Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014310.1 Kokia drynarioides strain JFW-HI SEQ_129347, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 253724
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:195 original size:71 final size:71
Alignment explanation
Indices: 79--220 Score: 241
Period size: 71 Copynumber: 2.0 Consensus size: 71
69 ATATAAAATT
*
79 CATAGAAATTACTCACCAAATTCCACTCCACAGTCCACCAATTAAAAAACTTCCTCCAGAAACCT
1 CATAGAAATTACTCACCAAATTCCACTCCACAGTCCACCAATTAAAAAACTTCCTCCAAAAACCT
144 TCAATG
66 TCAATG
* *
150 CATAGAAATTACTCACCAAGTTCCACTCCACCA-TCCACCAATTAAAAAACTTCCTCTAAAAACC
1 CATAGAAATTACTCACCAAATTCCACTCCA-CAGTCCACCAATTAAAAAACTTCCTCCAAAAACC
214 TTCAATG
65 TTCAATG
221 AACCTACATT
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
71 65 0.97
72 2 0.03
ACGTcount: A:0.39, C:0.32, G:0.05, T:0.23
Consensus pattern (71 bp):
CATAGAAATTACTCACCAAATTCCACTCCACAGTCCACCAATTAAAAAACTTCCTCCAAAAACCT
TCAATG
Found at i:4627 original size:53 final size:53
Alignment explanation
Indices: 4569--4788 Score: 230
Period size: 53 Copynumber: 4.2 Consensus size: 53
4559 TTTTTCGTTT
* * * *
4569 TATACTCACGATGACA-AAAAGTCATCGAACCTTTTAATCCGTAAGAAGATTCA
1 TATACTCACAATGATACAAAA-TCATCGAACCTATTAATCCGTAATAAGATTCA
* **
4622 TATACTCACAATGATACGAAATCATCGGGCCTATTAATCCGTAATAAGATTCA
1 TATACTCACAATGATACAAAATCATCGAACCTATTAATCCGTAATAAGATTCA
* ** * * * * *
4675 TATACTCACTATGATACGTAATCATCAAATCTATTAGTCCGTAATATG-GTCTA
1 TATACTCACAATGATACAAAATCATCGAACCTATTAATCCGTAATAAGATTC-A
* * *
4728 TATACTCACAATGATATAAAATCATC-AGACCTATTCATCCGTAATAGGATTCA
1 TATACTCACAATGATACAAAATCATCGA-ACCTATTAATCCGTAATAAGATTCA
4781 TATACTCA
1 TATACTCA
4789 TGATGACACA
Statistics
Matches: 138, Mismatches: 25, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
52 3 0.02
53 130 0.94
54 5 0.04
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.30
Consensus pattern (53 bp):
TATACTCACAATGATACAAAATCATCGAACCTATTAATCCGTAATAAGATTCA
Found at i:11368 original size:53 final size:52
Alignment explanation
Indices: 11275--11464 Score: 236
Period size: 53 Copynumber: 3.6 Consensus size: 52
11265 AATTGTTTAC
* * *
11275 ATCCATAAGAGGATTCATATACTCACGATGATACGCAATCATCGGACCTATTA
1 ATCCATAATAGGATTCATATACTCACGATGATACG-AATCATCGGACTTGTTA
* * *
11328 ATCTATAATAGGATCCATATACTCACGATGATACGTAATCATTGGACTTGTTA
1 ATCCATAATAGGATTCATATACTCACGATGATACG-AATCATCGGACTTGTTA
* * * * * *
11381 ATCCGTAATAGGATTTATATACTCACGGTGATTCAGAATCATCGGACTTGGTC
1 ATCCATAATAGGATTCATATACTCACGATGATAC-GAATCATCGGACTTGTTA
*
11434 ATCCGTAATAGGATTCATATACTCACGATGA
1 ATCCATAATAGGATTCATATACTCACGATGA
11465 CACAAAGTCA
Statistics
Matches: 118, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
53 117 0.99
54 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (52 bp):
ATCCATAATAGGATTCATATACTCACGATGATACGAATCATCGGACTTGTTA
Found at i:22392 original size:2 final size:2
Alignment explanation
Indices: 22387--22421 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
22377 AAAATAGATA
22387 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
22422 GAATAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34017 original size:41 final size:41
Alignment explanation
Indices: 33911--34175 Score: 282
Period size: 41 Copynumber: 6.4 Consensus size: 41
33901 GTATAAAAAA
* * *
33911 GAAGACTCATGTCTC-AGGTTGAGAATGAGA-AATTGTATAAATG
1 GAAGACTCATGTCTCGA-GATGAGAATGAGATTA-TGAAT-AA-G
* * * *
33954 GAAGACTTATGTCTCAAAATGAGAATAAGATTATGAATAAG
1 GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
* ** *
33995 GAAGACCCATGTCTTTAGATGAGAATGAGTTTATGAATAAG
1 GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
* * *
34036 GAAGACTCATGTCTTGAGATGCGAATGAGATTTTGAATAAG
1 GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
* * *
34077 GAAGACTCATGTCTCGAAATGAGAATGAGATTATGATTATG
1 GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
* **
34118 GAAGACTCATGTCTCGAGATGAGAATGAGAATATGGTTAAG
1 GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
* *
34159 GAAGACTTATGACTCGA
1 GAAGACTCATGTCTCGA
34176 TAGAACATAA
Statistics
Matches: 190, Mismatches: 30, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
41 158 0.83
42 2 0.01
43 28 0.15
44 2 0.01
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.28
Consensus pattern (41 bp):
GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
Found at i:38053 original size:15 final size:16
Alignment explanation
Indices: 38028--38058 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
38018 GGAAATTCTT
38028 TAAATCAAGGGAGTTA
1 TAAATCAAGGGAGTTA
38044 TAAA-CAAGGGAGTTA
1 TAAATCAAGGGAGTTA
38059 CAATAGCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.06, G:0.26, T:0.23
Consensus pattern (16 bp):
TAAATCAAGGGAGTTA
Found at i:44805 original size:17 final size:18
Alignment explanation
Indices: 44783--44823 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
44773 TTAGTTTTCA
**
44783 TGCATTCTTA-TTGTGTC
1 TGCATTCTTACTTGTCAC
44800 TGCATT-TTACTTGTCAC
1 TGCATTCTTACTTGTCAC
44817 TGCATTC
1 TGCATTC
44824 CTTTTGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.15, C:0.22, G:0.15, T:0.49
Consensus pattern (18 bp):
TGCATTCTTACTTGTCAC
Found at i:53183 original size:123 final size:125
Alignment explanation
Indices: 52990--53257 Score: 344
Period size: 123 Copynumber: 2.2 Consensus size: 125
52980 GGTGAATATA
* * * *
52990 AAAGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTATAAATGGAAGACTCATCTCTCAAAA
1 AAAGAAGACTCATGTCTCGAGATGAGAATGAGAAATTGAATAAATGGAAGACTCATCTCTCAAAA
* * *
53055 TGAGAATGAGATTATGAATAAGAAAGACTCGTGTCTCAAGATGAGAATGAGATTATGAAT
66 TGAGAATAAGATTATGAATAAGAAAGACTCATGTCTCAAGATGAGAATGAGAATATGAAT
* *
53115 AAAGAAGACTCATGTCTCGAGATGAGAATGAG-ATTATGAAT-AA-GGAAGACTCATGTCTCAAA
1 AAAGAAGACTCATGTCTCGAGATGAGAATGAGAAAT-TGAATAAATGGAAGACTCATCTCTCAAA
* * * * **
53177 ATGAGAATAAGATTATGATTAAGGAGGACTCATGTCTCGAGATGAGAATGAGAATATGGTT
65 ATGAGAATAAGATTATGAATAAGAAAGACTCATGTCTCAAGATGAGAATGAGAATATGAAT
* * *
53238 AAGGAAGACTTATGACTCGA
1 AAAGAAGACTCATGTCTCGA
53258 TAGAGCATAA
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
123 87 0.70
124 4 0.03
125 33 0.27
ACGTcount: A:0.40, C:0.11, G:0.24, T:0.25
Consensus pattern (125 bp):
AAAGAAGACTCATGTCTCGAGATGAGAATGAGAAATTGAATAAATGGAAGACTCATCTCTCAAAA
TGAGAATAAGATTATGAATAAGAAAGACTCATGTCTCAAGATGAGAATGAGAATATGAAT
Found at i:53240 original size:41 final size:41
Alignment explanation
Indices: 52993--53257 Score: 298
Period size: 41 Copynumber: 6.4 Consensus size: 41
52983 GAATATAAAA
* * * * *
52993 GAAGACTCATGTCTCGGGTTGAGCATGAGA-AATTGTATAAATG
1 GAAGACTCATGTCTCGAGATGAGAATGAGATTA-TGAAT-AA-G
* * *
53036 GAAGACTCATCTCTCAAAATGAGAATGAGATTATGAATAAG
1 GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
* * * *
53077 AAAGACTCGTGTCTCAAGATGAGAATGAGATTATGAATAAA
1 GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
53118 GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
1 GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
* * * *
53159 GAAGACTCATGTCTCAAAATGAGAATAAGATTATGATTAAG
1 GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
* * **
53200 GAGGACTCATGTCTCGAGATGAGAATGAGAATATGGTTAAG
1 GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
* *
53241 GAAGACTTATGACTCGA
1 GAAGACTCATGTCTCGA
53258 TAGAGCATAA
Statistics
Matches: 191, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
41 160 0.84
42 2 0.01
43 28 0.15
44 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (41 bp):
GAAGACTCATGTCTCGAGATGAGAATGAGATTATGAATAAG
Found at i:57352 original size:21 final size:22
Alignment explanation
Indices: 57327--57370 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
57317 TACATTTTCA
57327 GACACGTTC-CTGGATTCATTT
1 GACACGTTCTCTGGATTCATTT
* * *
57348 GACACTTTCTTTGGATTCCTTT
1 GACACGTTCTCTGGATTCATTT
57370 G
1 G
57371 CTTCTCCGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.16, C:0.23, G:0.18, T:0.43
Consensus pattern (22 bp):
GACACGTTCTCTGGATTCATTT
Found at i:59094 original size:15 final size:16
Alignment explanation
Indices: 59067--59101 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
59057 TAAAATTATA
59067 AATTTATTATTTTAAT
1 AATTTATTATTTTAAT
*
59083 AATTTA-TATTTTTAT
1 AATTTATTATTTTAAT
59098 AATT
1 AATT
59102 AAAATAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
AATTTATTATTTTAAT
Found at i:59096 original size:24 final size:24
Alignment explanation
Indices: 59036--59120 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
59026 ATTGAAATTG
*
59036 AATTGTATATTTTTATTATAATAA-
1 AATT-TATATTTTTATTATTATAAT
** *
59060 AA-TTATAAATTTATTATTTTAAT
1 AATTTATATTTTTATTATTATAAT
* *
59083 AATTTATATTTTTATAATTAAAAT
1 AATTTATATTTTTATTATTATAAT
*
59107 AAGTTTTTATTTTT
1 AA-TTTATATTTTT
59121 TTTAAGTTTA
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
22 15 0.31
23 3 0.06
24 20 0.42
25 10 0.21
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
AATTTATATTTTTATTATTATAAT
Found at i:59131 original size:28 final size:25
Alignment explanation
Indices: 59080--59161 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 25
59070 TTATTATTTT
*
59080 AATAATTTATATTTTTA-TAA-TTAA
1 AATAATTT-TATTATTATTAATTTAA
* *
59104 AATAAGTTTTTATTTTTTTTAAGTTTAA
1 AATAA--TTTTATTATTATTAA-TTTAA
59132 AGTATAATTTTATTATTATTAATTTAA
1 A--ATAATTTTATTATTATTAATTTAA
59159 AAT
1 AAT
59162 TTCATAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
24 5 0.10
25 9 0.19
26 6 0.12
27 6 0.12
28 18 0.38
30 4 0.08
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (25 bp):
AATAATTTTATTATTATTAATTTAA
Found at i:59748 original size:16 final size:18
Alignment explanation
Indices: 59709--59742 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59699 TAAGTTTATA
59709 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
59726 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
59743 AATTTAAAAT
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:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:59856 original size:15 final size:16
Alignment explanation
Indices: 59825--59858 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
59815 AAATGAGTAT
59825 ATAAAAAATTTCAATAA
1 ATAAAAAATTT-AATAA
59842 ATAAAAAATTT-ATAA
1 ATAAAAAATTTAATAA
59857 AT
1 AT
59859 TTATTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
17 11 0.65
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAAAAATTTAATAA
Found at i:60428 original size:39 final size:39
Alignment explanation
Indices: 60382--60465 Score: 150
Period size: 39 Copynumber: 2.2 Consensus size: 39
60372 TTAAATAGGG
*
60382 TTTTAATGTGTCTTAGTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCCTAGTTTGATACATATTTAATAGTTGT
*
60421 TTTTAATGTGTCCTATTTTGATACATATTTAATAGTTGT
1 TTTTAATGTGTCCTAGTTTGATACATATTTAATAGTTGT
60460 TTTTAA
1 TTTTAA
60466 GTTGTCTAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.55
Consensus pattern (39 bp):
TTTTAATGTGTCCTAGTTTGATACATATTTAATAGTTGT
Found at i:66811 original size:41 final size:41
Alignment explanation
Indices: 66754--67218 Score: 592
Period size: 41 Copynumber: 11.3 Consensus size: 41
66744 TCACTTTAAA
*
66754 TATATTAAAAGAAGACTCATGTCTCGGGATGAGCATGAGAT
1 TATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
* ***
66795 TATATTAAAGGAAGACTCATGACTCAAAATGAGCATGAGAT
1 TATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
* *** *
66836 TATATTAAAGGAAGACTCATGACTCAAAATGAGTATGAGAT
1 TATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
66877 TATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
1 TATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
* * *** * *
66918 TATATTAAAGGAAGACTCGTGACTCAAAATAAGCATGAGAC
1 TATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
* *
66959 TAAATTAAAGGAAGAATCATGTCTCGGGATGAGCATGAGAT
1 TATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
*
67000 TATATTAAAGGAAGACTCGTGTCTCGGGATGAGCATGAGAT
1 TATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
* **
67041 TAAATTAAAGGAAGACTCATGTCTAAGGATGAGCATGAGAT
1 TATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
* * * * *
67082 TATACTAAAGGAAGGCTCATTTCTTGGGATGAGCATCAGAT
1 TATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
* *
67123 TATATTAAAGGAAGACTCGTGACTCGGGATGAGCATGAGAT
1 TATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
* * * *
67164 TATATATAAAGGAAGACTTATGACTCGGTAT-AGCATAAGAT
1 TATAT-TAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
67205 TAT-TTAAAAGGAAG
1 TATATT-AAAGGAAG
67219 GTTTACGACT
Statistics
Matches: 370, Mismatches: 52, Indels: 5
0.87 0.12 0.01
Matches are distributed among these distances:
39 1 0.00
40 9 0.02
41 338 0.91
42 22 0.06
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (41 bp):
TATATTAAAGGAAGACTCATGTCTCGGGATGAGCATGAGAT
Found at i:70971 original size:75 final size:75
Alignment explanation
Indices: 70878--71021 Score: 225
Period size: 75 Copynumber: 1.9 Consensus size: 75
70868 ACACACTAAG
*
70878 ATTCCCTTATTAATAGAGAAGAAAAATGGAAAGTTAGAAAAATAAATTATATTCTTTCCAAAAGA
1 ATTCCCTTATTAATAGAGAAGAAAAATGGAAAGTTAGAAAAAGAAATTATATTCTTTCCAAAAGA
70943 ATATAGGATT
66 ATATAGGATT
* ** * * *
70953 ATTCTCTTATTAATAGAGAAGGCAAATGGAAAGTTAGGAAAAGAAATTATATTTTTTCCAAAGGA
1 ATTCCCTTATTAATAGAGAAGAAAAATGGAAAGTTAGAAAAAGAAATTATATTCTTTCCAAAAGA
71018 ATAT
66 ATAT
71022 TAATTTTCAT
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 62 1.00
ACGTcount: A:0.46, C:0.08, G:0.15, T:0.31
Consensus pattern (75 bp):
ATTCCCTTATTAATAGAGAAGAAAAATGGAAAGTTAGAAAAAGAAATTATATTCTTTCCAAAAGA
ATATAGGATT
Found at i:71364 original size:138 final size:138
Alignment explanation
Indices: 70997--71557 Score: 899
Period size: 138 Copynumber: 4.1 Consensus size: 138
70987 TAGGAAAAGA
* * * **
70997 AATTATATTTTTTCCAAAGGAATATTAATTTTCATGTCTTTTATATTTTAACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
* *
71062 TATAAATGTTTATATTAATAAATTCTGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
71127 CATATATT
131 CATATATT
* * * *
71135 AGTTATATTTTTCTCCAAAAGAATATTAATTTTCATGTGTTTTATATTTTGTCCAAAATTAATTA
1 AATTATATTCTT-TCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTA
* ** *
71200 ATATAATTGTTTATATAAATGGATTCGGTAAAATATATACAATTAATATTTTATATGAATCAAAT
65 ATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
71265 TCATATATT
130 TCATATATT
*
71274 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTTG-CTAAAATTAATTA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATA-TTTTGACCAAAATTAATTA
71338 ATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
65 ATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
71403 TCATATATT
130 TCATATATT
* *
71412 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
* * **
71477 TATAATTGTTTATATTAATAAATTTGGTAAAATGTATATTATTAATATTTTGTATGAATCAAATT
66 TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
71542 CATATATT
131 CATATATT
71550 AATTATAT
1 AATTATAT
71558 CTATGTTCTC
Statistics
Matches: 392, Mismatches: 28, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
137 5 0.01
138 258 0.66
139 129 0.33
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCAAAATTAATTAA
TATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:80088 original size:41 final size:41
Alignment explanation
Indices: 79907--80088 Score: 229
Period size: 41 Copynumber: 4.4 Consensus size: 41
79897 TTATGCTCTA
* * * ** *
79907 TCGAGTCATAAGTCTTCATTAACCATATTCTCATTCTCATC
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
* *
79948 TCGAGACATGAGTCTTCCTTAATCATAATCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
* * *
79989 TTGAGACATGAGTATTCCTTATTCATAATCTCATTCTCAAC
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
*
80030 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATT
1 TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
* * *
80071 TCAAGAGATCAGTCTTCC
1 TCGAGACATGAGTCTTCC
80089 ATTTATACAA
Statistics
Matches: 123, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 123 1.00
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (41 bp):
TCGAGACATGAGTCTTCCTTATTCATAATCTCATTCTCATC
Found at i:84823 original size:13 final size:13
Alignment explanation
Indices: 84805--84854 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
84795 TTGACCCACT
*
84805 ACTCGACCTGTTG
1 ACTCGACCTATTG
*
84818 ACTCGACC---CG
1 ACTCGACCTATTG
*
84828 ACTCGACCCATTG
1 ACTCGACCTATTG
84841 ACTCGACCTATTG
1 ACTCGACCTATTG
84854 A
1 A
84855 TCGTTAACCG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
10 9 0.29
13 22 0.71
ACGTcount: A:0.22, C:0.36, G:0.18, T:0.24
Consensus pattern (13 bp):
ACTCGACCTATTG
Found at i:84835 original size:23 final size:23
Alignment explanation
Indices: 84805--84848 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
84795 TTGACCCACT
**
84805 ACTCGACCTGTTGACTCGACCCG
1 ACTCGACCCATTGACTCGACCCG
84828 ACTCGACCCATTGACTCGACC
1 ACTCGACCCATTGACTCGACC
84849 TATTGATCGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.41, G:0.18, T:0.20
Consensus pattern (23 bp):
ACTCGACCCATTGACTCGACCCG
Found at i:88557 original size:17 final size:17
Alignment explanation
Indices: 88532--88566 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
88522 AATATTTATA
*
88532 TATATTTTTAAATATTT
1 TATACTTTTAAATATTT
*
88549 TATACTTTTATATATTT
1 TATACTTTTAAATATTT
88566 T
1 T
88567 TTATTATTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TATACTTTTAAATATTT
Found at i:93803 original size:17 final size:18
Alignment explanation
Indices: 93781--93814 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
93771 ATAACAATTA
93781 TGAAGATTTTGG-ATATG
1 TGAAGATTTTGGCATATG
93798 TGAAGATTTTGGCATAT
1 TGAAGATTTTGGCATAT
93815 TCCTTGAAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.41
Consensus pattern (18 bp):
TGAAGATTTTGGCATATG
Found at i:103497 original size:43 final size:43
Alignment explanation
Indices: 103414--103526 Score: 199
Period size: 43 Copynumber: 2.6 Consensus size: 43
103404 GCTCATAATA
* *
103414 AATCATATACTTTCAATAATAGGGAAACAATGTTCCTCTCAATC
1 AATCACATACTTTCAATAATA-GGAAACAATGTTACTCTCAATC
103458 AATCACATACTTTCAATAATAGGAAACAATGTTACTCTCAATC
1 AATCACATACTTTCAATAATAGGAAACAATGTTACTCTCAATC
103501 AATCACATACTTTCAATAATAGGAAA
1 AATCACATACTTTCAATAATAGGAAA
103527 TAGTGTTCCA
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
43 47 0.70
44 20 0.30
ACGTcount: A:0.42, C:0.19, G:0.08, T:0.30
Consensus pattern (43 bp):
AATCACATACTTTCAATAATAGGAAACAATGTTACTCTCAATC
Found at i:106011 original size:40 final size:39
Alignment explanation
Indices: 105967--106187 Score: 185
Period size: 40 Copynumber: 5.5 Consensus size: 39
105957 TCATAGCTTA
* *
105967 CTAAGCCATAGCTTGAATTTTAACACCGACTTGTAGCCTG
1 CTAAGCCA-AGCTTGAATTCTATCACCGACTTGTAGCCTG
** * *
106007 CTAAGTCGTAGCTTGAATT-TATTCACCGACTCGTAGCGTG
1 CTAAG-CCAAGCTTGAATTCTA-TCACCGACTTGTAGCCTG
** * * *
106047 CTAAGCCAAAGCTTGAATTCTATCATTG-GTTCGAAGCTTG
1 CTAAGCC-AAGCTTGAATTCTATCACCGACTT-GTAGCCTG
* * *
106087 CTAAGCCGAAGCTTGAATTCTATCACCGGCTCGTAGCCTA
1 CTAAGCC-AAGCTTGAATTCTATCACCGACTTGTAGCCTG
* * * *
106127 CTAAGTCAAAGCTTGAATTCTATCACTGGCTTGTAGCCTA
1 CTAAG-CCAAGCTTGAATTCTATCACCGACTTGTAGCCTG
*
106167 CTAAGCCGAAGCTTGACTTCT
1 CTAAGCC-AAGCTTGAATTCT
106188 TTCAACGTAA
Statistics
Matches: 147, Mismatches: 26, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
39 5 0.03
40 137 0.93
41 5 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (39 bp):
CTAAGCCAAGCTTGAATTCTATCACCGACTTGTAGCCTG
Found at i:106171 original size:80 final size:81
Alignment explanation
Indices: 105947--106191 Score: 291
Period size: 80 Copynumber: 3.1 Consensus size: 81
105937 CTTCTAATCA
* * * * * * *
105947 ATTCACCGGCTCATAGCTTACTAAGCCATAGCTTGAATTTTAACACCGACTTGTAGCCTGCTAAG
1 ATTCACCGGCTCGTAGCCTACTAAGCCAAAGCTTGAATTCTATCACTGGCTTGTAGCCTGCTAAG
* *
106012 TCGTAGCTTGAATT-T
66 CCGAAGCTTGAATTCT
* * * * * *
106027 ATTCACCGACTCGTAGCGTGCTAAGCCAAAGCTTGAATTCTATCATTGG-TTCGAAGCTTGCTAA
1 ATTCACCGGCTCGTAGCCTACTAAGCCAAAGCTTGAATTCTATCACTGGCTT-GTAGCCTGCTAA
106091 GCCGAAGCTTGAATTCT
65 GCCGAAGCTTGAATTCT
* *
106108 A-TCACCGGCTCGTAGCCTACTAAGTCAAAGCTTGAATTCTATCACTGGCTTGTAGCCTACTAAG
1 ATTCACCGGCTCGTAGCCTACTAAGCCAAAGCTTGAATTCTATCACTGGCTTGTAGCCTGCTAAG
*
106172 CCGAAGCTTGACTTCT
66 CCGAAGCTTGAATTCT
106188 -TTCA
1 ATTCA
106192 ACGTAACTTA
Statistics
Matches: 138, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
79 2 0.01
80 132 0.96
81 4 0.03
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.31
Consensus pattern (81 bp):
ATTCACCGGCTCGTAGCCTACTAAGCCAAAGCTTGAATTCTATCACTGGCTTGTAGCCTGCTAAG
CCGAAGCTTGAATTCT
Found at i:106179 original size:120 final size:120
Alignment explanation
Indices: 105961--106187 Score: 287
Period size: 120 Copynumber: 1.9 Consensus size: 120
105951 ACCGGCTCAT
* * * **
105961 AGCTTACTAAGCCATAGCTTGAATTTTAACACCGACTTGTAGCCTGCTAAGTCGTAGCTTGAATT
1 AGCTTACTAAGCCATAGCTTGAATTCTAACACCGACTCGTAGCCTACTAAGTCAAAGCTTGAATT
* *
106026 TATTCACCGACTCGTAGCGTGCTAAGCCAAAGCTTGAATTCTATCATTGGTTCGA
66 TATTCACCGACTCGTAGCCTACTAAGCCAAAGCTTGAATTCTATCATTGGTTCGA
* * *
106081 AGCTTGCTAAGCCGA-AGCTTGAATTCTATCACCGGCTCGTAGCCTACTAAGTCAAAGCTTGAAT
1 AGCTTACTAAGCC-ATAGCTTGAATTCTAACACCGACTCGTAGCCTACTAAGTCAAAGCTTGAAT
* * * * *
106145 TCTA-TCACTGGCTTGTAGCCTACTAAGCCGAAGCTTGACTTCT
65 T-TATTCACCGACTCGTAGCCTACTAAGCCAAAGCTTGAATTCT
106188 TTCAACGTAA
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
120 87 0.97
121 3 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.30
Consensus pattern (120 bp):
AGCTTACTAAGCCATAGCTTGAATTCTAACACCGACTCGTAGCCTACTAAGTCAAAGCTTGAATT
TATTCACCGACTCGTAGCCTACTAAGCCAAAGCTTGAATTCTATCATTGGTTCGA
Found at i:112939 original size:7 final size:6
Alignment explanation
Indices: 112918--113094 Score: 178
Period size: 6 Copynumber: 28.5 Consensus size: 6
112908 AGTGCATGAT
*
112918 AAAATA AAAATA AAAATA AAAAT- AATA-A AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
* * * *
112964 AATATA AATATGA AAAATGA AAAATGA AAAATGG AAAATGT AAAATA AAAATGA
1 AAAATA AAAAT-A AAAAT-A AAAAT-A AAAAT-A AAAAT-A AAAATA AAAAT-A
* * * * *
113018 AAAATAA AAAATAA AAAATG AAAATG AAAATG AAAATG AAAATG AAAATA
1 AAAAT-A AAAAT-A AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA
113068 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
113095 GTACTAATTT
Statistics
Matches: 157, Mismatches: 10, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
5 6 0.04
6 101 0.64
7 50 0.32
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:112941 original size:33 final size:28
Alignment explanation
Indices: 112918--113086 Score: 152
Period size: 28 Copynumber: 5.9 Consensus size: 28
112908 AGTGCATGAT
112918 AAAATAAAAATAAAAATAAAAATAATAA
1 AAAATAAAAATAAAAATAAAAATAATAA
*
112946 AAAATAAAAATAAAAATAAATATAAATATGA
1 AAAATAAAAATAAAAATAAAAAT-AATA--A
* *
112977 AAAATGAAAAATGAAAAATGGAAAAT-GT--
1 AAAAT-AAAAAT-AAAAAT-AAAAATAATAA
113005 AAAATAAAAATGAAAAAT-AAAA-AATAA
1 AAAATAAAAAT-AAAAATAAAAATAATAA
* * *
113032 AAAATGAAAATGAAAATGAAAATGAA-AA
1 AAAATAAAAATAAAAATAAAAAT-AATAA
113060 TGAAAATAAAAATAAAAATAAAAATAA
1 --AAAATAAAAATAAAAATAAAAATAA
113087 AAATAAAAGT
Statistics
Matches: 117, Mismatches: 10, Indels: 27
0.76 0.06 0.18
Matches are distributed among these distances:
25 5 0.04
26 5 0.04
27 27 0.23
28 29 0.25
29 8 0.07
30 20 0.17
31 6 0.05
32 7 0.06
33 6 0.05
34 4 0.03
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.18
Consensus pattern (28 bp):
AAAATAAAAATAAAAATAAAAATAATAA
Found at i:112950 original size:16 final size:16
Alignment explanation
Indices: 112929--112988 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
112919 AAATAAAAAT
112929 AAAAATAAAAATAATA
1 AAAAATAAAAATAATA
112945 AAAAATAAAAATAA-A
1 AAAAATAAAAATAATA
* *
112960 AATAAATATAAAT-ATG
1 AA-AAATAAAAATAATA
112976 AAAAATGAAAAAT
1 AAAAAT-AAAAAT
112989 GAAAAATGGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
15 8 0.21
16 30 0.79
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (16 bp):
AAAAATAAAAATAATA
Found at i:115883 original size:14 final size:14
Alignment explanation
Indices: 115864--115922 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
115854 AGAAGAGAAA
115864 AAAAATTAAAATAT
1 AAAAATTAAAATAT
115878 AAAAATT-AAAT-T
1 AAAAATTAAAATAT
**
115890 AAAAATGCAAATAT
1 AAAAATTAAAATAT
* **
115904 TAAAACAAAAATA-
1 AAAAATTAAAATAT
115917 AAAAAT
1 AAAAAT
115923 GGCTAAAGTA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
12 7 0.19
13 12 0.33
14 17 0.47
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (14 bp):
AAAAATTAAAATAT
Found at i:120592 original size:16 final size:16
Alignment explanation
Indices: 120547--120593 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 16
120537 TTAGTACAAA
120547 AAGATATAAAAATAAC
1 AAGATATAAAAATAAC
*
120563 AAGAATTTTAAAAATAAC
1 AAG-A-TATAAAAATAAC
120581 AAGATATAAAAAT
1 AAGATATAAAAAT
120594 GGTGTATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 11 0.41
17 2 0.07
18 14 0.52
ACGTcount: A:0.66, C:0.04, G:0.06, T:0.23
Consensus pattern (16 bp):
AAGATATAAAAATAAC
Found at i:120955 original size:15 final size:14
Alignment explanation
Indices: 120926--120983 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
120916 TTTATCATAA
*
120926 TTTTTT-TTCTTCT
1 TTTTTTCTTTTTCT
120939 TTTTATTCTTTTTCT
1 TTTT-TTCTTTTTCT
120954 TTTTCTTCCTTTTTCT
1 TTTT-TT-CTTTTTCT
*
120970 CATTTTTCTTTTTC
1 -TTTTTTCTTTTTC
120984 AAGTGACTGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
13 4 0.11
14 2 0.05
15 19 0.50
16 10 0.26
17 3 0.08
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTCTTTTTCT
Found at i:120965 original size:25 final size:24
Alignment explanation
Indices: 120929--120983 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
120919 ATCATAATTT
*
120929 TTTTTCTTCTTTTTATTC-TTTTTC
1 TTTTTCTTCTTTTT-CTCATTTTTC
120953 TTTTTCTTCCTTTTTCTCATTTTTC
1 TTTTTCTT-CTTTTTCTCATTTTTC
120978 TTTTTC
1 TTTTTC
120984 AAGTGACTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTCTTCTTTTTCTCATTTTTC
Found at i:121738 original size:24 final size:24
Alignment explanation
Indices: 121706--121756 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
121696 CTCACCCTCG
*
121706 TCCTGGTG-CTTCTTCTTCTTTTTA
1 TCCTGGTGCCTT-TTCCTCTTTTTA
*
121730 TCCTTGTGCCTTTTCCTCTTTTTA
1 TCCTGGTGCCTTTTCCTCTTTTTA
121754 TCC
1 TCC
121757 ATCGTACCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 21 0.88
25 3 0.12
ACGTcount: A:0.04, C:0.29, G:0.10, T:0.57
Consensus pattern (24 bp):
TCCTGGTGCCTTTTCCTCTTTTTA
Found at i:122074 original size:15 final size:15
Alignment explanation
Indices: 122054--122082 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
122044 CTCTTCATTC
122054 TCTTCTTCCTTTTCT
1 TCTTCTTCCTTTTCT
122069 TCTTCTTCCTTTTC
1 TCTTCTTCCTTTTC
122083 CTTCAGCTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (15 bp):
TCTTCTTCCTTTTCT
Found at i:144054 original size:43 final size:43
Alignment explanation
Indices: 144006--144109 Score: 111
Period size: 49 Copynumber: 2.3 Consensus size: 43
143996 TGAATCCAAT
144006 ACCCTAAAGATGGAAAGATTGAAGCCGCAATGACAAATCTTGC
1 ACCCTAAAGATGGAAAGATTGAAGCCGCAATGACAAATCTTGC
* * *
144049 ACCCTAGAAATGTGAAGGGAAAGATTGAAGCCGCAATGACGAATCTTGT
1 ACCCT--AAA---G-ATGGAAAGATTGAAGCCGCAATGACAAATCTTGC
144098 ACCC-AAGAGATG
1 ACCCTAA-AGATG
144110 TGAAGGGAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
43 7 0.14
44 1 0.02
45 3 0.06
46 2 0.04
47 1 0.02
48 1 0.02
49 35 0.70
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.18
Consensus pattern (43 bp):
ACCCTAAAGATGGAAAGATTGAAGCCGCAATGACAAATCTTGC
Found at i:144094 original size:49 final size:49
Alignment explanation
Indices: 144017--144583 Score: 527
Period size: 49 Copynumber: 11.6 Consensus size: 49
144007 CCCTAAAGAT
* * *
144017 GGAAAGATTGAAGCCGCAATGACAAATCTTGCACCCTAGAAATGTGAAG
1 GGAAAGATTGAAGCCGCAATGGCGAATCTTGCACCCTAGAGATGTGAAG
* * *
144066 GGAAAGATTGAAGCCGCAATGACGAATCTTGTACCCAAGAGATGTGAAG
1 GGAAAGATTGAAGCCGCAATGGCGAATCTTGCACCCTAGAGATGTGAAG
* * * * * *
144115 GG-AAGATTGAAGCTGTAATGGCGAATCTTGTACCTTGGAGATGTAAAG
1 GGAAAGATTGAAGCCGCAATGGCGAATCTTGCACCCTAGAGATGTGAAG
* * *
144163 GGAAAGATTGAAGCCACAATGG-AAGATCTTGCACCCTAGAAATGTGAAG
1 GGAAAGATTGAAGCCGCAATGGCGA-ATCTTGCACCCTAGAGATGTGAAG
* * *
144212 GGAAAGATTGAAGTCGTAATGGCGAATCTTGTACCCTAGAGATGTGAAG
1 GGAAAGATTGAAGCCGCAATGGCGAATCTTGCACCCTAGAGATGTGAAG
* * * * * *
144261 GGAAAGATCGAAGTCGTAATGACGAATCTTGCACCTTAGAGATATGAAG
1 GGAAAGATTGAAGCCGCAATGGCGAATCTTGCACCCTAGAGATGTGAAG
* * * ** *
144310 GG-AAGATTGAAGTCACAATGGCGAATCTTGTACGTTGGAGATGTGAAG
1 GGAAAGATTGAAGCCGCAATGGCGAATCTTGCACCCTAGAGATGTGAAG
* * * * * *
144358 GGAAATATTGAAGCTGTAATGG-TAAGTCTTGCACCTTAGAAATGTGAAG
1 GGAAAGATTGAAGCCGCAATGGCGAA-TCTTGCACCCTAGAGATGTGAAG
* * * * * *
144407 GGAAAGATTGAAGTCACAATGGCAAATCTTGTACCCTAGAGATATGGAG
1 GGAAAGATTGAAGCCGCAATGGCGAATCTTGCACCCTAGAGATGTGAAG
* * * *
144456 GGAAAGATTGAAGGCGCAATGGCGGATCTTGCACCCTAGAAATGTG-GG
1 GGAAAGATTGAAGCCGCAATGGCGAATCTTGCACCCTAGAGATGTGAAG
* * * * ** *
144504 GGTAAAGATTGAAGTCACAACGGTGAATCTTATACCCTAAAGAT-TGTAGAG
1 GG-AAAGATTGAAGCCGCAATGGCGAATCTTGCACCCTAGAGATGTG-A-AG
* * *
144555 GGCCAA-ATTGAAGCCGCAAAGGCAAATCT
1 GG-AAAGATTGAAGCCGCAATGGCGAATCT
144584 CACACCCCTA
Statistics
Matches: 423, Mismatches: 85, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
48 89 0.21
49 308 0.73
50 21 0.05
51 5 0.01
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.22
Consensus pattern (49 bp):
GGAAAGATTGAAGCCGCAATGGCGAATCTTGCACCCTAGAGATGTGAAG
Found at i:144316 original size:146 final size:147
Alignment explanation
Indices: 144017--144547 Score: 592
Period size: 146 Copynumber: 3.6 Consensus size: 147
144007 CCCTAAAGAT
* * *
144017 GGAAAGATTGAAGCCGCAAT-GACAAATCTTGCACCCTAGAAATGTGAAGGGAAAGATTGAAGCC
1 GGAAAGATTGAAGCCACAATGGA-AGATCTTGCACCCTAGAAATGTGAAGGGAAAGATTGAAGTC
* *
144081 GCAATGACGAATCTTGTACCCAAGAGATGTGAAGGG-AAGATTGAAG-CTGTAATGGCGAATCTT
65 GCAATGGCGAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGTC-GTAATGGCGAATCTT
* * *
144144 GTACCTTGGAGATGTAAAG
129 GTACCTTAGAGATATGAAG
144163 GGAAAGATTGAAGCCACAATGGAAGATCTTGCACCCTAGAAATGTGAAGGGAAAGATTGAAGTCG
1 GGAAAGATTGAAGCCACAATGGAAGATCTTGCACCCTAGAAATGTGAAGGGAAAGATTGAAGTCG
* * * *
144228 TAATGGCGAATCTTGTACCCTAGAGATGTGAAGGGAAAGATCGAAGTCGTAATGACGAATCTTGC
66 CAATGGCGAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGTCGTAATGGCGAATCTTGT
144293 ACCTTAGAGATATGAAG
131 ACCTTAGAGATATGAAG
* * * ** * * *
144310 GG-AAGATTGAAGTCACAATGG-CGAATCTTGTACGTTGGAGATGTGAAGGGAAATATTGAAG-C
1 GGAAAGATTGAAGCCACAATGGAAG-ATCTTGCACCCTAGAAATGTGAAGGGAAAGATTGAAGTC
* * * * * ** *
144372 TGTAATGG-TAAGTCTTGCACCTTAGAAATGTGAAGGGAAAGATTGAAGTCACAATGGCAAATCT
65 -GCAATGGCGAA-TCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGTCGTAATGGCGAATCT
* *
144436 TGTACCCTAGAGATATGGAG
128 TGTACCTTAGAGATATGAAG
* * ** *
144456 GGAAAGATTGAAGGCGCAATGGCGGATCTTGCACCCTAGAAATGTG-GGGGTAAAGATTGAAGTC
1 GGAAAGATTGAAGCCACAATGGAAGATCTTGCACCCTAGAAATGTGAAGGG-AAAGATTGAAGTC
* * * * *
144520 ACAACGGTGAATCTTATACCCTAAAGAT
65 GCAATGGCGAATCTTGTACCCTAGAGAT
144548 TGTAGAGGGC
Statistics
Matches: 323, Mismatches: 51, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
145 4 0.01
146 213 0.66
147 101 0.31
148 5 0.02
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (147 bp):
GGAAAGATTGAAGCCACAATGGAAGATCTTGCACCCTAGAAATGTGAAGGGAAAGATTGAAGTCG
CAATGGCGAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGTCGTAATGGCGAATCTTGT
ACCTTAGAGATATGAAG
Found at i:144350 original size:195 final size:195
Alignment explanation
Indices: 144017--144539 Score: 692
Period size: 195 Copynumber: 2.7 Consensus size: 195
144007 CCCTAAAGAT
* * * *
144017 GGAAAGATTGAAGCCGCAATGACAAATCTTGCACCCTAGAAATGTGAAGGGAAAGATTGAAGCCG
1 GGAAAGATTGAAGTCGCAATGGCAAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGCCG
* * **
144082 CAATGACGAATCTTGTACCCAAGAGATGTGAAGGGAAGATTGAAG-CTGTAATGGCGAATCTTGT
66 CAATGACGAATCTTGCACCCTAGAGATGTGAAGGGAAGATTGAAGTC-ACAATGGCGAATCTTGT
144146 ACCTTGGAGATGTAAAGGGAAAGATTGAAGCCACAATGG-AAGATCTTGCACCCTAGAAATGTGA
130 ACCTTGGAGATGTAAAGGGAAAGATTGAAGCCACAATGGTAAG-TCTTGCACCCTAGAAATGTGA
144210 AG
194 AG
* * * *
144212 GGAAAGATTGAAGTCGTAATGGCGAATCTTGTACCCTAGAGATGTGAAGGGAAAGATCGAAGTCG
1 GGAAAGATTGAAGTCGCAATGGCAAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGCCG
* * *
144277 TAATGACGAATCTTGCACCTTAGAGATATGAAGGGAAGATTGAAGTCACAATGGCGAATCTTGTA
66 CAATGACGAATCTTGCACCCTAGAGATGTGAAGGGAAGATTGAAGTCACAATGGCGAATCTTGTA
* * * *** *
144342 CGTTGGAGATGTGAAGGGAAATATTGAAGCTGTAATGGTAAGTCTTGCACCTTAGAAATGTGAAG
131 CCTTGGAGATGTAAAGGGAAAGATTGAAGCCACAATGGTAAGTCTTGCACCCTAGAAATGTGAAG
* * * *
144407 GGAAAGATTGAAGTCACAATGGCAAATCTTGTACCCTAGAGATATGGAGGGAAAGATTGAAGGCG
1 GGAAAGATTGAAGTCGCAATGGCAAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGCCG
* * * * * * *
144472 CAATGGCGGATCTTGCACCCTAGAAATGTG-GGGGTAAAGATTGAAGTCACAACGGTGAATCTTA
66 CAATGACGAATCTTGCACCCTAGAGATGTGAAGGG--AAGATTGAAGTCACAATGGCGAATCTTG
144536 TACC
129 TACC
144540 CTAAAGATTG
Statistics
Matches: 284, Mismatches: 40, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
194 3 0.01
195 249 0.88
196 32 0.11
ACGTcount: A:0.35, C:0.14, G:0.28, T:0.23
Consensus pattern (195 bp):
GGAAAGATTGAAGTCGCAATGGCAAATCTTGTACCCTAGAGATGTGAAGGGAAAGATTGAAGCCG
CAATGACGAATCTTGCACCCTAGAGATGTGAAGGGAAGATTGAAGTCACAATGGCGAATCTTGTA
CCTTGGAGATGTAAAGGGAAAGATTGAAGCCACAATGGTAAGTCTTGCACCCTAGAAATGTGAAG
Found at i:159443 original size:22 final size:22
Alignment explanation
Indices: 159418--159460 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
159408 AAAATATTTC
159418 ATTA-ATAAATTGGGTTTAATTA
1 ATTATATAAATTGGG-TTAATTA
*
159440 ATTATTTAAATTGGGTTAATT
1 ATTATATAAATTGGGTTAATT
159461 TTATTTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.37, C:0.00, G:0.14, T:0.49
Consensus pattern (22 bp):
ATTATATAAATTGGGTTAATTA
Found at i:167772 original size:35 final size:35
Alignment explanation
Indices: 167722--167834 Score: 118
Period size: 40 Copynumber: 3.1 Consensus size: 35
167712 TGCTGGGCAC
* *
167722 ATATTTTTCGGTTTATCCGACTAGCATTAGGCGCAA
1 ATATTGTT-GGTTTATCCGACTAGCACTAGGCGCAA
* * * *
167758 ATATTGTTGGTTTATCCAACTAGAACTGGGCTCACATTTA
1 ATATTGTTGGTTTATCCGACTAGCACTAGG--CGCA---A
167798 ATATTGTTGGTTTATCCGACTAGCACTAGGCGCAA
1 ATATTGTTGGTTTATCCGACTAGCACTAGGCGCAA
167833 AT
1 AT
167835 TCTTTCGCGG
Statistics
Matches: 62, Mismatches: 10, Indels: 11
0.75 0.12 0.13
Matches are distributed among these distances:
35 21 0.34
36 7 0.11
37 3 0.05
38 3 0.05
40 28 0.45
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (35 bp):
ATATTGTTGGTTTATCCGACTAGCACTAGGCGCAA
Found at i:170416 original size:43 final size:43
Alignment explanation
Indices: 170357--170629 Score: 174
Period size: 43 Copynumber: 6.4 Consensus size: 43
170347 TAAAGACTTA
* *
170357 ATATATAAATGGAAGACTCATG-CTTCGGGATGAGCATGAGATT
1 ATATATAAATGGAAGACTCATGTC-TCGAGATAAGCATGAGATT
* *
170400 GTATATAAATGAAAGACTCATGTCTCGAGATAAGCATGAGATT
1 ATATATAAATGGAAGACTCATGTCTCGAGATAAGCATGAGATT
* * *
170443 ATGTATAAATGGAAGACTTATGTCTCG-G-TAAGAGCATAAGATT
1 ATATATAAATGGAAGACTCATGTCTCGAGAT-A-AGCATGAGATT
* * * * *
170486 AT-TGTAAATGGAAGAAATTAAGTCTCG-G-TAAGAGCATAAGATT
1 ATATATAAATGGAAG-ACTCATGTCTCGAGAT-A-AGCATGAGATT
* * * *
170529 AT-TGTAAATGGAAGAACTTATGTCTCG-GTAAAAGCATAAGATT
1 ATATATAAATGGAAG-ACTCATGTCTCGAG-ATAAGCATGAGATT
* * * *
170572 AT-TGTAAATGGAAGAACTTATGTCT-TAG-TAAGAGCATAAGATT
1 ATATATAAATGGAAG-ACTCATGTCTCGAGAT-A-AGCATGAGATT
*
170615 AT-TGTAAATGGAAGA
1 ATATATAAATGGAAGA
170630 ACTTATGACT
Statistics
Matches: 204, Mismatches: 17, Indels: 19
0.85 0.07 0.08
Matches are distributed among these distances:
41 1 0.00
42 15 0.07
43 186 0.91
44 2 0.01
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (43 bp):
ATATATAAATGGAAGACTCATGTCTCGAGATAAGCATGAGATT
Found at i:170511 original size:86 final size:87
Alignment explanation
Indices: 170360--170654 Score: 327
Period size: 86 Copynumber: 3.4 Consensus size: 87
170350 AGACTTAATA
* * * * * * * *
170360 TATAAATGGAAG-ACTCATG-CTTCGGGATGAGCATGAGATTGTATATAAATGAAAG-ACTCATG
1 TATAAATGGAAGAACTTATGTC-TCGGTAAGAGCATAAGATTAT-TGTAAATGGAAGAACTTATG
*
170422 TCTCGAG-ATA-AGCATGAGATTAT
64 TCTCGAGTA-AGAGCATAAGATTAT
* *
170445 GTATAAATGGAAG-ACTTATGTCTCGGTAAGAGCATAAGATTATTGTAAATGGAAGAAATTAAGT
1 -TATAAATGGAAGAACTTATGTCTCGGTAAGAGCATAAGATTATTGTAAATGGAAGAACTTATGT
170509 CTCG-GTAAGAGCATAAGATTAT
65 CTCGAGTAAGAGCATAAGATTAT
* *
170531 TGTAAATGGAAGAACTTATGTCTCGGTAAAAGCATAAGATTATTGTAAATGGAAGAACTTATGTC
1 TATAAATGGAAGAACTTATGTCTCGGTAAGAGCATAAGATTATTGTAAATGGAAGAACTTATGTC
*
170596 T-TAGTAAGAGCATAAGATTAT
66 TCGAGTAAGAGCATAAGATTAT
* * * **
170617 TGTAAATGGAAGAACTTATGACTCAGTCGGAGCATAAG
1 TATAAATGGAAGAACTTATGTCTCGGTAAGAGCATAAG
170655 GTTAATTCAG
Statistics
Matches: 182, Mismatches: 21, Indels: 12
0.85 0.10 0.06
Matches are distributed among these distances:
85 23 0.13
86 158 0.87
87 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (87 bp):
TATAAATGGAAGAACTTATGTCTCGGTAAGAGCATAAGATTATTGTAAATGGAAGAACTTATGTC
TCGAGTAAGAGCATAAGATTAT
Found at i:170630 original size:43 final size:43
Alignment explanation
Indices: 170432--170654 Score: 331
Period size: 43 Copynumber: 5.2 Consensus size: 43
170422 TCTCGAGATA
* *
170432 AGCATGAGATTATGTATAAATGGAAG-ACTTATGTCTCGGTAAG
1 AGCATAAGATTAT-TGTAAATGGAAGAACTTATGTCTCGGTAAG
* *
170475 AGCATAAGATTATTGTAAATGGAAGAAATTAAGTCTCGGTAAG
1 AGCATAAGATTATTGTAAATGGAAGAACTTATGTCTCGGTAAG
*
170518 AGCATAAGATTATTGTAAATGGAAGAACTTATGTCTCGGTAAA
1 AGCATAAGATTATTGTAAATGGAAGAACTTATGTCTCGGTAAG
**
170561 AGCATAAGATTATTGTAAATGGAAGAACTTATGTCTTAGTAAG
1 AGCATAAGATTATTGTAAATGGAAGAACTTATGTCTCGGTAAG
* * **
170604 AGCATAAGATTATTGTAAATGGAAGAACTTATGACTCAGTCGG
1 AGCATAAGATTATTGTAAATGGAAGAACTTATGTCTCGGTAAG
170647 AGCATAAG
1 AGCATAAG
170655 GTTAATTCAG
Statistics
Matches: 165, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
42 11 0.07
43 154 0.93
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (43 bp):
AGCATAAGATTATTGTAAATGGAAGAACTTATGTCTCGGTAAG
Found at i:170650 original size:129 final size:128
Alignment explanation
Indices: 170405--170654 Score: 342
Period size: 129 Copynumber: 1.9 Consensus size: 128
170395 AGATTGTATA
* * *
170405 TAAATGAAAGACTCATGTCTCGAGATAAGCATGAGATTATGTATAAATGGAAGACTTATGTCTCG
1 TAAATGAAAGACTCATGTCTCGAGAAAAGCATAAGATTATGTATAAATGGAAGACTTATGTCTCA
* *
170470 GTAAGAGCATAAGATTATTGTAAATGGAAGAAATTAAGTCTCGGTAAGAGCATAAGATTATTG
66 GTAAGAGCATAAGATTATTGTAAATGGAAGAAATTAAGACTCAGTAAGAGCATAAGATTATTG
* * *
170533 TAAATGGAAGAACTTATGTCTCG-GTAAAAGCATAAGATTAT-TGTAAATGGAAGAACTTATGTC
1 TAAATGAAAG-ACTCATGTCTCGAG-AAAAGCATAAGATTATGTATAAATGGAAG-ACTTATGTC
* * * **
170596 TTAGTAAGAGCATAAGATTATTGTAAATGGAAGAACTTATGACTCAGTCGGAGCATAAG
63 TCAGTAAGAGCATAAGATTATTGTAAATGGAAGAAATTAAGACTCAGTAAGAGCATAAG
170655 GTTAATTCAG
Statistics
Matches: 106, Mismatches: 13, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
128 21 0.20
129 85 0.80
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (128 bp):
TAAATGAAAGACTCATGTCTCGAGAAAAGCATAAGATTATGTATAAATGGAAGACTTATGTCTCA
GTAAGAGCATAAGATTATTGTAAATGGAAGAAATTAAGACTCAGTAAGAGCATAAGATTATTG
Found at i:172123 original size:34 final size:34
Alignment explanation
Indices: 172085--172153 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
172075 GGATACTTAG
172085 TATGTGTTTAAGGATGGGGAATTCAGGTATATTA
1 TATGTGTTTAAGGATGGGGAATTCAGGTATATTA
172119 TATGTGTTTAAGGATGGGGAATTCAGGTATATTA
1 TATGTGTTTAAGGATGGGGAATTCAGGTATATTA
172153 T
1 T
172154 TATGGTATCT
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:0.29, C:0.03, G:0.29, T:0.39
Consensus pattern (34 bp):
TATGTGTTTAAGGATGGGGAATTCAGGTATATTA
Found at i:176729 original size:9 final size:9
Alignment explanation
Indices: 176717--176790 Score: 58
Period size: 9 Copynumber: 7.6 Consensus size: 9
176707 ATTTTAAATT
176717 TTTTTAAAA
1 TTTTTAAAA
*
176726 TTTTTAACAT
1 TTTTTAA-AA
176736 TATTTTAAAA
1 T-TTTTAAAA
176746 TTTTTTAAAA
1 -TTTTTAAAA
**
176756 TTTTTAACT
1 TTTTTAAAA
176765 TTTTTATATAA
1 TTTTTA-A-AA
*
176776 TCTTTAGAAA
1 TTTTTA-AAA
176786 TTTTT
1 TTTTT
176791 TATGATATTC
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
9 20 0.39
10 18 0.35
11 13 0.25
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:176738 original size:30 final size:30
Alignment explanation
Indices: 176704--176770 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
176694 GACCAAAAAT
*
176704 ATTATTTTAAATTTTTTTAAAATTTTTAAC
1 ATTATTTTAAAATTTTTTAAAATTTTTAAC
176734 ATTATTTTAAAATTTTTTAAAATTTTTAAC
1 ATTATTTTAAAATTTTTTAAAATTTTTAAC
176764 -TT-TTTTA
1 ATTATTTTA
176771 TATAATCTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 5 0.14
29 2 0.06
30 29 0.81
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (30 bp):
ATTATTTTAAAATTTTTTAAAATTTTTAAC
Found at i:176743 original size:20 final size:19
Alignment explanation
Indices: 176708--176790 Score: 69
Period size: 20 Copynumber: 4.2 Consensus size: 19
176698 AAAAATATTA
*
176708 TTTTAAATTTTTTTAAAAT
1 TTTTAAATTATTTTAAAAT
176727 TTTTAACATTATTTTAAAATT
1 TTTTAA-ATTATTTTAAAA-T
* **
176748 TTTTAAAAT-TTTTAACTT
1 TTTTAAATTATTTTAAAAT
* *
176766 TTTTATATAATCTTTAGAAAT
1 TTTTAAATTAT-TTTA-AAAT
176787 TTTT
1 TTTT
176791 TATGATATTC
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
18 7 0.14
19 13 0.26
20 17 0.34
21 13 0.26
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (19 bp):
TTTTAAATTATTTTAAAAT
Found at i:176787 original size:30 final size:30
Alignment explanation
Indices: 176704--176790 Score: 99
Period size: 30 Copynumber: 2.9 Consensus size: 30
176694 GACCAAAAAT
* *
176704 ATTATTTTAAATTTTTTTAAAATTTTTAAC
1 ATTATTTTAAAATTCTTTAAAATTTTTAAC
*
176734 ATTATTTTAAAATTTTTTAAAATTTTTAAC
1 ATTATTTTAAAATTCTTTAAAATTTTTAAC
176764 -TT-TTTTATATAA-TCTTTAGAAATTTTT
1 ATTATTTTA-A-AATTCTTTA-AAATTTTT
176791 TATGATATTC
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
28 5 0.10
29 8 0.15
30 39 0.75
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (30 bp):
ATTATTTTAAAATTCTTTAAAATTTTTAAC
Found at i:189737 original size:21 final size:21
Alignment explanation
Indices: 189711--189761 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
189701 ACAAAACATT
189711 ATGTTTGTAACTCTCATCATA
1 ATGTTTGTAACTCTCATCATA
* * * *
189732 ATGTTTTGTAATTGTCCTCATT
1 ATG-TTTGTAACTCTCATCATA
189754 ATGTTTGT
1 ATGTTTGT
189762 TTTAAATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 8 0.32
22 17 0.68
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.51
Consensus pattern (21 bp):
ATGTTTGTAACTCTCATCATA
Found at i:191308 original size:3 final size:3
Alignment explanation
Indices: 191302--191331 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
191292 TATTAAAATA
191302 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
191332 TTCGGTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:193926 original size:69 final size:69
Alignment explanation
Indices: 193784--193988 Score: 218
Period size: 69 Copynumber: 3.0 Consensus size: 69
193774 TTAATGAAGT
* * * * *
193784 ATAAGGTATAAGATCATAGCTTGGCTATGACAACTAATAGTGTCTGCCAGGATAATAAACACAAG
1 ATAAGGTATAAGATCATAGCTCGGCTATGGCAACTAATAGAGTCTGTCAGGACAATAAACACAAG
*
193849 AATT
66 AATC
* * * * *
193853 ATAAGGAATAAGACCATAGCTCGGCTATGGTAACCAATAGAGTCTGTCAGGACAATAAACA-TAG
1 ATAAGGTATAAGATCATAGCTCGGCTATGGCAACTAATAGAGTCTGTCAGGACAATAAACACAAG
*
193917 TGATC
66 -AATC
* * * *
193922 ATAAGGTGTAAGATCATAGCTCGACTATGGCAACTAGTAGAGT-TCGTC-GAGACAATAAACACG
1 ATAAGGTATAAGATCATAGCTCGGCTATGGCAACTAATAGAGTCT-GTCAG-GACAATAAACACA
193985 AGAA
64 AGAA
193989 AGTCCGTAAA
Statistics
Matches: 111, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
68 4 0.04
69 105 0.95
70 2 0.02
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (69 bp):
ATAAGGTATAAGATCATAGCTCGGCTATGGCAACTAATAGAGTCTGTCAGGACAATAAACACAAG
AATC
Found at i:197285 original size:16 final size:16
Alignment explanation
Indices: 197266--197306 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
197256 GAAAAAAATT
197266 TAATTTA-AATATTTTA
1 TAATTTATAA-ATTTTA
197282 TAATTTATAAATTTTA
1 TAATTTATAAATTTTA
*
197298 -AATTAATAA
1 TAATTTATAA
197307 TGATAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 8 0.35
16 13 0.57
17 2 0.09
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATTTATAAATTTTA
Found at i:197381 original size:81 final size:82
Alignment explanation
Indices: 197251--197405 Score: 183
Period size: 81 Copynumber: 1.9 Consensus size: 82
197241 GATTTCTCTT
* * * * *
197251 AAAATGAAAAAAATTTAATTTAAATATTTTATAATTTATAAATTTTAAATTAAT--AATGATAAA
1 AAAATGAAAAAAATTTAATTTAAATATTTTAAAAATAATAAATTATAAATTAATAAAATAAT-AA
197314 ATTATATTTTGATCCCTC
65 ATTATATTTTGATCCCTC
* * *
197332 AAAAT-AATAAAAATTTGATTTAACT-TTTTAAAAATAATAAATATATAAATTATTAAAATAATA
1 AAAATGAA-AAAAATTTAATTTAAATATTTTAAAAATAATAAAT-TATAAATTAATAAAATAATA
197395 AATTATATTTT
64 AATTATATTTT
197406 TATTATTATA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
80 16 0.26
81 29 0.47
82 12 0.19
83 5 0.08
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.43
Consensus pattern (82 bp):
AAAATGAAAAAAATTTAATTTAAATATTTTAAAAATAATAAATTATAAATTAATAAAATAATAAA
TTATATTTTGATCCCTC
Found at i:198022 original size:64 final size:64
Alignment explanation
Indices: 197949--198077 Score: 258
Period size: 64 Copynumber: 2.0 Consensus size: 64
197939 AATTTATAGC
197949 TTAATATTTGATTCGAATTCGGTCGAATATTTATTTTTAAGTTTGCATTAAAATATAATCGAGT
1 TTAATATTTGATTCGAATTCGGTCGAATATTTATTTTTAAGTTTGCATTAAAATATAATCGAGT
198013 TTAATATTTGATTCGAATTCGGTCGAATATTTATTTTTAAGTTTGCATTAAAATATAATCGAGT
1 TTAATATTTGATTCGAATTCGGTCGAATATTTATTTTTAAGTTTGCATTAAAATATAATCGAGT
198077 T
1 T
198078 ATTCAAAAAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.46
Consensus pattern (64 bp):
TTAATATTTGATTCGAATTCGGTCGAATATTTATTTTTAAGTTTGCATTAAAATATAATCGAGT
Found at i:200344 original size:29 final size:29
Alignment explanation
Indices: 200302--200453 Score: 164
Period size: 30 Copynumber: 5.1 Consensus size: 29
200292 GTTTTATTTA
*
200302 AAAATTATATTTTGACCCATAAACTTCCC
1 AAAATTACATTTTGACCCATAAACTTCCC
200331 AAAATTACATTTTGACCCATAAACTTCCC
1 AAAATTACATTTTGACCCATAAACTTCCC
* * *
200360 AAAATTACATTTTAACCTC-TAAAATTTTCC
1 AAAATTACATTTTGACC-CAT-AAACTTCCC
* * *
200390 AAAATTACATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTGACCCATAAAC-TTCCC
* *
200420 AAAATTA-AGTTTTGACCCTTAAAATTCTCC
1 AAAATTACA-TTTTGACCCATAAACTTC-CC
200450 AAAA
1 AAAA
200454 CTTCAATTTC
Statistics
Matches: 108, Mismatches: 9, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
29 52 0.48
30 56 0.52
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (29 bp):
AAAATTACATTTTGACCCATAAACTTCCC
Found at i:200451 original size:60 final size:59
Alignment explanation
Indices: 200302--200453 Score: 184
Period size: 60 Copynumber: 2.6 Consensus size: 59
200292 GTTTTATTTA
* * * *
200302 AAAATTATATTTTGACCCATAAACTTC-CCAAAATTACATTTTGACCCATAAACTTCCC
1 AAAATTACATTTTGACCCTTAAAATTCTCCAAAATTACATTTTAACCCATAAACTTCCC
* * * *
200360 AAAATTACATTTT-AACCTCTAAAATTTTCCAAAATTACATTTTAACCCCTAAACTTTTCC
1 AAAATTACATTTTGACCCT-TAAAATTCTCCAAAATTACATTTTAACCCATAAAC-TTCCC
200420 AAAATTA-AGTTTTGACCCTTAAAATTCTCCAAAA
1 AAAATTACA-TTTTGACCCTTAAAATTCTCCAAAA
200454 CTTCAATTTC
Statistics
Matches: 79, Mismatches: 10, Indels: 8
0.81 0.10 0.08
Matches are distributed among these distances:
57 3 0.04
58 18 0.23
59 25 0.32
60 29 0.37
61 4 0.05
ACGTcount: A:0.39, C:0.23, G:0.03, T:0.35
Consensus pattern (59 bp):
AAAATTACATTTTGACCCTTAAAATTCTCCAAAATTACATTTTAACCCATAAACTTCCC
Found at i:205199 original size:19 final size:18
Alignment explanation
Indices: 205177--205215 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
205167 AAAAAAGAGG
205177 AAAAAGAAAGAAAGAAGAA
1 AAAAAGAAAGAAA-AAGAA
*
205196 AAAAATAAAGAAAAAGAA
1 AAAAAGAAAGAAAAAGAA
205214 AA
1 AA
205216 GGGGTCGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (18 bp):
AAAAAGAAAGAAAAAGAA
Found at i:206162 original size:7 final size:6
Alignment explanation
Indices: 206141--206201 Score: 79
Period size: 6 Copynumber: 9.7 Consensus size: 6
206131 AAAGAGAGGG
206141 AAAAG- AAAAGA AAAAGGAA AAAGAGAA AAAAGA AAAAGA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAA-G-A AAA-AG-A AAAAGA AAAAGA AAAAGA AAAAGA
206192 AAAAGA AAAA
1 AAAAGA AAAA
206202 TGAGAGGTCA
Statistics
Matches: 52, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
5 5 0.10
6 33 0.63
7 3 0.06
8 10 0.19
9 1 0.02
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:206169 original size:15 final size:14
Alignment explanation
Indices: 206146--206201 Score: 66
Period size: 13 Copynumber: 4.2 Consensus size: 14
206136 GAGGGAAAAG
206146 AAAAGAAAAAG-GA
1 AAAAGAAAAAGAGA
*
206159 AAAAGAGAAAAAAGA
1 AAAAGA-AAAAGAGA
206174 AAAAG-AAAA-AGA
1 AAAAGAAAAAGAGA
206186 AAAAGAAAAAGA-A
1 AAAAGAAAAAGAGA
206199 AAA
1 AAA
206202 TGAGAGGTCA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
12 8 0.21
13 18 0.47
14 5 0.13
15 7 0.18
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAAGAGA
Found at i:206173 original size:27 final size:26
Alignment explanation
Indices: 206141--206195 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
206131 AAAGAGAGGG
206141 AAAAG-AAAAGAAAAAGGAAAAAGAGAA
1 AAAAGAAAAAGAAAAA-GAAAAAGA-AA
206168 AAAAGAAAAAGAAAAAGAAAAAGAAA
1 AAAAGAAAAAGAAAAAGAAAAAGAAA
206194 AA
1 AA
206196 GAAAAATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 4 0.15
27 13 0.48
28 10 0.37
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (26 bp):
AAAAGAAAAAGAAAAAGAAAAAGAAA
Found at i:207167 original size:50 final size:49
Alignment explanation
Indices: 207068--207225 Score: 158
Period size: 49 Copynumber: 3.2 Consensus size: 49
207058 GAAGGGAAAG
* * **
207068 ATCTCGTACCCTAGGAATATGAAGGGAAAGATTGAGGTAG-TAACGGCGA
1 ATCTCATACCCTAGGAATGTGAAGGGAAAGATTGAGGCCGCT-ACGGCGA
* *
207117 ATCTCATACCGCTAGGAATGTGAAAGGAAAGATTGAGGCCGCTACAGCGA
1 ATCTCATACC-CTAGGAATGTGAAGGGAAAGATTGAGGCCGCTACGGCGA
** * * *
207167 ATCTTGTACCCTA-AAGATGTGAAGGGAAAGGTTGAGGCCGCAACGGCGA
1 ATCTCATACCCTAGGA-ATGTGAAGGGAAAGATTGAGGCCGCTACGGCGA
* *
207216 ACCTTATACC
1 ATCTCATACC
207226 TTAGAAATAA
Statistics
Matches: 91, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
48 1 0.01
49 49 0.54
50 40 0.44
51 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.28, T:0.20
Consensus pattern (49 bp):
ATCTCATACCCTAGGAATGTGAAGGGAAAGATTGAGGCCGCTACGGCGA
Found at i:207346 original size:97 final size:98
Alignment explanation
Indices: 207133--207355 Score: 270
Period size: 97 Copynumber: 2.3 Consensus size: 98
207123 TACCGCTAGG
* * * * *
207133 AATGTGAAAGGAAAGATTGAGGCCGCTACAGCGAATCTTGTACCCTAAAGATGTGAAGGGAAAGG
1 AATGTGAAAGGAAAGATTGAGGCCACAACAGCGAATCTTGAACCCTAAAGATATGAAGGAAAAGG
* * *
207198 TTGAGGCCGCAACGGCGAACCTTATACCTTAGA
66 TTGAGCCCACAACGGCAAACCTTATACCTTAGA
** ** * * *
207231 AATAAGAAAGCCAA-ATTGAAGTCACAACGGCGAATCTTGAACCCTAAAGATATGAAGGAAAAGG
1 AATGTGAAAGGAAAGATTGAGGCCACAACAGCGAATCTTGAACCCTAAAGATATGAAGGAAAAGG
* *
207295 TTGAGCCCACAATGGTAAACCTTATACCTTAGA
66 TTGAGCCCACAACGGCAAACCTTATACCTTAGA
*
207328 GATGTG-AAGGAAAGATTGAGGCCACAAC
1 AATGTGAAAGGAAAGATTGAGGCCACAAC
207356 TATGAATCTT
Statistics
Matches: 100, Mismatches: 24, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
96 5 0.05
97 85 0.85
98 10 0.10
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.19
Consensus pattern (98 bp):
AATGTGAAAGGAAAGATTGAGGCCACAACAGCGAATCTTGAACCCTAAAGATATGAAGGAAAAGG
TTGAGCCCACAACGGCAAACCTTATACCTTAGA
Found at i:207367 original size:48 final size:48
Alignment explanation
Indices: 207087--207379 Score: 182
Period size: 49 Copynumber: 6.0 Consensus size: 48
207077 CCTAGGAATA
* * * *
207087 TGAAGGGAAAGATTGAGG-TAGTAACGGCGAATCTCATACCGCT-AGGAATG
1 TGAA-GGAAAGATTGAGGCCA-CAACGGCGAATCTTATACC-CTAAAG-ATG
* * * *
207137 TGAAAGGAAAGATTGAGGCCGCTACAGCGAATCTTGTACCCTAAAGATG
1 TG-AAGGAAAGATTGAGGCCACAACGGCGAATCTTATACCCTAAAGATG
* * * * *
207186 TGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTTATACCTTAGAA-ATA
1 TGAA-GGAAAGATTGAGGCCACAACGGCGAATCTTATACCCTA-AAGATG
* ** * * *
207235 AGAAAGCCAA-ATTGAAGTCACAACGGCGAATCTTGA-ACCCTAAAGATA
1 TG-AAGGAAAGATTGAGGCCACAACGGCGAATCTT-ATACCCTAAAGATG
* * * ** * * *
207283 TGAAGGAAAAGGTTGAGCCCACAATGGTAAACCTTATACCTTAGAGATG
1 TGAAGG-AAAGATTGAGGCCACAACGGCGAATCTTATACCCTAAAGATG
*** *
207332 TGAAGGAAAGATTGAGGCCACAACTATGAATCTTATACCCTGAAGATG
1 TGAAGGAAAGATTGAGGCCACAACGGCGAATCTTATACCCTAAAGATG
207380 AAGCAAATTG
Statistics
Matches: 184, Mismatches: 48, Indels: 24
0.72 0.19 0.09
Matches are distributed among these distances:
47 5 0.03
48 65 0.35
49 77 0.42
50 35 0.19
51 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.20
Consensus pattern (48 bp):
TGAAGGAAAGATTGAGGCCACAACGGCGAATCTTATACCCTAAAGATG
Found at i:225139 original size:3 final size:3
Alignment explanation
Indices: 225131--225174 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
225121 TCCTTAAATA
225131 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
225175 ATGTTGTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:231498 original size:48 final size:48
Alignment explanation
Indices: 231441--231534 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
231431 TTCAAACCCC
* * **
231441 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAAATGATGAAGTGGT
1 CATCTTCTTGATGAGATACAGAAAAGTGGACCAAAACAATGAAGTGGT
231489 CATCTTCTTGATGAGATACAGAAAAGTGGACCAAAACAATGAAGTG
1 CATCTTCTTGATGAGATACAGAAAAGTGGACCAAAACAATGAAGTG
231535 AAGCTCAACG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.38, C:0.13, G:0.24, T:0.24
Consensus pattern (48 bp):
CATCTTCTTGATGAGATACAGAAAAGTGGACCAAAACAATGAAGTGGT
Found at i:231616 original size:124 final size:123
Alignment explanation
Indices: 231391--231722 Score: 466
Period size: 124 Copynumber: 2.7 Consensus size: 123
231381 AATGATATCA
* * * *
231391 TGGACTAAAATAATGAAGTGGAGCTCAACGTGAATGAAACTTCAAACCCCCATCTTCTTGATGAG
1 TGGACCAAAACAATGAAGTGAAGCTCAACGTGAGTGAAACTTC-AACCCCCATCTTCTTGATGAG
* * * *
231456 ATACAGAGAAGTGGATCAAAATGATGAAGTGGTCATCTTCTTGATGAGATACAGAAAAG
65 ATACAGAGAAGTGGATCAAAATGATAAAGCGATCATCTTCTTGACGAGATACAGAAAAG
231515 TGGACCAAAACAATGAAGTGAAGCTCAACGTGAGTGAAACTTCATACCCCCATCTTCTTGATGAG
1 TGGACCAAAACAATGAAGTGAAGCTCAACGTGAGTGAAACTTCA-ACCCCCATCTTCTTGATGAG
231580 ATACAGAGAAGTGGATCAAAATGATAAAGCGATCATCTTCTTGACGAGATACAGAAAAG
65 ATACAGAGAAGTGGATCAAAATGATAAAGCGATCATCTTCTTGACGAGATACAGAAAAG
* * * ** * ** * *
231639 TAGACCAAATCAACGTTGCGAAGCTCAATATGAGTGAAACTTCAAACCCCATCTTCCTGATGAGA
1 TGGACCAAAACAATGAAGTGAAGCTCAACGTGAGTGAAACTTCAACCCCCATCTTCTTGATGAGA
* *
231704 TATAGAGAAGTGGACCAAA
66 TACAGAGAAGTGGATCAAA
231723 TCTGTCTTCT
Statistics
Matches: 187, Mismatches: 20, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
123 37 0.20
124 150 0.80
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (123 bp):
TGGACCAAAACAATGAAGTGAAGCTCAACGTGAGTGAAACTTCAACCCCCATCTTCTTGATGAGA
TACAGAGAAGTGGATCAAAATGATAAAGCGATCATCTTCTTGACGAGATACAGAAAAG
Found at i:231837 original size:85 final size:85
Alignment explanation
Indices: 231688--231873 Score: 250
Period size: 85 Copynumber: 2.2 Consensus size: 85
231678 CTTCAAACCC
* * * * *
231688 CATCTTCCTGATGAGATATAGAGAAGTGGACCAAATCTGTCTTCTTAATGAGATACAGATAAGTG
1 CATCTTCCTAATGAGAAATAGAGAAGTGGACCAAATCTGTCTTCCTAATAAGATACAGAGAAGTG
**
231753 GATCAAAGTAA-GAAAGTGGT
66 GATCAAAACAATG-AAGTGGT
* *
231773 CATCTTCCTAATGAGAAATAGAGAAGTGGATCAAAT-TCGTCTTCCTAATAAGATATAGAGAAGT
1 CATCTTCCTAATGAGAAATAGAGAAGTGGACCAAATCT-GTCTTCCTAATAAGATACAGAGAAGT
231837 GGATCAAAACAATGAAGTGGT
65 GGATCAAAACAATGAAGTGGT
*
231858 CATTTTCCTAATGAGA
1 CATCTTCCTAATGAGA
231874 TACAGATAAG
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
84 1 0.01
85 87 0.98
86 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.27
Consensus pattern (85 bp):
CATCTTCCTAATGAGAAATAGAGAAGTGGACCAAATCTGTCTTCCTAATAAGATACAGAGAAGTG
GATCAAAACAATGAAGTGGT
Found at i:231994 original size:75 final size:77
Alignment explanation
Indices: 231862--232053 Score: 230
Period size: 75 Copynumber: 2.5 Consensus size: 77
231852 AGTGGTCATT
* * * *
231862 TTCCTAATGAGATACAGATAAGTAGACCTAAACAATGAAG-CGAAGCTCAATGCGAGTGAAACGT
1 TTCCTAATGAGATACAGAAAAGTGGACCAAAACAATGAAGTAGAAGCTCAATGCGAGTGAAACGT
231926 C-AAAC-CCTATC
66 CAAAACTCC-ATC
* * * * *
231937 TTCTTGATGAGATACAGAAAAGTGGACCAAAATAATGAAGTAG-AGCTCAATGTGAGTGAAACTT
1 TTCCTAATGAGATACAGAAAAGTGGACCAAAACAATGAAGTAGAAGCTCAATGCGAGTGAAACGT
*
232001 CAAAACTCCATT
66 CAAAACTCCATC
* * *
232013 TTCCTAATGAGATACAGAGAAGTGGATCAAAACAATAAAGT
1 TTCCTAATGAGATACAGAAAAGTGGACCAAAACAATGAAGT
232054 GGTCATCTTC
Statistics
Matches: 98, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
75 54 0.55
76 42 0.43
77 2 0.02
ACGTcount: A:0.42, C:0.17, G:0.19, T:0.22
Consensus pattern (77 bp):
TTCCTAATGAGATACAGAAAAGTGGACCAAAACAATGAAGTAGAAGCTCAATGCGAGTGAAACGT
CAAAACTCCATC
Found at i:232076 original size:199 final size:200
Alignment explanation
Indices: 231814--232179 Score: 536
Period size: 199 Copynumber: 1.8 Consensus size: 200
231804 CAAATTCGTC
* * * *
231814 TTCCTAATAAGATATAGAGAAGTGGATCAAAACAATGAAGTGGTCATTTTCCTAATGAGATACAG
1 TTCCTAATAAGATACAGAGAAGTGGATCAAAACAATAAAGTGGTCATCTTCCTAATAAGATACAG
* * * * * *
231879 ATAAGTAGACCTAAACAATGAAGCGAAGCTCAATGCGAGTGAAACGTCA-AACCCTATCTTCTTG
66 AGAAGTAGACCAAAACAATGAAGCAAAGCTCAACGCGAGTGAAACGTCACAACCCCATCTTCCTG
* *
231943 ATGAGATACAGAAAAGTGGACCAAAATAATGAAGTAGAGCTCAATGTGAGTGAAACTTCAAAACT
131 ATGAAATACAGAAAAGTAGACCAAAATAATGAAGTAGAGCTCAATGTGAGTGAAACTTCAAAACT
232008 CCATT
196 CCATT
* *
232013 TTCCTAATGAGATACAGAGAAGTGGATCAAAACAATAAAGTGGTCATCTTCCTATTAAGATACAG
1 TTCCTAATAAGATACAGAGAAGTGGATCAAAACAATAAAGTGGTCATCTTCCTAATAAGATACAG
* * * *
232078 AGAAGTAGACCAAAACATTGAAGCAAAGCTCAACGTGAGTGAAACTTCACACCCCCATCTTCCTG
66 AGAAGTAGACCAAAACAATGAAGCAAAGCTCAACGCGAGTGAAACGTCACAACCCCATCTTCCTG
* * *
232143 ATGAAATACAGAGAAGTAGATCAAAATGATGAAGTAG
131 ATGAAATACAGAAAAGTAGACCAAAATAATGAAGTAG
232180 TCATCTTCCT
Statistics
Matches: 145, Mismatches: 21, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
199 101 0.70
200 44 0.30
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (200 bp):
TTCCTAATAAGATACAGAGAAGTGGATCAAAACAATAAAGTGGTCATCTTCCTAATAAGATACAG
AGAAGTAGACCAAAACAATGAAGCAAAGCTCAACGCGAGTGAAACGTCACAACCCCATCTTCCTG
ATGAAATACAGAAAAGTAGACCAAAATAATGAAGTAGAGCTCAATGTGAGTGAAACTTCAAAACT
CCATT
Found at i:232154 original size:124 final size:123
Alignment explanation
Indices: 231934--232338 Score: 508
Period size: 124 Copynumber: 3.3 Consensus size: 123
231924 GTCAAACCCT
* * * * * *
231934 ATCTTCTTGATGAGATACAGAAAAGTGGACCAAAATAATGAAGTAGAGCTCAATGTGAGTGAAAC
1 ATCTTCCTGATTAGATACAGAGAAGTAGACCAAAACAATGAAGCAGAGCTCAATGTGAGTGAAAC
* * * *
231999 TTCAAAACTCCATTTTCCTAATGAGATACAGAGAAGTGGATCAAAACAATAAAGTGGTC
66 TTC-AAACCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGTAGTC
* * *
232058 ATCTTCCT-ATTAAGATACAGAGAAGTAGACCAAAACATTGAAGCAAAGCTCAACGTGAGTGAAA
1 ATCTTCCTGATT-AGATACAGAGAAGTAGACCAAAACAATGAAGCAGAGCTCAATGTGAGTGAAA
* * * ** *
232122 CTTCACACCCCCATCTTCCTGATGAAATACAGAGAAGTAGATCAAAATGATGAAGTAGTC
65 CTTCA-AACCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGTAGTC
* * * * *
232182 ATCTTCCTGATGAGATATAAAGAAGTAGACCAAATCAATGAAGC-GAGACTCAATATGAGTGAAA
1 ATCTTCCTGATTAGATACAGAGAAGTAGACCAAAACAATGAAGCAGAG-CTCAATGTGAGTGAAA
* * * *
232246 CTTCAAGCCCCATCTTCCTGATGAGATACAGAGAAGTGGCTCAAAGCAATAAAGCAGTC
65 CTTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGTAGTC
232305 ATCTTCCTGATTAGATACAGAGAAGTAGACCAAA
1 ATCTTCCTGATTAGATACAGAGAAGTAGACCAAA
232339 TTCGTCTTCC
Statistics
Matches: 238, Mismatches: 39, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
123 81 0.34
124 155 0.65
125 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (123 bp):
ATCTTCCTGATTAGATACAGAGAAGTAGACCAAAACAATGAAGCAGAGCTCAATGTGAGTGAAAC
TTCAAACCCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATAAAGTAGTC
Found at i:232223 original size:48 final size:48
Alignment explanation
Indices: 232133--232224 Score: 123
Period size: 48 Copynumber: 1.9 Consensus size: 48
232123 TTCACACCCC
* *
232133 CATCTTCCTGATGAAATACAGAGAAGTAGATCAAAATGATGAAGTAGT
1 CATCTTCCTGATGAAATACAAAGAAGTAGATCAAAATAATGAAGTAGT
* * *
232181 CATCTTCCTGATGAGATATAAAGAAGTAGA-CCAAATCAATGAAG
1 CATCTTCCTGATGAAATACAAAGAAGTAGATCAAAAT-AATGAAG
232225 CGAGACTCAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
47 5 0.13
48 33 0.87
ACGTcount: A:0.42, C:0.14, G:0.20, T:0.24
Consensus pattern (48 bp):
CATCTTCCTGATGAAATACAAAGAAGTAGATCAAAATAATGAAGTAGT
Found at i:232358 original size:37 final size:37
Alignment explanation
Indices: 232306--232452 Score: 123
Period size: 37 Copynumber: 3.7 Consensus size: 37
232296 AAAGCAGTCA
*
232306 TCTTCCTGATTAGATACAGAGAAGTAGACCAAATTCG
1 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATTCG
* * * *
232343 TCTTCCTGATGAGATATAGAGAATTGGATCAGAGCAATAAAGCAGTCA
1 TCTTCCTGATGAGATACAGAGAA---G-T-AGA-C---CAA--ATTCG
* * *
232391 TCTTTCTGATGAGATATAGAGAAGTAGATCAAATTCG
1 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATTCG
232428 TCTTCCTGATGAGATACAGAGAAGT
1 TCTTCCTGATGAGATACAGAGAAGT
232453 GGATCAAAAT
Statistics
Matches: 87, Mismatches: 12, Indels: 22
0.72 0.10 0.18
Matches are distributed among these distances:
37 47 0.54
39 2 0.02
40 1 0.01
41 1 0.01
42 3 0.03
43 4 0.05
44 1 0.01
45 1 0.01
46 2 0.02
48 25 0.29
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (37 bp):
TCTTCCTGATGAGATACAGAGAAGTAGACCAAATTCG
Found at i:232406 original size:85 final size:85
Alignment explanation
Indices: 232258--232509 Score: 380
Period size: 85 Copynumber: 3.0 Consensus size: 85
232248 TCAAGCCCCA
* * *
232258 TCTTCCTGATGAGATACAGAGAAGTGGCTCAAAGCAATAAAGCAGTCATCTTCCTGATTAGATAC
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCAGTCATCTTTCTGATGAGATAC
232323 AGAGAAGTAGACCAAATTCG
66 AGAGAAGTAGACCAAATTCG
* * * *
232343 TCTTCCTGATGAGATATAGAGAATTGGATCAGAGCAATAAAGCAGTCATCTTTCTGATGAGATAT
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCAGTCATCTTTCTGATGAGATAC
*
232408 AGAGAAGTAGATCAAATTCG
66 AGAGAAGTAGACCAAATTCG
** *
232428 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCAGTCATC-TTCTTGATGAGATA
1 TCTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCAGTCATCTTTC-TGATGAGATA
*
232492 CAGAAAAGTAGACCAAAT
65 CAGAGAAGTAGACCAAAT
232510 CAATGAAGCG
Statistics
Matches: 149, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
84 3 0.02
85 146 0.98
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (85 bp):
TCTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCAGTCATCTTTCTGATGAGATAC
AGAGAAGTAGACCAAATTCG
Found at i:232653 original size:123 final size:123
Alignment explanation
Indices: 232419--232878 Score: 600
Period size: 123 Copynumber: 3.7 Consensus size: 123
232409 GAGAAGTAGA
* * *
232419 TCAAATT-CGTCTTCCTGATGAGATACAGAGAAGTGGATCAAAATAATGAAGCAGTCATCTTCTT
1 TCAAATTCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCTT
*
232483 GATGAGATACAGAAAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACT
66 GATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACT
* * *
232541 TCAAATTCCATCTTCCTAATGAGATACAGAGAAGTGGATCAAAACAATGAGGCGGTCATCTTCCT
1 TCAAATTCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCTT
* * *
232606 GATGAGATACAGAGAAGTGGAGCAAAT-AATGAAGCGAAGCTCAAATGTGAGTAAAACT
66 GATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTC-AATGTGAGTGAAACT
** * * * * * *
232664 TCAAACCCCCATCTTCTTGATGATATACAGAAAAATGGATCAAAACAGTGAGGCGGTCATCTTCT
1 TCAAA-TTCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCT
* ** * *
232729 TGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGTTCAATGCAAGAGAAATT
65 TGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACT
* * * ** * *
232788 TCAAATTTCATCTTCCTGATGAGATACAAAGAAGTGGGTCAAAGTAATAAAGCGGTCATCTTCGT
1 TCAAATTCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCTT
* *
232853 GATGAGATAAAAAGAAGTAGACCAAA
66 GATGAGATACAGAGAAGTAGACCAAA
232879 AGATGAAGTT
Statistics
Matches: 290, Mismatches: 44, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
122 22 0.08
123 163 0.56
124 91 0.31
125 14 0.05
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (123 bp):
TCAAATTCCATCTTCCTGATGAGATACAGAGAAGTGGATCAAAACAATGAAGCGGTCATCTTCTT
GATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCAATGTGAGTGAAACT
Found at i:234719 original size:29 final size:29
Alignment explanation
Indices: 234686--234777 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 29
234676 ATTTTATTTA
* * *
234686 AAAATTATATTTGACCCTTGAACTTTTCT
1 AAAATTATATTTGACCCCTAAACTTTTCC
*
234715 AAAATTATATTTTGACCCCTAAATTTTTCC
1 AAAATTATA-TTTGACCCCTAAACTTTTCC
* *
234745 AAAATTAATATTTGACCCC-AAAATTCTCC
1 AAAATT-ATATTTGACCCCTAAACTTTTCC
234774 AAAA
1 AAAA
234778 CTTCAATTTC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
29 21 0.38
30 31 0.56
31 3 0.05
ACGTcount: A:0.38, C:0.20, G:0.04, T:0.38
Consensus pattern (29 bp):
AAAATTATATTTGACCCCTAAACTTTTCC
Found at i:243758 original size:18 final size:18
Alignment explanation
Indices: 243735--243769 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
243725 TTAAAGTAAA
243735 AAATATATAAAAATTAAT
1 AAATATATAAAAATTAAT
* *
243753 AAATATCTCAAAATTAA
1 AAATATATAAAAATTAA
243770 AGCATAAGGG
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:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATATATAAAAATTAAT
Found at i:244253 original size:3 final size:3
Alignment explanation
Indices: 244245--244292 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
244235 TCTAGAAATC
244245 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
244293 AGAAGTAGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:251118 original size:29 final size:28
Alignment explanation
Indices: 251060--251118 Score: 64
Period size: 29 Copynumber: 2.1 Consensus size: 28
251050 AAATATCAAG
* * **
251060 TTTATACATGAACTTTGATTTTATGTAA
1 TTTATACATAAACTTTGATTTAATCCAA
*
251088 TTTATACATAAAATTTTGATTTAATCCAA
1 TTTATACAT-AAACTTTGATTTAATCCAA
251117 TT
1 TT
251119 CCTGTAAATT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (28 bp):
TTTATACATAAACTTTGATTTAATCCAA
Found at i:251356 original size:31 final size:29
Alignment explanation
Indices: 251301--251362 Score: 79
Period size: 31 Copynumber: 2.1 Consensus size: 29
251291 GTTTCACGTG
* *
251301 TATAATTACACCAAATTAAAGTTCATGTA
1 TATAATTACACCAAATCAAAGTTCATATA
*
251330 TATAATTACACATTAAATCAAAGTTCATATA
1 TATAATTACAC--CAAATCAAAGTTCATATA
251361 TA
1 TA
251363 CTTTTGAGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 11 0.39
31 17 0.61
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (29 bp):
TATAATTACACCAAATCAAAGTTCATATA
Found at i:251360 original size:29 final size:28
Alignment explanation
Indices: 251301--251362 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 28
251291 GTTTCACGTG
*
251301 TATAATTACACCAAATTAAAGTTCATGTA
1 TATAATTACACCAAATCAAAGTTCA-GTA
*
251330 TATAATTACACATTAAATCAAAGTTCA-TA
1 TATAATTACAC--CAAATCAAAGTTCAGTA
251359 TATA
1 TATA
251363 CTTTTGAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 17 0.59
31 12 0.41
ACGTcount: A:0.47, C:0.13, G:0.05, T:0.35
Consensus pattern (28 bp):
TATAATTACACCAAATCAAAGTTCAGTA
Found at i:251680 original size:17 final size:16
Alignment explanation
Indices: 251657--251726 Score: 67
Period size: 16 Copynumber: 4.6 Consensus size: 16
251647 TATTAAAATT
251657 ATTTTTTAAAATATAA
1 ATTTTTTAAAATATAA
*
251673 ATTTTTTTAAAT-T--
1 ATTTTTTAAAATATAA
251686 ATTTTTTAAAATATAA
1 ATTTTTTAAAATATAA
* * *
251702 AATTATTAAAAT-TAT
1 ATTTTTTAAAATATAA
*
251717 TTTTTTTAAA
1 ATTTTTTAAA
251727 TAATAAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
15 10 0.23
16 21 0.49
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTTTTAAAATATAA
Found at i:251725 original size:31 final size:29
Alignment explanation
Indices: 251641--251742 Score: 150
Period size: 29 Copynumber: 3.4 Consensus size: 29
251631 CACTTAATTT
251641 TAAAATTATTAAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
* * *
251670 TAAATTTTTTTAAATTATTTTTTAAAATA
1 TAAAATTATTAAAATTATTTTTTAAAATA
*
251699 TAAAATTATTAAAATTATTTTTTTTAAATAA
1 TAAAATTATTAAAATTA-TTTTTTAAAAT-A
251730 TAAAATTATTAAA
1 TAAAATTATTAAA
251743 TAATTTTAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
29 40 0.62
30 10 0.16
31 14 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TAAAATTATTAAAATTATTTTTTAAAATA
Found at i:251749 original size:30 final size:30
Alignment explanation
Indices: 251641--251749 Score: 102
Period size: 30 Copynumber: 3.7 Consensus size: 30
251631 CACTTAATTT
251641 TAAAATTATT-AA-AATTATTTTTTAAA-ATA
1 TAAAATTATTAAATAATT-TTTTTTAAATA-A
* * * *
251670 TAAATTTTTTTAAATTA-TTTTTTAAAAT-A
1 TAAA-ATTATTAAATAATTTTTTTTAAATAA
*
251699 TAAAATTATTAAAATTATTTTTTTTAAATAA
1 TAAAATTATT-AAATAATTTTTTTTAAATAA
251730 TAAAATTATTAAATAATTTT
1 TAAAATTATTAAATAATTTT
251750 AATTTCCAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
28 4 0.06
29 15 0.23
30 31 0.48
31 14 0.22
32 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TAAAATTATTAAATAATTTTTTTTAAATAA
Found at i:252824 original size:29 final size:30
Alignment explanation
Indices: 252776--252848 Score: 112
Period size: 29 Copynumber: 2.5 Consensus size: 30
252766 AATTAAAATC
252776 ATTTAATAATTTTATTATTTCAAAAAAAAA
1 ATTTAATAATTTTATTATTTCAAAAAAAAA
* *
252806 ATTTAATAATTTTA-TATTTTAAAAAATAA
1 ATTTAATAATTTTATTATTTCAAAAAAAAA
*
252835 TTTTAATAATTTTA
1 ATTTAATAATTTTA
252849 AAATTTTTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 26 0.65
30 14 0.35
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTAATAATTTTATTATTTCAAAAAAAAA
Found at i:252835 original size:20 final size:22
Alignment explanation
Indices: 252810--252851 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
252800 AAAAAAATTT
252810 AATAATTTT-AT-ATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
252830 AATAATTTTAATAATTTTAAAA
1 AATAATTTTAATAATTTTAAAA
252852 TTTTTTGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 9 0.45
21 2 0.10
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AATAATTTTAATAATTTTAAAA
Done.