Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009609.1 Hibiscus syriacus cultivar Beakdansim tig00116995_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: 1078827
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:338356 original size:21 final size:21
Alignment explanation
Indices: 338330--338373 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
338320 TCGGTAAAAA
*
338330 TTATTTAAAATATTATTATTT
1 TTATTTAAAATATTAATATTT
338351 TTATTTAAAATATTAATATTT
1 TTATTTAAAATATTAATATTT
338372 TT
1 TT
338374 TAATATTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTATTTAAAATATTAATATTT
Found at i:338805 original size:2 final size:2
Alignment explanation
Indices: 338798--338875 Score: 149
Period size: 2 Copynumber: 39.5 Consensus size: 2
338788 TTGTAGAAAT
338798 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
338839 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 T
338876 GTTTAGGCCT
Statistics
Matches: 75, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.01
2 74 0.99
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:343834 original size:24 final size:24
Alignment explanation
Indices: 343821--343939 Score: 177
Period size: 24 Copynumber: 5.0 Consensus size: 24
343811 AAGCATAATT
*
343821 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
* *
343845 CAGGTCAAGTATCAAATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
*
343869 CAAGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
343893 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCATATCAGAATC
*
343917 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
343940 TCAAATCGAA
Statistics
Matches: 86, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
23 2 0.02
24 82 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:343936 original size:48 final size:48
Alignment explanation
Indices: 343807--343939 Score: 178
Period size: 48 Copynumber: 2.8 Consensus size: 48
343797 TATATCAAAA
* * * *
343807 ATCAAAGCATAATTCATGTCAAGTATCATATCAAAATCCAGGTCAAGT
1 ATCAAATCAGAATCCATGTCAAGTATCATATCAGAATCCAGGTCAAGT
* *
343855 ATCAAATCAGAATCCAAGTCAAGTATCATATCAGAATCCATGTC-AGAT
1 ATCAAATCAGAATCCATGTCAAGTATCATATCAGAATCCAGGTCAAG-T
* *
343903 ATCATATCAGAATCCATGTCAAGTATCAGATCAGAAT
1 ATCAAATCAGAATCCATGTCAAGTATCATATCAGAAT
343940 TCAAATCGAA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
47 2 0.03
48 73 0.97
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (48 bp):
ATCAAATCAGAATCCATGTCAAGTATCATATCAGAATCCAGGTCAAGT
Found at i:364751 original size:29 final size:29
Alignment explanation
Indices: 364717--364772 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
364707 TTTTAAAAAA
*
364717 ATTAATTCGATTAACAGTTAA-TAAATTTG
1 ATTAATTCAATTAACAG-TAATTAAATTTG
*
364746 ATTAATTCAATTAATAGTAATTAAATT
1 ATTAATTCAATTAACAGTAATTAAATT
364773 AGGTCGGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.45, C:0.05, G:0.07, T:0.43
Consensus pattern (29 bp):
ATTAATTCAATTAACAGTAATTAAATTTG
Found at i:365012 original size:18 final size:20
Alignment explanation
Indices: 364974--365013 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
364964 CACCCTCCTA
364974 AATTTATGTACTAATAATTT
1 AATTTATGTACTAATAATTT
*
364994 AATTTAT-TA-TAATATTTT
1 AATTTATGTACTAATAATTT
365012 AA
1 AA
365014 ACTTATCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 2 0.11
20 7 0.37
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (20 bp):
AATTTATGTACTAATAATTT
Found at i:367241 original size:31 final size:31
Alignment explanation
Indices: 367203--367261 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
367193 GGGGAAATGA
* *
367203 TCCCTAACGTTATCGATCCATTCGATTTGAT
1 TCCCTAACATTATCGATCCATTCAATTTGAT
*
367234 TCCCTAACATTATCGATCCGTTCAATTT
1 TCCCTAACATTATCGATCCATTCAATTT
367262 TAGTCCCTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.24, C:0.27, G:0.10, T:0.39
Consensus pattern (31 bp):
TCCCTAACATTATCGATCCATTCAATTTGAT
Found at i:367269 original size:31 final size:31
Alignment explanation
Indices: 367203--367269 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
367193 GGGGAAATGA
* * *
367203 TCCCTAACGTTATCGATCCATTCGATTTGAT
1 TCCCTAACATTATCGATCCATTCAATTTGAG
* *
367234 TCCCTAACATTATCGATCCGTTCAATTTTAG
1 TCCCTAACATTATCGATCCATTCAATTTGAG
367265 TCCCT
1 TCCCT
367270 CAGTCATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.28, G:0.10, T:0.39
Consensus pattern (31 bp):
TCCCTAACATTATCGATCCATTCAATTTGAG
Found at i:372335 original size:57 final size:58
Alignment explanation
Indices: 372221--372341 Score: 149
Period size: 57 Copynumber: 2.1 Consensus size: 58
372211 GTTGGGTGGC
*
372221 CATTTTGTAACTTTAATAGTCGAGGAACTCAACAAAACAACTCCCTATAGTCAGGGGAT
1 CATTTTATAACTTTAATAGTC-AGGAACTCAACAAAACAACTCCCTATAGTCAGGGGAT
* * **
372280 TATTTTATAACTTTTAATAGT-TGGAACTCAACAAAA-AA-TATTCTATAGTCAGGGGAT
1 CATTTTATAAC-TTTAATAGTCAGGAACTCAACAAAACAACT-CCCTATAGTCAGGGGAT
372337 CATTT
1 CATTT
372342 GTGTAATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
56 1 0.02
57 21 0.39
58 14 0.26
59 9 0.17
60 9 0.17
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (58 bp):
CATTTTATAACTTTAATAGTCAGGAACTCAACAAAACAACTCCCTATAGTCAGGGGAT
Found at i:377844 original size:48 final size:48
Alignment explanation
Indices: 377773--377869 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
377763 AAACCGAAAG
377773 AAAGACTAGGCAATATGAATGAGTTGCTCCAAACTCGAAATGTAGTAT
1 AAAGACTAGGCAATATGAATGAGTTGCTCCAAACTCGAAATGTAGTAT
377821 AAAGACTAGGCAATATGAATGAGTTGCTCCAAACTCGAAATGTAGTAT
1 AAAGACTAGGCAATATGAATGAGTTGCTCCAAACTCGAAATGTAGTAT
377869 A
1 A
377870 TTCAATGTTC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (48 bp):
AAAGACTAGGCAATATGAATGAGTTGCTCCAAACTCGAAATGTAGTAT
Found at i:378454 original size:15 final size:16
Alignment explanation
Indices: 378434--378463 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
378424 ATATAACAAC
378434 AAGAAGAAA-GAGAAG
1 AAGAAGAAACGAGAAG
378449 AAGAAGAAACGAGAA
1 AAGAAGAAACGAGAA
378464 CGATAAGCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.03, G:0.30, T:0.00
Consensus pattern (16 bp):
AAGAAGAAACGAGAAG
Found at i:379192 original size:4 final size:4
Alignment explanation
Indices: 379183--379207 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
379173 TTAATTGTGT
379183 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
379208 AAGTTTGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:382781 original size:29 final size:29
Alignment explanation
Indices: 382729--382811 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 29
382719 ACAGTGGCCG
* * **
382729 TAGGTCGCCATACACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCGGCGACCAAC
* *
382758 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCGGCGACCAAC
* *
382787 GAGGTCGCCATGCACTCGCGGCGAC
1 TAGGTCGCCATGCACTCCCGGCGAC
382812 ATCCCCTGCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.19, C:0.40, G:0.28, T:0.13
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCGGCGACCAAC
Found at i:383073 original size:29 final size:29
Alignment explanation
Indices: 383031--383136 Score: 203
Period size: 29 Copynumber: 3.7 Consensus size: 29
383021 ATGCAGGAGG
383031 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
383060 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
383089 AGGAGTGCATGGCGACCTACAAGGTCGCC
1 AGGAGTGCATGGCGACCTACAAGGTCGCC
*
383118 CGGAGTGCATGGCGACCTA
1 AGGAGTGCATGGCGACCTA
383137 TGCTGGGAAG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.24, C:0.27, G:0.35, T:0.14
Consensus pattern (29 bp):
AGGAGTGCATGGCGACCTACAAGGTCGCC
Found at i:386448 original size:22 final size:22
Alignment explanation
Indices: 386423--386484 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
386413 ATTGTTAGTA
* *
386423 TTTTATCTTGAAATTTAACAACT
1 TTTTAT-TCGAAAATTAACAACT
386446 TTTTATTCGAAAATTAACAACT
1 TTTTATTCGAAAATTAACAACT
*
386468 TTTTATTCAAAAATTAA
1 TTTTATTCGAAAATTAA
386485 TATGAATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
22 30 0.83
23 6 0.17
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.45
Consensus pattern (22 bp):
TTTTATTCGAAAATTAACAACT
Found at i:395570 original size:15 final size:16
Alignment explanation
Indices: 395550--395583 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
395540 TTCAATTCGG
395550 TTAAGTTGG-TATTCA
1 TTAAGTTGGCTATTCA
*
395565 TTAAGTTGGCTATTGA
1 TTAAGTTGGCTATTCA
395581 TTA
1 TTA
395584 TTAAAAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (16 bp):
TTAAGTTGGCTATTCA
Found at i:396710 original size:29 final size:29
Alignment explanation
Indices: 396677--396737 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
396667 CGTCGCTGCT
*
396677 TTCCGGGTGACCTACTAGGTCGTC-ATGTC
1 TTCCGGGTGACCTACTAAGTCG-CAATGTC
396706 TTCCGGGTGACCTACTAAGTCGCAATGTC
1 TTCCGGGTGACCTACTAAGTCGCAATGTC
396735 TTC
1 TTC
396738 TCGGCGAGCT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 1 0.03
29 29 0.97
ACGTcount: A:0.16, C:0.28, G:0.25, T:0.31
Consensus pattern (29 bp):
TTCCGGGTGACCTACTAAGTCGCAATGTC
Found at i:402519 original size:15 final size:15
Alignment explanation
Indices: 402499--402533 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
402489 ATGATAAGAA
402499 AGATAGTGTAAAGCC
1 AGATAGTGTAAAGCC
402514 AGATAGTGTAAAGCC
1 AGATAGTGTAAAGCC
402529 AGATA
1 AGATA
402534 TTGAAGCACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.43, C:0.11, G:0.26, T:0.20
Consensus pattern (15 bp):
AGATAGTGTAAAGCC
Found at i:406915 original size:3 final size:3
Alignment explanation
Indices: 406907--406938 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
406897 CAGATCTCTT
406907 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
406939 TAATTGTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:412030 original size:10 final size:10
Alignment explanation
Indices: 412015--412039 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
412005 TAATGAGTTG
412015 TTATATTTTT
1 TTATATTTTT
412025 TTATATTTTT
1 TTATATTTTT
412035 TTATA
1 TTATA
412040 ATTTAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (10 bp):
TTATATTTTT
Found at i:413933 original size:155 final size:154
Alignment explanation
Indices: 413652--413962 Score: 471
Period size: 155 Copynumber: 2.0 Consensus size: 154
413642 TATCATTTAC
* * * *
413652 TTATCGTACAGTCTTGAACCTTGATATGCATATATACCGTAAACCGGATCCAAGGCTCTAATCAG
1 TTATCGTACAGTCTCGAACCTTGATATGCATAAAAACCGTAAACCAGATCCAAGGCTCTAATCAG
* *
413717 TGCTGTGCTATTCTTACTAAGGACAGAAAATTCAAGCTAAGACTTAACATTCATATAAATATGAT
66 TGCTGTGCTATTCTTACTAAGGACAGAAAATCCAAGCTAAAACTTAACATTCATATAAATATGAT
413782 GAACATCCATTGCTATTCAACCAT
131 GAACATCCATTGCTATTCAACCAT
* * * * * *
413806 TTATCTTACAGTCTCGAATCTTGATATGCCGTAAAAACCTTAAACCATATCCAAGGCTCTGATCA
1 TTATCGTACAGTCTCGAACCTTGATATG-CATAAAAACCGTAAACCAGATCCAAGGCTCTAATCA
* *
413871 GTGCTTTGCTATTCTTACTAAGGACAGCAAATCCAAGCTAAAACTTAACATTTCA-ATAAATATG
65 GTGCTGTGCTATTCTTACTAAGGACAGAAAATCCAAGCTAAAACTTAACA-TTCATATAAATATG
413935 ATGAACATCCATTGCTATTCAACCAT
129 ATGAACATCCATTGCTATTCAACCAT
413961 TT
1 TT
413963 GAACAACTAA
Statistics
Matches: 141, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
154 25 0.18
155 112 0.79
156 4 0.03
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.31
Consensus pattern (154 bp):
TTATCGTACAGTCTCGAACCTTGATATGCATAAAAACCGTAAACCAGATCCAAGGCTCTAATCAG
TGCTGTGCTATTCTTACTAAGGACAGAAAATCCAAGCTAAAACTTAACATTCATATAAATATGAT
GAACATCCATTGCTATTCAACCAT
Found at i:424222 original size:2 final size:2
Alignment explanation
Indices: 424215--424252 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
424205 GGTATAAGTA
424215 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
424253 GTTTACATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:424794 original size:17 final size:18
Alignment explanation
Indices: 424764--424801 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
424754 TAGGAAATGG
*
424764 AATTAAGTAAATAAATTA
1 AATTAAGTAAATAAATAA
*
424782 AATT-AGTATATAAATAA
1 AATTAAGTAAATAAATAA
424799 AAT
1 AAT
424802 ACTATTAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (18 bp):
AATTAAGTAAATAAATAA
Found at i:427680 original size:22 final size:23
Alignment explanation
Indices: 427626--427687 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 23
427616 TGAATATGGG
* * *
427626 TATTGAAATTTAGAGATTTAGAG
1 TATTGAGATTTAGGGATTTAGAA
427649 T-TTG-GATTTAGGGATTTA-AA
1 TATTGAGATTTAGGGATTTAGAA
427669 TATTGAGATTTAGGGATTT
1 TATTGAGATTTAGGGATTT
427688 GAGATAATGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 2 0.06
21 15 0.44
22 16 0.47
23 1 0.03
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.44
Consensus pattern (23 bp):
TATTGAGATTTAGGGATTTAGAA
Found at i:430585 original size:28 final size:29
Alignment explanation
Indices: 430553--430607 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
430543 TAATAAGATT
430553 ATAAAT-AGATAATTCAATTTAA-AAAATC
1 ATAAATGA-ATAATTCAATTTAACAAAATC
*
430581 ATAAATGAATCATTCAATTTAACAAAA
1 ATAAATGAATAATTCAATTTAACAAAA
430608 ATAAAATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (29 bp):
ATAAATGAATAATTCAATTTAACAAAATC
Found at i:437927 original size:21 final size:21
Alignment explanation
Indices: 437901--437945 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
437891 GATTTCTGGG
* *
437901 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
437922 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
437943 CAA
1 CAA
437946 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:439684 original size:149 final size:149
Alignment explanation
Indices: 439447--439750 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
439437 GAGTCGATGG
439447 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
439512 ACTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
439577 TATGGCACTACAGTGCAAT
131 TATGGCACTACAGTGCAAT
439596 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
*
439661 ACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
*
439726 TATGGCACTACGGTGCAAT
131 TATGGCACTACAGTGCAAT
439745 TCTACG
1 TCTACG
439751 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTTCTTTGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
ACTTGATCCATAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACAGTGCAAT
Found at i:439773 original size:23 final size:23
Alignment explanation
Indices: 439729--439773 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
439719 ATCATTATAT
*
439729 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
439752 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
439774 AGCTGTGGTG
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:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:442855 original size:21 final size:21
Alignment explanation
Indices: 442829--442873 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
442819 GATTTCTGGG
* *
442829 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
442850 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
442871 CAA
1 CAA
442874 ACGAACAAGA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:444534 original size:16 final size:16
Alignment explanation
Indices: 444513--444543 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
444503 TTCTACGCAG
*
444513 TTCTTTGGGACATGTA
1 TTCTTTGGAACATGTA
444529 TTCTTTGGAACATGT
1 TTCTTTGGAACATGT
444544 GTGAAGTCTT
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:0.19, C:0.13, G:0.23, T:0.45
Consensus pattern (16 bp):
TTCTTTGGAACATGTA
Found at i:444622 original size:143 final size:141
Alignment explanation
Indices: 444358--444649 Score: 466
Period size: 143 Copynumber: 2.0 Consensus size: 141
444348 GAGTCGAGGG
*
444358 TCTACGCGGTTCTTTGGGACATATGTATATTCTTGGAACATGTGTGAAGTCTTGAAAGACACATA
1 TCTACGCAGTTCTTTGGGACA-ATGTATATTCTTGGAACATGTGTGAAGTCTTGAAAGACACATA
*
444423 CTTGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGGGTCCTTATGACATCATTATAT
65 CTTGATCCATAG-ATATGTATATGATTCTTAAGGAATTCTATGGGTCCTTATGACATCA-T-TAT
444488 GGCACTACGGTGCAAT
127 GGCACTACGGTGC-AT
444504 TCTACGCAGTTCTTTGGGAC-ATG--TATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACATA
1 TCTACGCAGTTCTTTGGGACAATGTATATTC-TTGGAACATGTGTGAAGTCTTGAAAGACACATA
444566 CTTGATCCATAG-TATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTATG
65 CTTGATCCATAGATATGTATATGATTCTTAAGGAATTCTATG-GGTCCTTAT-GACATCATTATG
444630 GCACTACGGTGCAT
128 GCACTACGGTGCAT
444644 TCTACG
1 TCTACG
444650 GGGCACTTCG
Statistics
Matches: 141, Mismatches: 2, Indels: 12
0.91 0.01 0.08
Matches are distributed among these distances:
140 8 0.06
141 45 0.32
142 15 0.11
143 51 0.36
144 3 0.02
146 19 0.13
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (141 bp):
TCTACGCAGTTCTTTGGGACAATGTATATTCTTGGAACATGTGTGAAGTCTTGAAAGACACATAC
TTGATCCATAGATATGTATATGATTCTTAAGGAATTCTATGGGTCCTTATGACATCATTATGGCA
CTACGGTGCAT
Found at i:450147 original size:255 final size:255
Alignment explanation
Indices: 449696--450205 Score: 1004
Period size: 255 Copynumber: 2.0 Consensus size: 255
449686 CCAATTAATC
449696 CAATATCAACCCAGAATCTCAAAAAAATTTGCCCAAATTACAAAAAAAAAATCATTCGGGAACTT
1 CAATATCAACCCAGAATCTCAAAAAAATTTGCCCAAATTACAAAAAAAAAATCATTCGGGAACTT
449761 ACCCCAAACAGTGGAGACGGTGACGCAACGAAGAGGCGGTGATCCTTACTGGATTTTGGTCGCAG
66 ACCCCAAACAGTGGAGACGGTGACGCAACGAAGAGGCGGTGATCCTTACTGGATTTTGGTCGCAG
449826 GATGTCAGAGAAGCCAACGGAGGTGACGATGTATTGAATGACCGGTTGGATCGAGGAAAATCCGA
131 GATGTCAGAGAAGCCAACGGAGGTGACGATGTATTGAATGACCGGTTGGATCGAGGAAAATCCGA
449891 GCGTCATGTGGGGTTTTGACAGGATTTCAACGACTTTTCCACGACGATCGATGGTACTTT
196 GCGTCATGTGGGGTTTTGACAGGATTTCAACGACTTTTCCACGACGATCGATGGTACTTT
449951 CAATATCAACCCAGAATCTC-AAAAAATTTGCCCAAATTACAAAAAAAAAAATCATTCGGGAACT
1 CAATATCAACCCAGAATCTCAAAAAAATTTGCCCAAATTAC-AAAAAAAAAATCATTCGGGAACT
450015 TACCCCAAACAGTGGAGACGGTGACGCAACGAAGAGGCGGTGATCCTTACTGGATTTTGGTCGCA
65 TACCCCAAACAGTGGAGACGGTGACGCAACGAAGAGGCGGTGATCCTTACTGGATTTTGGTCGCA
450080 GGATGTCAGAGAAGCCAACGGAGGTGACGATGTATTGAATGACCGGTTGGATCGAGGAAAATCCG
130 GGATGTCAGAGAAGCCAACGGAGGTGACGATGTATTGAATGACCGGTTGGATCGAGGAAAATCCG
450145 AGCGTCATGTGGGGTTTTGACAGGATTTCAACGACTTTTCCACGACGATCGATGGTACTTT
195 AGCGTCATGTGGGGTTTTGACAGGATTTCAACGACTTTTCCACGACGATCGATGGTACTTT
450206 TCAAAGCGAG
Statistics
Matches: 254, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
254 20 0.08
255 234 0.92
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (255 bp):
CAATATCAACCCAGAATCTCAAAAAAATTTGCCCAAATTACAAAAAAAAAATCATTCGGGAACTT
ACCCCAAACAGTGGAGACGGTGACGCAACGAAGAGGCGGTGATCCTTACTGGATTTTGGTCGCAG
GATGTCAGAGAAGCCAACGGAGGTGACGATGTATTGAATGACCGGTTGGATCGAGGAAAATCCGA
GCGTCATGTGGGGTTTTGACAGGATTTCAACGACTTTTCCACGACGATCGATGGTACTTT
Found at i:452329 original size:2 final size:2
Alignment explanation
Indices: 452322--452358 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
452312 CATTATTTCG
452322 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 T
452359 TTACTATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:452503 original size:22 final size:22
Alignment explanation
Indices: 452478--452528 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
452468 CATTTTGTTT
452478 ATTTTATACACTGTTTATCTTC
1 ATTTTATACACTGTTTATCTTC
*
452500 ATTTTATACACTGTTTATCTTT
1 ATTTTATACACTGTTTATCTTC
452522 ATTTTAT
1 ATTTTAT
452529 TGCTTCCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.24, C:0.14, G:0.04, T:0.59
Consensus pattern (22 bp):
ATTTTATACACTGTTTATCTTC
Found at i:463924 original size:105 final size:105
Alignment explanation
Indices: 463742--464528 Score: 1466
Period size: 105 Copynumber: 7.5 Consensus size: 105
463732 AGGTTTTACC
*
463742 CAGAGCCAATTTCAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
463807 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
463847 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
463912 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
463952 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
464017 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
464057 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
464122 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
464162 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
464227 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
464267 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
464332 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
464372 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
464437 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* ** * * *
464477 CAGAGCCAATTACTGCTTCACAACGAAGGATATTGGCCTCGAAACAACGCAA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAA
464529 CTTGTATGGG
Statistics
Matches: 667, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 667 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:466247 original size:2 final size:2
Alignment explanation
Indices: 466240--466270 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
466230 CATTATTTCG
466240 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 T
466271 TTACTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:466417 original size:22 final size:22
Alignment explanation
Indices: 466392--466439 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
466382 CATTTTGTTT
466392 ATTTTATACACTGTTTATCTTC
1 ATTTTATACACTGTTTATCTTC
*
466414 ATTTTATACACTGTTTATCTTT
1 ATTTTATACACTGTTTATCTTC
466436 ATTT
1 ATTT
466440 ATTGCTTCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.23, C:0.15, G:0.04, T:0.58
Consensus pattern (22 bp):
ATTTTATACACTGTTTATCTTC
Found at i:495829 original size:27 final size:27
Alignment explanation
Indices: 495789--495849 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
495779 AACAACAACA
* *
495789 AAAAACACCTTAAATTTCATAAAATTC-C
1 AAAAA-ACCATAAA-TTCATAAAAATCTC
*
495817 AAAAAACCATAAATTCCTAAAAATCTC
1 AAAAAACCATAAATTCATAAAAATCTC
495844 AAAAAA
1 AAAAAA
495850 ATTATAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 10 0.34
27 14 0.48
28 5 0.17
ACGTcount: A:0.57, C:0.20, G:0.00, T:0.23
Consensus pattern (27 bp):
AAAAAACCATAAATTCATAAAAATCTC
Found at i:495848 original size:28 final size:26
Alignment explanation
Indices: 495787--495864 Score: 68
Period size: 28 Copynumber: 2.8 Consensus size: 26
495777 CCAACAACAA
*
495787 CAAAAAACACCTTAAATT-TCATAAAATT
1 CAAAAAA-ACCATAAATTCT-A-AAAATT
*
495815 CCAAAAAACCATAAATTCCTAAAAATCT
1 CAAAAAAACCATAAATT-CTAAAAAT-T
**
495843 CAAAAAAATTATAAATTCTAAA
1 CAAAAAAACCATAAATTCTAAA
495865 TCACAATCCC
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
27 19 0.45
28 22 0.52
29 1 0.02
ACGTcount: A:0.56, C:0.18, G:0.00, T:0.26
Consensus pattern (26 bp):
CAAAAAAACCATAAATTCTAAAAATT
Found at i:497484 original size:21 final size:21
Alignment explanation
Indices: 497458--497502 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
497448 GATTTATGGG
* *
497458 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
497479 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
497500 CAA
1 CAA
497503 ACGAACAAAA
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:503067 original size:2 final size:2
Alignment explanation
Indices: 503060--503087 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
503050 TTCGACATAA
503060 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
503088 TATTAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:507018 original size:40 final size:40
Alignment explanation
Indices: 506963--507146 Score: 251
Period size: 40 Copynumber: 4.5 Consensus size: 40
506953 ACCAGTTGTT
506963 GCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAAC
*
507003 GCGAACTTCGACTATCGCAACGAATTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAAC
* ** * * **
507043 GTGAACTTGGAAAATCGCAACGCGAACTTCGACTATCGCAAC
1 GCGAACTTGGACTATCGCAA--CGAATTTGGAAAATCGCAAC
*
507085 GTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAAC
* *
507125 GCGAACTTCGACTATCACAACG
1 GCGAACTTGGACTATCGCAACG
507147 TGAACTTGGA
Statistics
Matches: 124, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
40 90 0.73
42 34 0.27
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.20
Consensus pattern (40 bp):
GCGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAAC
Found at i:507019 original size:21 final size:21
Alignment explanation
Indices: 506963--507240 Score: 199
Period size: 21 Copynumber: 14.0 Consensus size: 21
506953 ACCAGTTGTT
506963 GCGAACTTGGACTATCGCAA-
1 GCGAACTTGGACTATCGCAAC
* **
506983 -CGAATTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAAC
*
507003 GCGAACTTCGACTATCGCAA-
1 GCGAACTTGGACTATCGCAAC
* **
507023 -CGAATTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAAC
* **
507043 GTGAACTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAAC
*
507064 GCGAACTTCGACTATCGCAAC
1 GCGAACTTGGACTATCGCAAC
*
507085 GTGAACTTGGACTATCGCAA-
1 GCGAACTTGGACTATCGCAAC
* **
507105 -CGAATTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAAC
* *
507125 GCGAACTTCGACTATCACAAC
1 GCGAACTTGGACTATCGCAAC
* *
507146 GTGAACTTGGACTAGCGCAA-
1 GCGAACTTGGACTATCGCAAC
*
507166 -CGAATTTGGAC--T---AAC
1 GCGAACTTGGACTATCGCAAC
** * **
507181 GTAAATTTGGAAAATCGCAA-
1 GCGAACTTGGACTATCGCAAC
* **
507201 -CGAATTTGGAAAATCGCAAC
1 GCGAACTTGGACTATCGCAAC
507221 GCGAACTTGGACTATCGCAA
1 GCGAACTTGGACTATCGCAA
507241 AATCGCGTTG
Statistics
Matches: 200, Mismatches: 43, Indels: 29
0.74 0.16 0.11
Matches are distributed among these distances:
14 2 0.01
16 8 0.04
18 1 0.00
19 72 0.36
21 117 0.58
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.21
Consensus pattern (21 bp):
GCGAACTTGGACTATCGCAAC
Found at i:507062 original size:61 final size:59
Alignment explanation
Indices: 506964--507175 Score: 280
Period size: 61 Copynumber: 3.5 Consensus size: 59
506954 CCAGTTGTTG
**
506964 CGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAACTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAA
* *
507023 CGAATTTGGAAAATCGCAACGTGAACTTGGAAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAACTTGGAAAATCGCAAC--GAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAA
** *
507084 CGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCACAA
1 C--GAACTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAA
** *
507145 CGTGAACTTGGACTAGCGCAACGAATTTGGA
1 C--GAACTTGGAAAATCGCAACGAATTTGGA
507176 CTAACGTAAA
Statistics
Matches: 139, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
59 17 0.12
61 106 0.76
63 16 0.12
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.21
Consensus pattern (59 bp):
CGAACTTGGAAAATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAA
Found at i:507090 original size:42 final size:42
Alignment explanation
Indices: 506965--507240 Score: 195
Period size: 40 Copynumber: 6.9 Consensus size: 42
506955 CAGTTGTTGC
* ** *
506965 GAACTTGGACTATCGCAA--CGAATTTGGAAAATCGCAACGC
1 GAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGT
* * **
507005 GAACTTCGACTATCGCAA--CGAATTTGGAAAATCGCAACGT
1 GAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGT
** *
507045 GAACTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGT
1 GAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGT
* ** *
507087 GAACTTGGACTATCGCAA--CGAATTTGGAAAATCGCAACGC
1 GAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGT
* * * *
507127 GAACTTCGACTATCACAACGTGAACTTGGACTAGCGCAAC--
1 GAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGT
* ** * **
507167 GAATTTGGAC--T---AACGTAAATTTGGAAAATCGCAAC--
1 GAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGT
* **
507202 GAATTTGGAAAATCGCAACGCGAACTTGGACTATCGCAA
1 GAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAA
507241 AATCGCGTTG
Statistics
Matches: 191, Mismatches: 36, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
35 28 0.15
37 1 0.01
38 1 0.01
40 112 0.59
42 49 0.26
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (42 bp):
GAACTTGGACTATCGCAACGCGAACTTGGACTATCGCAACGT
Found at i:507100 original size:82 final size:80
Alignment explanation
Indices: 506965--507240 Score: 314
Period size: 82 Copynumber: 3.5 Consensus size: 80
506955 CAGTTGTTGC
** * ** *
506965 GAACTTGGACTATCGCAA--CGAATTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGAAT
1 GAACTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACG-GAACTTGGACTATCGCAACGAAT
507028 TTGGAAAATCGCAACG
65 TTGGAAAATCGCAACG
*
507044 TGAACTTGGAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAA
1 -GAACTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACG-GAACTTGGACTATCGCAACGAA
507109 TTTGGAAAATCGCAACG
64 TTTGGAAAATCGCAACG
* ** * * * * * *
507126 CGAACTTCGACTATCACAACGTGAACTTGGACTAGCGCAAC-GAATTTGGACTAACG-TA--AAT
1 -GAACTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGGAACTTGGACTATCGCAACGAAT
507187 TTGGAAAATCGCAAC-
65 TTGGAAAATCGCAACG
*
507202 GAATTTGGAAAATCGCAACGCGAACTTGGACTATCGCAA
1 GAACTTGGAAAATCGCAACGCGAACTTGGACTATCGCAA
507241 AATCGCGTTG
Statistics
Matches: 168, Mismatches: 26, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
75 32 0.19
77 18 0.11
79 1 0.01
80 29 0.17
82 88 0.52
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.21
Consensus pattern (80 bp):
GAACTTGGAAAATCGCAACGCGAACTTGGACTATCGCAACGGAACTTGGACTATCGCAACGAATT
TGGAAAATCGCAACG
Found at i:507191 original size:35 final size:35
Alignment explanation
Indices: 507143--507210 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
507133 CGACTATCAC
* **
507143 AACGTGAACTTGGACTAGCGCAACGAATTTGGACT
1 AACGTAAACTTGGAAAAGCGCAACGAATTTGGACT
* *
507178 AACGTAAATTTGGAAAATCGCAACGAATTTGGA
1 AACGTAAACTTGGAAAAGCGCAACGAATTTGGA
507211 AAATCGCAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (35 bp):
AACGTAAACTTGGAAAAGCGCAACGAATTTGGACT
Found at i:507409 original size:4 final size:4
Alignment explanation
Indices: 507400--507425 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
507390 TATTTTCTCT
507400 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
507426 ATGTAAAGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:508609 original size:25 final size:24
Alignment explanation
Indices: 508556--508618 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 24
508546 AACGAGAAAA
*
508556 AAAAGGAAAATTAATAAATAATAAAT
1 AAAAGGAAAA--AACAAATAATAAAT
508582 AAAAGGAAAAAACAAATAAATAAAT
1 AAAAGGAAAAAACAAAT-AATAAAT
508607 AAAAGGAAAAAA
1 AAAAGGAAAAAA
508619 TATTTTTTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
24 6 0.17
25 19 0.54
26 10 0.29
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.14
Consensus pattern (24 bp):
AAAAGGAAAAAACAAATAATAAAT
Found at i:508893 original size:39 final size:37
Alignment explanation
Indices: 508677--508914 Score: 168
Period size: 38 Copynumber: 6.3 Consensus size: 37
508667 AAATCATATA
* *
508677 ATATAATATA-ATATATTTTCAAAAAATATTTTAAAATT
1 ATATAATATATAT-TGTTTTC-AAAAATATTTTAAAACT
* * * *
508715 ACATATTATATATAT-TTTTCAAAATGTTTTTTTAAAAAACT
1 ATATAATATATAT-TGTTTTCAAAA--ATATTTT--AAAACT
* *
508756 -T-T-ATATATA-AGTTTTCAAAAACAGTTTTAAAAACT
1 ATATAATATATATTGTTTTCAAAAATA-TTTT-AAAACT
* * *
508791 ATATAATATGTA-TATTTTCTAAAATATTTTCAAAACT
1 ATATAATATATATTGTTTTCAAAAATATTTT-AAAACT
*
508828 ATAT-ATATTATATAGTTTTCAAAAATATTTTAAAGACT
1 ATATAATA-TATATTGTTTTCAAAAATATTTTAAA-ACT
* *
508866 ATATATTATATACTTGTTTTCAAAAATAATTTACAAACT
1 ATATAATATATA-TTGTTTTCAAAAATATTTTA-AAACT
508905 ATATAATATA
1 ATATAATATA
508915 CATATATATA
Statistics
Matches: 159, Mismatches: 25, Indels: 31
0.74 0.12 0.14
Matches are distributed among these distances:
35 7 0.04
36 8 0.05
37 34 0.21
38 61 0.38
39 42 0.26
40 2 0.01
41 5 0.03
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.45
Consensus pattern (37 bp):
ATATAATATATATTGTTTTCAAAAATATTTTAAAACT
Found at i:517497 original size:27 final size:27
Alignment explanation
Indices: 517459--517539 Score: 153
Period size: 27 Copynumber: 3.0 Consensus size: 27
517449 TTCTTTTTTT
*
517459 AAACACCTATTTGGGTAGAGTTTCTTG
1 AAACACCTATTTGGGTAGAGTTTATTG
517486 AAACACCTATTTGGGTAGAGTTTATTG
1 AAACACCTATTTGGGTAGAGTTTATTG
517513 AAACACCTATTTGGGTAGAGTTTATTG
1 AAACACCTATTTGGGTAGAGTTTATTG
517540 GTACCTTACA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.37
Consensus pattern (27 bp):
AAACACCTATTTGGGTAGAGTTTATTG
Found at i:521122 original size:15 final size:15
Alignment explanation
Indices: 521089--521122 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
521079 TTTAGTTGGG
* *
521089 CGGGCGGATGTGGGG
1 CGGGCGGATGCGGGA
521104 CGGGCGGATGCGGGA
1 CGGGCGGATGCGGGA
521119 CGGG
1 CGGG
521123 TAATGTCTCA
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:0.09, C:0.18, G:0.65, T:0.09
Consensus pattern (15 bp):
CGGGCGGATGCGGGA
Found at i:523690 original size:9 final size:9
Alignment explanation
Indices: 523676--523700 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
523666 TTTGAATTAT
523676 TTTTGAAAA
1 TTTTGAAAA
523685 TTTTGAAAA
1 TTTTGAAAA
523694 TTTTGAA
1 TTTTGAA
523701 TAAATTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (9 bp):
TTTTGAAAA
Found at i:523909 original size:10 final size:10
Alignment explanation
Indices: 523896--523931 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
523886 ATTTATGTTT
523896 ATTTTAATTA
1 ATTTTAATTA
523906 ATTTTAATTA
1 ATTTTAATTA
523916 ATTTTTAATT-
1 A-TTTTAATTA
523926 ATTTTA
1 ATTTTA
523932 TATTTAACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 5 0.20
10 12 0.48
11 8 0.32
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTAATTA
Found at i:524182 original size:2 final size:2
Alignment explanation
Indices: 524175--524204 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
524165 TTTAAATTAA
524175 AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
524205 ATCCTAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:524453 original size:65 final size:65
Alignment explanation
Indices: 524349--524490 Score: 257
Period size: 65 Copynumber: 2.2 Consensus size: 65
524339 CCGCAGTTGT
524349 CATCGATTGATCATCAAAATCGCGTGGGATCTCGATTTTCGTCCTAGAGTTCACGATGTACAAAA
1 CATCGATTGATCATCAAAATCGCGTGGGATCTCGATTTTCGTCCTAGAGTTCACGATGTACAAAA
* *
524414 CATCGTTTGATCATCGAAATCGCGTGGGATCTCGATTTTCGTCCTAGAGTTCACGATGTACAAAA
1 CATCGATTGATCATCAAAATCGCGTGGGATCTCGATTTTCGTCCTAGAGTTCACGATGTACAAAA
*
524479 CATTGATTGATC
1 CATCGATTGATC
524491 GTATATCGGT
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 73 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (65 bp):
CATCGATTGATCATCAAAATCGCGTGGGATCTCGATTTTCGTCCTAGAGTTCACGATGTACAAAA
Found at i:529026 original size:108 final size:108
Alignment explanation
Indices: 528837--529052 Score: 378
Period size: 108 Copynumber: 2.0 Consensus size: 108
528827 GTATGAAGAG
* * *
528837 TATTAAGGAGGATGCATTTAAGTAAACTAAAAGAAGTTAACCCGGAGCAAAGTTCTTGATTTCAG
1 TATTAAGGAGGATGCATTTAAGGAAACTAAAAAAAGTTAACCCGGAGCAAAGTTCTCGATTTCAG
*
528902 CCTAGTTTGGTTCTATAGTTTACTATTAAGGAAGAAAATAGAC
66 CCTAGTTTGGTTCTATAGTGTACTATTAAGGAAGAAAATAGAC
* *
528945 TATTAAGGAGGATGCATTTAAGGAAATTAAAAAAAGTTAACCCGGAGCAAAGTTCTCGATTTTAG
1 TATTAAGGAGGATGCATTTAAGGAAACTAAAAAAAGTTAACCCGGAGCAAAGTTCTCGATTTCAG
529010 CCTAGTTTGGTTCTATAGTGTACTATTAAGGAAGAAAATAGAC
66 CCTAGTTTGGTTCTATAGTGTACTATTAAGGAAGAAAATAGAC
529053 AATCCATGCA
Statistics
Matches: 102, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
108 102 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.30
Consensus pattern (108 bp):
TATTAAGGAGGATGCATTTAAGGAAACTAAAAAAAGTTAACCCGGAGCAAAGTTCTCGATTTCAG
CCTAGTTTGGTTCTATAGTGTACTATTAAGGAAGAAAATAGAC
Found at i:533629 original size:2 final size:2
Alignment explanation
Indices: 533624--533687 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
533614 ACCATATAAA
533624 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
533666 AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
533688 GAGTCGAGAG
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:534105 original size:20 final size:20
Alignment explanation
Indices: 534080--534189 Score: 114
Period size: 20 Copynumber: 5.5 Consensus size: 20
534070 AATTTGGAAA
*
534080 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
534100 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
534121 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
534141 TTCGCAATGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
* *
534161 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
534181 TTCGCAACG
1 ATCGCAACG
534190 AGATTCTGAA
Statistics
Matches: 78, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 2 0.03
20 59 0.76
21 15 0.19
22 2 0.03
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:534194 original size:20 final size:20
Alignment explanation
Indices: 534122--534198 Score: 127
Period size: 20 Copynumber: 3.9 Consensus size: 20
534112 TAATACAAAA
*
534122 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
534142 TCGCAATGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
534162 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
*
534182 TCGCAACGAGATTCTGA
1 TCGCAACGCGATTCTGA
534199 AAATCGCAAT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:534205 original size:20 final size:20
Alignment explanation
Indices: 534162--534207 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
534152 ATTCTGACTT
* ***
534162 TCGCAACGCGATTCTGACTT
1 TCGCAACGAGATTCTGAAAA
534182 TCGCAACGAGATTCTGAAAA
1 TCGCAACGAGATTCTGAAAA
534202 TCGCAA
1 TCGCAA
534208 TCATCTTCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (20 bp):
TCGCAACGAGATTCTGAAAA
Found at i:534206 original size:40 final size:40
Alignment explanation
Indices: 534076--534207 Score: 156
Period size: 40 Copynumber: 3.3 Consensus size: 40
534066 TACGAATTTG
* * **
534076 GAAAATCGCAATGCGATACTGACTATCGCAACGCGATAAT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
* *
534116 ACAAAATCGCAACGCGATACTGACTTTCGCAATGCGATTCT
1 -GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
*** * *
534157 GACTTTCGCAACGCGATTCTGACTTTCGCAACGAGATTCT
1 GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
534197 GAAAATCGCAA
1 GAAAATCGCAA
534208 TCATCTTCAA
Statistics
Matches: 75, Mismatches: 16, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
40 41 0.55
41 34 0.45
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (40 bp):
GAAAATCGCAACGCGATACTGACTTTCGCAACGCGATTCT
Found at i:534439 original size:20 final size:20
Alignment explanation
Indices: 534406--534462 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
534396 TTCATTTGAC
*
534406 TATCGCAACACGAAAATGGA
1 TATCGCAACGCGAAAATGGA
* *
534426 TATTGCAACGCGAAAATGGC
1 TATCGCAACGCGAAAATGGA
*
534446 TATCGCAACGAGAAAAT
1 TATCGCAACGCGAAAAT
534463 CGCAATGCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (20 bp):
TATCGCAACGCGAAAATGGA
Found at i:534516 original size:20 final size:20
Alignment explanation
Indices: 534491--534566 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
534481 TCGCATTGCG
*
534491 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
* *
534511 ATTTTCGCGTTGCAATAGTC
1 ATTTTCGCGTTGCGATAGCC
*
534531 ATTTTCGTGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
534551 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
534567 TCTCTCGTTG
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:535166 original size:21 final size:21
Alignment explanation
Indices: 535137--535197 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
535127 GAACGGTGGG
*
535137 GGGGACTCTTGAGGGATGATA
1 GGGGACTCTTGAGGGATGAGA
* **
535158 GGGGTCTCTTGAATGACTG-GA
1 GGGGACTCTTGAGGGA-TGAGA
535179 GGGGACTCTTGAGGGATGA
1 GGGGACTCTTGAGGGATGA
535198 CAGGTGAGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.11, G:0.43, T:0.25
Consensus pattern (21 bp):
GGGGACTCTTGAGGGATGAGA
Found at i:535586 original size:20 final size:20
Alignment explanation
Indices: 535563--535637 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
535553 AAACTTACTT
535563 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
535583 TCGCAACGCGAAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
535603 TCACAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGGCTA
*
535623 TCGCAATGC-GAAATG
1 TCGCAACGCGGAAATG
535638 AAAATCGCAG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 6 0.12
20 44 0.88
ACGTcount: A:0.33, C:0.24, G:0.27, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGGCTA
Found at i:535587 original size:40 final size:40
Alignment explanation
Indices: 535543--535628 Score: 118
Period size: 40 Copynumber: 2.1 Consensus size: 40
535533 TAGTTTACTT
* * * *
535543 TCGCAACACGAAACTTACTTTCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTATCACAACGCGGAAATGGCTA
* *
535583 TCGCAACGCGAAAATGGCTATCACAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTATCACAACGCGGAAATGGCTA
535623 TCGCAA
1 TCGCAA
535629 TGCGAAATGA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (40 bp):
TCGCAACACGAAAATGACTATCACAACGCGGAAATGGCTA
Found at i:535672 original size:19 final size:19
Alignment explanation
Indices: 535642--535726 Score: 72
Period size: 19 Copynumber: 4.6 Consensus size: 19
535632 GAAATGAAAA
535642 TCGCAGTTGCGATTTTCATT
1 TCGCA-TTGCGATTTTCATT
*
535662 TCGCATTGCGA-TTT--TG
1 TCGCATTGCGATTTTCATT
*
535678 TAG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
***
535695 TCGCATTGCGATAGCCATT
1 TCGCATTGCGATTTTCATT
535714 TCCGCATTGCGAT
1 T-CGCATTGCGAT
535727 AGTCATTTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
14 6 0.12
15 3 0.06
16 3 0.06
17 3 0.06
18 3 0.06
19 18 0.35
20 16 0.31
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.41
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:535745 original size:20 final size:20
Alignment explanation
Indices: 535691--535734 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
535681 TTGCGATTTT
535691 CATTT-CGCATTGCGATAGC
1 CATTTCCGCATTGCGATAGC
*
535710 CATTTCCGCATTGCGATAGT
1 CATTTCCGCATTGCGATAGC
535730 CATTT
1 CATTT
535735 TCGTGTTGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 5 0.22
20 18 0.78
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CATTTCCGCATTGCGATAGC
Found at i:536302 original size:18 final size:18
Alignment explanation
Indices: 536279--536326 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
536269 TCGGTCGATC
536279 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
536297 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
536315 AGGTGATGGCTC
1 AGGTGATGGCTC
536327 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:537693 original size:20 final size:20
Alignment explanation
Indices: 537645--537687 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
537635 AATAGTTTCT
* *
537645 GAAAATGAAAATCGCAACAC
1 GAAAATGACAATCGCAACGC
537665 GAAAATGACAATCGCAACGC
1 GAAAATGACAATCGCAACGC
537685 GAA
1 GAA
537688 TTTGACTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.21, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGACAATCGCAACGC
Found at i:537992 original size:22 final size:22
Alignment explanation
Indices: 537965--538008 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
537955 AGATGGAGAT
537965 AGACGGATTTCGCCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
*
537987 AGACGGATTTCGTCGGAGATGG
1 AGACGGATTTCGCCGGAGATGG
538009 GTGAGAGAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.16, G:0.41, T:0.20
Consensus pattern (22 bp):
AGACGGATTTCGCCGGAGATGG
Found at i:538263 original size:40 final size:41
Alignment explanation
Indices: 538216--538292 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
538206 CGAAAGTCAG
*
538216 TATCGCGTTGCGA-AGTCAGTATTGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTGTAT
538256 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTT
1 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTT
538293 CCAAATTCGC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 13 0.37
41 22 0.63
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.39
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTGTAT
Found at i:538289 original size:20 final size:20
Alignment explanation
Indices: 538196--538289 Score: 111
Period size: 20 Copynumber: 4.7 Consensus size: 20
538186 GATTATGTAT
* *
538196 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
538216 TATCGCGTTGCGA-AGTCAG
1 TATCGCGTTGCGATAGTCAG
* * *
538235 TATTGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
538256 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
538276 TATCGCGTTGCGAT
1 TATCGCGTTGCGAT
538290 TTTCCAAATT
Statistics
Matches: 63, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
19 21 0.33
20 27 0.43
21 13 0.21
22 2 0.03
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:538308 original size:41 final size:41
Alignment explanation
Indices: 538216--538310 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
538206 CGAAAGTCAG
* ** *
538216 TATCGCGTTGCGA-AGTCAGTATTGCGTTGCGATTTTGTAT
1 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCAAA
538256 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCCAAA
1 TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTT-CAAA
*
538298 T-TCGCATTGCGAT
1 TATCGCGTTGCGAT
538311 TAACTTATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 13 0.27
41 33 0.69
42 2 0.04
ACGTcount: A:0.19, C:0.19, G:0.25, T:0.37
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTCAGTATCGCGTTGCGATTTTCAAA
Found at i:539281 original size:2 final size:2
Alignment explanation
Indices: 539274--539303 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
539264 GGATGTGGCA
539274 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
539304 GTTAGGATCC
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:542623 original size:16 final size:15
Alignment explanation
Indices: 542598--542627 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
542588 AAGAGGAGTA
542598 AATATTATTATTTTG
1 AATATTATTATTTTG
542613 AATAGTTATTATTTT
1 AATA-TTATTATTTT
542628 TCACTCGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (15 bp):
AATATTATTATTTTG
Found at i:545881 original size:14 final size:14
Alignment explanation
Indices: 545862--545890 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
545852 TTCTTTTTTT
545862 TAATTTATTAATAA
1 TAATTTATTAATAA
545876 TAATTTATTAATAA
1 TAATTTATTAATAA
545890 T
1 T
545891 TTAGTGGCCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATTTATTAATAA
Found at i:546214 original size:31 final size:31
Alignment explanation
Indices: 546177--546235 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
546167 AGTTGTATGG
* *
546177 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
546208 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
546236 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:546354 original size:22 final size:22
Alignment explanation
Indices: 546326--546369 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
546316 ATTTATTCAG
546326 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
546348 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
546370 AAATTTATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:546875 original size:14 final size:14
Alignment explanation
Indices: 546836--546874 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
546826 TCTTTAAACA
546836 TCACAATTTTTTCTT
1 TCAC-ATTTTTTCTT
*
546851 TCCCATTTTTTCTT
1 TCACATTTTTTCTT
546865 TCAC-TTTTTT
1 TCACATTTTTT
546875 TTGTTGGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 6 0.27
14 13 0.59
15 3 0.14
ACGTcount: A:0.13, C:0.23, G:0.00, T:0.64
Consensus pattern (14 bp):
TCACATTTTTTCTT
Found at i:547257 original size:15 final size:15
Alignment explanation
Indices: 547237--547279 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
547227 CGAAAGATCA
547237 ATTAATAATTAATTT
1 ATTAATAATTAATTT
547252 ATTAATAATTAA-TT
1 ATTAATAATTAATTT
*
547266 ATAAATAA-TAATTT
1 ATTAATAATTAATTT
547280 TAATTCAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 3 0.12
14 11 0.42
15 12 0.46
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTAATAATTAATTT
Found at i:547707 original size:14 final size:15
Alignment explanation
Indices: 547672--547709 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
547662 AGATCGATGT
*
547672 TAGAATTAAAAATAA
1 TAGAATTAAAAAAAA
*
547687 TACAATTAAAAAAAA
1 TAGAATTAAAAAAAA
547702 T-GAATTAA
1 TAGAATTAA
547710 TTGAGTGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.26
Consensus pattern (15 bp):
TAGAATTAAAAAAAA
Found at i:551941 original size:170 final size:169
Alignment explanation
Indices: 551613--551951 Score: 653
Period size: 169 Copynumber: 2.0 Consensus size: 169
551603 ATTGTAAAAT
551613 ATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTTTTACAAAATTAAA
1 ATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTTTTACAAAATTAAA
551678 ATATAAAAAAAGGTTTAATAAAAGGGTAAAAAAAATTAACCCTTGAACTTCATATAAAATTTTAA
66 ATATAAAAAAAGGTTTAATAAAAGGGTAAAAAAAATTAACCCTTGAACTTCATATAAAATTTTAA
551743 TTATAGACTTTTTTTTGTAAATCTAAAATAATTTTAGGA
131 TTATAGACTTTTTTTTGTAAATCTAAAATAATTTTAGGA
551782 ATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTTTTACAAAATTAAA
1 ATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTTTTACAAAATTAAA
551847 A-ATATAAAAAAGGTTTAATAAAAGGGTAAAAAAAATTTAACCCTTGAACTTCATATAAAATTTT
66 ATATA-AAAAAAGGTTTAATAAAAGGGTAAAAAAAA-TTAACCCTTGAACTTCATATAAAATTTT
551911 AATTATAGACTTTTTTTTGTAAATCTAAAATAATTTTAGGA
129 AATTATAGACTTTTTTTTGTAAATCTAAAATAATTTTAGGA
551952 TAAATTTGTA
Statistics
Matches: 168, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
168 3 0.02
169 96 0.57
170 69 0.41
ACGTcount: A:0.46, C:0.06, G:0.06, T:0.42
Consensus pattern (169 bp):
ATTTATATATTTTCTTTAAAAAATTAAATTCATAATATTTATATAATTTTTTTTACAAAATTAAA
ATATAAAAAAAGGTTTAATAAAAGGGTAAAAAAAATTAACCCTTGAACTTCATATAAAATTTTAA
TTATAGACTTTTTTTTGTAAATCTAAAATAATTTTAGGA
Found at i:553349 original size:32 final size:32
Alignment explanation
Indices: 553313--553413 Score: 114
Period size: 32 Copynumber: 3.2 Consensus size: 32
553303 TCCAAGGCAT
*
553313 TTCCTTGGGTAGGCTCTAAGGCCCCAATATAC
1 TTCCTTGGGTAGGCTCTAAGGCCCCAAAATAC
** * *
553345 TTCCTTATGTAGGCTCTTAGGCCCTAAAATAC
1 TTCCTTGGGTAGGCTCTAAGGCCCCAAAATAC
* * * *
553377 TCCCTTGGATAGGCTCTCAGGCCCCAAGATA-
1 TTCCTTGGGTAGGCTCTAAGGCCCCAAAATAC
553408 TTCCTT
1 TTCCTT
553414 TAGGTTGGCA
Statistics
Matches: 56, Mismatches: 13, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
31 5 0.09
32 51 0.91
ACGTcount: A:0.22, C:0.29, G:0.19, T:0.31
Consensus pattern (32 bp):
TTCCTTGGGTAGGCTCTAAGGCCCCAAAATAC
Found at i:559008 original size:29 final size:30
Alignment explanation
Indices: 558941--559017 Score: 84
Period size: 30 Copynumber: 2.6 Consensus size: 30
558931 AAATTAACGG
* * *
558941 TCGGTGGTTTGATTAAATCAATTAAATAGT
1 TCGGTGGTCTGATTGATTCAATTAAATAGT
* *
558971 TGGGTGGTCTGATTGATTCAATTGAA-AGT
1 TCGGTGGTCTGATTGATTCAATTAAATAGT
**
559000 TCGGTGGTCACATTGATT
1 TCGGTGGTCTGATTGATT
559018 TTTGACCATT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
29 18 0.46
30 21 0.54
ACGTcount: A:0.26, C:0.09, G:0.26, T:0.39
Consensus pattern (30 bp):
TCGGTGGTCTGATTGATTCAATTAAATAGT
Found at i:561732 original size:16 final size:16
Alignment explanation
Indices: 561713--561744 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
561703 GGGCGACGAT
*
561713 TGTGGCAGCCGACGGC
1 TGTGGCAGCCAACGGC
561729 TGTGGCAGCCAACGGC
1 TGTGGCAGCCAACGGC
561745 AGCAGGATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.16, C:0.31, G:0.41, T:0.12
Consensus pattern (16 bp):
TGTGGCAGCCAACGGC
Found at i:561839 original size:18 final size:18
Alignment explanation
Indices: 561818--561872 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
561808 AATTTTAGGG
561818 ATTTTTAAAAAATATAAT
1 ATTTTTAAAAAATATAAT
* *
561836 ATTTTTTAAAAAACAAAAT
1 A-TTTTTAAAAAATATAAT
*
561855 A-TTTTAACATAATATAAT
1 ATTTTTAA-AAAATATAAT
561873 CAATTAACGG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 6 0.20
18 8 0.27
19 16 0.53
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTTTAAAAAATATAAT
Found at i:561841 original size:19 final size:19
Alignment explanation
Indices: 561819--561859 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
561809 ATTTTAGGGA
* *
561819 TTTTTAAAAAATATAATAT
1 TTTTTAAAAAACAAAATAT
561838 TTTTTAAAAAACAAAATAT
1 TTTTTAAAAAACAAAATAT
561857 TTT
1 TTT
561860 AACATAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTTTAAAAAACAAAATAT
Found at i:563577 original size:19 final size:17
Alignment explanation
Indices: 563545--563579 Score: 52
Period size: 19 Copynumber: 1.9 Consensus size: 17
563535 ACCTAATACT
563545 AATTTAAATTTAAATTC
1 AATTTAAATTTAAATTC
563562 AATTTAAAAGTTTAAATT
1 AATTT-AAA-TTTAAATT
563580 GATTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.31
18 3 0.19
19 8 0.50
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
AATTTAAATTTAAATTC
Found at i:563942 original size:15 final size:14
Alignment explanation
Indices: 563917--563953 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
563907 AACTGATGAC
563917 TTAAAAACATAAAA
1 TTAAAAACATAAAA
563931 TTAAACAACATAAAA
1 TTAAA-AACATAAAA
563946 TATAAAAA
1 T-TAAAAA
563954 TATATATGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 12 0.57
16 4 0.19
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.22
Consensus pattern (14 bp):
TTAAAAACATAAAA
Found at i:564045 original size:32 final size:32
Alignment explanation
Indices: 564001--564066 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
563991 ATAAAAATTT
* * *
564001 AAAAATAAATAATTATTACTTAATTATAAAAA
1 AAAAATAAATAATGATTACATAATGATAAAAA
* *
564033 AAAAATACATAATGATTACATAATGATAAGAA
1 AAAAATAAATAATGATTACATAATGATAAAAA
564065 AA
1 AA
564067 CTTTAATAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (32 bp):
AAAAATAAATAATGATTACATAATGATAAAAA
Found at i:565855 original size:26 final size:27
Alignment explanation
Indices: 565826--565884 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
565816 TAATTCTTAT
565826 AATTTAGGGTT-TAATTTAAAATTTAA
1 AATTTAGGGTTATAATTTAAAATTTAA
* * *
565852 AATTTAGGGTTATGATTTTAAATTTTA
1 AATTTAGGGTTATAATTTAAAATTTAA
565879 AATTTA
1 AATTTA
565885 TGATTAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 11 0.38
27 18 0.62
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (27 bp):
AATTTAGGGTTATAATTTAAAATTTAA
Found at i:565881 original size:27 final size:26
Alignment explanation
Indices: 565813--565884 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 26
565803 TGTGTTCAGG
565813 TTTT-AATTCTTATAATTTAGGGTTTAA
1 TTTTAAATT-TTA-AATTTAGGGTTTAA
* * *
565840 TTTAAAATTTAAAATTTAGGGTTATGA
1 TTTTAAATTTTAAATTTAGGGTT-TAA
565867 TTTTAAATTTTAAATTTA
1 TTTTAAATTTTAAATTTA
565885 TGATTAAAGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 11 0.29
27 23 0.61
28 4 0.11
ACGTcount: A:0.36, C:0.01, G:0.10, T:0.53
Consensus pattern (26 bp):
TTTTAAATTTTAAATTTAGGGTTTAA
Found at i:566124 original size:4 final size:4
Alignment explanation
Indices: 566115--566142 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
566105 GTTGGGACAT
566115 GAGG GAGG GAGG GAGG GAGG GAGG GAGG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG
566143 AGAAAAGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.75, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:567894 original size:18 final size:18
Alignment explanation
Indices: 567855--567894 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
567845 AATTTATAAT
* *
567855 ATATTTTGACAGGTTCAT
1 ATATTTTGACAGGTCCAC
*
567873 ATATTTTGATAGGTCCAC
1 ATATTTTGACAGGTCCAC
567891 ATAT
1 ATAT
567895 AATGAGATTT
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:0.30, C:0.12, G:0.15, T:0.42
Consensus pattern (18 bp):
ATATTTTGACAGGTCCAC
Found at i:569074 original size:18 final size:19
Alignment explanation
Indices: 569051--569090 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
569041 AAGATTAACA
*
569051 TTTGATTGTAACA-TTTAT
1 TTTGATCGTAACATTTTAT
*
569069 TTTGATCGTAATATTTTAT
1 TTTGATCGTAACATTTTAT
569088 TTT
1 TTT
569091 TAAAGAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (19 bp):
TTTGATCGTAACATTTTAT
Found at i:569401 original size:13 final size:14
Alignment explanation
Indices: 569383--569411 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
569373 GGTCCATCTC
569383 TATTTTAAA-TATT
1 TATTTTAAATTATT
569396 TATTTTAAATTATT
1 TATTTTAAATTATT
569410 TA
1 TA
569412 AAAATTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATTTTAAATTATT
Found at i:570034 original size:22 final size:22
Alignment explanation
Indices: 570006--570056 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
569996 TACCAGAATA
570006 ACATCTAAGTTTGAATGAGGCG
1 ACATCTAAGTTTGAATGAGGCG
570028 ACATCTAAGTTTGAATGAGGCG
1 ACATCTAAGTTTGAATGAGGCG
570050 ACATCTA
1 ACATCTA
570057 GATCCATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Consensus pattern (22 bp):
ACATCTAAGTTTGAATGAGGCG
Found at i:580110 original size:42 final size:42
Alignment explanation
Indices: 580058--580182 Score: 178
Period size: 42 Copynumber: 3.0 Consensus size: 42
580048 CAACCGAATC
* **
580058 ATTAGGTGAATCATTGGAATTTCCAATATTATTATTAGAAGT
1 ATTAGATGAATCATTGGAATTTCCAATAGGATTATTAGAAGT
* * *
580100 ATTATATGAATCATTGAAATTTCTAATAGGATTATTAGAAGT
1 ATTAGATGAATCATTGGAATTTCCAATAGGATTATTAGAAGT
* *
580142 ATTAGGTGAATCATTGGAATTTCCAATCGGATTATTAGAAG
1 ATTAGATGAATCATTGGAATTTCCAATAGGATTATTAGAAG
580183 GTTTAATCGG
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (42 bp):
ATTAGATGAATCATTGGAATTTCCAATAGGATTATTAGAAGT
Found at i:581442 original size:48 final size:48
Alignment explanation
Indices: 581388--581487 Score: 173
Period size: 48 Copynumber: 2.1 Consensus size: 48
581378 TTTTCCACCG
581388 AATCCTGATTGTCCTCTTGTTGATTTTCTTCGTTATTTGGTGAAGTGA
1 AATCCTGATTGTCCTCTTGTTGATTTTCTTCGTTATTTGGTGAAGTGA
* * *
581436 AATCCTGCTTGTCCTCTTGTTGATTTTCTTCGTTATTTGTTGAAGTTA
1 AATCCTGATTGTCCTCTTGTTGATTTTCTTCGTTATTTGGTGAAGTGA
581484 AATC
1 AATC
581488 TCGAAAATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.17, C:0.16, G:0.18, T:0.49
Consensus pattern (48 bp):
AATCCTGATTGTCCTCTTGTTGATTTTCTTCGTTATTTGGTGAAGTGA
Found at i:604913 original size:22 final size:21
Alignment explanation
Indices: 604866--604936 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 21
604856 GCGATCATGC
*
604866 ATGCGATTTTCCAAATTCGCG
1 ATGCGATTTTCCAAATTCGCA
* * *
604887 TTGCGATTTTCCGACTATCGCA
1 ATGCGATTTTCCAAAT-TCGCA
* * **
604909 ATGCGAATATGTAAA-TCGCA
1 ATGCGATTTTCCAAATTCGCA
604929 ATGCGATT
1 ATGCGATT
604937 ATGACTATCG
Statistics
Matches: 37, Mismatches: 12, Indels: 3
0.71 0.23 0.06
Matches are distributed among these distances:
20 12 0.32
21 13 0.35
22 12 0.32
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (21 bp):
ATGCGATTTTCCAAATTCGCA
Found at i:604946 original size:20 final size:20
Alignment explanation
Indices: 604923--605036 Score: 138
Period size: 20 Copynumber: 5.7 Consensus size: 20
604913 GAATATGTAA
* *
604923 ATCGCAATGCGATTATGACT
1 ATCGCAACGCGATTCTGACT
* *
604943 ATCGCAACGCAATTCTAACT
1 ATCGCAACGCGATTCTGACT
* *
604963 ATCGCAACGAGATTCTTACT
1 ATCGCAACGCGATTCTGACT
* *
604983 ATCGTAACGCAATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
605003 ATCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTCTGACT
*
605023 ATCGCAATGCGATT
1 ATCGCAACGCGATT
605037 TTCAAAGCGC
Statistics
Matches: 78, Mismatches: 16, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 78 1.00
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.27
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:605602 original size:20 final size:20
Alignment explanation
Indices: 605577--605632 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
605567 TGCGATTTGT
605577 TTCGCGTTGCGATTTTCAAA
1 TTCGCGTTGCGATTTTCAAA
** **
605597 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATTTTCAAA
*
605617 TTCGTGTTGCGATTTT
1 TTCGCGTTGCGATTTT
605633 AAGTTTCAGG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.14, C:0.18, G:0.23, T:0.45
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCAAA
Found at i:605639 original size:20 final size:20
Alignment explanation
Indices: 605575--605639 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
605565 AATGCGATTT
605575 GTTTCGCGTTGCGATTTTCAA
1 GTTTCGCGTTGCGATTTT-AA
* ** *
605596 -ATTCGCGTTGCGATAGTCA
1 GTTTCGCGTTGCGATTTTAA
* *
605615 TTTTCGTGTTGCGATTTTAA
1 GTTTCGCGTTGCGATTTTAA
605635 GTTTC
1 GTTTC
605640 AGGAACTATT
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
19 1 0.03
20 32 0.97
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
GTTTCGCGTTGCGATTTTAA
Found at i:608062 original size:20 final size:20
Alignment explanation
Indices: 608037--608084 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
608027 GTGATTCTCT
608037 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
**
608057 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
608077 TGTTGCGA
1 CGTTGCGA
608085 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:608308 original size:20 final size:20
Alignment explanation
Indices: 608279--608317 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
608269 TTACTTTCGC
608279 AACGCAAAAATGACTATCGT
1 AACGCAAAAATGACTATCGT
*
608299 AACGCGAAAATGACTATCG
1 AACGCAAAAATGACTATCG
608318 CAATGAAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (20 bp):
AACGCAAAAATGACTATCGT
Found at i:608374 original size:308 final size:308
Alignment explanation
Indices: 607816--608697 Score: 1279
Period size: 308 Copynumber: 2.9 Consensus size: 308
607806 ATTTCACTTA
* *
607816 GATTGCTTAGTAAATTCATTCGATTGCTGTCAATACTGCTAAACTGTTTATTCTTTAACCCTGTG
1 GATTGCTTAGTAAATTCATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACCCTGTG
*
607881 AAGTTAGTATTTGTTTTTGGTTATCTTTTGGTTGAAGTAATGCAATCCATTCAAGTTTCAATTTG
66 AAGTTAGTATTTGTTTTTTGTTATCTTTTGGTTGAAGTAATGCAATCCATTCAAGTTTCAATTTG
607946 CAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCGCAACGAAAGAATCACAATGCG
131 CAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCGCAACGAAAGAATCACAATGCG
* ** * *****
608011 AAATGAAAATCGCATTGTGATTCTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTC
196 AAATGAAAATCGCAATGAAAATCGAAAATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTC
*
608076 GTGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAATG
261 GCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAATG
* * *
608124 GATTGCTTAGTAAATTTATTCGGTTGCTGCCAATACTGCTAAATTGTTTATTCTTTAACTCTGTG
1 GATTGCTTAGTAAATTCATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACCCTGTG
* *
608189 AAGTTAGTATTTGTTTTTTGTTATCTTTTGGATGAAGTATTGCAATCCATTCAAGTTTCAATTTG
66 AAGTTAGTATTTGTTTTTTGTTATCTTTTGGTTGAAGTAATGCAATCCATTCAAGTTTCAATTTG
* * * * *
608254 CAGAAGAAGAATAGTTTACTTTCGCAACGCAAAAATGACTATCGTAACGCGAA-AATGACTAT-C
131 CAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCGCAACG-AAAGAATCACAATGC
* * * * * *
608317 GCAATGAAAGAATCGTAATGCAAAAT-GAAAATTGC-ATTG-CGATTCTCTCGTTGCGATAGTCA
195 GAAATG-AA-AATCGCAATG-AAAATCGAAAATTGCGATAGTCAAAT-TCGCGTTGCGATAGTCA
608379 TTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAATG
256 TTTTCGCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAATG
* *
608432 GATTGGTTAGTAAATTCATTTGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACCCTGTG
1 GATTGCTTAGTAAATTCATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACCCTGTG
*
608497 AAGTTAGTATTTGTTTTTTGTTGTCTTTTGGTTGAAGTAATGCAATCCATTCAAGTTTCAATTTG
66 AAGTTAGTATTTGTTTTTTGTTATCTTTTGGTTGAAGTAATGCAATCCATTCAAGTTTCAATTTG
* * *
608562 CAGAAGAATAATAGTTTACTTTCGCAACGCGAAAATGACTATCGCAACAAAAGAATCGCAATGCG
131 CAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCGCAACGAAAGAATCACAATGCG
* * ** * *****
608627 AAATAAAAATCGCATTGCGATTCTCTCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTC
196 AAATGAAAATCGCAATGAAAATCGAAAATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTC
608692 GCGTTG
261 GCGTTG
608698 TGATAGTCAT
Statistics
Matches: 503, Mismatches: 61, Indels: 20
0.86 0.10 0.03
Matches are distributed among these distances:
306 2 0.00
307 23 0.05
308 454 0.90
309 22 0.04
310 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.36
Consensus pattern (308 bp):
GATTGCTTAGTAAATTCATTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACCCTGTG
AAGTTAGTATTTGTTTTTTGTTATCTTTTGGTTGAAGTAATGCAATCCATTCAAGTTTCAATTTG
CAGAAGAAGAATAGTTTACTTTCGCAACGCGAAAATGACTATCGCAACGAAAGAATCACAATGCG
AAATGAAAATCGCAATGAAAATCGAAAATTGCGATAGTCAAATTCGCGTTGCGATAGTCATTTTC
GCGTTGCGAAAGTAAACTATTCTTCTTCTGCAAATTGAAACTTGAATG
Found at i:608678 original size:20 final size:19
Alignment explanation
Indices: 608653--608719 Score: 82
Period size: 20 Copynumber: 3.5 Consensus size: 19
608643 GCGATTCTCT
608653 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTC-AATTCG
*
608673 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCA-ATTCG
*
608693 CGTTGTGATAGTC-ATTCG
1 CGTTGCGATAGTCAATTCG
*
608711 TGTTGCGAT
1 CGTTGCGAT
608720 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 11 0.27
19 1 0.02
20 29 0.71
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCAATTCG
Found at i:609249 original size:18 final size:19
Alignment explanation
Indices: 609210--609251 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
609200 CTCACCTGTC
609210 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
609231 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
609249 ATC
1 ATC
609252 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:610890 original size:20 final size:20
Alignment explanation
Indices: 610867--610904 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
610857 ACGTTAAACT
*
610867 CAAAATCGCAATGCGAAAGA
1 CAAAATCGCAACGCGAAAGA
610887 CAAAATCGCAACGCGAAA
1 CAAAATCGCAACGCGAAA
610905 CCGTTGCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.50, C:0.24, G:0.18, T:0.08
Consensus pattern (20 bp):
CAAAATCGCAACGCGAAAGA
Found at i:610931 original size:20 final size:20
Alignment explanation
Indices: 610906--611185 Score: 248
Period size: 20 Copynumber: 15.2 Consensus size: 20
610896 AACGCGAAAC
*
610906 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
610926 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
610946 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
* *
610960 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
610980 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
611000 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
* *
611014 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
611034 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
611054 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
611074 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
*
611088 CGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
611108 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
611128 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* * *
611142 AGTTGCGATAATCAAATTCA
1 CGTTGCGATAGTCAAATTCG
611162 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
611182 CGTT
1 CGTT
611186 ACAATATTCA
Statistics
Matches: 209, Mismatches: 27, Indels: 48
0.74 0.10 0.17
Matches are distributed among these distances:
14 47 0.22
16 4 0.02
18 4 0.02
20 154 0.74
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:610969 original size:54 final size:54
Alignment explanation
Indices: 610906--611058 Score: 270
Period size: 54 Copynumber: 2.8 Consensus size: 54
610896 AACGCGAAAC
* * *
610906 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
610960 CGTTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
1 CGTTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
*
611014 CGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTG
611059 TGATAGTCAA
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 95 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (54 bp):
CGTTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:611018 original size:34 final size:34
Alignment explanation
Indices: 610980--611116 Score: 150
Period size: 34 Copynumber: 3.9 Consensus size: 34
610970 GTCAAATACC
610980 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* * *
611014 CGTTGCGATAGTCAAATACCCGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT--T----TTCT
*
611054 CGTTGTGATAGTCAAATTCGCGTTGCGATTTT-T
1 CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
* *
611087 GCGTTGCGATAGTCATATTCGTGTTGCGAT
1 -CGTTGCGATAGTCAAATTCGCGTTGCGAT
611117 AGTCAAATTC
Statistics
Matches: 86, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
34 55 0.64
36 1 0.01
38 1 0.01
40 29 0.34
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (34 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT
Found at i:611038 original size:74 final size:74
Alignment explanation
Indices: 610960--611136 Score: 266
Period size: 74 Copynumber: 2.4 Consensus size: 74
610950 GCGATTTTCT
* *
610960 CGTTGCGATAGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT-CGTTGCGATA
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGCGTTGCGATA
611024 GTCAAATACC
65 GTCAAATACC
* *
611034 CGTTGCGATAATCAAATTCGCGTTGTGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGCGATAG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGCGATAG
* * *
611099 TCATATTCG
66 TCAAATACC
*
611108 TGTTGCGATAGTCAAATTCGCGTTGCGAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGAT
611137 TTTTGAGTTG
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
73 1 0.01
74 91 0.99
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.34
Consensus pattern (74 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGCGTTGCGATAG
TCAAATACC
Found at i:611092 original size:54 final size:54
Alignment explanation
Indices: 611034--611185 Score: 250
Period size: 54 Copynumber: 2.8 Consensus size: 54
611024 GTCAAATACC
*
611034 CGTTGCGATAATCAAATTCGCGTTGTGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
* * *
611088 CGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
* *
611142 AGTTGCGATAATCAAATTCACGTTGCGATAGTCAAATTCGCGTT
1 CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
611186 ACAATATTCA
Statistics
Matches: 89, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 89 1.00
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (54 bp):
CGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTG
Found at i:611133 original size:128 final size:128
Alignment explanation
Indices: 610905--611185 Score: 440
Period size: 128 Copynumber: 2.2 Consensus size: 128
610895 CAACGCGAAA
610905 CCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATA
1 CCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATA
* *
610970 GTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT-CGTTGCGATAGTCAAATAC
66 GTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTT-TGAGTTGCGATAATCAAATAC
*
611033 CCGTTGCGATAATCAAATTCGCGTTGTGATAGTCAAATTCGCGTTGCGATTTT-TGCGTTGCGAT
1 CCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCT-CGTTGCGAT
* * ** *
611097 AGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTGCGATAATCAAATTC
65 AGTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTGCGATAATCAAATAC
* *
611161 ACGTTGCGATAGTCAAATTCGCGTT
1 CCGTTGCGATAATCAAATTCGCGTT
611186 ACAATATTCA
Statistics
Matches: 141, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
127 2 0.01
128 139 0.99
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (128 bp):
CCGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATA
GTCAAATACCCGTTGCGATAGTCAAATTCGCGTTGCGATTTTTGAGTTGCGATAATCAAATAC
Found at i:611196 original size:20 final size:20
Alignment explanation
Indices: 611153--611198 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
611143 GTTGCGATAA
* *
611153 TCAAATTCACGTTGCGATAG
1 TCAAATTCACGTTACAATAG
* *
611173 TCAAATTCGCGTTACAATAT
1 TCAAATTCACGTTACAATAG
611193 TCAAAT
1 TCAAAT
611199 GAATGTGTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (20 bp):
TCAAATTCACGTTACAATAG
Found at i:611421 original size:140 final size:140
Alignment explanation
Indices: 611169--611438 Score: 486
Period size: 140 Copynumber: 1.9 Consensus size: 140
611159 TCACGTTGCG
*
611169 ATAGTCAAATTCGCGTTACAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCA
1 ATAGTCAAATTCGCGTTACAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
611234 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
611299 AATACACATA
131 AATACACATA
* *** *
611309 ATAGTCAAATTCGTGTTGTGATATTCAAATGAATGTGTAATAAGTGATAATAACTGAACAGATCA
1 ATAGTCAAATTCGCGTTACAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
611374 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
611439 TACAATGTTT
Statistics
Matches: 124, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTACAATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:613545 original size:14 final size:15
Alignment explanation
Indices: 613526--613562 Score: 67
Period size: 14 Copynumber: 2.5 Consensus size: 15
613516 TCCCGTGGCA
613526 TTTTCTTCGGGGAC-
1 TTTTCTTCGGGGACT
613540 TTTTCTTCGGGGACT
1 TTTTCTTCGGGGACT
613555 TTTTCTTC
1 TTTTCTTC
613563 TTCTTTTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (15 bp):
TTTTCTTCGGGGACT
Done.