Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold407
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: 362590
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.30
Warning! 33360 characters in sequence are not A, C, G, or T
Found at i:2097 original size:15 final size:15
Alignment explanation
Indices: 2077--2112 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
2067 ATCTAAGGCC
2077 TTGTTTATAGTTTAA
1 TTGTTTATAGTTTAA
2092 TTGTTTATAGTTTAA
1 TTGTTTATAGTTTAA
*
2107 TAGTTT
1 TTGTTT
2113 GGAGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.14, T:0.61
Consensus pattern (15 bp):
TTGTTTATAGTTTAA
Found at i:9026 original size:3 final size:3
Alignment explanation
Indices: 9018--9057 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
9008 TCTTTTAATC
9018 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
9058 CATCATCATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:9214 original size:37 final size:37
Alignment explanation
Indices: 9169--9275 Score: 151
Period size: 37 Copynumber: 2.9 Consensus size: 37
9159 ATTTTTATAC
9169 TTTGTAATTTATATATACATATATACATACATACATT
1 TTTGTAATTTATATATACATATATACATACATACATT
* *
9206 TTTGTAATTTATACATATATATATACATACATACATT
1 TTTGTAATTTATATATACATATATACATACATACATT
* * * * *
9243 TTTATAATCTATATATACGTAGATACGTACATA
1 TTTGTAATTTATATATACATATATACATACATA
9276 TTTTTATAGC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.40, C:0.11, G:0.05, T:0.44
Consensus pattern (37 bp):
TTTGTAATTTATATATACATATATACATACATACATT
Found at i:9257 original size:33 final size:34
Alignment explanation
Indices: 9180--9293 Score: 106
Period size: 37 Copynumber: 3.2 Consensus size: 34
9170 TTGTAATTTA
* *
9180 TATATACATATATACATACATACATTTTTGTAATT
1 TATATATATATATACATACATACATTTTTATAA-T
9215 TATACATATATATATACATACATACATTTTTATAAT
1 TAT--ATATATATATACATACATACATTTTTATAAT
* * *
9251 CTATATATACGTAGATACGTACAT--ATTTTTATAGCT
1 -TATATATA--TATATACATACATACATTTTTATA-AT
9287 TATATAT
1 TATATAT
9294 GCATCCTTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
35 24 0.35
36 2 0.03
37 42 0.62
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.45
Consensus pattern (34 bp):
TATATATATATATACATACATACATTTTTATAAT
Found at i:11105 original size:16 final size:15
Alignment explanation
Indices: 11084--11114 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
11074 GTTTTCGCTG
11084 CATGGCATTTCGATTA
1 CATGGCATTTC-ATTA
11100 CATGGCATTTCATTA
1 CATGGCATTTCATTA
11115 TAAAATGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.26, C:0.19, G:0.16, T:0.39
Consensus pattern (15 bp):
CATGGCATTTCATTA
Found at i:21834 original size:42 final size:44
Alignment explanation
Indices: 21787--21890 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 44
21777 ATTGTATCTT
* *
21787 CCTGAAGATGCAGTGGAGCA-GAT-CGACTACGAA-TCCTATTTC
1 CCTGAAGATGCAGTGGAGCAGGATGAGAATAC-AAGTCCTATTTC
* * *
21829 CCTGAAGTTGCAGTGGAGCAGGTTGAGAATACAAGTCTTATTTC
1 CCTGAAGATGCAGTGGAGCAGGATGAGAATACAAGTCCTATTTC
*
21873 CCTAAAGATGCAGTGGAG
1 CCTGAAGATGCAGTGGAG
21891 TAGACCGAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
42 19 0.37
43 4 0.08
44 29 0.56
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (44 bp):
CCTGAAGATGCAGTGGAGCAGGATGAGAATACAAGTCCTATTTC
Found at i:23704 original size:3 final size:3
Alignment explanation
Indices: 23696--23787 Score: 148
Period size: 3 Copynumber: 30.7 Consensus size: 3
23686 TCTTTTAATC
23696 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
23744 TTA TTA TTA TTA TTA TTA TTA TTA TCA TCA TCA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23788 TAACTCATTT
Statistics
Matches: 85, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 85 1.00
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:23922 original size:37 final size:37
Alignment explanation
Indices: 23877--23968 Score: 121
Period size: 37 Copynumber: 2.5 Consensus size: 37
23867 ATTTTTATAC
23877 TTTGTAATTTATATATACACATATACATACATACATT
1 TTTGTAATTTATATATACACATATACATACATACATT
* ** * *
23914 TTTGTAATTTATACATTTATATATATATACATACATT
1 TTTGTAATTTATATATACACATATACATACATACATT
* *
23951 TTTATAATATATATATAC
1 TTTGTAATTTATATATAC
23969 GTAGATACGT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (37 bp):
TTTGTAATTTATATATACACATATACATACATACATT
Found at i:25202 original size:95 final size:95
Alignment explanation
Indices: 25039--25218 Score: 360
Period size: 95 Copynumber: 1.9 Consensus size: 95
25029 AATTTTGTAA
25039 ACCAAAAGCATTGTTTTAATAAACCTAAACCGTTTATTAAAAACAACCATTTTACGAGGTGACCC
1 ACCAAAAGCATTGTTTTAATAAACCTAAACCGTTTATTAAAAACAACCATTTTACGAGGTGACCC
25104 GATCACACCTCATAAAAAAATTCTGAATTT
66 GATCACACCTCATAAAAAAATTCTGAATTT
25134 ACCAAAAGCATTGTTTTAATAAACCTAAACCGTTTATTAAAAACAACCATTTTACGAGGTGACCC
1 ACCAAAAGCATTGTTTTAATAAACCTAAACCGTTTATTAAAAACAACCATTTTACGAGGTGACCC
25199 GATCACACCTCATAAAAAAA
66 GATCACACCTCATAAAAAAA
25219 GATTGGTGGC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 85 1.00
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.27
Consensus pattern (95 bp):
ACCAAAAGCATTGTTTTAATAAACCTAAACCGTTTATTAAAAACAACCATTTTACGAGGTGACCC
GATCACACCTCATAAAAAAATTCTGAATTT
Found at i:33680 original size:44 final size:45
Alignment explanation
Indices: 33615--33705 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
33605 ACCTCTATTC
* * *
33615 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
33659 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
33704 CA
1 CA
33706 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:33707 original size:16 final size:16
Alignment explanation
Indices: 33686--33737 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
33676 GATTAGCTAT
33686 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
33702 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
33718 TACACCTCAAATCCAA
1 TACACCTCTAATCCAA
33734 TACA
1 TACA
33738 GCGAACCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:38475 original size:13 final size:13
Alignment explanation
Indices: 38457--38485 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
38447 AATTGTTATT
38457 AATGAATTATTAA
1 AATGAATTATTAA
38470 AATGAATTATTAA
1 AATGAATTATTAA
38483 AAT
1 AAT
38486 ATAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (13 bp):
AATGAATTATTAA
Found at i:50416 original size:49 final size:49
Alignment explanation
Indices: 50354--50449 Score: 156
Period size: 49 Copynumber: 2.0 Consensus size: 49
50344 GACATTCAAG
* *
50354 AATGGATAAATAGTGATAAGATTGTAGACAGTGGAAGACTAAGTTTAAC
1 AATGGATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAAC
* *
50403 AATGTATAAATAGTGATAAGAGTGTAGATAGTGGAAGACCAAGTTTA
1 AATGGATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTA
50450 GAAATGCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 43 1.00
ACGTcount: A:0.43, C:0.05, G:0.25, T:0.27
Consensus pattern (49 bp):
AATGGATAAATAGTGATAAGAGTGTAGACAGTGGAAGACCAAGTTTAAC
Found at i:60053 original size:22 final size:22
Alignment explanation
Indices: 60013--60069 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
60003 GGGTTAGGAA
* **
60013 TTTGCATCTGTATTTGATCTAT
1 TTTGCATCTATATCCGATCTAT
*
60035 TTTGCATCTATATCCGATCTGT
1 TTTGCATCTATATCCGATCTAT
* *
60057 TCTGCAACTATAT
1 TTTGCATCTATAT
60070 TGGATATCCT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.47
Consensus pattern (22 bp):
TTTGCATCTATATCCGATCTAT
Found at i:63857 original size:3 final size:3
Alignment explanation
Indices: 63849--63888 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
63839 TAAATTTTAA
*
63849 AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
63889 TGCATATGGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:66151 original size:18 final size:18
Alignment explanation
Indices: 66128--66170 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
66118 TGTCAGGTGC
*
66128 GTATCCTAGCCCTTATAT
1 GTATCCTAACCCTTATAT
66146 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
66164 GTTTCCT
1 GTATCCT
66171 TTTCCAGTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.09, T:0.42
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:66657 original size:62 final size:60
Alignment explanation
Indices: 66541--66657 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 60
66531 TTGTACAAAC
* ****
66541 TATTTTTATATTGTTTCATTTAATAAAATAAAAGTTGTTTTGAATATTTTAATAGTATAT
1 TATTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAGTATAT
*
66601 TATTTTTATATT-TTGTCCTATTTAATAAAATAGAAGTTCTTTTGAATAAGGCAATAG
1 TATTTTTATATTGTT-T-C-ATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAG
66658 AAATAATGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.04
60 13 0.27
61 1 0.02
62 32 0.67
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.50
Consensus pattern (60 bp):
TATTTTTATATTGTTTCATTTAATAAAATAAAAGTTCTTTTGAATAAGGCAATAGTATAT
Found at i:70084 original size:126 final size:125
Alignment explanation
Indices: 69710--70094 Score: 567
Period size: 126 Copynumber: 3.1 Consensus size: 125
69700 AGAACTACTA
*
69710 TAGAAAAAGAGCGTCCACGTAGGAGCTCTTTTCAGTAATTTTGCTAATAGTGCATCCTGCTTGAA
1 TAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTAATAGTGCATCCTGCTTGAA
* * *
69775 GCGTTTTTTACACTATTTTTTTCAAAATCATCTTCTCAAAATTATTTTTC-AAGAACCATCG
66 GCGTTTTTGACACTA-TTTTTTCAAAATCATCTTCTCAAAATTATTTTTCTAA-AACTATTG
* *
69836 TAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTTAGTAATTTTGCTAATAGTGCATCCTGCTTGAA
1 TAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTAATAGTGCATCCTGCTTGAA
* **
69901 GCGTTTTTGACACTATTTTTTCAAAATCATCTTCTCAAAATTATTTTTTTGGGAACTATTG
66 GCGTTTTTGACACTATTTTTTCAAAATCATCTTCTCAAAATTATTTTTCT-AAAACTATTG
* * * *
69962 TAGAAAAATAACGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTAACAGTGCATTCTGCTTGAA
1 TAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTAATAGTGCATCCTGCTTGAA
* * *
70027 GCGTTTTTGACATTATCTTTTC-AAATCCATCTTCTCAAAATTAATTTTTCTAAAACTACTG
66 GCGTTTTTGACACTATTTTTTCAAAAT-CATCTTCTCAAAATT-ATTTTTCTAAAACTATTG
70088 TAGAAAA
1 TAGAAAA
70095 GAAACAAAAT
Statistics
Matches: 234, Mismatches: 21, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
125 37 0.16
126 190 0.81
127 7 0.03
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (125 bp):
TAGAAAAAGAGCGTCCACGTAGGAGCTTTTTTCAGTAATTTTGCTAATAGTGCATCCTGCTTGAA
GCGTTTTTGACACTATTTTTTCAAAATCATCTTCTCAAAATTATTTTTCTAAAACTATTG
Found at i:71458 original size:13 final size:13
Alignment explanation
Indices: 71442--71476 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
71432 AAAAGACCAT
71442 ACCAAAAAATTTA
1 ACCAAAAAATTTA
71455 ACCAAAAAATTTA
1 ACCAAAAAATTTA
71468 A--AAAAAATT
1 ACCAAAAAATT
71477 ATAATTGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 8 0.36
13 14 0.64
ACGTcount: A:0.66, C:0.11, G:0.00, T:0.23
Consensus pattern (13 bp):
ACCAAAAAATTTA
Found at i:73534 original size:15 final size:15
Alignment explanation
Indices: 73514--73545 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
73504 GCGCTTTTTG
*
73514 AATTGAAATTGAGTT
1 AATTGAAATCGAGTT
73529 AATTGAAATCGAGTT
1 AATTGAAATCGAGTT
73544 AA
1 AA
73546 CTTTAAGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (15 bp):
AATTGAAATCGAGTT
Found at i:76026 original size:12 final size:13
Alignment explanation
Indices: 76009--76067 Score: 59
Period size: 12 Copynumber: 4.5 Consensus size: 13
75999 TGTGCAGAAC
76009 TCATAAAAT-AAA
1 TCATAAAATGAAA
*
76021 TCATAATATGAAA
1 TCATAAAATGAAA
*
76034 TACATAAAAT-AAT
1 T-CATAAAATGAAA
*
76047 TCATAATATGAAA
1 TCATAAAATGAAA
76060 TACATAAA
1 T-CATAAA
76068 TTGTTAGCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
12 15 0.41
13 10 0.27
14 12 0.32
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.29
Consensus pattern (13 bp):
TCATAAAATGAAA
Found at i:76040 original size:26 final size:26
Alignment explanation
Indices: 76010--76067 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
76000 GTGCAGAACT
76010 CATAAAATAAATCATAATATGAAATA
1 CATAAAATAAATCATAATATGAAATA
*
76036 CATAAAATAATTCATAATATGAAATA
1 CATAAAATAAATCATAATATGAAATA
76062 CATAAA
1 CATAAA
76068 TTGTTAGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.60, C:0.09, G:0.03, T:0.28
Consensus pattern (26 bp):
CATAAAATAAATCATAATATGAAATA
Found at i:86597 original size:22 final size:22
Alignment explanation
Indices: 86528--86599 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
86518 AAGGTATATG
* * *
86528 TCTCAAGAAAAATACACAATTT
1 TCTCGAGACAAATACATAATTT
* * *
86550 TCTTGAGACACATACACT-GTTT
1 TCTCGAGACAAATACA-TAATTT
*
86572 TCTCGAGACAAATACATAATTA
1 TCTCGAGACAAATACATAATTT
86594 TCTCGA
1 TCTCGA
86600 CACATGGCTC
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
21 1 0.03
22 37 0.97
ACGTcount: A:0.39, C:0.21, G:0.10, T:0.31
Consensus pattern (22 bp):
TCTCGAGACAAATACATAATTT
Found at i:89511 original size:19 final size:19
Alignment explanation
Indices: 89487--89526 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
89477 AATGTTTCAC
89487 TTTAATTAAAATTAATTAA
1 TTTAATTAAAATTAATTAA
*
89506 TTTAATTAAAATTAGTTAA
1 TTTAATTAAAATTAATTAA
89525 TT
1 TT
89527 AAGCTTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (19 bp):
TTTAATTAAAATTAATTAA
Found at i:90493 original size:90 final size:90
Alignment explanation
Indices: 90334--90529 Score: 243
Period size: 90 Copynumber: 2.2 Consensus size: 90
90324 AAGTGAATAC
* * * * *
90334 ATTGCTCAGACAAGTTGACATTATAATAAGGTTTCTCACACAAGCTGACATTATGATGGAATTGC
1 ATTGCTCACACAAGCTAACATTATAATAAGGTTTCTCACACAAGCTGACATTATAATAGAATTGC
* *
90399 TCACACAAGCTGACATTATGAT-GG
66 TCACACAAGCTGACATTATAATAAG
* * * * *
90423 AATTGCTCATACAAGCTAATATTATAAT-AGTTTTACTCACACAAGTTGACATTATAATAGTATT
1 -ATTGCTCACACAAGCTAACATTATAATAAGGTTT-CTCACACAAGCTGACATTATAATAGAATT
*
90487 GTTCACACAAGCTGACATTATAATAAG
64 GCTCACACAAGCTGACATTATAATAAG
90514 ATTGCTCACACAAGCT
1 ATTGCTCACACAAGCT
90530 GACAATAAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
89 5 0.05
90 85 0.93
91 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (90 bp):
ATTGCTCACACAAGCTAACATTATAATAAGGTTTCTCACACAAGCTGACATTATAATAGAATTGC
TCACACAAGCTGACATTATAATAAG
Found at i:90542 original size:30 final size:30
Alignment explanation
Indices: 90334--90533 Score: 215
Period size: 30 Copynumber: 6.7 Consensus size: 30
90324 AAGTGAATAC
* *
90334 ATTGCTCAGACAAGTTGACATTATAATA-A
1 ATTGCTCACACAAGCTGACATTATAATAGA
* * * *
90363 GGTTTCTCACACAAGCTGACATTATGATGGA
1 -ATTGCTCACACAAGCTGACATTATAATAGA
* *
90394 ATTGCTCACACAAGCTGACATTATGATGGA
1 ATTGCTCACACAAGCTGACATTATAATAGA
* * * *
90424 ATTGCTCATACAAGCTAATATTATAATAGT
1 ATTGCTCACACAAGCTGACATTATAATAGA
* * * *
90454 TTTACTCACACAAGTTGACATTATAATAGT
1 ATTGCTCACACAAGCTGACATTATAATAGA
*
90484 ATTGTTCACACAAGCTGACATTATAATA-A
1 ATTGCTCACACAAGCTGACATTATAATAGA
90513 GATTGCTCACACAAGCTGACA
1 -ATTGCTCACACAAGCTGACA
90534 ATAAAATAAC
Statistics
Matches: 142, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
30 141 0.99
31 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (30 bp):
ATTGCTCACACAAGCTGACATTATAATAGA
Found at i:94853 original size:11 final size:11
Alignment explanation
Indices: 94837--94862 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
94827 AATTAGAGTT
94837 CTTTCTCAGTC
1 CTTTCTCAGTC
94848 CTTTCTCAGTC
1 CTTTCTCAGTC
94859 CTTT
1 CTTT
94863 TACCCCCATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.35, G:0.08, T:0.50
Consensus pattern (11 bp):
CTTTCTCAGTC
Found at i:95604 original size:32 final size:33
Alignment explanation
Indices: 95563--95634 Score: 112
Period size: 32 Copynumber: 2.2 Consensus size: 33
95553 AATTTGTTAG
95563 AATTGATTATGTTTTAAGCTTGTTAGATATT-A
1 AATTGATTATGTTTTAAGCTTGTTAGATATTGA
* *
95595 AATTTATTATGTTTTAAGCTTGTTGGATATTGA
1 AATTGATTATGTTTTAAGCTTGTTAGATATTGA
95628 AA-TGATT
1 AATTGATT
95635 GACAATGACA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 33 0.92
33 3 0.08
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.50
Consensus pattern (33 bp):
AATTGATTATGTTTTAAGCTTGTTAGATATTGA
Found at i:99520 original size:20 final size:20
Alignment explanation
Indices: 99491--99530 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
99481 AAATATTTTC
99491 AGTAAATCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
*
99511 AGTAAGTCATTTTCCAGAAA
1 AGTAAATCATTTTCCAGAAA
99531 TTATTTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (20 bp):
AGTAAATCATTTTCCAGAAA
Found at i:100026 original size:16 final size:14
Alignment explanation
Indices: 99997--100030 Score: 50
Period size: 16 Copynumber: 2.3 Consensus size: 14
99987 ATCAACAAAA
99997 TAAATTTTAAACTT
1 TAAATTTTAAACTT
100011 TAAATTTTTAAAACTT
1 TAAA-TTTT-AAACTT
100027 TAAA
1 TAAA
100031 ATTAACTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 4 0.22
16 10 0.56
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAATTTTAAACTT
Found at i:105861 original size:19 final size:21
Alignment explanation
Indices: 105837--105875 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
105827 CATCAATGTA
105837 ATTTTA-AAAAATAA-AAATT
1 ATTTTACAAAAATAATAAATT
105856 ATTTTACAAAAATAATAAAT
1 ATTTTACAAAAATAATAAAT
105876 ATTATTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
ATTTTACAAAAATAATAAATT
Found at i:105953 original size:16 final size:17
Alignment explanation
Indices: 105932--105964 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
105922 CTTAACCGCT
105932 TTTTAAAA-AAATTACC
1 TTTTAAAAGAAATTACC
105948 TTTTAAAAGAAATTACC
1 TTTTAAAAGAAATTACC
105965 GTTATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (17 bp):
TTTTAAAAGAAATTACC
Found at i:106416 original size:28 final size:28
Alignment explanation
Indices: 106371--106431 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
106361 ACTACCCATA
106371 TTTTTTTCATTTTATTTTCT-TTCTTTC
1 TTTTTTTCATTTTATTTTCTATTCTTTC
*
106398 TTTTTTTCACGTTTT-TTTTCTATTGTTTC
1 TTTTTTTCA--TTTTATTTTCTATTCTTTC
106427 TTTTT
1 TTTTT
106432 CTTTTCTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 9 0.30
28 6 0.20
29 15 0.50
ACGTcount: A:0.07, C:0.13, G:0.03, T:0.77
Consensus pattern (28 bp):
TTTTTTTCATTTTATTTTCTATTCTTTC
Found at i:106676 original size:22 final size:23
Alignment explanation
Indices: 106637--106683 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
106627 AAAGATATAA
* *
106637 ATTTAAATAATAATTTAAAATAT
1 ATTTAAATAATAAATTAAAAAAT
*
106660 ATTT-AATATTAAATTAAAAAAT
1 ATTTAAATAATAAATTAAAAAAT
106682 AT
1 AT
106684 ATTATTAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
ATTTAAATAATAAATTAAAAAAT
Found at i:107138 original size:2 final size:2
Alignment explanation
Indices: 107131--107155 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
107121 TTATAAATTA
107131 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 A
107156 ACAAATAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:115484 original size:19 final size:19
Alignment explanation
Indices: 115460--115496 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
115450 GAAATCTGAT
115460 TGTTTTCATTTGATTTTTC
1 TGTTTTCATTTGATTTTTC
* *
115479 TGTTTTCCTTTTATTTTT
1 TGTTTTCATTTGATTTTT
115497 TATTTATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.11, G:0.08, T:0.73
Consensus pattern (19 bp):
TGTTTTCATTTGATTTTTC
Found at i:116471 original size:26 final size:26
Alignment explanation
Indices: 116416--116486 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
116406 CATTTAAACA
*
116416 GTTTTAT-TATTATTTATTTTAAGAT
1 GTTTTATGTATTATTTATATTAAGAT
*
116441 TTTTTATGTATTATTTATATTAA-AT
1 GTTTTATGTATTATTTATATTAAGAT
*
116466 CGTTTTA-GT-TTATATATATTA
1 -GTTTTATGTATTATTTATATTA
116487 TTTTAAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 11 0.28
25 10 0.25
26 19 0.47
ACGTcount: A:0.30, C:0.01, G:0.07, T:0.62
Consensus pattern (26 bp):
GTTTTATGTATTATTTATATTAAGAT
Found at i:118033 original size:24 final size:23
Alignment explanation
Indices: 117984--118033 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
117974 TCTCATTGCA
* *
117984 TTTCATCTGTTTTGAGTTATAGT
1 TTTCATCTGTTTTGACTTATAAT
118007 TTTCATCATGTTTTGTACTT-TAAT
1 TTTCATC-TGTTTTG-ACTTATAAT
118031 TTT
1 TTT
118034 TTATATATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 7 0.30
24 13 0.57
25 3 0.13
ACGTcount: A:0.18, C:0.10, G:0.12, T:0.60
Consensus pattern (23 bp):
TTTCATCTGTTTTGACTTATAAT
Found at i:124512 original size:3 final size:3
Alignment explanation
Indices: 124498--124583 Score: 104
Period size: 3 Copynumber: 28.7 Consensus size: 3
124488 TATTTTAATG
* **
124498 TTA TTA TCA TTA TTA TT- TTA -TA CCA TTA TTTA TTA TTTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA -TTA TTA TTA
*
124543 TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
124584 TCTATACATA
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
2 4 0.06
3 62 0.86
4 6 0.08
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:124517 original size:51 final size:51
Alignment explanation
Indices: 124475--124570 Score: 126
Period size: 51 Copynumber: 1.9 Consensus size: 51
124465 TAGCTATTTT
*
124475 TTATTTA--ATTAATTATT-TTAATGTTATTATCATTATTATTTTATACCA
1 TTATTTATTATTAATTATTATTAATATTATTATCATTATTATTTTATACCA
* * *
124523 TTATTTATTATTTATTATTATTACTATTATTATTATTATTATTATTAT
1 TTATTTATTATTAATTATTATTAATATTATTATCATTATTATT-TTAT
124571 TATTATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
48 7 0.17
50 9 0.22
51 20 0.50
52 4 0.10
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (51 bp):
TTATTTATTATTAATTATTATTAATATTATTATCATTATTATTTTATACCA
Found at i:124527 original size:36 final size:37
Alignment explanation
Indices: 124486--124555 Score: 90
Period size: 36 Copynumber: 1.9 Consensus size: 37
124476 TATTTAATTA
*
124486 ATTATTT-TAATGTTATTATCATTATTATT-TTATACC
1 ATTATTTATAAT-TTATTATCATTACTATTATTATACC
* *
124522 ATTATTTATTATTTATTATTATTACTATTATTAT
1 ATTATTTATAATTTATTATCATTACTATTATTAT
124556 TATTATTATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 22 0.76
37 7 0.24
ACGTcount: A:0.31, C:0.06, G:0.01, T:0.61
Consensus pattern (37 bp):
ATTATTTATAATTTATTATCATTACTATTATTATACC
Found at i:124950 original size:17 final size:18
Alignment explanation
Indices: 124925--124958 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
124915 ATTTCAAAAT
*
124925 TTATTTATATAT-CATAC
1 TTATATATATATACATAC
124942 TTATATATATATACATA
1 TTATATATATATACATA
124959 TTTTGTAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATATATATATACATAC
Found at i:131178 original size:88 final size:88
Alignment explanation
Indices: 131011--131180 Score: 227
Period size: 88 Copynumber: 1.9 Consensus size: 88
131001 GGTGAAACTT
* * *
131011 CAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGTAGATCTTGTCTTCTTGTATTG
1 CAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCGTGTATTG
* *
131076 GTATCGAAGTAGATCGAATATAC
66 CTATCGAAGCAGATCGAATATAC
* * * *
131099 CAGCCTTGTCTCCCTGAGCAGTAGTTGAGTAGGTTGACAATAGCAGATCTTGCCTTCGTGTACTT
1 CAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCGTGTA-TT
131164 -CTAGT-GAAGCAGATCGA
65 GCTA-TCGAAGCAGATCGA
131181 GGACACCAGT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
88 68 0.96
89 3 0.04
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (88 bp):
CAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCGTGTATTG
CTATCGAAGCAGATCGAATATAC
Found at i:131258 original size:50 final size:50
Alignment explanation
Indices: 131204--131307 Score: 127
Period size: 50 Copynumber: 2.1 Consensus size: 50
131194 ATCGCCTTTA
** * *
131204 CGTTGCAATGGAAAAGATTGAAGCCACAACAGCGAATCTTATTTCCCTGG
1 CGTTGCAACAGAAAAGATTGAAGCCACAACAGCAAATCTTATCTCCCTGG
* ** * *
131254 CGTTGTAACAGAGCAGATTGAAGCCACGACGGCAAATCTTATCTCCCTGG
1 CGTTGCAACAGAAAAGATTGAAGCCACAACAGCAAATCTTATCTCCCTGG
131304 CGTT
1 CGTT
131308 AAGGCTTGAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.24
Consensus pattern (50 bp):
CGTTGCAACAGAAAAGATTGAAGCCACAACAGCAAATCTTATCTCCCTGG
Found at i:131552 original size:44 final size:43
Alignment explanation
Indices: 131504--131746 Score: 140
Period size: 41 Copynumber: 5.7 Consensus size: 43
131494 CCAATAATTC
* *
131504 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATGATGGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAAATGACGGATCT
* * * * ***
131548 TATCTCTCTGAAGGTGCAGTAGAGTAGATCGCAT--CTGG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATAAAATGAC-GGATCT
* ** *
131589 TATCTCCCTGAAGTTGCAGTGGAGCAGACAAAA-GAAACCAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATAAAATG--ACGGATCT
* * ** * *
131633 TATCTCCTTGAGGTTGCAGTGGAGTGGATTAAAAATCACAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-T-AAAATGACGGATCT
* * ** * *
131678 TATCTCTCTGAAGTTGCAGTAGAGCAGACT-GCATCA-AG-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TAAAATGACGGATCT
*
131719 TATCTCCCTAAAGTTGCAGTGGAGCAGA
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA
131747 CTAGAGATAA
Statistics
Matches: 149, Mismatches: 41, Indels: 21
0.71 0.19 0.10
Matches are distributed among these distances:
41 56 0.38
42 4 0.03
43 7 0.05
44 50 0.34
45 28 0.19
46 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATAAAATGACGGATCT
Found at i:131733 original size:130 final size:129
Alignment explanation
Indices: 131503--131747 Score: 366
Period size: 130 Copynumber: 1.9 Consensus size: 129
131493 GCCAATAATT
* **
131503 CTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATGATGGATCTTATCTCTCTGAAGGTGCAGT
1 CTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGGTGCAGT
* ** *
131568 AGAGTAGATCGCATCTGGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAAAAGAAACCAATC
66 AGAGCAGATCGCATCAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACAAAAGAAACCAATC
* * * *
131632 CTATCTCCTTGAGGTTGCAGTGGAGTGGATTAAAAATCACAGATCTTATCTCTCTGAAGTTGCAG
1 CTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAATCACAGATCTTATCTCTCTGAAGGTGCAG
131697 TAGAGCAGA-CTGCATCAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGAC
65 TAGAGCAGATC-GCATCAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGAC
131748 TAGAGATAAC
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
129 29 0.28
130 74 0.72
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (129 bp):
CTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGGTGCAGT
AGAGCAGATCGCATCAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACAAAAGAAACCAATC
Found at i:133573 original size:17 final size:18
Alignment explanation
Indices: 133548--133581 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
133538 ATTTCAAAAT
*
133548 TTATTTATATAT-CATAC
1 TTATATATATATACATAC
133565 TTATATATATATACATA
1 TTATATATATATACATA
133582 TTTTGTAAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATATATATATACATAC
Found at i:139509 original size:18 final size:17
Alignment explanation
Indices: 139488--139521 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
139478 AGTTAATCAT
139488 ATATATAAAAACAAATAC
1 ATATATAAAAA-AAATAC
*
139506 ATATATACAAAAAATA
1 ATATATAAAAAAAATA
139522 AAATAAAAGA
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:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (17 bp):
ATATATAAAAAAAATAC
Found at i:139573 original size:26 final size:27
Alignment explanation
Indices: 139522--139579 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
139512 ACAAAAAATA
*
139522 AAAT-AAAAGAAATTAGTAACAGTAAT
1 AAATAAAAAGAAATAAGTAACAGTAAT
* **
139548 ACATAAAAAGAAATAAGTATGA-TAAT
1 AAATAAAAAGAAATAAGTAACAGTAAT
139574 AAATAA
1 AAATAA
139580 TAATAATATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.64, C:0.03, G:0.10, T:0.22
Consensus pattern (27 bp):
AAATAAAAAGAAATAAGTAACAGTAAT
Found at i:149654 original size:18 final size:19
Alignment explanation
Indices: 149618--149655 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
149608 GTGGATTTTA
149618 ATGCATATGATGCAATGTG
1 ATGCATATGATGCAATGTG
149637 ATGCA-ATGCATG-AATGTG
1 ATGCATATG-ATGCAATGTG
149655 A
1 A
149656 AAAGGCGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (19 bp):
ATGCATATGATGCAATGTG
Found at i:153438 original size:18 final size:17
Alignment explanation
Indices: 153417--153450 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
153407 AGTTAATCAT
153417 ATATATAAAAACAAATAC
1 ATATATAAAAA-AAATAC
*
153435 ATATATACAAAAAATA
1 ATATATAAAAAAAATA
153451 AAATAAAAGA
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:0.68, C:0.09, G:0.00, T:0.24
Consensus pattern (17 bp):
ATATATAAAAAAAATAC
Found at i:157176 original size:45 final size:46
Alignment explanation
Indices: 157127--157631 Score: 473
Period size: 45 Copynumber: 11.3 Consensus size: 46
157117 ATTGTAGCAG
* * * *
157127 AGTAGACT-AAAAATAGCAGATCTTATCTTTCTATATTGGCAGCGA
1 AGTAGACTCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *
157172 AGTAGA-TCGAAGATAGTA-AGTCTTGTCTTCCTGTATTGACAGCGA
1 AGTAGACTCAAAGATAGCAGA-TCTTGTCTTCCTGTATTGGCAGCGA
* * *
157217 AATAGACT-AAAGATAGCAGATCTTATCTTCCTGTATTGGCAGCAA
1 AGTAGACTCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *
157262 AGTA-AGTCAAAGATAGCAGATCTTATCTTCCTATATTGGCAGCGA
1 AGTAGACTCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * * **
157307 AGTAGA-TCGAAGATAACAGGTCTTGTCTTCCTGTATTGATAGCGA
1 AGTAGACTCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *
157352 AGTAGACT-GAAGATAACAGATCTTGTCTTCCTGTATTGGTAGCGA
1 AGTAGACTCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *
157397 AGTAG-GTCAAAGATAGTAGATCTTGTCTTCTTGTATTGGCAGCGA
1 AGTAGACTCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * *
157442 AGTAG-GTCGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCGA
1 AGTAGACTCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * * **** * *
157487 AGTAGA-TTAAAAATAGCAGATCTTGTCTCCCTG-AGCAACAGTGG
1 AGTAGACTCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * * *
157531 AGTAG-GTCGAAGATTA-TAGATCTTGTCTTCTTGTATTGGCAGCGA
1 AGTAGACTCAAAGA-TAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
* * * * *
157576 AGTAGA-TCGAAGATAGCAAATCTTGTCTTCTTGTACTGGCAGTGA
1 AGTAGACTCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
*
157621 AGCAGA-TCAAA
1 AGTAGACTCAAA
157632 AGCTGGTCCT
Statistics
Matches: 381, Mismatches: 65, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
44 35 0.09
45 342 0.90
46 4 0.01
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (46 bp):
AGTAGACTCAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGA
Found at i:157344 original size:135 final size:135
Alignment explanation
Indices: 157139--157610 Score: 588
Period size: 135 Copynumber: 3.5 Consensus size: 135
157129 TAGACTAAAA
* * *
157139 ATAGCAGATCTTATCTTTCTATATTGGCAGCGAAGTAGATCGAAGATAGTAAGTCTTGTCTTCCT
1 ATAGCAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTGTCTTCCT
* * * *
157204 GTATTGACAGCGAAATAGACTAAAGATAGCAGATCTTATCTTCCTGTATTGGCAGCAAAGTAAGT
66 GTATTGACAGCGAAGTAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGGT
157269 CAAAG
131 CAAAG
* **
157274 ATAGCAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAACAGGTCTTGTCTTCCT
1 ATAGCAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTGTCTTCCT
* * * *
157339 GTATTGATAGCGAAGTAGACTGAAGATAACAGATCTTGTCTTCCTGTATTGGTAGCGAAGTAGGT
66 GTATTGACAGCGAAGTAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGGT
157404 CAAAG
131 CAAAG
* * * * * *
157409 ATAGTAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGGTCGAAGATAGCAGATCTTGTCTTCCT
1 ATAGCAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTGTCTTCCT
* * * * * **** * *
157474 ATATTGGCAGCGAAGTAGATTAAAAATAGCAGATCTTGTCTCCCTG-AGCAACAGTGGAGTAGGT
66 GTATTGACAGCGAAGTAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGGT
*
157538 CGAAG
131 CAAAG
* * * * *
157543 ATTA-TAGATCTTGTCTTCTTGTATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTGTCTTCT
1 A-TAGCAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTGTCTTCC
157607 TGTA
65 TGTA
157611 CTGGCAGTGA
Statistics
Matches: 297, Mismatches: 39, Indels: 3
0.88 0.12 0.01
Matches are distributed among these distances:
134 76 0.26
135 221 0.74
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (135 bp):
ATAGCAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAAGATAGCAAATCTTGTCTTCCT
GTATTGACAGCGAAGTAGACTAAAGATAGCAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGGT
CAAAG
Found at i:157883 original size:86 final size:86
Alignment explanation
Indices: 157619--157887 Score: 213
Period size: 86 Copynumber: 3.1 Consensus size: 86
157609 TACTGGCAGT
* * ***
157619 GAAGCAGATCAAAAGCTGGTCCTGTCTCCCTAAGAAGTAGTGGAGCAGATCGAAGACGGTGAATC
1 GAAGCAGATCAAAAGCTGGTCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAAACGACAAATC
*
157684 TTATGTTCCCAAGGTAGTAGG
66 TTATCTTCCCAAGGTAGTAGG
** * * * * * * * ** *
157705 GAAGCAGAT-TTAAGCCACTAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAG
1 GAAGCAGATCAAAAG---CTGGTCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAA-AACG-AC
* ** * * *
157769 ATAT-TT-TCTTCCTGTA-CTGGTAGT
61 AAATCTTATCTTCC-CAAGGTAGTAGG
* * *
157793 GAAGCAGATCGAAAGCTGGTCTTGTTTCCCTAAGCAGTAGTGGAGCAGATCGAAAACGACAAATC
1 GAAGCAGATCAAAAGCTGGTCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAAACGACAAATC
157858 TTATCTTCCCAAGGTAGTAGG
66 TTATCTTCCCAAGGTAGTAGG
157879 GAAGCAGAT
1 GAAGCAGAT
157888 TTAAGCCACC
Statistics
Matches: 130, Mismatches: 43, Indels: 20
0.67 0.22 0.10
Matches are distributed among these distances:
84 4 0.03
85 8 0.06
86 59 0.45
88 50 0.38
89 7 0.05
90 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (86 bp):
GAAGCAGATCAAAAGCTGGTCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAAACGACAAATC
TTATCTTCCCAAGGTAGTAGG
Found at i:157946 original size:44 final size:44
Alignment explanation
Indices: 157898--158015 Score: 150
Period size: 44 Copynumber: 2.7 Consensus size: 44
157888 TTAAGCCACC
* * *
157898 AGTCTGATCCCCCTGAAGTTGCAGTGGGGCAGATTGAGGATAC-A
1 AGTCT-ATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTA
*
157942 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACTA
1 AGTC-TATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTA
*
157987 A-TCCTATCTCCTTGAAGTTGCAGTGGAGC
1 AGT-CTATCTCCCTGAAGTTGCAGTGGAGC
158016 GAATTAAAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
44 62 0.94
45 4 0.06
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (44 bp):
AGTCTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACTA
Found at i:157975 original size:174 final size:174
Alignment explanation
Indices: 157610--157975 Score: 448
Period size: 174 Copynumber: 2.1 Consensus size: 174
157600 GTCTTCTTGT
*
157610 ACTGGCAGTGAAGCAGATCAAAAGCTGGTCCTGTCTCCCTAAGAAGTAGTGGAGCAGATCGAAGA
1 ACTGGCAGTGAAGCAGATCAAAAGCTGGTCCTGTCTCCCTAAGAAGTAGTGGAGCAGATCGAAAA
*** * * *
157675 CGGTGAATCTTATGTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACTAGTCCTATCTCCCTGA
66 CGACAAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCCCCCTGA
* * *** * * *
157740 GCAGCAGTGGAGTAGGTTGAAGATTGTAGATATTTTCTTCCTGT
131 GCAGCAGTGGAGCAGATTGAAGATACAAGATATTATCTCCCTGA
* * * * *
157784 ACTGGTAGTGAAGCAGATCGAAAGCTGGTCTTGTTTCCCTAAGCAGTAGTGGAGCAGATCGAAAA
1 ACTGGCAGTGAAGCAGATCAAAAGCTGGTCCTGTCTCCCTAAGAAGTAGTGGAGCAGATCGAAAA
157849 CGACAAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGT-CTGATCCCCCTG
66 CGACAAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCT-ATCCCCCTG
** * * *
157913 AAGTTGCAGTGGGGCAGATTGAGGATACAAG-TCTTATCTCCCTGA
130 -AGCAGCAGTGGAGCAGATTGAAGATACAAGATATTATCTCCCTGA
* * *
157958 AGTTGCAGTGGAGCAGAT
1 ACTGGCAGTGAAGCAGAT
157976 TGAAGCTACT
Statistics
Matches: 161, Mismatches: 29, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
173 2 0.01
174 138 0.86
175 21 0.13
ACGTcount: A:0.28, C:0.20, G:0.27, T:0.25
Consensus pattern (174 bp):
ACTGGCAGTGAAGCAGATCAAAAGCTGGTCCTGTCTCCCTAAGAAGTAGTGGAGCAGATCGAAAA
CGACAAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCCCCCTGA
GCAGCAGTGGAGCAGATTGAAGATACAAGATATTATCTCCCTGA
Found at i:159801 original size:26 final size:25
Alignment explanation
Indices: 159746--159816 Score: 74
Period size: 26 Copynumber: 2.8 Consensus size: 25
159736 CATTTAAACA
* *
159746 GTTTTATTATTATTTATTTTAAGAT
1 GTTTTAGTATTATTTATATTAAGAT
*
159771 TTTTTACGTATTATTTATATTAA-AT
1 GTTTTA-GTATTATTTATATTAAGAT
*
159796 CGTTTTAGT-TTATATATATTA
1 -GTTTTAGTATTATTTATATTA
159817 TTTTAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
24 11 0.28
25 9 0.23
26 19 0.49
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.61
Consensus pattern (25 bp):
GTTTTAGTATTATTTATATTAAGAT
Found at i:163115 original size:25 final size:25
Alignment explanation
Indices: 163081--163133 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 25
163071 ATTTAATTAG
*
163081 AAAAAAATA-TATTTTA-AAATTATA
1 AAAAAAATATTATTTAATAAATT-TA
163105 AAAAAATATATTATTTAATAAATTTA
1 AAAAAA-ATATTATTTAATAAATTTA
163131 AAA
1 AAA
163134 TTTAAACACG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 6 0.24
25 3 0.12
26 11 0.44
27 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAAAAATATTATTTAATAAATTTA
Found at i:163352 original size:119 final size:120
Alignment explanation
Indices: 163134--163373 Score: 473
Period size: 119 Copynumber: 2.0 Consensus size: 120
163124 AAATTTAAAA
163134 TTTAAACACGTAAAATCACATGCAACGCACGCGGCTCAAGAATAGACCTAATCATGGGTCAAATC
1 TTTAAACACGTAAAATCACATGCAACGCACGCGGCTCAAGAATAGACCTAATCATGGGTCAAATC
163199 ACCCGCCTGCTCGAAAAATGGGAGGGTTTGAGAAAAAAGGTATGAAAAATGGGCT
66 ACCCGCCTGCTCGAAAAATGGGAGGGTTTGAGAAAAAAGGTATGAAAAATGGGCT
163254 TTTAAA-ACGTAAAATCACATGCAACGCACGCGGCTCAAGAATAGACCTAATCATGGGTCAAATC
1 TTTAAACACGTAAAATCACATGCAACGCACGCGGCTCAAGAATAGACCTAATCATGGGTCAAATC
163318 ACCCGCCTGCTCGAAAAATGGGAGGGTTTGAGAAAAAAGGTATGAAAAATGGGCT
66 ACCCGCCTGCTCGAAAAATGGGAGGGTTTGAGAAAAAAGGTATGAAAAATGGGCT
163373 T
1 T
163374 GGACGGAAAA
Statistics
Matches: 120, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
119 114 0.95
120 6 0.05
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (120 bp):
TTTAAACACGTAAAATCACATGCAACGCACGCGGCTCAAGAATAGACCTAATCATGGGTCAAATC
ACCCGCCTGCTCGAAAAATGGGAGGGTTTGAGAAAAAAGGTATGAAAAATGGGCT
Found at i:164350 original size:266 final size:263
Alignment explanation
Indices: 163803--164617 Score: 1140
Period size: 265 Copynumber: 3.1 Consensus size: 263
163793 GAAAATTTTT
* * * *
163803 TTCAGAGAAGGTTGTATTTCTATTCAGTGTGAAAAGAATGAAGAAATCAACCCTCTATTTATACT
1 TTCAAAGAGGGTTGTGTTTCTGTTCAGTGTGAAAAGAATGAAGAAATCAACCCTCTATTTATACT
* * *
163868 AGTAACAGAAGGTCAAAACGGTAAATAAGTAGGGGAAAAGAAGTAAAAAACGCACTGAAATTGCC
66 AGTAATAGAAGGGCAAAACGGTAAATAAGTAGGGGCAAAGAAGTAAAAAA-GCACTGAAATTGCC
* * * * *
163933 CTACTATTTCTG-GCCAACAGCAAAAAAAAAAATTCCAATTTCAGATTTTTCGGAACAGTAAAAC
130 CCACTATTTCTGCCCCAACAGC--CAAAAAATATTCCAATTCCAGATTTTTCGGAACAGTAAAAC
*
163997 TAGAAAAATAAATAGCTTAAAGATTTTATTTTTTTTGAAAAATAATTAAAA-TTTTATAAAAAAA
193 TAGAAAAATAAATAGTTTAAAGATTTTATTTTTTTTGAAAAATAA-TAAAACTTTTAT-AAAAAA
164061 AATATGCAC
256 AA-ATGCAC
*
164070 TTC--AGAGGGTTGTGTTTTTGTTCAGTGTGAAAAGAATGAAGAAATCAACCCTCTATCTTATAC
1 TTCAAAGAGGGTTGTGTTTCTGTTCAGTGTGAAAAGAATGAAGAAATCAACCCTCTAT-TTATAC
*
164133 TAGTAATAGAAGGGAAAAACGGTAAATAAGTAGGGGCAAAGAAGTAAAAAATGCACTGAAATTGC
65 TAGTAATAGAAGGGCAAAACGGTAAATAAGTAGGGGCAAAGAAGTAAAAAA-GCACTGAAATTGC
* * * *
164198 CCCACTATTTCTGCTCCAACAGCCAAAAAATATTCCAGTTCCAGATTTTTCGAAACAGTAAAATT
129 CCCACTATTTCTGCCCCAACAGCCAAAAAATATTCCAATTCCAGATTTTTCGGAACAGTAAAACT
*
164263 AGAAAAATAAATAATTTAAAGATTTTATTTCTTTCTTGAAAAATAATAAAACTTTTAT-AAAAAA
194 AGAAAAATAAATAGTTTAAAGATTTTATTT-TTT-TTGAAAAATAATAAAACTTTTATAAAAAAA
164327 AATGCAC
257 AATGCAC
* * * *
164334 TTCAAAAAGAGTTGTGTTTCTGTTCAGTGTGAAAAGAATGAAGAAATCAACCATCTATTTATACG
1 TTCAAAGAGGGTTGTGTTTCTGTTCAGTGTGAAAAGAATGAAGAAATCAACCCTCTATTTATACT
* ** * *
164399 AGTAATAGAAGGGCAAAATGGTAAATAAGTAGGGGCAAAGAAGTAAAAAA-CACAAAAAAATGGC
66 AGTAATAGAAGGGCAAAACGGTAAATAAGTAGGGGCAAAGAAGTAAAAAAGCAC-TGAAATTGCC
* *
164463 CCACTATTTCTGCCCCAATAGCCCAAAAAAAATATTCCAATTCCAGATTTTTTGGAACAGTAAAA
130 CCACTATTTCTGCCCCAACAG-CC--AAAAAATATTCCAATTCCAGATTTTTCGGAACAGTAAAA
* * * *
164528 CTGGAAAATTGAATAGTTTAAAGATTTT-TTTTTTTTTAAAAATAATAAAACTTTTATAAAAAAA
192 CTAGAAAAATAAATAGTTTAAAGATTTTATTTTTTTTGAAAAATAATAAAACTTTTATAAAAAAA
164592 AATGCAC
257 AATGCAC
164599 TTCAAAGAGGGTTGTGTTT
1 TTCAAAGAGGGTTGTGTTT
164618 GTGTATAACT
Statistics
Matches: 493, Mismatches: 43, Indels: 26
0.88 0.08 0.05
Matches are distributed among these distances:
263 3 0.01
264 56 0.11
265 209 0.42
266 138 0.28
267 87 0.18
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.29
Consensus pattern (263 bp):
TTCAAAGAGGGTTGTGTTTCTGTTCAGTGTGAAAAGAATGAAGAAATCAACCCTCTATTTATACT
AGTAATAGAAGGGCAAAACGGTAAATAAGTAGGGGCAAAGAAGTAAAAAAGCACTGAAATTGCCC
CACTATTTCTGCCCCAACAGCCAAAAAATATTCCAATTCCAGATTTTTCGGAACAGTAAAACTAG
AAAAATAAATAGTTTAAAGATTTTATTTTTTTTGAAAAATAATAAAACTTTTATAAAAAAAAATG
CAC
Found at i:185378 original size:169 final size:170
Alignment explanation
Indices: 185180--185519 Score: 673
Period size: 169 Copynumber: 2.0 Consensus size: 170
185170 TAGAAAAAGC
185180 AATTAATAATTATTTTTTATATGAAATTATAAAGTGAAATAAATTTAAAAAATGTTAATTCTGAA
1 AATTAATAATTATTTTTTATATGAAATTATAAAGTGAAATAAATTTAAAAAATGTTAATTCTGAA
185245 TATACAATAGTTATATATGTATAAAAAATTACAAAATTAACAATTATTCAAATAAATAAAATCTA
66 TATACAATAGTTATATATGTATAAAAAATTACAAAATTAACAATTATTCAAATAAATAAAATCTA
185310 TATTAAATTTATAATGATATCTATACTACTACATATAAGA
131 TATTAAATTTATAATGATATCTATACTACTACATATAAGA
185350 AATTAATAATT-TTTTTTATATGAAATTATAAAGTGAAATAAATTTAAAAAATGTTAATTCTGAA
1 AATTAATAATTATTTTTTATATGAAATTATAAAGTGAAATAAATTTAAAAAATGTTAATTCTGAA
185414 TATACAATAGTTATATATGTATAAAAAATTACAAAATTAACAATTATTCAAATAAATAAAATCTA
66 TATACAATAGTTATATATGTATAAAAAATTACAAAATTAACAATTATTCAAATAAATAAAATCTA
185479 TATTAAATTTATAATGATATCTATACTACTACATATAAGA
131 TATTAAATTTATAATGATATCTATACTACTACATATAAGA
185519 A
1 A
185520 GAAGGCCCTA
Statistics
Matches: 170, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
169 159 0.94
170 11 0.06
ACGTcount: A:0.51, C:0.06, G:0.05, T:0.38
Consensus pattern (170 bp):
AATTAATAATTATTTTTTATATGAAATTATAAAGTGAAATAAATTTAAAAAATGTTAATTCTGAA
TATACAATAGTTATATATGTATAAAAAATTACAAAATTAACAATTATTCAAATAAATAAAATCTA
TATTAAATTTATAATGATATCTATACTACTACATATAAGA
Found at i:185471 original size:82 final size:82
Alignment explanation
Indices: 185216--185473 Score: 221
Period size: 82 Copynumber: 3.1 Consensus size: 82
185206 TTATAAAGTG
185216 AAATAAATTTAAAAAATGTTAATTCTGAATATACAATAGTTATATATGTATAAAAAATTACAAAA
1 AAATAAATTTAAAAAATGTTAATTCTGAATATACAATAGTTATATATGTATAAAAAATTACAAAA
185281 TTAACAATTATTCAAAT
66 TTAACAATTATTCAAAT
** ** * * * *
185298 AAATAAAATCTATATTAAAT-TT-ATAATG-ATAT-CTATA-CTACTACA--TATAAGAAATTA-
1 AAAT-AAAT-T-TAAAAAATGTTAATTCTGAATATACAATAGTTA-TATATGTATAAAAAATTAC
* *
185355 ATAATTTTTTTTATATGAAATTA-T-AAAGT
62 A-AA-----ATTA-A--CAATTATTCAAA-T
185384 GAAATAAATTTAAAAAATGTTAATTCTGAATATACAATAGTTATATATGTATAAAAAATTACAAA
1 -AAATAAATTTAAAAAATGTTAATTCTGAATATACAATAGTTATATATGTATAAAAAATTACAAA
185449 ATTAACAATTATTCAAAT
65 ATTAACAATTATTCAAAT
185467 AAATAAA
1 AAATAAA
185474 ATCTATATTA
Statistics
Matches: 131, Mismatches: 20, Indels: 50
0.65 0.10 0.25
Matches are distributed among these distances:
78 1 0.01
79 13 0.10
80 2 0.02
81 7 0.05
82 20 0.15
83 10 0.08
84 16 0.12
85 16 0.12
86 10 0.08
87 13 0.10
88 7 0.05
89 2 0.02
90 13 0.10
91 1 0.01
ACGTcount: A:0.52, C:0.06, G:0.05, T:0.37
Consensus pattern (82 bp):
AAATAAATTTAAAAAATGTTAATTCTGAATATACAATAGTTATATATGTATAAAAAATTACAAAA
TTAACAATTATTCAAAT
Found at i:186585 original size:22 final size:22
Alignment explanation
Indices: 186541--186585 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
186531 ACGGCTAACT
* * * *
186541 AAAAATATAGCTATCTATGTAA
1 AAAAAAATAGATATATATATAA
186563 AAAAAAATAGATATATATATAA
1 AAAAAAATAGATATATATATAA
186585 A
1 A
186586 TATACCAACA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (22 bp):
AAAAAAATAGATATATATATAA
Found at i:199868 original size:22 final size:22
Alignment explanation
Indices: 199811--199887 Score: 79
Period size: 22 Copynumber: 3.5 Consensus size: 22
199801 AAACTAATCC
* *
199811 TCTCTCAAATTTTCTCTTAATT
1 TCTCTCAAATTTCCTCTCAATT
199833 TCT-TCTAAATTTCCTCTCAATT
1 TCTCTC-AAATTTCCTCTCAATT
199855 TGCTCTCAAA-TTCCT-TCAAAATT
1 T-CTCTCAAATTTCCTCTC--AATT
199878 TCTCTCAAAT
1 TCTCTCAAAT
199888 CCATATTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
21 4 0.09
22 31 0.66
23 10 0.21
24 2 0.04
ACGTcount: A:0.26, C:0.26, G:0.01, T:0.47
Consensus pattern (22 bp):
TCTCTCAAATTTCCTCTCAATT
Found at i:199883 original size:33 final size:32
Alignment explanation
Indices: 199811--199885 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 32
199801 AAACTAATCC
* * * *
199811 TCTCTCAAATTTTCTCTTAATTTCTTCTAAATT
1 TCTCTC-AATTTGCTCTAAATTCCTTCAAAATT
199844 TCCTCTCAATTTGCTCTCAAATTCCTTCAAAATT
1 T-CTCTCAATTTGCTCT-AAATTCCTTCAAAATT
199878 TCTCTCAA
1 TCTCTCAA
199886 ATCCATATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 17 0.47
34 19 0.53
ACGTcount: A:0.25, C:0.27, G:0.01, T:0.47
Consensus pattern (32 bp):
TCTCTCAATTTGCTCTAAATTCCTTCAAAATT
Found at i:199887 original size:11 final size:11
Alignment explanation
Indices: 199811--199887 Score: 63
Period size: 11 Copynumber: 6.9 Consensus size: 11
199801 AAACTAATCC
199811 TCTCTCAAATT
1 TCTCTCAAATT
*
199822 T-TCTCTTAATT
1 TCTCTC-AAATT
199833 TCT-TCTAAATT
1 TCTCTC-AAATT
199844 TCCTCTC-AATT
1 T-CTCTCAAATT
199855 TGCTCTCAAATT
1 T-CTCTCAAATT
*
199867 CCT-TCAAAATT
1 TCTCTC-AAATT
199878 TCTCTCAAAT
1 TCTCTCAAAT
199888 CCATATTTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
10 6 0.11
11 37 0.69
12 9 0.17
13 2 0.04
ACGTcount: A:0.26, C:0.26, G:0.01, T:0.47
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:199956 original size:51 final size:51
Alignment explanation
Indices: 199851--199957 Score: 121
Period size: 51 Copynumber: 2.1 Consensus size: 51
199841 ATTTCCTCTC
**
199851 AATTTGCTCTCAAATTCCTTCAAAATTTCTCTCAAATCCATATTTATTTTT
1 AATTTGCTCTCAAATTCCTTCAAAATTTCTCTCAAATCCATATTTATTAAT
* * *
199902 AATTTGCTCTCAAGTTCC-TCTTAAATTTCTCTTAAAT-CACTATTT-TTAAAT
1 AATTTGCTCTCAAATTCCTTC-AAAATTTCTCTCAAATCCA-TATTTATT-AAT
199953 AATTT
1 AATTT
199958 TAAAAAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
50 6 0.12
51 42 0.88
ACGTcount: A:0.30, C:0.20, G:0.03, T:0.48
Consensus pattern (51 bp):
AATTTGCTCTCAAATTCCTTCAAAATTTCTCTCAAATCCATATTTATTAAT
Found at i:202387 original size:6 final size:7
Alignment explanation
Indices: 202358--202400 Score: 61
Period size: 7 Copynumber: 6.0 Consensus size: 7
202348 CTAAAATTAA
202358 AAACCCT
1 AAACCCT
202365 AAACCCT
1 AAACCCT
202372 AAACCCT
1 AAACCCT
202379 AAA-CCT
1 AAACCCT
202385 AAAAACCCT
1 --AAACCCT
202394 AAACCCT
1 AAACCCT
202401 TAACTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
6 3 0.09
7 24 0.73
8 3 0.09
9 3 0.09
ACGTcount: A:0.47, C:0.40, G:0.00, T:0.14
Consensus pattern (7 bp):
AAACCCT
Found at i:202390 original size:22 final size:22
Alignment explanation
Indices: 202365--202880 Score: 616
Period size: 22 Copynumber: 24.0 Consensus size: 22
202355 TAAAAACCCT
* *
202365 AAACCCTAAACCCTAAACCTAA
1 AAACCCTAAACCCTTAACTTAA
202387 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
**
202409 AAACCCTAGCCCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
202431 AAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
**
202453 AAACCCTAGCCCCTTAA-TCTAA
1 AAACCCTAAACCCTTAACT-TAA
* *
202475 AAACCCT-AACCCTTGACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
202496 AAATCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
202518 AAACCCT-AACCCTTAATTTTA
1 AAACCCTAAACCCTTAACTTAA
*
202539 AAACCCTAAACCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
*
202561 AAATCCTAAACCCTTAACTT-A
1 AAACCCTAAACCCTTAACTTAA
*
202582 AAACCCATAAACCCTTAACCTAA
1 AAACCC-TAAACCCTTAACTTAA
*
202605 AAATCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
202627 AAACCCTAAACCCTTAA-TT-A
1 AAACCCTAAACCCTTAACTTAA
202647 AAACCCATAAACCCTTAACTTAA
1 AAACCC-TAAACCCTTAACTTAA
*
202670 AAACACT-AACCCTTAACTT-A
1 AAACCCTAAACCCTTAACTTAA
* *
202690 AAACCAT-AACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
* *
202711 AAACTCTAAACCCTT--TTTAA
1 AAACCCTAAACCCTTAACTTAA
* *
202731 AATCCCT-AACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
*
202752 AAACCCTAAACCCTTAAATT-A
1 AAACCCTAAACCCTTAACTTAA
202773 AAACCCATAAACCCTTAACTTAA
1 AAACCC-TAAACCCTTAACTTAA
*
202796 AAACACT-AACCCTTAACTT-A
1 AAACCCTAAACCCTTAACTTAA
* *
202816 AAACCAT-AACCCTTAACTTTA
1 AAACCCTAAACCCTTAACTTAA
* *
202837 AAACTCTAAACCCTTAAATTAA
1 AAACCCTAAACCCTTAACTTAA
*
202859 AAA-CCTTAACCCTTAACTTAA
1 AAACCCTAAACCCTTAACTTAA
202880 A
1 A
202881 TATAATTTGA
Statistics
Matches: 425, Mismatches: 51, Indels: 37
0.83 0.10 0.07
Matches are distributed among these distances:
19 7 0.02
20 51 0.12
21 121 0.28
22 228 0.54
23 18 0.04
ACGTcount: A:0.44, C:0.30, G:0.01, T:0.25
Consensus pattern (22 bp):
AAACCCTAAACCCTTAACTTAA
Found at i:202392 original size:15 final size:14
Alignment explanation
Indices: 202316--202398 Score: 64
Period size: 15 Copynumber: 5.9 Consensus size: 14
202306 GACAAATCTT
*
202316 AAACCCTTAACCTA
1 AAACCCTAAACCTA
*
202330 TAAACCCTAACCCT-
1 -AAACCCTAAACCTA
* **
202344 -AACTCTAAAATTAA
1 AAACCCTAAACCT-A
202358 AAACCCTAAACCCT-
1 AAACCCTAAA-CCTA
202372 AAACCCTAAACCTAA
1 AAACCCTAAACCT-A
202387 AAACCCTAAACC
1 AAACCCTAAACC
202399 CTTAACTTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
12 8 0.15
13 3 0.06
14 10 0.19
15 31 0.58
16 1 0.02
ACGTcount: A:0.47, C:0.35, G:0.00, T:0.18
Consensus pattern (14 bp):
AAACCCTAAACCTA
Found at i:202510 original size:43 final size:44
Alignment explanation
Indices: 202365--202877 Score: 555
Period size: 43 Copynumber: 12.0 Consensus size: 44
202355 TAAAAACCCT
* * *
202365 AAACCCTAAACCCTAAACCTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAATCTAAAAACCCTAAACCCTTAACTTTA
** *
202409 AAACCCTAGCCCCTTAA-CTTAAAAACCCTAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAATC-TAAAAACCCTAAACCCTTAACTTTA
** *
202453 AAACCCTAGCCCCTTAATCTAAAAACCCT-AACCCTTGACTTTA
1 AAACCCTAAACCCTTAATCTAAAAACCCTAAACCCTTAACTTTA
* *
202496 AAATCCTAAACCCTTAA-CTTAAAAACCCT-AACCCTTAATTTTA
1 AAACCCTAAACCCTTAATC-TAAAAACCCTAAACCCTTAACTTTA
*
202539 AAACCCTAAACCCTTAAAT-TAAAAATCCTAAACCCTTAAC-TTA
1 AAACCCTAAACCCTT-AATCTAAAAACCCTAAACCCTTAACTTTA
* * *
202582 AAACCCATAAACCCTTAACCTAAAAATCCTAAACCCTTAACTTAA
1 AAACCC-TAAACCCTTAATCTAAAAACCCTAAACCCTTAACTTTA
*
202627 AAACCCTAAACCCTTAAT-T-AAAACCCATAAACCCTTAACTTAA
1 AAACCCTAAACCCTTAATCTAAAAACCC-TAAACCCTTAACTTTA
* * *
202670 AAACACT-AACCCTTAA-CTTAAAACCAT-AACCCTTAACTTTA
1 AAACCCTAAACCCTTAATCTAAAAACCCTAAACCCTTAACTTTA
* * *
202711 AAACTCTAAACCCTT--TTTAAAATCCCT-AACCCTTAACTTTA
1 AAACCCTAAACCCTTAATCTAAAAACCCTAAACCCTTAACTTTA
*
202752 AAACCCTAAACCCTTAAAT-T-AAAACCCATAAACCCTTAACTTAA
1 AAACCCTAAACCCTT-AATCTAAAAACCC-TAAACCCTTAACTTTA
* * *
202796 AAACACT-AACCCTTAA-CTTAAAACCAT-AACCCTTAACTTTA
1 AAACCCTAAACCCTTAATCTAAAAACCCTAAACCCTTAACTTTA
* *
202837 AAACTCTAAACCCTTAAAT-TAAAAA-CCTTAACCCTTAACTT
1 AAACCCTAAACCCTT-AATCTAAAAACCCTAAACCCTTAACTT
202878 AAATATAATT
Statistics
Matches: 410, Mismatches: 34, Indels: 51
0.83 0.07 0.10
Matches are distributed among these distances:
41 73 0.18
42 44 0.11
43 146 0.36
44 138 0.34
45 9 0.02
ACGTcount: A:0.43, C:0.30, G:0.01, T:0.26
Consensus pattern (44 bp):
AAACCCTAAACCCTTAATCTAAAAACCCTAAACCCTTAACTTTA
Found at i:204306 original size:126 final size:125
Alignment explanation
Indices: 204049--204859 Score: 1089
Period size: 126 Copynumber: 6.5 Consensus size: 125
204039 CCTAAGCATG
* *
204049 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGCTTTGACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* *
204114 TAGAAGCG--ATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTA-TTTTTCTAGGAC
66 TAGAA-CGTTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTC-AGGAC
* * *
204173 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATGCTT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* * *
204237 CTTGTAACGTTTTTTTATACTATTTGCTCAGAAACGTCACCTCAAAATTATTTTTTCAGGAC
65 CTAG-AACGTTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
204299 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
** * ** * * *
204364 TAGAA-GCAATTTTATACTATTTTCTCAGAAACGTCATGTCGAAATTATTTTTCCAGAAC
66 TAGAACGTTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* *
204423 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATGCTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* * * *
204487 GTTGCAGCGTTGTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
65 CTAG-AACGTTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
204549 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
** * ** * * *
204614 TAGAA-GCAATTTTATACTATTTTCTCAGAAACGTCATGTCGAAATTATTTTTCCAGAAC
66 TAGAACGTTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * *
204673 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCA-AATAGCATGCTA
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTG
* * * * * *
204737 CTTGCAGCGTTGTTTTATACCATTTGCTCAGAAATGTCAACTCAAAATTATTTTTTCAGGTC
65 CTAG-AACGTTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * * *
204799 CTACTGTAGCAAAAGCGCGTCCACGTGGACGCGACTTCACAAATTCTTCTTATAAATCATC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATC
204860 ATGTTTGAGC
Statistics
Matches: 599, Mismatches: 74, Indels: 26
0.86 0.11 0.04
Matches are distributed among these distances:
123 6 0.01
124 273 0.46
125 7 0.01
126 301 0.50
127 12 0.02
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (125 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TAGAACGTTATTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
Found at i:204505 original size:250 final size:250
Alignment explanation
Indices: 204049--204859 Score: 1433
Period size: 250 Copynumber: 3.2 Consensus size: 250
204039 CCTAAGCATG
* *
204049 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGCTTTGACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
* * * * *
204114 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCTAGGACCTACTG
66 TAGAAGCAATTTTATACTATTTTCTCAGAAACGTCATGTCGAAATTATTTTTCCAGAACCTACTG
* * *
204179 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATGCTTCTTGTAA
131 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATGCTACTTGCAG
* *
204244 CGTTTTTTTATACTATTTGCTCAGAAACGTCACCTCAAAATTATTTTTTCAGGAC
196 CGTTGTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
204299 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
204364 TAGAAGCAATTTTATACTATTTTCTCAGAAACGTCATGTCGAAATTATTTTTCCAGAACCTACTG
66 TAGAAGCAATTTTATACTATTTTCTCAGAAACGTCATGTCGAAATTATTTTTCCAGAACCTACTG
**
204429 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATGCTGGTTGCAG
131 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATGCTACTTGCAG
204494 CGTTGTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
196 CGTTGTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
204549 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
204614 TAGAAGCAATTTTATACTATTTTCTCAGAAACGTCATGTCGAAATTATTTTTCCAGAACCTACTG
66 TAGAAGCAATTTTATACTATTTTCTCAGAAACGTCATGTCGAAATTATTTTTCCAGAACCTACTG
204679 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATGCTACTTGCAG
131 TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATGCTACTTGCAG
* * *
204744 CGTTGTTTTATACCATTTGCTCAGAAATGTCAACTCAAAATTATTTTTTCAGGTC
196 CGTTGTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
* * * *
204799 CTACTGTAGCAAAAGCGCGTCCACGTGGACGCGACTTCACAAATTCTTCTTATAAATCATC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATC
204860 ATGTTTGAGC
Statistics
Matches: 539, Mismatches: 22, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
250 539 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (250 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
TAGAAGCAATTTTATACTATTTTCTCAGAAACGTCATGTCGAAATTATTTTTCCAGAACCTACTG
TAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATGCTACTTGCAG
CGTTGTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGAC
Found at i:213256 original size:18 final size:17
Alignment explanation
Indices: 213206--213270 Score: 78
Period size: 18 Copynumber: 3.7 Consensus size: 17
213196 AACATAGAAT
*
213206 ATAAGAAAAAAACATCAA
1 ATAATAAAAAAACAT-AA
*
213224 ATAA-AAAATAACATAA
1 ATAATAAAAAAACATAA
213240 ATAATACAAAAAACATAA
1 ATAATA-AAAAAACATAA
213258 ATAAATAAAAAAA
1 AT-AATAAAAAAA
213271 GATTCAAATC
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
16 6 0.14
17 10 0.24
18 22 0.52
19 4 0.10
ACGTcount: A:0.75, C:0.08, G:0.02, T:0.15
Consensus pattern (17 bp):
ATAATAAAAAAACATAA
Found at i:217969 original size:3 final size:3
Alignment explanation
Indices: 217961--217999 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
217951 TGATTTTGGT
217961 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
218000 GCTTAAGGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:218524 original size:9 final size:9
Alignment explanation
Indices: 218445--218525 Score: 50
Period size: 9 Copynumber: 9.4 Consensus size: 9
218435 AAAATAAAAA
*
218445 AAAAACTAT
1 AAAAATTAT
*
218454 AAAAACTAT
1 AAAAATTAT
218463 AAAAA-TATT
1 AAAAATTA-T
**
218472 GTAAA-TA-
1 AAAAATTAT
218479 AAAAATT-T
1 AAAAATTAT
218487 AAAAATT-T
1 AAAAATTAT
218495 AAAAATTA-
1 AAAAATTAT
218503 AAATTAA-TAT
1 AAA--AATTAT
218513 AAAAATTAT
1 AAAAATTAT
218522 AAAA
1 AAAA
218526 CATATCGATT
Statistics
Matches: 60, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
7 3 0.05
8 23 0.38
9 29 0.48
10 5 0.08
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:218530 original size:18 final size:17
Alignment explanation
Indices: 218445--218530 Score: 63
Period size: 18 Copynumber: 5.0 Consensus size: 17
218435 AAAATAAAAA
*
218445 AAAAACTATAAAAACTAT
1 AAAAATTATAAAAA-TAT
**
218463 AAAAA-TATTGTAAATA-
1 AAAAATTA-TAAAAATAT
*
218479 AAAAATT-TAAAAATTT
1 AAAAATTATAAAAATAT
218495 AAAAATTA-AAATTAATAT
1 AAAAATTATAAA--AATAT
218513 AAAAATTATAAAACATAT
1 AAAAATTATAAAA-ATAT
218531 CGATTAACTC
Statistics
Matches: 54, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
15 5 0.09
16 15 0.28
17 6 0.11
18 25 0.46
19 3 0.06
ACGTcount: A:0.65, C:0.03, G:0.01, T:0.30
Consensus pattern (17 bp):
AAAAATTATAAAAATAT
Found at i:218858 original size:279 final size:274
Alignment explanation
Indices: 218317--218861 Score: 647
Period size: 279 Copynumber: 2.0 Consensus size: 274
218307 GGTCTTAATC
* * *
218317 GAAACTAGCAATCAATTAATTATTCGGATTTGTTTTTTTCATTGAAGCTCTTCAAATTAACTTTG
1 GAAACTAGAAATCAATTAATTATTCGAAATTGTTTTTTTCATTGAAGCTCTTCAAATTAAC-TTG
* * * *
218382 TGCTAACTAGGTAAAAGATGAGGCGACATGATATGAGGTTGGAAAAATATTGAAAAATAAAAAAA
65 TGCTAACAAGGTAAAAGAAGAGGCGACATGATATGAAGTAGGAAAAATATT--AAAATAAAAAAA
* *
218447 AAACTATAAAAACTATAAAAATATTGTAAATAAAAAATTTAAAAATTTAAAAATTAAAATTAATA
128 AAACTATAAAAACTATAAAAATATTGTAAATAAAAAATTTAAAAAATTAAAAATTAAAATTAAAA
*
218512 TAAAAATTATAAAACATATCGATTAACTCAAAATTTATAATTGCAATTCATATAACTACAAATCA
193 TAAAAATTATAAAACATATCAATTAACTCAAAATTTATAATTGCAATTCATATAACTACAAATCA
218577 TATTTAAGCTACTGATT
258 TATTTAAGCTACTGATT
* * * * *
218594 GAAACTA-AAATCAATTAGTTATTTGAAATTGTTTTTTTCGTTGGAA-CTCTTGATATTAAC-TG
1 GAAACTAGAAATCAATTAATTATTCGAAATTGTTTTTTTCATT-GAAGCTCTTCAAATTAACTTG
* * * *
218656 TGTTAACAAGGTAAAAGAAGGGGCG-TATGATATGAAAGTAGGAAAAATATT-AAA-AAATAAAA
65 TGCTAACAAGGTAAAAGAAGAGGCGACATGATATG-AAGTAGGAAAAATATTAAAATAAAAAAAA
*
218718 AACTATAAAAATATTATAAAAATATTGTAAATAAAAAA-TTAAAAAATTACAATTAATATAAAAC
129 AACTAT-AAAA-ACTATAAAAATATTGTAAATAAAAAATTTAAAAAATTA-AA--AAT-TAAAA-
* * * * *
218782 TAATAAAAGCTATAAATTAT-AAACATGTCAATTAACTCATAGTTTATAATTGCAATTTATATAA
187 T--TAAAA--TAAAAATTATAAAACATATCAATTAACTCAAAATTTATAATTGCAATTCATATAA
* *
218846 CTTCATATCATATTTA
248 CTACAAATCATATTTA
218862 TGTTGTTGTA
Statistics
Matches: 228, Mismatches: 27, Indels: 24
0.82 0.10 0.09
Matches are distributed among these distances:
270 13 0.06
271 17 0.07
272 27 0.12
273 8 0.04
274 40 0.18
275 5 0.02
276 42 0.18
277 10 0.04
278 4 0.02
279 53 0.23
280 9 0.04
ACGTcount: A:0.48, C:0.08, G:0.10, T:0.33
Consensus pattern (274 bp):
GAAACTAGAAATCAATTAATTATTCGAAATTGTTTTTTTCATTGAAGCTCTTCAAATTAACTTGT
GCTAACAAGGTAAAAGAAGAGGCGACATGATATGAAGTAGGAAAAATATTAAAATAAAAAAAAAA
CTATAAAAACTATAAAAATATTGTAAATAAAAAATTTAAAAAATTAAAAATTAAAATTAAAATAA
AAATTATAAAACATATCAATTAACTCAAAATTTATAATTGCAATTCATATAACTACAAATCATAT
TTAAGCTACTGATT
Found at i:222292 original size:15 final size:15
Alignment explanation
Indices: 222272--222351 Score: 58
Period size: 15 Copynumber: 5.4 Consensus size: 15
222262 GGGGTAGAAT
*
222272 TGATATGTTAAGATA
1 TGATATGATAAGATA
222287 TGATATGATAAGATA
1 TGATATGATAAGATA
* *
222302 T-A-A-AATGAGATA
1 TGATATGATAAGATA
* * *
222314 TGACATTATATGAAATA
1 TGATATGATA--AGATA
222331 TGATATGATAAGATA
1 TGATATGATAAGATA
*
222346 CGATAT
1 TGATAT
222352 AAGATATGCC
Statistics
Matches: 50, Mismatches: 10, Indels: 10
0.71 0.14 0.14
Matches are distributed among these distances:
12 8 0.16
13 2 0.04
14 2 0.04
15 26 0.52
17 12 0.24
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.34
Consensus pattern (15 bp):
TGATATGATAAGATA
Found at i:222316 original size:22 final size:22
Alignment explanation
Indices: 222284--222345 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
222274 ATATGTTAAG
222284 ATATGATATGATAAGATATAAA
1 ATATGATATGATAAGATATAAA
* ** *
222306 ATGA-GATATGACATTATATGAA
1 AT-ATGATATGATAAGATATAAA
222328 ATATGATATGATAAGATA
1 ATATGATATGATAAGATA
222346 CGATATAAGA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.16, T:0.32
Consensus pattern (22 bp):
ATATGATATGATAAGATATAAA
Found at i:228189 original size:9 final size:9
Alignment explanation
Indices: 228162--228327 Score: 70
Period size: 9 Copynumber: 17.4 Consensus size: 9
228152 AAAATATTTT
*
228162 AAAATAATA
1 AAAATTATA
* *
228171 AAAGTAATA
1 AAAATTATA
228180 AAAATTATA
1 AAAATTATA
228189 AAAA-TATA
1 AAAATTATA
*
228197 AAACGATTTTTTA
1 AAA--A--TTATA
228210 AAAA-TATA
1 AAAATTATA
*
228218 GAAAATAATA
1 -AAAATTATA
228228 AATAATTATA
1 AA-AATTATA
*
228238 GAAATTTACATA
1 -AAAATT--ATA
228250 AAAATTATA
1 AAAATTATA
*
228259 TAGAATTATA
1 -AAAATTATA
*
228269 AAAATAATA
1 AAAATTATA
*
228278 AATA-TATA
1 AAAATTATA
*
228286 CAAAATAAT-
1 -AAAATTATA
*
228295 AAAATTACAA
1 AAAATTA-TA
*
228305 AAAATTAAA
1 AAAATTATA
*
228314 GAAAATTCTA
1 -AAAATTATA
228324 AAAA
1 AAAA
228328 GATAGAAAAT
Statistics
Matches: 120, Mismatches: 20, Indels: 34
0.69 0.11 0.20
Matches are distributed among these distances:
8 19 0.16
9 47 0.39
10 37 0.31
11 8 0.07
12 3 0.03
13 6 0.05
ACGTcount: A:0.64, C:0.03, G:0.04, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:228190 original size:26 final size:27
Alignment explanation
Indices: 228143--228199 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
228133 AAATTTGTTA
*
228143 AAAATGTAAAAAATATT-TTAAAATAAT
1 AAAATGTAAAAAATATTATAAAAAT-AT
228170 AAAA-GTAATAAAA-ATTATAAAAATAT
1 AAAATGTAA-AAAATATTATAAAAATAT
228196 AAAA
1 AAAA
228200 CGATTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 13 0.48
27 14 0.52
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (27 bp):
AAAATGTAAAAAATATTATAAAAATAT
Found at i:228283 original size:25 final size:26
Alignment explanation
Indices: 228214--228285 Score: 64
Period size: 25 Copynumber: 2.8 Consensus size: 26
228204 TTTTTAAAAA
228214 TATAGAAAATAATAAATAATTATAGAAAT
1 TATA-AAAATAATAAAT-A-TATAGAAAT
*
228243 T-T--ACATAA-AAATTATATAG-AAT
1 TATAAAAATAATAAA-TATATAGAAAT
228265 TATAAAAATAATAAATATATA
1 TATAAAAATAATAAATATATA
228286 CAAAATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 14
0.69 0.04 0.27
Matches are distributed among these distances:
22 4 0.11
23 6 0.17
24 4 0.11
25 17 0.47
26 3 0.08
28 1 0.03
29 1 0.03
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (26 bp):
TATAAAAATAATAAATATATAGAAAT
Found at i:256357 original size:3 final size:3
Alignment explanation
Indices: 256349--256417 Score: 52
Period size: 3 Copynumber: 23.0 Consensus size: 3
256339 ATGCATAAAC
* * * * *
256349 AAT AAT AAT AAT GAT GAA- AAC GAT AAT -AT AAAT AAC AAT AAT GAT
1 AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT
*
256394 AAT AAC AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
256418 CTAAATTTTG
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
2 4 0.08
3 44 0.86
4 3 0.06
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:256389 original size:15 final size:15
Alignment explanation
Indices: 256349--256413 Score: 71
Period size: 15 Copynumber: 4.3 Consensus size: 15
256339 ATGCATAAAC
*
256349 AATAATAATAATGAT
1 AATAACAATAATGAT
*
256364 GAA-AACGATAAT-AT
1 -AATAACAATAATGAT
256378 AAATAACAATAATGAT
1 -AATAACAATAATGAT
*
256394 AATAACAATAATAAT
1 AATAACAATAATGAT
256409 AATAA
1 AATAA
256414 TAATCTAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
14 4 0.10
15 34 0.81
16 4 0.10
ACGTcount: A:0.63, C:0.05, G:0.06, T:0.26
Consensus pattern (15 bp):
AATAACAATAATGAT
Found at i:256389 original size:30 final size:30
Alignment explanation
Indices: 256349--256406 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
256339 ATGCATAAAC
* *
256349 AATAATAATAATGATGAA-AACGATAATATA
1 AATAACAATAATGAT-AATAACAATAATATA
256379 AATAACAATAATGATAATAACAATAATA
1 AATAACAATAATGATAATAACAATAATA
256407 ATAATAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.26
Consensus pattern (30 bp):
AATAACAATAATGATAATAACAATAATATA
Found at i:261258 original size:36 final size:38
Alignment explanation
Indices: 261181--261276 Score: 92
Period size: 37 Copynumber: 2.6 Consensus size: 38
261171 GTATTGTAGA
* * * *
261181 TTTTACAA-AATAATCCATAAAATTTCAATTTTCTATT
1 TTTTACAATATTAGTCCCTAAAATTTCAATTTTCTATG
261218 TTTTACAAT-TTAGTCCCTAAAA-TTCAATTTT-TACTG
1 TTTTACAATATTAGTCCCTAAAATTTCAATTTTCTA-TG
** *
261254 TTTTATGATATTAGTCTCTAAAA
1 TTTTACAATATTAGTCCCTAAAA
261277 ATAGAATTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
35 2 0.04
36 17 0.35
37 30 0.61
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (38 bp):
TTTTACAATATTAGTCCCTAAAATTTCAATTTTCTATG
Found at i:261782 original size:30 final size:30
Alignment explanation
Indices: 261748--261807 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
261738 ATTTTTGGAC
261748 TAAAGTTCATAACATG-CAATAATATACAAA
1 TAAAGTTCATAACA-GACAATAATATACAAA
*
261778 TAAAGTTCATACCAGACAATAATATACAAA
1 TAAAGTTCATAACAGACAATAATATACAAA
261808 GAATGAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.53, C:0.15, G:0.07, T:0.25
Consensus pattern (30 bp):
TAAAGTTCATAACAGACAATAATATACAAA
Found at i:266048 original size:188 final size:189
Alignment explanation
Indices: 265731--266103 Score: 739
Period size: 188 Copynumber: 2.0 Consensus size: 189
265721 AACTCTTTAT
265731 GCAACTAAGTCTCTGGCTAACCGTTTAGTGTTGAAACAACGTCTACTTACGTTTCGCATGAACGG
1 GCAACTAAGTCTCTGGCTAACCGTTTAGTGTTGAAACAACGTCTACTTACGTTTCGCATGAACGG
265796 ATGTGAGCTTTTTAGAGATCACATCAGTCAATTCATTACTCTTTTAAATGATTTAAAGAACGTTG
66 ATGTGAGCTTTTTAGAGATCACATCAGTCAATTCATTACTCTTTTAAATGATTTAAAGAACGTTG
265861 AGGTTCATATTGATGATGAAGATCAAGCTATGCTATTATTGTGCTCTTT-ACCCCATTC
131 AGGTTCATATTGATGATGAAGATCAAGCTATGCTATTATTGTGCTCTTTAACCCCATTC
265919 GCAACTAAGTCTCTGGCTAACCGTTTAGTGTTGAAACAACGTCTACTTACGTTTCGCATGAACGG
1 GCAACTAAGTCTCTGGCTAACCGTTTAGTGTTGAAACAACGTCTACTTACGTTTCGCATGAACGG
265984 ATGTGAGCTTTTTAGAGATCACATCAGTCAATTCATTACTCTTTTAAATGATTTAAAGAACGTTG
66 ATGTGAGCTTTTTAGAGATCACATCAGTCAATTCATTACTCTTTTAAATGATTTAAAGAACGTTG
266049 AGGTTCATATTGATGATGAAGATCAAGCTATGCTATTATTGTGCTCTTTAACCCC
131 AGGTTCATATTGATGATGAAGATCAAGCTATGCTATTATTGTGCTCTTTAACCCC
266104 TTCATACAAG
Statistics
Matches: 184, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
188 179 0.97
189 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (189 bp):
GCAACTAAGTCTCTGGCTAACCGTTTAGTGTTGAAACAACGTCTACTTACGTTTCGCATGAACGG
ATGTGAGCTTTTTAGAGATCACATCAGTCAATTCATTACTCTTTTAAATGATTTAAAGAACGTTG
AGGTTCATATTGATGATGAAGATCAAGCTATGCTATTATTGTGCTCTTTAACCCCATTC
Found at i:267471 original size:27 final size:27
Alignment explanation
Indices: 267424--267481 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
267414 TAAAACAGTA
267424 ATTTTACCTCTTAAGGATATTTTGGTC
1 ATTTTACCTCTTAAGGATATTTTGGTC
* *
267451 ATTTTACC-CTTCGAGGGTATTTTGGTC
1 ATTTTACCTCTT-AAGGATATTTTGGTC
267478 ATTT
1 ATTT
267482 AACAACCTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.19, C:0.16, G:0.17, T:0.48
Consensus pattern (27 bp):
ATTTTACCTCTTAAGGATATTTTGGTC
Found at i:269231 original size:76 final size:77
Alignment explanation
Indices: 269132--269284 Score: 299
Period size: 76 Copynumber: 2.0 Consensus size: 77
269122 TATGACTTTT
269132 TTTAACACAATAATTTAAAAGGCCTACATCTAAGCATCCAGGGTTTTATCCACTTAAAACCAAAA
1 TTTAACACAATAATTTAAAAGGCCTACATCTAAGCATCCAGGGTTTTATCCACTTAAAACCAAAA
269197 TTTTTACTAAAG
66 TTTTTACTAAAG
269209 TTTAACACAA-AATTTAAAAGGCCTACATCTAAGCATCCAGGGTTTTATCCACTTAAAACCAAAA
1 TTTAACACAATAATTTAAAAGGCCTACATCTAAGCATCCAGGGTTTTATCCACTTAAAACCAAAA
269273 TTTTTACTAAAG
66 TTTTTACTAAAG
269285 CCAGGTTTGA
Statistics
Matches: 76, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 66 0.87
77 10 0.13
ACGTcount: A:0.41, C:0.20, G:0.09, T:0.31
Consensus pattern (77 bp):
TTTAACACAATAATTTAAAAGGCCTACATCTAAGCATCCAGGGTTTTATCCACTTAAAACCAAAA
TTTTTACTAAAG
Found at i:274929 original size:47 final size:47
Alignment explanation
Indices: 274906--275067 Score: 306
Period size: 47 Copynumber: 3.4 Consensus size: 47
274896 TCAAATCGGT
274906 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
1 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
*
274953 CAGCATTTATACACTAAAATTTGACAGCATATATATACAAAATTGGA
1 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
275000 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
1 CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
*
275047 CAGCATTTATGCACCAAAATT
1 CAGCATTTATACACCAAAATT
275068 GGATAACTCT
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 112 1.00
ACGTcount: A:0.44, C:0.17, G:0.10, T:0.28
Consensus pattern (47 bp):
CAGCATTTATACACCAAAATTTGACAGCATATATATACAAAATTGGA
Found at i:275068 original size:24 final size:24
Alignment explanation
Indices: 274889--275070 Score: 210
Period size: 23 Copynumber: 7.8 Consensus size: 24
274879 TTGATAGCTC
* * *
274889 TTATACATC-AAATCGGTCAGCAT
1 TTATACACCAAAATTGGACAGCAT
*
274912 TTATACACCAAAATTTGACAGCAT
1 TTATACACCAAAATTGGACAGCAT
* *
274936 ATATATA-CAAAATTGGACAGCAT
1 TTATACACCAAAATTGGACAGCAT
* *
274959 TTATACACTAAAATTTGACAGCAT
1 TTATACACCAAAATTGGACAGCAT
* *
274983 ATATATA-CAAAATTGGACAGCAT
1 TTATACACCAAAATTGGACAGCAT
*
275006 TTATACACCAAAATTTGACAGCAT
1 TTATACACCAAAATTGGACAGCAT
* *
275030 ATATATA-CAAAATTGGACAGCAT
1 TTATACACCAAAATTGGACAGCAT
*
275053 TTATGCACCAAAATTGGA
1 TTATACACCAAAATTGGA
275071 TAACTCTATA
Statistics
Matches: 131, Mismatches: 24, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
23 66 0.50
24 65 0.50
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.29
Consensus pattern (24 bp):
TTATACACCAAAATTGGACAGCAT
Found at i:276687 original size:44 final size:43
Alignment explanation
Indices: 276588--276704 Score: 157
Period size: 44 Copynumber: 2.7 Consensus size: 43
276578 GTTTCGTACA
* *
276588 ATGCCATCGTCCCAGACGTGGTCTTACAGGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
**
276631 ATGCC-ACTGTCCCAGACAAGGTCTTACACGTAAATCACA-AGTCG
1 ATGCCAAC-GTCCCAGACGTGGTCTTACACGT-AATCACATA-TCG
276675 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
276705 ACAACACATA
Statistics
Matches: 64, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
42 1 0.02
43 26 0.41
44 35 0.55
45 2 0.03
ACGTcount: A:0.27, C:0.30, G:0.21, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCACATATCG
Found at i:278154 original size:24 final size:23
Alignment explanation
Indices: 278123--278169 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
278113 CCATTGTTAT
*
278123 TTGTATCTTTATTTTCATCTCCA
1 TTGTATCTTTATCTTCATCTCCA
*
278146 TTGTCATCTTTGTCTTCATCTCCA
1 TTGT-ATCTTTATCTTCATCTCCA
278170 CCATCGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.15, C:0.26, G:0.06, T:0.53
Consensus pattern (23 bp):
TTGTATCTTTATCTTCATCTCCA
Found at i:281595 original size:41 final size:42
Alignment explanation
Indices: 281456--281651 Score: 260
Period size: 41 Copynumber: 4.7 Consensus size: 42
281446 AACTCACACA
* * * *
281456 ATGCC-ATATCCCAGATATGGTCTTACATGCTATCATATATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AATCATATATCG
281498 ATGCCAATAG-CCCAG-CTATGGTCTTACACGAATC-TCATATCG
1 ATGCCAAT-GTCCCAGAC-ATGGTCTTACACGAATCAT-ATATCG
*
281540 ATGCCAATGTCCCAGGCATGGTCTTACACGAATCATATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATCATATATCG
281581 ATGCCAATGTCCCAGACATGGTCTTACACGAATCATATA-CG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAATCATATATCG
*
281622 ATGCAAATGTCCCAGACATGGTCTTACACG
1 ATGCCAATGTCCCAGACATGGTCTTACACG
281652 TCCGAAGTTC
Statistics
Matches: 141, Mismatches: 6, Indels: 15
0.87 0.04 0.09
Matches are distributed among these distances:
41 73 0.52
42 47 0.33
43 21 0.15
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAATCATATATCG
Found at i:281602 original size:83 final size:84
Alignment explanation
Indices: 281464--281651 Score: 260
Period size: 83 Copynumber: 2.2 Consensus size: 84
281454 CAATGCCATA
* * *
281464 TCCCAGATATGGTCTTACATGCTATCATATATCGATGCCAATAGCCCAGCTATGGTCTTACACGA
1 TCCCAGACATGGTCTTACACGCAATCATATATCGATGCCAATAGCCCAGCTATGGTCTTACACGA
*
281529 ATC-TCATATCGATGCCAATG
66 ATCAT-ATA-CGATGCAAATG
*
281549 TCCCAGGCATGGTCTTACACG-AATCATATA-CGATGCCAAT-GTCCCAGAC-ATGGTCTTACAC
1 TCCCAGACATGGTCTTACACGCAATCATATATCGATGCCAATAG-CCCAG-CTATGGTCTTACAC
281610 GAATCATATACGATGCAAATG
64 GAATCATATACGATGCAAATG
281631 TCCCAGACATGGTCTTACACG
1 TCCCAGACATGGTCTTACACG
281652 TCCGAAGTTC
Statistics
Matches: 94, Mismatches: 6, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
82 31 0.33
83 35 0.37
84 10 0.11
85 18 0.19
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (84 bp):
TCCCAGACATGGTCTTACACGCAATCATATATCGATGCCAATAGCCCAGCTATGGTCTTACACGA
ATCATATACGATGCAAATG
Found at i:281837 original size:30 final size:30
Alignment explanation
Indices: 281782--281902 Score: 120
Period size: 31 Copynumber: 4.0 Consensus size: 30
281772 TTCAACAATT
* *
281782 TATATTCATATACGAATCAAATTTGGCAAC
1 TATAATCATATACGAATCAAATTCGGCAAC
* * *
281812 ATATAATCATACACAAATC-AATTTGGCAATC
1 -TATAATCATATACGAATCAAATTCGGCAA-C
* * * *
281843 TATAACCATATATGAATCAAATTCGACAATG
1 TATAATCATATACGAATCAAATTCGGCAA-C
281874 TATAATCATATACGAATC-AATTCGGCAAC
1 TATAATCATATACGAATCAAATTCGGCAAC
281903 CTATTTTCTT
Statistics
Matches: 74, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
30 33 0.45
31 41 0.55
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (30 bp):
TATAATCATATACGAATCAAATTCGGCAAC
Found at i:281916 original size:61 final size:61
Alignment explanation
Indices: 281788--281956 Score: 176
Period size: 61 Copynumber: 2.8 Consensus size: 61
281778 AATTTATATT
* * * ** * * *
281788 CATATACGAATCAAATTTGGCAACATATAATCATACACAAATCAATTTGGCAATCTATAAC
1 CATATATGAATCAAATTCGACAATGTATAATCATATACAAATCAATTCGGCAACCTATAAC
* ***
281849 CATATATGAATCAAATTCGACAATGTATAATCATATACGAATCAATTCGGCAACCTATTTT
1 CATATATGAATCAAATTCGACAATGTATAATCATATACAAATCAATTCGGCAACCTATAAC
* * * * * *
281910 CTTATATAAATCAACTTCGATAATGTATAACCATATACAAATAAATT
1 CATATATGAATCAAATTCGACAATGTATAATCATATACAAATCAATT
281957 TCAGTAATGT
Statistics
Matches: 89, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 89 1.00
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.31
Consensus pattern (61 bp):
CATATATGAATCAAATTCGACAATGTATAATCATATACAAATCAATTCGGCAACCTATAAC
Found at i:281939 original size:92 final size:89
Alignment explanation
Indices: 281770--282061 Score: 244
Period size: 92 Copynumber: 3.2 Consensus size: 89
281760 TGCTCAAGTC
* * *
281770 AATTCAACAATTTATATTCATATACGAATCAAATTTGGCAACATATAATCATACACAAATCAATT
1 AATTC-ACAATGTATAATCATATACGAATC-AATTCGGCAACATATAATCATACACAAATCAATT
* * **
281835 TGGCAATCTATAACCATATATGAATCA
64 CGACAATCTATAACCATATACAAAT-A
* ** * * *
281862 AATTCGACAATGTATAATCATATACGAATCAATTCGGCAACCTATTTTCTTATATAAATCAACTT
1 AATTC-ACAATGTATAATCATATACGAATCAATTCGGCAACATATAATCATACACAAATCAA-TT
* *
281927 CGATAATGTATAACCATATACAAATA
64 CGACAATCTATAACCATATACAAATA
* * * * * * * * *
281953 AATTTCAGTAATGTATAATTATATACGAATTATTTCGGCAACTTAT-ATCCACATACAATTCTAT
1 AA-TTCA-CAATGTATAATCATATACGAATCAATTCGGCAACATATAAT-CATACACAAATC-AA
* *
282017 TTCAACAATGTATAACCATATACAAATA
62 TTCGACAATCTATAACCATATACAAATA
282045 AATTTCAGCAATGTATA
1 AA-TTCA-CAATGTATA
282062 TAATATATAC
Statistics
Matches: 165, Mismatches: 30, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
91 30 0.18
92 134 0.81
93 1 0.01
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (89 bp):
AATTCACAATGTATAATCATATACGAATCAATTCGGCAACATATAATCATACACAAATCAATTCG
ACAATCTATAACCATATACAAATA
Found at i:281966 original size:31 final size:31
Alignment explanation
Indices: 281931--282061 Score: 131
Period size: 31 Copynumber: 4.3 Consensus size: 31
281921 CAACTTCGAT
*
281931 AATGTATAACCATATACAAATAAATTTCAGT
1 AATGTATAACCATATACAAATAAATTTCAGC
** * * *
281962 AATGTATAATTATATACGAAT-TATTTCGGC
1 AATGTATAACCATATACAAATAAATTTCAGC
* * * ** *
281992 AACT-TATATCCACATACAATTCTATTTCAAC
1 AA-TGTATAACCATATACAAATAAATTTCAGC
282023 AATGTATAACCATATACAAATAAATTTCAGC
1 AATGTATAACCATATACAAATAAATTTCAGC
282054 AATGTATA
1 AATGTATA
282062 TAATATATAC
Statistics
Matches: 77, Mismatches: 20, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
30 20 0.26
31 57 0.74
ACGTcount: A:0.44, C:0.15, G:0.07, T:0.34
Consensus pattern (31 bp):
AATGTATAACCATATACAAATAAATTTCAGC
Found at i:299323 original size:12 final size:13
Alignment explanation
Indices: 299306--299338 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
299296 CATATTTAAG
299306 TTTTTA-ATAAAT
1 TTTTTACATAAAT
299318 TTTTTACATAAA-
1 TTTTTACATAAAT
299330 TTTTTACAT
1 TTTTTACAT
299339 CTATATCGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 15 0.75
13 5 0.25
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (13 bp):
TTTTTACATAAAT
Found at i:300493 original size:41 final size:40
Alignment explanation
Indices: 300436--300756 Score: 234
Period size: 41 Copynumber: 7.8 Consensus size: 40
300426 ATTTTTAAAC
* * * * *
300436 CTTTAGCGGTGTTTTTATTTTAGAGCCGCTAATGGTCCGAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCT-CGAT
* * * *
300477 CTTTAGCGGCGTTTTTATCTGAGCGCCACTAATGCTATGAC
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCT-CGAT
*
300518 CTTTAGCGGCGTTTTTCTCTAAGCGCCGCTAATGCTCGTAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCG-AT
* * * **
300559 CTTTAGTGGCGTTTTTATCTGAA-CGCCACTAATTCTCTGGC
1 CTTTAGCGGCGTTTTTATCT-AAGCGCCGCTAATGCTC-GAT
* * *
300600 CTTTAGCGGCAATTTTT-TCTAAGCGCCGCTAATGTTAGTAT
1 CTTTAGCGGC-GTTTTTATCTAAGCGCCGCTAATGCTCG-AT
* * * * *
300641 CTTTAGTGGTGTTTTTATCTGAGCGCCACTAATGCTCTG-G
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTC-GAT
** * ** *
300681 CTTTTAGCGGCGTTTTATAGGTAAGCGCCGCGAATGCATTTAC
1 C-TTTAGCGGCGTTTT-TATCTAAGCGCCGCTAATGC-TCGAT
** *
300724 CTTTAGCGGCGTTTTTGCCGAAGCGCCGCTAAT
1 CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAAT
300757 AGTAACAAAA
Statistics
Matches: 217, Mismatches: 51, Indels: 24
0.74 0.17 0.08
Matches are distributed among these distances:
40 10 0.05
41 167 0.77
42 38 0.18
43 2 0.01
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.37
Consensus pattern (40 bp):
CTTTAGCGGCGTTTTTATCTAAGCGCCGCTAATGCTCGAT
Found at i:300571 original size:82 final size:81
Alignment explanation
Indices: 300434--300696 Score: 339
Period size: 82 Copynumber: 3.2 Consensus size: 81
300424 CGATTTTTAA
* * * * * *
300434 ACCTTTAGCGGTGTTTTTATTTTAGAGCCGCTAATGGTCCG-ATCTTTAGCGGCGTTTTTATCTG
1 ACCTTTAGCGGCGTTTTT-TCTAAGCGCCGCTAATGCT-CGTATCTTTAGTGGCGTTTTTATCTG
*
300498 AGCGCCACTAATGCTATG
64 AGCGCCACTAATGCTCTG
300516 ACCTTTAGCGGCGTTTTTCTCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGA
1 ACCTTTAGCGGCGTTTTT-TCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGA
* *
300581 ACGCCACTAATTCTCTG
65 GCGCCACTAATGCTCTG
* * * * *
300598 GCCTTTAGCGGCAATTTTTTCTAAGCGCCGCTAATGTTAGTATCTTTAGTGGTGTTTTTATCTGA
1 ACCTTTAGCGGC-GTTTTTTCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGA
300663 GCGCCACTAATGCTCTG
65 GCGCCACTAATGCTCTG
* *
300680 GCTTTTAGCGGCGTTTT
1 ACCTTTAGCGGCGTTTT
300697 ATAGGTAAGC
Statistics
Matches: 160, Mismatches: 19, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
81 6 0.04
82 149 0.93
83 5 0.03
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (81 bp):
ACCTTTAGCGGCGTTTTTTCTAAGCGCCGCTAATGCTCGTATCTTTAGTGGCGTTTTTATCTGAG
CGCCACTAATGCTCTG
Found at i:320727 original size:21 final size:21
Alignment explanation
Indices: 320702--320746 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
320692 ATTTGCGGCA
*
320702 CTAAAAAGCGCCGCTAAAGGC
1 CTAAAAAGCGCCGCTAAAAGC
320723 CTAAAAAGCGCCGCTAAAAGC
1 CTAAAAAGCGCCGCTAAAAGC
320744 CTA
1 CTA
320747 TTTTGGTGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.40, C:0.29, G:0.20, T:0.11
Consensus pattern (21 bp):
CTAAAAAGCGCCGCTAAAAGC
Found at i:322182 original size:17 final size:17
Alignment explanation
Indices: 322141--322183 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
322131 TTAATTGCTT
322141 ACAT-AACATCTATGTG
1 ACATCAACATCTATGTG
*
322157 ACAATCAACATGTATGTG
1 AC-ATCAACATCTATGTG
322175 ACATCAACA
1 ACATCAACA
322184 AAGTTAACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 2 0.08
17 9 0.38
18 13 0.54
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.26
Consensus pattern (17 bp):
ACATCAACATCTATGTG
Found at i:323143 original size:26 final size:26
Alignment explanation
Indices: 323107--323158 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
323097 ATATGAATTT
*
323107 AGCCTATAAATAGGCTCTTTTACAAC
1 AGCCTATAAATAGGCTCTTGTACAAC
323133 AGCCTATAAATAGGCTCTTGTACAAC
1 AGCCTATAAATAGGCTCTTGTACAAC
323159 CTTAGAAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (26 bp):
AGCCTATAAATAGGCTCTTGTACAAC
Found at i:330764 original size:17 final size:18
Alignment explanation
Indices: 330744--330777 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
330734 TGTTTAACTA
*
330744 TTTACTTAATT-TAATGG
1 TTTACTAAATTATAATGG
330761 TTTACTAAATTATAATG
1 TTTACTAAATTATAATG
330778 TAAATTAGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (18 bp):
TTTACTAAATTATAATGG
Found at i:334740 original size:17 final size:19
Alignment explanation
Indices: 334718--334752 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
334708 TTAAAATCTA
334718 TCAGAAAA-AT-TAAAAAT
1 TCAGAAAATATATAAAAAT
334735 TCAGAAAATATATAAAAA
1 TCAGAAAATATATAAAAA
334753 AAATTCTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 2 0.12
19 6 0.38
ACGTcount: A:0.66, C:0.06, G:0.06, T:0.23
Consensus pattern (19 bp):
TCAGAAAATATATAAAAAT
Found at i:335649 original size:2 final size:2
Alignment explanation
Indices: 335642--335672 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
335632 ATATCTGATA
*
335642 AT AT AT AT AT AT AT AT AT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
335673 AAAGACTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:336407 original size:10 final size:9
Alignment explanation
Indices: 336394--336458 Score: 60
Period size: 10 Copynumber: 6.8 Consensus size: 9
336384 TAAAAGCTTG
336394 TAAAAATTCA
1 TAAAAATT-A
336404 TAAAAACTTA
1 TAAAAA-TTA
336414 TAAATAA-TA
1 TAAA-AATTA
* *
336423 TAAAAACTC
1 TAAAAATTA
336432 TAATAAATTA
1 TAA-AAATTA
336442 TAAAAATATA
1 TAAAAAT-TA
336452 TAAAAAT
1 TAAAAAT
336459 AGAAATCATA
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
8 2 0.04
9 14 0.30
10 27 0.57
11 4 0.09
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (9 bp):
TAAAAATTA
Found at i:336417 original size:20 final size:20
Alignment explanation
Indices: 336370--336458 Score: 71
Period size: 19 Copynumber: 4.5 Consensus size: 20
336360 ATGTTTAAAG
* *
336370 TATATAAAATTTTATAAAAGC
1 TATATAAAA-ATTATAAAAAC
*
336391 T-TGTAAAAATTCATAAAAAC
1 TATATAAAAATT-ATAAAAAC
336411 T-TATAAATAA-TATAAAAAC
1 TATATAAA-AATTATAAAAAC
* *
336430 TCTA-ATAAATTATAAAAA-
1 TATATAAAAATTATAAAAAC
336448 TATATAAAAAT
1 TATATAAAAAT
336459 AGAAATCATA
Statistics
Matches: 56, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
18 5 0.09
19 26 0.46
20 22 0.39
21 3 0.05
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.34
Consensus pattern (20 bp):
TATATAAAAATTATAAAAAC
Found at i:336452 original size:29 final size:29
Alignment explanation
Indices: 336394--336457 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
336384 TAAAAGCTTG
* *
336394 TAAAAATTCATAAAAACTTATAAATAATA
1 TAAAAACTCATAAAAACTTATAAAAAATA
336423 TAAAAACTC-TAATAAA-TTATAAAAATATA
1 TAAAAACTCATAA-AAACTTATAAAAA-ATA
336452 TAAAAA
1 TAAAAA
336458 TAGAAATCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 11 0.35
29 20 0.65
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (29 bp):
TAAAAACTCATAAAAACTTATAAAAAATA
Found at i:336459 original size:10 final size:10
Alignment explanation
Indices: 336223--336329 Score: 71
Period size: 10 Copynumber: 10.9 Consensus size: 10
336213 TCATATAATC
336223 ATAAAAATAT
1 ATAAAAATAT
336233 AT-AAAATAT
1 ATAAAAATAT
*
336242 -TAATAAATAA
1 ATAA-AAATAT
**
336252 ATAAACTTAT
1 ATAAAAATAT
336262 A-AAAAATAT
1 ATAAAAATAT
*
336271 AGAAAAATGAT
1 ATAAAAAT-AT
*
336282 AAAAAAATAT
1 ATAAAAATAT
* **
336292 TTAAAGAATCC
1 ATAAA-AATAT
*
336303 ATAAAAA-CT
1 ATAAAAATAT
336312 -TAAAAATAT
1 ATAAAAATAT
336321 ATAAAAATA
1 ATAAAAATA
336330 AAAATAAAAA
Statistics
Matches: 75, Mismatches: 14, Indels: 16
0.71 0.13 0.15
Matches are distributed among these distances:
8 7 0.09
9 17 0.23
10 32 0.43
11 19 0.25
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:336660 original size:19 final size:20
Alignment explanation
Indices: 336628--336667 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
336618 GACTCTCTCC
*
336628 TTTTTATTGATAAATAATTT
1 TTTTTATTGATAAAAAATTT
*
336648 TTTTTATT-TTAAAAAATTT
1 TTTTTATTGATAAAAAATTT
336667 T
1 T
336668 AACTTTCAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTTATTGATAAAAAATTT
Found at i:336942 original size:28 final size:29
Alignment explanation
Indices: 336909--336972 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
336899 CTTGTTTTGA
*
336909 AATTTTTACAAGTT-TTATAATTACTAGT
1 AATTTTTACAACTTGTTATAATTACTAGT
336937 AATTTTTACAACTTGTTATAATTACTAGT
1 AATTTTTACAACTTGTTATAATTACTAGT
336966 AATTTTT
1 AATTTTT
336973 TTTATAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 13 0.38
29 21 0.62
ACGTcount: A:0.34, C:0.08, G:0.06, T:0.52
Consensus pattern (29 bp):
AATTTTTACAACTTGTTATAATTACTAGT
Found at i:339509 original size:29 final size:29
Alignment explanation
Indices: 339464--339539 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
339454 TTAAAATTTT
339464 ATAAAAACATATTAAAATTCTATA-AAAATA
1 ATAAAAA-ATATTAAAATT-TATATAAAATA
* * *
339494 ATAAAAAGTATTAAAATTTATATAAACTT
1 ATAAAAAATATTAAAATTTATATAAAATA
* *
339523 ATAAAAATTATAAAAAT
1 ATAAAAAATATTAAAAT
339540 AAAAATAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 4 0.10
29 29 0.73
30 7 0.17
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (29 bp):
ATAAAAAATATTAAAATTTATATAAAATA
Found at i:349548 original size:29 final size:29
Alignment explanation
Indices: 349503--349578 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
349493 TTAAAATTTT
349503 ATAAAAACATATTAAAATTCTATA-AAAATA
1 ATAAAAA-ATATTAAAATT-TATATAAAATA
* * *
349533 ATAAAAAGTATTAAAATTTATATAAACTT
1 ATAAAAAATATTAAAATTTATATAAAATA
* *
349562 ATAAAAATTATAAAAAT
1 ATAAAAAATATTAAAAT
349579 AAAAATAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 4 0.10
29 29 0.73
30 7 0.17
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (29 bp):
ATAAAAAATATTAAAATTTATATAAAATA
Done.