Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 16 of 193
Found at i:5642129 original size:58 final size:59
Alignment explanation
Indices: 5642067--5642196 Score: 169
Period size: 58 Copynumber: 2.2 Consensus size: 59
5642057 CAAACTTTCC
*
5642067 AAAATT-CCATTTTTAACCTCGAA-CCTCTTAAAATTCCA-TTTTAACCCCGATTTCACAA
1 AAAATTACCATTTTTAACCTCGAAGCCTC-GAAAATTCCATTTTTAACCCCGATTTCAC-A
* * * *
5642125 AAAATTACCA-TTTTACCCTCGAAGCCTCGAAAATTCCATTTTTAACCTCGATTTTACC
1 AAAATTACCATTTTTAACCTCGAAGCCTCGAAAATTCCATTTTTAACCCCGATTTCACA
5642183 AAAATTACCATTTT
1 AAAATTACCATTTT
5642197 GCCCCCGGGT
Statistics
Matches: 63, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
58 37 0.59
59 26 0.41
ACGTcount: A:0.34, C:0.26, G:0.05, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTTAACCTCGAAGCCTCGAAAATTCCATTTTTAACCCCGATTTCACA
Found at i:5642172 original size:87 final size:87
Alignment explanation
Indices: 5642009--5642175 Score: 264
Period size: 87 Copynumber: 1.9 Consensus size: 87
5641999 CAAACTTTCC
** *
5642009 AAAATTCCATTTTAACCCCGATTTCACCTAAAATTACCATTTTACCCCCAAACTTTCCAAAATTC
1 AAAATTCCATTTTAACCCCGATTTCACAAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTC
5642074 CATTTTTAACCTCGAACCTCTT
66 CATTTTTAACCTCGAACCTCTT
* * *
5642096 AAAATTCCATTTTAACCCCGATTTCACAAAAAATTACCATTTTACCCTCGAAGC-CTCGAAAATT
1 AAAATTCCATTTTAACCCCGATTTCACAAAAAATTACCATTTTACCC-CCAAACTCTCCAAAATT
5642160 CCATTTTTAACCTCGA
65 CCATTTTTAACCTCGA
5642176 TTTTACCAAA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
87 69 0.95
88 4 0.05
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.33
Consensus pattern (87 bp):
AAAATTCCATTTTAACCCCGATTTCACAAAAAATTACCATTTTACCCCCAAACTCTCCAAAATTC
CATTTTTAACCTCGAACCTCTT
Found at i:5654063 original size:92 final size:92
Alignment explanation
Indices: 5653915--5654718 Score: 1274
Period size: 92 Copynumber: 8.9 Consensus size: 92
5653905 GAGCAACGTC
* * ** * *
5653915 ATCCTCTTGAAATTGAAGTAGAG-TGGATAACAAGTCTTTAT-ATCTCTGAAATTGAAGTAGGAG
1 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCT-TCTGAAATTGAAGTAAGAG
* *
5653978 TAAGATGAAGTATCAACGTCATTTTCCC
65 TAAGATGAAGCATCAACGTCATTTTCCT
* *
5654006 ATCCTCTTGAAATTGAAGTAAAGCTGAATAACAAGCCTTCGTCCATCTGAAATTGAAGTAAGAGT
1 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAAATTGAAGTAAGAGT
5654071 AAGATGAAGCATCAACGTCATTTTCCT
66 AAGATGAAGCATCAACGTCATTTTCCT
5654098 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAAATTGAAGTAAGAGT
1 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAAATTGAAGTAAGAGT
5654163 AAGATGAAGCATCAACGTCATTTTCCT
66 AAGATGAAGCATCAACGTCATTTTCCT
* *
5654190 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCTTTCGTCCTTCTGAAATTGAAGTAAGAAT
1 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAAATTGAAGTAAGAGT
*
5654255 AAGATGAAACATCAACGTCATTTTCCT
66 AAGATGAAGCATCAACGTCATTTTCCT
*
5654282 ATCCTCTTGAAATTGAAGTAAAGCTGAATAACAAGCCTTCGTCCTTCTGAAATTGAAGTAAGAGT
1 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAAATTGAAGTAAGAGT
* *
5654347 AAGATGAAACATCAACGACATTTTCCT
66 AAGATGAAGCATCAACGTCATTTTCCT
*
5654374 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTTGTCCTTCTGAAATTGAAGTAAGAGT
1 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAAATTGAAGTAAGAGT
*
5654439 AAGATGAAACATCAACGTCATTTTCCT
66 AAGATGAAGCATCAACGTCATTTTCCT
5654466 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAAATT---G-AAGA-T
1 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAAATTGAAGTAAGAGT
5654526 --GA--AA-CATCAACGTCATTTTCCT
66 AAGATGAAGCATCAACGTCATTTTCCT
* * *
5654548 ATCCTCTTGAAATTGAAGTACAGCTGGATAATAAGCCTTCGTCCTTTTGAAATTGAAGTAAGAGT
1 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAAATTGAAGTAAGAGT
5654613 AAGATGAAGCATCAACGTCATTTTCCT
66 AAGATGAAGCATCAACGTCATTTTCCT
* * *
5654640 ATCCTCTTGAAATTGAAGTAAAGCTGGATAGCAAGCCTTCGTCCTTTTGAAATT-AAATAAGAGT
1 ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAAATTGAAGTAAGAGT
* *
5654704 TAGGTGAAGCATCAA
66 AAGATGAAGCATCAA
5654719 ACCTACTGTT
Statistics
Matches: 669, Mismatches: 32, Indels: 24
0.92 0.04 0.03
Matches are distributed among these distances:
82 69 0.10
83 2 0.00
85 3 0.00
86 4 0.01
87 2 0.00
88 4 0.01
89 3 0.00
91 46 0.07
92 536 0.80
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (92 bp):
ATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCTTCTGAAATTGAAGTAAGAGT
AAGATGAAGCATCAACGTCATTTTCCT
Found at i:5654560 original size:42 final size:42
Alignment explanation
Indices: 5654439--5654565 Score: 110
Period size: 42 Copynumber: 3.1 Consensus size: 42
5654429 AAGTAAGAGT
5654439 AAGATGAAACATCAACGTCATTTTCCTATCCTCTTGAAATTG
1 AAGATGAAACATCAACGTCATTTTCCTATCCTCTTGAAATTG
* *
5654481 AAG-T-AAAGCTGGAT-AACAAG-C--CTT-C-GTCCT-TCTGAAATTG
1 AAGATGAAA-C---ATCAAC--GTCATTTTCCTATCCTCT-TGAAATTG
5654521 AAGATGAAACATCAACGTCATTTTCCTATCCTCTTGAAATTG
1 AAGATGAAACATCAACGTCATTTTCCTATCCTCTTGAAATTG
5654563 AAG
1 AAG
5654566 TACAGCTGGA
Statistics
Matches: 65, Mismatches: 4, Indels: 32
0.64 0.04 0.32
Matches are distributed among these distances:
37 1 0.02
38 3 0.05
39 4 0.06
40 20 0.31
41 6 0.09
42 23 0.35
43 4 0.06
44 3 0.05
45 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (42 bp):
AAGATGAAACATCAACGTCATTTTCCTATCCTCTTGAAATTG
Found at i:5654576 original size:82 final size:84
Alignment explanation
Indices: 5654436--5654694 Score: 396
Period size: 82 Copynumber: 3.0 Consensus size: 84
5654426 TTGAAGTAAG
5654436 AGTAAGATGAAACATCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAG
1 AGTAAGATGAAACATCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAG
*
5654501 CCTTCGTCCTTCTGAAATT
66 CCTTCGTCCTTTTGAAATT
* *
5654520 -G-AAGATGAAACATCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTACAGCTGGATAATAAG
1 AGTAAGATGAAACATCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAG
5654583 CCTTCGTCCTTTTGAAATT
66 CCTTCGTCCTTTTGAAATT
5654602 GAAGTAAGAGTAAGATGAAGCATCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGG
1 --AGTAAGA-T--GA--AA-CATCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGG
*
5654667 ATAGCAAGCCTTCGTCCTTTTGAAATT
58 ATAACAAGCCTTCGTCCTTTTGAAATT
5654694 A
1 A
5654695 AATAAGAGTT
Statistics
Matches: 159, Mismatches: 6, Indels: 14
0.89 0.03 0.08
Matches are distributed among these distances:
82 78 0.49
83 1 0.01
85 1 0.01
86 4 0.03
87 1 0.01
89 2 0.01
90 1 0.01
91 2 0.01
92 69 0.43
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (84 bp):
AGTAAGATGAAACATCAACGTCATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAG
CCTTCGTCCTTTTGAAATT
Found at i:5655046 original size:26 final size:26
Alignment explanation
Indices: 5655002--5655053 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5654992 TTATGTTAAA
* *
5655002 GTTAAATTTATTTTAAATTTAGATTT
1 GTTAAATTTAATTTAAATTTAAATTT
5655028 GTTAAATTTAAATTT-AATTTAAATTT
1 GTTAAATTT-AATTTAAATTTAAATTT
5655054 AGAATTAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (26 bp):
GTTAAATTTAATTTAAATTTAAATTT
Found at i:5655048 original size:5 final size:6
Alignment explanation
Indices: 5654962--5655059 Score: 62
Period size: 6 Copynumber: 16.3 Consensus size: 6
5654952 GCCAAATTGT
* * * *
5654962 TTTAAA ATTAAA TTT-AT TTTAAA ATTAAA TTT--A TGTTAAA GTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
* *
5655008 TTT-AT TTTAAA TTTAGATT TGTTAAA TTTAAA TTT-AA TTTAAA TTTAGAA
1 TTTAAA TTTAAA TTTA-A-A T-TTAAA TTTAAA TTTAAA TTTAAA TTTA-AA
5655058 TT
1 TT
5655060 AATGTAAATT
Statistics
Matches: 70, Mismatches: 12, Indels: 19
0.69 0.12 0.19
Matches are distributed among these distances:
4 2 0.03
5 15 0.21
6 41 0.59
7 7 0.10
8 2 0.03
9 3 0.04
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (6 bp):
TTTAAA
Found at i:5655048 original size:11 final size:11
Alignment explanation
Indices: 5654969--5655054 Score: 59
Period size: 11 Copynumber: 7.8 Consensus size: 11
5654959 TGTTTTAAAA
*
5654969 TTAAATTTATT
1 TTAAATTTAAT
*
5654980 TTAAAATTAAAT
1 TT-AAATTTAAT
** * *
5654992 TTATGTTAAAG
1 TTAAATTTAAT
*
5655003 TTAAATTTATT
1 TTAAATTTAAT
5655014 TTAAATTTAGAT
1 TTAAATTTA-AT
* *
5655026 TT--GTTAAAT
1 TTAAATTTAAT
5655035 TTAAATTTAAT
1 TTAAATTTAAT
5655046 TTAAATTTA
1 TTAAATTTA
5655055 GAATTAATGT
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
9 4 0.07
10 3 0.05
11 37 0.66
12 12 0.21
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:5655051 original size:17 final size:17
Alignment explanation
Indices: 5654962--5655090 Score: 106
Period size: 17 Copynumber: 7.6 Consensus size: 17
5654952 GCCAAATTGT
* *
5654962 TTTAAAATTAAATTTAT
1 TTTAAATTTAAATTTAA
*
5654979 TTTAAAATTAAATTT-A
1 TTTAAATTTAAATTTAA
* *
5654995 TGTTAAAGTTAAATTTAT
1 T-TTAAATTTAAATTTAA
*
5655013 TTTAAATTTAGATTT--
1 TTTAAATTTAAATTTAA
*
5655028 GTTAAATTTAAATTTAA
1 TTTAAATTTAAATTTAA
5655045 TTTAAATTTAGAA-TTAA
1 TTTAAATTTA-AATTTAA
* *
5655062 TGTAAATTTTAAAATT-A
1 TTTAAA-TTTAAATTTAA
5655079 TTATAAATTTAA
1 TT-TAAATTTAA
5655091 TAGAGTGTCC
Statistics
Matches: 94, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
15 13 0.14
16 1 0.01
17 67 0.71
18 13 0.14
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
TTTAAATTTAAATTTAA
Found at i:5657111 original size:29 final size:28
Alignment explanation
Indices: 5657066--5657370 Score: 185
Period size: 29 Copynumber: 10.4 Consensus size: 28
5657056 GAACTTCTAG
5657066 AATTCCATTTTTAACCCCAATTTTACCAAA
1 AATTCCA-TTTTAACCCCAATTTT-CCAAA
*
5657096 AATTACCATTTT-ACCCTCGAACTTTCC-AA
1 AATT-CCATTTTAACCC-C-AATTTTCCAAA
*
5657125 AATTCCATTTTTAACCCCAATTTCACCAAA
1 AATTCCA-TTTTAACCCCAATTT-TCCAAA
* * *
5657155 AATTACCATTTTACCCCCAAACTTT-CTAA
1 AATT-CCATTTTAACCCC-AATTTTCCAAA
* * *
5657184 AATTCCATTTTTAACCCCGATTTCACCTAA
1 AATTCCA-TTTTAACCCCAATTT-TCCAAA
* * *
5657214 AATTACTATTTTACCCCCGAACTTTCC-AA
1 AATT-CCATTTTAACCCC-AATTTTCCAAA
* ** *
5657243 AATTCCATTTTTAACCTCGAA-CCTCCTAA
1 AATTCCA-TTTTAACC-CCAATTTTCCAAA
*
5657272 AATTCCATTTTAACCCCAATTTCACCAAA
1 AATTCCATTTTAACCCCAATTT-TCCAAA
**
5657301 AATTACCATTTT-ACCCTCGAAGATT-CAAA
1 AATT-CCATTTTAACCC-C-AATTTTCCAAA
*
5657330 AATTCCATTTTTAACCCCAA-TTTCACCAA
1 AATTCCA-TTTTAACCCCAATTTTC-CAAA
5657359 AATTACCATTTT
1 AATT-CCATTTT
5657371 GCCCTTAGGT
Statistics
Matches: 217, Mismatches: 31, Indels: 55
0.72 0.10 0.18
Matches are distributed among these distances:
27 5 0.02
28 31 0.14
29 93 0.43
30 65 0.30
31 23 0.11
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.35
Consensus pattern (28 bp):
AATTCCATTTTAACCCCAATTTTCCAAA
Found at i:5657153 original size:59 final size:59
Alignment explanation
Indices: 5657036--5657258 Score: 358
Period size: 59 Copynumber: 3.8 Consensus size: 59
5657026 AAAATTTTAG
* * *
5657036 AAAATTACCATTTTACCCCCGAAC-TTCTAGAATTCCATTTTTAACCCCAATTTTACCA
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCA
*
5657094 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCA
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCA
* * * *
5657153 AAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCT
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCA
*
5657212 AAAATTACTATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACC
5657259 TCGAACCTCC
Statistics
Matches: 152, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
58 23 0.15
59 129 0.85
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCA
Found at i:5657301 original size:146 final size:146
Alignment explanation
Indices: 5657094--5657370 Score: 425
Period size: 146 Copynumber: 1.9 Consensus size: 146
5657084 AATTTTACCA
* *
5657094 AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATT
1 AAAATTACCATTTTAACCTCGAACTCTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATT
* * * *
5657159 ACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCTAAAATTACTATT
66 ACCATTTTACCCCCAAACATTCAAAAATTCCATTTTTAACCCCAATTTCACC-AAAATTACCATT
5657224 TTACCCCCGAACTTTCC
130 TTACCCCCGAACTTTCC
5657241 AAAATT-CCATTTTTAACCTCGAAC-CTCCTAAAATTCCA-TTTTAACCCCAATTTCACCAAAAA
1 AAAATTACCA-TTTTAACCTCGAACTCTCC-AAAATTCCATTTTTAACCCCAATTTCACCAAAAA
* * *
5657303 TTACCATTTTACCCTCGAAGATTCAAAAATTCCATTTTTAACCCCAATTTCACCAAAATTACCAT
64 TTACCATTTTACCCCCAAACATTCAAAAATTCCATTTTTAACCCCAATTTCACCAAAATTACCAT
5657368 TTT
129 TTT
5657371 GCCCTTAGGT
Statistics
Matches: 119, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
145 13 0.11
146 78 0.66
147 28 0.24
ACGTcount: A:0.34, C:0.29, G:0.02, T:0.34
Consensus pattern (146 bp):
AAAATTACCATTTTAACCTCGAACTCTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAATT
ACCATTTTACCCCCAAACATTCAAAAATTCCATTTTTAACCCCAATTTCACCAAAATTACCATTT
TACCCCCGAACTTTCC
Found at i:5657304 original size:87 final size:88
Alignment explanation
Indices: 5657180--5657345 Score: 262
Period size: 87 Copynumber: 1.9 Consensus size: 88
5657170 CCCAAACTTT
* * * * *
5657180 CTAAAATTCCATTTTTAACCCCGATTTCACCTAAAATTACTATTTTACCCCCGAACTTTCCAAAA
1 CTAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAACATTCAAAAA
5657245 TTCCATTTTTAACCTCGAACCTC
66 TTCCATTTTTAACCTCGAACCTC
* *
5657268 CTAAAATTCCA-TTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCTCGAAGATTCAAAAA
1 CTAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAACATTCAAAAA
5657332 TTCCATTTTTAACC
66 TTCCATTTTTAACC
5657346 CCAATTTCAC
Statistics
Matches: 71, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
87 60 0.85
88 11 0.15
ACGTcount: A:0.34, C:0.29, G:0.03, T:0.34
Consensus pattern (88 bp):
CTAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCATTTTACCCCCGAACATTCAAAAA
TTCCATTTTTAACCTCGAACCTC
Found at i:5657312 original size:118 final size:117
Alignment explanation
Indices: 5657036--5657290 Score: 336
Period size: 118 Copynumber: 2.2 Consensus size: 117
5657026 AAAATTTTAG
* * * * *
5657036 AAAATTACCATTTTACCCCCGAAC-TTCTAGAATTCCATTTTTAACCCCAATTTTACCAAAAATT
1 AAAATTACCATTTTAACCCCAAACTTTCAAAAATTCCATTTTTAACCCCAATTTCACCAAAAATT
* *
5657100 ACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCA
66 ACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCAA-TCCACCA
* * * *
5657153 AAAATTACCATTTTACCCCCAAACTTTCTAAAATTCCATTTTTAACCCCGATTTCACCTAAAATT
1 AAAATTACCATTTTAACCCCAAACTTTCAAAAATTCCATTTTTAACCCCAATTTCACCAAAAATT
* * * *
5657218 ACTATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCGAA-CCTCCT
66 ACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACC-CCAATCCACCA
5657270 AAAATT-CCATTTTAACCCCAA
1 AAAATTACCATTTTAACCCCAA
5657291 TTTCACCAAA
Statistics
Matches: 124, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
116 14 0.11
117 32 0.26
118 75 0.60
119 3 0.02
ACGTcount: A:0.33, C:0.30, G:0.02, T:0.34
Consensus pattern (117 bp):
AAAATTACCATTTTAACCCCAAACTTTCAAAAATTCCATTTTTAACCCCAATTTCACCAAAAATT
ACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCCCAATCCACCA
Found at i:5662348 original size:60 final size:58
Alignment explanation
Indices: 5662246--5662913 Score: 492
Period size: 59 Copynumber: 11.2 Consensus size: 58
5662236 GGTGTTGGCC
** * ** *
5662246 ATGGCCGACACCCCTTTTAAATCTGATAAAAAAATCAAATTTTTGGGTGTTGGCCATGCA
1 ATGGCCGACACCCCTTTT-TGTCAGAT-AAAAAATTTAATTTTTTGGTGTTGGCCATGCA
* * **
5662306 ATGACTGACACCTCCTTTTTTGTCAGATAAAAAATTTAATTTTTTTGGTGTTGATCATGTCA
1 ATGGCCGACACC-CC-TTTTTGTCAGATAAAAAATTTAA-TTTTTTGGTGTTGGCCATG-CA
* * * *
5662368 A-GGCCAACACCCCCTTCTTGTCAGATAAAAAATTTAATTTTTTTGGTGTTGGTCATGCC
1 ATGGCCGACA-CCCCTTTTTGTCAGATAAAAAATTTAA-TTTTTTGGTGTTGGCCATGCA
* * * * * ** * *
5662427 ATGGGCAACACCCCTATTT-ACTGATAAAAAAATCAAACTTTTT-GTGTTGGTCATGCA
1 ATGGCCGACACCCCTTTTTGTCAGAT-AAAAAATTTAATTTTTTGGTGTTGGCCATGCA
**
5662484 ATGGGTGACA-CCCTCTTTT-TCAGATAAAAAATTTTTAAAATTTTTTGGTGTTGGCCATTGC-
1 ATGGCCGACACCCCT-TTTTGTCAGATAAAAAA--TTT--AATTTTTTGGTGTTGGCCA-TGCA
* * * * * * * * *
5662545 ATGGTCGACACCTCTTTTTATCTAAAT-AAAAATTCAAATATTTGGGTGTTAGCCATGCC
1 ATGGCCGACACCCCTTTTTGTC-AGATAAAAAATT-TAATTTTTTGGTGTTGGCCATGCA
* * * *
5662604 ATAGCCGACACCCCTTTTTGTCAGATAAAAAATTCAAATTTTTTTTGGTGTTGGTCATGCC
1 ATGGCCGACACCCCTTTTTGTCAGATAAAAAATT-TAA--TTTTTTGGTGTTGGCCATGCA
* * * * **
5662665 ATGGCCGACATCCCC-TTTT-TCTGGTAAAAAAATCAATTTTTTTTAATGTTGGCCATGCA
1 ATGGCCGACA-CCCCTTTTTGTCAGATAAAAAATTTAA--TTTTTTGGTGTTGGCCATGCA
* * * * * *
5662724 ATGGCCGACGCCCCTTTTTATCTAAATAAAAAATTAAATTTTTAGGTGTTGACCATGTC-
1 ATGGCCGACACCCCTTTTTGTC-AGATAAAAAATTTAATTTTTTGGTGTTGGCCATG-CA
* *
5662783 ATGGCCGACACCCCCTTTTTGTCAGATAAAAAATTTAATTTTTTTGGTGTTAGCCATGCC
1 ATGGCCGACA-CCCCTTTTTGTCAGATAAAAAATTTAA-TTTTTTGGTGTTGGCCATGCA
* * * * * *
5662843 ATGACCGACACCCCTATTTATCTGATAAAAAAATCTAATATTTTGGTGTTGGCCATGCA
1 ATGGCCGACACCCCTTTTTGTCAGAT-AAAAAATTTAATTTTTTGGTGTTGGCCATGCA
5662902 ATGGCCGACACC
1 ATGGCCGACACC
5662914 AACTTTCCCT
Statistics
Matches: 491, Mismatches: 86, Indels: 63
0.77 0.13 0.10
Matches are distributed among these distances:
56 10 0.02
57 28 0.06
58 20 0.04
59 177 0.36
60 136 0.28
61 91 0.19
62 26 0.05
63 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (58 bp):
ATGGCCGACACCCCTTTTTGTCAGATAAAAAATTTAATTTTTTGGTGTTGGCCATGCA
Found at i:5662634 original size:120 final size:118
Alignment explanation
Indices: 5662243--5662913 Score: 476
Period size: 120 Copynumber: 5.6 Consensus size: 118
5662233 ATTGGTGTTG
* * * * * *
5662243 GCCATGGCCGACACCCCTTTTAAATCTGATAAAAAAATCAAATTTTTGGGTGTTGGCCATGCAAT
1 GCCAT-GCCGACACCCCTTTT-TATCAGATAAAAAATTTAAATTTTTTGGTGTTGGCCATGCCAT
* * * * * * *
5662308 GACTGACACCTCCTTTTT-TGTCAGATAAAAAATTTAATTTTTTTGGTGTT-GATCAT
64 GGCCGACACCCCCTTTTTATCT-AAAT-AAAAATTCAATTTTTTTGGTGTTAG-CCAT
* * * * * * *
5662364 GTCAAGGCCAACACCCCCTTCTTGTCAGATAAAAAATTTAATTTTTTTGGTGTTGGTCATGCCAT
1 G-CCATGCCGACA-CCCCTTTTTATCAGATAAAAAATTTAAATTTTTTGGTGTTGGCCATGCCAT
* * * ** * *
5662429 GGGCAACA-CCCCTATTTA-CTGATAA-AAAAA-TCAAACTTTTT-GTGTTGGTCAT
64 GGCCGACACCCCCTTTTTATCT-A-AATAAAAATTCAATTTTTTTGGTGTTAGCCAT
* **
5662481 GCAATGGGTGACA-CCCTCTTTT-TCAGATAAAAAATTTTTAAAATTTTTTGGTGTTGGCCATTG
1 GCCAT-GCCGACACCCCT-TTTTATCAGATAAAAAA--TTT-AAATTTTTTGGTGTTGGCCA-TG
* * * * *
5662544 -CATGGTCGACA-CCTCTTTTTATCTAAATAAAAATTCAAATATTTGGGTGTTAGCCAT
60 CCATGGCCGACACCCCCTTTTTATCTAAATAAAAATTCAATTTTTTTGGTGTTAGCCAT
* * *
5662601 GCCATAGCCGACACCCCTTTTTGTCAGATAAAAAATTCAAATTTTTTTTGGTGTTGGTCATGCCA
1 GCCAT-GCCGACACCCCTTTTTATCAGATAAAAAATTTAAA--TTTTTTGGTGTTGGCCATGCCA
* * * ** *
5662666 TGGCCGACATCCCCTTTTTCTGGT-AA-AAAAA-TCAATTTTTTTTAATGTTGGCCAT
63 TGGCCGACACCCCCTTTTTAT-CTAAATAAAAATTCAA-TTTTTTTGGTGTTAGCCAT
* * * * * *
5662721 GCAATGGCCGACGCCCCTTTTTATCTAAATAAAAAA-TTAAATTTTTAGGTGTTGACCATGTCAT
1 GCCAT-GCCGACACCCCTTTTTATC-AGATAAAAAATTTAAATTTTTTGGTGTTGGCCATGCCAT
* * *
5662785 GGCCGACACCCCCTTTTTGTC-AGATAAAAAATTTAATTTTTTTGGTGTTAGCCAT
64 GGCCGACACCCCCTTTTTATCTAAAT-AAAAATTCAATTTTTTTGGTGTTAGCCAT
* * * * *
5662840 GCCATGACCGACACCCCTATTTATCTGATAAAAAAATCT-AATATTTTGGTGTTGGCCATGCAAT
1 GCCATG-CCGACACCCCTTTTTATCAGAT-AAAAAATTTAAATTTTTTGGTGTTGGCCATGCCAT
5662904 GGCCGACACC
64 GGCCGACACC
5662914 AACTTTCCCT
Statistics
Matches: 433, Mismatches: 86, Indels: 64
0.74 0.15 0.11
Matches are distributed among these distances:
115 16 0.04
116 6 0.01
117 20 0.05
118 93 0.21
119 102 0.24
120 104 0.24
121 82 0.19
122 10 0.02
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.35
Consensus pattern (118 bp):
GCCATGCCGACACCCCTTTTTATCAGATAAAAAATTTAAATTTTTTGGTGTTGGCCATGCCATGG
CCGACACCCCCTTTTTATCTAAATAAAAATTCAATTTTTTTGGTGTTAGCCAT
Found at i:5664242 original size:24 final size:24
Alignment explanation
Indices: 5664215--5664270 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
5664205 ACTCGGGTTG
* *
5664215 GTCCTGAGCCTCGTAATCGGGCTC
1 GTCCTCAGCCTCGTAAGCGGGCTC
* *
5664239 GTCCTCAGGCTCGTTAGCGGGCTC
1 GTCCTCAGCCTCGTAAGCGGGCTC
*
5664263 GTACTCAG
1 GTCCTCAG
5664271 GTTCGTCATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.12, C:0.32, G:0.30, T:0.25
Consensus pattern (24 bp):
GTCCTCAGCCTCGTAAGCGGGCTC
Found at i:5664837 original size:21 final size:21
Alignment explanation
Indices: 5664788--5664839 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
5664778 TTTTAAAAAA
*
5664788 TTCAAAAATATAAAAAAATAT
1 TTCAAAAATAAAAAAAAATAT
*
5664809 TTCGAAAATAAAAAAAAATAT
1 TTCAAAAATAAAAAAAAATAT
*
5664830 TATAAAAAAT
1 T-TCAAAAAT
5664840 TCGAAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCAAAAATAAAAAAAAATAT
Found at i:5666550 original size:59 final size:58
Alignment explanation
Indices: 5666414--5667112 Score: 414
Period size: 60 Copynumber: 11.8 Consensus size: 58
5666404 GGAAAGTTGC
* * * * *
5666414 TGTCGGCCATTACATAGCCAACACAAAAAAAATT-AATTTTTTACCAGATA-AAAAAGAAGG
1 TGTCGGCCATTGCATGGCCAACAC--AAAAAATTGAATTTTTTATCTGA-ACAAAAAG-GGG
* **
5666474 TGTCGGCCA-TGCAATGGCCAACACCAAAAATTCGAATTTTTTATCTGAACAAAAAGAAG
1 TGTCGGCCATTGC-ATGGCCAACACAAAAAATT-GAATTTTTTATCTGAACAAAAAGGGG
* * *
5666533 TGTCGGCAATTGCATGGCCAACACAAAAAAAAATTG-ATTTTTTA-C-CAAAAAAAAGGGG
1 TGTCGGCCATTGCATGGCCAACAC---AAAAAATTGAATTTTTTATCTGAACAAAAAGGGG
* * * * * * * *
5666591 TGTCAGCTATGGCATGGCCAACACCCAAAAATTTAAATTTTTAT-TCAGATAAAAAGGGG
1 TGTCGGCCATTGCATGGCCAACA-CAAAAAATTGAATTTTTTATCTGA-ACAAAAAGGGG
* * *
5666650 TGTCGGTCA-TGCAATGGCCAATATCAAAAAAATTTAAAATTTTTTTATCTG-A-AAAAAGGAGG
1 TGTCGGCCATTGC-ATGGCCAACA-C-AAAAAA-TT-GAA-TTTTTTATCTGAACAAAAAGG-GG
* * **
5666712 TGTCGACCA-TGCAACGGCCAACACAAAAAATTTGAATTTTTTATCTGAACAAAAAGAAG
1 TGTCGGCCATTGC-ATGGCCAACACAAAAAA-TTGAATTTTTTATCTGAACAAAAAGGGG
* * * *
5666771 TGTCGGCAATTGCATGGTCAATACAAAAAAAATTG-ATTTTTTA-C-CAA-AAAAAGGGG
1 TGTCGGCCATTGCATGG-CCA-ACACAAAAAATTGAATTTTTTATCTGAACAAAAAGGGG
* * * * * * * *
5666827 TGTCAGCTATGGCATGGCCAACACCCAAAAATTTAAATTTTTAT-TCAGATAAAAAGGGG
1 TGTCGGCCATTGCATGGCCAACA-CAAAAAATTGAATTTTTTATCTGA-ACAAAAAGGGG
** * * *
5666886 TGTCGATCA-TGCAATGGCCAATACCAAAAAATTTTAAAATTTTTTATCTG-A-AAAAGGGGG
1 TGTCGGCCATTGC-ATGGCCAACA-CAAAAAA--TT-GAATTTTTTATCTGAACAAAAAGGGG
* * *
5666946 TGTCGGTCATGGCATGGCCAACACTAAAAAAATTGAATTTTTTATCTG-ACAAGAAGGGGG
1 TGTCGGCCATTGCATGGCCAACAC--AAAAAATTGAATTTTTTATCTGAACAA-AAAGGGG
* * * * * *
5667006 TGTCAGCCATGGCATGACCAACACAAAAAAAATTAAATTTTTTATTTG-ACAAGAAGGGG
1 TGTCGGCCATTGCATGGCCAACAC--AAAAAATTGAATTTTTTATCTGAACAAAAAGGGG
* * *
5667065 ATGTCGACCATTGCATGGCCAACACCCAAAAATTTGATTTTTCTTATC
1 -TGTCGGCCATTGCATGGCCAACA--CAAAAAATTGAATTTT-TTATC
5667113 AAATTAAAAG
Statistics
Matches: 511, Mismatches: 83, Indels: 89
0.75 0.12 0.13
Matches are distributed among these distances:
54 3 0.01
55 9 0.02
56 35 0.07
57 11 0.02
58 69 0.14
59 114 0.22
60 185 0.36
61 35 0.07
62 41 0.08
63 8 0.02
64 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (58 bp):
TGTCGGCCATTGCATGGCCAACACAAAAAATTGAATTTTTTATCTGAACAAAAAGGGG
Found at i:5666870 original size:236 final size:237
Alignment explanation
Indices: 5666463--5667099 Score: 901
Period size: 236 Copynumber: 2.7 Consensus size: 237
5666453 TTTACCAGAT
* * *
5666463 AAAAAAGAAGGTGTCGGCCATGCAATGGCCAACACCAAAAATTCGAATTTTTTATCTGAACAAAA
1 AAAAAAGGAGGTGTCGGCCATGCAATGGCCAACACAAAAAATTTGAATTTTTTATCTGAACAAAA
5666528 AGAAGTGTCGGCAATTGCATGGCCAACACAAAAAAAAATTGATTTTTTACCAAAAAAAAGGGGTG
66 AGAAGTGTCGGCAATTGCATGGCCAACACAAAAAAAAATTGATTTTTTACCAAAAAAAAGGGGTG
*
5666593 TCAGCTATGGCATGGCCAACACCCAAAAATTTAAATTTTTATTCAGATAAAAAGGGGTGTCGGTC
131 TCAGCTATGGCATGGCCAACACCCAAAAATTTAAATTTTTATTCAGATAAAAAGGGGTGTCGATC
*
5666658 ATGCAATGGCCAATATCAAAAAAATTTAAAATTTTTTTATCTG
196 ATGCAATGGCCAATACCAAAAAAATTTAAAA-TTTTTTATCTG
* *
5666701 AAAAAAGGAGGTGTCGACCATGCAACGGCCAACACAAAAAATTTGAATTTTTTATCTGAACAAAA
1 AAAAAAGGAGGTGTCGGCCATGCAATGGCCAACACAAAAAATTTGAATTTTTTATCTGAACAAAA
* *
5666766 AGAAGTGTCGGCAATTGCATGGTCAATAC-AAAAAAAATTGATTTTTTACC-AAAAAAAGGGGTG
66 AGAAGTGTCGGCAATTGCATGGCCAACACAAAAAAAAATTGATTTTTTACCAAAAAAAAGGGGTG
5666829 TCAGCTATGGCATGGCCAACACCCAAAAATTTAAATTTTTATTCAGATAAAAAGGGGTGTCGATC
131 TCAGCTATGGCATGGCCAACACCCAAAAATTTAAATTTTTATTCAGATAAAAAGGGGTGTCGATC
*
5666894 ATGCAATGGCCAATACCAAAAAATTTTAAAATTTTTTATCTG
196 ATGCAATGGCCAATACCAAAAAAATTTAAAATTTTTTATCTG
* * *
5666936 -AAAAAGGGGGTGTCGGTCATGGC-ATGGCCAACACTAAAAAAATTGAATTTTTTATCTG-ACAA
1 AAAAAAGGAGGTGTCGGCCAT-GCAATGGCCAACAC-AAAAAATTTGAATTTTTTATCTGAACAA
* ** * * * * * *** * *
5666998 GAAGGGGGTGTCAGCCATGGCATGACCAACAC-AAAAAAAATTAAATTTTTTATTTGACAAGAAG
64 -AAAGAAGTGTCGGCAATTGCATGGCCAACACAAAAAAAAATT-GATTTTTTA-CCAAAAAAAAG
* *
5667062 GGGATGTC-GACCATTGCATGGCCAACACCCAAAAATTT
126 GGG-TGTCAG-CTATGGCATGGCCAACACCCAAAAATTT
5667100 GATTTTTCTT
Statistics
Matches: 360, Mismatches: 31, Indels: 15
0.89 0.08 0.04
Matches are distributed among these distances:
234 31 0.09
235 67 0.19
236 114 0.32
237 21 0.06
238 97 0.27
239 30 0.08
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (237 bp):
AAAAAAGGAGGTGTCGGCCATGCAATGGCCAACACAAAAAATTTGAATTTTTTATCTGAACAAAA
AGAAGTGTCGGCAATTGCATGGCCAACACAAAAAAAAATTGATTTTTTACCAAAAAAAAGGGGTG
TCAGCTATGGCATGGCCAACACCCAAAAATTTAAATTTTTATTCAGATAAAAAGGGGTGTCGATC
ATGCAATGGCCAATACCAAAAAAATTTAAAATTTTTTATCTG
Found at i:5670397 original size:39 final size:39
Alignment explanation
Indices: 5670354--5670433 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
5670344 ATCGATTGGC
* *
5670354 TACCAATCACCGTAACATTATCTGTAATAATTATATATA
1 TACCAATCACCCTAACATTATCTATAATAATTATATATA
5670393 TACCAATCACCCTAACATTATCTATAATAATTATATATA
1 TACCAATCACCCTAACATTATCTATAATAATTATATATA
5670432 TA
1 TA
5670434 TATATATATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.42, C:0.19, G:0.03, T:0.36
Consensus pattern (39 bp):
TACCAATCACCCTAACATTATCTATAATAATTATATATA
Found at i:5670431 original size:2 final size:2
Alignment explanation
Indices: 5670424--5670491 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
5670414 CTATAATAAT
5670424 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5670466 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5670492 AAATAAGTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5671817 original size:23 final size:23
Alignment explanation
Indices: 5671787--5671831 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5671777 AATAAAAAAT
5671787 ATAAATTTA-AAAAATAATATATA
1 ATAAATTTATAAAAATAA-ATATA
*
5671810 ATAAATTTATATAAATAAATAT
1 ATAAATTTATAAAAATAAATAT
5671832 TGTTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
ATAAATTTATAAAAATAAATATA
Found at i:5674914 original size:16 final size:16
Alignment explanation
Indices: 5674867--5674916 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
5674857 ATAATAAAAT
5674867 TATATTATAAAACCTTA
1 TATATTATAAAA-CTTA
**
5674884 T-T-TTATAAAGGTTA
1 TATATTATAAAACTTA
*
5674898 TATATTATAAAATTTA
1 TATATTATAAAACTTA
5674914 TAT
1 TAT
5674917 TACTTTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 4 0.15
15 8 0.30
16 14 0.52
17 1 0.04
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (16 bp):
TATATTATAAAACTTA
Found at i:5675728 original size:14 final size:13
Alignment explanation
Indices: 5675709--5675741 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
5675699 AAGTCAGACC
5675709 GTTGACCGTTAACT
1 GTTGACC-TTAACT
5675723 GTTGACCTTAACT
1 GTTGACCTTAACT
5675736 -TTGACC
1 GTTGACC
5675742 CGTTGACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 6 0.32
14 7 0.37
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (13 bp):
GTTGACCTTAACT
Found at i:5687257 original size:17 final size:17
Alignment explanation
Indices: 5687235--5687267 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5687225 AGCAAACAAA
5687235 AATTCA-TATATGAAAAT
1 AATTCATTA-ATGAAAAT
5687252 AATTCATTAATGAAAA
1 AATTCATTAATGAAAA
5687268 GATCTGCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.33
Consensus pattern (17 bp):
AATTCATTAATGAAAAT
Found at i:5690492 original size:3 final size:3
Alignment explanation
Indices: 5690484--5690508 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5690474 AGCAATTTAA
5690484 TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC T
5690509 CATTTCTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:5700166 original size:27 final size:27
Alignment explanation
Indices: 5700135--5700186 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
5700125 ATACAAGTAA
5700135 AAATTATTTTAAAATAATAATTACTAG
1 AAATTATTTTAAAATAATAATTACTAG
5700162 AAATTATTTTAAAATAATAATTACT
1 AAATTATTTTAAAATAATAATTACT
5700187 TAATCATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (27 bp):
AAATTATTTTAAAATAATAATTACTAG
Found at i:5704920 original size:5 final size:5
Alignment explanation
Indices: 5704910--5704959 Score: 84
Period size: 5 Copynumber: 10.2 Consensus size: 5
5704900 CAAACAAGAG
*
5704910 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA G-AAA GAAAA GCAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
5704959 G
1 G
5704960 TTTAAAGAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
4 4 0.09
5 39 0.91
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:5705279 original size:3 final size:3
Alignment explanation
Indices: 5705271--5705301 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
5705261 ATTAGGTTGT
5705271 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
5705302 TGATGACAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5706362 original size:30 final size:28
Alignment explanation
Indices: 5706328--5706396 Score: 86
Period size: 30 Copynumber: 2.4 Consensus size: 28
5706318 AGACTATATC
*
5706328 TTTATAGTTTTTAAAAGATTAAATCAAAAT
1 TTTATA-TTTTAAAAAGATTAAAT-AAAAT
*
5706358 TTTATTATTTTAAAAAGATTAAATATAAT
1 TTTA-TATTTTAAAAAGATTAAATAAAAT
5706387 TTTAT-TTTTA
1 TTTATATTTTA
5706397 CTAATTTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
27 5 0.14
28 1 0.03
29 8 0.22
30 20 0.56
31 2 0.06
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (28 bp):
TTTATATTTTAAAAAGATTAAATAAAAT
Found at i:5706371 original size:29 final size:29
Alignment explanation
Indices: 5706335--5706392 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
5706325 ATCTTTATAG
*
5706335 TTTTTAAAAGATTAAATCAAAATTTTATTA
1 TTTTAAAAAGATTAAAT-AAAATTTTATTA
*
5706365 TTTTAAAAAGATTAAATATAATTTTATT
1 TTTTAAAAAGATTAAATAAAATTTTATT
5706393 TTTACTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (29 bp):
TTTTAAAAAGATTAAATAAAATTTTATTA
Found at i:5706700 original size:18 final size:21
Alignment explanation
Indices: 5706674--5706719 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
5706664 GAAGAATTGA
*
5706674 AAATGAAAA-GTTTTT-A-AG
1 AAATTAAAATGTTTTTCATAG
5706692 AAATTAAAAATGTTTTTCATAG
1 AAATT-AAAATGTTTTTCATAG
5706714 AAATTA
1 AAATTA
5706720 CATAATTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 6 0.26
21 2 0.09
22 7 0.30
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (21 bp):
AAATTAAAATGTTTTTCATAG
Found at i:5706708 original size:20 final size:21
Alignment explanation
Indices: 5706679--5706719 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
5706669 ATTGAAAATG
5706679 AAAAGTTTTT-A-AGAAATTA
1 AAAAGTTTTTCATAGAAATTA
5706698 AAAATGTTTTTCATAGAAATTA
1 AAAA-GTTTTTCATAGAAATTA
5706720 CATAATTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 6 0.32
21 1 0.05
22 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (21 bp):
AAAAGTTTTTCATAGAAATTA
Found at i:5714693 original size:21 final size:20
Alignment explanation
Indices: 5714655--5714705 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
5714645 AAAAACGCAT
*
5714655 AAAAAATAACATCCAAACAA
1 AAAAAATAACAACCAAACAA
* *
5714675 CAAAAATAATAACCAAAACAA
1 AAAAAATAACAACC-AAACAA
5714696 AAAAAA-AACA
1 AAAAAATAACA
5714706 GTAACAAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.75, C:0.18, G:0.00, T:0.08
Consensus pattern (20 bp):
AAAAAATAACAACCAAACAA
Found at i:5714702 original size:23 final size:24
Alignment explanation
Indices: 5714676--5714730 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
5714666 TCCAAACAAC
*
5714676 AAAAATAATAACCAAAACAA-AAA
1 AAAAATAATAACAAAAACAATAAA
* * * *
5714699 AAAAACAGTAACAAAAATAATAAC
1 AAAAATAATAACAAAAACAATAAA
5714723 AAAAATAA
1 AAAAATAA
5714731 CAGTAAAAAT
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.76, C:0.11, G:0.02, T:0.11
Consensus pattern (24 bp):
AAAAATAATAACAAAAACAATAAA
Found at i:5714722 original size:12 final size:12
Alignment explanation
Indices: 5714673--5714730 Score: 64
Period size: 12 Copynumber: 4.9 Consensus size: 12
5714663 ACATCCAAAC
5714673 AACAAAAATAAT
1 AACAAAAATAAT
* *
5714685 AACCAAAACAA-
1 AACAAAAATAAT
* * *
5714696 AAAAAAAACAGT
1 AACAAAAATAAT
5714708 AACAAAAATAAT
1 AACAAAAATAAT
5714720 AACAAAAATAA
1 AACAAAAATAA
5714731 CAGTAAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
11 8 0.22
12 29 0.78
ACGTcount: A:0.76, C:0.12, G:0.02, T:0.10
Consensus pattern (12 bp):
AACAAAAATAAT
Found at i:5714791 original size:12 final size:11
Alignment explanation
Indices: 5714743--5714796 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
5714733 GTAAAAATAG
*
5714743 CACCAAAAAAA
1 CACCAAAACAA
*
5714754 CACCAAAACAG
1 CACCAAAACAA
* *
5714765 TA-AAAAACAA
1 CACCAAAACAA
5714775 CACCAAAACAA
1 CACCAAAACAA
5714786 CAACCAAAACA
1 C-ACCAAAACA
5714797 GTAAAAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 7 0.21
11 18 0.53
12 9 0.26
ACGTcount: A:0.67, C:0.30, G:0.02, T:0.02
Consensus pattern (11 bp):
CACCAAAACAA
Found at i:5714813 original size:34 final size:34
Alignment explanation
Indices: 5714735--5714822 Score: 137
Period size: 33 Copynumber: 2.6 Consensus size: 34
5714725 AAATAACAGT
*
5714735 AAAAATAGCACCAAAAAAAC-ACCAAAACAGTAA
1 AAAAATAGCACCAAAACAACAACCAAAACAGTAA
5714768 AAAACA-A-CACCAAAACAACAACCAAAACAGTAA
1 AAAA-ATAGCACCAAAACAACAACCAAAACAGTAA
5714801 AAAAATAGCACCAAAACAACAA
1 AAAAATAGCACCAAAACAACAA
5714823 TATAATTTTT
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
32 12 0.24
33 23 0.46
34 15 0.30
ACGTcount: A:0.67, C:0.24, G:0.05, T:0.05
Consensus pattern (34 bp):
AAAAATAGCACCAAAACAACAACCAAAACAGTAA
Found at i:5715435 original size:5 final size:5
Alignment explanation
Indices: 5715425--5715451 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5715415 TCTTTTCCTT
5715425 TTAGA TTAGA TTAGA TTAGA TTAGA TT
1 TTAGA TTAGA TTAGA TTAGA TTAGA TT
5715452 TTATTTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (5 bp):
TTAGA
Found at i:5718015 original size:2 final size:2
Alignment explanation
Indices: 5718008--5718032 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5717998 AAAGTTCATA
5718008 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5718033 AAAACACGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5724669 original size:22 final size:20
Alignment explanation
Indices: 5724644--5724684 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
5724634 ACAAGGTTAA
5724644 TAAGTAAATATGAAACAATAAT
1 TAAGTAAATA--AAACAATAAT
*
5724666 TAAGTAGATAAAACAATAA
1 TAAGTAAATAAAACAATAA
5724685 CCAAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.61, C:0.05, G:0.10, T:0.24
Consensus pattern (20 bp):
TAAGTAAATAAAACAATAAT
Found at i:5727542 original size:47 final size:52
Alignment explanation
Indices: 5727468--5727564 Score: 132
Period size: 47 Copynumber: 1.9 Consensus size: 52
5727458 CTTTTATTTA
*
5727468 TTATATTATATATAGATATATAGATATTAGTTAATAATA-ATAAAATAATAAT
1 TTATATTATATATA-ATATATAGATATTAATTAATAATAGATAAAATAATAAT
*
5727520 TTATATTAT-TAT-AT-TATA-ATATTAATTAATAATAGATTAAATAAT
1 TTATATTATATATAATATATAGATATTAATTAATAATAGATAAAATAAT
5727565 GAAAAATCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
47 15 0.36
48 13 0.31
49 2 0.05
51 3 0.07
52 9 0.21
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (52 bp):
TTATATTATATATAATATATAGATATTAATTAATAATAGATAAAATAATAAT
Found at i:5729290 original size:13 final size:13
Alignment explanation
Indices: 5729268--5729299 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
5729258 GTTGGGCTTG
*
5729268 TAATTGGAAGATT
1 TAATTTGAAGATT
5729281 TAATTTGAAGATT
1 TAATTTGAAGATT
5729294 TAATTT
1 TAATTT
5729300 TATTTTTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (13 bp):
TAATTTGAAGATT
Found at i:5735507 original size:17 final size:17
Alignment explanation
Indices: 5735466--5735501 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
5735456 TTTTGCATGA
5735466 CATGCCATGCAGCACGC
1 CATGCCATGCAGCACGC
5735483 CATGCCATGCAGCACGC
1 CATGCCATGCAGCACGC
5735500 CA
1 CA
5735502 ATCCATTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.25, C:0.42, G:0.22, T:0.11
Consensus pattern (17 bp):
CATGCCATGCAGCACGC
Found at i:5754142 original size:18 final size:18
Alignment explanation
Indices: 5754119--5754156 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
5754109 AATTTATTGG
5754119 AATGCCATTAATTAAATA
1 AATGCCATTAATTAAATA
5754137 AATGCCATTAATTAAATA
1 AATGCCATTAATTAAATA
5754155 AA
1 AA
5754157 AGGAATTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
AATGCCATTAATTAAATA
Found at i:5757296 original size:16 final size:16
Alignment explanation
Indices: 5757275--5757329 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
5757265 ATTAAAAACT
5757275 AAAATTAAAACTAAAA
1 AAAATTAAAACTAAAA
*
5757291 AAAATTAAAAACT-AAG
1 AAAATT-AAAACTAAAA
5757307 AAAA-TAAAA-TATAAA
1 AAAATTAAAACTA-AAA
5757322 AAAATTAA
1 AAAATTAA
5757330 TGAGGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
13 1 0.03
14 4 0.12
15 7 0.21
16 15 0.45
17 6 0.18
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (16 bp):
AAAATTAAAACTAAAA
Found at i:5757299 original size:29 final size:31
Alignment explanation
Indices: 5757264--5757329 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
5757254 GAGGTTTTAG
*
5757264 AATTAAAAACT-A-AAATTAAAACTA-AAAAA
1 AATTAAAAACTAAGAAAATAAAA-TATAAAAA
5757293 AATTAAAAACTAAGAAAATAAAATATAAAAA
1 AATTAAAAACTAAGAAAATAAAATATAAAAA
5757324 AATTAA
1 AATTAA
5757330 TGAGGAAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 11 0.33
30 3 0.09
31 19 0.58
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.21
Consensus pattern (31 bp):
AATTAAAAACTAAGAAAATAAAATATAAAAA
Found at i:5757482 original size:39 final size:39
Alignment explanation
Indices: 5757428--5757505 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
5757418 AATTGGTTAT
5757428 AGTCACTAACGAACTCTTAGCAAGCTAATCTCTCCTTAC
1 AGTCACTAACGAACTCTTAGCAAGCTAATCTCTCCTTAC
*
5757467 AGTCACTAACGAACTCTTAGCAAGTTAATCTCTCCTTAC
1 AGTCACTAACGAACTCTTAGCAAGCTAATCTCTCCTTAC
5757506 CTTCTCGATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.29
Consensus pattern (39 bp):
AGTCACTAACGAACTCTTAGCAAGCTAATCTCTCCTTAC
Found at i:5761747 original size:11 final size:11
Alignment explanation
Indices: 5761731--5761828 Score: 55
Period size: 11 Copynumber: 9.0 Consensus size: 11
5761721 CGAGCCTTCT
5761731 TTTTAAATTTA
1 TTTTAAATTTA
5761742 TTTT-AA---A
1 TTTTAAATTTA
*
5761749 -TTTAGATTTA
1 TTTTAAATTTA
5761759 TTTTAAATTTGA
1 TTTTAAATTT-A
* *
5761771 ATTTAAATTAA
1 TTTTAAATTTA
5761782 TTTTAAATTTTAA
1 TTTTAAA-TTT-A
*
5761795 ATTT-AATTTAA
1 TTTTAAATTT-A
*
5761806 ATTTAAATTTA
1 TTTTAAATTTA
*
5761817 TCTTCAAATTTA
1 T-TTTAAATTTA
5761829 AAGGAATCTA
Statistics
Matches: 68, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
6 3 0.04
7 2 0.03
10 3 0.04
11 29 0.43
12 27 0.40
13 4 0.06
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTTAAATTTA
Found at i:5761752 original size:6 final size:6
Alignment explanation
Indices: 5761732--5761830 Score: 89
Period size: 6 Copynumber: 17.0 Consensus size: 6
5761722 GAGCCTTCTT
* * * *
5761732 TTTAAA TTT-AT TTTAAA TTTAGA TTT-AT TTTAAA TTTGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** *
5761778 -TTAAT TTTAAA TTTTAAA TTT-AA TTTAAA TTTAAA TTTATC TTCAAA
1 TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
5761825 TTTAAA
1 TTTAAA
5761831 GGAATCTATT
Statistics
Matches: 72, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
5 16 0.22
6 50 0.69
7 6 0.08
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:5761773 original size:23 final size:22
Alignment explanation
Indices: 5761743--5761816 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 22
5761733 TTAAATTTAT
5761743 TTTAAATTTAGATTTATTTTAAA
1 TTTAAATTTA-ATTTATTTTAAA
* *
5761766 TTTGAATTTAAATTAATTTTAAA
1 TTTAAATTT-AATTTATTTTAAA
*
5761789 TTTTAAATTTAATTTAAATTTAAA
1 -TTTAAATTTAATTT-ATTTTAAA
5761813 TTTA
1 TTTA
5761817 TCTTCAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
23 27 0.63
24 16 0.37
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (22 bp):
TTTAAATTTAATTTATTTTAAA
Found at i:5763919 original size:28 final size:29
Alignment explanation
Indices: 5763843--5763965 Score: 126
Period size: 30 Copynumber: 4.1 Consensus size: 29
5763833 ATAAATAATA
* *
5763843 TTTTGACCCCAAAACTTTTCCAAAATTACAT
1 TTTTAACCCCAAAAC--TTCAAAAATTACAT
*
5763874 TTTTGACCCCAAAACTTCTAAAAATTACA-
1 TTTTAACCCCAAAACTTC-AAAAATTACAT
*
5763903 TTTT-ACCCTC-AAACTTCCAAAAATTCCAT
1 TTTTAACCC-CAAAACTT-CAAAAATTACAT
5763932 TTTTAACCCCAAAACTTACAAAAATTACCAT
1 TTTTAACCCCAAAACTT-CAAAAATTA-CAT
5763963 TTT
1 TTT
5763966 ACCCTTGAAT
Statistics
Matches: 81, Mismatches: 4, Indels: 14
0.82 0.04 0.14
Matches are distributed among these distances:
28 19 0.23
29 14 0.17
30 27 0.33
31 21 0.26
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.34
Consensus pattern (29 bp):
TTTTAACCCCAAAACTTCAAAAATTACAT
Found at i:5764093 original size:57 final size:59
Alignment explanation
Indices: 5763871--5764273 Score: 278
Period size: 59 Copynumber: 6.9 Consensus size: 59
5763861 TCCAAAATTA
* * * * *
5763871 CATTTTTGACCCCAAAAC-TTCTAAAAATTA-CATTTTA-CCCTCAAACT-TCCAAAAATTC
1 CATTTTTAACCTCGAAACTTTC-AAAAATTACCATTTTACCCCT-GAA-TGTCCAAAAACTC
* * * * *
5763929 CATTTTTAACCCCAAAACTTACAAAAATTACCATTTTACCCTTGAATATCCAAAAACTC
1 CATTTTTAACCTCGAAACTTTCAAAAATTACCATTTTACCCCTGAATGTCCAAAAACTC
* * * ** *
5763988 AATTTTTGACCTTGAAACTTTCAAAAATTATTATTTTACCCC-GAATGTCAAAAAACTC
1 CATTTTTAACCTCGAAACTTTCAAAAATTACCATTTTACCCCTGAATGTCCAAAAACTC
* * * * *
5764046 CA-TTTTAACCTCGAAAGTTT-TAAATTTACCATTTTACCCCTGGATGTCTAAAAACTC
1 CATTTTTAACCTCGAAACTTTCAAAAATTACCATTTTACCCCTGAATGTCCAAAAACTC
* * *
5764103 CATTTTTGATCC-CGAAACTTTCAAAAATTACCATTTTACCTCT-AGATGTCCAAAAATTC
1 CATTTTT-AACCTCGAAACTTTCAAAAATTACCATTTTACCCCTGA-ATGTCCAAAAACTC
** * ** * * **
5764162 TGTTTTTTATCCT-G-ATTTTTCTAAAAATTACCGTTTTACCCCTG-ATGTCTAAAATGT-
1 -CATTTTTAACCTCGAAACTTTC-AAAAATTACCATTTTACCCCTGAATGTCCAAAAACTC
* * * * *
5764219 CATTTTTAA-CTCCAAATTTTCCCAAAATTACCATTTTGCCCCCGAGA-GTCCAAAA
1 CATTTTTAACCTCGAAACTTT-CAAAAATTACCATTTTACCCCTGA-ATGTCCAAAA
5764274 TTATCATTTT
Statistics
Matches: 274, Mismatches: 53, Indels: 36
0.75 0.15 0.10
Matches are distributed among these distances:
55 2 0.01
56 22 0.08
57 54 0.20
58 76 0.28
59 112 0.41
60 8 0.03
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.36
Consensus pattern (59 bp):
CATTTTTAACCTCGAAACTTTCAAAAATTACCATTTTACCCCTGAATGTCCAAAAACTC
Found at i:5770296 original size:21 final size:21
Alignment explanation
Indices: 5770264--5770312 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5770254 GGTGTGAACT
5770264 TTTTC-ATCAATTTTACTTTC-
1 TTTTCTAT-AATTTTACTTTCA
*
5770284 TTTCTCTATAATTTTTCTTTCA
1 TTT-TCTATAATTTTACTTTCA
5770306 TTTTCTA
1 TTTTCTA
5770313 ATTTATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 17 0.68
22 5 0.20
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.63
Consensus pattern (21 bp):
TTTTCTATAATTTTACTTTCA
Found at i:5771003 original size:29 final size:30
Alignment explanation
Indices: 5770944--5771019 Score: 91
Period size: 29 Copynumber: 2.5 Consensus size: 30
5770934 CAAAACTATG
* *
5770944 CATGAATTATGATTTAATGTGTAATTGTATA
1 CATGAATTTTGATTT-ATGTGCAATTGTATA
*
5770975 CATGAATTTTGATTT-TGTGCAATTTTATA
1 CATGAATTTTGATTTATGTGCAATTGTATA
*
5771004 CATAAAATTTTGATTT
1 CAT-GAATTTTGATTT
5771020 GATTCAATTC
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
29 15 0.38
30 11 0.28
31 14 0.35
ACGTcount: A:0.33, C:0.05, G:0.13, T:0.49
Consensus pattern (30 bp):
CATGAATTTTGATTTATGTGCAATTGTATA
Found at i:5775292 original size:22 final size:22
Alignment explanation
Indices: 5775260--5775316 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
5775250 ATTTTTACTG
* ***
5775260 TTTTGTCATTATTTTGCTGTTA
1 TTTTGTTATTATTTTGCAACTA
*
5775282 TTTTGTTATTATATTGCAACTA
1 TTTTGTTATTATTTTGCAACTA
*
5775304 TTTTGTTGTTATT
1 TTTTGTTATTATT
5775317 GTTTATATAT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.18, C:0.07, G:0.12, T:0.63
Consensus pattern (22 bp):
TTTTGTTATTATTTTGCAACTA
Found at i:5776363 original size:21 final size:21
Alignment explanation
Indices: 5776322--5776363 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5776312 CAAATACTCC
*
5776322 TTTTAAAGATACATATCAAAT
1 TTTTAAAGATACATATAAAAT
* *
5776343 TTTTAAAGTTACGTATAAAAT
1 TTTTAAAGATACATATAAAAT
5776364 AAAAAAACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTTAAAGATACATATAAAAT
Found at i:5777090 original size:11 final size:12
Alignment explanation
Indices: 5777067--5777108 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
5777057 TAAAAAAAAA
5777067 TTATTTAAATTT
1 TTATTTAAATTT
5777079 TTATTT-AATTT
1 TTATTTAAATTT
5777090 TTCATCTTAAATTT
1 TT-AT-TTAAATTT
*
5777104 GTATT
1 TTATT
5777109 ATTTATCAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 7 0.27
12 9 0.35
13 4 0.15
14 6 0.23
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (12 bp):
TTATTTAAATTT
Found at i:5777245 original size:6 final size:6
Alignment explanation
Indices: 5777234--5777285 Score: 56
Period size: 6 Copynumber: 9.0 Consensus size: 6
5777224 GGCTCAATAG
* *
5777234 AATTTA AATTT- ATTTTA AGTTTA AATTT- -ATTGTA AATTTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATT-TA AATTTA AATTTA
5777280 AATTTA
1 AATTTA
5777286 TTTAAACTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 3 0.08
5 5 0.13
6 28 0.72
7 3 0.08
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:5777258 original size:17 final size:17
Alignment explanation
Indices: 5777234--5777279 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
5777224 GGCTCAATAG
*
5777234 AATTTAAATTTATTTTA
1 AATTTAAATTTATTGTA
*
5777251 AGTTTAAATTTATTGTA
1 AATTTAAATTTATTGTA
5777268 AATTTAAATTTA
1 AATTTAAATTTA
5777280 AATTTATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
AATTTAAATTTATTGTA
Found at i:5777273 original size:23 final size:22
Alignment explanation
Indices: 5777247--5777291 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
5777237 TTAAATTTAT
*
5777247 TTTAAGTTTAAATTTATTGTAAA
1 TTTAAATTTAAATTTATT-TAAA
5777270 TTTAAATTTAAATTTATTTAAA
1 TTTAAATTTAAATTTATTTAAA
5777292 CTAATAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTAAATTTAAATTTATTTAAA
Found at i:5779202 original size:29 final size:28
Alignment explanation
Indices: 5779152--5779411 Score: 202
Period size: 29 Copynumber: 8.9 Consensus size: 28
5779142 GAAGGTCCCT
* *
5779152 AAACTGTCTAAAAATTACCATTTTACCCTC
1 AAACT-TCCAAAAATTA-CATTTTACCCCC
* * * **
5779182 GAACTTTTCAAAAATCACATTTTTACCCTA
1 AAAC-TTCCAAAAATTACA-TTTTACCCCC
*
5779212 AAACTTCCAAAAATTTCCA-TTTACCCCC
1 AAACTTCCAAAAA-TTACATTTTACCCCC
* *
5779240 AAACTTCCAAAAATTGCATTTTAACCCC
1 AAACTTCCAAAAATTACATTTTACCCCC
* * *
5779268 AAACTTTTCAAAAATCAAATTTTTACCCCC
1 AAAC-TTCCAAAAATTACA-TTTTACCCCC
* * * *
5779298 GAACCTCCAAAAATTACCATTTTGCCCTC
1 AAACTTCCAAAAATTA-CATTTTACCCCC
5779327 AAA-TATCCAAAAATTACATTTTTACCCCC
1 AAACT-TCCAAAAATTACA-TTTTACCCCC
* *
5779356 -GAGTGTCCAAAAATTACCATTTTACCCCC
1 AAACT-TCCAAAAATTA-CATTTTACCCCC
*
5779385 AAACCTCCAAAAATTACCATTTTACCC
1 AAACTTCCAAAAATTA-CATTTTACCC
5779412 TCGGGCATCC
Statistics
Matches: 184, Mismatches: 34, Indels: 25
0.76 0.14 0.10
Matches are distributed among these distances:
27 4 0.02
28 35 0.19
29 102 0.55
30 42 0.23
31 1 0.01
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (28 bp):
AAACTTCCAAAAATTACATTTTACCCCC
Found at i:5779424 original size:58 final size:58
Alignment explanation
Indices: 5779152--5779411 Score: 237
Period size: 58 Copynumber: 4.5 Consensus size: 58
5779142 GAAGGTCCCT
* * * * **
5779152 AAACTGTCTAAAAATTACCATTTTACCCTCGAACTTTTCAAAAATCA-CATTTTTACCCTA
1 AAACT-TCCAAAAATTACCATTTTACCCCCGAAC-TTCCAAAAATTACCA-TTTTACCCCC
* * * *
5779212 AAACTTCCAAAAATTTCCA-TTTACCCCCAAACTTCCAAAAATT-GCATTTTAACCCC
1 AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTACCATTTTACCCCC
* * * * * *
5779268 AAACTTTTCAAAAATCA-AATTTTTACCCCCGAACCTCCAAAAATTACCATTTTGCCCTC
1 AAAC-TTCCAAAAATTACCA-TTTTACCCCCGAACTTCCAAAAATTACCATTTTACCCCC
*
5779327 AAA-TATCCAAAAATTA-CATTTTTACCCCCG-AGTGTCCAAAAATTACCATTTTACCCCC
1 AAACT-TCCAAAAATTACCA-TTTTACCCCCGAACT-TCCAAAAATTACCATTTTACCCCC
*
5779385 AAACCTCCAAAAATTACCATTTTACCC
1 AAACTTCCAAAAATTACCATTTTACCC
5779412 TCGGGCATCC
Statistics
Matches: 164, Mismatches: 27, Indels: 20
0.78 0.13 0.09
Matches are distributed among these distances:
56 12 0.07
57 22 0.13
58 99 0.60
59 26 0.16
60 5 0.03
ACGTcount: A:0.37, C:0.30, G:0.03, T:0.30
Consensus pattern (58 bp):
AAACTTCCAAAAATTACCATTTTACCCCCGAACTTCCAAAAATTACCATTTTACCCCC
Found at i:5780752 original size:16 final size:16
Alignment explanation
Indices: 5780731--5780764 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5780721 ATAAATCTTT
5780731 AAAACAAAAAAAAATC
1 AAAACAAAAAAAAATC
* *
5780747 AAAACAACAAAAGATC
1 AAAACAAAAAAAAATC
5780763 AA
1 AA
5780765 TCCAAGTGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.15, G:0.03, T:0.06
Consensus pattern (16 bp):
AAAACAAAAAAAAATC
Found at i:5783711 original size:13 final size:14
Alignment explanation
Indices: 5783679--5783712 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
5783669 TTATATATAA
*
5783679 AAATAAATTCTCAT
1 AAATAAATTCTCAC
5783693 AAATAAATT-TCAC
1 AAATAAATTCTCAC
5783706 AAATAAA
1 AAATAAA
5783713 AATTTATCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (14 bp):
AAATAAATTCTCAC
Found at i:5785654 original size:23 final size:23
Alignment explanation
Indices: 5785624--5785707 Score: 82
Period size: 22 Copynumber: 3.6 Consensus size: 23
5785614 TGTTTCATTA
5785624 TTAAAAATAATAAATTTTATTTT
1 TTAAAAATAATAAATTTTATTTT
* **
5785647 TTAAAAAT-CTAAATTTTAAATT
1 TTAAAAATAATAAATTTTATTTT
5785669 TTAAAAA-AGTATAATATTTTATTTT
1 TTAAAAATA--ATAA-ATTTTATTTT
*
5785694 TAAAAAATTAATAA
1 TTAAAAA-TAATAA
5785708 TATGTATAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
22 18 0.38
23 8 0.17
24 3 0.06
25 18 0.38
27 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (23 bp):
TTAAAAATAATAAATTTTATTTT
Found at i:5785676 original size:24 final size:24
Alignment explanation
Indices: 5785626--5785710 Score: 68
Period size: 24 Copynumber: 3.5 Consensus size: 24
5785616 TTTCATTATT
**
5785626 AAAAATAATAA-ATTTT-ATTTTTT
1 AAAAAT-ATAATATTTTAATTTTAA
*
5785649 AAAAATCTAA-ATTTTAAATTTTAA
1 AAAAATATAATATTTT-AATTTTAA
* *
5785673 AAAAGTATAATATTTTATTTTTAA
1 AAAAATATAATATTTTAATTTTAA
*
5785697 AAAATTAATAATAT
1 AAAAAT-ATAATAT
5785711 GTATAAAATT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
22 8 0.16
23 6 0.12
24 25 0.49
25 12 0.24
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
AAAAATATAATATTTTAATTTTAA
Found at i:5785706 original size:22 final size:22
Alignment explanation
Indices: 5785626--5785701 Score: 89
Period size: 23 Copynumber: 3.3 Consensus size: 22
5785616 TTTCATTATT
*
5785626 AAAAATAATAAATTTTATTTTTT
1 AAAAAT-ATAAATTTTATTTTTA
* *
5785649 AAAAATCTAAATTTTAAATTTTA
1 AAAAATATAAATTTT-ATTTTTA
5785672 AAAAAGTATAATATTTTATTTTTA
1 AAAAA-TATAA-ATTTTATTTTTA
5785696 AAAAAT
1 AAAAAT
5785702 TAATAATATG
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
22 8 0.18
23 17 0.38
24 15 0.33
25 5 0.11
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (22 bp):
AAAAATATAAATTTTATTTTTA
Found at i:5791928 original size:17 final size:16
Alignment explanation
Indices: 5791902--5791933 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5791892 CAGGAGTCTC
5791902 TCTGGTTTTTTTTTCT
1 TCTGGTTTTTTTTTCT
5791918 TCTGTGTTTTTTTTTC
1 TCTG-GTTTTTTTTTC
5791934 GTTTTCTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.75
Consensus pattern (16 bp):
TCTGGTTTTTTTTTCT
Found at i:5796156 original size:17 final size:17
Alignment explanation
Indices: 5796134--5796167 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5796124 AGTCTCTGAT
5796134 CTGAAGGTCCTGGTTCA
1 CTGAAGGTCCTGGTTCA
5796151 CTGAAGGTCCTGGTTCA
1 CTGAAGGTCCTGGTTCA
5796168 TAGTCAAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (17 bp):
CTGAAGGTCCTGGTTCA
Found at i:5796415 original size:29 final size:29
Alignment explanation
Indices: 5796370--5796447 Score: 124
Period size: 29 Copynumber: 2.7 Consensus size: 29
5796360 ATTGGAAATT
5796370 AAAATAA-TTTAATAATTTTAT-TATTTAA
1 AAAATAATTTTAATAATTTTATAT-TTTAA
5796398 AAAATAATTTTAATAATTTTATATTTTAA
1 AAAATAATTTTAATAATTTTATATTTTAA
*
5796427 AAAATGATTTTAATAATTTTA
1 AAAATAATTTTAATAATTTTA
5796448 AAATCATTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
28 7 0.15
29 39 0.83
30 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
AAAATAATTTTAATAATTTTATATTTTAA
Found at i:5803526 original size:3 final size:3
Alignment explanation
Indices: 5803518--5803557 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
5803508 TATAAGGAGA
5803518 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
5803558 GTATTTGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:5807182 original size:7 final size:7
Alignment explanation
Indices: 5807170--5807198 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
5807160 CATACTTTTG
5807170 TTTAAAA
1 TTTAAAA
5807177 TTTAAAA
1 TTTAAAA
5807184 TTTAAAA
1 TTTAAAA
5807191 TTTAAAA
1 TTTAAAA
5807198 T
1 T
5807199 ATACTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (7 bp):
TTTAAAA
Found at i:5807714 original size:30 final size:28
Alignment explanation
Indices: 5807657--5807718 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 28
5807647 TCGTATATTT
* *
5807657 AAAATTTAATTTCATGCTTTTATTTTTA
1 AAAATTTAATTTCATACTTTTAATTTTA
*
5807685 AAAATTTAATCTTTATACTTTTTAATTTTA
1 AAAATTTAAT-TTCATAC-TTTTAATTTTA
5807715 AAAA
1 AAAA
5807719 ATTAGGCTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 10 0.34
29 5 0.17
30 14 0.48
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.53
Consensus pattern (28 bp):
AAAATTTAATTTCATACTTTTAATTTTA
Found at i:5808398 original size:30 final size:30
Alignment explanation
Indices: 5808362--5808419 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5808352 AATCATTGAA
* *
5808362 TTTTTATGTGATTGAATTTTACTATTAAAT
1 TTTTTATGTGATTCAATTTTACCATTAAAT
* *
5808392 TTTTTATTTTATTCAATTTTACCATTAA
1 TTTTTATGTGATTCAATTTTACCATTAA
5808420 TATTGATTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (30 bp):
TTTTTATGTGATTCAATTTTACCATTAAAT
Found at i:5808432 original size:30 final size:31
Alignment explanation
Indices: 5808376--5808461 Score: 77
Period size: 31 Copynumber: 2.8 Consensus size: 31
5808366 TATGTGATTG
* * * *
5808376 AATTTTACTATTAA-ATT-TTTTATTTTATTC
1 AATTTTACCATTAATATTAATTT-TTTAATTA
*
5808406 AATTTTACCATTAATATTGATTTTTTAATTA
1 AATTTTACCATTAATATTAATTTTTTAATTA
* *
5808437 AAATTTACCACTCAATATTAATTTT
1 AATTTTACCA-TTAATATTAATTTT
5808462 AATTATTTGA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
30 13 0.28
31 18 0.39
32 15 0.33
ACGTcount: A:0.35, C:0.09, G:0.01, T:0.55
Consensus pattern (31 bp):
AATTTTACCATTAATATTAATTTTTTAATTA
Found at i:5808533 original size:15 final size:14
Alignment explanation
Indices: 5808489--5808530 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
5808479 TTAATAATAA
*
5808489 TTTAATAATTTAAT
1 TTTAATAATTAAAT
5808503 TTATAA-ATATTAAAT
1 TT-TAATA-ATTAAAT
5808518 TTTAATAATTAAA
1 TTTAATAATTAAA
5808531 ATTAAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTAATAATTAAAT
Found at i:5810542 original size:44 final size:41
Alignment explanation
Indices: 5810467--5810552 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 41
5810457 TCTTAATTAA
* * *
5810467 TTTAAATTAATTAGAAAAATAAATATAACACATTATGATGT
1 TTTAAATTAATTAGAAAAATAAAAACAACACATTAAGATGT
5810508 TTTAAATTAATTAAGAGATAAATAAAAACAACACATTAAGATGT
1 TTTAAATTAATT-AGA-A-AAATAAAAACAACACATTAAGATGT
5810552 T
1 T
5810553 ATCATTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 12 0.31
42 3 0.08
43 1 0.03
44 23 0.59
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (41 bp):
TTTAAATTAATTAGAAAAATAAAAACAACACATTAAGATGT
Found at i:5811481 original size:123 final size:123
Alignment explanation
Indices: 5811254--5811486 Score: 342
Period size: 123 Copynumber: 1.9 Consensus size: 123
5811244 TGTATTTAGG
* * * * *
5811254 TCAGAGCATTAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTAGCGACGCTTATGG
1 TCAGAGCATTAACGACGCTTATGGGAAAACGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGA
5811319 GAAAGAGCCGCTAAAGGTCAAAGCATTAGCAGCGCTTATGGGAAAGCACTACTAAAGA
66 GAAAGAGCCGCTAAAGGTCAAAGCATTAGCAGCGCTTATGGGAAAGCACTACTAAAGA
* * *
5811377 TCAGAGCATTAACGACGTTTATGGGAAAACGCCGCTAAAGGTCAGAGTAATAGCGACGTTTATGA
1 TCAGAGCATTAACGACGCTTATGGGAAAACGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGA
* * * *
5811442 GAAA-ATGTCGCTAAATGTCAAAGCATTAGCTGCGTTTATGGGAAA
66 GAAAGA-GCCGCTAAAGGTCAAAGCATTAGCAGCGCTTATGGGAAA
5811487 AACGCCACTA
Statistics
Matches: 97, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
122 1 0.01
123 96 0.99
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.21
Consensus pattern (123 bp):
TCAGAGCATTAACGACGCTTATGGGAAAACGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGA
GAAAGAGCCGCTAAAGGTCAAAGCATTAGCAGCGCTTATGGGAAAGCACTACTAAAGA
Found at i:5811518 original size:41 final size:41
Alignment explanation
Indices: 5811251--5811519 Score: 272
Period size: 41 Copynumber: 6.6 Consensus size: 41
5811241 AGCTGTATTT
* *
5811251 AGGTCAGAGCATTAGCGGCGCTTATGGGAAAGCGCCGCTAA
1 AGGTCAGAGCATTAGCGGCGTTTATGGGAAAACGCCGCTAA
* *
5811292 AGGTCAGAGCATTAGCGACGCTTATGGGAAAGA-GCCGCTAA
1 AGGTCAGAGCATTAGCGGCGTTTATGGGAAA-ACGCCGCTAA
* * * * * **
5811333 AGGTCAAAGCATTAGCAGCGCTTATGGGAAAGCACTACTAA
1 AGGTCAGAGCATTAGCGGCGTTTATGGGAAAACGCCGCTAA
* * *
5811374 AGATCAGAGCATTAACGACGTTTATGGGAAAACGCCGCTAA
1 AGGTCAGAGCATTAGCGGCGTTTATGGGAAAACGCCGCTAA
* * * * * *
5811415 AGGTCAGAGTAATAGCGACGTTTATGAGAAAATGTCGCTAA
1 AGGTCAGAGCATTAGCGGCGTTTATGGGAAAACGCCGCTAA
* * * *
5811456 ATGTCAAAGCATTAGCTGCGTTTATGGGAAAAACGCCACTAA
1 AGGTCAGAGCATTAGCGGCGTTTATGGG-AAAACGCCGCTAA
* *
5811498 AGGTTA-AGCAATAGCGGCGTTT
1 AGGTCAGAGCATTAGCGGCGTTT
5811520 TCCATAAACG
Statistics
Matches: 185, Mismatches: 40, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
41 171 0.92
42 14 0.08
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (41 bp):
AGGTCAGAGCATTAGCGGCGTTTATGGGAAAACGCCGCTAA
Found at i:5811519 original size:123 final size:123
Alignment explanation
Indices: 5811254--5811519 Score: 338
Period size: 123 Copynumber: 2.2 Consensus size: 123
5811244 TGTATTTAGG
* * * *
5811254 TCAGAGCATTAGCGGCGCTTATGGGAAAGCGCCGCTAAAGGTCAGAGCATTAGCGACGCTTATGG
1 TCAGAGCATTAGCGGCGTTTATGGGAAAACGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGA
* *
5811319 GAAAGAGCCGCTAAAGGTCAAAGCATTAGCAGCGCTTATGGGAAAGCACTACTAAAGA
66 GAAAGAGCCGCTAAAGGTCAAAGCATTAGCAGCGCTTATGGGAAAACACCACTAAAGA
* * * *
5811377 TCAGAGCATTAACGACGTTTATGGGAAAACGCCGCTAAAGGTCAGAGTAATAGCGACGTTTATGA
1 TCAGAGCATTAGCGGCGTTTATGGGAAAACGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGA
* * * * * *
5811442 GAAA-ATGTCGCTAAATGTCAAAGCATTAGCTGCGTTTATGGGAAAAACGCCACTAAAGG
66 GAAAGA-GCCGCTAAAGGTCAAAGCATTAGCAGCGCTTATGGG-AAAACACCACTAAAGA
* *
5811501 TTA-AGCAATAGCGGCGTTT
1 TCAGAGCATTAGCGGCGTTT
5811520 TCCATAAACG
Statistics
Matches: 121, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
122 1 0.01
123 106 0.88
124 14 0.12
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.21
Consensus pattern (123 bp):
TCAGAGCATTAGCGGCGTTTATGGGAAAACGCCGCTAAAGGTCAGAGCAATAGCGACGCTTATGA
GAAAGAGCCGCTAAAGGTCAAAGCATTAGCAGCGCTTATGGGAAAACACCACTAAAGA
Found at i:5811951 original size:16 final size:16
Alignment explanation
Indices: 5811930--5811969 Score: 64
Period size: 16 Copynumber: 2.5 Consensus size: 16
5811920 CGTTTGGTTC
5811930 GCTGTAATGGAATA-G
1 GCTGTAATGGAATACG
5811945 AGCTGTAATGGAATACG
1 -GCTGTAATGGAATACG
5811962 GCTGTAAT
1 GCTGTAAT
5811970 CAGTATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 22 0.96
17 1 0.04
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATACG
Found at i:5812207 original size:56 final size:57
Alignment explanation
Indices: 5812139--5812289 Score: 171
Period size: 56 Copynumber: 2.6 Consensus size: 57
5812129 TTGTTAAATT
* * * *
5812139 TTAATAAAATTATTATTAAATATAATTTAATAAAAAATAAACATTTTAATCATATT-
1 TTAATATAATTATTATTAAATATAATTTAATAAAAAATAAACAATTTAATAACATTC
* * * * *
5812195 TTAACT-TGATTATTATTAAATATAATTCAATAAAACAGTATATAATTTAATAACATTC
1 TTAA-TATAATTATTATTAAATATAATTTAATAAAA-AATAAACAATTTAATAACATTC
*
5812253 TTAATATAATTATTATTAAAATATAAATTAATAAAAA
1 TTAATATAATTATTATT-AAATATAATTTAATAAAAA
5812290 TCATAATATA
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
56 30 0.38
57 17 0.22
58 15 0.19
59 16 0.21
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (57 bp):
TTAATATAATTATTATTAAATATAATTTAATAAAAAATAAACAATTTAATAACATTC
Found at i:5814855 original size:56 final size:56
Alignment explanation
Indices: 5814754--5814875 Score: 131
Period size: 56 Copynumber: 2.2 Consensus size: 56
5814744 AATTAATTAT
* * * * *
5814754 TTGACTCAAATCTCCTTATATAGTAATAATGTATATTAATCAATATTTAATAGTTAA
1 TTGACTC-AATCTCCTTATATACTAATAATATATATTAATCAATATTCAAGAGGTAA
* *
5814811 TTGACTCAATTTCCTCT-TATACTAAT-ATATATATTAATGTAATATTCAAGAGGTAA
1 TTGACTCAATCTCCT-TATATACTAATAATATATATTAAT-CAATATTCAAGAGGTAA
*
5814867 TTCACTCAA
1 TTGACTCAA
5814876 ACTATTAAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
55 11 0.20
56 36 0.65
57 8 0.15
ACGTcount: A:0.39, C:0.13, G:0.07, T:0.41
Consensus pattern (56 bp):
TTGACTCAATCTCCTTATATACTAATAATATATATTAATCAATATTCAAGAGGTAA
Found at i:5819458 original size:23 final size:23
Alignment explanation
Indices: 5819424--5819525 Score: 152
Period size: 23 Copynumber: 4.4 Consensus size: 23
5819414 TGCTGGGCAA
*
5819424 CAGAGAGCACACACAGTGCTAAAT
1 CAGAGAGCACACAAAGTGCT-AAT
* *
5819448 -AGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
5819470 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
5819493 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
5819516 CAGAGAGCAC
1 CAGAGAGCAC
5819526 GAGACGTGCT
Statistics
Matches: 71, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
22 3 0.04
23 68 0.96
ACGTcount: A:0.43, C:0.23, G:0.22, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:5819474 original size:46 final size:46
Alignment explanation
Indices: 5819424--5819543 Score: 154
Period size: 46 Copynumber: 2.6 Consensus size: 46
5819414 TGCTGGGCAA
*
5819424 CAGAGAGCACACACAGTGCTAAATAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACACAGTGCTAAATAGAGAGCACACAAAGTACTAAT
* * *
5819470 CAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAAT-AGAGAGCACACAAAGTACTAAT
* *
5819516 CAGAGAGCACGAGAC-GTGCTAAACAGAG
1 CAGAGAGCAC-ACACAGTGCTAAATAGAG
5819544 CGCGCTCTAG
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
45 3 0.05
46 57 0.89
47 4 0.06
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (46 bp):
CAGAGAGCACACACAGTGCTAAATAGAGAGCACACAAAGTACTAAT
Found at i:5819497 original size:69 final size:66
Alignment explanation
Indices: 5819378--5819522 Score: 186
Period size: 69 Copynumber: 2.1 Consensus size: 66
5819368 ACGGAACAAA
*
5819378 CAGAGAGTACCAAAGAACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAGTGC
1 CAGAGAGTACCAAAGAACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACACAGTGC
5819443 TAAAT
63 T-AAT
*
5819448 -AGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACACAGTG
1 CAGAGAGTAC-CAAAGAACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACACAGTG
5819511 CTAAT
62 CTAAT
5819516 CAGAGAG
1 CAGAGAG
5819523 CACGAGACGT
Statistics
Matches: 68, Mismatches: 2, Indels: 11
0.84 0.02 0.14
Matches are distributed among these distances:
68 5 0.07
69 35 0.51
70 10 0.15
71 11 0.16
72 7 0.10
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.12
Consensus pattern (66 bp):
CAGAGAGTACCAAAGAACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACACAGTGCTAA
T
Found at i:5819534 original size:23 final size:22
Alignment explanation
Indices: 5819424--5819543 Score: 109
Period size: 23 Copynumber: 5.2 Consensus size: 22
5819414 TGCTGGGCAA
*
5819424 CAGAGAGCACACACAGTGCTAAAT
1 CAGAGAGCACAAAC-GTGCT-AAT
*
5819448 -AGAGAGTACACAAA-GTACTAAT
1 CAGAGAG--CACAAACGTGCTAAT
*
5819470 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACA-AACGTGCTAAT
*
5819493 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACAAAC-GTGCTAAT
* *
5819516 CAGAGAGCACGAGACGTGCTAAA
1 CAGAGAGCAC-AAACGTGCTAAT
5819539 CAGAG
1 CAGAG
5819544 CGCGCTCTAG
Statistics
Matches: 82, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.05
22 6 0.07
23 64 0.78
24 3 0.04
25 5 0.06
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.12
Consensus pattern (22 bp):
CAGAGAGCACAAACGTGCTAAT
Found at i:5826539 original size:23 final size:23
Alignment explanation
Indices: 5826466--5826637 Score: 127
Period size: 23 Copynumber: 7.5 Consensus size: 23
5826456 TATACGGAAC
* * *
5826466 AAACAGAGAGTAC-CAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
*
5826488 -AACAGAGAGCACATA-AGTGCT
1 AAACAGAGAGCACACACAGTGCT
* *
5826509 GGGCAACAGAGAGAACACACAGTGCT
1 ---AAACAGAGAGCACACACAGTGCT
* * *
5826535 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACACAGTGCT
* * *
5826558 AATCAGAGAGCATACAAAGTGCT
1 AAACAGAGAGCACACACAGTGCT
* *
5826581 AATCAGAGAGTACACACAGTGCT
1 AAACAGAGAGCACACACAGTGCT
* * *
5826604 AATCATAGAGCACGAGAC-GTGCT
1 AAACAGAGAGCAC-ACACAGTGCT
5826627 AAACAGAGAGC
1 AAACAGAGAGC
5826638 GCGCTAGTGT
Statistics
Matches: 122, Mismatches: 21, Indels: 13
0.78 0.13 0.08
Matches are distributed among these distances:
21 16 0.13
22 1 0.01
23 83 0.68
24 3 0.02
25 13 0.11
26 6 0.05
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACACAGTGCT
Found at i:5826565 original size:46 final size:46
Alignment explanation
Indices: 5826515--5826636 Score: 156
Period size: 46 Copynumber: 2.7 Consensus size: 46
5826505 TGCTGGGCAA
*
5826515 CAGAGAGAACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
* * * * *
5826561 CAGAGAGCATACAAAGTGCTAATCAGAGAGTACACACAGTGCTAAT
1 CAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
* *
5826607 CATAGAGCACGAGAC-GTGCTAAACAGAGAG
1 CAGAGAGCAC-ACACAGTGCTAAACAGAGAG
5826637 CGCGCTAGTG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 62 0.97
47 2 0.03
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.14
Consensus pattern (46 bp):
CAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT
Found at i:5826588 original size:69 final size:66
Alignment explanation
Indices: 5826466--5826605 Score: 185
Period size: 69 Copynumber: 2.0 Consensus size: 66
5826456 TATACGGAAC
5826466 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGGGCAACAGAGAGAACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCT--G-AACAGAGAGAACACACAG
5826531 TGCT
63 TGCT
*
5826535 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCATACA-AAGTGCT-AATCAGAGAGTACACAC
1 AAACAGAGAGTAC-CAAAGTACTAA-CAGAGAGC--ACATAAGTGCTGAA-CAGAGAGAACACAC
5826598 AGTGCT
61 AGTGCT
5826604 AA
1 AA
5826606 TCATAGAGCA
Statistics
Matches: 65, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
68 2 0.03
69 34 0.52
70 11 0.17
71 8 0.12
72 7 0.11
73 3 0.05
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.14
Consensus pattern (66 bp):
AAACAGAGAGTACCAAAGTACTAACAGAGAGCACATAAGTGCTGAACAGAGAGAACACACAGTGC
T
Found at i:5832230 original size:43 final size:43
Alignment explanation
Indices: 5832176--5832514 Score: 298
Period size: 43 Copynumber: 8.0 Consensus size: 43
5832166 TCTGTTAATG
* *
5832176 TTAGTGGCGTTTGTGGGAAAAAG-GCTGCTAAAGAACATGTTCT
1 TTAGCGGCGTTTGTGGG-AAAAGCGCCGCTAAAGAACATGTTCT
* * * *
5832219 ATAGCGGCGTTTGTGGGAAAAGCGTC-CTAAAGATCATGGTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGTTCT
* * * * *
5832261 TTAGCAGCGTTTGTGGGAGAAGCACCGCTAAACAACATG-ACTT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGTTC-T
* * * * * *
5832304 TTAGGGGCGTTTGTAGGAAAAGCACCACTAAAGAACGTGGTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGTTCT
** * *
5832347 TTAGCGGTATTTGTGGTG-AAGGCGCCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGG-GAAAAGCGCCGCTAAAGAACATGTTCT
* *
5832390 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGATCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGTTCT
* * * *
5832433 TTAGCAGCGTTTGTGGTAAAAGTGTCGCTAAAGAACATG----
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGTTCT
* * * * * *
5832472 GTAGTGACGTTTGTGGGAAAAGTGTCGCTAAAGACCATGTTCT
1 TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGTTCT
5832515 ATAACGATGT
Statistics
Matches: 239, Mismatches: 47, Indels: 20
0.78 0.15 0.07
Matches are distributed among these distances:
39 33 0.14
42 42 0.18
43 162 0.68
44 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGAACATGTTCT
Found at i:5840495 original size:15 final size:14
Alignment explanation
Indices: 5840471--5840500 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
5840461 GAAAAATACT
5840471 TTTGGTATTTTTTA
1 TTTGGTATTTTTTA
5840485 TTTGAGTATTTTTTA
1 TTTG-GTATTTTTTA
5840500 T
1 T
5840501 AAATTATGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.17, C:0.00, G:0.13, T:0.70
Consensus pattern (14 bp):
TTTGGTATTTTTTA
Found at i:5843238 original size:36 final size:36
Alignment explanation
Indices: 5843189--5843260 Score: 85
Period size: 36 Copynumber: 2.0 Consensus size: 36
5843179 TTTTCATTAT
5843189 TAATTTTGAAAAATACGAAATA-AATTATAATAAAAA
1 TAATTTTGAAAAAT-CGAAATACAATTATAATAAAAA
** *
5843225 TAATTTT-AGAAAATCTTAATACAATTTTAATAAAAA
1 TAATTTTGA-AAAATCGAAATACAATTATAATAAAAA
5843261 AAGAGAGAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (36 bp):
TAATTTTGAAAAATCGAAATACAATTATAATAAAAA
Found at i:5843301 original size:18 final size:18
Alignment explanation
Indices: 5843270--5843304 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5843260 AAAGAGAGAG
*
5843270 TTGAGAGAGGAATAAAAA
1 TTGAGAGAGAAATAAAAA
*
5843288 TTGAGTGAGAAATAAAA
1 TTGAGAGAGAAATAAAA
5843305 GAGAACTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.26, T:0.20
Consensus pattern (18 bp):
TTGAGAGAGAAATAAAAA
Found at i:5847394 original size:15 final size:15
Alignment explanation
Indices: 5847370--5847400 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5847360 ACAGAAGATA
5847370 AAAAACAATTTTTTT
1 AAAAACAATTTTTTT
*
5847385 AAAAATAATTTTTTT
1 AAAAACAATTTTTTT
5847400 A
1 A
5847401 CTTTTAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
AAAAACAATTTTTTT
Found at i:5847816 original size:32 final size:36
Alignment explanation
Indices: 5847751--5847823 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 36
5847741 TTAAAATTTT
*
5847751 AAATTAATAAAAATAAAATTATACTTTAATCC-TTA
1 AAATTAATAAAAATAAAATTATAATTTAATCCTTTA
*
5847786 AAATTAAT-AAAA-AATATT-TAATTTAATCCTTTA
1 AAATTAATAAAAATAAAATTATAATTTAATCCTTTA
5847819 AAATT
1 AAATT
5847824 TTTTAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 10 0.29
33 13 0.37
34 4 0.11
35 8 0.23
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (36 bp):
AAATTAATAAAAATAAAATTATAATTTAATCCTTTA
Found at i:5855439 original size:18 final size:17
Alignment explanation
Indices: 5855415--5855477 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 17
5855405 ATAATATGCG
5855415 TTTTTTAATTTAAATTA
1 TTTTTTAATTTAAATTA
*
5855432 TATTTTTAAAATTTAATTTA
1 T-TTTTT--AATTTAAATTA
* *
5855452 TTATTTTAATTTGATTTA
1 TT-TTTTAATTTAAATTA
5855470 TTCTTTTA
1 TT-TTTTA
5855478 TCATATATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
17 1 0.03
18 22 0.56
19 1 0.03
20 15 0.38
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTTTAATTTAAATTA
Found at i:5855533 original size:18 final size:17
Alignment explanation
Indices: 5855502--5855558 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 17
5855492 AAAAAAACCT
5855502 ATTTAAAGAATAAATTA
1 ATTTAAAGAATAAATTA
5855519 ATTTAAAGCAATAAATTA
1 ATTTAAAG-AATAAATTA
* *
5855537 AATTAAAAAATAGAATTTA
1 ATTTAAAGAATA-AA-TTA
5855556 ATT
1 ATT
5855559 AATAAAATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
17 12 0.35
18 17 0.50
19 5 0.15
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (17 bp):
ATTTAAAGAATAAATTA
Found at i:5855559 original size:18 final size:18
Alignment explanation
Indices: 5855510--5855567 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
5855500 CTATTTAAAG
* *
5855510 AATAAATTAATTTAA-AGC
1 AATAAATTAAATTAATA-A
5855528 AATAAATTAAATTAA-AA
1 AATAAATTAAATTAATAA
*
5855545 AATAGAATTTAATTAATAA
1 AATA-AATTAAATTAATAA
5855564 AATA
1 AATA
5855568 CATATTTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.11
18 25 0.71
19 6 0.17
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (18 bp):
AATAAATTAAATTAATAA
Found at i:5855574 original size:20 final size:18
Alignment explanation
Indices: 5855528--5855575 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
5855518 AATTTAAAGC
*
5855528 AATA-AATTAAATTAAAA
1 AATACAATTTAATTAAAA
*
5855545 AATAGAATTTAATTAATAA
1 AATACAATTTAATTAA-AA
5855564 AATACATATTTA
1 AATACA-ATTTA
5855576 GAGAATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 4 0.15
18 10 0.38
19 7 0.27
20 5 0.19
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
AATACAATTTAATTAAAA
Found at i:5863165 original size:23 final size:23
Alignment explanation
Indices: 5863138--5863207 Score: 88
Period size: 23 Copynumber: 3.1 Consensus size: 23
5863128 ACAAAATATT
5863138 ATGACAGGAGAGTTACAAACATA
1 ATGACAGGAGAGTTACAAACATA
* *
5863161 ATGACAGGAAAGTTACAAACATT
1 ATGACAGGAGAGTTACAAACATA
** *
5863184 ATGGTAGGAGAGGTACAAA-ATA
1 ATGACAGGAGAGTTACAAACATA
5863206 AT
1 AT
5863208 AATAATTGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 4 0.10
23 36 0.90
ACGTcount: A:0.47, C:0.10, G:0.23, T:0.20
Consensus pattern (23 bp):
ATGACAGGAGAGTTACAAACATA
Found at i:5865268 original size:20 final size:19
Alignment explanation
Indices: 5865257--5865323 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 19
5865247 AACAACAACT
5865257 AAAACAGTAAAAAAACACC
1 AAAACAGTAAAAAAACACC
5865276 AAAACAGTAAAAAAAACAACAC
1 AAAACAGT-AAAAAAAC-AC-C
*
5865298 AAAAACAATAAAAAACAGCACC
1 -AAAACAGTAAAAAA-A-CACC
5865320 AAAA
1 AAAA
5865324 TAACAATATA
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
19 8 0.20
20 8 0.20
21 6 0.15
22 8 0.20
23 10 0.24
24 1 0.02
ACGTcount: A:0.72, C:0.19, G:0.04, T:0.04
Consensus pattern (19 bp):
AAAACAGTAAAAAAACACC
Found at i:5865271 original size:23 final size:21
Alignment explanation
Indices: 5865245--5865312 Score: 77
Period size: 23 Copynumber: 3.1 Consensus size: 21
5865235 AAACAACACG
5865245 AAAACAACAACTAAAACAGTAAA
1 AAAACAAC-AC-AAAACAGTAAA
5865268 AAAAC-AC-CAAAACAGTAAAA
1 AAAACAACACAAAACAGT-AAA
*
5865288 AAAACAACACAAAAACAATAAA
1 AAAACAACAC-AAAACAGTAAA
5865310 AAA
1 AAA
5865313 CAGCACCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 8 0.20
20 9 0.22
21 2 0.05
22 9 0.22
23 12 0.30
ACGTcount: A:0.74, C:0.18, G:0.03, T:0.06
Consensus pattern (21 bp):
AAAACAACACAAAACAGTAAA
Found at i:5865292 original size:31 final size:32
Alignment explanation
Indices: 5865199--5865293 Score: 95
Period size: 31 Copynumber: 3.0 Consensus size: 32
5865189 AAAGCAATAT
* *
5865199 TAAAAACAACA-AAAATAGCAACAAAAATAACAG
1 TAAAAACAACACCAAA-A-CAACAAAAAAAACAG
* **
5865232 TAAAAACAACACGAAAACAACAACTAAAACAG
1 TAAAAACAACACCAAAACAACAAAAAAAACAG
**
5865264 TAAAAA-AACACCAAAACAGTAAAAAAAACA
1 TAAAAACAACACCAAAACAACAAAAAAAACA
5865294 ACACAAAAAC
Statistics
Matches: 52, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
31 19 0.37
32 18 0.35
33 12 0.23
34 3 0.06
ACGTcount: A:0.69, C:0.18, G:0.05, T:0.07
Consensus pattern (32 bp):
TAAAAACAACACCAAAACAACAAAAAAAACAG
Found at i:5865311 original size:10 final size:10
Alignment explanation
Indices: 5865200--5865314 Score: 56
Period size: 11 Copynumber: 10.7 Consensus size: 10
5865190 AAGCAATATT
5865200 AAAAACAACA
1 AAAAACAACA
5865210 AAAATAGCAAC-
1 AAAA-A-CAACA
*
5865221 AAAAATAACA
1 AAAAACAACA
5865231 GTAAAAACAACA
1 --AAAAACAACA
*
5865243 CGAAAACAACA
1 -AAAAACAACA
5865254 ACTAAAACAGTA-A
1 A--AAAACA--ACA
*
5865267 AAAAACACCA
1 AAAAACAACA
**
5865277 AAACAGTAA-A
1 AAA-AACAACA
5865287 AAAAACAACA
1 AAAAACAACA
*
5865297 CAAAAACAATA
1 -AAAAACAACA
5865308 AAAAACA
1 AAAAACA
5865315 GCACCAAAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 26
0.68 0.10 0.22
Matches are distributed among these distances:
9 6 0.08
10 21 0.26
11 31 0.39
12 19 0.24
13 2 0.03
14 1 0.01
ACGTcount: A:0.71, C:0.18, G:0.04, T:0.06
Consensus pattern (10 bp):
AAAAACAACA
Found at i:5865331 original size:24 final size:21
Alignment explanation
Indices: 5865245--5865323 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 21
5865235 AAACAACACG
* *
5865245 AAAACAACAACTAAAACAGT-A
1 AAAACAAC-ACAAAAACAATAA
* *
5865266 AAAA-AACACCAAAACAGTAAAA
1 AAAACAACACAAAAACA--ATAA
5865288 AAAACAACACAAAAACAATAA
1 AAAACAACACAAAAACAATAA
* *
5865309 AAAACAGCACCAAAA
1 AAAACAACACAAAAA
5865324 TAACAATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
19 8 0.17
20 3 0.06
21 20 0.43
22 5 0.11
23 11 0.23
ACGTcount: A:0.71, C:0.20, G:0.04, T:0.05
Consensus pattern (21 bp):
AAAACAACACAAAAACAATAA
Found at i:5867283 original size:2 final size:2
Alignment explanation
Indices: 5867276--5867311 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5867266 GAAGAAGGTG
5867276 GA GA GA GA GA -A GA GA GA GA GA -A GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5867312 AGACATCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5867292 original size:11 final size:11
Alignment explanation
Indices: 5867276--5867311 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
5867266 GAAGAAGGTG
5867276 GAGAGAGAGAA
1 GAGAGAGAGAA
5867287 GAGAGAGAGAA
1 GAGAGAGAGAA
5867298 GAGAGAGAG-A
1 GAGAGAGAGAA
5867308 GAGA
1 GAGA
5867312 AGACATCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 5 0.20
11 20 0.80
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (11 bp):
GAGAGAGAGAA
Found at i:5867294 original size:13 final size:13
Alignment explanation
Indices: 5867276--5867314 Score: 62
Period size: 13 Copynumber: 3.0 Consensus size: 13
5867266 GAAGAAGGTG
5867276 GAGAGAGAGAAGA
1 GAGAGAGAGAAGA
5867289 GAGAGAGA-AGAGA
1 GAGAGAGAGA-AGA
5867302 GAGAGAGAGAAGA
1 GAGAGAGAGAAGA
5867315 CATCAACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (13 bp):
GAGAGAGAGAAGA
Found at i:5881058 original size:69 final size:69
Alignment explanation
Indices: 5880935--5881142 Score: 217
Period size: 69 Copynumber: 3.0 Consensus size: 69
5880925 ACTCCATATA
* * *
5880935 CTTCTTTCCCCGTTAAATTAATACCCA-TATTATCCGTGGCTCCCC-TATCACAAGTGGTTGGAT
1 CTTCTTACCCCATTAAATTAATACCCACT-TTATCCGTGG-TCCCCACATCACAAGTGGTTGGAT
5880998 CATGTT
64 CATGTT
* * ** *
5881004 CTTTTTACCCTATTAAATTAATTTCCACTTTATCCATGGTCCCCACATCACAAGTGGTTGTG-TC
1 CTTCTTACCCCATTAAATTAATACCCACTTTATCCGTGGTCCCCACATCACAAGTGGTTG-GATC
*
5881068 ATTTT
65 ATGTT
* * * * **
5881073 CTTCTTGCCCCATTAAAATAATACCCACTTTATTCGTGG-CCTCCACATCACAAGTGATTTTATC
1 CTTCTTACCCCATTAAATTAATACCCACTTTATCCGTGGTCC-CCACATCACAAGTGGTTGGATC
5881137 ATGTT
65 ATGTT
5881142 C
1 C
5881143 CATCACTGCA
Statistics
Matches: 113, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
68 7 0.06
69 104 0.92
70 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.12, T:0.38
Consensus pattern (69 bp):
CTTCTTACCCCATTAAATTAATACCCACTTTATCCGTGGTCCCCACATCACAAGTGGTTGGATCA
TGTT
Found at i:5885722 original size:14 final size:14
Alignment explanation
Indices: 5885703--5885731 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
5885693 AATAAATACA
5885703 AAGCAAACTATGAC
1 AAGCAAACTATGAC
5885717 AAGCAAACTATGAC
1 AAGCAAACTATGAC
5885731 A
1 A
5885732 GCTTGATAGA
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:0.52, C:0.21, G:0.14, T:0.14
Consensus pattern (14 bp):
AAGCAAACTATGAC
Found at i:5891087 original size:4 final size:4
Alignment explanation
Indices: 5891078--5891112 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
5891068 ACTCTAAATG
*
5891078 TTGT TTGT TTGT TTGT TTGT TTGT TT-A TTGT TTGT
1 TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT TTGT
5891113 GATTGCATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 2 0.07
4 26 0.93
ACGTcount: A:0.03, C:0.00, G:0.23, T:0.74
Consensus pattern (4 bp):
TTGT
Found at i:5896345 original size:7 final size:7
Alignment explanation
Indices: 5896333--5896359 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5896323 GGGACAACCA
5896333 CAAACAC
1 CAAACAC
5896340 CAAACAC
1 CAAACAC
5896347 CAAACAC
1 CAAACAC
5896354 CAAACA
1 CAAACA
5896360 TAGACAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.41, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAACAC
Found at i:5896845 original size:15 final size:15
Alignment explanation
Indices: 5896827--5896856 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5896817 ATAAAAAAGT
*
5896827 AAAGCAGAAAAGAAA
1 AAAGAAGAAAAGAAA
5896842 AAAGAAGAAAAGAAA
1 AAAGAAGAAAAGAAA
5896857 TGCACATTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (15 bp):
AAAGAAGAAAAGAAA
Found at i:5901065 original size:24 final size:24
Alignment explanation
Indices: 5901037--5901099 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
5901027 AGAAATAATC
5901037 TTTCAGTTAAACTCTATTTAATTG
1 TTTCAGTTAAACTCTATTTAATTG
* * * *
5901061 TTTCAATTAAAATCTGTTTATTTG
1 TTTCAGTTAAACTCTATTTAATTG
* *
5901085 TTTAAGTCAAACTCT
1 TTTCAGTTAAACTCT
5901100 TATTAGTCCA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (24 bp):
TTTCAGTTAAACTCTATTTAATTG
Found at i:5912566 original size:17 final size:17
Alignment explanation
Indices: 5912539--5912590 Score: 77
Period size: 17 Copynumber: 3.1 Consensus size: 17
5912529 AGTCCCAATC
*
5912539 AAATCATTTTAAATTTA
1 AAATTATTTTAAATTTA
*
5912556 AATTTATTTTAAATTTA
1 AAATTATTTTAAATTTA
*
5912573 AAATTATTATAAATTTA
1 AAATTATTTTAAATTTA
5912590 A
1 A
5912591 TTAAAAGTCC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTATTTTAAATTTA
Found at i:5913430 original size:15 final size:15
Alignment explanation
Indices: 5913386--5913437 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
5913376 AAATACATGC
* *
5913386 TAATAATAATAACAG
1 TAATGATAATAACAT
*
5913401 TATTGATAAT-A-AT
1 TAATGATAATAACAT
*
5913414 TACTGATAATAACAT
1 TAATGATAATAACAT
5913429 TAATGATAA
1 TAATGATAA
5913438 ATATTGGTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 10 0.33
14 2 0.07
15 18 0.60
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.35
Consensus pattern (15 bp):
TAATGATAATAACAT
Found at i:5914678 original size:31 final size:30
Alignment explanation
Indices: 5914632--5914874 Score: 116
Period size: 30 Copynumber: 8.2 Consensus size: 30
5914622 AACTGTTTAG
5914632 AAATTATA-TTTTGACCCTCAAACTTCTTCA
1 AAATTATATTTTTGACCCTCAAACTTC-TCA
* * * *
5914662 AAATTATATTTTTGACCTTAAAACTTTTGA
1 AAATTATATTTTTGACCCTCAAACTTCTCA
*
5914692 AAATTATA-TTTTAACCC-CAAAAACTTC-CAA
1 AAATTATATTTTTGACCCTC--AAACTTCTC-A
* * * * *
5914722 AAATTACATTTTTAACCCTAAAATTTCTAA
1 AAATTATATTTTTGACCCTCAAACTTCTCA
* *
5914752 AAAATATATTTTTG-CCCTCGAACTTC-CAA
1 AAATTATATTTTTGACCCTCAAACTTCTC-A
* ** * *
5914781 AAACTCCATTTTTGATCCC-GAAACTTCTAA
1 AAATTATATTTTTGA-CCCTCAAACTTCTCA
**
5914811 AAATTCCATTTTT-ACCC-CTAAACTTC-CA
1 AAATTATATTTTTGACCCTC-AAACTTCTCA
**
5914839 AAAGTT-TCATTTTT-A-CCTCAAAACTTCAAA
1 AAA-TTAT-ATTTTTGACCCTC-AAACTTCTCA
5914869 AAATTA
1 AAATTA
5914875 CCATTTTACC
Statistics
Matches: 164, Mismatches: 32, Indels: 34
0.71 0.14 0.15
Matches are distributed among these distances:
28 9 0.05
29 55 0.34
30 73 0.45
31 27 0.16
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.37
Consensus pattern (30 bp):
AAATTATATTTTTGACCCTCAAACTTCTCA
Done.