Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007712.1 Hibiscus syriacus cultivar Beakdansim tig00109936_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 920388
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:143157 original size:37 final size:36
Alignment explanation
Indices: 143117--143199 Score: 103
Period size: 39 Copynumber: 2.2 Consensus size: 36
143107 AATCATTCCT
*
143117 AAAATTTAGTTTTTGTTTCATTTTAGTCCCCACTGTTA
1 AAAATTTAGTTTTTGTTTCATTTTAGT-ACC-CTGTTA
* * *
143155 AAAACTTCATTTTTTGTTTCATTTTAGTACCCTGTTC
1 AAAA-TTTAGTTTTTGTTTCATTTTAGTACCCTGTTA
143192 AAAATTTA
1 AAAATTTA
143200 ACGTTAAGTT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
36 3 0.08
37 9 0.23
38 6 0.15
39 21 0.54
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.49
Consensus pattern (36 bp):
AAAATTTAGTTTTTGTTTCATTTTAGTACCCTGTTA
Found at i:143318 original size:144 final size:144
Alignment explanation
Indices: 143153--143445 Score: 426
Period size: 144 Copynumber: 2.0 Consensus size: 144
143143 TCCCCACTGT
*
143153 TAAAAACTTCATTTTTTGTTTCATTTTAGTAC-CCTGTTCAAAATTTAACGTTAAGTTTCAAAAA
1 TAAAAACTTCAGTTTTTGTTTCATTTTAGTACTCC-GTTCAAAATTTAACGTTAAGTTTCAAAAA
* * * * *
143217 AAATGAAAGTTTAGGTACTAAAACGGATCAAAATTGATAGCTTAGGTACTAAACACATTAAGTTT
65 AAATGAAAGTTTAGGTACTAAAACGGACCAAAACTAATAGCTTAGATACTAAACACATTAAATTT
*
143282 TTAATGGTGGGGTAC
130 TTAATGGCGGGGTAC
* **
143297 TAAAAACTTTAGTTTTTGTTTCATTTTAGTACTCCGTTCAAAATTTAACGTTAAGTTTTGAAAAA
1 TAAAAACTTCAGTTTTTGTTTCATTTTAGTACTCCGTTCAAAATTTAACGTTAAGTTTCAAAAAA
* * * * * *
143362 ATTGAAAGTTTATGTACTAAAACGGGCCAAAACTAATAGTTTATATACTAAACGCATTAAATTTT
66 AATGAAAGTTTAGGTACTAAAACGGACCAAAACTAATAGCTTAGATACTAAACACATTAAATTTT
143427 TAATGGCGGGGTAC
131 TAATGGCGGGGTAC
143441 TAAAA
1 TAAAA
143446 TGAAAATGAT
Statistics
Matches: 132, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
144 130 0.98
145 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (144 bp):
TAAAAACTTCAGTTTTTGTTTCATTTTAGTACTCCGTTCAAAATTTAACGTTAAGTTTCAAAAAA
AATGAAAGTTTAGGTACTAAAACGGACCAAAACTAATAGCTTAGATACTAAACACATTAAATTTT
TAATGGCGGGGTAC
Found at i:145476 original size:21 final size:21
Alignment explanation
Indices: 145436--145479 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
145426 TGGTAAAAAA
* * *
145436 TTACTTAAAATATTATTATTT
1 TTACTTAAAACATCAATATTT
145457 TTACTTAAAACATCAATATTT
1 TTACTTAAAACATCAATATTT
145478 TT
1 TT
145480 TAGTATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (21 bp):
TTACTTAAAACATCAATATTT
Found at i:151467 original size:15 final size:15
Alignment explanation
Indices: 151447--151479 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
151437 AAGAGAGAGA
151447 AAAAACTAAA-AAAAC
1 AAAAAC-AAACAAAAC
151462 AAAAACAAACAAAAC
1 AAAAACAAACAAAAC
151477 AAA
1 AAA
151480 GGGAAAGCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAAACAAACAAAAC
Found at i:151918 original size:30 final size:30
Alignment explanation
Indices: 151871--151966 Score: 131
Period size: 30 Copynumber: 3.2 Consensus size: 30
151861 GCATTCTGGT
*
151871 CTTTAATTTTCTGTTTTAGTTATTTTAGTC
1 CTTTAAGTTTCTGTTTTAGTTATTTTAGTC
* *
151901 CATTAAGTTTCTATTTTAGTTATTTTAGTC
1 CTTTAAGTTTCTGTTTTAGTTATTTTAGTC
* *
151931 CTTTAAGTTTATGTATTT-GTTATTTTGGTC
1 CTTTAAGTTTCTGT-TTTAGTTATTTTAGTC
151961 CTTTAA
1 CTTTAA
151967 CTTTTTGTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 55 0.95
31 3 0.05
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.59
Consensus pattern (30 bp):
CTTTAAGTTTCTGTTTTAGTTATTTTAGTC
Found at i:151976 original size:30 final size:30
Alignment explanation
Indices: 151871--151979 Score: 123
Period size: 30 Copynumber: 3.6 Consensus size: 30
151861 GCATTCTGGT
151871 CTTTAA-TTTTCTGTTTTAGTTATTTTAGTC
1 CTTTAAGTTTT-TGTTTTAGTTATTTTAGTC
* * *
151901 CATTAAGTTTCTATTTTAGTTATTTTAGTC
1 CTTTAAGTTTTTGTTTTAGTTATTTTAGTC
* *
151931 CTTTAAGTTTATGTATTT-GTTATTTTGGTC
1 CTTTAAGTTTTTGT-TTTAGTTATTTTAGTC
*
151961 CTTTAACTTTTTGTATTTA
1 CTTTAAGTTTTTGT-TTTA
151980 CTGTTCAACC
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
30 61 0.91
31 6 0.09
ACGTcount: A:0.19, C:0.09, G:0.11, T:0.61
Consensus pattern (30 bp):
CTTTAAGTTTTTGTTTTAGTTATTTTAGTC
Found at i:153326 original size:38 final size:36
Alignment explanation
Indices: 153274--153628 Score: 204
Period size: 38 Copynumber: 9.3 Consensus size: 36
153264 GTGATTAACG
* *
153274 TGGAAACCTAATTTTAGGATTAGAAACTCGTTTTAGGT
1 TGGAAACCTGATTTTA-GATTGGAAACT-GTTTTAGGT
*
153312 TGGAAACCTGATTTTTAGTTTGGAAAACATGTTTTAGGT
1 TGGAAACCTGA-TTTTAGATTGG-AAAC-TGTTTTAGGT
* * * *
153351 TGAAAACCTGGTTCT-GAGTTGGAAATCTGATTTTGGGAT
1 TGGAAACCTGATTTTAGA-TTGGAAA-CTG-TTTTAGG-T
* *
153390 TGGAAA--TAAGTTTTAGGTTGGAAAACTGATTTTAGGT
1 TGGAAACCTGA-TTTTAGATTGG-AAACTG-TTTTAGGT
** * *
153427 TGGAAACCAAATTTTTAGTTTGGATAACAAGTTTTAGGT
1 TGGAAACCTGA-TTTTAGATTGGA-AAC-TGTTTTAGGT
*
153466 TGGAAACCTGATTTTGGGATTGGAAA-TAGGTTTTAGGT
1 TGGAAACCTGATTTT-AGATTGGAAACT--GTTTTAGGT
* * * *
153504 TGGAAACATGATTTTTAGTTTGTAAAATAGGTTTTAGGT
1 TGGAAACCTGA-TTTTAGATTGGAAACT--GTTTTAGGT
*
153543 AT-GAAACATGATTTT-GAGTTGGAAACCTGATTTTAGGAT
1 -TGGAAACCTGATTTTAGA-TTGGAAA-CTG-TTTTAGG-T
* *
153582 T-GAGAACATG-TTTTAGGTTGGAAAACTGATTTTAGGT
1 TGGA-AACCTGATTTTAGATTGG-AAACTG-TTTTAGGT
153619 TGGAAACCTG
1 TGGAAACCTG
153629 CCTTTGGGAT
Statistics
Matches: 257, Mismatches: 32, Indels: 57
0.74 0.09 0.16
Matches are distributed among these distances:
37 23 0.09
38 119 0.46
39 112 0.44
40 3 0.01
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (36 bp):
TGGAAACCTGATTTTAGATTGGAAACTGTTTTAGGT
Found at i:153601 original size:192 final size:191
Alignment explanation
Indices: 153274--153626 Score: 523
Period size: 192 Copynumber: 1.8 Consensus size: 191
153264 GTGATTAACG
*
153274 TGGAAACCTAATTTTAGGATTAGAAACTCGTTTTAGGTTGGAAACCTGATTTTTAGTTTGGAAAA
1 TGGAAACCTAATTTTAGGATTAGAAACTCGTTTTAGGTTGGAAACATGATTTTTAGTTTGGAAAA
* * * * *
153339 CATGTTTTAGGTTGAAAACCTGGTTCTGAGTTGGAAATCTGATTTTGGGATTGGAAATAAGTTTT
66 CAGGTTTTAGGTTGAAAACATGATTCTGAGTTGGAAACCTGATTTTAGGATTGGAAAT-AGTTTT
153404 AGGTTGGAAAACTGATTTTAGGTTGGAAACCAAATTTTTAGTTTGGATAACAAGTTTTAGGT
130 AGGTTGGAAAACTGATTTTAGGTTGGAAACCAAATTTTTAGTTTGGATAACAAGTTTTAGGT
* * * * *
153466 TGGAAACCTGATTTTGGGATTGGAAA-TAGGTTTTAGGTTGGAAACATGATTTTTAGTTTGTAAA
1 TGGAAACCTAATTTTAGGATTAGAAACT-CGTTTTAGGTTGGAAACATGATTTTTAGTTTGGAAA
* *
153530 ATAGGTTTTAGGTATG-AAACATGATTTTGAGTTGGAAACCTGATTTTAGGATTGAGAACAT-GT
65 ACAGGTTTTAGGT-TGAAAACATGATTCTGAGTTGGAAACCTGATTTTAGGATTG-GAA-ATAGT
153593 TTTAGGTTGGAAAACTGATTTTAGGTTGGAAACC
127 TTTAGGTTGGAAAACTGATTTTAGGTTGGAAACC
153627 TGCCTTTGGG
Statistics
Matches: 144, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
191 1 0.01
192 136 0.94
193 5 0.03
194 2 0.01
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (191 bp):
TGGAAACCTAATTTTAGGATTAGAAACTCGTTTTAGGTTGGAAACATGATTTTTAGTTTGGAAAA
CAGGTTTTAGGTTGAAAACATGATTCTGAGTTGGAAACCTGATTTTAGGATTGGAAATAGTTTTA
GGTTGGAAAACTGATTTTAGGTTGGAAACCAAATTTTTAGTTTGGATAACAAGTTTTAGGT
Found at i:153645 original size:96 final size:93
Alignment explanation
Indices: 153274--153625 Score: 360
Period size: 96 Copynumber: 3.7 Consensus size: 93
153264 GTGATTAACG
* * * * *
153274 TGGAAACCTAATTTTAGGATTAGAAACTCGTTTTAGGTTGGAAACCTGATTTTTAGTTTGGAAAA
1 TGGAAACCTGATTTTAGGATTGGAAA-TAGTTTTAGGTTGGAAAACTGATTTTTAGGTTGG-AAA
* * *
153339 CATGTTTTAGGTTGAAAACCTGGTTCTGAGT
64 CATGTTTTAGGTTGGAAACAT-GTTTTGAGT
* *
153370 TGGAAATCTGATTTTGGGATTGGAAATAAGTTTTAGGTTGGAAAACTGA-TTTTAGGTTGGAAAC
1 TGGAAACCTGATTTTAGGATTGGAAAT-AGTTTTAGGTTGGAAAACTGATTTTTAGGTTGGAAA-
* *
153434 CAAAT-TTTTAGTTTGGATAACAAGTTTT-AGGT
64 C--ATGTTTTAGGTTGGA-AACATGTTTTGA-GT
* * *
153466 TGGAAACCTGATTTTGGGATTGGAAATAGGTTTTAGGTTGG-AAACATGATTTTTAGTTTGTAAA
1 TGGAAACCTGATTTTAGGATTGGAAATA-GTTTTAGGTTGGAAAAC-TGATTTTTAGGTTGGAAA
153530 -ATAGGTTTTAGGTAT-GAAACATGATTTTGAGT
64 CAT--GTTTTAGGT-TGGAAACATG-TTTTGAGT
153562 TGGAAACCTGATTTTAGGATTGAGAACAT-GTTTTAGGTTGGAAAACTGA-TTTTAGGTTGGAAA
1 TGGAAACCTGATTTTAGGATTG-GAA-ATAGTTTTAGGTTGGAAAACTGATTTTTAGGTTGGAAA
153625 C
64 C
153626 CTGCCTTTGG
Statistics
Matches: 217, Mismatches: 20, Indels: 38
0.79 0.07 0.14
Matches are distributed among these distances:
93 2 0.01
94 3 0.01
95 35 0.16
96 149 0.69
97 26 0.12
98 2 0.01
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (93 bp):
TGGAAACCTGATTTTAGGATTGGAAATAGTTTTAGGTTGGAAAACTGATTTTTAGGTTGGAAACA
TGTTTTAGGTTGGAAACATGTTTTGAGT
Found at i:153807 original size:38 final size:38
Alignment explanation
Indices: 153756--153845 Score: 139
Period size: 38 Copynumber: 2.4 Consensus size: 38
153746 TGGGAACACG
153756 TAATCATAATTATTTCAGGTGACTCGCA-CATGAGTACC
1 TAATCATAATTATTTCAGGTGACTCGCATCA-GAGTACC
* *
153794 TAATCATAATTATTCCAGGTGACTCGCATGAGAGTACC
1 TAATCATAATTATTTCAGGTGACTCGCATCAGAGTACC
153832 TAATCA-AATTATTT
1 TAATCATAATTATTT
153846 TTTATATTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
37 7 0.15
38 40 0.83
39 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (38 bp):
TAATCATAATTATTTCAGGTGACTCGCATCAGAGTACC
Found at i:155956 original size:38 final size:38
Alignment explanation
Indices: 155914--156035 Score: 163
Period size: 38 Copynumber: 3.2 Consensus size: 38
155904 GTTAGAAACT
155914 TGATTTTGGGATTAGAAACAGGTTTTAGGTTGGAAAAA
1 TGATTTTGGGATTAGAAACAGGTTTTAGGTTGGAAAAA
** * * * * *
155952 TGATTTTTAGCTTGGAAAACAAGTTTTAAGTTGGAAACA
1 TGATTTTGGGATTAG-AAACAGGTTTTAGGTTGGAAAAA
*
155991 TGATTTTGGGATTAGAAACAGGTTTTAGGTTGGAAAAT
1 TGATTTTGGGATTAGAAACAGGTTTTAGGTTGGAAAAA
156029 TGATTTT
1 TGATTTT
156036 AGTTTGGAAA
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
38 37 0.54
39 31 0.46
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (38 bp):
TGATTTTGGGATTAGAAACAGGTTTTAGGTTGGAAAAA
Found at i:155961 original size:77 final size:76
Alignment explanation
Indices: 155860--156066 Score: 247
Period size: 77 Copynumber: 2.7 Consensus size: 76
155850 GAAACCTGAT
* * * * * *
155860 TTTTAGTTTGAAAAAAAGGTTTTAGGCTGGAAACCCGATTTTGAGTTAGAAACTTGATTTTGGGA
1 TTTTAGGTTGGAAAAATGATTTTAGGCTGGAAACACGATTTTGAGTTGGAAACTTGATTTTGGGA
155925 TTAGAAACAGG
66 TTAGAAACAGG
* * *
155936 TTTTAGGTTGGAAAAATGATTTTTA-GCTTGGAAA-ACAAGTTTTAAGTTGGAAACATGATTTTG
1 TTTTAGGTTGGAAAAATGA-TTTTAGGC-TGGAAACACGA-TTTTGAGTTGGAAACTTGATTTTG
155999 GGATTAGAAACAGG
63 GGATTAGAAACAGG
* ** **
156013 TTTTAGGTTGGAAAATTGATTTTAGTTTGGAAACTTGATTTTGAGTTGGAAACT
1 TTTTAGGTTGGAAAAATGATTTTAGGCTGGAAACACGATTTTGAGTTGGAAACT
156067 AGACTTTATG
Statistics
Matches: 109, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
76 44 0.40
77 65 0.60
ACGTcount: A:0.32, C:0.06, G:0.25, T:0.37
Consensus pattern (76 bp):
TTTTAGGTTGGAAAAATGATTTTAGGCTGGAAACACGATTTTGAGTTGGAAACTTGATTTTGGGA
TTAGAAACAGG
Found at i:155978 original size:39 final size:39
Alignment explanation
Indices: 155929--156045 Score: 139
Period size: 39 Copynumber: 3.1 Consensus size: 39
155919 TTGGGATTAG
*
155929 AAACAGGTTTTAGGTTGGAAAAATGATTTTTAGCTTGGA
1 AAACAGGTTTTAGGTTGGAAAAATGATTTTTAGATTGGA
* * * ** *
155968 AAACAAGTTTTAAGTTGGAAACATGATTTTGGGATTAG-
1 AAACAGGTTTTAGGTTGGAAAAATGATTTTTAGATTGGA
* *
156006 AAACAGGTTTTAGGTTGGAAAATTGA-TTTTAGTTTGGA
1 AAACAGGTTTTAGGTTGGAAAAATGATTTTTAGATTGGA
156044 AA
1 AA
156046 CTTGATTTTG
Statistics
Matches: 62, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
37 7 0.11
38 24 0.39
39 31 0.50
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (39 bp):
AAACAGGTTTTAGGTTGGAAAAATGATTTTTAGATTGGA
Found at i:156083 original size:20 final size:19
Alignment explanation
Indices: 155838--156091 Score: 89
Period size: 19 Copynumber: 13.2 Consensus size: 19
155828 TAACGTACTT
155838 GATTTTGAGTTGGAAACCT-
1 GATTTTGAGTTGGAAA-CTA
* * **
155857 GATTTTTAGTTTGAAAAAAA
1 GATTTTGAG-TTGGAAACTA
* * **
155877 GGTTTT-AGGCTGGAAACCC
1 GATTTTGA-GTTGGAAACTA
* *
155896 GATTTTGAGTTAGAAACTT
1 GATTTTGAGTTGGAAACTA
* *
155915 GATTTTGGGATTAGAAAC-A
1 GATTTTGAG-TTGGAAACTA
* *
155934 GGTTTT-AGGTTGGAAA-AA
1 GATTTTGA-GTTGGAAACTA
* *
155952 TGATTTTTAGCTTGGAAAACAA
1 -GATTTTGAG-TTGG-AAACTA
*
155974 G-TTTTAAGTTGGAAAC-A
1 GATTTTGAGTTGGAAACTA
* *
155991 TGATTTTGGGATTAGAAAC-A
1 -GATTTTGAG-TTGGAAACTA
* * *
156011 GGTTTT-AGGTTGGAAAATT
1 GATTTTGA-GTTGGAAACTA
*
156030 GATTTT-AGTTTGGAAACTT
1 GATTTTGAG-TTGGAAACTA
156049 GATTTTGAGTTGGAAACTA
1 GATTTTGAGTTGGAAACTA
*
156068 GACTTTATGA-TTGGAAACCA
1 GA-TTT-TGAGTTGGAAACTA
156088 GATT
1 GATT
156092 CTGCGAAGGA
Statistics
Matches: 180, Mismatches: 34, Indels: 42
0.70 0.13 0.16
Matches are distributed among these distances:
17 1 0.01
18 19 0.11
19 95 0.53
20 56 0.31
21 7 0.04
22 2 0.01
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.37
Consensus pattern (19 bp):
GATTTTGAGTTGGAAACTA
Found at i:156219 original size:69 final size:69
Alignment explanation
Indices: 156095--156278 Score: 221
Period size: 69 Copynumber: 2.7 Consensus size: 69
156085 CCAGATTCTG
* * * * * * *
156095 CGAAGGATAAGAGTAACTCACA-ATGGAGCACTTAATCATAACTATTTCGGGTGACTCGCACGGG
1 CGAAAGATTAGAGTAACTCGCACA-GGAGCACCTAATCATAATTATTTCGAGTGACTCACACGGG
156159 AGCCT
65 AGCCT
*
156164 CGAAAGATTAGATTAACTCGCACAGGAGCACCTAATCATAATTA-TTCTGAGTGACTCACACGGG
1 CGAAAGATTAGAGTAACTCGCACAGGAGCACCTAATCATAATTATTTC-GAGTGACTCACACGGG
156228 AGCCT
65 AGCCT
* * * *
156233 CGAAGGATTAGAGTGACTCGCACGGGAGAACCTAATCAT-ATTATTT
1 CGAAAGATTAGAGTAACTCGCACAGGAGCACCTAATCATAATTATTT
156279 TCATATTCGG
Statistics
Matches: 99, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
68 7 0.07
69 91 0.92
70 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (69 bp):
CGAAAGATTAGAGTAACTCGCACAGGAGCACCTAATCATAATTATTTCGAGTGACTCACACGGGA
GCCT
Found at i:160015 original size:14 final size:14
Alignment explanation
Indices: 159996--160026 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
159986 CTAAATTTAT
159996 TTTAATTTAATATA
1 TTTAATTTAATATA
160010 TTTAATTTAATATA
1 TTTAATTTAATATA
160024 TTT
1 TTT
160027 TATGTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTAATTTAATATA
Found at i:160313 original size:31 final size:31
Alignment explanation
Indices: 160275--160335 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
160265 TTACCACATC
*
160275 TTTAATTAAATAAAA-ATGAAAGTGATCATAT
1 TTTAATTAAATAAAAGA-GAAAGTGACCATAT
160306 TTTAATTAAATAAAAGAGAAAGTGACCATA
1 TTTAATTAAATAAAAGAGAAAGTGACCATA
160336 CATTATGGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.52, C:0.05, G:0.11, T:0.31
Consensus pattern (31 bp):
TTTAATTAAATAAAAGAGAAAGTGACCATAT
Found at i:162006 original size:83 final size:83
Alignment explanation
Indices: 161887--162129 Score: 328
Period size: 83 Copynumber: 2.9 Consensus size: 83
161877 TTGTTATCTA
* * * * *
161887 TTTAAATTTAGATATTAAAA-AAGTGTTGGTTGGAGTAAAACTCTCAGTTTTATTATTATAAATT
1 TTTAAATTGAGATATTAAAAGAA-TTTTGGTTAGAGTAAAACTCTCAGATTTAATATTATAAATT
* *
161951 TATAATATATTATAATATG
65 TAAAAGATATTATAATATG
* * *
161970 TTTAGATTTA-ACTATTAAAAGAATTTTGGTTAGAGTAAAACTCTCAGGTTTAATATTATAAATT
1 TTTAAATTGAGA-TATTAAAAGAATTTTGGTTAGAGTAAAACTCTCAGATTTAATATTATAAATT
162034 TAAAAGATATTATAATATG
65 TAAAAGATATTATAATATG
* * * *
162053 TTTAAATTGAGATATTAAAAGAGTTTTGGTTAGAATAAAACTCTCAAATTTAATATTTTAAATTT
1 TTTAAATTGAGATATTAAAAGAATTTTGGTTAGAGTAAAACTCTCAGATTTAATATTATAAATTT
162118 AAAAGATATTAT
66 AAAAGATATTAT
162130 TATCTATTTT
Statistics
Matches: 143, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
82 1 0.01
83 139 0.97
84 3 0.02
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (83 bp):
TTTAAATTGAGATATTAAAAGAATTTTGGTTAGAGTAAAACTCTCAGATTTAATATTATAAATTT
AAAAGATATTATAATATG
Found at i:162928 original size:4 final size:4
Alignment explanation
Indices: 162919--162945 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
162909 CAATGCATGT
162919 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
162946 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:171089 original size:83 final size:82
Alignment explanation
Indices: 170980--171266 Score: 380
Period size: 83 Copynumber: 3.5 Consensus size: 82
170970 GGAAATATAT
* *
170980 GTTTAATATT-TAAATTTAAACA-ATATTATTATCTATTTAAATTTAGATATTAGAAGAGTTTTG
1 GTTTAATATTATAAATTTAAA-AGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTG
171043 GTTGTAGTAAAACTCTCAG
65 GTTG-AGTAAAACTCTCAG
* * *
171062 GTTTAATATTATAAATTTAAAAGATATTATAATTTGTTTAAATTTAGATATTAAAAGAATTTTGG
1 GTTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
*
171127 TTGGAGTAAAACTCTCAA
66 TT-GAGTAAAACTCTCAG
* * * *
171145 GTTTAATATTATAAATTTAAAAGATATTATAATTTGTTTAAATTTAGATATCAAAATAGTTTTGG
1 GTTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
* *
171210 TTAGAATGAAACTCTCAG
66 TT-GAGTAAAACTCTCAG
* * * *
171228 ATTTAATATTTTAAATTTAAAAGATACTATTATCTATTT
1 GTTTAATATTATAAATTTAAAAGATATTATAATCTATTT
171267 TTAAATATTA
Statistics
Matches: 183, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
82 11 0.06
83 171 0.93
84 1 0.01
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (82 bp):
GTTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
TTGAGTAAAACTCTCAG
Found at i:171188 original size:166 final size:161
Alignment explanation
Indices: 170980--171304 Score: 411
Period size: 166 Copynumber: 2.0 Consensus size: 161
170970 GGAAATATAT
* * *
170980 GTTTAATATTTAAATTTAAACAATATTATTATCTATTTAAATTTAGATATTAGAAGAGTTTTGGT
1 GTTTAATATTTAAATTTAAACAATATTATAATCTATTTAAATTTAGATATCAAAAGAGTTTTGGT
* * * * * *
171045 T-GTAGTAAAACTCTCAGGTTTAATATTATAAATTTAAAAGATATTATAATTTGTTTAAATTTAG
66 TAG-AATAAAACTCTCAGATTTAATATTATAAATTTAAAAGATACTATAATCT-ATT---TTTAA
* *
171109 ATATTAAAAGAATTTTGGTTGGAGTAAAACTCTCAA
126 ATATTAAAACAATTTTAGTTGGAGTAAAACTCTCAA
* * *
171145 GTTTAATATTATAAATTTAAA-AGATATTATAATTTGTTTAAATTTAGATATCAAAATAGTTTTG
1 GTTTAATATT-TAAATTTAAACA-ATATTATAATCTATTTAAATTTAGATATCAAAAGAGTTTTG
* * *
171209 GTTAGAATGAAACTCTCAGATTTAATATTTTAAATTTAAAAGATACTATTATCTATTTTTAAATA
64 GTTAGAATAAAACTCTCAGATTTAATATTATAAATTTAAAAGATACTATAATCTATTTTTAAATA
*
171274 TTAAAACAATTTTAGTTGGAGTAAAATTCTC
129 TTAAAACAATTTTAGTTGGAGTAAAACTCTC
171305 TCGAAATTCT
Statistics
Matches: 139, Mismatches: 18, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
162 35 0.25
165 13 0.09
166 90 0.65
167 1 0.01
ACGTcount: A:0.41, C:0.05, G:0.11, T:0.43
Consensus pattern (161 bp):
GTTTAATATTTAAATTTAAACAATATTATAATCTATTTAAATTTAGATATCAAAAGAGTTTTGGT
TAGAATAAAACTCTCAGATTTAATATTATAAATTTAAAAGATACTATAATCTATTTTTAAATATT
AAAACAATTTTAGTTGGAGTAAAACTCTCAA
Found at i:172725 original size:14 final size:13
Alignment explanation
Indices: 172696--172729 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
172686 AACTTTAAAA
*
172696 TTTAAAAATTATT
1 TTTAAAAATAATT
172709 TTTAAATAATAATT
1 TTTAAA-AATAATT
172723 TTTAAAA
1 TTTAAAA
172730 TAAAAGCGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TTTAAAAATAATT
Found at i:183013 original size:3 final size:3
Alignment explanation
Indices: 183005--183030 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
182995 AATATTACGG
183005 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
183031 TTTGAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:183492 original size:29 final size:29
Alignment explanation
Indices: 183453--183525 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
183443 AGAATTCACC
183453 GAAGCCAAGAAATCTGATCCAACTCTGAA
1 GAAGCCAAGAAATCTGATCCAACTCTGAA
* *
183482 GAAGCCGAGAAATCTGATCCAAGTCTGAA
1 GAAGCCAAGAAATCTGATCCAACTCTGAA
* *
183511 GACGCCAAGAGATCT
1 GAAGCCAAGAAATCT
183526 CAAAATCATA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.16
Consensus pattern (29 bp):
GAAGCCAAGAAATCTGATCCAACTCTGAA
Found at i:184017 original size:14 final size:15
Alignment explanation
Indices: 183993--184023 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
183983 GATTTATTCA
183993 AAAATTAATTTAAAT
1 AAAATTAATTTAAAT
184008 AAAA-TAATTTAAAT
1 AAAATTAATTTAAAT
184022 AA
1 AA
184024 TTATTATAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATTAATTTAAAT
Found at i:186213 original size:20 final size:20
Alignment explanation
Indices: 186190--186241 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
186180 AACGCGATCC
186190 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
186210 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
186230 CCAAAATCGCAA
1 CCAGAATCGCAA
186242 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:186322 original size:20 final size:20
Alignment explanation
Indices: 186297--186490 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
186287 GATTTTCCAT
* *
186297 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
186317 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
186337 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
186357 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
186377 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
186397 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
186417 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
186437 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
186458 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
186478 AATCGCAACGCGA
1 AATCGCAACGCGA
186491 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:186342 original size:40 final size:39
Alignment explanation
Indices: 186293--186490 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
186283 TTGCGATTTT
* ** *
186293 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
186331 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
186372 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
186412 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
186451 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
186491 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:186380 original size:60 final size:60
Alignment explanation
Indices: 186297--186489 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
186287 GATTTTCCAT
* ** * *
186297 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
186357 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
186417 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
186478 AATCGCAACGCG
1 AATCGCAACGCG
186490 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:186910 original size:33 final size:33
Alignment explanation
Indices: 186871--186941 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
186861 TTCACTTAGA
*
186871 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
186904 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
186937 TTTCA
1 TTTCA
186942 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:187081 original size:14 final size:14
Alignment explanation
Indices: 187062--187116 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
187052 AGAATGACTG
187062 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
187076 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
187095 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
187109 TCGCAACG
1 TCGCAACG
187117 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:187099 original size:33 final size:33
Alignment explanation
Indices: 187062--187132 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
187052 AGAATGACTG
**
187062 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
187095 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
187128 TCGCA
1 TCGCA
187133 TTGCGATTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:187150 original size:19 final size:19
Alignment explanation
Indices: 187128--187225 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
187118 GAAACCAAAA
*
187128 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
187147 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
187161 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
187180 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
187194 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
187213 TCGCGTTGCGATT
1 TCGCGTTGCGATT
187226 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:187169 original size:14 final size:14
Alignment explanation
Indices: 187150--187239 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
187140 TTTCATTTCG
187150 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
187164 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
187183 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
187197 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
187214 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
187230 CGTTGCGATT
1 CGTTGCGATT
187240 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:187175 original size:33 final size:33
Alignment explanation
Indices: 187133--187247 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
187123 CAAAATCGCA
187133 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
187166 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
187199 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
187232 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
187248 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:189258 original size:93 final size:93
Alignment explanation
Indices: 188944--189414 Score: 903
Period size: 93 Copynumber: 5.1 Consensus size: 93
188934 TAGATTGCTT
*
188944 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
189009 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
189037 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
189101 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
189129 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
189194 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
189222 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
189286 -TTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
189313 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
189378 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
189406 AGTAAATTT
1 AGTAAATTT
189415 ATCCATTCAA
Statistics
Matches: 372, Mismatches: 3, Indels: 6
0.98 0.01 0.02
Matches are distributed among these distances:
91 89 0.24
92 95 0.26
93 188 0.51
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:189411 original size:184 final size:185
Alignment explanation
Indices: 188944--189414 Score: 917
Period size: 185 Copynumber: 2.6 Consensus size: 185
188934 TAGATTGCTT
*
188944 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
189009 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
189074 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
189129 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
189194 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
189259 GTGTATTCTTTAACACTGTGAAATATA-TTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
189313 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
189378 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
189415 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
184 129 0.45
185 155 0.55
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:189498 original size:19 final size:19
Alignment explanation
Indices: 189458--189586 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
189448 TAGTTTACTT
* *
189458 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
189478 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
189497 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
189516 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
189530 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
189549 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
189563 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
189582 TCGCA
1 TCGCA
189587 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:189537 original size:33 final size:32
Alignment explanation
Indices: 189494--189586 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
189484 CGCGAAACCA
**
189494 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
189526 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
189559 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
189587 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:189584 original size:52 final size:52
Alignment explanation
Indices: 189458--189586 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
189448 TAGTTTACTT
**
189458 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
189510 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
189563 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
189587 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:189604 original size:19 final size:19
Alignment explanation
Indices: 189582--189716 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
189572 GAAACCAAAA
*
189582 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
189601 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
189617 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
189634 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
189650 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
189667 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
189686 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
189706 TCGTGTTGCGA
1 TCGCGTTGCGA
189717 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:189623 original size:14 final size:14
Alignment explanation
Indices: 189604--189660 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
189594 TTTCATTTCG
189604 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
189618 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
189635 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
189651 CGTTGCGATT
1 CGTTGCGATT
189661 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:189629 original size:33 final size:33
Alignment explanation
Indices: 189587--189679 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
189577 CAAAATCGCA
*
189587 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
189620 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
189653 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
189680 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:191640 original size:14 final size:14
Alignment explanation
Indices: 191621--191656 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
191611 ATTGTTTAAT
191621 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
191635 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
191649 TGATTTGT
1 TGATTTGT
191657 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:191779 original size:19 final size:19
Alignment explanation
Indices: 191763--191864 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
191753 AAAAATGACT
191763 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
191782 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
191801 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
191815 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
191834 ATCGCAATACGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
191854 ATCGCAATGCG
1 ATCGCAATGCG
191865 TTTATAATTT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:191917 original size:19 final size:19
Alignment explanation
Indices: 191893--192185 Score: 392
Period size: 19 Copynumber: 16.4 Consensus size: 19
191883 GATTATCTCG
191893 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
191912 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
191931 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
191945 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
191964 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
191983 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
192002 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
192021 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
192040 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
192059 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
192073 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
192092 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
192111 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
192125 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
192145 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
192159 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
192178 TTGCGATT
1 TTGCGATT
192186 GTATTTTCCG
Statistics
Matches: 245, Mismatches: 8, Indels: 42
0.83 0.03 0.14
Matches are distributed among these distances:
14 29 0.12
16 24 0.10
17 20 0.08
18 3 0.01
19 157 0.64
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:191933 original size:52 final size:52
Alignment explanation
Indices: 191871--192185 Score: 330
Period size: 52 Copynumber: 5.9 Consensus size: 52
191861 TGCGTTTATA
*
191871 ATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
191923 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
191975 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
192032 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
192084 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-ATTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
192136 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTATTTC--GTTGCGATTTTCATTTCGCATTGCGATT
192186 GTATTTTCCG
Statistics
Matches: 241, Mismatches: 9, Indels: 25
0.88 0.03 0.09
Matches are distributed among these distances:
48 9 0.04
50 5 0.02
51 4 0.02
52 129 0.54
53 18 0.07
54 6 0.02
55 8 0.03
57 62 0.26
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTATTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:192041 original size:128 final size:122
Alignment explanation
Indices: 191893--192157 Score: 194
Period size: 128 Copynumber: 2.1 Consensus size: 122
191883 GATTATCTCG
*
191893 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TGTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
191955 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
192019 CA
121 CA
* * *
192021 TTGCGATTTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TTC-TGTCG-TTGCGATTTT
1 TTGCGATTTTCATTTCGCATTGCGA--TT-CTGTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
192083 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATTT-CG
192143 CA
121 CA
192145 TTGCGATTTTCAT
1 TTGCGATTTTCAT
192158 GTTGGGATTT
Statistics
Matches: 125, Mismatches: 5, Indels: 18
0.84 0.03 0.12
Matches are distributed among these distances:
121 7 0.06
122 4 0.03
123 18 0.14
124 18 0.14
125 2 0.02
126 2 0.02
128 74 0.59
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (122 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTGTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
Found at i:194046 original size:12 final size:12
Alignment explanation
Indices: 194029--194053 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
194019 TCTTCGGGGA
194029 CTTTTTCTTCTT
1 CTTTTTCTTCTT
194041 CTTTTTCTTCTT
1 CTTTTTCTTCTT
194053 C
1 C
194054 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:194262 original size:24 final size:24
Alignment explanation
Indices: 194228--194274 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
194218 CTGAAACATC
194228 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
194252 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
194275 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:194985 original size:20 final size:20
Alignment explanation
Indices: 194957--195325 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
194947 AAATTTAAGT
* * * *
194957 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
194977 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
194997 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
195017 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
195037 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
195057 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
195077 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
195097 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
195117 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
195137 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
195157 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
195177 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
195197 GTTGCGATATACAGATACGC
1 GTTGCGATTTACGGATACGC
* **
195217 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
195237 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
195257 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
195277 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
195297 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
195317 GTTGCGATT
1 GTTGCGATT
195326 ATGGAAAATC
Statistics
Matches: 308, Mismatches: 31, Indels: 20
0.86 0.09 0.06
Matches are distributed among these distances:
19 6 0.02
20 296 0.96
21 6 0.02
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:201249 original size:29 final size:29
Alignment explanation
Indices: 201206--201288 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
201196 CTCACCTAAC
201206 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
201236 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
201265 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
201289 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:206019 original size:29 final size:29
Alignment explanation
Indices: 205976--206058 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
205966 CTCACCTAAC
205976 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
206006 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
206035 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
206059 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:209392 original size:3 final size:3
Alignment explanation
Indices: 209380--209415 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
209370 ACAAACAATA
209380 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
209416 TCTCAACAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:210795 original size:23 final size:24
Alignment explanation
Indices: 210721--210795 Score: 93
Period size: 23 Copynumber: 3.2 Consensus size: 24
210711 TTGACTAACT
*
210721 TGTTGACCTTGATTGACTTGACC-
1 TGTTGACTTTGATTGACTTGACCA
***
210744 TGTTGACTTTGACCAACTTGA-CA
1 TGTTGACTTTGATTGACTTGACCA
210767 TGTTGACTTTGATTGACTTGACCA
1 TGTTGACTTTGATTGACTTGACCA
210791 T-TTGA
1 TGTTGA
210796 TCATTAACTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 1 0.02
23 39 0.91
24 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.20, T:0.40
Consensus pattern (24 bp):
TGTTGACTTTGATTGACTTGACCA
Found at i:211627 original size:87 final size:85
Alignment explanation
Indices: 211438--211742 Score: 273
Period size: 87 Copynumber: 3.5 Consensus size: 85
211428 ATCCCCATCC
* * * * * * *
211438 TGATTCTGCAT-GAGATTATATCTCCGTCCTGATTTTGCATGGGATTTGAT-CTCGTCCTGATTC
1 TGATTCTACATGGA-ATTATATCCCCATCCTGATTCTGCATGGGATTTGATCCCCGTCCTAATTT
*
211501 TGCATAGGATTTGA-CCCTCGT
65 TGCATGGGATTTGATCCCTC-T
* *
211522 TCTATTCCTACATGGAATTATATCCCCATCCTGATTCTGCATAGGATTTGATCCCCGTCCTAATT
1 T-GATT-CTACATGGAATTATATCCCCATCCTGATTCTGCATGGGATTTGATCCCCGTCCTAATT
211587 TTGCATGGGATTTGATCTCCGTCT
64 TTGCATGGGATTTGATC-CC-TCT
** * *
211611 TGATTCTACATGGAATTATATCCCTGTCCTGATTCTGTATGAGATTTGATCTCCC-TCCTAATTC
1 TGATTCTACATGGAATTATATCCCCATCCTGATTCTGCATGGGATTTGATC-CCCGTCCTAATT-
*
211675 TT-CATGGGATTAT-ATCCCCTTCC
64 TTGCATGGGATT-TGAT-CCC-TCT
* * ** *
211698 TGATTTTGCATTGG-ATTATATGTCCATCCTGATTTTGCATGGGAT
1 TGATTCTACA-TGGAATTATATCCCCATCCTGATTCTGCATGGGAT
211743 CCTCTATAGA
Statistics
Matches: 182, Mismatches: 27, Indels: 21
0.79 0.12 0.09
Matches are distributed among these distances:
84 1 0.01
85 3 0.02
86 37 0.20
87 121 0.66
88 14 0.08
89 4 0.02
90 2 0.01
ACGTcount: A:0.20, C:0.23, G:0.18, T:0.40
Consensus pattern (85 bp):
TGATTCTACATGGAATTATATCCCCATCCTGATTCTGCATGGGATTTGATCCCCGTCCTAATTTT
GCATGGGATTTGATCCCTCT
Found at i:211742 original size:29 final size:28
Alignment explanation
Indices: 211435--211742 Score: 219
Period size: 29 Copynumber: 10.7 Consensus size: 28
211425 ATAATCCCCA
*
211435 TCCTGATTCTGCATGAGATTATATCTCCG
1 TCCTGATTCTGCATGGGATT-TATCTCCG
*
211464 TCCTGATTTTGCATGGGATTTGATCT-CG
1 TCCTGATTCTGCATGGGATTT-ATCTCCG
* *
211492 TCCTGATTCTGCATAGGATTTGA-CCCTCG
1 TCCTGATTCTGCATGGGATTT-ATCTC-CG
* * * * *
211521 TTCT-ATTCCTACATGGAATTATATCCCCA
1 TCCTGATT-CTGCATGGGATT-TATCTCCG
* *
211550 TCCTGATTCTGCATAGGATTTGATCCCCG
1 TCCTGATTCTGCATGGGATTT-ATCTCCG
* *
211579 TCCTAATTTTGCATGGGATTTGATCTCCG
1 TCCTGATTCTGCATGGGATTT-ATCTCCG
* * *
211608 TCTTGATTCTACATGGAATTATATC-CCTG
1 TCCTGATTCTGCATGGGATT-TATCTCC-G
* * *
211637 TCCTGATTCTGTATGAGATTTGATCTCCC
1 TCCTGATTCTGCATGGGATTT-ATCTCCG
* * * *
211666 TCCTAATTCTTCATGGGATTATATCCCCT
1 TCCTGATTCTGCATGGGATT-TATCTCCG
* * * *
211695 TCCTGATTTTGCATTGGATTATATGTCCA
1 TCCTGATTCTGCATGGGATT-TATCTCCG
*
211724 TCCTGATTTTGCATGGGAT
1 TCCTGATTCTGCATGGGAT
211743 CCTCTATAGA
Statistics
Matches: 222, Mismatches: 44, Indels: 26
0.76 0.15 0.09
Matches are distributed among these distances:
27 1 0.00
28 31 0.14
29 179 0.81
30 11 0.05
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (28 bp):
TCCTGATTCTGCATGGGATTTATCTCCG
Found at i:215710 original size:2 final size:2
Alignment explanation
Indices: 215703--215733 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
215693 TTTCCATGTA
*
215703 TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
215734 TGCACGTAAG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
TC
Found at i:217166 original size:18 final size:18
Alignment explanation
Indices: 217143--217182 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
217133 TTTTATTAAT
217143 ATTTATGTATGATGTGAC
1 ATTTATGTATGATGTGAC
*
217161 ATTTATGTATGATGTGAT
1 ATTTATGTATGATGTGAC
217179 ATTT
1 ATTT
217183 TTTCTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.28, C:0.03, G:0.20, T:0.50
Consensus pattern (18 bp):
ATTTATGTATGATGTGAC
Found at i:217459 original size:20 final size:22
Alignment explanation
Indices: 217436--217475 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
217426 TAATTTTAAA
217436 ATTTTAATT-TA-ATTAATATT
1 ATTTTAATTATATATTAATATT
217456 ATTTTAATTATATATTAATA
1 ATTTTAATTATATATTAATA
217476 AAATAAGAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTAATTATATATTAATATT
Found at i:220546 original size:22 final size:22
Alignment explanation
Indices: 220492--220548 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 22
220482 GCAACACGAT
*
220492 TTTGAAAAATGTGTTGCGATAG
1 TTTGAAAAATGTGTTGCGAGAG
220514 -TT--AAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
220533 TTTGAAAAACGTGTTG
1 TTTGAAAAATGTGTTG
220549 TTGCGATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 16 0.53
20 2 0.07
21 2 0.07
22 10 0.33
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:220885 original size:19 final size:19
Alignment explanation
Indices: 220858--220895 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
220848 AATCGCAACG
*
220858 CGAACTTGGACTATCGTAA
1 CGAACTTGGACTAACGTAA
*
220877 CGAATTTGGACTAACGTAA
1 CGAACTTGGACTAACGTAA
220896 ATTTGGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.26
Consensus pattern (19 bp):
CGAACTTGGACTAACGTAA
Found at i:220974 original size:20 final size:19
Alignment explanation
Indices: 220951--220996 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
220941 GGAAACTGAT
* *
220951 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
220971 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
220990 TTGCGAT
1 TTGCGAT
220997 TTCGATTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:220986 original size:19 final size:19
Alignment explanation
Indices: 220962--220998 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
220952 TGCGATACTG
*
220962 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
220981 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
220999 CGATTTGCCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:221092 original size:20 final size:19
Alignment explanation
Indices: 221069--221114 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
221059 AGAAACTGAT
* *
221069 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
221089 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
221108 TTGCGAT
1 TTGCGAT
221115 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:221104 original size:19 final size:19
Alignment explanation
Indices: 221080--221116 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
221070 TGCGATACTG
*
221080 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
221099 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
221117 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:221110 original size:118 final size:118
Alignment explanation
Indices: 220902--221116 Score: 421
Period size: 118 Copynumber: 1.8 Consensus size: 118
220892 GTAAATTTGG
*
220902 AAAATCGCAATGCGAATATGTAAATCGCAACGCGATTCTGGAAACTGATTTGCGATACTGGAGAT
1 AAAATCGCAATGCGAATATGTAAATCGCAACGCGATTCTAGAAACTGATTTGCGATACTGGAGAT
220967 CGCGTTGCGATTTAGAGATCGCATTGCGATTTCGATTTGCCAAAATGACCAAC
66 CGCGTTGCGATTTAGAGATCGCATTGCGATTTCGATTTGCCAAAATGACCAAC
221020 AAAATCGCAATGCGAATATGTAAATCGCAACGCGATTCTAGAAACTGATTTGCGATACTGGAGAT
1 AAAATCGCAATGCGAATATGTAAATCGCAACGCGATTCTAGAAACTGATTTGCGATACTGGAGAT
221085 CGCGTTGCGATTTAGAGATCGCATTGCGATTT
66 CGCGTTGCGATTTAGAGATCGCATTGCGATTT
221117 TGTTGGTCAT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
118 96 1.00
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (118 bp):
AAAATCGCAATGCGAATATGTAAATCGCAACGCGATTCTAGAAACTGATTTGCGATACTGGAGAT
CGCGTTGCGATTTAGAGATCGCATTGCGATTTCGATTTGCCAAAATGACCAAC
Found at i:224784 original size:239 final size:234
Alignment explanation
Indices: 224355--224816 Score: 690
Period size: 239 Copynumber: 2.0 Consensus size: 234
224345 TACAATCTGT
* *
224355 ATTCACTGTGTTGTCAAACTGGTGCATTTAACATAATGTTTTTACTATTAACATTAAAAGAGTGC
1 ATTCACTGTGTTGTCAAACTAGTGCATTTAACATAATGTTTTTACTATTAACATTAAAAGAGTAC
* * *
224420 TACGAAGAAATGAAACCGTAGCTCGATATGAATCAATCGAACTAAGATTCAGTTAAAAGGATCGC
66 TACGAACAAACGAAACCGTAGCTCGACATGAATCAATCGAACTAAGATTCAGTTAAAAGGATCGC
*** * * *
224485 GAATGTTGGGATTCAAATCCCATACCTGCTAGATGGAAGCATTCAAAAATGAATGTATGAACCAC
131 GAATGGCAGGATTCAAATCCCATACATGCTAAATGCAAGCATTCAAAAATGAATGTATGAACCAC
224550 TTAAGCTATGTTCTGAACTCCCTAAAGAGTACTATCAGC
196 TTAAGCTATGTTCTGAACTCCCTAAAGAGTACTATCAGC
* *
224589 ATTCACTGTGTTGTCAAACTATTGCATTTAACATAATGTTTTTACTATTAAATAACATTAAGAGA
1 ATTCACTGTGTTGTCAAACTAGTGCATTTAACATAATGTTTTTACTA-T---TAACATTAAAAGA
* *
224654 GTACTATGAACAAACGAAACCGTAGCTCGACATGAATCAATCGAAGTAAGATTCAGTTTAAAAGG
62 GTACTACGAACAAACGAAACCGTAGCTCGACATGAATCAATCGAACTAAGATTCAG-TTAAAAGG
* * * *
224719 ATTGTGAATGGCAGGATTCAAATCCCATACATGCTAAATGCAAGCATTTAAAAATGGATGTATGA
126 ATCGCGAATGGCAGGATTCAAATCCCATACATGCTAAATGCAAGCATTCAAAAATGAATGTATGA
* *
224784 ACCACTTAAGCTATGTTCTGCATTCCCTAAAGA
191 ACCACTTAAGCTATGTTCTGAACTCCCTAAAGA
224817 AGATACAATA
Statistics
Matches: 202, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
234 45 0.22
235 1 0.00
238 62 0.31
239 94 0.47
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (234 bp):
ATTCACTGTGTTGTCAAACTAGTGCATTTAACATAATGTTTTTACTATTAACATTAAAAGAGTAC
TACGAACAAACGAAACCGTAGCTCGACATGAATCAATCGAACTAAGATTCAGTTAAAAGGATCGC
GAATGGCAGGATTCAAATCCCATACATGCTAAATGCAAGCATTCAAAAATGAATGTATGAACCAC
TTAAGCTATGTTCTGAACTCCCTAAAGAGTACTATCAGC
Found at i:230023 original size:3 final size:3
Alignment explanation
Indices: 230017--230079 Score: 74
Period size: 3 Copynumber: 21.0 Consensus size: 3
230007 TTTCCTTATT
* * *
230017 TAA TAA TAA TAA TAA T-A TATA TAA TAA TAA TAA TAA TTA TTA TTA
1 TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
230062 TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
230080 ATAAAAATGG
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:230043 original size:21 final size:23
Alignment explanation
Indices: 230012--230078 Score: 95
Period size: 21 Copynumber: 3.0 Consensus size: 23
230002 TATTTTTTCC
230012 TTATT-TAATAATAATAATAATA
1 TTATTATAATAATAATAATAATA
230034 -TA-TATAATAATAATAATAATTA
1 TTATTATAATAATAATAATAA-TA
*
230056 TTATTATTATAATAATAATAATA
1 TTATTATAATAATAATAATAATA
230079 AATAAAAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
20 1 0.03
21 17 0.43
22 2 0.05
23 4 0.10
24 16 0.40
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTATTATAATAATAATAATAATA
Found at i:230452 original size:124 final size:121
Alignment explanation
Indices: 230223--230515 Score: 346
Period size: 124 Copynumber: 2.4 Consensus size: 121
230213 GTTGAATAAA
* * *
230223 TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCCGCTGG---GGATGATGTTGAC
1 TTCTT-TCTTT-TTCAGATGAGTTCTTCTCATTATGAACTTT-CTCTGGAAAGGATGATGCTAAC
* * * * *
230285 CTATTTCCTTTTGTGATAGAGTCATTCAAAAGGTTGAATAAGCTCTTCTCATTATGAAC
63 ATATTTCCTTCTGTGATAAAATCATTCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
* *
230344 TTTTTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGTTGATGCTAAT
1 ---TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAAC
* * *
230409 ATATCTT-CTTCTGTGATAAAATTATGT-AAAAGGTTGAACAAGCTCTTGTCATTGTGAAC
63 ATAT-TTCCTTCTGTGATAAAATCAT-TCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
*
230468 TTC-TTCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
1 TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
230516 AGCTAATCCA
Statistics
Matches: 150, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
120 44 0.29
121 8 0.05
122 30 0.20
123 5 0.03
124 60 0.40
125 3 0.02
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.43
Consensus pattern (121 bp):
TTCTTTCTTTTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGATGATGCTAACATA
TTTCCTTCTGTGATAAAATCATTCAAAAGGTTGAACAAGCTCTTCTCATTATGAAC
Found at i:230751 original size:116 final size:116
Alignment explanation
Indices: 230436--231059 Score: 1009
Period size: 116 Copynumber: 5.5 Consensus size: 116
230426 AAAATTATGT
** * *
230436 AAAAGGTTGAACAAGCTCTTGTCATTGTGAA---CTTCTT-CTTCTTCAGAT---GAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGGAGTTCTTCT
* * * * * * * * * ** *
230494 CATTATGAACTTTCTCTGGAAAAGCTAATCCATCAAGTGATGGATTTGAGC
66 CATTATGAACTATATCTAGCAATGTTGATCCATCAAATGATGAATTCAAAC
*
230545 AAAAGGTTGAACAAATTCTTCTCATTATGAA--T-TTCTTCC-TCTTCAGATGACGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGGAGTTCTTCT
230606 CATTATGAACTATATCTAGCAATGTTGATCCATCAAATGATGAATTCAAAC
66 CATTATGAACTATATCTAGCAATGTTGATCCATCAAATGATGAATTCAAAC
*
230657 AAAAGGTTGAAAAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGGAGTTCTTCT
230722 CATTATGAACTATATCTAGCAATGTTGATCCATCAAATGATGAATTCAAAC
66 CATTATGAACTATATCTAGCAATGTTGATCCATCAAATGATGAATTCAAAC
230773 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGGAGTTCTTCT
230838 CATTATGAACTATATCTAGCAATGTTGATCCATCAAATGATGAATTCAAAC
66 CATTATGAACTATATCTAGCAATGTTGATCCATCAAATGATGAATTCAAAC
230889 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGGAGTTCTTCT
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGGAGTTCTTCT
230954 CATTATGAACTATATCTAGCAATGTTGATCCATCAAATGATGAATTCAAAC
66 CATTATGAACTATATCTAGCAATGTTGATCCATCAAATGATGAATTCAAAC
231005 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
1 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
231060 TTCTTATCAT
Statistics
Matches: 487, Mismatches: 19, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
109 41 0.08
110 1 0.00
112 79 0.16
114 1 0.00
115 7 0.01
116 358 0.74
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.36
Consensus pattern (116 bp):
AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGGAGTTCTTCT
CATTATGAACTATATCTAGCAATGTTGATCCATCAAATGATGAATTCAAAC
Found at i:231993 original size:114 final size:114
Alignment explanation
Indices: 231828--232055 Score: 352
Period size: 114 Copynumber: 2.0 Consensus size: 114
231818 ACGATCATGC
* * * *
231828 AATTCATCTTTCAATTCCAATGATTGGTTTTGTGGTTCTTACCGAACCAGATCAGATGACTCAAA
1 AATTCATCTTTCAATTCCAATGATTGATTTTGTGGTTCATACCAAACCAGATCAGATAACTCAAA
* *
231893 GAACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTGCTATGAGCA
66 GAACACTTCCAGAAGATGCTATTGGGTATTCTTATTTCTACTATGAGCA
* *
231942 AATTCATTTTTCAAATT-CAATGATTGATTTTAG-GGTTCATACCAAATCAGATCAGATAACTCA
1 AATTCATCTTTC-AATTCCAATGATTGATTTT-GTGGTTCATACCAAACCAGATCAGATAACTCA
232005 AAGAACACTTCCAGAAGATGCTATTGGGTATTCTTATTTCTACTATGAGCA
64 AAGAACACTTCCAGAAGATGCTATTGGGTATTCTTATTTCTACTATGAGCA
232056 CATGGCACTT
Statistics
Matches: 104, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
114 99 0.95
115 5 0.05
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (114 bp):
AATTCATCTTTCAATTCCAATGATTGATTTTGTGGTTCATACCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGGGTATTCTTATTTCTACTATGAGCA
Found at i:240748 original size:15 final size:15
Alignment explanation
Indices: 240725--240756 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
240715 TGAAATGAAT
240725 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
240740 AATGTATGTATGCAA
1 AATGAATGTATGCAA
240755 AA
1 AA
240757 AGGTATTGAT
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:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:247606 original size:99 final size:99
Alignment explanation
Indices: 247279--247918 Score: 615
Period size: 99 Copynumber: 6.4 Consensus size: 99
247269 ATATCAATCG
* * * * * * *
247279 TTTAAATTATAAGTATGAAATCATTTATATGATGCAATAGTAAGTTCAAAATAGGTTTTTCTTGA
1 TTTAAGTTATAAGTATGAAATCATTTATATTATGCAAAAGTAAG-ACAAAACAGGTTTCTCATGA
** *
247344 TAACGTAGTAGGTA-TCACCTTTTTTATGTCAACTA
65 TAACGTAGTAGGTAGT-GTCTTTTTTATGTCAACAA
* * * * * *
247379 TTTAAGTTATAAGTATGAATTCGTTTATATTATGAAAAAGTAAGAC-AAACAGATTGCTCGTGAT
1 TTTAAGTTATAAGTATGAAATCATTTATATTATGCAAAAGTAAGACAAAACAGGTTTCTCATGAT
* * * * **
247443 AACATACTAAGTAGAACT-TTTTTTTTAATGTCAACCG
66 AACGTAGTAGGTAG---TGTCTTTTTT-ATGTCAACAA
* * * * * * * * *
247480 TTTAAGTTGTAAGTACGAAACCGTTTATATTATGCAAAGGTAAAACAAAATATGTTTTTCATGAT
1 TTTAAGTTATAAGTATGAAATCATTTATATTATGCAAAAGTAAGACAAAACAGGTTTCTCATGAT
* *
247545 AACATCGTAGGTAGTGTCTTTTTTATGTCAACAA
66 AACGTAGTAGGTAGTGTCTTTTTTATGTCAACAA
* *
247579 TTTAAGTTATAAGTATGAAATCATTTATATTATGCAAAAGTAAGACACAACAGGTTGCTCATGAT
1 TTTAAGTTATAAGTATGAAATCATTTATATTATGCAAAAGTAAGACAAAACAGGTTTCTCATGAT
* *** * **
247644 AACGTATTAGGTAACATATTTTTCTAATGTCAACCG
66 AACGTAGTAGGTAGTGTCTTTTT-T-ATGTCAACAA
* * * * * *
247680 TTTAAGTTATAAGTATAAAAACATTTATTTTATGCAAAAGTAAGACAAAACATGTTTTTCATAAT
1 TTTAAGTTATAAGTATGAAATCATTTATATTATGCAAAAGTAAGACAAAACAGGTTTCTCATGAT
* *
247745 AACGTAATAGGTAGCGTCTTTTTTATGTCAACAA
66 AACGTAGTAGGTAGTGTCTTTTTTATGTCAACAA
* * * *
247779 TTTAAGTTATAAGTATGAAACCATTTATATTATACAAAAATAAGACAAAACAAGTTTCTCATGAT
1 TTTAAGTTATAAGTATGAAATCATTTATATTATGCAAAAGTAAGACAAAACAGGTTTCTCATGAT
* * * *
247844 AACGTAGGAGGTAATGTTTTTTTTATATCAACAA
66 AACGTAGTAGGTAGTGTCTTTTTTATGTCAACAA
* * *
247878 TTTAAATTATAA-TATGAAA-CCTGTTATATTATGAAAAAGTA
1 TTTAAGTTATAAGTATGAAATCAT-TTATATTATGCAAAAGTA
247919 GGTCAAACCA
Statistics
Matches: 439, Mismatches: 91, Indels: 22
0.80 0.16 0.04
Matches are distributed among these distances:
97 2 0.00
98 45 0.10
99 184 0.42
100 53 0.12
101 131 0.30
102 24 0.05
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.37
Consensus pattern (99 bp):
TTTAAGTTATAAGTATGAAATCATTTATATTATGCAAAAGTAAGACAAAACAGGTTTCTCATGAT
AACGTAGTAGGTAGTGTCTTTTTTATGTCAACAA
Found at i:247847 original size:200 final size:199
Alignment explanation
Indices: 247237--248009 Score: 759
Period size: 200 Copynumber: 3.9 Consensus size: 199
247227 TTTGTTATGT
* * * * * * * *
247237 TCATAATAACGTAGTAGGTATCACATTTTTTAATATCAATCGTTTAAATTATAAGTATGAAATCA
1 TCATGATAACGTACTAGGTAACATATTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAAACA
* * * * * * **
247302 TTTATATGATGCAATAGTAAGTTCAAAATAGGTTTTTCTTGATAACGTAGTAGGTATCACCTTTT
66 TTTATATTATGCAAAAGTAAG-ACAAAATATGTTTTTCATGATAACGTAGTAGGTAGCGTCTTTT
* * *
247367 TTATGTCAACTATTTAAGTTATAAGTATGAATTCGTTTATATTATGA-AAAAGTAAGAC-AAAC-
130 TTATGTCAACAATTTAAGTTATAAGTATGAAATCATTTATATTAT-ACAAAAGTAAGACAAAACA
247429 AGATTGC
194 AG-TTGC
* * * * * * * *
247436 TCGTGATAACATACTAAGTAGAACTTTTTTTTTAATGTCAACCGTTTAAGTTGTAAGTACGAAAC
1 TCATGATAACGTACTAGGT--AACATATTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAAA
* * * * * *
247501 CGTTTATATTATGCAAAGGTAAAACAAAATATGTTTTTCATGATAACATCGTAGGTAGTGTCTTT
64 CATTTATATTATGCAAAAGTAAGACAAAATATGTTTTTCATGATAACGTAGTAGGTAGCGTCTTT
* *
247566 TTTATGTCAACAATTTAAGTTATAAGTATGAAATCATTTATATTATGCAAAAGTAAGACACAACA
129 TTTATGTCAACAATTTAAGTTATAAGTATGAAATCATTTATATTATACAAAAGTAAGACAAAACA
*
247631 GGTTGC
194 AGTTGC
* *
247637 TCATGATAACGTATTAGGTAACATATTTTTCTAATGTCAACCGTTTAAGTTATAAGTATAAAAAC
1 TCATGATAACGTACTAGGTAACATATTTTT-TAATGTCAACCGTTTAAGTTATAAGTATGAAAAC
* * * *
247702 ATTTATTTTATGCAAAAGTAAGACAAAACATGTTTTTCATAATAACGTAATAGGTAGCGTCTTTT
65 ATTTATATTATGCAAAAGTAAGACAAAATATGTTTTTCATGATAACGTAGTAGGTAGCGTCTTTT
* *
247767 TTATGTCAACAATTTAAGTTATAAGTATGAAACCATTTATATTATACAAAAATAAGACAAAACAA
130 TTATGTCAACAATTTAAGTTATAAGTATGAAATCATTTATATTATACAAAAGTAAGACAAAACAA
*
247832 GTTTC
195 GTTGC
** ** * * ** * *
247837 TCATGATAACGTAGGAGGTAATGT-TTTTTTTATATCAACAATTTAAATTATAA-TATG-AAACC
1 TCATGATAACGTACTAGGTAACATATTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAAACA
* * * ** * * * * * * *
247899 TGTTATATTATGAAAAAGTAGGTCAAACCAAGTTGTTCATGATAATGTAATACGTAAC-ACATTT
66 T-TTATATTATGCAAAAGTAAGACAAAATATGTTTTTCATGATAACGTAGTAGGTAGCGTC--TT
* * ** * *
247963 TTTTATATCATCCGTTTAAGTTATAAGTATGAAAGCGTTTATATTAT
128 TTTTATGTCAACAATTTAAGTTATAAGTATGAAATCATTTATATTAT
248010 TGAATAGTAA
Statistics
Matches: 475, Mismatches: 90, Indels: 19
0.81 0.15 0.03
Matches are distributed among these distances:
196 6 0.01
197 48 0.10
198 62 0.13
199 28 0.06
200 256 0.54
201 74 0.16
202 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (199 bp):
TCATGATAACGTACTAGGTAACATATTTTTTAATGTCAACCGTTTAAGTTATAAGTATGAAAACA
TTTATATTATGCAAAAGTAAGACAAAATATGTTTTTCATGATAACGTAGTAGGTAGCGTCTTTTT
TATGTCAACAATTTAAGTTATAAGTATGAAATCATTTATATTATACAAAAGTAAGACAAAACAAG
TTGC
Found at i:248066 original size:299 final size:300
Alignment explanation
Indices: 247262--248052 Score: 737
Period size: 299 Copynumber: 2.6 Consensus size: 300
247252 AGGTATCACA
* * * * *
247262 TTTTTTAATATCAATC-GTTTAAATTATAAGTATGAAATCATTTATATGATGCAATAGTAAGTTC
1 TTTTTT-ATATCAA-CAATTTAAATTATAAGTATGAAATCATTTATATTATGAAAAAGTAAG-AC
* * * ** * * * * * * **
247326 AAAATAGGTTTTTCTTGATAACGTAGTAGGTATCACCTTTTT-T-ATGTCAACTATTTAAGTTAT
63 ACAACAAGTTGCTCATGATAACGTAATACGTAACACATTTTTCTAATATCAACCGTTTAAGTTAT
* ** * * ** * * *
247389 AAGTATGAATTCGTTTATATTATGAAAAAGTAAGAC-AAACA-GATTGCTCGTGATAACA-TACT
128 AAGTATAAAAACATTTATATTATGCAAAAGTAAGACAAAACATG-TTTTTCATAATAA-AGTAAT
* * * ** * * *
247451 AAGTAGAACTTTTTTTTTAATGTCAACCGTTTAAGTTGTAAGTACGAAACCGTTTATATTATGCA
191 AGGTAG--CGTCTTTTTTAATGTCAACAATTTAAGTTATAAGTACGAAACCATTTATATTATACA
** * * * * * *
247516 AAGGTAAAACAAAATATGTTTTTCATGATAACATCGTAGGTAGTGTC
254 AAAATAAAACAAAACAAGTTTCTCATGATAACATAGGAGGTAATGTC
* * *
247563 TTTTTTATGTCAACAATTTAAGTTATAAGTATGAAATCATTTATATTATGCAAAAGTAAGACACA
1 TTTTTTATATCAACAATTTAAATTATAAGTATGAAATCATTTATATTATGAAAAAGTAAGACACA
* * * * *
247628 ACAGGTTGCTCATGATAACGTATTAGGTAACATATTTTTCTAATGTCAACCGTTTAAGTTATAAG
66 ACAAGTTGCTCATGATAACGTAATACGTAACACATTTTTCTAATATCAACCGTTTAAGTTATAAG
* *
247693 TATAAAAACATTTATTTTATGCAAAAGTAAGACAAAACATGTTTTTCATAATAACGTAATAGGTA
131 TATAAAAACATTTATATTATGCAAAAGTAAGACAAAACATGTTTTTCATAATAAAGTAATAGGTA
*
247758 GCGTCTTTTTT-ATGTCAACAATTTAAGTTATAAGTATGAAACCATTTATATTATACAAAAATAA
196 GCGTCTTTTTTAATGTCAACAATTTAAGTTATAAGTACGAAACCATTTATATTATACAAAAATAA
* * *
247822 GACAAAACAAGTTTCTCATGATAACGTAGGAGGTAATGTT
261 AACAAAACAAGTTTCTCATGATAACATAGGAGGTAATGTC
* * *
247862 TTTTTTATATCAACAATTTAAATTATAA-TATGAAA-CCTGTTATATTATGAAAAAGTAGGTCA-
1 TTTTTTATATCAACAATTTAAATTATAAGTATGAAATCAT-TTATATTATGAAAAAGTAAGACAC
* * * *
247924 AACCAAGTTGTTCATGATAATGTAATACGTAACACATTTTT-TTATATCATCCGTTTAAGTTATA
65 AA-CAAGTTGCTCATGATAACGTAATACGTAACACATTTTTCTAATATCAACCGTTTAAGTTATA
* * * * * * *
247988 AGTATGAAAGCGTTTATATTATTG-AATAGTAATAC-AAATATGATTTTTC-TAGTAAAGTAATA
129 AGTATAAAAACATTTATATTA-TGCAAAAGTAAGACAAAACATG-TTTTTCATAATAAAGTAATA
248050 GGT
192 GGT
248053 TCAATCTTCT
Statistics
Matches: 407, Mismatches: 73, Indels: 25
0.81 0.14 0.05
Matches are distributed among these distances:
296 20 0.05
297 56 0.14
298 61 0.15
299 137 0.34
300 56 0.14
301 54 0.13
302 22 0.05
303 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (300 bp):
TTTTTTATATCAACAATTTAAATTATAAGTATGAAATCATTTATATTATGAAAAAGTAAGACACA
ACAAGTTGCTCATGATAACGTAATACGTAACACATTTTTCTAATATCAACCGTTTAAGTTATAAG
TATAAAAACATTTATATTATGCAAAAGTAAGACAAAACATGTTTTTCATAATAAAGTAATAGGTA
GCGTCTTTTTTAATGTCAACAATTTAAGTTATAAGTACGAAACCATTTATATTATACAAAAATAA
AACAAAACAAGTTTCTCATGATAACATAGGAGGTAATGTC
Found at i:248645 original size:187 final size:186
Alignment explanation
Indices: 248304--248667 Score: 498
Period size: 187 Copynumber: 2.0 Consensus size: 186
248294 ACTTTCGAAT
** * * * *
248304 TTAAAAAAATATTAATATTTTAGATCTCAACCTACTTTCTTAGTGAACCATGACATTCTTGGGCG
1 TTAAAAAAATATTAATATTCAACATCTCAACCTACTTTCTTAGTGAACCATAACATTATGGGGCG
* * * **
248369 CAATCTTATTTATTATAGATATTCATAACATTTTTGGCTTTTAACATATTTTATTATCGTGGGAA
66 CAACCGTATTTATTATAGATATTCATAACATTTTTAGCTTTTAACATATTTTATTATCGTAAGAA
* ** * * *
248434 AATCTAAGGCTTCATCAGCTTAAACTTTGGTAACATTTTAGGCGCAATCCATTTTG
131 AATCTAAAGCCCCATCAACTTAAACTCTAGTAACATTTTAGGCGCAATCCATTTTG
248490 TTAATAAAAATATTAATATTCAACAT-TGCAACCTACTTTCTTAGTGAACCATAACATTATGGGG
1 TTAA-AAAAATATTAATATTCAACATCT-CAACCTACTTTCTTAGTGAACCATAACATTATGGGG
* * *
248554 CGTAACCGTATTTATTATAGA-ATTCATAACATTTTCTAGCTTTTAACTTATTTTGTTATCGTAA
64 CGCAACCGTATTTATTATAGATATTCATAACATTTT-TAGCTTTTAACATATTTTATTATCGTAA
*
248618 GAAAATTTAAAGCCCCATCAACTTAAACTCTAGTAACATTTTAGGCGCAA
128 GAAAATCTAAAGCCCCATCAACTTAAACTCTAGTAACATTTTAGGCGCAA
248668 CCTAAAATGT
Statistics
Matches: 154, Mismatches: 21, Indels: 5
0.86 0.12 0.03
Matches are distributed among these distances:
186 19 0.12
187 135 0.88
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (186 bp):
TTAAAAAAATATTAATATTCAACATCTCAACCTACTTTCTTAGTGAACCATAACATTATGGGGCG
CAACCGTATTTATTATAGATATTCATAACATTTTTAGCTTTTAACATATTTTATTATCGTAAGAA
AATCTAAAGCCCCATCAACTTAAACTCTAGTAACATTTTAGGCGCAATCCATTTTG
Found at i:248806 original size:77 final size:78
Alignment explanation
Indices: 248654--248822 Score: 243
Period size: 77 Copynumber: 2.2 Consensus size: 78
248644 ACTCTAGTAA
*
248654 CATTTTAGGCGCAACCTAAAATGTTAATAATATCCATAATATTCATCATTTATAACTTATTTTCT
1 CATTTTAGGCGCAACCTAAAATATTAATAATATCCATAATATTCATCATTTATAACTTATTTTCT
** *
248719 TATTGTTTATA-T
66 TACAGCTTATAGT
** * *
248731 CATTTTAGGCGCAACCTAAAATATTAATAATATTTATAATATTTATCGTTTATAACTTATTTTCT
1 CATTTTAGGCGCAACCTAAAATATTAATAATATCCATAATATTCATCATTTATAACTTATTTTCT
248796 TACAGCTTATAGT
66 TACAGCTTATAGT
*
248809 -ATTTTAGGAGCAAC
1 CATTTTAGGCGCAAC
248823 ATGTTATGTT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
77 81 0.99
78 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (78 bp):
CATTTTAGGCGCAACCTAAAATATTAATAATATCCATAATATTCATCATTTATAACTTATTTTCT
TACAGCTTATAGT
Found at i:250640 original size:29 final size:29
Alignment explanation
Indices: 250604--250670 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
250594 CATTTTACAC
* *
250604 AAATAGCACACTTTTTAAAATAATTACCA
1 AAATAGCACACATTTCAAAATAATTACCA
* *
250633 AAATAGCACACATTTCGAATTAATTACCA
1 AAATAGCACACATTTCAAAATAATTACCA
*
250662 GAATAGCAC
1 AAATAGCAC
250671 CAAAACTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.27
Consensus pattern (29 bp):
AAATAGCACACATTTCAAAATAATTACCA
Found at i:250681 original size:29 final size:29
Alignment explanation
Indices: 250649--250729 Score: 144
Period size: 29 Copynumber: 2.8 Consensus size: 29
250639 CACACATTTC
*
250649 GAATTAATTACCAGAATAGCACCAAAACT
1 GAATTATTTACCAGAATAGCACCAAAACT
250678 GAATTATTTACCAGAATAGCACCAAAACT
1 GAATTATTTACCAGAATAGCACCAAAACT
*
250707 GAATTATTTACCATAATAGCACC
1 GAATTATTTACCAGAATAGCACC
250730 GGTCAACGGT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.44, C:0.21, G:0.10, T:0.25
Consensus pattern (29 bp):
GAATTATTTACCAGAATAGCACCAAAACT
Found at i:250773 original size:18 final size:18
Alignment explanation
Indices: 250737--250789 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
250727 ACCGGTCAAC
* *
250737 GGTCAAC-GATCGAGTCG
1 GGTCAACGGGTCGGGTCG
250754 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
250772 GGTCAACGGGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
250790 TGACCGGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
17 7 0.21
18 26 0.79
ACGTcount: A:0.15, C:0.23, G:0.45, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:258124 original size:29 final size:29
Alignment explanation
Indices: 258092--258197 Score: 122
Period size: 29 Copynumber: 3.7 Consensus size: 29
258082 CTTTTTAAAA
* ***
258092 TAATTACCAAAATAGCACCCATTTCGAAT
1 TAATTACCAAAATAGCACCAAAACCGAAT
* *
258121 TAATTACTAGAATAGCACCAAAACCGAAT
1 TAATTACCAAAATAGCACCAAAACCGAAT
* * *
258150 TATTTAACAGAATAGCACCAAAACCGAAT
1 TAATTACCAAAATAGCACCAAAACCGAAT
*
258179 TATTTACCAAAATAGCACC
1 TAATTACCAAAATAGCACC
258198 GGTCAACGGT
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.45, C:0.23, G:0.08, T:0.24
Consensus pattern (29 bp):
TAATTACCAAAATAGCACCAAAACCGAAT
Found at i:258237 original size:18 final size:18
Alignment explanation
Indices: 258216--258256 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
258206 GTCAACGATC
258216 GGTCGGGTCAACGGGTCG
1 GGTCGGGTCAACGGGTCG
*
258234 GGTCGGGTCAACGGGTTG
1 GGTCGGGTCAACGGGTCG
258252 GGTCG
1 GGTCG
258257 TGACCGGTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.10, C:0.20, G:0.51, T:0.20
Consensus pattern (18 bp):
GGTCGGGTCAACGGGTCG
Found at i:265468 original size:29 final size:29
Alignment explanation
Indices: 265432--265498 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
265422 CATTTTACAC
* *
265432 AAATAGCACACTTTTTAAAATAATTACCA
1 AAATAGCACACATTTCAAAATAATTACCA
* * *
265461 AAATAGCACCCATTTCGAATTAATTACCA
1 AAATAGCACACATTTCAAAATAATTACCA
*
265490 GAATAGCAC
1 AAATAGCAC
265499 CAAAACCAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.45, C:0.21, G:0.07, T:0.27
Consensus pattern (29 bp):
AAATAGCACACATTTCAAAATAATTACCA
Found at i:265499 original size:29 final size:29
Alignment explanation
Indices: 265478--265557 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
265468 ACCCATTTCG
265478 AATTAATTACCAGAATAGCACCAAAACCA
1 AATTAATTACCAGAATAGCACCAAAACCA
* *
265507 AATTATTTACCAGAATAGCACCAAAACAA
1 AATTAATTACCAGAATAGCACCAAAACCA
*
265536 AATTATTTACCAGAATAGCACC
1 AATTAATTACCAGAATAGCACC
265558 GGTCAACGGT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.49, C:0.23, G:0.07, T:0.21
Consensus pattern (29 bp):
AATTAATTACCAGAATAGCACCAAAACCA
Found at i:265600 original size:18 final size:18
Alignment explanation
Indices: 265567--265613 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
265557 CGGTCAACGG
*
265567 TCAAC-GATCGGGTCGGA
1 TCAACGGATCGGATCGGA
* *
265584 TCAACGGGTCGGATCGGG
1 TCAACGGATCGGATCGGA
265602 TCAACGGATCGG
1 TCAACGGATCGG
265614 GTCTTGACCG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 5 0.20
18 20 0.80
ACGTcount: A:0.21, C:0.23, G:0.38, T:0.17
Consensus pattern (18 bp):
TCAACGGATCGGATCGGA
Found at i:289187 original size:15 final size:15
Alignment explanation
Indices: 289159--289200 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
289149 TTTTTTTTAG
289159 ATTTTATAAAAAAATGA
1 ATTTT-TAAAAAAAT-A
289176 ATTTTTAAAAAAATA
1 ATTTTTAAAAAAATA
*
289191 TTTTTTAAAA
1 ATTTTTAAAA
289201 TCTCAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 10 0.42
16 9 0.38
17 5 0.21
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (15 bp):
ATTTTTAAAAAAATA
Found at i:289770 original size:3 final size:3
Alignment explanation
Indices: 289762--289786 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
289752 TGAACAGGAA
289762 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
289787 GAAAGAGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:293343 original size:19 final size:19
Alignment explanation
Indices: 293319--293361 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
293309 GAGTGATGAC
293319 GTGGTTGAACTCAGCATCT
1 GTGGTTGAACTCAGCATCT
293338 GTGGTTGAACTCAGCATCT
1 GTGGTTGAACTCAGCATCT
293357 GTGGT
1 GTGGT
293362 AGCCTCATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (19 bp):
GTGGTTGAACTCAGCATCT
Found at i:300034 original size:67 final size:66
Alignment explanation
Indices: 299954--300098 Score: 184
Period size: 66 Copynumber: 2.2 Consensus size: 66
299944 TAGCTTACCC
** * *
299954 TGAGGTAGAGTGATAA-TGAAATATTGTAGAAGATCACTCAATGTGACTCGTGTACCTTTGTGGT
1 TGAGGTAGAGTGATAATTG-AATATCATA-AAGATCACTCAATGTGACTCGCGTACCTTAGTGGT
*
300018 GCA
64 ACA
* *
300021 TGAGGTGGAGTGATAATTGAATATCATACAGATCACTCAATGTGACTCGCGTACCTTAGTGGTAC
1 TGAGGTAGAGTGATAATTGAATATCATAAAGATCACTCAATGTGACTCGCGTACCTTAGTGGTAC
300086 A
66 A
* *
300087 CGAGGTTGAGTG
1 TGAGGTAGAGTG
300099 TATCGTGTAC
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
66 44 0.65
67 22 0.32
68 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.30
Consensus pattern (66 bp):
TGAGGTAGAGTGATAATTGAATATCATAAAGATCACTCAATGTGACTCGCGTACCTTAGTGGTAC
A
Found at i:300899 original size:19 final size:19
Alignment explanation
Indices: 300877--300940 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
300867 TAAGGAAATT
300877 TATAAGTATGATGGAAAAC
1 TATAAGTATGATGGAAAAC
* *
300896 TATAA-TAATAGTTGGAAAATT
1 TATAAGT-AT-GATGGAAAA-C
*
300917 TATATGTATGATGGAAAAC
1 TATAAGTATGATGGAAAAC
300936 TATAA
1 TATAA
300941 TAATAGTTGT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 11 0.31
20 16 0.46
21 6 0.17
22 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (19 bp):
TATAAGTATGATGGAAAAC
Found at i:300913 original size:20 final size:20
Alignment explanation
Indices: 300888--300949 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
300878 ATAAGTATGA
300888 TGGAAAACTATAATAATAGT
1 TGGAAAACTATAATAATAGT
* * *
300908 TGGAAAA-T-TTATATGTATGA
1 TGGAAAACTATAATA-ATA-GT
300928 TGGAAAACTATAATAATAGT
1 TGGAAAACTATAATAATAGT
300948 TG
1 TG
300950 TTGTATGTGG
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
18 4 0.12
19 3 0.09
20 18 0.56
21 3 0.09
22 4 0.12
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.34
Consensus pattern (20 bp):
TGGAAAACTATAATAATAGT
Found at i:300926 original size:40 final size:40
Alignment explanation
Indices: 300872--300949 Score: 147
Period size: 40 Copynumber: 1.9 Consensus size: 40
300862 TAACTTAAGG
300872 AAATTTATAAGTATGATGGAAAACTATAATAATAGTTGGA
1 AAATTTATAAGTATGATGGAAAACTATAATAATAGTTGGA
*
300912 AAATTTATATGTATGATGGAAAACTATAATAATAGTTG
1 AAATTTATAAGTATGATGGAAAACTATAATAATAGTTG
300950 TTGTATGTGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.46, C:0.03, G:0.17, T:0.35
Consensus pattern (40 bp):
AAATTTATAAGTATGATGGAAAACTATAATAATAGTTGGA
Found at i:301784 original size:11 final size:12
Alignment explanation
Indices: 301752--301776 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
301742 TAGGTAAAAA
301752 AAATAATTTTTT
1 AAATAATTTTTT
301764 AAATAATTTTTT
1 AAATAATTTTTT
301776 A
1 A
301777 CTAATTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATAATTTTTT
Found at i:304518 original size:40 final size:34
Alignment explanation
Indices: 304430--304516 Score: 158
Period size: 34 Copynumber: 2.6 Consensus size: 34
304420 AAAAGTAAGC
304430 TCAA-TTCAACTCAAACTCACGAGCTAAAATTTA
1 TCAAGTTCAACTCAAACTCACGAGCTAAAATTTA
304463 TCAAGTTCAACTCAAACTCACGAGCTAAAATTTA
1 TCAAGTTCAACTCAAACTCACGAGCTAAAATTTA
*
304497 TCAAGTTCAACTCGAACTCA
1 TCAAGTTCAACTCAAACTCA
304517 AAATATAATA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
33 4 0.08
34 48 0.92
ACGTcount: A:0.40, C:0.25, G:0.08, T:0.26
Consensus pattern (34 bp):
TCAAGTTCAACTCAAACTCACGAGCTAAAATTTA
Found at i:312798 original size:30 final size:30
Alignment explanation
Indices: 312743--312800 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
312733 AAGTTTTGAA
*
312743 AAAATTGAAAGTTTATTTATAAAATGGACT
1 AAAATTGAAAGTTTATGTATAAAATGGACT
*
312773 AAAATTGATAGTTTATGTACT-AAATGGA
1 AAAATTGAAAGTTTATGTA-TAAAATGGA
312801 TTAAGTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 24 0.96
31 1 0.04
ACGTcount: A:0.45, C:0.03, G:0.16, T:0.36
Consensus pattern (30 bp):
AAAATTGAAAGTTTATGTATAAAATGGACT
Found at i:313777 original size:22 final size:22
Alignment explanation
Indices: 313736--313882 Score: 120
Period size: 22 Copynumber: 6.5 Consensus size: 22
313726 AGTTCTATCA
*
313736 AAAAATA-AT-ATATTATTTTTT
1 AAAAATATATAATA-TAGTTTTT
*
313757 GAAAATATATAATATAGTTTTT
1 AAAAATATATAATATAGTTTTT
*
313779 AAAAACATATAATATAGTTTTT
1 AAAAATATATAATATAGTTTTT
* ** *
313801 GAAAATATATAGCATAGTTTTA
1 AAAAATATATAATATAGTTTTT
* *
313823 AAAACATATTGTTATATA-TTTTT
1 AAAA-ATA-TATAATATAGTTTTT
313846 AAAAACATATAATATATATAGTTTTT
1 -AAAA-ATAT-ATA-ATATAGTTTTT
313872 CAAAAATATAT
1 -AAAAATATAT
313883 GTAATATATA
Statistics
Matches: 100, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
21 6 0.06
22 49 0.49
23 11 0.11
24 16 0.16
25 9 0.09
26 9 0.09
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (22 bp):
AAAAATATATAATATAGTTTTT
Found at i:313936 original size:19 final size:21
Alignment explanation
Indices: 313892--313943 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
313882 TGTAATATAT
313892 ATATATATATATATTTGTAAAC
1 ATAT-TATATATATTTGTAAAC
313914 ATATTATATGAT-TTTG-AAA-
1 ATATTATAT-ATATTTGTAAAC
*
313933 ATATAATATAT
1 ATATTATATAT
313944 TATATAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.07
19 8 0.29
20 3 0.11
21 9 0.32
22 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.06, T:0.46
Consensus pattern (21 bp):
ATATTATATATATTTGTAAAC
Found at i:313944 original size:26 final size:28
Alignment explanation
Indices: 313914--313971 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 28
313904 ATTTGTAAAC
313914 ATATTATAT-GATTTTGAAAATATA-AT
1 ATATTATATAGATTTTGAAAATATATAT
* * *
313940 ATATTATATAGTTTTTTAATATATATAT
1 ATATTATATAGATTTTGAAAATATATAT
313968 ATAT
1 ATAT
313972 ATAACTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 9 0.33
27 12 0.44
28 6 0.22
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (28 bp):
ATATTATATAGATTTTGAAAATATATAT
Found at i:315847 original size:18 final size:18
Alignment explanation
Indices: 315824--315876 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
315814 CGTAGAATTT
*
315824 TGTCCCGAAGGACCATTA
1 TGTCCCGAAGGACCACTA
*
315842 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
315860 TGTCCC-ATAGGACCACT
1 TGTCCCGA-AGGACCACT
315877 GATAATCCGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.25, C:0.32, G:0.21, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:321151 original size:2 final size:2
Alignment explanation
Indices: 321144--321177 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
321134 TCGTACATGC
321144 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
321178 GTTGTTTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:322237 original size:27 final size:28
Alignment explanation
Indices: 322186--322238 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
322176 TCTGTTTACA
**
322186 TTATGTCGTCGACTCAGTGTTTGAAATG
1 TTATGTCGTCGACTCAGTACTTGAAATG
322214 TTATGTCGTCGA-TCAGTACTTGAAA
1 TTATGTCGTCGACTCAGTACTTGAAA
322239 GCAACAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (28 bp):
TTATGTCGTCGACTCAGTACTTGAAATG
Found at i:324171 original size:34 final size:34
Alignment explanation
Indices: 324127--324194 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
324117 AAAATGAACA
*
324127 AAAATTTCCCAATTTGTGCACTGATTTAGCAGCT
1 AAAATCTCCCAATTTGTGCACTGATTTAGCAGCT
*
324161 AAAATCTCCCAATTTGTGCACTGATTTAGTAGCT
1 AAAATCTCCCAATTTGTGCACTGATTTAGCAGCT
324195 GGGAAATGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (34 bp):
AAAATCTCCCAATTTGTGCACTGATTTAGCAGCT
Found at i:325891 original size:140 final size:139
Alignment explanation
Indices: 325655--326063 Score: 638
Period size: 140 Copynumber: 2.9 Consensus size: 139
325645 ACCTAGAGGA
* * * * *
325655 CTAAAGTAGAAGCTCTAATATTAATCCTAATTTGTTTTAACTAATTATTAAGTCGGATAATCGAA
1 CTAAAGTGGAGGCTCTAATATTAATCCTAATTTATTTTAACTAATTATTGAGTCGAATAATCGAA
* * *
325720 ATGATCCCTTGGGCATGTTAATGTGAGAGCCAAATCAAATTATTCCCAAATTAAAGGACTAAAGT
66 ATGGT-CCTTGGGCATGTTAATGCGAGAGCCAAATCAAATTATTCCCAAATTAAAGGACTAAACT
325785 AAAATTAAAC
130 AAAATTAAAC
* *
325795 CTAAAGTGGAGGCTCTAATATTAATCCTAATTTATTTTAGCTAATTATTGAGTCGAATAATCGAC
1 CTAAAGTGGAGGCTCTAATATTAATCCTAATTTATTTTAACTAATTATTGAGTCGAATAATCGAA
* * *
325860 ATGGTCTCTCGGGCATGTTAATGGGAGAGCCAAATCAAATTATTCCCTAATTAAAGGACTAAACT
66 ATGGTC-CTTGGGCATGTTAATGCGAGAGCCAAATCAAATTATTCCCAAATTAAAGGACTAAACT
325925 AAAATTAAAC
130 AAAATTAAAC
*
325935 CTAAAGTGGAGGCTCTAATATTAATCCTAATTTATTTTAACCAATTATTGAGTCGAATAATCGAA
1 CTAAAGTGGAGGCTCTAATATTAATCCTAATTTATTTTAACTAATTATTGAGTCGAATAATCGAA
* *
326000 ATGGTCCATTGGGCATGTTAATGCGAGAGCCAAATCAAATTATTCTCTAAACTAAAGGACTAAA
66 ATGGTCC-TTGGGCATGTTAATGCGAGAGCCAAATCAAATTATTC-CCAAATTAAAGGACTAAA
326064 TGTGAGAAAT
Statistics
Matches: 246, Mismatches: 20, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
139 2 0.01
140 229 0.93
141 15 0.06
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (139 bp):
CTAAAGTGGAGGCTCTAATATTAATCCTAATTTATTTTAACTAATTATTGAGTCGAATAATCGAA
ATGGTCCTTGGGCATGTTAATGCGAGAGCCAAATCAAATTATTCCCAAATTAAAGGACTAAACTA
AAATTAAAC
Found at i:326588 original size:35 final size:35
Alignment explanation
Indices: 326542--326617 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
326532 AAAACAGTCC
* *
326542 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
326577 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
326612 TCAATT
1 TCAATT
326618 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:327160 original size:130 final size:130
Alignment explanation
Indices: 327014--327261 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
327004 TATTTATATA
* **
327014 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
327079 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
327144 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
327209 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
327262 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:327292 original size:130 final size:129
Alignment explanation
Indices: 327028--327292 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
327018 ATTTGGTCCT
* ** *
327028 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
327093 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
327158 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
327223 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
327287 -A
128 CA
327288 AAATT
1 AAATT
327293 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:327728 original size:16 final size:18
Alignment explanation
Indices: 327707--327740 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
327697 ATTTCTTATT
327707 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
327723 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
327741 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:330986 original size:18 final size:17
Alignment explanation
Indices: 330963--331042 Score: 66
Period size: 18 Copynumber: 4.9 Consensus size: 17
330953 GAAATATATG
330963 AATATAGATTATAATAAA
1 AATATA-ATTATAATAAA
330981 AATATAA--A-AAGTAAA
1 AATATAATTATAA-TAAA
*
330996 AGTA-AA-TAT-A-AAA
1 AATATAATTATAATAAA
331009 AATATAATTATAATAAA
1 AATATAATTATAATAAA
*
331026 AATATATTTTATAATAA
1 AATATA-ATTATAATAA
331043 CTCACTATTA
Statistics
Matches: 51, Mismatches: 3, Indels: 16
0.73 0.04 0.23
Matches are distributed among these distances:
13 6 0.12
14 6 0.12
15 13 0.25
16 1 0.02
17 10 0.20
18 15 0.29
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.33
Consensus pattern (17 bp):
AATATAATTATAATAAA
Found at i:335318 original size:22 final size:22
Alignment explanation
Indices: 335261--335322 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
335251 GGTATGATAT
*
335261 TATATTAAAAATA-T-AGAATAT
1 TATA-TAAAAATATTAAGAATAA
*
335282 TA-AAAAAAACT-TTAAGAATAA
1 TATATAAAAA-TATTAAGAATAA
335303 TATATAAAAATATTAAGAAT
1 TATATAAAAATATTAAGAAT
335323 TTATCATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
19 5 0.15
20 3 0.09
21 11 0.33
22 14 0.42
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (22 bp):
TATATAAAAATATTAAGAATAA
Found at i:336143 original size:91 final size:91
Alignment explanation
Indices: 336038--336218 Score: 317
Period size: 91 Copynumber: 2.0 Consensus size: 91
336028 TTTTTTATAT
336038 TGTCATAATCTTATTATAATTTTAATAAAAATATTATACACATTAAACTTATGTGCTTTAAATAA
1 TGTCATAATCTTATTATAATTTTAATAAAAATATTATACACATTAAACTTATGTGCTTTAAATAA
* *
336103 TAATTCTTCAATTAAATTTTATTTTA
66 TAATTCTGCAATTAAACTTTATTTTA
* * *
336129 TGTCATAATCTTATTATAATTTTAATCAAAATATTATACACATTAAAGTTATGTGTTTTAAATAA
1 TGTCATAATCTTATTATAATTTTAATAAAAATATTATACACATTAAACTTATGTGCTTTAAATAA
336194 TAATTCTGCAATTAAACTTTATTTT
66 TAATTCTGCAATTAAACTTTATTTT
336219 TTATGTTATT
Statistics
Matches: 85, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 85 1.00
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (91 bp):
TGTCATAATCTTATTATAATTTTAATAAAAATATTATACACATTAAACTTATGTGCTTTAAATAA
TAATTCTGCAATTAAACTTTATTTTA
Found at i:344393 original size:20 final size:20
Alignment explanation
Indices: 344353--344394 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
344343 CGGTTATAAT
* * *
344353 ATCCGGTTTTAAAATATCCG
1 ATCCGGTTTAAAAAAAACCG
344373 ATCCGGTTTAAAAAAAACCG
1 ATCCGGTTTAAAAAAAACCG
344393 AT
1 AT
344395 TTTTCCCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (20 bp):
ATCCGGTTTAAAAAAAACCG
Found at i:347950 original size:17 final size:18
Alignment explanation
Indices: 347922--347955 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
347912 ATTATTTTTT
347922 AAATTCATTTTTTAAATA
1 AAATTCATTTTTTAAATA
347940 AAATTCA-TTTTTAAAT
1 AAATTCATTTTTTAAAT
347956 TATAGTAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTCATTTTTTAAATA
Found at i:349846 original size:29 final size:29
Alignment explanation
Indices: 349813--349868 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
349803 TCCCAACACA
*
349813 TAGGTCGCCATGCCCTCCGGGCGACCTTG
1 TAGGTCGCCATGCACTCCGGGCGACCTTG
349842 TAGGTCGCCATGCACTCCGGGCGACCT
1 TAGGTCGCCATGCACTCCGGGCGACCT
349869 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.12, C:0.38, G:0.30, T:0.20
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCGGGCGACCTTG
Found at i:349955 original size:33 final size:33
Alignment explanation
Indices: 349872--349996 Score: 124
Period size: 33 Copynumber: 3.8 Consensus size: 33
349862 GCGACCTACC
* * * *
349872 CTCGCTCGGCTGCCCTCGGATTCCCTTGCATAG
1 CTCGCTCGGATGGCCTCGGATGCCCTCGCATAG
* **
349905 CTCGCTCGGTTACCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGATGGCCTCGGATGCCCTCGCATAG
* * * * *
349938 CTCGTTCGAATGGCCTCGGATGCTCTCGAATGG
1 CTCGCTCGGATGGCCTCGGATGCCCTCGCATAG
*
349971 CCTCGGTCGGATGGCCTCGGATGCCC
1 -CTCGCTCGGATGGCCTCGGATGCCC
349997 AGCGTGTTGG
Statistics
Matches: 76, Mismatches: 15, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
33 54 0.71
34 22 0.29
ACGTcount: A:0.11, C:0.36, G:0.28, T:0.25
Consensus pattern (33 bp):
CTCGCTCGGATGGCCTCGGATGCCCTCGCATAG
Found at i:349990 original size:34 final size:33
Alignment explanation
Indices: 349918--349996 Score: 104
Period size: 34 Copynumber: 2.4 Consensus size: 33
349908 GCTCGGTTAC
* *
349918 CCTCGGATGCCCTCGCATAGCTCGTTCGAATGG
1 CCTCGGATGCCCTCGAATAGCTCGGTCGAATGG
* * *
349951 CCTCGGATGCTCTCGAATGGCCTCGGTCGGATGG
1 CCTCGGATGCCCTCGAATAG-CTCGGTCGAATGG
349985 CCTCGGATGCCC
1 CCTCGGATGCCC
349997 AGCGTGTTGG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 17 0.44
34 22 0.56
ACGTcount: A:0.13, C:0.34, G:0.30, T:0.23
Consensus pattern (33 bp):
CCTCGGATGCCCTCGAATAGCTCGGTCGAATGG
Found at i:350070 original size:29 final size:29
Alignment explanation
Indices: 350033--350090 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
350023 GCAATCTCTT
* *
350033 GTAGCTCGCCGGGAAGACATGGCGACCTA
1 GTAGCTCGCCCGAAAGACATGGCGACCTA
* *
350062 GTAGGTCGCCCGAAAGGCATGGCGACCTA
1 GTAGCTCGCCCGAAAGACATGGCGACCTA
350091 CGGCCAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.24, C:0.28, G:0.34, T:0.14
Consensus pattern (29 bp):
GTAGCTCGCCCGAAAGACATGGCGACCTA
Found at i:355681 original size:37 final size:37
Alignment explanation
Indices: 355609--355724 Score: 119
Period size: 37 Copynumber: 3.1 Consensus size: 37
355599 TTTGATGTTG
** *
355609 TTTCTCTTAAAAATAAAGTGTCATCTCGCTAGAGACAAT
1 TTTCTCTTAAAAA-AAA-TGTTGTCTCGCTTGAGACAAT
*
355648 TTT-TCTTAAAAACAAATGTTGTCTCGCTTGAGACAGT
1 TTTCTCTTAAAAA-AAATGTTGTCTCGCTTGAGACAAT
* * **
355685 TTTCTCTTAAAAATAATTTTGTCTTACTTGAGAC-AT
1 TTTCTCTTAAAAAAAATGTTGTCTCGCTTGAGACAAT
355721 TTTC
1 TTTC
355725 CCTCAGGACA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
36 5 0.08
37 37 0.56
38 21 0.32
39 3 0.05
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (37 bp):
TTTCTCTTAAAAAAAATGTTGTCTCGCTTGAGACAAT
Found at i:355955 original size:66 final size:65
Alignment explanation
Indices: 355872--356197 Score: 402
Period size: 66 Copynumber: 5.0 Consensus size: 65
355862 AACAAAATTG
* ** * *
355872 ATAATCTTTGATATTGTTTGTCTTGAAACAAGTTTGTCTCCCTTGAGACAGTTTCACTTGAAACA
1 ATAATCTTTGAGATTGTTTCCCTTGAAACAAGTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
* * * *
355937 TATAATCTTTGAGATTGTTTCTCTTGAAACAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAAC
1 -ATAATCTTTGAGATTGTTTCCCTTGAAACAAGTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
356002 A
65 A
*** ** * *
356003 CCCATCTTTGAGATCATTTCCCTTGAAACGAATTTTGTCTCTCTTGGGACAGTTTCTCTTGAAAC
1 ATAATCTTTGAGATTGTTTCCCTTGAAAC-AAGTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
356068 A
65 A
* * *
356069 ATCATCTTTGAG-TCGTTTCCCTTGAAACGAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
1 ATAATCTTTGAGATTGTTTCCCTTGAAACAAG-TTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
356133 A
65 A
** * * *
356134 CCAATCTTTGTGTTTGTTTCCCTTGAAACAAGTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 ATAATCTTTGAGATTGTTTCCCTTGAAACAAGTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC
356198 CATTTCCCTA
Statistics
Matches: 230, Mismatches: 27, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
64 1 0.00
65 109 0.47
66 120 0.52
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.40
Consensus pattern (65 bp):
ATAATCTTTGAGATTGTTTCCCTTGAAACAAGTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACA
Done.