Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011431.1 Corchorus capsularis cultivar CVL-1 contig11452, 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: 132585
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1316 original size:457 final size:457
Alignment explanation
Indices: 453--1367 Score: 1785
Period size: 457 Copynumber: 2.0 Consensus size: 457
443 CTACTAGTCA
453 ACCTTTCTCTGATCGGTCCAAAGATCAACACTTTTATTCCATCAACCAGTTCCAGAATAAAGCAT
1 ACCTTTCTCTGATCGGTCCAAAGATCAACACTTTTATTCCATCAACCAGTTCCAGAATAAAGCAT
518 TAAGATTATTATATGCTTGCATGCTTAATTAAATTAAAACCAAACTTACCTACACCTATTTCTGT
66 TAAGATTATTATATGCTTGCATGCTTAATTAAATTAAAACCAAACTTACCTACACCTATTTCTGT
583 TCGGCCTATAGGTTTCAATAAGGTTTGATATCCCATTGAACTAGGACTCCTAAGCTCAATTGTTA
131 TCGGCCTATAGGTTTCAATAAGGTTTGATATCCCATTGAACTAGGACTCCTAAGCTCAATTGTTA
648 CTTTGAATAAAGATTCTAACTATAGCATCCATATTTATCAAGATTAGTAGCGCTCCTAACCAATC
196 CTTTGAATAAAGATTCTAACTATAGCATCCATATTTATCAAGATTAGTAGCGCTCCTAACCAATC
713 AAACATGAACACAAAAGATGAAGTACAGAGATAAGAAACATATTCAAGTAAAAATCAAATTATTA
261 AAACATGAACACAAAAGATGAAGTACAGAGATAAGAAACATATTCAAGTAAAAATCAAATTATTA
778 AGAACAAAAGTCTCCCCATAAATAAAATGTCAAGAGATCAATATGATCCTACATTGGAGAAATAA
326 AGAACAAAAGTCTCCCCATAAATAAAATGTCAAGAGATCAATATGATCCTACATTGGAGAAATAA
* *
843 AAGATTAGCTACTCATTAATTGAGTAGTCATCAAAAGGAAAAAGGAATAGAAAAACCTAGGAAAG
391 AAGATTAACCACTCATTAATTGAGTAGTCATCAAAAGGAAAAAGGAATAGAAAAACCTAGGAAAG
908 AT
456 AT
*
910 ACCTTTCTCTGTTCGGTCCAAAGATCAACACTTTTATTCCATCAACCAGTTCCAGAATAAAGCAT
1 ACCTTTCTCTGATCGGTCCAAAGATCAACACTTTTATTCCATCAACCAGTTCCAGAATAAAGCAT
975 TAAGATTATTATATGCTTGCATGCTTAATTAAATTAAAACCAAACTTACCTACACCTATTTCTGT
66 TAAGATTATTATATGCTTGCATGCTTAATTAAATTAAAACCAAACTTACCTACACCTATTTCTGT
*
1040 TCGGTCTATAGGTTTCAATAAGGTTTGATATCCCATTGAACTAGGACTCCTAAGCTCAATTGTTA
131 TCGGCCTATAGGTTTCAATAAGGTTTGATATCCCATTGAACTAGGACTCCTAAGCTCAATTGTTA
1105 CTTTGAATAAAGATTCTAACTATAGCATCCATATTTATCAAGATTAGTAGCGCTCCTAACCAATC
196 CTTTGAATAAAGATTCTAACTATAGCATCCATATTTATCAAGATTAGTAGCGCTCCTAACCAATC
*
1170 AAACATGAACAGAAAAGATGAAGTACAGAGATAAGAAACATATTCAAGTAAAAATCAAATTATTA
261 AAACATGAACACAAAAGATGAAGTACAGAGATAAGAAACATATTCAAGTAAAAATCAAATTATTA
1235 AGAACAAAAGTCTCCCCATAAATAAAATGTCAAGAGATCAATATGATCCTACATTGGAGAAATAA
326 AGAACAAAAGTCTCCCCATAAATAAAATGTCAAGAGATCAATATGATCCTACATTGGAGAAATAA
1300 AAGATTAACCACTCATTAATTGAGTAGTCATCAAAAGGAAAAAGGAATAGAAAAACCTAGGAAAG
391 AAGATTAACCACTCATTAATTGAGTAGTCATCAAAAGGAAAAAGGAATAGAAAAACCTAGGAAAG
1365 AT
456 AT
1367 A
1 A
1368 GTCTGGCCGG
Statistics
Matches: 453, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
457 453 1.00
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.28
Consensus pattern (457 bp):
ACCTTTCTCTGATCGGTCCAAAGATCAACACTTTTATTCCATCAACCAGTTCCAGAATAAAGCAT
TAAGATTATTATATGCTTGCATGCTTAATTAAATTAAAACCAAACTTACCTACACCTATTTCTGT
TCGGCCTATAGGTTTCAATAAGGTTTGATATCCCATTGAACTAGGACTCCTAAGCTCAATTGTTA
CTTTGAATAAAGATTCTAACTATAGCATCCATATTTATCAAGATTAGTAGCGCTCCTAACCAATC
AAACATGAACACAAAAGATGAAGTACAGAGATAAGAAACATATTCAAGTAAAAATCAAATTATTA
AGAACAAAAGTCTCCCCATAAATAAAATGTCAAGAGATCAATATGATCCTACATTGGAGAAATAA
AAGATTAACCACTCATTAATTGAGTAGTCATCAAAAGGAAAAAGGAATAGAAAAACCTAGGAAAG
AT
Found at i:4208 original size:20 final size:19
Alignment explanation
Indices: 4166--4209 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4156 AATTGGATCT
* *
4166 TCCAAGATGATTTTCTCGA
1 TCCAACATGATTCTCTCGA
*
4185 TCCAACATGATTGCTCTCGC
1 TCCAACATGATT-CTCTCGA
4205 TCCAA
1 TCCAA
4210 GAATGGTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.32
Consensus pattern (19 bp):
TCCAACATGATTCTCTCGA
Found at i:15085 original size:26 final size:24
Alignment explanation
Indices: 15032--15085 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
15022 AAAATTAGTC
**
15032 TTTCAAAATAAAAACTAAAAAGGT
1 TTTCAAAATAAAAACTAAAAAGAA
15056 TTTCAAAATTCAAAAA-TAAGAAAGAA
1 TTTCAAAA-T-AAAAACTAA-AAAGAA
15082 TTTC
1 TTTC
15086 CTTCAAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
24 8 0.32
25 4 0.16
26 13 0.52
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (24 bp):
TTTCAAAATAAAAACTAAAAAGAA
Found at i:21525 original size:53 final size:53
Alignment explanation
Indices: 21459--21560 Score: 179
Period size: 53 Copynumber: 1.9 Consensus size: 53
21449 TGGATCTCTA
21459 TATATAAACCACAATAGATC-CTCACATCCTCATGATGTGGGATCTTGGGGCGT
1 TATATAAACCACAATAGATCAC-CACATCCTCATGATGTGGGATCTTGGGGCGT
*
21512 TATATAAACCACAATAGATCACCACATCCTCCTGATGTGGGATCTTGGG
1 TATATAAACCACAATAGATCACCACATCCTCATGATGTGGGATCTTGGG
21561 ACGTCACAGT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
53 46 0.98
54 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (53 bp):
TATATAAACCACAATAGATCACCACATCCTCATGATGTGGGATCTTGGGGCGT
Found at i:28056 original size:37 final size:37
Alignment explanation
Indices: 27878--28044 Score: 277
Period size: 37 Copynumber: 4.5 Consensus size: 37
27868 TTGACTTCAA
* *
27878 TTAATTACCCTGAATTAAG--CCTGTTATTGACTCCAC
1 TTAATTACCCTGAATTAAGTCCCT-TTATTGACGCTAC
27914 TTAATTACCCAT-AATTAAGTCCCTTTATTGACGCTAC
1 TTAATTACCC-TGAATTAAGTCCCTTTATTGACGCTAC
27951 TTAATTACCCTGAATTAAGTCCCTTTATTGACGCTAC
1 TTAATTACCCTGAATTAAGTCCCTTTATTGACGCTAC
27988 TTAATTACCCTGAATTAAGTCCCTTTATTGACGCTAC
1 TTAATTACCCTGAATTAAGTCCCTTTATTGACGCTAC
28025 TTAATTACCCTGAATTAAGT
1 TTAATTACCCTGAATTAAGT
28045 TCCTAACTTG
Statistics
Matches: 125, Mismatches: 2, Indels: 7
0.93 0.01 0.05
Matches are distributed among these distances:
36 18 0.14
37 104 0.83
38 3 0.02
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (37 bp):
TTAATTACCCTGAATTAAGTCCCTTTATTGACGCTAC
Found at i:28071 original size:32 final size:32
Alignment explanation
Indices: 28023--28099 Score: 100
Period size: 32 Copynumber: 2.4 Consensus size: 32
28013 TATTGACGCT
* *
28023 ACTTAATTACCCTGAATTAAGTTCCTAACTTG
1 ACTTAATTACCTTGAATTAAGTCCCTAACTTG
* *
28055 ACTTAATTGCCTTGAATTAAGTCCCTGACTTG
1 ACTTAATTACCTTGAATTAAGTCCCTAACTTG
* *
28087 ACATAATTTCCTT
1 ACTTAATTACCTT
28100 CCTTGAAATT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.29, C:0.22, G:0.10, T:0.39
Consensus pattern (32 bp):
ACTTAATTACCTTGAATTAAGTCCCTAACTTG
Found at i:28131 original size:37 final size:37
Alignment explanation
Indices: 28064--28256 Score: 204
Period size: 37 Copynumber: 5.4 Consensus size: 37
28054 GACTTAATTG
* * *
28064 CCTTG-AATTAAGTCCCTGACT-TGACATAATTTCCTT
1 CCTTGAAATTAAGTCCTTAACTCT-ACTTAATTTCCTT
* *
28100 CCTTGAAATTAAATCCTTAACTCTACTTAATTCCCTT
1 CCTTGAAATTAAGTCCTTAACTCTACTTAATTTCCTT
* *
28137 CCTTGGAATCAAGT-C----CTCTACTTAATTTCCTT
1 CCTTGAAATTAAGTCCTTAACTCTACTTAATTTCCTT
* ** *
28169 CCTTGAAATTAAGCCCTTTCCTCTACTTAATTCCCCTT
1 CCTTGAAATTAAGTCCTTAACTCTACTTAATT-TCCTT
*
28207 -CTTGGAATTAAGTCCTTAACTCTACTTAATTTCCTT
1 CCTTGAAATTAAGTCCTTAACTCTACTTAATTTCCTT
28243 CCTTGAAATTAAGT
1 CCTTGAAATTAAGT
28257 TCTTTGTCTG
Statistics
Matches: 129, Mismatches: 19, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
32 27 0.21
33 1 0.01
36 10 0.08
37 86 0.67
38 5 0.04
ACGTcount: A:0.25, C:0.26, G:0.08, T:0.40
Consensus pattern (37 bp):
CCTTGAAATTAAGTCCTTAACTCTACTTAATTTCCTT
Found at i:28163 original size:69 final size:71
Alignment explanation
Indices: 28090--28254 Score: 228
Period size: 69 Copynumber: 2.3 Consensus size: 71
28080 TGACTTGACA
*
28090 TAATTTCCTTCCTTGAAATTAAATCCTTAACTCTACTTAATT-CCCTTCCTTGGAATCAAGT-C-
1 TAATTTCCTTCCTTGAAATTAAACCCTTAACTCTACTTAATTCCCCTT-CTTGGAATCAAGTCCA
28152 CTCTACT
65 CTCTACT
* ** *
28159 TAATTTCCTTCCTTGAAATTAAGCCCTTTCCTCTACTTAATTCCCCTTCTTGGAATTAAGTCCTT
1 TAATTTCCTTCCTTGAAATTAAACCCTTAACTCTACTTAATTCCCCTTCTTGGAATCAAGTCC--
28224 AACTCTACT
64 -ACTCTACT
28233 TAATTTCCTTCCTTGAAATTAA
1 TAATTTCCTTCCTTGAAATTAA
28255 GTTCTTTGTC
Statistics
Matches: 85, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
69 50 0.59
70 6 0.07
74 29 0.34
ACGTcount: A:0.25, C:0.27, G:0.06, T:0.42
Consensus pattern (71 bp):
TAATTTCCTTCCTTGAAATTAAACCCTTAACTCTACTTAATTCCCCTTCTTGGAATCAAGTCCAC
TCTACT
Found at i:28179 original size:106 final size:105
Alignment explanation
Indices: 28064--28256 Score: 248
Period size: 106 Copynumber: 1.8 Consensus size: 105
28054 GACTTAATTG
*
28064 CCTTGAATTAAGTCCC-TGACT-TGACATAATT-TCCTTCCTTGAAATTAAATCCTTAACTCTAC
1 CCTTGAATTAAG-CCCTTGACTCT-ACATAATTCCCCTT-CTTGAAATTAAATCCTTAACTCTAC
*
28126 TTAATTCCCTTCCTTGGAATCAAGTCCTCTACTTAATTTCCTT
63 TTAATTCCCTTCCTTGAAATCAAGTCCTCTACTTAATTTCCTT
** * * *
28169 CCTTGAAATTAAGCCCTTTCCTCTACTTAATTCCCCTTCTTGGAATTAAGTCCTTAACTCTACTT
1 CCTTG-AATTAAGCCCTTGACTCTACATAATTCCCCTTCTTGAAATTAAATCCTTAACTCTACTT
* *
28234 AATTTCCTTCCTTGAAATTAAGT
65 AATTCCCTTCCTTGAAATCAAGT
28257 TCTTTGTCTG
Statistics
Matches: 75, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
105 8 0.11
106 62 0.83
107 5 0.07
ACGTcount: A:0.25, C:0.26, G:0.08, T:0.40
Consensus pattern (105 bp):
CCTTGAATTAAGCCCTTGACTCTACATAATTCCCCTTCTTGAAATTAAATCCTTAACTCTACTTA
ATTCCCTTCCTTGAAATCAAGTCCTCTACTTAATTTCCTT
Found at i:28381 original size:36 final size:37
Alignment explanation
Indices: 28288--28432 Score: 93
Period size: 36 Copynumber: 3.9 Consensus size: 37
28278 TCATCTTTGG
* **
28288 ATTAAGTCTCTGC-TGACTTTACTTAATTCTTGTGAA
1 ATTAAGTCTCTGCTTGTCTTTACTTAATTCTCCTGAA
* **
28324 ATTAAGTCTTTGCTAAT-TTTACTTAATTAC-CCTG-A
1 ATTAAGTCTCTGCTTGTCTTTACTTAATT-CTCCTGAA
* *
28359 ATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTTGAA
1 ATTAAGTCTCTGCTTGTCTTTACTTAA-TT-C-TCC-TGAA
* * * * *
28400 ATTTACTCTGTGCTTATCTTTACCTAA-TCTCCT
1 ATTAAGTCTCTGCTTGTCTTTACTTAATTCTCCT
28433 TCCTTGGATT
Statistics
Matches: 87, Mismatches: 14, Indels: 16
0.74 0.12 0.14
Matches are distributed among these distances:
35 15 0.17
36 34 0.39
37 7 0.08
38 1 0.01
39 3 0.03
40 2 0.02
41 25 0.29
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (37 bp):
ATTAAGTCTCTGCTTGTCTTTACTTAATTCTCCTGAA
Found at i:28538 original size:37 final size:37
Alignment explanation
Indices: 28440--28629 Score: 235
Period size: 37 Copynumber: 5.2 Consensus size: 37
28430 CCTTCCTTGG
* * *
28440 ATTAAGT-TCTTTATTGACTCCACTTAATTACCCTGA
1 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
* * * *
28476 ATTAAG--CATGTTATTGACTCCACTTAATTATCCAT-A
1 ATTAAGTCCCT-TTATTGACGCTACTTAATTA-CCCTGA
*
28512 ATTAAGTCCCTTTATTAACGCTACTTAATTACCCTGA
1 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
* *
28549 ATTAAGTACCTTTATTGACGCTACTTAATTACCCTAA
1 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
*
28586 ATTAAGTCTCTTTATTGACGCTACTTAATTACCCTGA
1 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
28623 ATTAAGT
1 ATTAAGT
28630 TCCTAACTTG
Statistics
Matches: 135, Mismatches: 14, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
35 1 0.01
36 36 0.27
37 96 0.71
38 2 0.01
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (37 bp):
ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
Found at i:28599 original size:74 final size:74
Alignment explanation
Indices: 28440--28629 Score: 262
Period size: 74 Copynumber: 2.6 Consensus size: 74
28430 CCTTCCTTGG
* * *
28440 ATTAAGT-TCTTTATTGACTCCACTTAATTACCCTGAATTAAG-CATGTTATTGACTCCACTTAA
1 ATTAAGTCTCTTTATTGACGCTACTTAATTACCCTGAATTAAGTCATGTTATTGACGCCACTTAA
*
28503 TTATCCATA
66 TTACCCATA
* * * *
28512 ATTAAGTCCCTTTATTAACGCTACTTAATTACCCTGAATTAAGTACCT-TTATTGACGCTACTTA
1 ATTAAGTCTCTTTATTGACGCTACTTAATTACCCTGAATTAAGT-CATGTTATTGACGCCACTTA
28576 ATTACCC-TAA
65 ATTACCCAT-A
28586 ATTAAGTCTCTTTATTGACGCTACTTAATTACCCTGAATTAAGT
1 ATTAAGTCTCTTTATTGACGCTACTTAATTACCCTGAATTAAGT
28630 TCCTAACTTG
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
72 7 0.07
73 32 0.31
74 63 0.61
75 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.09, T:0.39
Consensus pattern (74 bp):
ATTAAGTCTCTTTATTGACGCTACTTAATTACCCTGAATTAAGTCATGTTATTGACGCCACTTAA
TTACCCATA
Found at i:28653 original size:32 final size:32
Alignment explanation
Indices: 28608--28679 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
28598 TATTGACGCT
*
28608 ACTTAATTACCCTGAATTAAGTTCCTAACTTG
1 ACTTAATTACCCTGAATTAAGTCCCTAACTTG
* * *
28640 CCTTAATTGCCCTGAATTAAGTCCCTGACTTG
1 ACTTAATTACCCTGAATTAAGTCCCTAACTTG
28672 ACTTAATT
1 ACTTAATT
28680 TCCTTCCTTG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.28, C:0.24, G:0.11, T:0.38
Consensus pattern (32 bp):
ACTTAATTACCCTGAATTAAGTCCCTAACTTG
Found at i:28706 original size:69 final size:70
Alignment explanation
Indices: 28653--28845 Score: 248
Period size: 69 Copynumber: 2.7 Consensus size: 70
28643 TAATTGCCCT
28653 GAATTAAGTCCCTGACTTGACTTAATTTCCTTCCTTGAAATTAAGTCTTTAACTCTACTTAATTC
1 GAATTAAGTCCCT-ACTT-ACTTAATTTCCTTCCTTGAAATTAAGTCTTTAACTCTACTTAATTC
28718 CCTTCCTTG
64 CC--CCTTG
* * **
28727 GAATCAAGT-CCT-C-TACTTAATTTCCTTCCTTGAAATTAAGCCTTTTCCTCTACTTAATTCCC
1 GAATTAAGTCCCTACTTACTTAATTTCCTTCCTTGAAATTAAGTCTTTAACTCTACTTAATTCCC
28789 CTTCTTG
66 C--CTTG
*
28796 GAATTAAGTCCTTAACTCTACTTAATTTCCTTCCTTGAAATTAAGTCTTT
1 GAATTAAGTCCCT-ACT-TACTTAATTTCCTTCCTTGAAATTAAGTCTTT
28846 GTCTGATCTC
Statistics
Matches: 105, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
67 1 0.01
69 57 0.54
70 3 0.03
71 1 0.01
72 1 0.01
73 3 0.03
74 39 0.37
ACGTcount: A:0.24, C:0.25, G:0.08, T:0.42
Consensus pattern (70 bp):
GAATTAAGTCCCTACTTACTTAATTTCCTTCCTTGAAATTAAGTCTTTAACTCTACTTAATTCCC
CCTTG
Found at i:28713 original size:37 final size:37
Alignment explanation
Indices: 28672--28845 Score: 216
Period size: 37 Copynumber: 4.8 Consensus size: 37
28662 CCCTGACTTG
28672 ACTTAATTTCCTTCCTTGAAATTAAGTCTTTAACTCT
1 ACTTAATTTCCTTCCTTGAAATTAAGTCTTTAACTCT
* * *
28709 ACTTAATTCCCTTCCTTGGAATCAAGTC-----CTCT
1 ACTTAATTTCCTTCCTTGAAATTAAGTCTTTAACTCT
* **
28741 ACTTAATTTCCTTCCTTGAAATTAAGCCTTTTCCTCT
1 ACTTAATTTCCTTCCTTGAAATTAAGTCTTTAACTCT
* * *
28778 ACTTAATTCCCCTT-CTTGGAATTAAGTCCTTAACTCT
1 ACTTAATT-TCCTTCCTTGAAATTAAGTCTTTAACTCT
28815 ACTTAATTTCCTTCCTTGAAATTAAGTCTTT
1 ACTTAATTTCCTTCCTTGAAATTAAGTCTTT
28846 GTCTGATCTC
Statistics
Matches: 114, Mismatches: 16, Indels: 14
0.79 0.11 0.10
Matches are distributed among these distances:
32 28 0.25
36 4 0.04
37 78 0.68
38 4 0.04
ACGTcount: A:0.24, C:0.25, G:0.07, T:0.44
Consensus pattern (37 bp):
ACTTAATTTCCTTCCTTGAAATTAAGTCTTTAACTCT
Found at i:28967 original size:585 final size:584
Alignment explanation
Indices: 27835--29033 Score: 2159
Period size: 585 Copynumber: 2.0 Consensus size: 584
27825 CTTTTATTGT
* * * * *
27835 TTTACTTAATCT-CTTTTTGGATTAAATTCTTTATTGACTTCAATTAATTACCCTGAATTAAGCC
1 TTTACCTAATCTCCTTCTTGGATTAAGTTCTTTATTGACTCCAATTAATTACCCTGAATTAAGCA
*
27899 TGTTATTGACTCCACTTAATTACCCATAATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGA
66 TGTTATTGACTCCACTTAATTACCCATAATTAAGTCCCTTTATTAACGCTACTTAATTACCCTGA
* *
27964 ATTAAGTCCCTTTATTGACGCTACTTAATTACCCTGAATTAAGTCCCTTTATTGACGCTACTTAA
131 ATTAAGTACCTTTATTGACGCTACTTAATTACCCTAAATTAAGTCCCTTTATTGACGCTACTTAA
*
28029 TTACCCTGAATTAAGTTCCTAACTTGACTTAATTGCCTTGAATTAAGTCCCTGACTTGACATAAT
196 TTACCCTGAATTAAGTTCCTAACTTGACTTAATTGCCCTGAATTAAGTCCCTGACTTGACATAAT
28094 TTCCTTCCTTGAAATTAAATCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTCCTCTACT
261 TTCCTTCCTTGAAATTAAATCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTCCTCTACT
28159 TAATTTCCTTCCTTGAAATTAAGCCCTTTCCTCTACTTAATTCCCCTTCTTGGAATTAAGTCCTT
326 TAATTTCCTTCCTTGAAATTAAGCCCTTTCCTCTACTTAATTCCCCTTCTTGGAATTAAGTCCTT
28224 AACTCTACTTAATTTCCTTCCTTGAAATTAAGTTCTTTGTCTGATCTCACTTAATCATCTTTGGA
391 AACTCTACTTAATTTCCTTCCTTGAAATTAAGTTCTTTGTCTGATCTCACTTAATCATCTTTGGA
28289 TTAAGTCTCTGCTGACTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTAC
456 TTAAGTCTCTGCTGACTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTAC
*
28354 CCTGAATTAAGTCTGTGCTTGTCTTTACCTAATTTCCTTCCTTGAAATTTACTCTGTGCTTATC
521 CCTGAATTAAGTCTGTGCTTGCCTTTACCTAATTTCCTTCCTTGAAATTTACTCTGTGCTTATC
*
28418 TTTACCTAATCTCCTTCCTTGGATTAAGTTCTTTATTGACTCCACTTAATTACCCTGAATTAAGC
1 TTTACCTAATCTCCTT-CTTGGATTAAGTTCTTTATTGACTCCAATTAATTACCCTGAATTAAGC
*
28483 ATGTTATTGACTCCACTTAATTATCCATAATTAAGTCCCTTTATTAACGCTACTTAATTACCCTG
65 ATGTTATTGACTCCACTTAATTACCCATAATTAAGTCCCTTTATTAACGCTACTTAATTACCCTG
*
28548 AATTAAGTACCTTTATTGACGCTACTTAATTACCCTAAATTAAGTCTCTTTATTGACGCTACTTA
130 AATTAAGTACCTTTATTGACGCTACTTAATTACCCTAAATTAAGTCCCTTTATTGACGCTACTTA
* *
28613 ATTACCCTGAATTAAGTTCCTAACTTGCCTTAATTGCCCTGAATTAAGTCCCTGACTTGACTTAA
195 ATTACCCTGAATTAAGTTCCTAACTTGACTTAATTGCCCTGAATTAAGTCCCTGACTTGACATAA
* *
28678 TTTCCTTCCTTGAAATTAAGTCTTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTCCTCTAC
260 TTTCCTTCCTTGAAATTAAATCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTCCTCTAC
*
28743 TTAATTTCCTTCCTTGAAATTAAGCCTTTTCCTCTACTTAATTCCCCTTCTTGGAATTAAGTCCT
325 TTAATTTCCTTCCTTGAAATTAAGCCCTTTCCTCTACTTAATTCCCCTTCTTGGAATTAAGTCCT
28808 TAACTCTACTTAATTTCCTTCCTTGAAATTAAG-TCTTTGTCTGATCTCACTTAATCATCTTTGG
390 TAACTCTACTTAATTTCCTTCCTTGAAATTAAGTTCTTTGTCTGATCTCACTTAATCATCTTTGG
28872 ATTAAGTCTCTGCTGACTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTA
455 ATTAAGTCTCTGCTGACTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTA
* *
28937 CCCTGAATTGAGTCTGTGCTTTGCCTTTACCTAATTTCCTTCCTTGAAATTTAGTCTGTGCTTAT
520 CCCTGAATTAAGTCTGTGC-TTGCCTTTACCTAATTTCCTTCCTTGAAATTTACTCTGTGCTTAT
29002 C
584 C
*
29003 TTTACCTAATCTCCTTTCTTGAAATTAAGTT
1 TTTACCTAATCTCC-TTCTTG-GATTAAGTT
29034 TGTGATTACT
Statistics
Matches: 590, Mismatches: 21, Indels: 7
0.95 0.03 0.01
Matches are distributed among these distances:
583 11 0.02
584 117 0.20
585 452 0.77
586 10 0.02
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.42
Consensus pattern (584 bp):
TTTACCTAATCTCCTTCTTGGATTAAGTTCTTTATTGACTCCAATTAATTACCCTGAATTAAGCA
TGTTATTGACTCCACTTAATTACCCATAATTAAGTCCCTTTATTAACGCTACTTAATTACCCTGA
ATTAAGTACCTTTATTGACGCTACTTAATTACCCTAAATTAAGTCCCTTTATTGACGCTACTTAA
TTACCCTGAATTAAGTTCCTAACTTGACTTAATTGCCCTGAATTAAGTCCCTGACTTGACATAAT
TTCCTTCCTTGAAATTAAATCCTTAACTCTACTTAATTCCCTTCCTTGGAATCAAGTCCTCTACT
TAATTTCCTTCCTTGAAATTAAGCCCTTTCCTCTACTTAATTCCCCTTCTTGGAATTAAGTCCTT
AACTCTACTTAATTTCCTTCCTTGAAATTAAGTTCTTTGTCTGATCTCACTTAATCATCTTTGGA
TTAAGTCTCTGCTGACTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTAC
CCTGAATTAAGTCTGTGCTTGCCTTTACCTAATTTCCTTCCTTGAAATTTACTCTGTGCTTATC
Found at i:29012 original size:41 final size:41
Alignment explanation
Indices: 28942--29193 Score: 357
Period size: 41 Copynumber: 6.1 Consensus size: 41
28932 AATTACCCTG
* *
28942 AATTGAGTCTGTGCTTTGCCTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTT-ACTTTACCTAATTTCCTTCCTTGA
* * *
28984 AATTTAGTCTGTGC-TTATCTTTACCTAATCTCCTTTCTTGA
1 AATTAAGTCTGTGCTTTA-CTTTACCTAATTTCCTTCCTTGA
* *
29025 AATTAAGTTTGTG-ATTACTTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTTAC-TTTACCTAATTTCCTTCCTTGA
*
29066 AATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTCA
1 AATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTGA
29107 AATTAAGTCTGTGC-TTACTTTTACCTAATTTCCTTCCTTGA
1 AATTAAGTCTGTGCTTTAC-TTTACCTAATTTCCTTCCTTGA
* *
29148 AATTAAGTCTGGGCTTTACTTTACCTAATTTCCTGCCTTGA
1 AATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTGA
29189 AATTA
1 AATTA
29194 GTCCTTTAAC
Statistics
Matches: 190, Mismatches: 14, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
40 5 0.03
41 164 0.86
42 21 0.11
ACGTcount: A:0.22, C:0.21, G:0.11, T:0.46
Consensus pattern (41 bp):
AATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTGA
Found at i:29210 original size:82 final size:81
Alignment explanation
Indices: 28962--29221 Score: 346
Period size: 82 Copynumber: 3.2 Consensus size: 81
28952 GTGCTTTGCC
* * *
28962 TTTACCTAATTTCCTTCCTTGAAATTTAGTCTGTGC-TTATCTTTACCTAATCTCCTTTCTTGAA
1 TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTA-CTTTACCTAATTTCCTTCCTTGAA
*
29026 ATTAAGT-TTGTGATTACT
65 ATTAAGTCTT-T-ACTACT
*
29044 TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTCAAA
1 TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTGAAA
* *
29109 TTAAGTCTGTGCTTACT
66 TTAAGTCTTTAC-TACT
* *
29126 TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGGGCTTTACTTTACCTAATTTCCTGCCTTGAAA
1 TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTGAAA
*
29191 TT-AGTCCTTTAACTGCT
66 TTAAGT-CTTT-ACTACT
*
29208 TTTACTTAATTTCC
1 TTTACCTAATTTCC
29222 CTGAATTAAG
Statistics
Matches: 159, Mismatches: 14, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
81 3 0.02
82 151 0.95
83 5 0.03
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.47
Consensus pattern (81 bp):
TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTTACTTTACCTAATTTCCTTCCTTGAAA
TTAAGTCTTTACTACT
Found at i:29212 original size:41 final size:39
Alignment explanation
Indices: 28962--29221 Score: 243
Period size: 41 Copynumber: 6.4 Consensus size: 39
28952 GTGCTTTGCC
* * *
28962 TTTACCTAATTTCCTTCCTTGAAATTTAGTCTGTGCTTAT
1 TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTAC-TCT
* * * *
29002 CTTTACCTAATCTCCTTTCTTGAAATTAAGTTTGTGATTACT
1 -TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGT-ACT-CT
* *
29044 TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTGCTTT
1 TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTACTCT
* *
29083 ACTTTACCTAATTTCCTTCCTTCAAATTAAGTCTGTGCTTACT
1 --TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTAC-T-CT
** *
29126 TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGGGCTTT
1 TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTACTCT
* *
29165 ACTTTACCTAATTTCCTGCCTTGAAATT-AGTCCTTTAACTGCT
1 --TTTACCTAATTTCCTTCCTTGAAATTAAGT-CTGT-ACT-CT
*
29208 TTTACTTAATTTCC
1 TTTACCTAATTTCC
29222 CTGAATTAAG
Statistics
Matches: 184, Mismatches: 24, Indels: 22
0.80 0.10 0.10
Matches are distributed among these distances:
39 2 0.01
40 5 0.03
41 171 0.93
42 4 0.02
43 2 0.01
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.47
Consensus pattern (39 bp):
TTTACCTAATTTCCTTCCTTGAAATTAAGTCTGTACTCT
Found at i:29253 original size:37 final size:36
Alignment explanation
Indices: 29189--29303 Score: 151
Period size: 37 Copynumber: 3.1 Consensus size: 36
29179 CCTGCCTTGA
29189 AATT-AGTCCTTTAACTGCTTTTACTTAATTTCCCTG
1 AATTAAGTCCTTTAACTG-TTTTACTTAATTTCCCTG
* * *
29225 AATTAAGTCCTTTGACTGTGTTTTCTTAATTTCCCAG
1 AATTAAGTCCTTTAACTGT-TTTACTTAATTTCCCTG
* *
29262 AATTAAGCCCTTTAACTGTCTTTACTTAATTGCCCTG
1 AATTAAGTCCTTTAACTGT-TTTACTTAATTTCCCTG
29299 AATTA
1 AATTA
29304 CTTAATTACC
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
36 5 0.07
37 63 0.93
ACGTcount: A:0.24, C:0.21, G:0.10, T:0.44
Consensus pattern (36 bp):
AATTAAGTCCTTTAACTGTTTTACTTAATTTCCCTG
Found at i:29306 original size:18 final size:18
Alignment explanation
Indices: 29283--29321 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
29273 TTAACTGTCT
* *
29283 TTACTTAATTGCCCTGAA
1 TTACTTAATTACCCAGAA
29301 TTACTTAATTACCCAGAA
1 TTACTTAATTACCCAGAA
29319 TTA
1 TTA
29322 AGTCCTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (18 bp):
TTACTTAATTACCCAGAA
Found at i:29333 original size:55 final size:55
Alignment explanation
Indices: 29249--29358 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 55
29239 ACTGTGTTTT
*
29249 CTTAATTTCCCAGAATTAAGCCCTTTAACTG-TCTTTACTTAATTGCCCTGAATTA
1 CTTAATTACCCAGAATTAAGCCCTTTAACTGCT-TTTACTTAATTGCCCTGAATTA
* *
29304 CTTAATTACCCAGAATTAAGTCCTTTAACTGCTTTTACTTAATTTCCCTGAATTA
1 CTTAATTACCCAGAATTAAGCCCTTTAACTGCTTTTACTTAATTGCCCTGAATTA
29359 AGTTCTCTGA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
55 50 0.98
56 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (55 bp):
CTTAATTACCCAGAATTAAGCCCTTTAACTGCTTTTACTTAATTGCCCTGAATTA
Found at i:29357 original size:37 final size:37
Alignment explanation
Indices: 29301--29700 Score: 522
Period size: 37 Copynumber: 10.8 Consensus size: 37
29291 TTGCCCTGAA
* * *
29301 TTACTTAATTACCCAGAATTAAGTCCTTTAACTGCT-T
1 TTACTTAATTTCCCTGAATTAAGTTCTTTAACTG-TGT
* *
29338 TTACTTAATTTCCCTGAATTAAGTTCTCTGACTGTGT
1 TTACTTAATTTCCCTGAATTAAGTTCTTTAACTGTGT
* * *
29375 TTACTTAATTACCCTGAATTAAGTTCTCTGACTGTGT
1 TTACTTAATTTCCCTGAATTAAGTTCTTTAACTGTGT
*
29412 TTACTTAATTTCCCTGAATTAAGTTCTCTAACTGTGT
1 TTACTTAATTTCCCTGAATTAAGTTCTTTAACTGTGT
*
29449 TTACTTAATTACCCTGAATTAAGTTCTTTAACTGTGT
1 TTACTTAATTTCCCTGAATTAAGTTCTTTAACTGTGT
* * *
29486 TTAATTAATTTCCATGAATTAAGTTCTTTAATTGTGT
1 TTACTTAATTTCCCTGAATTAAGTTCTTTAACTGTGT
*
29523 TTGCTTAATTTCCCTGAATTAAGTTCTTTAACTGCT-T
1 TTACTTAATTTCCCTGAATTAAGTTCTTTAACTG-TGT
* *
29560 TTACTTAATTGCCCTTAATTAAGTTCTTTAACTGCT-T
1 TTACTTAATTTCCCTGAATTAAGTTCTTTAACTG-TGT
* **
29597 TTACTTAATTTCCCTGAGTTAAGTTCTTTAACAACT-T
1 TTACTTAATTTCCCTGAATTAAGTTCTTTAAC-TGTGT
* *
29634 TTACTTAATTTCCCTGAGTTAAGTTCTTTAATTGCT-T
1 TTACTTAATTTCCCTGAATTAAGTTCTTTAACTG-TGT
*
29671 TTACTTAATTTCCCTGAGTTAAGTTCTTTA
1 TTACTTAATTTCCCTGAATTAAGTTCTTTA
29701 CTGATTACCC
Statistics
Matches: 330, Mismatches: 29, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
36 1 0.00
37 328 0.99
38 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (37 bp):
TTACTTAATTTCCCTGAATTAAGTTCTTTAACTGTGT
Found at i:29372 original size:92 final size:92
Alignment explanation
Indices: 29209--29395 Score: 259
Period size: 92 Copynumber: 2.0 Consensus size: 92
29199 TTAACTGCTT
* * * * *
29209 TTACTTAATTTCCCTGAATTAAGTCCTTTGACTGTGTTTTCTTAATTTCCCAGAATTAAGCCCTT
1 TTACTTAATTACCCAGAATTAAGTCCTTTAACTGTGTTTACTTAATTTCCCAGAATTAAGCCCTC
*
29274 TAACTGTCTTTACTTAATTGCCCTGAA
66 TAACTGTCTTTACTTAATTACCCTGAA
* **
29301 TTACTTAATTACCCAGAATTAAGTCCTTTAACTGCT-TTTACTTAATTTCCCTGAATTAAGTTCT
1 TTACTTAATTACCCAGAATTAAGTCCTTTAACTG-TGTTTACTTAATTTCCCAGAATTAAGCCCT
* *
29365 CTGACTGTGTTTACTTAATTACCCTGAA
65 CTAACTGTCTTTACTTAATTACCCTGAA
29393 TTA
1 TTA
29396 AGTTCTCTGA
Statistics
Matches: 83, Mismatches: 11, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
92 82 0.99
93 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (92 bp):
TTACTTAATTACCCAGAATTAAGTCCTTTAACTGTGTTTACTTAATTTCCCAGAATTAAGCCCTC
TAACTGTCTTTACTTAATTACCCTGAA
Found at i:29427 original size:129 final size:128
Alignment explanation
Indices: 29189--29432 Score: 380
Period size: 129 Copynumber: 1.9 Consensus size: 128
29179 CCTGCCTTGA
* *
29189 AATTAGTCCTTTAACTGCTTTTACTTAATTTCCCTGAATTAAGTCCTTTGACTGTGTTTTCTTAA
1 AATTAGTCCTTTAACTGCTTTTACTTAATTTCCCTGAATTAAGTCCTCTGACTGTGTTTACTTAA
* *
29254 TTTCCCAGAATTAAGCCCTTTAACTGTCTTTACTTAATTGCCCTGAATTACTTAATTACCCAG
66 TTACCCAGAATTAAGCCCTCTAACTGTCTTTACTTAATTGCCCTGAATTACTTAATTACCCAG
*
29317 AATTAAGTCCTTTAACTGCTTTTACTTAATTTCCCTGAATTAAGTTCTCTGACTGTGTTTACTTA
1 AATT-AGTCCTTTAACTGCTTTTACTTAATTTCCCTGAATTAAGTCCTCTGACTGTGTTTACTTA
* ** * * *
29382 ATTACCCTGAATTAAGTTCTCTGACTGTGTTTACTTAATTTCCCTGAATTA
65 ATTACCCAGAATTAAGCCCTCTAACTGTCTTTACTTAATTGCCCTGAATTA
29433 AGTTCTCTAA
Statistics
Matches: 104, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
128 4 0.04
129 100 0.96
ACGTcount: A:0.25, C:0.20, G:0.11, T:0.44
Consensus pattern (128 bp):
AATTAGTCCTTTAACTGCTTTTACTTAATTTCCCTGAATTAAGTCCTCTGACTGTGTTTACTTAA
TTACCCAGAATTAAGCCCTCTAACTGTCTTTACTTAATTGCCCTGAATTACTTAATTACCCAG
Found at i:29834 original size:41 final size:42
Alignment explanation
Indices: 29714--29843 Score: 201
Period size: 43 Copynumber: 3.0 Consensus size: 42
29704 ATTACCCTGA
29714 ATTTTGACTGACTATGTTTACTTTTCTTAATTACCCTGAATTAAG
1 ATTTTGACTGAC--TG-TTACTTTTCTTAATTACCCTGAATTAAG
29759 ATTTTGACTGACTGGTTACTTTTCTTAATTACCCTGAATTAAG
1 ATTTTGACTGACT-GTTACTTTTCTTAATTACCCTGAATTAAG
29802 ATTTTGACTGTACT-TT-CTTTTCTTAATTACCCTGAATTAAG
1 ATTTTGACTG-ACTGTTACTTTTCTTAATTACCCTGAATTAAG
29843 A
1 A
29844 CTTTACTCTT
Statistics
Matches: 83, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
41 26 0.31
42 2 0.02
43 39 0.47
44 4 0.05
45 12 0.14
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (42 bp):
ATTTTGACTGACTGTTACTTTTCTTAATTACCCTGAATTAAG
Found at i:29856 original size:31 final size:31
Alignment explanation
Indices: 29813--30002 Score: 84
Period size: 31 Copynumber: 5.6 Consensus size: 31
29803 TTTTGACTGT
*
29813 ACTTT-CTTTTCTTAATTACCCTGAATTAAG
1 ACTTTACTCTTCTTAATTACCCTGAATTAAG
*
29843 ACTTTACTCTTCTTAATTGCCC--AACTTAGGACCTTG
1 ACTTTACTCTTCTTAATTACCCTGAA-TTA--A----G
* *
29879 ACTGTACTTTCTTTTTTTAATTACCCTGAATTAAG
1 ACTTTAC--TC--TTCTTAATTACCCTGAATTAAG
**
29914 ACTTTACTCTTCTTAATTGTCC--AACTTAGGACCTTG
1 ACTTTACTCTTCTTAATTACCCTGAA-TTA--A----G
*
29950 ACTGTACTTTCTTTCCTTAATTACCCTGAATTAAG
1 ACTTTAC--TC-TT-CTTAATTACCCTGAATTAAG
29985 ACTTTACTCTTCTTAATT
1 ACTTTACTCTTCTTAATT
30003 TCTCTTAAAT
Statistics
Matches: 120, Mismatches: 13, Indels: 53
0.65 0.07 0.28
Matches are distributed among these distances:
29 4 0.03
30 11 0.09
31 31 0.26
32 4 0.03
33 4 0.03
35 14 0.12
36 14 0.12
38 4 0.03
39 4 0.03
40 20 0.17
41 6 0.05
42 4 0.03
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.45
Consensus pattern (31 bp):
ACTTTACTCTTCTTAATTACCCTGAATTAAG
Found at i:29889 original size:71 final size:71
Alignment explanation
Indices: 29805--30002 Score: 369
Period size: 71 Copynumber: 2.8 Consensus size: 71
29795 AATTAAGATT
29805 TTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTT
1 TTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTT
29870 AGGACC
66 AGGACC
* *
29876 TTGACTGTACTTTCTTTTTTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGTCCAACTT
1 TTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTT
29941 AGGACC
66 AGGACC
*
29947 TTGACTGTACTTTCTTTCCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATT
1 TTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATT
30003 TCTCTTAAAT
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 123 1.00
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (71 bp):
TTGACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTGCCCAACTT
AGGACC
Found at i:30358 original size:4 final size:4
Alignment explanation
Indices: 30349--30376 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
30339 TCAAATTTAC
30349 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA
30377 AAAGGAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:32967 original size:17 final size:18
Alignment explanation
Indices: 32940--32977 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
32930 TTAAATACTT
*
32940 AATTCTTCTTTATTAAGC
1 AATTCTTCTTTATTAACC
32958 AATT-TTCTTTATTAACC
1 AATTCTTCTTTATTAACC
32975 AAT
1 AAT
32978 GTAAATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.50
Consensus pattern (18 bp):
AATTCTTCTTTATTAACC
Found at i:40968 original size:20 final size:20
Alignment explanation
Indices: 40943--40989 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
40933 AAACCAGGTG
*
40943 GGGCGCCAAGCTTGCCGCAT
1 GGGCGCCAAGCTTGCCACAT
40963 GGGCGCCAAGCTTGCCACAT
1 GGGCGCCAAGCTTGCCACAT
40983 GGGCGCC
1 GGGCGCC
40990 CAGTGCCAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.15, C:0.36, G:0.36, T:0.13
Consensus pattern (20 bp):
GGGCGCCAAGCTTGCCACAT
Found at i:46570 original size:11 final size:11
Alignment explanation
Indices: 46554--46609 Score: 55
Period size: 11 Copynumber: 5.2 Consensus size: 11
46544 TGCTTCTTGA
46554 AATAATTCTTC
1 AATAATTCTTC
46565 AATAA-TCTTC
1 AATAATTCTTC
*
46575 AATTATTCTTC
1 AATAATTCTTC
*
46586 AA-ATTATCTTC
1 AATAAT-TCTTC
46597 AATTAA-TCTTC
1 AA-TAATTCTTC
46608 AA
1 AA
46610 ACACGAACTT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 10 0.27
11 26 0.70
13 1 0.03
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.45
Consensus pattern (11 bp):
AATAATTCTTC
Found at i:46610 original size:22 final size:22
Alignment explanation
Indices: 46560--46610 Score: 77
Period size: 22 Copynumber: 2.4 Consensus size: 22
46550 TTGAAATAAT
*
46560 TCTTC-AATAATCTTCAATTAT
1 TCTTCAAATAATCTTCAATTAA
*
46581 TCTTCAAATTATCTTCAATTAA
1 TCTTCAAATAATCTTCAATTAA
46603 TCTTCAAA
1 TCTTCAAA
46611 CACGAACTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.35, C:0.20, G:0.00, T:0.45
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAATTAA
Found at i:47727 original size:21 final size:21
Alignment explanation
Indices: 47688--47728 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
47678 TGGATGGTGA
*
47688 GAAAACTTTTTCTCTCTTTTG
1 GAAAACTTTTTCTCCCTTTTG
47709 GAAAACTTTTTC-CACCTTTT
1 GAAAACTTTTTCTC-CCTTTT
47729 ACTGGGAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.22, C:0.22, G:0.07, T:0.49
Consensus pattern (21 bp):
GAAAACTTTTTCTCCCTTTTG
Found at i:48335 original size:3 final size:3
Alignment explanation
Indices: 48327--48360 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
48317 TATATATTTA
48327 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
48361 GTATCCATAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:61281 original size:50 final size:50
Alignment explanation
Indices: 61227--61327 Score: 193
Period size: 50 Copynumber: 2.0 Consensus size: 50
61217 CAAGAATAGA
61227 ATAGAAGAAAAATCTTGCTAGAACTTGAAGAGCTCTTATTCAACTAAGCT
1 ATAGAAGAAAAATCTTGCTAGAACTTGAAGAGCTCTTATTCAACTAAGCT
*
61277 ATAGAAGAAAAATCTTGCTAGAACTTGAAGAGCTCTTATTTAACTAAGCT
1 ATAGAAGAAAAATCTTGCTAGAACTTGAAGAGCTCTTATTCAACTAAGCT
61327 A
1 A
61328 AGACAGCCAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.29
Consensus pattern (50 bp):
ATAGAAGAAAAATCTTGCTAGAACTTGAAGAGCTCTTATTCAACTAAGCT
Found at i:66072 original size:29 final size:28
Alignment explanation
Indices: 66038--66139 Score: 96
Period size: 29 Copynumber: 3.5 Consensus size: 28
66028 GGCTAATTGC
66038 TCAAATAAGGGCTCGATCTTTTAATTTGG
1 TCAAATAAGGGC-CGATCTTTTAATTTGG
* * * ** *
66067 TCAAATAAGGGCCTAACGTTATCGAAAATGC
1 TCAAATAAGGGCCGATC-TT-T-TAATTTGG
66098 TCAAATAAGGGCCCGATCTTTTAATTTGG
1 TCAAATAAGGG-CCGATCTTTTAATTTGG
*
66127 CCAAATAAGGGCC
1 TCAAATAAGGGCC
66140 TAACATTATC
Statistics
Matches: 56, Mismatches: 13, Indels: 9
0.72 0.17 0.12
Matches are distributed among these distances:
28 5 0.09
29 28 0.50
30 2 0.04
31 17 0.30
32 4 0.07
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (28 bp):
TCAAATAAGGGCCGATCTTTTAATTTGG
Found at i:66105 original size:31 final size:30
Alignment explanation
Indices: 66067--66172 Score: 110
Period size: 31 Copynumber: 3.5 Consensus size: 30
66057 TTTAATTTGG
66067 TCAAATAAGGGCCTAACGTTATCGAAAATGC
1 TCAAATAAGGGCCTAAC-TTATCGAAAATGC
* * * **
66098 TCAAATAAGGGCCCGATCTT-T-TAATTTGGC
1 TCAAATAAGGG-CCTAACTTATCGAAAAT-GC
66128 -CAAATAAGGGCCTAACATTATCGAAAATGC
1 TCAAATAAGGGCCTAAC-TTATCGAAAATGC
66158 TCAAATAAGGGCCTA
1 TCAAATAAGGGCCTA
66173 GCGTCAGTTA
Statistics
Matches: 59, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
28 4 0.07
29 15 0.25
30 6 0.10
31 30 0.51
32 4 0.07
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.25
Consensus pattern (30 bp):
TCAAATAAGGGCCTAACTTATCGAAAATGC
Found at i:66132 original size:60 final size:60
Alignment explanation
Indices: 66035--66170 Score: 245
Period size: 60 Copynumber: 2.3 Consensus size: 60
66025 GATGGCTAAT
* * *
66035 TGCTCAAATAAGGGCTCGATCTTTTAATTTGGTCAAATAAGGGCCTAACGTTATCGAAAA
1 TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGGGCCTAACATTATCGAAAA
66095 TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGGGCCTAACATTATCGAAAA
1 TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGGGCCTAACATTATCGAAAA
66155 TGCTCAAATAAGGGCC
1 TGCTCAAATAAGGGCC
66171 TAGCGTCAGT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 73 1.00
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (60 bp):
TGCTCAAATAAGGGCCCGATCTTTTAATTTGGCCAAATAAGGGCCTAACATTATCGAAAA
Found at i:71039 original size:27 final size:27
Alignment explanation
Indices: 71009--71082 Score: 112
Period size: 27 Copynumber: 2.7 Consensus size: 27
70999 AAGTGGATTC
*
71009 AAAATGACCAAAATGCGCCTGAATGCA
1 AAAATGACCAAAATGCCCCTGAATGCA
* **
71036 AAAATGACTAAAATGCCCCTGAATGTG
1 AAAATGACCAAAATGCCCCTGAATGCA
71063 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
71083 AGGTGACCCT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.43, C:0.23, G:0.16, T:0.18
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGCA
Found at i:77599 original size:27 final size:27
Alignment explanation
Indices: 77569--77642 Score: 139
Period size: 27 Copynumber: 2.7 Consensus size: 27
77559 AAGTGGATTC
77569 AAAATGACCAAAATGCCCCTGAATGCA
1 AAAATGACCAAAATGCCCCTGAATGCA
*
77596 AAAATGACCAAAATACCCCTGAATGCA
1 AAAATGACCAAAATGCCCCTGAATGCA
77623 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
77643 ACGTGACCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.46, C:0.27, G:0.12, T:0.15
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGCA
Found at i:78368 original size:22 final size:22
Alignment explanation
Indices: 78343--78417 Score: 69
Period size: 22 Copynumber: 3.3 Consensus size: 22
78333 AATTAATACA
*
78343 CGGAGGTTTCTGAATTTGTGCC
1 CGGAGGTTTCTGAATTTGCGCC
* * ** *
78365 CGGAGGACTTGACAGAATTAACACC
1 CGGAGG--TT-TCTGAATTTGCGCC
78390 CGGAGGTTTCTGAATTTGCGCC
1 CGGAGGTTTCTGAATTTGCGCC
78412 CGGAGG
1 CGGAGG
78418 ACTTACCAAT
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
22 21 0.54
23 2 0.05
24 2 0.05
25 14 0.36
ACGTcount: A:0.21, C:0.21, G:0.32, T:0.25
Consensus pattern (22 bp):
CGGAGGTTTCTGAATTTGCGCC
Found at i:78369 original size:47 final size:46
Alignment explanation
Indices: 78314--78423 Score: 175
Period size: 47 Copynumber: 2.3 Consensus size: 46
78304 TTTTACCAAT
*
78314 TGCCCGGAGGACTTATCAGAATTAATACACGGAGGTTTCTGAATTTG
1 TGCCCGGAGGACTTA-CAGAATTAACACACGGAGGTTTCTGAATTTG
*
78361 TGCCCGGAGGACTTGACAGAATTAACACCCGGAGGTTTCTGAATTTG
1 TGCCCGGAGGACTT-ACAGAATTAACACACGGAGGTTTCTGAATTTG
*
78408 CGCCCGGAGGACTTAC
1 TGCCCGGAGGACTTAC
78424 CAATGCAAAC
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
46 2 0.03
47 56 0.95
48 1 0.02
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (46 bp):
TGCCCGGAGGACTTACAGAATTAACACACGGAGGTTTCTGAATTTG
Found at i:78572 original size:22 final size:22
Alignment explanation
Indices: 78547--78620 Score: 76
Period size: 22 Copynumber: 3.2 Consensus size: 22
78537 AGGACTTACA
*
78547 GAATTAATACCCGAAGGTTTCT
1 GAATTAATACCCGGAGGTTTCT
** * *
78569 GAATTTGTGCCCGGAGGACTTATCA
1 GAATTAATACCCGGAGG--TT-TCT
78594 GAATTAATACCCGGAGGTTTCT
1 GAATTAATACCCGGAGGTTTCT
78616 GAATT
1 GAATT
78621 TGTGCCCGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
22 20 0.50
23 2 0.05
24 2 0.05
25 16 0.40
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (22 bp):
GAATTAATACCCGGAGGTTTCT
Found at i:78606 original size:47 final size:46
Alignment explanation
Indices: 78530--78638 Score: 191
Period size: 47 Copynumber: 2.3 Consensus size: 46
78520 TTTTACCAAT
78530 TGCCCGGAGGACTTACAGAATTAATACCCGAAGGTTTCTGAATTTG
1 TGCCCGGAGGACTTACAGAATTAATACCCGAAGGTTTCTGAATTTG
*
78576 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTG
1 TGCCCGGAGGACTTA-CAGAATTAATACCCGAAGGTTTCTGAATTTG
*
78623 TGCCCGAAGGACTTAC
1 TGCCCGGAGGACTTAC
78639 CAATGCAAAC
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
46 16 0.27
47 44 0.73
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.28
Consensus pattern (46 bp):
TGCCCGGAGGACTTACAGAATTAATACCCGAAGGTTTCTGAATTTG
Found at i:78608 original size:215 final size:210
Alignment explanation
Indices: 78154--78703 Score: 828
Period size: 215 Copynumber: 2.6 Consensus size: 210
78144 TTTTACCCAT
**
78154 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTACCGGAGGACTTACCAA
1 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGGCCCGGAGGACTTACCAA
* * *
78219 TGCAAACTCTGAACTGCCACCTTCAATCAAGGATTTTAAACTT-AAAT--ATGATAAAAACTTGA
66 TGCAAACTCTGAATTGTCACCTTCGATCAAGGATTTTAAACTTAAAATGAATGATAAAAACTTGA
* * *
78281 TGGAATGAAATGGTACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATCAGAATTAATACACGG
131 TGAAATGAAATGGCACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATCAGAATTAATACACGA
78346 AGGTTTCTGAATTTG
196 AGGTTTCTGAATTTG
*
78361 TGCCCGGAGGACTTGA-CAGAATTAACACCCGGAGGTTTCTGAATTTGCGCCCGGAGGACTTACC
1 TGCCCGGAGGACTT-ATCAGAATTAATACCCGGAGGTTTCTGAATTTG-GCCCGGAGGACTTACC
* *
78425 AATGCAAACTCTGAATTGTTACCTTCGATCAAGGATTTTAAACTTAAACATGAATTTTTGATGAA
64 AATGCAAACTCTGAATTGTCACCTTCGATCAAGGATTTTAAACTTAAA-ATGAA----TGATAAA
* *
78490 AACTTGGTTAAATGAAATGGCACCCGGAGGTTTTACCAATTGCCCGGAGGACTTA-CAGAATTAA
124 AACTTGATGAAATGAAATGGCACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATCAGAATTAA
*
78554 TACCCGAAGGTTTCTGAATTTG
189 TACACGAAGGTTTCTGAATTTG
*
78576 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGTGCCCGAAGGACTTACCA
1 TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTG-GCCCGGAGGACTTACCA
*
78641 ATGCAAACTCTGAATTGTCACCTTCGATCAAGGATTTTAAACTT-AAAT--ATGATTAAAACTTG
65 ATGCAAACTCTGAATTGTCACCTTCGATCAAGGATTTTAAACTTAAAATGAATGATAAAAACTTG
78703 A
130 A
78704 ACTAACTCGT
Statistics
Matches: 312, Mismatches: 20, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
207 56 0.18
208 56 0.18
209 2 0.01
210 2 0.01
211 1 0.00
212 1 0.00
213 2 0.01
214 3 0.01
215 132 0.42
216 57 0.18
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (210 bp):
TGCCCGGAGGACTTATCAGAATTAATACCCGGAGGTTTCTGAATTTGGCCCGGAGGACTTACCAA
TGCAAACTCTGAATTGTCACCTTCGATCAAGGATTTTAAACTTAAAATGAATGATAAAAACTTGA
TGAAATGAAATGGCACCCGGAGGTTTTACCAATTGCCCGGAGGACTTATCAGAATTAATACACGA
AGGTTTCTGAATTTG
Found at i:78628 original size:22 final size:22
Alignment explanation
Indices: 78556--78628 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
78546 AGAATTAATA
*
78556 CCCGAAGGTTTCTGAATTTGTG
1 CCCGGAGGTTTCTGAATTTGTG
* ** *
78578 CCCGGAGGACTTATCAGAATTAATA
1 CCCGGAGG--TT-TCTGAATTTGTG
78603 CCCGGAGGTTTCTGAATTTGTG
1 CCCGGAGGTTTCTGAATTTGTG
78625 CCCG
1 CCCG
78629 AAGGACTTAC
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
22 19 0.49
23 2 0.05
24 2 0.05
25 16 0.41
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (22 bp):
CCCGGAGGTTTCTGAATTTGTG
Found at i:80019 original size:8 final size:8
Alignment explanation
Indices: 80002--80062 Score: 70
Period size: 8 Copynumber: 7.5 Consensus size: 8
79992 TATTCTTTTC
*
80002 TTTTCTTT
1 TTTTCATT
80010 TTTTCATT
1 TTTTCATT
*
80018 TTTTTA-T
1 TTTTCATT
*
80025 TTTTAATT
1 TTTTCATT
80033 TTTCATCATT
1 TTT--TCATT
80043 TTTTCATT
1 TTTTCATT
80051 TTTTCATT
1 TTTTCATT
80059 TTTT
1 TTTT
80063 TCACGGCACT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
7 6 0.13
8 33 0.72
10 7 0.15
ACGTcount: A:0.13, C:0.10, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTCATT
Found at i:80122 original size:12 final size:13
Alignment explanation
Indices: 80094--80122 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
80084 AGTTAACCCG
80094 AAAACTCTTTTCA
1 AAAACTCTTTTCA
80107 AAAACTCTTTTCA
1 AAAACTCTTTTCA
80120 AAA
1 AAA
80123 GTTTTGACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (13 bp):
AAAACTCTTTTCA
Found at i:80408 original size:14 final size:14
Alignment explanation
Indices: 80388--80460 Score: 77
Period size: 13 Copynumber: 5.6 Consensus size: 14
80378 CATTTTTTTC
80388 ATTTTTTTTGA-TG
1 ATTTTTTTTGATTG
80401 ATTTTTTTTGATTG
1 ATTTTTTTTGATTG
80415 A--TTTTTTGATTG
1 ATTTTTTTTGATTG
* *
80427 A-TTTTTTTGTTTT
1 ATTTTTTTTGATTG
*
80440 ATTTTTATT-ATT-
1 ATTTTTTTTGATTG
80452 ATTTTTTTT
1 ATTTTTTTT
80461 TGAAAATTCT
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
12 20 0.38
13 23 0.44
14 9 0.17
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.75
Consensus pattern (14 bp):
ATTTTTTTTGATTG
Found at i:80408 original size:25 final size:25
Alignment explanation
Indices: 80380--80461 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
80370 CATTTCATCA
80380 TTTTTTTCATTTTTTTTGATGA--T
1 TTTTTTTCATTTTTTTTGATGATTT
*
80403 TTTTTTTGATTGATTTTTTGATTGATTT
1 TTTTTTTCATT--TTTTTTGA-TGATTT
* * *
80431 TTTTGTTTTATTTTTATT-ATTATTT
1 TTTT-TTTCATTTTTTTTGATGATTT
80456 TTTTTT
1 TTTTTT
80462 GAAAATTCTC
Statistics
Matches: 49, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
23 10 0.20
24 2 0.04
25 17 0.35
26 4 0.08
27 5 0.10
28 5 0.10
29 6 0.12
ACGTcount: A:0.13, C:0.01, G:0.09, T:0.77
Consensus pattern (25 bp):
TTTTTTTCATTTTTTTTGATGATTT
Found at i:80445 original size:12 final size:12
Alignment explanation
Indices: 80391--80433 Score: 61
Period size: 12 Copynumber: 3.5 Consensus size: 12
80381 TTTTTTCATT
80391 TTTTTTGA-TGA
1 TTTTTTGATTGA
80402 TTTTTTTTGATTGA
1 --TTTTTTGATTGA
80416 TTTTTTGATTGA
1 TTTTTTGATTGA
80428 TTTTTT
1 TTTTTT
80434 TGTTTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 18 0.62
13 8 0.28
14 3 0.10
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (12 bp):
TTTTTTGATTGA
Found at i:80752 original size:14 final size:14
Alignment explanation
Indices: 80735--80773 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
80725 ACGGGTTTCG
*
80735 AAAACCATTTTTGA
1 AAAACCACTTTTGA
80749 AAAA-CACTTTTGA
1 AAAACCACTTTTGA
*
80762 AAAACCCCTTTT
1 AAAACCACTTTT
80774 TTTTACTTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (14 bp):
AAAACCACTTTTGA
Found at i:80891 original size:9 final size:9
Alignment explanation
Indices: 80877--80928 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 9
80867 TTCCAAGTGC
80877 TTTTTTTCA
1 TTTTTTTCA
80886 TTTTTTTCA
1 TTTTTTTCA
80895 TCATTTTGCATTCA
1 T--TTTT---TTCA
80909 TTTTTTTTCA
1 -TTTTTTTCA
80919 TTTTTTTCA
1 TTTTTTTCA
80928 T
1 T
80929 CATTTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
9 20 0.54
10 4 0.11
11 4 0.11
13 4 0.11
14 4 0.11
15 1 0.03
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.71
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:80898 original size:12 final size:12
Alignment explanation
Indices: 80883--80937 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 12
80873 GTGCTTTTTT
80883 TCATTTTTTTCA
1 TCATTTTTTTCA
*
80895 TCA--TTTTGCA
1 TCATTTTTTTCA
80905 TTCATTTTTTT--
1 -TCATTTTTTTCA
80916 TCATTTTTTTCA
1 TCATTTTTTTCA
80928 TCATTTTTTT
1 TCATTTTTTT
80938 TGGGAATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
10 16 0.44
11 3 0.08
12 13 0.36
13 4 0.11
ACGTcount: A:0.15, C:0.15, G:0.02, T:0.69
Consensus pattern (12 bp):
TCATTTTTTTCA
Found at i:80908 original size:23 final size:22
Alignment explanation
Indices: 80882--80937 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
80872 AGTGCTTTTT
80882 TTCATTTTTTTCATCATTTTGCA
1 TTCATTTTTTTCAT-ATTTTGCA
* *
80905 TTCATTTTTTTTCATTTTTTTCA
1 TTCA-TTTTTTTCATATTTTGCA
80928 -TCATTTTTTT
1 TTCATTTTTTT
80938 TGGGAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 7 0.23
22 3 0.10
23 10 0.33
24 10 0.33
ACGTcount: A:0.14, C:0.14, G:0.02, T:0.70
Consensus pattern (22 bp):
TTCATTTTTTTCATATTTTGCA
Found at i:88549 original size:27 final size:27
Alignment explanation
Indices: 88519--88592 Score: 148
Period size: 27 Copynumber: 2.7 Consensus size: 27
88509 AAGTGGACTC
88519 AAAATGACCAAAATGCCCCTGAATGCA
1 AAAATGACCAAAATGCCCCTGAATGCA
88546 AAAATGACCAAAATGCCCCTGAATGCA
1 AAAATGACCAAAATGCCCCTGAATGCA
88573 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
88593 ACGTGACCCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.45, C:0.27, G:0.14, T:0.15
Consensus pattern (27 bp):
AAAATGACCAAAATGCCCCTGAATGCA
Found at i:90075 original size:27 final size:27
Alignment explanation
Indices: 90041--90107 Score: 134
Period size: 27 Copynumber: 2.5 Consensus size: 27
90031 CTGTTGTCGC
90041 AGTGGATCCTCCCACTTCGACCCCAGT
1 AGTGGATCCTCCCACTTCGACCCCAGT
90068 AGTGGATCCTCCCACTTCGACCCCAGT
1 AGTGGATCCTCCCACTTCGACCCCAGT
90095 AGTGGATCCTCCC
1 AGTGGATCCTCCC
90108 GCTTTGCCTC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.18, C:0.40, G:0.19, T:0.22
Consensus pattern (27 bp):
AGTGGATCCTCCCACTTCGACCCCAGT
Found at i:96189 original size:11 final size:11
Alignment explanation
Indices: 96173--96250 Score: 66
Period size: 12 Copynumber: 6.7 Consensus size: 11
96163 TTATATATGT
*
96173 TCATGCATCAA
1 TCATGCATTAA
96184 TCATGCATTAA
1 TCATGCATTAA
* *
96195 TCCATTCATTAC
1 T-CATGCATTAA
*
96207 TACATGCATCAA
1 T-CATGCATTAA
96219 TCATGCATTAA
1 TCATGCATTAA
* *
96230 TCCATTCATTAC
1 T-CATGCATTAA
96242 TACATGCAT
1 T-CATGCAT
96251 CCATCTTGCA
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
11 21 0.40
12 32 0.60
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.35
Consensus pattern (11 bp):
TCATGCATTAA
Found at i:96213 original size:35 final size:35
Alignment explanation
Indices: 96174--96263 Score: 162
Period size: 35 Copynumber: 2.6 Consensus size: 35
96164 TATATATGTT
96174 CATGCATCAATCATGCATTAATCCATTCATTACTA
1 CATGCATCAATCATGCATTAATCCATTCATTACTA
96209 CATGCATCAATCATGCATTAATCCATTCATTACTA
1 CATGCATCAATCATGCATTAATCCATTCATTACTA
* *
96244 CATGCATCCATCTTGCATTA
1 CATGCATCAATCATGCATTA
96264 CCTTTATCTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.32, C:0.27, G:0.07, T:0.34
Consensus pattern (35 bp):
CATGCATCAATCATGCATTAATCCATTCATTACTA
Found at i:96790 original size:27 final size:27
Alignment explanation
Indices: 96758--96831 Score: 80
Period size: 27 Copynumber: 2.7 Consensus size: 27
96748 GGTCGAGTTA
96758 GCATTTTGGTCTTTTTTGCA-TCTAGGG
1 GCATTTTGGTCTTTTTTGCACTC-AGGG
* *
96785 GTATTTTGGTC-ATTTTGACACTCAGGG
1 GCATTTTGGTCTTTTTTG-CACTCAGGG
*
96812 GCATTTTGGTCATTCTTTGC
1 GCATTTTGGTC-TTTTTTGC
96832 GTTTAAGGAT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
26 5 0.13
27 26 0.68
28 3 0.08
29 4 0.11
ACGTcount: A:0.14, C:0.16, G:0.24, T:0.46
Consensus pattern (27 bp):
GCATTTTGGTCTTTTTTGCACTCAGGG
Found at i:96959 original size:23 final size:23
Alignment explanation
Indices: 96933--96976 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
96923 TTTGCATATT
*
96933 TGCATTTAGTAACTTGGTATTAC
1 TGCACTTAGTAACTTGGTATTAC
*
96956 TGCACTTAGTAATTTGGTATT
1 TGCACTTAGTAACTTGGTATT
96977 GTTGCATCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.11, G:0.18, T:0.45
Consensus pattern (23 bp):
TGCACTTAGTAACTTGGTATTAC
Found at i:96982 original size:23 final size:23
Alignment explanation
Indices: 96932--96982 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
96922 TTTTGCATAT
*
96932 TTGCATTTAGTAACTTGGTATTA
1 TTGCACTTAGTAACTTGGTATTA
* * *
96955 CTGCACTTAGTAATTTGGTATTG
1 TTGCACTTAGTAACTTGGTATTA
96978 TTGCA
1 TTGCA
96983 TCTCCATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.20, T:0.45
Consensus pattern (23 bp):
TTGCACTTAGTAACTTGGTATTA
Found at i:99256 original size:55 final size:55
Alignment explanation
Indices: 99191--99377 Score: 340
Period size: 55 Copynumber: 3.4 Consensus size: 55
99181 TAAAAGGGGC
99191 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAG-AATTAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAA-TAGTAATCAGTA
*
99246 AATCGGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
*
99301 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTTAAAGTAATAGTAATCAGTA
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
99356 AATCAGTAATTAAGTAAAAAGA
1 AATCAGTAATTAAGTAAAAAGA
99378 TAGTAATTAG
Statistics
Matches: 128, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
55 126 0.98
56 2 0.02
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (55 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAAGTAATAGTAATCAGTA
Found at i:99286 original size:26 final size:25
Alignment explanation
Indices: 99257--99343 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 25
99247 ATCGGTAATT
99257 AAGTAAAAAGAGATTAATCAGAGTCA
1 AAGTAAAAAGAGATTAATCAGAGT-A
* * * *
99283 AAGTAATAGTAATCAG-TAAATCAGTAATT
1 AAGTAA-A--AA-GAGATTAATCAG-AGTA
99312 AAGTAAAAAGAGATTAATCAGAGTTA
1 AAGTAAAAAGAGATTAATCAGAG-TA
99338 AAGTAA
1 AAGTAA
99344 TAGTAATCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 22 0.48
27 1 0.02
28 1 0.02
29 15 0.33
30 4 0.09
ACGTcount: A:0.53, C:0.06, G:0.17, T:0.24
Consensus pattern (25 bp):
AAGTAAAAAGAGATTAATCAGAGTA
Found at i:99306 original size:29 final size:28
Alignment explanation
Indices: 99272--99361 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 28
99262 AAAAGAGATT
99272 AATCAGAGTCAAAGTAATAGTAATCAGTA
1 AATCAGAGT-AAAGTAATAGTAATCAGTA
* * * *
99301 AATCAGTAATTAAGTAA-A--AA-GAGATT
1 AATCAG-AGTAAAGTAATAGTAATCAG-TA
99327 AATCAGAGTTAAAGTAATAGTAATCAGTA
1 AATCAGAG-TAAAGTAATAGTAATCAGTA
99356 AATCAG
1 AATCAG
99362 TAATTAAGTA
Statistics
Matches: 46, Mismatches: 8, Indels: 14
0.68 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 16 0.35
27 1 0.02
28 1 0.02
29 21 0.46
30 4 0.09
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.26
Consensus pattern (28 bp):
AATCAGAGTAAAGTAATAGTAATCAGTA
Found at i:99746 original size:21 final size:21
Alignment explanation
Indices: 99722--99778 Score: 80
Period size: 21 Copynumber: 2.7 Consensus size: 21
99712 AAAAAGGCAA
*
99722 TCAGTAAGAGTAAGAAGGTTG
1 TCAGTAAGAGTAAGAAGGTAG
*
99743 TCAGTAAAAAGTAA-AAGGTAG
1 TCAGT-AAGAGTAAGAAGGTAG
99764 TCAGTAAGAGTAAGA
1 TCAGTAAGAGTAAGA
99779 GAGTAATTAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 7 0.23
21 17 0.55
22 7 0.23
ACGTcount: A:0.46, C:0.05, G:0.28, T:0.21
Consensus pattern (21 bp):
TCAGTAAGAGTAAGAAGGTAG
Found at i:99805 original size:22 final size:20
Alignment explanation
Indices: 99720--99841 Score: 77
Period size: 21 Copynumber: 5.8 Consensus size: 20
99710 AAAAAAAGGC
99720 AATCAGTAAGAGTAAGA-AGGT
1 AATCAGTAAGAGTAA-ATA-GT
** *
99741 TGTCAGTAAAAAGTAAA-AGGT
1 AATCAGT-AAGAGTAAATA-GT
* *
99762 AGTCAGTAAGAGTAAGAGAGT
1 AATCAGTAAGAGTAA-ATAGT
*
99783 AATTAGTAAAGAAGTAAATAGT
1 AATCAGT-AAG-AGTAAATAGT
* *
99805 AATCAGTAAGAGTAAAAGAGC
1 AATCAGTAAGAGT-AAATAGT
99826 AATCAGTAAAGAGTAA
1 AATCAGT-AAGAGTAA
99842 CCAGTAAAGA
Statistics
Matches: 83, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
20 10 0.12
21 41 0.49
22 27 0.33
23 5 0.06
ACGTcount: A:0.50, C:0.05, G:0.25, T:0.20
Consensus pattern (20 bp):
AATCAGTAAGAGTAAATAGT
Found at i:99812 original size:43 final size:43
Alignment explanation
Indices: 99713--99841 Score: 149
Period size: 43 Copynumber: 3.0 Consensus size: 43
99703 AGAAAGTAAA
* **
99713 AAAAGGCAATCAGTAAGAGTAAGA-AGGTTGTCAGTAAA-AAGT
1 AAAAGGTAATCAGTAAGAGTAAGAGA-GTAATCAGTAAAGAAGT
* *
99755 AAAAGGTAGTCAGTAAGAGTAAGAGAGTAATTAGTAAAGAAGT
1 AAAAGGTAATCAGTAAGAGTAAGAGAGTAATCAGTAAAGAAGT
* *
99798 AAATA-GTAATCAGTAAGAGTAAAAGAGCAATCAGTAAAG-AGT
1 AAA-AGGTAATCAGTAAGAGTAAGAGAGTAATCAGTAAAGAAGT
99840 AA
1 AA
99842 CCAGTAAAGA
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
42 36 0.48
43 38 0.51
44 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.25, T:0.19
Consensus pattern (43 bp):
AAAAGGTAATCAGTAAGAGTAAGAGAGTAATCAGTAAAGAAGT
Found at i:99870 original size:7 final size:7
Alignment explanation
Indices: 99769--99942 Score: 61
Period size: 7 Copynumber: 24.4 Consensus size: 7
99759 GGTAGTCAGT
99769 AAGAGTA
1 AAGAGTA
99776 AGAGAGTA
1 A-AGAGTA
**
99784 ATTAGTA
1 AAGAGTA
99791 AAGAAGTA
1 AAG-AGTA
*
99799 AATAGTA
1 AAGAGTA
**
99806 ATCAGT-
1 AAGAGTA
99812 AAGAGTAA
1 AAGAGT-A
*
99820 AAGAGCA
1 AAGAGTA
**
99827 ATCAGTA
1 AAGAGTA
99834 AAGAGTA
1 AAGAGTA
**
99841 ACCAGTA
1 AAGAGTA
99848 AAGA--A
1 AAGAGTA
*
99853 AAAATGTA
1 AAGA-GTA
99861 AAGAGTA
1 AAGAGTA
99868 AAGAGTA
1 AAGAGTA
** *
99875 ATCAGTG
1 AAGAGTA
**
99882 AAGAAAA
1 AAGAGTA
99889 AATG-GTA
1 AA-GAGTA
* *
99896 AAGAATG
1 AAGAGTA
99903 AAGAGTA
1 AAGAGTA
**
99910 ATTAGTA
1 AAGAGTA
99917 AA-ATGGTA
1 AAGA--GTA
99925 AAGAGTA
1 AAGAGTA
99932 AAGAAGTA
1 AAG-AGTA
99940 AAG
1 AAG
99943 TAAAGGGAGA
Statistics
Matches: 116, Mismatches: 38, Indels: 25
0.65 0.21 0.14
Matches are distributed among these distances:
5 4 0.03
6 6 0.05
7 70 0.60
8 35 0.30
9 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.24, T:0.18
Consensus pattern (7 bp):
AAGAGTA
Found at i:99873 original size:34 final size:35
Alignment explanation
Indices: 99830--99910 Score: 119
Period size: 34 Copynumber: 2.3 Consensus size: 35
99820 AAGAGCAATC
99830 AGTAAAGAGTAACCAGTAAAGAAAAAAT-GTAAAG
1 AGTAAAGAGTAACCAGTAAAGAAAAAATGGTAAAG
* *
99864 AGTAAAGAGTAATCAGTGAAGAAAAAATGGTAAAG
1 AGTAAAGAGTAACCAGTAAAGAAAAAATGGTAAAG
* *
99899 AATGAAGAGTAA
1 AGTAAAGAGTAA
99911 TTAGTAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
34 26 0.62
35 16 0.38
ACGTcount: A:0.57, C:0.04, G:0.23, T:0.16
Consensus pattern (35 bp):
AGTAAAGAGTAACCAGTAAAGAAAAAATGGTAAAG
Found at i:99982 original size:40 final size:40
Alignment explanation
Indices: 99929--100022 Score: 111
Period size: 40 Copynumber: 2.3 Consensus size: 40
99919 ATGGTAAAGA
*
99929 GTAAAGAAGTAAAGT-AAAGGGAGATCAGTAAA-AAGAAAATG
1 GTAAAG-AGTAAAGTAAAAAGGA-ATCAGTAAAGAA-AAAATG
*
99970 GTAAAGAGTAAAGTAAAAAGTAATCAGTAAAGAAAAAATG
1 GTAAAGAGTAAAGTAAAAAGGAATCAGTAAAGAAAAAATG
**
100010 GTAATCAGTAAAG
1 GTAAAGAGTAAAG
100023 AGTAATAGTA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
40 34 0.72
41 13 0.28
ACGTcount: A:0.56, C:0.03, G:0.23, T:0.17
Consensus pattern (40 bp):
GTAAAGAGTAAAGTAAAAAGGAATCAGTAAAGAAAAAATG
Found at i:99988 original size:21 final size:21
Alignment explanation
Indices: 99952--100122 Score: 104
Period size: 22 Copynumber: 8.2 Consensus size: 21
99942 GTAAAGGGAG
99952 ATCAGTAAA-AAGAAAATGGTA
1 ATCAGTAAAGAA-AAAATGGTA
** *
99973 AAGAGTAAAGTAAAAA--GTA
1 ATCAGTAAAGAAAAAATGGTA
99992 ATCAGTAAAGAAAAAATGGTA
1 ATCAGTAAAGAAAAAATGGTA
** *
100013 ATCAGTAAAG-AGTAATAGTA
1 ATCAGTAAAGAAAAAATGGTA
** *
100033 ATCAGT-AAGAAGTAGTGGTA
1 ATCAGTAAAGAAAAAATGGTA
* * * *
100053 ATTAGAAAAGAGTAAAAGGGTA
1 ATCAGTAAAGA-AAAAATGGTA
100075 ATCAGTAAA-AAGTAAAATGGTA
1 ATCAGTAAAGAA--AAAATGGTA
* *
100097 ATTAGAAAAGAGTAAAAA-GGTA
1 ATCAGTAAAGA--AAAAATGGTA
100119 ATCA
1 ATCA
100123 ACAAAAAGTA
Statistics
Matches: 114, Mismatches: 25, Indels: 21
0.71 0.16 0.13
Matches are distributed among these distances:
19 19 0.17
20 25 0.22
21 29 0.25
22 35 0.31
23 5 0.04
25 1 0.01
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.20
Consensus pattern (21 bp):
ATCAGTAAAGAAAAAATGGTA
Found at i:100035 original size:20 final size:20
Alignment explanation
Indices: 99988--100089 Score: 80
Period size: 20 Copynumber: 5.0 Consensus size: 20
99978 TAAAGTAAAA
**
99988 AGTAATCAGTAAAGAAAAAAT
1 AGTAATCAGTAAAG-AGTAAT
*
100009 GGTAATCAGTAAAGAGTAAT
1 AGTAATCAGTAAAGAGTAAT
*
100029 AGTAATCAGT-AAGAAGTAGT
1 AGTAATCAGTAAAG-AGTAAT
* * * *
100049 GGTAATTAGAAAAGAGTAAA
1 AGTAATCAGTAAAGAGTAAT
*
100069 AGGGTAATCAGTAAAAAGTAA
1 A--GTAATCAGTAAAGAGTAA
100090 AATGGTAATT
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
19 3 0.05
20 29 0.46
21 16 0.25
22 15 0.24
ACGTcount: A:0.52, C:0.04, G:0.23, T:0.22
Consensus pattern (20 bp):
AGTAATCAGTAAAGAGTAAT
Found at i:100043 original size:40 final size:41
Alignment explanation
Indices: 99952--100180 Score: 189
Period size: 44 Copynumber: 5.4 Consensus size: 41
99942 GTAAAGGGAG
*
99952 ATCAGTAAAAAGAAAATGGTAA--AGAGTAA-AGTAAAAAGTA
1 ATCAGTAAAAAGAAAATGGTAATTAGA-AAAGAGT-AAAAGTA
* * *
99992 ATCAGTAAAGAA-AAAATGGTAATCAGTAAAGAGTAATAGTA
1 ATCAGTAAA-AAGAAAATGGTAATTAGAAAAGAGTAAAAGTA
* * *
100033 ATCAGTAAGAAG-TAGTGGTAATTAGAAAAGAGTAAAAGGGTA
1 ATCAGTAAAAAGAAAATGGTAATTAGAAAAGAGTAAAA--GTA
100075 ATCAGTAAAAAGTAAAATGGTAATTAGAAAAGAGTAAAAAGGTA
1 ATCAGTAAAAAG-AAAATGGTAATTAGAAAAGAGT-AAAA-GTA
** * * *
100119 ATCAACAAAAAGTAAAATGGAAATTAATAAAAAAAAGTAAAGAGTA
1 ATCAGTAAAAAG-AAAATGGTAA-T--TAGAAAAGAGTAAA-AGTA
*
100165 ATCAGTAAAGAGAAAA
1 ATCAGTAAAAAGAAAA
100181 AATAGTAAAG
Statistics
Matches: 155, Mismatches: 20, Indels: 23
0.78 0.10 0.12
Matches are distributed among these distances:
40 41 0.26
41 18 0.12
42 19 0.12
44 43 0.28
45 9 0.06
46 15 0.10
47 10 0.06
ACGTcount: A:0.57, C:0.03, G:0.20, T:0.19
Consensus pattern (41 bp):
ATCAGTAAAAAGAAAATGGTAATTAGAAAAGAGTAAAAGTA
Found at i:100107 original size:44 final size:43
Alignment explanation
Indices: 99952--100144 Score: 197
Period size: 44 Copynumber: 4.6 Consensus size: 43
99942 GTAAAGGGAG
* *
99952 ATCAGTAAAAAG-AAAATGGTAA--AGAGTAA-AGTAAAAAGTA
1 ATCAGTAAAAAGTAAAATGGTAATTAGA-AAAGAGTAAAAGGTA
* * *
99992 ATCAGTAAAGAA--AAAATGGTAATCAGTAAAGAGTAATA-GTA
1 ATCAGTAAA-AAGTAAAATGGTAATTAGAAAAGAGTAAAAGGTA
* *
100033 ATCAGTAAGAAGT--AGTGGTAATTAGAAAAGAGTAAAAGGGTA
1 ATCAGTAAAAAGTAAAATGGTAATTAGAAAAGAGTAAAA-GGTA
100075 ATCAGTAAAAAGTAAAATGGTAATTAGAAAAGAGTAAAAAGGTA
1 ATCAGTAAAAAGTAAAATGGTAATTAGAAAAGAGT-AAAAGGTA
** *
100119 ATCAACAAAAAGTAAAATGGAAATTA
1 ATCAGTAAAAAGTAAAATGGTAATTA
100145 ATAAAAAAAA
Statistics
Matches: 129, Mismatches: 13, Indels: 18
0.81 0.08 0.11
Matches are distributed among these distances:
40 41 0.32
41 15 0.12
42 23 0.18
44 46 0.36
45 4 0.03
ACGTcount: A:0.55, C:0.04, G:0.21, T:0.20
Consensus pattern (43 bp):
ATCAGTAAAAAGTAAAATGGTAATTAGAAAAGAGTAAAAGGTA
Found at i:100150 original size:22 final size:22
Alignment explanation
Indices: 100048--100151 Score: 95
Period size: 22 Copynumber: 4.7 Consensus size: 22
100038 TAAGAAGTAG
*
100048 TGGTAATTAGA-AAAGAGTAAAA
1 TGGTAATTA-ATAAAAAGTAAAA
* * *
100070 GGGTAATCAGTAAAAAGTAAAA
1 TGGTAATTAATAAAAAGTAAAA
*
100092 TGGTAATTAGA-AAAGAGTAAAA
1 TGGTAATTA-ATAAAAAGTAAAA
* * *
100114 AGGTAATCAACAAAAAGTAAAA
1 TGGTAATTAATAAAAAGTAAAA
*
100136 TGGAAATTAATAAAAA
1 TGGTAATTAATAAAAA
100152 AAAGTAAAGA
Statistics
Matches: 64, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
21 1 0.02
22 63 0.98
ACGTcount: A:0.58, C:0.03, G:0.19, T:0.20
Consensus pattern (22 bp):
TGGTAATTAATAAAAAGTAAAA
Found at i:100173 original size:14 final size:14
Alignment explanation
Indices: 100154--100233 Score: 81
Period size: 14 Copynumber: 5.6 Consensus size: 14
100144 AATAAAAAAA
100154 AGTAAAGAGTAATC
1 AGTAAAGAGTAATC
*
100168 AGTAAAGAGAAAAAAT-
1 AGTAAAGAG---TAATC
*
100184 AGTAAAGAGTAATT
1 AGTAAAGAGTAATC
**
100198 AGTAAAGAGTAAAG
1 AGTAAAGAGTAATC
*
100212 AGTAAAAAGTAATC
1 AGTAAAGAGTAATC
100226 AGTAAAGA
1 AGTAAAGA
100234 AAAAATAGTA
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
13 3 0.06
14 39 0.72
16 9 0.17
17 3 0.06
ACGTcount: A:0.57, C:0.03, G:0.21, T:0.19
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:100208 original size:7 final size:7
Alignment explanation
Indices: 100154--100233 Score: 61
Period size: 7 Copynumber: 11.1 Consensus size: 7
100144 AATAAAAAAA
100154 AGTAAAG
1 AGTAAAG
**
100161 AGTAATC
1 AGTAAAG
100168 AGTAAAG
1 AGTAAAG
* *
100175 AGAAAAAAT
1 AG--TAAAG
100184 AGTAAAG
1 AGTAAAG
**
100191 AGTAATT
1 AGTAAAG
100198 AGTAAAG
1 AGTAAAG
100205 AGTAAAG
1 AGTAAAG
*
100212 AGTAAAA
1 AGTAAAG
**
100219 AGTAATC
1 AGTAAAG
100226 AGTAAAG
1 AGTAAAG
100233 A
1 A
100234 AAAAATAGTA
Statistics
Matches: 54, Mismatches: 17, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
7 49 0.91
9 5 0.09
ACGTcount: A:0.57, C:0.03, G:0.21, T:0.19
Consensus pattern (7 bp):
AGTAAAG
Found at i:100243 original size:14 final size:14
Alignment explanation
Indices: 100175--100244 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 14
100165 ATCAGTAAAG
100175 AGAAAAAATAGTAA
1 AGAAAAAATAGTAA
** *
100189 AGAGTAATTAGTAA
1 AGAAAAAATAGTAA
** *
100203 AGAGTAAAGAGTAA
1 AGAAAAAATAGTAA
**
100217 A-AAGTAATCAGTAA
1 AGAAAAAAT-AGTAA
100231 AGAAAAAATAGTAA
1 AGAAAAAATAGTAA
100245 GGAGTGAGAA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
13 3 0.07
14 35 0.81
15 5 0.12
ACGTcount: A:0.61, C:0.01, G:0.19, T:0.19
Consensus pattern (14 bp):
AGAAAAAATAGTAA
Found at i:100243 original size:21 final size:21
Alignment explanation
Indices: 100205--100301 Score: 56
Period size: 21 Copynumber: 4.6 Consensus size: 21
100195 ATTAGTAAAG
*
100205 AGTAAAGAGTAAAA-AGTAATC
1 AGTAAAGA-AAAAATAGTAATC
**
100226 AGTAAAGAAAAAATAGTAAGG
1 AGTAAAGAAAAAATAGTAATC
* *
100247 AGT-GAGAAGAAATCAGTAAAAT-
1 AGTAAAGAAAAAAT-AGT--AATC
* * * *
100269 GGTAAAGGATAAAGAGTAATC
1 AGTAAAGAAAAAATAGTAATC
100290 AGTAAAGAAAAA
1 AGTAAAGAAAAA
100302 TGGTAAAGAG
Statistics
Matches: 56, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
20 15 0.27
21 28 0.50
22 5 0.09
23 8 0.14
ACGTcount: A:0.58, C:0.03, G:0.23, T:0.16
Consensus pattern (21 bp):
AGTAAAGAAAAAATAGTAATC
Found at i:100329 original size:64 final size:64
Alignment explanation
Indices: 100191--100336 Score: 151
Period size: 64 Copynumber: 2.3 Consensus size: 64
100181 AATAGTAAAG
* *
100191 AGTAATTAGT-AAAGAGTAAAGAGTAAAAAGTAATCAGTAAAGAAAAAATAGTAAGGAGTGAGA
1 AGTAATTAGTAAAAGAGTAAAGAGTAAAAAGTAATCAGTAAAGAAAAAATAGTAAAGAGTGAAA
* * * *
100254 AGAAATCAGTAAAATG-GTAAAG-GATAAAGAGTAATCAGTAAAG-AAAAATGGTAAAGAGT-AA
1 AGTAATTAGTAAAA-GAGTAAAGAG-TAAAAAGTAATCAGTAAAGAAAAAATAGTAAAGAGTGAA
100315 A
64 A
*
100316 ATCTTAATTAGTAAAA-AGTAA
1 A--GTAATTAGTAAAAGAGTAA
100337 TGGCAACCAG
Statistics
Matches: 68, Mismatches: 9, Indels: 12
0.76 0.10 0.13
Matches are distributed among these distances:
62 3 0.04
63 27 0.40
64 37 0.54
65 1 0.01
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (64 bp):
AGTAATTAGTAAAAGAGTAAAGAGTAAAAAGTAATCAGTAAAGAAAAAATAGTAAAGAGTGAAA
Found at i:101953 original size:24 final size:23
Alignment explanation
Indices: 101926--101972 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
101916 AAGAGACGAA
101926 AAAAAAGATGA-AAATTGAAAGTGG
1 AAAAAA-ATGAGAAA-TGAAAGTGG
101950 AAAAAAATGATGAAATGAAAGTG
1 AAAAAAATGA-GAAATGAAAGTG
101973 ATGGATTTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 14 0.67
25 3 0.14
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (23 bp):
AAAAAAATGAGAAATGAAAGTGG
Found at i:101953 original size:25 final size:24
Alignment explanation
Indices: 101923--101972 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
101913 AAAAAGAGAC
*
101923 GAAAAAAAAGATGAAAATTGAAAGTG
1 GAAAAAAATGATG-AAA-TGAAAGTG
101949 GAAAAAAATGATGAAATGAAAGTG
1 GAAAAAAATGATGAAATGAAAGTG
101973 ATGGATTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.35
25 3 0.13
26 12 0.52
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (24 bp):
GAAAAAAATGATGAAATGAAAGTG
Found at i:102391 original size:18 final size:19
Alignment explanation
Indices: 102368--102406 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
102358 TTCTTGAAAT
*
102368 AATTCTTC-AATTGTCTTC
1 AATTCTTCAAATTATCTTC
102386 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATTATCTTC
102405 AA
1 AA
102407 ATAATCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.46
Consensus pattern (19 bp):
AATTCTTCAAATTATCTTC
Found at i:102405 original size:11 final size:11
Alignment explanation
Indices: 102389--102418 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
102379 TGTCTTCAAT
*
102389 TCTTCAAATTA
1 TCTTCAAATAA
102400 TCTTCAAATAA
1 TCTTCAAATAA
102411 TCTTCAAA
1 TCTTCAAA
102419 CACGAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:102417 original size:22 final size:22
Alignment explanation
Indices: 102359--102418 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
102349 AATTCTTGCT
* *
102359 TCTTGAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
102381 TCTTC-AAT--TCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
102400 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
102419 CACGAATTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 9 0.28
20 3 0.09
21 3 0.09
22 12 0.38
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.43
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Found at i:105361 original size:15 final size:15
Alignment explanation
Indices: 105341--105381 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
105331 TCCAAGTTGT
*
105341 TCATCTTCTTGTGGC
1 TCATCTTCTGGTGGC
105356 TCATCTTCTGGTGGC
1 TCATCTTCTGGTGGC
105371 TCATCTTCTGG
1 TCATCTTCTGG
105382 CTTGGCAAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.07, C:0.27, G:0.22, T:0.44
Consensus pattern (15 bp):
TCATCTTCTGGTGGC
Found at i:106495 original size:18 final size:19
Alignment explanation
Indices: 106463--106502 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
106453 CCTAAATTGA
106463 TTTTCGACACAAATTTTTT
1 TTTTCGACACAAATTTTTT
*
106482 TTTTCGACGC-AATTTTTT
1 TTTTCGACACAAATTTTTT
106500 TTT
1 TTT
106503 ATTTAGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (19 bp):
TTTTCGACACAAATTTTTT
Found at i:108190 original size:18 final size:19
Alignment explanation
Indices: 108167--108205 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
108157 TTCTTGAAAT
*
108167 AATTCTTC-AATTGTCTTC
1 AATTCTTCAAATTATCTTC
108185 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATTATCTTC
108204 AA
1 AA
108206 ATAATCTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.31, C:0.21, G:0.03, T:0.46
Consensus pattern (19 bp):
AATTCTTCAAATTATCTTC
Found at i:108204 original size:11 final size:11
Alignment explanation
Indices: 108188--108217 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
108178 TGTCTTCAAT
*
108188 TCTTCAAATTA
1 TCTTCAAATAA
108199 TCTTCAAATAA
1 TCTTCAAATAA
108210 TCTTCAAA
1 TCTTCAAA
108218 CACGAACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (11 bp):
TCTTCAAATAA
Found at i:108216 original size:22 final size:22
Alignment explanation
Indices: 108158--108217 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
108148 AATTCTTGCT
* *
108158 TCTTGAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
108180 TCTTC-AAT--TCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
108199 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
108218 CACGAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 9 0.28
20 3 0.09
21 3 0.09
22 12 0.38
ACGTcount: A:0.35, C:0.18, G:0.03, T:0.43
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Found at i:110706 original size:2 final size:2
Alignment explanation
Indices: 110699--110730 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
110689 AACTTAACTG
110699 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
110731 AATGCCACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:112862 original size:12 final size:12
Alignment explanation
Indices: 112845--112871 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
112835 TTACATCTCC
112845 TGAATACATTGA
1 TGAATACATTGA
112857 TGAATACATTGA
1 TGAATACATTGA
112869 TGA
1 TGA
112872 GATAAAGATA
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:0.41, C:0.07, G:0.19, T:0.33
Consensus pattern (12 bp):
TGAATACATTGA
Found at i:113193 original size:2 final size:2
Alignment explanation
Indices: 113188--113231 Score: 65
Period size: 2 Copynumber: 22.5 Consensus size: 2
113178 TGGGTTTTTT
113188 TA TA TA TA TA CTA TA TA -A TA -A 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
113229 TA T
1 TA T
113232 CTAATACTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 2 0.05
2 35 0.90
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:115722 original size:29 final size:29
Alignment explanation
Indices: 115689--115746 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
115679 TTTTGGGCCA
*
115689 AACTAAAATTATGGGAATATTCTTGATTT
1 AACTAAAATTATGGGAATATTCCTGATTT
115718 AACTAAAATTATGGGAATATTCCTGATTT
1 AACTAAAATTATGGGAATATTCCTGATTT
115747 TATGACAAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.40
Consensus pattern (29 bp):
AACTAAAATTATGGGAATATTCCTGATTT
Found at i:119558 original size:27 final size:27
Alignment explanation
Indices: 119528--119580 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
119518 CAAGTTCATT
119528 CTTTACACTAGCGATTAAATTTCTCTC
1 CTTTACACTAGCGATTAAATTTCTCTC
119555 CTTTACACTAGCGATTAAATTTCTCT
1 CTTTACACTAGCGATTAAATTTCTCT
119581 GCAAAAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.42
Consensus pattern (27 bp):
CTTTACACTAGCGATTAAATTTCTCTC
Found at i:121976 original size:28 final size:28
Alignment explanation
Indices: 121945--121999 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
121935 CGTTTTTTCT
*
121945 AAAAAA-AAAAAAAATTTTGCGTCGAAA
1 AAAAAATAAAAAAAAATTTGCGTCGAAA
*
121972 AAAAAATTAAAAAAAATTTGCGTCGAAA
1 AAAAAATAAAAAAAAATTTGCGTCGAAA
122000 TAAATTTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.62, C:0.07, G:0.11, T:0.20
Consensus pattern (28 bp):
AAAAAATAAAAAAAAATTTGCGTCGAAA
Found at i:123062 original size:15 final size:15
Alignment explanation
Indices: 123042--123112 Score: 106
Period size: 15 Copynumber: 4.7 Consensus size: 15
123032 CCTTGCTAAG
123042 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
123057 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
* *
123072 ACAGAAGATGAGCAA
1 CCAGAAGATGAGCCA
*
123087 CTAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
*
123102 CAAGAAGATGA
1 CCAGAAGATGA
123113 ACAACTTGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 50 1.00
ACGTcount: A:0.45, C:0.20, G:0.27, T:0.08
Consensus pattern (15 bp):
CCAGAAGATGAGCCA
Found at i:124172 original size:25 final size:25
Alignment explanation
Indices: 124140--124192 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
124130 GCGCCACGCC
*
124140 CACCTATCACCATGCCACCACCGGT
1 CACCTATCACCATGCCACCACCAGT
* *
124165 CACCTATCACCGTGCCATCACCAGT
1 CACCTATCACCATGCCACCACCAGT
124190 CAC
1 CAC
124193 ATCCGAGCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.25, C:0.47, G:0.11, T:0.17
Consensus pattern (25 bp):
CACCTATCACCATGCCACCACCAGT
Found at i:124301 original size:16 final size:16
Alignment explanation
Indices: 124280--124311 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
124270 TTTTCCTTGC
124280 ATTGCTTTGAGTGATT
1 ATTGCTTTGAGTGATT
*
124296 ATTGCTTTGATTGATT
1 ATTGCTTTGAGTGATT
124312 GTCTATTCCT
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:0.19, C:0.06, G:0.22, T:0.53
Consensus pattern (16 bp):
ATTGCTTTGAGTGATT
Found at i:128645 original size:44 final size:44
Alignment explanation
Indices: 128582--128671 Score: 171
Period size: 44 Copynumber: 2.0 Consensus size: 44
128572 TCACCTAACA
*
128582 CTTAAAGTAACAAGAGAATGATTATAAAGATGTGTAGAGTAATC
1 CTTAAAGTAACAAGAGAATGATTATAAAAATGTGTAGAGTAATC
128626 CTTAAAGTAACAAGAGAATGATTATAAAAATGTGTAGAGTAATC
1 CTTAAAGTAACAAGAGAATGATTATAAAAATGTGTAGAGTAATC
128670 CT
1 CT
128672 AAGTAGTATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.46, C:0.08, G:0.19, T:0.28
Consensus pattern (44 bp):
CTTAAAGTAACAAGAGAATGATTATAAAAATGTGTAGAGTAATC
Found at i:129622 original size:23 final size:23
Alignment explanation
Indices: 129591--129645 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
129581 GATTTACAAA
129591 AGAGATTTGAAAGCTAAGG-GCTTG
1 AGAG-TTTGAAAGC-AAGGAGCTTG
*
129615 AGAGTTTGAAAGCACGGAGCTTG
1 AGAGTTTGAAAGCAAGGAGCTTG
129638 AGA-TTTGA
1 AGAGTTTGA
129646 TTTGCGCGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 8 0.28
23 17 0.59
24 4 0.14
ACGTcount: A:0.33, C:0.09, G:0.33, T:0.25
Consensus pattern (23 bp):
AGAGTTTGAAAGCAAGGAGCTTG
Done.