Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013048.1 Kokia drynarioides strain JFW-HI SEQ_128066, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 145146
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:35 original size:20 final size:20
Alignment explanation
Indices: 10--61 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1 TTAATTATT
*
10 TGTAAAATCTAATTTAAATA
1 TGTAAAATATAATTTAAATA
* *
30 TGTAAATTATATTTTAAATA
1 TGTAAAATATAATTTAAATA
50 T-TAAAATATAAT
1 TGTAAAATATAAT
62 CATTACAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 9 0.33
20 18 0.67
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
TGTAAAATATAATTTAAATA
Found at i:75 original size:22 final size:21
Alignment explanation
Indices: 45--101 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 21
35 ATTATATTTT
45 AAATATTAAAATATAATCATTAC
1 AAAT-TTAAAATATAAT-ATTAC
* *
68 AAATTTAAATATATTATATTAT
1 AAATTTAAA-ATATAATATTAC
*
90 ATATTTAAAATA
1 AAATTTAAAATA
102 AATTTCAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 3 0.10
22 17 0.57
23 10 0.33
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATTTAAAATATAATATTAC
Found at i:10115 original size:15 final size:12
Alignment explanation
Indices: 10104--10128 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10094 AAAAAGAGGG
10104 AAAGGAAGAAGA
1 AAAGGAAGAAGA
10116 AAAGGAAGAAGA
1 AAAGGAAGAAGA
10128 A
1 A
10129 GAGCTTGCTG
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:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (12 bp):
AAAGGAAGAAGA
Found at i:15834 original size:52 final size:52
Alignment explanation
Indices: 15767--16004 Score: 318
Period size: 52 Copynumber: 4.6 Consensus size: 52
15757 GTAAATGAAT
* *
15767 GGTCCGATGATTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGAATTATGA
* * * * *
15819 GGTCCGATGACTATGTGTCATTGTGAGTATATGAATCCTTTATGGATAATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGAATTATGA
* *
15871 GGTCTGATGACTTTGTGTCATCGTGAGTATATGAATCATTTAC-AGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGA-ATTATGA
* * *
15923 GGTCCGATGACTAAGTGTCATCTTGAGTATATGAATCATTTACGGATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGAATTATGA
* *
15975 GGTTCGATTG-CTATGTGTCATCATGAGTAT
1 GGTCCGA-TGACTATGTGTCATCGTGAGTAT
16005 TAAATGAAAT
Statistics
Matches: 163, Mismatches: 20, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
52 161 0.99
53 2 0.01
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.37
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGAATTATGA
Found at i:30253 original size:52 final size:52
Alignment explanation
Indices: 30171--30461 Score: 395
Period size: 52 Copynumber: 5.6 Consensus size: 52
30161 CGTAAATGAA
* * * * *
30171 AGGTCCGATGATTATGTGTCATTGTGAGTATATGAATCATTTAAGGATTATG
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
30223 AGGTCCTAGGACTATGTGTCATCATAAGTATATGAATCCTTTACGGATTATG
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
30275 AGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTATGGATTTTA
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* *
30327 AGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
1 AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
* * * *
30379 AGTTTCGAA-GGCTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATG
1 AG-GTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
30431 AGGTCCAATGACTATGTGTCATCGTGAGTAT
1 AGGTCCAATGACTATGTGTCATCGTGAGTAT
30462 TTAATAAAAT
Statistics
Matches: 209, Mismatches: 28, Indels: 4
0.87 0.12 0.02
Matches are distributed among these distances:
51 4 0.02
52 203 0.97
53 2 0.01
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (52 bp):
AGGTCCAATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATG
Found at i:30454 original size:156 final size:156
Alignment explanation
Indices: 30170--30461 Score: 460
Period size: 156 Copynumber: 1.9 Consensus size: 156
30160 CCGTAAATGA
* * *
30170 AAGGTCCGATGATTATGTGTCATTGTGAGTATATGAATCATTTAAGGATTATGAGGTCCTAGGAC
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTAAGGATTATGAGGTCCAAGGAC
* *
30235 TATGTGTCATCATAAGTATATGAATCCTTTACGGATTATGAGGTCCGATGACTATGTGTCATCGT
66 TATGTGTCATCATAAGTATATGAATCCTTTACGAATTATGAGGTCCAATGACTATGTGTCATCGT
30300 GAGTATATGAATCCTTTATGGATTTT
131 GAGTATATGAATCCTTTATGGATTTT
* * * * *
30326 AAGGTTCGATGACTATGTGTCATCGTGAGTATATGAATCCTTTACGGATTATGAGTTTCGAAGG-
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTAAGGATTATGAG-GTCCAAGGA
* *
30390 CTATGTGTCATCGTGAGTATATGAATCCTTTACGAATTATGAGGTCCAATGACTATGTGTCATCG
65 CTATGTGTCATCATAAGTATATGAATCCTTTACGAATTATGAGGTCCAATGACTATGTGTCATCG
30455 TGAGTAT
130 TGAGTAT
30462 TTAATAAAAT
Statistics
Matches: 123, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
156 118 0.96
157 5 0.04
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (156 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTAAGGATTATGAGGTCCAAGGAC
TATGTGTCATCATAAGTATATGAATCCTTTACGAATTATGAGGTCCAATGACTATGTGTCATCGT
GAGTATATGAATCCTTTATGGATTTT
Found at i:32747 original size:21 final size:21
Alignment explanation
Indices: 32723--32787 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
32713 GGAGTTTTTA
32723 GTATCGGTAGAAGTTACACTT
1 GTATCGGTAGAAGTTACACTT
* * * **
32744 GTATTGGTAGAACTTACTCAG
1 GTATCGGTAGAAGTTACACTT
*
32765 GTATCAGTAGAAGTCTACA-TT
1 GTATCGGTAGAAGT-TACACTT
32786 GT
1 GT
32788 TTCTAAGATT
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
21 29 0.91
22 3 0.09
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (21 bp):
GTATCGGTAGAAGTTACACTT
Found at i:49243 original size:22 final size:22
Alignment explanation
Indices: 49199--49244 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
49189 TCTTTGTAAT
* *
49199 TTAGGTTTTAGTATTTTCTTTC
1 TTAGGTTTCAGTATTTTCGTTC
49221 TTAGGTTTCAGTTATTTT-GTTC
1 TTAGGTTTCAG-TATTTTCGTTC
49243 TT
1 TT
49245 TCATTATTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.13, C:0.09, G:0.15, T:0.63
Consensus pattern (22 bp):
TTAGGTTTCAGTATTTTCGTTC
Found at i:56612 original size:26 final size:26
Alignment explanation
Indices: 56581--56764 Score: 178
Period size: 26 Copynumber: 7.2 Consensus size: 26
56571 AGATAGTACT
*
56581 TGCTAAACATTCACCGGCTCGAAGCC
1 TGCTAAATATTCACCGGCTCGAAGCC
* * *
56607 TGCT-AACATTCACCAGCTC-AAGGCT
1 TGCTAAATATTCACCGGCTCGAA-GCC
* *
56632 TGCTAAACATTCACCGGCTCAAAGCC
1 TGCTAAATATTCACCGGCTCGAAGCC
* **
56658 TGCTAAATATACA-TAGCTCGAAGCC
1 TGCTAAATATTCACCGGCTCGAAGCC
* * *
56683 TACTAAATATACACCGGCTCGAAGCA
1 TGCTAAATATTCACCGGCTCGAAGCC
* *
56709 TGCTAAATATAT-ACCGGCTCAAAGCT
1 TGCTAAATAT-TCACCGGCTCGAAGCC
* *
56735 TGCTAAATATACACCAGCTCGAAGCC
1 TGCTAAATATTCACCGGCTCGAAGCC
56761 TGCT
1 TGCT
56765 CATGTATCTC
Statistics
Matches: 131, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
24 2 0.02
25 41 0.31
26 86 0.66
27 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.22
Consensus pattern (26 bp):
TGCTAAATATTCACCGGCTCGAAGCC
Found at i:56639 original size:51 final size:49
Alignment explanation
Indices: 56579--56764 Score: 194
Period size: 51 Copynumber: 3.7 Consensus size: 49
56569 GTAGATAGTA
*
56579 CTTGCTAAACATTCACCGGCTCGAAGCCTGCTAACAT-TCACCAGCTCAAGG
1 CTTGCTAAACATACACCGGCTCGAAGCCTGCTAA-ATAT-ACCAGCTCAA-G
* * *
56630 CTTGCTAAACATTCACCGGCTCAAAGCCTGCTAAATATACATAGCTCGAAG
1 CTTGCTAAACATACACCGGCTCGAAGCCTGCTAAATATAC-CAGCTC-AAG
* * * * *
56681 CCTACTAAATATACACCGGCTCGAAGCATGCTAAATATATACCGGCTCAAAG
1 CTTGCTAAACATACACCGGCTCGAAGCCTGCT-AA-ATATACCAGCTC-AAG
* *
56733 CTTGCTAAATATACACCAGCTCGAAGCCTGCT
1 CTTGCTAAACATACACCGGCTCGAAGCCTGCT
56765 CATGTATCTC
Statistics
Matches: 115, Mismatches: 15, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
50 4 0.03
51 66 0.57
52 39 0.34
53 6 0.05
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.23
Consensus pattern (49 bp):
CTTGCTAAACATACACCGGCTCGAAGCCTGCTAAATATACCAGCTCAAG
Found at i:56713 original size:77 final size:77
Alignment explanation
Indices: 56581--56761 Score: 217
Period size: 77 Copynumber: 2.4 Consensus size: 77
56571 AGATAGTACT
* * * * *
56581 TGCTAAACATTCACCGGCTCGAAGCCTGCTAACATTCACCAGCTCAAGGCTTGCTAAACAT-TCA
1 TGCTAAATATACACCAGCTCGAAGCCTACTAACATTCACCAGCTCAAGGCATGCTAAACATAT-A
56645 CCGGCTCAAAGCC
65 CCGGCTCAAAGCC
* * *
56658 TGCTAAATATACA-TAGCTCGAAGCCTACTAA-ATATACACCGGCTCGAA-GCATGCTAAATATA
1 TGCTAAATATACACCAGCTCGAAGCCTACTAACAT-T-CACCAGCTC-AAGGCATGCTAAACATA
*
56720 TACCGGCTCAAAGCT
63 TACCGGCTCAAAGCC
56735 TGCTAAATATACACCAGCTCGAAGCCT
1 TGCTAAATATACACCAGCTCGAAGCCT
56762 GCTCATGTAT
Statistics
Matches: 89, Mismatches: 10, Indels: 9
0.82 0.09 0.08
Matches are distributed among these distances:
75 2 0.02
76 16 0.18
77 56 0.63
78 15 0.17
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (77 bp):
TGCTAAATATACACCAGCTCGAAGCCTACTAACATTCACCAGCTCAAGGCATGCTAAACATATAC
CGGCTCAAAGCC
Found at i:60242 original size:17 final size:17
Alignment explanation
Indices: 60203--60250 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
60193 TGATATATGG
**
60203 AAATGCAATGACAATGT
1 AAATGCAATGACAATAA
* *
60220 ACATGCAGTGACAATAA
1 AAATGCAATGACAATAA
60237 AAATGCAATGACAA
1 AAATGCAATGACAA
60251 AGGAAATGTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.50, C:0.15, G:0.17, T:0.19
Consensus pattern (17 bp):
AAATGCAATGACAATAA
Found at i:60257 original size:17 final size:17
Alignment explanation
Indices: 60201--60258 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
60191 AATGATATAT
*
60201 GGAAATGCAATGACAAT
1 GGAAATGCAATGACAAA
* * *
60218 GTACATGCAGTGACAATA
1 GGAAATGCAATGACAA-A
*
60236 -AAAATGCAATGACAAA
1 GGAAATGCAATGACAAA
60252 GGAAATG
1 GGAAATG
60259 TGGTGACAAT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
16 1 0.03
17 30 0.97
ACGTcount: A:0.48, C:0.12, G:0.22, T:0.17
Consensus pattern (17 bp):
GGAAATGCAATGACAAA
Found at i:60265 original size:34 final size:34
Alignment explanation
Indices: 60203--60268 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
60193 TGATATATGG
* * *
60203 AAATGCAATGACAATGTACATGCAGTGACAATAA
1 AAATGCAATGACAAAGGAAATGCAGTGACAATAA
**
60237 AAATGCAATGACAAAGGAAATGTGGTGACAAT
1 AAATGCAATGACAAAGGAAATGCAGTGACAAT
60269 TACATTACAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.47, C:0.12, G:0.21, T:0.20
Consensus pattern (34 bp):
AAATGCAATGACAAAGGAAATGCAGTGACAATAA
Found at i:73138 original size:48 final size:48
Alignment explanation
Indices: 73055--73146 Score: 121
Period size: 48 Copynumber: 1.9 Consensus size: 48
73045 TTCAAAACCC
** * ** *
73055 CATCTTCCTGATGCGATACAGAGAAGTGGGTCAAAATAATGAAGTGTT
1 CATCTTCCTGATAAGATACAGAGAAGTAGACCAAAACAATGAAGTGTT
*
73103 CATCTTTCTGATAAGATACAGAGAAGTAGACCAAAACAATGAAG
1 CATCTTCCTGATAAGATACAGAGAAGTAGACCAAAACAATGAAG
73147 CAAAGCTCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 37 1.00
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.24
Consensus pattern (48 bp):
CATCTTCCTGATAAGATACAGAGAAGTAGACCAAAACAATGAAGTGTT
Found at i:73278 original size:123 final size:123
Alignment explanation
Indices: 72906--73393 Score: 516
Period size: 123 Copynumber: 4.0 Consensus size: 123
72896 TATAGTAAGA
* * * *
72906 AAAGCTCAATG-CACGTGAAACTTTAAACCCGATCTTCCTAATGAGATACA-AGGAAGTAGGTCA
1 AAAGCTCAATGTCA-GTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGA-GAAGTAGATCA
* * *
72969 AAACAATCAAG-CGGACATCTTCTTGATGAGAT--ATAG-AG--GACCAAAATAATGAAGC
64 AAACAATCAAGTC-GTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGC
* ** * * *
73024 GAAGCTCAATGTCAGCAAAACTTCAAAACCCCATCTTCCTGATGCGATACAGAGAAGTGGGTCAA
1 AAAGCTCAATGTCAGTGAAACTTC-AAACCCCATCTTCCTGATGAGATACAGAGAAGTAGATCAA
* * *
73089 AATAATGAAGT-GTTCATCTT-TCTGATAAGATACAGAGAAGTAGACCAAAACAATGAAGC
65 AACAATCAAGTCG-TCATCTTCT-TGATGAGATACAGAGAAGTAGACCAAAACAATGAAGC
* * *
73148 AAAGCTCAATGTGAGTGAAACTTCAAACCCCTATCTTCTTGGTGAGATACAGAGAAGTAGATC-A
1 AAAGCTCAATGTCAGTGAAACTTCAAACCCC-ATCTTCCTGATGAGATACAGAGAAGTAGATCAA
* * *
73212 AACAATCAAGTCGTCATATTCCTT-ATGAGATATAGAGAAGTATACCAAAACAATGAAGC
65 AACAATCAAGTCGTCATCTT-CTTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGC
** * * * *
73271 AAAGCTCAACCTGAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATACAAAGAAATGGATC-A
1 AAAGCTCAATGTCAGTGAAACTTCAAA-CCCCATCTTCCTGATGAGATACAGAGAAGTAGATCAA
** * *
73335 AACAATCAAGAGGTCATCTTCTTGAAGAGATACAGAGAAGTAGACCAAAATAATGAAGC
65 AACAATCAAGTCGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGC
73394 GAACATCTTC
Statistics
Matches: 310, Mismatches: 43, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
118 19 0.06
119 58 0.19
120 1 0.00
121 3 0.01
122 5 0.02
123 155 0.50
124 68 0.22
125 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (123 bp):
AAAGCTCAATGTCAGTGAAACTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTAGATCAAA
ACAATCAAGTCGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAAACAATGAAGC
Found at i:73413 original size:48 final size:48
Alignment explanation
Indices: 73302--73489 Score: 243
Period size: 48 Copynumber: 3.9 Consensus size: 48
73292 TTCAAACCCC
* * * * * *
73302 CATCTTCCTGATGAGATACAAAGAAATGGATC-AAACAATCAAGAGGT
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGCGGT
* * * **
73349 CATCTTCTTGAAGAGATACAGAGAAGTAGACCAAAATAATGAAGCGAA
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGCGGT
**
73397 CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAATAATGAAGCGGT
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGCGGT
*
73445 CATCTTCCTGATGAGATATAGAGAAGTGGACCAAAATAATGAAGC
1 CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGC
73490 AGAGCTCAAT
Statistics
Matches: 119, Mismatches: 21, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
47 26 0.22
48 93 0.78
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.21
Consensus pattern (48 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGACCAAAATAATGAAGCGGT
Found at i:73477 original size:96 final size:95
Alignment explanation
Indices: 73302--73489 Score: 277
Period size: 96 Copynumber: 2.0 Consensus size: 95
73292 TTCAAACCCC
*
73302 CATCTTCCTGATGAGATACAAAGAAATGGATCAAACAATCAAGAGGTCATCTTCTTGAAGAGATA
1 CATCTTCCTGATGAGATACAAAGAAATGGATCAAACAATCAAGAGGTCATCTTCCTGAAGAGATA
73367 CAGAGAAGTAGACCAAAATAATGAAGCGAA
66 CAGAGAAGTAGACCAAAATAATGAAGCGAA
* * * * * * *
73397 CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAATAATGAAGCGGTCATCTTCCTGATGAGAT
1 CATCTTCCTGATGAGATACAAAGAAATGGATC-AAACAATCAAGAGGTCATCTTCCTGAAGAGAT
* *
73462 ATAGAGAAGTGGACCAAAATAATGAAGC
65 ACAGAGAAGTAGACCAAAATAATGAAGC
73490 AGAGCTCAAT
Statistics
Matches: 82, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
95 29 0.35
96 53 0.65
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.21
Consensus pattern (95 bp):
CATCTTCCTGATGAGATACAAAGAAATGGATCAAACAATCAAGAGGTCATCTTCCTGAAGAGATA
CAGAGAAGTAGACCAAAATAATGAAGCGAA
Found at i:73723 original size:123 final size:121
Alignment explanation
Indices: 73397--73856 Score: 580
Period size: 123 Copynumber: 3.7 Consensus size: 121
73387 ATGAAGCGAA
*
73397 CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAAATAATGAAGCGGTCATCTTCCTGATGAGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGGTC-AAACAATGAAGCGGTCATCTTCCTGATGAGAT
* * *
73462 ATAGAGAAGTGGACCAAAATAATGAAGCAGAGCTCAATGTGAATGAAACTTCAAAACCC
65 ACAGAGAAGTAGACCAAAATAATGAAGCA-AGTTCAATGT-AATGAAACTTCAAAACCC
* * * * *
73521 CATTTTCCTGATGAGATGCAGAGAAGCGGGTCAAAACAATGAAGTGGTCATCTTCCTAATGAGAT
1 CATCTTCCTGATGAGATACAGAGAAGTGGGTC-AAACAATGAAGCGGTCATCTTCCTGATGAGAT
* * * *
73586 ATAGAGAAGTAGACCAAAATAATGAAGCGAAGTTCAATGTCAACGAAACTCCAAACCCC
65 ACAGAGAAGTAGACCAAAATAATGAAGC-AAGTTCAATGT-AATGAAACTTCAAAACCC
* * * * * * * * *
73645 CATCTTCGTAATAAGATATAGAGAAGTGGATCAAACATTCAAGTGGTCATTTTCCTGATGAGATA
1 CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAACAATGAAGCGGTCATCTTCCTGATGAGATA
*
73710 CAGAGAAGTAGACCAAAATAATGAAGCAAAGTTCAATGTAAGTGAAACTTCAAAACTC
66 CAGAGAAGTAGACCAAAATAATGAAGC-AAGTTCAATGTAA-TGAAACTTCAAAACCC
* * * *
73768 CATCTTCCTGATGAGATAGAGAGAAATGGGTCAAACAATGAAGCAGTCATCTTCCTGAGGAGATA
1 CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAACAATGAAGCGGTCATCTTCCTGATGAGATA
* *
73833 CAGAGAAATAGACAAAAAT-ATGAA
66 CAGAGAAGTAGACCAAAATAATGAA
73857 ACTACGATGC
Statistics
Matches: 290, Mismatches: 44, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
122 7 0.02
123 148 0.51
124 134 0.46
125 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.22
Consensus pattern (121 bp):
CATCTTCCTGATGAGATACAGAGAAGTGGGTCAAACAATGAAGCGGTCATCTTCCTGATGAGATA
CAGAGAAGTAGACCAAAATAATGAAGCAAGTTCAATGTAATGAAACTTCAAAACCC
Found at i:74880 original size:13 final size:14
Alignment explanation
Indices: 74862--74910 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
74852 TCACCGATTC
74862 AAAAAAGA-AAATA
1 AAAAAAGACAAATA
*
74875 AAAAAAGAGAAATA
1 AAAAAAGACAAATA
*
74889 ACAAAAACAACAAATA
1 A-AAAAA-GACAAATA
74905 AAAAAA
1 AAAAAA
74911 TCATCAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 8 0.26
14 6 0.19
15 10 0.32
16 7 0.23
ACGTcount: A:0.82, C:0.06, G:0.06, T:0.06
Consensus pattern (14 bp):
AAAAAAGACAAATA
Found at i:75732 original size:30 final size:29
Alignment explanation
Indices: 75696--75825 Score: 111
Period size: 29 Copynumber: 4.4 Consensus size: 29
75686 AACTCCATTA
*
75696 AAAATTACATTTTAACCTTTAAACTTTTCC
1 AAAATTACATTTTAACC-CTAAACTTTTCC
* * **
75726 AAAATTA-AGTTTGACCCTAAACTTTTTT
1 AAAATTACATTTTAACCCTAAACTTTTCC
* *
75754 AAAATTATATTTTAACCCCTAAATTTTTCC
1 AAAATTACATTTTAA-CCCTAAACTTTTCC
* * * *
75784 AAAATTACAATTTCA-CCTCAAAATTCTCC
1 AAAATTACATTTTAACCCT-AAACTTTTCC
*
75813 AAAATTTCATTTT
1 AAAATTACATTTT
75826 TGACCCTTTT
Statistics
Matches: 80, Mismatches: 17, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
28 19 0.24
29 31 0.39
30 30 0.38
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.42
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTTCC
Found at i:75749 original size:28 final size:30
Alignment explanation
Indices: 75696--75790 Score: 95
Period size: 30 Copynumber: 3.2 Consensus size: 30
75686 AACTCCATTA
* * **
75696 AAAATTACATTTTAACCTTTAAACTTTTCC
1 AAAATTATAGTTTAACCCCTAAACTTTTCC
* **
75726 AAAATTA-AGTTTGA-CCCTAAACTTTTTT
1 AAAATTATAGTTTAACCCCTAAACTTTTCC
* *
75754 AAAATTATATTTTAACCCCTAAATTTTTCC
1 AAAATTATAGTTTAACCCCTAAACTTTTCC
75784 AAAATTA
1 AAAATTA
75791 CAATTTCACC
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
28 17 0.33
29 10 0.19
30 25 0.48
ACGTcount: A:0.39, C:0.17, G:0.02, T:0.42
Consensus pattern (30 bp):
AAAATTATAGTTTAACCCCTAAACTTTTCC
Found at i:79921 original size:20 final size:21
Alignment explanation
Indices: 79896--79939 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
79886 TGGCAATATA
79896 TTTCTTCTTT-TTTCTCTTTT
1 TTTCTTCTTTCTTTCTCTTTT
*
79916 TTTCTTCTTTCTTTTTCTTTT
1 TTTCTTCTTTCTTTCTCTTTT
79937 TTT
1 TTT
79940 TATAAGTGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTCTTCTTTCTTTCTCTTTT
Found at i:79940 original size:10 final size:10
Alignment explanation
Indices: 79896--79940 Score: 54
Period size: 11 Copynumber: 4.2 Consensus size: 10
79886 TGGCAATATA
79896 TTTCTTCTTTT
1 TTTCTT-TTTT
79907 TTCTCTTTTTT
1 TT-TCTTTTTT
*
79918 TCTTCTTTCTT
1 T-TTCTTTTTT
79929 TTTCTTTTTT
1 TTTCTTTTTT
79939 TT
1 TT
79941 ATAAGTGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
10 10 0.33
11 15 0.50
12 5 0.17
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:87335 original size:14 final size:14
Alignment explanation
Indices: 87306--87339 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
87296 CTGTTGATTG
87306 TTGTTATAACTCCC
1 TTGTTATAACTCCC
*
87320 TTGTCTATAACTCCT
1 TTGT-TATAACTCCC
87335 TTGTT
1 TTGTT
87340 GTGTGGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.18, C:0.24, G:0.09, T:0.50
Consensus pattern (14 bp):
TTGTTATAACTCCC
Found at i:95856 original size:35 final size:34
Alignment explanation
Indices: 95805--96068 Score: 145
Period size: 35 Copynumber: 7.6 Consensus size: 34
95795 ACCCCATAAA
* *
95805 ACCTATATGTCATTTACACGGTGTCGCCTTGAAG
1 ACCTGTATATCATTTACACGGTGTCGCCTTGAAG
* ** * * * *
95839 AACTTGTATATTGTTTACACGGTATTGCCCTAAAGG
1 -ACCTGTATATCATTTACACGGTGTCGCCTTGAA-G
* * *
95875 ACCTGTATA-CTATTTACACGATGTCACCTCGGAAG
1 ACCTGTATATC-ATTTACACGGTGTCGCCT-TGAAG
* * * **
95910 ACCTGTATATCGTTTACATGGTATTAC-CCTAAAAG
1 ACCTGTATATCATTTACACGGT-GT-CGCCTTGAAG
* * * * * *
95945 ACATGTATACCGTTTACACGATGTCACCTCGGAAG
1 ACCTGTATATCATTTACACGGTGTCGCCT-TGAAG
* * *
95980 ACCTGTATATTATTTACATGGTGTCGCCTCGAAGG
1 ACCTGTATATCATTTACACGGTGTCGCCTTGAA-G
* * *
96015 ACTTGTATATCATTTACACAGTGTCGCCCTGAAGG
1 ACCTGTATATCATTTACACGGTGTCGCCTTGAA-G
* * *
96050 ACCTATCTATCGTTTACAC
1 ACCTGTATATCATTTACAC
96069 AATGTCACCT
Statistics
Matches: 170, Mismatches: 50, Indels: 18
0.71 0.21 0.08
Matches are distributed among these distances:
33 1 0.01
34 7 0.04
35 153 0.90
36 8 0.05
37 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.18, T:0.32
Consensus pattern (34 bp):
ACCTGTATATCATTTACACGGTGTCGCCTTGAAG
Found at i:95933 original size:70 final size:70
Alignment explanation
Indices: 95815--96001 Score: 250
Period size: 70 Copynumber: 2.7 Consensus size: 70
95805 ACCTATATGT
* * * * * * * *
95815 CATTTACACGGTGTCGCCT-TGAAGAACTTGTATATTGTTTACACGGTATTGCCCTAAAGGACCT
1 CATTTACACGATGTCACCTCGGAAG-ACCTGTATATTGTTTACATGGTATTACCCTAAAAGACAT
95879 GTATAC
65 GTATAC
* *
95885 TATTTACACGATGTCACCTCGGAAGACCTGTATATCGTTTACATGGTATTACCCTAAAAGACATG
1 CATTTACACGATGTCACCTCGGAAGACCTGTATATTGTTTACATGGTATTACCCTAAAAGACATG
95950 TATAC
66 TATAC
* *
95955 CGTTTACACGATGTCACCTCGGAAGACCTGTATATTATTTACATGGT
1 CATTTACACGATGTCACCTCGGAAGACCTGTATATTGTTTACATGGT
96002 GTCGCCTCGA
Statistics
Matches: 102, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
70 98 0.96
71 4 0.04
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (70 bp):
CATTTACACGATGTCACCTCGGAAGACCTGTATATTGTTTACATGGTATTACCCTAAAAGACATG
TATAC
Found at i:96053 original size:70 final size:70
Alignment explanation
Indices: 95814--96033 Score: 225
Period size: 70 Copynumber: 3.1 Consensus size: 70
95804 AACCTATATG
* * * * * *
95814 TCATTTACACGGTGTCGCCT-TGAAGAACTTGTATATTGTTTACACGGTATTGCC-CTAAAGGAC
1 TCATTTACACGATGTCACCTCGGAAG-ACCTGTATATTGTTTACATGGTATCGCCTC-AAAGGAC
*
95877 CTGTATA
64 ATGTATA
* *
95884 -CTATTTACACGATGTCACCTCGGAAGACCTGTATATCGTTTACATGGTATTAC-CCT-AAAAGA
1 TC-ATTTACACGATGTCACCTCGGAAGACCTGTATATTGTTTACATGGTA-T-CGCCTCAAAGGA
95946 CATGTATA
63 CATGTATA
* * * * * *
95954 CCGTTTACACGATGTCACCTCGGAAGACCTGTATATTATTTACATGGTGTCGCCTCGAAGGACTT
1 TCATTTACACGATGTCACCTCGGAAGACCTGTATATTGTTTACATGGTATCGCCTCAAAGGACAT
96019 GTATA
66 GTATA
96024 TCATTTACAC
1 TCATTTACAC
96034 AGTGTCGCCC
Statistics
Matches: 124, Mismatches: 18, Indels: 16
0.78 0.11 0.10
Matches are distributed among these distances:
68 1 0.01
69 5 0.04
70 110 0.89
71 8 0.06
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (70 bp):
TCATTTACACGATGTCACCTCGGAAGACCTGTATATTGTTTACATGGTATCGCCTCAAAGGACAT
GTATA
Found at i:100944 original size:112 final size:112
Alignment explanation
Indices: 100747--100970 Score: 448
Period size: 112 Copynumber: 2.0 Consensus size: 112
100737 TAGTTTTGGG
100747 CTAGATTTTATTACTTCTTTCATAGCTAGCATAAATGACTTAGACTTAATTTATGATCCCATAGC
1 CTAGATTTTATTACTTCTTTCATAGCTAGCATAAATGACTTAGACTTAATTTATGATCCCATAGC
100812 TCAAGCGTTCCTAATAGATGCAGATCCAAAAACCTATGATGAGGCTA
66 TCAAGCGTTCCTAATAGATGCAGATCCAAAAACCTATGATGAGGCTA
100859 CTAGATTTTATTACTTCTTTCATAGCTAGCATAAATGACTTAGACTTAATTTATGATCCCATAGC
1 CTAGATTTTATTACTTCTTTCATAGCTAGCATAAATGACTTAGACTTAATTTATGATCCCATAGC
100924 TCAAGCGTTCCTAATAGATGCAGATCCAAAAACCTATGATGAGGCTA
66 TCAAGCGTTCCTAATAGATGCAGATCCAAAAACCTATGATGAGGCTA
100971 TAAGGTCAAT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 112 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (112 bp):
CTAGATTTTATTACTTCTTTCATAGCTAGCATAAATGACTTAGACTTAATTTATGATCCCATAGC
TCAAGCGTTCCTAATAGATGCAGATCCAAAAACCTATGATGAGGCTA
Found at i:112857 original size:30 final size:33
Alignment explanation
Indices: 112821--112882 Score: 85
Period size: 35 Copynumber: 1.9 Consensus size: 33
112811 AAAAATTTTA
112821 ATAAATA-AAAAATG-TAT-AAAATAATATAAT
1 ATAAATATAAAAATGTTATAAAAATAATATAAT
112851 ATAAATATTTAAAAATGTTATAAAAATAATAT
1 ATAAATA--TAAAAATGTTATAAAAATAATAT
112883 GGACAGGTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 7 0.26
33 7 0.26
34 3 0.11
35 10 0.37
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (33 bp):
ATAAATATAAAAATGTTATAAAAATAATATAAT
Found at i:113254 original size:31 final size:31
Alignment explanation
Indices: 113215--113318 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
113205 CCCTTTTTTC
113215 TTCCATTTTCTTCACTACTGTCGGAGTTATT
1 TTCCATTTTCTTCACTACTGTCGGAGTTATT
* *****
113246 TTTCATTTTCTTC-C-A-T-TTTTTTTTCCATT
1 TTCCATTTTCTTCACTACTGTCGGAGTT--ATT
113275 TTCCATTTTCTTCACTACTGTCGGAGTTATT
1 TTCCATTTTCTTCACTACTGTCGGAGTTATT
113306 TTCCATTTTCTTC
1 TTCCATTTTCTTC
113319 CATTTTTTCC
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
27 3 0.05
28 1 0.02
29 16 0.29
30 2 0.04
31 29 0.53
32 1 0.02
33 3 0.05
ACGTcount: A:0.13, C:0.23, G:0.08, T:0.56
Consensus pattern (31 bp):
TTCCATTTTCTTCACTACTGTCGGAGTTATT
Found at i:113321 original size:10 final size:10
Alignment explanation
Indices: 113306--113337 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
113296 CGGAGTTATT
113306 TTCCATTTTC
1 TTCCATTTTC
113316 TTCCATTTT-
1 TTCCATTTTC
113325 TTCCATTTTC
1 TTCCATTTTC
113335 TTC
1 TTC
113338 ACTACAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.09, C:0.28, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCCATTTTC
Found at i:113330 original size:9 final size:9
Alignment explanation
Indices: 113304--113333 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
113294 GTCGGAGTTA
113304 TTTTCCATT
1 TTTTCCATT
113313 TTCTTCCATT
1 TT-TTCCATT
113323 TTTTCCATT
1 TTTTCCATT
113332 TT
1 TT
113334 CTTCACTACA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (9 bp):
TTTTCCATT
Found at i:115853 original size:9 final size:9
Alignment explanation
Indices: 115839--115877 Score: 60
Period size: 9 Copynumber: 4.1 Consensus size: 9
115829 GCAAATGATT
115839 TTAAAATTA
1 TTAAAATTA
115848 TTAAAATTA
1 TTAAAATTA
115857 TTAAAATTA
1 TTAAAATTA
115866 TTTTAAAATTA
1 --TTAAAATTA
115877 T
1 T
115878 AATCATCATC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 19 0.68
11 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TTAAAATTA
Found at i:115862 original size:18 final size:19
Alignment explanation
Indices: 115839--115877 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
115829 GCAAATGATT
115839 TTAAAATTA-TTAAAATTA
1 TTAAAATTATTTAAAATTA
115857 TTAAAATTATTTTAAAATTA
1 TTAAAATTA-TTTAAAATTA
115877 T
1 T
115878 AATCATCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAATTATTTAAAATTA
Found at i:116836 original size:99 final size:99
Alignment explanation
Indices: 116661--116858 Score: 342
Period size: 99 Copynumber: 2.0 Consensus size: 99
116651 TTCCTAAGAA
**
116661 ATGAGATTGAAATAAAGAACCTTGAAGGGTTGGAAGAGTGATGAAAGAAGAAGAAGTCATGGTTT
1 ATGAGATTGAAATAAAGAACCTTGAAGGGTTGGAAGAGTGATGAAAGAAGAAGAAACCATGGTTT
*
116726 GGTTCAGAATCCAAGTGGAGAAGTAGCCATGGTT
66 GGTTCAAAATCCAAGTGGAGAAGTAGCCATGGTT
* * *
116760 ATGAGATTGAAATAGAGAACCTTGAAGGGTTGGGAGAGTGATGGAAGAAGAAGAAACCATGGTTT
1 ATGAGATTGAAATAAAGAACCTTGAAGGGTTGGAAGAGTGATGAAAGAAGAAGAAACCATGGTTT
116825 GGTTCAAAATCCAAGTGGAGAAGTAGCCATGGTT
66 GGTTCAAAATCCAAGTGGAGAAGTAGCCATGGTT
116859 TGGTTCAAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 93 1.00
ACGTcount: A:0.37, C:0.09, G:0.32, T:0.23
Consensus pattern (99 bp):
ATGAGATTGAAATAAAGAACCTTGAAGGGTTGGAAGAGTGATGAAAGAAGAAGAAACCATGGTTT
GGTTCAAAATCCAAGTGGAGAAGTAGCCATGGTT
Found at i:117067 original size:16 final size:16
Alignment explanation
Indices: 117018--117071 Score: 60
Period size: 15 Copynumber: 3.6 Consensus size: 16
117008 TATTTAATAA
*
117018 TTTTAATAATTT-TAT
1 TTTTAAAAATTTATAT
* *
117033 CTTTAAAAA-ATAT-T
1 TTTTAAAAATTTATAT
117047 TTTTAAAAATTTATAT
1 TTTTAAAAATTTATAT
117063 TTTTAAAAA
1 TTTTAAAAA
117072 ATAATTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
14 10 0.32
15 11 0.35
16 10 0.32
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
TTTTAAAAATTTATAT
Found at i:117070 original size:30 final size:28
Alignment explanation
Indices: 117013--117089 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 28
117003 AAAATTATTT
117013 AATAATTTTAATAATTTTATCTTTAAAA
1 AATAATTTTAATAATTTTATCTTTAAAA
* * *
117041 AATATTTTTTAAAAATTTATATTTTTAAAA
1 AATA-ATTTTAATAATTT-TATCTTTAAAA
117071 AATAATTTTAATAATTTTA
1 AATAATTTTAATAATTTTA
117090 AAATAATTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 6 0.14
29 22 0.52
30 14 0.33
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (28 bp):
AATAATTTTAATAATTTTATCTTTAAAA
Found at i:117081 original size:13 final size:13
Alignment explanation
Indices: 117034--117081 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 13
117024 TAATTTTATC
117034 TTTAAAAAATATTT
1 TTTAAAAAATA-TT
117048 TTTAAAAATTTATATT
1 TTTAAAAA---ATATT
*
117064 TTTAAAAAATAAT
1 TTTAAAAAATATT
117077 TTTAA
1 TTTAA
117082 TAATTTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 9 0.30
14 8 0.27
16 10 0.33
17 3 0.10
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAAAAAATATT
Found at i:118090 original size:22 final size:22
Alignment explanation
Indices: 118059--118137 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
118049 ATATGATCTG
*
118059 ATTGAGTGTTTTAATGCAAGAA
1 ATTGAATGTTTTAATGCAAGAA
118081 ATTGAATGTTTTAATGCAAGAA
1 ATTGAATGTTTTAATGCAAGAA
*
118103 ATTGAATGTTTTAATGCAAGAT
1 ATTGAATGTTTTAATGCAAGAA
*
118125 ATTGAATGATTTA
1 ATTGAATGTTTTA
118138 TGGATGTAGA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.38, C:0.04, G:0.19, T:0.39
Consensus pattern (22 bp):
ATTGAATGTTTTAATGCAAGAA
Found at i:120050 original size:18 final size:19
Alignment explanation
Indices: 120027--120079 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 19
120017 AAAAGGCAGG
*
120027 AAATGATGTTAACATTT-T
1 AAATGATGTTAACATTTCA
120045 AAATGATGTTCAA-ATTTCA
1 AAATGATGTT-AACATTTCA
120064 AAATGATGTTAACATT
1 AAATGATGTTAACATT
120080 GATGGAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 16 0.52
19 15 0.48
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (19 bp):
AAATGATGTTAACATTTCA
Found at i:121630 original size:39 final size:40
Alignment explanation
Indices: 121569--121776 Score: 197
Period size: 40 Copynumber: 5.2 Consensus size: 40
121559 ATCTTGTATC
* * * * *
121569 TTAACACTGGCTCTTAGCTTGCTAAGTCGAAGCTTGAATG
1 TTAACACCGACTCATAGCTTACTAAGTCGAAGCTTGAATA
* * * * *
121609 TT-ACACCGGCTCATGGTTTGCTAAG-CTAAAGCTTGAATA
1 TTAACACCGACTCATAGCTTACTAAGTC-GAAGCTTGAATA
* * * * *
121648 TTAACACCAACTCATAGCCTACTGAGCCGAAGCTTGAACA
1 TTAACACCGACTCATAGCTTACTAAGTCGAAGCTTGAATA
* *
121688 TT-ACACCGACTCATGGCTTACTAAGTTGAAGCTTGAATA
1 TTAACACCGACTCATAGCTTACTAAGTCGAAGCTTGAATA
* * *
121727 TTAACACCGGCTCATAGCCTACTAAGTCGAAGCTTGAACA
1 TTAACACCGACTCATAGCTTACTAAGTCGAAGCTTGAATA
*
121767 TTAAAACCGA
1 TTAACACCGA
121777 ATCTAACAAT
Statistics
Matches: 135, Mismatches: 29, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
38 1 0.01
39 63 0.47
40 70 0.52
41 1 0.01
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (40 bp):
TTAACACCGACTCATAGCTTACTAAGTCGAAGCTTGAATA
Found at i:121679 original size:79 final size:79
Alignment explanation
Indices: 121590--121769 Score: 252
Period size: 79 Copynumber: 2.3 Consensus size: 79
121580 TCTTAGCTTG
* ** * * *
121590 CTAAGTCGAAGCTTGAATGTTACACCGGCTCATGGTTTGCTAAGCTAAAGCTTGAATATTAACAC
1 CTAAGCCGAAGCTTGAACATTACACCGACTCATGGCTTACTAAGCTAAAGCTTGAATATTAACAC
121655 CAACTCATAGCCTA
66 CAACTCATAGCCTA
* * *
121669 CTGAGCCGAAGCTTGAACATTACACCGACTCATGGCTTACTAAGTTGAAGCTTGAATATTAACAC
1 CTAAGCCGAAGCTTGAACATTACACCGACTCATGGCTTACTAAGCTAAAGCTTGAATATTAACAC
**
121734 CGGCTCATAGCCTA
66 CAACTCATAGCCTA
*
121748 CTAAGTCGAAGCTTGAACATTA
1 CTAAGCCGAAGCTTGAACATTA
121770 AAACCGAATC
Statistics
Matches: 88, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 88 1.00
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.27
Consensus pattern (79 bp):
CTAAGCCGAAGCTTGAACATTACACCGACTCATGGCTTACTAAGCTAAAGCTTGAATATTAACAC
CAACTCATAGCCTA
Found at i:123296 original size:66 final size:70
Alignment explanation
Indices: 123145--123322 Score: 267
Period size: 72 Copynumber: 2.6 Consensus size: 70
123135 CAATGCTAAA
*
123145 CTAGTTTTATCTATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTA-
123210 GTGTAAT
65 GTGT-AT
123217 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTA-
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAG
123281 T-T-T
66 TGTAT
* * *
123284 C-AGTTTTATCAATAGTTATTTATATTT-GATTTTGGATAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATAT
123323 AAAATTTGTT
Statistics
Matches: 102, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
65 11 0.11
66 24 0.24
67 2 0.02
69 1 0.01
70 1 0.01
72 63 0.62
ACGTcount: A:0.22, C:0.06, G:0.15, T:0.57
Consensus pattern (70 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTGGTTTTTGGATATTGAATTTATGTTCTACTTATTTAG
TGTAT
Found at i:126674 original size:16 final size:16
Alignment explanation
Indices: 126650--126681 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
126640 TCCTTACAAA
*
126650 TTTATTCCTTTAACAT
1 TTTAGTCCTTTAACAT
126666 TTTAGTCCTTTAACAT
1 TTTAGTCCTTTAACAT
126682 AAAAATTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.19, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGTCCTTTAACAT
Found at i:127473 original size:11 final size:11
Alignment explanation
Indices: 127459--127536 Score: 72
Period size: 11 Copynumber: 6.9 Consensus size: 11
127449 GCCCCTTTTT
*
127459 AATTTATTTTA
1 AATTTAATTTA
127470 AATTTAGATTT-
1 AATTTA-ATTTA
*
127481 ATTTTAAATTTA
1 AATTT-AATTTA
127493 AA-TTAATCTTA
1 AATTTAAT-TTA
127504 AATTTAAATTT-
1 AATTT-AATTTA
127515 AATTTAAATTTA
1 AATTT-AATTTA
127527 AATTTAATTT
1 AATTTAATTT
127537 CAAAATTAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
10 3 0.05
11 37 0.65
12 14 0.25
13 3 0.05
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.55
Consensus pattern (11 bp):
AATTTAATTTA
Found at i:127482 original size:17 final size:17
Alignment explanation
Indices: 127459--127546 Score: 113
Period size: 17 Copynumber: 5.1 Consensus size: 17
127449 GCCCCTTTTT
127459 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
*
127476 GATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
* *
127493 AATTAATCTTAAATTTA
1 AATTTATTTTAAATTTA
*
127510 AATTTAATTTAAATTTA
1 AATTTATTTTAAATTTA
* *
127527 AATTTAATTTCAAAATTA
1 AATTT-ATTTTAAATTTA
127545 AA
1 AA
127547 AAGTCCAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
17 49 0.82
18 11 0.18
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.51
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:127547 original size:6 final size:6
Alignment explanation
Indices: 127466--127546 Score: 82
Period size: 6 Copynumber: 14.0 Consensus size: 6
127456 TTTAATTTAT
* *
127466 TTTAAA TTTAGA TTT-AT TTTAAA TTTAAA -TT-AA TCTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA
*
127512 TTT-AA TTTAAA TTTAAA TTT-AA TTTCAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
127547 AAGTCCAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
4 2 0.03
5 15 0.24
6 39 0.62
7 7 0.11
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:129242 original size:29 final size:28
Alignment explanation
Indices: 129210--129353 Score: 113
Period size: 30 Copynumber: 5.2 Consensus size: 28
129200 AAAATTCTGC
129210 TTTTACCCCAGAACTTCCAAAAATCCCAT
1 TTTTACCCC-GAACTTCCAAAAATCCCAT
* *
129239 TTTT-----G-AC-CCCAAAAATTCCAT
1 TTTTACCCCGAACTTCCAAAAATCCCAT
* *
129260 TTTTACCCTCAAACTTTCAAAAATCCCAT
1 TTTTACCC-CGAACTTCCAAAAATCCCAT
* * *
129289 TTTTAACCTCGAAACTTCCAAAAATTCTAT
1 TTTT-ACCCCG-AACTTCCAAAAATCCCAT
*
129319 TTTTGATCCCCGAACTTCCAAAAATCTCAT
1 TTTT-A-CCCCGAACTTCCAAAAATCCCAT
129349 TTTTA
1 TTTTA
129354 TTCCCGAATG
Statistics
Matches: 88, Mismatches: 16, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
21 16 0.18
22 2 0.02
23 1 0.01
28 2 0.02
29 21 0.24
30 42 0.48
31 4 0.05
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.35
Consensus pattern (28 bp):
TTTTACCCCGAACTTCCAAAAATCCCAT
Found at i:129256 original size:50 final size:50
Alignment explanation
Indices: 129197--129292 Score: 140
Period size: 50 Copynumber: 1.9 Consensus size: 50
129187 CTTAAACTGT
**
129197 CCAAAAATTCTGCTTTTACCC-CAGAACTTCCAAAAATCCCATTTTTGACC
1 CCAAAAATTCCACTTTTACCCTCA-AACTTCCAAAAATCCCATTTTTGACC
* *
129247 CCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTT
1 CCAAAAATTCCACTTTTACCCTCAAACTTCCAAAAATCCCATTTTT
129293 AACCTCGAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 39 0.95
51 2 0.05
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (50 bp):
CCAAAAATTCCACTTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACC
Found at i:129262 original size:20 final size:21
Alignment explanation
Indices: 129226--129272 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
129216 CCCAGAACTT
129226 CCAAAAATCCCATTTTTGACC
1 CCAAAAATCCCATTTTTGACC
*
129247 CCAAAAATTCCATTTTT-ACC
1 CCAAAAATCCCATTTTTGACC
129267 CTCAAA
1 C-CAAA
129273 CTTTCAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.36, C:0.32, G:0.02, T:0.30
Consensus pattern (21 bp):
CCAAAAATCCCATTTTTGACC
Found at i:129311 original size:30 final size:30
Alignment explanation
Indices: 129247--129353 Score: 119
Period size: 30 Copynumber: 3.6 Consensus size: 30
129237 ATTTTTGACC
* *
129247 CCAAAAATTCCATTTTTACCCTC-AAACTT
1 CCAAAAATCCCATTTTTAACCTCGAAACTT
*
129276 TCAAAAATCCCATTTTTAACCTCGAAACTT
1 CCAAAAATCCCATTTTTAACCTCGAAACTT
* * * *
129306 CCAAAAATTCTATTTTTGATCCCCG-AACTT
1 CCAAAAATCCCATTTTT-AACCTCGAAACTT
*
129336 CCAAAAATCTCATTTTTA
1 CCAAAAATCCCATTTTTA
129354 TTCCCGAATG
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
29 21 0.32
30 39 0.60
31 5 0.08
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.36
Consensus pattern (30 bp):
CCAAAAATCCCATTTTTAACCTCGAAACTT
Found at i:129359 original size:29 final size:29
Alignment explanation
Indices: 129247--129387 Score: 110
Period size: 29 Copynumber: 4.8 Consensus size: 29
129237 ATTTTTGACC
* * *
129247 CCAAAAATTCCATTTTTA-CCCTCAAACTT
1 CCAAAAATTCTATTTTTATACC-CGAACTT
* * *
129276 TCAAAAATCCCATTTTTA-ACCTCGAAACTT
1 CCAAAAATTCTATTTTTATACC-CG-AACTT
*
129306 CCAAAAATTCTATTTTTGATCCCCGAACTT
1 CCAAAAATTCTATTTTT-ATACCCGAACTT
*
129336 CCAAAAA-TCTCATTTTTATTCCCGAA-TGT
1 CCAAAAATTCT-ATTTTTATACCCGAACT-T
* *
129365 CTAAAAATTCTATTTTTAAACCC
1 CCAAAAATTCTATTTTTATACCC
129388 TAAATTTTCC
Statistics
Matches: 94, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
28 1 0.01
29 48 0.51
30 40 0.43
31 3 0.03
32 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.04, T:0.36
Consensus pattern (29 bp):
CCAAAAATTCTATTTTTATACCCGAACTT
Found at i:129371 original size:59 final size:59
Alignment explanation
Indices: 129247--129382 Score: 154
Period size: 59 Copynumber: 2.3 Consensus size: 59
129237 ATTTTTGACC
* *
129247 CCAAAAATTCCATTTTTACCCTCAAACTTTCAAAAATCCCATTTTTAACCTCGAAACTT
1 CCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCTCGAAACTT
* * *
129306 CCAAAAATTCTATTTTTGATCCC-CGAACTTCCAAAAATCTCATTTTTATTCC-CG-AA-TGT
1 CCAAAAATTCTATTTTT-A-CCCTCAAACTTCCAAAAATCCCATTTTTA-ACCTCGAAACT-T
*
129365 CTAAAAATTCTATTTTTA
1 CCAAAAATTCTATTTTTA
129383 AACCCTAAAT
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
58 2 0.03
59 35 0.52
60 25 0.37
61 5 0.07
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.38
Consensus pattern (59 bp):
CCAAAAATTCTATTTTTACCCTCAAACTTCCAAAAATCCCATTTTTAACCTCGAAACTT
Found at i:140626 original size:27 final size:27
Alignment explanation
Indices: 140595--140649 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
140585 TCAACTAACG
*
140595 ATTGTTTCCTTTGATCCTCTTTTTAAT
1 ATTGTTTCCTTTGATCCTCTTCTTAAT
140622 ATTGTTTCCTTTGATCCTCTTCTTAAT
1 ATTGTTTCCTTTGATCCTCTTCTTAAT
140649 A
1 A
140650 GAATTTTTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.16, C:0.20, G:0.07, T:0.56
Consensus pattern (27 bp):
ATTGTTTCCTTTGATCCTCTTCTTAAT
Found at i:141490 original size:207 final size:207
Alignment explanation
Indices: 141135--141924 Score: 1314
Period size: 207 Copynumber: 3.8 Consensus size: 207
141125 GCGATTATCC
* * *
141135 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGA
1 ACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGA
** * * * * * * *
141200 TGTGAGCAAATTTTCGAATCCTAGCTTCCTGACGAGACACCGAGAA-CTAGGTTGAAGCAATAAA
66 CATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGC-AGGTCGAAGCAATAAA
*
141264 ATGGTTAGCTTCTTGATGAGATACTAAAAAGTGGACCAAATTCGTCTTCCTGATGAGATAACAGA
130 ATGGTTAGCTTCTTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAACAGA
141329 GAAGCGAATTGAA
195 GAAGCGAATTGAA
141342 ACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGA
1 ACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGA
*
141407 CATGAGCAAATCTTCGAACCCCAGCTTACTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
66 CATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
141472 TGGTTAGCTTCTTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAACAGAG
131 TGGTTAGCTTCTTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAACAGAG
141537 AAGCGAATTGAA
196 AAGCGAATTGAA
*
141549 ACAAACAATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGA
1 ACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGA
*
141614 CATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAA
66 CATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
*
141679 TGGTTAGCTTCTTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGTTGAGAT-ACAGAG
131 TGGTTAGCTTCTTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAACAGAG
141743 AAGCGAATTGAA
196 AAGCGAATTGAA
*
141755 ACAAACGATGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGA
1 ACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGA
* * * * *
141820 TATGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGAAGGTCAAAGTAATAAAA
66 CATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
** **
141885 TGGTTAGCTTCCAGATGAGATACTAAGAAGAAGACCAAAT
131 TGGTTAGCTTCTTGATGAGATACTAAGAAGTGGACCAAAT
141925 CAGTAAAACT
Statistics
Matches: 552, Mismatches: 30, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
206 176 0.32
207 375 0.68
208 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (207 bp):
ACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGA
CATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA
TGGTTAGCTTCTTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGATGAGATAACAGAG
AAGCGAATTGAA
Found at i:141912 original size:413 final size:414
Alignment explanation
Indices: 141135--141924 Score: 1316
Period size: 413 Copynumber: 1.9 Consensus size: 414
141125 GCGATTATCC
* *
141135 ACAAACGACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAGTCAAACCCACGCTCGA
1 ACAAACAACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
** * * * * *
141200 TGTGAGCAAATTTTCGAATCCTAGCTTCCTGACGAGACACCGAGAACTAGGTTGAAGCAATAAAA
66 CATGAGCAAATCTTCGAACCCCAGCTTCCTGACGAGACACCGAGAACTAAGTCGAAGCAATAAAA
141265 TGGTTAGCTTCTTGATGAGATACTAAAAAGTGGACCAAATTCGTCTTCCTGATGAGATAACAGAG
131 TGGTTAGCTTCTTGATGAGATACTAAAAAGTGGACCAAATTCGTCTTCCTGATGAGATAACAGAG
*
141330 AAGCGAATTGAAACAAACGATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
196 AAGCGAATTGAAACAAACGATGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
*
141395 ACCCATGCTCGACATGAGCAAATCTTCGAACCCCAGCTTACTGATGAGATACTGAGAAGCAGGTC
261 ACCCATGCTCGACATGAGCAAATCTTCGAACCCCAGCTTACTGATGAGATACTGAGAAGAAGGTC
* ** **
141460 GAAGCAATAAAATGGTTAGCTTCTTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGAT
326 AAAGCAATAAAATGGTTAGCTTCCAGATGAGATACTAAGAAGAAGACCAAATTCGTCTTCCTGAT
141525 GAGATAACAGAGAAGCGAATTGAA
391 GAGATAACAGAGAAGCGAATTGAA
* *
141549 ACAAACAATGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCATGCTCGA
1 ACAAACAACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
* * *
141614 CATGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAGAAGC-AAGTCGAAGCAATAAA
66 CATGAGCAAATCTTCGAACCCCAGCTTCCTGACGAGACACCGAGAA-CTAAGTCGAAGCAATAAA
* *
141678 ATGGTTAGCTTCTTGATGAGATACTAAGAAGTGGACCAAATTCGTCTTCCTGTTGAGAT-ACAGA
130 ATGGTTAGCTTCTTGATGAGATACTAAAAAGTGGACCAAATTCGTCTTCCTGATGAGATAACAGA
141742 GAAGCGAATTGAAACAAACGATGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCA
195 GAAGCGAATTGAAACAAACGATGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCA
*
141807 AACCCATGCTCGATATGAGCAAATCTTCGAACCCCAGCTT-CTTGATGAGATACTGAGAAGAAGG
260 AACCCATGCTCGACATGAGCAAATCTTCGAACCCCAGCTTAC-TGATGAGATACTGAGAAGAAGG
*
141871 TCAAAGTAATAAAATGGTTAGCTTCCAGATGAGATACTAAGAAGAAGACCAAAT
324 TCAAAGCAATAAAATGGTTAGCTTCCAGATGAGATACTAAGAAGAAGACCAAAT
141925 CAGTAAAACT
Statistics
Matches: 349, Mismatches: 25, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
412 1 0.00
413 177 0.51
414 170 0.49
415 1 0.00
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (414 bp):
ACAAACAACGCAGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGCTCGA
CATGAGCAAATCTTCGAACCCCAGCTTCCTGACGAGACACCGAGAACTAAGTCGAAGCAATAAAA
TGGTTAGCTTCTTGATGAGATACTAAAAAGTGGACCAAATTCGTCTTCCTGATGAGATAACAGAG
AAGCGAATTGAAACAAACGATGCAATCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
ACCCATGCTCGACATGAGCAAATCTTCGAACCCCAGCTTACTGATGAGATACTGAGAAGAAGGTC
AAAGCAATAAAATGGTTAGCTTCCAGATGAGATACTAAGAAGAAGACCAAATTCGTCTTCCTGAT
GAGATAACAGAGAAGCGAATTGAA
Found at i:142592 original size:30 final size:29
Alignment explanation
Indices: 142556--142985 Score: 453
Period size: 30 Copynumber: 14.6 Consensus size: 29
142546 CCCTGGATTG
*
142556 TCCAAAAATTCTATTTTTGACCTCGAAACT
1 TCCAAAAATTCCATTTTT-ACCTCGAAACT
* *
142586 TCCAAAAATTCTATTTTTACCTCAAAACT
1 TCCAAAAATTCCATTTTTACCTCGAAACT
* * *
142615 TCC-AAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTT-ACCTCGAAACT
* *
142644 TCCAAAAATTCCATTTTTACCCCTAAACT
1 TCCAAAAATTCCATTTTTACCTCGAAACT
* * * * *
142673 TTCAAAGATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTT-ACCTCGAAACT
* *
142703 TCCAAAAATTCTATTTTTACCCTTG-AACT
1 TCCAAAAATTCCATTTTTA-CCTCGAAACT
* *
142732 TCCAAAAATCCCATTTTTAACC-CTAAAACT
1 TCCAAAAATTCCATTTTT-ACCTC-GAAACT
142762 TCCAAAAATTCCATTTTTACCCCTCG-AACT
1 TCCAAAAATTCCATTTTTA--CCTCGAAACT
*
142792 TCCAAAAATCCCATTTTTGACCTCGAAACT
1 TCCAAAAATTCCATTTTT-ACCTCGAAACT
* *
142822 TCCAAAAATTTCGTTTTTACCTTCG-AACT
1 TCCAAAAATTCCATTTTTACC-TCGAAACT
*
142851 TCC-AAAATTTCATTTTTGACCTCGAAACT
1 TCCAAAAATTCCATTTTT-ACCTCGAAACT
* *
142880 TCCAAAAATTCCATTTTTACCCCCAAACT
1 TCCAAAAATTCCATTTTTACCTCGAAACT
142909 TCC-AAAATTCCCATTTTTAACCTCGAAACT
1 TCCAAAAATT-CCATTTTT-ACCTCGAAACT
*
142939 TCCAAAAATTCCGTTTTTACCCTCG-AACT
1 TCCAAAAATTCCATTTTTA-CCTCGAAACT
*
142968 TCCAAAAATCCCATTTTT
1 TCCAAAAATTCCATTTTT
142986 GTTCTCGAGT
Statistics
Matches: 344, Mismatches: 36, Indels: 41
0.82 0.09 0.10
Matches are distributed among these distances:
28 34 0.10
29 141 0.41
30 159 0.46
31 9 0.03
32 1 0.00
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTACCTCGAAACT
Found at i:142992 original size:29 final size:29
Alignment explanation
Indices: 142556--143045 Score: 399
Period size: 30 Copynumber: 16.6 Consensus size: 29
142546 CCCTGGATTG
*
142556 TCCAAAAATTCTATTTTTGACCTCGAAACT
1 TCCAAAAATTCCATTTTTGACCTCG-AACT
* *
142586 TCCAAAAATTCTATTTTT-ACCTCAAAACT
1 TCCAAAAATTCCATTTTTGACCTC-GAACT
* * *
142615 TCC-AAAATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTTGACCTC-GAACT
* *
142644 TCCAAAAATTCCATTTTT-ACCCCTAAACT
1 TCCAAAAATTCCATTTTTGACCTC-GAACT
* * * * *
142673 TTCAAAGATCCCATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTTGACCTC-GAACT
* *
142703 TCCAAAAATTCTATTTTT-ACCCTTGAACT
1 TCCAAAAATTCCATTTTTGA-CCTCGAACT
* * **
142732 TCCAAAAATCCCATTTTTAACCCTAAAACT
1 TCCAAAAATTCCATTTTTGA-CCTCGAACT
142762 TCCAAAAATTCCATTTTT-ACCCCTCGAACT
1 TCCAAAAATTCCATTTTTGA--CCTCGAACT
*
142792 TCCAAAAATCCCATTTTTGACCTCGAAACT
1 TCCAAAAATTCCATTTTTGACCTCG-AACT
* *
142822 TCCAAAAATTTCGTTTTT-ACCTTCGAACT
1 TCCAAAAATTCCATTTTTGACC-TCGAACT
*
142851 TCC-AAAATTTCATTTTTGACCTCGAAACT
1 TCCAAAAATTCCATTTTTGACCTCG-AACT
* *
142880 TCCAAAAATTCCATTTTT-ACCCCCAAACT
1 TCCAAAAATTCCATTTTTGA-CCTCGAACT
*
142909 TCC-AAAATTCCCATTTTTAACCTCGAAACT
1 TCCAAAAATT-CCATTTTTGACCTCG-AACT
*
142939 TCCAAAAATTCCGTTTTT-ACCCTCGAACT
1 TCCAAAAATTCCATTTTTGA-CCTCGAACT
* ** *
142968 TCCAAAAATCCCATTTTTGTTCTCG-AGT
1 TCCAAAAATTCCATTTTTGACCTCGAACT
* * * *
142996 GTCTAAAAATTCTATTTTTAAACCTCGAATTT
1 -TCCAAAAATTCCATTTTT-GACCTCGAA-CT
*
143028 TCCCAAAATTACCATTTT
1 TCCAAAAATT-CCATTTT
143046 GCCCCTCGAG
Statistics
Matches: 385, Mismatches: 50, Indels: 48
0.80 0.10 0.10
Matches are distributed among these distances:
28 36 0.09
29 156 0.41
30 170 0.44
31 16 0.04
32 7 0.02
ACGTcount: A:0.33, C:0.28, G:0.04, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTCCATTTTTGACCTCGAACT
Found at i:142993 original size:59 final size:59
Alignment explanation
Indices: 142556--142986 Score: 566
Period size: 59 Copynumber: 7.3 Consensus size: 59
142546 CCCTGGATTG
* * * *
142556 TCCAAAAATTCTATTTTTGACCTCGAAACTTCCAAAAATTCTATTTTTA-CCTCAAAACT
1 TCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTC-GAACT
* * *
142615 TCC-AAAATCCCATTTTTGACCCCAAAACTTCCAAAAATTCCATTTTTACCC-CTAAACT
1 TCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTC-GAACT
* * * * * *
142673 TTCAAAGATCCCATTTTTGACCCCAAAACTTCCAAAAATTCTATTTTTACCCTTGAACT
1 TCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACT
* *
142732 TCCAAAAATCCCATTTTTAACC-CTAAAACTTCCAAAAATTCCATTTTTACCCCTCGAACT
1 TCCAAAAATCCCATTTTTGACCTC-GAAACTTCCAAAAATTCCATTTTTA-CCCTCGAACT
* * *
142792 TCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTTCGTTTTTACCTTCGAACT
1 TCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACT
** * *
142851 TCC-AAAATTTCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCCCAAACT
1 TCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACT
* * *
142909 TCCAAAATTCCCATTTTTAACCTCGAAACTTCCAAAAATTCCGTTTTTACCCTCGAACT
1 TCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACT
142968 TCCAAAAATCCCATTTTTG
1 TCCAAAAATCCCATTTTTG
142987 TTCTCGAGTG
Statistics
Matches: 328, Mismatches: 37, Indels: 14
0.87 0.10 0.04
Matches are distributed among these distances:
58 100 0.30
59 175 0.53
60 52 0.16
61 1 0.00
ACGTcount: A:0.33, C:0.29, G:0.04, T:0.34
Consensus pattern (59 bp):
TCCAAAAATCCCATTTTTGACCTCGAAACTTCCAAAAATTCCATTTTTACCCTCGAACT
Done.