Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011700.1 Kokia drynarioides strain JFW-HI SEQ_126694, 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: 364021
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 11 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:6328 original size:21 final size:21
Alignment explanation
Indices: 6287--6330 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6277 TGGCTCGAAA
**
6287 GACAAAAAGAGAAAGCGCAAG
1 GACAAAAAGAGAAAGAACAAG
6308 GACAAAAAGA-AGAAGAACAAG
1 GACAAAAAGAGA-AAGAACAAG
6329 GA
1 GA
6331 GGAAGGAAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.61, C:0.11, G:0.27, T:0.00
Consensus pattern (21 bp):
GACAAAAAGAGAAAGAACAAG
Found at i:24355 original size:15 final size:16
Alignment explanation
Indices: 24335--24375 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
24325 AAAGTTTTCT
24335 ATAGTTTCACAATT-C-
1 ATAGTTTCAC-ATTCCA
24350 ATAGTTTTCACATTCCA
1 ATAG-TTTCACATTCCA
24367 ATAGTTTCA
1 ATAGTTTCA
24376 AAGTTTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 7 0.30
16 12 0.52
17 4 0.17
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (16 bp):
ATAGTTTCACATTCCA
Found at i:29569 original size:3 final size:3
Alignment explanation
Indices: 29563--29597 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
29553 AATCATTATT
*
29563 ATC ATC ATC ACC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
29598 TATTATTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
ATC
Found at i:30538 original size:148 final size:146
Alignment explanation
Indices: 30046--30702 Score: 705
Period size: 150 Copynumber: 4.5 Consensus size: 146
30036 TATTTTGGGA
* * *
30046 AAAGTTTTGGTTTTTTTAA-TAATTTCCAAATAAAAGCTTT-GATTTTTAAGTAAAATACTGATT
1 AAAGTTTTGGTTTTTTTAACT-ATTTCGAAATAAAAG-TTTAGATTTTTAAGTAAAGTAGTGATT
* * *
30109 TT-TTTAAAAAAAAAGAGAAGTTTAGATTTTTAAAAATAAAAA-TA---TGTTTTTTTT--AG-A
64 TTCATTAAAAAATAAGA-AAGTTTAGATTTTTAAAAATAAAAACTATTTTTTTTTTTTTAAAGAA
30166 AAAGTTTAAATTTTTAAAC
128 AAAGTTTAAATTTTTAAAC
* * * * * * *
30185 AAAGTTTTGATTTTTTTTAACCACTTCGAAATAAAAGTTTGGATTTTTAAGTAAAATAGCGATTC
1 AAAGTTTTG-GTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTT
* * * * *
30250 TCTTTAAACAA-AAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTTACTTATTTTACAG
65 TCATTAAAAAATAAGAAAGTTTAGATTTTTAAAAATAAAAA-CTATTTTTTT--TT-TTTTAAAG
*
30314 AAAAAGTTTAAATTTTTAAAT
126 AAAAAGTTTAAATTTTTAAAC
* * * *
30335 AAAATTTTGATTTTTTTTAACTATTTCGAAATAAAATTTTAGATTTTTCAG-AAAGTAGTGATTT
1 AAAGTTTTG-GTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTT
* *
30399 TCATTAAAAAATGAGAAAGTTTATA-TTTTAAAAATAAAAATCTATTTTTTAATTTTTTTAAAGA
65 TCATTAAAAAATAAGAAAGTTTAGATTTTTAAAAATAAAAA-CTATTTTTT--TTTTTTTAAAGA
*
30463 AAAAGTTTAAATTTTTAAAT
127 AAAAGTTTAAATTTTTAAAC
* *
30483 AAAGTTTTGGTTTTTTTAACTATTTTGAAATAAAAGTTTAGATTTTTAAGTAAAGTAATGATTTT
1 AAAGTTTTGGTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTT
* *
30548 CATTAAAAAAATAAAGAAAATTTAGATTTTTAAAAAATAAGAAACTGTTTTTTTTTTAGTGATTT
66 CATT-AAAAAAT-AAGAAAGTTTAGATTTTT-AAAAATAA-AAACT-ATTTTTTTTT--T--TTT
30613 AAAGAAAAA-TTTAAATTTTTAAAC
122 AAAGAAAAAGTTTAAATTTTTAAAC
* * * *
30637 AAAGTTTT-GATTTTTTAACTATTTCGAAATAAAAAGTTTTGATTTTGAAGTAAAGTAGTAATTT
1 AAAGTTTTGGTTTTTTTAACTATTTCGAAAT-AAAAGTTTAGATTTTTAAGTAAAGTAGTGATTT
30701 TC
65 TC
30703 TTTTAATCAA
Statistics
Matches: 445, Mismatches: 43, Indels: 45
0.83 0.08 0.08
Matches are distributed among these distances:
139 36 0.08
140 48 0.11
141 9 0.02
144 3 0.01
146 2 0.00
147 41 0.09
148 53 0.12
149 54 0.12
150 86 0.19
151 8 0.02
152 10 0.02
153 30 0.07
154 53 0.12
155 12 0.03
ACGTcount: A:0.42, C:0.04, G:0.10, T:0.44
Consensus pattern (146 bp):
AAAGTTTTGGTTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTT
CATTAAAAAATAAGAAAGTTTAGATTTTTAAAAATAAAAACTATTTTTTTTTTTTTAAAGAAAAA
GTTTAAATTTTTAAAC
Found at i:40011 original size:13 final size:14
Alignment explanation
Indices: 39993--40021 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39983 TAGTAGAGAA
39993 TTTCATACCTT-AT
1 TTTCATACCTTGAT
40006 TTTCATACCTTGAT
1 TTTCATACCTTGAT
40020 TT
1 TT
40022 CTACTTTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.21, C:0.21, G:0.03, T:0.55
Consensus pattern (14 bp):
TTTCATACCTTGAT
Found at i:42313 original size:10 final size:9
Alignment explanation
Indices: 42289--42337 Score: 55
Period size: 10 Copynumber: 5.2 Consensus size: 9
42279 TTAAATCAAG
*
42289 AAAAAAATA
1 AAAAAAAGA
42298 CAAAAAAAGA
1 -AAAAAAAGA
42308 AGAAAAAAG-
1 A-AAAAAAGA
42317 AAAAAAAGA
1 AAAAAAAGA
42326 AAAAAATAGA
1 AAAAAA-AGA
42336 AA
1 AA
42338 GAGAGAGCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
8 7 0.20
9 8 0.23
10 20 0.57
ACGTcount: A:0.84, C:0.02, G:0.10, T:0.04
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:42325 original size:15 final size:16
Alignment explanation
Indices: 42301--42330 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
42291 AAAAATACAA
42301 AAAAAGAAGAAAAAAG
1 AAAAAGAAGAAAAAAG
42317 AAAAA-AAGAAAAAA
1 AAAAAGAAGAAAAAA
42331 ATAGAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAAGAAGAAAAAAG
Found at i:42336 original size:18 final size:18
Alignment explanation
Indices: 42286--42337 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
42276 TGTTTAAATC
*
42286 AAGAAAAAAATACAAAAA
1 AAGAAAAAAATAGAAAAA
42304 AAGAAGAAAAA-AGAAAAA
1 AAGAA-AAAAATAGAAAAA
42322 AAGAAAAAAATAGAAA
1 AAGAAAAAAATAGAAA
42338 GAGAGAGCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
17 5 0.16
18 21 0.68
19 5 0.16
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.04
Consensus pattern (18 bp):
AAGAAAAAAATAGAAAAA
Found at i:42798 original size:42 final size:42
Alignment explanation
Indices: 42739--43320 Score: 700
Period size: 42 Copynumber: 13.9 Consensus size: 42
42729 AAGGAAAGCA
* * *
42739 TTCATTGCATTTAGAGGCCCAAGTGTTGAGTTCCATTTACTT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
** * *
42781 TTCATCACATTCAGAGGCCCAAGTATGGAGGCCCATTTACTT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * *
42823 TTCATTGCATTTAG-GGCCTAGGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * * **
42864 TTCATCGCTTTTAGAGGAACAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * *
42906 TTCACTGCATTCAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* *
42948 TTCATTGCATTCGGAGACCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* *
42990 TTCATTGCATTCAGAGGCCAAAGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
** * * *
43032 TTCATCACATTCAAAGGCCTAAGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * *
43074 TTCATTGTATTTAGAGGCCCAAATGTGGAGGTCCATTTACTT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
** * *
43116 TTCATTGCATTTGGAGG-CCTAGAAGTGGAGGTCCATTTACTT
1 TTCATTGCATTCAGAGGCCCAAG-TGTGGAGGTCCATTTACTT
* * *
43158 TTCATCGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
** * * * *
43200 TTCACCGCATTCAAAGGCCTAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
* * *
43242 TTCATTGCATTCAGAAGCCTAAGTGTGGAGGTCCATTTATTT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
** *
43284 TTCATTGCATTCAGAGGCTTAGGTGTGGAGGTCCATT
1 TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATT
43321 ACAAGTGTGG
Statistics
Matches: 461, Mismatches: 76, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
41 38 0.08
42 419 0.91
43 4 0.01
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.34
Consensus pattern (42 bp):
TTCATTGCATTCAGAGGCCCAAGTGTGGAGGTCCATTTACTT
Found at i:43034 original size:126 final size:126
Alignment explanation
Indices: 42739--43551 Score: 767
Period size: 126 Copynumber: 6.3 Consensus size: 126
42729 AAGGAAAGCA
* * * *
42739 TTCATTGCATTTAGAGGCCCAAGTGTTGAGTTCCATTTACTTTTCATCACATTCAGAGGCCCAAG
1 TTCATTGCATTTAGAGGCCAAAGTGTGGAGGTCCATTTACTTTTCATCGCATTCAGAGGCCCAAG
* * *
42804 TATGGAGGCCCATTTACTTTTCATTGCATTTAG-GGCCTAGGTGTGGAGGTCCATTTACTT
66 TGTGGAGGCCCATTTACTTTTCATTGCATTCAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
42864 TTCATCGCTTTTAGAGG-AACAAGTGTGGAGGTCCATTTACTTTTCA-CTGCATTCAGAGGCCCA
1 TTCATTGCATTTAGAGGCCA-AAGTGTGGAGGTCCATTTACTTTTCATC-GCATTCAGAGGCCCA
* * * *
42927 GGTGTGGAGGCCCATTTACTTTTCATTGCATTCGGAGACCCAAGTGTGGAGGTCCATTTACTT
64 AGTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * *
42990 TTCATTGCATTCAGAGGCCAAAGTGTGGAGGCCCATTTACTTTTCATCACATTCAAAGGCCTAAG
1 TTCATTGCATTTAGAGGCCAAAGTGTGGAGGTCCATTTACTTTTCATCGCATTCAGAGGCCCAAG
* * **
43055 TGTGGAGGCCCATTTACTTTTCATTGTATTTAGAGGCCCAAATGTGGAGGTCCATTTACTT
66 TGTGGAGGCCCATTTACTTTTCATTGCATTCAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
43116 TTCATTGCATTTGGAGGCCTAGAA--GTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCCA
1 TTCATTGCATTTAGAGGCC-A-AAGTGTGGAGGTCCATTTACTTTTCATCGCATTCAGAGGCCCA
* * ** * * *
43179 AGTGTAGAGGTCCATTTACTTTTCACCGCATTCAAAGGCCTAGGTGTGGAGGCCCATTTACTT
64 AGTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * * * ** *
43242 TTCATTGCATTCAGAAGCCTAAGTGTGGAGGTCCATTTATTTTTCATTGCATTCAGAGGCTTAGG
1 TTCATTGCATTTAGAGGCCAAAGTGTGGAGGTCCATTTACTTTTCATCGCATTCAGAGGCCCAAG
* * *
43307 TGTGGAGGTCCATTACAAGTGTGGAGGTCCATTTACTTTTCATTGCACTTAGAGGCCCAGGTGTG
66 TGTGGAGG-CC----C-A-T-T-----T--A-C---TTTTCATTGCATTCAGAGGCCCAGGTGTG
43372 GAGG-CACATTTACTT
112 GAGGTC-CATTTACTT
* * * * * * * *
43387 TTCATTGAATTTAGAGGCTC-AGGTGTGGAGGCCCATTTACTTTTCGTTGCATTTAGAGGCCTAG
1 TTCATTGCATTTAGAGGC-CAAAGTGTGGAGGTCCATTTACTTTTCATCGCATTCAGAGGCCCAA
* * * * * * * *
43451 GTGAGAAGGTCTATTTACTTTTCCTTGCAATCGGAGGCCTAGGTGTGGAGGTCCATTTACTT
65 GTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * ** *
43513 TTCATTACAATTAGAGGCCTAAGCATAGAGGTCCATTTA
1 TTCATTGCATTTAGAGGCCAAAGTGTGGAGGTCCATTTA
43552 TTTATTTATT
Statistics
Matches: 564, Mismatches: 92, Indels: 63
0.78 0.13 0.09
Matches are distributed among these distances:
124 3 0.01
125 85 0.15
126 359 0.64
127 5 0.01
128 2 0.00
130 1 0.00
131 1 0.00
132 2 0.00
133 1 0.00
134 1 0.00
137 1 0.00
138 1 0.00
139 2 0.00
141 1 0.00
144 2 0.00
145 96 0.17
146 1 0.00
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (126 bp):
TTCATTGCATTTAGAGGCCAAAGTGTGGAGGTCCATTTACTTTTCATCGCATTCAGAGGCCCAAG
TGTGGAGGCCCATTTACTTTTCATTGCATTCAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:43403 original size:103 final size:103
Alignment explanation
Indices: 43222--43423 Score: 291
Period size: 103 Copynumber: 2.0 Consensus size: 103
43212 AAAGGCCTAG
* *
43222 GTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAAGCCTAAGTGTGGAGGTCCATTTATTTTTC
1 GTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAAGCCCAAGTGTGGAGGTCCATTTACTTTTC
* * *
43287 ATTGCATTCAGAGGCTTAGGTGTGGAGGTCCATTACAA
66 ATTGAATTCAGAGGCTCAGGTGTGGAGGCCCATTACAA
* * *
43325 GTGTGGAGGTCCATTTACTTTTCATTGCACTT-AGAGGCCCAGGTGTGGAGG-CACATTTACTTT
1 GTGTGGAGGCCCATTTACTTTTCATTGCA-TTCAGAAGCCCAAGTGTGGAGGTC-CATTTACTTT
*
43388 TCATTGAATTTAGAGGCTCAGGTGTGGAGGCCCATT
64 TCATTGAATTCAGAGGCTCAGGTGTGGAGGCCCATT
43424 TACTTTTCGT
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
102 1 0.01
103 85 0.97
104 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.27, T:0.34
Consensus pattern (103 bp):
GTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAAGCCCAAGTGTGGAGGTCCATTTACTTTTC
ATTGAATTCAGAGGCTCAGGTGTGGAGGCCCATTACAA
Found at i:43445 original size:145 final size:145
Alignment explanation
Indices: 43177--43453 Score: 387
Period size: 145 Copynumber: 1.9 Consensus size: 145
43167 TTTAGAGGCC
* *
43177 CAAGTGTAGAGGTCCATTTACTTTTCACCGCATTCAAAGGCCTAGGTGTGGAGGCCCATTTACTT
1 CAAGTGTAGAGGTCCATTTACTTTTCACCGCATTCAAAGGCCCAGGTGTGGAGGCACATTTACTT
* * * *
43242 TTCATTGCATTCAGAAGCCTAAGTGTGGAGGTCCATTTATTTTTCATTGCATTCAGAGGCTTAGG
66 TTCATTGAATTCAGAAGCCTAAGTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAGGCCTAGG
43307 TGTGGAGGTCCATTA
131 TGTGGAGGTCCATTA
* ** *
43322 CAAGTGTGGAGGTCCATTTACTTTTCATTGCACTT-AGAGGCCCAGGTGTGGAGGCACATTTACT
1 CAAGTGTAGAGGTCCATTTACTTTTCACCGCA-TTCAAAGGCCCAGGTGTGGAGGCACATTTACT
* * * * *
43386 TTTCATTGAATTTAG-AGGCTCAGGTGTGGAGGCCCATTTACTTTTCGTTGCATTTAGAGGCCTA
65 TTTCATTGAATTCAGAAGCCT-AAGTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAGGCCTA
43450 GGTG
129 GGTG
43454 AGAAGGTCTA
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
144 4 0.03
145 109 0.95
146 2 0.02
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (145 bp):
CAAGTGTAGAGGTCCATTTACTTTTCACCGCATTCAAAGGCCCAGGTGTGGAGGCACATTTACTT
TTCATTGAATTCAGAAGCCTAAGTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAGGCCTAGG
TGTGGAGGTCCATTA
Found at i:43496 original size:187 final size:187
Alignment explanation
Indices: 43140--43507 Score: 515
Period size: 187 Copynumber: 2.0 Consensus size: 187
43130 AGGCCTAGAA
*
43140 GTGGAGGTCCATTTACTTTTCATCGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTACTTTTCAC
1 GTGGAGGTCCATTTACTTTTCATCGCACTTAGAGGCCCAAGTGTAGAGGTCCATTTACTTTTCAC
* * *
43205 CGCATTCAAAGGCCTAGGTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAAGCCTAAGTGTGG
66 CGAATTCAAAGGCCTAGGTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAAGCCTAAGTGAGA
* * *
43270 AGGTCCATTTATTTTTCATTGCATTCAGAGGCTTAGGTGTGGAGGTCCATTACAAGT
131 AGGTCCATTTACTTTTCATTGCAATCAGAGGCCTAGGTGTGGAGGTCCATTACAAGT
* * *
43327 GTGGAGGTCCATTTACTTTTCATTGCACTTAGAGGCCCAGGTGTGGAGG-CACATTTACTTTTCA
1 GTGGAGGTCCATTTACTTTTCATCGCACTTAGAGGCCCAAGTGTAGAGGTC-CATTTACTTTTCA
** * * * * * *
43391 TTGAATTTAGAGG-CTCAGGTGTGGAGGCCCATTTACTTTTCGTTGCATTTAGAGGCCTAGGTGA
65 CCGAATTCAAAGGCCT-AGGTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAAGCCTAAGTGA
* * *
43455 GAAGGTCTATTTACTTTTCCTTGCAATCGGAGGCCTAGGTGTGGAGGTCCATT
129 GAAGGTCCATTTACTTTTCATTGCAATCAGAGGCCTAGGTGTGGAGGTCCATT
43508 TACTTTTCAT
Statistics
Matches: 158, Mismatches: 21, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
186 3 0.02
187 155 0.98
ACGTcount: A:0.21, C:0.19, G:0.26, T:0.34
Consensus pattern (187 bp):
GTGGAGGTCCATTTACTTTTCATCGCACTTAGAGGCCCAAGTGTAGAGGTCCATTTACTTTTCAC
CGAATTCAAAGGCCTAGGTGTGGAGGCCCATTTACTTTTCATTGCATTCAGAAGCCTAAGTGAGA
AGGTCCATTTACTTTTCATTGCAATCAGAGGCCTAGGTGTGGAGGTCCATTACAAGT
Found at i:43499 original size:229 final size:229
Alignment explanation
Indices: 43097--43518 Score: 594
Period size: 229 Copynumber: 1.8 Consensus size: 229
43087 GAGGCCCAAA
* * *
43097 TGTGGAGGTCCATTTACTTTTCATTGCATTTGGAGGCCTAGAAGTGGAGGTCCATTTACTTTTCA
1 TGTGGAGGTCCATTTACTTTTCATTGCACTTAGAGGCCCAGAAGTGGAGGTCCATTTACTTTTCA
* * *
43162 TCGCATTTAGAGGCCCAAGTGTAGAGGTCCATTTACTTTTCACCGCATTCAAAGGCCTAGGTGTG
66 TCGAATTTAGAGGCCCAAGTGTAGAGGCCCATTTACTTTTCACCGCATTCAAAGGCCTAGGTGAG
* * *
43227 GAGGCCCATTTACTTTTCATTGCATTCAGAAGCCTAAGTGTGGAGGTCCATTTATTTTTCATTGC
131 AAGGCCCATTTACTTTTCATTGCAATCAGAAGCCTAAGTGTGGAGGTCCATTTACTTTTCATTGC
43292 ATTCAGAGGCTTAGGTGTGGAGGTCCATTACAAG
196 ATTCAGAGGCTTAGGTGTGGAGGTCCATTACAAG
**
43326 TGTGGAGGTCCATTTACTTTTCATTGCACTTAGAGGCCCAGGTGTGGAGG-CACATTTACTTTTC
1 TGTGGAGGTCCATTTACTTTTCATTGCACTTAGAGGCCCAGAAGTGGAGGTC-CATTTACTTTTC
* * * * *** * *
43390 ATTGAATTTAGAGGCTCAGGTGTGGAGGCCCATTTACTTTTCGTTGCATTTAGAGGCCTAGGTGA
65 ATCGAATTTAGAGGCCCAAGTGTAGAGGCCCATTTACTTTTCACCGCATTCAAAGGCCTAGGTGA
* * * * * *
43455 GAAGGTCTATTTACTTTTCCTTGCAATCGGAGGCCTAGGTGTGGAGGTCCATTTACTTTTCATT
130 GAAGGCCCATTTACTTTTCATTGCAATCAGAAGCCTAAGTGTGGAGGTCCATTTACTTTTCATT
43519 ACAATTAGAG
Statistics
Matches: 166, Mismatches: 26, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
228 1 0.01
229 165 0.99
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (229 bp):
TGTGGAGGTCCATTTACTTTTCATTGCACTTAGAGGCCCAGAAGTGGAGGTCCATTTACTTTTCA
TCGAATTTAGAGGCCCAAGTGTAGAGGCCCATTTACTTTTCACCGCATTCAAAGGCCTAGGTGAG
AAGGCCCATTTACTTTTCATTGCAATCAGAAGCCTAAGTGTGGAGGTCCATTTACTTTTCATTGC
ATTCAGAGGCTTAGGTGTGGAGGTCCATTACAAG
Found at i:43532 original size:42 final size:42
Alignment explanation
Indices: 43325--43551 Score: 262
Period size: 42 Copynumber: 5.4 Consensus size: 42
43315 TCCATTACAA
* *
43325 GTGTGGAGGTCCATTTACTTTTCATTGCACTTAGAGGCCCAG
1 GTGTGGAGGTCCATTTACTTTTCATTGCAATTAGAGGCCTAG
43367 GTGTGGAGG-CACATTTACTTTTCATTG-AATTTAGAGG-CTCAG
1 GTGTGGAGGTC-CATTTACTTTTCATTGCAA-TTAGAGGCCT-AG
* * *
43409 GTGTGGAGGCCCATTTACTTTTCGTTGCATTTAGAGGCCTAG
1 GTGTGGAGGTCCATTTACTTTTCATTGCAATTAGAGGCCTAG
* * * * **
43451 GTGAGAAGGTCTATTTACTTTTCCTTGCAATCGGAGGCCTAG
1 GTGTGGAGGTCCATTTACTTTTCATTGCAATTAGAGGCCTAG
* *
43493 GTGTGGAGGTCCATTTACTTTTCATTACAATTAGAGGCCTAA
1 GTGTGGAGGTCCATTTACTTTTCATTGCAATTAGAGGCCTAG
** *
43535 GCATAGAGGTCCATTTA
1 GTGTGGAGGTCCATTTA
43552 TTTATTTATT
Statistics
Matches: 156, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
41 3 0.02
42 149 0.96
43 4 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (42 bp):
GTGTGGAGGTCCATTTACTTTTCATTGCAATTAGAGGCCTAG
Found at i:43885 original size:16 final size:15
Alignment explanation
Indices: 43861--43895 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
43851 AAATAGAGGT
43861 TTTTATTTTTCTTTTC
1 TTTTATTTTTC-TTTC
*
43877 TTTTCTTTTTCTTTC
1 TTTTATTTTTCTTTC
43892 TTTT
1 TTTT
43896 TGGGCTTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTATTTTTCTTTC
Found at i:43930 original size:3 final size:3
Alignment explanation
Indices: 43916--43975 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
43906 AAGGGCCCAA
* * * * *
43916 ATT ATA ATT ATT ATT ATT ATC ATC ATC ATT CTT ATT CA-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
43961 ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT
43976 GTTGTTGTTG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
2 1 0.02
3 47 0.96
4 1 0.02
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:44593 original size:3 final size:3
Alignment explanation
Indices: 44587--44615 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
44577 CTTATTATTA
44587 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
44616 TTTAGGGTTT
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:45293 original size:149 final size:146
Alignment explanation
Indices: 45024--45517 Score: 673
Period size: 137 Copynumber: 3.4 Consensus size: 146
45014 AAAGATTTGT
* * *
45024 TTTTTTTAAACAATTTTGAAATAAAAGCTTTGATTTTTAAGTAAAATAATGATTTTCTTTAAAAA
1 TTTTTTT-AACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAATGATTTTCTTTAAAAA
45089 AGAGAAAGTTTAGATTTTTAAAAATAAAAATCTG----T--TT-TTTT--AAAAAAGTTTAAATT
65 AGAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTAGTTATTTTAAAAAAAAGTTTAAATT
45145 TTTAAACAAAATTTTTA
130 TTTAAACAAAATTTTTA
* *
45162 TTTTTTTAACTATTTCGAAATAAAAATTTGGATTTTTAAGTAAAATAATGATTTTCTTTAAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAATGATTTTCTTTAAAAAA
*
45227 GAGAAAGTTTATATTTTTAAAAATAAAAATCTGTTTTTTAGTTATTTTAAAGAAAAAAGTTTAAA
66 GAGAAAGTTTAGATTTTTAAAAATAAAAATCTG-TTTTTAGTTATTTT-AA-AAAAAAGTTTAAA
* *
45292 TTTTTAAATAAAGTTTTTA
128 TTTTTAAACAAAATTTTTA
* * *
45311 TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAATGATTTTC-TT-TAAAA
* *
45376 AAGAAAGAAAGTTTAGATTTTTAAAAAATAAAAATCTATTTTTAGTGATTTTAAAAAAAAGTTTA
64 AAG--AGAAAGTTTAGATTTTT-AAAAATAAAAATCTGTTTTTAGTTATTTTAAAAAAAAGTTTA
*
45441 AATTTTTAAACAAAATTTTGA
126 AATTTTTAAACAAAATTTTTA
* * * *
45462 TTTTTTTTAACTATTTCAAAATAAAAGTTTTGATTTTGAAGTAAAGTAGTGATTTT
1 -TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAATGATTTT
45518 ATTTTAATCA
Statistics
Matches: 317, Mismatches: 21, Indels: 22
0.88 0.06 0.06
Matches are distributed among these distances:
137 85 0.27
138 7 0.02
142 1 0.00
144 2 0.01
145 4 0.01
149 82 0.26
150 2 0.01
151 36 0.11
152 55 0.17
153 29 0.09
154 14 0.04
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (146 bp):
TTTTTTTAACTATTTCGAAATAAAAGTTTTGATTTTTAAGTAAAATAATGATTTTCTTTAAAAAA
GAGAAAGTTTAGATTTTTAAAAATAAAAATCTGTTTTTAGTTATTTTAAAAAAAAGTTTAAATTT
TTAAACAAAATTTTTA
Found at i:45365 original size:51 final size:51
Alignment explanation
Indices: 45281--45517 Score: 135
Period size: 51 Copynumber: 4.7 Consensus size: 51
45271 TTTTAAAGAA
* ** *
45281 AAAAGTTTAAATTTTTAAATAAAGTTTTTATTTTTTTAACTATTTCGAAAT
1 AAAAGTTTAGATTTTTAAATAAAGTAGTGATTTTTTTAACTATTTCGAAAT
* * * * ****
45332 AAAAGTTTTGATTTTTAAGTAAAGTAGTGATTTTCATTAA-AAAAAAGAAA-
1 AAAAGTTTAGATTTTTAAATAAAGTAGTGATTTT-TTTAACTATTTCGAAAT
* *** * * *
45382 GAAAGTTTAGATTTTTAAA-AAA-TAAAAATCTATTTTT-AGTGATTT-TAAAA
1 AAAAGTTTAGATTTTTAAATAAAGTAGTGAT-T-TTTTTAACT-ATTTCGAAAT
* * * ** *
45432 AAAAGTTTAAATTTTTAAACAAAATTTTGATTTTTTTTAACTATTTCAAAAT
1 AAAAGTTTAGATTTTTAAATAAAGTAGTGA-TTTTTTTAACTATTTCGAAAT
* * *
45484 AAAAGTTTTGATTTTGAAGTAAAGTAGTGATTTT
1 AAAAGTTTAGATTTTTAAATAAAGTAGTGATTTT
45518 ATTTTAATCA
Statistics
Matches: 134, Mismatches: 41, Indels: 22
0.68 0.21 0.11
Matches are distributed among these distances:
48 5 0.04
49 9 0.07
50 36 0.27
51 49 0.37
52 34 0.25
53 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.10, T:0.44
Consensus pattern (51 bp):
AAAAGTTTAGATTTTTAAATAAAGTAGTGATTTTTTTAACTATTTCGAAAT
Found at i:47741 original size:53 final size:53
Alignment explanation
Indices: 47683--47790 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
47673 ATTCGTGGAA
47683 AAGTCAATTATTGCAATGGTATCATGAACCAAAAGTAGCAGGACAGTGTGATG
1 AAGTCAATTATTGCAATGGTATCATGAACCAAAAGTAGCAGGACAGTGTGATG
47736 AAGTCAATTATTGCAATGGTATCATGAACCAAAAGTAGCAGGACAGTGTGATG
1 AAGTCAATTATTGCAATGGTATCATGAACCAAAAGTAGCAGGACAGTGTGATG
47789 AA
1 AA
47791 AACTATGGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (53 bp):
AAGTCAATTATTGCAATGGTATCATGAACCAAAAGTAGCAGGACAGTGTGATG
Found at i:50998 original size:16 final size:15
Alignment explanation
Indices: 50973--51003 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
50963 CCTATTCTCA
50973 ATTTTTTATTTTATT
1 ATTTTTTATTTTATT
50988 ATTTGTTTATTTTATT
1 ATTT-TTTATTTTATT
51004 TTAATTGTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (15 bp):
ATTTTTTATTTTATT
Found at i:51020 original size:21 final size:20
Alignment explanation
Indices: 50976--51021 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
50966 ATTCTCAATT
50976 TTTTATTTTATTATTTGTTTA
1 TTTTATTTTA-TATTTGTTTA
50997 TTTTATTTTA-ATTGTGTTTAA
1 TTTTATTTTATATT-TGTTT-A
51018 TTTT
1 TTTT
51022 TTCTTTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.13
20 5 0.22
21 15 0.65
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.74
Consensus pattern (20 bp):
TTTTATTTTATATTTGTTTA
Found at i:70783 original size:14 final size:14
Alignment explanation
Indices: 70760--70796 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
70750 CATTTTTATA
70760 TTTCCTTTTA-TTG
1 TTTCCTTTTACTTG
70773 TTTCACTTTTACTTG
1 TTTC-CTTTTACTTG
70788 TTTCCTTTT
1 TTTCCTTTT
70797 CAATTTTATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.18
14 11 0.50
15 7 0.32
ACGTcount: A:0.08, C:0.19, G:0.05, T:0.68
Consensus pattern (14 bp):
TTTCCTTTTACTTG
Found at i:71827 original size:15 final size:15
Alignment explanation
Indices: 71807--71851 Score: 81
Period size: 15 Copynumber: 3.0 Consensus size: 15
71797 ACCGTACGTG
71807 CATTCTGCACTCAAT
1 CATTCTGCACTCAAT
*
71822 CATTCTACACTCAAT
1 CATTCTGCACTCAAT
71837 CATTCTGCACTCAAT
1 CATTCTGCACTCAAT
71852 TTTAAAGGGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.29, C:0.33, G:0.04, T:0.33
Consensus pattern (15 bp):
CATTCTGCACTCAAT
Found at i:74073 original size:137 final size:138
Alignment explanation
Indices: 73885--74287 Score: 598
Period size: 146 Copynumber: 2.9 Consensus size: 138
73875 ATATTTAAAA
*
73885 AAAAAATCAAAACTTTGTTAAAAATTTAAAC-TTTTCTTTAAAATAACTAAAAACCAGATTTTTA
1 AAAAAAT-AAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTA
* *
73949 TTTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAGATCACTATTTTTCTTAAAAATCCAAAC-T
65 TTTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATCCAAACTT
74013 -AAATAGTT
130 CAAATAGTT
74021 AGAAAAA-ATAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTT
1 A-AAAAATA-AAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTT
* *
74085 ATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATCTAAACT
64 ATTTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATCCAAAC-
74150 TTTATTTCGAAATAGTT
128 -----TTC-AAATAGTT
* *
74167 AAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATATATTTTTA
1 AAAAAAT-AAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTA
* *
74232 TTTTTAAAAATCTAAGCTTTCTCTTTTTTAAAGAAAATCACTATTTTGCTTAAAAA
65 TTTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAA
74288 AATCAAAACT
Statistics
Matches: 243, Mismatches: 10, Indels: 18
0.90 0.04 0.07
Matches are distributed among these distances:
135 1 0.00
136 23 0.09
137 96 0.40
144 1 0.00
145 5 0.02
146 116 0.48
147 1 0.00
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (138 bp):
AAAAAATAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTAT
TTTTAAAAATCTAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATCCAAACTTC
AAATAGTT
Found at i:74183 original size:146 final size:146
Alignment explanation
Indices: 74013--74322 Score: 489
Period size: 146 Copynumber: 2.1 Consensus size: 146
74003 AATCCAAACT
74013 AAATAGTTAGAAAAAATAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACA
1 AAATAGTTA-AAAAAATAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACA
74078 GATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTT-AAAAA
65 GATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAAA
* *
74142 TCTAAACTTTTATTTCG
130 TCAAAACTTTTATTTCA
*
74159 AAATAGTT-AAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAT
1 AAATAGTTAAAAAAAT--AAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAC
* * * *
74223 ATATTTTTATTTTTAAAAATCTAAGCTTTCTCTTTTTTAAAGAAAATCACTATTTTGCTTAAAAA
64 AGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTT-AAAA
74288 AATCAAAACTTTTATTTCA
128 AATCAAAACTTTTATTTCA
*
74307 AAATTGTTTAAAAAAA
1 AAATAG-TTAAAAAAA
74323 CCAAAACATG
Statistics
Matches: 150, Mismatches: 8, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
144 7 0.05
146 110 0.73
148 25 0.17
149 2 0.01
150 6 0.04
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.41
Consensus pattern (146 bp):
AAATAGTTAAAAAAATAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAG
ATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAAAT
CAAAACTTTTATTTCA
Found at i:74212 original size:49 final size:50
Alignment explanation
Indices: 74030--74222 Score: 123
Period size: 49 Copynumber: 3.9 Consensus size: 50
74020 TAGAAAAAAT
*
74030 AAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAA-CAG
1 AAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAATTAAAAAATCAG
*** * * * ** *
74079 ATTTTTATTTTTAAAAATATAAACTTTCTCTTT--TTTAA--AGAAAATCA-
1 A-AACT-TTGTTAAAAATTTAAACTTTTTCTTTAAAATAATTAAAAAATCAG
** * * * ** *
74126 CTATTTTACTTAAAAATCTAAACTTTTAT-TTCGAAATAGTTAAAAAATCA-
1 AAACTTT-GTTAAAAATTTAAACTTTT-TCTTTAAAATAATTAAAAAATCAG
*
74176 AAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAT
1 AAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAATTAAAAAAT
74223 ATATTTTTAT
Statistics
Matches: 106, Mismatches: 28, Indels: 20
0.69 0.18 0.13
Matches are distributed among these distances:
45 2 0.02
46 21 0.20
47 6 0.06
48 5 0.05
49 36 0.34
50 13 0.12
51 23 0.22
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (50 bp):
AAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAATTAAAAAATCAG
Found at i:74375 original size:146 final size:145
Alignment explanation
Indices: 74013--74361 Score: 418
Period size: 146 Copynumber: 2.4 Consensus size: 145
74003 AATCCAAACT
* * *
74013 AAATAGTTAGAAAAA--ATAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAA
1 AAATAGTTA-AAAAACCA-AAACTATGTCAAAAATTCAAACTTTTTCTTTAAAATAAC-AAAAAA
* *
74076 CAGATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAA
63 TATATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAA
* *
74141 ATCTAAACTTTTATTTCG
128 ATCAAAACTTTTATTTCA
* * * *
74159 AAATAGTTAAAAAATCAAAACTTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATA
1 AAATAGTTAAAAAACCAAAACTATGTCAAAAATTCAAACTTTTTCTTTAAAATAAC-AAAAAATA
* * *
74224 TATTTTTATTTTTAAAAATCTAAGCTTTCTCTTTTTTAAAGAAAATCACTATTTTGCTTAAAAAA
65 TATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTT--AAAA
74289 ATCAAAACTTTTATTTCA
128 ATCAAAACTTTTATTTCA
* * *
74307 AAATTGTTTAAAAAAACCAAAAC-ATGTCCCAAAA-TCAAACTGTTTTTCTTAAAAA
1 AAATAG-TT-AAAAAACCAAAACTATGT-CAAAAATTCAAAC--TTTTTCTTTAAAA
74362 AAAACTTTTA
Statistics
Matches: 180, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
145 5 0.03
146 111 0.62
147 1 0.01
148 25 0.14
149 10 0.06
150 16 0.09
151 12 0.07
ACGTcount: A:0.45, C:0.11, G:0.04, T:0.40
Consensus pattern (145 bp):
AAATAGTTAAAAAACCAAAACTATGTCAAAAATTCAAACTTTTTCTTTAAAATAACAAAAAATAT
ATTTTTATTTTTAAAAATATAAACTTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATC
AAAACTTTTATTTCA
Found at i:75237 original size:42 final size:43
Alignment explanation
Indices: 75191--75353 Score: 199
Period size: 42 Copynumber: 3.9 Consensus size: 43
75181 CTATTCTTAG
*
75191 GCCTCT-AATTGCAATGAAAAGTAAATGGACCTCCACACCTAA
1 GCCTCTAAATTGCAATGAAAAATAAATGGACCTCCACACCTAA
* * * **
75233 GCCTCTGAA-TGTAATGAAAAATAAATGGACCTCCACACTTGG
1 GCCTCTAAATTGCAATGAAAAATAAATGGACCTCCACACCTAA
*
75275 GCCTCTAAATT-CAATGAAAAATAAATGGGCCTCCACACCTAA
1 GCCTCTAAATTGCAATGAAAAATAAATGGACCTCCACACCTAA
* * * *
75317 GCCTCTAAA-TGTAATGAAAATTAAGTGGGCCTCCACA
1 GCCTCTAAATTGCAATGAAAAATAAATGGACCTCCACA
75354 AACTACAACA
Statistics
Matches: 104, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.01
42 100 0.96
43 3 0.03
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (43 bp):
GCCTCTAAATTGCAATGAAAAATAAATGGACCTCCACACCTAA
Found at i:75309 original size:84 final size:84
Alignment explanation
Indices: 75190--75353 Score: 258
Period size: 84 Copynumber: 2.0 Consensus size: 84
75180 TCTATTCTTA
* *
75190 GGCCTCTAATTGCAATGAAAAGTAAATGGACCTCCACACCTAAGCCTCTGAATGTAATGAAAAAT
1 GGCCTCTAATTGCAATGAAAAATAAATGGACCTCCACACCTAAGCCTCTAAATGTAATGAAAAAT
75255 AAATGGACCTCCACACTTG
66 AAATGGACCTCCACACTTG
* *
75274 GGCCTCTAAATT-CAATGAAAAATAAATGGGCCTCCACACCTAAGCCTCTAAATGTAATGAAAAT
1 GGCCTCT-AATTGCAATGAAAAATAAATGGACCTCCACACCTAAGCCTCTAAATGTAATGAAAAA
* *
75338 TAAGTGGGCCTCCACA
65 TAAATGGACCTCCACA
75354 AACTACAACA
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
84 69 0.95
85 4 0.05
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (84 bp):
GGCCTCTAATTGCAATGAAAAATAAATGGACCTCCACACCTAAGCCTCTAAATGTAATGAAAAAT
AAATGGACCTCCACACTTG
Found at i:75514 original size:41 final size:41
Alignment explanation
Indices: 75455--75712 Score: 372
Period size: 41 Copynumber: 6.3 Consensus size: 41
75445 AAACGCCACA
*
75455 AAAGGTCAGAGCATTAGCGGCGCTTATGGGCAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCT
*
75496 AAAGGTCAAAGCAATAGCGGCGCTTATGGGCAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCT
* * *
75537 AAAGGTTAGAGCAATAGCGACGCTAATGGGCAAGCGCCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCT
* * * * *
75578 AACGGTCAGAGCAATAGTGGCGCTTTTGGGCAATCGTCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCT
* *
75619 AAAGGTCAGAGCAATAGCGGCGCTTATGGACAAGCGTCGCT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCT
* * *
75660 AAAGGTCAGATCAATAGCGGCGCTTATGGGCAAGCTCCGTT
1 AAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCT
*
75701 AAAGGTTAGAGC
1 AAAGGTCAGAGC
75713 CCAAAAGCGC
Statistics
Matches: 191, Mismatches: 26, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 191 1.00
ACGTcount: A:0.28, C:0.22, G:0.32, T:0.18
Consensus pattern (41 bp):
AAAGGTCAGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCT
Found at i:75861 original size:41 final size:41
Alignment explanation
Indices: 75768--75944 Score: 160
Period size: 41 Copynumber: 4.3 Consensus size: 41
75758 TCAGAGCATT
* * * * * *
75768 AAGCGCTGCTAAAGGTCAAAGCATTAACGGTGCTTATGGGC
1 AAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGTGA
*** * *
75809 AAGCAATGCTAAAAGTCAGAGCATTTGCGGCGCTTATGTGA
1 AAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGTGA
* * * *
75850 AAGCTCCGCTAAAGGTCAGAGCAATAGCGGTG-AT-TGTGAA
1 AAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGTG-A
*
75890 CAATCGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGTGAA
1 -AAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGTG-A
*
75933 AAACGCCGCTAA
1 AAGCGCCGCTAA
75945 TTTATTTAAA
Statistics
Matches: 109, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
39 4 0.04
40 2 0.02
41 85 0.78
42 12 0.11
43 6 0.06
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.21
Consensus pattern (41 bp):
AAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGCTTATGTGA
Found at i:81447 original size:43 final size:43
Alignment explanation
Indices: 81399--81609 Score: 194
Period size: 43 Copynumber: 5.0 Consensus size: 43
81389 TGTTAACGTC
*** *
81399 AGTGGCGTTTGTGGGAAAAATATCGCTAAAGATCATGTTCTTT
1 AGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCTTT
* * * *
81442 AGTGGCGGTTGTGAGATAAGCGTCACTAAAGACCATGTTCTTT
1 AGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCTTT
* * * * *
81485 ACTGGCATTTGTGAGATAAGCGTTGCTAAAGACCATGCTT-TTT
1 AGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGACCATG-TTCTTT
* * **
81528 AATGGCGTTTTTGGG-AAAGCACCGCTAAAGACCATGTTCTTT
1 AGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCTTT
* * * * *
81570 AGCGGCATTTTTGGG-AAAGTGCCGCTAAAGACCATGTTCT
1 AGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCT
81610 ATAGCGGTAT
Statistics
Matches: 140, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
41 2 0.01
42 55 0.39
43 81 0.58
44 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
AGTGGCGTTTGTGGGAAAAGCGTCGCTAAAGACCATGTTCTTT
Found at i:81562 original size:42 final size:42
Alignment explanation
Indices: 81467--81623 Score: 156
Period size: 42 Copynumber: 3.7 Consensus size: 42
81457 ATAAGCGTCA
* * ***
81467 CTAAAGACCATGTTCTTT-ACTGGCATTTGTGAGATAAGCGTTG
1 CTAAAGACCATGTTCTTTAAC-GGCATTTTTGGGA-AAGCACCG
* *
81510 CTAAAGACCATGCTT-TTTAATGGCGTTTTTGGGAAAGCACCG
1 CTAAAGACCATG-TTCTTTAACGGCATTTTTGGGAAAGCACCG
* **
81552 CTAAAGACCATGTTCTTTAGCGGCATTTTTGGGAAAGTGCCG
1 CTAAAGACCATGTTCTTTAACGGCATTTTTGGGAAAGCACCG
* * *
81594 CTAAAGACCATGTTCTATAGCGGTATTTTT
1 CTAAAGACCATGTTCTTTAACGGCATTTTT
81624 CCTCATAAAT
Statistics
Matches: 97, Mismatches: 14, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
41 2 0.02
42 67 0.69
43 25 0.26
44 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (42 bp):
CTAAAGACCATGTTCTTTAACGGCATTTTTGGGAAAGCACCG
Found at i:81831 original size:42 final size:42
Alignment explanation
Indices: 81772--82007 Score: 364
Period size: 42 Copynumber: 5.6 Consensus size: 42
81762 TCCTGTAGTG
81772 ACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCC
1 ACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCC
* *
81814 ACACCTACGCCTCTAAATGCAATGAAAAGTAAATGGACCTCT
1 ACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCC
* *
81856 ACACCTGGGCCTCTAAATGCGATGAAAAGTAAATGGACCTCC
1 ACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCC
* *
81898 ACACCTGGGCCTCTAAATGCAATGAAAAGTAAATGGGCCTCC
1 ACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCC
* ** * * *
81940 ACACATAGGCCTCCGAATGCAACGAAAAATAAATGGACCTTC
1 ACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCC
81982 ACACCTAGGCCTCTAAATGCAATGAA
1 ACACCTAGGCCTCTAAATGCAATGAA
82008 TGTTTCCTTT
Statistics
Matches: 174, Mismatches: 20, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 174 1.00
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (42 bp):
ACACCTAGGCCTCTAAATGCAATGAAAAGTAAATGGACCTCC
Found at i:82423 original size:25 final size:21
Alignment explanation
Indices: 82389--82444 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 21
82379 TTCAATATAG
82389 TTTTTTTTCTTGCTCTCTATTTCT
1 TTTTTTTTCTT-CTCT-TATTT-T
*
82413 ATTTTTTTTCTTCTCTTCTTTT
1 -TTTTTTTTCTTCTCTTATTTT
82435 TTTTTTTTCT
1 TTTTTTTTCT
82445 ATTTTTTCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 10 0.33
22 1 0.03
23 4 0.13
24 4 0.13
25 11 0.37
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTTTTTCTTCTCTTATTTT
Found at i:82427 original size:22 final size:21
Alignment explanation
Indices: 82389--82444 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
82379 TTCAATATAG
*
82389 TTTTTTTTCTTGCTCTCTATTTCTA
1 TTTTTTTTCTT-CTCT-T-CTT-TA
*
82414 TTTTTTTTCTTCTCTTCTTTT
1 TTTTTTTTCTTCTCTTCTTTA
82435 TTTTTTTTCT
1 TTTTTTTTCT
82445 ATTTTTTCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 11 0.38
22 2 0.07
23 1 0.03
24 4 0.14
25 11 0.38
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.77
Consensus pattern (21 bp):
TTTTTTTTCTTCTCTTCTTTA
Found at i:82436 original size:19 final size:18
Alignment explanation
Indices: 82409--82444 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
82399 TGCTCTCTAT
82409 TTCTATTTTTTTTCTTCTC
1 TTCTATTTTTTTT-TTCTC
*
82428 TTCTTTTTTTTTTTTCT
1 TTCTATTTTTTTTTTCT
82445 ATTTTTTCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (18 bp):
TTCTATTTTTTTTTTCTC
Found at i:82450 original size:16 final size:16
Alignment explanation
Indices: 82408--82451 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
82398 TTGCTCTCTA
82408 TTTCTATTTTTTTTCT
1 TTTCTATTTTTTTTCT
* *
82424 TCTCT-TCTTTTTTTTT
1 TTTCTAT-TTTTTTTCT
82440 TTTCTATTTTTT
1 TTTCTATTTTTT
82452 CCTTGATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 1 0.04
16 21 0.91
17 1 0.04
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTATTTTTTTTCT
Found at i:94621 original size:41 final size:41
Alignment explanation
Indices: 94576--94654 Score: 158
Period size: 41 Copynumber: 1.9 Consensus size: 41
94566 TATTATTTAT
94576 AATTTTTCTAGGGTAAATAATCGATAAGCTCTTAAAAAATA
1 AATTTTTCTAGGGTAAATAATCGATAAGCTCTTAAAAAATA
94617 AATTTTTCTAGGGTAAATAATCGATAAGCTCTTAAAAA
1 AATTTTTCTAGGGTAAATAATCGATAAGCTCTTAAAAA
94655 CTAACATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.34
Consensus pattern (41 bp):
AATTTTTCTAGGGTAAATAATCGATAAGCTCTTAAAAAATA
Found at i:95674 original size:157 final size:153
Alignment explanation
Indices: 95315--95830 Score: 677
Period size: 157 Copynumber: 3.4 Consensus size: 153
95305 TTGATTAAAC
* *
95315 AAAAATCACTAATTTACTT-AAAATCCAAACA-TTTATTTCAAAATAGTT-AAAAAAATCAAAAC
1 AAAAATCACTATTTTACTTAAAAATCCAAA-ATTTTATTTCGAAATAGTTAAAAAAAATCAAAAC
* * *
95377 TTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACATATTTTTACTTTTTAAAAATC
65 TTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTA-TTTTTAAAAATA
95442 TAAACTTT-C-----TCTTTTTTAA
129 TAAACTTTCCTTTTTTCTTTTTTAA
* * *
95461 AGAAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTTAGAAAAAATCAAAAC
1 A-AAAATCACTATTTTACTTAAAAATCCAAAATTTTATTTCGAAATAGTTAAAAAAAATCAAAAC
* *
95526 TTTGTTAAAAATTTAAACTTTTTCTTTAAAATAAGTAAAACATAGATTTTTATTTTTAAAAATAT
65 TTTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATAT
*
95591 AAACTTTCGCTTTTTTCTTTTTTTTTTA
130 AAACTTTC-CTTTTTTC---TTTTTTAA
95619 AAAAATCACTATTTTACTTAAAAATCCAAAATTTTATTTCGAAATAGTTAAAAAAAATCAAAACT
1 AAAAATCACTATTTTACTTAAAAATCCAAAATTTTATTTCGAAATAGTTAAAAAAAATCAAAACT
*
95684 TTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTAATTTTTAAAAATATA
66 TTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATATA
*
95749 AA------TTTTCTCTTTTTTAA
131 AACTTTCCTTTTTTCTTTTTTAA
* * * * *
95766 AGAAAATCACTATTTTGCTTAAAAAT-CAAAGCTTTTATTTCGAACTTGTTTAAAAAAATCAAAA
1 A-AAAATCACTATTTTACTTAAAAATCCAAA-ATTTTATTTCGAAATAGTTAAAAAAAATCAAAA
95830 C
64 C
95831 ATTTCCCAAA
Statistics
Matches: 330, Mismatches: 24, Indels: 30
0.86 0.06 0.08
Matches are distributed among these distances:
146 1 0.00
147 29 0.09
148 97 0.29
149 61 0.18
150 7 0.02
155 2 0.01
157 125 0.38
158 8 0.02
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.41
Consensus pattern (153 bp):
AAAAATCACTATTTTACTTAAAAATCCAAAATTTTATTTCGAAATAGTTAAAAAAAATCAAAACT
TTGTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAATAGATTTTTATTTTTAAAAATATA
AACTTTCCTTTTTTCTTTTTTAA
Found at i:96269 original size:18 final size:18
Alignment explanation
Indices: 96246--96307 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
96236 CATGAAACCT
96246 TAAAAATTAAGATAATAA
1 TAAAAATTAAGATAATAA
*
96264 TAAAAA-TAAGAATAAGAA
1 TAAAAATTAAG-ATAATAA
* * * *
96282 TAATAATGATGATGATAA
1 TAAAAATTAAGATAATAA
*
96300 TAATAATT
1 TAAAAATT
96308 TGGGCCCTTG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
17 4 0.11
18 29 0.83
19 2 0.06
ACGTcount: A:0.61, C:0.00, G:0.10, T:0.29
Consensus pattern (18 bp):
TAAAAATTAAGATAATAA
Found at i:120545 original size:20 final size:20
Alignment explanation
Indices: 120504--120549 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 20
120494 CCTACGATCT
120504 GCTCTTTTTCACTCGTCTTTC
1 GCTCTTTTTCACTCG-CTTTC
120525 GCTCGTTTTTCACTC-CTTTC
1 GCTC-TTTTTCACTCGCTTTC
120545 GCTCT
1 GCTCT
120550 CAAATGCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.04
20 9 0.38
21 4 0.17
22 10 0.42
ACGTcount: A:0.04, C:0.35, G:0.11, T:0.50
Consensus pattern (20 bp):
GCTCTTTTTCACTCGCTTTC
Found at i:121343 original size:16 final size:15
Alignment explanation
Indices: 121305--121353 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 15
121295 TTCCTTTTTC
121305 TTTTTTC-TTTCAAT
1 TTTTTTCTTTTCAAT
**
121319 TCATTT-TTTTCAAT
1 TTTTTTCTTTTCAAT
*
121333 TTTTTTCTTTTCGAT
1 TTTTTTCTTTTCAAT
121348 TTTTTT
1 TTTTTT
121354 TATTTTGAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
14 15 0.54
15 13 0.46
ACGTcount: A:0.12, C:0.12, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTTTTCTTTTCAAT
Found at i:134526 original size:19 final size:18
Alignment explanation
Indices: 134493--134536 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
134483 TAATACTATT
134493 ATAAATATAAAATAAAAA
1 ATAAATATAAAATAAAAA
** *
134511 AGTAAATATACGATAAATA
1 A-TAAATATAAAATAAAAA
134530 ATAAATA
1 ATAAATA
134537 AAGGCCACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (18 bp):
ATAAATATAAAATAAAAA
Found at i:135270 original size:32 final size:32
Alignment explanation
Indices: 135234--135295 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
135224 AGCTTTTGGT
*
135234 TTTTTCATGTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATATTGTCAAAGAGTTGAACAATGGA
*
135266 TTTTTCGTATTGTCAAAGAGTTGAACAATG
1 TTTTTCATATTGTCAAAGAGTTGAACAATG
135296 AAAATAGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.39
Consensus pattern (32 bp):
TTTTTCATATTGTCAAAGAGTTGAACAATGGA
Found at i:135814 original size:22 final size:22
Alignment explanation
Indices: 135771--135816 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
135761 ACCTTTAAGT
**
135771 ATTCATCTCGAATTTCGTCATG
1 ATTCATCTCGAATTTCAACATG
* *
135793 ATTCATCTCTACTTTCAACATG
1 ATTCATCTCGAATTTCAACATG
135815 AT
1 AT
135817 ATCAAAGCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.09, T:0.41
Consensus pattern (22 bp):
ATTCATCTCGAATTTCAACATG
Found at i:139047 original size:12 final size:12
Alignment explanation
Indices: 139030--139056 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
139020 GAATTTTGGG
139030 ATTCAATTCCCT
1 ATTCAATTCCCT
139042 ATTCAATTCCCT
1 ATTCAATTCCCT
139054 ATT
1 ATT
139057 TTTAGTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (12 bp):
ATTCAATTCCCT
Found at i:140183 original size:32 final size:32
Alignment explanation
Indices: 140147--140213 Score: 116
Period size: 32 Copynumber: 2.1 Consensus size: 32
140137 TTAACAAATA
*
140147 TACAGTCTCTGTGGAGACAATAACTTGATACT
1 TACAGTCCCTGTGGAGACAATAACTTGATACT
*
140179 TACAGTCCCTGTGGAGACAATAACTTGGTACT
1 TACAGTCCCTGTGGAGACAATAACTTGATACT
140211 TAC
1 TAC
140214 TTATTACTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (32 bp):
TACAGTCCCTGTGGAGACAATAACTTGATACT
Found at i:145263 original size:27 final size:27
Alignment explanation
Indices: 145225--145278 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
145215 GATAACTAAC
145225 AAATACTAATCTAATACTAATAGAATA
1 AAATACTAATCTAATACTAATAGAATA
145252 AAATACTAATCTAATACTAATAGAATA
1 AAATACTAATCTAATACTAATAGAATA
145279 GAAAAAATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.30
Consensus pattern (27 bp):
AAATACTAATCTAATACTAATAGAATA
Found at i:145265 original size:5 final size:6
Alignment explanation
Indices: 145226--145273 Score: 50
Period size: 5 Copynumber: 8.7 Consensus size: 6
145216 ATAACTAACA
* *
145226 AATACT AAT-CT AATACT AATA-G AATA-A AATACT AAT-CT AATACT
1 AATACT AATACT AATACT AATACT AATACT AATACT AATACT AATACT
145270 AATA
1 AATA
145274 GAATAGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
5 18 0.50
6 18 0.50
ACGTcount: A:0.54, C:0.12, G:0.02, T:0.31
Consensus pattern (6 bp):
AATACT
Found at i:145289 original size:14 final size:14
Alignment explanation
Indices: 145270--145297 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
145260 ATCTAATACT
145270 AATAGAATAGAAAA
1 AATAGAATAGAAAA
145284 AATAGAATAGAAAA
1 AATAGAATAGAAAA
145298 TACTAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
AATAGAATAGAAAA
Found at i:146608 original size:24 final size:25
Alignment explanation
Indices: 146559--146609 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
146549 TTAACCCAAT
*
146559 AATAAAAAAAATTTAAGATTATATA
1 AATAAAAAAAATTTAAGATTACATA
*
146584 AATAAAAAAAATTTAA-ATTCCATA
1 AATAAAAAAAATTTAAGATTACATA
146608 AA
1 AA
146610 AAATTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (25 bp):
AATAAAAAAAATTTAAGATTACATA
Found at i:156759 original size:2 final size:2
Alignment explanation
Indices: 156752--156780 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
156742 CATTATCCAT
156752 TC TC TC TC TC 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 T
156781 TTCTTGCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:159622 original size:28 final size:28
Alignment explanation
Indices: 159569--159651 Score: 96
Period size: 28 Copynumber: 3.0 Consensus size: 28
159559 ACAACCAGAC
* *
159569 AAGCCTCC-TTAATAGAGCCAGCCACAA
1 AAGCTTCCTTTAATAGAGTCAGCCACAA
* * *
159596 AAGCTTCCTTTAACAGAGTCAGTCACAG
1 AAGCTTCCTTTAATAGAGTCAGCCACAA
* *
159624 AGGCTTCCTTTAATAGAGTCAACCACAA
1 AAGCTTCCTTTAATAGAGTCAGCCACAA
159652 GGGCTTTCTG
Statistics
Matches: 45, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 7 0.16
28 38 0.84
ACGTcount: A:0.35, C:0.28, G:0.16, T:0.22
Consensus pattern (28 bp):
AAGCTTCCTTTAATAGAGTCAGCCACAA
Found at i:159748 original size:28 final size:28
Alignment explanation
Indices: 159717--159855 Score: 102
Period size: 28 Copynumber: 4.9 Consensus size: 28
159707 AAGGTGTGCC
* *
159717 CTTTCAGAGTTTTGCCATAAAGGCATTT
1 CTTTCAGAGATTTGCCACAAAGGCATTT
* * * ** *
159745 CTTTGAAAGGTTCACCAAAAAGGC-TTAT
1 CTTTCAGAGATTTGCCACAAAGGCATT-T
* *
159773 CTTTCAAGAGATTTGCCACAAAGGCAGTC
1 CTTTC-AGAGATTTGCCACAAAGGCATTT
* * * *
159802 CTTTGAGAG-TTTCACCACAAAGACGTTT
1 CTTTCAGAGATTT-GCCACAAAGGCATTT
159830 CTTTCCAGAGATTTGCCACAAAGGCA
1 CTTT-CAGAGATTTGCCACAAAGGCA
159856 ATCCTTTGAA
Statistics
Matches: 81, Mismatches: 24, Indels: 11
0.70 0.21 0.09
Matches are distributed among these distances:
27 5 0.06
28 41 0.51
29 31 0.38
30 4 0.05
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (28 bp):
CTTTCAGAGATTTGCCACAAAGGCATTT
Found at i:159796 original size:29 final size:29
Alignment explanation
Indices: 159763--159854 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
159753 GGTTCACCAA
159763 AAAGGCTTATCTTTCAAGAGATTTGCCAC
1 AAAGGCTTATCTTTCAAGAGATTTGCCAC
* *
159792 AAAGGC--AGTCCTTT-GAGAG-TTTCACCAC
1 AAAGGCTTA-T-CTTTCAAGAGATTT-GCCAC
* *
159820 AAAGACGTT-TCTTTCCAGAGATTTGCCAC
1 AAAGGC-TTATCTTTCAAGAGATTTGCCAC
159849 AAAGGC
1 AAAGGC
159855 AATCCTTTGA
Statistics
Matches: 49, Mismatches: 6, Indels: 16
0.69 0.08 0.23
Matches are distributed among these distances:
27 4 0.08
28 18 0.37
29 24 0.49
30 3 0.06
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (29 bp):
AAAGGCTTATCTTTCAAGAGATTTGCCAC
Found at i:159862 original size:29 final size:29
Alignment explanation
Indices: 159773--159862 Score: 85
Period size: 29 Copynumber: 3.1 Consensus size: 29
159763 AAAGGCTTAT
*
159773 CTTTCAAGAGATTTGCCACAAAGGCAGTC
1 CTTTCAAGAGATTTGCCACAAAGGCAATC
* * * ** *
159802 CTTT-GAGAG-TTTCACCACAAAGACGTTT
1 CTTTCAAGAGATTT-GCCACAAAGGCAATC
*
159830 CTTTCCAGAGATTTGCCACAAAGGCAATC
1 CTTTCAAGAGATTTGCCACAAAGGCAATC
159859 CTTT
1 CTTT
159863 GAAAGGTTCG
Statistics
Matches: 46, Mismatches: 12, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
27 3 0.07
28 18 0.39
29 22 0.48
30 3 0.07
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (29 bp):
CTTTCAAGAGATTTGCCACAAAGGCAATC
Found at i:159881 original size:28 final size:28
Alignment explanation
Indices: 159850--159947 Score: 74
Period size: 28 Copynumber: 3.5 Consensus size: 28
159840 ATTTGCCACA
159850 AAGGCAATCCTTTGAAAGGTTCGCCATG
1 AAGGCAATCCTTTGAAAGGTTCGCCATG
** * * *
159878 AAGGCTTTCATTCT-AAGAGATT-GTCCATA
1 AAGGCAATCCTT-TGAA-AGGTTCG-CCATG
** *
159907 AAGATAATCCTTTGAAAGGTTCGTCATG
1 AAGGCAATCCTTTGAAAGGTTCGCCATG
*
159935 AAGGCATTCCTTT
1 AAGGCAATCCTTT
159948 CCAAAGATTT
Statistics
Matches: 49, Mismatches: 16, Indels: 10
0.65 0.21 0.13
Matches are distributed among these distances:
28 30 0.61
29 19 0.39
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (28 bp):
AAGGCAATCCTTTGAAAGGTTCGCCATG
Found at i:159897 original size:57 final size:57
Alignment explanation
Indices: 159717--159969 Score: 237
Period size: 57 Copynumber: 4.5 Consensus size: 57
159707 AAGGTGTGCC
* * * * *
159717 CTTTC-AGAGTTTTGCCATAAAGGCATTTCTTTGAAAGGTTCACCAAAAAGGC-TTAT
1 CTTTCAAGAGATTTGCCACAAAGGCAATCCTTTGAAAGGTTCACCATAAAGGCATT-T
* * * * * *
159773 CTTTCAAGAGATTTGCCACAAAGGCAGTCCTTTGAGAGTTTCACCACAAAGACGTTT
1 CTTTCAAGAGATTTGCCACAAAGGCAATCCTTTGAAAGGTTCACCATAAAGGCATTT
* * *
159830 CTTTCCAGAGATTTGCCACAAAGGCAATCCTTTGAAAGGTTCGCCATGAAGGC-TTT
1 CTTTCAAGAGATTTGCCACAAAGGCAATCCTTTGAAAGGTTCACCATAAAGGCATTT
* * ** ** * *
159886 CATTCTAAGAGA-TTGTCCATAAAGATAATCCTTTGAAAGGTTCGTCATGAAGGCATTC
1 CTTTC-AAGAGATTTG-CCACAAAGGCAATCCTTTGAAAGGTTCACCATAAAGGCATTT
159944 CTTTCCAA-AGATTTGCCACAAAGGCA
1 CTTT-CAAGAGATTTGCCACAAAGGCA
159970 GTCTTTTGCT
Statistics
Matches: 163, Mismatches: 27, Indels: 13
0.80 0.13 0.06
Matches are distributed among these distances:
56 15 0.09
57 135 0.83
58 12 0.07
59 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (57 bp):
CTTTCAAGAGATTTGCCACAAAGGCAATCCTTTGAAAGGTTCACCATAAAGGCATTT
Found at i:159918 original size:114 final size:114
Alignment explanation
Indices: 159716--159969 Score: 271
Period size: 114 Copynumber: 2.2 Consensus size: 114
159706 AAAGGTGTGC
* * * * *
159716 CCTTT-CAGAGTTTTGCCATAAAGGCATTTCTTTGAAAGGTTCACCAAAAAGGCTTATCTTTCAA
1 CCTTTCCAGAGATTTGCCACAAAGGCAATCCTTTGAAAGGTTCACCAAAAAGGCTTATCATTCAA
* * * * *
159780 GAGATTTGCCACAAAGGCAGTCCTTTGAGAGTTTCACCACAAAGACGTT
66 GAGATTTGCCACAAAGACAATCCTTTGAAAGGTTCACCACAAAGACATT
* * **
159829 TCTTTCCAGAGATTTGCCACAAAGGCAATCCTTTGAAAGGTTCGCCATGAAGGCTT-TCATTCTA
1 CCTTTCCAGAGATTTGCCACAAAGGCAATCCTTTGAAAGGTTCACCAAAAAGGCTTATCATTC-A
* * ** ** *
159893 AGAGA-TTGTCCATAAAGATAATCCTTTGAAAGGTTCGTCATGAAGGCATT
65 AGAGATTTG-CCACAAAGACAATCCTTTGAAAGGTTCACCACAAAGACATT
*
159943 CCTTTCCAAAGATTTGCCACAAAGGCA
1 CCTTTCCAGAGATTTGCCACAAAGGCA
159970 GTCTTTTGCT
Statistics
Matches: 115, Mismatches: 23, Indels: 5
0.80 0.16 0.03
Matches are distributed among these distances:
113 12 0.10
114 103 0.90
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (114 bp):
CCTTTCCAGAGATTTGCCACAAAGGCAATCCTTTGAAAGGTTCACCAAAAAGGCTTATCATTCAA
GAGATTTGCCACAAAGACAATCCTTTGAAAGGTTCACCACAAAGACATT
Found at i:173574 original size:16 final size:16
Alignment explanation
Indices: 173553--173589 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
173543 CTCTGTACCA
*
173553 AAATAATTGCAATGTT
1 AAATAAGTGCAATGTT
*
173569 AAATAAGTGTAATGTT
1 AAATAAGTGCAATGTT
173585 AAATA
1 AAATA
173590 TTTAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.03, G:0.14, T:0.35
Consensus pattern (16 bp):
AAATAAGTGCAATGTT
Found at i:178453 original size:20 final size:20
Alignment explanation
Indices: 178405--178459 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
178395 TGAAGTGTTA
*
178405 AAATGATTTTGACTTGGTTC
1 AAATCATTTTGACTTGGTTC
* *
178425 AAATTATTTTGACTT-GTTT
1 AAATCATTTTGACTTGGTTC
*
178444 AACATCATTTTAACTT
1 AA-ATCATTTTGACTT
178460 AATTTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 5 0.17
20 25 0.83
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (20 bp):
AAATCATTTTGACTTGGTTC
Found at i:184712 original size:55 final size:55
Alignment explanation
Indices: 184651--184765 Score: 221
Period size: 55 Copynumber: 2.1 Consensus size: 55
184641 AGGCTTCATT
184651 TCATTCATCAAACACACCATTGAACACCTAGTTCCATATCAATTTACAGAGAAAA
1 TCATTCATCAAACACACCATTGAACACCTAGTTCCATATCAATTTACAGAGAAAA
184706 TCATTCATCAAACACACCATTGAACACCTAGTTCCATATCAATTTACAGAGAAAA
1 TCATTCATCAAACACACCATTGAACACCTAGTTCCATATCAATTTACAGAGAAAA
*
184761 GCATT
1 TCATT
184766 GAGTATTCTT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 59 1.00
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (55 bp):
TCATTCATCAAACACACCATTGAACACCTAGTTCCATATCAATTTACAGAGAAAA
Found at i:186363 original size:19 final size:20
Alignment explanation
Indices: 186339--186387 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
186329 GCAAAATTGA
*
186339 TATCGATATGAAATTTT-GG
1 TATCGATATAAAATTTTAGG
186358 TATCGATA-AAAATTTTAGAGG
1 TATCGATATAAAATTTT--AGG
186379 TATCGATAT
1 TATCGATAT
186388 TGATTGTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.28
19 8 0.32
21 10 0.40
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (20 bp):
TATCGATATAAAATTTTAGG
Found at i:189071 original size:15 final size:16
Alignment explanation
Indices: 189043--189072 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
189033 AAATCAAGAA
189043 CAAAATTATAAAAAAT
1 CAAAATTATAAAAAAT
189059 CAAAATT-TAAAAAA
1 CAAAATTATAAAAAA
189073 CACTATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (16 bp):
CAAAATTATAAAAAAT
Found at i:190665 original size:13 final size:13
Alignment explanation
Indices: 190647--190671 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
190637 TGAAAATTCG
190647 TTAATGGTACATC
1 TTAATGGTACATC
190660 TTAATGGTACAT
1 TTAATGGTACAT
190672 TTTCCTCTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (13 bp):
TTAATGGTACATC
Found at i:198858 original size:23 final size:23
Alignment explanation
Indices: 198653--198904 Score: 197
Period size: 23 Copynumber: 11.2 Consensus size: 23
198643 GAACACTAGC
* *
198653 GTGCTCTCTGATTAGCACTGTGT
1 GTGCCCTCTGATTAGCACTTTGT
*
198676 GTGCTCTCTGATTAGCA-TTGTGT
1 GTGCCCTCTGATTAGCACTT-TGT
*
198699 GTGCCCTCT-ATTTAGCACGTTT-C
1 GTGCCCTCTGA-TTAGCAC-TTTGT
*
198722 GTGCCCTCTG-TTCAGCACTATGT
1 GTGCCCTCTGATT-AGCACTTTGT
* *
198745 GTGCCCTCTGTTTAGCACATTT-C
1 GTGCCCTCTGATTAGCAC-TTTGT
*
198768 GTGCCCTCTG-TTCAGCACTGTGT
1 GTGCCCTCTGATT-AGCACTTTGT
*
198791 GTGCCCTCTGTTATTAGCACTTCGT
1 GTGCCCTCTG--ATTAGCACTTTGT
*
198816 GTGCTCTCTGATTAGCACTTTGT
1 GTGCCCTCTGATTAGCACTTTGT
** *
198839 GTGATCTCTGATTAGCACTTTAT
1 GTGCCCTCTGATTAGCACTTTGT
*
198862 GTG--CTC-----AGTACTTTGT
1 GTGCCCTCTGATTAGCACTTTGT
* *
198878 GTACTCTCTGATTAGCACTTTGT
1 GTGCCCTCTGATTAGCACTTTGT
198901 GTGC
1 GTGC
198905 TCCCTGTTAC
Statistics
Matches: 188, Mismatches: 20, Indels: 42
0.75 0.08 0.17
Matches are distributed among these distances:
16 10 0.05
18 3 0.02
21 3 0.02
22 10 0.05
23 136 0.72
24 5 0.03
25 19 0.10
26 2 0.01
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.40
Consensus pattern (23 bp):
GTGCCCTCTGATTAGCACTTTGT
Found at i:198886 original size:39 final size:39
Alignment explanation
Indices: 198832--198906 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
198822 TCTGATTAGC
198832 ACTTTGTGTGATCTCTGATTAGCACTTTATGTGCTCAGT
1 ACTTTGTGTGATCTCTGATTAGCACTTTATGTGCTCAGT
*
198871 ACTTTGTGT-ACTCTCTGATTAGCACTTTGTGTGCTC
1 ACTTTGTGTGA-TCTCTGATTAGCACTTTATGTGCTC
198907 CCTGTTACCC
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.16, C:0.20, G:0.20, T:0.44
Consensus pattern (39 bp):
ACTTTGTGTGATCTCTGATTAGCACTTTATGTGCTCAGT
Found at i:200505 original size:20 final size:21
Alignment explanation
Indices: 200460--200508 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
200450 AACTCAATGC
200460 GTATCGATACTTTTTAAATAA
1 GTATCGATACTTTTTAAATAA
*
200481 GTATCGATATTTTTTAAA-AA
1 GTATCGATACTTTTTAAATAA
*
200501 TTATCGAT
1 GTATCGAT
200509 TAAATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (21 bp):
GTATCGATACTTTTTAAATAA
Found at i:209016 original size:20 final size:20
Alignment explanation
Indices: 208975--209043 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
208965 AAAGCTTGTG
*
208975 GTATCGATATTTTT-TCACAA
1 GTATCGATATTTTTAT-AAAA
*
208995 GTATCGATATTTTTATAGAA
1 GTATCGATATTTTTATAAAA
* *
209015 GTATCAATAATTTTA-AAATA
1 GTATCGATATTTTTATAAA-A
209035 GTATCGATA
1 GTATCGATA
209044 CCAAATTGCA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.05
20 39 0.93
21 1 0.02
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (20 bp):
GTATCGATATTTTTATAAAA
Found at i:214875 original size:37 final size:38
Alignment explanation
Indices: 214825--214928 Score: 102
Period size: 37 Copynumber: 2.7 Consensus size: 38
214815 TTCGAAGCAA
* *
214825 TAAAGTAACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAGTGACACCCAGTGTCTCATCGAACCTAGCCGAAG
* ** * *
214862 TAAAGTGATACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAGTGACACCCAGTGTCTCATCGAACCTAGCCGAAG
*
214900 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AGTGACACCCAGTGTCTCATCGA
214929 CTCGAGGACG
Statistics
Matches: 52, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
37 21 0.40
38 10 0.19
40 2 0.04
41 19 0.37
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (38 bp):
TAAAGTGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:214925 original size:41 final size:38
Alignment explanation
Indices: 214832--214928 Score: 97
Period size: 41 Copynumber: 2.5 Consensus size: 38
214822 CAATAAAGTA
* *
214832 ACACCCAGTGTCTCATCG-GCCTAGCCGAAGTAAAGTG
1 ACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAATG
* ** * *
214869 ATACCCAGTACCTCATCGAATCTATCCGAAGTAAAATAATG
1 ACACCCAGTGTCTCATCGAACCTAGCCGAAGT--AA-AATG
214910 ACACCCAGTGTCTCATCGA
1 ACACCCAGTGTCTCATCGA
214929 CTCGAGGACG
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
37 15 0.33
38 10 0.22
40 2 0.04
41 19 0.41
ACGTcount: A:0.32, C:0.29, G:0.18, T:0.22
Consensus pattern (38 bp):
ACACCCAGTGTCTCATCGAACCTAGCCGAAGTAAAATG
Found at i:215054 original size:18 final size:18
Alignment explanation
Indices: 215031--215067 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
215021 ATAATGCATA
*
215031 TCACTTTCAATTTCGATT
1 TCACTTTCAATTTCAATT
*
215049 TCACTTTCACTTTCAATT
1 TCACTTTCAATTTCAATT
215067 T
1 T
215068 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.24, G:0.03, T:0.51
Consensus pattern (18 bp):
TCACTTTCAATTTCAATT
Found at i:218138 original size:20 final size:20
Alignment explanation
Indices: 218110--218165 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
218100 TGAAATGTTA
* *
218110 AAATGATTTTGACTTGGTTG
1 AAATCATTTTGACTTGGTTC
** *
218130 AAATCATTTTGTTTTGTTTC
1 AAATCATTTTGACTTGGTTC
*
218150 AAATCATTTTAACTTG
1 AAATCATTTTGACTTG
218166 ATTTTAAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (20 bp):
AAATCATTTTGACTTGGTTC
Found at i:220806 original size:18 final size:17
Alignment explanation
Indices: 220779--220812 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
220769 TTATTAAATC
*
220779 TTGTGTTTATTCTTTCTG
1 TTGTGATTATT-TTTCTG
220797 TTGTGATTATTTTTCT
1 TTGTGATTATTTTTCT
220813 TCAAAATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.09, C:0.09, G:0.15, T:0.68
Consensus pattern (17 bp):
TTGTGATTATTTTTCTG
Found at i:222500 original size:42 final size:38
Alignment explanation
Indices: 222424--222515 Score: 94
Period size: 40 Copynumber: 2.3 Consensus size: 38
222414 TATTGCCGCG
* * *
222424 AAAGGTAAAGAGCAATAGCGGCGTTTATGAAAAAGCGCCACA
1 AAAGGT-AA-AGCAATAACAGCGTTTATCAAAAAGC-CCA-A
*
222466 AAAGGTAAAGCAATAACAGCGTTTTATCATAAAAGCCGAA
1 AAAGGTAAAGCAATAACAGCG-TTTATCA-AAAAGCCCAA
222506 AAAGGTAAAG
1 AAAGGTAAAG
222516 ATCAATAGCG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
40 22 0.50
41 10 0.23
42 12 0.27
ACGTcount: A:0.47, C:0.14, G:0.23, T:0.16
Consensus pattern (38 bp):
AAAGGTAAAGCAATAACAGCGTTTATCAAAAAGCCCAA
Found at i:222522 original size:42 final size:41
Alignment explanation
Indices: 222424--222571 Score: 151
Period size: 42 Copynumber: 3.6 Consensus size: 41
222414 TATTGCCGCG
* *
222424 AAAGGTAAAGAGCAATAGCGGCG-TTTATGA-AAAAGCGCCACA
1 AAAGGTAAAGA-CAATAGCGGCGTTTTATCATAAAAGC-CGA-A
* *
222466 AAAGGTAAAG-CAATAACAGCGTTTTATCATAAAAGCCGAA
1 AAAGGTAAAGACAATAGCGGCGTTTTATCATAAAAGCCGAA
* * * *
222506 AAAGGTAAAGATCAATAGCGGCATTTTACCATAAACGCCGTA
1 AAAGGTAAAGA-CAATAGCGGCGTTTTATCATAAAAGCCGAA
*
222548 AAATGTAAAG-CAATAGCGGCGTTT
1 AAAGGTAAAGACAATAGCGGCGTTT
222572 ATGGATAAAA
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
40 33 0.37
41 8 0.09
42 49 0.54
ACGTcount: A:0.43, C:0.16, G:0.22, T:0.20
Consensus pattern (41 bp):
AAAGGTAAAGACAATAGCGGCGTTTTATCATAAAAGCCGAA
Found at i:222580 original size:82 final size:83
Alignment explanation
Indices: 222424--222602 Score: 193
Period size: 82 Copynumber: 2.2 Consensus size: 83
222414 TATTGCCGCG
**
222424 AAAGGTAAAGAGCAATAGCGGCGTTTATGAAAAAGCGCCACAAAAGGTAAAGCAATAACAGCGTT
1 AAAGGTAAAGAGCAATAGCGGCGTTTACCAAAAAGCGCCACAAAAGGTAAAGCAATAACAGCGTT
222489 TTATCATAAAA-GCCGAA
66 TTATCATAAAATGCCGAA
* * * ** * * *
222506 AAAGGTAAAGATCAATAGCGGCATTTTACCATAAA-CGCCGTAAAATGTAAAGCAATAGCGGCG-
1 AAAGGTAAAGAGCAATAGCGGC-GTTTACCAAAAAGCGCCACAAAAGGTAAAGCAATAACAGCGT
* * *
222569 TTTATGGATAAAATGTCGCA
65 TTTAT-CATAAAATGCCGAA
*
222589 AAATGTAAAGAGCA
1 AAAGGTAAAGAGCA
222603 TTAGTGGTGT
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
81 5 0.06
82 50 0.63
83 24 0.30
ACGTcount: A:0.44, C:0.15, G:0.22, T:0.20
Consensus pattern (83 bp):
AAAGGTAAAGAGCAATAGCGGCGTTTACCAAAAAGCGCCACAAAAGGTAAAGCAATAACAGCGTT
TTATCATAAAATGCCGAA
Found at i:224276 original size:41 final size:41
Alignment explanation
Indices: 224231--224357 Score: 116
Period size: 41 Copynumber: 3.1 Consensus size: 41
224221 AATAATGACA
*
224231 TTTATGGGAAAAATGCCGCTAAAGGTTAAGCAATAGCGGCG
1 TTTATGGGAAAAACGCCGCTAAAGGTTAAGCAATAGCGGCG
* * * *
224272 TTTATGGG-AAAACGCC-ATAAAAGGTAAAGAGAATTAGAGGCG
1 TTTATGGGAAAAACGCCGCT-AAAGGTTAAG-CAA-TAGCGGCG
** * *
224314 TTTAT-GGAAAAAGCGCCGCTAAAAATTAAGCAATAACGGTG
1 TTTATGGGAAAAA-CGCCGCTAAAGGTTAAGCAATAGCGGCG
224355 TTT
1 TTT
224358 TCCCATAAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
39 1 0.01
40 16 0.24
41 20 0.30
42 18 0.27
43 11 0.16
44 1 0.01
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (41 bp):
TTTATGGGAAAAACGCCGCTAAAGGTTAAGCAATAGCGGCG
Found at i:227232 original size:26 final size:26
Alignment explanation
Indices: 227203--227318 Score: 101
Period size: 26 Copynumber: 4.5 Consensus size: 26
227193 AATTATTTAA
227203 TTAAATATTTAATTATTAAAAACAAC
1 TTAAATATTTAATTATTAAAAACAAC
*
227229 TTAAATATTTAATTATTCAAAACAAC
1 TTAAATATTTAATTATTAAAAACAAC
** * * * ** *
227255 CCAATTATTGAATTATT--GAATTAT
1 TTAAATATTTAATTATTAAAAACAAC
* *
227279 TTCATTATTTAATTATTAAAAACAAC
1 TTAAATATTTAATTATTAAAAACAAC
**
227305 CCAAATATTTAATT
1 TTAAATATTTAATT
227319 CAAAATATTT
Statistics
Matches: 67, Mismatches: 21, Indels: 4
0.73 0.23 0.04
Matches are distributed among these distances:
24 16 0.24
26 51 0.76
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.41
Consensus pattern (26 bp):
TTAAATATTTAATTATTAAAAACAAC
Found at i:227270 original size:8 final size:8
Alignment explanation
Indices: 227257--227295 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
227247 AAAACAACCC
227257 AATTATTG
1 AATTATTG
227265 AATTATTG
1 AATTATTG
*
227273 AATTATTT
1 AATTATTG
* *
227281 CATTATTT
1 AATTATTG
227289 AATTATT
1 AATTATT
227296 AAAAACAACC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (8 bp):
AATTATTG
Found at i:227397 original size:72 final size:73
Alignment explanation
Indices: 227321--227474 Score: 222
Period size: 72 Copynumber: 2.1 Consensus size: 73
227311 ATTTAATTCA
* *** *
227321 AAATATTTAATTTTTTAATTATTTAATT-ACATTTATTTATTTAATT-AAATATTTAATTATTAA
1 AAATATTTAATTATTTAATTATTTAATTCA-ACCCAATTATTTAATTAAAATATTTAATTATTAA
227384 AAACAACTC
65 AAACAACTC
227393 AAATATTTAATTATTTAATTATTTAATTCAACCCAATTATTTAATTCAAAATATTTAATTATTAA
1 AAATATTTAATTATTTAATTATTTAATTCAACCCAATTATTTAATT-AAAATATTTAATTATTAA
*
227458 AAATAACTC
65 AAACAACTC
227467 AAATATTT
1 AAATATTT
227475 GATTCAAATT
Statistics
Matches: 73, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
72 39 0.53
73 1 0.01
74 33 0.45
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (73 bp):
AAATATTTAATTATTTAATTATTTAATTCAACCCAATTATTTAATTAAAATATTTAATTATTAAA
AACAACTC
Found at i:227438 original size:8 final size:8
Alignment explanation
Indices: 227324--227420 Score: 58
Period size: 8 Copynumber: 12.1 Consensus size: 8
227314 TAATTCAAAA
227324 TATTTAAT
1 TATTTAAT
*
227332 TTTTTAAT
1 TATTTAAT
227340 TATTTAAT
1 TATTTAAT
*
227348 TACATTTATT
1 T--ATTTAAT
227358 TATTTAAT
1 TATTTAAT
227366 TA---AA-
1 TATTTAAT
227370 TATTTAAT
1 TATTTAAT
* *
227378 TATTAAAAAC
1 TATT--TAAT
* * * *
227388 AACTCAAA
1 TATTTAAT
227396 TATTTAAT
1 TATTTAAT
227404 TATTTAAT
1 TATTTAAT
227412 TATTTAAT
1 TATTTAAT
227420 T
1 T
227421 CAACCCAATT
Statistics
Matches: 67, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
7 2 0.03
8 50 0.75
10 11 0.16
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (8 bp):
TATTTAAT
Found at i:228368 original size:139 final size:139
Alignment explanation
Indices: 228118--228394 Score: 545
Period size: 139 Copynumber: 2.0 Consensus size: 139
228108 TAAGAGTTGG
228118 ATGAAATTGTCAAGGGTAAGCAACGACTATCGAAATGGAGTACAAACTTTTCTAAATTTTGCATT
1 ATGAAATTGTCAAGGGTAAGCAACGACTATCGAAATGGAGTACAAACTTTTCTAAATTTTGCATT
*
228183 TCAAAATGCAAGCCAAGAGAATATGATTCTTTGCCCGTGTAAGAAGTGTGGCAACATCAATTGGC
66 TCAAAATGCAAGCCAAGAGAATATGATTCTTTGCCCGTGTAAGAAGTGTGACAACATCAATTGGC
228248 ATATTCGTT
131 ATATTCGTT
228257 ATGAAATTGTCAAGGGTAAGCAACGACTATCGAAATGGAGTACAAACTTTTCTAAATTTTGCATT
1 ATGAAATTGTCAAGGGTAAGCAACGACTATCGAAATGGAGTACAAACTTTTCTAAATTTTGCATT
228322 TCAAAATGCAAGCCAAGAGAATATGATTCTTTGCCCGTGTAAGAAGTGTGACAACATCAATTGGC
66 TCAAAATGCAAGCCAAGAGAATATGATTCTTTGCCCGTGTAAGAAGTGTGACAACATCAATTGGC
228387 ATATTCGT
131 ATATTCGT
228395 GAAGTTGTCT
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 137 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (139 bp):
ATGAAATTGTCAAGGGTAAGCAACGACTATCGAAATGGAGTACAAACTTTTCTAAATTTTGCATT
TCAAAATGCAAGCCAAGAGAATATGATTCTTTGCCCGTGTAAGAAGTGTGACAACATCAATTGGC
ATATTCGTT
Found at i:234085 original size:42 final size:43
Alignment explanation
Indices: 234016--234103 Score: 142
Period size: 42 Copynumber: 2.1 Consensus size: 43
234006 ATGTTAATGT
234016 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTA
* * *
234059 TAGCGGCGTTTGT-TGAAAAGCGCCGCTAAATATCATGTTCTA
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTA
234101 TAG
1 TAG
234104 TAGCGTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
42 29 0.69
43 13 0.31
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.27
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTA
Found at i:236064 original size:23 final size:23
Alignment explanation
Indices: 236038--236082 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
236028 AATTTTGAAT
**
236038 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
236061 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
236083 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:236370 original size:42 final size:42
Alignment explanation
Indices: 236323--236406 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
236313 CAAATATTTT
*
236323 TAAACCTAAATATAATTTCATTCCTAAAAAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
* *
236365 TAAACCCAAATATAATTTTATTCCTAAATAACACTCATAAAC
1 TAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
236407 AACTCATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (42 bp):
TAAACCCAAATATAATTTCATTCCTAAAAAACACTCATAAAC
Found at i:238004 original size:13 final size:14
Alignment explanation
Indices: 237985--238021 Score: 58
Period size: 13 Copynumber: 2.7 Consensus size: 14
237975 CAAAAATTTT
237985 AATTTTATTAAA-A
1 AATTTTATTAAATA
*
237998 TATTTTATTAAATA
1 AATTTTATTAAATA
238012 AATTTTATTA
1 AATTTTATTA
238022 TCATTTATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AATTTTATTAAATA
Found at i:247814 original size:67 final size:67
Alignment explanation
Indices: 247693--247826 Score: 216
Period size: 67 Copynumber: 2.0 Consensus size: 67
247683 TTGGAAACTC
* *
247693 AATCAAGAAAAAGTACTAAACTGTAATTATGACAAAAAGTCATAAAATCTTACACTCACATTTTC
1 AATCAAGAAAAAGTACTAAACTGTAATTATGAAAAAAAGCCATAAAATCTTACACTCACATTTTC
247758 TT
66 TT
* *
247760 AATCAAGAAAAA-TACTAAATTGTAATTATGAAAAAAAGCCATGCAAATCTTACACTCACATTTT
1 AATCAAGAAAAAGTACTAAACTGTAATTATGAAAAAAAGCCAT-AAAATCTTACACTCACATTTT
247824 CTT
65 CTT
247827 TCTGCAAGCA
Statistics
Matches: 62, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
66 27 0.44
67 35 0.56
ACGTcount: A:0.46, C:0.16, G:0.07, T:0.30
Consensus pattern (67 bp):
AATCAAGAAAAAGTACTAAACTGTAATTATGAAAAAAAGCCATAAAATCTTACACTCACATTTTC
TT
Found at i:250144 original size:76 final size:74
Alignment explanation
Indices: 250048--250200 Score: 263
Period size: 76 Copynumber: 2.0 Consensus size: 74
250038 GTAATTCACT
250048 TTTTGAAAAAAAAAAGATTTTCATAAAATGGTCCAATTCTTATTTCAGTCCCTATATTTTTTTTT
1 TTTTGAAAAAAAAAAGATTTTCATAAAATGGTCCAATTCTTATTTCAGTCCCTATA---TTTTTT
250113 GTATATTTAAAA
63 GTATATTTAAAA
*
250125 TTTTG-AAAAAAAAATATTTTCATAAAATGGTCCAATTCTTATTTCAGTCCCTATATTTTTTGTA
1 TTTTGAAAAAAAAAAGATTTTCATAAAATGGTCCAATTCTTATTTCAGTCCCTATATTTTTTGTA
250189 TATTTAAAA
66 TATTTAAAA
250198 TTT
1 TTT
250201 AGTCTTTGTT
Statistics
Matches: 75, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
73 21 0.28
76 49 0.65
77 5 0.07
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.46
Consensus pattern (74 bp):
TTTTGAAAAAAAAAAGATTTTCATAAAATGGTCCAATTCTTATTTCAGTCCCTATATTTTTTGTA
TATTTAAAA
Found at i:253652 original size:21 final size:21
Alignment explanation
Indices: 253623--253696 Score: 139
Period size: 21 Copynumber: 3.5 Consensus size: 21
253613 ATAGGGGGTA
*
253623 TGTCGCGACATAGGAGGACCG
1 TGTCACGACATAGGAGGACCG
253644 TGTCACGACATAGGAGGACCG
1 TGTCACGACATAGGAGGACCG
253665 TGTCACGACATAGGAGGACCG
1 TGTCACGACATAGGAGGACCG
253686 TGTCACGACAT
1 TGTCACGACAT
253697 CGAGGGCAGT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 52 1.00
ACGTcount: A:0.27, C:0.24, G:0.32, T:0.16
Consensus pattern (21 bp):
TGTCACGACATAGGAGGACCG
Found at i:259960 original size:23 final size:23
Alignment explanation
Indices: 259901--260024 Score: 85
Period size: 23 Copynumber: 5.2 Consensus size: 23
259891 AAGTACTTAA
259901 CAGAGGGCACAC-AAGTGCTGGGTAA-
1 CAGAGGGCACACAAAGTGC----TAAT
*
259926 CAGAGGGTACACAAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
* **
259949 CAAAGGGCACACGTAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
*
259972 AACAGAGGGCAAACACAA-TGCTAAAT
1 --CAGAGGGCACACA-AAGTGCT-AAT
* *
259998 -AGAGAGCACACACAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
260020 CAGAG
1 CAGAG
260025 AGTGCACTAG
Statistics
Matches: 79, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
22 7 0.09
23 37 0.47
25 25 0.32
26 10 0.13
ACGTcount: A:0.40, C:0.20, G:0.27, T:0.14
Consensus pattern (23 bp):
CAGAGGGCACACAAAGTGCTAAT
Found at i:260136 original size:24 final size:26
Alignment explanation
Indices: 260089--260137 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
260079 GTCTACATGG
260089 TCATAATCTATCATATTCATCATTTC
1 TCATAATCTATCATATTCATCATTTC
260115 TCATAAT-T-TCATATATCA-CATTT
1 TCATAATCTATCATAT-TCATCATTT
260138 ACATTTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 11 0.50
25 4 0.18
26 7 0.32
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (26 bp):
TCATAATCTATCATATTCATCATTTC
Found at i:262638 original size:21 final size:21
Alignment explanation
Indices: 262614--262663 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
262604 CCTATAATAG
* * *
262614 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
*
262635 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
262656 TTCTACCG
1 TTCTACCG
262664 GTACTAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:263257 original size:28 final size:28
Alignment explanation
Indices: 263213--263268 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
263203 GATATCCGAT
*
263213 TTACTCCCTGTTGACCCAAAGGTCATGC
1 TTACTCCCTGTTAACCCAAAGGTCATGC
263241 TTACTCCCTGTTAACCCAAAGGTCATGC
1 TTACTCCCTGTTAACCCAAAGGTCATGC
263269 ATGTTACTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.29
Consensus pattern (28 bp):
TTACTCCCTGTTAACCCAAAGGTCATGC
Found at i:267789 original size:90 final size:89
Alignment explanation
Indices: 267666--267871 Score: 274
Period size: 90 Copynumber: 2.3 Consensus size: 89
267656 TAAAAAGCTT
** *
267666 TCAAACTTTTTCAAAAAAAGCAATTAAGCCCCTT-CTTTTTTTTTGCACTCAATT-GAGCACTTT
1 TCAAACTTTTT-AAAAAAAGCAATTAAGCCCCTTAC-TTTTTTTCCCACTCAATTGGA-CACTTG
267729 AACTTTCAAAATGCATAAAAAAGACCC
63 AACTTTCAAAATGCATAAAAAAGACCC
*
267756 TCAAACTTCTTTAAAAAAAAGCAATTAAG-CCCTTACTTTTTTTCCCACTCAATTGGATACTTGA
1 TCAAACTT-TTT-AAAAAAAGCAATTAAGCCCCTTACTTTTTTTCCCACTCAATTGGACACTTGA
* *
267820 ACTTTCAAAATGTATCAAAAAGACCC
64 ACTTTCAAAATGCATAAAAAAGACCC
* *
267846 TCAAAATTTTTCAAAAAAGCAATTAA
1 TCAAACTTTTTAAAAAAAGCAATTAA
267872 ACCTTTGCTC
Statistics
Matches: 104, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
88 14 0.13
89 3 0.03
90 65 0.62
91 22 0.21
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (89 bp):
TCAAACTTTTTAAAAAAAGCAATTAAGCCCCTTACTTTTTTTCCCACTCAATTGGACACTTGAAC
TTTCAAAATGCATAAAAAAGACCC
Found at i:268324 original size:10 final size:10
Alignment explanation
Indices: 268242--268426 Score: 81
Period size: 10 Copynumber: 19.3 Consensus size: 10
268232 GGACGATAAC
268242 TTTTATAATT
1 TTTTATAATT
*
268252 CTTTT-TACATA
1 -TTTTATA-ATT
*
268263 TTTTGT-ATT
1 TTTTATAATT
268272 TCTTTAT-ATT
1 T-TTTATAATT
*
268282 TTGTATAATT
1 TTTTATAATT
**
268292 TTCTTACGA--
1 TT-TTATAATT
**
268301 TTTTATAAAA
1 TTTTATAATT
268311 TTTTATAATT
1 TTTTATAATT
268321 TTTT-T-ATAT
1 TTTTATAAT-T
* *
268330 TTCTAT-ATA
1 TTTTATAATT
268339 TTTTATAA-T
1 TTTTATAATT
*
268348 TTTTATGA-T
1 TTTTATAATT
**
268357 TTTTATAAAA
1 TTTTATAATT
*
268367 TTTTACAA-T
1 TTTTATAATT
268376 TTTTAT-ATT
1 TTTTATAATT
*
268385 TTTTATGA-T
1 TTTTATAATT
*
268394 TTTTATATTT
1 TTTTATAATT
*
268404 TTTTCTAATT
1 TTTTATAATT
*
268414 TTTAATAATT
1 TTTTATAATT
268424 TTT
1 TTT
268427 ATTAAAATTT
Statistics
Matches: 133, Mismatches: 27, Indels: 29
0.70 0.14 0.15
Matches are distributed among these distances:
8 7 0.05
9 53 0.40
10 63 0.47
11 10 0.08
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:268331 original size:28 final size:28
Alignment explanation
Indices: 268285--268425 Score: 112
Period size: 28 Copynumber: 5.0 Consensus size: 28
268275 TTATATTTTG
* *
268285 TATAATTTTCTTACGATTTTATAAAATTT
1 TATAATTTTTTTA-TATTTTATAAAATTT
*
268314 TATAATTTTTTTATATTTCTAT-ATATTT
1 TATAATTTTTTTATATTT-TATAAAATTT
*
268342 TATAATTTTTATGAT-TTTTATAAAATTT
1 TATAATTTTT-TTATATTTTATAAAATTT
* * * * *
268370 TACAATTTTTATATTTTTTAT-GATTTT
1 TATAATTTTTTTATATTTTATAAAATTT
*
268397 TAT-ATTTTTTTCTAATTTT-TAATAATTT
1 TATAATTTTTTTAT-ATTTTATAA-AATTT
268425 T
1 T
268426 TATTAAAATT
Statistics
Matches: 89, Mismatches: 16, Indels: 15
0.74 0.13 0.12
Matches are distributed among these distances:
26 9 0.10
27 15 0.17
28 47 0.53
29 18 0.20
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.64
Consensus pattern (28 bp):
TATAATTTTTTTATATTTTATAAAATTT
Found at i:268380 original size:37 final size:37
Alignment explanation
Indices: 268339--268428 Score: 119
Period size: 37 Copynumber: 2.4 Consensus size: 37
268329 TTTCTATATA
268339 TTTTATAATTTTTATGATTTTTATAAAATTTTAC-AAT
1 TTTTATAATTTTTATGATTTTTAT-AAATTTTACTAAT
* ** *
268376 TTTTATATTTTTTATGATTTTTATATTTTTTTCTAAT
1 TTTTATAATTTTTATGATTTTTATAAATTTTACTAAT
268413 TTTTAATAATTTTTAT
1 TTTT-ATAATTTTTAT
268429 TAAAATTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
36 6 0.13
37 30 0.65
38 10 0.22
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (37 bp):
TTTTATAATTTTTATGATTTTTATAAATTTTACTAAT
Found at i:268427 original size:10 final size:9
Alignment explanation
Indices: 268301--268428 Score: 105
Period size: 9 Copynumber: 13.7 Consensus size: 9
268291 TTTCTTACGA
*
268301 TTTTATAAAA
1 TTTTAT-AAT
268311 TTTTATAAT
1 TTTTATAAT
*
268320 TTTTTTATAT
1 TTTTATA-AT
*
268330 TTCTAT-AT
1 TTTTATAAT
268338 ATTTTATAAT
1 -TTTTATAAT
*
268348 TTTTATGAT
1 TTTTATAAT
*
268357 TTTTATAAAA
1 TTTTAT-AAT
*
268367 TTTTACAAT
1 TTTTATAAT
*
268376 TTTTATATT
1 TTTTATAAT
*
268385 TTTTATGAT
1 TTTTATAAT
*
268394 TTTTATATTT
1 TTTTATA-AT
*
268404 TTTTCTAAT
1 TTTTATAAT
268413 TTTTAATAAT
1 TTTT-ATAAT
268423 TTTTAT
1 TTTTAT
268429 TAAAATTTAA
Statistics
Matches: 93, Mismatches: 19, Indels: 13
0.74 0.15 0.10
Matches are distributed among these distances:
8 2 0.02
9 56 0.60
10 35 0.38
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (9 bp):
TTTTATAAT
Found at i:268493 original size:66 final size:64
Alignment explanation
Indices: 268339--268491 Score: 166
Period size: 67 Copynumber: 2.3 Consensus size: 64
268329 TTTCTATATA
* * ** * *
268339 TTTTATAATTTTTATGATTTTTATAAAATTTTACAATTTTTATATTTTTTATGATTTTTATATTT
1 TTTTATAATTTTTAT-ATTTTTATAAAATTTAACAATATTTATACCTTATATGATTTTAATATTT
* *
268404 TTTTCTAATTTTTAATAATTTTTATTAAAATTTAATAATATTTATAACCTTAT-TGATTTTAAT-
1 TTTTATAATTTTT-AT-ATTTTTA-TAAAATTTAACAATATTTAT-ACCTTATATGATTTTAATA
268467 TTT
62 TTT
268470 TTTTATATATTTTTATATTTTT
1 TTTTATA-ATTTTTATATTTTT
268492 TAATAAAACC
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
65 18 0.24
66 20 0.27
67 32 0.43
68 4 0.05
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (64 bp):
TTTTATAATTTTTATATTTTTATAAAATTTAACAATATTTATACCTTATATGATTTTAATATTT
Found at i:268723 original size:89 final size:86
Alignment explanation
Indices: 268522--268726 Score: 234
Period size: 89 Copynumber: 2.3 Consensus size: 86
268512 TTGTTTTTTT
** * * *
268522 TTTTTTTGAAAAAGTTTGAGGGTCCTTTTATTGCATTTTAAAAGTTCAAGTACCCAATTGAGTCT
1 TTTTTTTG-AAAAGTTTGAGGGTTTTTTTAATGCATTTTAAAAGTTCAAGTACCCAAATGAGTCA
268587 GAAAAAAAGTAGGGGCTTAATTGC
65 GAAAAAAAGT--GGGCTTAATTGC
* * *
268611 TTTTTTTGAAAAGGTTTGAGGGTTTTTTTAATGCATTTTTAATGTTTAAGTACCCAAATGAGTGC
1 TTTTTTTGAAAA-GTTTGAGGGTTTTTTTAATGCATTTTAAAAGTTCAAGTACCCAAATGAGT-C
268676 AAGAAAATCAAA-T-GGCTTAATTGC
64 -AGAAAA--AAAGTGGGCTTAATTGC
*
268700 TTTTTTTGAGAGAGTTTGAGGGTTTTT
1 TTTTTTTGA-AAAGTTTGAGGGTTTTT
268727 GCACCCTTAA
Statistics
Matches: 101, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
88 4 0.04
89 85 0.84
90 3 0.03
91 5 0.05
92 1 0.01
93 3 0.03
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (86 bp):
TTTTTTTGAAAAGTTTGAGGGTTTTTTTAATGCATTTTAAAAGTTCAAGTACCCAAATGAGTCAG
AAAAAAAGTGGGCTTAATTGC
Found at i:272384 original size:64 final size:64
Alignment explanation
Indices: 272305--272433 Score: 222
Period size: 64 Copynumber: 2.0 Consensus size: 64
272295 CATTAACGGG
* *
272305 TGTAAAAGCTCAACGTTTAAGCCAGGTCGTGGACTTAAACAAGGTGACCCTTTAAGCCCCTTTT
1 TGTAAAAGCTCAACGTTCAAGCCAGGTCGTGGACTTAAACAAGGTGACCCCTTAAGCCCCTTTT
* *
272369 TGTAAAAGCTCAACGTTCAAGCCAGGTCGTGGACTTAGACAAGGTGACCCCTTAAGCCCTTTTT
1 TGTAAAAGCTCAACGTTCAAGCCAGGTCGTGGACTTAAACAAGGTGACCCCTTAAGCCCCTTTT
272433 T
1 T
272434 TGTTTTTAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (64 bp):
TGTAAAAGCTCAACGTTCAAGCCAGGTCGTGGACTTAAACAAGGTGACCCCTTAAGCCCCTTTT
Found at i:273976 original size:82 final size:82
Alignment explanation
Indices: 273834--273998 Score: 249
Period size: 82 Copynumber: 2.0 Consensus size: 82
273824 TTTGATTTGA
* * * *
273834 ACTATGACCGTGCCACGGATCGAGGAAAAAGAAAATTAACGGAGCAGTTCTTGGAATCCATTCAC
1 ACTACGACCGTGCCACGGATCGAGGAAAAAGAAAATTAACGGAGCAGTCCCTAGAATCCATTCAC
*
273899 AACTGCAATCCAGTCCG
66 AACCGCAATCCAGTCCG
** * *
273916 ACTACGACCGTGCCACGGATCTTGGAAAAGGAAAATTAACGGAGTAGTCCCTAGAATCCATTCAC
1 ACTACGACCGTGCCACGGATCGAGGAAAAAGAAAATTAACGGAGCAGTCCCTAGAATCCATTCAC
273981 AACCGCAATCCAGTCCG
66 AACCGCAATCCAGTCCG
273998 A
1 A
273999 TAAGTTCGTA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.34, C:0.26, G:0.21, T:0.19
Consensus pattern (82 bp):
ACTACGACCGTGCCACGGATCGAGGAAAAAGAAAATTAACGGAGCAGTCCCTAGAATCCATTCAC
AACCGCAATCCAGTCCG
Found at i:274322 original size:51 final size:52
Alignment explanation
Indices: 274138--274332 Score: 257
Period size: 52 Copynumber: 3.8 Consensus size: 52
274128 GCTATAAACG
*
274138 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAACGAATCCTTTACGGATT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
** * * *
274190 AAAGGGTTTGATGACTAAGTGTCATCGTGAGTAAATTAGTCCTTTACGGGTT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
274242 AAAGGGTCCGATAACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
** * *
274294 AAA-GGTCCGATGACTCTGTGTAATCGTGAGTATATGAAT
1 AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAAT
274333 TCCTATATGG
Statistics
Matches: 123, Mismatches: 20, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
51 31 0.25
52 92 0.75
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (52 bp):
AAAGGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:280859 original size:82 final size:82
Alignment explanation
Indices: 280695--281010 Score: 357
Period size: 82 Copynumber: 3.9 Consensus size: 82
280685 TACAATCGTG
* * * * * *
280695 CCACGGATTGAGGAAAAAGAAAATTAGCGAAGTAATCACTAGAA-CCATTCACAACCACAATCCA
1 CCACGGATCGAGGAAAAGGAAAATTAGAGAAGTACTCCCTAGAATCCATTCACAACCGCAATCCA
* * *
280759 ATTCAACTACAATCGTC
66 ATCCAACTACGACCGTC
* * * *
280776 CCACGAATCAAGGAAAAGGAAAATTTGAGGAGTACTCCCTAGAATCCATTCACAACCGCAATCCA
1 CCACGGATCGAGGAAAAGGAAAATTAGAGAAGTACTCCCTAGAATCCATTCACAACCGCAATCCA
* *
280841 CTCCAAGTACGACCGTC
66 ATCCAACTACGACCGTC
* * * ** * * *
280858 CCACGGATCGAGGGAAAGGAAAATTAGAAAAATACTCTTTAAAATCCATTCACAACTGCAATCTA
1 CCACGGATCGAGGAAAAGGAAAATTAGAGAAGTACTCCCTAGAATCCATTCACAACCGCAATCCA
* *
280923 GTCCAACTATGACCGTC
66 ATCCAACTACGACCGTC
* * *
280940 CCACGGATCGAGGAAAAGGAAAATTAAAGGAGTACT-CCTTGAAATCCATTCACAACCGCAATCC
1 CCACGGATCGAGGAAAAGGAAAATTAGAGAAGTACTCCCTAG-AATCCATTCACAACCGCAATCC
281004 AATCCAA
65 AATCCAA
281011 TAAATTCGTA
Statistics
Matches: 191, Mismatches: 42, Indels: 3
0.81 0.18 0.01
Matches are distributed among these distances:
81 36 0.19
82 155 0.81
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.19
Consensus pattern (82 bp):
CCACGGATCGAGGAAAAGGAAAATTAGAGAAGTACTCCCTAGAATCCATTCACAACCGCAATCCA
ATCCAACTACGACCGTC
Found at i:294614 original size:13 final size:13
Alignment explanation
Indices: 294596--294620 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
294586 TTAACTTGAA
294596 ATTTATTTACTCG
1 ATTTATTTACTCG
294609 ATTTATTTACTC
1 ATTTATTTACTC
294621 AAAATTCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.16, G:0.04, T:0.56
Consensus pattern (13 bp):
ATTTATTTACTCG
Found at i:296839 original size:21 final size:21
Alignment explanation
Indices: 296791--296844 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
296781 GAAGTTTTTA
* *
296791 GTATCGGTAGAAGTATGACTT
1 GTATCGGTAGAAGTATCACCT
*
296812 GTTTCGGTAGAAGT-TACACCT
1 GTATCGGTAGAAGTAT-CACCT
296833 GTATCGGTAGAA
1 GTATCGGTAGAA
296845 CTTTCCCAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 1 0.04
21 27 0.96
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTATCACCT
Found at i:302802 original size:18 final size:18
Alignment explanation
Indices: 302743--302806 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
302733 CTCTTATGAT
302743 CCAGTATGCTCAAACGAG
1 CCAGTATGCTCAAACGAG
* *
302761 CTAATATGCTCAAACGAG
1 CCAGTATGCTCAAACGAG
**
302779 TTAGTATGCTCAAACGAG
1 CCAGTATGCTCAAACGAG
302797 CCAGTATGCT
1 CCAGTATGCT
302807 ATTCCTTACA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (18 bp):
CCAGTATGCTCAAACGAG
Found at i:308302 original size:17 final size:17
Alignment explanation
Indices: 308280--308331 Score: 86
Period size: 17 Copynumber: 3.1 Consensus size: 17
308270 ATTGAACATT
308280 TATCCTTCTATTTATCA
1 TATCCTTCTATTTATCA
308297 TATCCTTCTATTTATCA
1 TATCCTTCTATTTATCA
* *
308314 TATCCATCGATTTATCA
1 TATCCTTCTATTTATCA
308331 T
1 T
308332 TCCATCTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.25, C:0.23, G:0.02, T:0.50
Consensus pattern (17 bp):
TATCCTTCTATTTATCA
Found at i:319555 original size:144 final size:144
Alignment explanation
Indices: 319368--319801 Score: 832
Period size: 144 Copynumber: 3.0 Consensus size: 144
319358 GATATATCAG
*
319368 ATGACTTATGTGATGAAGACATTAGTTGTTCCAAGCTTACCCCAGTGCTAATATTGGTATGGAAA
1 ATGACTCATGTGATGAAGACATTAGTTGTTCCAAGCTTACCCCAGTGCTAATATTGGTATGGAAA
319433 AAATTAAGTGATAAGTTATGTTGGTTATCAAATATGACTTTATTGTCCTTTGGGGGGACTTGATA
66 AAATTAAGTGATAAGTTATGTTGGTTATCAAATATGACTTTATTGTCCTTTGGGGGGACTTGATA
319498 TTGCAACTAGAGCT
131 TTGCAACTAGAGCT
319512 ATGACTCATGTGATGAAGACATTAGTTGTTCCAAGCTTACCCCAGTGCTAATATTGGTATGGAAA
1 ATGACTCATGTGATGAAGACATTAGTTGTTCCAAGCTTACCCCAGTGCTAATATTGGTATGGAAA
*
319577 AAGTTAAGTGATAAGTTATGTTGGTTATCAAATATGACTTTATTGTCCTTTGGGGGGACTTGATA
66 AAATTAAGTGATAAGTTATGTTGGTTATCAAATATGACTTTATTGTCCTTTGGGGGGACTTGATA
319642 TTGCAACTAGAGCT
131 TTGCAACTAGAGCT
*
319656 ATGACTCACGTGATGAAGACATTAGTTGTTCCAAGCTTACCCCAGTGCTAATATTGGTATGGAAA
1 ATGACTCATGTGATGAAGACATTAGTTGTTCCAAGCTTACCCCAGTGCTAATATTGGTATGGAAA
*
319721 AAATTAAGTGATAAGTTATGTTGGTTATCAAATATGACTTTATTGTCCTTTGGGGGTACTTGATA
66 AAATTAAGTGATAAGTTATGTTGGTTATCAAATATGACTTTATTGTCCTTTGGGGGGACTTGATA
319786 TTGCAACTAGAGCT
131 TTGCAACTAGAGCT
319800 AT
1 AT
319802 TAGGTTTAGA
Statistics
Matches: 285, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
144 285 1.00
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (144 bp):
ATGACTCATGTGATGAAGACATTAGTTGTTCCAAGCTTACCCCAGTGCTAATATTGGTATGGAAA
AAATTAAGTGATAAGTTATGTTGGTTATCAAATATGACTTTATTGTCCTTTGGGGGGACTTGATA
TTGCAACTAGAGCT
Found at i:321937 original size:15 final size:15
Alignment explanation
Indices: 321903--321937 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
321893 GTTTGATAAA
*
321903 TTGAAAAATTAAGTG
1 TTGAAAAATTAAGGG
*
321918 CTGAAAAATTAAGGG
1 TTGAAAAATTAAGGG
321933 TTGAA
1 TTGAA
321938 TATTTTAAGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.46, C:0.03, G:0.23, T:0.29
Consensus pattern (15 bp):
TTGAAAAATTAAGGG
Found at i:323036 original size:46 final size:46
Alignment explanation
Indices: 322984--323071 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
322974 AAGGGAAATA
* *
322984 AAAACCTAATATAATAAGGAAAATAACTAAAACTAAAACTCTTAAT
1 AAAACCTAATATAATAAAGAAAATAAATAAAACTAAAACTCTTAAT
* * *
323030 AAAACCTGATATAATAAAGAAATTAAATAAATCTAAAACTCT
1 AAAACCTAATATAATAAAGAAAATAAATAAAACTAAAACTCT
323072 AATTGCAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
46 37 1.00
ACGTcount: A:0.58, C:0.12, G:0.05, T:0.25
Consensus pattern (46 bp):
AAAACCTAATATAATAAAGAAAATAAATAAAACTAAAACTCTTAAT
Found at i:324468 original size:46 final size:46
Alignment explanation
Indices: 324416--324503 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
324406 TAGGGAAATA
*
324416 AAAACCTAATACAAT-AAGAAAAATAACTAAAACTAAAACTCTTAAT
1 AAAACCTAATACAATAAAG-AAAATAAATAAAACTAAAACTCTTAAT
* * * *
324462 AAAACCTGATATAATAAAGAAATTAAATAAATCTAAAACTCT
1 AAAACCTAATACAATAAAGAAAATAAATAAAACTAAAACTCT
324504 AATTGCAATA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
46 33 0.92
47 3 0.08
ACGTcount: A:0.59, C:0.14, G:0.03, T:0.24
Consensus pattern (46 bp):
AAAACCTAATACAATAAAGAAAATAAATAAAACTAAAACTCTTAAT
Found at i:326540 original size:2 final size:2
Alignment explanation
Indices: 326533--326558 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
326523 ATTTCTTATT
326533 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
326559 GAACTCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:344780 original size:49 final size:49
Alignment explanation
Indices: 344686--345188 Score: 329
Period size: 49 Copynumber: 10.2 Consensus size: 49
344676 AGCTGCAATG
* * * * * * *** *
344686 ATCTTACACCTTAAAATTAAAGAGGGATAGCTTAAAGCTGTAACGGTGG
1 ATCTAACACCCTAAAACTAAAGAGGGAAAGATTGAAGCCACAACGGTGA
* *
344735 ACCTAACACCCTAAAACTAAAGAGGGAAAGATTAAAGCCACAACGGT-A
1 ATCTAACACCCTAAAACTAAAGAGGGAAAGATTGAAGCCACAACGGTGA
* * * * * **
344783 GATCTTACACCTTAAAA-TCGAAGAGGGATAGATTGAAGCCATAATAGTGA
1 -ATCTAACACCCTAAAACT-AAAGAGGGAAAGATTGAAGCCACAACGGTGA
* * * * ** ** *
344833 ATCTAACACCCTAAAATTGAGGAAGGAAAGATTGAAGCCGTAACGACGG
1 ATCTAACACCCTAAAACTAAAGAGGGAAAGATTGAAGCCACAACGGTGA
* * * * *
344882 ATCTAACACCCTAAAA-TAGAAAAGGGATAGATTGAAGCCGCAACGATAA
1 ATCTAACACCCTAAAACTA-AAGAGGGAAAGATTGAAGCCACAACGGTGA
* * * * * *
344931 ATCTAACACCTTAAAATCGAAA-AGGGAAAGATTGAAGCAACAATGGCGG
1 ATCTAACACCCTAAAA-CTAAAGAGGGAAAGATTGAAGCCACAACGGTGA
* * * **
344980 ATCTAACACCTTAAAATCGT-TA-AGGGAAAGATTGAAGCCGCAACGACGA
1 ATCTAACACCCTAAAA-C-TAAAGAGGGAAAGATTGAAGCCACAACGGTGA
** * *** **
345029 ATCTTTCACCCTAGAAAC-AAAGA-GGATAGATTGAAGTTGCAACGACGA
1 ATCTAACACCCTA-AAACTAAAGAGGGAAAGATTGAAGCCACAACGGTGA
*
345077 ATCTAACACCCTAAAACTGAAGAGGGAAAGATTGAAGCCACAACGGTGA
1 ATCTAACACCCTAAAACTAAAGAGGGAAAGATTGAAGCCACAACGGTGA
* * * *
345126 ATCTTACACCCTAAAAAAATTGAAGAGGGAATAGATTGAAGCCACAACGGCGA
1 ATCTAACACCCT---AAAACTAAAGAGGGAA-AGATTGAAGCCACAACGGTGA
*
345179 ATCTTACACC
1 ATCTAACACC
345189 ATATAAAAAA
Statistics
Matches: 362, Mismatches: 75, Indels: 30
0.78 0.16 0.06
Matches are distributed among these distances:
47 4 0.01
48 40 0.11
49 265 0.73
50 7 0.02
51 1 0.00
52 15 0.04
53 30 0.08
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (49 bp):
ATCTAACACCCTAAAACTAAAGAGGGAAAGATTGAAGCCACAACGGTGA
Found at i:344839 original size:98 final size:96
Alignment explanation
Indices: 344685--345269 Score: 378
Period size: 98 Copynumber: 5.9 Consensus size: 96
344675 AAGCTGCAAT
* ** * * * * * *
344685 GATCTTACACCTTAAAATTAAAGAGGGATAGCTTAAAGCTGTAACGGTGGACCTAACACCCTAAA
1 GATCTAACACCTTAAAATCGAAGAGGGATAGATTGAAGCCGCAAC-GTGAATCTAACACCCTAAA
*
344750 ACTAAAGAGGGAAAGATTAAAGCCACAACGGTA
65 ACTAAAGAGGGAAAGATTGAAGCCACAACGG-A
* ** *
344783 GATCTTACACCTTAAAATCGAAGAGGGATAGATTGAAGCCATAATAGTGAATCTAACACCCTAAA
1 GATCTAACACCTTAAAATCGAAGAGGGATAGATTGAAGCCGCAA-CGTGAATCTAACACCCTAAA
* * * * **
344848 ATTGAGGAAGGAAAGATTGAAGCCGTAAC-GA
65 ACTAAAGAGGGAAAGATTGAAGCCACAACGGA
* * * * *
344879 CGGATCTAACACCCTAAAATAGAAAAGGGATAGATTGAAGCCGCAACGATAAATCTAACACCTTA
1 --GATCTAACACCTTAAAATCGAAGAGGGATAGATTGAAGCCGCAACG-TGAATCTAACACCCTA
* * * *
344944 AAATCGAAA-AGGGAAAGATTGAAGCAACAATGGCG
63 AAA-CTAAAGAGGGAAAGATTGAAGCCACAACGG-A
* * * **
344979 GATCTAACACCTTAAAATCGTTA-AGGGAAAGATTGAAGCCGCAACGACGAATCTTTCACCCTAG
1 GATCTAACACCTTAAAATCG-AAGAGGGATAGATTGAAGCCGCAACG-TGAATCTAACACCCTA-
* ***
345043 AAAC-AAAGA-GGATAGATTGAAGTTGCAAC-GA
63 AAACTAAAGAGGGAAAGATTGAAGCCACAACGGA
* * * *
345074 CGAATCTAACACCCTAAAA-CTGAAGAGGGAAAGATTGAAGCCACAACGGTGAATCTTACACCCT
1 -G-ATCTAACACCTTAAAATC-GAAGAGGGATAGATTGAAGCCGCAAC-GTGAATCTAACACCCT
* * *
345138 AAAAAAATTGAAGAGGGAATAGATTGAAGCCACAACGGC
62 ---AAAACTAAAGAGGGAA-AGATTGAAGCCACAACGGA
* * *
345177 GAATCTTACACCATATAAAAAATACTGAAGAGGGAATAGATTGAAGCTGCAAAGGTGAATCGT-A
1 G-ATCTAACACC-T-T--AAAAT-C-GAAGAGGG-ATAGATTGAAGCCGC-AACGTGAATC-TAA
** *
345241 CA-CCTGAAAACTGTAGAGGGACAGATTGA
56 CACCCT-AAAACTAAAGAGGGAAAGATTGA
345270 TCCTATTTTC
Statistics
Matches: 384, Mismatches: 72, Indels: 55
0.75 0.14 0.11
Matches are distributed among these distances:
96 5 0.01
97 70 0.18
98 204 0.53
99 9 0.02
100 5 0.01
101 3 0.01
102 24 0.06
103 1 0.00
104 1 0.00
105 7 0.02
106 17 0.04
108 13 0.03
109 22 0.06
110 3 0.01
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.19
Consensus pattern (96 bp):
GATCTAACACCTTAAAATCGAAGAGGGATAGATTGAAGCCGCAACGTGAATCTAACACCCTAAAA
CTAAAGAGGGAAAGATTGAAGCCACAACGGA
Found at i:344963 original size:147 final size:146
Alignment explanation
Indices: 344737--345188 Score: 480
Period size: 147 Copynumber: 3.1 Consensus size: 146
344727 AACGGTGGAC
* * * * * * *
344737 CTAACACCCTAAAACTAAAGAGGGAAAGATTAAAGCCACAACGGTAGATCTTACACCTTAAAATC
1 CTAACACCCTAAAA-TAAAAAGGGATAGATTGAAGCCGCAACGATAAATCTAACACCTTAAAATC
* * * *
344802 GAAGAGGGATAGATTGAAGCCATAATAGTGAATCTAACACCCTAAAATTGAGGAAGGAAAGATTG
65 GAAGAGGGAAAGATTGAAGCCACAATGGTGAATCTAACACCCTAAAATTGAAGAAGGAAAGATTG
* *
344867 AAGCCGTAACGACGGAT
130 AAGCCGCAACGACGAAT
344884 CTAACACCCTAAAATAGAAAAGGGATAGATTGAAGCCGCAACGATAAATCTAACACCTTAAAATC
1 CTAACACCCTAAAATA-AAAAGGGATAGATTGAAGCCGCAACGATAAATCTAACACCTTAAAATC
* * * * * *
344949 GAAAAGGGAAAGATTGAAGCAACAATGGCGGATCTAACACCTTAAAATCGTTAAG--GGAAAGAT
65 GAAGAGGGAAAGATTGAAGCCACAATGGTGAATCTAACACCCTAAAAT--TGAAGAAGGAAAGAT
345012 TGAAGCCGCAACGACGAAT
128 TGAAGCCGCAACGACGAAT
** * * ** ** *
345031 CTTTCACCCTAGAA-ACAAAGAGGATAGATTGAAGTTGCAACGACGAATCTAACACCCTAAAA-C
1 CTAACACCCTAAAATAAAAAG-GGATAGATTGAAGCCGCAACGATAAATCTAACACCTTAAAATC
* * *
345094 TGAAGAGGGAAAGATTGAAGCCACAACGGTGAATCTTACACCCTAAAAAAATTGAAGAGGGAATA
65 -GAAGAGGGAAAGATTGAAGCCACAATGGTGAATCTAACACCCT---AAAATTGAAGAAGGAA-A
* *
345159 GATTGAAGCCACAACGGCGAAT
125 GATTGAAGCCGCAACGACGAAT
*
345181 CTTACACC
1 CTAACACC
345189 ATATAAAAAA
Statistics
Matches: 255, Mismatches: 39, Indels: 19
0.81 0.12 0.06
Matches are distributed among these distances:
145 5 0.02
146 75 0.29
147 135 0.53
149 12 0.05
150 28 0.11
ACGTcount: A:0.43, C:0.19, G:0.21, T:0.18
Consensus pattern (146 bp):
CTAACACCCTAAAATAAAAAGGGATAGATTGAAGCCGCAACGATAAATCTAACACCTTAAAATCG
AAGAGGGAAAGATTGAAGCCACAATGGTGAATCTAACACCCTAAAATTGAAGAAGGAAAGATTGA
AGCCGCAACGACGAAT
Done.