Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005237.1 Hibiscus syriacus cultivar Beakdansim tig00011857_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: 107108
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:8244 original size:26 final size:23
Alignment explanation
Indices: 8171--8244 Score: 76
Period size: 24 Copynumber: 3.0 Consensus size: 23
8161 ATCATTAAAA
* *
8171 TTTAGATAATTCTTTAAAAATCAT
1 TTTAGAAAATTCATTAAAAAT-AT
*
8195 TTTAGAAAATTCATTCAAATATAT
1 TTTAGAAAATTCATT-AAAAATAT
8219 TTTCAGAAAATATCATATAAAAATAT
1 TTT-AGAAAAT-TCAT-TAAAAATAT
8245 ATAGGCTAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
24 18 0.43
25 12 0.29
26 11 0.26
27 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (23 bp):
TTTAGAAAATTCATTAAAAATAT
Found at i:11165 original size:2 final size:2
Alignment explanation
Indices: 11158--11197 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
11148 AATCTCTTTG
*
11158 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11198 CAGCATAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13136 original size:20 final size:20
Alignment explanation
Indices: 13086--13136 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
13076 AGTCTTTCGT
*
13086 TATGGGGACCATTCCTACGA
1 TATGGAGACCATTCCTACGA
* * *
13106 TATGAAAACCATTCCTTCTG-
1 TATGGAGACCATTCCTAC-GA
13126 TATGGAGACCA
1 TATGGAGACCA
13137 ATTGGTCTCA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (20 bp):
TATGGAGACCATTCCTACGA
Found at i:23014 original size:97 final size:94
Alignment explanation
Indices: 22912--23232 Score: 255
Period size: 97 Copynumber: 3.3 Consensus size: 94
22902 ACTTTGTTAC
*
22912 AATTTATTATTGTGAAAGAATGTTATGTCATGATTTTTCTATATTGA-AAATTTAATATTTTTTA
1 AATTTATTATT-TGAAAGAATATTATGTCATGA-TTTT-TATATTGACAAATTTAATATTTTTTA
*
22976 TAAATTGTTATTATGATTAAATAAATTTGTCAT
63 TAAATT-TTATTATGACTAAATAAATTTGTCAT
** * ***
23009 AATTTATTA-TTCCAAGAA-ACTAT-T-ATGACTAAATATATTTGACATAATTTTTAAT-TTTGA
1 AATTTATTATTTGAAAGAATATTATGTCATGA-TTTTTATA-TTGACA-AA--TTTAATATTT--
* * *
23069 TTAAATTTAATATTTTATTATGACTAAATAAATTTTTTAT
59 TT---TATAA-ATTTTATTATGACTAAATAAATTTGTCAT
* *
23109 AATTTATTATTATGAAA-AATATTATTTGTCATAAATTTTTATATTGAGAAA-TTAATATTTTTT
1 AATTTATTATT-TGAAAGAATATTA--TGTCAT-GATTTTTATATTGACAAATTTAATATTTTTT
*
23172 ATAAATTTTTATTATAACTAAATAAATTTGTCAT
62 ATAAA-TTTTATTATGACTAAATAAATTTGTCAT
23206 AATTTATTATTTTGAGAA-AATATTATG
1 AATTTATTA-TTTGA-AAGAATATTATG
23233 ATTAAATAAA
Statistics
Matches: 177, Mismatches: 24, Indels: 47
0.71 0.10 0.19
Matches are distributed among these distances:
91 4 0.02
92 9 0.05
93 2 0.01
94 5 0.03
95 9 0.05
96 10 0.06
97 52 0.29
98 11 0.06
100 38 0.21
101 11 0.06
102 9 0.05
104 3 0.02
105 6 0.03
106 7 0.04
107 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.07, T:0.50
Consensus pattern (94 bp):
AATTTATTATTTGAAAGAATATTATGTCATGATTTTTATATTGACAAATTTAATATTTTTTATAA
ATTTTATTATGACTAAATAAATTTGTCAT
Found at i:23096 original size:23 final size:23
Alignment explanation
Indices: 23053--23105 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
23043 ATATTTGACA
* *
23053 TAATTTTTAATTTTGATTAAATT
1 TAATTTTTAATTATGACTAAATT
23076 TAATATTTT-ATTATGACTAAA-T
1 TAAT-TTTTAATTATGACTAAATT
*
23098 AAATTTTT
1 TAATTTTT
23106 TATAATTTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 4 0.15
22 4 0.15
23 14 0.54
24 4 0.15
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (23 bp):
TAATTTTTAATTATGACTAAATT
Found at i:23168 original size:33 final size:31
Alignment explanation
Indices: 23109--23224 Score: 92
Period size: 33 Copynumber: 3.5 Consensus size: 31
23099 AATTTTTTAT
* *
23109 AATTTATTATTATGAAAAATATTATTTGTCATA
1 AATTT-TTATT-TGAGAAATAATATTTGTCATA
* *
23142 AATTTTTATATTGAGAAATTAATATTTTTTATA
1 AATTTTTAT-TTGAGAAA-TAATATTTGTCATA
* *
23175 AATTTTTATTATAACTAAATAA-ATTTGTCAT-
1 AATTTTTATT-TGA-GAAATAATATTTGTCATA
23206 AATTTATTATTTTGAGAAA
1 AATTT-TTA-TTTGAGAAA
23225 ATATTATGAT
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
31 8 0.12
32 23 0.34
33 33 0.49
34 3 0.04
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (31 bp):
AATTTTTATTTGAGAAATAATATTTGTCATA
Found at i:23184 original size:65 final size:64
Alignment explanation
Indices: 23100--23224 Score: 166
Period size: 65 Copynumber: 1.9 Consensus size: 64
23090 GACTAAATAA
*
23100 ATTTTTTATAATTTATTATTATGAA-AAATATTATTTGTCATAAATTT-TTATATTGAGAAATTA
1 ATTTTTTATAATTTATTATTAT-AACAAATA-AATTTGTCAT-AATTTATTATATTGAGAAATTA
23163 AT
63 AT
*
23165 ATTTTTTATAAATTT-TTATTATAACTAAATAAATTTGTCATAATTTATTATTTTGAGAAA
1 ATTTTTTAT-AATTTATTATTATAAC-AAATAAATTTGTCATAATTTATTATATTGAGAAA
23225 ATATTATGAT
Statistics
Matches: 54, Mismatches: 2, Indels: 8
0.84 0.03 0.12
Matches are distributed among these distances:
64 7 0.13
65 37 0.69
66 10 0.19
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (64 bp):
ATTTTTTATAATTTATTATTATAACAAATAAATTTGTCATAATTTATTATATTGAGAAATTAAT
Found at i:23227 original size:32 final size:32
Alignment explanation
Indices: 23081--23227 Score: 113
Period size: 32 Copynumber: 4.6 Consensus size: 32
23071 AAATTTAATA
** * *
23081 TTTTATTATGACTAAATAAATTTTTTAT-AAT
1 TTTTATTATGAGAAAATAAATTTGTCATAAAT
*
23112 TTATTATTATGA-AAAATATTATTTGTCATAAAT
1 TT-TTATTATGAGAAAATA-AATTTGTCATAAAT
* * *
23145 TTTTA-TATTGAGAAATTAATATTTTTTATAAAT
1 TTTTATTA-TGAGAAAATAA-ATTTGTCATAAAT
* **
23178 TTTTATTATAACTAAATAAATTTGTCAT-AAT
1 TTTTATTATGAGAAAATAAATTTGTCATAAAT
*
23209 TTATTATTTTGAGAAAATA
1 TT-TTATTATGAGAAAATA
23228 TTATGATTAA
Statistics
Matches: 90, Mismatches: 18, Indels: 15
0.73 0.15 0.12
Matches are distributed among these distances:
31 14 0.16
32 41 0.46
33 33 0.37
34 2 0.02
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (32 bp):
TTTTATTATGAGAAAATAAATTTGTCATAAAT
Found at i:23248 original size:197 final size:197
Alignment explanation
Indices: 22912--23299 Score: 548
Period size: 197 Copynumber: 2.0 Consensus size: 197
22902 ACTTTGTTAC
* * * *
22912 AATTTATTATTGTGAAAGAATGTTATGTCATGATTTTTCTATATTGAAAATTTAATATTTTTTAT
1 AATTTATTATTATGAAAGAATATTATGTCATAAATTTTCTATATTGAAAATTTAATATTTTTTAT
* * *
22977 AAATTGTTATTATGATTAAATAAATTTGTCATAATTTATTATTCCAAGAAACTATTATGACTAAA
66 AAATTGTTATTATAACTAAATAAATTTGTCATAATTTATTATTCCAAGAAAATATTATGACTAAA
* * * * *
23042 TATATTTGACATAATTTTTAATTTTGATTAAATTTAATATTTTATTATGACTAAATAAATTTTTT
131 TAAATTTGACATAATTTTTAATTTTGACTAAATTTAATATATTATTAGGAATAAATAAATTTTTT
23107 AT
196 AT
23109 AATTTATTATTATGAAA-AATATTATTTGTCATAAATTTT-TATATTGAGAAA-TTAATATTTTT
1 AATTTATTATTATGAAAGAATATTA--TGTCATAAATTTTCTATATTGA-AAATTTAATATTTTT
* *** *
23171 TATAAATTTTTATTATAACTAAATAAATTTGTCATAATTTATTATTTTGAGAAAATATTATGATT
63 TATAAATTGTTATTATAACTAAATAAATTTGTCATAATTTATTATTCCAAGAAAATATTATGACT
* * *
23236 AAATAAATTTGACATAATTTTTTATTTTGACTAGATTTAATATATTATTGGGAATAAATAAATT
128 AAATAAATTTGACATAATTTTTAATTTTGACTAAATTTAATATATTATTAGGAATAAATAAATT
23300 AATATTAAAT
Statistics
Matches: 168, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
196 6 0.04
197 148 0.88
198 14 0.08
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (197 bp):
AATTTATTATTATGAAAGAATATTATGTCATAAATTTTCTATATTGAAAATTTAATATTTTTTAT
AAATTGTTATTATAACTAAATAAATTTGTCATAATTTATTATTCCAAGAAAATATTATGACTAAA
TAAATTTGACATAATTTTTAATTTTGACTAAATTTAATATATTATTAGGAATAAATAAATTTTTT
AT
Found at i:23282 original size:97 final size:96
Alignment explanation
Indices: 22984--23283 Score: 274
Period size: 97 Copynumber: 3.1 Consensus size: 96
22974 TATAAATTGT
* *** * *
22984 TATTATGATTAAATAAATTTGTCATAATTTATTATTCCAAGAAACTATTATGACTAAATATATTT
1 TATTATGACTAAATAAATTTGTCATAATTTATTATTATGAGAAAATATTATGATTAAATATATTT
*
23049 GACATAATTTTTAATTTTGATTAAATTTAATA
66 GACATAATTTTTTATTTTGA-TAAATTTAATA
* *
23081 TTTTATTATGACTAAATAAATTTTTTATAATTTATTATTATGA-AAAATATTATTTG-TCATAAA
1 ---TATTATGACTAAATAAATTTGTCATAATTTATTATTATGAGAAAATATTA--TGAT--TAAA
* * *
23144 TTTTTATATTGAGA-AATTAATATT-TTTT-ATAAATTT--T-
59 --TATAT-TTGACATAATT--TTTTATTTTGATAAATTTAATA
* * *
23181 TATTATAACTAAATAAATTTGTCATAATTTATTATTTTGAGAAAATATTATGATTAAATAAATTT
1 TATTATGACTAAATAAATTTGTCATAATTTATTATTATGAGAAAATATTATGATTAAATATATTT
*
23246 GACATAATTTTTTATTTTGACTAGATTTAATA
66 GACATAATTTTTTATTTTGA-TAAATTTAATA
23278 TATTAT
1 TATTAT
23284 TGGGAATAAA
Statistics
Matches: 161, Mismatches: 21, Indels: 39
0.73 0.10 0.18
Matches are distributed among these distances:
91 3 0.02
92 9 0.06
93 8 0.05
94 6 0.04
95 4 0.02
96 3 0.02
97 43 0.27
98 9 0.06
99 8 0.05
100 34 0.21
101 3 0.02
102 4 0.02
103 7 0.04
104 9 0.06
105 9 0.06
106 2 0.01
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (96 bp):
TATTATGACTAAATAAATTTGTCATAATTTATTATTATGAGAAAATATTATGATTAAATATATTT
GACATAATTTTTTATTTTGATAAATTTAATA
Found at i:23331 original size:22 final size:21
Alignment explanation
Indices: 23305--23353 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 21
23295 AAATTAATAT
23305 TAAATATCATTAAAATAAACATA
1 TAAATAT--TTAAAATAAACATA
*
23328 -AAATATTTAGAATAAACATA
1 TAAATATTTAAAATAAACATA
23348 TAAATA
1 TAAATA
23354 CATAAAGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 13 0.54
21 5 0.21
22 6 0.25
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (21 bp):
TAAATATTTAAAATAAACATA
Found at i:24070 original size:4 final size:4
Alignment explanation
Indices: 24061--24085 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
24051 TCATTTTATC
24061 TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT T
24086 CATTTTTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:25358 original size:22 final size:22
Alignment explanation
Indices: 25332--25374 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
25322 AATAATAGAA
* * *
25332 ATATAATTTATAAATTAAAATT
1 ATATAATCTAAAAAATAAAATT
25354 ATATAATCTAAAAAATAAAAT
1 ATATAATCTAAAAAATAAAAT
25375 AAAATTATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (22 bp):
ATATAATCTAAAAAATAAAATT
Found at i:25365 original size:15 final size:13
Alignment explanation
Indices: 25339--25398 Score: 54
Period size: 13 Copynumber: 4.6 Consensus size: 13
25329 GAAATATAAT
25339 TTATAAATTAAAA
1 TTATAAATTAAAA
25352 TTATATAATCTAAAA
1 TTATA-AAT-TAAAA
* *
25367 -AATAAAATAAAA
1 TTATAAATTAAAA
25379 TTAT-AATT-AAA
1 TTATAAATTAAAA
25390 TTGATAAAT
1 TT-ATAAAT
25399 CCTTTTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
11 5 0.13
12 10 0.26
13 12 0.32
14 6 0.16
15 5 0.13
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (13 bp):
TTATAAATTAAAA
Found at i:25411 original size:2 final size:2
Alignment explanation
Indices: 25404--25446 Score: 61
Period size: 2 Copynumber: 21.5 Consensus size: 2
25394 TAAATCCTTT
*
25404 TA TA TA TA TA TA TA TA TCC T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA
25446 T
1 T
25447 CATGAAATCC
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
1 1 0.03
2 36 0.95
3 1 0.03
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25423 original size:22 final size:22
Alignment explanation
Indices: 25397--25442 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
25387 AAATTGATAA
*
25397 ATCCTTTTATATATATATATAT
1 ATCCTTATATATATATATATAT
25419 ATCCTTATATATATATATATAT
1 ATCCTTATATATATATATATAT
25441 AT
1 AT
25443 ATATCATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (22 bp):
ATCCTTATATATATATATATAT
Found at i:25928 original size:13 final size:13
Alignment explanation
Indices: 25910--25939 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
25900 TAATTTTGAA
25910 AAAATTAAAAATT
1 AAAATTAAAAATT
*
25923 AAAATTAAAATTT
1 AAAATTAAAAATT
25936 AAAA
1 AAAA
25940 AACCCGATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:26034 original size:14 final size:14
Alignment explanation
Indices: 26005--26045 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
25995 ATGCTAGATA
26005 AAAAATAAAA-ACAT
1 AAAAATAAAATA-AT
26019 AAAAATAAAATAAT
1 AAAAATAAAATAAT
*
26033 AATAA-AAAATAAT
1 AAAAATAAAATAAT
26046 TGAAGGGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 8 0.32
14 16 0.64
15 1 0.04
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAAATAAAATAAT
Found at i:26080 original size:11 final size:11
Alignment explanation
Indices: 26065--26117 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
26055 AAATAATATA
26065 AAAAATATAAAG
1 AAAAAT-TAAAG
26077 AAAAATTAAAG
1 AAAAATTAAAG
*
26088 AAAAAAATTAAAA
1 --AAAAATTAAAG
* *
26101 AAAAAGTAAAC
1 AAAAATTAAAG
26112 AAAAAT
1 AAAAAT
26118 GTTAAATTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
11 19 0.54
12 6 0.17
13 10 0.29
ACGTcount: A:0.77, C:0.02, G:0.06, T:0.15
Consensus pattern (11 bp):
AAAAATTAAAG
Found at i:26080 original size:12 final size:12
Alignment explanation
Indices: 26052--26092 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
26042 TAATTGAAGG
*
26052 GAAAAATAATATA
1 GAAAAAT-ATAAA
26065 -AAAAATATAAA
1 GAAAAATATAAA
26076 GAAAAAT-TAAA
1 GAAAAATATAAA
26087 GAAAAA
1 GAAAAA
26093 AATTAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 14 0.54
12 12 0.46
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
GAAAAATATAAA
Found at i:26123 original size:24 final size:24
Alignment explanation
Indices: 26064--26116 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
26054 AAAATAATAT
* * *
26064 AAAAAATATAAAGAAAAATTAAAGA
1 AAAAAAT-TAAAAAAAAAGTAAACA
26089 AAAAAATTAAAAAAAAAGTAAACA
1 AAAAAATTAAAAAAAAAGTAAACA
26113 AAAA
1 AAAA
26117 TGTTAAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.79, C:0.02, G:0.06, T:0.13
Consensus pattern (24 bp):
AAAAAATTAAAAAAAAAGTAAACA
Found at i:27210 original size:16 final size:16
Alignment explanation
Indices: 27189--27219 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27179 AAAAAATAAC
*
27189 AAATAACAAATAAAAT
1 AAATAAAAAATAAAAT
27205 AAATAAAAAATAAAA
1 AAATAAAAAATAAAA
27220 AACATTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (16 bp):
AAATAAAAAATAAAAT
Found at i:27215 original size:7 final size:7
Alignment explanation
Indices: 27179--27221 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
27169 GGAAAAAAGA
27179 AAAAAAT
1 AAAAAAT
*
27186 AACAAAT
1 AAAAAAT
*
27193 AACAAAT
1 AAAAAAT
27200 AAAATAAAT
1 -AAA-AAAT
27209 AAAAAAT
1 AAAAAAT
27216 AAAAAA
1 AAAAAA
27222 CATTTTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 23 0.72
8 5 0.16
9 4 0.12
ACGTcount: A:0.81, C:0.05, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAAAT
Found at i:27433 original size:38 final size:38
Alignment explanation
Indices: 27310--27510 Score: 240
Period size: 39 Copynumber: 5.4 Consensus size: 38
27300 TTTAAAACTA
*
27310 ATATATATTTTCAGAAATATTTTC-AAAA-T-TATAT-T
1 ATATATATTTTCA-AAATGTTTTCAAAAACTATATATAT
* *
27345 ATATACATTTTCAAAATGTTTTTAAAAACTATATAT-T
1 ATATATATTTTCAAAATGTTTTCAAAAACTATATATAT
27382 ATATA-AGTTTTCAAAATG-TTTCAAAAACTATATTATAT
1 ATATATA-TTTTCAAAATGTTTTCAAAAACTATA-TATAT
* *
27420 ATATATATATTCAAAATGTTTTCAAAAACTATATATTAA
1 ATATATATTTTCAAAATGTTTTCAAAAACTATATA-TAT
*
27459 ATATATATTTTCAAAATATTTT-AAAAACTATATAT-T
1 ATATATATTTTCAAAATGTTTTCAAAAACTATATATAT
*
27495 ATATATATTTTAAAAA
1 ATATATATTTTCAAAA
27511 AATTATACCA
Statistics
Matches: 147, Mismatches: 10, Indels: 17
0.84 0.06 0.10
Matches are distributed among these distances:
34 8 0.05
35 16 0.11
36 30 0.20
37 26 0.18
38 30 0.20
39 37 0.25
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.45
Consensus pattern (38 bp):
ATATATATTTTCAAAATGTTTTCAAAAACTATATATAT
Found at i:27485 original size:77 final size:74
Alignment explanation
Indices: 27308--27502 Score: 263
Period size: 75 Copynumber: 2.6 Consensus size: 74
27298 GTTTTAAAAC
* * * *
27308 TAATATATATTTTCAGAAATATTTTCAAAA-T-TATATTATATACATTTTCAAAATGTTTTTAAA
1 TAATATATATTTTCA-AAATATTTTAAAAACTATATATTATATATATATTCAAAATGTTTTCAAA
27371 AACTATATAT
65 AACTATATAT
* *
27381 T-ATATA-AGTTTTCAAAATGTTTCAAAAACTATATTATATATATATATATTCAAAATGTTTTCA
1 TAATATATA-TTTTCAAAATATTTTAAAAACTATA-TAT-TATATATATATTCAAAATGTTTTCA
27444 AAAACTATATAT
63 AAAACTATATAT
27456 TAAATATATATTTTCAAAATATTTTAAAAACTATATATTATATATAT
1 T-AATATATATTTTCAAAATATTTTAAAAACTATATATTATATATAT
27503 TTTAAAAAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
71 12 0.11
72 12 0.11
73 3 0.03
74 3 0.03
75 44 0.42
76 3 0.03
77 28 0.26
78 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (74 bp):
TAATATATATTTTCAAAATATTTTAAAAACTATATATTATATATATATTCAAAATGTTTTCAAAA
ACTATATAT
Found at i:27513 original size:38 final size:36
Alignment explanation
Indices: 27310--27510 Score: 201
Period size: 38 Copynumber: 5.4 Consensus size: 36
27300 TTTAAAACTA
* *
27310 ATATATATTTTCAGAAATATTTTCAAAA-T-TATATT
1 ATATATATTTT-AAAAATATTTTAAAAACTATATATT
* * *
27345 ATATACATTTTCAAAATGTTTTTAAAAACTATATATT
1 ATATATATTTTAAAAAT-ATTTTAAAAACTATATATT
* * *
27382 ATATA-AGTTTTCAAAATGTTTCAAAAACTATATTATAT
1 ATATATA-TTTTAAAAATATTTTAAAAACTATA-TAT-T
* * *
27420 ATATATATATTCAAAATGTTTTCAAAAACTATATATT
1 ATATATATTTTAAAAATATTTT-AAAAACTATATATT
*
27457 AAATATATATTTTCAAAATATTTTAAAAACTATATATT
1 --ATATATATTTTAAAAATATTTTAAAAACTATATATT
27495 ATATATATTTTAAAAA
1 ATATATATTTTAAAAA
27511 AATTATACCA
Statistics
Matches: 144, Mismatches: 12, Indels: 19
0.82 0.07 0.11
Matches are distributed among these distances:
34 4 0.03
35 18 0.12
36 30 0.21
37 25 0.17
38 36 0.25
39 31 0.22
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.45
Consensus pattern (36 bp):
ATATATATTTTAAAAATATTTTAAAAACTATATATT
Found at i:28754 original size:45 final size:46
Alignment explanation
Indices: 28705--28795 Score: 139
Period size: 46 Copynumber: 2.0 Consensus size: 46
28695 AAACATCGAA
* * *
28705 TGCATTTTATGCATCGATGCA-CATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCATAAAACCATGCATCGATGCACTCAG
*
28750 TGCATTTGATGCATTGATGCATAAAACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCATAAAACCATGCATCGATGCACTCAG
28796 GTTTTTCAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 19 0.46
46 22 0.54
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.29
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCATAAAACCATGCATCGATGCACTCAG
Found at i:36196 original size:21 final size:21
Alignment explanation
Indices: 36154--36197 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
36144 ACTCTGGGAG
* *
36154 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
36175 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
36196 CT
1 CT
36198 CCTCCTCCGA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:37388 original size:19 final size:20
Alignment explanation
Indices: 37364--37416 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
37354 AATGCATTTT
*
37364 ATGCATCGATGCAC-ATACC
1 ATGCATCGATGCACAAGACC
37383 ATGCATCGATGCACAAGACC
1 ATGCATCGATGCACAAGACC
37403 ATGCATCGATGCAC
1 ATGCATCGATGCAC
37417 TCAGGTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.32, C:0.30, G:0.19, T:0.19
Consensus pattern (20 bp):
ATGCATCGATGCACAAGACC
Found at i:39045 original size:12 final size:12
Alignment explanation
Indices: 39028--39077 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
39018 TCCAATTGGA
39028 TTTATTTTATTT
1 TTTATTTTATTT
39040 TTTATTTT-TATT
1 TTTATTTTAT-TT
*
39052 TTTATTTAAATTT
1 TTTATTT-TATTT
*
39065 TTGATTTTATTT
1 TTTATTTTATTT
39077 T
1 T
39078 AAAAAAAAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
11 1 0.03
12 22 0.69
13 8 0.25
14 1 0.03
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:39047 original size:6 final size:6
Alignment explanation
Indices: 39028--39077 Score: 50
Period size: 6 Copynumber: 8.3 Consensus size: 6
39018 TCCAATTGGA
**
39028 TTTA-T TTTATTT TTTATT TTTATT TTTATT TAAATT TTTGA-T TTTATT
1 TTTATT TTTA-TT TTTATT TTTATT TTTATT TTTATT TTT-ATT TTTATT
39076 TT
1 TT
39078 AAAAAAAAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
5 5 0.14
6 26 0.70
7 6 0.16
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:39078 original size:19 final size:18
Alignment explanation
Indices: 39028--39080 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
39018 TCCAATTGGA
**
39028 TTTATTTTATTTTTTATT
1 TTTATTTTATTTTAAATT
39046 TTTATTTT-TATTTAAATT
1 TTTATTTTAT-TTTAAATT
39064 TTTGATTTTATTTTAAA
1 TTT-ATTTTATTTTAAA
39081 AAAAAGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 1 0.03
18 17 0.57
19 11 0.37
20 1 0.03
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.74
Consensus pattern (18 bp):
TTTATTTTATTTTAAATT
Found at i:39313 original size:3 final size:3
Alignment explanation
Indices: 39305--39333 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
39295 CCAATTTATT
39305 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
39334 GTGAAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (3 bp):
TGA
Found at i:40766 original size:6 final size:6
Alignment explanation
Indices: 40755--40782 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
40745 CTCAATTACA
40755 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
40783 GATTCGACTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:41151 original size:11 final size:11
Alignment explanation
Indices: 41137--41179 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
41127 AGAATATCAC
*
41137 AAGAAAGAAAT
1 AAGAAAAAAAT
41148 AAGAAAAAAAT
1 AAGAAAAAAAT
*
41159 AAGAAATAAA-
1 AAGAAAAAAAT
*
41169 AACAAAAAAAT
1 AAGAAAAAAAT
41180 TGAATTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 8 0.30
11 19 0.70
ACGTcount: A:0.79, C:0.02, G:0.09, T:0.09
Consensus pattern (11 bp):
AAGAAAAAAAT
Found at i:41190 original size:20 final size:21
Alignment explanation
Indices: 41137--41179 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41127 AGAATATCAC
* *
41137 AAGAAAGAAATAAGAAAAAAAT
1 AAGAAATAAA-AACAAAAAAAT
41159 AAGAAATAAAAACAAAAAAAT
1 AAGAAATAAAAACAAAAAAAT
41180 TGAATTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.79, C:0.02, G:0.09, T:0.09
Consensus pattern (21 bp):
AAGAAATAAAAACAAAAAAAT
Found at i:41968 original size:37 final size:37
Alignment explanation
Indices: 41917--41995 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
41907 GTGTTATCGC
41917 TTGGTTTT--TTCGGTGTTTAGCTATTGTGGTTGTTT
1 TTGGTTTTGCTTCGGTGTTTAGCTATTGTGGTTGTTT
* *
41952 TTTGTTTTGCTTCGGTGTTTGGCTATTGTGGTTGTTT
1 TTGGTTTTGCTTCGGTGTTTAGCTATTGTGGTTGTTT
41989 TTGGTTT
1 TTGGTTT
41996 GATGTTCAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
35 7 0.18
37 32 0.82
ACGTcount: A:0.04, C:0.06, G:0.29, T:0.61
Consensus pattern (37 bp):
TTGGTTTTGCTTCGGTGTTTAGCTATTGTGGTTGTTT
Found at i:42284 original size:15 final size:15
Alignment explanation
Indices: 42264--42302 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
42254 TTGGACCTGG
42264 AAATAAAAAATAAA-A
1 AAATAAAAAA-AAATA
42279 AAATAAAAAAAAATA
1 AAATAAAAAAAAATA
42294 ACAATAAAA
1 A-AATAAAA
42303 TGAATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 3 0.14
15 12 0.55
16 7 0.32
ACGTcount: A:0.85, C:0.03, G:0.00, T:0.13
Consensus pattern (15 bp):
AAATAAAAAAAAATA
Found at i:42351 original size:35 final size:35
Alignment explanation
Indices: 42312--42567 Score: 196
Period size: 35 Copynumber: 6.9 Consensus size: 35
42302 ATGAATAATA
*
42312 ATATATTATATATTTTTAAAAATAGTTCCAAAACT
1 ATATATTATATATTTTTAAAAATAGTTTCAAAACT
* * * *
42347 ATATAATATATATATTCAAAAATA-TTTTAAAACT
1 ATATATTATATATTTTTAAAAATAGTTTCAAAACT
* * *
42381 ATACATTATAT-CTTTTAAAAAT-GTTTTTTAAAACT
1 ATATATTATATATTTTTAAAAATAG--TTTCAAAACT
*
42416 ATATATTATATATATTTTCAAAAT-GTTTTCAAAAACT
1 ATATATTATATAT-TTTTAAAAATAG-TTTC-AAAACT
* *
42453 ATATATTATATATTTTCAAAAATAATTTTCAAAACTAT
1 ATATATTATATATTTTTAAAAAT-AGTTTCAAAAC--T
* *
42491 ATATATATATATATATATATTCAAAAATCATTTTCAAAACC
1 ATATAT-TATATAT-T-T-TT-AAAAAT-AGTTTCAAAACT
* *
42532 ATATAGTATATATATTTTCAAAAATAATTTTCAAAA
1 ATATA-T-TATATATTTTTAAAAAT-AGTTTCAAAA
42568 GTACATAATA
Statistics
Matches: 183, Mismatches: 22, Indels: 29
0.78 0.09 0.12
Matches are distributed among these distances:
33 8 0.04
34 17 0.09
35 41 0.22
36 17 0.09
37 33 0.18
38 23 0.13
39 8 0.04
40 2 0.01
41 7 0.04
42 10 0.05
43 17 0.09
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (35 bp):
ATATATTATATATTTTTAAAAATAGTTTCAAAACT
Found at i:42439 original size:37 final size:36
Alignment explanation
Indices: 42340--42554 Score: 181
Period size: 37 Copynumber: 5.8 Consensus size: 36
42330 AAAATAGTTC
* *
42340 CAAAACTATATA-ATATATATATTCAAAAAT-ATTTT
1 CAAAACTATATATATATATATTTTC-AAAATGTTTTT
* * *
42375 -AAAACTATACAT-TATATCTTTTAAAAATGTTTTT
1 CAAAACTATATATATATATATTTTCAAAATGTTTTT
*
42409 TAAAACTATATATTATATATATTTTCAAAATG-TTTT
1 CAAAACTATATA-TATATATATTTTCAAAATGTTTTT
**
42445 CAAAAACTATATAT-TATATATTTTCAAAAATAATTTT
1 C-AAAACTATATATATATATATTTTC-AAAATGTTTTT
**
42482 CAAAACTATATATATATATATATATATATTCAAAAATCATTTT
1 CAAAAC----TATATATATATATAT-T-TTC-AAAATGTTTTT
*
42525 CAAAACCATATAGTATATATATTTTCAAAA
1 CAAAACTATATA-TATATATATTTTCAAAA
42555 ATAATTTTCA
Statistics
Matches: 152, Mismatches: 12, Indels: 30
0.78 0.06 0.15
Matches are distributed among these distances:
33 5 0.03
34 22 0.14
35 21 0.14
36 16 0.11
37 35 0.23
38 3 0.02
39 6 0.04
40 16 0.11
41 7 0.05
42 1 0.01
43 20 0.13
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.43
Consensus pattern (36 bp):
CAAAACTATATATATATATATTTTCAAAATGTTTTT
Found at i:42500 original size:44 final size:45
Alignment explanation
Indices: 42452--42547 Score: 151
Period size: 43 Copynumber: 2.2 Consensus size: 45
42442 TTTCAAAAAC
* *
42452 TATATATTATATATTTTCAAAAATAATTTTCAAAACTATATA-TA
1 TATATATTATATATATTCAAAAATAATTTTCAAAACCATATAGTA
*
42496 TATATA-TATATATATTCAAAAATCATTTTCAAAACCATATAGTA
1 TATATATTATATATATTCAAAAATAATTTTCAAAACCATATAGTA
42540 TATATATT
1 TATATATT
42548 TTCAAAAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
43 32 0.68
44 14 0.30
45 1 0.02
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (45 bp):
TATATATTATATATATTCAAAAATAATTTTCAAAACCATATAGTA
Found at i:43349 original size:85 final size:85
Alignment explanation
Indices: 43260--43603 Score: 329
Period size: 85 Copynumber: 4.1 Consensus size: 85
43250 TCTCGACTTA
* * *
43260 AGCTATGTTGTAAATTTGACATGCCCTTGAGCTGAATGAAATCGAAATCGAAGGTATTTGTTGAC
1 AGCTATGCTATAAATTTGATATGCCCTTGAGCTGAATGAAATCGAAATCGAAGGTATTTGTTGAC
*
43325 AGATAACCCTTATTACCTTG
66 AGATAACCCTTCTTACCTTG
* * * * * * *
43345 AGCTATGCTGTAAATTTGATATGTCCTCGAGCTGAATGTAATC-AAACTTGAAGG-A-TTATTGG
1 AGCTATGCTATAAATTTGATATGCCCTTGAGCTGAATGAAATCGAAA-TCGAAGGTATTTGTTGA
* * *
43407 CTGATAGCCCTTCTCACCTTG
65 CAGATAACCCTTCTTACCTTG
* * * * *
43428 AGCTATGATATAAATTTGATATGCCTTTGAGCTGAAT-ATAATCGAACTCGAAGGTCTTGGTTGA
1 AGCTATGCTATAAATTTGATATGCCCTTGAGCTGAATGA-AATCGAAATCGAAGGTATTTGTTGA
* *
43492 CAGATAACCCTTCTTGCTTTG
65 CAGATAACCCTTCTTACCTTG
* * * * * * * **
43513 AGTTATGCTATAAATTTGATATGTCCTTGAGCTAAATGTAATTGAACTCGAAGGTCTTCATT-AG
1 AGCTATGCTATAAATTTGATATGCCCTTGAGCTGAATGAAATCGAAATCGAAGGTATTTGTTGA-
* **
43577 CAGATTACCCTTCTCGCCTTG
65 CAGATAACCCTTCTTACCTTG
43598 AGCTAT
1 AGCTAT
43604 ACTGCAAATA
Statistics
Matches: 210, Mismatches: 42, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
83 64 0.30
84 7 0.03
85 139 0.66
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (85 bp):
AGCTATGCTATAAATTTGATATGCCCTTGAGCTGAATGAAATCGAAATCGAAGGTATTTGTTGAC
AGATAACCCTTCTTACCTTG
Found at i:43538 original size:168 final size:170
Alignment explanation
Indices: 43260--43603 Score: 453
Period size: 168 Copynumber: 2.0 Consensus size: 170
43250 TCTCGACTTA
* * *
43260 AGCTATGTTGTAAATTTGACATGCCCTTGAGCTGAATGAAATCGAAATCGAAGGTATTTGTTGAC
1 AGCTATGATATAAATTTGACATGCCCTTGAGCTGAATGAAATCGAAATCGAAGGTATTGGTTGAC
* *
43325 AGATAACCCTTATTACCTTGAGCTATGCTGTAAATTTGATATGTCCTCGAGCTGAATGTAATCAA
66 AGATAACCCTTATTACCTTGAGCTATGCTATAAATTTGATATGTCCTCGAGCTAAATGTAATCAA
* * *
43390 ACTTGAAGG-ATT-ATTGGCTGA-TAGCCCTTCTCACCTTG
131 ACTCGAAGGTATTCATTAGCAGATTA-CCCTTCTCACCTTG
* * * *
43428 AGCTATGATATAAATTTGATATGCCTTTGAGCTGAAT-ATAATCGAACTCGAAGGTCTTGGTTGA
1 AGCTATGATATAAATTTGACATGCCCTTGAGCTGAATGA-AATCGAAATCGAAGGTATTGGTTGA
* * * * * **
43492 CAGATAACCCTTCTTGCTTTGAGTTATGCTATAAATTTGATATGTCCTTGAGCTAAATGTAATTG
65 CAGATAACCCTTATTACCTTGAGCTATGCTATAAATTTGATATGTCCTCGAGCTAAATGTAATCA
* *
43557 AACTCGAAGGTCTTCATTAGCAGATTACCCTTCTCGCCTTG
130 AACTCGAAGGTATTCATTAGCAGATTACCCTTCTCACCTTG
43598 AGCTAT
1 AGCTAT
43604 ACTGCAAATA
Statistics
Matches: 151, Mismatches: 21, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
167 1 0.01
168 120 0.79
169 2 0.01
170 26 0.17
171 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (170 bp):
AGCTATGATATAAATTTGACATGCCCTTGAGCTGAATGAAATCGAAATCGAAGGTATTGGTTGAC
AGATAACCCTTATTACCTTGAGCTATGCTATAAATTTGATATGTCCTCGAGCTAAATGTAATCAA
ACTCGAAGGTATTCATTAGCAGATTACCCTTCTCACCTTG
Found at i:43721 original size:42 final size:42
Alignment explanation
Indices: 43675--43853 Score: 128
Period size: 42 Copynumber: 4.2 Consensus size: 42
43665 TAAATGACTT
* *
43675 CCCTTCATGGGAAAGCCAAGTGGTATATTATTCAGGTGGTTC
1 CCCTTCACGGGAAAGCCAACTGGTATATTATTCAGGTGGTTC
** *** * ** * *
43717 CCCTTCGTGGGTCTG--AACTAGGTGAGACGATCTCTAGATGATTC
1 CCCTTCACGGGAAAGCCAACT-GGT-ATATTAT-TC-AGGTGGTTC
* * * * *
43761 CCTTTCACGGGAAAGCCAAGTGGTATATTCTTCATGTGGTTA
1 CCCTTCACGGGAAAGCCAACTGGTATATTATTCAGGTGGTTC
* * *
43803 CCCTTCACGGGAAAGCCAACTGATATATTCTTCACGTGGTTC
1 CCCTTCACGGGAAAGCCAACTGGTATATTATTCAGGTGGTTC
43845 CCCTTCACG
1 CCCTTCACG
43854 TGTCTGAACC
Statistics
Matches: 101, Mismatches: 30, Indels: 12
0.71 0.21 0.08
Matches are distributed among these distances:
40 3 0.03
41 3 0.03
42 66 0.65
43 4 0.04
44 19 0.19
45 3 0.03
46 3 0.03
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.30
Consensus pattern (42 bp):
CCCTTCACGGGAAAGCCAACTGGTATATTATTCAGGTGGTTC
Found at i:43896 original size:128 final size:128
Alignment explanation
Indices: 43675--43906 Score: 329
Period size: 128 Copynumber: 1.8 Consensus size: 128
43665 TAAATGACTT
* * * * ** *
43675 CCCTTCATGGGAAAGCCAAGTGGTATATTATTCAGGTGGTTCCCCTTCGTGGGTCTGAACTAGGT
1 CCCTTCACGGGAAAGCCAACTGATATATTATTCACGTGGTTCCCCTTCACGGGTCTGAACCAGGT
* * * *
43740 GAGACGATCTCTAGATGATTCCCTTTCACGGGAAAGCCAAGTGGTATATTCTTCATGTGGTTA
66 GAGACAATCTCTAGATGACTCCCCTTCACAGGAAAGCCAAGTGGTATATTCTTCATGTGGTTA
* *
43803 CCCTTCACGGGAAAGCCAACTGATATATTCTTCACGTGGTTCCCCTTCACGTGTCTGAACCAGGT
1 CCCTTCACGGGAAAGCCAACTGATATATTATTCACGTGGTTCCCCTTCACGGGTCTGAACCAGGT
* *
43868 GAGACAATCTTTGGATGACTCCCCTTCACAGGAAAGCCA
66 GAGACAATCTCTAGATGACTCCCCTTCACAGGAAAGCCA
43907 CATGGGATGT
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
128 89 1.00
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.28
Consensus pattern (128 bp):
CCCTTCACGGGAAAGCCAACTGATATATTATTCACGTGGTTCCCCTTCACGGGTCTGAACCAGGT
GAGACAATCTCTAGATGACTCCCCTTCACAGGAAAGCCAAGTGGTATATTCTTCATGTGGTTA
Found at i:49180 original size:22 final size:21
Alignment explanation
Indices: 49137--49179 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
49127 GGAAAAATGT
49137 TAATTACAAAATTAAATAAAAA
1 TAATTACAAAA-TAAATAAAAA
49159 TAATTACTAAAA-AAATAAAAA
1 TAATTAC-AAAATAAATAAAAA
49180 AAAATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.45
22 7 0.35
23 4 0.20
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (21 bp):
TAATTACAAAATAAATAAAAA
Found at i:49194 original size:22 final size:22
Alignment explanation
Indices: 49175--49251 Score: 64
Period size: 22 Copynumber: 3.3 Consensus size: 22
49165 CTAAAAAAAT
*
49175 AAAAAAAAATTAAAAGAAAACA
1 AAAAAAAAATAAAAAGAAAACA
* *
49197 ATAAAATAATAAAAAGAAAATCA
1 AAAAAAAAATAAAAAGAAAA-CA
* *
49220 AAAGAAAGAAATAAGGAATAATAACA
1 AAA-AAA-AAATAA-AAAGAA-AACA
49246 AAAAAA
1 AAAAAA
49252 TTGAATTAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
22 17 0.40
23 4 0.09
24 3 0.07
25 8 0.19
26 9 0.21
27 2 0.05
ACGTcount: A:0.77, C:0.04, G:0.08, T:0.12
Consensus pattern (22 bp):
AAAAAAAAATAAAAAGAAAACA
Found at i:49202 original size:32 final size:32
Alignment explanation
Indices: 49166--49253 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 32
49156 AAATAATTAC
*
49166 TAAAAAAATAAAAAAAAATTAAAAGAAA-ACAA
1 TAAAATAATAAAAAAAAATTAAAAGAAAGA-AA
*
49198 TAAAATAATAAAAAGAAAATCAAAAGAAAGAAA
1 TAAAATAATAAAAA-AAAATTAAAAGAAAGAAA
49231 TAAGGAATAATAACAAAAAAATT
1 TAA--AATAATAA-AAAAAAATT
49254 GAATTAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
32 13 0.27
33 18 0.38
34 1 0.02
35 13 0.27
36 3 0.06
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (32 bp):
TAAAATAATAAAAAAAAATTAAAAGAAAGAAA
Found at i:49361 original size:16 final size:15
Alignment explanation
Indices: 49329--49377 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 15
49319 GTTAGTTAAG
*
49329 AAAATAAGAATAAAAA
1 AAAATAA-AATAGAAA
49345 AAGAATAAAATAGAAA
1 AA-AATAAAATAGAAA
49361 ATAAAT-AAATAGAAA
1 A-AAATAAAATAGAAA
49376 AA
1 AA
49378 TTAAATTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
14 1 0.03
15 10 0.33
16 13 0.43
17 6 0.20
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (15 bp):
AAAATAAAATAGAAA
Found at i:52867 original size:31 final size:30
Alignment explanation
Indices: 52832--52899 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
52822 CAAAGATCAA
52832 AAAAGTTTAGAGACAAAAAGTGTAATTTCCC
1 AAAAGTTTAGAGACAAAAAGTGTAATTT-CC
* * *
52863 AAAAGTTTAGGGACTAAAAGTGTAATTTTC
1 AAAAGTTTAGAGACAAAAAGTGTAATTTCC
52893 AAAAGTT
1 AAAAGTT
52900 ATGCATTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 8 0.24
31 26 0.76
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (30 bp):
AAAAGTTTAGAGACAAAAAGTGTAATTTCC
Found at i:54337 original size:22 final size:23
Alignment explanation
Indices: 54311--54355 Score: 83
Period size: 22 Copynumber: 2.0 Consensus size: 23
54301 ATCGGGAGGG
54311 GTATCGATACCATAGT-AGGGTA
1 GTATCGATACCATAGTAAGGGTA
54333 GTATCGATACCATAGTAAGGGTA
1 GTATCGATACCATAGTAAGGGTA
54356 TCGATATCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (23 bp):
GTATCGATACCATAGTAAGGGTA
Found at i:54358 original size:20 final size:20
Alignment explanation
Indices: 54309--54361 Score: 79
Period size: 22 Copynumber: 2.5 Consensus size: 20
54299 ATATCGGGAG
*
54309 GGGTATCGATACCATAGTAG
1 GGGTATCGATACCATAGTAA
54329 GGTAGTATCGATACCATAGTAA
1 GG--GTATCGATACCATAGTAA
54351 GGGTATCGATA
1 GGGTATCGATA
54362 TCAAGAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 11 0.37
22 19 0.63
ACGTcount: A:0.32, C:0.13, G:0.28, T:0.26
Consensus pattern (20 bp):
GGGTATCGATACCATAGTAA
Found at i:55116 original size:68 final size:68
Alignment explanation
Indices: 55042--55238 Score: 277
Period size: 68 Copynumber: 2.9 Consensus size: 68
55032 AAAGATTAAT
**
55042 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGTTAGTTAGATGAAAGGCTAAATGCCT
1 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCT
55107 TTG
66 TTG
* * *
55110 AGGCCTAACAGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCT
55175 TTG
66 TTG
* * * ** * * *
55178 AGGCCTAACTGTGCAATTGGTAGAAAGATACCAATTATTCCAGTTAGATGAACGGTTAAAT
1 AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAAT
55239 ATCATTGAGT
Statistics
Matches: 113, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 113 1.00
ACGTcount: A:0.32, C:0.14, G:0.24, T:0.29
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATGCCT
TTG
Found at i:55318 original size:81 final size:81
Alignment explanation
Indices: 55179--55750 Score: 867
Period size: 81 Copynumber: 7.0 Consensus size: 81
55169 GTGCCTTTGA
* * * *
55179 GGCCTAACTGTGCAATTGGTAGAAAGATACCAATTATTCCAGTTAGATGAACGGTTAAATATCAT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
55244 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * *
55260 GGCCTAACTGTGCAATTGGTAGAAATGTACCAATTA-GTCCATTTAGATTAACGATTAAATACCG
1 GGCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATG-CCAGTTAGATGAACGGTTAAATACCG
55324 TTGAGTAAAAGAATAAT
65 TTGAGTAAAAGAATAAT
*
55341 GGCCTAACTGTGCAATTGGTAGAAAGATACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
55406 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* *
55422 GGCCTAACTGTGGAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACAGTTAAATACCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
55487 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * *
55503 GGCCTAACTGTGCAATTGATAGAAAGGTACCAATTATGCCAATTAGATGAATGGTTAAATACTGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
55568 TGAGTAAAAGAATAATAAT
66 TGAGTAAAAG---AATAAT
* * * * *
55587 AGCCTAACTGTGCCATTGGTAGAAAAGTACCAATTATGCCAGTTAGATGAATGGTTAAATACCTT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
*
55652 TGAGTAAAATAATAAT
66 TGAGTAAAAGAATAAT
* * * *
55668 GGCATAATTGTGCAATTGGTAGAGAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATAGCGT
1 GGCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
*
55733 TGAGCAAAAGAATAAT
66 TGAGTAAAAGAATAAT
55749 GG
1 GG
55751 ATTAGCTATG
Statistics
Matches: 445, Mismatches: 41, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
81 371 0.83
82 1 0.00
84 73 0.16
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (81 bp):
GGCCTAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGT
TGAGTAAAAGAATAAT
Found at i:55701 original size:246 final size:243
Alignment explanation
Indices: 55183--55750 Score: 870
Period size: 246 Copynumber: 2.3 Consensus size: 243
55173 CTTTGAGGCC
* * * *
55183 TAACTGTGCAATTGGTAGAAAGATACCAATTATTCCAGTTAGATGAACGGTTAAATATCATTGAG
1 TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
* * * *
55248 TAAAAGAATAATGGCCTAACTGTGCAATTGGTAGAAATGTACCAATTAGTCCATTTAGATTAACG
66 TAAAAGAATAATGGCCTAACTGTGCAATTGATAGAAAGGTACCAATTAGTCCAATTAGATGAACG
*
55313 ATTAAATACCGTTGAGTAAAAGAATAATGGCCTAACTGTGCAATTGGTAGAAAGATACCAATTAT
131 ATTAAATACCGTTGAGTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAGATACCAATTAT
*
55378 GCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGCC
196 GCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGCA
* *
55426 TAACTGTGGAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACAGTTAAATACCGTTGAG
1 TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
*
55491 TAAAAGAATAATGGCCTAACTGTGCAATTGATAGAAAGGTACCAATTA-TGCCAATTAGATGAAT
66 TAAAAGAATAATGGCCTAACTGTGCAATTGATAGAAAGGTACCAATTAGT-CCAATTAGATGAAC
* * *
55555 GGTTAAATACTGTTGAGTAAAAGAATAATAATAGCCTAACTGTGCCATTGGTAGAAA-AGTACCA
130 GATTAAATACCGTTGAGTAAAAG---AATAATAGCCTAACTGTGCAATTGGTAGAAAGA-TACCA
* * *
55619 ATTATGCCAGTTAGATGAATGGTTAAATACCTTTGAGTAAAATAATAATGGCA
191 ATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGCA
* * *
55672 TAATTGTGCAATTGGTAGAGAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATAGCGTTGAG
1 TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
*
55737 CAAAAGAATAATGG
66 TAAAAGAATAATGG
55751 ATTAGCTATG
Statistics
Matches: 295, Mismatches: 25, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
242 1 0.00
243 137 0.46
245 1 0.00
246 156 0.53
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (243 bp):
TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
TAAAAGAATAATGGCCTAACTGTGCAATTGATAGAAAGGTACCAATTAGTCCAATTAGATGAACG
ATTAAATACCGTTGAGTAAAAGAATAATAGCCTAACTGTGCAATTGGTAGAAAGATACCAATTAT
GCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGCA
Found at i:55808 original size:246 final size:245
Alignment explanation
Indices: 55183--55828 Score: 810
Period size: 246 Copynumber: 2.6 Consensus size: 245
55173 CTTTGAGGCC
* * * *
55183 TAACTGTGCAATTGGTAGAAAGATACCAATTATTCCAGTTAGATGAACGGTTAAATATCATTGAG
1 TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
* * * *
55248 TAAAAGAATAATGGCCTAACTGTGCAATTGGTAGAAA-TGTACCAAT-TAGTCCATTTAGAT-TA
66 TAAAAGAATAATGGCCTAACTGTGCAATTGATAGAAAGTGTACAAATAT-GT--AATTAGATGAA
* * *
55310 ACGATTAAATACCGTTGAGTAAAAG---AATAATGGCCTAACTGTGCAATTGGTAGAAAGATACC
128 AAG-TTAAATACTGTTGAGTAAAAGAATAATAATAGCCTAACTGTGCAATTGGTAGAAAGATACC
*
55372 AATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGCC
192 AATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGCA
* *
55426 TAACTGTGGAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACAGTTAAATACCGTTGAG
1 TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
* * *
55491 TAAAAGAATAATGGCCTAACTGTGCAATTGATAGAAAG-GTACCAATTATGCCAATTAGATGAAT
66 TAAAAGAATAATGGCCTAACTGTGCAATTGATAGAAAGTGTA-CAAATATG-TAATTAGATGAAA
* *
55555 GGTTAAATACTGTTGAGTAAAAGAATAATAATAGCCTAACTGTGCCATTGGTAGAAA-AGTACCA
129 AGTTAAATACTGTTGAGTAAAAGAATAATAATAGCCTAACTGTGCAATTGGTAGAAAGA-TACCA
* * *
55619 ATTATGCCAGTTAGATGAATGGTTAAATACCTTTGAGTAAAATAATAATGGCA
193 ATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGCA
* * *
55672 TAATTGTGCAATTGGTAGAGAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATAGCGTTGAG
1 TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
* ** * * * *
55737 CAAAAGAATAATGGATTAGCTATGC-ATCTGACAGGAAAGTGT-CAAATATGTAAGTTAAATGAA
66 TAAAAGAATAATGGCCTAACTGTGCAAT-TGATA-GAAAGTGTACAAATATGTAA-TTAGATGAA
* *
55800 AAGTTAAATATCT-TTGTGTAAAATAATAA
128 AAGTTAAATA-CTGTTGAGTAAAAGAATAA
55829 AGGAATTATA
Statistics
Matches: 350, Mismatches: 39, Indels: 25
0.85 0.09 0.06
Matches are distributed among these distances:
243 125 0.36
244 6 0.02
245 6 0.02
246 204 0.58
247 7 0.02
248 2 0.01
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (245 bp):
TAACTGTGCAATTGGTAGAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAG
TAAAAGAATAATGGCCTAACTGTGCAATTGATAGAAAGTGTACAAATATGTAATTAGATGAAAAG
TTAAATACTGTTGAGTAAAAGAATAATAATAGCCTAACTGTGCAATTGGTAGAAAGATACCAATT
ATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGCA
Found at i:55889 original size:2 final size:2
Alignment explanation
Indices: 55882--55936 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
55872 TGAAAGGATG
55882 AT AT AT AT 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 AT AT AT AT
55924 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
55937 ATGTTCAAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:56871 original size:84 final size:86
Alignment explanation
Indices: 56746--56908 Score: 213
Period size: 84 Copynumber: 1.9 Consensus size: 86
56736 GACGCACAAA
* ** * * *
56746 TGCGCGTCATTGAAGCTACCGTCATAAATCTCATATGACACATAATTGCGTGTCATAAATCTATG
1 TGCGCATCATTGAAGCTACCGTCATAAATCGAAGATGACACACAATTACGTGTCATAAATCTATG
*
56811 ACACGCATTTATGATGCGCAT
66 ACAAGCATTTATGATGCGCAT
* * * *
56832 TGCGCATCATTGAAGC-CCCGTCATAAAT-GAAGATGACACACATTTATGTGTCATAAATTTATG
1 TGCGCATCATTGAAGCTACCGTCATAAATCGAAGATGACACACAATTACGTGTCATAAATCTATG
56895 ACAAGCATTTATGA
66 ACAAGCATTTATGA
56909 CTTACATTTA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
84 40 0.61
85 11 0.17
86 15 0.23
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (86 bp):
TGCGCATCATTGAAGCTACCGTCATAAATCGAAGATGACACACAATTACGTGTCATAAATCTATG
ACAAGCATTTATGATGCGCAT
Found at i:56916 original size:13 final size:13
Alignment explanation
Indices: 56900--56929 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
56890 TTATGACAAG
*
56900 CATTTATGACTTA
1 CATTTACGACTTA
56913 CATTTACGACTTA
1 CATTTACGACTTA
56926 CATT
1 CATT
56930 GCGTGTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.20, G:0.07, T:0.43
Consensus pattern (13 bp):
CATTTACGACTTA
Found at i:57007 original size:2 final size:2
Alignment explanation
Indices: 57000--57026 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
56990 ATGTTGTATG
57000 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
57027 TGTATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:60612 original size:31 final size:31
Alignment explanation
Indices: 60574--60665 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 31
60564 CCCGAAGTAC
* *
60574 CAGTCCATAGGTCTCGAAGAACCTAGGTAAT
1 CAGTCCATATGTCACGAAGAACCTAGGTAAT
* *
60605 CAGTCCATATGTCCCAAAGAACCTAGGTAAT
1 CAGTCCATATGTCACGAAGAACCTAGGTAAT
* *
60636 CAGTCCATATATCACGAAGAACATAGGTAA
1 CAGTCCATATGTCACGAAGAACCTAGGTAA
60666 CCCTCGACTC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 54 1.00
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTCACGAAGAACCTAGGTAAT
Found at i:61623 original size:31 final size:32
Alignment explanation
Indices: 61566--61626 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
61556 AATTATTTGC
* * *
61566 AACTTTTCCAAAATTGCTAAATTGGTCCCCCT
1 AACTTTTCAAAAATTACTAAAATGGTCCCCCT
61598 AACTTTTCAAAAATTAC-AAAATGGTCCCC
1 AACTTTTCAAAAATTACTAAAATGGTCCCC
61627 AAATTTTCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.31
Consensus pattern (32 bp):
AACTTTTCAAAAATTACTAAAATGGTCCCCCT
Found at i:72130 original size:48 final size:47
Alignment explanation
Indices: 72070--72215 Score: 177
Period size: 48 Copynumber: 3.1 Consensus size: 47
72060 CAAAGTACTG
* *
72070 ATACGAAAATGAAATATAGGCATTAAACAAAACCGATCGATAACCATC
1 ATACGAAAATGAAAT-TATGCATTAAACAAAATCGATCGATAACCATC
* * *
72118 ATATGAAAATGAAACTTATGCATTAAACAAATTCGATCGATAATCATC
1 ATACGAAAATGAAA-TTATGCATTAAACAAAATCGATCGATAACCATC
* * * *
72166 ATACAAAAATGCAACTTATGCATTAAAC-AAATCGATCAATAACCGTC
1 ATACGAAAATG-AAATTATGCATTAAACAAAATCGATCGATAACCATC
72213 ATA
1 ATA
72216 AACAAAGTAT
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
47 18 0.21
48 63 0.75
49 3 0.04
ACGTcount: A:0.48, C:0.18, G:0.10, T:0.24
Consensus pattern (47 bp):
ATACGAAAATGAAATTATGCATTAAACAAAATCGATCGATAACCATC
Found at i:78641 original size:53 final size:53
Alignment explanation
Indices: 78540--78644 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 53
78530 AAGTGCTCAA
* * * *
78540 ATGGTAATTCACAAACTCATTATGAATCCCATGGATGCGCATATAGTGCCGAC
1 ATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACACAGTGCCGAC
* * *
78593 ATGGTCATTCATAAACTCATTATGAATACCATGGATTCACACACAGTGCCGA
1 ATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACACAGTGCCGA
78645 AAGTACATAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (53 bp):
ATGGTAATTCACAAACTCATTATGAATACCATGGATGCACACACAGTGCCGAC
Found at i:78734 original size:48 final size:48
Alignment explanation
Indices: 78662--78809 Score: 210
Period size: 48 Copynumber: 3.1 Consensus size: 48
78652 TATAGTACTG
78662 ATACGAAAATGCAAC--ATCGACATTAAACAAAATCGATCGATAATCATC
1 ATACGAAAATGCAACTTAT-G-CATTAAACAAAATCGATCGATAATCATC
*
78710 ATACGAAAATGCAACTTATGCATTAAACAAATTCGATCGATAATCATC
1 ATACGAAAATGCAACTTATGCATTAAACAAAATCGATCGATAATCATC
* * * **
78758 ATGCAAAAATGCAACTTATGCATTAAACCAAATCGATCGATAGCCATC
1 ATACGAAAATGCAACTTATGCATTAAACAAAATCGATCGATAATCATC
78806 ATAC
1 ATAC
78810 ACAAAGTATG
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
48 87 0.97
49 1 0.01
50 2 0.02
ACGTcount: A:0.45, C:0.21, G:0.11, T:0.24
Consensus pattern (48 bp):
ATACGAAAATGCAACTTATGCATTAAACAAAATCGATCGATAATCATC
Found at i:86921 original size:21 final size:21
Alignment explanation
Indices: 86895--86958 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
86885 TTTTTGTGCA
*
86895 GAGGGAATCGATCCCCCCCAT
1 GAGGGAACCGATCCCCCCCAT
* **
86916 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATCCCCCCCAT
*
86937 GAAGGGGAACCGATTCCCCCCA
1 G-A-GGGAACCGATCCCCCCCA
86959 CAGGGGAATC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 18 0.51
22 1 0.03
23 16 0.46
ACGTcount: A:0.23, C:0.36, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATCCCCCCCAT
Found at i:86965 original size:21 final size:21
Alignment explanation
Indices: 86897--86977 Score: 60
Period size: 21 Copynumber: 3.8 Consensus size: 21
86887 TTTGTGCAGA
*
86897 GGGAATCGA-TCCCCCC-CATG
1 GGGAACCGATTCCCCCCACA-G
*
86917 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC---CACAG
86941 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
86962 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
86978 TAGGGTTCTG
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 1 0.02
21 24 0.49
22 6 0.12
23 16 0.33
24 1 0.02
25 1 0.02
ACGTcount: A:0.23, C:0.37, G:0.25, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:87391 original size:24 final size:26
Alignment explanation
Indices: 87345--87393 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
87335 AGAATTTTCC
*
87345 AAAAAATTTTAAATTTTCGAAATTAA
1 AAAAAATGTTAAATTTTCGAAATTAA
87371 AAAAAATGTT-AATTTTC-AAATTA
1 AAAAAATGTTAAATTTTCGAAATTA
87394 TTGTGTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 6 0.27
25 7 0.32
26 9 0.41
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (26 bp):
AAAAAATGTTAAATTTTCGAAATTAA
Found at i:95329 original size:15 final size:15
Alignment explanation
Indices: 95305--95337 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
95295 AAACCATTTA
95305 ATAATCTTCTTTATT
1 ATAATCTTCTTTATT
*
95320 ATAATTTTCTTTATT
1 ATAATCTTCTTTATT
95335 ATA
1 ATA
95338 GGGTTAAGTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (15 bp):
ATAATCTTCTTTATT
Done.