Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008350.1 Hibiscus syriacus cultivar Beakdansim tig00111084_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: 573897
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:31 original size:19 final size:19
Alignment explanation
Indices: 9--58 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
1 TTTTTTCC
9 ATTTTTTCATTTTT-TTATT
1 ATTTTTTCATTTTTATT-TT
28 ATTTTTT-ATTTTTATTTT
1 ATTTTTTCATTTTTATTTT
*
46 TTTTTTTCATTTT
1 ATTTTTTCATTTT
59 CACTCATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 14 0.50
19 14 0.50
ACGTcount: A:0.14, C:0.04, G:0.00, T:0.82
Consensus pattern (19 bp):
ATTTTTTCATTTTTATTTT
Found at i:32 original size:18 final size:19
Alignment explanation
Indices: 11--58 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
1 TTTTTTCCAT
11 TTTTTCATTTTT-TTATTA
1 TTTTTCATTTTTATTATTA
* * *
29 TTTTTTATTTTTATTTTTT
1 TTTTTCATTTTTATTATTA
48 TTTTTCATTTT
1 TTTTTCATTTT
59 CACTCATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 11 0.44
19 14 0.56
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTCATTTTTATTATTA
Found at i:42 original size:13 final size:12
Alignment explanation
Indices: 18--58 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 12
8 CATTTTTTCA
*
18 TTTTTTTATTAT
1 TTTTTTTTTTAT
30 TTTTTATTTTTAT
1 TTTTT-TTTTTAT
43 TTTTTTTTTTCAT
1 TTTTTTTTTT-AT
56 TTT
1 TTT
59 CACTCATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 10 0.38
13 16 0.62
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTTTTTTTAT
Found at i:50 original size:16 final size:16
Alignment explanation
Indices: 20--49 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10 TTTTTTCATT
20 TTTTTATTATTTTTTA
1 TTTTTATTATTTTTTA
36 TTTTTATT-TTTTTT
1 TTTTTATTATTTTTT
50 TTTCATTTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTATTATTTTTTA
Found at i:17108 original size:60 final size:59
Alignment explanation
Indices: 17035--17189 Score: 161
Period size: 60 Copynumber: 2.6 Consensus size: 59
17025 TTAAATTGGT
* * * *
17035 TCCTAAACGTTTGAATA-TTCTGATTTTATCTCCAAACCATGACTCATATTT-TAATTTAG
1 TCCTAAACTTTTGAATATTTC-AATTTCATCTCAAAACCATGAC-CATATTTCTAATTTAG
* * * * *
17094 TCCTTAAACTTTTGAACATTTCAATTTCATCTCAAAACTATGACCCTTTTTCTAATTTGG
1 TCC-TAAACTTTTGAATATTTCAATTTCATCTCAAAACCATGACCATATTTCTAATTTAG
* *
17154 TCCCAAACTTTTGAATATTACAATTTCATCTTCAAA
1 TCCTAAACTTTTGAATATTTCAATTTCATC-TCAAA
17190 TTCATCCAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
59 32 0.40
60 45 0.56
61 3 0.04
ACGTcount: A:0.31, C:0.21, G:0.06, T:0.42
Consensus pattern (59 bp):
TCCTAAACTTTTGAATATTTCAATTTCATCTCAAAACCATGACCATATTTCTAATTTAG
Found at i:19172 original size:31 final size:31
Alignment explanation
Indices: 19131--19190 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
19121 TTTGACCACT
19131 TTCGGTTTTATTTAACTAAGATGTGATCATG
1 TTCGGTTTTATTTAACTAAGATGTGATCATG
* *
19162 TTCGTTTTTATTTAATTAAGATGTGATCA
1 TTCGGTTTTATTTAACTAAGATGTGATCA
19191 CTTTTGTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.08, G:0.17, T:0.48
Consensus pattern (31 bp):
TTCGGTTTTATTTAACTAAGATGTGATCATG
Found at i:27470 original size:2 final size:2
Alignment explanation
Indices: 27463--27513 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
27453 TTAGACGAGA
27463 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
27505 AT AT AT AT A
1 AT AT AT AT A
27514 CATTTCAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:35569 original size:26 final size:25
Alignment explanation
Indices: 35540--35599 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
35530 TAAATAATTT
* *
35540 TTTTTAATATTATAATATA-TATTAA
1 TTTTTAAAATTA-AATAAATTATTAA
35565 CTTTTTAAAATTAAATAAATTATTAA
1 -TTTTTAAAATTAAATAAATTATTAA
*
35591 TTTTAAAAA
1 TTTTTAAAA
35600 ATAATTATAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
25 13 0.43
26 17 0.57
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTTAAAATTAAATAAATTATTAA
Found at i:35581 original size:25 final size:25
Alignment explanation
Indices: 35540--35608 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 25
35530 TAAATAATTT
*
35540 TTTTTAATATTATAATATA-TATTAA
1 TTTTTAAAATTA-AATATATTATTAA
*
35565 CTTTTTAAAATTAAATAAATTATTAA
1 -TTTTTAAAATTAAATATATTATTAA
* * *
35591 TTTTAAAAAATAATTATA
1 TTTTTAAAATTAAATATA
35609 CCCATAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
25 19 0.53
26 17 0.47
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTTTAAAATTAAATATATTATTAA
Found at i:40119 original size:91 final size:89
Alignment explanation
Indices: 39964--40238 Score: 433
Period size: 91 Copynumber: 3.0 Consensus size: 89
39954 AAATTACATA
* * * * *
39964 ACTTTTAACATATTAGGTAGCTCTTTACCGTTTTTATCATAATAAAACTGATTTTGTCATATTTT
1 ACTTTCAACATATCAGGTAGCTCTTTACCG-TTTTGTCATAATGAAACTGGTTTTGTCATATTTT
40029 TACTTGTTATATTGTAAAGTATCGAT
65 TAC-TGTTATATTGTAAAGTATCGAT
40055 ACTTTCAACATATCAGGTAGCTCTTTACCAGTTTTGTCATAATGAAACTGGTTTTGTCATATTTT
1 ACTTTCAACATATCAGGTAGCTCTTTACC-GTTTTGTCATAATGAAACTGGTTTTGTCATATTTT
*
40120 TACATGTTATATTGTTAAGTATCGAT
65 TAC-TGTTATATTGTAAAGTATCGAT
*
40146 ACTTTCAACATATCAGGTAGCTCTTTACCGGTTTTGTCATAATGAAACTGGTTTTGCCATATTTT
1 ACTTTCAACATATCAGGTAGCTCTTTACC-GTTTTGTCATAATGAAACTGGTTTTGTCATATTTT
40211 TAACTGTTATATTGTAAAGTATCGAT
65 T-ACTGTTATATTGTAAAGTATCGAT
40237 AC
1 AC
40239 ATTTTTATAA
Statistics
Matches: 172, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
91 169 0.98
92 3 0.02
ACGTcount: A:0.28, C:0.14, G:0.13, T:0.44
Consensus pattern (89 bp):
ACTTTCAACATATCAGGTAGCTCTTTACCGTTTTGTCATAATGAAACTGGTTTTGTCATATTTTT
ACTGTTATATTGTAAAGTATCGAT
Found at i:40738 original size:197 final size:197
Alignment explanation
Indices: 40356--40993 Score: 865
Period size: 198 Copynumber: 3.2 Consensus size: 197
40346 GTAAACGTAT
* * * *
40356 GTGTCGATACATTT-TCTAAAAATATCGACCCCAAAAATATTGAAACAATAATTATAATGTAATA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCCAAAAACATCGAAACAATAATTATAATGTAATA
* * * *
40420 GGTAAATTAACAATGTAACCGGTATAAATATACCG-TTAATTAGAAAACATGTCAACATAATGTA
65 GGTAAATTTACAATGTAACCGGTATAAATATACCGTTTTATGAGAAAATATGTCAACATAATGTA
* ** * *
40484 TCGACACTTGTGGAATTTGTGTCGATACTTATTGTCTAGAATGAATCCCCAAACGAGGTGCACGC
130 TCGACACTTTTTAAATTTGTGTCGATACTT-TTGTCCAGAATGAAT-GCCAAACGAGGTGCACGC
40549 ATAAA
193 ATAAA
*
40554 GTGTCGATAAATTTATTAAAAGTATCGATCCCAAAAACATCGAAAC-ATAATTATAATGTAATAG
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAATAATTATAATGTAATAG
* *
40618 GTAAATTTACAATGTAACCGGTATAAATATACCGTTTTATGAGAGAATATGTCAACATATTGTAT
66 GTAAATTTACAATGTAACCGGTATAAATATACCGTTTTATGAGAAAATATGTCAACATAATGTAT
* *
40683 CGACACTTTTTAAATTTGTGTCGATACATTTTGTCCAGAATGAATGTCAAACGAGGTGCACTCAT
131 CGACACTTTTTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCAT
40748 AAA
195 AAA
* * * *
40751 GTGTCGATACATTTATTAAAAGTATCAATCCCAAAAACATTGAAACCGATAATTACAATGTAATA
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAA-CAATAATTATAATGTAATA
** * * * *
40816 GGTAAATTTACAATGTGCCCGGTAGAAATATACCGGTTTTATGAGAAAATAGGTCTACATAATAT
65 GGTAAATTTACAATGTAACCGGTATAAATATACC-GTTTTATGAGAAAATATGTCAACATAATGT
* * *
40881 ATCGACACTTTTTAAGTTTGTGTCGATACTTTT-TTCAGAATGAATGCCCAACGAGGTGCACGCA
129 ATCGACACTTTTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCA
40945 TAAA
194 TAAA
* * *
40949 GTGTCGATACGTTTA--AAATTGTATCGATCCAAAAAACATCGAAAC
1 GTGTCGATACATTTATTAAA-AGTATCGATCCCAAAAACATCGAAAC
40994 CGATAATATG
Statistics
Matches: 393, Mismatches: 40, Indels: 16
0.88 0.09 0.04
Matches are distributed among these distances:
196 4 0.01
197 134 0.34
198 148 0.38
199 54 0.14
200 53 0.13
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (197 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAACATCGAAACAATAATTATAATGTAATAG
GTAAATTTACAATGTAACCGGTATAAATATACCGTTTTATGAGAAAATATGTCAACATAATGTAT
CGACACTTTTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCATA
AA
Found at i:41229 original size:16 final size:16
Alignment explanation
Indices: 41208--41244 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
41198 TGATATAACA
41208 TAACCGATCTAAATTT
1 TAACCGATCTAAATTT
*
41224 TAACCGGTCTAAATTT
1 TAACCGATCTAAATTT
41240 TAACC
1 TAACC
41245 AGTCACTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (16 bp):
TAACCGATCTAAATTT
Found at i:41420 original size:19 final size:19
Alignment explanation
Indices: 41391--41438 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
41381 CATATATTTT
41391 TATTTTT-TATTTATTTAA
1 TATTTTTGTATTTATTTAA
41409 TATTTTTGTATTTATTTAA
1 TATTTTTGTATTTATTTAA
41428 TATTTTTGTAT
1 TATTTTTGTAT
41439 CCATTATCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 7 0.24
19 22 0.76
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
TATTTTTGTATTTATTTAA
Found at i:42736 original size:24 final size:24
Alignment explanation
Indices: 42709--42764 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
42699 CTATTCTTTC
42709 GCTTCAATTAAGCTCAAATTTTAG
1 GCTTCAATTAAGCTCAAATTTTAG
*
42733 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTAAGCTCAAATTTTAG
42757 GCTTCAAT
1 GCTTCAAT
42765 CGAACTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (24 bp):
GCTTCAATTAAGCTCAAATTTTAG
Found at i:50548 original size:20 final size:20
Alignment explanation
Indices: 50523--50562 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
50513 ACATACTTGT
* *
50523 TAAAAATTAAAAATATAATA
1 TAAAAAATAAAAAGATAATA
50543 TAAAAAATAAAAAGATAATA
1 TAAAAAATAAAAAGATAATA
50563 ATATAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (20 bp):
TAAAAAATAAAAAGATAATA
Found at i:50595 original size:24 final size:24
Alignment explanation
Indices: 50566--50612 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
50556 GATAATAATA
*
50566 TAATAATATTACATATTTAATTAT
1 TAATAATATTACATATTAAATTAT
* *
50590 TAATAATTTTATATATTAAATTA
1 TAATAATATTACATATTAAATTA
50613 AACTAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (24 bp):
TAATAATATTACATATTAAATTAT
Found at i:53646 original size:21 final size:21
Alignment explanation
Indices: 53620--53665 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
53610 TAATTTAGTT
53620 ATTTTTTATT-TATTATTAATA
1 ATTTTTTATTATATTATTAA-A
*
53641 A-TTTTTATTATATTCTTAAA
1 ATTTTTTATTATATTATTAAA
53661 ATTTT
1 ATTTT
53666 ATAAGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTTTATTATATTATTAAA
Found at i:53667 original size:19 final size:20
Alignment explanation
Indices: 53622--53665 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
53612 ATTTAGTTAT
53622 TTTTTATTTATTATTAATAA
1 TTTTTATTTATTATTAATAA
*
53642 TTTTTATTATATTCTTAA-AA
1 TTTTTATT-TATTATTAATAA
53662 TTTT
1 TTTT
53666 ATAAGTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTATTTATTATTAATAA
Found at i:60788 original size:2 final size:2
Alignment explanation
Indices: 60781--60815 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
60771 TAGCTCATAC
60781 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
60816 AACAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60975 original size:31 final size:31
Alignment explanation
Indices: 60877--60967 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
60867 CAATTTAAGG
60877 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
60908 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
60939 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
60968 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:61059 original size:19 final size:19
Alignment explanation
Indices: 61032--61097 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
61022 AATGTTTTTA
* *
61032 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
61051 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
61070 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
61089 TGAAC-GTAA
1 TGAACAGTAA
61098 CCCGAGGCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
18 4 0.09
19 39 0.91
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:61229 original size:21 final size:21
Alignment explanation
Indices: 61203--61244 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
61193 ATTTGAATAT
*
61203 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
61224 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
61245 CCATTCTGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:61305 original size:21 final size:21
Alignment explanation
Indices: 61272--61311 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
61262 TTTGAGTAGA
*
61272 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
61294 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
61312 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:64240 original size:22 final size:22
Alignment explanation
Indices: 64214--64260 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
64204 GTTTGGTTTG
64214 AAAAATTCAATTTCTTAATAAA
1 AAAAATTCAATTTCTTAATAAA
*
64236 AAAAATTCAATTTCTTAATGAA
1 AAAAATTCAATTTCTTAATAAA
64258 AAA
1 AAA
64261 GGGGGAGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (22 bp):
AAAAATTCAATTTCTTAATAAA
Found at i:64517 original size:31 final size:31
Alignment explanation
Indices: 64419--64509 Score: 168
Period size: 31 Copynumber: 3.0 Consensus size: 31
64409 CAATTTAAGG
64419 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
64450 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
64481 CAAAAT-GTTTTTGGACTT-AATTGAATTTA
1 CAAAATGGTTTTTGGACTTGAATTGAATTTA
64510 TTCAAAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.18
30 12 0.20
31 37 0.62
ACGTcount: A:0.33, C:0.07, G:0.18, T:0.43
Consensus pattern (31 bp):
CAAAATGGTTTTTGGACTTGAATTGAATTTA
Found at i:64601 original size:19 final size:19
Alignment explanation
Indices: 64574--64639 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
64564 AATGTTTTTA
* *
64574 TGAATAGTAATTTACTATT
1 TGAACAGTAAATTACTATT
64593 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
64612 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
64631 TGAAC-GTAA
1 TGAACAGTAA
64640 CCCGAGGCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
18 4 0.09
19 39 0.91
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:64847 original size:21 final size:21
Alignment explanation
Indices: 64814--64853 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
64804 TTTGAGTAGA
*
64814 AAAATCATTCCCAAACGGCTCC
1 AAAATCA-TCCCCAACGGCTCC
64836 AAAA-CATCCCCAACGGCT
1 AAAATCATCCCCAACGGCT
64854 AGATACGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 11 0.65
21 2 0.12
22 4 0.24
ACGTcount: A:0.38, C:0.38, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAATCATCCCCAACGGCTCC
Found at i:65107 original size:34 final size:32
Alignment explanation
Indices: 65068--65137 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
65058 TTTTGTAAAG
*
65068 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAATCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
65102 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
65134 GGGA
1 GGGA
65138 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.30, T:0.23
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:66570 original size:33 final size:31
Alignment explanation
Indices: 66515--66575 Score: 79
Period size: 33 Copynumber: 1.9 Consensus size: 31
66505 AGCAGATATT
*
66515 TATTATATTTAAATTTAAAAAATAATTAAAAA
1 TATTATATTTAAACTTAAAAAAT-ATTAAAAA
66547 TATTAATATTTAAAACTT-AAAAATATTAA
1 TATT-ATATTT-AAACTTAAAAAATATTAA
66576 TATTTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
32 9 0.35
33 12 0.46
34 5 0.19
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (31 bp):
TATTATATTTAAACTTAAAAAATATTAAAAA
Found at i:66842 original size:2 final size:2
Alignment explanation
Indices: 66835--66859 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
66825 CTTCGTTTGT
66835 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
66860 TCGTTTTTGC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:73712 original size:3 final size:3
Alignment explanation
Indices: 73704--73732 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
73694 AATTACAATA
73704 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
73733 AGGGTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:90194 original size:33 final size:33
Alignment explanation
Indices: 90157--90222 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
90147 CTATTTGCAT
90157 GTTTAAGTACAATAAATATCAGCTTAAAAAGAA
1 GTTTAAGTACAATAAATATCAGCTTAAAAAGAA
*
90190 GTTTAAGTACAATAAGTATCAGCTTAAAAAGAA
1 GTTTAAGTACAATAAATATCAGCTTAAAAAGAA
90223 TACCTCCATC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.14, T:0.27
Consensus pattern (33 bp):
GTTTAAGTACAATAAATATCAGCTTAAAAAGAA
Found at i:94169 original size:26 final size:26
Alignment explanation
Indices: 94133--94189 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
94123 ATCATGTTAG
94133 CTTAAGTGATCAGCAGTTTGATATGA
1 CTTAAGTGATCAGCAGTTTGATATGA
94159 CTTAAGTGATCAGCAGTTTGATATGA
1 CTTAAGTGATCAGCAGTTTGATATGA
94185 CTTAA
1 CTTAA
94190 ATAAGATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (26 bp):
CTTAAGTGATCAGCAGTTTGATATGA
Found at i:96676 original size:16 final size:17
Alignment explanation
Indices: 96645--96677 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
96635 AAAATTTTAA
*
96645 TTTAAACTTCTAAATTT
1 TTTAAAATTCTAAATTT
96662 TTTAAAATT-TAAATTT
1 TTTAAAATTCTAAATTT
96678 ACCTCAAACG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TTTAAAATTCTAAATTT
Found at i:103462 original size:50 final size:50
Alignment explanation
Indices: 103387--103481 Score: 190
Period size: 50 Copynumber: 1.9 Consensus size: 50
103377 AGGAAGCGAC
103387 AGCCTTTTTACCTTTGATTTCACTTTTAATCAATGCTCAAGTGTAGTGAT
1 AGCCTTTTTACCTTTGATTTCACTTTTAATCAATGCTCAAGTGTAGTGAT
103437 AGCCTTTTTACCTTTGATTTCACTTTTAATCAATGCTCAAGTGTA
1 AGCCTTTTTACCTTTGATTTCACTTTTAATCAATGCTCAAGTGTA
103482 AGATTGAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.24, C:0.19, G:0.13, T:0.44
Consensus pattern (50 bp):
AGCCTTTTTACCTTTGATTTCACTTTTAATCAATGCTCAAGTGTAGTGAT
Found at i:105591 original size:60 final size:59
Alignment explanation
Indices: 105442--105631 Score: 170
Period size: 60 Copynumber: 3.2 Consensus size: 59
105432 AATTTGGATG
* * * *
105442 AGTTTAGGGATAAAATTGTAATATTCAAAAGTTTGAGGACAAATTCAAGAA-GAGGGTCAT
1 AGTTTAGGGATAAAATTGAAATATTCAAAAGTTTAAGAAC-AATT-TAGAATGAGGGTCAT
* * *** * *
105502 AGTTTAAGGATGAAATT-AGAATGCACAAAAGTTTAAGAACTAGTTTGGAATGAGGGTCAT
1 AGTTTAGGGATAAAATTGA-AATATTCAAAAGTTTAAGAAC-AATTTAGAATGAGGGTCAT
* * *
105562 AGTTTGGGGATAAAATTGAAATATTCAAAAGTTTAAAGATCAATTTAAAATGAGGGAT-AT
1 AGTTTAGGGATAAAATTGAAATATTCAAAAGTTT-AAGAACAATTTAGAATGAGGG-TCAT
*
105622 AGTTTGGGGA
1 AGTTTAGGGA
105632 CATGTGATGC
Statistics
Matches: 103, Mismatches: 22, Indels: 10
0.76 0.16 0.07
Matches are distributed among these distances:
59 3 0.03
60 93 0.90
61 7 0.07
ACGTcount: A:0.41, C:0.05, G:0.24, T:0.29
Consensus pattern (59 bp):
AGTTTAGGGATAAAATTGAAATATTCAAAAGTTTAAGAACAATTTAGAATGAGGGTCAT
Found at i:107708 original size:27 final size:29
Alignment explanation
Indices: 107677--107736 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
107667 TCTTAATTTA
107677 AATA-TTGTAAATC-AAAAATAATATCAG
1 AATATTTGTAAATCAAAAAATAATATCAG
* *
107704 AATATTTGTAAATCAAAAAATAATGTCGG
1 AATATTTGTAAATCAAAAAATAATATCAG
107733 AATA
1 AATA
107737 ATTTCATCTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 4 0.14
28 9 0.31
29 16 0.55
ACGTcount: A:0.53, C:0.07, G:0.10, T:0.30
Consensus pattern (29 bp):
AATATTTGTAAATCAAAAAATAATATCAG
Found at i:116587 original size:2 final size:2
Alignment explanation
Indices: 116582--116614 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
116572 TGGAAGTGTG
*
116582 TA TA TA TA TA TA TA TA TA TA TA -A TA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
116615 GCATTTGAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:117816 original size:21 final size:20
Alignment explanation
Indices: 117790--117834 Score: 81
Period size: 21 Copynumber: 2.2 Consensus size: 20
117780 CTTAAGTTAT
117790 GGTTAGGGCTAATGGTTTAGA
1 GGTTAGGGCTAATGGTTTA-A
117811 GGTTAGGGCTAATGGTTTAA
1 GGTTAGGGCTAATGGTTTAA
117831 GGTT
1 GGTT
117835 TAAAATTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 5 0.21
21 19 0.79
ACGTcount: A:0.22, C:0.04, G:0.38, T:0.36
Consensus pattern (20 bp):
GGTTAGGGCTAATGGTTTAA
Found at i:120020 original size:11 final size:12
Alignment explanation
Indices: 119990--120023 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
119980 GTTATTTAAA
119990 CGGGTATTGGGT
1 CGGGTATTGGGT
120002 CGGGTATTGGGT
1 CGGGTATTGGGT
120014 C-GGTATTGGG
1 CGGGTATTGGG
120024 CCGTGAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 9 0.41
12 13 0.59
ACGTcount: A:0.09, C:0.09, G:0.50, T:0.32
Consensus pattern (12 bp):
CGGGTATTGGGT
Found at i:120101 original size:24 final size:25
Alignment explanation
Indices: 120041--120101 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
120031 TCGGGCCGGG
120041 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
120064 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
120088 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
120102 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:120958 original size:12 final size:12
Alignment explanation
Indices: 120941--120970 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
120931 CGTCCAATTT
120941 TTTTTTAAAATA
1 TTTTTTAAAATA
120953 TTTTTT-AAATA
1 TTTTTTAAAATA
120964 TTTTTTA
1 TTTTTTA
120971 TTTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTTTTAAAATA
Found at i:135189 original size:19 final size:19
Alignment explanation
Indices: 135165--135202 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
135155 GCGATTTTAA
*
135165 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGAGAGTT
135184 AAAATGTGTTGCGAGAGTT
1 AAAATGTGTTGCGAGAGTT
135203 TGAAAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.29, T:0.34
Consensus pattern (19 bp):
AAAATGTGTTGCGAGAGTT
Found at i:135730 original size:19 final size:19
Alignment explanation
Indices: 135706--135743 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
135696 GACTAACGTA
135706 AATTTGAAAAATCGCAACG
1 AATTTGAAAAATCGCAACG
135725 AATTTGAAAAATCGCAACG
1 AATTTGAAAAATCGCAACG
135744 CGAACTTGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.16, T:0.21
Consensus pattern (19 bp):
AATTTGAAAAATCGCAACG
Found at i:137165 original size:12 final size:12
Alignment explanation
Indices: 137148--137189 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
137138 TATTTCAAAA
137148 ATATTAATTAAT
1 ATATTAATTAAT
137160 ATATTAATTAAT
1 ATATTAATTAAT
* *
137172 ATATTTATTAAA
1 ATATTAATTAAT
137184 ATATTA
1 ATATTA
137190 TTAGATTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATATTAATTAAT
Found at i:137175 original size:35 final size:34
Alignment explanation
Indices: 137131--137221 Score: 91
Period size: 35 Copynumber: 2.6 Consensus size: 34
137121 TTAATAGTGT
*
137131 TATATTATATTTCAAAAATATTAATTA-ATATATTA
1 TATAATATATTT-AAAAATATTAATTAGAT-TATTA
137166 -ATTAATATATTTATTAAAATATT-ATTAGATTATTA
1 TA-TAATATATTTA--AAAATATTAATTAGATTATTA
*
137201 TATAATA-ATTTAATAATATTA
1 TATAATATATTTAAAAATATTA
137222 TTTCTATGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
32 7 0.15
34 7 0.15
35 23 0.48
36 11 0.23
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (34 bp):
TATAATATATTTAAAAATATTAATTAGATTATTA
Found at i:137354 original size:22 final size:22
Alignment explanation
Indices: 137326--137369 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
137316 TTGATTATTT
137326 TATTATAATATTAAAAATATAA
1 TATTATAATATTAAAAATATAA
* *
137348 TATTATATTATTAGAAATATAA
1 TATTATAATATTAAAAATATAA
137370 ATAAATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTATAATATTAAAAATATAA
Found at i:137359 original size:30 final size:34
Alignment explanation
Indices: 137309--137378 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 34
137299 ATATTATTAT
* * *
137309 AATATAATTGATTATTTTATTA-TAATATTAA-A
1 AATATAATTGATTATATTATTAGAAATATAAATA
137341 AATATAA-T-ATTATATTATTAGAAATATAAATA
1 AATATAATTGATTATATTATTAGAAATATAAATA
137373 AATATA
1 AATATA
137379 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 11 0.33
31 8 0.24
32 14 0.42
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (34 bp):
AATATAATTGATTATATTATTAGAAATATAAATA
Found at i:140705 original size:32 final size:32
Alignment explanation
Indices: 140652--140729 Score: 93
Period size: 32 Copynumber: 2.4 Consensus size: 32
140642 AAGGCTAATG
** * * *
140652 GACTAAAATCGAATGGGAGTTAACGGTTAAGA
1 GACTAAAATCGAATGAAAGTTAAAGATCAAGA
*
140684 GACTAAAATCGAATGAAAGTTAAAGATCAAGG
1 GACTAAAATCGAATGAAAGTTAAAGATCAAGA
*
140716 GGCTAAAATCGAAT
1 GACTAAAATCGAAT
140730 AGATCAATAA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.45, C:0.10, G:0.24, T:0.21
Consensus pattern (32 bp):
GACTAAAATCGAATGAAAGTTAAAGATCAAGA
Found at i:146863 original size:87 final size:87
Alignment explanation
Indices: 146717--146882 Score: 269
Period size: 87 Copynumber: 1.9 Consensus size: 87
146707 CATTTCATTG
* *
146717 ATTTCAACATTGACTTTGACATCAATATTAGATAATAGTAGTAAGGTATATAACTTTATGTACTC
1 ATTTCAACATTGACTTTGACATCAATATTAGATAATAGTAGTAAGGCATAGAACTTTATGTACTC
146782 AGCATGAATTTGCTCAATAATC
66 AGCATGAATTTGCTCAATAATC
* ** *
146804 ATTTCAATATTGTTTTTGACATCAATATTAGATAATAGTAGTAAGGCATAGAACTTTATGTTCTC
1 ATTTCAACATTGACTTTGACATCAATATTAGATAATAGTAGTAAGGCATAGAACTTTATGTACTC
*
146869 AGGATGAATTTGCT
66 AGCATGAATTTGCT
146883 GGCTTTCTGA
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 72 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (87 bp):
ATTTCAACATTGACTTTGACATCAATATTAGATAATAGTAGTAAGGCATAGAACTTTATGTACTC
AGCATGAATTTGCTCAATAATC
Found at i:154937 original size:30 final size:29
Alignment explanation
Indices: 154901--154975 Score: 105
Period size: 30 Copynumber: 2.6 Consensus size: 29
154891 TTAGAACCTA
154901 AAATCTTAAATCTTCCTTCAGACAAAAACC
1 AAATCTTAAATCTTCCTTCAGACAAAAA-C
* * * *
154931 AAATCTTAAGTCATCCTTCAGACCAAAAT
1 AAATCTTAAATCTTCCTTCAGACAAAAAC
154960 AAATCTTAAATCTTCC
1 AAATCTTAAATCTTCC
154976 AATGAATATC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 14 0.36
30 25 0.64
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.29
Consensus pattern (29 bp):
AAATCTTAAATCTTCCTTCAGACAAAAAC
Found at i:157343 original size:24 final size:24
Alignment explanation
Indices: 157316--157374 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
157306 GCCATAACAT
157316 AAGAAGCTCACACTTTTTCCCTTC
1 AAGAAGCTCACACTTTTTCCCTTC
157340 AAGAAGCTCACACTTTTTCCCTTC
1 AAGAAGCTCACACTTTTTCCCTTC
* *
157364 AAAAACCTCAC
1 AAGAAGCTCAC
157375 TCTTCTTCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.34, G:0.07, T:0.29
Consensus pattern (24 bp):
AAGAAGCTCACACTTTTTCCCTTC
Found at i:158317 original size:35 final size:37
Alignment explanation
Indices: 158255--158323 Score: 88
Period size: 35 Copynumber: 1.9 Consensus size: 37
158245 TAAAATTGTC
*
158255 ATTATATTTTTTAGATGATTATAATAACATTAAATTT
1 ATTATATTTTTTAGATAATTATAATAACATTAAATTT
* * *
158292 ATTAT-TTTTTTA-ATATTTATTATAACTTTAAA
1 ATTATATTTTTTAGATAATTATAATAACATTAAA
158324 ATAATCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
35 16 0.57
36 7 0.25
37 5 0.18
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (37 bp):
ATTATATTTTTTAGATAATTATAATAACATTAAATTT
Found at i:161686 original size:116 final size:116
Alignment explanation
Indices: 161482--161713 Score: 464
Period size: 116 Copynumber: 2.0 Consensus size: 116
161472 TTTAATTTTA
161482 TGCTGTTTTAGGGTTCAAGTGTCCCTCTCGTTGTCAAATGGGTGGATACAGAAAAGGAAAGACAA
1 TGCTGTTTTAGGGTTCAAGTGTCCCTCTCGTTGTCAAATGGGTGGATACAGAAAAGGAAAGACAA
161547 GCTCGGAGGGTCCAGAAAGCTCAATCTCAAGCTTCGAACATACCAATTGCT
66 GCTCGGAGGGTCCAGAAAGCTCAATCTCAAGCTTCGAACATACCAATTGCT
161598 TGCTGTTTTAGGGTTCAAGTGTCCCTCTCGTTGTCAAATGGGTGGATACAGAAAAGGAAAGACAA
1 TGCTGTTTTAGGGTTCAAGTGTCCCTCTCGTTGTCAAATGGGTGGATACAGAAAAGGAAAGACAA
161663 GCTCGGAGGGTCCAGAAAGCTCAATCTCAAGCTTCGAACATACCAATTGCT
66 GCTCGGAGGGTCCAGAAAGCTCAATCTCAAGCTTCGAACATACCAATTGCT
161714 GATTCACCAC
Statistics
Matches: 116, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (116 bp):
TGCTGTTTTAGGGTTCAAGTGTCCCTCTCGTTGTCAAATGGGTGGATACAGAAAAGGAAAGACAA
GCTCGGAGGGTCCAGAAAGCTCAATCTCAAGCTTCGAACATACCAATTGCT
Found at i:163714 original size:31 final size:31
Alignment explanation
Indices: 163676--163739 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 31
163666 AACTCGTTAA
*
163676 CTTCAACAAATAAGGCCCATTCAATCTGTTT
1 CTTCAACAAATAAGCCCCATTCAATCTGTTT
163707 CTTCAACAAATAAGCCCCATTCAATCTGTTT
1 CTTCAACAAATAAGCCCCATTCAATCTGTTT
163738 CT
1 CT
163740 GACATGCATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (31 bp):
CTTCAACAAATAAGCCCCATTCAATCTGTTT
Found at i:168781 original size:18 final size:20
Alignment explanation
Indices: 168758--168804 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 20
168748 CGTCCTGAAG
168758 GACCACT-AT-GTCTCGAAT
1 GACCACTAATAGTCTCGAAT
168776 GACCACTAGATACGTCTCGAAT
1 GACCACTA-ATA-GTCTCGAAT
168798 GACCACT
1 GACCACT
168805 GGATACGTCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 7 0.28
20 2 0.08
22 16 0.64
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (20 bp):
GACCACTAATAGTCTCGAAT
Found at i:168795 original size:22 final size:22
Alignment explanation
Indices: 168767--168818 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
168757 GGACCACTAT
168767 GTCTCGAATGACCACTAGATAC
1 GTCTCGAATGACCACTAGATAC
*
168789 GTCTCGAATGACCACTGGATAC
1 GTCTCGAATGACCACTAGATAC
*
168811 GTCCCGAA
1 GTCTCGAA
168819 GGACTAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (22 bp):
GTCTCGAATGACCACTAGATAC
Found at i:170294 original size:64 final size:64
Alignment explanation
Indices: 170200--170320 Score: 163
Period size: 64 Copynumber: 1.9 Consensus size: 64
170190 GCATAAAATA
** *
170200 CATTCGATGTTTCAATATTAAGGTGATGCATCGATACACGCCTTATGCATCGATACATTAATTG
1 CATTCGATGTTTCAATATTAAGAAGATGCATCGATACACGACTTATGCATCGATACATTAATTG
* * * *
170264 CATTCGATGTTTCTATTATTAAGAAG-TGCATCGATGCACTACTTGTGCATCGATACA
1 CATTCGATGTTTC-AATATTAAGAAGATGCATCGATACACGACTTATGCATCGATACA
170321 CCTTCAATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
64 40 0.82
65 9 0.18
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (64 bp):
CATTCGATGTTTCAATATTAAGAAGATGCATCGATACACGACTTATGCATCGATACATTAATTG
Found at i:175395 original size:3 final size:3
Alignment explanation
Indices: 175387--175440 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
175377 ACAAGCGATG
175387 ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
175434 ATA ATA A
1 ATA ATA A
175441 AACCCAAAGT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 48 0.96
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:185409 original size:20 final size:20
Alignment explanation
Indices: 185352--185419 Score: 77
Period size: 20 Copynumber: 3.4 Consensus size: 20
185342 AACAAATACA
*
185352 TTGCGAATTT-AAAATCGTG
1 TTGCGAATTTGATAATCGTG
* *
185371 TTGCGATTTTTGACT-ATCGCG
1 TTGCGA-ATTTGA-TAATCGTG
185392 TTGCGAATTTGATAATCGTG
1 TTGCGAATTTGATAATCGTG
185412 TTGCGAAT
1 TTGCGAAT
185420 CTGGAAACTG
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.17
20 21 0.52
21 12 0.30
ACGTcount: A:0.24, C:0.13, G:0.24, T:0.40
Consensus pattern (20 bp):
TTGCGAATTTGATAATCGTG
Found at i:189155 original size:21 final size:21
Alignment explanation
Indices: 189131--189177 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
189121 ATTTAACGCT
189131 AAATTTTAAAAAAAAATATAA
1 AAATTTTAAAAAAAAATATAA
** * *
189152 AAATTTTATTAAAACATATCA
1 AAATTTTAAAAAAAAATATAA
189173 AAATT
1 AAATT
189178 GATAATTTAA
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:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (21 bp):
AAATTTTAAAAAAAAATATAA
Found at i:191674 original size:43 final size:44
Alignment explanation
Indices: 191545--191747 Score: 142
Period size: 43 Copynumber: 4.7 Consensus size: 44
191535 GGGCTTAAAC
* *
191545 TATAAAAGTAAAAAGTGTA-ATTGAAAAAAATTAG-AG-ACACCAAT
1 TATAAAATTAAAAAGTG-AGATTG-AAAAAATTAGAAGTTCA-CAAT
** * * * *
191589 TATAAAGGTAAAAAGTGAGA-T-AAAAAATCAG-GGGTCTCAAT
1 TATAAAATTAAAAAGTGAGATTGAAAAAATTAGAAGTTCACAAT
191630 TATAAAATTAAAAAGTGAGATTGAAAAAATTAGAAGTTCA-AAT
1 TATAAAATTAAAAAGTGAGATTGAAAAAATTAGAAGTTCACAAT
* * * *
191673 TAT-AAATATATAAAGTGAGACTG-AAAAATT-TAAGCTCATCAAT
1 TATAAAAT-TAAAAAGTGAGATTGAAAAAATTAGAAGTTCA-CAAT
*
191716 TAT-AAATGTAAAAAAT-AGGATTGAAAAAATTA
1 TATAAAAT-TAAAAAGTGA-GATTGAAAAAATTA
191748 AGGGTTTATT
Statistics
Matches: 129, Mismatches: 19, Indels: 21
0.76 0.11 0.12
Matches are distributed among these distances:
41 38 0.29
42 14 0.11
43 50 0.39
44 27 0.21
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.26
Consensus pattern (44 bp):
TATAAAATTAAAAAGTGAGATTGAAAAAATTAGAAGTTCACAAT
Found at i:196974 original size:30 final size:30
Alignment explanation
Indices: 196874--196974 Score: 79
Period size: 30 Copynumber: 3.4 Consensus size: 30
196864 ATTTATATAA
* *
196874 TTTAAATACCTATTTTGAC--ATAAAATATT
1 TTTAAATACTTATTTTGACTAAAAAAATA-T
*
196903 TTTGAAATA--TATTTTGA-TAGAAAATGATAT
1 TTT-AAATACTTATTTTGACTA-AAAA-AATAT
*
196933 TTTAAGA-ACTTATTTTGACTAAAAAAATAC
1 TTTAA-ATACTTATTTTGACTAAAAAAATAT
196963 TTTAAATACTTA
1 TTTAAATACTTA
196975 AATAAAAAGG
Statistics
Matches: 58, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
28 8 0.14
29 7 0.12
30 26 0.45
31 15 0.26
32 2 0.03
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.43
Consensus pattern (30 bp):
TTTAAATACTTATTTTGACTAAAAAAATAT
Found at i:197990 original size:17 final size:16
Alignment explanation
Indices: 197968--198044 Score: 61
Period size: 17 Copynumber: 4.7 Consensus size: 16
197958 TCATCATTTT
197968 TTATTAAACTAAAGTGA
1 TTATTAAA-TAAAGTGA
*
197985 TTATTAAATAATGTG-
1 TTATTAAATAAAGTGA
*
198000 TT-TTAAAT-AATTGAA
1 TTATTAAATAAAGTG-A
198015 TTTTATTAAACTAAAGTGA
1 --TTATTAAA-TAAAGTGA
*
198034 TTATAAAATAA
1 TTATTAAATAA
198045 TATGCGTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
13 3 0.06
14 6 0.12
15 2 0.04
16 9 0.19
17 17 0.35
18 5 0.10
19 2 0.04
20 4 0.08
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.42
Consensus pattern (16 bp):
TTATTAAATAAAGTGA
Found at i:198228 original size:89 final size:89
Alignment explanation
Indices: 198069--198240 Score: 224
Period size: 89 Copynumber: 1.9 Consensus size: 89
198059 ATTTTTAATT
** *
198069 ATTTGACAATGAACTCTTAATCACCTTGTTGCAGTCGTTTGTCTTCGAACTGTGACCTCTACGAA
1 ATTTGACAATGAACTCTTAATCACCTTGTTGCAGTCGTTTGTCTTCGAACTGAAACCTATACGAA
198134 CAACAACGATTCCTTTAATTACTG
66 CAACAACGATTCCTTTAATTACTG
* * *
198158 ATTTGACAATGAA-TGCTTAATTACAC-TGTTGCAGTCG-TTGATGTTCGAACTGAAACCTATAG
1 ATTTGACAATGAACT-CTTAATCAC-CTTGTTGCAGTCGTTTG-TCTTCGAACTGAAACCTATAC
* *
198220 GAATAACAACGATTCTTTTAA
63 GAACAACAACGATTCCTTTAA
198241 CTATTGAGAT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
88 4 0.06
89 67 0.93
90 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (89 bp):
ATTTGACAATGAACTCTTAATCACCTTGTTGCAGTCGTTTGTCTTCGAACTGAAACCTATACGAA
CAACAACGATTCCTTTAATTACTG
Found at i:200111 original size:216 final size:210
Alignment explanation
Indices: 199726--200146 Score: 689
Period size: 216 Copynumber: 2.0 Consensus size: 210
199716 TAAAGTAAGT
* * *
199726 CCTTAATTTAATATTGTAAATAAAAGTATGTTTCTAGAATCTTTTGCTGCAAACCTTGCTGGAGA
1 CCTTAACTTAATAATGTAAATAAAAGTATGTTTCTAAAATCTTTTGCTGCAAACCTTGCTGGAGA
* * * *
199791 TGTTACACACACACAAAAATTGTTCTCTTATTACAACTTCAATTTTACTTCTACTGCTAGTCTTA
66 TGTTACACACAAAAAAAAATTGTTCTCTTATTAAAACTTCAATATTACTTCTACTGCTAGTCTTA
199856 TCCATTTTCACAAACTTAGGCACCGATACTAAACATCTTGAATTGTTGTTTCATATTTTATTTTA
131 TCCATTTTCACAAACTTAGGCACCGATACTAAACATCTTGAATTGTTGTTTCATATTTTATTTTA
199921 TTAATGCACAGCAGC
196 TTAATGCACAGCAGC
199936 CCTTAACTTAATAATGTAAATAAAAGTATGTTTCTAAAATCTTTTGCTGCCAAACCTTGCTGGAG
1 CCTTAACTTAATAATGTAAATAAAAGTATGTTTCTAAAATCTTTTGCTG-CAAACCTTGCTGGAG
*
200001 ATGTTACACGCACAAAAAAAGAAAATTGTTCTCTTATTAAAATTTCAATATTACTTCTACTGCTA
65 ATGTTACA--CAC--AAAAA-AAAATTGTTCTCTTATTAAAACTTCAATATTACTTCTACTGCTA
* * *
200066 GTCTTGTCCATTTTCTCAAACTTAGGCACCGATACTAATCATCTTGAATTGTTGTTTCATATTTT
125 GTCTTATCCATTTTCACAAACTTAGGCACCGATACTAAACATCTTGAATTGTTGTTTCATATTTT
200131 ATTTTATTAATGCACA
190 ATTTTATTAATGCACA
200147 ACACTATTCT
Statistics
Matches: 194, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
210 46 0.24
211 23 0.12
213 3 0.02
215 3 0.02
216 119 0.61
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (210 bp):
CCTTAACTTAATAATGTAAATAAAAGTATGTTTCTAAAATCTTTTGCTGCAAACCTTGCTGGAGA
TGTTACACACAAAAAAAAATTGTTCTCTTATTAAAACTTCAATATTACTTCTACTGCTAGTCTTA
TCCATTTTCACAAACTTAGGCACCGATACTAAACATCTTGAATTGTTGTTTCATATTTTATTTTA
TTAATGCACAGCAGC
Found at i:204268 original size:22 final size:22
Alignment explanation
Indices: 204231--204277 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
204221 AAAATTTAGT
** * *
204231 GAAACCGAAATTAACCTAAATC
1 GAAACCGAAAGAAACCCAAACC
204253 GAAACCGAAAGAAACCCAAACC
1 GAAACCGAAAGAAACCCAAACC
204275 GAA
1 GAA
204278 TTTTAACCCG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.53, C:0.26, G:0.13, T:0.09
Consensus pattern (22 bp):
GAAACCGAAAGAAACCCAAACC
Found at i:209905 original size:17 final size:18
Alignment explanation
Indices: 209860--209906 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
209850 TCCTCTATAT
209860 ATAATTTTTTTTAATTAA
1 ATAATTTTTTTTAATTAA
* *
209878 ATAACTATTTTT-ATTAA
1 ATAATTTTTTTTAATTAA
209895 ATAATTTTTTTT
1 ATAATTTTTTTT
209907 TATTTCGAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 15 0.60
18 10 0.40
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
ATAATTTTTTTTAATTAA
Found at i:220392 original size:7 final size:7
Alignment explanation
Indices: 220380--220427 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
220370 TGTGTTACTT
*
220380 TTTTTTC
1 TTTTTTA
*
220387 TTTTTTT
1 TTTTTTA
220394 TTTTTTA
1 TTTTTTA
**
220401 TTTTTGG
1 TTTTTTA
220408 TTTTTTA
1 TTTTTTA
220415 TTTTTTTA
1 -TTTTTTA
220423 TTTTT
1 TTTTT
220428 ACTTTCTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
7 27 0.79
8 7 0.21
ACGTcount: A:0.06, C:0.02, G:0.04, T:0.88
Consensus pattern (7 bp):
TTTTTTA
Found at i:220397 original size:14 final size:14
Alignment explanation
Indices: 220378--220449 Score: 74
Period size: 14 Copynumber: 5.2 Consensus size: 14
220368 GTTGTGTTAC
*
220378 TTTTTTTTCTTTTT
1 TTTTTTTTATTTTT
220392 TTTTTTTTATTTTT
1 TTTTTTTTATTTTT
**
220406 GGTTTTTTATTTTT
1 TTTTTTTTATTTTT
* *
220420 TTATTTTTA-CTTT
1 TTTTTTTTATTTTT
* *
220433 CTTTTGTTATTTTT
1 TTTTTTTTATTTTT
220447 TTT
1 TTT
220450 GTTAATTTGT
Statistics
Matches: 45, Mismatches: 12, Indels: 2
0.76 0.20 0.03
Matches are distributed among these distances:
13 9 0.20
14 36 0.80
ACGTcount: A:0.07, C:0.04, G:0.04, T:0.85
Consensus pattern (14 bp):
TTTTTTTTATTTTT
Found at i:220418 original size:27 final size:26
Alignment explanation
Indices: 220388--220449 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
220378 TTTTTTTTCT
* *
220388 TTTTTTTTTTTTA-TTTTTGGTTTTTTA
1 TTTTTTTTTTTTACTTTCT--TTTGTTA
220415 TTTTTTTATTTTTACTTTCTTTTGTTA
1 TTTTTTT-TTTTTACTTTCTTTTGTTA
220442 TTTTTTTT
1 TTTTTTTT
220450 GTTAATTTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 1 0.03
27 20 0.65
28 6 0.19
29 4 0.13
ACGTcount: A:0.08, C:0.03, G:0.05, T:0.84
Consensus pattern (26 bp):
TTTTTTTTTTTTACTTTCTTTTGTTA
Found at i:221255 original size:18 final size:18
Alignment explanation
Indices: 221205--221257 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
221195 TAATATTAAT
*
221205 TTTTATAACTTTAAAATAA
1 TTTTATAACTTT-TAATAA
* * *
221224 CTTT-TAATTTTTAATTA
1 TTTTATAACTTTTAATAA
221241 TTTTATAACTTTTAATA
1 TTTTATAACTTTTAATA
221258 GTCATATGAC
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
17 7 0.27
18 16 0.62
19 3 0.12
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTTATAACTTTTAATAA
Found at i:223185 original size:34 final size:35
Alignment explanation
Indices: 223147--223216 Score: 115
Period size: 37 Copynumber: 2.0 Consensus size: 35
223137 CAATTATTAG
223147 ATTAAATAAC-ATCATAAAAGTAGATGATCAAACA
1 ATTAAATAACAATCATAAAAGTAGATGATCAAACA
223181 ATTAAATAACAATATCATAAAAGTAGATGATCAAAC
1 ATTAAATAAC-A-ATCATAAAAGTAGATGATCAAAC
223217 GGTAAAGTGT
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 10 0.30
37 23 0.70
ACGTcount: A:0.56, C:0.11, G:0.09, T:0.24
Consensus pattern (35 bp):
ATTAAATAACAATCATAAAAGTAGATGATCAAACA
Found at i:232583 original size:10 final size:10
Alignment explanation
Indices: 232568--232594 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
232558 GCATCAACAT
232568 TGTGTCAAAC
1 TGTGTCAAAC
232578 TGTGTCAAAC
1 TGTGTCAAAC
232588 TGTGTCA
1 TGTGTCA
232595 TTGAAACCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (10 bp):
TGTGTCAAAC
Found at i:239722 original size:17 final size:18
Alignment explanation
Indices: 239702--239737 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
239692 TATTAATAAT
*
239702 ATAAT-TTATTTTAAAAA
1 ATAATATTACTTTAAAAA
239719 ATAATATTACTTTAAAAA
1 ATAATATTACTTTAAAAA
239737 A
1 A
239738 ATCATAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
ATAATATTACTTTAAAAA
Found at i:243243 original size:22 final size:22
Alignment explanation
Indices: 243218--243261 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
243208 TCGAACATTT
243218 AAATTTGTGTATATATTTTTTA
1 AAATTTGTGTATATATTTTTTA
243240 AAATTTGTGTATATATTTTTTA
1 AAATTTGTGTATATATTTTTTA
243262 GATTAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (22 bp):
AAATTTGTGTATATATTTTTTA
Found at i:244572 original size:2 final size:2
Alignment explanation
Indices: 244555--244599 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
244545 TTTAAATTAA
*
244555 AT AT AA AT AT -T 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
244596 AT AT
1 AT AT
244600 TTTTAATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:245220 original size:16 final size:16
Alignment explanation
Indices: 245199--245258 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
245189 TAATAAATAA
245199 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
245215 ACGAACATAAACAAAC
1 ACGAACATAAACAAAC
* *
245231 AGGAACATAAATAAAC
1 ACGAACATAAACAAAC
245247 ACGAACATAAAC
1 ACGAACATAAAC
245259 GTTGGAGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.62, C:0.22, G:0.08, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACAAAC
Found at i:246192 original size:14 final size:14
Alignment explanation
Indices: 246160--246186 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
246150 GAATGAACAT
246160 AAACGAACATAACC
1 AAACGAACATAACC
246174 AAACGAACATAAC
1 AAACGAACATAAC
246187 TGAACGTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.26, G:0.07, T:0.07
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:256069 original size:17 final size:19
Alignment explanation
Indices: 256041--256078 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
256031 TGGTTTAGGG
256041 TTGGTGATTT-GGGATTTT
1 TTGGTGATTTGGGGATTTT
256059 TTGGT-ATTTGGGGATTTT
1 TTGGTGATTTGGGGATTTT
256077 TT
1 TT
256079 TTAATTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.11, C:0.00, G:0.32, T:0.58
Consensus pattern (19 bp):
TTGGTGATTTGGGGATTTT
Found at i:265153 original size:21 final size:21
Alignment explanation
Indices: 265127--265166 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
265117 TAAATCACCA
265127 AGTGCTTATGGTTAAATTTAG
1 AGTGCTTATGGTTAAATTTAG
265148 AGTGCTTATGGTTAAATTT
1 AGTGCTTATGGTTAAATTT
265167 GGCCTACGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.05, G:0.23, T:0.45
Consensus pattern (21 bp):
AGTGCTTATGGTTAAATTTAG
Found at i:266133 original size:23 final size:23
Alignment explanation
Indices: 266084--266133 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 23
266074 TGAACAAGTG
***
266084 AAAATTAATATTAAAAATAAGTG
1 AAAATTAATATTAAAAATAAAAA
**
266107 AAAATTAATATTAAATTTAAAAA
1 AAAATTAATATTAAAAATAAAAA
266130 AAAA
1 AAAA
266134 GTAGAAATTG
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (23 bp):
AAAATTAATATTAAAAATAAAAA
Found at i:277460 original size:2 final size:2
Alignment explanation
Indices: 277449--277482 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
277439 TTCGCTTAGG
277449 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
277483 TTACCGACTG
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:292254 original size:19 final size:19
Alignment explanation
Indices: 292230--292267 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
292220 TTAAATTTAA
292230 ATTTAA-ATTATTTTATTTT
1 ATTTAATATT-TTTTATTTT
292249 ATTTAATATTTTTTATTTT
1 ATTTAATATTTTTTATTTT
292268 GTTATGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTAATATTTTTTATTTT
Found at i:295913 original size:42 final size:42
Alignment explanation
Indices: 295847--295930 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 42
295837 TTTGCAGCCC
*
295847 CACCGTTAACCACCGCACAAAGGCATTGA-GGCAACGATTGAA
1 CACCGTTAACCACCACACAAAGGCATT-ACGGCAACGATTGAA
* * * *
295889 CACCGTTAACCGCCACGCATAGGCATTACGGCGACGATTGAA
1 CACCGTTAACCACCACACAAAGGCATTACGGCAACGATTGAA
295931 TTAGACACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 35 0.97
ACGTcount: A:0.32, C:0.30, G:0.23, T:0.15
Consensus pattern (42 bp):
CACCGTTAACCACCACACAAAGGCATTACGGCAACGATTGAA
Found at i:297854 original size:21 final size:21
Alignment explanation
Indices: 297830--297877 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
297820 TTAACATGTT
297830 AGTCCACAATGCTGACATGGC
1 AGTCCACAATGCTGACATGGC
* *
297851 AGTCCACATTGCTGACATGGT
1 AGTCCACAATGCTGACATGGC
297872 AGTCCA
1 AGTCCA
297878 GGGTGGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.27, G:0.23, T:0.23
Consensus pattern (21 bp):
AGTCCACAATGCTGACATGGC
Found at i:298664 original size:49 final size:49
Alignment explanation
Indices: 298606--298715 Score: 159
Period size: 49 Copynumber: 2.2 Consensus size: 49
298596 TTTTTAACCA
* *
298606 GTGACCAAAACATTACGTTAAGTATAATTTTGAAAAAAATAATAG-TTG
1 GTGACCAAAACATAACGTTAAATATAATTTTGAAAAAAATAATAGCTTG
** *
298654 GCTGACCAAAATGTAACGTTAAATATGATTTTGAAAAAAATAATAGCTTG
1 G-TGACCAAAACATAACGTTAAATATAATTTTGAAAAAAATAATAGCTTG
298704 GTGACCAAAACA
1 GTGACCAAAACA
298716 AAAACTAAGC
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
48 1 0.02
49 48 0.91
50 4 0.08
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.28
Consensus pattern (49 bp):
GTGACCAAAACATAACGTTAAATATAATTTTGAAAAAAATAATAGCTTG
Found at i:304634 original size:177 final size:181
Alignment explanation
Indices: 304440--304772 Score: 460
Period size: 187 Copynumber: 1.8 Consensus size: 181
304430 TATCAAACAA
** * *
304440 TCTATTAAATTTACCAACTTTAGTGTAATCATTATGCTTTTGTTTATTAAA-T-T-A-TGTCTTT
1 TCTATTAAACCTACCAACTTTAGTGTAATCATTAT-ATTTTGTTTATTAAATTATCATTATCTTT
*
304501 TT-ATTTTTTTTATAATTAAACAATAATTATTTATTTTTAAATTTTTGTTATCTTTTTTACTTAT
65 TTGATTTTTTTTATAATTAAACAATAATTATTTATTTTTAAATTTTTGTTATATTTTTTACTTAT
*
304565 TTAATCATTCATACATATATATAATTTGGGTTAGTCTAAATATACTAAGTAG
130 TTAATCATACATACATATATATAATTTGGGTTAGTCTAAATATACTAAGTAG
*
304617 TCTATTAAACCTACCAACTTTAGTGTAATCATTATATTTTTTTTATTAAAGTTTTCTTATCATTA
1 TCTATTAAACCTACCAACTTTAGTGTAATCATTATATTTTGTTTATTAAA------TTATCATTA
* * * *
304682 TGTTTTTGCTTTTTTTTATAATTAAATAATCATTATTTATTTTTAAATTTTTGTTATATTTTTTA
60 TCTTTTTGATTTTTTTTATAATTAAACAATAATTATTTATTTTTAAATTTTTGTTATATTTTTTA
*
304747 CTTATTTAATTATACATACATATATA
125 CTTATTTAATCATACATACATATATA
304773 ATTTTATATT
Statistics
Matches: 133, Mismatches: 12, Indels: 12
0.85 0.08 0.08
Matches are distributed among these distances:
176 13 0.10
177 33 0.25
183 1 0.01
184 1 0.01
185 1 0.01
186 7 0.05
187 77 0.58
ACGTcount: A:0.31, C:0.09, G:0.05, T:0.55
Consensus pattern (181 bp):
TCTATTAAACCTACCAACTTTAGTGTAATCATTATATTTTGTTTATTAAATTATCATTATCTTTT
TGATTTTTTTTATAATTAAACAATAATTATTTATTTTTAAATTTTTGTTATATTTTTTACTTATT
TAATCATACATACATATATATAATTTGGGTTAGTCTAAATATACTAAGTAG
Found at i:304785 original size:7 final size:7
Alignment explanation
Indices: 304773--304797 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
304763 TACATATATA
304773 ATTTTAT
1 ATTTTAT
304780 ATTTTAT
1 ATTTTAT
304787 ATTTTAT
1 ATTTTAT
304794 ATTT
1 ATTT
304798 ATGTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
ATTTTAT
Found at i:305082 original size:13 final size:14
Alignment explanation
Indices: 305064--305121 Score: 57
Period size: 13 Copynumber: 4.2 Consensus size: 14
305054 GTCTTTTTCA
305064 TTATTAAAGTT-TT
1 TTATTAAAGTTATT
*
305077 TTATTAAAGTATTTT
1 TTATTAAAGT-TATT
* * *
305092 TTATT-TATTTCTT
1 TTATTAAAGTTATT
305105 TTATTAAAGTTATT
1 TTATTAAAGTTATT
305119 TTA
1 TTA
305122 ATCAATTTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
13 18 0.50
14 11 0.31
15 7 0.19
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (14 bp):
TTATTAAAGTTATT
Found at i:305100 original size:32 final size:32
Alignment explanation
Indices: 305026--305100 Score: 80
Period size: 31 Copynumber: 2.3 Consensus size: 32
305016 TATTGAAAAA
* * *
305026 TTTTATCTATATAAAATTTTCTATTAAGGTCTT
1 TTTTATTTAT-TAAAATTTTCTATTAAAGTATT
* * *
305059 TTTCA-TTATTAAAGTTTTTTATTAAAGTATT
1 TTTTATTTATTAAAATTTTCTATTAAAGTATT
305090 TTTTATTTATT
1 TTTTATTTATT
305101 TCTTTTATTA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
31 22 0.65
32 8 0.24
33 4 0.12
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.60
Consensus pattern (32 bp):
TTTTATTTATTAAAATTTTCTATTAAAGTATT
Found at i:305129 original size:28 final size:28
Alignment explanation
Indices: 305075--305129 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
305065 TATTAAAGTT
* **
305075 TTTTATTAAAGTATTTTTTATTTATTTC
1 TTTTATTAAAGTATTTTTAATCAATTTC
305103 TTTTATTAAAGT-TATTTTAATCAATTT
1 TTTTATTAAAGTAT-TTTTAATCAATTT
305130 AAATTTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 1 0.04
28 22 0.96
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (28 bp):
TTTTATTAAAGTATTTTTAATCAATTTC
Found at i:305203 original size:15 final size:15
Alignment explanation
Indices: 305183--305214 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
305173 GGTCGCATGT
305183 TGAGATTACAAAACA
1 TGAGATTACAAAACA
305198 TGAGATTACAAAACA
1 TGAGATTACAAAACA
305213 TG
1 TG
305215 GGATGAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.12, G:0.16, T:0.22
Consensus pattern (15 bp):
TGAGATTACAAAACA
Found at i:319738 original size:14 final size:14
Alignment explanation
Indices: 319721--319748 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
319711 ACACTAAACC
319721 ATAATTTAAGGTTT
1 ATAATTTAAGGTTT
319735 ATAATTTAAGGTTT
1 ATAATTTAAGGTTT
319749 TAAGTTGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (14 bp):
ATAATTTAAGGTTT
Found at i:321075 original size:21 final size:21
Alignment explanation
Indices: 321049--321097 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
321039 CTAGATTCGT
*
321049 AACGCGAACTTCGACTATCGC
1 AACGCGAACTTCGACCATCGC
*
321070 AACGCGAACTTGGACCATCGC
1 AACGCGAACTTCGACCATCGC
*
321091 AATGCGA
1 AACGCGA
321098 TTGCGATAGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.31, G:0.22, T:0.16
Consensus pattern (21 bp):
AACGCGAACTTCGACCATCGC
Found at i:321124 original size:21 final size:21
Alignment explanation
Indices: 321098--321146 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
321088 CGCAATGCGA
*
321098 TTGCGATAGCCCAAGTTCGCG
1 TTGCGATAGCCCAAATTCGCG
***
321119 TTGCGATTTTCCAAATTCGCG
1 TTGCGATAGCCCAAATTCGCG
321140 TTGCGAT
1 TTGCGAT
321147 TTATTCAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.33
Consensus pattern (21 bp):
TTGCGATAGCCCAAATTCGCG
Found at i:321147 original size:21 final size:21
Alignment explanation
Indices: 321108--321148 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
321098 TTGCGATAGC
*
321108 CCAAGTTCGCGTTGCGATTTT
1 CCAAATTCGCGTTGCGATTTT
321129 CCAAATTCGCGTTGCGATTT
1 CCAAATTCGCGTTGCGATTT
321149 ATTCAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (21 bp):
CCAAATTCGCGTTGCGATTTT
Found at i:321161 original size:23 final size:21
Alignment explanation
Indices: 321113--321161 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 21
321103 ATAGCCCAAG
*
321113 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATTTTCAAAA
321134 TTCGCGTTGCGATTTATTCAAAA
1 TTCGCGTTGCGA-TT-TTCAAAA
321157 TTCGC
1 TTCGC
321162 AACGACTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 12 0.48
22 2 0.08
23 11 0.44
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.39
Consensus pattern (21 bp):
TTCGCGTTGCGATTTTCAAAA
Found at i:321792 original size:19 final size:19
Alignment explanation
Indices: 321725--321854 Score: 188
Period size: 19 Copynumber: 6.6 Consensus size: 19
321715 GCGATAGTCC
321725 AAAATCGCAACGAATTTGG
1 AAAATCGCAACGAATTTGG
* *
321744 AATAAATCGCAACGCGAACTTCG
1 -A-AAATCGCAA--CGAATTTGG
**
321767 ACTATCGCAACGAATTTGG
1 AAAATCGCAACGAATTTGG
321786 AAAATCGCAACGAATTTGG
1 AAAATCGCAACGAATTTGG
321805 AAAATCGCAACGAATTTGG
1 AAAATCGCAACGAATTTGG
321824 AAAATCGCAACGAATTTGG
1 AAAATCGCAACGAATTTGG
321843 AAAATCGCAACG
1 AAAATCGCAACG
321855 CGAACTTCGA
Statistics
Matches: 99, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
19 74 0.75
20 1 0.01
21 16 0.16
22 1 0.01
23 7 0.07
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.20
Consensus pattern (19 bp):
AAAATCGCAACGAATTTGG
Found at i:323984 original size:14 final size:14
Alignment explanation
Indices: 323965--323992 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
323955 AAGTGAAAAA
323965 ATAGTTATATAATT
1 ATAGTTATATAATT
323979 ATAGTTATATAATT
1 ATAGTTATATAATT
323993 TTGTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATAGTTATATAATT
Found at i:324449 original size:21 final size:22
Alignment explanation
Indices: 324424--324475 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 22
324414 AAAATTGAAT
*
324424 CTAAATCATAAAT-TCTAACAC
1 CTAAATCATAAATCCCTAACAC
* *
324445 CTAAATCCT-AATCCCTAACCC
1 CTAAATCATAAATCCCTAACAC
324466 CTAAATCATA
1 CTAAATCATA
324476 CATAAATCTC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 3 0.12
21 22 0.88
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.27
Consensus pattern (22 bp):
CTAAATCATAAATCCCTAACAC
Found at i:324572 original size:21 final size:22
Alignment explanation
Indices: 324532--324575 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
324522 AATTATTAAT
*
324532 ATAATATTTTTTTAATAATTAC
1 ATAATATTATTTTAATAATTAC
324554 ATAATATTATTTT-ATAATTAC
1 ATAATATTATTTTAATAATTAC
324575 A
1 A
324576 CATCCATCGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (22 bp):
ATAATATTATTTTAATAATTAC
Found at i:335185 original size:2 final size:2
Alignment explanation
Indices: 335178--335214 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
335168 ATCTAAAACA
335178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
335215 GACACACACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:339966 original size:21 final size:21
Alignment explanation
Indices: 339924--339966 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
339914 TTTCTAGGCT
* *
339924 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
339945 AGGGGAATCGATATCCC-CTCA
1 AGGGGAATCGATA-CCCACTCA
339966 A
1 A
339967 CGAATATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:340018 original size:20 final size:20
Alignment explanation
Indices: 339993--340030 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
339983 GAATGCTAGA
*
339993 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
340013 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
340031 TATAAAAAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:340729 original size:103 final size:103
Alignment explanation
Indices: 340504--340721 Score: 418
Period size: 103 Copynumber: 2.1 Consensus size: 103
340494 ATAGAGGGTC
*
340504 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
340569 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
340607 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
340672 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
340710 TATGTGGTCCTT
1 TATGTGGTCCTT
340722 ATGGACATTA
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 112 1.00
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:340771 original size:23 final size:23
Alignment explanation
Indices: 340738--340800 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
340728 ATTATTATAT
340738 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
340761 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
340784 GGCACTAAGGTGCAATT
1 GGCACTACGGTGCAATT
340801 ATATGAGCTG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:346883 original size:21 final size:21
Alignment explanation
Indices: 346841--346883 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
346831 TTTCTAGGCT
* *
346841 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
346862 AGGGGAATCGATATCCC-CTCA
1 AGGGGAATCGATA-CCCACTCA
346883 A
1 A
346884 CGAATATGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:346934 original size:21 final size:21
Alignment explanation
Indices: 346910--346949 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
346900 GAATGCTAGA
*
346910 GGGGAATCGATACCCCCATGG
1 GGGGAACCGATACCCCCATGG
*
346931 GGGGAACCGATTCCCCCAT
1 GGGGAACCGATACCCCCAT
346950 ATAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.33, G:0.30, T:0.15
Consensus pattern (21 bp):
GGGGAACCGATACCCCCATGG
Found at i:347547 original size:86 final size:86
Alignment explanation
Indices: 347402--347565 Score: 301
Period size: 86 Copynumber: 1.9 Consensus size: 86
347392 GTAGAGGGTC
*
347402 TATGTGGTCCTTCGGGACATATATGTATTATTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTATTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
347467 TTGATCATTGGTAAGGAATGA
66 TTGATCATTGGTAAGGAATGA
*
347488 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTATTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
*
347553 TTGATCCTTGGTA
66 TTGATCATTGGTA
347566 TATGTATATG
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 75 1.00
ACGTcount: A:0.25, C:0.13, G:0.27, T:0.35
Consensus pattern (86 bp):
TATGTGGTCATTCGGGACATATATGTATTATTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
TTGATCATTGGTAAGGAATGA
Found at i:347652 original size:23 final size:23
Alignment explanation
Indices: 347619--347681 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
347609 ATTATTATAT
*
347619 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACAC
* *
347642 GGCACTCCGGTGCAATTCTACAT
1 GGCACTACGGTGCAATTCTACAC
*
347665 GGCACTAAGGTGCAATT
1 GGCACTACGGTGCAATT
347682 ATATGAGCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.24, C:0.27, G:0.25, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACAC
Found at i:349835 original size:103 final size:103
Alignment explanation
Indices: 349656--349975 Score: 579
Period size: 103 Copynumber: 3.1 Consensus size: 103
349646 GTCGAGGGTC
*
349656 TATGTGGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
349721 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
349759 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
349824 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
*
349862 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACGCA-AC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * * *
349926 TTGATCCCTAGTATATGTATATGATTATTAAGGAATGA
66 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
349964 TATGTGGTCCTT
1 TATGTGGTCCTT
349976 ATGGACATTA
Statistics
Matches: 211, Mismatches: 6, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
102 48 0.23
103 163 0.77
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
Found at i:350025 original size:23 final size:23
Alignment explanation
Indices: 349991--350059 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
349981 CATTATTATA
349991 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
350014 TGGCACTCCGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
350037 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
350060 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:356603 original size:19 final size:21
Alignment explanation
Indices: 356567--356606 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
356557 ATTTTTTAGA
356567 AAAAAGTATAATTATAATTTT
1 AAAAAGTATAATTATAATTTT
356588 AAAAA-TATAA-TATAATTTT
1 AAAAAGTATAATTATAATTTT
356607 CCATAAACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.47
20 5 0.26
21 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (21 bp):
AAAAAGTATAATTATAATTTT
Found at i:357160 original size:13 final size:13
Alignment explanation
Indices: 357142--357175 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
357132 ACCACCATCT
357142 ACGGTAGTC-TACG
1 ACGGTAG-CATACG
357155 ACGGTAGCATACG
1 ACGGTAGCATACG
357168 ACGGTAGC
1 ACGGTAGC
357176 GTCTAGTCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 1 0.05
13 19 0.95
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.18
Consensus pattern (13 bp):
ACGGTAGCATACG
Found at i:368665 original size:2 final size:2
Alignment explanation
Indices: 368658--368683 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
368648 TTTTGGAATC
368658 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
368684 TTTTTGATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:372993 original size:21 final size:21
Alignment explanation
Indices: 372968--373015 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
372958 CCTAATATTG
372968 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
372989 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
373010 TAATGT
1 CAATGT
373016 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:381136 original size:80 final size:80
Alignment explanation
Indices: 380998--381154 Score: 190
Period size: 80 Copynumber: 2.0 Consensus size: 80
380988 TAACATTTTC
* * ** * *
380998 GTAAAGTGTCCAATAATAACAAAACTGGTAGAAAAAATAATGTTTTTGGTGACGTTTTACCGGAT
1 GTAAAGTGTCCAATAATAAAAAAACCGGTAGAAAAAATAATGTTTCCGATAACGTTTTACCGGAT
*
381063 ATGTTAACAAAACTG
66 ATGTTAAAAAAACTG
* ** *
381078 GTAAAGTG-CCTAATAATAAAAAAACCGGTAGAAATAATAATGTTTCCGATAATTTTTTACCGGT
1 GTAAAGTGTCC-AATAATAAAAAAACCGGTAGAAAAAATAATGTTTCCGATAACGTTTTACCGGA
*
381142 TTTGTTAAAAAAA
65 TATGTTAAAAAAA
381155 TAATAACAAA
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
79 2 0.03
80 62 0.97
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (80 bp):
GTAAAGTGTCCAATAATAAAAAAACCGGTAGAAAAAATAATGTTTCCGATAACGTTTTACCGGAT
ATGTTAAAAAAACTG
Found at i:383020 original size:15 final size:14
Alignment explanation
Indices: 382991--383025 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
382981 AGAGACTGCC
382991 TCTTTTTTTTATTT
1 TCTTTTTTTTATTT
*
383005 TCTTTTTTCTTTTTT
1 TCTTTTTT-TTATTT
383020 TCTTTT
1 TCTTTT
383026 CTTACCTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (14 bp):
TCTTTTTTTTATTT
Found at i:384887 original size:14 final size:14
Alignment explanation
Indices: 384870--384898 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
384860 AGCAAATGCT
384870 ACTGTATAAATTAG
1 ACTGTATAAATTAG
384884 ACTGTATAAATTAG
1 ACTGTATAAATTAG
384898 A
1 A
384899 AGAAAAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.14, T:0.34
Consensus pattern (14 bp):
ACTGTATAAATTAG
Done.