Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 2 of 190
Found at i:317865 original size:11 final size:11
Alignment explanation
Indices: 317849--317873 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
317839 TAATATATTT
317849 TTTTAATAATA
1 TTTTAATAATA
317860 TTTTAATAATA
1 TTTTAATAATA
317871 TTT
1 TTT
317874 ATATATATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAATAATA
Found at i:320253 original size:49 final size:49
Alignment explanation
Indices: 320197--320291 Score: 147
Period size: 49 Copynumber: 1.9 Consensus size: 49
320187 GAAAGGATAT
320197 ATCTTAGAAATAAACG-AGTGCATAAAGAAAAGGTAGCTAAATTGGTTAC
1 ATCTTAGAAATAAACGTA-TGCATAAAGAAAAGGTAGCTAAATTGGTTAC
** *
320246 ATCTTAGAAATAAGTGTATGCATAAAGAAAAGGTGGCTAAATTGGT
1 ATCTTAGAAATAAACGTATGCATAAAGAAAAGGTAGCTAAATTGGT
320292 ATTTCTCTGG
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
49 41 0.98
50 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.26
Consensus pattern (49 bp):
ATCTTAGAAATAAACGTATGCATAAAGAAAAGGTAGCTAAATTGGTTAC
Found at i:320482 original size:52 final size:53
Alignment explanation
Indices: 320379--320485 Score: 164
Period size: 52 Copynumber: 2.0 Consensus size: 53
320369 CAAGAGAGAT
*
320379 ATAGTTTAGATGCTAAGTAAAGTTGAAAAAGAAACAATGCAACTCTTATGCTG
1 ATAGTTTAAATGCTAAGTAAAGTTGAAAAAGAAACAATGCAACTCTTATGCTG
* *
320432 ATAGTTTAAATGCTAAGTAGAGTTG-GAAAG-AACAAATGCAACTCTTATGCTG
1 ATAGTTTAAATGCTAAGTAAAGTTGAAAAAGAAAC-AATGCAACTCTTATGCTG
320484 AT
1 AT
320486 GAATTTCAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
51 3 0.06
52 24 0.48
53 23 0.46
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.29
Consensus pattern (53 bp):
ATAGTTTAAATGCTAAGTAAAGTTGAAAAAGAAACAATGCAACTCTTATGCTG
Found at i:322553 original size:19 final size:20
Alignment explanation
Indices: 322529--322572 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
322519 TTTTTGCTTC
322529 TTCTTCT-CGTACGTTTCTT
1 TTCTTCTACGTACGTTTCTT
**
322548 TTCTTCTATTTACGTTTCTT
1 TTCTTCTACGTACGTTTCTT
322568 TTCTT
1 TTCTT
322573 TTCTCCATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.07, C:0.23, G:0.07, T:0.64
Consensus pattern (20 bp):
TTCTTCTACGTACGTTTCTT
Found at i:323608 original size:78 final size:78
Alignment explanation
Indices: 323487--323630 Score: 198
Period size: 78 Copynumber: 1.8 Consensus size: 78
323477 GTGTTGCTAT
* * *
323487 CTTACCAAAGGAAGCGAAGCCAAATAAGATAGAATCACCATTGCGAATTCAGTCCTCATTAACCC
1 CTTACCAAAGGAAGCGAAGCCAAATAAGATAGAATCACAATTGCAAATTCACTCCTCATTAACCC
323552 CGAGTGTCACTGC
66 CGAGTGTCACTGC
* * * * * **
323565 CTTATCAATGGAAGCTAAGCCAATTAAGTTAGAATCACAATTGCAAATTCACTCCTTGTTAACCC
1 CTTACCAAAGGAAGCGAAGCCAAATAAGATAGAATCACAATTGCAAATTCACTCCTCATTAACCC
323630 C
66 C
323631 TTGGCTGATA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
78 56 1.00
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (78 bp):
CTTACCAAAGGAAGCGAAGCCAAATAAGATAGAATCACAATTGCAAATTCACTCCTCATTAACCC
CGAGTGTCACTGC
Found at i:327553 original size:49 final size:49
Alignment explanation
Indices: 327496--327599 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
327486 TCATGTGTTA
* * * *
327496 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGGGTTCACCTTTTGATTCATGATATTAAACTTAATTT
327545 TAATTTTATAAAGGGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGGGTTCACCTTTTGATTCATGATATTAAACTTAATTT
327594 TAATTT
1 TAATTT
327600 GTTTTTTTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.49
Consensus pattern (49 bp):
TAATTTTATAAAGGGTTCACCTTTTGATTCATGATATTAAACTTAATTT
Found at i:329007 original size:21 final size:21
Alignment explanation
Indices: 328983--329025 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
328973 AATAAAGTAG
328983 ATTATATATTATG-TTTATAGT
1 ATTATATATTATGATTT-TAGT
329004 ATTATATATTATGATTTTAGT
1 ATTATATATTATGATTTTAGT
329025 A
1 A
329026 AATTCATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
ATTATATATTATGATTTTAGT
Found at i:329247 original size:45 final size:44
Alignment explanation
Indices: 329168--329256 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
329158 CATCATTCCG
329168 TTCAACCAAACACAAGAATACTATTACAGTTCTATTCCATTACA
1 TTCAACCAAACACAAGAATACTATTACAGTTCTATTCCATTACA
*
329212 TTCAACCAAACA-ATTGAATTACTATTAC-GTCTCTATTCCATTACA
1 TTCAACCAAACACA-AGAA-TACTATTACAGT-TCTATTCCATTACA
329257 CCTCAATTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
43 1 0.02
44 17 0.41
45 23 0.56
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (44 bp):
TTCAACCAAACACAAGAATACTATTACAGTTCTATTCCATTACA
Found at i:329467 original size:34 final size:33
Alignment explanation
Indices: 329421--329484 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
329411 AATAAAATGT
329421 AAATATTGTTAAATTATATTCATAATAAATAATA
1 AAATATTGTTAAATTAT-TTCATAATAAATAATA
* *
329455 AAATATAT-TTAAATTATTTTATATTAAATA
1 AAATAT-TGTTAAATTATTTCATAATAAATA
329485 TAATTAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 11 0.41
34 15 0.56
35 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (33 bp):
AAATATTGTTAAATTATTTCATAATAAATAATA
Found at i:329904 original size:18 final size:18
Alignment explanation
Indices: 329851--329904 Score: 65
Period size: 17 Copynumber: 3.0 Consensus size: 18
329841 GATGTAGATA
* *
329851 AAAATATTAAATTTAAGTA
1 AAAATA-TAAATTTAATTT
*
329870 AAAATTTAAATTT-ATTT
1 AAAATATAAATTTAATTT
329887 AAAATATAAATTTAATTT
1 AAAATATAAATTTAATTT
329905 GAACTTCAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 14 0.47
18 11 0.37
19 5 0.17
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
AAAATATAAATTTAATTT
Found at i:330355 original size:19 final size:19
Alignment explanation
Indices: 330331--330442 Score: 75
Period size: 19 Copynumber: 5.9 Consensus size: 19
330321 TGCAAACTCT
330331 TTTTTACAATTTTATATAA
1 TTTTTACAATTTTATATAA
** * *
330350 TTTTTACTTTTTTTTGTAA
1 TTTTTACAATTTTATATAA
* * * *
330369 TTTCTATAATTTTTTATAC
1 TTTTTACAATTTTATATAA
** *
330388 TTTTTGTAATTTTGTA-AA
1 TTTTTACAATTTTATATAA
* * *
330406 ATTTTGCAATTTTATATTA
1 TTTTTACAATTTTATATAA
330425 TTTTTA-ATATTTTATATA
1 TTTTTACA-ATTTTATATA
330443 TTTCTTAAAA
Statistics
Matches: 70, Mismatches: 21, Indels: 4
0.74 0.22 0.04
Matches are distributed among these distances:
18 15 0.21
19 55 0.79
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.63
Consensus pattern (19 bp):
TTTTTACAATTTTATATAA
Found at i:330450 original size:19 final size:19
Alignment explanation
Indices: 330414--330450 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
330404 AAATTTTGCA
330414 ATTTTATATTATTTTTAAT
1 ATTTTATATTATTTTTAAT
330433 ATTTTATA-TATTTCTTAA
1 ATTTTATATTATTT-TTAA
330451 AATTCTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (19 bp):
ATTTTATATTATTTTTAAT
Found at i:331907 original size:37 final size:34
Alignment explanation
Indices: 331848--331931 Score: 100
Period size: 38 Copynumber: 2.4 Consensus size: 34
331838 ATGCAACATG
331848 ACATGTTATAAC-AAATTAATACAGTAGCAA-TA
1 ACATGTTATAACAAAATTAATACAGTAGCAATTA
331880 ACATGTTTATAACAAATATATATATACAGTAGCAATTA
1 ACATG-TTATAACAAA-AT-TA-ATACAGTAGCAATTA
*
331918 TCATGCTTATAACA
1 ACATG-TTATAACA
331932 GATCATGACA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
32 5 0.11
33 7 0.16
34 2 0.05
35 2 0.05
36 2 0.05
37 12 0.27
38 14 0.32
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.32
Consensus pattern (34 bp):
ACATGTTATAACAAAATTAATACAGTAGCAATTA
Found at i:334165 original size:97 final size:97
Alignment explanation
Indices: 334034--334234 Score: 267
Period size: 97 Copynumber: 2.1 Consensus size: 97
334024 ACTGGATTGG
* * * ** * *
334034 GGAGTCGTGGATCTATTACGGAGAGGTTCCGATTGAATATGGTGGAAATATTTAAAGATGTTTTT
1 GGAGTCGTAGATCTATTACGGAGAGGCTCCGATTGAATAGGGAAGAAATATTTAAAGATATTGTT
* * *
334099 GGAACGACGCCTACTGTGGTCGAGTGCTGGAT
66 GGAACGACGCCTACTGTGGCCAAGTACTGGAT
* * * *
334131 GGAGTCGTAGATCTATTATGGAGAGGCTCTGATTGAATGGGGAAGAAATATTTAAAGGTATTGTT
1 GGAGTCGTAGATCTATTACGGAGAGGCTCCGATTGAATAGGGAAGAAATATTTAAAGATATTGTT
*
334196 GGAACGACTCCTACTGTGGCCAAGTACTGGAT
66 GGAACGACGCCTACTGTGGCCAAGTACTGGAT
334228 GGAGTCG
1 GGAGTCG
334235 ACGGAGAGGA
Statistics
Matches: 89, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
97 89 1.00
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.29
Consensus pattern (97 bp):
GGAGTCGTAGATCTATTACGGAGAGGCTCCGATTGAATAGGGAAGAAATATTTAAAGATATTGTT
GGAACGACGCCTACTGTGGCCAAGTACTGGAT
Found at i:335192 original size:34 final size:33
Alignment explanation
Indices: 335148--335244 Score: 131
Period size: 34 Copynumber: 2.8 Consensus size: 33
335138 ATACAATATG
335148 ACATGCTTATAACATATCAATAAGATAGCAATTA
1 ACATGCTTATAACATATCAATAAG-TAGCAATTA
* *
335182 GCATGCTTATAACAAATCAATATAGTAGCAATTA
1 ACATGCTTATAACATATCAATA-AGTAGCAATTA
* *
335216 ATATGCTTATAACATATAAATAAAGTAGC
1 ACATGCTTATAACATATCAAT-AAGTAGC
335245 TATAGACACC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
34 52 0.95
35 3 0.05
ACGTcount: A:0.46, C:0.13, G:0.10, T:0.30
Consensus pattern (33 bp):
ACATGCTTATAACATATCAATAAGTAGCAATTA
Found at i:335420 original size:12 final size:12
Alignment explanation
Indices: 335403--335427 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
335393 TAAGCAAGAT
335403 TGAAAAGTAGTA
1 TGAAAAGTAGTA
335415 TGAAAAGTAGTA
1 TGAAAAGTAGTA
335427 T
1 T
335428 ATATACATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (12 bp):
TGAAAAGTAGTA
Found at i:338078 original size:92 final size:91
Alignment explanation
Indices: 337958--338143 Score: 239
Period size: 92 Copynumber: 2.0 Consensus size: 91
337948 TGATAAAAAT
* * *
337958 ATATTGATGGATGAATCATTTGTCTGTGCAGATAAAAGCTACT-AATACGTTGTGGATGACCCAC
1 ATATTGATGGATGAACCATTCGTCTGTGCAGATAAAAG-TACTCAATACGTTGTGGATGAACCAC
*
338022 TAGTCAAACAGATAAACTTCTGACTAAA
65 TAGTCAAACAGAT-AACTACTGACTAAA
* * * **
338050 ATATTGGTGGATGAACCATTCGTTTGTGCATATAAAAGTTGTCAATACGTTGTGGATGAACCACT
1 ATATTGATGGATGAACCATTCGTCTGTGCAGATAAAAGTACTCAATACGTTGTGGATGAACCACT
* * *
338115 GGTTAAACAGATGACTACTGACTAAA
66 AGTCAAACAGATAACTACTGACTAAA
338141 ATA
1 ATA
338144 CGTAGTGAAT
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
91 17 0.21
92 64 0.79
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (91 bp):
ATATTGATGGATGAACCATTCGTCTGTGCAGATAAAAGTACTCAATACGTTGTGGATGAACCACT
AGTCAAACAGATAACTACTGACTAAA
Found at i:340761 original size:14 final size:14
Alignment explanation
Indices: 340744--340773 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
340734 AATTAACTTG
340744 ACATAGTTAACAAT
1 ACATAGTTAACAAT
340758 ACATAGTTAACAAT
1 ACATAGTTAACAAT
340772 AC
1 AC
340774 CTTGACACGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.27
Consensus pattern (14 bp):
ACATAGTTAACAAT
Found at i:340850 original size:2 final size:2
Alignment explanation
Indices: 340795--340837 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
340785 TCTATTTTCC
*
340795 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
340837 A
1 A
340838 AACAAGGTAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:342423 original size:16 final size:17
Alignment explanation
Indices: 342412--342443 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
342402 AATAATATTT
342412 TTAAT-TTTTAATTTTA
1 TTAATATTTTAATTTTA
342428 TTAATATTTT-ATTTTA
1 TTAATATTTTAATTTTA
342444 ATTTAATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTAATATTTTAATTTTA
Found at i:342458 original size:27 final size:28
Alignment explanation
Indices: 342428--342493 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 28
342418 TTTAATTTTA
342428 TTAATATTTTATTTT-AATT-TAATTAAG
1 TTAATATTTTATTTTAAATTCT-ATTAAG
*
342455 TTAATCA-ATTATTTTAAATTCTATTAAG
1 TTAAT-ATTTTATTTTAAATTCTATTAAG
* *
342483 ATAATTTTTTA
1 TTAATATTTTA
342494 GGATAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
27 12 0.39
28 18 0.58
29 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (28 bp):
TTAATATTTTATTTTAAATTCTATTAAG
Found at i:353286 original size:198 final size:198
Alignment explanation
Indices: 352917--353291 Score: 449
Period size: 198 Copynumber: 1.9 Consensus size: 198
352907 TAATGGTCTA
* * *
352917 CTGCACACTCACAAAGTATATTAGCTCATATTTAGGCCTCATTCGGCCCCTAAAGTCAATAAAAG
1 CTGCACACTCACAAAGCATATTAGCTCACACTTAGGCCTCATTCGGCCCCTAAAGTCAATAAAAG
* * ** ** **
352982 ACTCAAATTACACATTTTATTACACTTAACTGAACTTGTTGAAATGTAATTAAACACAACTAAAA
66 ACTCAAATTACACAGTTTATTACACTTAAATGAAAGTAATGAAATGTAACCAAACACAACTAAAA
* * *
353047 TGCTTATGTTCAACTTCCTAAAGTGCAAAAATTAATTTAATCTGCTATACCAAATTACGGCAGAT
131 TGCTTATATTCAACTTCCTAAAGTACAAAAACTAATTTAATCTGCTATACCAAATTACGGCAGAT
353112 CAC
196 CAC
* *
353115 CTGCACACTCACAAAGCATATTAGCTCACGCTTAGGCCTCATTCGGCCCCTAAGGTCAATAAAAG
1 CTGCACACTCACAAAGCATATTAGCTCACACTTAGGCCTCATTCGGCCCCTAAAGTCAATAAAAG
*
353180 ACTCAAATTAC-CAGTTTATTGA-ATTTAAAT-AAAGTAATGAAACCT-TAACCAAA-ATCTAAC
66 ACTCAAATTACACAGTTTATT-ACACTTAAATGAAAGTAATGAAA--TGTAACCAAACA-C-AAC
* * * *
353240 TAAAGTGCTTGTATTCAAGC-TCCTCAAA-TACGAAAACTAGTTTAATCTGCTA
126 TAAAATGCTTATATTCAA-CTTCCT-AAAGTACAAAAACTAATTTAATCTGCTA
353292 CATCGAATTA
Statistics
Matches: 149, Mismatches: 21, Indels: 14
0.81 0.11 0.08
Matches are distributed among these distances:
196 9 0.06
197 21 0.14
198 115 0.77
199 4 0.03
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (198 bp):
CTGCACACTCACAAAGCATATTAGCTCACACTTAGGCCTCATTCGGCCCCTAAAGTCAATAAAAG
ACTCAAATTACACAGTTTATTACACTTAAATGAAAGTAATGAAATGTAACCAAACACAACTAAAA
TGCTTATATTCAACTTCCTAAAGTACAAAAACTAATTTAATCTGCTATACCAAATTACGGCAGAT
CAC
Found at i:364819 original size:20 final size:20
Alignment explanation
Indices: 364779--364834 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
364769 TTTTTCTCTC
*
364779 ATTTTCTCTCTTGCCAAACACA
1 ATTTTCT-TCTT-CAAAACACA
*
364801 ATTTTCTTCTTCAAAACACC
1 ATTTTCTTCTTCAAAACACA
*
364821 ATTCTTCATCTTCA
1 ATT-TTCTTCTTCA
364835 CTACCAAACC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.33
21 13 0.43
22 7 0.23
ACGTcount: A:0.27, C:0.30, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTTCTTCTTCAAAACACA
Found at i:364834 original size:21 final size:20
Alignment explanation
Indices: 364794--364834 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
364784 CTCTCTTGCC
*
364794 AAACACAATTTTCTTCTTCA
1 AAACACAATTTTCATCTTCA
*
364814 AAACACCATTCTTCATCTTCA
1 AAACACAATT-TTCATCTTCA
364835 CTACCAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.34, C:0.29, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACACAATTTTCATCTTCA
Found at i:368930 original size:13 final size:13
Alignment explanation
Indices: 368912--368936 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
368902 ATCCAAGTAA
368912 AAATATAGATTTT
1 AAATATAGATTTT
368925 AAATATAGATTT
1 AAATATAGATTT
368937 GGATAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (13 bp):
AAATATAGATTTT
Found at i:372499 original size:57 final size:59
Alignment explanation
Indices: 372438--372560 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 59
372428 TGTCGACAGG
* * *
372438 TAAAAAAGTAA-T-TTTTTTGTGGT-GTCGTGTTGTCTAGCAACATTGGCGTCAGATAGT
1 TAAAAAAGTAATTCTTTTTTGT-GTCATCATGTTGTCTAGCAACACTGGCGTCAGATAGT
* * * *
372495 TAAAAAAGTAATTCTTTTTTGTGTCATCATGTTGTCTGGCGACACTGGTGTTAGATAGT
1 TAAAAAAGTAATTCTTTTTTGTGTCATCATGTTGTCTAGCAACACTGGCGTCAGATAGT
372554 TAAAAAA
1 TAAAAAA
372561 AAATTGTGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
57 11 0.20
58 3 0.05
59 42 0.75
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (59 bp):
TAAAAAAGTAATTCTTTTTTGTGTCATCATGTTGTCTAGCAACACTGGCGTCAGATAGT
Found at i:375387 original size:29 final size:29
Alignment explanation
Indices: 375298--375389 Score: 116
Period size: 29 Copynumber: 3.2 Consensus size: 29
375288 ATTTGTGTAT
*
375298 TTTGGTATATTTTTGTTTTGAAGATTATG
1 TTTGGTATATTTATGTTTTGAAGATTATG
* * **
375327 TTTGGTATA-TGATGTTTTGTA-ATGGTG
1 TTTGGTATATTTATGTTTTGAAGATTATG
375354 CTTTGGTATATTTATGTTTTGAAGATTATG
1 -TTTGGTATATTTATGTTTTGAAGATTATG
375384 TTTGGT
1 TTTGGT
375390 TGATGGACTT
Statistics
Matches: 51, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 4 0.08
28 18 0.35
29 25 0.49
30 4 0.08
ACGTcount: A:0.20, C:0.01, G:0.24, T:0.55
Consensus pattern (29 bp):
TTTGGTATATTTATGTTTTGAAGATTATG
Found at i:377258 original size:15 final size:15
Alignment explanation
Indices: 377220--377259 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
377210 GTGGTTGCTG
*
377220 TGAATCCTACAAATC
1 TGAATCCTGCAAATC
* *
377235 TGAATCCTGTAAATT
1 TGAATCCTGCAAATC
377250 TGAATCCTGC
1 TGAATCCTGC
377260 TGAATCGAGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.12, T:0.33
Consensus pattern (15 bp):
TGAATCCTGCAAATC
Found at i:379608 original size:46 final size:46
Alignment explanation
Indices: 379541--379702 Score: 267
Period size: 46 Copynumber: 3.6 Consensus size: 46
379531 TTTGAGTACT
379541 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
379587 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
* *
379633 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAACTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
*
379678 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
379703 ATCATATGTA
Statistics
Matches: 111, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
43 12 0.11
44 5 0.05
45 18 0.16
46 76 0.68
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
Found at i:385409 original size:24 final size:24
Alignment explanation
Indices: 385361--385410 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
385351 AAAGAATTAT
*
385361 TAATTTAAAATGAAAAACTTAAAA
1 TAATTTAAAATGAAAAACATAAAA
385385 TAATTTGAAAAT-AAAAA-ATACAAA
1 TAATTT-AAAATGAAAAACATA-AAA
385409 TA
1 TA
385411 TTAATAAGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 2 0.09
24 16 0.70
25 5 0.22
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (24 bp):
TAATTTAAAATGAAAAACATAAAA
Found at i:385937 original size:6 final size:6
Alignment explanation
Indices: 385926--385955 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
385916 ATCCAGAGTT
*
385926 CCGAAC CCGAAC CCGAAC CCGAAC TCGAAC
1 CCGAAC CCGAAC CCGAAC CCGAAC CCGAAC
385956 AGATAAGTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.33, C:0.47, G:0.17, T:0.03
Consensus pattern (6 bp):
CCGAAC
Found at i:393320 original size:3 final size:3
Alignment explanation
Indices: 393314--393395 Score: 164
Period size: 3 Copynumber: 27.3 Consensus size: 3
393304 GATGATGATG
393314 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
393362 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
393396 AGTGTATAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:393536 original size:7 final size:7
Alignment explanation
Indices: 393524--393548 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
393514 TTGTTTGAAT
393524 AATTTTA
1 AATTTTA
393531 AATTTTA
1 AATTTTA
393538 AATTTTA
1 AATTTTA
393545 AATT
1 AATT
393549 ATTTTAAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
AATTTTA
Found at i:400192 original size:29 final size:29
Alignment explanation
Indices: 400148--400203 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
400138 TAGCTATTTG
* *
400148 AACTAATTAATTACATTGTAAAAATATTA
1 AACTAATTAATAACATTATAAAAATATTA
400177 AACTAATTAATAACATTATAAAAATAT
1 AACTAATTAATAACATTATAAAAATAT
400204 AGAGACCAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (29 bp):
AACTAATTAATAACATTATAAAAATATTA
Found at i:422239 original size:23 final size:23
Alignment explanation
Indices: 422212--422287 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
422202 AGTGTTATTG
422212 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
422235 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
422258 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
422281 ATCAGTG
1 ATCAGTG
422288 TGGCACTTAT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.21, C:0.21, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:443652 original size:39 final size:39
Alignment explanation
Indices: 443593--443670 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
443583 ACGTATGTCT
* *
443593 TGATTTTTTGTCAAAAATATATTTGAACACTGAAACAAA
1 TGATCTTTTGTCAAAAATATATATGAACACTGAAACAAA
* *
443632 TGATCTTTTGTCAAAAATATATATGTACATTGAAACAAA
1 TGATCTTTTGTCAAAAATATATATGAACACTGAAACAAA
443671 ATTATAGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (39 bp):
TGATCTTTTGTCAAAAATATATATGAACACTGAAACAAA
Found at i:445831 original size:3 final size:3
Alignment explanation
Indices: 445823--445879 Score: 114
Period size: 3 Copynumber: 19.0 Consensus size: 3
445813 TTAAAACAAC
445823 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
445871 TAA TAA TAA
1 TAA TAA TAA
445880 AAGACGAAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 54 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:457952 original size:20 final size:20
Alignment explanation
Indices: 457927--457966 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
457917 CGTAAAATGA
*
457927 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
457947 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
457967 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:457956 original size:34 final size:35
Alignment explanation
Indices: 457912--457978 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
457902 CAGTAAAATA
*
457912 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
457946 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
457979 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:457982 original size:14 final size:15
Alignment explanation
Indices: 457906--457982 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
457896 GATTGCCAGT
* *
457906 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
457920 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
457934 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
457954 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
457969 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
457983 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:458832 original size:30 final size:32
Alignment explanation
Indices: 458796--458857 Score: 92
Period size: 30 Copynumber: 2.0 Consensus size: 32
458786 TATAAAAAAA
**
458796 ATTTATTTTAGCT-TTTCATTTA-ATTTTTTT
1 ATTTATTTTAGCTCTTAAATTTATATTTTTTT
458826 ATTTATTTTAGCTCTTAAATTTATATTTTTTT
1 ATTTATTTTAGCTCTTAAATTTATATTTTTTT
458858 TGTCAAATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 13 0.46
31 7 0.25
32 8 0.29
ACGTcount: A:0.23, C:0.06, G:0.03, T:0.68
Consensus pattern (32 bp):
ATTTATTTTAGCTCTTAAATTTATATTTTTTT
Found at i:467738 original size:31 final size:29
Alignment explanation
Indices: 467700--467775 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
467690 TTAACAGCTC
*
467700 AGTGACTAAAATGTTACAACACGATAACATA
1 AGTGACTAAAATGTAACAACAC-A-AACATA
* ***
467731 AGTGACTAAAACGTAACATTTCAAACATA
1 AGTGACTAAAATGTAACAACACAAACATA
467760 AGTGACTAAAATGTAA
1 AGTGACTAAAATGTAA
467776 ACTGAGGCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 21 0.54
30 1 0.03
31 17 0.44
ACGTcount: A:0.49, C:0.14, G:0.13, T:0.24
Consensus pattern (29 bp):
AGTGACTAAAATGTAACAACACAAACATA
Found at i:473118 original size:22 final size:22
Alignment explanation
Indices: 473092--473141 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
473082 GACTCACATA
473092 CTTTTCTTCT-AATCCGCAATAT
1 CTTTTCTTCTAAATCCGCAA-AT
**
473114 CTTTT-TTCTAAATCTTCAAAT
1 CTTTTCTTCTAAATCCGCAAAT
473135 CTTTTCT
1 CTTTTCT
473142 GACTGACATC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.22, C:0.24, G:0.02, T:0.52
Consensus pattern (22 bp):
CTTTTCTTCTAAATCCGCAAAT
Found at i:498550 original size:28 final size:25
Alignment explanation
Indices: 498505--498563 Score: 64
Period size: 28 Copynumber: 2.2 Consensus size: 25
498495 TACGTACATA
*
498505 TATATACCTATATACATACATTTTTTT
1 TATATACATATATACAT--ATTTTTTT
* *
498532 GTATATACATATTTTCATATTTTTTT
1 -TATATACATATATACATATTTTTTT
498558 TATATA
1 TATATA
498564 TTTAACAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.21
26 8 0.29
28 14 0.50
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (25 bp):
TATATACATATATACATATTTTTTT
Found at i:513846 original size:20 final size:18
Alignment explanation
Indices: 513811--513866 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 18
513801 ATATAAAAAA
*
513811 TAAAATTTAAAAAAATTAT
1 TAAATTTTAAAAAAATT-T
513830 TAAATTTTAATAAAAATTT
1 TAAATTTTAA-AAAAATTT
*
513849 TCAAATTTATTAAAAAAT
1 T-AAATTT-TAAAAAAAT
513867 AGATTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 11 0.34
20 19 0.59
21 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATTTTAAAAAAATTT
Found at i:513989 original size:11 final size:11
Alignment explanation
Indices: 513963--513999 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
513953 TGATAAAAAA
513963 ATAAAAATTA-
1 ATAAAAATTAT
*
513973 ATAAAAGTTAT
1 ATAAAAATTAT
513984 ATAAAAATTAT
1 ATAAAAATTAT
513995 A-AAAA
1 ATAAAA
514000 GTTTCTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 13 0.54
11 11 0.46
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (11 bp):
ATAAAAATTAT
Found at i:514111 original size:46 final size:45
Alignment explanation
Indices: 514033--514137 Score: 122
Period size: 46 Copynumber: 2.3 Consensus size: 45
514023 TATAAATTAT
* * *
514033 TTTATGAAATTTATATTTCTTTACATTGTATAATTTTCTTACGA-C
1 TTTATAAAATTTATATTTCTATACATTGTATAATTTT-ATACGATC
* * *
514078 TTTATAAAATTTTATATTTCTATATATTTTATAATTTTATACGATT
1 TTTATAAAA-TTTATATTTCTATACATTGTATAATTTTATACGATC
514124 TTTATAAAAGTTTA
1 TTTATAAAA-TTTA
514138 CAATTTTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 13 0.25
46 38 0.75
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (45 bp):
TTTATAAAATTTATATTTCTATACATTGTATAATTTTATACGATC
Found at i:514128 original size:19 final size:18
Alignment explanation
Indices: 514104--514174 Score: 61
Period size: 19 Copynumber: 3.8 Consensus size: 18
514094 TTTCTATATA
514104 TTTTATAATTTTATACGAT
1 TTTTATAATTTT-TACGAT
** *
514123 TTTTATAAAAGTTTACAAT
1 TTTTAT-AATTTTTACGAT
* *
514142 TTTTATATTTTTTTATGAT
1 TTTTATA-ATTTTTACGAT
*
514161 TTTTATATTTTTTA
1 TTTTATAATTTTTA
514175 ACTGTTAATA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
18 8 0.19
19 30 0.71
20 4 0.10
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (18 bp):
TTTTATAATTTTTACGAT
Found at i:514429 original size:93 final size:92
Alignment explanation
Indices: 514292--514502 Score: 266
Period size: 92 Copynumber: 2.3 Consensus size: 92
514282 TAATTGCTTT
* * * * *
514292 TTTTTTTGAAAAAGTTTGAAGG-TCTTTTTTATGCATTTTGAAAGTTCAAGTACCTAAATGAGTG
1 TTTTTTTAAAAAAGTTTGAGGGCTTTTTTTTATGCATTTTAAAAGTTCAAGTACCAAAATGAGTG
* * * * * *
514356 CAAAAAAAGAGAGTAGGGGTTTAATTGC-
66 -AAAAAAA-AAAGCAGAGGCTTAAATACA
*
514384 TTTTTTTAAAAAAGTTTGAGGGCTTTTTTTTATGCATTTTAAAAGTTTAAGTACCAAAATGAGTG
1 TTTTTTTAAAAAAGTTTGAGGGCTTTTTTTTATGCATTTTAAAAGTTCAAGTACCAAAATGAGTG
514449 AAAAAAAAAAGCAGAGGCTTAAATACA
66 AAAAAAAAAAGCAGAGGCTTAAATACA
*
514476 TTTTTTGAAAAAA-TTTGAGGGCTTTTT
1 TTTTTTTAAAAAAGTTTGAGGGCTTTTT
514503 ACATCATTAA
Statistics
Matches: 104, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
91 27 0.26
92 39 0.38
93 38 0.37
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (92 bp):
TTTTTTTAAAAAAGTTTGAGGGCTTTTTTTTATGCATTTTAAAAGTTCAAGTACCAAAATGAGTG
AAAAAAAAAAGCAGAGGCTTAAATACA
Found at i:514498 original size:91 final size:92
Alignment explanation
Indices: 514293--514502 Score: 264
Period size: 91 Copynumber: 2.3 Consensus size: 92
514283 AATTGCTTTT
* * * * *
514293 TTTTTTGAAAAAGTTTGAAGG-TCTTTTTTATGCATTTTGAAAGTTCAAGTACCTAAATGAGTGC
1 TTTTTTGAAAAAATTTGAGGGCTTTTTTTTATGCATTTTAAAAGTTCAAGTACCAAAATGAGTGC
* * * * * *
514357 AAAAAAAGAGAGTAGGGGTTTAATTGC
66 AAAAAAAGAAAGCAGAGGCTTAAATAC
* *
514384 TTTTTTTAAAAAAGTTTGAGGGCTTTTTTTTATGCATTTTAAAAGTTTAAGTACCAAAATGAGTG
1 TTTTTTGAAAAAA-TTTGAGGGCTTTTTTTTATGCATTTTAAAAGTTCAAGTACCAAAATGAGTG
514449 -AAAAAAA-AAAGCAGAGGCTTAAATAC
65 CAAAAAAAGAAAGCAGAGGCTTAAATAC
514475 ATTTTTTGAAAAAATTTGAGGGCTTTTT
1 -TTTTTTGAAAAAATTTGAGGGCTTTTT
514503 ACATCATTAA
Statistics
Matches: 102, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
91 38 0.37
92 26 0.25
93 38 0.37
ACGTcount: A:0.36, C:0.07, G:0.19, T:0.38
Consensus pattern (92 bp):
TTTTTTGAAAAAATTTGAGGGCTTTTTTTTATGCATTTTAAAAGTTCAAGTACCAAAATGAGTGC
AAAAAAAGAAAGCAGAGGCTTAAATAC
Found at i:527217 original size:20 final size:20
Alignment explanation
Indices: 527170--527224 Score: 67
Period size: 19 Copynumber: 2.7 Consensus size: 20
527160 TAATCATTCT
527170 TTAAAAAATTTAAAAAAAAAC
1 TTAAAAAA-TTAAAAAAAAAC
* *
527191 TT-AAAAATTAAAAAAGAAG
1 TTAAAAAATTAAAAAAAAAC
527210 TTAAAAAATATAAAA
1 TTAAAAAAT-TAAAA
527225 GTATATAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 12 0.40
20 11 0.37
21 7 0.23
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (20 bp):
TTAAAAAATTAAAAAAAAAC
Found at i:527308 original size:21 final size:22
Alignment explanation
Indices: 527267--527308 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
527257 AATTGAAAAT
*
527267 AAATAAATTAAATATGTTTAAA
1 AAATAAATTAAATATGGTTAAA
*
527289 AAATAAA-TAAATTTGGTTAA
1 AAATAAATTAAATATGGTTAA
527309 TTTTTTAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (22 bp):
AAATAAATTAAATATGGTTAAA
Found at i:527352 original size:15 final size:15
Alignment explanation
Indices: 527328--527361 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
527318 GAATTACAAG
*
527328 AAAATGTAAAAATTT
1 AAAATGTAAAAAATT
*
527343 AAAATTTAAAAAATT
1 AAAATGTAAAAAATT
527358 AAAA
1 AAAA
527362 AATATATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
AAAATGTAAAAAATT
Found at i:536347 original size:16 final size:16
Alignment explanation
Indices: 536326--536356 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
536316 TAATATTATT
536326 TAATATTAAATTTAAA
1 TAATATTAAATTTAAA
536342 TAATATTAAATTTAA
1 TAATATTAAATTTAA
536357 TTTAATACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAATATTAAATTTAAA
Found at i:540299 original size:24 final size:25
Alignment explanation
Indices: 540250--540299 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 25
540240 GTTATAACTT
540250 TTTTTTATTTACCAAAAAATATATAA
1 TTTTTTATTTACC-AAAAATATATAA
540276 TTTTTTATTTACC-AAAATATATAA
1 TTTTTTATTTACCAAAAATATATAA
540300 AAAAACAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 11 0.46
26 13 0.54
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (25 bp):
TTTTTTATTTACCAAAAATATATAA
Found at i:540474 original size:18 final size:17
Alignment explanation
Indices: 540451--540628 Score: 82
Period size: 18 Copynumber: 10.0 Consensus size: 17
540441 GAAGGAGAGG
540451 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
540469 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
540486 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
540502 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
** *
540520 GGAAAGAAAAGGAAAGGGGA
1 GG-AAG-AAA-GAAAAAGAA
*
540540 GGAAAGAAAGAAAAATAA
1 GG-AAGAAAGAAAAAGAA
*
540558 GGAAAGAAAAGGAAAGGAGAA
1 GG-AAG-AAA-GAAA-AAGAA
540579 GAGAA-AAA-AAAAAGAA
1 G-GAAGAAAGAAAAAGAA
* * *
540595 AGAAGAAA-AAGAGGAAA
1 GGAAGAAAGAAAAAG-AA
540612 GGAAGGAAA-AAAAAGAA
1 GGAA-GAAAGAAAAAGAA
540629 AATAAGGTAN
Statistics
Matches: 126, Mismatches: 20, Indels: 29
0.72 0.11 0.17
Matches are distributed among these distances:
15 12 0.10
16 15 0.12
17 14 0.11
18 36 0.29
19 26 0.21
20 16 0.13
21 6 0.05
22 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:540484 original size:10 final size:10
Alignment explanation
Indices: 540453--540524 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
540443 AGGAGAGGGG
*
540453 AAGAAGAAGA
1 AAGAAAAAGA
540463 AAGAAAGGAAGA
1 AAGAAA--AAGA
540475 AAGAAAAAGA
1 AAGAAAAAGA
* *
540485 AGGAAAAGGA
1 AAGAAAAAGA
540495 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
540509 AAGAAAAAGA
1 AAGAAAAAGA
*
540519 AGGAAA
1 AAGAAA
540525 GAAAAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:540484 original size:22 final size:23
Alignment explanation
Indices: 540453--540629 Score: 82
Period size: 24 Copynumber: 7.5 Consensus size: 23
540443 AGGAGAGGGG
*
540453 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
540475 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
540497 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
* ***
540523 AAGAAAAGGAAAGGGGAGGAAAGA
1 AAGAAAAAGAAAGAAAAGG-AAGA
540547 AAGAAAAATAAGGAAAGAAAAGGAAAGGA
1 AAG--AAA-AA-GAAAGAAAAGG-AA-GA
* *
540576 GAAGAGAAA-AAA-AAAAGAAAG-
1 -AAGAAAAAGAAAGAAAAGGAAGA
*
540597 AAGAAAAAG--AGGAAAGGAAGGA
1 AAGAAAAAGAAAGAAAAGGAA-GA
540619 AA-AAAAAGAAA
1 AAGAAAAAGAAA
540630 ATAAGGTANN
Statistics
Matches: 115, Mismatches: 22, Indels: 35
0.67 0.13 0.20
Matches are distributed among these distances:
19 1 0.01
20 13 0.11
21 7 0.06
22 15 0.13
23 13 0.11
24 33 0.29
25 8 0.07
26 4 0.03
27 3 0.03
28 13 0.11
29 2 0.02
30 3 0.03
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:540511 original size:28 final size:28
Alignment explanation
Indices: 540456--540630 Score: 87
Period size: 28 Copynumber: 6.0 Consensus size: 28
540446 AGAGGGGAAG
540456 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
540481 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G-AA--A-AGGAAAGAAAGAAA
** *
540515 AAGAAGGAAAGAAAAGGAAAG-GGGAGGA
1 AAGAAGGAAAGAAAAGGAAAGAAAGA-AA
*
540543 AAGAAAGAAA-AATAAGGAAAGAAAAGGAAA
1 AAGAAGGAAAGAA-AAGGAAAG-AAA-GAAA
* * *
540573 GGAGAAGAGAAAAAAAAAAGAAAG-AAGAAA
1 -AAGAAG-G-AAAGAAAAGGAAAGAAAGAAA
* *
540603 AAG-AGGAAAG-GAAGGAAAAAAAAGAAA
1 AAGAAGGAAAGAAAAGG-AAAGAAAGAAA
540630 A
1 A
540631 TAAGGTANNN
Statistics
Matches: 115, Mismatches: 15, Indels: 38
0.68 0.09 0.23
Matches are distributed among these distances:
25 8 0.07
26 7 0.06
27 15 0.13
28 28 0.24
29 3 0.03
30 6 0.05
31 10 0.09
32 3 0.03
33 16 0.14
34 19 0.17
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.01
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:540529 original size:38 final size:37
Alignment explanation
Indices: 540471--540630 Score: 177
Period size: 38 Copynumber: 4.3 Consensus size: 37
540461 GAAAGAAAGG
540471 AAGAAAGAAAAAGAAG---GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGAAAGAAAAGGAAAGGAGAGGA
*
540505 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAA-GAAAGAAAAGGAAAGGAGAGGA
*
540543 AAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGAAGAGA
1 AAGAAAGAAAAAGAA-GAAAGAAAAGGAAAGGAG-AG-GA
* * *
540583 AAAAAAAAAGAAAGAAGAAA-AAGAGGAAAGGA-AGGAA
1 AAGAAAGAA-AAAGAAGAAAGAAAAGGAAAGGAGAGG-A
*
540620 AAAAAAGAAAA
1 AAGAAAGAAAA
540631 TAAGGTANNN
Statistics
Matches: 110, Mismatches: 8, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
34 15 0.14
35 1 0.01
36 3 0.03
37 11 0.10
38 49 0.45
39 13 0.12
40 13 0.12
41 5 0.05
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.01
Consensus pattern (37 bp):
AAGAAAGAAAAAGAAGAAAGAAAAGGAAAGGAGAGGA
Found at i:540531 original size:10 final size:10
Alignment explanation
Indices: 540473--540573 Score: 79
Period size: 10 Copynumber: 10.5 Consensus size: 10
540463 AAGAAAGGAA
*
540473 GAAAGAAAAA
1 GAAAGAAAAG
*
540483 GAAGGAAAAG
1 GAAAGAAAAG
* *
540493 GAAAGGAGAG
1 GAAAGAAAAG
540503 GAAAG-AAA-
1 GAAAGAAAAG
540511 GAAA-AAGAAG
1 GAAAGAA-AAG
540521 GAAAGAAAAG
1 GAAAGAAAAG
***
540531 GAAAGGGGAG
1 GAAAGAAAAG
540541 GAAAG-AAA-
1 GAAAGAAAAG
540549 GAAA-AATAAG
1 GAAAGAA-AAG
540559 GAAAGAAAAG
1 GAAAGAAAAG
540569 GAAAG
1 GAAAG
540574 GAGAAGAGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 16
0.73 0.11 0.16
Matches are distributed among these distances:
8 10 0.14
9 7 0.10
10 51 0.71
11 4 0.06
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:540629 original size:18 final size:19
Alignment explanation
Indices: 540487--540629 Score: 86
Period size: 18 Copynumber: 7.5 Consensus size: 19
540477 GAAAAAGAAG
*
540487 GAAAAGGAAAGGAGAGGAAA
1 GAAAAAGAAAGGA-AGGAAA
540507 GAAAGAA-AAA-GAAGGAAA
1 GAAA-AAGAAAGGAAGGAAA
* *
540525 GAAAAGGAAAGGGGAGGAAA
1 GAAAAAGAAA-GGAAGGAAA
*
540545 GAAAGAA-AAA-TAAGGAAA
1 GAAA-AAGAAAGGAAGGAAA
*
540563 GAAAAGGAAAGGAGAAGAGAAAA
1 GAAAAAGAAA-G-GAAG-G-AAA
*
540586 AAAAAAGAAA-GAA-GAAA
1 GAAAAAGAAAGGAAGGAAA
* *
540603 -AAGAGGAAAGGAAGGAAA
1 GAAAAAGAAAGGAAGGAAA
540621 -AAAAAGAAA
1 GAAAAAGAAA
540630 ATAAGGTANN
Statistics
Matches: 96, Mismatches: 14, Indels: 28
0.70 0.10 0.20
Matches are distributed among these distances:
16 7 0.07
17 8 0.08
18 38 0.40
19 2 0.02
20 24 0.25
21 5 0.05
22 1 0.01
23 11 0.11
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (19 bp):
GAAAAAGAAAGGAAGGAAA
Found at i:541652 original size:17 final size:17
Alignment explanation
Indices: 541630--541666 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
541620 ATAGGGTAAG
541630 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
541647 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
541664 ATG
1 ATG
541667 ACATATTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:542672 original size:15 final size:14
Alignment explanation
Indices: 542632--542660 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
542622 TTTTTGTATC
542632 AATTTAATTATTCT
1 AATTTAATTATTCT
542646 AATTTAATTATTCT
1 AATTTAATTATTCT
542660 A
1 A
542661 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:545066 original size:18 final size:18
Alignment explanation
Indices: 545040--545077 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
545030 ATCCCAATGA
* *
545040 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
545058 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
545076 TC
1 TC
545078 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Found at i:545084 original size:18 final size:18
Alignment explanation
Indices: 545043--545084 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
545033 CCAATGATCG
* *
545043 CCACCACCTTCTTCTTCG
1 CCACCACATTCTTCTTCA
*
545061 CAACCACATTCTTCTTCA
1 CCACCACATTCTTCTTCA
545079 CCACCA
1 CCACCA
545085 ACCATATCAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.48, G:0.02, T:0.29
Consensus pattern (18 bp):
CCACCACATTCTTCTTCA
Found at i:545796 original size:3 final size:3
Alignment explanation
Indices: 545790--545836 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
545780 AGTTTTTTAC
545790 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
545837 TAAAATTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:546165 original size:27 final size:27
Alignment explanation
Indices: 546127--546228 Score: 87
Period size: 27 Copynumber: 3.8 Consensus size: 27
546117 CGAGTAGTGT
** **
546127 CGCCAACCTGGTTGGCAGGACTGGTGC
1 CGCCAACCTGGTTCCCACCACTGGTGC
*
546154 CGCCAACCTGGTTCCCTCCACTGGTGC
1 CGCCAACCTGGTTCCCACCACTGGTGC
* *****
546181 CGCCAACCTGCTTCCCTTGTTTGGTGC
1 CGCCAACCTGGTTCCCACCACTGGTGC
* *
546208 CGCCAACCTGCTTCCCTCCAC
1 CGCCAACCTGGTTCCCACCAC
546229 CCAGGGAGTT
Statistics
Matches: 61, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.12, C:0.41, G:0.24, T:0.24
Consensus pattern (27 bp):
CGCCAACCTGGTTCCCACCACTGGTGC
Found at i:546272 original size:13 final size:12
Alignment explanation
Indices: 546254--546286 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
546244 ATCAGTTCAG
546254 GTTTTTTTTTTCT
1 GTTTTTTTTTT-T
546267 GTTTTTTTTTTT
1 GTTTTTTTTTTT
546279 GTTTTTTT
1 GTTTTTTT
546287 ATATTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (12 bp):
GTTTTTTTTTTT
Found at i:546273 original size:12 final size:12
Alignment explanation
Indices: 546256--546286 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
546246 CAGTTCAGGT
546256 TTTTTTTTTCTG
1 TTTTTTTTTCTG
*
546268 TTTTTTTTTTTG
1 TTTTTTTTTCTG
546280 TTTTTTT
1 TTTTTTT
546287 ATATTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.03, G:0.06, T:0.90
Consensus pattern (12 bp):
TTTTTTTTTCTG
Found at i:552695 original size:17 final size:16
Alignment explanation
Indices: 552675--552717 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
552665 AACTATTTCA
*
552675 AATTTAAATTAATTTTG
1 AATTTAAATTAA-TTCG
* *
552692 AATTCAAATCAATTCG
1 AATTTAAATTAATTCG
552708 AATTTAAATT
1 AATTTAAATT
552718 TATCTTTTTT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (16 bp):
AATTTAAATTAATTCG
Found at i:558941 original size:21 final size:22
Alignment explanation
Indices: 558900--558941 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
558890 TAAATATTAG
*
558900 ATTAAATTTAATATTAAATTTT
1 ATTAAATTTAATATGAAATTTT
558922 ATTAAA-TTAATA-GAATATTT
1 ATTAAATTTAATATGAA-ATTT
558942 ATCTACAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.11
21 10 0.56
22 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATTAAATTTAATATGAAATTTT
Found at i:563056 original size:13 final size:13
Alignment explanation
Indices: 563038--563086 Score: 55
Period size: 13 Copynumber: 3.5 Consensus size: 13
563028 TTTCCTAAAT
563038 TAAAAAATAATTA
1 TAAAAAATAATTA
563051 TAAAAAATAATAATA
1 TAAAAAATAAT--TA
563066 TATTAAAAAT-ATTA
1 TA--AAAAATAATTA
563080 TAAAAAA
1 TAAAAAA
563087 AGTATGCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
12 5 0.16
13 11 0.34
14 4 0.12
15 4 0.12
16 2 0.06
17 6 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAAAAATAATTA
Found at i:563075 original size:17 final size:16
Alignment explanation
Indices: 563039--563076 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
563029 TTCCTAAATT
563039 AAAA-AATAATTATAA
1 AAAATAATAATTATAA
*
563054 AAAATAATAATATATTA
1 AAAATAATAAT-TATAA
563071 AAAATA
1 AAAATA
563077 TTATAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 6 0.30
17 10 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAATAATTATAA
Found at i:570813 original size:16 final size:15
Alignment explanation
Indices: 570787--570817 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
570777 AAAATTATTC
570787 AAAATATTAAAAATT
1 AAAATATTAAAAATT
570802 AAAATAATTAAAAATT
1 AAAAT-ATTAAAAATT
570818 TTAGTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AAAATATTAAAAATT
Found at i:571650 original size:20 final size:20
Alignment explanation
Indices: 571625--571667 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
571615 TTCGATTTCA
571625 AATATGTTTGTATGCAATGG
1 AATATGTTTGTATGCAATGG
*
571645 AATATGTTTGTATGTAATGG
1 AATATGTTTGTATGCAATGG
571665 AAT
1 AAT
571668 TTATAACATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.02, G:0.23, T:0.42
Consensus pattern (20 bp):
AATATGTTTGTATGCAATGG
Found at i:577644 original size:66 final size:66
Alignment explanation
Indices: 577538--577670 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
577528 AGGAAAAGCA
577538 AGCATTGATTCAGTGTATTGATTGACAATGTTGGTACATGTAACATTAGTTATATGGGAATCTCC
1 AGCATTGATTCAGTGTATTGATTGACAATGTTGGTACATGTAACATTAGTTATATGGGAATCTCC
577603 C
66 C
577604 AGCATTGATTCAGTGTATTGATTGACAATGTTGGTACATGTAACATTAGTTATATGGGAATCTCC
1 AGCATTGATTCAGTGTATTGATTGACAATGTTGGTACATGTAACATTAGTTATATGGGAATCTCC
577669 C
66 C
577670 A
1 A
577671 ATCTATTTAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (66 bp):
AGCATTGATTCAGTGTATTGATTGACAATGTTGGTACATGTAACATTAGTTATATGGGAATCTCC
C
Found at i:582575 original size:85 final size:84
Alignment explanation
Indices: 582406--582578 Score: 206
Period size: 85 Copynumber: 2.0 Consensus size: 84
582396 GAAGTGGTAG
* *
582406 AAAAAGTGAAAGAGGAGGCGAAAGGAAAATATTGCGCGAAGTATTGGCTTCCACCACCGCTACCT
1 AAAAAGTCAAAGAGGAGGCGAAAGGAAAAGATTGCGCGAAGTATTGGCTTCCACCACCGCTACCT
* *
582471 TTGTTGCCATTATGTTTAT
66 TTGCTGCCAGTATGTTTAT
* * ** * *
582490 AAAAATGTCAAAGAGGAGGCGGAAGGAAAAGATTGTGTTAAGTATTGGCTTCCACCGCTGCTACC
1 AAAAA-GTCAAAGAGGAGGCGAAAGGAAAAGATTGCGCGAAGTATTGGCTTCCACCACCGCTACC
*
582555 ATTT-CTGTCAGTATAG-TTAT
65 -TTTGCTGCCAGTAT-GTTTAT
582575 AAAA
1 AAAA
582579 GTTGAAATTG
Statistics
Matches: 75, Mismatches: 11, Indels: 5
0.82 0.12 0.05
Matches are distributed among these distances:
84 5 0.07
85 66 0.88
86 4 0.05
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.27
Consensus pattern (84 bp):
AAAAAGTCAAAGAGGAGGCGAAAGGAAAAGATTGCGCGAAGTATTGGCTTCCACCACCGCTACCT
TTGCTGCCAGTATGTTTAT
Found at i:583320 original size:168 final size:168
Alignment explanation
Indices: 583024--583348 Score: 418
Period size: 168 Copynumber: 1.9 Consensus size: 168
583014 ATTGGGCCTC
* ** * * *
583024 AGAACCCAAAACCGAGATTGAGACCCAAAAACTAGTTGAATCAGGCTTGGTATGTGAAACTGAGA
1 AGAACCCAAAACCAAGATCAAGACCCAAAAACTAGTCGAATCAGGCCTGATATGTGAAACTGAGA
** * * * * *
583089 CGATGATCCAACCGGTGGCTGGGCCGGACCAGTTAGGCCATCACTAGGTCAAGACCGAACCGGCT
66 AAATGATCCAACCAGTGGCTAGACCGGACCAGTGAGGCCATCACTAGGTCAAGACCAAACCGGCT
*
583154 CAGGGTGTCGTGAGGGTGTCGCACCTGTAATGGCACAT
131 CAGGGTGCCGTGAGGGTGTCGCACCTGTAATGGCACAT
* * *
583192 AGAACCCAAAACCAAGATCAATACCCAAAAACTGGTCGAATCAGGCCTGATATGTGAAACTGGGA
1 AGAACCCAAAACCAAGATCAAGACCCAAAAACTAGTCGAATCAGGCCTGATATGTGAAACTGAGA
** * * * *
583257 AAATGATCCAACCAGTGGCTAGATTGGACCAGTCGA-GCCGTCATTAGGTCCAGACTAAACCGGC
66 AAATGATCCAACCAGTGGCTAGACCGGACCAGT-GAGGCCATCACTAGGTCAAGACCAAACCGGC
*
583321 TCGGGGTGCCGTGAGGGTGTCGCACCTG
130 TCAGGGTGCCGTGAGGGTGTCGCACCTG
583349 CGATAGCACA
Statistics
Matches: 132, Mismatches: 24, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
168 131 0.99
169 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (168 bp):
AGAACCCAAAACCAAGATCAAGACCCAAAAACTAGTCGAATCAGGCCTGATATGTGAAACTGAGA
AAATGATCCAACCAGTGGCTAGACCGGACCAGTGAGGCCATCACTAGGTCAAGACCAAACCGGCT
CAGGGTGCCGTGAGGGTGTCGCACCTGTAATGGCACAT
Found at i:583485 original size:11 final size:11
Alignment explanation
Indices: 583458--583534 Score: 52
Period size: 11 Copynumber: 6.8 Consensus size: 11
583448 ATTTCAAAAA
583458 TAATATT-ATT
1 TAATATTAATT
*
583468 TTA-ATTAATT
1 TAATATTAATT
583478 TAATATTAAATT
1 TAATATT-AATT
583490 TAAT-TTAATT
1 TAATATTAATT
*
583500 CTTATATTAATAT
1 -TAATATTAAT-T
* *
583513 TACTTTATTAACT
1 TA--ATATTAATT
583526 TAATATTAA
1 TAATATTAA
583535 AGTGATTATC
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
9 3 0.06
10 11 0.21
11 14 0.27
12 14 0.27
13 4 0.08
14 6 0.12
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (11 bp):
TAATATTAATT
Found at i:583659 original size:58 final size:59
Alignment explanation
Indices: 583518--583667 Score: 141
Period size: 58 Copynumber: 2.6 Consensus size: 59
583508 AATATTACTT
* * * *
583518 TATTAACTTAATATTAAAGTGATT--ATCTTAATATTAATTTTAATTAAGATAAATATTC
1 TATTAATTTAATATTAAAGTGATTAAAT-TTAATACTAATTTTAATCAAGATAAATATTA
* ** *
583576 TATTAATTTAATAAATTCAA-T-ATTAAATTTAAT-CTAATATTT-ATCCTGATAAGTATTA
1 TATTAATTTAAT--ATTAAAGTGATTAAATTTAATACTAAT-TTTAATCAAGATAAATATTA
*
583634 TATTAATTTAATATTAAAGTGATTAAGTTTAATA
1 TATTAATTTAATATTAAAGTGATTAAATTTAATA
583668 ATAGTTGAAC
Statistics
Matches: 74, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
56 5 0.07
57 1 0.01
58 52 0.70
59 9 0.12
60 7 0.09
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (59 bp):
TATTAATTTAATATTAAAGTGATTAAATTTAATACTAATTTTAATCAAGATAAATATTA
Found at i:584064 original size:2 final size:2
Alignment explanation
Indices: 584057--584097 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
584047 AACCTTTTGC
584057 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
584098 TAATACTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:589059 original size:30 final size:30
Alignment explanation
Indices: 589018--589077 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
589008 AGTAATTTGT
* *
589018 AAAGGGTTTTAGTTAAGCTACAAAAACTAG
1 AAAGGGCTTTAGTTAAGCCACAAAAACTAG
*
589048 AAAGGGCTTTAGTTTAGCCACAAAAACTAG
1 AAAGGGCTTTAGTTAAGCCACAAAAACTAG
589078 GGGAAATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.25
Consensus pattern (30 bp):
AAAGGGCTTTAGTTAAGCCACAAAAACTAG
Found at i:590173 original size:20 final size:19
Alignment explanation
Indices: 590150--590202 Score: 52
Period size: 22 Copynumber: 2.6 Consensus size: 19
590140 TATCTCTCAA
*
590150 CAAAAATTATAAAAATAATT
1 CAAAAATTATAAAAA-AATC
590170 CAAAATATTTAATAAAAAAATC
1 CAAAA-A-TT-ATAAAAAAATC
*
590192 CAAAATTTATA
1 CAAAAATTATA
590203 TTTAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 3 0.11
20 7 0.25
21 1 0.04
22 10 0.36
23 7 0.25
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.30
Consensus pattern (19 bp):
CAAAAATTATAAAAAAATC
Found at i:592651 original size:14 final size:14
Alignment explanation
Indices: 592632--592658 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
592622 AAATATTTAA
592632 TATAAATTTTAGAT
1 TATAAATTTTAGAT
592646 TATAAATTTTAGA
1 TATAAATTTTAGA
592659 GCGGTGAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (14 bp):
TATAAATTTTAGAT
Found at i:595401 original size:22 final size:20
Alignment explanation
Indices: 595375--595422 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
595365 AGAAGAGAAT
595375 AGAAAATAAAGAGAGAAAAAAA
1 AGAAAATAAA-A-AGAAAAAAA
* * *
595397 AGAAAGTTAAAAGAATAAAA
1 AGAAAATAAAAAGAAAAAAA
595417 AGAAAA
1 AGAAAA
595423 CAATTAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 13 0.59
21 1 0.05
22 8 0.36
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (20 bp):
AGAAAATAAAAAGAAAAAAA
Found at i:609422 original size:20 final size:20
Alignment explanation
Indices: 609397--609436 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
609387 CGTAAAATAA
*
609397 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
609417 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
609437 GAAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:609426 original size:34 final size:35
Alignment explanation
Indices: 609382--609448 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
609372 CAGTAAAATA
* *
609382 TTTTCCGTAAAATAATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
* *
609416 TTTTCTGTAAAATGATTTACTGAAAAATATTTT
1 TTTTCCGTAAAATAATTTACTGAAAAATATTTT
609449 TTGGTGTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATAATTTACTGAAAAATATTTTAC
Found at i:617906 original size:21 final size:19
Alignment explanation
Indices: 617861--617909 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
617851 ATTTTAAAAA
617861 ATAATTTTTTGAATTTTTG
1 ATAATTTTTTGAATTTTTG
* *
617880 AAAATTATTTTGAACTTTTTT
1 ATAATT-TTTTGAA-TTTTTG
617901 ATAATTTTT
1 ATAATTTTT
617910 GTTGAGAGAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 5 0.20
20 10 0.40
21 10 0.40
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (19 bp):
ATAATTTTTTGAATTTTTG
Found at i:617914 original size:22 final size:20
Alignment explanation
Indices: 617861--617914 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
617851 ATTTTAAAAA
617861 ATAA-TTTTTTGAATTTTTG
1 ATAATTTTTTTGAATTTTTG
* * *
617880 AAAATTATTTTGAACTTTTTT
1 ATAATTTTTTTGAA-TTTTTG
617901 ATAATTTTTGTTGA
1 ATAATTTTT-TTGA
617915 GAGAGAGACC
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 3 0.11
20 8 0.30
21 12 0.44
22 4 0.15
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (20 bp):
ATAATTTTTTTGAATTTTTG
Found at i:618784 original size:53 final size:53
Alignment explanation
Indices: 618704--618812 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
618694 TAGTTGGACC
618704 ATGAAATGAATAAAGAAATAAAGAAAGAAACTATCTTGGATTAAAAGGAACCT
1 ATGAAATGAATAAAGAAATAAAGAAAGAAACTATCTTGGATTAAAAGGAACCT
618757 ATGAAATGAATAAAGAAATAAAGAAAGAAACTATCTTGGATTAAAAGGAACCT
1 ATGAAATGAATAAAGAAATAAAGAAAGAAACTATCTTGGATTAAAAGGAACCT
618810 ATG
1 ATG
618813 CTTGTGGGTC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.54, C:0.07, G:0.17, T:0.21
Consensus pattern (53 bp):
ATGAAATGAATAAAGAAATAAAGAAAGAAACTATCTTGGATTAAAAGGAACCT
Found at i:626674 original size:26 final size:28
Alignment explanation
Indices: 626626--626679 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 28
626616 GTTCTCCTCT
* *
626626 GTTTTCTTCTTTTTACCCACTCCTTTTG
1 GTTTTCCTCTTTTTAACCACTCCTTTTG
626654 GTTTTCCTC-TTTTAACC-CTCCTTTTG
1 GTTTTCCTCTTTTTAACCACTCCTTTTG
626680 TAAGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.38
27 7 0.29
28 8 0.33
ACGTcount: A:0.07, C:0.30, G:0.07, T:0.56
Consensus pattern (28 bp):
GTTTTCCTCTTTTTAACCACTCCTTTTG
Found at i:632439 original size:14 final size:14
Alignment explanation
Indices: 632403--632436 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
632393 TCATCATTTA
632403 CCTATAACCAAAAC
1 CCTATAACCAAAAC
632417 CCTATAACCAAAAC
1 CCTATAACCAAAAC
632431 CC-ATAA
1 CCTATAA
632437 ACCCATACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (14 bp):
CCTATAACCAAAAC
Found at i:639871 original size:21 final size:20
Alignment explanation
Indices: 639847--639887 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
639837 TTTTTTTGTA
639847 TTTATAGAAATGGATTGAATT
1 TTTAT-GAAATGGATTGAATT
* *
639868 TTTATTAAATTGATTGAATT
1 TTTATGAAATGGATTGAATT
639888 GATATCATGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
TTTATGAAATGGATTGAATT
Found at i:644368 original size:9 final size:9
Alignment explanation
Indices: 644354--644384 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
644344 GTTAAACGAA
644354 TCGAGTTAT
1 TCGAGTTAT
*
644363 TCGAGTTAA
1 TCGAGTTAT
644372 TCGAGTTAT
1 TCGAGTTAT
644381 TCGA
1 TCGA
644385 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:649252 original size:20 final size:19
Alignment explanation
Indices: 649227--649265 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
649217 TCCTATGCAA
649227 TGATGGATGGCATTAATTTC
1 TGATGG-TGGCATTAATTTC
* *
649247 TGATGGTGGGATTCATTTC
1 TGATGGTGGCATTAATTTC
649266 ATAAGCAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.21, C:0.10, G:0.28, T:0.41
Consensus pattern (19 bp):
TGATGGTGGCATTAATTTC
Found at i:652931 original size:16 final size:15
Alignment explanation
Indices: 652897--652947 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 15
652887 AACAGATTTT
652897 AAAAAAC-AAA-GAA
1 AAAAAACAAAATGAA
*
652910 ACAAAAACAAAATTAA
1 A-AAAAACAAAATGAA
*
652926 AGAAAAATAAAATGAA
1 A-AAAAACAAAATGAA
652942 AAAAAA
1 AAAAAA
652948 ATCCAAACCG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
13 1 0.03
14 6 0.19
15 8 0.26
16 16 0.52
ACGTcount: A:0.80, C:0.06, G:0.06, T:0.08
Consensus pattern (15 bp):
AAAAAACAAAATGAA
Found at i:661360 original size:2 final size:2
Alignment explanation
Indices: 661353--661399 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
661343 TGAATGCACC
* * **
661353 AT AT AT AT AC AT AT AC AT AT GC AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
661395 AT AT A
1 AT AT A
661400 ATAGTATAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (2 bp):
AT
Found at i:663681 original size:50 final size:47
Alignment explanation
Indices: 663589--663688 Score: 105
Period size: 50 Copynumber: 2.0 Consensus size: 47
663579 GAAATATAAG
663589 GATTAAAACTAAAATTTAACCATTATTATATAATCTCAAAAAAGTAAAAA
1 GATTAAAACTAAAATTTAACCA-TATTATATAATCTCAAAAAA--AAAAA
* * *
663639 GATTAGAACTAAAATTT-AGCA-ATTATATATTCTCATGTAAAAAAAAAA
1 GATTAAAACTAAAATTTAACCATATTATATAATCTCA---AAAAAAAAAA
663687 GA
1 GA
663689 GAAAAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
47 13 0.30
48 7 0.16
49 3 0.07
50 21 0.48
ACGTcount: A:0.54, C:0.09, G:0.07, T:0.30
Consensus pattern (47 bp):
GATTAAAACTAAAATTTAACCATATTATATAATCTCAAAAAAAAAAA
Found at i:665604 original size:21 final size:21
Alignment explanation
Indices: 665578--665622 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
665568 ACTTTATGGA
* *
665578 GAAAATGGTGTTGTACAGGAT
1 GAAAATGATGTTGTACAAGAT
*
665599 GAAAATGATGTTGTAGAAGAT
1 GAAAATGATGTTGTACAAGAT
665620 GAA
1 GAA
665623 GTACTTTGTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.40, C:0.02, G:0.31, T:0.27
Consensus pattern (21 bp):
GAAAATGATGTTGTACAAGAT
Found at i:665652 original size:36 final size:34
Alignment explanation
Indices: 665599--665693 Score: 113
Period size: 33 Copynumber: 2.8 Consensus size: 34
665589 TGTACAGGAT
*
665599 GAAAATGATGTTGTAGAAGATGAAGTACTTTGTGAA
1 GAAAATGATGTTGTAGAAGATGAAGTA--TTATGAA
* *
665635 GAAAATGATATTTTAGAAGAT-ATAG-ATTATGAA
1 GAAAATGATGTTGTAGAAGATGA-AGTATTATGAA
*
665668 GAAAATGGTGTTGTAGAAGATGAAGT
1 GAAAATGATGTTGTAGAAGATGAAGT
665694 TGAAGGAGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
33 26 0.52
34 1 0.02
35 2 0.04
36 21 0.42
ACGTcount: A:0.42, C:0.01, G:0.26, T:0.31
Consensus pattern (34 bp):
GAAAATGATGTTGTAGAAGATGAAGTATTATGAA
Found at i:671323 original size:15 final size:15
Alignment explanation
Indices: 671303--671356 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
671293 ATACTACAAA
671303 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
671318 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
671335 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
671352 ATATT
1 ATATT
671357 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:671443 original size:13 final size:13
Alignment explanation
Indices: 671427--671482 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
671417 AAAATTGAAA
671427 TATTAAATTAATT
1 TATTAAATTAATT
* *
671440 TATTAAAATAATA
1 TATTAAATTAATT
* *
671453 AATTATATTAATT
1 TATTAAATTAATT
671466 ATATT-AA-TAATT
1 -TATTAAATTAATT
671478 TATTA
1 TATTA
671483 TATGACAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
11 4 0.12
12 5 0.15
13 21 0.64
14 3 0.09
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATTAAATTAATT
Found at i:671473 original size:22 final size:22
Alignment explanation
Indices: 671419--671480 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 22
671409 ATTAAAATAA
* *
671419 AATTGAAATATTAAATTA-ATT
1 AATTAAAATAATAAATTATATT
*
671440 TATTAAAATAATAAATTATATT
1 AATTAAAATAATAAATTATATT
* * *
671462 AATTATATTAATAATTTAT
1 AATTAAAATAATAAATTAT
671481 TATATGACAA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
21 15 0.45
22 18 0.55
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (22 bp):
AATTAAAATAATAAATTATATT
Found at i:671547 original size:22 final size:22
Alignment explanation
Indices: 671522--671566 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
671512 ATATTTAATA
671522 ATATTGAAAATTATAAT-ATTTT
1 ATATT-AAAATTATAATAATTTT
* *
671544 ATATTAATATTTTAATAATTTT
1 ATATTAAAATTATAATAATTTT
671566 A
1 A
671567 AATACATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATATTAAAATTATAATAATTTT
Found at i:674073 original size:20 final size:20
Alignment explanation
Indices: 674050--674087 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
674040 ATTTGTTATT
* *
674050 TTAATTTTTTTATTATTAAA
1 TTAATTATTTTAATATTAAA
674070 TTAATTATTTTAATATTA
1 TTAATTATTTTAATATTA
674088 TTAATACTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
TTAATTATTTTAATATTAAA
Found at i:674131 original size:3 final size:3
Alignment explanation
Indices: 674123--674169 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
674113 ATCTTGTATC
674123 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
674170 ATTCATATGC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:674486 original size:16 final size:16
Alignment explanation
Indices: 674448--674478 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
674438 TATGTTATAA
*
674448 TATATATATATATATG
1 TATATTTATATATATG
674464 TATATTTATATATAT
1 TATATTTATATATAT
674479 TTTTATTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTTATATATATG
Found at i:679809 original size:21 final size:22
Alignment explanation
Indices: 679780--679820 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
679770 CCTATACACT
*
679780 CTCTCTCCTCTAATTTCCTCGG
1 CTCTCTCCTCTAATCTCCTCGG
*
679802 CTCT-TCCTCTCATCTCCTC
1 CTCTCTCCTCTAATCTCCTC
679821 TCTTGCAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.07, C:0.46, G:0.05, T:0.41
Consensus pattern (22 bp):
CTCTCTCCTCTAATCTCCTCGG
Found at i:696333 original size:19 final size:19
Alignment explanation
Indices: 696309--696345 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
696299 ATAACATATC
* *
696309 AATTAAATATAATTTAAAA
1 AATTAAAAAAAATTTAAAA
696328 AATTAAAAAAAATTTAAA
1 AATTAAAAAAAATTTAAA
696346 GTTAGGATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AATTAAAAAAAATTTAAAA
Found at i:705371 original size:68 final size:67
Alignment explanation
Indices: 705279--705486 Score: 218
Period size: 62 Copynumber: 3.1 Consensus size: 67
705269 ATTTTAATAA
* * *
705279 ATTTAATATTAAATTTAATTTAATACTTATCTCAATAGTATTTTATTAATTTAATATTAAAGTGA
1 ATTTAATATTAAATTTAATTTAATATTTATCTTAATAATATTTTATTAATTTAATATTAAAGTGA
705344 TT
66 TT
705346 ATCTTAATATTAAATTTAATTTAATATTTATCTTGTAGATAAATATTTTATTAATTT-A-A-T--
1 AT-TTAATATTAAATTTAATTTAATATTTATC-T-TA-AT-AATATTTTATTAATTTAATATTAA
705406 A---A-T
61 AGTGATT
* * * *
705409 ATTTAATATTAAATTTAATCTAATATTTATCTTGAGAATATTATATTAAATTTAATATTAAAGTG
1 ATTTAATATTAAATTTAATTTAATATTTATCTTAATAATATTTTATT-AATTTAATATTAAAGTG
705474 ATT
65 ATT
705477 AAGTTTAATA
1 -A-TTTAATA
705487 ATAATTGAAT
Statistics
Matches: 117, Mismatches: 7, Indels: 31
0.75 0.05 0.20
Matches are distributed among these distances:
58 10 0.09
59 6 0.05
60 2 0.02
61 2 0.02
62 29 0.25
63 3 0.03
64 2 0.02
67 4 0.03
68 29 0.25
69 3 0.03
70 9 0.08
71 3 0.03
72 15 0.13
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.50
Consensus pattern (67 bp):
ATTTAATATTAAATTTAATTTAATATTTATCTTAATAATATTTTATTAATTTAATATTAAAGTGA
TT
Found at i:705409 original size:19 final size:21
Alignment explanation
Indices: 705387--705438 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 21
705377 CTTGTAGATA
705387 AATATTT-TATT-AATTTAAT
1 AATATTTATATTAAATTTAAT
705406 AATATTTAATATTAAATTTAATCT
1 AATATTT-ATATTAAATTTAA--T
705430 AATATTTAT
1 AATATTTAT
705439 CTTGAGAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 7 0.25
21 4 0.14
22 7 0.25
23 2 0.07
24 8 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
AATATTTATATTAAATTTAAT
Found at i:705449 original size:32 final size:32
Alignment explanation
Indices: 705351--705467 Score: 102
Period size: 32 Copynumber: 3.7 Consensus size: 32
705341 TGATTATCTT
705351 AATATTAAATTTAATTTAATATTTATCTTGTAG
1 AATATTAAATTTAATTTAATATTTATCTTG-AG
** *
705384 ATAAATATTTTA-TTAATTTAATA-ATAT-TT---
1 ---AATATTAAATTTAATTTAATATTTATCTTGAG
*
705413 AATATTAAATTTAATCTAATATTTATCTTGAG
1 AATATTAAATTTAATTTAATATTTATCTTGAG
* *
705445 AATATTATATTAAATTTAATATT
1 AATATTAAATTTAATTTAATATT
705468 AAAGTGATTA
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
26 7 0.11
27 10 0.15
28 3 0.05
29 2 0.03
32 20 0.31
33 2 0.03
34 3 0.05
35 11 0.17
36 7 0.11
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (32 bp):
AATATTAAATTTAATTTAATATTTATCTTGAG
Found at i:707781 original size:29 final size:29
Alignment explanation
Indices: 707713--707785 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
707703 TCAAAAAAGC
* *
707713 ATAGGGACTAAAATTGAGCAATTTGAAAA
1 ATAGGGACTAAATTTGAGCAAATTGAAAA
*
707742 ATAAGGAGACTAAATTTGATCAAATT-AAAA
1 AT-AGG-GACTAAATTTGAGCAAATTGAAAA
707772 TATAGGGACTAAAT
1 -ATAGGGACTAAAT
707786 CTACAACTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
29 10 0.26
30 10 0.26
31 18 0.47
ACGTcount: A:0.49, C:0.07, G:0.18, T:0.26
Consensus pattern (29 bp):
ATAGGGACTAAATTTGAGCAAATTGAAAA
Found at i:708261 original size:2 final size:2
Alignment explanation
Indices: 708254--708304 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
708244 NNNNNNNNAG
708254 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
708296 TA TA TA TA T
1 TA TA TA TA T
708305 TAATTTTTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:713096 original size:3 final size:3
Alignment explanation
Indices: 713088--713121 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
713078 AATAAAGAGG
713088 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
713122 TCCCCACCTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:717027 original size:2 final size:2
Alignment explanation
Indices: 717020--717062 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
717010 ATCTTACGTT
717020 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
717061 TA
1 TA
717063 GAATTATTTC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:718443 original size:32 final size:29
Alignment explanation
Indices: 718402--718462 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 29
718392 TTTTCCAGAG
*
718402 TTTTTATATTTTTTTGAATTTTGAATATTAT
1 TTTTTATATTTTTAT-AATTTTGAA-ATTAT
*
718433 TTTTTAATATTTTTATAATTTTTAAATTAT
1 TTTTT-ATATTTTTATAATTTTGAAATTAT
718463 CTATTGGCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 5 0.19
31 13 0.48
32 9 0.33
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (29 bp):
TTTTTATATTTTTATAATTTTGAAATTAT
Found at i:720956 original size:2 final size:2
Alignment explanation
Indices: 720949--720979 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
720939 GAATAATAAA
720949 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
720980 GTACATGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:720999 original size:21 final size:21
Alignment explanation
Indices: 720975--721018 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
720965 ATATATATAT
*
720975 AATATGTACATGTATTTACAA
1 AATATGTACATATATTTACAA
*
720996 AATATGTACATATATTTATAA
1 AATATGTACATATATTTACAA
721017 AA
1 AA
721019 AAATAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.39
Consensus pattern (21 bp):
AATATGTACATATATTTACAA
Done.