Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008433.1 Hibiscus syriacus cultivar Beakdansim tig00111231_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 451884
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 3
Found at i:228077 original size:20 final size:20
Alignment explanation
Indices: 228039--228083 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
228029 TATATATTTT
* * *
228039 ATTAAAATTAATAATTAATA
1 ATTAAAATAAAAAAATAATA
228059 ATTAAAATAAAAAAATAATA
1 ATTAAAATAAAAAAATAATA
*
228079 GTTAA
1 ATTAA
228084 TTGGTGATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (20 bp):
ATTAAAATAAAAAAATAATA
Found at i:228976 original size:30 final size:30
Alignment explanation
Indices: 228877--228979 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 30
228867 GAAAGCAAAC
* *
228877 CAAAGAAAGAAGAAACCCACCACAAC-AAAC
1 CAAAGAAACAA-AAACCCACCACAACAAAAA
* * * * * *
228907 CAAAGAAAACAAAATCTC-TCACAGCAGAAG
1 CAAAG-AAACAAAAACCCACCACAACAAAAA
*
228937 CAAAGGAAACAAAAGCCCACCACAACAAAAA
1 CAAA-GAAACAAAAACCCACCACAACAAAAA
228968 CAAAGAAACAAA
1 CAAAGAAACAAA
228980 TATAGGGATA
Statistics
Matches: 56, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
29 5 0.09
30 33 0.59
31 18 0.32
ACGTcount: A:0.60, C:0.26, G:0.11, T:0.03
Consensus pattern (30 bp):
CAAAGAAACAAAAACCCACCACAACAAAAA
Found at i:231310 original size:48 final size:48
Alignment explanation
Indices: 231231--231480 Score: 296
Period size: 48 Copynumber: 5.3 Consensus size: 48
231221 GTAGGCATAA
* * * *
231231 GGAGGAGGTGGGGAGTGTAC---CGGTGGTGGAGATTTGTAAATATAG
1 GGAGGAGGTGGGGAGTGCACTGGAGGTGGAGGAGACTTGTAAATATAG
* * * * *
231276 GGAGGAGGCGGGGAGTGGACTGGTGGTGGAGGAGATTTGTAAATGTAG
1 GGAGGAGGTGGGGAGTGCACTGGAGGTGGAGGAGACTTGTAAATATAG
* *
231324 GGAGGAGGTGGTGAGTGCACTGGAGGTGGAGGAGACTTGTAAACATA-
1 GGAGGAGGTGGGGAGTGCACTGGAGGTGGAGGAGACTTGTAAATATAG
* * * *
231371 --AGGAGGCGGGGAGTGAACTGGCGGTGGAGGAGACTTGTAAATGTAG
1 GGAGGAGGTGGGGAGTGCACTGGAGGTGGAGGAGACTTGTAAATATAG
*
231417 GGAGGAGGTGGCGAGTGCACTGGAGGTGGAGGAGACTTGTAAATATAG
1 GGAGGAGGTGGGGAGTGCACTGGAGGTGGAGGAGACTTGTAAATATAG
*
231465 GGAGGTGGTGGAGGAG
1 GGAGGAGGTGG-GGAG
231481 ACTTGTAAAC
Statistics
Matches: 173, Mismatches: 25, Indels: 10
0.83 0.12 0.05
Matches are distributed among these distances:
45 57 0.33
48 113 0.65
49 3 0.02
ACGTcount: A:0.25, C:0.06, G:0.49, T:0.20
Consensus pattern (48 bp):
GGAGGAGGTGGGGAGTGCACTGGAGGTGGAGGAGACTTGTAAATATAG
Found at i:231378 original size:93 final size:93
Alignment explanation
Indices: 231278--231469 Score: 330
Period size: 93 Copynumber: 2.1 Consensus size: 93
231268 AAATATAGGG
* * * *
231278 AGGAGGCGGGGAGTGGACTGGTGGTGGAGGAGATTTGTAAATGTAGGGAGGAGGTGGTGAGTGCA
1 AGGAGGCGGGGAGTGAACTGGCGGTGGAGGAGACTTGTAAATGTAGGGAGGAGGTGGCGAGTGCA
231343 CTGGAGGTGGAGGAGACTTGTAAACATA
66 CTGGAGGTGGAGGAGACTTGTAAACATA
231371 AGGAGGCGGGGAGTGAACTGGCGGTGGAGGAGACTTGTAAATGTAGGGAGGAGGTGGCGAGTGCA
1 AGGAGGCGGGGAGTGAACTGGCGGTGGAGGAGACTTGTAAATGTAGGGAGGAGGTGGCGAGTGCA
*
231436 CTGGAGGTGGAGGAGACTTGTAAATATA
66 CTGGAGGTGGAGGAGACTTGTAAACATA
*
231464 GGGAGG
1 AGGAGG
231470 TGGTGGAGGA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.26, C:0.07, G:0.48, T:0.19
Consensus pattern (93 bp):
AGGAGGCGGGGAGTGAACTGGCGGTGGAGGAGACTTGTAAATGTAGGGAGGAGGTGGCGAGTGCA
CTGGAGGTGGAGGAGACTTGTAAACATA
Found at i:231477 original size:30 final size:30
Alignment explanation
Indices: 231438--231509 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
231428 CGAGTGCACT
*
231438 GGAGGTGGAGGAGACTTGTAAATATAGGGA
1 GGAGGTGGAGGAGACTTGTAAACATAGGGA
*
231468 GGTGGTGGAGGAGACTTGTAAACATAGGGA
1 GGAGGTGGAGGAGACTTGTAAACATAGGGA
231498 GGAGGTGG-GGAG
1 GGAGGTGGAGGAG
231510 TGGACTGGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 4 0.10
30 35 0.90
ACGTcount: A:0.29, C:0.04, G:0.49, T:0.18
Consensus pattern (30 bp):
GGAGGTGGAGGAGACTTGTAAACATAGGGA
Found at i:231488 original size:78 final size:78
Alignment explanation
Indices: 231393--231557 Score: 260
Period size: 78 Copynumber: 2.1 Consensus size: 78
231383 GTGAACTGGC
**
231393 GGTGGAGGAGACTTGTAAATGTAGGGAGGAGGTGGCGAGTGCACTGGAGGTGGAGGAGACTTGTA
1 GGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGCGAGTGCACTGGAGGTGGAGGAGACTTGTA
*
231458 AATATAGGGAGGT
66 AATATAGGGAGGA
* * *
231471 GGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTA
1 GGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGCGAGTGCACTGGAGGTGGAGGAGACTTGTA
*
231536 AATGTAGGGAGGA
66 AATATAGGGAGGA
231549 GGTGG-GGAG
1 GGTGGAGGAG
231558 TGAACTGGAG
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
77 4 0.05
78 76 0.95
ACGTcount: A:0.26, C:0.05, G:0.49, T:0.19
Consensus pattern (78 bp):
GGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGCGAGTGCACTGGAGGTGGAGGAGACTTGTA
AATATAGGGAGGA
Found at i:231519 original size:219 final size:220
Alignment explanation
Indices: 231252--231691 Score: 639
Period size: 219 Copynumber: 2.0 Consensus size: 220
231242 GGAGTGTACC
* * * *
231252 GGTGGTGGAGATTTGTAAATATAGGGAGGAGGCGGGGAGTGGACTGGTGGTGGAGGAGATTTGTA
1 GGTGGAGGAGACTTGTAAACATAGGGAGGAGGCGGGGAGTGGACTGGTGGTGGAGGAGACTTGTA
* * *
231317 AATGTAGGGAGGAGGTGGTGAGTGCACTGGAGGTGGAGGAGACTTGTAAACATA-AGGAGGCGGG
66 AATGTAGGGAGGAGGTGGGGAGTGAACTGGAGGTGGAGGAGACTTGTAAACATAGAGGAGGAGGG
* * * * *
231381 GAGTGAACTGGCGGTGGAGGAGACTTGTAAATGTAGGGAGGAGGTGGCGAGTGCACTGGAGGTGG
131 GAGTGAACTGGAGGTGGAGGAGACTTATAAATATAAGGAGGAGGTGGCGAGTGCACTGGAGGAGG
231446 AGGAGACTTGTAAATATAGGGAGGT
196 AGGAGACTTGTAAATATAGGGAGGT
*
231471 GGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTA
1 GGTGGAGGAGACTTGTAAACATAGGGAGGAGGCGGGGAGTGGACTGGTGGTGGAGGAGACTTGTA
* *
231536 AATGTAGGGAGGAGGTGGGGAGTGAACTGGAGGTGGTGGAGACTTGTAAATATAGGGAGGAGGAG
66 AATGTAGGGAGGAGGTGGGGAGTGAACTGGAGGTGGAGGAGACTTGTAAACATA--GAGGAGGAG
* * * * * *
231601 GTGAGTGAACTGGAGGTGGTGGAGACTTATAAATATAAGGAGGTGGTGGGGAGTGGACTGGTGGA
129 GGGAGTGAACTGGAGGTGGAGGAGACTTATAAATATAAGGAGGAGGTGGCGAGTGCACTGGAGGA
* * *
231666 GGAGGTGACTTGTAAATGTATGGAGG
194 GGAGGAGACTTGTAAATATAGGGAGG
231692 AGGCGGTGAG
Statistics
Matches: 194, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
219 110 0.57
222 84 0.43
ACGTcount: A:0.26, C:0.05, G:0.47, T:0.21
Consensus pattern (220 bp):
GGTGGAGGAGACTTGTAAACATAGGGAGGAGGCGGGGAGTGGACTGGTGGTGGAGGAGACTTGTA
AATGTAGGGAGGAGGTGGGGAGTGAACTGGAGGTGGAGGAGACTTGTAAACATAGAGGAGGAGGG
GAGTGAACTGGAGGTGGAGGAGACTTATAAATATAAGGAGGAGGTGGCGAGTGCACTGGAGGAGG
AGGAGACTTGTAAATATAGGGAGGT
Found at i:231520 original size:48 final size:48
Alignment explanation
Indices: 231471--231820 Score: 423
Period size: 48 Copynumber: 7.3 Consensus size: 48
231461 ATAGGGAGGT
* * *
231471 GGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGGGAGTGGACTGGT
1 GGTGGTGGAGACTTGTAAATATAGGGAGGAGGTGGGGAGTGGACTGGA
* * *
231519 GGTGGAGGAGACTTGTAAATGTAGGGAGGAGGTGGGGAGTGAACTGGA
1 GGTGGTGGAGACTTGTAAATATAGGGAGGAGGTGGGGAGTGGACTGGA
* * *
231567 GGTGGTGGAGACTTGTAAATATAGGGAGGAGGAGGTGAGTGAACTGGA
1 GGTGGTGGAGACTTGTAAATATAGGGAGGAGGTGGGGAGTGGACTGGA
* * * *
231615 GGTGGTGGAGACTTATAAATATAAGGAGGTGGTGGGGAGTGGACTGGT
1 GGTGGTGGAGACTTGTAAATATAGGGAGGAGGTGGGGAGTGGACTGGA
* * * * * * *
231663 GGAGGAGGTGACTTGTAAATGTATGGAGGAGGCGGTGAGTGGACTGGA
1 GGTGGTGGAGACTTGTAAATATAGGGAGGAGGTGGGGAGTGGACTGGA
* * * *
231711 GGTGGTGGGGATTTGTAAATGTAAGGG-GGAGGTGGAGAGTGGACTGGA
1 GGTGGTGGAGACTTGTAAATAT-AGGGAGGAGGTGGGGAGTGGACTGGA
* * * * *
231759 GGTGGTGGAGACTTATAGATATAAGGAGGAGGTGGAGAGTGGACTAGA
1 GGTGGTGGAGACTTGTAAATATAGGGAGGAGGTGGGGAGTGGACTGGA
231807 GGTGGTGGAGACTT
1 GGTGGTGGAGACTT
231821 ATAGACATAG
Statistics
Matches: 261, Mismatches: 39, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
47 3 0.01
48 255 0.98
49 3 0.01
ACGTcount: A:0.26, C:0.05, G:0.48, T:0.21
Consensus pattern (48 bp):
GGTGGTGGAGACTTGTAAATATAGGGAGGAGGTGGGGAGTGGACTGGA
Found at i:231532 original size:126 final size:123
Alignment explanation
Indices: 231348--231595 Score: 415
Period size: 126 Copynumber: 2.0 Consensus size: 123
231338 GTGCACTGGA
231348 GGTGGAGGAGACTTGTAAACATAAGGAGGCGGGGAGTGAACTGGCGGTGGAGGAGACTTGTAAAT
1 GGTGGAGGAGACTTGTAAACATAAGGAGGCGGGGAGTGAACTGGCGGTGGAGGAGACTTGTAAAT
*
231413 GTAGGGAGGAGGTGGCGAGTGCACTGGAGGTGGAGGAGACTTGTAAATATAGGGAGGT
66 GTAGGGAGGAGGTGGCGAGTGAACTGGAGGTGGAGGAGACTTGTAAATATAGGGAGGT
* * *
231471 GGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTA
1 GGTGGAGGAGACTTGTAAACATA---AGGAGGCGGGGAGTGAACTGGCGGTGGAGGAGACTTGTA
* *
231536 AATGTAGGGAGGAGGTGGGGAGTGAACTGGAGGTGGTGGAGACTTGTAAATATAGGGAGG
63 AATGTAGGGAGGAGGTGGCGAGTGAACTGGAGGTGGAGGAGACTTGTAAATATAGGGAGG
231596 AGGAGGTGAG
Statistics
Matches: 116, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
123 23 0.20
126 93 0.80
ACGTcount: A:0.27, C:0.06, G:0.47, T:0.19
Consensus pattern (123 bp):
GGTGGAGGAGACTTGTAAACATAAGGAGGCGGGGAGTGAACTGGCGGTGGAGGAGACTTGTAAAT
GTAGGGAGGAGGTGGCGAGTGAACTGGAGGTGGAGGAGACTTGTAAATATAGGGAGGT
Found at i:231594 original size:27 final size:26
Alignment explanation
Indices: 231564--231649 Score: 65
Period size: 27 Copynumber: 3.4 Consensus size: 26
231554 GGAGTGAACT
231564 GGAGGTGGTGGAGACTTGTAAATATA
1 GGAGGTGGTGGAGACTTGTAAATATA
* * * * *
231590 GGGAGGAGGAGGTGA---GTGAA-CT-
1 -GGAGGTGGTGGAGACTTGTAAATATA
*
231612 GGAGGTGGTGGAGACTTATAAATATAA
1 GGAGGTGGTGGAGACTTGTAAATAT-A
231639 GGAGGTGGTGG
1 GGAGGTGGTGG
231650 GGAGTGGACT
Statistics
Matches: 42, Mismatches: 11, Indels: 12
0.65 0.17 0.18
Matches are distributed among these distances:
21 11 0.26
23 1 0.02
24 7 0.17
25 1 0.02
27 22 0.52
ACGTcount: A:0.29, C:0.03, G:0.45, T:0.22
Consensus pattern (26 bp):
GGAGGTGGTGGAGACTTGTAAATATA
Found at i:231627 original size:174 final size:171
Alignment explanation
Indices: 231297--231653 Score: 518
Period size: 174 Copynumber: 2.1 Consensus size: 171
231287 GGAGTGGACT
* ** *
231297 GGTGGTGGAGGAGATTTGTAAATGTAGGGAGGAGGTGGTGAGTGCACTGGAGGTGGAGGAGACTT
1 GGTGGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGGGAGTGCACTGGAGGTGGAGGAGACTT
* * *
231362 GTAAACATAAGGAGGCGGGGAGTGAACTGGCGGTGGAGGAGACTTGTAAATGTAGGGAGGAGGTG
66 GTAAACATAAGGAGGCGGGGAGTGAACTGGAGGTGGAGGAGACTTGTAAATATAGGGAGGAGGAG
* * *
231427 GCGAGTGCACTGGAGGTGGAGGAGACTTGTAAATATAGGGA
131 GCGAGTGAACTGGAGGTGGAGGAGACTTATAAATATAAGGA
* *
231468 GGTGGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTT
1 GGTGGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGGGAGTGCACTGGAGGTGGAGGAGACTT
** * *
231533 GTAAATGTAGGGAGGAGGTGGGGAGTGAACTGGAGGTGGTGGAGACTTGTAAATATAGGGAGGAG
66 GTAAACATA---AGGAGGCGGGGAGTGAACTGGAGGTGGAGGAGACTTGTAAATATAGGGAGGAG
* *
231598 GAGGTGAGTGAACTGGAGGTGGTGGAGACTTATAAATATAAGGA
128 GAGGCGAGTGAACTGGAGGTGGAGGAGACTTATAAATATAAGGA
231642 GGTGGTGG-GGAG
1 GGTGGTGGAGGAG
231654 TGGACTGGTG
Statistics
Matches: 165, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
171 66 0.40
173 4 0.02
174 95 0.58
ACGTcount: A:0.27, C:0.06, G:0.47, T:0.20
Consensus pattern (171 bp):
GGTGGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGGGAGTGCACTGGAGGTGGAGGAGACTT
GTAAACATAAGGAGGCGGGGAGTGAACTGGAGGTGGAGGAGACTTGTAAATATAGGGAGGAGGAG
GCGAGTGAACTGGAGGTGGAGGAGACTTATAAATATAAGGA
Found at i:231655 original size:144 final size:144
Alignment explanation
Indices: 231471--231820 Score: 486
Period size: 144 Copynumber: 2.4 Consensus size: 144
231461 ATAGGGAGGT
* * * *
231471 GGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTA
1 GGTGGTGGAGACTTATAAATATAAGGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTA
*
231536 AATGTAGGGAGGAGGTGGGGAGTGAACTGGAGGTGGTGGAGACTTGTAAATAT-AGGGAGGAGGA
66 AATGTAGGGAGGAGGCGGGGAGTGAACTGGAGGTGGTGGAGACTTGTAAATATAAGGG-GGAGGA
*
231600 GGTGAGTGAACTGGA
130 GGAGAGTGAACTGGA
* * *
231615 GGTGGTGGAGACTTATAAATATAAGGAGGTGGTGGGGAGTGGACTGGTGGAGGAGGTGACTTGTA
1 GGTGGTGGAGACTTATAAATATAAGGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTA
* * * * * * *
231680 AATGTATGGAGGAGGCGGTGAGTGGACTGGAGGTGGTGGGGATTTGTAAATGTAAGGGGGAGGTG
66 AATGTAGGGAGGAGGCGGGGAGTGAACTGGAGGTGGTGGAGACTTGTAAATATAAGGGGGAGGAG
*
231745 GAGAGTGGACTGGA
131 GAGAGTGAACTGGA
* * * * *
231759 GGTGGTGGAGACTTATAGATATAAGGAGGAGGTGGAGAGTGGACTAGAGGTGGTGGAGACTT
1 GGTGGTGGAGACTTATAAATATAAGGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTT
231821 ATAGACATAG
Statistics
Matches: 180, Mismatches: 25, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
144 176 0.98
145 4 0.02
ACGTcount: A:0.26, C:0.05, G:0.48, T:0.21
Consensus pattern (144 bp):
GGTGGTGGAGACTTATAAATATAAGGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTA
AATGTAGGGAGGAGGCGGGGAGTGAACTGGAGGTGGTGGAGACTTGTAAATATAAGGGGGAGGAG
GAGAGTGAACTGGA
Found at i:231786 original size:27 final size:26
Alignment explanation
Indices: 231756--231852 Score: 78
Period size: 27 Copynumber: 3.8 Consensus size: 26
231746 AGAGTGGACT
231756 GGAGGTGGTGGAGACTTATAGATATAA
1 GGAGGTGGTGGAGACTTATAGA-ATAA
* * * *
231783 GGAGGAGGTGGAGA---GTGGACT-A
1 GGAGGTGGTGGAGACTTATAGAATAA
*
231805 -GAGGTGGTGGAGACTTATAGACATAG
1 GGAGGTGGTGGAGACTTATAGA-ATAA
* *
231831 GGTGGTGGTGGAGATTTATAGA
1 GGAGGTGGTGGAGACTTATAGA
231853 CATACGGTGG
Statistics
Matches: 53, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
21 12 0.23
22 1 0.02
23 1 0.02
24 6 0.11
25 1 0.02
27 32 0.60
ACGTcount: A:0.29, C:0.04, G:0.43, T:0.24
Consensus pattern (26 bp):
GGAGGTGGTGGAGACTTATAGAATAA
Found at i:231853 original size:27 final size:27
Alignment explanation
Indices: 231807--231871 Score: 94
Period size: 27 Copynumber: 2.4 Consensus size: 27
231797 GTGGACTAGA
*
231807 GGTGGTGGAGACTTATAGACATAGGGT
1 GGTGGTGGAGACTTATAGACATACGGT
*
231834 GGTGGTGGAGATTTATAGACATACGGT
1 GGTGGTGGAGACTTATAGACATACGGT
* *
231861 GGAGGAGGAGA
1 GGTGGTGGAGA
231872 GTGAACCAGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.28, C:0.06, G:0.43, T:0.23
Consensus pattern (27 bp):
GGTGGTGGAGACTTATAGACATACGGT
Found at i:233087 original size:16 final size:16
Alignment explanation
Indices: 233066--233098 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
233056 TGTACTCGAC
233066 TCAAACTCAAAAAAAT
1 TCAAACTCAAAAAAAT
*
233082 TCAAACTTAAAAAAAT
1 TCAAACTCAAAAAAAT
233098 T
1 T
233099 TCGAGAGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.15, G:0.00, T:0.24
Consensus pattern (16 bp):
TCAAACTCAAAAAAAT
Found at i:234389 original size:21 final size:20
Alignment explanation
Indices: 234365--234420 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
234355 TCACATAATC
234365 ATATTAAGAGTTTAGGGTTTA
1 ATATT-AGAGTTTAGGGTTTA
*
234386 ATATTAGGGTTTAGGGTTTA
1 ATATTAGAGTTTAGGGTTTA
*
234406 AGATTTAGAGTTTAG
1 ATA-TTAGAGTTTAG
234421 TATTTAGGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 16 0.52
21 15 0.48
ACGTcount: A:0.30, C:0.00, G:0.27, T:0.43
Consensus pattern (20 bp):
ATATTAGAGTTTAGGGTTTA
Found at i:234399 original size:7 final size:7
Alignment explanation
Indices: 234389--234459 Score: 65
Period size: 7 Copynumber: 10.4 Consensus size: 7
234379 GGGTTTAATA
234389 TTAGGGT
1 TTAGGGT
234396 TTAGGGT
1 TTAGGGT
* *
234403 TTAAGAT
1 TTAGGGT
*
234410 TTAGAGT
1 TTAGGGT
**
234417 TTAGTAT
1 TTAGGGT
234424 TTAGGGT
1 TTAGGGT
234431 TTA-GGT
1 TTAGGGT
234437 TTA-GGT
1 TTAGGGT
*
234443 TTAAGGT
1 TTAGGGT
*
234450 TTGGGGT
1 TTAGGGT
234457 TTA
1 TTA
234460 ATCTAACATG
Statistics
Matches: 51, Mismatches: 12, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
6 12 0.24
7 39 0.76
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.46
Consensus pattern (7 bp):
TTAGGGT
Found at i:234399 original size:20 final size:21
Alignment explanation
Indices: 234371--234447 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 21
234361 AATCATATTA
*
234371 AGAGTTTAGGGTTTAATA-TT
1 AGAGTTTAGGGTTTAAGATTT
*
234391 AGGGTTTAGGGTTTAAGATTT
1 AGAGTTTAGGGTTTAAGATTT
** * *
234412 AGAGTTTAGTATTTAGGGTTT
1 AGAGTTTAGGGTTTAAGATTT
234433 AG-GTTTA-GGTTTAAG
1 AGAGTTTAGGGTTTAAG
234448 GTTTGGGGTT
Statistics
Matches: 46, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
19 5 0.11
20 21 0.46
21 20 0.43
ACGTcount: A:0.26, C:0.00, G:0.30, T:0.44
Consensus pattern (21 bp):
AGAGTTTAGGGTTTAAGATTT
Found at i:234563 original size:14 final size:14
Alignment explanation
Indices: 234532--234621 Score: 67
Period size: 14 Copynumber: 6.5 Consensus size: 14
234522 AGTTTAATGC
* * *
234532 TTAGGGATTAGTGC
1 TTAGGGTTTAGAGT
*
234546 TTAGGGTTTAGGGT
1 TTAGGGTTTAGAGT
*
234560 TTAGGGTTT-GATAT
1 TTAGGGTTTAGA-GT
*
234574 TTAGGGTTTATAGT
1 TTAGGGTTTAGAGT
*** *
234588 TTATAATTTATAGT
1 TTAGGGTTTAGAGT
234602 TTAGGGTTTAG-GT
1 TTAGGGTTTAGAGT
234615 TTAGGGT
1 TTAGGGT
234622 GTAATCTAAC
Statistics
Matches: 60, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
13 10 0.17
14 49 0.82
15 1 0.02
ACGTcount: A:0.21, C:0.01, G:0.31, T:0.47
Consensus pattern (14 bp):
TTAGGGTTTAGAGT
Found at i:234576 original size:21 final size:21
Alignment explanation
Indices: 234552--234611 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
234542 GTGCTTAGGG
234552 TTTAGGGTTTAGGGTTTGAT-A
1 TTTAGGGTTTAGGGTTT-ATAA
**
234573 TTTAGGGTTTATAGTTTATAA
1 TTTAGGGTTTAGGGTTTATAA
**
234594 TTTATAGTTTAGGGTTTA
1 TTTAGGGTTTAGGGTTTA
234612 GGTTTAGGGT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 2 0.06
21 30 0.94
ACGTcount: A:0.23, C:0.00, G:0.25, T:0.52
Consensus pattern (21 bp):
TTTAGGGTTTAGGGTTTATAA
Found at i:234577 original size:28 final size:27
Alignment explanation
Indices: 234546--234621 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 27
234536 GGATTAGTGC
234546 TTAGGGTTTAGGGTTTAGGGTTTGATA-T
1 TTAGGGTTTA-GGTTTAGGGTTT-ATAGT
* ***
234574 TTAGGGTTTATAGTTTATAATTTATAGT
1 TTAGGGTTTA-GGTTTAGGGTTTATAGT
234602 TTAGGGTTTAGGTTTAGGGT
1 TTAGGGTTTAGGTTTAGGGT
234622 GTAATCTAAC
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
27 9 0.24
28 29 0.76
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.49
Consensus pattern (27 bp):
TTAGGGTTTAGGTTTAGGGTTTATAGT
Found at i:238369 original size:42 final size:42
Alignment explanation
Indices: 238308--238416 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 42
238298 GATGATGCCA
* * *
238308 CAGGGGTACATGCCCAGCCCTCCAGTTCAGATGCCATCTCCT
1 CAGGGGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCCG
* * * *
238350 CAGGGGTATATGTCAAGCCCACCAGTTTATATGCCATCTCCG
1 CAGGGGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCCG
* * * *
238392 CAGGGTTACATTCCTAGCCCGCCAG
1 CAGGGGTACATGCCAAGCCCACCAG
238417 GTTACATGCC
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.21, C:0.34, G:0.22, T:0.23
Consensus pattern (42 bp):
CAGGGGTACATGCCAAGCCCACCAGTTCAGATGCCATCTCCG
Found at i:238419 original size:21 final size:21
Alignment explanation
Indices: 238395--238434 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
238385 ATCTCCGCAG
*
238395 GGTTACATTCCTAGCCCGCCA
1 GGTTACATGCCTAGCCCGCCA
238416 GGTTACATGCCTAGCCCGC
1 GGTTACATGCCTAGCCCGC
238435 ATGGTTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.38, G:0.23, T:0.23
Consensus pattern (21 bp):
GGTTACATGCCTAGCCCGCCA
Found at i:238440 original size:21 final size:20
Alignment explanation
Indices: 238389--238440 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 20
238379 TATGCCATCT
*
238389 CCGCAGGGTTACATTCCTAGC
1 CCGCA-GGTTACATGCCTAGC
238410 CCGCCAGGTTACATGCCTAGC
1 CCG-CAGGTTACATGCCTAGC
238431 CCGCATGGTT
1 CCGCA-GGTT
238441 TTATGAAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.17, C:0.35, G:0.25, T:0.23
Consensus pattern (20 bp):
CCGCAGGTTACATGCCTAGC
Found at i:238997 original size:34 final size:34
Alignment explanation
Indices: 238958--239030 Score: 128
Period size: 34 Copynumber: 2.1 Consensus size: 34
238948 TTAAATGTTT
238958 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
* *
238992 TTAAAATACAAATTATAGTATTCGAAATTTAACA
1 TTAAAATACAAATTATAGTATTCAAAATTTAAAA
239026 TTAAA
1 TTAAA
239031 TTCAACTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (34 bp):
TTAAAATACAAATTATAGTATTCAAAATTTAAAA
Found at i:239255 original size:23 final size:23
Alignment explanation
Indices: 239242--239341 Score: 70
Period size: 23 Copynumber: 4.6 Consensus size: 23
239232 TCACTTCACA
*
239242 TTTATTCAATTTATCCATAACAT
1 TTTATCCAATTTATCCATAACAT
*
239265 TTTATCCAATTTATTC--AA-A-
1 TTTATCCAATTTATCCATAACAT
* * * * *
239284 --TAACCAACTGATCACTTCACA-
1 TTTATCCAATTTATC-CATAACAT
*
239305 TTTATTCAATTTATCCATAACAT
1 TTTATCCAATTTATCCATAACAT
239328 TTTATCCAATTTAT
1 TTTATCCAATTTAT
239342 TCAAACTTCA
Statistics
Matches: 56, Mismatches: 14, Indels: 14
0.67 0.17 0.17
Matches are distributed among these distances:
17 9 0.16
18 1 0.02
20 2 0.04
21 3 0.05
22 5 0.09
23 36 0.64
ACGTcount: A:0.35, C:0.20, G:0.01, T:0.44
Consensus pattern (23 bp):
TTTATCCAATTTATCCATAACAT
Found at i:239290 original size:63 final size:63
Alignment explanation
Indices: 239222--239346 Score: 241
Period size: 63 Copynumber: 2.0 Consensus size: 63
239212 TCAATGTCAC
*
239222 AACCAACTTATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAAAT
1 AACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAAAT
239285 AACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAAA
1 AACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAAA
239347 CTTCACATAA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.37, C:0.22, G:0.01, T:0.40
Consensus pattern (63 bp):
AACCAACTGATCACTTCACATTTATTCAATTTATCCATAACATTTTATCCAATTTATTCAAAT
Found at i:243124 original size:21 final size:21
Alignment explanation
Indices: 243098--243139 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
243088 AATAATTAAT
*
243098 ATTATTTATTATAAAAAATTA
1 ATTATTAATTATAAAAAATTA
* *
243119 ATTATTAATTTTAAAATATTA
1 ATTATTAATTATAAAAAATTA
243140 TAATAATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTATTAATTATAAAAAATTA
Found at i:245673 original size:5 final size:5
Alignment explanation
Indices: 245638--245662 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
245628 GTTCCTTTTG
245638 TCTTT TCTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT
245663 ATGTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TCTTT
Found at i:247391 original size:147 final size:147
Alignment explanation
Indices: 247044--247556 Score: 476
Period size: 147 Copynumber: 3.5 Consensus size: 147
247034 CCTCCTCCCC
* * * * * * * * *
247044 CTCCTCCGTATGTTTACAAATCACCTCCTCCCCCTCCATACGTCTACAAGTCTCCTCCTCCACCT
1 CTCCTCCTTATGTATACAAATCACCACCTCCCCCTCCATACATGTATAAGTCACCACCACCACCT
** * *** * *
247109 CTGTATGAGTACTAGTCACCTCCTCCTCCTCCTTATGTTTACGAA-TCACCTCCTCCCCTCCATA
66 CCATACGTCAACAAGTCACCTCCTCCTCCTCCATATGTTTAC-AAGTCACCTCCT--CCTCCATA
*
247173 TGAGTACAAGTCACCTCC-T
128 TGTGTACAAGTCACCTCCAT
* * * * *
247192 CCTCCTCCTTATGTCTACAAATCACCTCCTCCCCCTCCATATGA-GTACAAGTCACCACCACCTC
1 -CTCCTCCTTATGTATACAAATCACCACCTCCCCCTCCATA-CATGTATAAGTCACCACCACCAC
*
247256 CTCCATACGTCTACAAGTCACCTCCTCCTCCTCCATATGTTTACAAGTCACCTCCTCCTCCATAT
64 CTCCATACGTCAACAAGTCACCTCCTCCTCCTCCATATGTTTACAAGTCACCTCCTCCTCCATAT
*
247321 GTCTACAAGTCACCTCCAT
129 GTGTACAAGTCACCTCCAT
* * ** * * * *
247340 CTCCTCCATATGTTTATGAGTCACCACCTCCCCCTCCATACATGTATAAGTCTCCTCCTCCACCT
1 CTCCTCCTTATGTATACAAATCACCACCTCCCCCTCCATACATGTATAAGTCACCACCACCACCT
* * * * * ** * * *
247405 CCATATGTGAACAAATCACCTCCTCCCCCTCCATACGAGTATAAGTCACCACCACCTCCATATGT
66 CCATACGTCAACAAGTCACCTCCTCCTCCTCCATATGTTTACAAGTCACCTCCTCCTCCATATGT
* * *
247470 GTACAAATCTCCTCCAC
131 GTACAAGTCACCTCCAT
* * * * * *
247487 CACCTTCTTATGAATACAAATCACCACCTCCTCCGT-CATACATGTATAAGTCGCCGCCACCACC
1 CTCCTCCTTATGTATACAAATCACCACCTCC-CCCTCCATACATGTATAAGTCACCACCACCACC
247551 TCCATA
65 TCCATA
247557 TGTTTAGACG
Statistics
Matches: 302, Mismatches: 57, Indels: 12
0.81 0.15 0.03
Matches are distributed among these distances:
146 1 0.00
147 196 0.65
148 6 0.02
149 99 0.33
ACGTcount: A:0.23, C:0.41, G:0.08, T:0.28
Consensus pattern (147 bp):
CTCCTCCTTATGTATACAAATCACCACCTCCCCCTCCATACATGTATAAGTCACCACCACCACCT
CCATACGTCAACAAGTCACCTCCTCCTCCTCCATATGTTTACAAGTCACCTCCTCCTCCATATGT
GTACAAGTCACCTCCAT
Found at i:247466 original size:57 final size:59
Alignment explanation
Indices: 247360--247484 Score: 166
Period size: 57 Copynumber: 2.1 Consensus size: 59
247350 TGTTTATGAG
* * *
247360 TCACCACCTCCCCCTCCATACATGTATAAGTCTCCTCCTCCACCTCCATATGTGAACAAA
1 TCACCTCCTCCCCCTCCATACATGTATAAG-CTCCACCACCACCTCCATATGTGAACAAA
*
247420 TCACCTCCTCCCCCTCCATACGA-GTATAAG-T-CACCACCACCTCCATATGTGTACAAA
1 TCACCTCCTCCCCCTCCATAC-ATGTATAAGCTCCACCACCACCTCCATATGTGAACAAA
*
247477 TCTCCTCC
1 TCACCTCC
247485 ACCACCTTCT
Statistics
Matches: 59, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
57 30 0.51
58 1 0.02
60 27 0.46
61 1 0.02
ACGTcount: A:0.26, C:0.42, G:0.07, T:0.25
Consensus pattern (59 bp):
TCACCTCCTCCCCCTCCATACATGTATAAGCTCCACCACCACCTCCATATGTGAACAAA
Found at i:247486 original size:27 final size:27
Alignment explanation
Indices: 247394--247487 Score: 89
Period size: 27 Copynumber: 3.4 Consensus size: 27
247384 TATAAGTCTC
*
247394 CTCCTCCACCTCCATATGTGAACAAAT
1 CTCCTCCACCTCCATATGTGTACAAAT
* * * * *
247421 CACCTCCTCCCCCTCCATACGAGTATAAGT
1 ---CTCCTCCACCTCCATATGTGTACAAAT
* *
247451 CACCACCACCTCCATATGTGTACAAAT
1 CTCCTCCACCTCCATATGTGTACAAAT
247478 CTCCTCCACC
1 CTCCTCCACC
247488 ACCTTCTTAT
Statistics
Matches: 49, Mismatches: 15, Indels: 3
0.73 0.22 0.04
Matches are distributed among these distances:
27 28 0.57
30 21 0.43
ACGTcount: A:0.27, C:0.43, G:0.07, T:0.23
Consensus pattern (27 bp):
CTCCTCCACCTCCATATGTGTACAAAT
Found at i:247489 original size:30 final size:30
Alignment explanation
Indices: 247012--247520 Score: 397
Period size: 30 Copynumber: 17.1 Consensus size: 30
247002 TTTGACGATT
* * *
247012 TCCTCCTTATGTTTACAAATCACCTCCTCCCCC
1 TCCTCCATATGTGTACAAGTCACCTCCT---CC
* * *
247045 TCCTCCGTATGTTTACAAATCACCTCCTCC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
* * * *
247075 CCCTCCATACGTCTACAAGTCTCCTCCTCC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
* ** * *
247105 ACCTCTGTATGAGTACTAGTCACCTCCTCC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
* *
247135 TCCTCCTTATGTTTACGAA-TCACCTCCTCC
1 TCCTCCATATGTGTAC-AAGTCACCTCCTCC
*
247165 -CCTCCATATGAGTACAAGTCACCTCCTCC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
* * *
247194 TCCTCCTTATGTCTACAAATCACCTCCTCC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
* * * *
247224 CCCTCCATATGAGTACAAGTCACCACCACC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
* *
247254 TCCTCCATACGTCTACAAGTCACCTCCTCC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
*
247284 TCCTCCATATGTTTACAAGTCA---CCTCC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
*
247311 TCCTCCATATGTCTACAAGTCACCTCCAT-C
1 TCCTCCATATGTGTACAAGTCACCTCC-TCC
* ** *
247341 TCCTCCATATGTTTATGAGTCACCACCTCC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
* ** * *
247371 CCCTCCATACATGTATAAGTCTCCTCCTCC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
* * *
247401 ACCTCCATATGTGAACAAATCACCTCCTCC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
* * * * *
247431 CCCTCCATACGAGTATAAGTCA---CCACC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
* * * *
247458 ACCTCCATATGTGTACAAATCTCCTCCACC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
* * * ** * *
247488 ACCTTCTTATGAATACAAATCACCACCTCC
1 TCCTCCATATGTGTACAAGTCACCTCCTCC
247518 TCC
1 TCC
247521 GTCATACATG
Statistics
Matches: 382, Mismatches: 83, Indels: 25
0.78 0.17 0.05
Matches are distributed among these distances:
27 46 0.12
28 2 0.01
29 24 0.06
30 281 0.74
31 2 0.01
33 27 0.07
ACGTcount: A:0.23, C:0.41, G:0.07, T:0.28
Consensus pattern (30 bp):
TCCTCCATATGTGTACAAGTCACCTCCTCC
Found at i:247511 original size:57 final size:57
Alignment explanation
Indices: 247399--247520 Score: 145
Period size: 57 Copynumber: 2.1 Consensus size: 57
247389 GTCTCCTCCT
* * * * *
247399 CCACCTCCATATGTGAACAAATCACCTCCTCCCCCTCCATACGAGTATAAGTCACCA
1 CCACCTCCATATGTGAACAAATCACCTCCACCACCTCCATACGAATACAAATCACCA
* * * * *
247456 CCACCTCCATATGTGTACAAATCTCCTCCACCACCTTCTTATGAATACAAATCACCA
1 CCACCTCCATATGTGAACAAATCACCTCCACCACCTCCATACGAATACAAATCACCA
*
247513 CCTCCTCC
1 CCACCTCC
247521 GTCATACATG
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
57 54 1.00
ACGTcount: A:0.29, C:0.41, G:0.07, T:0.24
Consensus pattern (57 bp):
CCACCTCCATATGTGAACAAATCACCTCCACCACCTCCATACGAATACAAATCACCA
Found at i:250566 original size:21 final size:21
Alignment explanation
Indices: 250542--250597 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
250532 GTAAATATAG
250542 GGAGGAGGAGGTGAGTGAACT
1 GGAGGAGGAGGTGAGTGAACT
* * * *
250563 GGAGGTGGTGGGGAGTGGACT
1 GGAGGAGGAGGTGAGTGAACT
*
250584 GGTGGAGGAGGTGA
1 GGAGGAGGAGGTGA
250598 CTTGTAAATG
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.04, G:0.59, T:0.16
Consensus pattern (21 bp):
GGAGGAGGAGGTGAGTGAACT
Found at i:250567 original size:69 final size:69
Alignment explanation
Indices: 250501--250645 Score: 218
Period size: 69 Copynumber: 2.1 Consensus size: 69
250491 TAGGGAGGAA
* *
250501 GTGGGGAGTGGACTGGAGGTGGTGGAGACTTGTAAATATAGGGAGGAGGAGGTGAGTGAACTGGA
1 GTGGGGAGTGGACTGGAGGAGGAGGAGACTTGTAAATATAGGGAGGAGGAGGTGAGTGAACTGGA
250566 GGTG
66 GGTG
* * * * * *
250570 GTGGGGAGTGGACTGGTGGAGGAGGTGACTTGTAAATGTATGGAGGAGGCGGTGAGTGGACTGGA
1 GTGGGGAGTGGACTGGAGGAGGAGGAGACTTGTAAATATAGGGAGGAGGAGGTGAGTGAACTGGA
250635 GGTG
66 GGTG
250639 GTGGGGA
1 GTGGGGA
250646 TTTGTAAATG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.22, C:0.05, G:0.52, T:0.21
Consensus pattern (69 bp):
GTGGGGAGTGGACTGGAGGAGGAGGAGACTTGTAAATATAGGGAGGAGGAGGTGAGTGAACTGGA
GGTG
Found at i:250573 original size:48 final size:48
Alignment explanation
Indices: 250206--250570 Score: 487
Period size: 48 Copynumber: 7.6 Consensus size: 48
250196 GTAGGCATAA
* * * *
250206 GGAGGAGGTGGGGAGTGTACCGGTGGTGGAGGAGATTTGTAAACATAG
1 GGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTAAATATAG
* * *
250254 GGAGGAGGCGGGGAGTGGACTGGTGGTGGAGGAGATTTGTAAATGTAG
1 GGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTAAATATAG
* * * * *
250302 GGAGGAGGTGGTGAGTGCACTGGAGGTGGAGGAGACTTGTAAACATAA
1 GGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTAAATATAG
* * *
250350 GGAGGAGGCGGGGAGTGAACTGGCGGTGGAGGAGACTTGTAAATATAG
1 GGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTAAATATAG
* * *
250398 GGAGGTGATGGGGAGTGGACTGGTGGTGGAGGAGACTTGTAAACATAG
1 GGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTAAATATAG
* *
250446 GGAGGAGGTGGGGAGTGGACTGGTGGTGGTGGAGACTTGTAAATGTAG
1 GGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTAAATATAG
* * *
250494 GGAGGAAGTGGGGAGTGGACTGGAGGTGGTGGAGACTTGTAAATATAG
1 GGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTAAATATAG
* * * *
250542 GGAGGAGGAGGTGAGTGAACTGGAGGTGG
1 GGAGGAGGTGGGGAGTGGACTGGTGGTGG
250571 TGGGGAGTGG
Statistics
Matches: 280, Mismatches: 37, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 280 1.00
ACGTcount: A:0.25, C:0.06, G:0.49, T:0.20
Consensus pattern (48 bp):
GGAGGAGGTGGGGAGTGGACTGGTGGTGGAGGAGACTTGTAAATATAG
Found at i:250577 original size:165 final size:165
Alignment explanation
Indices: 250398--250738 Score: 486
Period size: 165 Copynumber: 2.1 Consensus size: 165
250388 GTAAATATAG
* * *
250398 GGAGGTGATGGGGAGTGGACTGGTGGTGGAGGAGACTTGTAAACATAGGGAGGAGGTGGGGAGTG
1 GGAGGTGGTGGGGAGTGGACTGGTGGAGGAGGAGACTTGTAAACATAGGGAGGAGGCGGGGAGTG
* * *
250463 GACTGGTGGTGGTGGAGACTTGTAAATGT-AGGGAGGAAGTGGGGAGTGGACTGGAGGTGGTGGA
66 GACTGGAGGTGGTGGAGACTTGTAAATGTAAGGG-GGAAGTGGAGAGTGGACTGGAGGTGGAGGA
* * *
250527 GACTTGTAAATATAGGGAGGAGGAGGTGAGTGAACT
130 GACTTATAAATATAAGGAGGAGGAGGGGAGTGAACT
* ** * *
250563 GGAGGTGGTGGGGAGTGGACTGGTGGAGGAGGTGACTTGTAAATGTATGGAGGAGGCGGTGAGTG
1 GGAGGTGGTGGGGAGTGGACTGGTGGAGGAGGAGACTTGTAAACATAGGGAGGAGGCGGGGAGTG
* * *
250628 GACTGGAGGTGGTGGGGATTTGTAAATGTAAGGGGGAGGTGGAGAGTGGACTGGAGGTGGAGGAG
66 GACTGGAGGTGGTGGAGACTTGTAAATGTAAGGGGGAAGTGGAGAGTGGACTGGAGGTGGAGGAG
* * *
250693 ACTTATAGATATAAGGAGGAGGTGGGGAGTGGACT
131 ACTTATAAATATAAGGAGGAGGAGGGGAGTGAACT
250728 GGAGGTGGTGG
1 GGAGGTGGTGG
250739 AGACTTATAG
Statistics
Matches: 155, Mismatches: 20, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
165 151 0.97
166 4 0.03
ACGTcount: A:0.24, C:0.04, G:0.51, T:0.21
Consensus pattern (165 bp):
GGAGGTGGTGGGGAGTGGACTGGTGGAGGAGGAGACTTGTAAACATAGGGAGGAGGCGGGGAGTG
GACTGGAGGTGGTGGAGACTTGTAAATGTAAGGGGGAAGTGGAGAGTGGACTGGAGGTGGAGGAG
ACTTATAAATATAAGGAGGAGGAGGGGAGTGAACT
Found at i:250614 original size:48 final size:48
Alignment explanation
Indices: 250563--250869 Score: 227
Period size: 48 Copynumber: 6.3 Consensus size: 48
250553 TGAGTGAACT
* * * * * * * *
250563 GGAGGTGGTGGGGAGTGGACTGGTGGAGGAGGTGACTTGTAAATGTAT
1 GGAGGAGGTGGAGAGTGGACTGGAGGTGGAGGAGACTTATAAATATAA
* * * * * * *
250611 GGAGGAGGCGGTGAGTGGACTGGAGGTGGTGGGGATTTGTAAATGTAA
1 GGAGGAGGTGGAGAGTGGACTGGAGGTGGAGGAGACTTATAAATATAA
* *
250659 GGGGGAGGTGGAGAGTGGACTGGAGGTGGAGGAGACTTATAGATATAA
1 GGAGGAGGTGGAGAGTGGACTGGAGGTGGAGGAGACTTATAAATATAA
* * * * *
250707 GGAGGAGGTGGGGAGTGGACTGGAGGTGGTGGAGACTTATAGACATAG
1 GGAGGAGGTGGAGAGTGGACTGGAGGTGGAGGAGACTTATAAATATAA
* * * * * * * * *
250755 GGAGGTGGTGGAGAATGGACTGGTGGTGGTGGAGATTTGTAGACATAC
1 GGAGGAGGTGGAGAGTGGACTGGAGGTGGAGGAGACTTATAAATATAA
* * * * * * * *
250803 GGTGGAGGAGGAGAGTGAACCGGGGGTGGAGGAGATTTGTAAATGTAA
1 GGAGGAGGTGGAGAGTGGACTGGAGGTGGAGGAGACTTATAAATATAA
*
250851 TGTGGAGGAGGTGGTGAGT
1 ---GGAGGAGGTGGAGAGT
250870 ATTCGGGCGG
Statistics
Matches: 211, Mismatches: 45, Indels: 3
0.81 0.17 0.01
Matches are distributed among these distances:
48 198 0.94
51 13 0.06
ACGTcount: A:0.24, C:0.05, G:0.49, T:0.22
Consensus pattern (48 bp):
GGAGGAGGTGGAGAGTGGACTGGAGGTGGAGGAGACTTATAAATATAA
Found at i:250666 original size:117 final size:117
Alignment explanation
Indices: 250446--250687 Score: 342
Period size: 117 Copynumber: 2.1 Consensus size: 117
250436 GTAAACATAG
* * * *
250446 GGAGGAGGTGGGGAGTGGACTGGTGGTGGTGGAGACTTGTAAATGTAGGGAGGAAGTGGGGAGTG
1 GGAGGTGGTGGGGAGTGGACTGGTGGAGGAGGAGACTTGTAAATGTAGGGAGGAAGCGGGGAGTG
*
250511 GACTGGAGGTGGTGGAGACTTGTAAATATAGGGAGGAGGAGGTGAGTGAACT
66 GACTGGAGGTGGTGGAGACTTGTAAATATAGGGAGGAGGAGGAGAGTGAACT
* * * *
250563 GGAGGTGGTGGGGAGTGGACTGGTGGAGGAGGTGACTTGTAAATGTATGGAGGAGGCGGTGAGTG
1 GGAGGTGGTGGGGAGTGGACTGGTGGAGGAGGAGACTTGTAAATGTAGGGAGGAAGCGGGGAGTG
* * * * *
250628 GACTGGAGGTGGTGGGGATTTGTAAATGTAAGGG-GGAGGTGGAGAGTGGACT
66 GACTGGAGGTGGTGGAGACTTGTAAATAT-AGGGAGGAGGAGGAGAGTGAACT
250680 GGAGGTGG
1 GGAGGTGG
250688 AGGAGACTTA
Statistics
Matches: 110, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
117 106 0.96
118 4 0.04
ACGTcount: A:0.23, C:0.04, G:0.52, T:0.21
Consensus pattern (117 bp):
GGAGGTGGTGGGGAGTGGACTGGTGGAGGAGGAGACTTGTAAATGTAGGGAGGAAGCGGGGAGTG
GACTGGAGGTGGTGGAGACTTGTAAATATAGGGAGGAGGAGGAGAGTGAACT
Found at i:250711 original size:144 final size:144
Alignment explanation
Indices: 250563--250837 Score: 325
Period size: 144 Copynumber: 1.9 Consensus size: 144
250553 TGAGTGAACT
* * * * ** * * *
250563 GGAGGTGGTGGGGAGTGGACTGGTGGAGGAGGTGACTTGTAAATGTATGGAGGAGGCGGTGAGTG
1 GGAGGAGGTGGGGAGTGGACTGGAGGAGGAGGAGACTTATAAACATAGGGAGGAGGCGGAGAATG
* ** * * *
250628 GACTGGAGGTGGTGGGGATTTGTAAATGTAAGGGGGAGGTGGAGAGTGGACTGGAGGTGGAGGAG
66 GACTGGAGGTGGTGGAGATTTGTAAACATAAGGGGGAGGAGGAGAGTGAACCGGAGGTGGAGGAG
250693 ACTTATAGATATAA
131 ACTTATAGATATAA
* * * * *
250707 GGAGGAGGTGGGGAGTGGACTGGAGGTGGTGGAGACTTATAGACATAGGGAGGTGGTGGAGAATG
1 GGAGGAGGTGGGGAGTGGACTGGAGGAGGAGGAGACTTATAAACATAGGGAGGAGGCGGAGAATG
* * * * *
250772 GACTGGTGGTGGTGGAGATTTGTAGACATACGGTGGAGGAGGAGAGTGAACCGGGGGTGGAGGAG
66 GACTGGAGGTGGTGGAGATTTGTAAACATAAGGGGGAGGAGGAGAGTGAACCGGAGGTGGAGGAG
250837 A
131 A
250838 TTTGTAAATG
Statistics
Matches: 106, Mismatches: 25, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
144 106 1.00
ACGTcount: A:0.24, C:0.05, G:0.50, T:0.20
Consensus pattern (144 bp):
GGAGGAGGTGGGGAGTGGACTGGAGGAGGAGGAGACTTATAAACATAGGGAGGAGGCGGAGAATG
GACTGGAGGTGGTGGAGATTTGTAAACATAAGGGGGAGGAGGAGAGTGAACCGGAGGTGGAGGAG
ACTTATAGATATAA
Found at i:250810 original size:96 final size:97
Alignment explanation
Indices: 250563--250837 Score: 275
Period size: 96 Copynumber: 2.9 Consensus size: 97
250553 TGAGTGAACT
* * * * * * * *
250563 GGAGGTGGTGGGGAGTGGACTGGTGGAGGAGGTGACTTGTAAATGTATGGAGGAGGCGGTGAGTG
1 GGAGGTGGTGGAGAGTGGACTGGTGGTGGAGGAGACTTGTAGATATAAGGAGGAGGAGGAGAGTG
* * * **
250628 GACTGGAGGTGGTGGGGATTTGTAAATGTAAG
66 GACTGGAGGTGGTGGAGACTTATAAACATAAG
* * * * *
250660 GG-GGAGGTGGAGAGTGGACTGGAGGTGGAGGAGACTTATAGATATAAGGAGGAGGTGGGGAGTG
1 GGAGGTGGTGGAGAGTGGACTGGTGGTGGAGGAGACTTGTAGATATAAGGAGGAGGAGGAGAGTG
*
250724 GACTGGAGGTGGTGGAGACTTATAGACAT-AG
66 GACTGGAGGTGGTGGAGACTTATAAACATAAG
* * * * * *
250755 GGAGGTGGTGGAGAATGGACTGGTGGTGGTGGAGATTTGTAGACATACGGTGGAGGAGGAGAGTG
1 GGAGGTGGTGGAGAGTGGACTGGTGGTGGAGGAGACTTGTAGATATAAGGAGGAGGAGGAGAGTG
* * * *
250820 AACCGGGGGTGGAGGAGA
66 GACTGGAGGTGGTGGAGA
250838 TTTGTAAATG
Statistics
Matches: 145, Mismatches: 32, Indels: 3
0.81 0.18 0.02
Matches are distributed among these distances:
95 4 0.03
96 139 0.96
97 2 0.01
ACGTcount: A:0.24, C:0.05, G:0.50, T:0.20
Consensus pattern (97 bp):
GGAGGTGGTGGAGAGTGGACTGGTGGTGGAGGAGACTTGTAGATATAAGGAGGAGGAGGAGAGTG
GACTGGAGGTGGTGGAGACTTATAAACATAAG
Found at i:253463 original size:29 final size:29
Alignment explanation
Indices: 253443--253532 Score: 126
Period size: 29 Copynumber: 3.1 Consensus size: 29
253433 ACAAAACTAA
* *
253443 CACCCTTTTAAAAATGTTTACTAAAATAG
1 CACCCTTTTAAAAATATTTACGAAAATAG
***
253472 CACCCTTTTAAAAATATTTTTAAAAATAG
1 CACCCTTTTAAAAATATTTACGAAAATAG
*
253501 CACCATTTTAAAAATATTTACGAAAATAG
1 CACCCTTTTAAAAATATTTACGAAAATAG
253530 CAC
1 CAC
253533 TCGGTTCGGG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (29 bp):
CACCCTTTTAAAAATATTTACGAAAATAG
Found at i:253496 original size:28 final size:30
Alignment explanation
Indices: 253399--253532 Score: 125
Period size: 29 Copynumber: 4.6 Consensus size: 30
253389 ACGGTCAACT
* **
253399 TTTACAAAAAATAGCACCC-TAAAAGAAATTA
1 TTTACTAAAAATAGCACCCTTTTAA-AAA-TA
* * * *
253430 ATTAC-AAAACTAACACCCTTTTAAAAATG
1 TTTACTAAAAATAGCACCCTTTTAAAAATA
253459 TTTACT-AAAATAGCACCCTTTTAAAAATA
1 TTTACTAAAAATAGCACCCTTTTAAAAATA
* *
253488 TTT-TTAAAAATAGCACCATTTTAAAAATA
1 TTTACTAAAAATAGCACCCTTTTAAAAATA
*
253517 TTTAC-GAAAATAGCAC
1 TTTACTAAAAATAGCAC
253533 TCGGTTCGGG
Statistics
Matches: 85, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
28 1 0.01
29 63 0.74
30 14 0.16
31 7 0.08
ACGTcount: A:0.49, C:0.16, G:0.05, T:0.30
Consensus pattern (30 bp):
TTTACTAAAAATAGCACCCTTTTAAAAATA
Found at i:260688 original size:29 final size:29
Alignment explanation
Indices: 260613--260770 Score: 176
Period size: 29 Copynumber: 5.4 Consensus size: 29
260603 ACATTCAACT
* **
260613 TTTACAAAAATAGCACCC-TAAAAGAAATTA
1 TTTACGAAAATAGCACCCTTTTAA-AAA-TA
* *
260643 ATTAC-AAAACTAACACCCTTTTAAAAATA
1 TTTACGAAAA-TAGCACCCTTTTAAAAATA
*
260672 TTTACTAAAATAGCACCCTTTTAAAAATA
1 TTTACGAAAATAGCACCCTTTTAAAAATA
*
260701 TTTACGAAAATATCACCCTTTTAAAAATA
1 TTTACGAAAATAGCACCCTTTTAAAAATA
* * * *
260730 TTTACGAAAATAGTATCATTTTAAAATTA
1 TTTACGAAAATAGCACCCTTTTAAAAATA
260759 TTTACGAAAATA
1 TTTACGAAAATA
260771 ACACTCGGGT
Statistics
Matches: 112, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
29 91 0.81
30 18 0.16
31 3 0.03
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.32
Consensus pattern (29 bp):
TTTACGAAAATAGCACCCTTTTAAAAATA
Found at i:262637 original size:21 final size:20
Alignment explanation
Indices: 262551--262708 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
262541 AAATGACCAA
**
262551 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
262570 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
262590 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
262610 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
262631 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
262652 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
262672 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
262693 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
262709 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:262701 original size:20 final size:20
Alignment explanation
Indices: 262676--262909 Score: 74
Period size: 20 Copynumber: 11.7 Consensus size: 20
262666 GATTTTCCAG
* *
262676 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
262696 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
262716 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * * *
262736 AACCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
262756 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
262776 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
262796 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * * *
262816 AATCGCAATGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
262836 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
262856 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAACACAT-A
* *
262877 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
262897 AATCGCAACGCGA
1 AATCGCAACGCGA
262910 TTTTTTAAAG
Statistics
Matches: 189, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
19 3 0.02
20 168 0.89
21 17 0.09
22 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:262743 original size:40 final size:40
Alignment explanation
Indices: 262676--262908 Score: 308
Period size: 40 Copynumber: 5.8 Consensus size: 40
262666 GATTTTCCAG
* ** * * *
262676 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATC-CGTA
* *
262716 AATCGCAACGCGTATCCGTAAACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
*
262756 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* *
262796 AATCGCAACGCGTATCCGTAAATCGCAATGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
* *
262836 AATCGCAACGCGTATCCGTAAATCGCAACGAC-AATACGTAA
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGTATCCGT-A
262877 AATCGCAACGCGTATCCGTAAATCGCAACGCG
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG
262909 ATTTTTTAAA
Statistics
Matches: 173, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
40 140 0.81
41 33 0.19
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.19
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTA
Found at i:262759 original size:60 final size:60
Alignment explanation
Indices: 262695--262908 Score: 304
Period size: 60 Copynumber: 3.5 Consensus size: 60
262685 GCGAATATGA
* * * *
262695 AAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTAAACCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATC-CGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCGT
* *
262755 AAATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCGT
* * ** *
262815 AAATCGCAATGTGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGACAATACGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCGT
262875 AAAATCGCAACGCGTATCCGTAAATCGCAACGCG
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCG
262909 ATTTTTTAAA
Statistics
Matches: 138, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
60 105 0.76
61 33 0.24
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGAGTATCCGT
Found at i:263307 original size:14 final size:14
Alignment explanation
Indices: 263288--263344 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
263278 TTTCATTTCG
263288 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
263302 CGTTGCGATTTTCATTCCG
1 CGTTGCGA--TTC--T-CT
*
263321 CGTTGCTATTCTCT
1 CGTTGCGATTCTCT
263335 CGTTGCGATT
1 CGTTGCGATT
263345 TTCAAGTTAG
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 3 0.09
17 3 0.09
18 1 0.03
19 8 0.24
ACGTcount: A:0.09, C:0.26, G:0.21, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:263317 original size:33 final size:33
Alignment explanation
Indices: 263278--263348 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
263268 TTCACTTAGA
*
263278 TTTCATTTCGCGTTGCGATTCTCTCGTTGCGAT
1 TTTCATTCCGCGTTGCGATTCTCTCGTTGCGAT
*
263311 TTTCATTCCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTCCGCGTTGCGATTCTCTCGTTGCGAT
263344 TTTCA
1 TTTCA
263349 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.10, C:0.25, G:0.18, T:0.46
Consensus pattern (33 bp):
TTTCATTCCGCGTTGCGATTCTCTCGTTGCGAT
Found at i:263466 original size:14 final size:14
Alignment explanation
Indices: 263447--263503 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
263437 GAGAAATGAA
263447 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
263461 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
263480 AATCGCAACGAGAG
1 AATCGCAACGAGAG
263494 AATCGCAACG
1 AATCGCAACG
263504 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:263479 original size:33 final size:33
Alignment explanation
Indices: 263439--263519 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
263429 CGCAACGAGA
263439 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
263472 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
263505 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
263520 TTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:263590 original size:21 final size:21
Alignment explanation
Indices: 263564--263628 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
263554 CGCGTTGCGA
*
263564 TTCTCTCGTTGTGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
263585 TTCTCTCGTTGCGATAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
263605 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
263626 TTC
1 TTC
263629 AACCAAAAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 18 0.47
21 20 0.53
ACGTcount: A:0.11, C:0.23, G:0.15, T:0.51
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:263625 original size:20 final size:20
Alignment explanation
Indices: 263520--263626 Score: 104
Period size: 19 Copynumber: 5.7 Consensus size: 20
263510 CAAAATCGCA
*
263520 TTGCGATTTTCATT-TCGCG
1 TTGCGATTTTCATTCTCTCG
*
263539 TTGCGATTTTCATT-TCGCG
1 TTGCGATTTTCATTCTCTCG
263558 TTGCG------ATTCTCTCG
1 TTGCGATTTTCATTCTCTCG
*
263572 TTGTGATTTTCATTTCTCTCG
1 TTGCGATTTTCA-TTCTCTCG
**
263593 TTGCGATAGTCATTCTCTCG
1 TTGCGATTTTCATTCTCTCG
263613 TTGCGATTTTCATT
1 TTGCGATTTTCATT
263627 TCAACCAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
13 3 0.04
14 8 0.11
19 24 0.33
20 21 0.29
21 17 0.23
ACGTcount: A:0.11, C:0.21, G:0.19, T:0.49
Consensus pattern (20 bp):
TTGCGATTTTCATTCTCTCG
Found at i:265594 original size:19 final size:19
Alignment explanation
Indices: 265554--265701 Score: 154
Period size: 19 Copynumber: 8.3 Consensus size: 19
265544 TAGTTTACTT
* *
265554 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
265574 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
265593 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
**
265612 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
265631 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
265645 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
265664 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAACCAAAA
265678 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
265697 TCGCA
1 TCGCA
265702 TTGCAATTTT
Statistics
Matches: 111, Mismatches: 7, Indels: 21
0.80 0.05 0.15
Matches are distributed among these distances:
14 20 0.18
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 66 0.59
20 13 0.12
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:265648 original size:14 final size:14
Alignment explanation
Indices: 265627--265685 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
265617 ACGCGAAATG
265627 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
265641 AGAATCGCAACGCGAAACC
1 AAAATCGCAA--CG--A-C
265660 AAAATCGCAACGAC
1 AAAATCGCAACGAC
265674 AAAATCGCAACG
1 AAAATCGCAACG
265686 CGAAACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.47, C:0.29, G:0.17, T:0.07
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:265652 original size:33 final size:33
Alignment explanation
Indices: 265572--265701 Score: 179
Period size: 33 Copynumber: 3.8 Consensus size: 33
265562 CGAAACTTAA
*
265572 AATCGCAACGCGAAACCAAAATCGCAACGCGAAATG
1 AATCGCAACGCGAAACCAAAATCGCAA--CGACA-G
**
265608 AAAATCGCAACGCGAAATGAAAATCGCAACGACAG
1 --AATCGCAACGCGAAACCAAAATCGCAACGACAG
*
265643 AATCGCAACGCGAAACCAAAATCGCAACGACAA
1 AATCGCAACGCGAAACCAAAATCGCAACGACAG
265676 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAACCAAAATCGCA
265702 TTGCAATTTT
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
33 56 0.65
35 1 0.01
36 4 0.05
38 25 0.29
ACGTcount: A:0.47, C:0.28, G:0.18, T:0.08
Consensus pattern (33 bp):
AATCGCAACGCGAAACCAAAATCGCAACGACAG
Found at i:265699 original size:52 final size:51
Alignment explanation
Indices: 265570--265701 Score: 158
Period size: 52 Copynumber: 2.5 Consensus size: 51
265560 CACGAAACTT
**
265570 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
* * ** * *
265621 GAAAT-GAAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 AAAATCGCAACGCGAAAC--CAAAATCGCAACGCGAAACCAAAATCGCAACG-C
265674 AAAATCGCAACGCGAAACCAAAATCGCA
1 AAAATCGCAACGCGAAACCAAAATCGCA
265702 TTGCAATTTT
Statistics
Matches: 63, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
50 8 0.13
51 4 0.06
52 38 0.60
53 5 0.08
54 8 0.13
ACGTcount: A:0.48, C:0.27, G:0.17, T:0.08
Consensus pattern (51 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
Found at i:265719 original size:19 final size:19
Alignment explanation
Indices: 265697--265836 Score: 146
Period size: 19 Copynumber: 7.6 Consensus size: 19
265687 GAAACCAAAA
* *
265697 TCGCATTGCAATTTTCATT
1 TCGCGTTGCGATTTTCATT
265716 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
265735 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
265751 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
265768 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
265787 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
265806 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
265826 TCGTGTTGCGA
1 TCGCGTTGCGA
265837 AAGTAAACTA
Statistics
Matches: 99, Mismatches: 16, Indels: 11
0.79 0.13 0.09
Matches are distributed among these distances:
14 7 0.07
16 5 0.05
17 5 0.05
19 70 0.71
20 12 0.12
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:265761 original size:33 final size:35
Alignment explanation
Indices: 265719--265818 Score: 132
Period size: 33 Copynumber: 2.8 Consensus size: 35
265709 TTTCATTTCG
*
265719 CGTTGCGATTTTCATTTCGCATTGCGATTCT-G-T
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTGGTT
*
265752 CGTTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTGG--T-T
*
265790 CGTTGCGATTCTCATTTCGCGTTGCGATT
1 CGTTGCGATTTTCATTTCGCGTTGCGATT
265819 TTAAGTTTCG
Statistics
Matches: 59, Mismatches: 3, Indels: 5
0.88 0.04 0.07
Matches are distributed among these distances:
33 29 0.49
34 1 0.02
38 29 0.49
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (35 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTGGTT
Found at i:265769 original size:52 final size:52
Alignment explanation
Indices: 265702--265801 Score: 155
Period size: 52 Copynumber: 1.9 Consensus size: 52
265692 CAAAATCGCA
265702 TTGCAATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCAATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGTCG
* ** * *
265754 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCTCGTTGCGATTCT
1 TTGCAATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCT
265802 CATTTCGCGT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 43 1.00
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.48
Consensus pattern (52 bp):
TTGCAATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGTCG
Found at i:269585 original size:24 final size:24
Alignment explanation
Indices: 269551--269597 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
269541 CTGAAACATC
269551 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
269575 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
269598 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:270318 original size:20 final size:20
Alignment explanation
Indices: 270303--270480 Score: 221
Period size: 20 Copynumber: 8.9 Consensus size: 20
270293 GTGATTTATA
270303 GATTCTCGTTGCGATTTACG
1 GATTCTCGTTGCGATTTACG
* *
270323 GATTATCGTTGCGATTTACA
1 GATTCTCGTTGCGATTTACG
270343 GATTCTCGTTGCGATTTACG
1 GATTCTCGTTGCGATTTACG
*
270363 GATTATCGTTGCGATTTACG
1 GATTCTCGTTGCGATTTACG
* *
270383 GATACGCGTTGCGATTTACG
1 GATTCTCGTTGCGATTTACG
* * *
270403 GATACGCATTGCGATTTACG
1 GATTCTCGTTGCGATTTACG
* *
270423 GATACGCGTTGCGATTTACG
1 GATTCTCGTTGCGATTTACG
* * *
270443 GATACACGTTGCGGTTTACG
1 GATTCTCGTTGCGATTTACG
* *
270463 GATACGCGTTGCGATTTA
1 GATTCTCGTTGCGATTTA
270481 TGTGTTCGCG
Statistics
Matches: 144, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 144 1.00
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GATTCTCGTTGCGATTTACG
Found at i:270350 original size:40 final size:39
Alignment explanation
Indices: 270309--270480 Score: 247
Period size: 40 Copynumber: 4.3 Consensus size: 39
270299 TATAGATTCT
* * *
270309 CGTTGCGATTTACGGATTATCGTTGCGATTTACAGATTCT
1 CGTTGCGATTTACGGA-TATCGTTGCGATTTACGGATACG
270349 CGTTGCGATTTACGGATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGA-TATCGTTGCGATTTACGGATACG
270389 CGTTGCGATTTACGGATA-CGCATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATATCG--TTGCGATTTACGGATACG
* *
270429 CGTTGCGATTTACGGATACACGTTGCGGTTTACGGATACG
1 CGTTGCGATTTACGGATA-TCGTTGCGATTTACGGATACG
270469 CGTTGCGATTTA
1 CGTTGCGATTTA
270481 TGTGTTCGCG
Statistics
Matches: 124, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
38 2 0.02
39 2 0.02
40 118 0.95
42 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (39 bp):
CGTTGCGATTTACGGATATCGTTGCGATTTACGGATACG
Found at i:270490 original size:20 final size:20
Alignment explanation
Indices: 270467--270518 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
270457 TTTACGGATA
* *
270467 CGCGTTGCGATTTAT-GTGTT
1 CGCGTTGCGATTT-TCATATT
*
270487 CGCGTTACGATTTTCATATT
1 CGCGTTGCGATTTTCATATT
270507 CGCGTTGCGATT
1 CGCGTTGCGATT
270519 CTGGAAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.42
Consensus pattern (20 bp):
CGCGTTGCGATTTTCATATT
Found at i:270491 original size:60 final size:60
Alignment explanation
Indices: 270303--270499 Score: 245
Period size: 60 Copynumber: 3.3 Consensus size: 60
270293 GTGATTTATA
* * * * *
270303 GATTCTCGTTGCGATTTACGGATTA-TCGTTGCGATTTACAGATTCTCGTTGCGATTTACG
1 GATTCGCGTTGCGATTTACGGA-TACACGTTGCGATTTACGGATACGCGTTGCGATTTACG
** * *
270363 GATTATCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCATTGCGATTTACG
1 GATTCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTACG
* * *
270423 GATACGCGTTGCGATTTACGGATACACGTTGCGGTTTACGGATACGCGTTGCGATTTATG
1 GATTCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTACG
*
270483 TG-TTCGCGTTACGATTT
1 -GATTCGCGTTGCGATTT
270500 TCATATTCGC
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
59 2 0.02
60 117 0.98
61 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.26, T:0.36
Consensus pattern (60 bp):
GATTCGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTACG
Found at i:270949 original size:18 final size:18
Alignment explanation
Indices: 270911--270950 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
270901 GATCAATAAC
**
270911 AATATTAAACCTATCTTT
1 AATATTAAACCTATCAAT
*
270929 AATATTAAGCCTATCAAT
1 AATATTAAACCTATCAAT
270947 AATA
1 AATA
270951 GCCAACCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.38
Consensus pattern (18 bp):
AATATTAAACCTATCAAT
Found at i:274211 original size:23 final size:23
Alignment explanation
Indices: 274167--274211 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
274157 CTGATTGGAT
* *
274167 CTTCTAGAAGCTATTGACTGAGC
1 CTTCTAGAAACTATTAACTGAGC
* *
274190 CTTCTAGAAACTGTTAATTGAG
1 CTTCTAGAAACTATTAACTGAG
274212 TCCCACGTCA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (23 bp):
CTTCTAGAAACTATTAACTGAGC
Found at i:274254 original size:23 final size:23
Alignment explanation
Indices: 274219--274263 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
274209 GAGTCCCACG
274219 TCAGCTACCACGTCATCACCATA
1 TCAGCTACCACGTCATCACCATA
* * *
274242 TCAGCTGCTACGTCATCGCCAT
1 TCAGCTACCACGTCATCACCAT
274264 GTTAGTTGCC
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:0.24, C:0.38, G:0.13, T:0.24
Consensus pattern (23 bp):
TCAGCTACCACGTCATCACCATA
Found at i:274684 original size:15 final size:15
Alignment explanation
Indices: 274666--274718 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
274656 AAGCAAGGCA
274666 AAATCAATTAAGTGT
1 AAATCAATTAAGTGT
* * *
274681 AAATCAATCATG-GC
1 AAATCAATTAAGTGT
274695 ATAATCAATTAAGTGT
1 A-AATCAATTAAGTGT
274711 AAATCAAT
1 AAATCAAT
274719 CATGGCATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
14 2 0.07
15 26 0.87
16 2 0.07
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.30
Consensus pattern (15 bp):
AAATCAATTAAGTGT
Found at i:274701 original size:30 final size:30
Alignment explanation
Indices: 274652--274726 Score: 123
Period size: 30 Copynumber: 2.5 Consensus size: 30
274642 ATTCAAGATC
* * *
274652 AATCAAGCAAGGCAAAATCAATTAAGTGTA
1 AATCAATCATGGCATAATCAATTAAGTGTA
274682 AATCAATCATGGCATAATCAATTAAGTGTA
1 AATCAATCATGGCATAATCAATTAAGTGTA
274712 AATCAATCATGGCAT
1 AATCAATCATGGCAT
274727 TTCAAACATC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 42 1.00
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (30 bp):
AATCAATCATGGCATAATCAATTAAGTGTA
Found at i:286437 original size:21 final size:21
Alignment explanation
Indices: 286373--286454 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
286363 CAGGGTTATG
* *
286373 TTTAGGATTTAAGGTTTA-AGA
1 TTTA-GATTTAAGGTTTAGGGT
*
286394 TTTAAACTTTAAGGTTT-GGGT
1 TTTAGA-TTTAAGGTTTAGGGT
* *
286415 TTTGGATTTATGGTTTAGGGT
1 TTTAGATTTAAGGTTTAGGGT
* *
286436 TTTATATTTAGGGTTTAGG
1 TTTAGATTTAAGGTTTAGG
286455 ATAGAGTTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 10 0.20
21 39 0.80
ACGTcount: A:0.23, C:0.01, G:0.27, T:0.49
Consensus pattern (21 bp):
TTTAGATTTAAGGTTTAGGGT
Found at i:286556 original size:24 final size:23
Alignment explanation
Indices: 286528--286573 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
286518 TATTTATTTA
*
286528 TAAGTTATATATTTTAATTAAATC
1 TAAGTAATATA-TTTAATTAAATC
* *
286552 TAAGTAATTTATTTATTTAAAT
1 TAAGTAATATATTTAATTAAAT
286574 GTAATGACTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (23 bp):
TAAGTAATATATTTAATTAAATC
Found at i:295853 original size:2 final size:2
Alignment explanation
Indices: 295846--295875 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
295836 GACAAGAATG
295846 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
295876 TAATGTGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:298576 original size:30 final size:30
Alignment explanation
Indices: 298540--298605 Score: 132
Period size: 30 Copynumber: 2.2 Consensus size: 30
298530 CCATATGGAT
298540 GATTTCGTCGGTAATCGACGGCTTTAGTTC
1 GATTTCGTCGGTAATCGACGGCTTTAGTTC
298570 GATTTCGTCGGTAATCGACGGCTTTAGTTC
1 GATTTCGTCGGTAATCGACGGCTTTAGTTC
298600 GATTTC
1 GATTTC
298606 TTTGCTATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.38
Consensus pattern (30 bp):
GATTTCGTCGGTAATCGACGGCTTTAGTTC
Found at i:316691 original size:36 final size:36
Alignment explanation
Indices: 316644--316721 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
316634 TTGGAAAACT
316644 AATTTTCAAAACTGTTGATATTGAAGACATAATAAG
1 AATTTTCAAAACTGTTGATATTGAAGACATAATAAG
*
316680 AATTTTCAAAACTGTTGCTATTGAAGACATAATAAG
1 AATTTTCAAAACTGTTGATATTGAAGACATAATAAG
316716 AATTTT
1 AATTTT
316722 TTTAAACTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (36 bp):
AATTTTCAAAACTGTTGATATTGAAGACATAATAAG
Found at i:324960 original size:21 final size:21
Alignment explanation
Indices: 324934--324975 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
324924 TTCCGACGTA
324934 TTTCTTCTCTTTCTTTT-ATCT
1 TTTCTT-TCTTTCTTTTGATCT
*
324955 TTTCTTTTTTTCTTTTGATCT
1 TTTCTTTCTTTCTTTTGATCT
324976 GTTTTCCTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.74
Consensus pattern (21 bp):
TTTCTTTCTTTCTTTTGATCT
Found at i:327273 original size:17 final size:18
Alignment explanation
Indices: 327251--327293 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
327241 TTCAATATTT
*
327251 AAATATTTT-TTATTTTA
1 AAATATTTTATAATTTTA
327268 AAATATTTTATAATTTTA
1 AAATATTTTATAATTTTA
*
327286 AAGTATTT
1 AAATATTT
327294 ACTAAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
AAATATTTTATAATTTTA
Found at i:329308 original size:25 final size:25
Alignment explanation
Indices: 329278--329345 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
329268 AAAATAAGTA
*
329278 TAAATTTGATTT-GAATTTTATAAAT
1 TAAATTTGATTTAAAATTTT-TAAAT
* *
329303 TTAATTCGATTTAAAATTTTTAAAT
1 TAAATTTGATTTAAAATTTTTAAAT
*
329328 TAAATTTGAATTATAAAT
1 TAAATTTGATTTA-AAAT
329346 ATATGACTCG
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
25 25 0.71
26 10 0.29
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (25 bp):
TAAATTTGATTTAAAATTTTTAAAT
Found at i:329566 original size:21 final size:21
Alignment explanation
Indices: 329527--329569 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
329517 TAGATTCTTT
329527 TTATAAAATAATGTAAATAAC
1 TTATAAAATAATGTAAATAAC
*
329548 TTATACAAATAATTTAATATAA
1 TTATA-AAATAATGTAA-ATAA
329570 TTTTCAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 10 0.53
23 4 0.21
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (21 bp):
TTATAAAATAATGTAAATAAC
Found at i:337886 original size:21 final size:22
Alignment explanation
Indices: 337862--337902 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
337852 CTGATTGTTG
337862 TATATGA-TATTATCATGAACA
1 TATATGATTATTATCATGAACA
*
337883 TATATGATTTTTATCATGAA
1 TATATGATTATTATCATGAA
337903 TAATATTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (22 bp):
TATATGATTATTATCATGAACA
Found at i:338295 original size:44 final size:44
Alignment explanation
Indices: 338245--338368 Score: 198
Period size: 44 Copynumber: 2.8 Consensus size: 44
338235 TGTAATCATG
338245 AAAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATA-TGAGT
1 AAAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTG-GT
*
338289 AAAATAAGCTTACAAGCTTATGGAATAATGGTAAGTATATTGGT
1 AAAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGT
338333 AAAATAAGCTTACGAGCTTAT-GAGATAAATGGTAAG
1 AAAATAAGCTTACGAGCTTATGGA-AT-AATGGTAAG
338369 AGATTTTATA
Statistics
Matches: 75, Mismatches: 2, Indels: 5
0.91 0.02 0.06
Matches are distributed among these distances:
43 2 0.03
44 62 0.83
45 11 0.15
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (44 bp):
AAAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGT
Found at i:341548 original size:16 final size:16
Alignment explanation
Indices: 341527--341637 Score: 61
Period size: 16 Copynumber: 6.9 Consensus size: 16
341517 AGAAATTAAA
341527 AATTTAAAATATATTT
1 AATTTAAAATATATTT
*
341543 AATTTATAATCATA-TT
1 AATTTAAAAT-ATATTT
* *
341559 ATTTTAAAATTATAATT
1 AATTTAAAA-TATATTT
**
341576 -ATGAAAAATATATATT
1 AATTTAAAATATAT-TT
*
341592 AATTT-ATATATATTT
1 AATTTAAAATATATTT
**
341607 ATAAATAAAATATTTATTT
1 A-ATTTAAAATA--TATTT
341626 -ATTTAAAA-ATAT
1 AATTTAAAATATAT
341638 CAGAAAATGA
Statistics
Matches: 71, Mismatches: 15, Indels: 20
0.67 0.14 0.19
Matches are distributed among these distances:
14 3 0.04
15 7 0.10
16 38 0.54
17 18 0.25
19 5 0.07
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (16 bp):
AATTTAAAATATATTT
Found at i:341835 original size:120 final size:120
Alignment explanation
Indices: 341592--341828 Score: 286
Period size: 120 Copynumber: 2.0 Consensus size: 120
341582 AATATATATT
* * *
341592 AATTTATATAT-ATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACTTCTAG
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAG
* * * * * *
341655 GTGTCTTAAGACAGCTATTTTCTTCGATATTAAAAAATAAATAACTAATTAAAAC
66 GTATCTTAAAACAGCTACTTTATTCAATATTAAAAAATAAATAAATAATTAAAAC
**
341710 AATTAATATATAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATAGACATCCA
1 AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAT-GACATCCA
* * * * *
341775 GTTATTTTAAAACTGC-CCTTTATT-AATATTGAAAAATAAATAAAT-ATTAAAAC
65 GGTATCTTAAAACAGCTACTTTATTCAATATTAAAAAATAAATAAATAATTAAAAC
341828 A
1 A
341829 GGATTAAAAT
Statistics
Matches: 100, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
118 19 0.19
119 24 0.24
120 40 0.40
121 17 0.17
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (120 bp):
AATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATCCAG
GTATCTTAAAACAGCTACTTTATTCAATATTAAAAAATAAATAAATAATTAAAAC
Found at i:343285 original size:18 final size:18
Alignment explanation
Indices: 343241--343287 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
343231 TAATGTTTGT
343241 AATTAT-TTAAT-AATAA
1 AATTATATTAATAAATAA
* *
343257 TA-TATAATAATAAATAA
1 AATTATATTAATAAATAA
343274 AATTATATTAATAA
1 AATTATATTAATAA
343288 TAATATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 5 0.21
17 6 0.25
18 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTATATTAATAAATAA
Found at i:343299 original size:24 final size:24
Alignment explanation
Indices: 343247--343299 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 24
343237 TTGTAATTAT
*
343247 TTAATAATAATATATAATAATAAA
1 TTAAAAATAATATATAATAATAAA
*
343271 -T-AAAATTATAT-TAATAATAATA
1 TTAAAAATAATATATAATAATAA-A
343293 TTAAAAA
1 TTAAAAA
343300 CAAATGGGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
21 9 0.38
22 9 0.38
23 2 0.08
24 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
TTAAAAATAATATATAATAATAAA
Found at i:344061 original size:113 final size:113
Alignment explanation
Indices: 343936--344501 Score: 819
Period size: 113 Copynumber: 5.0 Consensus size: 113
343926 ATCCATTTTA
*
343936 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
344001 CATTATGAACTTTCTCTGGAAATGATGATCCATCGAGTGATGGATTTG
66 CATTATGAACTTTCTCTGGAAATGATGATCCATCGAGTGATGGATTTG
* *
344049 AGCAAAAGGTTGAACAAGCTCTTTTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * **
344114 CATTATGAACTTTCTCTGGCAATGCTGATCCATCGGGTGATGAATTAA
66 CATTATGAACTTTCTCTGGAAATGATGATCCATCGAGTGATGGATTTG
* * * * *
344162 AGTAAAAGGTTGAACAAGTTCTTCTTATTATAAACTTCTTCTTCCTTATTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * **
344227 CATTATGAACTTTCTCTTGAAAT-ACTGATCCATCAAATGATGAATTAA
66 CATTATGAACTTTCTCTGGAAATGA-TGATCCATCGAGTGATGGATTTG
* * *
344275 AGTAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * * * *
344340 CATTATGAACTTTCTCTTGAAATGTTGATCCATCAAATGATAGATTTG
66 CATTATGAACTTTCTCTGGAAATGATGATCCATCGAGTGATGGATTTG
* *
344388 AGCAAAAGGTTGAACAAGCTTTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCT
1 AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
* * *
344453 CATTATGAACTTTCTCTGGAAAAGCTGATCCATCGAGTGATAGATTTG
66 CATTATGAACTTTCTCTGGAAATGATGATCCATCGAGTGATGGATTTG
344501 A
1 A
344502 ATCTTTGCTA
Statistics
Matches: 413, Mismatches: 38, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
113 413 1.00
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.39
Consensus pattern (113 bp):
AGCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCT
CATTATGAACTTTCTCTGGAAATGATGATCCATCGAGTGATGGATTTG
Found at i:344418 original size:339 final size:327
Alignment explanation
Indices: 343612--344493 Score: 1165
Period size: 339 Copynumber: 2.7 Consensus size: 327
343602 ATCTCCTTAT
* * *
343612 GCAAAAGGTTGAACAAGCTATTCTCATTATGAACTTCTTCTTGC-TCTTCAGATAAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* ** * *
343676 ATTATGAAC-TTCTCTGGAAAAGTTGATCCATCGAATGATGAATTCAAACAAAAAGTTGAACAA-
66 ATTATGAACTTTCTCTGGAAATGTTGATCCATCGAATGATG-ATTTGAGCAAAAGGTTGAACAAG
* *
343739 ATTCTTCTCATTATGAA--T-TTCTT-CTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTA
130 CTT-TTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT-TT
* * * * *
343800 C-CTGGCAATGTTAATCCATCAAATGATGAATTTAAACAAAAGGTTGAACAAGCTCTTCTCATTG
190 CTCTGGCAATGCTGATCCATCGAGTGATGAATTTAAACAAAAGGTTGAACAAGCTCTTCTCATTA
* * *
343864 TGAACTTCTTTTTCCTTCTTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATC
255 TAAACTTCTTCTTCCTTATTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATC
343929 CATTTTAA
320 CATTTTAA
*
343937 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTTTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
344002 ATTATGAACTTTCTCTGGAAATGATGATCCATCGAGTGATGGATTTGAGCAAAAGGTTGAACAAG
66 ATTATGAACTTTCTCTGGAAATGTTGATCCATCGAATGAT-GATTTGAGCAAAAGGTTGAACAAG
*
344067 CTCTTT-TCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
130 CT-TTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCT
* * * *
344131 GGCAATGCTGATCCATCGGGTGATGAA-TTAAAGTAAAAGGTTGAACAAGTTCTTCTTATTATAA
194 GGCAATGCTGATCCATCGAGTGATGAATTTAAA-CAAAAGGTTGAACAAGCTCTTCTCATTATAA
* *
344195 ACTTCTTCTTCCTTATTCAGATGAGTTCTTCTCATTATGAACTTTCTCTTGAAATA-CTGATCCA
258 ACTTCTTCTTCCTTATTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAA-AGCTGAT-C-
344259 TCAAATGATGAATTAAA
320 -C--AT--T---TT-AA
* * *
344276 GTAAAAGGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
344341 ATTATGAACTTTCTCTTGAAATGTTGATCCATCAAATGATAGATTTGAGCAAAAGGTTGAACAAG
66 ATTATGAACTTTCTCTGGAAATGTTGATCCATCGAATGAT-GATTTGAGCAAAAGGTTGAACAAG
*
344406 CTTTTCTCATTATGAACTTCTTCTTCCTTCTTCATATGAGTTCTTCTCATTATGAACTTTCTCTG
130 CTTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
344471 GAAAAGCTGATCCATCGAGTGAT
195 GCAATGCTGATCCATCGAGTGAT
344494 AGATTTGAAT
Statistics
Matches: 491, Mismatches: 42, Indels: 34
0.87 0.07 0.06
Matches are distributed among these distances:
325 41 0.08
326 28 0.06
327 62 0.13
328 130 0.26
329 4 0.01
330 4 0.01
331 12 0.02
333 2 0.00
335 1 0.00
338 5 0.01
339 202 0.41
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.38
Consensus pattern (327 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAATGTTGATCCATCGAATGATGATTTGAGCAAAAGGTTGAACAAGC
TTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGG
CAATGCTGATCCATCGAGTGATGAATTTAAACAAAAGGTTGAACAAGCTCTTCTCATTATAAACT
TCTTCTTCCTTATTCAGATAAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATTTT
AA
Found at i:345355 original size:114 final size:114
Alignment explanation
Indices: 345192--345411 Score: 359
Period size: 114 Copynumber: 1.9 Consensus size: 114
345182 GATCATGCAG
* * * * *
345192 TTCATCTTTTAATTCCAATGATTGGTTATGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
345257 ACACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * *
345306 TTCATCTTTCAAATCTAATGATTGATTTTGGGGTTCATACCAAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGATTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
345371 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTA
345412 CGAGAACGTG
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGATTATGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:346108 original size:6 final size:6
Alignment explanation
Indices: 346097--346123 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
346087 ATTTCTTTTC
346097 TTCCTT TTCCTT TTCCTT TTCCTT TTC
1 TTCCTT TTCCTT TTCCTT TTCCTT TTC
346124 TTCTTCTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (6 bp):
TTCCTT
Found at i:358982 original size:3 final size:3
Alignment explanation
Indices: 358974--359022 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
358964 TGTAATTATT
* *
358974 TAA TAA TAA TATA TAA TAA TAAA TAA -AA TTA TAT TAA TAA TAA TAA
1 TAA TAA TAA TA-A TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
359020 TAA
1 TAA
359023 AAACAAATGG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.79
4 6 0.15
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:359011 original size:18 final size:18
Alignment explanation
Indices: 358967--359013 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
358957 TGTTATTTGT
358967 AATTAT-TTAAT-AATAA
1 AATTATATTAATAAATAA
* *
358983 TA-TATAATAATAAATAA
1 AATTATATTAATAAATAA
359000 AATTATATTAATAA
1 AATTATATTAATAA
359014 TAATAATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 5 0.21
17 6 0.25
18 10 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATTATATTAATAAATAA
Found at i:359768 original size:30 final size:30
Alignment explanation
Indices: 359734--359835 Score: 118
Period size: 30 Copynumber: 3.4 Consensus size: 30
359724 TGTTCGTAAC
*
359734 CGTTTATTTATTTTTGAATGTGTTCGTGTT
1 CGTTTATTTATTTTTAAATGTGTTCGTGTT
* * *
359764 CGTTTA--AATTTTCAATATCGTGTTCATGTT
1 CGTTTATTTATTTTTAA-AT-GTGTTCGTGTT
*
359794 CGTTTATTTATTTTTAAAGGTGTTCGTGTT
1 CGTTTATTTATTTTTAAATGTGTTCGTGTT
*
359824 CTTTTATTTATT
1 CGTTTATTTATT
359836 GTTCATGAAC
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
28 6 0.10
29 2 0.03
30 43 0.73
31 1 0.02
32 7 0.12
ACGTcount: A:0.18, C:0.09, G:0.16, T:0.58
Consensus pattern (30 bp):
CGTTTATTTATTTTTAAATGTGTTCGTGTT
Found at i:359861 original size:23 final size:23
Alignment explanation
Indices: 359830--359946 Score: 92
Period size: 24 Copynumber: 5.0 Consensus size: 23
359820 TGTTCTTTTA
* *
359830 TTTATTGTTCATGAACATGTTCT
1 TTTAATGTTCATGAACATGTTCG
*
359853 TTTAATGTT-TTGCGAACATGTTCG
1 TTTAATGTTCAT--GAACATGTTCG
*
359877 TTTATATGTTCATAAACATGTTCG
1 TTTA-ATGTTCATGAACATGTTCG
** * **
359901 TTTAATGTTCGCGAACTTACTCG
1 TTTAATGTTCATGAACATGTTCG
* *
359924 TTTATATGTTCACGAACGTGTTC
1 TTTA-ATGTTCATGAACATGTTC
359947 ATTAACAAGT
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
22 1 0.01
23 25 0.34
24 42 0.57
25 5 0.07
26 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.45
Consensus pattern (23 bp):
TTTAATGTTCATGAACATGTTCG
Found at i:359946 original size:47 final size:48
Alignment explanation
Indices: 359830--359946 Score: 148
Period size: 47 Copynumber: 2.5 Consensus size: 48
359820 TGTTCTTTTA
* * **
359830 TTTAT-TGTTCATGAACATGTTCTTTTAATGTTTTGCGAACATGTTCG
1 TTTATATGTTCATGAACATGTTCGTTTAATGTTTCGCGAACATACTCG
* *
359877 TTTATATGTTCATAAACATGTTCGTTTAATG-TTCGCGAACTTACTCG
1 TTTATATGTTCATGAACATGTTCGTTTAATGTTTCGCGAACATACTCG
* *
359924 TTTATATGTTCACGAACGTGTTC
1 TTTATATGTTCATGAACATGTTC
359947 ATTAACAAGT
Statistics
Matches: 60, Mismatches: 9, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
47 37 0.62
48 23 0.38
ACGTcount: A:0.23, C:0.15, G:0.16, T:0.45
Consensus pattern (48 bp):
TTTATATGTTCATGAACATGTTCGTTTAATGTTTCGCGAACATACTCG
Found at i:360780 original size:25 final size:25
Alignment explanation
Indices: 360732--360780 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
360722 AAATTTATAA
*
360732 AATTTTAGAGAAAATAAACTTAAAG
1 AATTTTAGAGAAAATAAACATAAAG
*
360757 AATTTTATAGAAAA-AGAACATAAA
1 AATTTTAGAGAAAATA-AACATAAA
360781 TTACATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.59, C:0.04, G:0.10, T:0.27
Consensus pattern (25 bp):
AATTTTAGAGAAAATAAACATAAAG
Found at i:361275 original size:21 final size:20
Alignment explanation
Indices: 361251--361317 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 20
361241 TATCTTTCAA
361251 ATTTACTCTTATACTGTAAGT
1 ATTTA-TCTTATACTGTAAGT
* *
361272 ATTTTATTTTATGCTGTAAGT
1 A-TTTATCTTATACTGTAAGT
* * *
361293 ATTTTATTTTATGCTATAAGT
1 A-TTTATCTTATACTGTAAGT
361314 ATTT
1 ATTT
361318 TATTTTATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
20 3 0.07
21 35 0.83
22 4 0.10
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.55
Consensus pattern (20 bp):
ATTTATCTTATACTGTAAGT
Found at i:361318 original size:21 final size:21
Alignment explanation
Indices: 361267--361325 Score: 109
Period size: 21 Copynumber: 2.8 Consensus size: 21
361257 TCTTATACTG
*
361267 TAAGTATTTTATTTTATGCTG
1 TAAGTATTTTATTTTATGCTA
361288 TAAGTATTTTATTTTATGCTA
1 TAAGTATTTTATTTTATGCTA
361309 TAAGTATTTTATTTTAT
1 TAAGTATTTTATTTTAT
361326 ATTTTCATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.27, C:0.03, G:0.10, T:0.59
Consensus pattern (21 bp):
TAAGTATTTTATTTTATGCTA
Found at i:362146 original size:39 final size:37
Alignment explanation
Indices: 362103--362312 Score: 214
Period size: 37 Copynumber: 5.5 Consensus size: 37
362093 TGAAAATACG
362103 TATATAATATATAGTTTTTTTAAAACATTTTTGAATATA
1 TATATAATATATAGTTTTTTTAAAACATTTTTGAA-A-A
362142 TATATATATATATTA-TATAGTTTTTAAAACATTTTTGAAAA
1 TATATA-ATATA-TAGT-T--TTTTTAAAACATTTTTGAAAA
*
362183 TGATATAATATATAG--TTTTTAAAACATTTTAGAAAA
1 T-ATATAATATATAGTTTTTTTAAAACATTTTTGAAAA
* *
362219 TATATAATGTATATA-TAATTTTTGAAATCA-TTTTGAAAA
1 TATATAA--TATATAGT--TTTTTTAAAACATTTTTGAAAA
* *
362258 TATATAATATATAGTTTTTTAAAAATATTTTTGAAAA
1 TATATAATATATAGTTTTTTTAAAACATTTTTGAAAA
* *
362295 CATATATTATATAGTTTT
1 TATATAATATATAGTTTT
362313 GAAAATATAT
Statistics
Matches: 147, Mismatches: 9, Indels: 32
0.78 0.05 0.17
Matches are distributed among these distances:
35 6 0.04
36 30 0.20
37 37 0.25
38 1 0.01
39 21 0.14
40 17 0.12
41 10 0.07
42 6 0.04
43 19 0.13
ACGTcount: A:0.43, C:0.02, G:0.06, T:0.48
Consensus pattern (37 bp):
TATATAATATATAGTTTTTTTAAAACATTTTTGAAAA
Found at i:362163 original size:45 final size:43
Alignment explanation
Indices: 362103--362270 Score: 157
Period size: 36 Copynumber: 4.1 Consensus size: 43
362093 TGAAAATACG
*
362103 TATATAATATATAGTTTTTTTAAAACATTTTTGAATAT-ATATATA
1 TATATAATATATAG--TTTTTAAAACATTTTTGAAAATGATATA-A
*
362148 TATATATTATATAGTTTTTAAAACATTTTTGAAAATG------
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAATGATATAA
*
362185 -ATATAATATATAGTTTTTAAAACATTTTAGAAAAT-ATATAA
1 TATATAATATATAGTTTTTAAAACATTTTTGAAAATGATATAA
* *
362226 TGTAT-ATATA-A-TTTTTGAAATCA-TTTTGAAAAT-ATATAA
1 TATATAATATATAGTTTTT-AAAACATTTTTGAAAATGATATAA
362265 TATATA
1 TATATA
362271 GTTTTTTAAA
Statistics
Matches: 105, Mismatches: 8, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
36 33 0.31
39 24 0.23
40 6 0.06
41 5 0.05
42 3 0.03
43 21 0.20
45 13 0.12
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (43 bp):
TATATAATATATAGTTTTTAAAACATTTTTGAAAATGATATAA
Found at i:362195 original size:36 final size:35
Alignment explanation
Indices: 362147--362317 Score: 191
Period size: 36 Copynumber: 4.7 Consensus size: 35
362137 ATATATATAT
*
362147 ATATATATTATATAGTTTTTAAAACATTTTTGAAA
1 ATATATAATATATAGTTTTTAAAACATTTTTGAAA
*
362182 ATGATATAATATATAGTTTTTAAAACATTTTAGAAA
1 AT-ATATAATATATAGTTTTTAAAACATTTTTGAAA
* *
362218 ATATATAATGTATATATAATTTTTGAAATCA-TTTTGAAA
1 ATATAT-A---ATATATAGTTTTT-AAAACATTTTTGAAA
*
362257 ATATATAATATATAGTTTTTTAAAAATATTTTTGAAA
1 ATATATAATATATAG-TTTTT-AAAACATTTTTGAAA
* * *
362294 ACATATATTATATAGTTTTGAAAA
1 ATATATAATATATAGTTTTTAAAA
362318 TATATATAAT
Statistics
Matches: 116, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
35 17 0.15
36 47 0.41
37 21 0.18
38 1 0.01
39 25 0.22
40 5 0.04
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.46
Consensus pattern (35 bp):
ATATATAATATATAGTTTTTAAAACATTTTTGAAA
Found at i:362330 original size:25 final size:24
Alignment explanation
Indices: 362286--362343 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
362276 TTAAAAATAT
362286 TTTTGAAAACATATATTATAT-AG
1 TTTTGAAAACATATATTATATAAG
* *
362309 TTTTGAAAATATATATAATATATAAT
1 TTTTGAAAACATATAT--TATATAAG
362335 TTTTGAAAA
1 TTTTGAAAA
362344 AACATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
23 15 0.50
25 5 0.17
26 10 0.33
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (24 bp):
TTTTGAAAACATATATTATATAAG
Found at i:362384 original size:46 final size:44
Alignment explanation
Indices: 362309--362417 Score: 123
Period size: 48 Copynumber: 2.4 Consensus size: 44
362299 TATTATATAG
*
362309 TTTTGAAAATATATATAATATATAA-TTTTTGAAAAAA-CATTT
1 TTTTGAAAATATATATAATATATAATTTTTTAAAAAAATCATTT
* *
362351 TTTTGAAATCATATATATACTATATAGATTTTTTTTAAAAAAATTATTT
1 TTTTGAAA--ATATATATAATATATA-A--TTTTTTAAAAAAATCATTT
362400 TTTTGAAAAATATATATA
1 TTTTG-AAAATATATATA
362418 TTTTGAAAAC
Statistics
Matches: 56, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
42 8 0.14
44 15 0.27
45 1 0.02
48 20 0.36
49 9 0.16
50 3 0.05
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (44 bp):
TTTTGAAAATATATATAATATATAATTTTTTAAAAAAATCATTT
Found at i:363708 original size:22 final size:20
Alignment explanation
Indices: 363651--363708 Score: 53
Period size: 22 Copynumber: 2.8 Consensus size: 20
363641 CCCCGAATTC
* *
363651 TTATTTTATTTTATTTATTA
1 TTATTATATTTTTTTTATTA
* *
363671 TTATTATCATGCTTTTTAATTA
1 TTATTAT-AT-TTTTTTTATTA
363693 TTATTAGTATTTTTTT
1 TTATTA-TATTTTTTT
363709 CCTCATATTG
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
20 6 0.20
21 7 0.23
22 16 0.53
23 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.69
Consensus pattern (20 bp):
TTATTATATTTTTTTTATTA
Found at i:371469 original size:99 final size:99
Alignment explanation
Indices: 371298--371493 Score: 392
Period size: 99 Copynumber: 2.0 Consensus size: 99
371288 ATGCTACACA
371298 ATTTATTGCTTGTAATGCTTTCTATTTGAGATTTTGAATAATCCTTAACCTTGATAAATGCATTT
1 ATTTATTGCTTGTAATGCTTTCTATTTGAGATTTTGAATAATCCTTAACCTTGATAAATGCATTT
371363 AATGCAGACCATTTTTGGGGCTAGTAAGGATGCG
66 AATGCAGACCATTTTTGGGGCTAGTAAGGATGCG
371397 ATTTATTGCTTGTAATGCTTTCTATTTGAGATTTTGAATAATCCTTAACCTTGATAAATGCATTT
1 ATTTATTGCTTGTAATGCTTTCTATTTGAGATTTTGAATAATCCTTAACCTTGATAAATGCATTT
371462 AATGCAGACCATTTTTGGGGCTAGTAAGGATG
66 AATGCAGACCATTTTTGGGGCTAGTAAGGATG
371494 GCAATATTTA
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
99 97 1.00
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.41
Consensus pattern (99 bp):
ATTTATTGCTTGTAATGCTTTCTATTTGAGATTTTGAATAATCCTTAACCTTGATAAATGCATTT
AATGCAGACCATTTTTGGGGCTAGTAAGGATGCG
Found at i:376161 original size:21 final size:21
Alignment explanation
Indices: 376135--376234 Score: 73
Period size: 21 Copynumber: 4.8 Consensus size: 21
376125 ATCAGTTCCC
376135 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATGA
*
376156 AGAATCGCAATGCGA-TA-GTA
1 AGAATCGCAACGCGATTATG-A
** * * **
376176 CA-AATTCGCATTGTGATTTTTC
1 -AGAA-TCGCAACGCGATTATGA
*
376198 AGAATCGCAACGCGAATATGA
1 AGAATCGCAACGCGATTATGA
376219 A-AATCGCAACGCGATT
1 AGAATCGCAACGCGATT
376235 CTGACTATCG
Statistics
Matches: 59, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
19 1 0.02
20 19 0.32
21 36 0.61
22 3 0.05
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (21 bp):
AGAATCGCAACGCGATTATGA
Found at i:376225 original size:20 final size:20
Alignment explanation
Indices: 376200--376455 Score: 139
Period size: 20 Copynumber: 12.7 Consensus size: 20
376190 GATTTTTCAG
*
376200 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATATGTA
* *
376220 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATATGTA
*
376239 CTATCGCAA--CGAATATTCGTAA
1 -AATCGCAACGCGAATA-T-GT-A
* *
376261 AATTGCAACGCGTAT-TCGTA
1 AATCGCAACGCGAATAT-GTA
* *
376281 AATCGTAACGAC-AATACGTAA
1 AATCGCAACG-CGAATATGT-A
* * ** * **
376302 AATTGTAACATGTATCCGTA
1 AATCGCAACGCGAATATGTA
* *
376322 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGTA
* *
376342 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATATGTA
* *
376362 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATATGTA
* *
376382 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGAATATGTA
*
376402 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATATGT-A
* *
376423 AATGGCAACGCGTAT-TCGTA
1 AATCGCAACGCGAATAT-GTA
376443 AATCGCAACGCGA
1 AATCGCAACGCGA
376456 TCTTCGGTAT
Statistics
Matches: 180, Mismatches: 41, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
18 4 0.02
19 2 0.01
20 130 0.72
21 39 0.22
22 1 0.01
23 4 0.02
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGAATATGTA
Found at i:376368 original size:40 final size:41
Alignment explanation
Indices: 376200--376452 Score: 261
Period size: 41 Copynumber: 6.2 Consensus size: 41
376190 GATTTTTCAG
* *
376200 AATCGCAACGCGAATATG-AAAATCGCAACGCG-ATTCTG-A
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTA-TCTGTA
* * *
376239 CTATCGCAACGA-ATATTCGTAAAATTGCAACGCGTAT-TCGTA
1 -AATCGCAACGAGA-ATACGTAAAATCGCAACGCGTATCT-GTA
* * * * ** *
376281 AATCGTAACGACAATACGTAAAATTGTAACATGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTA
376322 AATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTA
* *
376362 AATCGCAACGAGAATACGT-AAATCGCAACGAGAATCTGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTA
* *
376402 AATCGCAACGACAATACGTAAAATGGCAACGCGTAT-TCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCT-GTA
376443 AATCGCAACG
1 AATCGCAACG
376453 CGATCTTCGG
Statistics
Matches: 179, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
39 1 0.01
40 86 0.48
41 89 0.50
42 3 0.02
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (41 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCTGTA
Found at i:377338 original size:24 final size:24
Alignment explanation
Indices: 377311--377364 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
377301 GTATTTGAAA
377311 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
377335 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
377359 TTTGAT
1 TTTGAT
377365 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:379820 original size:20 final size:20
Alignment explanation
Indices: 379795--379883 Score: 103
Period size: 20 Copynumber: 4.5 Consensus size: 20
379785 CAACGCAGAA
379795 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAATATGACT
379815 ATCGCAACATG-GAA-ATGACT
1 ATCGCAAC--GCGAATATGACT
*
379835 ATCGCAATGCGGAAT-TGACT
1 ATCGCAACGC-GAATATGACT
* *
379855 ATCGCAACGCGAAAATAACT
1 ATCGCAACGCGAATATGACT
379875 ATCGCAACG
1 ATCGCAACG
379884 AGAGAATCGC
Statistics
Matches: 59, Mismatches: 4, Indels: 12
0.79 0.05 0.16
Matches are distributed among these distances:
18 1 0.02
19 3 0.05
20 51 0.86
21 3 0.05
22 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:379854 original size:40 final size:40
Alignment explanation
Indices: 379795--379883 Score: 117
Period size: 40 Copynumber: 2.2 Consensus size: 40
379785 CAACGCAGAA
* * *
379795 ATCGCAACGCGAATATGACTATCGCAACATGGAAATGACT
1 ATCGCAACGCGAATATGACTATCGCAACACGAAAATAACT
* *
379835 ATCGCAATGCGGAAT-TGACTATCGCAACGCGAAAATAACT
1 ATCGCAACGC-GAATATGACTATCGCAACACGAAAATAACT
379875 ATCGCAACG
1 ATCGCAACG
379884 AGAGAATCGC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 38 0.90
41 4 0.10
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (40 bp):
ATCGCAACGCGAATATGACTATCGCAACACGAAAATAACT
Found at i:380114 original size:14 final size:14
Alignment explanation
Indices: 380095--380131 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
380085 CATCAATTAA
380095 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
380109 ACAAATCATCTTTT
1 ACAAATCAACATTT
380123 ACAAATCAA
1 ACAAATCAA
380132 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:381575 original size:42 final size:42
Alignment explanation
Indices: 381479--381579 Score: 105
Period size: 42 Copynumber: 2.4 Consensus size: 42
381469 GGGAGTGACA
* * * *
381479 TCTTCAACGATGACAGTGGCCTCTTGAACGGTGGGAGGGGAC
1 TCTTGAACGATGACAGGGGCCTCTTGAACGATGGGAGAGGAC
** * * *
381521 TCTTGAGGGATGATAGGGGCCTCTTGAACGATAGGG-GATGCC
1 TCTTGAACGATGACAGGGGCCTCTTGAACGAT-GGGAGAGGAC
381563 TCTTGAACGATGACAGG
1 TCTTGAACGATGACAGG
381580 TGAGTCGGGC
Statistics
Matches: 46, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
42 43 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.23
Consensus pattern (42 bp):
TCTTGAACGATGACAGGGGCCTCTTGAACGATGGGAGAGGAC
Found at i:382082 original size:20 final size:20
Alignment explanation
Indices: 382067--382165 Score: 162
Period size: 20 Copynumber: 5.0 Consensus size: 20
382057 AAATCGTAAA
382067 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
382087 GCGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
*
382107 GTGAAAATGACTATCGCAAT
1 GCGAAAATGACTATCGCAAT
*
382127 GCGAAAATGACTATCGTAAT
1 GCGAAAATGACTATCGCAAT
**
382147 GCGAATTTGACTATCGCAA
1 GCGAAAATGACTATCGCAA
382166 CGAGAGAATC
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 73 1.00
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.23
Consensus pattern (20 bp):
GCGAAAATGACTATCGCAAT
Found at i:382222 original size:19 final size:19
Alignment explanation
Indices: 382200--382243 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
382190 AAATCGCAAC
382200 GCGATTATAGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
* *
382219 GCGATTTTGGTTTCGCGTT
1 GCGATTATAGTTTCGCGTT
382238 GCGATT
1 GCGATT
382244 TTCATTTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.11, C:0.16, G:0.30, T:0.43
Consensus pattern (19 bp):
GCGATTATAGTTTCGCGTT
Found at i:382244 original size:19 final size:19
Alignment explanation
Indices: 382209--382245 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
382199 CGCGATTATA
382209 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
382228 GTTTCGCGTTGCGATTTT
1 GTTTCGCGTTGCGATTTT
382246 CATTTCTCGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.16, G:0.30, T:0.49
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:382251 original size:19 final size:19
Alignment explanation
Indices: 382210--382258 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
382200 GCGATTATAG
**
382210 TTTCGCGTTGCGATTTTGG
1 TTTCGCGTTGCGATTTTCA
382229 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
382248 TTTCTCGTTGC
1 TTTCGCGTTGC
382259 AATTCTCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.06, C:0.20, G:0.24, T:0.49
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:382526 original size:94 final size:94
Alignment explanation
Indices: 382380--382759 Score: 656
Period size: 94 Copynumber: 4.1 Consensus size: 94
382370 ATGGATTGCA
* * *
382380 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACATAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
382444 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
382473 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
382538 TTAGCAGAAATGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
382567 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACATAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
382632 TTAGCAGAATTGGCAGCAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
382661 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
382725 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCGAACAAAT
382755 TTACT
1 TTACT
382760 AAGCAATCTA
Statistics
Matches: 274, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
93 23 0.08
94 251 0.92
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:384419 original size:82 final size:81
Alignment explanation
Indices: 384324--384851 Score: 325
Period size: 82 Copynumber: 6.4 Consensus size: 81
384314 CAAAATGGTA
** * ** *
384324 ACTTTAGCAGCGTTTTTATAAAAACGCCG-TAATAGGTTCATCGA-TAGTGGCATTTTT-TCAAC
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAA-AGACTCAT-AATTAGTGGCATTTTTAT--AC
*
384386 AAACGCCGTAAAAGAGTAGT
62 AAACGCCGTAAAAGAATAGT
384406 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAATTTAGTGGCATTTTTATACAAA
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAA-TTAGTGGCATTTTTATACAAA
* * *
384471 CGCCGTTATAGAATTGT
65 CGCCGTAAAAGAATAGT
* * * * * * * *
384488 ACTTTAGTGGTGTTTTTATACAAACGTCGTTATACATA-T-GTACTATAGTGGCGTTTGTGTTTA
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTA-A-AGACTCATAAT-TAGTGGCATTT-T-TATA
* * *
384551 AAAACGCCGTTAAAGACTCA-T
61 CAAACGCCGTAAAAGAAT-AGT
* * * * *
384572 AATTTAGTGGCGTTTTTATACAAATGCCGTTAAAGACTCATACTTTAGTGGCGTTTTTATACAAA
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATA-ATTAGTGGCATTTTTATACAAA
* ***
384637 CTCCGCT-AAAGACGCGT
65 CGCCG-TAAAAGAATAGT
* * * * * ** * * *
384654 ACTTTAGTGGCATTTTTATTCAAACGCCGTTATACACTTGTACTATAGTGGCGTTTGTGTTTACA
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAAT-TAGTGGCATTT-T-TATACA
* * *
384719 AACGTCGCT-AAAGACTCGT
63 AACGCCG-TAAAAGAATAGT
* * * * * * * *
384738 AATTTAGTGGCATTTTTATACAAATGCCGCTAAAGGCCCATACTTTATTGACATTTTTATACAAA
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATA-ATTAGTGGCATTTTTATACAAA
* * * *
384803 CACCGTTAAAGACTCGT
65 CGCCGTAAAAGAATAGT
* *
384820 ACTTTAGTGGCGTTTTTATTCAAACGTCGCTA
1 ACTTTAGTGGCGTTTTTATACAAACGCCGCTA
384852 TACACTTGTA
Statistics
Matches: 357, Mismatches: 69, Indels: 40
0.77 0.15 0.09
Matches are distributed among these distances:
81 4 0.01
82 202 0.57
83 25 0.07
84 124 0.35
85 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (81 bp):
ACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGACTCATAATTAGTGGCATTTTTATACAAAC
GCCGTAAAAGAATAGT
Done.