Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 102 of 125
Found at i:30811813 original size:16 final size:16
Alignment explanation
Indices: 30811794--30811887 Score: 50
Period size: 16 Copynumber: 6.0 Consensus size: 16
30811784 GATTACTATT
30811794 AAATATAATTTAATAA
1 AAATATAATTTAATAA
**
30811810 AAATATTAA-TTAATTT
1 AAATA-TAATTTAATAA
* * *
30811826 AATTATATTTTAATAT
1 AAATATAATTTAATAA
* * *
30811842 AATTATTATTAAAT-A
1 AAATATAATTTAATAA
* **
30811857 AAATTTAATAAAAT-A
1 AAATATAATTTAATAA
*
30811872 ATATATAATTTAATAA
1 AAATATAATTTAATAA
30811888 TATTTTTAAT
Statistics
Matches: 58, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
15 23 0.40
16 32 0.55
17 3 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATAATTTAATAA
Found at i:30811838 original size:32 final size:31
Alignment explanation
Indices: 30811792--30811911 Score: 83
Period size: 32 Copynumber: 4.0 Consensus size: 31
30811782 AAGATTACTA
30811792 TTAAATATAATTTAATAAAAATATTAATTAAT
1 TTAAATATAATTTAATAAAAATATT-ATTAAT
* * *
30811824 TTAATTATATTTTAAT--ATA-ATTATT-A-
1 TTAAATATAATTTAATAAAAATATTATTAAT
* *
30811850 TTAAATAAAATTTAAT-AAAATAATATATAAT
1 TTAAATATAATTTAATAAAAATATTAT-TAAT
* * *
30811881 TT-AATAATATTTTTAATATAATTATTATTAA
1 TTAAAT-ATA-ATTTAATAAAAATATTATTAA
30811912 AATATGAATT
Statistics
Matches: 67, Mismatches: 13, Indels: 16
0.70 0.14 0.17
Matches are distributed among these distances:
26 13 0.19
27 3 0.04
28 7 0.10
29 4 0.06
30 6 0.09
31 4 0.06
32 23 0.34
33 7 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TTAAATATAATTTAATAAAAATATTATTAAT
Found at i:30811839 original size:58 final size:58
Alignment explanation
Indices: 30811769--30811939 Score: 197
Period size: 58 Copynumber: 2.9 Consensus size: 58
30811759 GATTATTCTT
* * *
30811769 ATTAAATTTTAATA-AGATTACTATTAAATATAATTTAATAAAAATATTA-ATTAATTTA
1 ATTATATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATAATATA-TAATTTA
*
30811827 ATTATATTTTAATATAATTATTATTAAATAAAATTTAAT-AAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTA
* * *
30811884 ATAATATTTTTAATATAATTATTATTAAAATATGAA-TTAGTAAAAATTATAATATA
1 ATTATA-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAATAAT-ATATA
30811940 TAATATTAGA
Statistics
Matches: 98, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
57 20 0.20
58 54 0.55
59 10 0.10
60 9 0.09
61 5 0.05
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.46
Consensus pattern (58 bp):
ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAATATATAATTTA
Found at i:30811906 original size:15 final size:15
Alignment explanation
Indices: 30811819--30811911 Score: 52
Period size: 15 Copynumber: 6.3 Consensus size: 15
30811809 AAAATATTAA
*
30811819 TTAATTTAATTATATT
1 TTAATATAATTAT-TT
*
30811835 TTAATATAATTATTA
1 TTAATATAATTATTT
*
30811850 TTAA-ATAA-AATTT
1 TTAATATAATTATTT
* * *
30811863 AATAAAATAATATATAAT
1 -TTAATATAAT-TAT-TT
30811881 TT-A-ATAA-TATTT
1 TTAATATAATTATTT
*
30811893 TTAATATAATTATTA
1 TTAATATAATTATTT
30811908 TTAA
1 TTAA
30811912 AATATGAATT
Statistics
Matches: 59, Mismatches: 10, Indels: 17
0.69 0.12 0.20
Matches are distributed among these distances:
12 3 0.05
13 7 0.12
14 11 0.19
15 21 0.36
16 13 0.22
17 3 0.05
18 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TTAATATAATTATTT
Found at i:30815092 original size:31 final size:31
Alignment explanation
Indices: 30815037--30815115 Score: 110
Period size: 31 Copynumber: 2.6 Consensus size: 31
30815027 TAACATAGAT
* *
30815037 ACTTATTTAACTACAA-A-AATAATTTAAGA
1 ACTTATTTAAATAAAATATAATAATTTAAGA
30815066 ACTTATTTAAATAAAATATAATAATTTAAGA
1 ACTTATTTAAATAAAATATAATAATTTAAGA
30815097 ACTTATTTAAA-AAATATAT
1 ACTTATTTAAATAAA-ATAT
30815116 TAGCCATTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 14 0.31
30 4 0.09
31 27 0.60
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (31 bp):
ACTTATTTAAATAAAATATAATAATTTAAGA
Found at i:30818081 original size:21 final size:20
Alignment explanation
Indices: 30818049--30818091 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
30818039 ATGCATGCTA
*
30818049 TTTTTTATTTTTTGAA-TAT
1 TTTTTTATTTTTTAAATTAT
30818068 TTTTTTATAATTTTTAAATTAT
1 TTTTTTAT--TTTTTAAATTAT
30818090 TT
1 TT
30818092 ATTGTCGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 8 0.40
21 7 0.35
22 5 0.25
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTTTTATTTTTTAAATTAT
Found at i:30818409 original size:6 final size:6
Alignment explanation
Indices: 30818398--30818424 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
30818388 ATAATTTGAT
30818398 ATGTCC ATGTCC ATGTCC ATGTCC ATG
1 ATGTCC ATGTCC ATGTCC ATGTCC ATG
30818425 ATGATCATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.30, G:0.19, T:0.33
Consensus pattern (6 bp):
ATGTCC
Found at i:30825298 original size:62 final size:61
Alignment explanation
Indices: 30825232--30825366 Score: 200
Period size: 62 Copynumber: 2.2 Consensus size: 61
30825222 ACTTTGACAA
30825232 TTTTTCCTTGTACTTCATGC-TAAAGTTTCTCCAACGACAGATGTAATTGATGATTAACTCGT
1 TTTTTCCTTGTACTTCATGCTTAAA-TTTCTCCAACGACAGATGTAATTGATGATTAACT-GT
* * * *
30825294 TTTTTTCTTGTAGTTCATGCTTAAATTTCTCCAACGACAGATGTAATTGATGATTAGCTTT
1 TTTTTCCTTGTACTTCATGCTTAAATTTCTCCAACGACAGATGTAATTGATGATTAACTGT
30825355 TCTTTTCCTTGT
1 T-TTTTCCTTGT
30825367 CATGAGCTTG
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
61 2 0.03
62 60 0.91
63 4 0.06
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (61 bp):
TTTTTCCTTGTACTTCATGCTTAAATTTCTCCAACGACAGATGTAATTGATGATTAACTGT
Found at i:30826242 original size:22 final size:22
Alignment explanation
Indices: 30826216--30826260 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
30826206 ACTTTTTTCA
*
30826216 TTTAAATTTA-TAATTATAAAAT
1 TTTAAA-TTAGTAATAATAAAAT
30826238 TTTAAATTAGTAATAATAAAAT
1 TTTAAATTAGTAATAATAAAAT
30826260 T
1 T
30826261 ACATTTTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTAAATTAGTAATAATAAAAT
Found at i:30826292 original size:31 final size:29
Alignment explanation
Indices: 30826249--30826318 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
30826239 TTAAATTAGT
30826249 AATAATAAAATTACATTTTAATCTTTTAAA
1 AATAATAAAATTACA-TTTAATCTTTTAAA
* *
30826279 AATAATTAAAATTAGATTTAATTTTTTAAA
1 AATAA-TAAAATTACATTTAATCTTTTAAA
* *
30826309 ATTTATAAAA
1 AATAATAAAA
30826319 ATATAAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 5 0.14
30 21 0.60
31 9 0.26
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.44
Consensus pattern (29 bp):
AATAATAAAATTACATTTAATCTTTTAAA
Found at i:30832322 original size:84 final size:84
Alignment explanation
Indices: 30832218--30832383 Score: 269
Period size: 84 Copynumber: 2.0 Consensus size: 84
30832208 CCACTACCAC
* * **
30832218 TAGTTCCACCACTTAAATTCTGTCCACAATCTTGCAACTCATCATTGTCCTTCACATCACCTTCT
1 TAGTTCCACCACTTAAATTCTGCCCACAATCTTGCAACTCACCATCATCCTTCACATCACCTTCT
30832283 CTTCTATTCACCACCTCAT
66 CTTCTATTCACCACCTCAT
* *
30832302 TAGTTCCACCATTTAGATTCTGCCCACAATCTTGCAACTCACCATCATCCTTCACATCACCTTCT
1 TAGTTCCACCACTTAAATTCTGCCCACAATCTTGCAACTCACCATCATCCTTCACATCACCTTCT
*
30832367 CTTTTATTCACCACCTC
66 CTTCTATTCACCACCTC
30832384 CTCATTAACC
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.23, C:0.37, G:0.05, T:0.35
Consensus pattern (84 bp):
TAGTTCCACCACTTAAATTCTGCCCACAATCTTGCAACTCACCATCATCCTTCACATCACCTTCT
CTTCTATTCACCACCTCAT
Found at i:30832994 original size:228 final size:219
Alignment explanation
Indices: 30832607--30833055 Score: 686
Period size: 228 Copynumber: 2.0 Consensus size: 219
30832597 CTCTCCACCA
* * *
30832607 CCACCACCAACACTCTTAGACTGTTCGCTGCCTGAATCCCGTGACCATGTTGGCGACCTTGACTT
1 CCACCACCAACACTCTTAGACTGCTCACTGCCCGAATCCCGTGACCATGTTGGCGACCTTGACTT
* *
30832672 AGACTTCGACTTGGAGCTTCTCCTCTTCAAATCCTCCTCCCTTGATTCCCCAACAACCCTCCCTG
66 AGACTTCGACTTGGAGCTTCTCCTCCTCAAATCCCCCTCCCTTGATTCCCCAACAACCCTCCCTG
*
30832737 CCCCCAAAGAATCCCTTGACCGTGTAGGTGAGCTCACATCCCTAACATCCTTCAGATGCACCTTA
131 CCCCCAAAGAATCCCTTGACCGTGTAGGTGAGCTCACATCCCTAACATCCCTCAGATGCACCTTA
*
30832802 CTACTACCTCTAGTC-TCATCAATT
196 CTACTACCTCTA-ACATCATCAATT
*
30832826 CCACCACCAACACTCTTAGACTGCTCACTGCCCGAATCTCGTGACCATGTTGGCGACCTTGACAT
1 CCACCACCAACACTCTTAGACTGCTCACTGCCCGAATCCCGTGACCATGTTGGCGACCTTGAC-T
*
30832891 AGACGTAGACATT-GCCTTGGAGCTTCTCCTCCTCAAATCTTCCCTCTCCCTTGATTCCCCAACA
65 -----TAGAC-TTCGACTTGGAGCTTCTCCTCCTCAAATC--CCC-CTCCCTTGATTCCCCAACA
30832955 ACCCTCCCTGCCCCCAAAGAATCCCTTGACCGTGTAGGTGAGCTCACATCCCTAACATCCCTCAG
121 ACCCTCCCTGCCCCCAAAGAATCCCTTGACCGTGTAGGTGAGCTCACATCCCTAACATCCCTCAG
* *
30833020 TTGCACCTTACTACTCCCTCTAACATCATCAATT
186 ATGCACCTTACTACTACCTCTAACATCATCAATT
30833054 CC
1 CC
30833056 CAACCTTCGC
Statistics
Matches: 208, Mismatches: 11, Indels: 13
0.90 0.05 0.06
Matches are distributed among these distances:
219 59 0.28
220 1 0.00
225 29 0.14
226 2 0.01
227 3 0.01
228 114 0.55
ACGTcount: A:0.22, C:0.38, G:0.13, T:0.27
Consensus pattern (219 bp):
CCACCACCAACACTCTTAGACTGCTCACTGCCCGAATCCCGTGACCATGTTGGCGACCTTGACTT
AGACTTCGACTTGGAGCTTCTCCTCCTCAAATCCCCCTCCCTTGATTCCCCAACAACCCTCCCTG
CCCCCAAAGAATCCCTTGACCGTGTAGGTGAGCTCACATCCCTAACATCCCTCAGATGCACCTTA
CTACTACCTCTAACATCATCAATT
Found at i:30837003 original size:31 final size:31
Alignment explanation
Indices: 30836968--30837033 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
30836958 AAAAATAGAT
30836968 ACATGTGACAAATAAAGTAATTTCTGAGCAA
1 ACATGTGACAAATAAAGTAATTTCTGAGCAA
** * *
30836999 ACATGTGACAAATGGAGTAATTTTTTAGCAA
1 ACATGTGACAAATAAAGTAATTTCTGAGCAA
30837030 ACAT
1 ACAT
30837034 AATCATATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (31 bp):
ACATGTGACAAATAAAGTAATTTCTGAGCAA
Found at i:30838349 original size:16 final size:16
Alignment explanation
Indices: 30838299--30838349 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
30838289 AAATCTGAAA
*
30838299 AAATTTAAAATAATCA
1 AAATTTAAAATAATCT
* * *
30838315 AAAGTTAAAAAAACCCT
1 AAATTTAAAATAA-TCT
30838332 AAATTTAAAATAATCT
1 AAATTTAAAATAATCT
30838348 AA
1 AA
30838350 TCAAACACTC
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
16 15 0.56
17 12 0.44
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (16 bp):
AAATTTAAAATAATCT
Found at i:30839204 original size:13 final size:14
Alignment explanation
Indices: 30839186--30839217 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
30839176 ATCAAATTCA
30839186 AAGACAAGGA-AAG
1 AAGACAAGGAGAAG
30839199 AAGACAAGGAGAAG
1 AAGACAAGGAGAAG
30839213 -AGACA
1 AAGACA
30839218 GTTGTTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.59, C:0.09, G:0.31, T:0.00
Consensus pattern (14 bp):
AAGACAAGGAGAAG
Found at i:30841281 original size:20 final size:20
Alignment explanation
Indices: 30841244--30841282 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
30841234 ATTTGTTACG
*
30841244 CCCTTATAATTTTTTATATT
1 CCCTTATAATTTTGTATATT
30841264 CCCTTAT-ATATTTGTATAT
1 CCCTTATAAT-TTTGTATAT
30841283 CTTCATATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.26, C:0.15, G:0.03, T:0.56
Consensus pattern (20 bp):
CCCTTATAATTTTGTATATT
Found at i:30841579 original size:40 final size:39
Alignment explanation
Indices: 30841521--30841626 Score: 110
Period size: 40 Copynumber: 2.6 Consensus size: 39
30841511 ACCTTCGTGT
30841521 TTTTTTGGTACTTT-TTCATATTTTTCGACA-TTCTCTTATAA
1 TTTTTT-GTA-TTTCTTCATATTTTT-GACATTTC-CTTATAA
* *
30841562 TTTTTTGTATTTCTTCATATTTTTTATATTTCCTTATAA
1 TTTTTTGTATTTCTTCATATTTTTGACATTTCCTTATAA
*
30841601 GTTTTTGTATTCTCTT-ATAATTTTTG
1 TTTTTTGTATT-TCTTCAT-ATTTTTG
30841627 GTACATTATT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
39 24 0.42
40 27 0.47
41 6 0.11
ACGTcount: A:0.19, C:0.11, G:0.07, T:0.63
Consensus pattern (39 bp):
TTTTTTGTATTTCTTCATATTTTTGACATTTCCTTATAA
Found at i:30841605 original size:20 final size:20
Alignment explanation
Indices: 30841555--30841625 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
30841545 TCGACATTCT
30841555 CTTATAATTTTTTGTATTT-
1 CTTATAATTTTTTGTATTTC
*
30841574 CTTCAT-ATTTTTTATATTTC
1 CTT-ATAATTTTTTGTATTTC
*
30841594 CTTATAAGTTTTTGTA-TTC
1 CTTATAATTTTTTGTATTTC
30841613 TCTTATAATTTTT
1 -CTTATAATTTTT
30841626 GGTACATTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
19 20 0.45
20 24 0.55
ACGTcount: A:0.21, C:0.10, G:0.04, T:0.65
Consensus pattern (20 bp):
CTTATAATTTTTTGTATTTC
Found at i:30841769 original size:40 final size:38
Alignment explanation
Indices: 30841725--30841818 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 38
30841715 GTATTTATTG
* *
30841725 ATATTACTTCATAATTATTGGTGCATCTCATATTTTTTTT
1 ATATTACTTCATAATTATTGGT-AATCTC-TATTCTTTTT
** *
30841765 ATATTTTTTCATAATTTTTGGTAATCTCTATTCTTTTT
1 ATATTACTTCATAATTATTGGTAATCTCTATTCTTTTT
*
30841803 GTATTCAC-TCATAATT
1 ATATT-ACTTCATAATT
30841819 TTGATACTCC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
38 21 0.47
39 5 0.11
40 19 0.42
ACGTcount: A:0.24, C:0.13, G:0.06, T:0.56
Consensus pattern (38 bp):
ATATTACTTCATAATTATTGGTAATCTCTATTCTTTTT
Found at i:30841846 original size:21 final size:21
Alignment explanation
Indices: 30841810--30841875 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 21
30841800 TTTGTATTCA
*
30841810 CTCATA-A-TTTTGATACTCC
1 CTCATATATTTTTTATACTCC
*
30841829 CTCATATATTTTTTATACTTC
1 CTCATATATTTTTTATACTCC
* *
30841850 TTCATAT-TTTTTTATATTCC
1 CTCATATATTTTTTATACTCC
30841870 CTCATA
1 CTCATA
30841876 ATTATTCGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
19 6 0.15
20 17 0.44
21 16 0.41
ACGTcount: A:0.24, C:0.21, G:0.02, T:0.53
Consensus pattern (21 bp):
CTCATATATTTTTTATACTCC
Found at i:30843180 original size:19 final size:19
Alignment explanation
Indices: 30843156--30843195 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
30843146 TTTAAACTTA
*
30843156 AACAAAAACAAAATATTAT
1 AACAAAAACAAAAAATTAT
*
30843175 AACAAATACAAAAAATTAT
1 AACAAAAACAAAAAATTAT
30843194 AA
1 AA
30843196 AAAGATAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.70, C:0.10, G:0.00, T:0.20
Consensus pattern (19 bp):
AACAAAAACAAAAAATTAT
Found at i:30845885 original size:20 final size:20
Alignment explanation
Indices: 30845862--30845915 Score: 56
Period size: 20 Copynumber: 2.7 Consensus size: 20
30845852 TTATTGTTTG
30845862 AATCGATTTATCTTAATTTA
1 AATCGATTTATCTTAATTTA
* * *
30845882 AATCAATTCAT-TGTGATTTA
1 AATCGATTTATCT-TAATTTA
*
30845902 AATTGATTTATCTT
1 AATCGATTTATCTT
30845916 GGATTAACTC
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
19 1 0.04
20 24 0.92
21 1 0.04
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.50
Consensus pattern (20 bp):
AATCGATTTATCTTAATTTA
Found at i:30846847 original size:18 final size:17
Alignment explanation
Indices: 30846820--30846855 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
30846810 AACCTTTTTG
*
30846820 TTTTATTTTAATTATTT
1 TTTTATTTTAATAATTT
30846837 TTTTAATTTTAATAATTT
1 TTTT-ATTTTAATAATTT
30846855 T
1 T
30846856 GGGAGCGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTATTTTAATAATTT
Found at i:30862341 original size:18 final size:18
Alignment explanation
Indices: 30862318--30862355 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
30862308 TCTTAAGTTA
30862318 AAGGGACTGCATAATTTT
1 AAGGGACTGCATAATTTT
30862336 AAGGGACTGCATAATTTT
1 AAGGGACTGCATAATTTT
30862354 AA
1 AA
30862356 TTGCAGGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (18 bp):
AAGGGACTGCATAATTTT
Found at i:30863480 original size:54 final size:54
Alignment explanation
Indices: 30863414--30863523 Score: 184
Period size: 54 Copynumber: 2.0 Consensus size: 54
30863404 GTCACTGCCC
* *
30863414 CTGATTTTTCCAATGCTGATGATGAGGAAGATGATATTGCTTCAGAAACCGGTT
1 CTGATTTGTCCAATGCTGATGATGAGGAAGATCATATTGCTTCAGAAACCGGTT
* *
30863468 CTGATTTGTCCAATGCTGATGATGAGGAAGATCATGTTGCTTCAGAAACTGGTT
1 CTGATTTGTCCAATGCTGATGATGAGGAAGATCATATTGCTTCAGAAACCGGTT
30863522 CT
1 CT
30863524 TCTAAGGATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.34
Consensus pattern (54 bp):
CTGATTTGTCCAATGCTGATGATGAGGAAGATCATATTGCTTCAGAAACCGGTT
Found at i:30864343 original size:75 final size:75
Alignment explanation
Indices: 30864220--30864368 Score: 226
Period size: 75 Copynumber: 2.0 Consensus size: 75
30864210 CAAGTCGCCT
* * * * * *
30864220 CTTGAAGCCCTTTTGTCTGACGTGCAAGTAACAGATACTGCTGCTTCCTGCTCTAAGAAAAGTGA
1 CTTGAAGCCCTTTTGTCAGACATGCAAGTAACAGATACTGCTACTTCCTGCTCCAAAAAAAGCGA
*
30864285 TGATGGTTCC
66 TGATAGTTCC
*
30864295 CTTGAAGCCCTTTTGTCAGACATGCAAGTCACAGATACTGCTACTTCCTGCTCCAAAAAAAGCGA
1 CTTGAAGCCCTTTTGTCAGACATGCAAGTAACAGATACTGCTACTTCCTGCTCCAAAAAAAGCGA
30864360 TGATAGTTC
66 TGATAGTTC
30864369 TCAACCTGGT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (75 bp):
CTTGAAGCCCTTTTGTCAGACATGCAAGTAACAGATACTGCTACTTCCTGCTCCAAAAAAAGCGA
TGATAGTTCC
Found at i:30873160 original size:34 final size:34
Alignment explanation
Indices: 30873117--30873185 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
30873107 AAAACCAAGA
30873117 TAGCATTAATATCCAATGAACGCAAAGCACAGGG
1 TAGCATTAATATCCAATGAACGCAAAGCACAGGG
30873151 TAGCATTAATATCCAATGAACGCAAAGCACAGGG
1 TAGCATTAATATCCAATGAACGCAAAGCACAGGG
30873185 T
1 T
30873186 TTGTATGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.19
Consensus pattern (34 bp):
TAGCATTAATATCCAATGAACGCAAAGCACAGGG
Found at i:30878335 original size:6 final size:6
Alignment explanation
Indices: 30878317--30878346 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
30878307 TCTGTCAAAT
*
30878317 TCCTTC TCTTTC TCCTTC TCCTTC TCCTTC
1 TCCTTC TCCTTC TCCTTC TCCTTC TCCTTC
30878347 CGTTTTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (6 bp):
TCCTTC
Found at i:30883967 original size:21 final size:23
Alignment explanation
Indices: 30883925--30883967 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
30883915 ATATTCAAAT
*
30883925 AATATTAAAAACGACAATAAAAC
1 AATAGTAAAAACGACAATAAAAC
30883948 AATAGTAAAAACG-C-ATAAAA
1 AATAGTAAAAACGACAATAAAA
30883968 ATAACATCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 12 0.63
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.16
Consensus pattern (23 bp):
AATAGTAAAAACGACAATAAAAC
Found at i:30883985 original size:12 final size:12
Alignment explanation
Indices: 30883964--30884060 Score: 74
Period size: 12 Copynumber: 8.3 Consensus size: 12
30883954 AAAAACGCAT
30883964 AAAAATAACATC
1 AAAAATAACATC
* *
30883976 CAAAACAACATC
1 AAAAATAACATC
*
30883988 AAAAATAAAATC
1 AAAAATAACATC
* *
30884000 -AAAAGAACAAC
1 AAAAATAACATC
*
30884011 AAAAATAACAAC
1 AAAAATAACATC
*
30884023 AAAAACAACA-C
1 AAAAATAACATC
* * *
30884034 TAAAATAGCA-A
1 AAAAATAACATC
*
30884045 AAAAACAACATC
1 AAAAATAACATC
30884057 AAAA
1 AAAA
30884061 CAACAAAAGC
Statistics
Matches: 65, Mismatches: 18, Indels: 4
0.75 0.21 0.05
Matches are distributed among these distances:
11 23 0.35
12 42 0.65
ACGTcount: A:0.70, C:0.19, G:0.02, T:0.09
Consensus pattern (12 bp):
AAAAATAACATC
Found at i:30883991 original size:23 final size:24
Alignment explanation
Indices: 30883964--30884060 Score: 101
Period size: 23 Copynumber: 4.2 Consensus size: 24
30883954 AAAAACGCAT
*
30883964 AAAAATAACATCCAAAACAACATC
1 AAAAATAACATCAAAAACAACATC
* * *
30883988 AAAAATAAAATC-AAAAGAACAAC
1 AAAAATAACATCAAAAACAACATC
*
30884011 AAAAATAACAACAAAAACAACA-C
1 AAAAATAACATCAAAAACAACATC
* * *
30884034 TAAAATAGCA-AAAAAACAACATC
1 AAAAATAACATCAAAAACAACATC
30884057 AAAA
1 AAAA
30884061 CAACAAAAGC
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
22 10 0.16
23 32 0.52
24 19 0.31
ACGTcount: A:0.70, C:0.19, G:0.02, T:0.09
Consensus pattern (24 bp):
AAAAATAACATCAAAAACAACATC
Found at i:30885635 original size:30 final size:30
Alignment explanation
Indices: 30885601--30885663 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
30885591 TAATAATTAG
*
30885601 ATATACATGAAATTAGAAAGAAAAATTAAA
1 ATATACAAGAAATTAGAAAGAAAAATTAAA
* ** *
30885631 ATATACAAGAAATTCGAAATTAAATTTAAA
1 ATATACAAGAAATTAGAAAGAAAAATTAAA
30885661 ATA
1 ATA
30885664 AAAACGAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.60, C:0.05, G:0.08, T:0.27
Consensus pattern (30 bp):
ATATACAAGAAATTAGAAAGAAAAATTAAA
Found at i:30885673 original size:30 final size:30
Alignment explanation
Indices: 30885626--30885691 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
30885616 GAAAGAAAAA
*
30885626 TTAAAATATACAAGAAATT-CGAAATTAAAT
1 TTAAAATATAAAAGAAATTAC-AAATTAAAT
30885656 TTAAAATA-AAAACGAAATTACAAATTAAAT
1 TTAAAATATAAAA-GAAATTACAAATTAAAT
30885686 TTAAAA
1 TTAAAA
30885692 AGTAAAGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 3 0.09
30 29 0.88
31 1 0.03
ACGTcount: A:0.61, C:0.06, G:0.05, T:0.29
Consensus pattern (30 bp):
TTAAAATATAAAAGAAATTACAAATTAAAT
Found at i:30886830 original size:14 final size:15
Alignment explanation
Indices: 30886804--30886832 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
30886794 TGTGTTTTTT
30886804 ATATTTCGAAAAAAA
1 ATATTTCGAAAAAAA
30886819 ATATTT-GAAAAAAA
1 ATATTTCGAAAAAAA
30886833 TATCAGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (15 bp):
ATATTTCGAAAAAAA
Found at i:30888234 original size:83 final size:82
Alignment explanation
Indices: 30888095--30888366 Score: 377
Period size: 83 Copynumber: 3.3 Consensus size: 82
30888085 TATAAAATAC
* *
30888095 GATAAAAATTGTAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATATTGTATTGT
1 GATAAAAATTGTAATATAAT-AAAATTTTTATTTAAAAATATAAAATTAATAAATATTGTATTGT
*
30888160 CAAATCAACACATTATAT
65 CAAATCAATACATTATAT
30888178 GATAAAAATTGTAATATAATAAAATTTTTTATTTAAAAATATAAAATTAATAAATATTGTATTGT
1 GATAAAAATTGTAATATAATAAAA-TTTTTATTTAAAAATATAAAATTAATAAATATTGTATTGT
30888243 CAAATCAATACATTATAT
65 CAAATCAATACATTATAT
* * * *
30888261 GATAAAAATTATAATATAATAATAATTTATACTTT--AAATATGAAAATTTGATAAATAATGTAT
1 GATAAAAATTGTAATATAATAA-AATTTTTA-TTTAAAAATAT-AAAA-TTAATAAATATTGTAT
* * *
30888324 TGTCAAATTAATACAATATTT
62 TGTCAAATCAATACATTATAT
*
30888345 GATATAAATTGTAATATAATAA
1 GATAAAAATTGTAATATAATAA
30888367 CTATCTTTTT
Statistics
Matches: 172, Mismatches: 12, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
82 10 0.06
83 105 0.61
84 57 0.33
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (82 bp):
GATAAAAATTGTAATATAATAAAATTTTTATTTAAAAATATAAAATTAATAAATATTGTATTGTC
AAATCAATACATTATAT
Found at i:30888514 original size:12 final size:12
Alignment explanation
Indices: 30888497--30888544 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
30888487 AAACATGTAC
30888497 ATTAATTTCCAA
1 ATTAATTTCCAA
30888509 ATTAATTTCAACTTAA
1 ATTAATTTC--C--AA
*
30888525 ATTAATTTTCAA
1 ATTAATTTCCAA
30888537 ATTAATTT
1 ATTAATTT
30888545 TTACACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAATTTCCAA
Found at i:30888543 original size:16 final size:16
Alignment explanation
Indices: 30888507--30888541 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
30888497 ATTAATTTCC
*
30888507 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
30888523 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
30888540 AA
1 AA
30888542 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:30888554 original size:28 final size:28
Alignment explanation
Indices: 30888497--30888554 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
30888487 AAACATGTAC
**
30888497 ATTAATTTCCAAATTAATTTCAACTTAA
1 ATTAATTTCCAAATTAATTTCAACACAA
* **
30888525 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTCCAAATTAATTTCAACACAA
30888553 AT
1 AT
30888555 ATACTTCGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTAATTTCCAAATTAATTTCAACACAA
Found at i:30892423 original size:61 final size:59
Alignment explanation
Indices: 30892270--30892596 Score: 396
Period size: 61 Copynumber: 5.5 Consensus size: 59
30892260 AGGAGAAGTT
* ** ** * *
30892270 GGTGTCGACCATTTGATGTTCAACATAAAAAAAATTTGAATTTTTTTCTCCAGAACAAGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAA-TTGAATTTTTTTCTCGAGAAAAAGG
30892330 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAAATTGAAATTTTTTTCTCGAGAAAAATGG
1 GGTGTCGGCCATTTGATGGCCAACACC-AAAAAAATTG-AATTTTTTTCTCGAGAAAAA-GG
* *
30892392 GCTGTCGGCCA-TTGCATGGCCAACACCAAAAAAATTGAATTTTTTTCTCGAGAAATAGG
1 GGTGTCGGCCATTTG-ATGGCCAACACCAAAAAAATTGAATTTTTTTCTCGAGAAAAAGG
*
30892451 GGATGTCGGCCATTTGATGGCCGAACACAAAAAAAAATTG-ATTTTTTTCTCGAGAAATAAGG
1 GG-TGTCGGCCATTTGATGGCC-AACAC-CAAAAAAATTGAATTTTTTTCTCGAGAAA-AAGG
* * *
30892513 GGTGTCGGCCATTTGATGGCCAACACC-AAAAAA-TGTAATTTTTTT-TTGCA-AATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTG-AATTTTTTTCTCG-AGAAAAAGG
30892570 GGTGTCGGCCATTTGATGGCCAACACC
1 GGTGTCGGCCATTTGATGGCCAACACC
30892597 CCAAAATTTT
Statistics
Matches: 239, Mismatches: 16, Indels: 27
0.85 0.06 0.10
Matches are distributed among these distances:
57 32 0.13
58 10 0.04
59 12 0.05
60 64 0.27
61 82 0.34
62 39 0.16
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.29
Consensus pattern (59 bp):
GGTGTCGGCCATTTGATGGCCAACACCAAAAAAATTGAATTTTTTTCTCGAGAAAAAGG
Found at i:30892519 original size:121 final size:120
Alignment explanation
Indices: 30892272--30892595 Score: 421
Period size: 121 Copynumber: 2.7 Consensus size: 120
30892262 GAGAAGTTGG
* ** ** *
30892272 TGTCGACCATTTGATGTTCAACATAAAAAAAATTTGAATTTTTTTCTCCAGAACA-AGGGGTGTC
1 TGTCGGCCATTTGATGGCCAACACCAAAAAAA-TTGAATTTTTTTCTCGAGAA-ATAGGGGTGTC
*
30892336 GGCCATTTGATGGCCAACACCAAAAAAAATTGAAATTTTTTTCTCGAGAAAAATGGGC
64 GGCCATTTGATGGCCAACACAAAAAAAAATTG-AATTTTTTTCTCGAGAAAAATGGGC
30892394 TGTCGGCCA-TTGCATGGCCAACACCAAAAAAATTGAATTTTTTTCTCGAGAAATAGGGGATGTC
1 TGTCGGCCATTTG-ATGGCCAACACCAAAAAAATTGAATTTTTTTCTCGAGAAATAGGGG-TGTC
*
30892458 GGCCATTTGATGGCCGAACACAAAAAAAAATTG-ATTTTTTTCTCGAGAAATAA-GGGG
64 GGCCATTTGATGGCC-AACACAAAAAAAAATTGAATTTTTTTCTCGAGAAA-AATGGGC
* *
30892515 TGTCGGCCATTTGATGGCCAACACC-AAAAAA-TGTAATTTTTTT-TTG-CAAATAGGGGGTGTC
1 TGTCGGCCATTTGATGGCCAACACCAAAAAAATTG-AATTTTTTTCTCGAGAAATA-GGGGTGTC
30892576 GGCCATTTGATGGCCAACAC
64 GGCCATTTGATGGCCAACAC
30892596 CCCAAAATTT
Statistics
Matches: 184, Mismatches: 10, Indels: 21
0.86 0.05 0.10
Matches are distributed among these distances:
117 5 0.03
118 24 0.13
119 8 0.04
120 16 0.09
121 68 0.37
122 47 0.26
123 16 0.09
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (120 bp):
TGTCGGCCATTTGATGGCCAACACCAAAAAAATTGAATTTTTTTCTCGAGAAATAGGGGTGTCGG
CCATTTGATGGCCAACACAAAAAAAAATTGAATTTTTTTCTCGAGAAAAATGGGC
Found at i:30897876 original size:13 final size:15
Alignment explanation
Indices: 30897858--30897894 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
30897848 GTTTTTTTCT
30897858 AAAATA-ATA-CAAA
1 AAAATATATATCAAA
30897871 AAAATATATATCAAA
1 AAAATATATATCAAA
*
30897886 ATAATATAT
1 AAAATATAT
30897895 TCTCCTCGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 6 0.29
14 3 0.14
15 12 0.57
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (15 bp):
AAAATATATATCAAA
Found at i:30898227 original size:34 final size:34
Alignment explanation
Indices: 30898150--30898227 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
30898140 CTACGCCCTG
*
30898150 CTGCTGCTGCCGTGACTGCTGTTGCCCCTGCGTC
1 CTGCTGCTGCCGTGACTGCTGTTGCCCCTACGTC
*
30898184 CT-ATCGCTGCCGTGACTGCTGTTGCCCCTACGTC
1 CTGCT-GCTGCCGTGACTGCTGTTGCCCCTACGTC
30898218 CTGCTGCTGC
1 CTGCTGCTGC
30898228 TGCTGCCCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
33 1 0.03
34 37 0.95
35 1 0.03
ACGTcount: A:0.05, C:0.38, G:0.27, T:0.29
Consensus pattern (34 bp):
CTGCTGCTGCCGTGACTGCTGTTGCCCCTACGTC
Found at i:30898454 original size:21 final size:23
Alignment explanation
Indices: 30898425--30898469 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 23
30898415 AAAAAATGTA
*
30898425 TGTTGTTT-ATGGTTTG-ATTGT
1 TGTTATTTAATGGTTTGTATTGT
*
30898446 TGTTATTTAATGTTTTGTATTGT
1 TGTTATTTAATGGTTTGTATTGT
30898469 T
1 T
30898470 CTTGAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 7 0.35
23 6 0.30
ACGTcount: A:0.13, C:0.00, G:0.22, T:0.64
Consensus pattern (23 bp):
TGTTATTTAATGGTTTGTATTGT
Found at i:30898506 original size:17 final size:17
Alignment explanation
Indices: 30898484--30898517 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
30898474 AAAAAAATTC
*
30898484 ATTTAAATGTTATTTAA
1 ATTTAAATATTATTTAA
30898501 ATTTAAATATTATTTAA
1 ATTTAAATATTATTTAA
30898518 TTATTGTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTAAATATTATTTAA
Found at i:30903370 original size:13 final size:13
Alignment explanation
Indices: 30903352--30903377 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
30903342 CCACGAACAG
30903352 AAGTGACATGTGT
1 AAGTGACATGTGT
30903365 AAGTGACATGTGT
1 AAGTGACATGTGT
30903378 GCCCCAGCAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
AAGTGACATGTGT
Found at i:30905027 original size:12 final size:12
Alignment explanation
Indices: 30905010--30905079 Score: 61
Period size: 12 Copynumber: 5.9 Consensus size: 12
30905000 ATAACATCTA
*
30905010 AACAACCAAAAT
1 AACAACAAAAAT
*
30905022 AACAACCAAAAT
1 AACAACAAAAAT
* **
30905034 AGCAGTAAAAAT
1 AACAACAAAAAT
* *
30905046 AA-TAGAAAAAT
1 AACAACAAAAAT
30905057 AACAACAAAAAT
1 AACAACAAAAAT
*
30905069 AACAATAAAAA
1 AACAACAAAAA
30905080 ACAGCAACCA
Statistics
Matches: 46, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
11 8 0.17
12 38 0.83
ACGTcount: A:0.70, C:0.14, G:0.04, T:0.11
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:30905107 original size:17 final size:17
Alignment explanation
Indices: 30905085--30905118 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
30905075 AAAAAACAGC
30905085 AACCAAAACAGTAAAAA
1 AACCAAAACAGTAAAAA
30905102 AACCAAAACAGTAAAAA
1 AACCAAAACAGTAAAAA
30905119 CATAACACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.18, G:0.06, T:0.06
Consensus pattern (17 bp):
AACCAAAACAGTAAAAA
Found at i:30905153 original size:22 final size:21
Alignment explanation
Indices: 30905075--30905177 Score: 79
Period size: 22 Copynumber: 4.9 Consensus size: 21
30905065 AAATAACAAT
*
30905075 AAAAAACAGCAACCAAAACAG-
1 AAAAAATAGC-ACCAAAACAGC
* *
30905096 TAAAAA-A--ACCAAAACAGT
1 AAAAAATAGCACCAAAACAGC
*
30905114 AAAAACATAACACCAAAACAGC
1 AAAAA-ATAGCACCAAAACAGC
* *
30905136 AAAAAATAGCAACTAAAATAGC
1 AAAAAATAGC-ACCAAAACAGC
*
30905158 AAAAAAACAGCACCAAAACA
1 -AAAAAATAGCACCAAAACA
30905178 ACAATATAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
17 10 0.15
18 4 0.06
19 1 0.02
20 2 0.03
21 9 0.14
22 31 0.47
23 9 0.14
ACGTcount: A:0.66, C:0.21, G:0.07, T:0.06
Consensus pattern (21 bp):
AAAAAATAGCACCAAAACAGC
Found at i:30905886 original size:24 final size:23
Alignment explanation
Indices: 30905866--30905916 Score: 75
Period size: 24 Copynumber: 2.2 Consensus size: 23
30905856 CAACAACAGC
30905866 AAAAACAACAAAAATAGCAACAA
1 AAAAACAACAAAAATAGCAACAA
**
30905889 AAATAACTGCAAAAATAGCAACAA
1 AAA-AACAACAAAAATAGCAACAA
30905913 AAAA
1 AAAA
30905917 TCACATCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.71, C:0.16, G:0.06, T:0.08
Consensus pattern (23 bp):
AAAAACAACAAAAATAGCAACAA
Found at i:30905900 original size:15 final size:12
Alignment explanation
Indices: 30905871--30905915 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
30905861 ACAGCAAAAA
30905871 CAACAAAAATAG
1 CAACAAAAATAG
*
30905883 CAACAAAAATAA
1 CAACAAAAATAG
**
30905895 CTGCAAAAATAG
1 CAACAAAAATAG
30905907 CAACAAAAA
1 CAACAAAAA
30905916 ATCACATCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.67, C:0.18, G:0.07, T:0.09
Consensus pattern (12 bp):
CAACAAAAATAG
Found at i:30905948 original size:21 final size:21
Alignment explanation
Indices: 30905933--30905992 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
30905923 CAAAATAACA
*
30905933 ACCAAAATAGTAAAAAAAAAT
1 ACCAAAACAGTAAAAAAAAAT
*
30905954 ACCAAAACAGTAAAAAATAAT
1 ACCAAAACAGTAAAAAAAAAT
* * *
30905975 ATCAAAGCAGCAAAAAAA
1 ACCAAAACAGTAAAAAAA
30905993 GTAAAATAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.68, C:0.13, G:0.07, T:0.12
Consensus pattern (21 bp):
ACCAAAACAGTAAAAAAAAAT
Found at i:30916254 original size:38 final size:37
Alignment explanation
Indices: 30916186--30916261 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 37
30916176 AAAGTGAAAA
30916186 ATAGTTTTGAATTATTCGAATCAATTTAAATAAAATTT
1 ATAGTTTTGAATTATTCGAATCAA-TTAAATAAAATTT
* *
30916224 ATAGTTTTGAGTTATTCGAAATTGAA-TAAATAAAATTT
1 ATAGTTTTGAATTATTCG-AA-TCAATTAAATAAAATTT
30916262 TGTTTAGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 29 0.85
39 2 0.06
40 3 0.09
ACGTcount: A:0.42, C:0.04, G:0.11, T:0.43
Consensus pattern (37 bp):
ATAGTTTTGAATTATTCGAATCAATTAAATAAAATTT
Found at i:30918201 original size:5 final size:5
Alignment explanation
Indices: 30918191--30918216 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
30918181 CAGCCTTAGT
30918191 TTGTA TTGTA TTGTA TTGTA TTGTA T
1 TTGTA TTGTA TTGTA TTGTA TTGTA T
30918217 GTGTGAAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.62
Consensus pattern (5 bp):
TTGTA
Found at i:30923354 original size:4 final size:4
Alignment explanation
Indices: 30923347--30923375 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
30923337 ACACACCTAT
30923347 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
30923376 AAAGAAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:30936536 original size:3 final size:3
Alignment explanation
Indices: 30936528--30936555 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
30936518 CCCTTGTCCT
30936528 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA T
30936556 TTTGATCACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:30949903 original size:56 final size:56
Alignment explanation
Indices: 30949843--30949978 Score: 209
Period size: 56 Copynumber: 2.4 Consensus size: 56
30949833 AAAATACGAA
* *
30949843 TAAAAATTTTTTTTGGATGTTTGTCACCCAATGGCCTACACCACCTTTCCCACATT
1 TAAAAATTTTTTTTGGGTGTTTGTCACCCAATGACCTACACCACCTTTCCCACATT
* * *
30949899 TAAAAATATTTTTTGGGTGTTTGTCACCCAATGACCTACATCACCTTTCCCAGATT
1 TAAAAATTTTTTTTGGGTGTTTGTCACCCAATGACCTACACCACCTTTCCCACATT
*
30949955 TAAAAATATTTATTTGGGTGTTTG
1 TAAAAAT-TTTTTTTGGGTGTTTG
30949979 GCAAGCAATA
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
56 58 0.81
57 14 0.19
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (56 bp):
TAAAAATTTTTTTTGGGTGTTTGTCACCCAATGACCTACACCACCTTTCCCACATT
Found at i:30950326 original size:12 final size:12
Alignment explanation
Indices: 30950309--30950338 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
30950299 CACATTTCAC
30950309 AATAAAATATTT
1 AATAAAATATTT
30950321 AATAAAATATTT
1 AATAAAATATTT
30950333 ATATAA
1 A-ATAA
30950339 TTTGAATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AATAAAATATTT
Found at i:30951594 original size:57 final size:58
Alignment explanation
Indices: 30951529--30951646 Score: 186
Period size: 57 Copynumber: 2.1 Consensus size: 58
30951519 AACCATCAAC
* *
30951529 AAACTAAACCCAAATATTTTTAAACCCAAATATAATTTCA-TTCTTCAA-AACACTCAT
1 AAACTAAACCCAAATATTTGTAAACCCAAATATAATTTCATTTC-TAAATAACACTCAT
*
30951586 AAACTAAACCCAAATATTTGTAAACCCAAATATAATTTTATTTCTAAATAACACTCAT
1 AAACTAAACCCAAATATTTGTAAACCCAAATATAATTTCATTTCTAAATAACACTCAT
30951644 AAA
1 AAA
30951647 TAACTCATTT
Statistics
Matches: 56, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 41 0.73
58 15 0.27
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.31
Consensus pattern (58 bp):
AAACTAAACCCAAATATTTGTAAACCCAAATATAATTTCATTTCTAAATAACACTCAT
Found at i:30956622 original size:2 final size:2
Alignment explanation
Indices: 30956615--30956647 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30956605 CTTTGTGTTG
30956615 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30956648 CTTCCCGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30960179 original size:31 final size:29
Alignment explanation
Indices: 30960144--30960212 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
30960134 AAAATAGTAT
30960144 TGATAAAA-TTACACTTTAACCTCTTTAAAAA
1 TGATAAAATTTA-A-TTTAA-CTCTTTAAAAA
*
30960175 TGATAAAAATTTAATTTAATTCTTTAAAAA
1 TGAT-AAAATTTAATTTAACTCTTTAAAAA
*
30960205 TAATAAAA
1 TGATAAAA
30960213 ATATATACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
29 4 0.12
30 13 0.38
31 9 0.26
32 5 0.15
33 3 0.09
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.38
Consensus pattern (29 bp):
TGATAAAATTTAATTTAACTCTTTAAAAA
Found at i:30962547 original size:29 final size:26
Alignment explanation
Indices: 30962478--30962547 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 26
30962468 AATCATGAAA
*
30962478 TTTTTTTAAATACACTTAAAATAAAT
1 TTTTTTTAAATAAACTTAAAATAAAT
* *
30962504 TTAATTTTAAATAAACTTTAAAATTTTAAT
1 TT-TTTTTAAATAAAC-TTAAAA--TAAAT
30962534 TTTTTTTAAATAAA
1 TTTTTTTAAATAAA
30962548 TATATAGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.06
27 11 0.31
28 6 0.17
29 11 0.31
30 6 0.17
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTTTTAAATAAACTTAAAATAAAT
Found at i:30966964 original size:42 final size:42
Alignment explanation
Indices: 30966917--30967000 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 42
30966907 AAAAGGAGTT
*
30966917 GTTTATAAGTGTTATTT-AGGAATAAAATTATATTTGGGTTTA
1 GTTTATAAGTGTT-TTTGAAGAATAAAATTATATTTGGGTTTA
* *
30966959 GTTTATGAGTGTTTTTGAATAATAAAATTATATTTGGGTTTA
1 GTTTATAAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTA
30967001 AAAATATTTG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 3 0.08
42 35 0.92
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (42 bp):
GTTTATAAGTGTTTTTGAAGAATAAAATTATATTTGGGTTTA
Found at i:30967267 original size:33 final size:33
Alignment explanation
Indices: 30967177--30967268 Score: 87
Period size: 37 Copynumber: 2.7 Consensus size: 33
30967167 CGAATTATTA
30967177 GAATAATTCG-AATTCGAAAATTAAACTCGATTC
1 GAATAATTCGAAATTC-AAAATTAAACTCGATTC
*** * *
30967210 GAACTCAAAATTCGAAAAAAAAAATTCAACTCGATTT
1 GAA-T---AATTCGAAATTCAAAATTAAACTCGATTC
30967247 GAATAATTCGAAATTCAAAATT
1 GAATAATTCGAAATTCAAAATT
30967269 TTTTTCGAAT
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
33 18 0.39
34 1 0.02
36 1 0.02
37 24 0.52
38 2 0.04
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.28
Consensus pattern (33 bp):
GAATAATTCGAAATTCAAAATTAAACTCGATTC
Found at i:30967406 original size:17 final size:17
Alignment explanation
Indices: 30967392--30967427 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
30967382 AAAAAATATT
30967392 AAATAA-AATAAAATAA
1 AAATAACAATAAAATAA
30967408 AAATAACAATAAAATCAA
1 AAATAACAATAAAAT-AA
30967426 AA
1 AA
30967428 CCTAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 8 0.44
18 4 0.22
ACGTcount: A:0.78, C:0.06, G:0.00, T:0.17
Consensus pattern (17 bp):
AAATAACAATAAAATAA
Found at i:30968233 original size:4 final size:4
Alignment explanation
Indices: 30968224--30968274 Score: 102
Period size: 4 Copynumber: 12.8 Consensus size: 4
30968214 TAAAATAATA
30968224 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
30968272 TAT
1 TAT
30968275 TGTTTGTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:30968339 original size:24 final size:23
Alignment explanation
Indices: 30968309--30968375 Score: 89
Period size: 24 Copynumber: 2.9 Consensus size: 23
30968299 ATTAACATTG
30968309 TTAATGTTCATGAACATGTTCAA
1 TTAATGTTCATGAACATGTTCAA
* *
30968332 TTATATGTTCATGAACATTTTCAT
1 TTA-ATGTTCATGAACATGTTCAA
* *
30968356 TTAATTTTCGTGAACATGTT
1 TTAATGTTCATGAACATGTT
30968376 TGATTAAGTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
23 17 0.45
24 21 0.55
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (23 bp):
TTAATGTTCATGAACATGTTCAA
Found at i:30968806 original size:24 final size:26
Alignment explanation
Indices: 30968779--30968834 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 26
30968769 CACTATACAT
* *
30968779 TTAAAAAGTA-GATTAATTTTT-TTA
1 TTAAAAAGTATCATCAATTTTTATTA
*
30968803 TT-AAAATTATCATCAATTTTTATTA
1 TTAAAAAGTATCATCAATTTTTATTA
30968828 TTAAAAA
1 TTAAAAA
30968835 TTAATTTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 6 0.23
24 11 0.42
25 5 0.19
26 4 0.15
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.48
Consensus pattern (26 bp):
TTAAAAAGTATCATCAATTTTTATTA
Found at i:30972297 original size:23 final size:19
Alignment explanation
Indices: 30972248--30972285 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
30972238 AATTTGATAG
*
30972248 AATTTAAATAAAAATATTA
1 AATTTAAATAAAAAAATTA
30972267 AATTTAAATAAAAAAATTA
1 AATTTAAATAAAAAAATTA
30972286 GATCTATTTA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AATTTAAATAAAAAAATTA
Found at i:30976967 original size:6 final size:6
Alignment explanation
Indices: 30976956--30976981 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
30976946 CAACACAAAG
30976956 TGAGGC TGAGGC TGAGGC TGAGGC TG
1 TGAGGC TGAGGC TGAGGC TGAGGC TG
30976982 GTCGGATAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.50, T:0.19
Consensus pattern (6 bp):
TGAGGC
Found at i:30980543 original size:58 final size:59
Alignment explanation
Indices: 30980407--30980841 Score: 378
Period size: 59 Copynumber: 7.2 Consensus size: 59
30980397 TTGGCCATTG
* ** * * * * *
30980407 CATGGCCGACACTCCCTTTTAATTTGATAAAAAAAAATCAAATTTTTGGGTGTTGACCATGC
1 CATGGCCGACAC-CCCTTTTTATCAGAT--AAAAAATTTAATTTTTTTGGTGTTGATCATGC
* ** * *
30980469 AATGGTTGACACCCCCTTTTT-TCAGATAAAAAATTTAATTTTTTTTGTGTTGGTCATGC
1 CATGGCCGACA-CCCCTTTTTATCAGATAAAAAATTTAATTTTTTTGGTGTTGATCATGC
** * * ** *
30980528 CATGGTTGACACCCCTATTTAT-TGATAAAAAAATCAAATTTTTTT-GTGTTGGTCATGC
1 CATGGCCGACACCCCTTTTTATCAGAT-AAAAAATTTAATTTTTTTGGTGTTGATCATGC
* * * *
30980586 AATGGCCAACACCCCTTTTTGTCAGATAAAAAATCTAATTTTTTTGGTGTTGATCATGC
1 CATGGCCGACACCCCTTTTTATCAGATAAAAAATTTAATTTTTTTGGTGTTGATCATGC
* *
30980645 CATGGCCGACA-CCCTTATTTATCAGATAAAAAAATTTTAAATTTTTTTTTGTGTTGACCATGC
1 CATGGCCGACACCCCTT-TTTATCAGAT-AAAAAA-TTT-AA-TTTTTTTGGTGTTGATCATGC
* * * *
30980708 TATGGGCGACACCCCTATTTATCAGATGAAAAAATTTTAAATTTTCTTGGTGTTGATCATTG-
1 CATGGCCGACACCCCTTTTTATCAGAT-AAAAAA-TTT-AATTTTTTTGGTGTTGATCA-TGC
* * * * *
30980770 CATGGCCGACACCCCTTTTTATCTAAATAAAAAA-TTAAATTTTTGGGTATTGGTCATGC
1 CATGGCCGACACCCCTTTTTATC-AGATAAAAAATTTAATTTTTTTGGTGTTGATCATGC
30980829 CATGGCCGACACC
1 CATGGCCGACACC
30980842 AACTTTCCCT
Statistics
Matches: 310, Mismatches: 49, Indels: 31
0.79 0.13 0.08
Matches are distributed among these distances:
58 64 0.21
59 113 0.36
60 8 0.03
61 6 0.02
62 58 0.19
63 57 0.18
64 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (59 bp):
CATGGCCGACACCCCTTTTTATCAGATAAAAAATTTAATTTTTTTGGTGTTGATCATGC
Found at i:30980611 original size:117 final size:117
Alignment explanation
Indices: 30980407--30980841 Score: 437
Period size: 117 Copynumber: 3.6 Consensus size: 117
30980397 TTGGCCATTG
*
30980407 CATGGCCGACACTCCCT-TTTAATTTGATAAAAAAAAATCAAATTTTTGGGTGTTGACCATGCAA
1 CATGGCCGACAC-CCCTATTT-ATCTGAT--AAAAAAATCAAATTTTTGGGTGTTGACCATGCAA
** * *
30980471 TGGTTGACACCCCCTTTTTTCAGATAAAAAATTTAATTTTTTTTGTGTTGGTCATGC
62 TGGCCGACA-CCCCTTTTTTCAGATAAAAAATTTAATTTTTTTGGTGTTGATCATGC
** ** **
30980528 CATGGTTGACACCCCTATTTAT-TGATAAAAAAATCAAATTTTTTTGTGTTGGTCATGCAATGGC
1 CATGGCCGACACCCCTATTTATCTGATAAAAAAATCAAATTTTTGGGTGTTGACCATGCAATGGC
* *
30980592 CAACACCCCTTTTTGTCAGATAAAAAATCTAATTTTTTTGGTGTTGATCATGC
66 CGACACCCCTTTTT-TCAGATAAAAAATTTAATTTTTTTGGTGTTGATCATGC
* * * ** *
30980645 CATGGCCGACACCCTTATTTATCAGATAAAAAAATTTTAAATTTTTTTTTGTGTTGACCATGCTA
1 CATGGCCGACACCCCTATTTATCTGATAAAAAAA--TCAAA--TTTTTGGGTGTTGACCATGCAA
* * *
30980710 TGGGCGACACCCCTATTTATCAGATGAAAAAATTTTAAATTTTCTTGGTGTTGATCATTG-
62 TGGCCGACACCCCT-TTTTTCAGAT-AAAAAA-TTT-AATTTTTTTGGTGTTGATCA-TGC
* * * * ** *
30980770 CATGGCCGACACCCCTTTTTATCT-AAATAAAAAATTAAATTTTTGGGTATTGGTCATGCCATGG
1 CATGGCCGACACCCCTATTTATCTGATA-AAAAAATCAAATTTTTGGGTGTTGACCATGCAATGG
30980834 CCGACACC
65 CCGACACC
30980842 AACTTTCCCT
Statistics
Matches: 265, Mismatches: 36, Indels: 26
0.81 0.11 0.08
Matches are distributed among these distances:
116 9 0.03
117 90 0.34
118 10 0.04
119 4 0.02
120 10 0.04
121 39 0.15
122 37 0.14
123 14 0.05
124 4 0.02
125 46 0.17
126 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (117 bp):
CATGGCCGACACCCCTATTTATCTGATAAAAAAATCAAATTTTTGGGTGTTGACCATGCAATGGC
CGACACCCCTTTTTTCAGATAAAAAATTTAATTTTTTTGGTGTTGATCATGC
Found at i:30984498 original size:18 final size:18
Alignment explanation
Indices: 30984458--30984500 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
30984448 AACTCATATA
* * *
30984458 ATATTTCTTCTTCAAGAT
1 ATATTTCCTCTTCAAAAC
*
30984476 TTATTTCCTCTTCAAAAC
1 ATATTTCCTCTTCAAAAC
30984494 ATATTTC
1 ATATTTC
30984501 TAGATTTTCT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.02, T:0.49
Consensus pattern (18 bp):
ATATTTCCTCTTCAAAAC
Found at i:30987041 original size:28 final size:28
Alignment explanation
Indices: 30987010--30987066 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 28
30987000 TTTTGACACC
*
30987010 TCTTGTTTGAAATCAATG-CTTTGATTTT
1 TCTTCTTTGAAATCAATGAC-TTGATTTT
30987038 TCTTCTTTGAAATCAATGACTTGATTTT
1 TCTTCTTTGAAATCAATGACTTGATTTT
30987066 T
1 T
30987067 ACTTTATAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 26 0.96
29 1 0.04
ACGTcount: A:0.23, C:0.12, G:0.12, T:0.53
Consensus pattern (28 bp):
TCTTCTTTGAAATCAATGACTTGATTTT
Found at i:30989607 original size:29 final size:29
Alignment explanation
Indices: 30989569--30989636 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 29
30989559 ATAAAATCTA
30989569 AAAAATACATAC-TCAAGATAAGATTCGAAC
1 AAAAA-ACATACAT-AAGATAAGATTCGAAC
*
30989599 AAAAAACATACATAAGATAATATTCGAAC
1 AAAAAACATACATAAGATAAGATTCGAAC
30989628 AAAAAACAT
1 AAAAAACAT
30989637 CATGAACTCC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
29 30 0.83
30 6 0.17
ACGTcount: A:0.59, C:0.15, G:0.07, T:0.19
Consensus pattern (29 bp):
AAAAAACATACATAAGATAAGATTCGAAC
Found at i:30989876 original size:25 final size:22
Alignment explanation
Indices: 30989829--30989880 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 22
30989819 GTTTCACTGA
*
30989829 TACAAGACAATACAATTGTAAG
1 TACAAGACAATACAATTGCAAG
30989851 TACAAGACAAGGTACAAATTGCAAG
1 TACAAGACAA--TAC-AATTGCAAG
30989876 TACAA
1 TACAA
30989881 ATGTAAGTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 10 0.38
24 3 0.12
25 13 0.50
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.19
Consensus pattern (22 bp):
TACAAGACAATACAATTGCAAG
Found at i:30996634 original size:22 final size:22
Alignment explanation
Indices: 30996608--30996649 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30996598 TTGAAAATGT
30996608 TAAATTGAT-TTTATTTTAAAAA
1 TAAATT-ATCTTTATTTTAAAAA
*
30996630 TAAATTATCTTTTTTTTAAA
1 TAAATTATCTTTATTTTAAA
30996650 GAAAAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TAAATTATCTTTATTTTAAAAA
Found at i:31004623 original size:28 final size:28
Alignment explanation
Indices: 31004558--31004641 Score: 73
Period size: 28 Copynumber: 2.9 Consensus size: 28
31004548 CCAATATTAT
* * *
31004558 TTTACAGTATTAATATATTTTT-ATTTAG
1 TTTACA-TTTTAATATTTTTTTAATGTAG
31004586 TCATTA-ATTTTAATATTTTTTTAATGTAG
1 T--TTACATTTTAATATTTTTTTAATGTAG
31004615 TTTACATTTTATATGATTTATTTTAAT
1 TTTACATTTTA-AT-ATTT-TTTTAAT
31004642 TATTAATGTC
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
27 3 0.07
28 20 0.43
29 9 0.20
30 7 0.15
31 7 0.15
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.60
Consensus pattern (28 bp):
TTTACATTTTAATATTTTTTTAATGTAG
Found at i:31020016 original size:18 final size:20
Alignment explanation
Indices: 31019985--31020021 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
31019975 AATGAACAAA
31019985 TTATTTTTTCAA-TTAAATT
1 TTATTTTTTCAATTTAAATT
31020004 TTATTTTTT-AATTTAAAT
1 TTATTTTTTCAATTTAAAT
31020022 ATATTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTTTTCAATTTAAATT
Found at i:31020026 original size:18 final size:16
Alignment explanation
Indices: 31019982--31020053 Score: 54
Period size: 19 Copynumber: 4.1 Consensus size: 16
31019972 TCAAATGAAC
31019982 AAATTATTTTTTCAATT
1 AAATTATTTTTT-AATT
31019999 AAATTTTATTTTTTAATTT
1 AAA--TTATTTTTTAA-TT
31020018 AAATATATTGTTTTAAATT
1 AAAT-TATT-TTTT-AATT
* * *
31020037 GATTTATTATTTAATT
1 AAATTATTTTTTAATT
31020053 A
1 A
31020054 TTATTTAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
16 4 0.09
17 7 0.16
18 10 0.22
19 22 0.49
20 2 0.04
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (16 bp):
AAATTATTTTTTAATT
Found at i:31020085 original size:66 final size:66
Alignment explanation
Indices: 31019983--31020110 Score: 177
Period size: 66 Copynumber: 1.9 Consensus size: 66
31019973 CAAATGAACA
* * * * * *
31019983 AATTATTTTTTCAATTAAATTTTATTTTTTAATTTAAATATATTGTTTTAAATTGATTTATTATT
1 AATTATTATTTCAATTAAATTCTATTTTTTAATTTAAATACAGTGCTTTAAATTGATATATTATT
31020048 T
66 T
*
31020049 AATTATTATTT-AGTTAAATTCTATTTTTTTAATTTAAATACAGTGCTTTAAATTGATATATT
1 AATTATTATTTCAATTAAATTCTA-TTTTTTAATTTAAATACAGTGCTTTAAATTGATATATT
31020111 GCATAAATTC
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 10 0.19
66 44 0.81
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (66 bp):
AATTATTATTTCAATTAAATTCTATTTTTTAATTTAAATACAGTGCTTTAAATTGATATATTATT
T
Found at i:31021316 original size:168 final size:168
Alignment explanation
Indices: 31021037--31021372 Score: 521
Period size: 168 Copynumber: 2.0 Consensus size: 168
31021027 AACAGCTAGA
*
31021037 ACAGTAACAATGAAAATAGCGCCCTCTTTAGTGAGATTATATGAACAAATGCCCGAACCTAAATA
1 ACAGTAACAATGAAAATAGCGCCCTCTTTAGTGAGATTATATGAACAAATCCCCGAACCTAAATA
* * * * * *
31021102 TGTTATTGCTATGGGCGCGTGTACAATTGCAGGAGGGTTTTTCAGTACTGATTCTTATAGTATTG
66 TGTTAATGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAGTACTGATTCTTATAATACTG
* * *
31021167 TTCGGGGGGTCGATAAGCTAATTCTCGTGGATGTCTAT
131 TTCGGGGGATCGATAAGCTAATTCCCGTAGATGTCTAT
31021205 ACAGTAACAATGAAAAT-GACGCCCTCTTTAGTGAGATTATATGAACAAATCCCCGAACCTAAAT
1 ACAGTAACAATGAAAATAG-CGCCCTCTTTAGTGAGATTATATGAACAAATCCCCGAACCTAAAT
* * * *
31021269 ATGTTAATGCTCTGGGTGTGTGTACAATTACAGGAGGGATGTTCAGTATTGATTCTTATAATACT
65 ATGTTAATGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAGTACTGATTCTTATAATACT
*
31021334 GTTCGGGGGATGGATAAGCTAATTCCCGTAGATGTCTAT
130 GTTCGGGGGATCGATAAGCTAATTCCCGTAGATGTCTAT
31021373 TTGTCGAGCT
Statistics
Matches: 152, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
167 1 0.01
168 151 0.99
ACGTcount: A:0.29, C:0.16, G:0.23, T:0.32
Consensus pattern (168 bp):
ACAGTAACAATGAAAATAGCGCCCTCTTTAGTGAGATTATATGAACAAATCCCCGAACCTAAATA
TGTTAATGCTATGGGCGCGTGTACAATTACAGGAGGGATGTTCAGTACTGATTCTTATAATACTG
TTCGGGGGATCGATAAGCTAATTCCCGTAGATGTCTAT
Found at i:31022054 original size:19 final size:19
Alignment explanation
Indices: 31022022--31022076 Score: 101
Period size: 19 Copynumber: 2.8 Consensus size: 19
31022012 TTTAAATATA
31022022 TAAAAAATTAAAAATAAATT
1 TAAAAAATT-AAAATAAATT
31022042 TAAAAAATTAAAATAAATT
1 TAAAAAATTAAAATAAATT
31022061 TAAAAAATTAAAATAA
1 TAAAAAATTAAAATAA
31022077 TAAGTTCTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 26 0.74
20 9 0.26
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TAAAAAATTAAAATAAATT
Found at i:31024540 original size:8 final size:8
Alignment explanation
Indices: 31024529--31024651 Score: 75
Period size: 8 Copynumber: 14.4 Consensus size: 8
31024519 AAATTAACAA
31024529 ATTTAATT
1 ATTTAATT
31024537 ATTTAATT
1 ATTTAATT
* *
31024545 AATTAAAT
1 ATTTAATT
31024553 ATTTAATT
1 ATTTAATT
*
31024561 ACTAATAAAATTT
1 A-T--T-TAA-TT
*
31024574 ATTTAAAT
1 ATTTAATT
*
31024582 ATTTAATA
1 ATTTAATT
31024590 ATTTAATT
1 ATTTAATT
* **
31024598 ATTAAAACA
1 ATT-TAATT
* *
31024607 ATTCAAAT
1 ATTTAATT
31024615 ATTTAATT
1 ATTTAATT
*
31024623 AGTTAATT
1 ATTTAATT
31024631 ATTTAATTAT
1 ATTTAA-T-T
31024641 ATTTAATT
1 ATTTAATT
31024649 ATT
1 ATT
31024652 AAAAATAACC
Statistics
Matches: 87, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
8 62 0.71
9 10 0.11
10 8 0.09
11 1 0.01
12 3 0.03
13 3 0.03
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (8 bp):
ATTTAATT
Found at i:31024573 original size:41 final size:40
Alignment explanation
Indices: 31024527--31024639 Score: 101
Period size: 37 Copynumber: 2.9 Consensus size: 40
31024517 TAAAATTAAC
31024527 AAATTTAATTATTTAATTAATTAAATATTTAATTACTAATA
1 AAATTTAATTATTTAATTAATTAAATATTTAATTACTAA-A
* * *
31024568 AAA--T--TTATTTAAAT-ATTTAATAATTTAATTATTAAA
1 AAATTTAATTATTTAATTAATTAAAT-ATTTAATTACTAAA
* * * *
31024604 ACAATTCAAATATTTAATTAGTTAATTATTTAATTA
1 A-AATTTAATTATTTAATTAATTAAATATTTAATTA
31024640 TATTTAATTA
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
36 8 0.14
37 23 0.41
39 1 0.02
41 20 0.36
42 4 0.07
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.49
Consensus pattern (40 bp):
AAATTTAATTATTTAATTAATTAAATATTTAATTACTAAA
Found at i:31024679 original size:23 final size:22
Alignment explanation
Indices: 31024649--31025079 Score: 130
Period size: 22 Copynumber: 19.2 Consensus size: 22
31024639 ATATTTAATT
*
31024649 ATTAAAAATAACCCAAATATTTA
1 ATTAAAAATAA-TCAAATATTTA
* ** *
31024672 ATTAAAAATATTTTATTATTTA
1 ATTAAAAATAATCAAATATTTA
* * *
31024694 ATTATATATAATTAAATATTTA
1 ATTAAAAATAATCAAATATTTA
*
31024716 ATAATAAAAACAATCCAAATATTTA
1 AT--TAAAAATAAT-CAAATATTTA
* * * *
31024741 A--ATAAATAATTAATTAATT-
1 ATTAAAAATAATCAAATATTTA
31024760 ATTAAAAATAACTCAAATATTTA
1 ATTAAAAATAA-TCAAATATTTA
* ** *
31024783 ATTAAAAATATTTTATTATTTA
1 ATTAAAAATAATCAAATATTTA
* ** *
31024805 ATTATATTTAATTAAATATTTAATA
1 ATTAAAAATAATCAAATA-TT--TA
*
31024830 ATTAAAAACAATCCAAATATTTCA
1 ATTAAAAATAAT-CAAATATTT-A
* * *
31024854 A-T--AAATAATTAATTAATT-
1 ATTAAAAATAATCAAATATTTA
*
31024872 ATTAAAAAATAACCCAAATATTTA
1 ATT-AAAAATAA-TCAAATATTTA
* ** * *
31024896 ATTAAAAATATTTTATTAGTTA
1 ATTAAAAATAATCAAATATTTA
* ** *
31024918 ATTATATTTAATTAAATATTTA
1 ATTAAAAATAATCAAATATTTA
31024940 A-TAATTAAA-AATGCCAAATATTTA
1 ATTAA--AAATAAT--CAAATATTTA
* ** * **
31024964 A--ATATTTAATTATTTATTT-
1 ATTAAAAATAATCAAATATTTA
* *
31024983 ATTAAAAACAACCCAAATATTTA
1 ATTAAAAATAA-TCAAATATTTA
* ** *
31025006 ATTAAAAATATTTTATTATTTA
1 ATTAAAAATAATCAAATATTTA
* ** *
31025028 ATTACATTTAATTAAATATTTA
1 ATTAAAAATAATCAAATATTTA
*
31025050 ATTATTAAAACAATCCAAATATTTA
1 ATTA--AAAATAAT-CAAATATTTA
31025075 ATTAA
1 ATTAA
31025080 TTATTTATTT
Statistics
Matches: 284, Mismatches: 94, Indels: 60
0.65 0.21 0.14
Matches are distributed among these distances:
18 1 0.00
19 3 0.01
20 18 0.06
21 27 0.10
22 120 0.42
23 49 0.17
24 26 0.09
25 35 0.12
26 5 0.02
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTAAAAATAATCAAATATTTA
Found at i:31024695 original size:66 final size:68
Alignment explanation
Indices: 31024611--31024764 Score: 181
Period size: 69 Copynumber: 2.3 Consensus size: 68
31024601 AAAACAATTC
* *
31024611 AAATATTTAATTAGTTAATTAT-T-TAATT-ATATTTAATTATTAAAAATAACCCAAATATTTAA
1 AAATATTTAATTAGTTAATTATATATAATTAATATTTAA-TAATAAAAACAACCCAAATATTTAA
*
31024673 TTAA
65 ATAA
* * *
31024677 AAATATTTTATTATTTAATTATATATAATTAAATATTTAATAATAAAAACAATCCAAATATTTAA
1 AAATATTTAATTAGTTAATTATATATAATT-AATATTTAATAATAAAAACAACCCAAATATTTAA
31024742 ATAA
65 ATAA
*
31024746 ATAATTAATTAATTA-TTAA
1 A-AA-TATTTAATTAGTTAA
31024765 AAATAACTCA
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
66 20 0.27
67 1 0.01
68 5 0.07
69 26 0.35
70 14 0.19
71 8 0.11
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (68 bp):
AAATATTTAATTAGTTAATTATATATAATTAATATTTAATAATAAAAACAACCCAAATATTTAAA
TAA
Found at i:31024777 original size:111 final size:111
Alignment explanation
Indices: 31024634--31025280 Score: 814
Period size: 111 Copynumber: 5.6 Consensus size: 111
31024624 GTTAATTATT
*
31024634 TAATTATATTTAATTATTAAAAATAACCCAAATATTTAATTAAAAATATTTTATTATTTAATTAT
1 TAATTA-A-TTAATTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTATTTAATTAT
*
31024699 ATATAATTAAATATTTAATAATAAAAACAATCCAAATATTTAAATAAA
64 ATTTAATTAAATATTTAATAATAAAAACAATCCAAATATTTAAATAAA
* *
31024747 TAATTAATTAATTATTAAAAATAACTCAAATATTTAATTAAAAATATTTTATTATTTAATTATAT
1 TAATTAATTAATTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTATTTAATTATAT
*
31024812 TTAATTAAATATTTAATAATTAAAAACAATCCAAATATTTCAATAAA
66 TTAATTAAATATTTAATAA-TAAAAACAATCCAAATATTTAAATAAA
* *
31024859 TAATTAATTAATTATTAAAAAATAACCCAAATATTTAATTAAAAATATTTTATTAGTTAATTATA
1 TAATTAATTAATTATT-AAAAACAACCCAAATATTTAATTAAAAATATTTTATTATTTAATTATA
* **
31024924 TTTAATTAAATATTTAATAAT-TAAA-AATGCCAAATATTTAAATATT
65 TTTAATTAAATATTTAATAATAAAAACAAT-CCAAATATTTAAATAAA
* * *
31024970 TAATTATTTATTTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTATTTAATTACAT
1 TAATTAATTAATTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTATTTAATTATAT
* * *
31025035 TTAATTAAATATTTAATTATTAAAACAATCCAAATATTTAATTAATTA
66 TTAATTAAATATTTAATAATAAAAACAATCCAAATATTTAAATAA--A
* * * * *
31025083 TTTATTTAACTAGTTAATTATTAACAACAATCCAAATATTTAATTCAAAATATTTAATTATTTAA
1 --TAATT-A--A-TTAATTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTATTTAA
*
31025148 TTATATTTAA-TATAATATTTAATTATTAAAAACAATCCAAATATTTAATTATTTAATTTAA
60 TTATATTTAATTA-AATATTTAA-TAATAAAAACAATCCAAATATTTAA--A--T-A---AA
* * * * * *
31025209 TAATTAGTTATTTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTACTTAATTATAT
1 TAATTAATTAATTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTATTTAATTATAT
31025274 TTAATTA
66 TTAATTA
31025281 TTAAAACAAC
Statistics
Matches: 474, Mismatches: 36, Indels: 40
0.86 0.07 0.07
Matches are distributed among these distances:
110 68 0.14
111 123 0.26
112 47 0.10
113 72 0.15
115 4 0.01
116 1 0.00
118 2 0.00
119 65 0.14
120 81 0.17
121 2 0.00
123 1 0.00
124 5 0.01
125 1 0.00
126 1 0.00
128 1 0.00
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (111 bp):
TAATTAATTAATTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTATTTAATTATAT
TTAATTAAATATTTAATAATAAAAACAATCCAAATATTTAAATAAA
Found at i:31025022 original size:334 final size:344
Alignment explanation
Indices: 31024625--31025280 Score: 935
Period size: 334 Copynumber: 1.9 Consensus size: 344
31024615 ATTTAATTAG
* *
31024625 TTAATTATTTAATTATATTTAATTATTAAAAATAACCCAAATATTTAATTAAAAATATTTTATTA
1 TTAAATATTTAATTATATTTAATTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTA
*
31024690 TTTAATTATATATAATTAAATATTTAATAATAAAAACAATCCAAATATTTAAATAA-A-TAATT-
66 TTTAATTACATATAATTAAATATTTAATAATAAAAACAATCCAAATATTTAAATAATATTAATTA
* *
31024752 A-A-TTAATTATTAAAAATAA-CTCAAATATTTAATTAAAAATATTTTATTATTTAATTATATTT
131 ACAGTTAATTATTAAAAACAATC-CAAATATTTAATTAAAAATATTTAATTATTTAATTATATTT
31024814 AAT-TAAATATTTAATAATTAAAAACAATCCAAATATTTCAA-TA-AA-TAATTAATTAATTA-T
195 AATAT-AATATTTAATAATTAAAAACAATCCAAATATTT-AATTATAATTAA-TAATTAATTATT
* * *
31024874 TA-AAAAATAACCCAAATATTTAATTAAAAATATTTTATTAGTTAATTATATTTAATTAAATATT
257 TATAAAAACAACCCAAATATTTAATTAAAAATATTTAATTACTTAATTATATTTAATTAAATATT
31024938 TAATAATTAAAAATGCCAAATAT
322 TAATAATTAAAAATGCCAAATAT
*
31024961 TTAAATATTTAA-T-TATTTATTTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTA
1 TTAAATATTTAATTATATTTAATTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTA
* * * * *
31025024 TTTAATTACATTTAATTAAATATTTAATTATTAAAACAATCCAAATATTTAATTAATTATTTATT
66 TTTAATTACATATAATTAAATATTTAATAATAAAAACAATCCAAATATTTAAATAA-TA-TTAAT
* *
31025089 TAACTAGTTAATTATTAACAACAATCCAAATATTTAATTCAAAATATTTAATTATTTAATTATAT
129 TAAC-AGTTAATTATTAAAAACAATCCAAATATTTAATTAAAAATATTTAATTATTTAATTATAT
* *
31025154 TTAATATAATATTTAATTATTAAAAACAATCCAAATATTTAATTATTTAATTTAATAATTAGTTA
193 TTAATATAATATTTAATAATTAAAAACAATCCAAATATTTAATTA--TAA-TTAATAATTAATTA
* *
31025219 TTTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTACTTAATTATATTTAATTA
255 TTTA-TAAAAACAACCCAAATATTTAATTAAAAATATTTAATTACTTAATTATATTTAATTA
31025281 TTAAAACAAC
Statistics
Matches: 281, Mismatches: 20, Indels: 25
0.86 0.06 0.08
Matches are distributed among these distances:
334 99 0.35
335 1 0.00
336 12 0.04
338 4 0.01
339 1 0.00
341 3 0.01
342 91 0.32
343 2 0.01
345 2 0.01
346 9 0.03
347 6 0.02
349 51 0.18
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (344 bp):
TTAAATATTTAATTATATTTAATTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTA
TTTAATTACATATAATTAAATATTTAATAATAAAAACAATCCAAATATTTAAATAATATTAATTA
ACAGTTAATTATTAAAAACAATCCAAATATTTAATTAAAAATATTTAATTATTTAATTATATTTA
ATATAATATTTAATAATTAAAAACAATCCAAATATTTAATTATAATTAATAATTAATTATTTATA
AAAACAACCCAAATATTTAATTAAAAATATTTAATTACTTAATTATATTTAATTAAATATTTAAT
AATTAAAAATGCCAAATAT
Found at i:31025023 original size:223 final size:225
Alignment explanation
Indices: 31024590--31025280 Score: 865
Period size: 223 Copynumber: 3.0 Consensus size: 225
31024580 ATATTTAATA
* * *
31024590 ATTTAATTATTAAAACAATTCAAATATTTAATTAGTTAATTATTTAATTATATTTAATTATTAAA
1 ATTTAATAATTAAAACAATCCAAATATTT-A--A-TTAA-TA-TTAATTATAGTTAATTATTAAA
*
31024655 AATAACCCAAATATTTAATTAAAAATATTTTATTATTTAATTATATATAATTAAATATTTAATAA
60 AATAACCCAAATATTTAATTAAAAATATTTTATTATTTAATTATATTTAATTAAATATTTAATAA
* ** * * *
31024720 TAAAAACAATCCAAATATTTAAATAAATAATTAATTAATTATTAAAAATAACTCAAATATTTAAT
125 T-TAAACAATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAACAACCCAAATATTTAAT
31024785 TAAAAATATTTTATTATTTAATTATATTTAATTAAAT
189 TAAAAATATTTTATTATTTAATTATATTTAATTAAAT
31024822 ATTTAATAATTAAAAACAATCCAAATATTTCAA-TAA-A-TAATTA-A-TTAATTATTAAAAAAT
1 ATTTAATAATT-AAAACAATCCAAATATTT-AATTAATATTAATTATAGTTAATTATT-AAAAAT
*
31024882 AACCCAAATATTTAATTAAAAATATTTTATTAGTTAATTATATTTAATTAAATATTTAATAATTA
63 AACCCAAATATTTAATTAAAAATATTTTATTATTTAATTATATTTAATTAAATATTTAATAATTA
*
31024947 AA-AATGCCAAATATTTAAATATTTAATTATTTATTTATTAAAAACAACCCAAATATTTAATTAA
128 AACAAT-CCAAATATTTAAATATTTAATTAATTATTTATTAAAAACAACCCAAATATTTAATTAA
*
31025011 AAATATTTTATTATTTAATTACATTTAATTAAAT
192 AAATATTTTATTATTTAATTATATTTAATTAAAT
* * *
31025045 ATTTAATTATTAAAACAATCCAAATATTTAATTAATTATTTATTTAACTAGTTAATTATTAACAA
1 ATTTAATAATTAAAACAATCCAAATATTTAATTAA-TA-TTAATT-A-TAGTTAATTATTAAAAA
* * * * *
31025110 CAATCCAAATATTTAATTCAAAATATTTAATTATTTAATTATATTTAA-TATAATATTTAATTAT
62 TAACCCAAATATTTAATTAAAAATATTTTATTATTTAATTATATTTAATTA-AATATTTAATAAT
* *
31025174 TAAAAACAATCCAAATATTTAATTATTTAATTTAATAATTAGTTATTTATTAACAACAACCCAAA
126 T--AAACAATCCAAATATTTAA--A--T-A-TT--TAATTAATTATTTATTAAAAACAACCCAAA
* * *
31025239 TATTTAATTCAAAATATTTAATTACTTAATTATATTTAATTA
181 TATTTAATTAAAAATATTTTATTATTTAATTATATTTAATTA
31025281 TTAAAACAAC
Statistics
Matches: 407, Mismatches: 28, Indels: 41
0.86 0.06 0.09
Matches are distributed among these distances:
221 2 0.00
222 24 0.06
223 107 0.26
224 69 0.17
225 6 0.01
226 4 0.01
227 2 0.00
228 2 0.00
229 64 0.16
230 9 0.02
231 16 0.04
232 13 0.03
233 19 0.05
235 1 0.00
236 1 0.00
237 2 0.00
239 66 0.16
ACGTcount: A:0.49, C:0.06, G:0.01, T:0.44
Consensus pattern (225 bp):
ATTTAATAATTAAAACAATCCAAATATTTAATTAATATTAATTATAGTTAATTATTAAAAATAAC
CCAAATATTTAATTAAAAATATTTTATTATTTAATTATATTTAATTAAATATTTAATAATTAAAC
AATCCAAATATTTAAATATTTAATTAATTATTTATTAAAAACAACCCAAATATTTAATTAAAAAT
ATTTTATTATTTAATTATATTTAATTAAAT
Found at i:31025104 original size:119 final size:122
Alignment explanation
Indices: 31024966--31025281 Score: 498
Period size: 120 Copynumber: 2.6 Consensus size: 122
31024956 AATATTTAAA
* * * *
31024966 TATTTAATTATTTATTTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTATTTAATT
1 TATTTAATTAGTTATTTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATT
*
31025031 ACATTTAATTA-AATATTTAATTATT-AAAACAATCCAAATATTTAATTAATT-ATT
66 ATATTTAATTATAATATTTAATTATTAAAAACAATCCAAATATTTAATTAATTAATT
* * *
31025085 TATTTAACTAGTTAATTATTAACAACAATCCAAATATTTAATTCAAAATATTTAATTATTTAATT
1 TATTTAATTAGTTATTTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATT
*
31025150 ATATTTAA-TATAATATTTAATTATTAAAAACAATCCAAATATTTAATTATTTAATT
66 ATATTTAATTATAATATTTAATTATTAAAAACAATCCAAATATTTAATTAATTAATT
* *
31025206 TA-ATAATTAGTTATTTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTACTTAATT
1 TATTTAATTAGTTATTTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATT
31025270 ATATTTAATTAT
66 ATATTTAATTAT
31025282 TAAAACAACC
Statistics
Matches: 179, Mismatches: 14, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
118 2 0.01
119 79 0.44
120 90 0.50
121 8 0.04
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.46
Consensus pattern (122 bp):
TATTTAATTAGTTATTTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATT
ATATTTAATTATAATATTTAATTATTAAAAACAATCCAAATATTTAATTAATTAATT
Found at i:31025167 original size:12 final size:10
Alignment explanation
Indices: 31025132--31025173 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
31025122 TTAATTCAAA
31025132 ATATTTAA-T
1 ATATTTAATT
31025141 -TATTTAATT
1 ATATTTAATT
31025150 ATATTTAATAT
1 ATATTTAAT-T
31025161 AATATTTAATT
1 -ATATTTAATT
31025172 AT
1 AT
31025174 TAAAAACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.24
9 1 0.03
10 10 0.34
11 2 0.07
12 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
ATATTTAATT
Found at i:31025190 original size:56 final size:55
Alignment explanation
Indices: 31025130--31025338 Score: 177
Period size: 58 Copynumber: 3.8 Consensus size: 55
31025120 ATTTAATTCA
*
31025130 AAATATTTAATTATTTAATTA-TATTTAATATAATATTTAATTATTAAAAACAATCC
1 AAATATTTAATTATATAATTATTATTTAAT-TAATATTTAATTATTAAAAACAA-CC
* * *
31025186 AAATATTTAA-T-TAT--TTA--ATTTAA-TAATTAGTTATTTATTAACAACAACCC
1 AAATATTTAATTATATAATTATTATTTAATTAA-TATTTAATTATTAAAAACAA-CC
* * *
31025236 AAATATTTAATTCAAAATATTTAATTACTTAATT-ATATTTAATTATT-AAAACAACC
1 AAATATTTAATT--ATATAATT-ATTATTTAATTAATATTTAATTATTAAAAACAACC
*
31025292 TAAAATATTTAATTATATAATTATTTATTTAATTATATAATTAATTA
1 --AAATATTTAATTATATAATTA-TTATTTAATTA-ATATTTAATTA
31025339 ATTATTTATA
Statistics
Matches: 123, Mismatches: 14, Indels: 30
0.74 0.08 0.18
Matches are distributed among these distances:
49 3 0.02
50 29 0.24
51 7 0.06
52 3 0.02
54 4 0.03
55 2 0.02
56 29 0.24
57 7 0.06
58 32 0.26
59 6 0.05
60 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.46
Consensus pattern (55 bp):
AAATATTTAATTATATAATTATTATTTAATTAATATTTAATTATTAAAAACAACC
Found at i:31025210 original size:46 final size:49
Alignment explanation
Indices: 31025141--31025247 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 49
31025131 AATATTTAAT
*
31025141 TATTTAATTATATTTAATATAAT-A-T-TTAATTATTAAAAACAATCCAAA
1 TATTTAA-T-TATTTAATATAATAATTATTAATTATTAAAAACAACCCAAA
* * *
31025189 TATTTAATTATTTAATTTAATAATTAGTTATTTATTAACAACAACCCAAA
1 TATTTAATTATTTAATATAATAATTA-TTAATTATTAAAAACAACCCAAA
31025239 TATTTAATT
1 TATTTAATT
31025248 CAAAATATTT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
46 12 0.24
47 2 0.04
48 8 0.16
50 29 0.57
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (49 bp):
TATTTAATTATTTAATATAATAATTATTAATTATTAAAAACAACCCAAA
Found at i:31025320 original size:120 final size:118
Alignment explanation
Indices: 31024970--31025344 Score: 402
Period size: 120 Copynumber: 3.1 Consensus size: 118
31024960 TTTAAATATT
* * * * * *
31024970 TAATTATTTATTTATTAAAAACAACCCAAATATTTAATTAAAAATATTTTATTATTTAATTACAT
1 TAATTAGTTAATTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATTATAT
* *
31025035 TTAATTAAATATTTAATTATTAAAACAATCCAAATATTTAATTAATTATTT-ATT--
66 TTAATT-AATATTTAATTATT-AAA-AAT-CAATTATATAATTAATTATTTAATTAA
* *
31025089 TAACTAGTTAATTATTAACAACAATCCAAATATTTAATTCAAAATATTTAATTATTTAATTATAT
1 TAATTAGTTAATTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATTATAT
* * *
31025154 TTAATATAATATTTAATTATTAAAAA-CAATCCAAATATTTAATTATTTAATTTAA
66 TTAAT-TAATATTTAATTATTAAAAATCAAT-TATATAATTAATTATTTAA-TTAA
* *
31025209 TAATTAGTTATTTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTACTTAATTATAT
1 TAATTAGTTAATTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATTATAT
** ** * * *
31025274 TTAATT-AT-TAAAACAACCTAAAATATTTAATTATATAATTATTTATTTAATTATA
66 TTAATTAATATTTAATTA-TTAAAA-A-TCAATTATATAATTAATTATTTAATTA-A
*
31025329 TAATTAATTAATTATT
1 TAATTAGTTAATTATT
31025345 TATAACTACG
Statistics
Matches: 216, Mismatches: 29, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
115 3 0.01
116 13 0.06
117 7 0.03
118 12 0.06
119 81 0.38
120 97 0.45
121 3 0.01
ACGTcount: A:0.46, C:0.07, G:0.01, T:0.46
Consensus pattern (118 bp):
TAATTAGTTAATTATTAACAACAACCCAAATATTTAATTCAAAATATTTAATTATTTAATTATAT
TTAATTAATATTTAATTATTAAAAATCAATTATATAATTAATTATTTAATTAA
Found at i:31025322 original size:20 final size:20
Alignment explanation
Indices: 31025297--31025348 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
31025287 CAACCTAAAA
*
31025297 TATTTAATTATATAATTATT
1 TATTTAATTATATAATTAAT
31025317 TATTTAATTATATAATTAAT
1 TATTTAATTATATAATTAAT
* *
31025337 TAATTATTTATA
1 TATTTAATTATA
31025349 ACTACGTGCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTAATTATATAATTAAT
Found at i:31025324 original size:12 final size:12
Alignment explanation
Indices: 31025304--31025346 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
31025294 AAATATTTAA
*
31025304 TTATATAATTAT
1 TTATTTAATTAT
31025316 TTATTTAATTAT
1 TTATTTAATTAT
* * *
31025328 ATAATTAATTAA
1 TTATTTAATTAT
31025340 TTATTTA
1 TTATTTA
31025347 TAACTACGTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATTTAATTAT
Found at i:31025729 original size:16 final size:16
Alignment explanation
Indices: 31025708--31025739 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
31025698 ATTGGCATAT
*
31025708 TCGTGAAGTTTTCTAC
1 TCGTGAAGTTGTCTAC
31025724 TCGTGAAGTTGTCTAC
1 TCGTGAAGTTGTCTAC
31025740 GAACATCTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (16 bp):
TCGTGAAGTTGTCTAC
Found at i:31031371 original size:13 final size:14
Alignment explanation
Indices: 31031348--31031390 Score: 52
Period size: 13 Copynumber: 3.0 Consensus size: 14
31031338 ATAAACGCCG
31031348 TTACTTTTAGCGGCA
1 TTAC-TTTAGCGGCA
*
31031363 TTA-TTTAGCGGCG
1 TTACTTTAGCGGCA
31031376 TTATCTTTAGCGGCA
1 TTA-CTTTAGCGGCA
31031391 CTTTTTGCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 12 0.50
15 12 0.50
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (14 bp):
TTACTTTAGCGGCA
Found at i:31031412 original size:28 final size:28
Alignment explanation
Indices: 31031346--31031402 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
31031336 TCATAAACGC
*
31031346 CGTTACTTTTAGCGGCATTATTTAGCGG
1 CGTTATTTTTAGCGGCATTATTTAGCGG
*
31031374 CGTTATCTTTAGCGGCACTT-TTT-GCGG
1 CGTTATTTTTAGCGGCA-TTATTTAGCGG
31031401 CG
1 CG
31031403 CTTTGTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 6 0.23
28 18 0.69
29 2 0.08
ACGTcount: A:0.14, C:0.21, G:0.26, T:0.39
Consensus pattern (28 bp):
CGTTATTTTTAGCGGCATTATTTAGCGG
Found at i:31035108 original size:6 final size:6
Alignment explanation
Indices: 31035099--31035124 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
31035089 TTCTCAGTCT
31035099 CCAATC CCAATC CCAATC CCAATC CC
1 CCAATC CCAATC CCAATC CCAATC CC
31035125 CTCCTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.54, G:0.00, T:0.15
Consensus pattern (6 bp):
CCAATC
Found at i:31041058 original size:19 final size:19
Alignment explanation
Indices: 31041036--31041074 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
31041026 CCAAAATGTA
31041036 AAAATAATAATAAA-ACAAT
1 AAAA-AATAATAAATACAAT
*
31041055 AAAAACTAATAAATACAAT
1 AAAAAATAATAAATACAAT
31041074 A
1 A
31041075 TAGAGTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAAATAATAAATACAAT
Found at i:31042503 original size:3 final size:3
Alignment explanation
Indices: 31042497--31042531 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31042487 TATACCCCAA
31042497 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
31042532 TTTTATATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:31044090 original size:20 final size:21
Alignment explanation
Indices: 31044062--31044106 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
31044052 CTCCGTTTAG
*
31044062 TTTACGAAAAT-ATTTTTCATT
1 TTTACGAAAATAACTTTT-ATT
31044083 TTTA-GAAAATAACTTTTATT
1 TTTACGAAAATAACTTTTATT
31044103 TTTA
1 TTTA
31044107 TAATTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTACGAAAATAACTTTTATT
Found at i:31044465 original size:42 final size:44
Alignment explanation
Indices: 31044388--31044473 Score: 108
Period size: 44 Copynumber: 2.0 Consensus size: 44
31044378 TTTTCTAATT
31044388 TCTATATTTTCATTTTTAAAAAAATTTAATCCAAAAC-AATTTTC
1 TCTATATTTTCATTTTTAAAAAAA-TTAATCCAAAACGAATTTTC
*
31044432 TCTATGTTTTCAATTTTCTAAAAAAA-T-A-CCAAAACGAATTTT
1 TCTATATTTTC-ATTTT-TAAAAAAATTAATCCAAAACGAATTTT
31044474 TTTAAAAACC
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
42 7 0.18
43 7 0.18
44 11 0.29
45 5 0.13
46 8 0.21
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.43
Consensus pattern (44 bp):
TCTATATTTTCATTTTTAAAAAAATTAATCCAAAACGAATTTTC
Found at i:31047031 original size:10 final size:10
Alignment explanation
Indices: 31047013--31047047 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
31047003 AAACTTAAAA
*
31047013 TTTAAATTAT
1 TTTATATTAT
31047023 TTTATATTAT
1 TTTATATTAT
*
31047033 TTTATATTTT
1 TTTATATTAT
31047043 TTTAT
1 TTTAT
31047048 GAAATTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTATATTAT
Found at i:31049354 original size:18 final size:18
Alignment explanation
Indices: 31049321--31049355 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31049311 ACTTTATCAA
* *
31049321 ATCCGATTTAATTAATAG
1 ATCCGATTGAAATAATAG
31049339 ATCCGATTGAAATAATA
1 ATCCGATTGAAATAATA
31049356 CTATTATTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (18 bp):
ATCCGATTGAAATAATAG
Found at i:31050070 original size:16 final size:17
Alignment explanation
Indices: 31050049--31050094 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
31050039 ATTTCAATTA
*
31050049 TTAATATTATTTAT-TT
1 TTAATATTATTTATCAT
*
31050065 TTAATATT-TTAATCAT
1 TTAATATTATTTATCAT
31050081 TTACATATTATTTA
1 TTA-ATATTATTTA
31050095 AATTATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 4 0.17
16 12 0.50
17 5 0.21
18 3 0.12
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (17 bp):
TTAATATTATTTATCAT
Found at i:31050113 original size:14 final size:14
Alignment explanation
Indices: 31050096--31050139 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
31050086 TATTATTTAA
*
31050096 ATTATATTTTAATC
1 ATTAAATTTTAATC
*
31050110 ATTAAATTTTAAATT
1 ATTAAATTTT-AATC
*
31050125 ATTACATTTTAATC
1 ATTAAATTTTAATC
31050139 A
1 A
31050140 ATAATATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
14 13 0.52
15 12 0.48
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTAAATTTTAATC
Found at i:31050168 original size:31 final size:31
Alignment explanation
Indices: 31050039--31050170 Score: 128
Period size: 31 Copynumber: 4.3 Consensus size: 31
31050029 TGATCGTTAA
* * *
31050039 ATTTCAATTATTAATATTATTTATTTTTAAT
1 ATTTTAATCATTAATATTATTTATTTATAAT
* *
31050070 ATTTTAATCATTTACATATTATTTA--AATTAT
1 ATTTTAATCA-TTA-ATATTATTTATTTATAAT
* * * *
31050101 ATTTTAATCATTAA-ATT-TTAAATTATTAC
1 ATTTTAATCATTAATATTATTTATTTATAAT
*
31050130 ATTTTAATCAATAATATTATTTATTTATAAT
1 ATTTTAATCATTAATATTATTTATTTATAAT
31050161 ATTTTAATCA
1 ATTTTAATCA
31050171 CTCAATCACT
Statistics
Matches: 82, Mismatches: 13, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
27 3 0.04
28 3 0.04
29 18 0.22
30 6 0.07
31 39 0.48
32 3 0.04
33 10 0.12
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTTTAATCATTAATATTATTTATTTATAAT
Found at i:31051562 original size:99 final size:98
Alignment explanation
Indices: 31051383--31051564 Score: 231
Period size: 99 Copynumber: 1.8 Consensus size: 98
31051373 ACAAATAAGA
* * *
31051383 GTAAACTATAAAAATAGTCATTTTTTTTATTTCAGATTATATTTTAGTTATTTATGTTTAAAATA
1 GTAAACTATAAAAATAGTCATTTTGTTTATTTCAGATTACATTTTAGTTACTTATGTTTAAAATA
*
31051448 TTATATTTTAATCACTTACATTATCGTTTTAGG
66 TTACATTTTAATCACTTACATTATCGTTTTAGG
* * * * *
31051481 GTAAATTATAAAAATAGTCACTTTTGTTTGTCTT-AGGTTACATTTTTGTTACTTATGTTTGAAA
1 GTAAACTATAAAAATAGTCA-TTTTGTTTAT-TTCAGATTACATTTTAGTTACTTATGTTTAAAA
* * *
31051545 TGTTACGTTTTAGTCACTTA
64 TATTACATTTTAATCACTTA
31051565 TGTTATTATT
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
98 19 0.27
99 49 0.70
100 2 0.03
ACGTcount: A:0.31, C:0.08, G:0.11, T:0.50
Consensus pattern (98 bp):
GTAAACTATAAAAATAGTCATTTTGTTTATTTCAGATTACATTTTAGTTACTTATGTTTAAAATA
TTACATTTTAATCACTTACATTATCGTTTTAGG
Found at i:31058234 original size:6 final size:6
Alignment explanation
Indices: 31058225--31058257 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
31058215 CTTCTCCTTT
31058225 ATAAAA ATAAAA ATAAAA AT-AAA AT-AAA ATAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAA
31058258 GGGTTTTTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
ATAAAA
Found at i:31068173 original size:29 final size:28
Alignment explanation
Indices: 31068090--31068174 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 28
31068080 AAAAAATTAT
* *
31068090 TTTAAATCTTTTAAAAGTTAGTAAAAAGAA
1 TTTAGATCCTTTAAAAGTTAGT-AAAA-AA
* * * **
31068120 TTTTGATCC-CTAAAAGCTAAAAAAAAA
1 TTTAGATCCTTTAAAAGTTAGTAAAAAA
31068147 TTTGAGATCCTTTAAAAGTTAGTAAAAA
1 TTT-AGATCCTTTAAAAGTTAGTAAAAA
31068175 TTTTTTGGCC
Statistics
Matches: 41, Mismatches: 12, Indels: 5
0.71 0.21 0.09
Matches are distributed among these distances:
27 5 0.12
28 9 0.22
29 21 0.51
30 6 0.15
ACGTcount: A:0.48, C:0.08, G:0.11, T:0.33
Consensus pattern (28 bp):
TTTAGATCCTTTAAAAGTTAGTAAAAAA
Found at i:31070811 original size:20 final size:21
Alignment explanation
Indices: 31070786--31070833 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
31070776 ATAATTATTA
*
31070786 TTGAAGAAAGAGAATA-TTTT
1 TTGAAGAAAGAGAACATTTTT
* *
31070806 TTGAAGAGAGATAACATTTTT
1 TTGAAGAAAGAGAACATTTTT
31070827 TTGAAGA
1 TTGAAGA
31070834 TGAAGAGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.42, C:0.02, G:0.21, T:0.35
Consensus pattern (21 bp):
TTGAAGAAAGAGAACATTTTT
Found at i:31074477 original size:21 final size:22
Alignment explanation
Indices: 31074453--31074493 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31074443 AACAAATTTA
31074453 AGTA-TGTTGCATTGCAAAAGC
1 AGTATTGTTGCATTGCAAAAGC
*
31074474 AGTATTGTTGTATTGCAAAA
1 AGTATTGTTGCATTGCAAAA
31074494 AGCTGATTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (22 bp):
AGTATTGTTGCATTGCAAAAGC
Found at i:31077737 original size:39 final size:39
Alignment explanation
Indices: 31077677--31077756 Score: 115
Period size: 39 Copynumber: 2.1 Consensus size: 39
31077667 ATCCGTGCCT
*
31077677 AAATCTGAGGGAGAAGATAATGTGGCAACAGACTCTTCA
1 AAATCCGAGGGAGAAGATAATGTGGCAACAGACTCTTCA
* * * *
31077716 AAATCCGAGGGAGAGGTTAATGTGGCAACTGATTCTTCA
1 AAATCCGAGGGAGAAGATAATGTGGCAACAGACTCTTCA
31077755 AA
1 AA
31077757 GGATGCTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (39 bp):
AAATCCGAGGGAGAAGATAATGTGGCAACAGACTCTTCA
Found at i:31093661 original size:3 final size:3
Alignment explanation
Indices: 31093653--31093677 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31093643 TTATGTTTTA
31093653 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
31093678 AAAAAACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:31093792 original size:9 final size:9
Alignment explanation
Indices: 31093778--31093808 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
31093768 TCAATCCTCA
31093778 TATTTATAT
1 TATTTATAT
31093787 TATTTATAT
1 TATTTATAT
31093796 TATTTATAT
1 TATTTATAT
31093805 TATT
1 TATT
31093809 CATTTCCGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TATTTATAT
Found at i:31098749 original size:19 final size:20
Alignment explanation
Indices: 31098709--31098749 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
31098699 TGTAATTTTA
**
31098709 TAATTTTATAACATGTATTT
1 TAATTTTATAACATACATTT
31098729 TAATTTTATAA-ATACATTT
1 TAATTTTATAACATACATTT
31098748 TA
1 TA
31098750 TTATAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (20 bp):
TAATTTTATAACATACATTT
Found at i:31104559 original size:43 final size:43
Alignment explanation
Indices: 31104511--31104596 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
31104501 GTTCATCTAG
31104511 AACTTGCAGTTAAAAGGGTAATTCAGCTGTACTTCTAATAATT
1 AACTTGCAGTTAAAAGGGTAATTCAGCTGTACTTCTAATAATT
31104554 AACTTGCAGTTAAAAGGGTAATTCAGCTGTACTTCTAATAATT
1 AACTTGCAGTTAAAAGGGTAATTCAGCTGTACTTCTAATAATT
31104597 TGAGTTTTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (43 bp):
AACTTGCAGTTAAAAGGGTAATTCAGCTGTACTTCTAATAATT
Found at i:31107269 original size:17 final size:17
Alignment explanation
Indices: 31107247--31107295 Score: 98
Period size: 17 Copynumber: 2.9 Consensus size: 17
31107237 CGGACCACAA
31107247 AAACACAACACTAATCG
1 AAACACAACACTAATCG
31107264 AAACACAACACTAATCG
1 AAACACAACACTAATCG
31107281 AAACACAACACTAAT
1 AAACACAACACTAAT
31107296 ATTGAACCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 32 1.00
ACGTcount: A:0.55, C:0.29, G:0.04, T:0.12
Consensus pattern (17 bp):
AAACACAACACTAATCG
Done.