Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 100 of 163
Found at i:28088136 original size:30 final size:29
Alignment explanation
Indices: 28088080--28088174 Score: 88
Period size: 30 Copynumber: 3.2 Consensus size: 29
28088070 CCTTGAAGGT
**
28088080 CCCTAAACTATC-CAAAAATTGTATTTTAAC
1 CCCTAAACT-TCTCAAAAATTACATTTT-AC
*
28088110 CCCTAAACTTCTCTAAAATTACATTTTTGA-
1 CCCTAAACTTCTCAAAAATTACA-TTTT-AC
28088140 CCCTGAAACTTCT-AAAAATTACCATTTTAC
1 CCCT-AAACTTCTCAAAAATTA-CATTTTAC
28088170 CCCTA
1 CCCTA
28088175 TATGTCCAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 11
0.77 0.07 0.15
Matches are distributed among these distances:
29 4 0.07
30 36 0.65
31 15 0.27
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
CCCTAAACTTCTCAAAAATTACATTTTAC
Found at i:28088152 original size:31 final size:30
Alignment explanation
Indices: 28088110--28088167 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
28088100 GTATTTTAAC
*
28088110 CCCTAAACTTCTCTAAAATTA-CATTTTTGA
1 CCCTAAACTTCT-AAAAATTACCATTTTTGA
28088140 CCCTGAAACTTCTAAAAATTACCATTTT
1 CCCT-AAACTTCTAAAAATTACCATTTT
28088168 ACCCCTATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 11 0.44
31 14 0.56
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.38
Consensus pattern (30 bp):
CCCTAAACTTCTAAAAATTACCATTTTTGA
Found at i:28088412 original size:146 final size:145
Alignment explanation
Indices: 28088122--28088634 Score: 520
Period size: 147 Copynumber: 3.5 Consensus size: 145
28088112 CTAAACTTCT
* * **
28088122 CTAAAATTA-CATTTTTGACCCT-GAAACTTCTAAAAATTACCATTTTA-CCCCTATATGTCCAA
1 CTAAAATTACCA-TTTTG-CCCTCGAAA-GTCT-AAAATTACCATTTTACCCCCGA-ACATCCAA
* * * * * *
28088184 AAA-TCCCATTTTTGATCTCGATTTTTCTAAAAATTACCG-TTTTACCCTTAA-TTTTCTAAAAT
61 AAAGTCTCATTTTTTATCTCGATTCTTCCAAAAATTA-CGTTTTTACCCTCAACATTTC--AAAT
28088246 GTCATTTCTAACCCCAAATTTTC
123 GTCATTTCTAACCCCAAATTTTC
28088269 CTAAAATTACCATTTTGCCCTCGAAAGTCTAAAATTACCATTTTACCCTCCGAACATCCAAAAAG
1 CTAAAATTACCATTTTGCCCTCGAAAGTCTAAAATTACCATTTTACCC-CCGAACATCCAAAAAG
* *
28088334 TCTCATTTTTTATCCCGATTCTTCCAAAAATTACGTTTTTACCCCCAACATTTCAAATGTCATTT
65 TCTCATTTTTTATCTCGATTCTTCCAAAAATTACGTTTTTACCCTCAACATTTCAAATGTCATTT
**
28088399 CTAACCTTAAATTTTTC
130 CTAACCCCAAA-TTTTC
* * * * * *
28088416 CT-AAATTTCCATTTTACCCTCAAAAGTCTAAAATTACCATTTTGCCCCCAAACATCCAAAAGGT
1 CTAAAATTACCATTTTGCCCTCGAAAGTCTAAAATTACCATTTTACCCCCGAACATCCAAAAAGT
* * * * ** *
28088480 CACGTTTTTTTATCTCGATTCTTCCAAAAGTTATGTTTTTACCCTTGGACATTTAAAATGTCAAT
66 CTC-ATTTTTTATCTCGATTCTTCCAAAAATTACGTTTTTACCC-TCAACATTTCAAATGTC-AT
28088545 TT-TAACCCCAAATTTTC
128 TTCTAACCCCAAATTTTC
* * * * * * * ***
28088562 CCAAAATTACCATTTTGCCCTTGAGAGTTTAAAATTATCATTTTGCCCTCGGGTATCCAAAAAGT
1 CTAAAATTACCATTTTGCCCTCGAAAGTCTAAAATTACCATTTTACCCCCGAACATCCAAAAAGT
28088627 CTCATTTT
66 CTCATTTT
28088635 CAACCCCGAT
Statistics
Matches: 307, Mismatches: 47, Indels: 25
0.81 0.12 0.07
Matches are distributed among these distances:
145 32 0.10
146 127 0.41
147 138 0.45
148 10 0.03
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (145 bp):
CTAAAATTACCATTTTGCCCTCGAAAGTCTAAAATTACCATTTTACCCCCGAACATCCAAAAAGT
CTCATTTTTTATCTCGATTCTTCCAAAAATTACGTTTTTACCCTCAACATTTCAAATGTCATTTC
TAACCCCAAATTTTC
Found at i:28088476 original size:28 final size:28
Alignment explanation
Indices: 28088418--28088476 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
28088408 AATTTTTCCT
* * *
28088418 AAATTTCCATTTTACCCTCAAAAGTCTA
1 AAATTACCATTTTACCCCCAAAAGTCCA
*
28088446 AAATTACCATTTTGCCCCCAAACA-TCCA
1 AAATTACCATTTTACCCCCAAA-AGTCCA
28088474 AAA
1 AAA
28088477 GGTCACGTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 25 0.96
29 1 0.04
ACGTcount: A:0.39, C:0.29, G:0.03, T:0.29
Consensus pattern (28 bp):
AAATTACCATTTTACCCCCAAAAGTCCA
Found at i:28100589 original size:92 final size:92
Alignment explanation
Indices: 28100370--28100920 Score: 1023
Period size: 92 Copynumber: 6.0 Consensus size: 92
28100360 GGTGGATTAG
28100370 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
28100435 GAAGTTGTAGT-AGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
* *
28100461 ATCAAACATCAATTCCTATCCTCTTAAAGTTGTAGTAAGGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
28100526 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
* *
28100553 ATCAAACATCAATTCTTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
28100618 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
*
28100645 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAATTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
28100710 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
28100737 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
28100802 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
* * *
28100829 ATCAAACATAAATTCTTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTGTCTCTCT
1 ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
28100894 GAAGTTGTAGTAAGAGCAAGATGAAGC
66 GAAGTTGTAGTAAGAGCAAGATGAAGC
28100921 CCTAACATCA
Statistics
Matches: 446, Mismatches: 13, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
91 74 0.17
92 372 0.83
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (92 bp):
ATCAAACATCAATTCCTATCCTCTTGAAGTTGTAGTAAAGTTGGATAGCAAGTCTTTATCTCTCT
GAAGTTGTAGTAAGAGCAAGATGAAGC
Found at i:28101246 original size:17 final size:17
Alignment explanation
Indices: 28101207--28101266 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
28101197 TAAAATGGAT
*
28101207 TTTAAATTTATTTCTAAA
1 TTTAAATTTACTT-TAAA
*
28101225 ATTAAATTTACTTTAAA
1 TTTAAATTTACTTTAAA
*
28101242 TTTAAATTTAGTTTAAA
1 TTTAAATTTACTTTAAA
28101259 TTTGAAAT
1 TTT-AAAT
28101267 AATTTTTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
17 22 0.59
18 15 0.41
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (17 bp):
TTTAAATTTACTTTAAA
Found at i:28101837 original size:21 final size:22
Alignment explanation
Indices: 28101808--28101849 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
28101798 ATCAGGTATT
*
28101808 AATGCATGTTT-GCTACCATTC
1 AATGCATGTTTAACTACCATTC
*
28101829 AATGTATGTTTAACTACCATT
1 AATGCATGTTTAACTACCATT
28101850 TATGTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (22 bp):
AATGCATGTTTAACTACCATTC
Found at i:28102237 original size:16 final size:17
Alignment explanation
Indices: 28102206--28102242 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
28102196 ACAAACGAAA
*
28102206 TAAAAGGAGGTTTTTTT
1 TAAAAGGAGCTTTTTTT
28102223 TAAAAGGA-CTTTTTTT
1 TAAAAGGAGCTTTTTTT
28102239 TAAA
1 TAAA
28102243 CTCCCAGATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (17 bp):
TAAAAGGAGCTTTTTTT
Found at i:28103156 original size:30 final size:31
Alignment explanation
Indices: 28103130--28103200 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
28103120 CAAAAATTGT
*
28103130 ATTTTGACCCCCAAACTTCTCCAAAATTACA
1 ATTTTGACCCCAAAACTTCTCCAAAATTACA
* *
28103161 ATTTTGACCCCAAAACTTCT-AAAAATTACC
1 ATTTTGACCCCAAAACTTCTCCAAAATTACA
28103191 ATTTT-ACCCC
1 ATTTTGACCCC
28103201 TTGAATGTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 5 0.14
30 13 0.35
31 19 0.51
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.31
Consensus pattern (31 bp):
ATTTTGACCCCAAAACTTCTCCAAAATTACA
Found at i:28103409 original size:148 final size:147
Alignment explanation
Indices: 28103138--28103665 Score: 568
Period size: 148 Copynumber: 3.6 Consensus size: 147
28103128 GTATTTTGAC
* * * * * *
28103138 CCCCAAACTTCTCC-AAAATTACAATTTTGACCCCAAAACTTCTAAAAATTACCATTTTACCCCT
1 CCCCAAATTTTTCCTAAAATTACCATTTT-ATCCTAAAA-GTCT-AAAATTACCATTTTACCCCT
* * * * * * *
28103202 TGAATGTCCAAAAA-TCCCATTTTTGATCTCGATTTTTCTAAAAATTACCG-TTTTACCCTCGAT
63 CGAATATCCAAAAAGTCACATTTTTTATCTCGATTCTTCCAAAAATTA-CGTTTTTACCCTCGAA
* *
28103265 TATCTAAAATGTCATTTCTAA
127 CATTTAAAATGTCATTTCTAA
* * * *
28103286 CCCTAAATTTTTCCTAAAATTACCATTTTGTTCCTAAAAGTCCAATATTACCATTTTACCCCTCG
1 CCCCAAATTTTTCCTAAAATTACCATTTT-ATCCTAAAAGTCTAAAATTACCATTTTACCCCTCG
* *
28103351 AATATCCAAAAAGTCACATTTTTTATCCCAATTCTTCCAAAAATTACGTTTTTACCCTCGAACAT
65 AATATCCAAAAAGTCACATTTTTTATCTCGATTCTTCCAAAAATTACGTTTTTACCCTCGAACAT
28103416 TTAAAATGTCATTTCTAA
130 TTAAAATGTCATTTCTAA
* * * *
28103434 CCCCAAATTTTTCCTAAAATTTCCATTTTA-CTCTCGAAAGTTTAAAATTACCATTTTTCCCC-C
1 CCCCAAATTTTTCCTAAAATTACCATTTTATC-CT-AAAAGTCTAAAATTACCATTTTACCCCTC
* * * * *
28103497 GAACATCTAAAAAGTCACGTTTTTTTATCTCGATTCTTCCAAAAATTACGTTTTTACCCCCTAAC
64 GAATATCCAAAAAGTCAC-ATTTTTTATCTCGATTCTTCCAAAAATTACGTTTTTACCCTCGAAC
*
28103562 ATTTAAAATGTCAATTCTAA
128 ATTTAAAATGTCATTTCTAA
* * * * *
28103582 CCCCAAA--TTTCCCAAAATTACCATTTTACCCTAGAGAGTCTAAAATTACCATTTT-GCCCTTG
1 CCCCAAATTTTTCCTAAAATTACCATTTTATCCTA-AAAGTCTAAAATTACCATTTTACCCCTCG
** *
28103644 GGTATCCAAAAAGTCTCATTTT
65 AATATCCAAAAAGTCACATTTT
28103666 CAACCCCGAT
Statistics
Matches: 321, Mismatches: 50, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
145 7 0.02
146 54 0.17
147 53 0.17
148 187 0.58
149 20 0.06
ACGTcount: A:0.32, C:0.25, G:0.06, T:0.37
Consensus pattern (147 bp):
CCCCAAATTTTTCCTAAAATTACCATTTTATCCTAAAAGTCTAAAATTACCATTTTACCCCTCGA
ATATCCAAAAAGTCACATTTTTTATCTCGATTCTTCCAAAAATTACGTTTTTACCCTCGAACATT
TAAAATGTCATTTCTAA
Found at i:28107161 original size:29 final size:29
Alignment explanation
Indices: 28107122--28107187 Score: 73
Period size: 30 Copynumber: 2.3 Consensus size: 29
28107112 TAGAGTTTCA
* *
28107122 CATGTAT-AATTGCAC-CAAATTAAAATT
1 CATGTATAAATTACACACAAATCAAAATT
* *
28107149 CATGTATACAATTACACATAAATCAAAGTT
1 CATGTATA-AATTACACACAAATCAAAATT
28107179 CATGTATAA
1 CATGTATAA
28107188 TTTTGAGATT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 7 0.22
29 8 0.25
30 17 0.53
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (29 bp):
CATGTATAAATTACACACAAATCAAAATT
Found at i:28117393 original size:22 final size:22
Alignment explanation
Indices: 28117365--28117412 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
28117355 AATTTAAAAT
28117365 AAATTATCGAACAAATTTATGA
1 AAATTATCGAACAAATTTATGA
28117387 AAATTATCGAACAAATTTATGA
1 AAATTATCGAACAAATTTATGA
28117409 AAAT
1 AAAT
28117413 AAAATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.31
Consensus pattern (22 bp):
AAATTATCGAACAAATTTATGA
Found at i:28117706 original size:21 final size:23
Alignment explanation
Indices: 28117682--28117725 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
28117672 TGAACAAATA
28117682 GATAAT-ACAATT-AAAAT-TTTC
1 GATAATCA-AATTGAAAATATTTC
28117703 GATAATCAAATTGAAAATATTTC
1 GATAATCAAATTGAAAATATTTC
28117726 TATTAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 10 0.50
22 6 0.30
23 4 0.20
ACGTcount: A:0.48, C:0.09, G:0.07, T:0.36
Consensus pattern (23 bp):
GATAATCAAATTGAAAATATTTC
Found at i:28117732 original size:24 final size:21
Alignment explanation
Indices: 28117682--28117743 Score: 56
Period size: 21 Copynumber: 2.9 Consensus size: 21
28117672 TGAACAAATA
28117682 GATAAT-ACAATTAAAATTTTC
1 GATAATCA-AATTAAAATTTTC
28117703 GATAATCAAATTGAAAATATTTC
1 GATAATCAAATT-AAAAT-TTTC
* *
28117726 TATTAATGAAA-TAAAATT
1 GA-TAATCAAATTAAAATT
28117744 AAAAAACTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
21 11 0.31
22 11 0.31
23 6 0.17
24 7 0.20
ACGTcount: A:0.50, C:0.06, G:0.06, T:0.37
Consensus pattern (21 bp):
GATAATCAAATTAAAATTTTC
Found at i:28123240 original size:43 final size:44
Alignment explanation
Indices: 28123179--28123278 Score: 139
Period size: 44 Copynumber: 2.3 Consensus size: 44
28123169 CACAAGACAG
* * * *
28123179 AGGAAGCTACATG-GAAAAAGCCACATCCAAGAAACGACAAAGA
1 AGGAAGCTACGTGAAAAAAAACCACATCCAAGAAACGACAAAAA
* *
28123222 AGGAAGCTACGTGAAAAAAAACCACTTCCAAGAAATGACAAAAA
1 AGGAAGCTACGTGAAAAAAAACCACATCCAAGAAACGACAAAAA
28123266 AGGAAGCTACGTG
1 AGGAAGCTACGTG
28123279 GAAATCACTC
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
43 12 0.24
44 38 0.76
ACGTcount: A:0.50, C:0.19, G:0.21, T:0.10
Consensus pattern (44 bp):
AGGAAGCTACGTGAAAAAAAACCACATCCAAGAAACGACAAAAA
Found at i:28136546 original size:12 final size:12
Alignment explanation
Indices: 28136529--28136563 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28136519 ATCATTAATA
*
28136529 AATAAACGAGTC
1 AATAAACGAGCC
*
28136541 AATAAATGAGCC
1 AATAAACGAGCC
28136553 AATAAACGAGC
1 AATAAACGAGC
28136564 TTTTAAACGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.14
Consensus pattern (12 bp):
AATAAACGAGCC
Found at i:28138596 original size:25 final size:25
Alignment explanation
Indices: 28138545--28138596 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
28138535 TATTTTATTT
*
28138545 TATTTATTTAATATTAATACAATTA
1 TATTTATTTAATATTAATACAAATA
*
28138570 TATTTA-TTAATATTAAATATAAATA
1 TATTTATTTAATATT-AATACAAATA
28138595 TA
1 TA
28138597 AATATACAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (25 bp):
TATTTATTTAATATTAATACAAATA
Found at i:28140123 original size:26 final size:26
Alignment explanation
Indices: 28140066--28140123 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
28140056 ATTCGAAAGA
**
28140066 ATAAAAAAAATTAAGTATCACTTATG
1 ATAAAAAAAATTAAGTATCACAAATG
* *
28140092 ACAAAAAAATTTAAGTATCA-AAATG
1 ATAAAAAAAATTAAGTATCACAAATG
28140117 ATAAAAA
1 ATAAAAA
28140124 TAATATAGCA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 9 0.33
26 18 0.67
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (26 bp):
ATAAAAAAAATTAAGTATCACAAATG
Found at i:28140951 original size:10 final size:9
Alignment explanation
Indices: 28140924--28140965 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
28140914 AATTTAAAAT
*
28140924 TAAAATTTA
1 TAAAATATA
28140933 TAAAA-ATA
1 TAAAATATA
28140941 TAAAAATATA
1 T-AAAATATA
*
28140951 TAAAATAAA
1 TAAAATATA
28140960 TAAAAT
1 TAAAAT
28140966 TTTATAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 3 0.10
9 22 0.76
10 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAATATA
Found at i:28141163 original size:16 final size:16
Alignment explanation
Indices: 28141126--28141164 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
28141116 AATAATATTA
28141126 TTAATTTATATATTTT
1 TTAATTTATATATTTT
** *
28141142 AAAATTTATCTATTTT
1 TTAATTTATATATTTT
28141158 TTAATTT
1 TTAATTT
28141165 CACAAAAATA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (16 bp):
TTAATTTATATATTTT
Found at i:28144126 original size:22 final size:21
Alignment explanation
Indices: 28144101--28144157 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
28144091 TTTCCCAAAG
*
28144101 CAGCGATTCT-TTCTCTTTAAGC
1 CAGCGATGCTCTTCTC-TT-AGC
*
28144123 CAGCGCTGCTCTTCTCTTAGC
1 CAGCGATGCTCTTCTCTTAGC
*
28144144 CAGCGTTGCTCTTC
1 CAGCGATGCTCTTC
28144158 ACGGAGCCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 16 0.52
22 10 0.32
23 5 0.16
ACGTcount: A:0.12, C:0.33, G:0.18, T:0.37
Consensus pattern (21 bp):
CAGCGATGCTCTTCTCTTAGC
Found at i:28144146 original size:21 final size:21
Alignment explanation
Indices: 28144111--28144175 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
28144101 CAGCGATTCT
28144111 TTCTCTTTAAGCCAGCGCTGCTC
1 TTCTC-TT-AGCCAGCGCTGCTC
*
28144134 TTCTCTTAGCCAGCGTTGCTC
1 TTCTCTTAGCCAGCGCTGCTC
* ** *
28144155 TTCACGGAGCCATCGCTGCTC
1 TTCTCTTAGCCAGCGCTGCTC
28144176 CTCGCGAAGC
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 29 0.81
22 2 0.06
23 5 0.14
ACGTcount: A:0.12, C:0.35, G:0.20, T:0.32
Consensus pattern (21 bp):
TTCTCTTAGCCAGCGCTGCTC
Found at i:28148730 original size:21 final size:21
Alignment explanation
Indices: 28148678--28148730 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 21
28148668 AACTAAATCA
*
28148678 TCGTATCATGCATGTTTTTAT
1 TCGTATCATGAATGTTTTTAT
*
28148699 TCGTCTAATCATGAATTTTTTTAT
1 TCG--T-ATCATGAATGTTTTTAT
28148723 TCGTATCA
1 TCGTATCA
28148731 ATTGGGATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 7 0.26
22 1 0.04
23 1 0.04
24 18 0.67
ACGTcount: A:0.23, C:0.15, G:0.11, T:0.51
Consensus pattern (21 bp):
TCGTATCATGAATGTTTTTAT
Found at i:28148954 original size:18 final size:18
Alignment explanation
Indices: 28148920--28148953 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
28148910 AAAAGAAATC
28148920 GAAAAAATTGGGAAAAAG
1 GAAAAAATTGGGAAAAAG
28148938 GAAAAAA-TGGGAAAAA
1 GAAAAAATTGGGAAAAA
28148954 ATAGAGGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.09
Consensus pattern (18 bp):
GAAAAAATTGGGAAAAAG
Found at i:28150233 original size:19 final size:19
Alignment explanation
Indices: 28150211--28150257 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
28150201 TGAAAGGTAT
*
28150211 TAAAGATTATATT-CTTTCA
1 TAAAGATTAT-TTACTTCCA
*
28150230 TAAAGAATATTTACTTCCA
1 TAAAGATTATTTACTTCCA
*
28150249 TAAATATTA
1 TAAAGATTA
28150258 ACTCTGGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (19 bp):
TAAAGATTATTTACTTCCA
Found at i:28176250 original size:23 final size:24
Alignment explanation
Indices: 28176210--28176255 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
28176200 TTTACTTTAT
** *
28176210 TTACATTTTTATTTTTAT-TGTAG
1 TTACATTTCCATTCTTATATGTAG
28176233 TTACATTTCCATTCTTATATGTA
1 TTACATTTCCATTCTTATATGTA
28176256 TAGTATTGTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.24, C:0.11, G:0.07, T:0.59
Consensus pattern (24 bp):
TTACATTTCCATTCTTATATGTAG
Found at i:28185403 original size:11 final size:11
Alignment explanation
Indices: 28185387--28185414 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
28185377 TTGATCTGAG
28185387 AAGAATCGAGC
1 AAGAATCGAGC
28185398 AAGAATCGAGC
1 AAGAATCGAGC
28185409 AAGAAT
1 AAGAAT
28185415 GACGAAGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.50, C:0.14, G:0.25, T:0.11
Consensus pattern (11 bp):
AAGAATCGAGC
Found at i:28185519 original size:12 final size:12
Alignment explanation
Indices: 28185502--28185526 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28185492 TGTTATTATC
28185502 ATGAATGCTATT
1 ATGAATGCTATT
28185514 ATGAATGCTATT
1 ATGAATGCTATT
28185526 A
1 A
28185527 ATTATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.40
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:28192429 original size:19 final size:20
Alignment explanation
Indices: 28192382--28192429 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
28192372 TTGATAATTC
28192382 TTAA-TATTA-AATTATAAA
1 TTAATTATTATAATTATAAA
*
28192400 TTAAATT-TTATAATT-TATA
1 TT-AATTATTATAATTATAAA
28192419 TTAATTATTAT
1 TTAATTATTAT
28192430 CAAGAGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 14 0.56
20 5 0.20
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAATTATTATAATTATAAA
Found at i:28199552 original size:21 final size:20
Alignment explanation
Indices: 28199503--28199555 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
28199493 TTGTACTAGC
*
28199503 TCTACTGATACAAGTATGATT
1 TCTACCGATACAAGTATGA-T
*
28199524 TCTTCCGATACAAGTCATGCA-
1 TCTACCGATACAAGT-ATG-AT
28199545 TCTACCGATAC
1 TCTACCGATAC
28199556 TAGAAACTCC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 23 0.85
22 3 0.11
23 1 0.04
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (20 bp):
TCTACCGATACAAGTATGAT
Found at i:28199732 original size:50 final size:50
Alignment explanation
Indices: 28199657--28199767 Score: 195
Period size: 50 Copynumber: 2.2 Consensus size: 50
28199647 TGCAATTCAA
*
28199657 CTACCAATACAACTCAAGTCAGAGAACAACCTCTCTCCTACCCTGTACTT
1 CTACCGATACAACTCAAGTCAGAGAACAACCTCTCTCCTACCCTGTACTT
* *
28199707 CTACCGATATAACTTAAGTCAGAGAACAACCTCTCTCCTACCCTGTACTT
1 CTACCGATACAACTCAAGTCAGAGAACAACCTCTCTCCTACCCTGTACTT
28199757 CTACCGATACA
1 CTACCGATACA
28199768 TGCATAAATT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 57 1.00
ACGTcount: A:0.32, C:0.34, G:0.09, T:0.25
Consensus pattern (50 bp):
CTACCGATACAACTCAAGTCAGAGAACAACCTCTCTCCTACCCTGTACTT
Found at i:28200921 original size:128 final size:128
Alignment explanation
Indices: 28200693--28200940 Score: 478
Period size: 128 Copynumber: 1.9 Consensus size: 128
28200683 TTACCAAACT
28200693 GGATTGCTGTTTAGGAAAGACTTCAAGGACTAATACGCCAATTTCCCTTTTTCGCGGTCTGTAGC
1 GGATTGCTGTTTAGGAAAGACTTCAAGGACTAATACGCCAATTTCCCTTTTTCGCGGTCTGTAGC
*
28200758 ACGATTGTAGTCTACATTTACAAATCATTCAATTCTCACATTAAGTCACATAATTACTAGACA
66 ACGATCGTAGTCTACATTTACAAATCATTCAATTCTCACATTAAGTCACATAATTACTAGACA
*
28200821 GGATTGCTGTTTAGGAAAGACTTCAAGGACTAATCCGCCAATTTCCCTTTTTCGCGGTCTGTAGC
1 GGATTGCTGTTTAGGAAAGACTTCAAGGACTAATACGCCAATTTCCCTTTTTCGCGGTCTGTAGC
28200886 ACGATCGTAGTCTACATTTACAAATCATTCAATTCTCACATTAAGTCACATAATT
66 ACGATCGTAGTCTACATTTACAAATCATTCAATTCTCACATTAAGTCACATAATT
28200941 TAGTCTTTCA
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 118 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (128 bp):
GGATTGCTGTTTAGGAAAGACTTCAAGGACTAATACGCCAATTTCCCTTTTTCGCGGTCTGTAGC
ACGATCGTAGTCTACATTTACAAATCATTCAATTCTCACATTAAGTCACATAATTACTAGACA
Found at i:28221992 original size:3 final size:3
Alignment explanation
Indices: 28221980--28222020 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
28221970 CAAACGTTTT
28221980 ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28222021 ATAACAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:28223285 original size:30 final size:30
Alignment explanation
Indices: 28223246--28223394 Score: 128
Period size: 30 Copynumber: 5.0 Consensus size: 30
28223236 ATTATCTAAG
*
28223246 ATTATATTTTGACCCTCGAACTTTCTAAAA
1 ATTATATTTTGACCCTCAAACTTTCTAAAA
* *
28223276 ATTACATTTTAACCC-CTAAACTTTCTAAAA
1 ATTATATTTTGACCCTC-AAACTTTCTAAAA
* *
28223306 ATTATATTTTTACCCTTAAAC-TTCTTAAAA
1 ATTATATTTTGACCCTCAAACTTTC-TAAAA
* * * *
28223336 AATACAATTTTG-CCCCCAAAC-TTCCAAAA
1 ATTA-TATTTTGACCCTCAAACTTTCTAAAA
* *
28223365 ATCATATTTTCGA-CCTCAAATTTTCTAAAA
1 ATTATATTTT-GACCCTCAAACTTTCTAAAA
28223395 GTTCAATTTT
Statistics
Matches: 94, Mismatches: 18, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
28 5 0.05
29 17 0.18
30 67 0.71
31 5 0.05
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (30 bp):
ATTATATTTTGACCCTCAAACTTTCTAAAA
Found at i:28223335 original size:60 final size:59
Alignment explanation
Indices: 28223246--28223394 Score: 160
Period size: 60 Copynumber: 2.5 Consensus size: 59
28223236 ATTATCTAAG
* * * *
28223246 ATTATATTTTGACCCTCGAACTTTCTAAAAATTAC-ATTTTAACCCCTAAACTTTCTAAAA
1 ATTATATTTTGACCCTCAAACTTTCTAAAAAATACAATTTT-ACCCCCAAAC-TTCCAAAA
* * *
28223306 ATTATATTTTTACCCTTAAAC-TTCTTAAAAAATACAATTTTGCCCCCAAACTTCCAAAA
1 ATTATATTTTGACCCTCAAACTTTC-TAAAAAATACAATTTTACCCCCAAACTTCCAAAA
* *
28223365 ATCATATTTTCGA-CCTCAAATTTTCTAAAA
1 ATTATATTTT-GACCCTCAAACTTTCTAAAA
28223395 GTTCAATTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 9
0.79 0.12 0.10
Matches are distributed among these distances:
59 30 0.41
60 39 0.53
61 5 0.07
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (59 bp):
ATTATATTTTGACCCTCAAACTTTCTAAAAAATACAATTTTACCCCCAAACTTCCAAAA
Found at i:28227929 original size:14 final size:15
Alignment explanation
Indices: 28227910--28227940 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
28227900 TTTTACTTTA
28227910 TTTTATTTTTAT-CT
1 TTTTATTTTTATGCT
28227924 TTTTATTTTTATGCT
1 TTTTATTTTTATGCT
28227939 TT
1 TT
28227941 CAAACAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (15 bp):
TTTTATTTTTATGCT
Found at i:28237103 original size:15 final size:15
Alignment explanation
Indices: 28237078--28237112 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
28237068 GCAAAGAAAT
*
28237078 TAAAA-TGAAACAAG
1 TAAAAGTGAAACAAA
28237092 TAAAAGTGAAACAAA
1 TAAAAGTGAAACAAA
28237107 TAAAAG
1 TAAAAG
28237113 AAAATGTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.66, C:0.06, G:0.14, T:0.14
Consensus pattern (15 bp):
TAAAAGTGAAACAAA
Found at i:28242316 original size:17 final size:17
Alignment explanation
Indices: 28242270--28242335 Score: 60
Period size: 17 Copynumber: 3.9 Consensus size: 17
28242260 ATATATATGG
**
28242270 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* **
28242287 AGATGCAGCGACAATAA
1 AAATGCAATGACAATAA
*
28242304 AAATGCAATGACATTAA
1 AAATGCAATGACAATAA
* *
28242321 TAATGCAAGGACAAT
1 AAATGCAATGACAAT
28242336 TATACTACAG
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:28242327 original size:34 final size:34
Alignment explanation
Indices: 28242270--28242335 Score: 82
Period size: 34 Copynumber: 1.9 Consensus size: 34
28242260 ATATATATGG
*
28242270 AAATGCAATGACAATGTAGATGC-AGCGACAATAA
1 AAATGCAATGACAATATAGATGCAAG-GACAATAA
*
28242304 AAATGCAATGACATTAATA-ATGCAAGGACAAT
1 AAATGCAATGACAAT-ATAGATGCAAGGACAAT
28242336 TATACTACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 24 0.86
35 4 0.14
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (34 bp):
AAATGCAATGACAATATAGATGCAAGGACAATAA
Found at i:28260566 original size:215 final size:215
Alignment explanation
Indices: 28260195--28260624 Score: 806
Period size: 215 Copynumber: 2.0 Consensus size: 215
28260185 ACCTTTGCCA
*
28260195 GAATTCCTAATCTTCCCTCCGATCATCAGGGAAACAGAACCTTCAACTGATGAAATTGATTCTGA
1 GAATTCCTAATCTTCCCTCCGATAATCAGGGAAACAGAACCTTCAACTGATGAAATTGATTCTGA
28260260 AGAGAAGGATCACTCCATAGCTTCTTCACCAAGACTAAATATTCGGATGAAAGAGGAGAGGTGGA
66 AGAGAAGGATCACTCCATAGCTTCTTCACCAAGACTAAATATTCGGATGAAAGAGGAGAGGTGGA
28260325 ATCAAATGAGGTAGAGGATTGCTTAAGGAACATTGCCAGTTAATTCGAGGAGGATTTCCTTGCTA
131 ATCAAATGAGGTAGAGGATTGCTTAAGGAACATTGCCAGTTAATTCGAGGAGGATTTCCTTGCTA
28260390 ATCTTGAGACTACTGATGCT
196 ATCTTGAGACTACTGATGCT
* *
28260410 GAATTCCTGATCTTCCCTCCGATAATCAGGGAAGCAGAACCTTCAACTGATGAAATTGATTCTGA
1 GAATTCCTAATCTTCCCTCCGATAATCAGGGAAACAGAACCTTCAACTGATGAAATTGATTCTGA
*
28260475 AGAGAAGGATCACTCCATAGCTTCTTCACCAAGACTACATATTCGGATGAAAGAGGAGAGGTGGA
66 AGAGAAGGATCACTCCATAGCTTCTTCACCAAGACTAAATATTCGGATGAAAGAGGAGAGGTGGA
* *
28260540 ATTAAATGAGGTAGAGGATTGCTTAAGGAACATTGCCAGTTAATTTGAGGAGGATTTCCTTGCTA
131 ATCAAATGAGGTAGAGGATTGCTTAAGGAACATTGCCAGTTAATTCGAGGAGGATTTCCTTGCTA
28260605 ATCTTGAGACTACTGATGCT
196 ATCTTGAGACTACTGATGCT
28260625 ATTGCAGAAG
Statistics
Matches: 209, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
215 209 1.00
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (215 bp):
GAATTCCTAATCTTCCCTCCGATAATCAGGGAAACAGAACCTTCAACTGATGAAATTGATTCTGA
AGAGAAGGATCACTCCATAGCTTCTTCACCAAGACTAAATATTCGGATGAAAGAGGAGAGGTGGA
ATCAAATGAGGTAGAGGATTGCTTAAGGAACATTGCCAGTTAATTCGAGGAGGATTTCCTTGCTA
ATCTTGAGACTACTGATGCT
Found at i:28261168 original size:17 final size:17
Alignment explanation
Indices: 28261157--28261192 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
28261147 TTGCATTTTT
*
28261157 ATTGTCACTGCATCTCC
1 ATTGTCACTGCATTTCC
*
28261174 ATTGTCATTGCATTTCC
1 ATTGTCACTGCATTTCC
28261191 AT
1 AT
28261193 ATATATTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.28, G:0.11, T:0.42
Consensus pattern (17 bp):
ATTGTCACTGCATTTCC
Found at i:28261646 original size:14 final size:14
Alignment explanation
Indices: 28261627--28261657 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
28261617 AATCTAGTCA
28261627 AAGGCTGTCACTGC
1 AAGGCTGTCACTGC
28261641 AAGGCTGTCACTGC
1 AAGGCTGTCACTGC
28261655 AAG
1 AAG
28261658 AGTATAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (14 bp):
AAGGCTGTCACTGC
Found at i:28261718 original size:21 final size:20
Alignment explanation
Indices: 28261692--28261735 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
28261682 TCAGTCACAT
28261692 AAAAAAAAGAAAAAGAAAGAA
1 AAAAAAAAGAAAAAGAAA-AA
** *
28261713 AAAAAAGGGGAAAAGAAAAA
1 AAAAAAAAGAAAAAGAAAAA
28261733 AAA
1 AAA
28261736 TATATGAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAAAAGAAAAAGAAAAA
Found at i:28263774 original size:15 final size:14
Alignment explanation
Indices: 28263750--28263779 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
28263740 CATCTAACCA
28263750 TTTTACCAATTCCT
1 TTTTACCAATTCCT
28263764 TTTTCACCAATTCCT
1 TTTT-ACCAATTCCT
28263779 T
1 T
28263780 AATGGCCGAA
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:0.20, C:0.30, G:0.00, T:0.50
Consensus pattern (14 bp):
TTTTACCAATTCCT
Found at i:28266602 original size:12 final size:12
Alignment explanation
Indices: 28266584--28266619 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
28266574 GTTCTGAGAG
28266584 CATAAAATAAAA
1 CATAAAATAAAA
*
28266596 GATAAAATAAAA
1 CATAAAATAAAA
*
28266608 CAGAAAATAAAA
1 CATAAAATAAAA
28266620 AAAAACACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.75, C:0.06, G:0.06, T:0.14
Consensus pattern (12 bp):
CATAAAATAAAA
Found at i:28270773 original size:23 final size:23
Alignment explanation
Indices: 28270747--28270917 Score: 158
Period size: 23 Copynumber: 7.7 Consensus size: 23
28270737 GCACATTAAC
* *
28270747 CACATTATCATTTGAGCATAAAT
1 CACATTATCTTTTAAGCATAAAT
*
28270770 CACATTAACTTTTAAGCATAAAT
1 CACATTATCTTTTAAGCATAAAT
* *
28270793 CACA-TA----TTAAGAAAAAAT
1 CACATTATCTTTTAAGCATAAAT
*
28270811 CACATTAACTTTTAAGCATAAAT
1 CACATTATCTTTTAAGCATAAAT
* *
28270834 GACA-TATACTTTTAAGCAAAAAT
1 CACATTAT-CTTTTAAGCATAAAT
*
28270857 CACATTAAT-TTTTAATCATAAAT
1 CACATT-ATCTTTTAAGCATAAAT
** *
28270880 CACATTAAATTCTAAGCATAAAT
1 CACATTATCTTTTAAGCATAAAT
*
28270903 CACATTAACTTTTAA
1 CACATTATCTTTTAA
28270918 CACATTTAAT
Statistics
Matches: 121, Mismatches: 18, Indels: 18
0.77 0.11 0.11
Matches are distributed among these distances:
18 14 0.12
19 2 0.02
22 5 0.04
23 97 0.80
24 1 0.01
25 2 0.02
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.34
Consensus pattern (23 bp):
CACATTATCTTTTAAGCATAAAT
Found at i:28270870 original size:46 final size:44
Alignment explanation
Indices: 28270761--28270917 Score: 185
Period size: 46 Copynumber: 3.5 Consensus size: 44
28270751 TTATCATTTG
* *
28270761 AGCATAAATCACATTAACTTTTAAGCATAAAT-CACATA--TTA
1 AGCAAAAATCACATTAACTTTTAAGCATAAATACATATATTTTA
*
28270802 AGAAAAAATCACATTAACTTTTAAGCATAAATGACATATACTTTTA
1 AGCAAAAATCACATTAACTTTTAAGCATAAAT-ACATATA-TTTTA
* * * *
28270848 AGCAAAAATCACATTAATTTTTAATCATAAATCACATTAAATTCTA
1 AGCAAAAATCACATTAACTTTTAAGCATAAAT-ACA-TATATTTTA
*
28270894 AGCATAAATCACATTAACTTTTAA
1 AGCAAAAATCACATTAACTTTTAA
28270918 CACATTTAAT
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
41 30 0.30
43 5 0.05
46 61 0.62
47 3 0.03
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.33
Consensus pattern (44 bp):
AGCAAAAATCACATTAACTTTTAAGCATAAATACATATATTTTA
Found at i:28279282 original size:10 final size:10
Alignment explanation
Indices: 28279246--28279322 Score: 52
Period size: 11 Copynumber: 7.4 Consensus size: 10
28279236 ATAATTAAAA
28279246 ATTAAAAATT
1 ATTAAAAATT
*
28279256 CA-TATAAAATC
1 -ATTA-AAAATT
28279267 ATTTAAAAATT
1 A-TTAAAAATT
*
28279278 ATTAAGAATT
1 ATTAAAAATT
*
28279288 A-TAAAAA-A
1 ATTAAAAATT
28279296 AGTTAATAAATT
1 A-TTAA-AAATT
28279308 ATTTAAAAATT
1 A-TTAAAAATT
28279319 ATTA
1 ATTA
28279323 CGAATTATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
8 1 0.02
9 5 0.10
10 18 0.35
11 21 0.40
12 7 0.13
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.38
Consensus pattern (10 bp):
ATTAAAAATT
Found at i:28279294 original size:19 final size:19
Alignment explanation
Indices: 28279270--28279332 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
28279260 TAAAATCATT
28279270 TAAAAATTATTAAGAATTA
1 TAAAAATTATTAAGAATTA
* *
28279289 TAAAAA-AAGTTAATAAATTA
1 TAAAAATTA-TTAA-GAATTA
*
28279309 TTTAAAAATTATTACGAATTA
1 --TAAAAATTATTAAGAATTA
28279330 TAA
1 TAA
28279333 GAAGGGTTCG
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
18 1 0.03
19 13 0.38
20 5 0.15
21 5 0.15
22 9 0.26
23 1 0.03
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.37
Consensus pattern (19 bp):
TAAAAATTATTAAGAATTA
Found at i:28287493 original size:18 final size:17
Alignment explanation
Indices: 28287466--28287499 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
28287456 GTTGAAATGC
28287466 CAAAATGGTACCAATAT
1 CAAAATGGTACCAATAT
*
28287483 CAAAGATGGTATCAATA
1 CAAA-ATGGTACCAATA
28287500 AAAATACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (17 bp):
CAAAATGGTACCAATAT
Found at i:28291901 original size:28 final size:27
Alignment explanation
Indices: 28291820--28291943 Score: 80
Period size: 24 Copynumber: 4.7 Consensus size: 27
28291810 TGATATGTTT
* * *
28291820 ACCATAATTAGTTTCCATGATATAAATTC
1 ACCATAATTAG-TTACATAATAT-AATTA
* * *
28291849 ATCATAATCAATT-CAT-ATAT-ATTA
1 ACCATAATTAGTTACATAATATAATTA
28291873 ACCATAATTAGTTCACATAATATAATTA
1 ACCATAATTAGTT-ACATAATATAATTA
* * * *
28291901 ATCATAATTACTTA-AT-ATA-CATTT
1 ACCATAATTAGTTACATAATATAATTA
28291925 ACCATAATTAGTTTACATA
1 ACCATAATTAG-TTACATA
28291944 TTTACAATAA
Statistics
Matches: 75, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
24 25 0.33
25 6 0.08
26 11 0.15
27 8 0.11
28 17 0.23
29 8 0.11
ACGTcount: A:0.43, C:0.15, G:0.03, T:0.40
Consensus pattern (27 bp):
ACCATAATTAGTTACATAATATAATTA
Found at i:28291929 original size:52 final size:53
Alignment explanation
Indices: 28291817--28291943 Score: 159
Period size: 52 Copynumber: 2.4 Consensus size: 53
28291807 ACTTGATATG
* * * *
28291817 TTTACCATAATTAGTTTC-CATGATATAAATTCATCATAATCAATTCATATATA
1 TTTACCATAATTAG-TTCACATAATATAAATTAATCATAATCAATTAATATACA
* * *
28291870 TTAACCATAATTAGTTCACATAATAT-AATTAATCATAATTACTTAATATACA
1 TTTACCATAATTAGTTCACATAATATAAATTAATCATAATCAATTAATATACA
*
28291922 TTTACCATAATTAGTTTACATA
1 TTTACCATAATTAGTTCACATA
28291944 TTTACAATAA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
52 44 0.69
53 20 0.31
ACGTcount: A:0.42, C:0.14, G:0.03, T:0.41
Consensus pattern (53 bp):
TTTACCATAATTAGTTCACATAATATAAATTAATCATAATCAATTAATATACA
Found at i:28291949 original size:28 final size:27
Alignment explanation
Indices: 28291869--28291945 Score: 72
Period size: 28 Copynumber: 2.9 Consensus size: 27
28291859 ATTCATATAT
*
28291869 ATTAACCATAATTAGTTCACATAATATA-
1 ATTAACCATAATTAGTTTACAT-AT-TAC
* *
28291897 ATTAATCATAATTA-CTTA-ATA-TAC
1 ATTAACCATAATTAGTTTACATATTAC
*
28291921 ATTTACCATAATTAGTTTACATATT
1 ATTAACCATAATTAGTTTACATATT
28291946 TACAATAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
23 2 0.05
24 12 0.31
25 4 0.10
26 5 0.13
27 3 0.08
28 13 0.33
ACGTcount: A:0.43, C:0.13, G:0.03, T:0.42
Consensus pattern (27 bp):
ATTAACCATAATTAGTTTACATATTAC
Found at i:28307830 original size:13 final size:14
Alignment explanation
Indices: 28307800--28307835 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
28307790 AAACATTTGC
28307800 TTTTA-TTT-TCTA
1 TTTTATTTTATCTA
28307812 TTTTATTTTATCT-
1 TTTTATTTTATCTA
28307825 TTTTATTTTAT
1 TTTTATTTTAT
28307836 GCTCTCAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 5 0.23
13 14 0.64
14 3 0.14
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTATTTTATCTA
Found at i:28307984 original size:14 final size:14
Alignment explanation
Indices: 28307965--28307995 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
28307955 GAAATACTAC
*
28307965 TAATTGTTCCTTTG
1 TAATTGTTCCGTTG
28307979 TAATTGTTCCGTTG
1 TAATTGTTCCGTTG
28307993 TAA
1 TAA
28307996 CACACTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.13, G:0.16, T:0.52
Consensus pattern (14 bp):
TAATTGTTCCGTTG
Found at i:28321237 original size:16 final size:15
Alignment explanation
Indices: 28321206--28321246 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
28321196 CGACAAAAGC
28321206 AAAAAT-AAAACAAA
1 AAAAATGAAAACAAA
*
28321220 AACAATGAAAACCAAA
1 AAAAATGAAAA-CAAA
28321236 AAAAATGAAAA
1 AAAAATGAAAA
28321247 ATTCCTATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 5 0.22
15 4 0.17
16 14 0.61
ACGTcount: A:0.78, C:0.10, G:0.05, T:0.07
Consensus pattern (15 bp):
AAAAATGAAAACAAA
Found at i:28330329 original size:21 final size:22
Alignment explanation
Indices: 28330297--28330338 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
28330287 ATTCACATGT
28330297 TTTCTAACTCATGATTCTTTTG
1 TTTCTAACTCATGATTCTTTTG
**
28330319 TTTCT-ACTCATTTTTCTTTT
1 TTTCTAACTCATGATTCTTTT
28330339 CTTTTTCTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.14, C:0.19, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTCTAACTCATGATTCTTTTG
Found at i:28342736 original size:25 final size:25
Alignment explanation
Indices: 28342702--28342754 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
28342692 ATATATTGTG
28342702 CATTAGAATTGTCAGCACAGGAACT
1 CATTAGAATTGTCAGCACAGGAACT
* *
28342727 CATTAGAATTGTCAGCGCCGGAACT
1 CATTAGAATTGTCAGCACAGGAACT
28342752 CAT
1 CAT
28342755 CTCAGAAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (25 bp):
CATTAGAATTGTCAGCACAGGAACT
Found at i:28353663 original size:58 final size:59
Alignment explanation
Indices: 28353594--28353728 Score: 186
Period size: 58 Copynumber: 2.3 Consensus size: 59
28353584 ATTTAATAAC
* *
28353594 AATAATAATTATATTAAAAATGTTATTAAATTATATATTA-TTTTATTAAATTGTATTT
1 AATAATAATTATATTAAAAATATAATTAAATTATATATTATTTTTATTAAATTGTATTT
* * *
28353652 AATAATAATTATGTT-AAAATATAATTAAATTATTTATTATTTTTATTAAATTTTATTT
1 AATAATAATTATATTAAAAATATAATTAAATTATATATTATTTTTATTAAATTGTATTT
*
28353710 AATAACAATCT-TATTAAAA
1 AATAATAAT-TATATTAAAA
28353729 TTTAATAATA
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
57 21 0.31
58 42 0.63
59 4 0.06
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.50
Consensus pattern (59 bp):
AATAATAATTATATTAAAAATATAATTAAATTATATATTATTTTTATTAAATTGTATTT
Found at i:28353941 original size:16 final size:16
Alignment explanation
Indices: 28353891--28353943 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
28353881 TGAATTATTG
*
28353891 ATTACAGC-CTTTTCC
1 ATTACAGCTCTATTCC
* *
28353906 ATCACAACTCTATTCC
1 ATTACAGCTCTATTCC
*
28353922 ATTACAGCTCTATTCT
1 ATTACAGCTCTATTCC
28353938 ATTACA
1 ATTACA
28353944 ACGAACCAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
15 6 0.19
16 25 0.81
ACGTcount: A:0.28, C:0.30, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:28354574 original size:17 final size:18
Alignment explanation
Indices: 28354544--28354581 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
28354534 TCGACGAATT
28354544 AAACTAAAACAAAT-CAA
1 AAACTAAAACAAATACAA
28354561 AAAC-AAAACAAAATACAA
1 AAACTAAAAC-AAATACAA
28354579 AAA
1 AAA
28354582 TTTAGTCTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 5 0.26
17 8 0.42
18 6 0.32
ACGTcount: A:0.76, C:0.16, G:0.00, T:0.08
Consensus pattern (18 bp):
AAACTAAAACAAATACAA
Found at i:28360138 original size:30 final size:29
Alignment explanation
Indices: 28360106--28360177 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 29
28360096 TAACAATGAT
28360106 AAAATTATACTTTAACTCTTTAAAAATAATA
1 AAAATT-TA-TTTAACTCTTTAAAAATAATA
* * *
28360137 AAAATTTATTTAATTTTTTAAAAAT-TTA
1 AAAATTTATTTAACTCTTTAAAAATAATA
28360165 AAAATATT-TTTAA
1 AAAAT-TTATTTAA
28360178 AATAATAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 12 0.32
29 17 0.46
30 2 0.05
31 6 0.16
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (29 bp):
AAAATTTATTTAACTCTTTAAAAATAATA
Found at i:28366322 original size:7 final size:7
Alignment explanation
Indices: 28366307--28366350 Score: 52
Period size: 7 Copynumber: 6.3 Consensus size: 7
28366297 ATATGCTTTT
28366307 ATCTATA
1 ATCTATA
*
28366314 ATTTATA
1 ATCTATA
28366321 ATCTATA
1 ATCTATA
*
28366328 ATCAATA
1 ATCTATA
*
28366335 ATCAATA
1 ATCTATA
*
28366342 ATATATA
1 ATCTATA
28366349 AT
1 AT
28366351 AGGGAGGGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (7 bp):
ATCTATA
Found at i:28369261 original size:20 final size:20
Alignment explanation
Indices: 28369227--28369280 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
28369217 GAACAAATGT
*
28369227 AAAAAATATGAAAAGAAATA-A
1 AAAAAATAT-TAAAG-AATACA
* *
28369248 AAAAATTATTAAAGAGTACA
1 AAAAAATATTAAAGAATACA
28369268 AAAAAATATTAAA
1 AAAAAATATTAAA
28369281 ATTGTAATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.11
20 17 0.61
21 8 0.29
ACGTcount: A:0.70, C:0.02, G:0.07, T:0.20
Consensus pattern (20 bp):
AAAAAATATTAAAGAATACA
Found at i:28369359 original size:25 final size:24
Alignment explanation
Indices: 28369315--28369362 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
28369305 AAAATGGTAA
* *
28369315 AAAAAACTTAAAATTTTGAAATTT
1 AAAAAACTTAAAAGTATGAAATTT
28369339 AAAAAACTTAAAAGGTATGAAATT
1 AAAAAACTTAAAA-GTATGAAATT
28369363 ATATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.31
Consensus pattern (24 bp):
AAAAAACTTAAAAGTATGAAATTT
Found at i:28370208 original size:15 final size:15
Alignment explanation
Indices: 28370169--28370210 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
28370159 TGATAAATTA
*
28370169 AAAAATTAAGTGTTG
1 AAAAATTAAGTATTG
*
28370184 AAAAAATAAGTATTG
1 AAAAATTAAGTATTG
*
28370199 AAAATTTAAGTA
1 AAAAATTAAGTA
28370211 CTAAATTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.55, C:0.00, G:0.14, T:0.31
Consensus pattern (15 bp):
AAAAATTAAGTATTG
Found at i:28374329 original size:16 final size:16
Alignment explanation
Indices: 28374308--28374338 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28374298 ATAATGTAAA
28374308 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
28374324 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
28374339 AGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:28375951 original size:27 final size:27
Alignment explanation
Indices: 28375913--28375965 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
28375903 AAACCCCCAA
*
28375913 GGAATGCGTAATT-AAGCCGACACACAG
1 GGAATACGTAATTGAA-CCGACACACAG
*
28375940 GGAATACGTAATTGCACCGACACACA
1 GGAATACGTAATTGAACCGACACACA
28375966 CTAATGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 22 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.25, G:0.23, T:0.15
Consensus pattern (27 bp):
GGAATACGTAATTGAACCGACACACAG
Found at i:28381578 original size:15 final size:15
Alignment explanation
Indices: 28381542--28381581 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
28381532 TAAGTCATTG
*
28381542 AATAAAGAATTTATT
1 AATAAATAATTTATT
28381557 AATAAATAATTTATT
1 AATAAATAATTTATT
28381572 AATAAATAAT
1 AATAAATAAT
28381582 AGTATAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
AATAAATAATTTATT
Found at i:28388736 original size:24 final size:24
Alignment explanation
Indices: 28388671--28388736 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
28388661 ATCTTATGAA
28388671 TTAATTG-AATATTTATTAACAAT
1 TTAATTGAAATATTTATTAACAAT
*
28388694 AT-ATTGAAA-ATATTATTAA-ATAT
1 TTAATTGAAATAT-TTATTAACA-AT
*
28388717 TTAATTGAAATATTTGTTAA
1 TTAATTGAAATATTTATTAA
28388737 TAATAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
22 7 0.20
23 13 0.37
24 13 0.37
25 2 0.06
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (24 bp):
TTAATTGAAATATTTATTAACAAT
Found at i:28402881 original size:16 final size:17
Alignment explanation
Indices: 28402860--28402909 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
28402850 AAATAGCATA
28402860 AAAATAACA-AAAT-AAT
1 AAAATAA-ATAAATAAAT
28402876 AAAATAAATAAATAAAT
1 AAAATAAATAAATAAAT
28402893 -AAATAAAATTAAATAAA
1 AAAAT-AAA-TAAATAAA
28402910 AGCAAGCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 1 0.03
16 15 0.50
17 6 0.20
18 8 0.27
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAATAAATAAATAAAT
Found at i:28402952 original size:4 final size:4
Alignment explanation
Indices: 28402943--28402979 Score: 58
Period size: 4 Copynumber: 9.2 Consensus size: 4
28402933 AAATAATAGC
28402943 AAAT AAAT AAAT AAAT AAAT -AAT AAAT ACAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT A
28402980 TATGAAATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 3 0.10
4 24 0.77
5 4 0.13
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:28402964 original size:16 final size:17
Alignment explanation
Indices: 28402943--28402990 Score: 64
Period size: 16 Copynumber: 2.9 Consensus size: 17
28402933 AAATAATAGC
28402943 AAATAAATAAATA-AAT
1 AAATAAATAAATACAAT
28402959 AAAT-AATAAATACAAT
1 AAATAAATAAATACAAT
*
28402975 AAATATATGAAATACA
1 AAATAAAT-AAATACA
28402991 CAAAATCTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 8 0.29
16 11 0.39
17 2 0.07
18 7 0.25
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (17 bp):
AAATAAATAAATACAAT
Found at i:28403165 original size:15 final size:15
Alignment explanation
Indices: 28403147--28403179 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
28403137 AATGTCATGA
28403147 AAATAAATAACAACT
1 AAATAAATAACAACT
28403162 AAATAAATAACAACT
1 AAATAAATAACAACT
28403177 AAA
1 AAA
28403180 AATTAAATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.70, C:0.12, G:0.00, T:0.18
Consensus pattern (15 bp):
AAATAAATAACAACT
Found at i:28403357 original size:5 final size:5
Alignment explanation
Indices: 28403347--28403390 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
28403337 GAGTGAATTA
* * *
28403347 AAAAT AAAAT AAAAT AAAAT AAAAT AAATT GAAAT TAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
28403391 ATTACAGGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:28407663 original size:21 final size:21
Alignment explanation
Indices: 28407639--28407681 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28407629 TTTCATCAAC
28407639 TTTTCTTTCT-TTTTTCATTTT
1 TTTTCTTTCTCTTTTTC-TTTT
*
28407660 TTTTCTTTTTCTTTTTCTTTT
1 TTTTCTTTCTCTTTTTCTTTT
28407681 T
1 T
28407682 GCGTCTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTCTTTCTCTTTTTCTTTT
Found at i:28407680 original size:17 final size:18
Alignment explanation
Indices: 28407639--28407680 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
28407629 TTTCATCAAC
28407639 TTTTC-TTTCTTTTTTCA
1 TTTTCTTTTCTTTTTTCA
*
28407656 TTTT-TTTTC-TTTTTCT
1 TTTTCTTTTCTTTTTTCA
28407672 TTTTCTTTT
1 TTTTCTTTT
28407681 TGCGTCTGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTTCA
Found at i:28408745 original size:24 final size:25
Alignment explanation
Indices: 28408700--28408760 Score: 70
Period size: 24 Copynumber: 2.4 Consensus size: 25
28408690 TTGGGGCATT
*
28408700 TTCTTCTTCTTTCTCCTCTTCTTTTCC
1 TTCTTCTTC-TTCT-CTCTTCTCTTCC
* *
28408727 TTCTTCTTCTTCT-TGTTCTCTTGC
1 TTCTTCTTCTTCTCTCTTCTCTTCC
28408751 TTCTTCTTCT
1 TTCTTCTTCT
28408761 ATTATAGCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 18 0.58
26 4 0.13
27 9 0.29
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (25 bp):
TTCTTCTTCTTCTCTCTTCTCTTCC
Found at i:28408774 original size:3 final size:3
Alignment explanation
Indices: 28408700--28408760 Score: 56
Period size: 3 Copynumber: 20.3 Consensus size: 3
28408690 TTGGGGCATT
* *
28408700 TTC TTC TTC TT- TCTC CTC TTC TT- TTCC TTC TTC TTC TTC TTG TTC
1 TTC TTC TTC TTC T-TC TTC TTC TTC TT-C TTC TTC TTC TTC TTC TTC
28408745 -TC TTGC TTC TTC TTC T
1 TTC TT-C TTC TTC TTC T
28408761 ATTATAGCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
2 5 0.10
3 38 0.79
4 5 0.10
ACGTcount: A:0.00, C:0.33, G:0.03, T:0.64
Consensus pattern (3 bp):
TTC
Found at i:28408780 original size:30 final size:30
Alignment explanation
Indices: 28408746--28408803 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
28408736 TTCTTGTTCT
28408746 CTTGCTTCTTCTTCT-ATTATAGCTTCTTCC
1 CTTGCTTCTTCTTCTCA-TATAGCTTCTTCC
*
28408776 CTTGCTTTTTCTTCTCATATAGCTTCTT
1 CTTGCTTCTTCTTCTCATATAGCTTCTT
28408804 TCGTTTCAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 25 0.96
31 1 0.04
ACGTcount: A:0.10, C:0.28, G:0.07, T:0.55
Consensus pattern (30 bp):
CTTGCTTCTTCTTCTCATATAGCTTCTTCC
Found at i:28421860 original size:16 final size:16
Alignment explanation
Indices: 28421830--28421884 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 16
28421820 ACACACTATT
28421830 AAAAGAGGAGAAAGAAAA
1 AAAAGA-GAG-AAGAAAA
28421848 AAAAGAGAGAAGAAGAA
1 AAAAGAGAGAAGAA-AA
28421865 GAAAAGA-A-AAGAAAGA
1 -AAAAGAGAGAAGAAA-A
28421881 AAAA
1 AAAA
28421885 TTCAAGATGA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
15 5 0.15
16 11 0.32
17 6 0.18
18 12 0.35
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (16 bp):
AAAAGAGAGAAGAAAA
Found at i:28423251 original size:112 final size:112
Alignment explanation
Indices: 28423117--28423418 Score: 480
Period size: 112 Copynumber: 2.7 Consensus size: 112
28423107 TTGTCATTTT
* * *
28423117 TAATCTTTTCATTCATAGGAGCTTTGCCTCCAATAAAATTTAATTTCATCTACCTTACAACCTTA
1 TAATCTTTTCATTCATACGAGCTTTGCCTCCAATAAAATTCAATTTCATCCACCTTACAACCTTA
28423182 TTCAAGCATTTTTGCATCAAAATAACGGTTAGTGGACCAATGATTCA
66 TTCAAGCATTTTTGCATCAAAATAACGGTTAGTGGACCAATGATTCA
*
28423229 TAATCCTTTT-ATTCATACGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTTACAACCTT
1 TAAT-CTTTTCATTCATACGAGCTTTGCCTCCAATAAAATTCAATTTCATCCACCTTACAACCTT
* * **
28423293 GTTCAAGCATTTTTGCATCAAAATAATGGTTAGTGTCCCAATGATTCA
65 ATTCAAGCATTTTTGCATCAAAATAACGGTTAGTGGACCAATGATTCA
* * *
28423341 TAATCTTTTCATTCATACGAGTTTTGCCTCCAATAAAACTCAATTTCATCCACCTTACGACCTTG
1 TAATCTTTTCATTCATACGAGCTTTGCCTCCAATAAAATTCAATTTCATCCACCTTACAACCTT-
28423406 ATTCAAGCATTTT
65 ATTCAAGCATTTT
28423419 CTTTGCATTT
Statistics
Matches: 174, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
111 5 0.03
112 152 0.87
113 17 0.10
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (112 bp):
TAATCTTTTCATTCATACGAGCTTTGCCTCCAATAAAATTCAATTTCATCCACCTTACAACCTTA
TTCAAGCATTTTTGCATCAAAATAACGGTTAGTGGACCAATGATTCA
Found at i:28424105 original size:98 final size:99
Alignment explanation
Indices: 28423998--28424183 Score: 257
Period size: 98 Copynumber: 1.9 Consensus size: 99
28423988 CCGCAATGGC
* * * * * *
28423998 GAACCCGGTACCTTAAAAGACGTGATGGGAAAGGTTGAGGCCGTAATGGTGAACCC-GTACCATT
1 GAACCCGGTACATTAAAAGACGTGATGGAAAAGGTTGAGGCCGCAACGGCGAACCCTGTACCATG
* * *
28424062 ATGACATGAATGGAAAGGTTGAGATCACAACGGT
66 AAGACATAAAGGGAAAGGTTGAGATCACAACGGT
* * *
28424096 GAACCCGGTACATTAGAAGATGTGATGGAAAAGGTTGAGGCCGCAACGGCGGACCCTGTACCATG
1 GAACCCGGTACATTAAAAGACGTGATGGAAAAGGTTGAGGCCGCAACGGCGAACCCTGTACCATG
28424161 AAGACATAAAGGGAAAGGTTGAG
66 AAGACATAAAGGGAAAGGTTGAG
28424184 GCCGTAATGA
Statistics
Matches: 75, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
98 48 0.64
99 27 0.36
ACGTcount: A:0.33, C:0.17, G:0.31, T:0.18
Consensus pattern (99 bp):
GAACCCGGTACATTAAAAGACGTGATGGAAAAGGTTGAGGCCGCAACGGCGAACCCTGTACCATG
AAGACATAAAGGGAAAGGTTGAGATCACAACGGT
Found at i:28424183 original size:49 final size:50
Alignment explanation
Indices: 28423877--28424344 Score: 220
Period size: 50 Copynumber: 9.5 Consensus size: 50
28423867 GATGTAATAT
* * * ** *
28423877 GAAAGGCTGAGGCCGCAACGACGAACCCGATACCAT-GAAGATATGAAAG
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGACGTGAAGG
* * *** * ** * * * * *
28423926 GAAATGTTAAGGCAATAATGATGAACCCGATACCTTATAAGACGTAAAGC
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGACGTGAAGG
* * * * *
28423976 GAAAGGTTAAGGCCGCAATGGCGAACCCGGTACCTTAAAAGACGTGATGG
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGACGTGAAGG
* * * * * * *
28424026 GAAAGGTTGAGGCCGTAATGGTGAACCC-GTACCAT-TATGACATGAATG
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGACGTGAAGG
** * * * *
28424074 GAAAGGTTGAGATCACAACGGTGAACCCGGTA-CATTAGAAGATGTGATGG
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCA-TAGAAGACGTGAAGG
* * * * *
28424124 AAAAGGTTGAGGCCGCAACGGCGGACCCTGTACCAT-GAAGACATAAAGG
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGACGTGAAGG
* * * * * * *
28424173 GAAAGGTTGAGGCCGTAATGACGAACCTGGTACCTTAGAAGACATGATA-A
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGACGTGA-AGG
* * * * * * **
28424223 GAAAGATAGAGGTCGTAACGGCGGATCTAGTACCAT-GTAA-A--TGAAGG
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAG-AAGACGTGAAGG
* * * * * * * * *
28424270 GAAAGGTTGAGGCTGTAATGGCGAACTCGATACCTTAAAAGATGTGATGG
1 GAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGACGTGAAGG
*
28424320 G-AAGGATTGAGGCCGCAACGACGAA
1 GAAAGG-TTGAGGCCGCAACGGCGAA
28424345 TCTTGTACCA
Statistics
Matches: 310, Mismatches: 95, Indels: 27
0.72 0.22 0.06
Matches are distributed among these distances:
46 1 0.00
47 29 0.09
48 34 0.11
49 80 0.26
50 163 0.53
51 3 0.01
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.18
Consensus pattern (50 bp):
GAAAGGTTGAGGCCGCAACGGCGAACCCGGTACCATAGAAGACGTGAAGG
Found at i:28424205 original size:99 final size:99
Alignment explanation
Indices: 28423964--28424339 Score: 332
Period size: 99 Copynumber: 3.8 Consensus size: 99
28423954 GATACCTTAT
* * * *
28423964 AAGACGTAAAGCGAAAGGTTAAGGCCGCAATGGCGAACCCGGTACCTTAAAAGACGTGATGGGAA
1 AAGACATAAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTAAAAGACGTGATGGAAA
* * * * *
28424029 AGGTTGAGGCCGTAATGGTGAACCC-GTACCATT
66 AGGTTGAGGCCGCAACGGCGGACCCTGTACCATG
* * * ** * * * * * *
28424062 ATGACATGAATGGAAAGGTTGAGATCACAACGGTGAACCCGGTACATTAGAAGATGTGATGGAAA
1 AAGACATAAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTAAAAGACGTGATGGAAA
28424127 AGGTTGAGGCCGCAACGGCGGACCCTGTACCATG
66 AGGTTGAGGCCGCAACGGCGGACCCTGTACCATG
* * * * * *
28424161 AAGACATAAAGGGAAAGGTTGAGGCCGTAATGACGAACCTGGTACCTTAGAAGACATGAT-AAGA
1 AAGACATAAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTAAAAGACGTGATGGA-A
* * * * *
28424225 AAGATAGAGGTCGTAACGGCGGA-TCTAGTACCATG
65 AAGGTTGAGGCCGCAACGGCGGACCCT-GTACCATG
* * * * * * * *
28424260 TA-A-ATGAAGGGAAAGGTTGAGGCTGTAATGGCGAACTCGATACCTTAAAAGATGTGATGG-GA
1 AAGACATAAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTAAAAGACGTGATGGAAA
28424322 AGGATTGAGGCCGCAACG
66 AGG-TTGAGGCCGCAACG
28424340 ACGAATCTTG
Statistics
Matches: 217, Mismatches: 56, Indels: 11
0.76 0.20 0.04
Matches are distributed among these distances:
96 3 0.01
97 57 0.26
98 75 0.35
99 82 0.38
ACGTcount: A:0.34, C:0.16, G:0.31, T:0.18
Consensus pattern (99 bp):
AAGACATAAAGGGAAAGGTTGAGGCCGCAATGGCGAACCCGGTACCTTAAAAGACGTGATGGAAA
AGGTTGAGGCCGCAACGGCGGACCCTGTACCATG
Found at i:28424569 original size:40 final size:40
Alignment explanation
Indices: 28424542--28425184 Score: 324
Period size: 40 Copynumber: 16.4 Consensus size: 40
28424532 TACCCTAGTT
*
28424542 AGAGGGCAGATTGAAGACACACTAATCTCTTACCCCGACC
1 AGAGGGCAGATTGAAGACACACTAATCTCTTACCCCGATC
**
28424582 ATG-GGGCAGATTGAAGGTACACTAATCTCTTACCCCGATC
1 A-GAGGGCAGATTGAAGACACACTAATCTCTTACCCCGATC
* * * *
28424622 AGAGGGCAAATTGAAGACACACCAATATCTTACCTCGATC
1 AGAGGGCAGATTGAAGACACACTAATCTCTTACCCCGATC
* * *
28424662 ATG-GGGCAAATTGAAGGCACACCAATCTCTTACCCCGATC
1 A-GAGGGCAGATTGAAGACACACTAATCTCTTACCCCGATC
** * **
28424702 ATTGGGCAGATTTAAGA-ATC-C-AATCTCTTA-CCTAATC
1 AGAGGGCAGATTGAAGACA-CACTAATCTCTTACCCCGATC
* ** * *
28424739 AGA-GGCAAATTGAAGACATTCCAATCTCTTACCCCAATC
1 AGAGGGCAGATTGAAGACACACTAATCTCTTACCCCGATC
* * * *
28424778 ATG-GGGTAGAATGAA-A-ATACCAATCTCTTACCCCGATC
1 A-GAGGGCAGATTGAAGACACACTAATCTCTTACCCCGATC
* * * **
28424816 ATAGGGCAGATTAAAAAC-CATCTAATCTCTTACGTCGATC
1 AGAGGGCAGATTGAAGACACA-CTAATCTCTTACCCCGATC
* *
28424856 ATG-GGGCAGATTGAA-A-ACACCAATCTCTTACCCTGATC
1 A-GAGGGCAGATTGAAGACACACTAATCTCTTACCCCGATC
* * **
28424894 ATG-GGGCAGATTGTAGTCATC-C-AATCTCTTACCCTAATC
1 A-GAGGGCAGATTGAAGACA-CACTAATCTCTTACCCCGATC
* * **
28424933 ATAGGGCAGATT-ATAGTCATC-C-AATCTCTTACCCTAATC
1 AGAGGGCAGATTGA-AGACA-CACTAATCTCTTACCCCGATC
* * * *
28424972 ATG-GGGTAGATTGAAAAC-CATCCAATCTCTTACCCCAATC
1 A-GAGGGCAGATTGAAGACACA-CTAATCTCTTACCCCGATC
* * * *
28425012 ATGA-GGTAGATTGAA-A-ACGCCAATCTCTTACTCCGATC
1 A-GAGGGCAGATTGAAGACACACTAATCTCTTACCCCGATC
* ** *
28425050 ATGA-GGCAGATTGAA-A-ATCATCCAATCTCTTACCTTGGTC
1 A-GAGGGCAGATTGAAGACA-CA-CTAATCTCTTACCCCGATC
* * * * **
28425090 ATAGGACAGATTGAAAAC-CATTCAATCTCTTACCCAAATC
1 AGAGGGCAGATTGAAGACACACT-AATCTCTTACCCCGATC
* * * *
28425130 ATG-GGGCAGATTAAAAAC-CATCCAATCTCTTACCCTGATC
1 A-GAGGGCAGATTGAAGACACA-CTAATCTCTTACCCCGATC
*
28425170 ATG-GGCCAGATTGAA
1 A-GAGGGCAGATTGAA
28425185 ACCATCGTCC
Statistics
Matches: 487, Mismatches: 79, Indels: 74
0.76 0.12 0.12
Matches are distributed among these distances:
36 11 0.02
37 9 0.02
38 110 0.23
39 83 0.17
40 270 0.55
41 4 0.01
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (40 bp):
AGAGGGCAGATTGAAGACACACTAATCTCTTACCCCGATC
Found at i:28424857 original size:78 final size:78
Alignment explanation
Indices: 28424545--28425185 Score: 519
Period size: 78 Copynumber: 8.2 Consensus size: 78
28424535 CCTAGTTAGA
* * ** *
28424545 GGGCAGATTGAAGACACACTAATCTCTTACCCCGACCATGGGGCAGATTGAAGGTA-CA-CTAAT
1 GGGCAGATTGAA-A-ACACCAATCTCTTACCCCGATCATGGGGCAGATT-AA-AAACCATCCAAT
*
28424608 CTCTTACCCCGATCA-G
62 CTCTTACCCCAATCATG
* * * * * **
28424624 AGGGCAAATTGAAGACACACCAATATCTTACCTCGATCATGGGGCAAATTGAAGGCACA-CCAAT
1 -GGGCAGATTGAA-A-ACACCAATCTCTTACCCCGATCATGGGGCAGATTAAAAAC-CATCCAAT
* *
28424688 CTCTTACCCCGATCATT
62 CTCTTACCCCAATCATG
* * ** * * * *
28424705 GGGCAGATTTAAGAA-TCCAATCTCTTA-CCTAATCA-GAGGCAAATTGAAGA-CATTCCAATCT
1 GGGCAGATTGAA-AACACCAATCTCTTACCCCGATCATGGGGCAGATTAAAAACCA-TCCAATCT
28424766 CTTACCCCAATCATG
64 CTTACCCCAATCATG
* * * * *
28424781 GGGTAGAATGAAAATACCAATCTCTTACCCCGATCATAGGGCAGATTAAAAACCATCTAATCTCT
1 GGGCAGATTGAAAACACCAATCTCTTACCCCGATCATGGGGCAGATTAAAAACCATCCAATCTCT
** *
28424846 TACGTCGATCATG
66 TACCCCAATCATG
* ** **
28424859 GGGCAGATTGAAAACACCAATCTCTTACCCTGATCATGGGGCAGATT-GTAGTCATCCAATCTCT
1 GGGCAGATTGAAAACACCAATCTCTTACCCCGATCATGGGGCAGATTAAAAACCATCCAATCTCT
* *
28424923 TACCCTAATCATA
66 TACCCCAATCATG
** ** * *
28424936 GGGCAGATT-ATAGTCATCCAATCTCTTACCCTAATCATGGGGTAGATTGAAAACCATCCAATCT
1 GGGCAGATTGA-AAACA-CCAATCTCTTACCCCGATCATGGGGCAGATTAAAAACCATCCAATCT
28425000 CTTACCCCAATCATG
64 CTTACCCCAATCATG
* * * * * * *
28425015 AGGTAGATTGAAAACGCCAATCTCTTACTCCGATCATGAGGCAGATTGAAAATCATCCAATCTCT
1 GGGCAGATTGAAAACACCAATCTCTTACCCCGATCATGGGGCAGATTAAAAACCATCCAATCTCT
**** *
28425080 TACCTTGGTCATA
66 TACCCCAATCATG
* * **
28425093 GGACAGATTGAAAACCATTCAATCTCTTACCCAAATCATGGGGCAGATTAAAAACCATCCAATCT
1 GGGCAGATTGAAAA-CA-CCAATCTCTTACCCCGATCATGGGGCAGATTAAAAACCATCCAATCT
**
28425158 CTTACCCTGATCATG
64 CTTACCCCAATCATG
*
28425173 GGCCAGATTGAAA
1 GGGCAGATTGAAA
28425186 CCATCGTCCA
Statistics
Matches: 452, Mismatches: 94, Indels: 30
0.78 0.16 0.05
Matches are distributed among these distances:
74 2 0.00
75 2 0.00
76 54 0.12
77 43 0.10
78 172 0.38
79 38 0.08
80 141 0.31
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (78 bp):
GGGCAGATTGAAAACACCAATCTCTTACCCCGATCATGGGGCAGATTAAAAACCATCCAATCTCT
TACCCCAATCATG
Found at i:28424998 original size:234 final size:228
Alignment explanation
Indices: 28424560--28425181 Score: 680
Period size: 234 Copynumber: 2.6 Consensus size: 228
28424550 GATTGAAGAC
* * ** *
28424560 ACACTAATCTCTTACCCCGACCATGGGGCAGATTGAAGGTACA-CTAATCTCTTACCCCGATCA-
1 ACACCAATCTCTTACCCCGATCAT-GGGCAGATT-AA-AAACATCTAATCTCTTACCTCGATCAT
* * *
28424623 GAGGGCAAATTGAAGACACACCAATATCTTA-CCTCGATCATGGGGCAAATTGAAGGCACA-CCA
63 G-GGGCAGATTGAA-A-ACACCAATCTCTTACCCT-GATCATGGGGCAGATTGAA-GC-CATCCA
*
28424686 ATCTCTTACCCCGATCATTGGGCAGATTTAAGAATCCAATCTCTTACCTAATCAGAGGCAAATTG
122 ATCTCTTACCCTGATCA-TGGGCAGATTTAAGAATCCAATCTCTTACCTAATCAGAGGCAAATTG
* *
28424751 AAGACATTCCAATCTCTTACCCCAATCATGGGGTAGAATGAAA
186 AAAACATTCCAATCTCTTACCCCAATCATGAGGTAGAATGAAA
* *
28424794 ATACCAATCTCTTACCCCGATCATAGGGCAGATTAAAAACCATCTAATCTCTTACGTCGATCATG
1 ACACCAATCTCTTACCCCGATCAT-GGGCAGATTAAAAA-CATCTAATCTCTTACCTCGATCATG
* *
28424859 GGGCAGATTGAAAACACCAATCTCTTACCCTGATCATGGGGCAGATTGTAGTCATCCAATCTCTT
64 GGGCAGATTGAAAACACCAATCTCTTACCCTGATCATGGGGCAGATTGAAGCCATCCAATCTCTT
* * * * *
28424924 ACCCTAATCATAGGGCAGA-TTATAGTCATCCAATCTCTTACCCTAATCATGGGGTAGATTGAAA
129 ACCCTGATCAT-GGGCAGATTTA-AG-AATCCAATCTCTTA-CCTAATCA-GAGGCAAATTGAAA
*
28424988 ACCA-TCCAATCTCTTACCCCAATCATGAGGTAGATTGAAA
189 A-CATTCCAATCTCTTACCCCAATCATGAGGTAGAATGAAA
* * * * * * *
28425028 ACGCCAATCTCTTACTCCGATCATGAGGCAGATTGAAAATCATCCAATCTCTTACCTTGGTCATA
1 ACACCAATCTCTTACCCCGATCATG-GGCAGATT-AAAAACATCTAATCTCTTACCTCGATCATG
* * ** * *
28425093 GGACAGATTGAAAACCATTCAATCTCTTACCCAAATCATGGGGCAGATTAAAAACCATCCAATCT
64 GGGCAGATTGAAAA-CA-CCAATCTCTTACCCTGATCATGGGGCAGATT-GAAGCCATCCAATCT
28425158 CTTACCCTGATCATGGGCCAGATT
126 CTTACCCTGATCATGGG-CAGATT
28425182 GAAACCATCG
Statistics
Matches: 330, Mismatches: 40, Indels: 32
0.82 0.10 0.08
Matches are distributed among these distances:
230 6 0.02
231 28 0.08
232 44 0.13
233 17 0.05
234 166 0.50
235 9 0.03
236 31 0.09
237 28 0.08
238 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (228 bp):
ACACCAATCTCTTACCCCGATCATGGGCAGATTAAAAACATCTAATCTCTTACCTCGATCATGGG
GCAGATTGAAAACACCAATCTCTTACCCTGATCATGGGGCAGATTGAAGCCATCCAATCTCTTAC
CCTGATCATGGGCAGATTTAAGAATCCAATCTCTTACCTAATCAGAGGCAAATTGAAAACATTCC
AATCTCTTACCCCAATCATGAGGTAGAATGAAA
Found at i:28436837 original size:31 final size:30
Alignment explanation
Indices: 28436789--28436861 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
28436779 AATTAGTAAA
28436789 GATAAAATTATACTTTAATCCCCTTAAAAAT
1 GATAAAATTATACTTTAAT-CCCTTAAAAAT
* **
28436820 GATAAAATTTTGA-TTTAATCTTTTAAAAAT
1 GATAAAATTAT-ACTTTAATCCCTTAAAAAT
* *
28436850 TATAAAAATATA
1 GATAAAATTATA
28436862 AACTATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 1 0.03
30 17 0.49
31 16 0.46
32 1 0.03
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (30 bp):
GATAAAATTATACTTTAATCCCTTAAAAAT
Found at i:28438304 original size:89 final size:89
Alignment explanation
Indices: 28438193--28438371 Score: 324
Period size: 89 Copynumber: 2.0 Consensus size: 89
28438183 ATGCACCCAT
*
28438193 TAGTATTCTTACGATCTTTTTTATTAAAGTGAAATTTTGATGGAAAGTC-TTTTTAATTTGTGAT
1 TAGTATTCTTACGATCTTTTTTATTAAAGTGAAATTTTGATGAAAAGTCTTTTTTAATTTGTGAT
28438257 CGAAATTGAAAAAAAAAACAGAATC
66 CGAAATTG-AAAAAAAAACAGAATC
28438282 TAGTATTCTTACGATCTTTTTTATTAAAGTGAAATTTTGATGAAAAGTCTTTTTTAATTTGTGAT
1 TAGTATTCTTACGATCTTTTTTATTAAAGTGAAATTTTGATGAAAAGTCTTTTTTAATTTGTGAT
*
28438347 CGAAATTGAAAAAGAAACAGAATC
66 CGAAATTGAAAAAAAAACAGAATC
28438371 T
1 T
28438372 CATTTCATTA
Statistics
Matches: 87, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
89 64 0.74
90 23 0.26
ACGTcount: A:0.37, C:0.08, G:0.15, T:0.40
Consensus pattern (89 bp):
TAGTATTCTTACGATCTTTTTTATTAAAGTGAAATTTTGATGAAAAGTCTTTTTTAATTTGTGAT
CGAAATTGAAAAAAAAACAGAATC
Found at i:28442683 original size:12 final size:12
Alignment explanation
Indices: 28442666--28442692 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
28442656 CATAAAAATA
28442666 TAAAAATAGTTT
1 TAAAAATAGTTT
28442678 TAAAAATAGTTT
1 TAAAAATAGTTT
28442690 TAA
1 TAA
28442693 GCTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (12 bp):
TAAAAATAGTTT
Found at i:28445375 original size:36 final size:35
Alignment explanation
Indices: 28445334--28445557 Score: 109
Period size: 36 Copynumber: 7.2 Consensus size: 35
28445324 CAATCCACCC
28445334 CCTGCACCTCCTCCCAGCCCATGGCCACCGCCAAGT
1 CCTGCACCTCCTCCCAGCCCATGGCCACC-CCAAGT
* *
28445370 CCTGCACCACCACCCA----AT--CCA-CCC----
1 CCTGCACCTCCTCCCAGCCCATGGCCACCCCAAGT
28445394 CCTGCACCTCCTCCCAGCCCATGGCCACCGCCAAGT
1 CCTGCACCTCCTCCCAGCCCATGGCCACC-CCAAGT
* *
28445430 CCTGCACCACCACCCA----AT--CCA--CC---T
1 CCTGCACCTCCTCCCAGCCCATGGCCACCCCAAGT
28445454 CCTGCACCTCCTCCCAGCCCATGGCCACCTCCAAGT
1 CCTGCACCTCCTCCCAGCCCATGGCCACC-CCAAGT
* * *
28445490 CCTCCACCACCACCCA----AT--CCA--CC---T
1 CCTGCACCTCCTCCCAGCCCATGGCCACCCCAAGT
28445514 CCTGCACCTCCTCCCAGCCCATGGCCACCGCCAAGT
1 CCTGCACCTCCTCCCAGCCCATGGCCACC-CCAAGT
*
28445550 CCTCCACC
1 CCTGCACC
28445558 ACCGCCCAAT
Statistics
Matches: 137, Mismatches: 15, Indels: 72
0.61 0.07 0.32
Matches are distributed among these distances:
24 43 0.31
27 4 0.03
28 8 0.06
29 1 0.01
30 18 0.13
31 1 0.01
32 8 0.06
33 4 0.03
36 50 0.36
ACGTcount: A:0.19, C:0.56, G:0.11, T:0.13
Consensus pattern (35 bp):
CCTGCACCTCCTCCCAGCCCATGGCCACCCCAAGT
Found at i:28445617 original size:60 final size:60
Alignment explanation
Indices: 28445180--28445587 Score: 640
Period size: 60 Copynumber: 6.8 Consensus size: 60
28445170 TCCTCCAGCT
* * * * * * *
28445180 CCACCACCAAGTCCTCCACCCCCTCCTAGTCCACCT-CTGCACCTCCACCAAGCCCATGG
1 CCACCGCCAAGTCCTCCACCACCACCCAATCCACCTCCTGCACCTCCTCCCAGCCCATGG
* * * *
28445239 CC-CCACCGAGTCCTCCACCACCACCCAATCCACCTCCTGCACCCCCACCCAGCCCATGG
1 CCACCGCCAAGTCCTCCACCACCACCCAATCCACCTCCTGCACCTCCTCCCAGCCCATGG
*
28445298 CCACCGCCAAGTCCTCCACCACCACCCAATCCACCCCCTGCACCTCCTCCCAGCCCATGG
1 CCACCGCCAAGTCCTCCACCACCACCCAATCCACCTCCTGCACCTCCTCCCAGCCCATGG
* *
28445358 CCACCGCCAAGTCCTGCACCACCACCCAATCCACCCCCTGCACCTCCTCCCAGCCCATGG
1 CCACCGCCAAGTCCTCCACCACCACCCAATCCACCTCCTGCACCTCCTCCCAGCCCATGG
*
28445418 CCACCGCCAAGTCCTGCACCACCACCCAATCCACCTCCTGCACCTCCTCCCAGCCCATGG
1 CCACCGCCAAGTCCTCCACCACCACCCAATCCACCTCCTGCACCTCCTCCCAGCCCATGG
*
28445478 CCACCTCCAAGTCCTCCACCACCACCCAATCCACCTCCTGCACCTCCTCCCAGCCCATGG
1 CCACCGCCAAGTCCTCCACCACCACCCAATCCACCTCCTGCACCTCCTCCCAGCCCATGG
* *
28445538 CCACCGCCAAGTCCTCCACCACCGCCCAATCCACCTCCTGCTCCTCCTCC
1 CCACCGCCAAGTCCTCCACCACCACCCAATCCACCTCCTGCACCTCCTCC
28445588 AAGCTTGTGG
Statistics
Matches: 328, Mismatches: 19, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
58 28 0.09
59 25 0.08
60 275 0.84
ACGTcount: A:0.20, C:0.57, G:0.10, T:0.13
Consensus pattern (60 bp):
CCACCGCCAAGTCCTCCACCACCACCCAATCCACCTCCTGCACCTCCTCCCAGCCCATGG
Found at i:28445724 original size:24 final size:24
Alignment explanation
Indices: 28445640--28445834 Score: 152
Period size: 24 Copynumber: 8.4 Consensus size: 24
28445630 AAGACCACCT
** * *
28445640 CCACCACCTAAACCTCCTCCCGCA
1 CCACCACCTAGGCCTCCACCAGCA
* * *
28445664 CCACCACCCAGG-CTCCACCAACT
1 CCACCACCTAGGCCTCCACCAGCA
28445687 CCACCACC-A-G----CACCAGCA
1 CCACCACCTAGGCCTCCACCAGCA
* * *
28445705 CCTCCACCTAGGCCTCCACCACCC
1 CCACCACCTAGGCCTCCACCAGCA
** * **
28445729 CCACCACCTAATCCTCCTCCCCCA
1 CCACCACCTAGGCCTCCACCAGCA
28445753 CCACCACCTAGGCCTCCACCAGCA
1 CCACCACCTAGGCCTCCACCAGCA
* * *
28445777 CCGCCACCAAGCCCTCCACCAGCA
1 CCACCACCTAGGCCTCCACCAGCA
* *
28445801 CCACCACCAAAGCCTCCACCAGCA
1 CCACCACCTAGGCCTCCACCAGCA
*
28445825 CCCCCACCTA
1 CCACCACCTA
28445835 AACCACCTCC
Statistics
Matches: 134, Mismatches: 31, Indels: 12
0.76 0.18 0.07
Matches are distributed among these distances:
18 13 0.10
19 1 0.01
20 1 0.01
21 1 0.01
22 1 0.01
23 15 0.11
24 102 0.76
ACGTcount: A:0.25, C:0.58, G:0.08, T:0.09
Consensus pattern (24 bp):
CCACCACCTAGGCCTCCACCAGCA
Found at i:28445770 original size:48 final size:47
Alignment explanation
Indices: 28445633--28445851 Score: 139
Period size: 48 Copynumber: 4.7 Consensus size: 47
28445623 CCCCACCAAG
* *
28445633 ACCACCTCCACCACCTAAACCTCCTCC-CGCACCACCACCCAGG-CTCC
1 ACCACC-CCCCCACCTAAACCTCCTCCAC-CACCACCACCTAGGCCTCC
* * ** * * *
28445680 ACCA--ACTCCACC---ACCAGCACCAGCACCTCCACCTAGGCCTCC
1 ACCACCCCCCCACCTAAACCTCCTCCACCACCACCACCTAGGCCTCC
* *
28445722 ACCACCCCCACCACCTAATCCTCCTCCCCCACCACCACCTAGGCCTCC
1 ACCACCCCC-CCACCTAAACCTCCTCCACCACCACCACCTAGGCCTCC
* * * * * * *
28445770 ACCAGCACCGCCACC-AAGCCCTCCACCAGCACCACCACCAAAGCCTCC
1 ACCA-CCCCCCCACCTAA-ACCTCCTCCACCACCACCACCTAGGCCTCC
* * *
28445818 ACCAGCACCCCCACCTAAACCACCTCCTCCACCA
1 ACCA-CCCCCCCACCTAAACCTCCTCCACCACCA
28445852 ATACCTCCAC
Statistics
Matches: 130, Mismatches: 31, Indels: 21
0.71 0.17 0.12
Matches are distributed among these distances:
41 18 0.14
42 8 0.06
44 7 0.05
45 5 0.04
47 6 0.05
48 81 0.62
49 5 0.04
ACGTcount: A:0.26, C:0.58, G:0.07, T:0.09
Consensus pattern (47 bp):
ACCACCCCCCCACCTAAACCTCCTCCACCACCACCACCTAGGCCTCC
Found at i:28445783 original size:12 final size:12
Alignment explanation
Indices: 28445765--28445832 Score: 68
Period size: 12 Copynumber: 5.7 Consensus size: 12
28445755 ACCACCTAGG
28445765 CCTCCACCAGCA
1 CCTCCACCAGCA
*
28445777 CCGCCACCAAGC-
1 CCTCCACC-AGCA
28445789 CCTCCACCAGCA
1 CCTCCACCAGCA
* *
28445801 CCACCACCA-AA
1 CCTCCACCAGCA
28445812 GCCTCCACCAGCA
1 -CCTCCACCAGCA
*
28445825 CCCCCACC
1 CCTCCACC
28445833 TAAACCACCT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
11 4 0.09
12 37 0.82
13 4 0.09
ACGTcount: A:0.26, C:0.60, G:0.09, T:0.04
Consensus pattern (12 bp):
CCTCCACCAGCA
Found at i:28445875 original size:12 final size:12
Alignment explanation
Indices: 28445860--28445894 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
28445850 CAATACCTCC
28445860 ACCACCACCAAA
1 ACCACCACCAAA
* *
28445872 ACCACCACCTAG
1 ACCACCACCAAA
28445884 ACCACCACCAA
1 ACCACCACCAA
28445895 TGCCATGCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.43, C:0.51, G:0.03, T:0.03
Consensus pattern (12 bp):
ACCACCACCAAA
Found at i:28445879 original size:18 final size:18
Alignment explanation
Indices: 28445818--28445880 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
28445808 CAAAGCCTCC
* * *
28445818 ACCAGCACCCCCACCTAA
1 ACCACCACCACCACCAAA
* * *
28445836 ACCACCTCCTCCACCAAT
1 ACCACCACCACCACCAAA
*
28445854 ACCTCCACCACCACCAAA
1 ACCACCACCACCACCAAA
28445872 ACCACCACC
1 ACCACCACC
28445881 TAGACCACCA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.33, C:0.57, G:0.02, T:0.08
Consensus pattern (18 bp):
ACCACCACCACCACCAAA
Found at i:28447575 original size:22 final size:22
Alignment explanation
Indices: 28447550--28447594 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
28447540 GTATTCAAAC
*
28447550 TTGACATTTTTTCCTAATTTGG
1 TTGACACTTTTTCCTAATTTGG
*
28447572 TTGACACTTTTTCTTAATTTGG
1 TTGACACTTTTTCCTAATTTGG
28447594 T
1 T
28447595 ATTTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.13, G:0.13, T:0.56
Consensus pattern (22 bp):
TTGACACTTTTTCCTAATTTGG
Found at i:28447914 original size:60 final size:57
Alignment explanation
Indices: 28447841--28447985 Score: 150
Period size: 60 Copynumber: 2.5 Consensus size: 57
28447831 GCATAGGTAC
* * * *
28447841 CAAATTAGGAAAAAATGTTAAGTTCAGGCACCAAATTGGGTCCAAAAAAGGTTT-AGATAT
1 CAAATTAGAAAAAAATGTCAAGTTCAGACACCAAATTGGGT--AAAAAA-ATTTAAG-TAT
* * *
28447901 CAAATTAGAAAAAAGTGTCAAGTTCAGATATCAAATTGGGTAAAAAAATTTAAGTAT
1 CAAATTAGAAAAAAATGTCAAGTTCAGACACCAAATTGGGTAAAAAAATTTAAGTAT
* *
28447958 CAAATTA-AGAAAAAGTGTCATGTTCAGA
1 CAAATTAGA-AAAAAATGTCAAGTTCAGA
28447986 TATGAAATAT
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
56 1 0.01
57 31 0.41
58 8 0.11
60 35 0.47
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.26
Consensus pattern (57 bp):
CAAATTAGAAAAAAATGTCAAGTTCAGACACCAAATTGGGTAAAAAAATTTAAGTAT
Found at i:28447973 original size:57 final size:59
Alignment explanation
Indices: 28447841--28447993 Score: 170
Period size: 57 Copynumber: 2.6 Consensus size: 59
28447831 GCATAGGTAC
* * * ** * *
28447841 CAAATTAGGAAAAAATGTTAAGTTCAGGCACCAAATTGGGTCCAAAAAAGGTTTAGATAT
1 CAAATTAAGAAAAAGTGTCAAGTTCAGATATCAAATTGGGT-CAAAAAAGATTTAGATAT
28447901 CAAATT-AGAAAAAAGTGTCAAGTTCAGATATCAAATTGGGT-AAAAAA-ATTTA-AGTAT
1 CAAATTAAG-AAAAAGTGTCAAGTTCAGATATCAAATTGGGTCAAAAAAGATTTAGA-TAT
* *
28447958 CAAATTAAGAAAAAGTGTCATGTTCAGATATGAAAT
1 CAAATTAAGAAAAAGTGTCAAGTTCAGATATCAAAT
28447994 ATTATATTAA
Statistics
Matches: 81, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
56 1 0.01
57 38 0.47
58 8 0.10
59 1 0.01
60 33 0.41
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.27
Consensus pattern (59 bp):
CAAATTAAGAAAAAGTGTCAAGTTCAGATATCAAATTGGGTCAAAAAAGATTTAGATAT
Found at i:28480357 original size:12 final size:12
Alignment explanation
Indices: 28480340--28480365 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28480330 GACCAAATTA
28480340 GATCGATTAATC
1 GATCGATTAATC
28480352 GATCGATTAATC
1 GATCGATTAATC
28480364 GA
1 GA
28480366 ATTAGATCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (12 bp):
GATCGATTAATC
Found at i:28491313 original size:5 final size:5
Alignment explanation
Indices: 28491303--28491328 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
28491293 TTTTAGCATT
28491303 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
28491329 ATATGTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:28496145 original size:16 final size:16
Alignment explanation
Indices: 28496124--28496165 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
28496114 TGTTGATTGG
28496124 TTGAATGGCCATTCAA
1 TTGAATGGCCATTCAA
*
28496140 TTGAATGGTCATTCAA
1 TTGAATGGCCATTCAA
28496156 TTGAATGGCC
1 TTGAATGGCC
28496166 TAATTTGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (16 bp):
TTGAATGGCCATTCAA
Found at i:28507533 original size:80 final size:79
Alignment explanation
Indices: 28507394--28507554 Score: 252
Period size: 80 Copynumber: 2.0 Consensus size: 79
28507384 TACCATCAAC
* * * *
28507394 CAAATTCGTCAATTCATGGCACCCGATGCCTAGCGGATAAACTGCGATAACTGAGCCCAGCTCTA
1 CAAATTCGTCAATTCATGGCACCAGATGCCTAGAGGATAAACCGCGATAAATGAGCCCAGCTCTA
28507459 GTTGGATTAACCAA
66 GTTGGATTAACCAA
*
28507473 CAAATTCCGTCAATTCATGGCACCTAG-TGCCTAGAGGATAAACCGTGATAAATGAGCCCAGCTC
1 CAAATT-CGTCAATTCATGGCACC-AGATGCCTAGAGGATAAACCGCGATAAATGAGCCCAGCTC
28507537 TAGTTGGATTAACCAA
64 TAGTTGGATTAACCAA
28507553 CA
1 CA
28507555 GTTTGCGCCA
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
79 6 0.08
80 68 0.91
81 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (79 bp):
CAAATTCGTCAATTCATGGCACCAGATGCCTAGAGGATAAACCGCGATAAATGAGCCCAGCTCTA
GTTGGATTAACCAA
Found at i:28515533 original size:22 final size:20
Alignment explanation
Indices: 28515496--28515535 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
28515486 GAATTAAATA
28515496 TAAATAAGGTTAATTAAGGC
1 TAAATAAGGTTAATTAAGGC
28515516 TAAATAAGTGATTAATTAAG
1 TAAATAAG-G-TTAATTAAG
28515536 TTAATTATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 1 0.06
22 9 0.50
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (20 bp):
TAAATAAGGTTAATTAAGGC
Found at i:28527481 original size:14 final size:15
Alignment explanation
Indices: 28527455--28527484 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
28527445 AATAATATAA
28527455 TGATAAGATGAACAG
1 TGATAAGATGAACAG
28527470 TGATAA-ATGAACAG
1 TGATAAGATGAACAG
28527484 T
1 T
28527485 AAAACACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.47, C:0.07, G:0.23, T:0.23
Consensus pattern (15 bp):
TGATAAGATGAACAG
Found at i:28532890 original size:52 final size:52
Alignment explanation
Indices: 28532779--28533017 Score: 304
Period size: 52 Copynumber: 4.6 Consensus size: 52
28532769 TTCCCATTTA
* * * *
28532779 ATACTCACGATGACACAAAGTCATCGGACCT-TAAATACGTAAAAAGA-TCTAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGT-AAAGGATTC-AT
* * * *
28532831 ATGCTCACGATGACACATAATCATCAGACATCTTAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
*
28532883 ATACTCACGATGACACATAGCCATCGGACCT-TATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCT-TAATCCGTAAAGGATTCAT
* * * *
28532935 ATACTCACGATGACACATAGCCATCGAACCTCATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
*
28532987 ATACTCATGATGACACATAGTCATCGGACCT
1 ATACTCACGATGACACATAGTCATCGGACCT
28533018 TTTTCATTTA
Statistics
Matches: 164, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
51 1 0.01
52 154 0.94
53 9 0.05
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCTTAATCCGTAAAGGATTCAT
Found at i:28533407 original size:35 final size:35
Alignment explanation
Indices: 28533361--28533431 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
28533351 TCCATATAAT
28533361 CCTTATTTATCAAACATAATATCGAATTAACTAAC
1 CCTTATTTATCAAACATAATATCGAATTAACTAAC
28533396 CCTTATTTATCAAACATAATATCGAATTAACTAAC
1 CCTTATTTATCAAACATAATATCGAATTAACTAAC
28533431 C
1 C
28533432 ATGCCATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (35 bp):
CCTTATTTATCAAACATAATATCGAATTAACTAAC
Found at i:28535479 original size:21 final size:19
Alignment explanation
Indices: 28535455--28535507 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
28535445 AGAGTTTTTA
28535455 GTATCGGTAGATGCATGACTT
1 GTATCGGTAGAT-CAT-ACTT
* *
28535476 GTATCGATAGAAATTATACTT
1 GTATCGGTAG--ATCATACTT
28535497 GTATCGGTAGA
1 GTATCGGTAGA
28535508 ACTAGCACAG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 1 0.04
21 22 0.81
22 2 0.07
23 2 0.07
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (19 bp):
GTATCGGTAGATCATACTT
Found at i:28535740 original size:14 final size:15
Alignment explanation
Indices: 28535716--28535745 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
28535706 AATAATATAA
28535716 TGATAAAATGAATAG
1 TGATAAAATGAATAG
28535731 TGAT-AAATGAATAG
1 TGATAAAATGAATAG
28535745 T
1 T
28535746 AAAACACTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (15 bp):
TGATAAAATGAATAG
Found at i:28541972 original size:2 final size:2
Alignment explanation
Indices: 28541965--28542012 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
28541955 CGAAATTAAT
28541965 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
28542007 TA TA TA
1 TA TA TA
28542013 CTACTATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28545163 original size:18 final size:17
Alignment explanation
Indices: 28545136--28545169 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
28545126 TAATATAAAT
28545136 ATAATTTTATTATTTTA
1 ATAATTTTATTATTTTA
28545153 ATAATTTTTATTATTTT
1 ATAA-TTTTATTATTTT
28545170 TAAAGGGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
ATAATTTTATTATTTTA
Found at i:28545191 original size:30 final size:31
Alignment explanation
Indices: 28545153--28545227 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 31
28545143 TATTATTTTA
* *
28545153 ATAATTTTTATTATTTTTAAAGGGTTAAATT
1 ATAATTTTTATCATTTTTAAAGGGTTAAAGT
**
28545184 A-AATTTTTATCATTTTTAGGGGGTTAAAGT
1 ATAATTTTTATCATTTTTAAAGGGTTAAAGT
28545214 ATAA-TTTTATCATT
1 ATAATTTTTATCATT
28545228 ACTAATTTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
30 36 0.92
31 3 0.08
ACGTcount: A:0.33, C:0.03, G:0.12, T:0.52
Consensus pattern (31 bp):
ATAATTTTTATCATTTTTAAAGGGTTAAAGT
Found at i:28549629 original size:18 final size:18
Alignment explanation
Indices: 28549609--28549643 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28549599 AGGTTCTTTT
*
28549609 TTTTCTTTC-TCTTCTTC
1 TTTTCCTTCTTCTTCTTC
28549626 TTTTCCTTCTTCTTCTTC
1 TTTTCCTTCTTCTTCTTC
28549644 CTCTTGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTCCTTCTTCTTCTTC
Found at i:28562112 original size:52 final size:52
Alignment explanation
Indices: 28562007--28562183 Score: 230
Period size: 52 Copynumber: 3.4 Consensus size: 52
28561997 ATGACTAAAG
* * * **
28562007 GTCATCATGAGTATATG-ATCCTTCACGGATAAAGAGGTCTGATGATTAAGT
1 GTCATCGTGAGTATATGAATCCTTCACGGATTAAGAGGTCTGATGACTCTGT
* * *
28562058 GTCATTGTGAGTATATGAATCCTTCAGGGATTAAGAGGTCTAATGACTCTGT
1 GTCATCGTGAGTATATGAATCCTTCACGGATTAAGAGGTCTGATGACTCTGT
* * * *
28562110 GTCATCGTGAGTATATGAATCCTTTACGAATTAAGAGGTCCGATGACTCTAT
1 GTCATCGTGAGTATATGAATCCTTCACGGATTAAGAGGTCTGATGACTCTGT
*
28562162 GTTATCGTGAGTATATGAATCC
1 GTCATCGTGAGTATATGAATCC
28562184 CTTGCAGATT
Statistics
Matches: 109, Mismatches: 16, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
51 15 0.14
52 94 0.86
ACGTcount: A:0.29, C:0.15, G:0.23, T:0.33
Consensus pattern (52 bp):
GTCATCGTGAGTATATGAATCCTTCACGGATTAAGAGGTCTGATGACTCTGT
Found at i:28562201 original size:52 final size:51
Alignment explanation
Indices: 28561987--28562233 Score: 161
Period size: 52 Copynumber: 4.8 Consensus size: 51
28561977 GCCATAAACA
* ** * * * *
28561987 AAGAGTTCCGATGACTAAAGGTCATCATGAGTATATG-AT-CCTTCACGGATA
1 AAGAGGTCCGATGACTCTATGTTATCGTGAGTATATGAATCCCTTCA--GATT
* * *
28562038 AAGAGGTCTGATGA-T-TAAGTGTCATTGTGAGTATATGAAT-CCTTCAGGGATT
1 AAGAGGTCCGATGACTCT-A-TGTTATCGTGAGTATATGAATCCCTTCA--GATT
** * * *
28562090 AAGAGGTCTAATGACTCTGTGTCATCGTGAGTATATGAAT-CCTTTACGAATT
1 AAGAGGTCCGATGACTCTATGTTATCGTGAGTATATGAATCCCTTCA-G-ATT
28562142 AAGAGGTCCGATGACTCTATGTTATCGTGAGTATATGAATCCCTTGCAGATT
1 AAGAGGTCCGATGACTCTATGTTATCGTGAGTATATGAATCCCTT-CAGATT
* * *
28562194 ATA-AGGTCCGGTG--GCTATGTTTCATTGTGAGTATATGAAT
1 A-AGAGGTCCGATGACTCTATG-TT-ATCGTGAGTATATGAAT
28562234 GAAGTAAAAT
Statistics
Matches: 164, Mismatches: 21, Indels: 21
0.80 0.10 0.10
Matches are distributed among these distances:
50 7 0.04
51 30 0.18
52 118 0.72
53 7 0.04
54 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (51 bp):
AAGAGGTCCGATGACTCTATGTTATCGTGAGTATATGAATCCCTTCAGATT
Found at i:28562201 original size:104 final size:103
Alignment explanation
Indices: 28562007--28562233 Score: 239
Period size: 104 Copynumber: 2.2 Consensus size: 103
28561997 ATGACTAAAG
* * * *
28562007 GTCATCATGAGTATATG-ATCCTTCACGGATAAAGAGGTCTGATGATTAAGTGTCATTGTGAGTA
1 GTCATCGTGAGTATATGAATCCTTCACGAATAAAGAGGTCCGATGATTAAGTGTCATCGTGAGTA
* *
28562071 TATGAATCCTTCAGGGATTAAGAGGTCTAATGACTCTGT
66 TATGAATCCTTCA-GGATTAAGAGGTCCAATGACTATGT
* * *
28562110 GTCATCGTGAGTATATGAATCCTTTACGAATTAAGAGGTCCGATGACTCT-A-TGTTATCGTGAG
1 GTCATCGTGAGTATATGAATCCTTCACGAATAAAGAGGTCCGATGA-T-TAAGTGTCATCGTGAG
** *
28562173 TATATGAATCCCTTGCA-GATTATA-AGGTCCGGTGGCTATGT
64 TATATGAAT-CCTT-CAGGATTA-AGAGGTCCAATGACTATGT
* *
28562214 TTCATTGTGAGTATATGAAT
1 GTCATCGTGAGTATATGAAT
28562234 GAAGTAAAAT
Statistics
Matches: 104, Mismatches: 14, Indels: 11
0.81 0.11 0.09
Matches are distributed among these distances:
103 16 0.15
104 78 0.75
105 7 0.07
106 3 0.03
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (103 bp):
GTCATCGTGAGTATATGAATCCTTCACGAATAAAGAGGTCCGATGATTAAGTGTCATCGTGAGTA
TATGAATCCTTCAGGATTAAGAGGTCCAATGACTATGT
Found at i:28565573 original size:17 final size:18
Alignment explanation
Indices: 28565542--28565579 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
28565532 TCTTTTTTTT
28565542 TCTTCTTCTTTCTTTCCA
1 TCTTCTTCTTTCTTTCCA
28565560 TCTTCTTC-TTCTTTCCA
1 TCTTCTTCTTTCTTTCCA
28565577 TCT
1 TCT
28565580 GTTACTGCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (18 bp):
TCTTCTTCTTTCTTTCCA
Found at i:28566532 original size:21 final size:20
Alignment explanation
Indices: 28566496--28566537 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 20
28566486 AGGCAGTAAC
28566496 AGATGGAAAGAAGAAGAAGA
1 AGATGGAAAGAAGAAGAAGA
28566516 AGATGGAAAGAAAGAAGAAGA
1 AGATGGAAAG-AAGAAGAAGA
28566537 A
1 A
28566538 AAAAACTGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.33, T:0.05
Consensus pattern (20 bp):
AGATGGAAAGAAGAAGAAGA
Done.