Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 60 of 135
Found at i:20306338 original size:111 final size:111
Alignment explanation
Indices: 20306115--20306337 Score: 295
Period size: 111 Copynumber: 2.0 Consensus size: 111
20306105 TATTCTTGAT
*
20306115 ATCATTAGACCACTAACCGTAATTTCAATGCAAAAATGCTTGAACAGGGTTGTAAGATGGATAAA
1 ATCATTAGACCACTAACCGTAATTTCAATGCAAAAATGCTTGAACAAGGTTGTAAGATGGATAAA
* **
20306180 ATTGAATTTATTATAGGCAAAGCTCGCGTGAATGAAAAGAATAAAA
66 ATTGAATTTATTAGAGGCAAAGCTCGCACGAATGAAAAGAATAAAA
* * * ** **
20306226 ATCATTAGTCCACTAACTGTTATTTCAATGCCGACGTGCTTGAACAAGGTTGTAA-AGTGGATAA
1 ATCATTAGACCACTAACCGTAATTTCAATGCAAAAATGCTTGAACAAGGTTGTAAGA-TGGATAA
* * *
20306290 AATTGAATTTTATTGGAGGCGAAGCTCGCACGAATGAAAAGATTAAAA
65 AATTGAA-TTTATTAGAGGCAAAGCTCGCACGAATGAAAAGAATAAAA
20306338 TGACAAACAT
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
110 1 0.01
111 61 0.64
112 34 0.35
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.27
Consensus pattern (111 bp):
ATCATTAGACCACTAACCGTAATTTCAATGCAAAAATGCTTGAACAAGGTTGTAAGATGGATAAA
ATTGAATTTATTAGAGGCAAAGCTCGCACGAATGAAAAGAATAAAA
Found at i:20307404 original size:16 final size:17
Alignment explanation
Indices: 20307380--20307443 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 17
20307370 TCATCTTGAC
20307380 TTTCTTTTTTCTTCCTT
1 TTTCTTTTTTCTTCCTT
*
20307397 TTTCTTTTCTTCTTCTTT
1 TTTCTTTT-TTCTTCCTT
*
20307415 TCTTCTTTTTTTCTT-TTCT
1 T-TTC-TTTTTTCTTCCT-T
20307434 TTTCTTTTTT
1 TTTCTTTTTT
20307444 TTTTAAAAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
17 14 0.33
18 14 0.33
19 10 0.24
20 4 0.10
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTCTTTTTTCTTCCTT
Found at i:20307417 original size:8 final size:8
Alignment explanation
Indices: 20307380--20307434 Score: 60
Period size: 8 Copynumber: 6.8 Consensus size: 8
20307370 TCATCTTGAC
20307380 TTTCTT-T
1 TTTCTTCT
20307387 TTTCTTCCTT
1 TTTCTT-C-T
20307397 TTTCTT-T
1 TTTCTTCT
20307404 TCTTCTTCT
1 T-TTCTTCT
20307413 TTTCTTCT
1 TTTCTTCT
*
20307421 TTTTTTCT
1 TTTCTTCT
20307429 TTTCTT
1 TTTCTT
20307435 TTCTTTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
7 8 0.20
8 24 0.59
9 2 0.05
10 7 0.17
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTCTTCT
Found at i:20307436 original size:11 final size:10
Alignment explanation
Indices: 20307380--20307446 Score: 71
Period size: 11 Copynumber: 6.3 Consensus size: 10
20307370 TCATCTTGAC
20307380 TTTCTTTTTT
1 TTTCTTTTTT
*
20307390 CTTCCTTTTTCT
1 -TTTCTTTTT-T
*
20307402 TTTCTTCTTCT
1 TTTCTT-TTTT
20307413 TTTCTTCTTTT
1 TTTCTT-TTTT
*
20307424 TTTCTTTTCT
1 TTTCTTTTTT
20307434 TTTCTTTTTT
1 TTTCTTTTTT
20307444 TTT
1 TTT
20307447 TAAAAATGCC
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
10 15 0.31
11 30 0.62
12 3 0.06
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:20307444 original size:21 final size:21
Alignment explanation
Indices: 20307380--20307447 Score: 84
Period size: 22 Copynumber: 3.1 Consensus size: 21
20307370 TCATCTTGAC
*
20307380 TTTCTTTT-TTCTTCCTTTTTCT
1 TTTCTTTTCTT-TT-CTTTTTTT
*
20307402 TTTCTTCTTCTTTTCTTCTTTT
1 TTTCTT-TTCTTTTCTTTTTTT
20307424 TTTCTTTTCTTTTCTTTTTTT
1 TTTCTTTTCTTTTCTTTTTTT
20307445 TTT
1 TTT
20307448 AAAAATGCCC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 17 0.41
22 18 0.44
23 4 0.10
24 2 0.05
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (21 bp):
TTTCTTTTCTTTTCTTTTTTT
Found at i:20307447 original size:5 final size:5
Alignment explanation
Indices: 20307396--20307445 Score: 66
Period size: 5 Copynumber: 9.8 Consensus size: 5
20307386 TTTTCTTCCT
*
20307396 TTTTC TTTTC TTCTTC TTTTC TTCTTT TTTTC TTTTC TTTTC TTTT- TTTT
1 TTTTC TTTTC TT-TTC TTTTC TT-TTC TTTTC TTTTC TTTTC TTTTC TTTT
20307446 TTAAAAATGC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
4 4 0.10
5 28 0.68
6 9 0.22
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTC
Found at i:20312785 original size:30 final size:30
Alignment explanation
Indices: 20312750--20312967 Score: 160
Period size: 30 Copynumber: 7.6 Consensus size: 30
20312740 CAAAATTTTT
*
20312750 TAAAATTATATTTTAACCCCTAAACTTTTCC
1 TAAAATTACATTTTAACCCCTAAAC-TTTCC
*
20312781 -AAAATTACATTTTAACCCTTAAACTTTCC
1 TAAAATTACATTTTAACCCCTAAACTTTCC
20312810 TAAAATTACATTTTAA-CCCT--A------
1 TAAAATTACATTTTAACCCCTAAACTTTCC
* *
20312831 -AAA-TCACATTTTAACTCCC-AAACCTTCC
1 TAAAATTACATTTTAAC-CCCTAAACTTTCC
* * * * *
20312859 CAAAATCACATTTTGA-CTCTCAAACCTTCC
1 TAAAATTACATTTTAACCCCT-AAACTTTCC
* * *
20312889 CAAAATCATATTTTAAACCCC-AAACTTTCC
1 TAAAATTACATTTT-AACCCCTAAACTTTCC
* *
20312919 TAAAATTACATTTTAACCCCTAAATTTTTC
1 TAAAATTACATTTTAACCCCTAAACTTTCC
*
20312949 TAAAATTACATTTTGACCC
1 TAAAATTACATTTTAACCC
20312968 TGAATTCTCC
Statistics
Matches: 153, Mismatches: 16, Indels: 37
0.74 0.08 0.18
Matches are distributed among these distances:
19 10 0.07
20 3 0.02
21 3 0.02
22 1 0.01
27 1 0.01
28 2 0.01
29 17 0.11
30 113 0.74
31 1 0.01
32 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.01, T:0.36
Consensus pattern (30 bp):
TAAAATTACATTTTAACCCCTAAACTTTCC
Found at i:20312832 original size:19 final size:19
Alignment explanation
Indices: 20312808--20312845 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
20312798 CTTAAACTTT
*
20312808 CCTAAAATTACATTTTAAC
1 CCTAAAATCACATTTTAAC
20312827 CCTAAAATCACATTTTAAC
1 CCTAAAATCACATTTTAAC
20312846 TCCCAAACCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.34
Consensus pattern (19 bp):
CCTAAAATCACATTTTAAC
Found at i:20312894 original size:79 final size:79
Alignment explanation
Indices: 20312750--20312904 Score: 186
Period size: 79 Copynumber: 2.0 Consensus size: 79
20312740 CAAAATTTTT
* * * * * * * *
20312750 TAAAATTATATTTTAACCCCTAAACTTTTCCAAAATTACATTTTAACCCTTAAACTTTCCTAAAA
1 TAAAATCACATTTTAACCCCTAAACCTTCCCAAAATCACATTTTAACCCTCAAACCTTCCCAAAA
*
20312815 TTACATTTTAACCC
66 TCACATTTTAACCC
* *
20312829 TAAAATCACATTTTAACTCCC-AAACCTTCCCAAAATCACATTTTGACTCTCAAACCTTCCCAAA
1 TAAAATCACATTTTAAC-CCCTAAACCTTCCCAAAATCACATTTTAACCCTCAAACCTTCCCAAA
*
20312893 ATCATATTTTAA
65 ATCACATTTTAA
20312905 ACCCCAAACT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
79 60 0.95
80 3 0.05
ACGTcount: A:0.38, C:0.26, G:0.01, T:0.35
Consensus pattern (79 bp):
TAAAATCACATTTTAACCCCTAAACCTTCCCAAAATCACATTTTAACCCTCAAACCTTCCCAAAA
TCACATTTTAACCC
Found at i:20319294 original size:41 final size:41
Alignment explanation
Indices: 20319152--20319422 Score: 310
Period size: 41 Copynumber: 6.5 Consensus size: 41
20319142 GGTGTATAAA
* * * * *
20319152 AAGGAAGACTCATGTCTCGGGTTTGAGCATGAGA-AACTGTAT
1 AAGGAAGACTCATGTCTCGAG-ATGAGAATGAGATTA-TGAAT
* * *
20319194 AAATGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATTT
1 -AA-GGAAGACTCATGTCTCGAGATGAGAATGAGATTATGA-AT
20319238 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
*
20319279 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGAAT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* * *
20319320 AAGGAAGACTCATGTCTCGAAATGAGAATGAGATTTTGATT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* * * **
20319361 AAGAAAGACTCATGTCTCGAGAAGAGAATGAGAATATGGTT
1 AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
* *
20319402 AAAGGAAGACTTATGACTCGA
1 -AAGGAAGACTCATGTCTCGA
20319423 AAGAGCATAA
Statistics
Matches: 201, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
41 115 0.57
42 52 0.26
43 16 0.08
44 18 0.09
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (41 bp):
AAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
Found at i:20319340 original size:124 final size:127
Alignment explanation
Indices: 20319151--20319422 Score: 381
Period size: 124 Copynumber: 2.2 Consensus size: 127
20319141 GGGTGTATAA
* * * *
20319151 AAAGGAAGACTCATGTCTCGGGTTTGAGCATGAGAAACTGTATAAATGGAAGACTCATGTCTCGA
1 AAAGGAAGACTCATGTCTCGAGTATGAGAATGAGAAACTGAATAAATGGAAGACTCATGTCTCGA
* * *
20319216 AATGAGAATGAGATTTTGATTTAAGGAAGACTCATGTCTCGAGATGAGAATGAGATTATGAAT
66 AATGAGAATGAGATTTTGA-TTAAGAAAGACTCATGTCTCGAGAAGAGAATGAGAATATGAAT
***
20319279 -AAGGAAGACTCATGTCTCGAG-ATGAGAATGAGATTTTGAAT-AA-GGAAGACTCATGTCTCGA
1 AAAGGAAGACTCATGTCTCGAGTATGAGAATGAGAAACTGAATAAATGGAAGACTCATGTCTCGA
**
20319340 AATGAGAATGAGATTTTGATTAAGAAAGACTCATGTCTCGAGAAGAGAATGAGAATATGGTT
66 AATGAGAATGAGATTTTGATTAAGAAAGACTCATGTCTCGAGAAGAGAATGAGAATATGAAT
* *
20319402 AAAGGAAGACTTATGACTCGA
1 AAAGGAAGACTCATGTCTCGA
20319423 AAGAGCATAA
Statistics
Matches: 129, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
123 38 0.29
124 55 0.43
125 2 0.02
126 14 0.11
127 20 0.16
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.26
Consensus pattern (127 bp):
AAAGGAAGACTCATGTCTCGAGTATGAGAATGAGAAACTGAATAAATGGAAGACTCATGTCTCGA
AATGAGAATGAGATTTTGATTAAGAAAGACTCATGTCTCGAGAAGAGAATGAGAATATGAAT
Found at i:20320035 original size:21 final size:21
Alignment explanation
Indices: 20319960--20320036 Score: 55
Period size: 21 Copynumber: 3.5 Consensus size: 21
20319950 CTGACTTGAG
* *
20319960 TTGTATCGGTAGTTAAAATTC
1 TTGTATCGGTAGTTAGAATAC
** * * *
20319981 AAGTTTCGGTAGTACTGAGCATAT
1 TTGTATCGGTAGT--T-AGAATAC
*
20320005 TTGTACCGGTAGTTAGAATAC
1 TTGTATCGGTAGTTAGAATAC
20320026 TTGTATCGGTA
1 TTGTATCGGTA
20320037 AAAGTTGTAA
Statistics
Matches: 39, Mismatches: 14, Indels: 6
0.66 0.24 0.10
Matches are distributed among these distances:
21 25 0.64
22 1 0.03
23 1 0.03
24 12 0.31
ACGTcount: A:0.27, C:0.12, G:0.23, T:0.38
Consensus pattern (21 bp):
TTGTATCGGTAGTTAGAATAC
Found at i:20326569 original size:39 final size:39
Alignment explanation
Indices: 20326455--20326577 Score: 149
Period size: 39 Copynumber: 3.2 Consensus size: 39
20326445 AGTTACATCA
* *
20326455 TCATCCAATCTCTTACCTAGATCATGGGGCAGATTACAG
1 TCATCCAATCTCTTACCTCGATCATGGGGCAGATTGCAG
* * * *
20326494 CCACCCGATCTTTTACAC-CGATCATGGGGCAGATTGCAG
1 TCATCCAATCTCTTAC-CTCGATCATGGGGCAGATTGCAG
* * *
20326533 TCATCCAATCTCTTACCTCGATCATGGGGAAAATTGCAA
1 TCATCCAATCTCTTACCTCGATCATGGGGCAGATTGCAG
20326572 TCATCC
1 TCATCC
20326578 GAAGCAATAA
Statistics
Matches: 69, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
38 1 0.01
39 67 0.97
40 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (39 bp):
TCATCCAATCTCTTACCTCGATCATGGGGCAGATTGCAG
Found at i:20326916 original size:171 final size:171
Alignment explanation
Indices: 20326631--20327002 Score: 564
Period size: 171 Copynumber: 2.2 Consensus size: 171
20326621 GAACCAAATC
* *
20326631 CATCTTCTTGATGAGATACAGAGAAGTGGATTGAAAAAATGAGGCGATCATCTTCCTGATGAGAT
1 CATCTTCTTGATGAGATACAGAGAAGTGAATTGAAAAAATGAGGCGATCATCTTCCTAATGAGAT
* * *
20326696 ACAGAGAAGTAGACCAAATCAATGAAGTAAAGCTCAATACGAATGAGACTTCAAACCGCATCTTC
66 ACAGAGAAGTAGACCAAATCAAAGAAGCAAAGCTCAATACGAATGAGACTTCAAACCCCATCTTC
* * * **
20326761 CTGATGAGATACAGAGAAGTGGGTCAAAGCAATAAATTGAT
131 CTAATGAGATACAAAAAAGTGGGTCAAAGCAATAAAGCGAT
* * *
20326802 CATCTTCTTGATGAGGTACAGAGAAGTGAATTGAAACAATGAGGCGGTCATCTTCCTAATGAGAT
1 CATCTTCTTGATGAGATACAGAGAAGTGAATTGAAAAAATGAGGCGATCATCTTCCTAATGAGAT
* *
20326867 ACAGAGAAGTAGACCAAATCAAAGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTTT
66 ACAGAGAAGTAGACCAAATCAAAGAAGCAAAGCTCAATACGAATGAGACTTCAAACCCCATCTTC
* *
20326932 CTAATGAGATACAAAAAAGTGGGTCAAAGTAATAAAGCGGT
131 CTAATGAGATACAAAAAAGTGGGTCAAAGCAATAAAGCGAT
* * *
20326973 CATCTTCCTGACGAGATGCAGAGAAGTGAA
1 CATCTTCTTGATGAGATACAGAGAAGTGAA
20327003 CCAAATCCGT
Statistics
Matches: 180, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
171 180 1.00
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (171 bp):
CATCTTCTTGATGAGATACAGAGAAGTGAATTGAAAAAATGAGGCGATCATCTTCCTAATGAGAT
ACAGAGAAGTAGACCAAATCAAAGAAGCAAAGCTCAATACGAATGAGACTTCAAACCCCATCTTC
CTAATGAGATACAAAAAAGTGGGTCAAAGCAATAAAGCGAT
Found at i:20327168 original size:208 final size:208
Alignment explanation
Indices: 20326804--20327368 Score: 735
Period size: 208 Copynumber: 2.7 Consensus size: 208
20326794 AAATTGATCA
* * *
20326804 TCTTCTTGATGAGGTACAGAGAAG-TGAATTGAAACAATGAGGCGGTCATCTTCCTAATGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTTG-ATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATA
* * *
20326868 CAGAGAAGTAGACCAAATCAAAGAAGCGAAGCTCAATACGAATGAGACTTCAAACCCCATCTT-T
65 CAGAGAAGTAGACCAAATCAATGAAGCGAAACTCAATACGAATGAGACTTCAAACCCTATCTTCT
* * * * * * *
20326932 CTAATGAGATACAAAAAAGTGGGTCAAAGTAATAAAGCGGTCATCTTCCTGACGAGATGCAGAGA
130 -TGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTAACGAGATACAGAAA
*
20326997 AGTGAACCAAATCCG
194 AGAGAACCAAATCCG
* *
20327012 TCTTCCTGATGAGATATAGAGAAGTTGATTGAAACAATGAGGTGGTCATCTTCCTGATGAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTTGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATAC
20327077 AGAGAAGTAGACCAAATCAATTG-AGCGAAACTCAATACGAATGAGACTTCAAACCCTATCTTCT
66 AGAGAAGTAGACCAAATCAA-TGAAGCGAAACTCAATACGAATGAGACTTCAAACCCTATCTTCT
* * * *
20327141 TGATAAGATACAGAGAAGTGGGTCAAAGCCATAAAGCGGTCATCTTCCTAATGAGATACATAAAA
130 TGATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTAACGAGATACAGAAAA
* *
20327206 GAGGACCAAATTCG
195 GAGAACCAAATCCG
* * * * *
20327220 TCTTCCTGATGAGATACAAAAAAGTGGATT-AAATCAATGAGACGGTCATCTTCTTGATGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTTGATTGAAA-CAATGAGGCGGTCATCTTCCTGATGAGATA
* * * * * *
20327284 TAGAGAAGTAGACCAAATCCATGAAGC-AAAGTTCAATGCGAGTGAAACTTCAAACCCCTATCTT
65 CAGAGAAGTAGACCAAATCAATGAAGCGAAA-CTCAATACGAATGAGACTTCAAA-CCCTATCTT
*
20327348 CCTGATGAGATACAGAGAAGT
128 CTTGATGAGATACAGAGAAGT
20327369 AGACCAAGAG
Statistics
Matches: 313, Mismatches: 37, Indels: 13
0.86 0.10 0.04
Matches are distributed among these distances:
207 8 0.03
208 273 0.87
209 32 0.10
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (208 bp):
TCTTCCTGATGAGATACAGAGAAGTTGATTGAAACAATGAGGCGGTCATCTTCCTGATGAGATAC
AGAGAAGTAGACCAAATCAATGAAGCGAAACTCAATACGAATGAGACTTCAAACCCTATCTTCTT
GATGAGATACAGAGAAGTGGGTCAAAGCAATAAAGCGGTCATCTTCCTAACGAGATACAGAAAAG
AGAACCAAATCCG
Found at i:20329394 original size:30 final size:30
Alignment explanation
Indices: 20329346--20329489 Score: 107
Period size: 30 Copynumber: 4.7 Consensus size: 30
20329336 GGTCCTGAAC
*
20329346 TTTCCAAAAATCATATTTTGACCAAC-AAACT
1 TTTCCAAAAAT-ACATTTTGACC-ACTAAACT
*
20329377 TTTCCAAAAATACATTTTGACCCCTAAACT
1 TTTCCAAAAATACATTTTGACCACTAAACT
* * * *
20329407 TTTTCAAAATTACAATTTTGATCC-TTAAAAT
1 TTTCCAAAAATAC-ATTTTGA-CCACTAAACT
* * *
20329438 TTTCTAAAATTACATTTTTG-CCCCTAAA-T
1 TTTCCAAAAATACA-TTTTGACCACTAAACT
**
20329467 TTTCCCAAATTTACATTTTGACC
1 TTT-CCAAAAATACATTTTGACC
20329490 CCAAAATCAC
Statistics
Matches: 95, Mismatches: 11, Indels: 15
0.79 0.09 0.12
Matches are distributed among these distances:
29 12 0.13
30 42 0.44
31 39 0.41
32 2 0.02
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (30 bp):
TTTCCAAAAATACATTTTGACCACTAAACT
Found at i:20329426 original size:61 final size:59
Alignment explanation
Indices: 20329346--20329489 Score: 141
Period size: 61 Copynumber: 2.4 Consensus size: 59
20329336 GGTCCTGAAC
* * *
20329346 TTTCCAAAAATCATATTTTGACC-AACAAACTTTTCCAAAAATACA-TTTTGACCCCTAAACT
1 TTTCCCAAAATTACATTTTGACCTAA-AAA-TTTTCCAAAAATACATTTTTG-CCCCTAAA-T
* * * *
20329407 TTT-TCAAAATTACAATTTTGATCCTTAAAATTTTCTAAAATTACATTTTTGCCCCTAAAT
1 TTTCCCAAAATTAC-ATTTTGA-CCTAAAAATTTTCCAAAAATACATTTTTGCCCCTAAAT
*
20329467 TTTCCCAAATTTACATTTTGACC
1 TTTCCCAAAATTACATTTTGACC
20329490 CCAAAATCAC
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
59 2 0.03
60 17 0.25
61 39 0.57
62 10 0.14
63 1 0.01
ACGTcount: A:0.35, C:0.22, G:0.03, T:0.40
Consensus pattern (59 bp):
TTTCCCAAAATTACATTTTGACCTAAAAATTTTCCAAAAATACATTTTTGCCCCTAAAT
Found at i:20329525 original size:30 final size:30
Alignment explanation
Indices: 20329489--20329574 Score: 109
Period size: 30 Copynumber: 2.9 Consensus size: 30
20329479 ACATTTTGAC
*
20329489 CCCAAAATCACATTTTGACTCTCAAACCTT
1 CCCAAAATCACATTTTGACCCTCAAACCTT
* *
20329519 CCCAAAATCACATTTTGACCCCCAAACTTT
1 CCCAAAATCACATTTTGACCCTCAAACCTT
* * * *
20329549 CCTAAAATTATATTTTAACCCTCAAA
1 CCCAAAATCACATTTTGACCCTCAAA
20329575 TTTTTTTAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.36, C:0.31, G:0.02, T:0.30
Consensus pattern (30 bp):
CCCAAAATCACATTTTGACCCTCAAACCTT
Found at i:20333960 original size:29 final size:30
Alignment explanation
Indices: 20333926--20333993 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
20333916 AAATTTGAAG
*
20333926 TTTAGTTTTTGTAC-TTTC-ATTTTTAAGAA
1 TTTAGTTTTTGTACTTTTCAAATTTTAA-AA
*
20333955 TTTAGTTTTTTTACTTTTCAAATTTTAAAA
1 TTTAGTTTTTGTACTTTTCAAATTTTAAAA
20333985 TTTATGTTT
1 TTTA-GTTT
20333994 AATTGTTAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 13 0.38
30 10 0.29
31 11 0.32
ACGTcount: A:0.25, C:0.06, G:0.07, T:0.62
Consensus pattern (30 bp):
TTTAGTTTTTGTACTTTTCAAATTTTAAAA
Found at i:20340437 original size:18 final size:19
Alignment explanation
Indices: 20340416--20340461 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
20340406 GAAAGAACTC
20340416 AAATTATAATAAA-TTTTA
1 AAATTATAATAAAGTTTTA
20340434 AAA-TA-AATTAAAGTTTTA
1 AAATTATAA-TAAAGTTTTA
20340452 AAATTATAAT
1 AAATTATAAT
20340462 CACGATTTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
16 2 0.08
17 6 0.25
18 11 0.46
19 3 0.12
20 2 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AAATTATAATAAAGTTTTA
Found at i:20341034 original size:16 final size:15
Alignment explanation
Indices: 20341013--20341050 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
20341003 TTTAGAATCT
20341013 ATAAAAATATTCAAAA
1 ATAAAAA-ATTCAAAA
20341029 AT-AAAAATTCAAAA
1 ATAAAAAATTCAAAA
*
20341043 TTAAAAAA
1 ATAAAAAA
20341051 ATAAAAAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 9 0.45
16 2 0.10
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (15 bp):
ATAAAAAATTCAAAA
Found at i:20341202 original size:31 final size:31
Alignment explanation
Indices: 20341185--20341269 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
20341175 AGATTGATGG
20341185 TCAAATTTGACTCTTTTTAAAAAATTAATAA
1 TCAAATTTGACTCTTTTTAAAAAATTAATAA
* * *
20341216 TTATATTTGACTCTTTTTCAAAAATTAATAA
1 TCAAATTTGACTCTTTTTAAAAAATTAATAA
* * *
20341247 TCATATTTGACTTTTTTTTAAAA
1 TCAAATTTGACTCTTTTTAAAAA
20341270 TTGAGAGTCA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (31 bp):
TCAAATTTGACTCTTTTTAAAAAATTAATAA
Found at i:20343279 original size:47 final size:48
Alignment explanation
Indices: 20343190--20343285 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
20343180 ATTAAAATTT
*
20343190 CCTCTTCACGTCTCTGCAACCCCTGCTGCTATTATTTCTTTCCGGCAA
1 CCTCTTCACGTCTCTGCAACCCCTGCTACTATTATTTCTTTCCGGCAA
* *
20343238 CCTCTTCACGTC-CTGCAACCCTTTGCTACTATTATTT-TTTCCTGCAA
1 CCTCTTCACGTCTCTGCAACCC-CTGCTACTATTATTTCTTTCCGGCAA
20343285 C
1 C
20343286 TACTTTGCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
47 19 0.43
48 25 0.57
ACGTcount: A:0.16, C:0.36, G:0.10, T:0.38
Consensus pattern (48 bp):
CCTCTTCACGTCTCTGCAACCCCTGCTACTATTATTTCTTTCCGGCAA
Found at i:20348906 original size:24 final size:24
Alignment explanation
Indices: 20348852--20348906 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
20348842 TATAATCACC
20348852 CTATTTTTCTTTCTTTTCTTCATT
1 CTATTTTTCTTTCTTTTCTTCATT
* *
20348876 TTGTTTTTCTTT-TCTTTCTTCCA-T
1 CTATTTTTCTTTCT-TTTCTT-CATT
20348900 CTATTTT
1 CTATTTT
20348907 CCTTAGAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.04
24 22 0.88
25 2 0.08
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (24 bp):
CTATTTTTCTTTCTTTTCTTCATT
Found at i:20349588 original size:198 final size:198
Alignment explanation
Indices: 20349318--20349933 Score: 814
Period size: 198 Copynumber: 3.1 Consensus size: 198
20349308 ATGAGTCAGC
* * *
20349318 CTAGTTTCGTTTAGAACAAACGGAGATTGATTTCAATTTGTAGTTCAAAATATATGATTTTTTGA
1 CTAGTTTTGTTTAGAACAAACGGAGATTGATTTCAATTTGTAGTTTAAAATATATGAATTTTTGA
* * *
20349383 GTGTTGAAATGTCATAAAAATCTTACAACAAAATTCTTATAAAACAGATTTAGCAGTGACTTTGA
66 ATGTTGAAAGGTCATAAAAATCTTACAACAGAATTCTTATAAAACAGATTTAGCAGTGACTTTGA
** *
20349448 AAAATCACCAATAATTGT-AAAAGATAAAATAGGAAATGAAACTTATATCCCTATAACA-GTATG
131 AAAATCACCAA-AATTGTCAAAAGATAAAATAGGAAATGAGCCTTATATCTCTATAA-ATGTATG
*
20349511 AAAGT
194 GAAGT
*
20349516 CTAGTTTTGTTTAGAACAAACGGAGATTGATTTCAATTTGTAGTTTAAAAGATATGAATTTTTGA
1 CTAGTTTTGTTTAGAACAAACGGAGATTGATTTCAATTTGTAGTTTAAAATATATGAATTTTTGA
* * *
20349581 ATGTTGAAAGGTCATATAAATC-TAGCAGCAGAATTCTTATAAAACAGTTTTAGCAGTGACTTTG
66 ATGTTGAAAGGTCATAAAAATCTTA-CAACAGAATTCTTATAAAACAGATTTAGCAGTGACTTTG
* * *
20349645 AAAAATCACC-AAA-TGCTGAACAAGATAAAATAGAAAATGAGCCTTAAATCTCTATAAATGTAT
130 AAAAATCACCAAAATTG-TCAA-AAGATAAAATAGGAAATGAGCCTTATATCTCTATAAATGTAT
20349708 GGAAGT
193 GGAAGT
* * * * * * * * * *
20349714 CTAGTTTTGTTTAGAATAAATGAATACTGAATTCAATTTTTGGTTTACAATATATGAATTTTTTA
1 CTAGTTTTGTTTAGAACAAACGGAGATTGATTTCAATTTGTAGTTTAAAATATATGAATTTTTGA
** *
20349779 ATGTTGAAAGGTCATAAAAATCTGGC-ACAGAATTCTTATAAAACAGATTTAACAGTGACTTTGA
66 ATGTTGAAAGGTCATAAAAATCTTACAACAGAATTCTTATAAAACAGATTTAGCAGTGACTTTGA
* *
20349843 AAAATCATCAAAAATT-TCAAAAGATAAAATAGGAAGTGAGCCTTATATCTCTATAAATGTATGG
131 AAAATCA-CCAAAATTGTCAAAAGATAAAATAGGAAATGAGCCTTATATCTCTATAAATGTATGG
20349907 AAGT
195 AAGT
* * *
20349911 TTAGTTTTGTTTAAAATAAACGG
1 CTAGTTTTGTTTAGAACAAACGG
20349934 TTCTCAATTT
Statistics
Matches: 367, Mismatches: 42, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
195 2 0.01
196 3 0.01
197 112 0.31
198 246 0.67
199 3 0.01
200 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (198 bp):
CTAGTTTTGTTTAGAACAAACGGAGATTGATTTCAATTTGTAGTTTAAAATATATGAATTTTTGA
ATGTTGAAAGGTCATAAAAATCTTACAACAGAATTCTTATAAAACAGATTTAGCAGTGACTTTGA
AAAATCACCAAAATTGTCAAAAGATAAAATAGGAAATGAGCCTTATATCTCTATAAATGTATGGA
AGT
Found at i:20365834 original size:18 final size:18
Alignment explanation
Indices: 20365811--20365879 Score: 84
Period size: 18 Copynumber: 3.8 Consensus size: 18
20365801 ACGGAAGGAA
20365811 TAGCATACTGGCTCGTTT
1 TAGCATACTGGCTCGTTT
* *
20365829 TAGCATATTGGCTCATTT
1 TAGCATACTGGCTCGTTT
* *
20365847 AAGCATACTGGCTCGTTA
1 TAGCATACTGGCTCGTTT
* *
20365865 GAGCATACTAGCTCG
1 TAGCATACTGGCTCG
20365880 CAAGAGCATT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (18 bp):
TAGCATACTGGCTCGTTT
Found at i:20365885 original size:18 final size:18
Alignment explanation
Indices: 20365848--20365888 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20365838 GGCTCATTTA
* **
20365848 AGCATACTGGCTCGTTAG
1 AGCATACTAGCTCGCAAG
20365866 AGCATACTAGCTCGCAAG
1 AGCATACTAGCTCGCAAG
20365884 AGCAT
1 AGCAT
20365889 TATTGGATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.24, T:0.22
Consensus pattern (18 bp):
AGCATACTAGCTCGCAAG
Found at i:20366676 original size:21 final size:21
Alignment explanation
Indices: 20366616--20366690 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
20366606 AGAGTTTTTA
* *
20366616 GTATCGGTAGAAGCATGACTT
1 GTATCGGTAGAATCATCACTT
* * *
20366637 GTTTCAGTAGAAGT-GTCACTT
1 GTATCGGTAGAA-TCATCACTT
*
20366658 GTATCGGTAGAATCATCACTA
1 GTATCGGTAGAATCATCACTT
*
20366679 GTATCGATAGAA
1 GTATCGGTAGAA
20366691 GTTTGCTACT
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 1 0.02
21 41 0.98
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAATCATCACTT
Found at i:20369338 original size:26 final size:25
Alignment explanation
Indices: 20369285--20369350 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 25
20369275 TTGGTTGCAC
*
20369285 AAAAATAAAAATATTAACTTATGGAA
1 AAAAAT-AAAATATTAAATTATGGAA
* *
20369311 AAAAATAAAATGATTAAATTTTGTAA
1 AAAAATAAAAT-ATTAAATTATGGAA
* *
20369337 AAGAAGAAAATATT
1 AAAAATAAAATATT
20369351 TTTTTATAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
25 8 0.24
26 26 0.76
ACGTcount: A:0.61, C:0.02, G:0.09, T:0.29
Consensus pattern (25 bp):
AAAAATAAAATATTAAATTATGGAA
Found at i:20370466 original size:43 final size:43
Alignment explanation
Indices: 20370405--20370717 Score: 340
Period size: 43 Copynumber: 7.3 Consensus size: 43
20370395 AAATTGGCAA
* * * * *
20370405 AAACGCAGCTAAAGAACATGATCTTTAACAGCACTTCTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCCCAC
* * *
20370448 AAACGCCGCTAAAGAACATGGTCTTTAGCGGTGCTTCTCCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCCCAC
* * * *
20370491 AAACGCTGCTAAAGAACATGGTATTTAGCAGCACTTTTCCCTC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCCCAC
* *
20370534 AAATGCCGCTAAAGAACATGGTCTTTAGC-GACGCTTTTTCCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCAG-CGCTTTTCCCAC
* * * *
20370577 AAACGTCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTCACAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCCCAC
* * * * * * **
20370620 AAATGCCGCTATAGAACATGGTCTTTAACGGTGTTTTTTACAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCCCAC
* * *
20370663 AAACGCCGCTATAGAACATGGTCTTTAGCAGCGTTTTTCTCAC
1 AAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCCCAC
*
20370706 AAACGCCACTAA
1 AAACGCCGCTAA
20370718 CATTAACAGA
Statistics
Matches: 230, Mismatches: 38, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
42 1 0.00
43 228 0.99
44 1 0.00
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGGTCTTTAGCAGCGCTTTTCCCAC
Found at i:20370550 original size:86 final size:86
Alignment explanation
Indices: 20370405--20370717 Score: 376
Period size: 86 Copynumber: 3.6 Consensus size: 86
20370395 AAATTGGCAA
* * * * *
20370405 AAACGCAGCTAAAGAACATGATCTTTAACAGCACTTCTCCCACAAACGCCGCTAAAGAACATGGT
1 AAACGCTGCTAAAGAACATGGTCTTTAGCAGCACTTTTCCCACAAATGCCGCTAAAGAACATGGT
* *
20370470 CTTTAGCGGTGCTTCTCCCAC
66 CTTTAGCGGTGCTTTTTCCAC
* *
20370491 AAACGCTGCTAAAGAACATGGTATTTAGCAGCACTTTTCCCTCAAATGCCGCTAAAGAACATGGT
1 AAACGCTGCTAAAGAACATGGTCTTTAGCAGCACTTTTCCCACAAATGCCGCTAAAGAACATGGT
**
20370556 CTTTAGCGACGCTTTTTCCAC
66 CTTTAGCGGTGCTTTTTCCAC
* ** * *
20370577 AAACG-TCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTCACACAAATGCCGCTATAGAACATGG
1 AAACGCT-GCTAAAGAACATGGTCTTTAGCAGCACTTTTCCCACAAATGCCGCTAAAGAACATGG
* * *
20370641 TCTTTAACGGTGTTTTTTACAC
65 TCTTTAGCGGTGCTTTTTCCAC
* * ** * * *
20370663 AAACGCCGCTATAGAACATGGTCTTTAGCAGCGTTTTTCTCACAAACGCCACTAA
1 AAACGCTGCTAAAGAACATGGTCTTTAGCAGCACTTTTCCCACAAATGCCGCTAA
20370718 CATTAACAGA
Statistics
Matches: 195, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
85 1 0.01
86 194 0.99
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.27
Consensus pattern (86 bp):
AAACGCTGCTAAAGAACATGGTCTTTAGCAGCACTTTTCCCACAAATGCCGCTAAAGAACATGGT
CTTTAGCGGTGCTTTTTCCAC
Found at i:20373921 original size:40 final size:41
Alignment explanation
Indices: 20373877--20373954 Score: 131
Period size: 40 Copynumber: 1.9 Consensus size: 41
20373867 GGAAAACGTC
*
20373877 GCTATTGCTTAATCATTAGCGGCG-TTTTCCCATAAACACT
1 GCTATTGCTTAACCATTAGCGGCGTTTTTCCCATAAACACT
*
20373917 GCTATTGCTTAACCTTTAGCGGCGTTTTTCCCATAAAC
1 GCTATTGCTTAACCATTAGCGGCGTTTTTCCCATAAAC
20373955 GCCGCTACTG
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 22 0.63
41 13 0.37
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (41 bp):
GCTATTGCTTAACCATTAGCGGCGTTTTTCCCATAAACACT
Found at i:20373967 original size:41 final size:40
Alignment explanation
Indices: 20373870--20373974 Score: 138
Period size: 41 Copynumber: 2.6 Consensus size: 40
20373860 GTTTATGGGA
* * *
20373870 AAACGTCGCTATTGCTTAATCATTAGCGGCGTTTTCCCAT
1 AAACGCCGCTATTGCTTAACCTTTAGCGGCGTTTTCCCAT
* *
20373910 AAACACTGCTATTGCTTAACCTTTAGCGGCGTTTTTCCCAT
1 AAACGCCGCTATTGCTTAACCTTTAGCGGCG-TTTTCCCAT
* *
20373951 AAACGCCGCTACTGCTTTACCTTT
1 AAACGCCGCTATTGCTTAACCTTT
20373975 TGCAGCCGTT
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
40 26 0.47
41 29 0.53
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (40 bp):
AAACGCCGCTATTGCTTAACCTTTAGCGGCGTTTTCCCAT
Found at i:20375420 original size:56 final size:57
Alignment explanation
Indices: 20375360--20375469 Score: 136
Period size: 56 Copynumber: 1.9 Consensus size: 57
20375350 TTACCTCTTG
* * *
20375360 AATATTACATTAATATATA-TATTAGTATA-AGAGGAGA-CTGAGTCAATTAACTATTA
1 AATATT-CATTAATATACATTATTACTATATA-AGGAGATCTGAGTCAAATAACTATTA
* *
20375416 AATATTGATTAATATACATTATTACTATATAAGGAGATTTGAGTCAAATAACTA
1 AATATTCATTAATATACATTATTACTATATAAGGAGATCTGAGTCAAATAACTA
20375470 ATTTCATATG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
55 10 0.22
56 21 0.46
57 15 0.33
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (57 bp):
AATATTCATTAATATACATTATTACTATATAAGGAGATCTGAGTCAAATAACTATTA
Found at i:20376677 original size:41 final size:41
Alignment explanation
Indices: 20376639--20376852 Score: 182
Period size: 41 Copynumber: 5.2 Consensus size: 41
20376629 AAAAACGCCG
* * * *
20376639 CTATTGCT-TAACCTTTAGCGGCATTTTCCCTATAAACGCCA
1 CTATTGCTCTGACCTTTAGCGGCGTTTTCTC-ATAAACGTCA
* * *
20376680 CTGA-TGCTCTGACCTTTAGCGGGGTTTTTTCATAAATGTCA
1 CT-ATTGCTCTGACCTTTAGCGGCGTTTTCTCATAAACGTCA
* * * *
20376721 CTATTACTCTGACCTTTAACGGCGCTTTCTCATAAATGTCA
1 CTATTGCTCTGACCTTTAGCGGCGTTTTCTCATAAACGTCA
* * * ** *
20376762 CTAATGCTCTAACCTTTAGTGGCACTTTCTCATAAACGTCG
1 CTATTGCTCTGACCTTTAGCGGCGTTTTCTCATAAACGTCA
* * * *
20376803 CTAATGCTCTGACCTTTAGCGGTGTTTT-TCCTATAAACGACG
1 CTATTGCTCTGACCTTTAGCGGCGTTTTCT-C-ATAAACGTCA
20376845 CTATTGCT
1 CTATTGCT
20376853 TTACTTTTTG
Statistics
Matches: 141, Mismatches: 27, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
40 2 0.01
41 105 0.74
42 34 0.24
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.36
Consensus pattern (41 bp):
CTATTGCTCTGACCTTTAGCGGCGTTTTCTCATAAACGTCA
Found at i:20377349 original size:15 final size:15
Alignment explanation
Indices: 20377329--20377361 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
20377319 TTTTCTTGTA
20377329 AATTCAAATCCAACC
1 AATTCAAATCCAACC
*
20377344 AATTCAAATCCAATC
1 AATTCAAATCCAACC
20377359 AAT
1 AAT
20377362 AACTTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (15 bp):
AATTCAAATCCAACC
Found at i:20377619 original size:21 final size:21
Alignment explanation
Indices: 20377595--20377634 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
20377585 ATTCGCTTTT
20377595 CTCGCTGTTGCCTCCGCTTCC
1 CTCGCTGTTGCCTCCGCTTCC
20377616 CTCGCTGTTGCCTCCGCTT
1 CTCGCTGTTGCCTCCGCTT
20377635 TAAGTTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.45, G:0.20, T:0.35
Consensus pattern (21 bp):
CTCGCTGTTGCCTCCGCTTCC
Found at i:20383436 original size:20 final size:20
Alignment explanation
Indices: 20383399--20383436 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20383389 GGTTGTTGTT
*
20383399 AATAAATAACTAATTATTAA
1 AATAAATAACTAAATATTAA
*
20383419 AATAAATAATTAAATATT
1 AATAAATAACTAAATATT
20383437 TGGATTGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (20 bp):
AATAAATAACTAAATATTAA
Found at i:20383454 original size:26 final size:26
Alignment explanation
Indices: 20383423--20383509 Score: 95
Period size: 26 Copynumber: 3.2 Consensus size: 26
20383413 TATTAAAATA
*
20383423 AATAATTAAATATTTGGATTGTTTTT
1 AATAATTAAATATTTGAATTGTTTTT
* *
20383449 AATAATTAAATATTT-AATTAAATATAATTA
1 AATAATTAAATATTTGAATT--GT-T--TTT
20383479 AATAATTAAATATTTGAATTGTTTTT
1 AATAATTAAATATTTGAATTGTTTTT
20383505 AATAA
1 AATAA
20383510 ATAACTAATT
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
25 3 0.06
26 22 0.44
27 1 0.02
28 2 0.04
29 1 0.02
30 17 0.34
31 4 0.08
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (26 bp):
AATAATTAAATATTTGAATTGTTTTT
Found at i:20383553 original size:102 final size:104
Alignment explanation
Indices: 20383309--20383597 Score: 352
Period size: 102 Copynumber: 2.7 Consensus size: 104
20383299 AGTTGCAAAT
* * *
20383309 AAATAACTAATTAAATATTTCGAGTTACTTTTAATAATTAAATA--TAATTAAATAATTAAATAT
1 AAATAA-TAATTAAATATTT-GGGTTATTTTTAATAATTAAATATTTAATTAAAT-A-TAATTA-
** **
20383372 TTTGAATTAAATATTTGGGTTGTTGTTAATAAATAACTAATTATTA
61 AAT-AATTAAATATTTGAATTGTTGTTAATAAATAACTAATTA-TA
* *
20383418 AAATAAATAATTAAATATTTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATA
1 AAAT-AATAATTAAATATTTGGGTTATTTTTAATAATTAAATATTTAATTAAATATAATTAAATA
*
20383483 ATTAAATATTTGAATTGTTTTTAATAAATAACTAATTA-A
65 ATTAAATATTTGAATTGTTGTTAATAAATAACTAATTATA
* * * *
20383522 AGAT-TTATTTAAATATTTGGGTTATTTTTAATAATTAAATATTTAATTAAATATAATTAACTAA
1 AAATAATAATTAAATATTTGGGTTATTTTTAATAATTAAATATTTAATTAAATATAATTAAATAA
20383586 TTAAATATTTGA
66 TTAAATATTTGA
20383598 GTTATTTTAA
Statistics
Matches: 161, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
102 67 0.42
104 4 0.02
106 36 0.22
107 1 0.01
108 24 0.15
109 18 0.11
110 11 0.07
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (104 bp):
AAATAATAATTAAATATTTGGGTTATTTTTAATAATTAAATATTTAATTAAATATAATTAAATAA
TTAAATATTTGAATTGTTGTTAATAAATAACTAATTATA
Found at i:20383602 original size:56 final size:55
Alignment explanation
Indices: 20383307--20383623 Score: 238
Period size: 50 Copynumber: 5.9 Consensus size: 55
20383297 ATAGTTGCAA
* *
20383307 ATAAATAACTAATTAAATATTTCGAGTTACTTTTAATAATTAAAT-A-TAATTAAAT
1 ATAATTAA-TAATTAAATATTT-GAGTTATTTTTAATAATTAAATAATTAATTAAAT
** * * * * *
20383362 AATTAAATATTTTGAATTAAATATTTGGGTTGTTGTTAATAAATAACTAATT-ATTAAA-
1 -A-T-AAT-TAAT-AATTAAATATTTGAGTTATTTTTAATAATTAAATAATTAATTAAAT
* *
20383420 AT-A--AATAATTAAATATTTG-GATTGTTTTTAATAATTAAATATTTAATTAAAT
1 ATAATTAATAATTAAATATTTGAG-TTATTTTTAATAATTAAATAATTAATTAAAT
* * * *
20383472 ATAATTAAATAATTAAATATTTGAATT-GTTTT--TAA-TAAATAACTAATTAAAG
1 ATAATT-AATAATTAAATATTTGAGTTATTTTTAATAATTAAATAATTAATTAAAT
* *
20383524 AT--TT-AT--TTAAATATTTGGGTTATTTTTAATAATTAAATATTTAATTAAAT
1 ATAATTAATAATTAAATATTTGAGTTATTTTTAATAATTAAATAATTAATTAAAT
* *
20383574 ATAATTAACTAATTAAATATTTGAGTTA-TTTTAATTTATTAAATTATTAA
1 ATAATTAA-TAATTAAATATTTGAGTTATTTTTAA-TAATTAAATAATTAA
20383624 ATATTTAAAT
Statistics
Matches: 206, Mismatches: 30, Indels: 50
0.72 0.10 0.17
Matches are distributed among these distances:
46 13 0.06
47 4 0.02
48 2 0.01
49 4 0.02
50 50 0.24
51 7 0.03
52 20 0.10
53 5 0.02
54 2 0.01
55 10 0.05
56 47 0.23
57 2 0.01
58 19 0.09
59 20 0.10
60 1 0.00
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (55 bp):
ATAATTAATAATTAAATATTTGAGTTATTTTTAATAATTAAATAATTAATTAAAT
Found at i:20383607 original size:26 final size:25
Alignment explanation
Indices: 20383530--20383617 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 25
20383520 AAAGATTTAT
*
20383530 TTAAATATTTGGGTTATTTTTAATAA
1 TTAAATATTTGAGTTA-TTTTAATAA
*
20383556 TTAAATATTT-AATTAAATATAATTAACTAA
1 TTAAATATTTGAGTT--AT-T--TTAA-TAA
*
20383586 TTAAATATTTGAGTTATTTTAATTTA
1 TTAAATATTTGAGTTATTTTAA-TAA
20383612 TTAAAT
1 TTAAAT
20383618 TATTAAATAT
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
25 2 0.04
26 23 0.46
27 2 0.04
28 1 0.02
29 6 0.12
30 13 0.26
31 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.51
Consensus pattern (25 bp):
TTAAATATTTGAGTTATTTTAATAA
Found at i:20383609 original size:30 final size:28
Alignment explanation
Indices: 20383530--20383609 Score: 76
Period size: 30 Copynumber: 2.8 Consensus size: 28
20383520 AAAGATTTAT
*
20383530 TTAAATATTTGGGTTATTT--TTAATAA
1 TTAAATATTTGAGTTATTTAATTAATAA
* *
20383556 TTAAATATTT-AATTAAATATAATTAACTAA
1 TTAAATATTTGAGTT--ATTTAATTAA-TAA
20383586 TTAAATATTTGAGTTATTTTAATT
1 TTAAATATTTGAGTTA-TTTAATT
20383610 TATTAAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
25 2 0.05
26 10 0.24
27 3 0.07
29 5 0.12
30 19 0.45
31 3 0.07
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.51
Consensus pattern (28 bp):
TTAAATATTTGAGTTATTTAATTAATAA
Found at i:20383630 original size:102 final size:102
Alignment explanation
Indices: 20383316--20383631 Score: 325
Period size: 102 Copynumber: 3.0 Consensus size: 102
20383306 AATAAATAAC
* * * **
20383316 TAATTAAATATTTCGAGTTACTTTTAATAATTAAATA--TAATTAAATAATTAAATATTTTGAAT
1 TAATTAAATATTTGGA-TTATTTTTAATAATTAAATATTTAATTAAAT-A-TAATTA-AAT-AAT
** **
20383379 TAAATATTTGGGTTG-TTGTTAATAAATAACTAATTATTAAAATAAA
61 TAAATATTTGAATTGATT-TTAATAAAT-A--AATTATT-AAATATT
*
20383425 TAATTAAATATTTGGATTGTTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATTAAAT
1 TAATTAAATATTTGGATTATTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATTAAAT
* * * *
20383490 ATTTGAATTGTTTTTAATAAATAACTAATTAAAGATT
66 ATTTGAATTGATTTTAATAAATAAATTATTAAATATT
* * *
20383527 TATTTAAATATTTGGGTTATTTTTAATAATTAAATATTTAATTAAATATAATTAACTAATTAAAT
1 TAATTAAATATTTGGATTATTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATTAAAT
* * *
20383592 ATTTGAGTT-ATTTTAATTTATTAAATTATTAAATATT
66 ATTTGAATTGATTTTAA-TAAATAAATTATTAAATATT
20383629 TAA
1 TAA
20383632 ATATTTAATT
Statistics
Matches: 178, Mismatches: 25, Indels: 15
0.82 0.11 0.07
Matches are distributed among these distances:
101 6 0.03
102 90 0.51
103 5 0.03
105 1 0.01
106 25 0.14
107 3 0.02
108 23 0.13
109 16 0.09
110 9 0.05
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (102 bp):
TAATTAAATATTTGGATTATTTTTAATAATTAAATATTTAATTAAATATAATTAAATAATTAAAT
ATTTGAATTGATTTTAATAAATAAATTATTAAATATT
Found at i:20383687 original size:72 final size:72
Alignment explanation
Indices: 20383551--20383690 Score: 160
Period size: 72 Copynumber: 1.9 Consensus size: 72
20383541 GGTTATTTTT
* ** *
20383551 AATAATTAAATATTTAATTAAATATAATTAACTAATTAAATATTTGAGTTATTTTAATTTATTAA
1 AATAATTAAATATTTAATTAAATATAATTAACTAATTAAACATTTGAAATATATTAATTTATTAA
20383616 ATTATTA
66 ATTATTA
* * * *
20383623 AATATTTAAATATTTAATTAAATGTTATT-AGTAATTAAACATTT-AAATA-ATTAACTTCTAAT
1 AATAATTAAATATTTAATTAAATATAATTAACTAATTAAACATTTGAAATATATTAA-TT-T-AT
20383685 TAAATT
63 TAAATT
20383691 TATACAATTT
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
69 4 0.07
70 5 0.09
71 14 0.25
72 34 0.60
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (72 bp):
AATAATTAAATATTTAATTAAATATAATTAACTAATTAAACATTTGAAATATATTAATTTATTAA
ATTATTA
Found at i:20386340 original size:41 final size:41
Alignment explanation
Indices: 20386294--20386486 Score: 206
Period size: 42 Copynumber: 4.7 Consensus size: 41
20386284 TTAGCGTTGT
* ** * *
20386294 TTTTCTCATAAGCGCCGTTAATGCTCTGATCATTAGCGGCG
1 TTTTCCCATAAGCGCCGCCAATGCTCTGACCTTTAGCGGCG
* ** * *
20386335 CTTTCTGATAAGCGCCGTCAATGCTCTAACCTTTAGCGGCG
1 TTTTCCCATAAGCGCCGCCAATGCTCTGACCTTTAGCGGCG
* * * *
20386376 TTTTTCCCAGAAGCGTCGCCAATGCTCTGATCTTTAACGGCG
1 -TTTTCCCATAAGCGCCGCCAATGCTCTGACCTTTAGCGGCG
* * *
20386418 TTTTCCACATAAACGCCGCTAATGCTCTGACCTTTAGCAGCG
1 TTTTCC-CATAAGCGCCGCCAATGCTCTGACCTTTAGCGGCG
*
20386460 TTTTCCCATAAACGCCGCCAATGCTCT
1 TTTTCCCATAAGCGCCGCCAATGCTCT
20386487 TTCCCATATT
Statistics
Matches: 127, Mismatches: 23, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
41 61 0.48
42 66 0.52
ACGTcount: A:0.21, C:0.30, G:0.19, T:0.31
Consensus pattern (41 bp):
TTTTCCCATAAGCGCCGCCAATGCTCTGACCTTTAGCGGCG
Found at i:20386380 original size:83 final size:84
Alignment explanation
Indices: 20386262--20386486 Score: 251
Period size: 83 Copynumber: 2.7 Consensus size: 84
20386252 TTTATGAGAA
* * ** * **
20386262 AAACGCCGCTATTGCT-TAACTTTTAGCGTTGTTTTTCTCATAAGCGCCGTTAATGCTCTGATCA
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGCGTTTTTCCCATAAGCGCCGCCAATGCTCTGATCA
* **
20386326 TTAGCGGCGCTTT-CTGAT
66 TTAACGGCGCTTTCCACAT
* * *
20386344 AAGCGCCG-TCAATGCTCTAACCTTTAGCGGCGTTTTTCCCAGAAGCGTCGCCAATGCTCTGATC
1 AAACGCCGCT-AATGCTCTAACCTTTAGCGGCGTTTTTCCCATAAGCGCCGCCAATGCTCTGATC
* *
20386408 TTTAACGGCGTTTTCCACAT
65 ATTAACGGCGCTTTCCACAT
* * *
20386428 AAACGCCGCTAATGCTCTGACCTTTAGCAGCG-TTTTCCCATAAACGCCGCCAATGCTCT
1 AAACGCCGCTAATGCTCTAACCTTTAGCGGCGTTTTTCCCATAAGCGCCGCCAATGCTCT
20386487 TTCCCATATT
Statistics
Matches: 118, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
81 1 0.01
82 12 0.10
83 74 0.63
84 30 0.25
85 1 0.01
ACGTcount: A:0.21, C:0.28, G:0.19, T:0.32
Consensus pattern (84 bp):
AAACGCCGCTAATGCTCTAACCTTTAGCGGCGTTTTTCCCATAAGCGCCGCCAATGCTCTGATCA
TTAACGGCGCTTTCCACAT
Found at i:20388471 original size:41 final size:41
Alignment explanation
Indices: 20388423--20388701 Score: 296
Period size: 41 Copynumber: 6.9 Consensus size: 41
20388413 GGCTTTTCCT
*
20388423 CATAAACGCCGCTAATGCTCTAACCTTTAGCGGCGCTTTGC
1 CATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTGC
* *
20388464 CAGAAACGTCGCTAATGCTCTGACCTTTAGCGGCGCTTTGC
1 CATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTGC
* * *
20388505 CAGAAACGCCGCTAATGCTCTGACCTTTACCGGCGC-TTAC
1 CATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTGC
* * **
20388545 CATAAACGCTGGTAATGCTCTGACCTTTAGCCACGC-TT-C
1 CATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTGC
* * * * *
20388584 TCATAAGCGTCGCTAATGATCTGACCTTTAGCGGTGCTTTTC
1 -CATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTGC
* * * * *
20388626 CACAAGCGCCGCTAATGCTCTGACTTTTAGCGGCGTTTTTTC
1 CATAAACGCCGCTAATGCTCTGACCTTTAGCGGCG-CTTTGC
* * * *
20388668 TATAAACGCCGCTATTGCT-TTACCTTTTGCGGCG
1 CATAAACGCCGCTAATGCTCTGACCTTTAGCGGCG
20388702 TTTATGAAAA
Statistics
Matches: 201, Mismatches: 33, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
39 1 0.00
40 63 0.31
41 116 0.58
42 21 0.10
ACGTcount: A:0.20, C:0.29, G:0.21, T:0.30
Consensus pattern (41 bp):
CATAAACGCCGCTAATGCTCTGACCTTTAGCGGCGCTTTGC
Found at i:20388638 original size:121 final size:121
Alignment explanation
Indices: 20388423--20388660 Score: 325
Period size: 121 Copynumber: 2.0 Consensus size: 121
20388413 GGCTTTTCCT
** *
20388423 CATAAACGCCGCTAATGCTCTAACCTTTAGCGGCGCTTTGCCAGAAACGTCGCTAATGCTCTGAC
1 CATAAACGCCGCTAATGCTCTAACCTTTAGCCACGCTTT-CCAGAAACGTCGCTAATGATCTGAC
*
20388488 CTTTAGCGGCGCTTTGCCAGAAACGCCGCTAATGCTCTGACCTTTACCGGCGCTTAC
65 CTTTAGCGGCGCTTTGCCACAAACGCCGCTAATGCTCTGACCTTTACCGGCGCTTAC
* * * * *
20388545 CATAAACGCTGGTAATGCTCTGACCTTTAGCCACGC-TTCTCATAAGCGTCGCTAATGATCTGAC
1 CATAAACGCCGCTAATGCTCTAACCTTTAGCCACGCTTTC-CAGAAACGTCGCTAATGATCTGAC
* * * * *
20388609 CTTTAGCGGTGCTTTTCCACAAGCGCCGCTAATGCTCTGACTTTTAGCGGCG
65 CTTTAGCGGCGCTTTGCCACAAACGCCGCTAATGCTCTGACCTTTACCGGCG
20388661 TTTTTTCTAT
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
120 1 0.01
121 69 0.68
122 31 0.31
ACGTcount: A:0.21, C:0.30, G:0.21, T:0.27
Consensus pattern (121 bp):
CATAAACGCCGCTAATGCTCTAACCTTTAGCCACGCTTTCCAGAAACGTCGCTAATGATCTGACC
TTTAGCGGCGCTTTGCCACAAACGCCGCTAATGCTCTGACCTTTACCGGCGCTTAC
Found at i:20395103 original size:21 final size:20
Alignment explanation
Indices: 20395079--20395122 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
20395069 GTCGTTCCAC
20395079 CTTTCTTTTTCTTTAGATTTT
1 CTTTCTTTTTCTTT-GATTTT
* *
20395100 CTTTTGTTTTTCTTTTATTTT
1 C-TTTCTTTTTCTTTGATTTT
20395121 CT
1 CT
20395123 CAAGCAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
20 1 0.05
21 7 0.35
22 12 0.60
ACGTcount: A:0.07, C:0.14, G:0.05, T:0.75
Consensus pattern (20 bp):
CTTTCTTTTTCTTTGATTTT
Found at i:20402981 original size:18 final size:17
Alignment explanation
Indices: 20402934--20402982 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
20402924 ATTTACAGGT
20402934 ATAAATAATAAGAAAACA
1 ATAAATAATAA-AAAACA
* *
20402952 ATATATACATAAAATACA
1 ATAAATA-ATAAAAAACA
20402970 ATAAGATAATAAA
1 ATAA-ATAATAAA
20402983 TTAAGTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 19 0.73
19 7 0.27
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.22
Consensus pattern (17 bp):
ATAAATAATAAAAAACA
Found at i:20403198 original size:30 final size:29
Alignment explanation
Indices: 20403162--20403408 Score: 206
Period size: 30 Copynumber: 8.2 Consensus size: 29
20403152 TTAATATCGA
*
20403162 GTCAAATTTGAATTTTTGGGAAGTTTAGG
1 GTCAAATTTGAATTTTTGGAAAGTTTAGG
* **
20403191 GATCAAATTGGAATTTTTGGAAAAAAATTAGGG
1 G-TCAAATTTGAATTTTTGG--AAAGTTTA-GG
*
20403224 GTTAAATTTGAATTTTTGGAAAGTTTAAGG
1 GTCAAATTTGAATTTTTGGAAAGTTT-AGG
* * *
20403254 GTTAAATTTGAATTTTTAGAAAATTTAGG
1 GTCAAATTTGAATTTTTGGAAAGTTTAGG
* * * *
20403283 GTCAAATTTAAAATTTTAGAAAGTTTGAAG
1 GTCAAATTTGAATTTTTGGAAAGTTT-AGG
** *
20403313 GTCAAATTCAAATTTTTGGAAGGTTTAGGG
1 GTCAAATTTGAATTTTTGGAAAGTTTA-GG
** *
20403343 GTCAAATTCAAAATTTTGGAAAGTTTAGGG
1 GTCAAATTTGAATTTTTGGAAAGTTTA-GG
** * * *
20403373 GTCAAATTCAAAATTTTAGAAAGCTTGAGG
1 GTCAAATTTGAATTTTTGGAAAG-TTTAGG
20403403 GTCAAA
1 GTCAAA
20403409 ACACAATTTT
Statistics
Matches: 186, Mismatches: 24, Indels: 15
0.83 0.11 0.07
Matches are distributed among these distances:
29 27 0.15
30 131 0.70
31 4 0.02
32 21 0.11
33 3 0.02
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.36
Consensus pattern (29 bp):
GTCAAATTTGAATTTTTGGAAAGTTTAGG
Found at i:20403406 original size:90 final size:89
Alignment explanation
Indices: 20403234--20403408 Score: 242
Period size: 89 Copynumber: 2.0 Consensus size: 89
20403224 GTTAAATTTG
* ** * *
20403234 AATTTTTGGAAAGTTTAAGGGTTAAATTTGAATTTTTAGAAAATTTAGGGTCAAATTTAAAATTT
1 AATTTTTGGAAAGTTTAAGGGTCAAATTCAAAATTTTAGAAAATTTAGGGTCAAATTCAAAATTT
*
20403299 TAGAAAGTTTGAAGGTCAAATTCA
66 TAGAAAGCTTGAAGGTCAAATTCA
* * * *
20403323 AATTTTTGGAAGGTTTAGGGGTCAAATTCAAAATTTTGGAAAGTTTAGGGGTCAAATTCAAAATT
1 AATTTTTGGAAAGTTTAAGGGTCAAATTCAAAATTTTAGAAAATTTA-GGGTCAAATTCAAAATT
*
20403388 TTAGAAAGCTTGAGGGTCAAA
65 TTAGAAAGCTTGAAGGTCAAA
20403409 ACACAATTTT
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
89 39 0.53
90 35 0.47
ACGTcount: A:0.38, C:0.05, G:0.21, T:0.36
Consensus pattern (89 bp):
AATTTTTGGAAAGTTTAAGGGTCAAATTCAAAATTTTAGAAAATTTAGGGTCAAATTCAAAATTT
TAGAAAGCTTGAAGGTCAAATTCA
Found at i:20404596 original size:4 final size:4
Alignment explanation
Indices: 20404589--20404640 Score: 52
Period size: 4 Copynumber: 12.5 Consensus size: 4
20404579 TTATTTATTT
* *
20404589 ATAA AT-A ATAA ATAA ATTAA ATAA TTAA ATTAA ATTAA ATGA ATAA ATAA
1 ATAA ATAA ATAA ATAA A-TAA ATAA ATAA A-TAA A-TAA ATAA ATAA ATAA
20404639 AT
1 AT
20404641 TTGAGCCTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 3 0.07
4 25 0.61
5 13 0.32
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (4 bp):
ATAA
Found at i:20404617 original size:13 final size:13
Alignment explanation
Indices: 20404595--20404640 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
20404585 ATTTATAAAT
20404595 AATAAATAAATTA
1 AATAAATAAATTA
*
20404608 AATAATTAAATTA
1 AATAAATAAATTA
*
20404621 AATTAAATGAA-TA
1 AA-TAAATAAATTA
20404634 AATAAAT
1 AATAAAT
20404641 TTGAGCCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 5 0.17
13 18 0.62
14 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
AATAAATAAATTA
Found at i:20405303 original size:28 final size:28
Alignment explanation
Indices: 20405263--20405339 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
20405253 GTTAGCTTTT
* * *
20405263 ATATATGGTCGACTGTGCTGCCTAAATG
1 ATATATGGTCGACTCTGCCGCCTAAATA
*
20405291 ATATATGGTCGACTCTGCCGCCTGAATA
1 ATATATGGTCGACTCTGCCGCCTAAATA
* *
20405319 ATATATGGTCAACCCTGCCGC
1 ATATATGGTCGACTCTGCCGC
20405340 TTGAATACTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.25, C:0.25, G:0.22, T:0.29
Consensus pattern (28 bp):
ATATATGGTCGACTCTGCCGCCTAAATA
Found at i:20405344 original size:28 final size:28
Alignment explanation
Indices: 20405263--20405351 Score: 88
Period size: 28 Copynumber: 3.2 Consensus size: 28
20405253 GTTAGCTTTT
* ** * * *
20405263 ATATATGGTCGACTGTGCTGCCTAAATG
1 ATATATGGTCAACCCTGCCGCCTGAATA
* *
20405291 ATATATGGTCGACTCTGCCGCCTGAATA
1 ATATATGGTCAACCCTGCCGCCTGAATA
*
20405319 ATATATGGTCAACCCTGCCGCTTGAATA
1 ATATATGGTCAACCCTGCCGCCTGAATA
*
20405347 CTATA
1 ATATA
20405352 GTGCATTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 53 1.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (28 bp):
ATATATGGTCAACCCTGCCGCCTGAATA
Found at i:20406097 original size:14 final size:13
Alignment explanation
Indices: 20406078--20406108 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
20406068 TGTTAAGAAA
20406078 TGTTTTTGACAAAG
1 TGTTTTTGA-AAAG
20406092 TGTTTTTGAAAAG
1 TGTTTTTGAAAAG
20406105 TGTT
1 TGTT
20406109 ATGGAAACTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (13 bp):
TGTTTTTGAAAAG
Found at i:20406986 original size:19 final size:18
Alignment explanation
Indices: 20406962--20406999 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20406952 ATTGTTTTGC
*
20406962 TTTTTAAAATTAAATTTTA
1 TTTTT-AAATTAAAATTTA
20406981 TTTTTAAATTAAAATTTA
1 TTTTTAAATTAAAATTTA
20406999 T
1 T
20407000 ATTATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTTAAATTAAAATTTA
Found at i:20409616 original size:36 final size:36
Alignment explanation
Indices: 20409566--20409854 Score: 141
Period size: 36 Copynumber: 8.0 Consensus size: 36
20409556 TATGTAAGGT
* *
20409566 GTTGTCATAAATAAGGTTTATCTTAATTTTTTTAAG
1 GTTGTCTTAGATAAGGTTTATCTTAATTTTTTTAAG
** *
20409602 GTTGTCTTAGATAAGGTTTAT-TTCAACCTTTTTAAA
1 GTTGTCTTAGATAAGGTTTATCTT-AATTTTTTTAAG
* * *
20409638 GTTGT-TATAG--ACGTGTTTATTTTAA-CTTTTTAAG
1 GTTGTCT-TAGATAAG-GTTTATCTTAATTTTTTTAAG
* * * *
20409672 GTTGTTTTAAATGA-GTTTATTTTAATTATTTTTAAAG
1 GTTGTCTTAGATAAGGTTTATCTTAATT-TTTTT-AAG
* * * *
20409709 GTTGTTTTAGATAAAGTTTATCTCAATCTTTTTAAG
1 GTTGTCTTAGATAAGGTTTATCTTAATTTTTTTAAG
* * *
20409745 GTT-ACTTTAGAT--GATTCTATCTCAATCTTTTTTAAAG
1 GTTGTC-TTAGATAAGGTT-TATCTTAAT-TTTTTT-AAG
* * * * * *
20409782 GTTGTCGTATACAAGGTTTAT-TTCAACTTTTTAAAA
1 GTTGTCTTAGATAAGGTTTATCTT-AATTTTTTTAAG
* ** *
20409818 GTTGTTTTAGA-CGGGTTTATCTCAACTTTTTTTAAG
1 GTTGTCTTAGATAAGGTTTATCTTAA-TTTTTTTAAG
20409854 G
1 G
20409855 GTAATTTATT
Statistics
Matches: 193, Mismatches: 39, Indels: 42
0.70 0.14 0.15
Matches are distributed among these distances:
34 30 0.16
35 30 0.16
36 79 0.41
37 35 0.18
38 16 0.08
39 3 0.02
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (36 bp):
GTTGTCTTAGATAAGGTTTATCTTAATTTTTTTAAG
Found at i:20409676 original size:34 final size:35
Alignment explanation
Indices: 20409581--20409837 Score: 151
Period size: 36 Copynumber: 7.2 Consensus size: 35
20409571 CATAAATAAG
* * * **
20409581 GTTTATCTTAATTTTTTTAAGGTTGTCTTAGATAA
1 GTTTATTTTAATCTTTTTAAGGTTGTTTTAGACGA
* * * * *
20409616 GGTTTATTTCAACCTTTTTAAAGTTGTTATAGACGT
1 -GTTTATTTTAATCTTTTTAAGGTTGTTTTAGACGA
* *
20409652 GTTTATTTTAA-CTTTTTAAGGTTGTTTTAAATGA
1 GTTTATTTTAATCTTTTTAAGGTTGTTTTAGACGA
* **
20409686 GTTTATTTTAATTATTTTTAAAGGTTGTTTTAGATAAA
1 GTTTATTTTAA-TCTTTTT-AAGGTTGTTTTAGA-CGA
* * ** *
20409724 GTTTATCTCAATCTTTTTAAGGTTACTTTAGATGA
1 GTTTATTTTAATCTTTTTAAGGTTGTTTTAGACGA
* * ** * *
20409759 -TTCTATCTCAATCTTTTTTAAAGGTTGTCGTATACAA
1 GTT-TATTTTAATC-TTTTT-AAGGTTGTTTTAGACGA
* * *
20409796 GGTTTATTTCAA-CTTTTTAAAAGTTGTTTTAGACGG
1 -GTTTATTTTAATCTTTTT-AAGGTTGTTTTAGACGA
20409832 GTTTAT
1 GTTTAT
20409838 CTCAACTTTT
Statistics
Matches: 171, Mismatches: 41, Indels: 19
0.74 0.18 0.08
Matches are distributed among these distances:
34 31 0.18
35 27 0.16
36 64 0.37
37 30 0.18
38 17 0.10
39 2 0.01
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (35 bp):
GTTTATTTTAATCTTTTTAAGGTTGTTTTAGACGA
Found at i:20409746 original size:73 final size:71
Alignment explanation
Indices: 20409566--20409852 Score: 222
Period size: 73 Copynumber: 4.0 Consensus size: 71
20409556 TATGTAAGGT
* * * * * * **
20409566 GTTGTCATAAATAAGGTTTATCTTAATTTTTTTAAGGTTGTCTTAGATAAGGTTTATTTCAACCT
1 GTTGTTATAGATAAGGTTTATCTCAA-CTTTTTAAGGTTGTTTTAGATGA-GTTTATTTCAATTT
20409631 TTTTAAA-
64 TTTTAAAG
* * * * *
20409638 GTTGTTATAG--ACGTGTTTATTTTAACTTTTTAAGGTTGTTTTAAATGAGTTTATTTTAATTAT
1 GTTGTTATAGATAAG-GTTTATCTCAACTTTTTAAGGTTGTTTTAGATGAGTTTATTTCAATT-T
20409701 TTTTAAAG
64 TTTTAAAG
* * ** *
20409709 GTTGTTTTAGATAAAGTTTATCTCAATCTTTTTAAGGTTACTTTAGATGA-TTCTATCTCAATCT
1 GTTGTTATAGATAAGGTTTATCTCAA-CTTTTTAAGGTTGTTTTAGATGAGTT-TATTTCAAT-T
20409773 TTTTTAAAG
63 TTTTTAAAG
** * * * * * * *
20409782 GTTGTCGTATACAAGGTTTATTTCAACTTTTTAAAAGTTGTTTTAGACGGGTTTATCTCAACTTT
1 GTTGTTATAGATAAGGTTTATCTCAACTTTTT-AAGGTTGTTTTAGATGAGTTTATTTCAA-TTT
20409847 TTTTAA
64 TTTTAA
20409853 GGGTAATTTA
Statistics
Matches: 172, Mismatches: 32, Indels: 21
0.76 0.14 0.09
Matches are distributed among these distances:
69 10 0.06
70 29 0.17
71 19 0.11
72 25 0.15
73 85 0.49
74 4 0.02
ACGTcount: A:0.27, C:0.08, G:0.14, T:0.50
Consensus pattern (71 bp):
GTTGTTATAGATAAGGTTTATCTCAACTTTTTAAGGTTGTTTTAGATGAGTTTATTTCAATTTTT
TTAAAG
Found at i:20410302 original size:60 final size:58
Alignment explanation
Indices: 20410224--20410438 Score: 196
Period size: 60 Copynumber: 3.6 Consensus size: 58
20410214 AAAATTTAAT
* * *
20410224 TTTTTTGGTGTTGTCCATGCAATGGTCGACACCTCTTATTTATTTGATAAAAAAATCAAA
1 TTTTTTGGTGTTGGCCATGCAATGGTCGACACC-CTT-TTTATCTGATAAAAAAATAAAA
* ***
20410284 TTTTTTGGTGTTGGCCATGCAATGGTCGACATTCCCTTTTTATCAGATAAAATTTTTTAAAA
1 TTTTTTGGTGTTGGCCATGCAATGGTCGACA--CCCTTTTTATCTGATAAAA--AAATAAAA
* * ** * *
20410346 TTTTTTGATGTTGGTCATGCAATGGTCGACACCACCTTCCTATCTGATAAAAAAATGAAT
1 TTTTTTGGTGTTGGCCATGCAATGGTCGACA-C-CCTTTTTATCTGATAAAAAAATAAAA
* * * * *
20410406 TTTTTTTGTATTGGCAATGCATTAGTCGACACC
1 TTTTTTGGTGTTGGCCATGCAATGGTCGACACC
20410439 AATTTTCTCT
Statistics
Matches: 125, Mismatches: 25, Indels: 12
0.77 0.15 0.07
Matches are distributed among these distances:
58 1 0.01
59 1 0.01
60 69 0.55
61 4 0.03
62 50 0.40
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.40
Consensus pattern (58 bp):
TTTTTTGGTGTTGGCCATGCAATGGTCGACACCCTTTTTATCTGATAAAAAAATAAAA
Found at i:20410395 original size:62 final size:62
Alignment explanation
Indices: 20410281--20410397 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 62
20410271 TAAAAAAATC
* * **
20410281 AAATTTTTTGGTGTTGGCCATGCAATGGTCGACATTCCCTTTTTATCAGATAAAATTTTTTA
1 AAATTTTTTGATGTTGGCCATGCAATGGTCGACATCCCCTTCCTATCAGATAAAATTTTTTA
* *
20410343 AAATTTTTTGATGTTGGTCATGCAATGGTCGACA-CCACCTTCCTATCTGATAAAA
1 AAATTTTTTGATGTTGGCCATGCAATGGTCGACATCC-CCTTCCTATCAGATAAAA
20410398 AAATGAATTT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
61 1 0.02
62 47 0.98
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (62 bp):
AAATTTTTTGATGTTGGCCATGCAATGGTCGACATCCCCTTCCTATCAGATAAAATTTTTTA
Found at i:20411262 original size:30 final size:29
Alignment explanation
Indices: 20411227--20411298 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 29
20411217 TAAATTTTCA
*
20411227 AGAAATAATAATTAGAATATA-TAAGAAATT
1 AGAAATAA-AATTAAAATATACT-AGAAATT
*
20411257 AGAAATTAAAATTAAAATATACTGGAAATT
1 AGAAA-TAAAATTAAAATATACTAGAAATT
*
20411287 AGAAATTAAATT
1 AGAAATAAAATT
20411299 TAAAGTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 6 0.16
30 27 0.73
31 4 0.11
ACGTcount: A:0.58, C:0.01, G:0.10, T:0.31
Consensus pattern (29 bp):
AGAAATAAAATTAAAATATACTAGAAATT
Found at i:20411302 original size:30 final size:30
Alignment explanation
Indices: 20411251--20411333 Score: 103
Period size: 30 Copynumber: 2.8 Consensus size: 30
20411241 GAATATATAA
* * ***
20411251 GAAATTAGAAATTAAAATTAAAATATACTG
1 GAAATTAGAAATTAAATTTAAAATAAAAAC
*
20411281 GAAATTAGAAATTAAATTTAAAGTAAAAAC
1 GAAATTAGAAATTAAATTTAAAATAAAAAC
*
20411311 GAAATTACAAATTAAATTTAAAA
1 GAAATTAGAAATTAAATTTAAAA
20411334 AGTAAACAGA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.59, C:0.04, G:0.08, T:0.29
Consensus pattern (30 bp):
GAAATTAGAAATTAAATTTAAAATAAAAAC
Found at i:20412099 original size:60 final size:59
Alignment explanation
Indices: 20411859--20412102 Score: 217
Period size: 59 Copynumber: 4.1 Consensus size: 59
20411849 ATGGCCAATA
* * * * * *
20411859 CAAAAAAATTAATTTTTT-ACCAGATAAAAAAGGAGGTGTCAGCCATGACAT-GACCAACAC
1 CAAAAAATTTGATTTTTTAATCAGAT-AAAAAGG-GGTGTCGGCCATGAAATAG-TCAACAC
* * * * * *
20411919 TAAAAAAAAATTGATTTTTTTATCTA-ACAAAAAGGGGTGTCGGCCATGATATAGCCAACAC
1 --CAAAAAATTTGATTTTTTAATC-AGATAAAAAGGGGTGTCGGCCATGAAATAGTCAACAC
* * *
20411980 TC-AAAAATTTGATTTTTTATTCAGATAAAAAGGGGTGTCGGCCATGTAATTGTCAACAC
1 -CAAAAAATTTGATTTTTTAATCAGATAAAAAGGGGTGTCGGCCATGAAATAGTCAACAC
** **
20412039 CAAAAAATTTGATTTTTTAATCAGATAAAAAGGGGATGTCGATCATGGCATAGTCAACAC
1 CAAAAAATTTGATTTTTTAATCAGATAAAAAGGGG-TGTCGGCCATGAAATAGTCAACAC
20412099 CAAA
1 CAAA
20412103 TTTTTTTTTG
Statistics
Matches: 154, Mismatches: 22, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
58 2 0.01
59 79 0.51
60 23 0.15
61 22 0.14
62 24 0.16
63 3 0.02
64 1 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (59 bp):
CAAAAAATTTGATTTTTTAATCAGATAAAAAGGGGTGTCGGCCATGAAATAGTCAACAC
Found at i:20412131 original size:55 final size:57
Alignment explanation
Indices: 20412059--20412182 Score: 141
Period size: 55 Copynumber: 2.2 Consensus size: 57
20412049 GATTTTTTAA
* * *
20412059 TCAGAT-AAAAAGGGGATGTC-GATCATGGCAT-AGTCAACACC-AAAT-TTTTTTTTG
1 TCAGATAAAAAAAGGGATGTCAG-CCATGGCATGA-CCAACACCAAAATCTTTTTTTTG
* *
20412113 TCATATAAAAAAAGGGATGTCAGCCATGGCATGACCAACACCAAAAATCTTTTTTTTT
1 TCAGATAAAAAAAGGGATGTCAGCCATGGCATGACCAACACC-AAAATCTTTTTTTTG
20412171 TCAGATAAAAAA
1 TCAGATAAAAAA
20412183 GAGGCACGGC
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
54 5 0.09
55 28 0.48
56 2 0.03
57 4 0.07
58 19 0.33
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (57 bp):
TCAGATAAAAAAAGGGATGTCAGCCATGGCATGACCAACACCAAAATCTTTTTTTTG
Found at i:20412827 original size:7 final size:7
Alignment explanation
Indices: 20412817--20412864 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
20412807 GTTTTAATTT
20412817 TTAAAAA
1 TTAAAAA
20412824 TTAAAAA
1 TTAAAAA
*
20412831 TCATAAAA
1 TTA-AAAA
20412839 TTAAAAA
1 TTAAAAA
20412846 TT-AAAA
1 TTAAAAA
*
20412852 TATAAAAT
1 T-TAAAAA
20412860 TTAAA
1 TTAAA
20412865 TCGAAATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
6 5 0.14
7 20 0.57
8 10 0.29
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (7 bp):
TTAAAAA
Found at i:20412845 original size:22 final size:20
Alignment explanation
Indices: 20412817--20412860 Score: 70
Period size: 22 Copynumber: 2.1 Consensus size: 20
20412807 GTTTTAATTT
20412817 TTAAAAATTAAAAATCATAAAA
1 TTAAAAATT-AAAAT-ATAAAA
20412839 TTAAAAATTAAAATATAAAA
1 TTAAAAATTAAAATATAAAA
20412859 TT
1 TT
20412861 TAAATCGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.36
21 5 0.23
22 9 0.41
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
TTAAAAATTAAAATATAAAA
Found at i:20412857 original size:14 final size:13
Alignment explanation
Indices: 20412820--20412864 Score: 54
Period size: 15 Copynumber: 3.2 Consensus size: 13
20412810 TTAATTTTTA
20412820 AAAATTAAAAATCAT
1 AAAATTAAAAAT--T
20412835 AAAATTAAAAATT
1 AAAATTAAAAATT
*
20412848 AAAATATAAAATTT
1 AAAAT-TAAAAATT
20412862 AAA
1 AAA
20412865 TCGAAATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 6 0.21
14 10 0.36
15 12 0.43
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:20417943 original size:13 final size:13
Alignment explanation
Indices: 20417925--20417949 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20417915 TGTTTTAACC
20417925 AAAAATATAAATA
1 AAAAATATAAATA
20417938 AAAAATATAAAT
1 AAAAATATAAAT
20417950 TTTGGTTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATATAAATA
Found at i:20419949 original size:32 final size:31
Alignment explanation
Indices: 20419890--20419950 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
20419880 GTTAATCAAG
* *
20419890 ATGAGTTTCAAATTAAATTAATTAATTTAAC
1 ATGAGTTTCAAATTAAAGTAATCAATTTAAC
* *
20419921 ATGAGTTATTAAATTCAAGTAATCAATTTA
1 ATGAGTT-TCAAATTAAAGTAATCAATTTA
20419951 TAAGTTTATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (31 bp):
ATGAGTTTCAAATTAAAGTAATCAATTTAAC
Found at i:20427158 original size:31 final size:30
Alignment explanation
Indices: 20427116--20427190 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 30
20427106 TCTCTTTTCT
* *
20427116 CTTTTTATGTATGGACTATAACTCC-TCGTAA
1 CTTTTT-TGTATGAACTATAAC-CCTTCATAA
20427147 CTTTTTCTGTATGAACTATAACCCTTCATAA
1 CTTTTT-TGTATGAACTATAACCCTTCATAA
20427178 CTTTCTTTGTATG
1 CTTT-TTTGTATG
20427191 CATAACATCC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 2 0.05
31 35 0.90
32 2 0.05
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.45
Consensus pattern (30 bp):
CTTTTTTGTATGAACTATAACCCTTCATAA
Found at i:20427862 original size:28 final size:29
Alignment explanation
Indices: 20427823--20427920 Score: 76
Period size: 28 Copynumber: 3.4 Consensus size: 29
20427813 CGTCCTTCAT
*
20427823 AGAATTAGCCACAGAGGCTT-ACTTTAAC
1 AGAATCAGCCACAGAGGCTTCACTTTAAC
* * * *
20427851 AGATTCGGCCAC-GAAGACTTCACTTTAAT
1 AGAATCAGCCACAG-AGGCTTCACTTTAAC
* * *
20427880 AGAATCAGCCACAAAGGCTCCA-TATAAC
1 AGAATCAGCCACAGAGGCTTCACTTTAAC
* *
20427908 ATAATAAGCCACA
1 AGAATCAGCCACA
20427921 AATGCCCTCT
Statistics
Matches: 53, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
27 1 0.02
28 29 0.55
29 23 0.43
ACGTcount: A:0.39, C:0.24, G:0.15, T:0.21
Consensus pattern (29 bp):
AGAATCAGCCACAGAGGCTTCACTTTAAC
Found at i:20427890 original size:29 final size:28
Alignment explanation
Indices: 20427821--20427892 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
20427811 GGCGTCCTTC
* *
20427821 ATAGAATTAGCCACAGAGGCTTACTTTA
1 ATAGAATCAGCCACAGAGACTTACTTTA
* * *
20427849 ACAGATTCGGCCAC-GAAGACTTCACTTTA
1 ATAGAATCAGCCACAG-AGACTT-ACTTTA
20427878 ATAGAATCAGCCACA
1 ATAGAATCAGCCACA
20427893 AAGGCTCCAT
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
27 1 0.03
28 15 0.45
29 17 0.52
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (28 bp):
ATAGAATCAGCCACAGAGACTTACTTTA
Found at i:20432993 original size:221 final size:221
Alignment explanation
Indices: 20432610--20433055 Score: 847
Period size: 221 Copynumber: 2.0 Consensus size: 221
20432600 TTAGGACGCA
* *
20432610 ACATTATTGTCACTGCCAGAAGTATCAAACCAGACTGTCATGTCACTAGTCTCTGGACATGTAAC
1 ACATTATTGTCACTGCCAGAAGTATCAAACCAGACTATCATGTCACTAGTCTCTAGACATGTAAC
20432675 TAAGCTTGTCTCCTCCCACTATAAAAGGACCATGCAAACAACTCATACACTCTCACGTGCACACT
66 TAAGCTTGTCTCCTCCCACTATAAAAGGACCATGCAAACAACTCATACACTCTCACGTGCACACT
20432740 TCTTCTTCATCAACTTAAAAATCTCTTACCAGCAGTCCGCCTTCCTCATCTCCACCCAAGTGCTC
131 TCTTCTTCATCAACTTAAAAATCTCTTACCAGCAGTCCGCCTTCCTCATCTCCACCCAAGTGCTC
20432805 CTCCTTACAAACCACCACCTACTTCC
196 CTCCTTACAAACCACCACCTACTTCC
*
20432831 ACATTATTGTCACTGCCAGAAGTATCAAACCAGACTATCATGTCATTAGTCTCTAGACATGTAAC
1 ACATTATTGTCACTGCCAGAAGTATCAAACCAGACTATCATGTCACTAGTCTCTAGACATGTAAC
20432896 TAAGCTTGTCTCCTCCCACTATAAAAGGACCATGCAAACAACTCATACACTCTCACGTGCACACT
66 TAAGCTTGTCTCCTCCCACTATAAAAGGACCATGCAAACAACTCATACACTCTCACGTGCACACT
* *
20432961 TCTTCTTCATCAACTTAAAAATCTCTTACCAGCAGTCCTCCTTCTTCATCTCCACCCAAGTGCTC
131 TCTTCTTCATCAACTTAAAAATCTCTTACCAGCAGTCCGCCTTCCTCATCTCCACCCAAGTGCTC
20433026 CTCCTTACAAACCACCACCTACTTCC
196 CTCCTTACAAACCACCACCTACTTCC
20433052 ACAT
1 ACAT
20433056 GTTAATCAAA
Statistics
Matches: 220, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
221 220 1.00
ACGTcount: A:0.29, C:0.34, G:0.10, T:0.27
Consensus pattern (221 bp):
ACATTATTGTCACTGCCAGAAGTATCAAACCAGACTATCATGTCACTAGTCTCTAGACATGTAAC
TAAGCTTGTCTCCTCCCACTATAAAAGGACCATGCAAACAACTCATACACTCTCACGTGCACACT
TCTTCTTCATCAACTTAAAAATCTCTTACCAGCAGTCCGCCTTCCTCATCTCCACCCAAGTGCTC
CTCCTTACAAACCACCACCTACTTCC
Found at i:20440168 original size:16 final size:16
Alignment explanation
Indices: 20440149--20440195 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
20440139 AAATTTCAAT
20440149 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
20440165 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
20440181 AAATAAAATAATATA
1 AAATAAAA-AATATA
20440196 AATATTTTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:20441500 original size:29 final size:30
Alignment explanation
Indices: 20441463--20441521 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
20441453 TATGATCTAA
*
20441463 TGTGCAATTTTATACATG-AACTTTGATTT
1 TGTGAAATTTTATACATGAAACTTTGATTT
*
20441492 TGTGAAATTTTATACATGAAATTTTGATTT
1 TGTGAAATTTTATACATGAAACTTTGATTT
20441522 GATTCAATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.31, C:0.07, G:0.14, T:0.49
Consensus pattern (30 bp):
TGTGAAATTTTATACATGAAACTTTGATTT
Found at i:20441748 original size:29 final size:30
Alignment explanation
Indices: 20441705--20441774 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 30
20441695 CAAATAGAAT
* * *
20441705 TTCATGTGTATAATTG-CATGAAATTAAAG
1 TTCATGTATACAATTGACATGAAATCAAAG
* *
20441734 TTTATGTATACAATTGCACATTAAATCAAAG
1 TTCATGTATACAATTG-ACATGAAATCAAAG
20441765 TTCATGTATA
1 TTCATGTATA
20441775 ATATTGATAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
29 13 0.39
31 20 0.61
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.39
Consensus pattern (30 bp):
TTCATGTATACAATTGACATGAAATCAAAG
Found at i:20442995 original size:5 final size:6
Alignment explanation
Indices: 20442969--20443009 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
20442959 TTTTTAAAAA
20442969 ATATTT ATATTT ATATTT ATA-TT ATA-TT AT-TTT AATATTT A
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT -ATATTT A
20443010 ATAATTTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 11 0.34
6 18 0.56
7 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
ATATTT
Found at i:20443006 original size:16 final size:18
Alignment explanation
Indices: 20442968--20443007 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 18
20442958 TTTTTTAAAA
20442968 AATATTTATATTTATATTT
1 AATA-TTATATTTATATTT
20442987 -ATATTATA-TTAT-TTT
1 AATATTATATTTATATTT
20443002 AATATT
1 AATATT
20443008 TAATAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
15 3 0.15
16 9 0.45
17 5 0.25
18 3 0.15
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATATTATATTTATATTT
Found at i:20451426 original size:17 final size:18
Alignment explanation
Indices: 20451394--20451427 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
20451384 TATTTACCAA
*
20451394 AAAAATTACATAATATAT
1 AAAAATAACATAATATAT
20451412 AAAAATAACAT-ATATA
1 AAAAATAACATAATATA
20451428 AAGTACTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAAAATAACATAATATAT
Found at i:20452535 original size:31 final size:31
Alignment explanation
Indices: 20452500--20452559 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
20452490 AACTTAACAG
20452500 TTCAATGACTTAAACAAAAACTTTTAAATGT
1 TTCAATGACTTAAACAAAAACTTTTAAATGT
**
20452531 TTCAATGACTTAAATGAAAACTTTTAAAT
1 TTCAATGACTTAAACAAAAACTTTTAAAT
20452560 AATTTAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.37
Consensus pattern (31 bp):
TTCAATGACTTAAACAAAAACTTTTAAATGT
Found at i:20455196 original size:29 final size:29
Alignment explanation
Indices: 20455164--20455222 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
20455154 GAATTTAACA
* *
20455164 TTTTTTTTATTTAATTTGGTACCTAAACT
1 TTTTTTTTACTCAATTTGGTACCTAAACT
* *
20455193 TTTTTTTTACTCAATTTGGTATCTGAACT
1 TTTTTTTTACTCAATTTGGTACCTAAACT
20455222 T
1 T
20455223 GACACTTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.22, C:0.12, G:0.08, T:0.58
Consensus pattern (29 bp):
TTTTTTTTACTCAATTTGGTACCTAAACT
Found at i:20455246 original size:61 final size:60
Alignment explanation
Indices: 20455175--20455338 Score: 179
Period size: 61 Copynumber: 2.7 Consensus size: 60
20455165 TTTTTTTATT
20455175 TAATTTGGTACCTAAACTTTTTTTTTACTCAATTTGGTATCTGAACTTGACACTTTTTTCC
1 TAATTTGGTACCTAAACTTTTTTTTTACTCAATTTGGTATCTGAACTTGACA-TTTTTTCC
** ** * * *
20455236 TAATTTGGTACCTAAACCATTTTTGGACCCAATGTGATA-CTTGAACTTGACATTTTTTCC
1 TAATTTGGTACCTAAACTTTTTTTTTACTCAATTTGGTATC-TGAACTTGACATTTTTTCC
* * * *
20455296 CAATTTGGAACCT-AAGTTTTTTTTTAGATTCAATTTGGTATCT
1 TAATTTGGTACCTAAACTTTTTTTTT--ACTCAATTTGGTATCT
20455339 AAATTTATTA
Statistics
Matches: 81, Mismatches: 18, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
59 7 0.09
60 20 0.25
61 53 0.65
62 1 0.01
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (60 bp):
TAATTTGGTACCTAAACTTTTTTTTTACTCAATTTGGTATCTGAACTTGACATTTTTTCC
Found at i:20455598 original size:90 final size:88
Alignment explanation
Indices: 20455492--20455679 Score: 229
Period size: 90 Copynumber: 2.1 Consensus size: 88
20455482 AAAAATTATG
20455492 TACCAAATTAGGAAAAAAAGTCAAGTTCATG-TACCAAATTGGATCCC-AA-AAAGTTTAAGTAC
1 TACCAAATTAGGAAAAAAAGTCAAGTT--TGATACCAAATTGGA-CCCAAACAAAGTTTAAGTAC
** *
20455554 CAGCTTAAAAAAAGGTGTCAAGTTTAGA
63 CAAATTAAAAAAA--TGTCAAGTTCAGA
* * *
20455582 TACCAAATTAGGAAAAAATGTCAAGTTTGAATACCAAATTGGACCCAAAACAAAGTTTAGGTATC
1 TACCAAATTAGGAAAAAAAGTCAAGTTTG-ATACCAAATTGGACCC-AAACAAAGTTTAAGTACC
*
20455647 AAATTAAAAAAATGTCAAGTTCAGG
64 AAATTAAAAAAATGTCAAGTTCAGA
20455672 TACCAAAT
1 TACCAAAT
20455680 GTTATATTAA
Statistics
Matches: 86, Mismatches: 7, Indels: 10
0.83 0.07 0.10
Matches are distributed among these distances:
88 2 0.02
89 3 0.03
90 57 0.66
91 2 0.02
92 22 0.26
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.24
Consensus pattern (88 bp):
TACCAAATTAGGAAAAAAAGTCAAGTTTGATACCAAATTGGACCCAAACAAAGTTTAAGTACCAA
ATTAAAAAAATGTCAAGTTCAGA
Found at i:20455604 original size:31 final size:31
Alignment explanation
Indices: 20455569--20455679 Score: 92
Period size: 31 Copynumber: 3.7 Consensus size: 31
20455559 TAAAAAAAGG
20455569 TGTCAAGTTTAGATACCAAATTAGGAAAAAA
1 TGTCAAGTTTAGATACCAAATTAGGAAAAAA
*
20455600 TGTCAAGTTT-GAATACCAAATT-GGACCCAAAA
1 TGTCAAGTTTAG-ATACCAAATTAGGA--AAAAA
* *
20455632 ---CAAAGTTTAGGTATCAAATTA--AAAAAA
1 TGTC-AAGTTTAGATACCAAATTAGGAAAAAA
* *
20455659 TGTCAAGTTCAGGTACCAAAT
1 TGTCAAGTTTAGATACCAAAT
20455680 GTTATATTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
27 4 0.06
29 17 0.26
30 19 0.29
31 21 0.32
32 4 0.06
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (31 bp):
TGTCAAGTTTAGATACCAAATTAGGAAAAAA
Found at i:20455859 original size:33 final size:33
Alignment explanation
Indices: 20455821--20455883 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
20455811 TTGGTGCAAT
*
20455821 TATATAAATGAAACTCTAATTATGGTTTAAATA
1 TATATAAATGAAACTCTAATTATGATTTAAATA
* * *
20455854 TATATAATTGAAACTTTAATTTTGATTTAA
1 TATATAAATGAAACTCTAATTATGATTTAA
20455884 TCATACATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.43, C:0.05, G:0.08, T:0.44
Consensus pattern (33 bp):
TATATAAATGAAACTCTAATTATGATTTAAATA
Found at i:20456052 original size:30 final size:29
Alignment explanation
Indices: 20456018--20456076 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
20456008 TAAATGAATC
*
20456018 AAATTAAAATTTCATATATAAAATTACATA
1 AAATTAAAATTT-ATATATAAAATCACATA
* *
20456048 AAATTAAAATTTATGTATACAATCACATA
1 AAATTAAAATTTATATATAAAATCACATA
20456077 TTAAATCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.54, C:0.08, G:0.02, T:0.36
Consensus pattern (29 bp):
AAATTAAAATTTATATATAAAATCACATA
Found at i:20456076 original size:29 final size:30
Alignment explanation
Indices: 20456018--20456098 Score: 92
Period size: 31 Copynumber: 2.7 Consensus size: 30
20456008 TAAATGAATC
* *
20456018 AAATTAAAATTTCATATATAAAATTACATA-
1 AAATTAAAATTT-ATGTATAAAATCACATAT
*
20456048 AAATTAAAATTTATGTATACAATCACATATT
1 AAATTAAAATTTATGTATAAAATCACATA-T
* *
20456079 AAATCATAATTTATGTATAA
1 AAATTAAAATTTATGTATAA
20456099 TTTTAATATT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 14 0.33
30 12 0.28
31 17 0.40
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.38
Consensus pattern (30 bp):
AAATTAAAATTTATGTATAAAATCACATAT
Found at i:20462123 original size:21 final size:21
Alignment explanation
Indices: 20462071--20462146 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
20462061 GGAGTTTTTA
* *
20462071 GTATCGATAGAAGCATGACTT
1 GTATCGATAGAAGCTTCACTT
* * *
20462092 ATTTCGGTAGAAGCTTCACTT
1 GTATCGATAGAAGCTTCACTT
**
20462113 GTATCGATAGAA-CTGTCACAA
1 GTATCGATAGAAGCT-TCACTT
*
20462134 GTATCGGTAGAAG
1 GTATCGATAGAAG
20462147 TCTGCACTAT
Statistics
Matches: 42, Mismatches: 11, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
20 2 0.05
21 40 0.95
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (21 bp):
GTATCGATAGAAGCTTCACTT
Found at i:20466878 original size:22 final size:23
Alignment explanation
Indices: 20466839--20466881 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
20466829 TTGGCTTCAA
*
20466839 AATCCCAAAAACGGCGTCATTAG
1 AATCCCAAAAACGACGTCATTAG
20466862 AATCCC-AAAACGACGTCATT
1 AATCCCAAAAACGACGTCATT
20466882 TTACTGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.19
Consensus pattern (23 bp):
AATCCCAAAAACGACGTCATTAG
Found at i:20468347 original size:9 final size:8
Alignment explanation
Indices: 20468329--20468401 Score: 60
Period size: 9 Copynumber: 8.6 Consensus size: 8
20468319 ATGCATGAAC
20468329 TAAAAAAA
1 TAAAAAAA
20468337 TAAACAAAA
1 TAAA-AAAA
20468346 TAAACATAAA
1 TAAA-A-AAA
20468356 TAAAAATAA
1 TAAAAA-AA
*
20468365 -AGATAAAA
1 TA-AAAAAA
20468373 TAAATAAAA
1 TAAA-AAAA
20468382 T-AAAAAA
1 TAAAAAAA
*
20468389 CAAAAAAA
1 TAAAAAAA
20468397 TAAAA
1 TAAAA
20468402 GGATTAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
7 4 0.07
8 21 0.39
9 22 0.41
10 7 0.13
ACGTcount: A:0.79, C:0.04, G:0.01, T:0.15
Consensus pattern (8 bp):
TAAAAAAA
Found at i:20468377 original size:21 final size:21
Alignment explanation
Indices: 20468345--20468385 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
20468335 AATAAACAAA
20468345 ATAAACATAAATAAAAATAAAG
1 ATAAACATAAAT-AAAATAAAG
20468367 ATAAA-ATAAATAAAATAAA
1 ATAAACATAAATAAAATAAA
20468386 AAACAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 6 0.32
22 5 0.26
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (21 bp):
ATAAACATAAATAAAATAAAG
Found at i:20468387 original size:15 final size:14
Alignment explanation
Indices: 20468333--20468401 Score: 75
Period size: 15 Copynumber: 4.6 Consensus size: 14
20468323 ATGAACTAAA
*
20468333 AAAATAAACAAAAT
1 AAAATAAAAAAAAT
20468347 AAACATAAATAAAAAT
1 AAA-ATAAA-AAAAAT
*
20468363 AAAGATAAAATAAAT
1 AAA-ATAAAAAAAAT
*
20468378 AAAATAAAAAACAAA
1 AAAATAAAAAA-AAT
20468393 AAAATAAAA
1 AAAATAAAA
20468402 GGATTAAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
14 10 0.21
15 24 0.51
16 13 0.28
ACGTcount: A:0.80, C:0.04, G:0.01, T:0.14
Consensus pattern (14 bp):
AAAATAAAAAAAAT
Found at i:20468422 original size:28 final size:27
Alignment explanation
Indices: 20468376--20468458 Score: 69
Period size: 29 Copynumber: 3.0 Consensus size: 27
20468366 GATAAAATAA
* *
20468376 ATAAAATAAAAAACAAAAAAATAAAAGG
1 ATAAATTAAAAAA-AAAAAAATAAAAGC
*
20468404 ATTAAATTAAAAAATAAAAAGAGT-AAAGC
1 A-TAAATTAAAAAA-AAAAA-AATAAAAGC
* * *
20468433 ATAAATTGAAAAAACAAAAATTAAAG
1 ATAAATTAAAAAAAAAAAAATAAAAG
20468459 GGACTGGATG
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
26 2 0.04
27 8 0.18
28 12 0.27
29 21 0.47
30 2 0.04
ACGTcount: A:0.71, C:0.04, G:0.08, T:0.17
Consensus pattern (27 bp):
ATAAATTAAAAAAAAAAAAATAAAAGC
Found at i:20468430 original size:21 final size:21
Alignment explanation
Indices: 20468391--20468430 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
20468381 ATAAAAAACA
* *
20468391 AAAAAATAAAAGGATTAAATT
1 AAAAAATAAAAAGAGTAAATT
20468412 AAAAAATAAAAAGAGTAAA
1 AAAAAATAAAAAGAGTAAA
20468431 GCATAAATTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAAAATAAAAAGAGTAAATT
Found at i:20468510 original size:30 final size:30
Alignment explanation
Indices: 20468474--20468555 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 30
20468464 GGATGAAATA
*
20468474 AATAAAGGATTAAATTAAAACAATAAACAT
1 AATAAAGGATTAAATTAAAACAATAAACAG
* ** **
20468504 ATTAAAGGCCTAAATT-TTA-AA-AAACAG
1 AATAAAGGATTAAATTAAAACAATAAACAG
*
20468531 AATAAAGAATTAAATTAAAACAATA
1 AATAAAGGATTAAATTAAAACAATA
20468556 TAAAAATGCA
Statistics
Matches: 37, Mismatches: 12, Indels: 6
0.67 0.22 0.11
Matches are distributed among these distances:
27 17 0.46
28 3 0.08
29 3 0.08
30 14 0.38
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.24
Consensus pattern (30 bp):
AATAAAGGATTAAATTAAAACAATAAACAG
Found at i:20469461 original size:13 final size:13
Alignment explanation
Indices: 20469441--20469473 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
20469431 AATTTTTTTG
20469441 TTTTTTTTC-CTA
1 TTTTTTTTCTCTA
20469453 TTCTTTTTTCTCTA
1 TT-TTTTTTCTCTA
20469467 TTTTTTT
1 TTTTTTT
20469474 GTAGGTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 12 0.63
14 5 0.26
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTTTTTCTCTA
Found at i:20469461 original size:14 final size:14
Alignment explanation
Indices: 20469441--20469473 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
20469431 AATTTTTTTG
20469441 TTTTTTTTC-CTAT
1 TTTTTTTTCTCTAT
*
20469454 TCTTTTTTCTCTAT
1 TTTTTTTTCTCTAT
20469468 TTTTTT
1 TTTTTT
20469474 GTAGGTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTTTCTCTAT
Found at i:20469969 original size:34 final size:34
Alignment explanation
Indices: 20469931--20469995 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
20469921 TTTATTATTA
20469931 TTACTA-TTACTATTACTATTTTATTTTATTTATG
1 TTACTACTTA-TATTACTATTTTATTTTATTTATG
*
20469965 TTACTACTTATATTATTATTTTATTTTATTT
1 TTACTACTTATATTACTATTTTATTTTATTT
20469996 TTGTCGATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 26 0.90
35 3 0.10
ACGTcount: A:0.26, C:0.08, G:0.02, T:0.65
Consensus pattern (34 bp):
TTACTACTTATATTACTATTTTATTTTATTTATG
Found at i:20472138 original size:59 final size:59
Alignment explanation
Indices: 20472077--20472624 Score: 791
Period size: 59 Copynumber: 9.3 Consensus size: 59
20472067 TGGATACCCG
* * * * * *
20472077 GGGGGCAAAATGGTAATTTT-GGTGTAATCGGGGTTGAAGATGGAATCTTAAAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
20472135 GGGGGTAAAATGGTAA-TTT-GGTGAAATCGGGGTTAAAAACGGAA-TTTAGAAGCTTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
20472191 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTCAAAAATAGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
20472250 GGGGGTAAAATGGTAATTTTCGATGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * * **
20472309 GGGGGTTAAAATGGTAATTTTCGGTGAAATTGGGATTAAAAATGGAATTTTGGAATTTTC
1 GGGGG-TAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * *
20472369 GAGGATAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* * * * *
20472428 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAGTTTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
20472487 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
* *
20472546 GGGGGTAAAATGGTAATTTTCGGTGAAATTGGGGTCAAAAATGGAATTTTAGAAGATTC
1 GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
*
20472605 GGGGGTTAAAAT-ATAATTTT
1 GGGGG-TAAAATGGTAATTTT
20472625 GGAAAAGTTT
Statistics
Matches: 442, Mismatches: 43, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
56 25 0.06
57 27 0.06
58 37 0.08
59 297 0.67
60 56 0.13
ACGTcount: A:0.34, C:0.05, G:0.30, T:0.31
Consensus pattern (59 bp):
GGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTC
Found at i:20472239 original size:30 final size:29
Alignment explanation
Indices: 20472192--20472595 Score: 237
Period size: 30 Copynumber: 13.7 Consensus size: 29
20472182 AGAAGCTTCG
20472192 GGGGT-AAAATGGTAATTTTCGGTGAAATC
1 GGGGTAAAAATGG-AATTTTCGGTGAAATC
* * ** *
20472221 GGGGTCAAAAATAGAATTTTAGAAG-ATTC
1 GGGGT-AAAAATGGAATTTTCGGTGAAATC
*
20472250 GGGGGT-AAAATGGTAATTTTCGATGAAATC
1 -GGGGTAAAAATGG-AATTTTCGGTGAAATC
* ** *
20472280 GGGGTCAAAAATGGAATTTTAGAAG-ATTC
1 GGGGT-AAAAATGGAATTTTCGGTGAAATC
* *
20472309 GGGGGTTAAAATGGTAATTTTCGGTGAAATT
1 -GGGGTAAAAATGG-AATTTTCGGTGAAATC
* *
20472340 GGGATTAAAAATGGAATTTT--G-GAATTTTC
1 GGG-GTAAAAATGGAATTTTCGGTGAA--ATC
* *
20472369 GAGG-ATAAAATGGTAATTTTTGGTGAAATC
1 GGGGTA-AAAATGG-AATTTTCGGTGAAATC
* ** *
20472399 GGGGTTAAAAATGGAATTTTAGAAG-ATTC
1 GGGG-TAAAAATGGAATTTTCGGTGAAATC
*
20472428 AGGGGT-AAAATGGTAATTTTTGGTGAAATC
1 -GGGGTAAAAATGG-AATTTTCGGTGAAATC
*
20472458 GGGGTCAAAAATGGAATTTT--G-GAAGTTTC
1 GGGGT-AAAAATGGAATTTTCGGTGAA--ATC
20472487 GGGGGT-AAAATGGTAATTTTCGGTGAAATC
1 -GGGGTAAAAATGG-AATTTTCGGTGAAATC
* ** *
20472517 GGGGTTAAAAATGGAATTTTAGAAG-ATTC
1 GGGG-TAAAAATGGAATTTTCGGTGAAATC
*
20472546 GGGGGT-AAAATGGTAATTTTCGGTGAAATT
1 -GGGGTAAAAATGG-AATTTTCGGTGAAATC
20472576 GGGGTCAAAAATGGAATTTT
1 GGGGT-AAAAATGGAATTTT
20472596 AGAAGATTCG
Statistics
Matches: 291, Mismatches: 45, Indels: 77
0.70 0.11 0.19
Matches are distributed among these distances:
27 7 0.02
28 36 0.12
29 87 0.30
30 101 0.35
31 53 0.18
32 7 0.02
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTCGGTGAAATC
Found at i:20472455 original size:237 final size:233
Alignment explanation
Indices: 20472140--20472595 Score: 777
Period size: 237 Copynumber: 1.9 Consensus size: 233
20472130 GATTCGGGGG
* *
20472140 TAAAATGGTAATTTGGTGAAATCGGGGTTAAAAACGGAATTTAGAAGCTTCGGGGGTAAAATGGT
1 TAAAATGGTAATTTGGTGAAATCGGGGTTAAAAACGGAATTTAGAAGATTCAGGGGTAAAATGGT
20472205 AATTTTCGGTGAAATCGGGGTCAAAAATAGAATTTTAGAAGATTCGGGGGTAAAATGGTAATTTT
66 AATTTTCGGTGAAATCGGGGTCAAAAATAGAATTTTAGAAGATTCGGGGGTAAAATGGTAATTTT
20472270 CGATGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTCGGGGGTTAAAATGGTAATTTTCGGTG
131 CGATGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTCGGGGG-TAAAATGGTAATTTTCGGTG
*
20472335 AAATTGGGATTAAAAATGGAATTTTGGAATTTTCGAGGA
195 AAATTGGGATCAAAAATGGAATTTTGGAATTTTCGAGGA
*
20472374 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAGGGGTAAAAT
1 TAAAATGGTAA--TTTGGTGAAATCGGGGTTAAAAACGGAA-TTTAGAAGATTCAGGGGTAAAAT
* * * *
20472439 GGTAATTTTTGGTGAAATCGGGGTCAAAAATGGAATTTTGGAAGTTTCGGGGGTAAAATGGTAAT
63 GGTAATTTTCGGTGAAATCGGGGTCAAAAATAGAATTTTAGAAGATTCGGGGGTAAAATGGTAAT
* *
20472504 TTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATGGTAATTTTCGG
128 TTTCGATGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATGGTAATTTTCGG
*
20472569 TGAAATTGGGGTCAAAAATGGAATTTT
193 TGAAATTGGGATCAAAAATGGAATTTT
20472596 AGAAGATTCG
Statistics
Matches: 208, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
234 11 0.05
236 70 0.34
237 127 0.61
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.31
Consensus pattern (233 bp):
TAAAATGGTAATTTGGTGAAATCGGGGTTAAAAACGGAATTTAGAAGATTCAGGGGTAAAATGGT
AATTTTCGGTGAAATCGGGGTCAAAAATAGAATTTTAGAAGATTCGGGGGTAAAATGGTAATTTT
CGATGAAATCGGGGTCAAAAATGGAATTTTAGAAGATTCGGGGGTAAAATGGTAATTTTCGGTGA
AATTGGGATCAAAAATGGAATTTTGGAATTTTCGAGGA
Found at i:20472622 original size:29 final size:29
Alignment explanation
Indices: 20472517--20472653 Score: 79
Period size: 30 Copynumber: 4.6 Consensus size: 29
20472507 CGGTGAAATC
20472517 GGGGTTAAAA-ATGGAATTTTAGAAGATTCG
1 GGGGTTAAAATAT--AATTTTAGAAGATTCG
* *
20472547 GGGG-TAAAATGGTAATTTTCGGTGAA-ATT--
1 GGGGTTAAAAT-ATAATTTT---AGAAGATTCG
*
20472576 GGGGTCAAAA-ATGGAATTTTAGAAGATTCG
1 GGGGTTAAAATAT--AATTTTAGAAGATTCG
* * **
20472606 GGGGTTAAAATATAATTTTGGAAAAGTTTT
1 GGGGTTAAAATATAATTTTAGAAGA-TTCG
*
20472636 AGGGTTAAAATATAATTT
1 GGGGTTAAAATATAATTT
20472654 CTGGATTGTT
Statistics
Matches: 83, Mismatches: 11, Indels: 26
0.69 0.09 0.22
Matches are distributed among these distances:
27 3 0.04
28 4 0.05
29 25 0.30
30 42 0.51
31 6 0.07
32 3 0.04
ACGTcount: A:0.36, C:0.03, G:0.27, T:0.34
Consensus pattern (29 bp):
GGGGTTAAAATATAATTTTAGAAGATTCG
Found at i:20473040 original size:161 final size:163
Alignment explanation
Indices: 20472747--20473064 Score: 554
Period size: 161 Copynumber: 2.0 Consensus size: 163
20472737 ACCCATTTGA
20472747 AAACCTTGAAAAATTTTAGGGCCAATTTCGTAATTAAATAATAGTTGATTTAAGGATTAAATTAA
1 AAACCTTGAAAAATTTTAGGGCCAATTTCGTAATTAAATAATAGTTGATTTAAGGATTAAATTAA
* *
20472812 AACAAATTAGAAATAAAAAGGACTAAATACAGAAATAATCCAAAAACATGACACGTGGCAACCTC
66 AACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAAATGACACGTGGCAACCTC
*
20472877 TGGTGCAGTCAAACAGTCAAAGGACTAGTTTAT
131 TGGTGCAATCAAACAGTCAAAGGACTAGTTTAT
*
20472910 AAACCTTGAAAAATTATT-GGGCCAATTTCGTAATTAAA-ACTAAGTTGATTT-AGGATTAAATT
1 AAACCTTGAAAAATT-TTAGGGCCAATTTCGTAATTAAATAAT-AGTTGATTTAAGGATTAAATT
20472972 AAAACAAATTAAAAAT-AAAAGGACTAAATACAGAAATAATCCAAAAAAATGACACGTGGCAACC
64 AAAACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAAATGACACGTGGCAACC
20473036 TCTGGTGCAATCAAACAGTCAAAGGACTA
129 TCTGGTGCAATCAAACAGTCAAAGGACTA
20473065 AAGTATAAAC
Statistics
Matches: 149, Mismatches: 4, Indels: 6
0.94 0.03 0.04
Matches are distributed among these distances:
161 75 0.50
162 28 0.19
163 44 0.30
164 2 0.01
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.25
Consensus pattern (163 bp):
AAACCTTGAAAAATTTTAGGGCCAATTTCGTAATTAAATAATAGTTGATTTAAGGATTAAATTAA
AACAAATTAAAAATAAAAAGGACTAAATACAGAAATAATCCAAAAAAATGACACGTGGCAACCTC
TGGTGCAATCAAACAGTCAAAGGACTAGTTTAT
Found at i:20473854 original size:10 final size:10
Alignment explanation
Indices: 20473839--20473873 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
20473829 TTAAAAGATT
20473839 TATTAATTAA
1 TATTAATTAA
20473849 TATTAATTAA
1 TATTAATTAA
*
20473859 TATTAATTAT
1 TATTAATTAA
20473869 TATTA
1 TATTA
20473874 TTATCATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
TATTAATTAA
Found at i:20474350 original size:20 final size:20
Alignment explanation
Indices: 20474325--20474363 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20474315 AGCTGGTGGG
* *
20474325 TGGAGCTGGTGGTCAGCAGA
1 TGGAGCGGGTGGCCAGCAGA
20474345 TGGAGCGGGTGGCCAGCAG
1 TGGAGCGGGTGGCCAGCAG
20474364 CAGTAGGCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.49, T:0.15
Consensus pattern (20 bp):
TGGAGCGGGTGGCCAGCAGA
Found at i:20474444 original size:14 final size:14
Alignment explanation
Indices: 20474406--20474458 Score: 65
Period size: 14 Copynumber: 3.9 Consensus size: 14
20474396 ATTTGGACTA
*
20474406 TTGTGATTGGGCCC
1 TTGTAATTGGGCCC
20474420 -T-TAATTGGGCCC
1 TTGTAATTGGGCCC
* *
20474432 TTGTAAATGGGCCA
1 TTGTAATTGGGCCC
20474446 TTGTAATTGGGCC
1 TTGTAATTGGGCC
20474459 GTGGGCCATG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 10 0.30
13 2 0.06
14 21 0.64
ACGTcount: A:0.17, C:0.19, G:0.30, T:0.34
Consensus pattern (14 bp):
TTGTAATTGGGCCC
Found at i:20474515 original size:6 final size:6
Alignment explanation
Indices: 20474481--20474582 Score: 86
Period size: 6 Copynumber: 17.0 Consensus size: 6
20474471 CATTTGGACT
* ** *
20474481 TTTAAA TTTAATA TTTTAAT TTTTTA TTTAAA TTTAAA TTCAAA -TTAAA
1 TTTAAA TTTAA-A -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
20474530 TTTAGATA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA TTTAAA --TAAA
1 TTTA-A-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
20474577 TTTAAA
1 TTTAAA
20474583 ATCAATTTAA
Statistics
Matches: 77, Mismatches: 11, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 52 0.68
7 3 0.04
8 10 0.13
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (6 bp):
TTTAAA
Found at i:20474530 original size:17 final size:16
Alignment explanation
Indices: 20474508--20474589 Score: 71
Period size: 17 Copynumber: 5.1 Consensus size: 16
20474498 AATTTTTTAT
*
20474508 TTAAATTTAAATTCAAA
1 TTAAATTTAAAAT-AAA
* *
20474525 TTAAATTT-AGAT-AT
1 TTAAATTTAAAATAAA
20474539 TTAAATTTAAAATAAA
1 TTAAATTTAAAATAAA
*
20474555 TCTAAATTTAAATTTAAA
1 T-TAAATTTAAA-ATAAA
*
20474573 -TAAATTTAAAATCAA
1 TTAAATTTAAAATAAA
20474588 TT
1 TT
20474590 TAACTCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
14 9 0.17
15 6 0.12
16 15 0.29
17 18 0.35
18 4 0.08
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (16 bp):
TTAAATTTAAAATAAA
Found at i:20474540 original size:25 final size:22
Alignment explanation
Indices: 20474506--20474582 Score: 100
Period size: 25 Copynumber: 3.3 Consensus size: 22
20474496 TTAATTTTTT
*
20474506 ATTTAAATTTAAATTCAAATTAA
1 ATTTAAATTTAAATTTAAA-TAA
20474529 ATTTAGATATTTAAATTTAAAATAA
1 ATTTA-A-ATTTAAATTT-AAATAA
*
20474554 ATCTAAATTTAAATTTAAATAA
1 ATTTAAATTTAAATTTAAATAA
20474576 ATTTAAA
1 ATTTAAA
20474583 ATCAATTTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
22 12 0.25
23 15 0.31
24 2 0.04
25 16 0.33
26 3 0.06
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (22 bp):
ATTTAAATTTAAATTTAAATAA
Found at i:20474543 original size:31 final size:30
Alignment explanation
Indices: 20474505--20474573 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 30
20474495 TTTAATTTTT
*
20474505 TATTTAAATTTAAATTCAAAT-TAAATTTAGA
1 TATTTAAATTTAAAAT-AAATCTAAATTTA-A
20474536 TATTTAAATTTAAAATAAATCTAAATTTAA
1 TATTTAAATTTAAAATAAATCTAAATTTAA
20474566 -ATTTAAAT
1 TATTTAAAT
20474574 AAATTTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 8 0.22
30 5 0.14
31 23 0.64
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (30 bp):
TATTTAAATTTAAAATAAATCTAAATTTAA
Found at i:20474589 original size:11 final size:11
Alignment explanation
Indices: 20474540--20474592 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
20474530 TTTAGATATT
20474540 TAAATTTAAAA
1 TAAATTTAAAA
* *
20474551 TAAATCTAAATT
1 TAAATTTAAA-A
20474563 TAAATTT-AAA
1 TAAATTTAAAA
20474573 TAAATTTAAAA
1 TAAATTTAAAA
*
20474584 TCAATTTAA
1 TAAATTTAA
20474593 CTCAAAAGTC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
10 7 0.20
11 22 0.63
12 6 0.17
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:20475025 original size:68 final size:68
Alignment explanation
Indices: 20474915--20475702 Score: 1375
Period size: 68 Copynumber: 11.6 Consensus size: 68
20474905 TGATCTTGCT
* * * *
20474915 CGTGTTATCCACTCTACTTCAATTTCAAAGGGATGACCTTGCTCTTATTTCAATTTCGGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
20474980 CGA
66 AGA
*
20474983 TGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
**
20475048 ATC
66 AGA
20475051 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
**
20475116 ATC
66 AGA
20475119 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTTACTTCAATTTCAGAGATG
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC-TTACTTCAATTTCAGAGATG
20475184 AAGA
65 AAGA
*
20475188 CGTGGT-TCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
20475252 AGA
66 AGA
*
20475255 CGTGTCATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
20475320 AGA
66 AGA
20475323 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTTACTTCAATTTCAGAGATG
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC-TTACTTCAATTTCAGAGATG
20475388 AAGA
65 AAGA
*
20475392 CGTGGT-TCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
20475456 ATA
66 AGA
*
20475459 CGTGTCATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
20475524 AAA
66 AGA
*
20475527 CGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
20475592 AGA
66 AGA
20475595 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
20475660 AGA
66 AGA
*
20475663 CGTGGT-TCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
20475703 AGATCTGCAA
Statistics
Matches: 691, Mismatches: 25, Indels: 9
0.95 0.03 0.01
Matches are distributed among these distances:
67 89 0.13
68 546 0.79
69 56 0.08
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (68 bp):
CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
AGA
Found at i:20476388 original size:1 final size:1
Alignment explanation
Indices: 20476382--20476478 Score: 86
Period size: 1 Copynumber: 97.0 Consensus size: 1
20476372 GACCTCTCCG
* * * * * * * *
20476382 TTTTTTTTTTGTTTTTGTTTTTGTTTTTTTTCTTTTTTTTTTGTTTTTGTTTTTGTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
20476447 TGTTTTTGTTTTTTTCTTTTTTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20476479 AGGTGTAATA
Statistics
Matches: 72, Mismatches: 24, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 72 1.00
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:20476396 original size:6 final size:6
Alignment explanation
Indices: 20476381--20476477 Score: 117
Period size: 6 Copynumber: 16.0 Consensus size: 6
20476371 TGACCTCTCC
* *
20476381 GTTTTT -TTTTT GTTTTT GTTTTT GTTTTTT TTCTTTT TTTTTT GTTTTT
1 GTTTTT GTTTTT GTTTTT GTTTTT G-TTTTT GT-TTTT GTTTTT GTTTTT
* *
20476430 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT -TTCTTT TTTTTT CTTTTT
1 GTTTTT GTTTTT GTTTTT GTTTTT GTTTTT GTT-TTT GTTTTT GTTTTT
20476478 TAGGTGTAAT
Statistics
Matches: 83, Mismatches: 3, Indels: 10
0.86 0.03 0.10
Matches are distributed among these distances:
5 7 0.08
6 63 0.76
7 13 0.16
ACGTcount: A:0.00, C:0.03, G:0.10, T:0.87
Consensus pattern (6 bp):
GTTTTT
Found at i:20486427 original size:68 final size:68
Alignment explanation
Indices: 20485965--20486747 Score: 1293
Period size: 67 Copynumber: 11.6 Consensus size: 68
20485955 AATGATCTTT
* * * *
20485965 CGTGTTATCCACTCTTACTTCAATTTCAAAGGGATGACCTTGCTCTTATTTCAATTT-GGAGATG
1 CGTGTTATCCACTC-TACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATG
*
20486029 ACGA
65 AAGA
*
20486033 TGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC-TACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
**
20486097 ATC
66 AGA
20486100 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
20486165 ATA
66 AGA
20486168 CGTGTTAT-CACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
20486232 AGA
66 AGA
20486235 CGTG-T-TCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
20486298 AGA
66 AGA
*
20486301 CGTGTCATCCACTCTA--TCAATTTCAAGGGGGATGACGTTGCTCTTACTTC-ATTTCAGAGATG
1 CGTGTTATCCACTCTACTTCAATTTCAA-GGGGATGACGTTGCTCTTACTTCAATTTCAGAGATG
20486363 AAGA
65 AAGA
20486367 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
20486432 AGA
66 AGA
*
20486435 CGTTGGT-TCCACTCTACTTCAATTTCAA-GGGATGACG-TGCTCTTTACTTCAATTTCAGAGAT
1 CG-TGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC-TTACTTCAATTTCAGAGA-
*
20486497 TGAATA
63 TGAAGA
20486503 CGTGTTCATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATG
1 CGTGTT-ATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATG
*
20486568 AAAA
65 AAGA
*
20486572 CGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
20486637 AGA
66 AGA
20486640 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
20486705 AGA
66 AGA
*
20486708 CGTGGT-TCCACTCTACTTCAATTTCAAGGGGATGACGTTG
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTG
20486748 AGATCTGCAA
Statistics
Matches: 678, Mismatches: 21, Indels: 33
0.93 0.03 0.05
Matches are distributed among these distances:
65 1 0.00
66 120 0.18
67 250 0.37
68 240 0.35
69 35 0.05
70 27 0.04
71 5 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (68 bp):
CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
AGA
Found at i:20486469 original size:267 final size:272
Alignment explanation
Indices: 20485965--20486747 Score: 1300
Period size: 267 Copynumber: 2.9 Consensus size: 272
20485955 AATGATCTTT
* * * *
20485965 CGTGTTATCCACTCTTACTTCAATTTCAAAGGGATGACCTTGCTCTTATTTCAATTT-GGAGATG
1 CGTGTTATCCACTC-TACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATG
* *
20486029 ACGATGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC-TACTTCAATTTCAGAG
65 AAGACGTGTTATCCACTCTAC-TCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG
**
20486093 ATGAATCCGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCA
129 ATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCA
* *
20486158 GAGATGAATACGT-GTTATCACTCTACTTCAATTTCAAGGGGATGACGTTGCTC-TTACTTCAAT
194 GAGATGAAGACGTGGTT-CCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTTACTTCAAT
20486221 TTCAGAGA-TGAAGA
258 TTCAGAGATTGAAGA
20486235 CGTG-T-TCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
1 CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
*
20486298 AGACGTGTCATCCACTCTA-TCAATTTCAAGGGGGATGACGTTGCTCTTACTTC-ATTTCAGAGA
66 AGACGTGTTATCCACTCTACTCAATTTCAA-GGGGATGACGTTGCTCTTACTTCAATTTCAGAGA
20486361 TGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAG
130 TGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAG
20486426 AGATGAAGACGTTGGTTCCACTCTACTTCAATTTCAA-GGGATGACG-TGCTCTTTACTTCAATT
195 AGATGAAGACG-TGGTTCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTTACTTCAATT
*
20486489 TCAGAGATTGAATA
259 TCAGAGATTGAAGA
20486503 CGTGTTCATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATG
1 CGTGTT-ATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATG
* *
20486568 AAAACGTGTTATCCACTCTACTTCAATTTCAAGGGAATGACGTTGCTCTTACTTCAATTTCAGAG
65 AAGACGTGTTATCCACTCTAC-TCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAG
20486633 ATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCA
129 ATGAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCA
20486698 GAGATGAAGACGTGGTTCCACTCTACTTCAATTTCAAGGGGATGACGTTG
194 GAGATGAAGACGTGGTTCCACTCTACTTCAATTTCAAGGGGATGACGTTG
20486748 AGATCTGCAA
Statistics
Matches: 483, Mismatches: 15, Indels: 26
0.92 0.03 0.05
Matches are distributed among these distances:
266 15 0.03
267 165 0.34
268 65 0.13
269 5 0.01
270 4 0.01
271 75 0.16
272 47 0.10
273 105 0.22
274 2 0.00
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (272 bp):
CGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGATGA
AGACGTGTTATCCACTCTACTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGAGAT
GAAGACGTGTTATCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTACTTCAATTTCAGA
GATGAAGACGTGGTTCCACTCTACTTCAATTTCAAGGGGATGACGTTGCTCTTTACTTCAATTTC
AGAGATTGAAGA
Done.