Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007837.1 Hibiscus syriacus cultivar Beakdansim tig00110186_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: 1003650
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:413551 original size:2 final size:2
Alignment explanation
Indices: 413544--413576 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
413534 TTTACATGTA
413544 AT AT AT AT AT AT AT -T 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
413577 GTTTATGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:414494 original size:20 final size:22
Alignment explanation
Indices: 414469--414526 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
414459 TTCCCCTTGA
414469 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
*
414489 AGTGCATCGATGTATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
414512 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
414527 CTACCCATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:419109 original size:21 final size:21
Alignment explanation
Indices: 419085--419132 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
419075 ATAATTCATG
* *
419085 ACAAATATAACCTTAAATATA
1 ACAAATATAACCCTAAATAAA
419106 ACAAATATAACCCTAAATAAA
1 ACAAATATAACCCTAAATAAA
419127 ACAAAT
1 ACAAAT
419133 TAATTTTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (21 bp):
ACAAATATAACCCTAAATAAA
Found at i:437530 original size:19 final size:18
Alignment explanation
Indices: 437492--437545 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
437482 AAATTTGTAT
*
437492 ATTTAAT-TTATGTTTTAA
1 ATTTAATATTAT-TTTAAA
437510 ATTCTAATATTATTTTAAA
1 ATT-TAATATTATTTTAAA
* *
437529 ATTTTAGATTATTTTAA
1 ATTTAATATTATTTTAA
437546 TTTGGTTTCG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
18 15 0.48
19 12 0.39
20 4 0.13
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (18 bp):
ATTTAATATTATTTTAAA
Found at i:438183 original size:60 final size:60
Alignment explanation
Indices: 438056--438192 Score: 134
Period size: 60 Copynumber: 2.3 Consensus size: 60
438046 ATAGTCAGGT
* * * * * *
438056 GACCATTTTATAACTTTTAATAGTTGTGAGACTTAACAAAACATCGTCCTATGGACTAAG
1 GACCATTTTGTAACTTTTAATAGTAGTGAGACTCAACAAAACATCGTCCTATAGACAAAA
* * * ** *
438116 GATCATTTTGTAACTTTTAATAGTCAG-GATACTCAATAAAGTATCGTCCTATAGTCAAAA
1 GACCATTTTGTAACTTTTAATAGT-AGTGAGACTCAACAAAACATCGTCCTATAGACAAAA
438176 GACCA-TTTGTATACTTT
1 GACCATTTTGTA-ACTTT
438193 ATCCTATTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
59 6 0.10
60 55 0.89
61 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTAGTGAGACTCAACAAAACATCGTCCTATAGACAAAA
Found at i:441055 original size:33 final size:31
Alignment explanation
Indices: 440963--441057 Score: 79
Period size: 33 Copynumber: 3.0 Consensus size: 31
440953 TATAATATTT
*
440963 TAAAA-TATAAGATATGATACATTTTAATTCAA
1 TAAAATTATAATA-ATGATACATTTTAATT-AA
* *
440995 TAAAATTATAATAATGAAGACA-ATTAATTAA
1 TAAAATTATAATAATG-ATACATTTTAATTAA
*
441026 TTTAAAATATGTAA-AATGATACATTTTAATTA
1 --TAAAAT-TATAATAATGATACATTTTAATTA
441058 TAACATATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
31 2 0.04
32 18 0.35
33 27 0.53
34 4 0.08
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (31 bp):
TAAAATTATAATAATGATACATTTTAATTAA
Found at i:444148 original size:15 final size:15
Alignment explanation
Indices: 444128--444159 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
444118 ATTTCATTAT
444128 ATTTTATATAATCAA
1 ATTTTATATAATCAA
444143 ATTTTATATAATCAA
1 ATTTTATATAATCAA
444158 AT
1 AT
444160 CTCACTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
ATTTTATATAATCAA
Found at i:444726 original size:94 final size:94
Alignment explanation
Indices: 444565--444755 Score: 382
Period size: 94 Copynumber: 2.0 Consensus size: 94
444555 GTTTACTACA
444565 AATCTCTACTAATTTCTGGGAAATTTTAAAGGGCTTTCCTTAAACCTTTATGTAGGAACCTGAGC
1 AATCTCTACTAATTTCTGGGAAATTTTAAAGGGCTTTCCTTAAACCTTTATGTAGGAACCTGAGC
444630 AAAATGCCATACGAAATTTACGGCCAATG
66 AAAATGCCATACGAAATTTACGGCCAATG
444659 AATCTCTACTAATTTCTGGGAAATTTTAAAGGGCTTTCCTTAAACCTTTATGTAGGAACCTGAGC
1 AATCTCTACTAATTTCTGGGAAATTTTAAAGGGCTTTCCTTAAACCTTTATGTAGGAACCTGAGC
444724 AAAATGCCATACGAAATTTACGGCCAATG
66 AAAATGCCATACGAAATTTACGGCCAATG
444753 AAT
1 AAT
444756 TTAGATGCGG
Statistics
Matches: 97, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 97 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.31
Consensus pattern (94 bp):
AATCTCTACTAATTTCTGGGAAATTTTAAAGGGCTTTCCTTAAACCTTTATGTAGGAACCTGAGC
AAAATGCCATACGAAATTTACGGCCAATG
Found at i:446148 original size:60 final size:60
Alignment explanation
Indices: 446040--446186 Score: 149
Period size: 60 Copynumber: 2.5 Consensus size: 60
446030 TGATCTTTAT
* * *
446040 TTTTAAATTGATCTAT-AAACTTTTAAATGATTCAATTTCATTCTCAAACTATAACCCAT-A
1 TTTTAAATTGATC-ATCAAACTTTTGAATGATTCAATTTAATTCCCAAACTATAA-CCATCA
* * *
446100 TTTTAAATTAATCATCAAACTTTTGAAT-ATTTCAGA-TTAATTCCCAAACTATGATCATCA
1 TTTTAAATTGATCATCAAACTTTTGAATGA-TTCA-ATTTAATTCCCAAACTATAACCATCA
* **
446160 TTCTAAATTGATCCCCAAACTTTTGAA
1 TTTTAAATTGATCATCAAACTTTTGAA
446187 AATTCCAATA
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
59 6 0.08
60 66 0.90
61 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.05, T:0.40
Consensus pattern (60 bp):
TTTTAAATTGATCATCAAACTTTTGAATGATTCAATTTAATTCCCAAACTATAACCATCA
Found at i:456579 original size:54 final size:54
Alignment explanation
Indices: 456521--456796 Score: 168
Period size: 54 Copynumber: 5.1 Consensus size: 54
456511 TTGGTTTTTG
* *
456521 GTAATGATCCCATCAGAAGCTGAGGTTGATTCCCTTCTAGAAATTAGATTTCCA
1 GTAATGATCCTATCAGAAGCTGAGGTTGATTCCCTTCTAGAAATTTGATTTCCA
* * ** * *
456575 GTAATGCTTCC-A-CTAGATGCAT-AATTTGATCCCCTTCTAGAAATTTGATTTACA
1 GTAATG-ATCCTATC-AGAAGC-TGAGGTTGATTCCCTTCTAGAAATTTGATTTCCA
* * * * * * * * *
456629 GTAACGATCCTATTAGATGC-AACGGTCGATTCCTTTCGAGAACTTTGATTTCGA
1 GTAATGATCCTATCAGAAGCTGA-GGTTGATTCCCTTCTAGAAATTTGATTTCCA
* * * * * * * *
456683 GCAGTCATCCTATCTG-AGGTGAAAGTTGATTCCCTTCTAGAAATTCGATCTCCA
1 GTAATGATCCTATCAGAAGCTG-AGGTTGATTCCCTTCTAGAAATTTGATTTCCA
* * * * * * *
456737 GTAATTATCCTGTCAGAAG-TAGGGGTTGTTTCCCTTCTAGGAATTGGACTTCCA
1 GTAATGATCCTATCAGAAGCT-GAGGTTGATTCCCTTCTAGAAATTTGATTTCCA
456791 GTAATG
1 GTAATG
456797 CCACCCTCGG
Statistics
Matches: 162, Mismatches: 49, Indels: 22
0.70 0.21 0.09
Matches are distributed among these distances:
53 6 0.04
54 148 0.91
55 8 0.05
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (54 bp):
GTAATGATCCTATCAGAAGCTGAGGTTGATTCCCTTCTAGAAATTTGATTTCCA
Found at i:457078 original size:239 final size:239
Alignment explanation
Indices: 456748--457229 Score: 820
Period size: 239 Copynumber: 2.0 Consensus size: 239
456738 TAATTATCCT
*
456748 GTCAGAAGTAGGGGTTGTTTCCCTTCTAGGAATTGGACTTCCAGTAATGCCACCCTCGGAACCAC
1 GTCAGAAGTAGGGGTTGTTTCCCTTCTAGGAATTGGACTTCCAGTAATGCCACCCTCAGAACCAC
*
456813 AAGCTGATTCTGCTGTAGAAATTAGACTTTCAACAGGACTAATATCATTGGCCGACATAGGGTCC
66 AAGCTGATTCCGCTGTAGAAATTAGACTTTCAACAGGACTAATATCATTGGCCGACATAGGGTCC
* * *
456878 GTTTTAGATATTTGTGTTCCTCCTTTCTGTCAGGTTAAAGCACAAGAAATAAATTTAATTCAATC
131 GTTTTAGATATTTGTGTTCCTCCTTTCTGTCAGGTTAAAACACAAGAAATAAACTCAATTCAATC
* * *
456943 ACAAAAATGTAGAATCTCGTGACCATGAACATCTATATTACTTG
196 ACAAAAATGCAGAATCTCGTGAACATGAAAATCTATATTACTTG
* * *
456987 GTCAGAAGTAGGGGTTGTTTCCCTTCTAGGAATTGGACTTCTAGTAATGCCACCCTCAGAGCCAG
1 GTCAGAAGTAGGGGTTGTTTCCCTTCTAGGAATTGGACTTCCAGTAATGCCACCCTCAGAACCAC
* * * *
457052 AAGCTGATTCCGTTGTAGAAATTAGACTTTCGACAGGACTTATATTATTGGCCGACATAGGGTCC
66 AAGCTGATTCCGCTGTAGAAATTAGACTTTCAACAGGACTAATATCATTGGCCGACATAGGGTCC
457117 GTTTTAGATATTTGTGTTCCTCCTTTCTGTCAGGTTAAAACACAAGAAATAAACTCAATTCAATC
131 GTTTTAGATATTTGTGTTCCTCCTTTCTGTCAGGTTAAAACACAAGAAATAAACTCAATTCAATC
*
457182 ACAAAAATGCGGAATCTCGTGAACATGAAAATCTATATTACTTG
196 ACAAAAATGCAGAATCTCGTGAACATGAAAATCTATATTACTTG
457226 GTCA
1 GTCA
457230 TGCAAAAACC
Statistics
Matches: 227, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
239 227 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (239 bp):
GTCAGAAGTAGGGGTTGTTTCCCTTCTAGGAATTGGACTTCCAGTAATGCCACCCTCAGAACCAC
AAGCTGATTCCGCTGTAGAAATTAGACTTTCAACAGGACTAATATCATTGGCCGACATAGGGTCC
GTTTTAGATATTTGTGTTCCTCCTTTCTGTCAGGTTAAAACACAAGAAATAAACTCAATTCAATC
ACAAAAATGCAGAATCTCGTGAACATGAAAATCTATATTACTTG
Found at i:460095 original size:15 final size:14
Alignment explanation
Indices: 460073--460103 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
460063 ATTTTTAATA
460073 ATTCAATAATAAAT
1 ATTCAATAATAAAT
460087 ATTCAAATAATAAAT
1 ATTC-AATAATAAAT
460102 AT
1 AT
460104 CATCTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (14 bp):
ATTCAATAATAAAT
Found at i:462057 original size:18 final size:18
Alignment explanation
Indices: 462030--462064 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
462020 CGGAATATAA
462030 GATTACCGGCGGGAATAT
1 GATTACCGGCGGGAATAT
*
462048 GATTATCGGCGGGAATA
1 GATTACCGGCGGGAATA
462065 AAATTGCTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.14, G:0.34, T:0.23
Consensus pattern (18 bp):
GATTACCGGCGGGAATAT
Found at i:462250 original size:19 final size:18
Alignment explanation
Indices: 462218--462255 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
462208 TGAATTCTAC
462218 TATATTTTACTAAATAATT
1 TATATTTTACTAAA-AATT
462237 TATATTTT-CTTAAAAATT
1 TATATTTTAC-TAAAAATT
462255 T
1 T
462256 TAATTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.55
Consensus pattern (18 bp):
TATATTTTACTAAAAATT
Found at i:463895 original size:15 final size:16
Alignment explanation
Indices: 463875--463915 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
463865 GTTTACTTCA
*
463875 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
463890 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
463906 GAATGATTCA
1 GAATGATTCA
463916 GAGGCTCCGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:477590 original size:253 final size:247
Alignment explanation
Indices: 477142--477668 Score: 776
Period size: 253 Copynumber: 2.1 Consensus size: 247
477132 CTTATTCATA
*
477142 TATTGAATAAAAATATTTTTTTTATTATTTCGGGTCGGGTCAGGTTTCTAATTCATATATTCGGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGG-CA-GTTTCTAATTCATATATTCGGG
477207 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGGTC
64 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAAGTGTGATATT---GTCGGGTC
* * *
477272 GAGTTCGGGTTTAGGGTGAAAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTTAG
126 GAGTTCAGGTTTAGGGTGAAAATACCCGACCCAAAAAAATATATAATTTTACCTTATATATTTAG
* *
477337 GAATAATTACAATAATATCCCTCTATATATAATTTTTTTTCAATTAAGTCACTGCTTT
191 GAATAATTACAATAATACCCCTCTATATATAA-TTTTTTTCAATTAAGTCAATGCTTT
477395 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTC-GG-A-TTTCTAATTCATATATTCGGGTC
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGCAGTTTCTAATTCATATATTCGGGTC
*
477457 GGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGTCGGGTTTTTTAAGTGTGATA-T-TCGGGTCG
66 GGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGT----TTTTTTAAGTGTGATATTGTCGGGTCG
477520 AGTTCAGGTTTAGGGTGAAAAAAATGGGACCCGACCCAAAAAAATATATAATTTTACCTTATATA
127 AGTTCAGGTTTAGGGTG---AAAAT---ACCCGACCCAAAAAAATATATAATTTTACCTTATATA
* *
477585 TTTAGGAATAATTATAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGTTTT
186 TTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGCTTT
*
477647 TATTGAATAAAAAATGATTTTT
1 TATTGAAT-AAAAATAATTTTT
477669 ATAATTTATT
Statistics
Matches: 253, Mismatches: 10, Indels: 22
0.89 0.04 0.08
Matches are distributed among these distances:
247 24 0.09
248 56 0.22
250 6 0.02
251 1 0.00
252 49 0.19
253 117 0.46
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.41
Consensus pattern (247 bp):
TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGGGCAGTTTCTAATTCATATATTCGGGTC
GGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGTTTTTTTAAGTGTGATATTGTCGGGTCGAGTT
CAGGTTTAGGGTGAAAATACCCGACCCAAAAAAATATATAATTTTACCTTATATATTTAGGAATA
ATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGCTTT
Found at i:477938 original size:18 final size:18
Alignment explanation
Indices: 477915--477961 Score: 94
Period size: 18 Copynumber: 2.6 Consensus size: 18
477905 ATGAAATTGG
477915 ATTTCAATTCTTTCACAT
1 ATTTCAATTCTTTCACAT
477933 ATTTCAATTCTTTCACAT
1 ATTTCAATTCTTTCACAT
477951 ATTTCAATTCT
1 ATTTCAATTCT
477962 ATCGTAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTCAATTCTTTCACAT
Found at i:482557 original size:13 final size:14
Alignment explanation
Indices: 482539--482576 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
482529 CATGGAGTCT
482539 ATAAAAATAA-AAA
1 ATAAAAATAATAAA
482552 ATAAAAA-AATAAA
1 ATAAAAATAATAAA
*
482565 ATAATAATAATA
1 ATAAAAATAATA
482577 TATAATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
12 2 0.09
13 16 0.73
14 4 0.18
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAAAATAATAAA
Found at i:508023 original size:18 final size:18
Alignment explanation
Indices: 508000--508042 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
507990 TGTGCCCTTG
*
508000 GAACTTTATTCTCGAAAT
1 GAACTTAATTCTCGAAAT
*
508018 GAACTTAATTCTCGAGAT
1 GAACTTAATTCTCGAAAT
508036 GAACTTA
1 GAACTTA
508043 GTTATATTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (18 bp):
GAACTTAATTCTCGAAAT
Found at i:510207 original size:24 final size:24
Alignment explanation
Indices: 510148--510207 Score: 111
Period size: 24 Copynumber: 2.5 Consensus size: 24
510138 GAATGCTCTT
*
510148 ATTAAAGAAGTCACAAGAGAGGAG
1 ATTAAAGAAGTTACAAGAGAGGAG
510172 ATTAAAGAAGTTACAAGAGAGGAG
1 ATTAAAGAAGTTACAAGAGAGGAG
510196 ATTAAAGAAGTT
1 ATTAAAGAAGTT
510208 GTTTTCTGCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.50, C:0.05, G:0.27, T:0.18
Consensus pattern (24 bp):
ATTAAAGAAGTTACAAGAGAGGAG
Found at i:520399 original size:20 final size:22
Alignment explanation
Indices: 520374--520422 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
520364 ATATGATAAT
520374 TTTAATTTT-ATCATCA-ATTA
1 TTTAATTTTGATCATCAGATTA
* *
520394 TTTAATTTTGTTTATCAGATTA
1 TTTAATTTTGATCATCAGATTA
520416 TTTAATT
1 TTTAATT
520423 ATTTAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.36
21 5 0.20
22 11 0.44
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (22 bp):
TTTAATTTTGATCATCAGATTA
Found at i:520728 original size:2 final size:2
Alignment explanation
Indices: 520721--520757 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
520711 GTGAATCACA
520721 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
520758 GTTAATGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:520861 original size:2 final size:2
Alignment explanation
Indices: 520854--520919 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
520844 TTTTAACTGG
520854 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
520896 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
520920 TGAATAATTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:523417 original size:25 final size:26
Alignment explanation
Indices: 523389--523445 Score: 100
Period size: 25 Copynumber: 2.3 Consensus size: 26
523379 GATAAGGACT
523389 TTTAAAAAATTT-AAAATAATATATA
1 TTTAAAAAATTTAAAAATAATATATA
523414 TTT-AAAAATTTAAAAATAATATATA
1 TTTAAAAAATTTAAAAATAATATATA
523439 TTTAAAA
1 TTTAAAA
523446 TTTTTATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
24 8 0.27
25 19 0.63
26 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (26 bp):
TTTAAAAAATTTAAAAATAATATATA
Found at i:523418 original size:16 final size:16
Alignment explanation
Indices: 523397--523446 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
523387 CTTTTAAAAA
523397 ATTTAAAATAATATAT
1 ATTTAAAATAATATAT
523413 ATTT-AAA-AAT-T-T
1 ATTTAAAATAATATAT
523425 A---AAAATAATATAT
1 ATTTAAAATAATATAT
523438 ATTTAAAAT
1 ATTTAAAAT
523447 TTTTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 14
0.66 0.00 0.34
Matches are distributed among these distances:
10 3 0.11
11 3 0.11
12 3 0.11
13 3 0.11
14 3 0.11
15 3 0.11
16 9 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAAATAATATAT
Found at i:523902 original size:17 final size:17
Alignment explanation
Indices: 523876--523910 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
523866 ACAATTATTT
*
523876 TCTTTCTATTATATTAG
1 TCTTTATATTATATTAG
523893 TCTTTATATTATATTAG
1 TCTTTATATTATATTAG
523910 T
1 T
523911 ATTTTCTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.26, C:0.09, G:0.06, T:0.60
Consensus pattern (17 bp):
TCTTTATATTATATTAG
Found at i:523920 original size:35 final size:35
Alignment explanation
Indices: 523878--523945 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
523868 AATTATTTTC
* *
523878 TTTCTATTATATTAGTCTTTATATTA-TATTAGTAT
1 TTTCTATTATATTAGT-ATTAGATTAGTATTAGTAT
*
523913 TTTCTATTCTATTAGTATTAGATTAGTATTAGT
1 TTTCTATTATATTAGTATTAGATTAGTATTAGT
523946 TAGTGAATCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 7 0.24
35 22 0.76
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (35 bp):
TTTCTATTATATTAGTATTAGATTAGTATTAGTAT
Found at i:524608 original size:18 final size:18
Alignment explanation
Indices: 524585--524635 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
524575 AGTTCTTTTC
524585 TTTCTATTATATTAGTAT
1 TTTCTATTATATTAGTAT
524603 TTTCTATTATA-T--T-T
1 TTTCTATTATATTAGTAT
*
524617 TTTCTATTCTATTAGTAT
1 TTTCTATTATATTAGTAT
524635 T
1 T
524636 AGTTAGTGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
14 11 0.39
15 2 0.07
17 2 0.07
18 13 0.46
ACGTcount: A:0.24, C:0.08, G:0.04, T:0.65
Consensus pattern (18 bp):
TTTCTATTATATTAGTAT
Found at i:526878 original size:6 final size:6
Alignment explanation
Indices: 526867--526922 Score: 67
Period size: 6 Copynumber: 9.0 Consensus size: 6
526857 CACGATGTAA
* *
526867 GTATAT GTATATGT GTATGT GTATAT GTATAT GTATAT TTATAT GTATAT
1 GTATAT GTATA--T GTATAT GTATAT GTATAT GTATAT GTATAT GTATAT
*
526917 GCATAT
1 GTATAT
526923 CTTTTCTTGT
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
6 38 0.88
8 5 0.12
ACGTcount: A:0.30, C:0.02, G:0.18, T:0.50
Consensus pattern (6 bp):
GTATAT
Found at i:526889 original size:14 final size:14
Alignment explanation
Indices: 526867--526900 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
526857 CACGATGTAA
*
526867 GTATATGTATATGT
1 GTATGTGTATATGT
526881 GTATGTGTATATGT
1 GTATGTGTATATGT
*
526895 ATATGT
1 GTATGT
526901 ATATTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (14 bp):
GTATGTGTATATGT
Found at i:526922 original size:18 final size:20
Alignment explanation
Indices: 526867--526922 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 20
526857 CACGATGTAA
*
526867 GTATATGTATATGTGTATGT
1 GTATATGTATATGTATATGT
526887 GTATATGTATATGTATAT-T
1 GTATATGTATATGTATATGT
*
526906 -TATATGTATATGCATAT
1 GTATATGTATATGTATAT
526923 CTTTTCTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 16 0.47
19 1 0.03
20 17 0.50
ACGTcount: A:0.30, C:0.02, G:0.18, T:0.50
Consensus pattern (20 bp):
GTATATGTATATGTATATGT
Found at i:527464 original size:20 final size:20
Alignment explanation
Indices: 527439--527478 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
527429 TCGGACACGA
*
527439 ACAAGGATCGCAGACCTCTG
1 ACAAGGATCACAGACCTCTG
527459 ACAAGGATCACAGACCTCTG
1 ACAAGGATCACAGACCTCTG
527479 TGTTAGTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.15
Consensus pattern (20 bp):
ACAAGGATCACAGACCTCTG
Found at i:535414 original size:15 final size:15
Alignment explanation
Indices: 535379--535415 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
535369 CATTTATAGT
*
535379 CTTCATCTCTTTCCA
1 CTTCATCTCTTTCAA
*
535394 CCTCATCTCTTTCAA
1 CTTCATCTCTTTCAA
535409 CTTCATC
1 CTTCATC
535416 AGCATCTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.16, C:0.41, G:0.00, T:0.43
Consensus pattern (15 bp):
CTTCATCTCTTTCAA
Found at i:538338 original size:51 final size:51
Alignment explanation
Indices: 538262--538362 Score: 193
Period size: 51 Copynumber: 2.0 Consensus size: 51
538252 TAAGGAAATG
*
538262 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGTTGAAATTCCTTGTAACTA
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
538313 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
1 ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACT
538363 CTCTCCCTGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 49 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.31
Consensus pattern (51 bp):
ATAGGCTGTAAAGAAATATCGGTTTGAACAGGCTGAAATTCCTTGTAACTA
Found at i:540144 original size:16 final size:14
Alignment explanation
Indices: 540123--540163 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 14
540113 CCTGATATCA
540123 TGTAGAAAACAAAC
1 TGTAGAAAACAAAC
*
540137 TGTGTAGAAAACAGAC
1 --TGTAGAAAACAAAC
540153 TGTAGAAAACA
1 TGTAGAAAACA
540164 GACAAGTCTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 11 0.46
16 13 0.54
ACGTcount: A:0.51, C:0.12, G:0.20, T:0.17
Consensus pattern (14 bp):
TGTAGAAAACAAAC
Found at i:540158 original size:14 final size:15
Alignment explanation
Indices: 540123--540166 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
540113 CCTGATATCA
*
540123 TGTAGAAAACAAACTG
1 TGTAGAAAACAGAC-G
540139 TGTAGAAAACAGAC-
1 TGTAGAAAACAGACG
540153 TGTAGAAAACAGAC
1 TGTAGAAAACAGAC
540167 AAGTCTGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 14 0.52
16 13 0.48
ACGTcount: A:0.50, C:0.14, G:0.20, T:0.16
Consensus pattern (15 bp):
TGTAGAAAACAGACG
Found at i:547603 original size:30 final size:31
Alignment explanation
Indices: 547564--547621 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
547554 CTAATTAGAA
* *
547564 ATTTAAATTTAA-TTTTTTATTCAGATTAAT
1 ATTTAAATTTAACTTTATAATTCAGATTAAT
*
547594 ATTTGAATTTAACTTTATAATTCAGATT
1 ATTTAAATTTAACTTTATAATTCAGATT
547622 TATTCAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (31 bp):
ATTTAAATTTAACTTTATAATTCAGATTAAT
Found at i:552279 original size:2 final size:2
Alignment explanation
Indices: 552272--552296 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
552262 TTTTTAAAAC
552272 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
552297 CCCCCATCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:552485 original size:24 final size:24
Alignment explanation
Indices: 552468--552603 Score: 193
Period size: 24 Copynumber: 5.7 Consensus size: 24
552458 ATCATAACAT
*
552468 AATCCATGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
*
552492 AATCCAAGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
552516 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCAGATCAA
*
552540 AATCCAGGTCAAGTATTC-GATCAG
1 AATCCAGGTCAAGTA-TCAGATCAA
* * *
552564 AATCCATGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCAGATCAA
*
552588 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
552604 TATAATAGAA
Statistics
Matches: 104, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
23 2 0.02
24 100 0.96
25 2 0.02
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.24
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCAGATCAA
Found at i:552515 original size:12 final size:12
Alignment explanation
Indices: 552476--552539 Score: 53
Period size: 12 Copynumber: 5.3 Consensus size: 12
552466 ATAATCCATG
552476 TCAAGTATCAGA
1 TCAAGTATCAGA
*
552488 TCAA-AATCCA-A
1 TCAAGTAT-CAGA
552499 GTCAAGTATCAGA
1 -TCAAGTATCAGA
* *
552512 TCAA-AATCCAGG
1 TCAAGTAT-CAGA
552524 TCAAGTATCAGA
1 TCAAGTATCAGA
552536 TCAA
1 TCAA
552540 AATCCAGGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
11 5 0.12
12 30 0.75
13 5 0.12
ACGTcount: A:0.44, C:0.20, G:0.14, T:0.22
Consensus pattern (12 bp):
TCAAGTATCAGA
Found at i:552551 original size:12 final size:12
Alignment explanation
Indices: 552488--552551 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
552478 AAGTATCAGA
*
552488 TCAAAATCCAAG
1 TCAAAATCCAGG
* *
552500 TCAAGTAT-CAGA
1 TCAA-AATCCAGG
552512 TCAAAATCCAGG
1 TCAAAATCCAGG
* *
552524 TCAAGTAT-CAGA
1 TCAA-AATCCAGG
552536 TCAAAATCCAGG
1 TCAAAATCCAGG
552548 TCAA
1 TCAA
552552 GTATTCGATC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
11 4 0.10
12 31 0.79
13 4 0.10
ACGTcount: A:0.44, C:0.22, G:0.14, T:0.20
Consensus pattern (12 bp):
TCAAAATCCAGG
Found at i:553738 original size:18 final size:18
Alignment explanation
Indices: 553717--553751 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
553707 TTCCATCCGG
*
553717 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
553735 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
553752 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:559052 original size:4 final size:5
Alignment explanation
Indices: 559026--559058 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
559016 TTTAGAACTA
559026 TAAAT TAAAT TAAAT TAAAT T-AAT TAAAAT TAA
1 TAAAT TAAAT TAAAT TAAAT TAAAT T-AAAT TAA
559059 GTGAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
4 4 0.15
5 18 0.69
6 4 0.15
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAAAT
Found at i:559174 original size:15 final size:15
Alignment explanation
Indices: 559143--559185 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
559133 GAAATTAGGA
559143 TTAAATTAATAAAATAT
1 TTAAA-TAAT-AAATAT
559160 TTAAATAATAAATAT
1 TTAAATAATAAATAT
* *
559175 TGAAAGAATAA
1 TTAAATAATAA
559186 TTATACAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 15 0.62
16 4 0.17
17 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (15 bp):
TTAAATAATAAATAT
Found at i:562024 original size:16 final size:16
Alignment explanation
Indices: 562025--562064 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
562015 TATTTATAAA
*
562025 TATAAATTCGACTAGT
1 TATAAATTCAACTAGT
* *
562041 TATAAATTCAATTATT
1 TATAAATTCAACTAGT
562057 TATAAATT
1 TATAAATT
562065 TGATTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.45
Consensus pattern (16 bp):
TATAAATTCAACTAGT
Found at i:562029 original size:22 final size:22
Alignment explanation
Indices: 562001--562047 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
561991 TAGTGGTTGG
*
562001 AATATAAATTCGACTATTTATA
1 AATATAAATTCGACTAGTTATA
562023 AATATAAATTCGACTAGTTATA
1 AATATAAATTCGACTAGTTATA
562045 AAT
1 AAT
562048 TCAATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.06, T:0.38
Consensus pattern (22 bp):
AATATAAATTCGACTAGTTATA
Found at i:562144 original size:13 final size:13
Alignment explanation
Indices: 562098--562135 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
562088 TTTAAATATT
562098 TAATCATTATTA-
1 TAATCATTATTAG
*
562110 -AATAATTATTAG
1 TAATCATTATTAG
562122 TAATCATTATTAG
1 TAATCATTATTAG
562135 T
1 T
562136 CATTATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
11 10 0.45
13 12 0.55
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (13 bp):
TAATCATTATTAG
Found at i:562176 original size:24 final size:23
Alignment explanation
Indices: 562099--562178 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 23
562089 TTAAATATTT
562099 AATCATTATTAAATAATTATTAGT-
1 AATCATTATT-AATAATTATTA-TA
* *
562123 AATCATTATTAGTCATTATTATGA
1 AATCATTATTAATAATTATTAT-A
** *
562147 TTTCATTATTACTAATTATTACTA
1 AATCATTATTAATAATTATTA-TA
562171 AATCATTA
1 AATCATTA
562179 GTATCAAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
22 1 0.02
23 9 0.20
24 34 0.76
25 1 0.02
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (23 bp):
AATCATTATTAATAATTATTATA
Found at i:562208 original size:21 final size:21
Alignment explanation
Indices: 562184--562274 Score: 66
Period size: 21 Copynumber: 4.4 Consensus size: 21
562174 CATTAGTATC
562184 AAATCATTAAATATTAATAAT
1 AAATCATTAAATATTAATAAT
* * *
562205 AAATCATT-ATTAGTAATCAT
1 AAATCATTAAATATTAATAAT
* * *
562225 -TA-CA--AAATCTTATTATTACT
1 AAATCATTAAA---TATTAATAAT
562245 AAATCATTAAATATTAATAAT
1 AAATCATTAAATATTAATAAT
562266 AAATCATTA
1 AAATCATTA
562275 GTAGTATCGG
Statistics
Matches: 50, Mismatches: 12, Indels: 16
0.64 0.15 0.21
Matches are distributed among these distances:
17 1 0.02
18 2 0.04
19 1 0.02
20 15 0.30
21 26 0.52
22 2 0.04
24 3 0.06
ACGTcount: A:0.51, C:0.09, G:0.01, T:0.40
Consensus pattern (21 bp):
AAATCATTAAATATTAATAAT
Found at i:562263 original size:61 final size:59
Alignment explanation
Indices: 562149--562280 Score: 185
Period size: 61 Copynumber: 2.2 Consensus size: 59
562139 TATTATGATT
* * *
562149 TCATTATTACTAATTATTACTAAATCATTAGTATCAAATCATTAAATATTAATAATAAA
1 TCATTATTAGTAATCATTACAAAATCATTAGTATCAAATCATTAAATATTAATAATAAA
*
562208 TCATTATTAGTAATCATTACAAAATC-TTATTATTACTAAATCATTAAATATTAATAATAAA
1 TCATTATTAGTAATCATTACAAAATCATTAGTA-T-C-AAATCATTAAATATTAATAATAAA
*
562269 TCATTAGTAGTA
1 TCATTATTAGTA
562281 TCGGTACCAT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
58 5 0.08
59 24 0.37
60 1 0.02
61 35 0.54
ACGTcount: A:0.46, C:0.10, G:0.03, T:0.41
Consensus pattern (59 bp):
TCATTATTAGTAATCATTACAAAATCATTAGTATCAAATCATTAAATATTAATAATAAA
Found at i:567153 original size:226 final size:227
Alignment explanation
Indices: 566790--567261 Score: 649
Period size: 235 Copynumber: 2.0 Consensus size: 227
566780 TTTATTTTGG
* *
566790 TCGGGTCTGGTCGGTTTTTTTTAAGTGTGATATTTGGGCCGGGTCGAGTTCGGGTTTAGGGTGAA
1 TCGGGTCGGGTCGGTTTTTTTTAAGTGTGATATTT--G-CGGGTCGAGGTCGGGTTTAGGGTGAA
* *
566855 AAATACCCGACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACC
63 AAATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAACACC
*
566920 CCTC-TATATATA-AT-TTTTT-CAATTAAGTCATTGTTTTTATTGAATAAAAAT-ATTTTTTTA
128 CCTCATATATATATATATTTTTCCAATTAAGTCATTGTTTTTATTGAATAAAAATAATTTTTTAA
566980 TTATTTTC-GGTC-AGGTCGGATTTCTAATTCATATAT
193 TTA-TTTCGGGTCGA-GTCGG-TTTCTAATTCATATAT
567016 TCGGGTCGGGTCGGTTTTTTTTAAGTGTGATA-TT-CGGGTCG-GGTCGGGTTTAGGGTGAAAAA
1 TCGGGTCGGGTCGGTTTTTTTTAAGTGTGATATTTGCGGGTCGAGGTCGGGTTTAGGGTGAAAAA
* *
567078 TACCCGACCCGATCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTATAATAACCC
66 TACCCGACCCG----AAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAACAC
567143 CTCTCTCTATATATATATATATATATTTTTCCAATTAAGTCATTGTTTTTATTGAATAAAAATAA
127 C-C-CTC-----ATATATATATATATTTTTCCAATTAAGTCATTGTTTTTATTGAATAAAAATAA
567208 TTTTTTAATTATTTCGGGTCGAGTCGGTTTCTAATTCATATAT
185 TTTTTTAATTATTTCGGGTCGAGTCGGTTTCTAATTCATATAT
*
567251 TCGGGTTGGGT
1 TCGGGTCGGGT
567262 GAAACTTTAT
Statistics
Matches: 220, Mismatches: 8, Indels: 27
0.86 0.03 0.11
Matches are distributed among these distances:
220 31 0.14
221 7 0.03
224 47 0.21
225 3 0.01
226 34 0.15
232 8 0.04
233 2 0.01
234 5 0.02
235 62 0.28
236 20 0.09
237 1 0.00
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.41
Consensus pattern (227 bp):
TCGGGTCGGGTCGGTTTTTTTTAAGTGTGATATTTGCGGGTCGAGGTCGGGTTTAGGGTGAAAAA
TACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAACACCCCT
CATATATATATATATTTTTCCAATTAAGTCATTGTTTTTATTGAATAAAAATAATTTTTTAATTA
TTTCGGGTCGAGTCGGTTTCTAATTCATATAT
Found at i:567690 original size:18 final size:18
Alignment explanation
Indices: 567645--567691 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
567635 TATGGAATTT
*
567645 GATTCCAATT-CTTGACA
1 GATTCCAATTCCTTCACA
* *
567662 AATTTCAATTCCTTCACA
1 GATTCCAATTCCTTCACA
567680 GATTCCAATTCC
1 GATTCCAATTCC
567692 CTCAGAAATA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 8 0.33
18 16 0.67
ACGTcount: A:0.30, C:0.28, G:0.06, T:0.36
Consensus pattern (18 bp):
GATTCCAATTCCTTCACA
Found at i:568031 original size:13 final size:14
Alignment explanation
Indices: 567994--568031 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
567984 GTGAAATTCT
*
567994 AAATATTTAAATAA
1 AAATATTTATATAA
568008 AAATTATTTATATAA
1 AAA-TATTTATATAA
568023 AAA-ATTTAT
1 AAATATTTAT
568032 TTGTTGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 6 0.27
14 3 0.14
15 13 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATATTTATATAA
Found at i:575967 original size:23 final size:23
Alignment explanation
Indices: 575941--575985 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
575931 CACCACAGCT
*
575941 CGTATAAATGCACCGAAGTGCCC
1 CGTAGAAATGCACCGAAGTGCCC
* *
575964 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
575986 ATATAATGAT
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:0.27, C:0.29, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCC
Found at i:576234 original size:149 final size:149
Alignment explanation
Indices: 575964--576267 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
575954 CGAAGTGCCC
575964 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
576029 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
576094 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
576113 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
*
576178 CATATACATATACTATGGATCAAGTATGTTTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
66 CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
576243 CATATGTCCTAAAGAACCG
131 CATATGTCCTAAAGAACCG
576262 CGTAGA
1 CGTAGA
576268 CCCTCTACCC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCCTTAAGAAT
CATATACATATACTATGGATCAAGTATGTGTCTTTCAAGACTTCACACAGGTTCCAAAGGATATA
CATATGTCCTAAAGAACCG
Found at i:576862 original size:67 final size:68
Alignment explanation
Indices: 576745--576898 Score: 238
Period size: 67 Copynumber: 2.3 Consensus size: 68
576735 TTTTTCTCAT
* *
576745 GGGGGAATCGGTTCCCCCTCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACG
1 GGGGGTATCGGTT-CCCCTCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATATACG
576810 ATGA
65 ATGA
* * * *
576814 GGGGGTATCGGTTCCCC-CCTGGGGGTATCGATTCCCCTCTAGCCTTCTGGAAATTCATATTCGT
1 GGGGGTATCGGTTCCCCTCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATATACGA
576878 TGA
66 TGA
576881 GGGGGTATCGGTTCCCCT
1 GGGGGTATCGGTTCCCCT
576899 TGAATGGGTA
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
67 62 0.79
68 4 0.05
69 12 0.15
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (68 bp):
GGGGGTATCGGTTCCCCTCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAAATTCATATACGA
TGA
Found at i:578488 original size:62 final size:62
Alignment explanation
Indices: 578391--578514 Score: 239
Period size: 62 Copynumber: 2.0 Consensus size: 62
578381 TTAGGGTTTT
578391 CTATTATCCCACCAACTCTTTAATTTGACATTCTTTAAAGGTGGTGTTATTTATTTATTTGA
1 CTATTATCCCACCAACTCTTTAATTTGACATTCTTTAAAGGTGGTGTTATTTATTTATTTGA
*
578453 CTATTATCCCACCAACTCTTTAATTTGGCATTCTTTAAAGGTGGTGTTATTTATTTATTTGA
1 CTATTATCCCACCAACTCTTTAATTTGACATTCTTTAAAGGTGGTGTTATTTATTTATTTGA
578515 ACGATCTTAT
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.25, C:0.16, G:0.12, T:0.47
Consensus pattern (62 bp):
CTATTATCCCACCAACTCTTTAATTTGACATTCTTTAAAGGTGGTGTTATTTATTTATTTGA
Found at i:586153 original size:2 final size:2
Alignment explanation
Indices: 586146--586178 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
586136 ACTAAGATTA
586146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
586179 ATAATGATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:599481 original size:3 final size:3
Alignment explanation
Indices: 599473--599536 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
599463 CTTTGAGCTT
599473 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
599521 TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA T
599537 ATCTTTATTT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:607539 original size:22 final size:20
Alignment explanation
Indices: 607514--607553 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
607504 GGTATTTATC
607514 GATAAAATAAAATAGATTGAAG
1 GATAAAA-AAAATAG-TTGAAG
*
607536 GATATAAAAAATAGTTGA
1 GATAAAAAAAATAGTTGA
607554 TCAATCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 7 0.41
22 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.17, T:0.25
Consensus pattern (20 bp):
GATAAAAAAAATAGTTGAAG
Found at i:613505 original size:30 final size:30
Alignment explanation
Indices: 613471--613531 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
613461 AATATAATCC
613471 CCCCAACATTTAGTCCGTTTAAAATATGGT
1 CCCCAACATTTAGTCCGTTTAAAATATGGT
* **
613501 CCCCAACATTTAGTCTGTTTGCAATATGGT
1 CCCCAACATTTAGTCCGTTTAAAATATGGT
613531 C
1 C
613532 TCCTACGTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (30 bp):
CCCCAACATTTAGTCCGTTTAAAATATGGT
Found at i:616535 original size:269 final size:266
Alignment explanation
Indices: 616035--616572 Score: 1049
Period size: 269 Copynumber: 2.0 Consensus size: 266
616025 CCCTTTCTTC
616035 TTTTGATTTTATTCTAAAGTCTTATTATTTTTAGGGTAAAGTATAATAATAGTCACTAAACTTTT
1 TTTTGATTTTATTCTAAAGTCTTATTATTTTTAGGGTAAAGTATAATAATAGTCACTAAACTTTT
616100 CTAAAGCTTTCATTTAGATCCCCACTTTAAAACTTGCAATACAATCTCCCAACATTTAGTCCGTT
66 CTAAAGCTTTCATTTAGATCCCCACTTTAAAACTTGCAATACAATCTCCCAACATTTAGTCCGTT
616165 TGTAATATGGTCCCCAACAGTTACGTCGGGGACCACATTACAAATGAACTAAATGTTTGAGGATC
131 TGTAATATGGTCCCCAACAGTTACGTCGGGGACCACATTACAAATGAACTAAATGTTTGAGGATC
616230 ATATTACAAACGGACTAAATGTTGGGGGACTGCATTGTAAGTTTTAAAAGTTAGAGGACCTAAAT
196 ATATTACAAACGGACTAAATGTTGGGGGACTGCATTGTAAGTTTTAAAAGTTAGAGGACCTAAAT
616295 GAAAGT
261 GAAAGT
616301 TTTTGATTTTATTCTAAAGTCTTATTATTTTTAGGGTAAAGTATAATAATAGTCACTAAACTTTT
1 TTTTGATTTTATTCTAAAGTCTTATTATTTTTAGGGTAAAGTATAATAATAGTCACTAAACTTTT
616366 CTAAAGCTTTCATTTAGATCCCCAACTTTTAAAACTTGCAATACAATCTCCCAACATTTAGTCCG
66 CTAAAGCTTTCATTTAGATCCCC-AC-TTTAAAACTTGCAATACAATCTCCCAACATTTAGTCCG
616431 TTTGTAATATGGTCCTCCAACAGTTACGTCGGGGACCACATTACAAATGAACTAAATGTTTGAGG
129 TTTGTAATATGGTCC-CCAACAGTTACGTCGGGGACCACATTACAAATGAACTAAATGTTTGAGG
616496 ATCATATTACAAACGGACTAAATGTTGGGGGACTGCATTGTAAGTTTTAAAAGTTAGAGGACCTA
193 ATCATATTACAAACGGACTAAATGTTGGGGGACTGCATTGTAAGTTTTAAAAGTTAGAGGACCTA
616561 AATGAAAGT
258 AATGAAAGT
616570 TTT
1 TTT
616573 AGAAAAGTTC
Statistics
Matches: 269, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
266 88 0.33
267 2 0.01
268 53 0.20
269 126 0.47
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (266 bp):
TTTTGATTTTATTCTAAAGTCTTATTATTTTTAGGGTAAAGTATAATAATAGTCACTAAACTTTT
CTAAAGCTTTCATTTAGATCCCCACTTTAAAACTTGCAATACAATCTCCCAACATTTAGTCCGTT
TGTAATATGGTCCCCAACAGTTACGTCGGGGACCACATTACAAATGAACTAAATGTTTGAGGATC
ATATTACAAACGGACTAAATGTTGGGGGACTGCATTGTAAGTTTTAAAAGTTAGAGGACCTAAAT
GAAAGT
Found at i:617442 original size:28 final size:28
Alignment explanation
Indices: 617410--617479 Score: 86
Period size: 31 Copynumber: 2.4 Consensus size: 28
617400 TCGACGTAAC
* *
617410 TGTTGGGGGATATTGCAAACGGACTAAA
1 TGTTGGGGGATATTACAAACAGACTAAA
617438 TGTTGGGGGACCATATTACAAACAGACTAAA
1 TGTTGGGGG---ATATTACAAACAGACTAAA
*
617469 TATTGGGGGAT
1 TGTTGGGGGAT
617480 TATATTGCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
28 11 0.31
31 25 0.69
ACGTcount: A:0.33, C:0.11, G:0.30, T:0.26
Consensus pattern (28 bp):
TGTTGGGGGATATTACAAACAGACTAAA
Found at i:617485 original size:31 final size:31
Alignment explanation
Indices: 617419--617478 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
617409 CTGTTGGGGG
* * *
617419 ATATTGCAAACGGACTAAATGTTGGGGGACC
1 ATATTACAAACAGACTAAATATTGGGGGACC
617450 ATATTACAAACAGACTAAATATTGGGGGA
1 ATATTACAAACAGACTAAATATTGGGGGA
617479 TTATATTGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.38, C:0.13, G:0.25, T:0.23
Consensus pattern (31 bp):
ATATTACAAACAGACTAAATATTGGGGGACC
Found at i:620530 original size:376 final size:376
Alignment explanation
Indices: 619836--620591 Score: 1471
Period size: 376 Copynumber: 2.0 Consensus size: 376
619826 AAACTCGTCC
619836 CAAACCGAACCGTGTAATAACTAAAATATCCCAATGACAACCTAACATCTATTTGCTGGTTCAAG
1 CAAACCGAACCGTGTAATAACTAAAATATCCCAATGACAACCTAACATCTATTTGCTGGTTCAAG
619901 CCATTTCTTCCATCACCAAATTCGCCAAACCGTAACTACAAGGTCCCATTGACCACCTAAAAGAT
66 CCATTTCTTCCATCACCAAATTCGCCAAACCGTAACTACAAGGTCCCATTGACCACCTAAAAGAT
619966 TATGCTAAGCACCAGATTCTATTCGCACACTCGGTTAAACGATTGTCTTTGGGACTATACTGACA
131 TATGCTAAGCACCAGATTCTATTCGCACACTCGGTTAAACGATTGTCTTTGGGACTATACTGACA
620031 GAATTATGAAGCAGGAAAGTAATGAATAGAGACGAAGTTTACGGCCGCCAGTGAAGTTCATCGGT
196 GAATTATGAAGCAGGAAAG-AATGAATAGAGACGAAGTTTACGGCCGCCAGTGAAGTTCATCGGT
620096 TTCTTGTAAACCATACTGTGGTAGAACTCACACAAGTCAACTAAATTACCACATGAAAACTCAAT
260 TTCTTGTAAACCATACTGTGGTAGAACTCACACAAGTCAACTAAATTACCACATGAAAACTCAAT
620161 TACAAGTTGGAGAAATATTGAGATTTGTTGATCAACACTCCAATTCTATGTT
325 TACAAGTTGGAGAAATATTGAGATTTGTTGATCAACACTCCAATTCTATGTT
620213 CAAACCGAACCGTGTAATAACTAAAATATCCCAATGACAACCTAACATCTATTTGCTGGTTCAAG
1 CAAACCGAACCGTGTAATAACTAAAATATCCCAATGACAACCTAACATCTATTTGCTGGTTCAAG
620278 CCATTTCTTCCATCACCAAATTCGCCAAACCGTAACTACAAGGTCCCATTGACCACCT-AAAGAT
66 CCATTTCTTCCATCACCAAATTCGCCAAACCGTAACTACAAGGTCCCATTGACCACCTAAAAGAT
620342 TATGCTAAGCACCAGATTCTATTCGCACACTCGGTTAAACGATTATGTCTTTGGGACTATACTGA
131 TATGCTAAGCACCAGATTCTATTCGCACACTCGGTTAAACGA-T-TGTCTTTGGGACTATACTGA
620407 CAGAATTATGAAGCAGGAAAG-ATGAATAGAGACGAAGTTTACGGCCGCCAGTGAAGTTCATCGG
194 CAGAATTATGAAGCAGGAAAGAATGAATAGAGACGAAGTTTACGGCCGCCAGTGAAGTTCATCGG
620471 TTTCTTGTAAACCATACTGTGGTAGAACTCACACAAGTCAACTAAATTACCACATGAAAACTCAA
259 TTTCTTGTAAACCATACTGTGGTAGAACTCACACAAGTCAACTAAATTACCACATGAAAACTCAA
620536 TTACAAGTTGGAGAAATATTGAGATTTGTTGATCAACACTCCAATTCTATGTT
324 TTACAAGTTGGAGAAATATTGAGATTTGTTGATCAACACTCCAATTCTATGTT
620589 CAA
1 CAA
620592 GCTATTCAAA
Statistics
Matches: 377, Mismatches: 0, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
376 212 0.56
377 124 0.33
378 41 0.11
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.27
Consensus pattern (376 bp):
CAAACCGAACCGTGTAATAACTAAAATATCCCAATGACAACCTAACATCTATTTGCTGGTTCAAG
CCATTTCTTCCATCACCAAATTCGCCAAACCGTAACTACAAGGTCCCATTGACCACCTAAAAGAT
TATGCTAAGCACCAGATTCTATTCGCACACTCGGTTAAACGATTGTCTTTGGGACTATACTGACA
GAATTATGAAGCAGGAAAGAATGAATAGAGACGAAGTTTACGGCCGCCAGTGAAGTTCATCGGTT
TCTTGTAAACCATACTGTGGTAGAACTCACACAAGTCAACTAAATTACCACATGAAAACTCAATT
ACAAGTTGGAGAAATATTGAGATTTGTTGATCAACACTCCAATTCTATGTT
Found at i:621212 original size:2 final size:2
Alignment explanation
Indices: 621205--621229 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
621195 TCGGTATGTG
621205 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 T
621230 GTTTTTATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:633591 original size:19 final size:19
Alignment explanation
Indices: 633567--633605 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
633557 TCAACCTTAG
633567 TTAAATAAATATAATTCAT
1 TTAAATAAATATAATTCAT
*
633586 TTAAATGAATATAATTCAT
1 TTAAATAAATATAATTCAT
633605 T
1 T
633606 AGCATGCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (19 bp):
TTAAATAAATATAATTCAT
Found at i:639511 original size:22 final size:22
Alignment explanation
Indices: 639486--639531 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
639476 TTAGAGATTT
*
639486 TATT-TTTATATTGTTAAAAATA
1 TATTCTTTA-ATTATTAAAAATA
639508 TATTCTTTAATTATTAAAAATA
1 TATTCTTTAATTATTAAAAATA
639530 TA
1 TA
639532 ATAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTCTTTAATTATTAAAAATA
Found at i:639550 original size:33 final size:32
Alignment explanation
Indices: 639502--639565 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
639492 TATATTGTTA
**
639502 AAAATATATTCTTTAATTATTAAAAATATAAT
1 AAAATATATTCTTTAACCATTAAAAATATAAT
* *
639534 AAAATATATTATTTTAACCATTTAAAATATAA
1 AAAATATATT-CTTTAACCATTAAAAATATAA
639566 CAAATAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 10 0.37
33 17 0.63
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (32 bp):
AAAATATATTCTTTAACCATTAAAAATATAAT
Found at i:652071 original size:8 final size:8
Alignment explanation
Indices: 652058--652098 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
652048 CTCATTTTTA
652058 GAGAATTT
1 GAGAATTT
652066 GAGAATTT
1 GAGAATTT
*
652074 -AGAGTTT
1 GAGAATTT
*
652081 GGGAATTT
1 GAGAATTT
652089 GAGAATTT
1 GAGAATTT
652097 GA
1 GA
652099 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:652482 original size:104 final size:104
Alignment explanation
Indices: 652302--652509 Score: 364
Period size: 104 Copynumber: 2.0 Consensus size: 104
652292 ATTTCTCAGG
* *
652302 GGACTTGAAGACGCGTTCCCGGGGGCGCGCTTTCCATTATTTTGTCAGAGAATATGTTATCATTG
1 GGACTTGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGCTATCATTG
*
652367 CCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCA
66 CCCTATTATGTCACTCATGTCCCTCGAGGACACTATTCA
*
652406 GGACTTGAA-AGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTTAGAGAATATGCTATCATT
1 GGACTTGAAGA-CGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGCTATCATT
652470 GCCCTATTATGTCACTCATGTCCCTCGAGGACACTATTCA
65 GCCCTATTATGTCACTCATGTCCCTCGAGGACACTATTCA
652510 TATCAGTACC
Statistics
Matches: 99, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
103 1 0.01
104 98 0.99
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (104 bp):
GGACTTGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGCTATCATTG
CCCTATTATGTCACTCATGTCCCTCGAGGACACTATTCA
Found at i:652633 original size:127 final size:128
Alignment explanation
Indices: 652406--652760 Score: 640
Period size: 127 Copynumber: 2.8 Consensus size: 128
652396 ACACTATTCA
* *
652406 GGACTTGAAAGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTTAGAGAATATGCTATCATTG
1 GGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTTAGAGAATATGTTATCATTG
*
652471 CCCTATTATGTCACTCATGTCCCTCGAGGACACTATTCATATCAGTACCTATTATTTCTCAGG
66 CCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGG
*
652534 GGACTTGAAGGCGCGTTCCTGGGGG-GCGCCTTCCATTATTTTGTTAGAGAATATGTTATCATTG
1 GGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTTAGAGAATATGTTATCATTG
652598 CCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGG
66 CCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGG
* * *
652661 GGACTTGAAGGCGTGTTCCCGGGGGTGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTG
1 GGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTTAGAGAATATGTTATCATTG
652726 CCCTATTATGTCACTCATGTCCCTCGGGGACACTA
66 CCCTATTATGTCACTCATGTCCCTCGGGGACACTA
652761 GATGGATTGT
Statistics
Matches: 219, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
127 123 0.56
128 96 0.44
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (128 bp):
GGACTTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTTAGAGAATATGTTATCATTG
CCCTATTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGG
Found at i:653195 original size:34 final size:34
Alignment explanation
Indices: 653156--653262 Score: 151
Period size: 34 Copynumber: 3.1 Consensus size: 34
653146 TAAGTTGAAA
* *
653156 TTTAATGTTAAATTTCGAATACTATAATTTATAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* * *
653190 TTTAATTTTAAATTTTGAATAATATTATTTTTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
* *
653224 TTTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTTAAATTTCGAATAATATAATTTATAT
653258 TTTAA
1 TTTAA
653263 AAACATTTAT
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 63 1.00
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
TTTAATTTTAAATTTCGAATAATATAATTTATAT
Found at i:653883 original size:21 final size:21
Alignment explanation
Indices: 653774--653888 Score: 151
Period size: 21 Copynumber: 5.5 Consensus size: 21
653764 TATGGTATAA
* *
653774 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTCGGAATGT
* *
653795 AA-CCTAGCGGGCTAGGAATAT
1 AACCCT-GCGGGCTCGGAATGT
* *
653816 AACCATGCGGGCTCGAAATGT
1 AACCCTGCGGGCTCGGAATGT
653837 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTCGGAATGT
*
653858 AACCCTACGGGCTCGGAATGT
1 AACCCTGCGGGCTCGGAATGT
653879 AACCCTGCGG
1 AACCCTGCGG
653889 AGATGGCATA
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
20 3 0.04
21 77 0.94
22 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.30, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTCGGAATGT
Found at i:653932 original size:21 final size:21
Alignment explanation
Indices: 653892--653939 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
653882 CCTGCGGAGA
* * *
653892 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAAATAGAGGGCT
653913 TGGCATATGAAATAGAGGGCT
1 TGGCATATGAAATAGAGGGCT
*
653934 GGGCAT
1 TGGCAT
653940 GTACCCCTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.12, G:0.38, T:0.25
Consensus pattern (21 bp):
TGGCATATGAAATAGAGGGCT
Found at i:655690 original size:34 final size:31
Alignment explanation
Indices: 655646--655734 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
655636 TTAATAATTC
*
655646 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTATATAAATA-TA--TTAA
* *
655680 TAAAAAAATAATATTTACATAAATATATTAA
1 TAAAAAAATAATAATTATATAAATATATTAA
* * *
655711 TATAAAATATAATAACTATTTAAA
1 TA-AAAAAATAATAATTATATAAA
655735 AAAATACTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 6 0.13
32 16 0.35
33 2 0.04
34 22 0.48
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.39
Consensus pattern (31 bp):
TAAAAAAATAATAATTATATAAATATATTAA
Found at i:655711 original size:31 final size:33
Alignment explanation
Indices: 655646--655725 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 33
655636 TTAATAATTC
* *
655646 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAAAAAATAATAATTACATAAATATTA-TTTAA
*
655680 TAAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAAATAATAATTACATAAATATTATTTAA
*
655711 TATAAAATATAATAA
1 TA-AAAAAATAATAA
655726 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
31 6 0.15
32 10 0.25
33 2 0.05
34 22 0.55
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TAAAAAAATAATAATTACATAAATATTATTTAA
Found at i:657290 original size:21 final size:21
Alignment explanation
Indices: 657266--657309 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
657256 AACCAAGGCA
657266 GTAATCTGTCACATGACAATT
1 GTAATCTGTCACATGACAATT
657287 GTAATCTGTCACATGACAATT
1 GTAATCTGTCACATGACAATT
657308 GT
1 GT
657310 TCTATCTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (21 bp):
GTAATCTGTCACATGACAATT
Found at i:663042 original size:21 final size:21
Alignment explanation
Indices: 663000--663042 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
662990 TTTATGGGCT
* *
663000 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
663021 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
663042 A
1 A
663043 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:663986 original size:4 final size:4
Alignment explanation
Indices: 663977--664934 Score: 1802
Period size: 4 Copynumber: 243.2 Consensus size: 4
663967 AAATGATGAC
663977 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664024 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664072 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664118 ATGT A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664164 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664212 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664260 ATGT ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664307 ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664353 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664401 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664449 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664497 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
664545 ATGT ATGT AT-T ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATAT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664590 ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664636 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664684 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664732 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664780 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664828 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664874 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
664922 ATGT ATGT ATGT A
1 ATGT ATGT ATGT A
664935 AGGGTTATAT
Statistics
Matches: 937, Mismatches: 2, Indels: 30
0.97 0.00 0.03
Matches are distributed among these distances:
2 12 0.01
3 9 0.01
4 916 0.98
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:665147 original size:31 final size:31
Alignment explanation
Indices: 665109--665182 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
665099 GCCAAAGAAC
**
665109 TACCTATG-TCTTTCGAGACATATGGATAGTA
1 TACCTATGTTCTAACGA-ACATATGGATAGTA
* *
665140 TACCTATGTTCTAAGGAACATATGGATAGTT
1 TACCTATGTTCTAACGAACATATGGATAGTA
*
665171 TACCTAGGTTCT
1 TACCTATGTTCT
665183 TCGGGACCTA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 32 0.86
32 5 0.14
ACGTcount: A:0.28, C:0.16, G:0.19, T:0.36
Consensus pattern (31 bp):
TACCTATGTTCTAACGAACATATGGATAGTA
Found at i:665195 original size:31 final size:31
Alignment explanation
Indices: 665120--665201 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
665110 ACCTATGTCT
* * *
665120 TTCGAGACATATGGATAGTATACCTATGTTC
1 TTCGGGACATATGGATAGTTTACCTAGGTTC
** *
665151 TAAGGAACATATGGATAGTTTACCTAGGTTC
1 TTCGGGACATATGGATAGTTTACCTAGGTTC
* *
665182 TTCGGGACCTATGGACAGTT
1 TTCGGGACATATGGATAGTT
665202 ACCGTGGATC
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (31 bp):
TTCGGGACATATGGATAGTTTACCTAGGTTC
Found at i:665221 original size:30 final size:30
Alignment explanation
Indices: 665187--665379 Score: 332
Period size: 30 Copynumber: 6.4 Consensus size: 30
665177 GGTTCTTCGG
* * *
665187 GACCTATGGACAGTTACCGTGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
665217 GACCTCTGGGTAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
665247 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
665277 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
665307 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
665337 GACCTCTGGATAGTTACCAAAGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
665367 GACCTCTGGATAG
1 GACCTCTGGATAG
665380 GTCCTTCAGA
Statistics
Matches: 156, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 156 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:668821 original size:21 final size:21
Alignment explanation
Indices: 668779--668821 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
668769 TTTCTAGGCT
* *
668779 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
668800 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
668821 A
1 A
668822 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:668874 original size:20 final size:20
Alignment explanation
Indices: 668849--668886 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
668839 GAATTCTAGA
*
668849 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
668869 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
668887 TAATGAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:669399 original size:2 final size:2
Alignment explanation
Indices: 669392--669452 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
669382 CATGTTACAG
669392 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
669434 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
669453 GAGTTGTGTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:669791 original size:4 final size:4
Alignment explanation
Indices: 669782--669942 Score: 322
Period size: 4 Copynumber: 40.2 Consensus size: 4
669772 AAATGATGAC
669782 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
669830 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
669878 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
669926 ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT A
669943 AGGGTTATAT
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 157 1.00
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:670203 original size:31 final size:31
Alignment explanation
Indices: 670128--670209 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
670118 ACCTATGTCT
* * *
670128 TTCGAGACATATGGATAGTATACCTATGTTC
1 TTCGGGACATATGGATAGTTTACCTAGGTTC
** *
670159 TAAGGAACATATGGATAGTTTACCTAGGTTC
1 TTCGGGACATATGGATAGTTTACCTAGGTTC
* *
670190 TTCGGGACCTATGGACAGTT
1 TTCGGGACATATGGATAGTT
670210 ACCGAGGATC
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (31 bp):
TTCGGGACATATGGATAGTTTACCTAGGTTC
Found at i:670229 original size:30 final size:30
Alignment explanation
Indices: 670195--670357 Score: 281
Period size: 30 Copynumber: 5.4 Consensus size: 30
670185 GGTTCTTCGG
* *
670195 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
670225 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
670255 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
*
670285 AACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
670315 GACCTCTGGATAGTTACCAAAGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
670345 GACCTCTGGATAG
1 GACCTCTGGATAG
670358 GTCCTTCGGA
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 127 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:674714 original size:4 final size:4
Alignment explanation
Indices: 674705--674835 Score: 248
Period size: 4 Copynumber: 33.2 Consensus size: 4
674695 AAATGATGAC
674705 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
674753 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT A-GT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
674799 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A
674836 AGGGTTATAT
Statistics
Matches: 126, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 6 0.05
4 120 0.95
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:675095 original size:31 final size:31
Alignment explanation
Indices: 675028--675101 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
675018 TCTTTCGAGA
* *
675028 CTATGGATAGTATACCTATGTTCTAAGGAAC
1 CTATGGATAGTTTACCTAGGTTCTAAGGAAC
* ** *
675059 ATATGGATAGTTTACCTAGGTTCTTCGGGAC
1 CTATGGATAGTTTACCTAGGTTCTAAGGAAC
*
675090 CTATGGACAGTT
1 CTATGGATAGTT
675102 ACGATGATCT
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (31 bp):
CTATGGATAGTTTACCTAGGTTCTAAGGAAC
Found at i:675119 original size:29 final size:30
Alignment explanation
Indices: 675087--675245 Score: 245
Period size: 29 Copynumber: 5.4 Consensus size: 30
675077 GGTTCTTCGG
* * *
675087 GACCTATGGACAGTTA-CGATGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
675116 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
675146 GACCTCTGGATAGTTACCGA-GATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
675175 GACCTCTGGATAGTTACCGAGGATC-TTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
* *
675204 GACCTCTGGATAGTTA-CAAAGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
675233 GACCTCTGGATAG
1 GACCTCTGGATAG
675246 GTCCTTCGGA
Statistics
Matches: 122, Mismatches: 5, Indels: 6
0.92 0.04 0.05
Matches are distributed among these distances:
28 6 0.05
29 80 0.66
30 36 0.30
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:675232 original size:58 final size:59
Alignment explanation
Indices: 675087--675245 Score: 257
Period size: 59 Copynumber: 2.7 Consensus size: 59
675077 GGTTCTTCGG
* * * *
675087 GACCTATGGACAGTTACGATGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACAAAGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTAT
**
675146 GACCTCTGGATAGTTACCGAGATCTTTATGACCTCTGGATAGTTACCGAGGATC-TTAT
1 GACCTCTGGATAGTTACAAAGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTAT
675204 GACCTCTGGATAGTTACAAAGATCTTTATGACCTCTGGATAG
1 GACCTCTGGATAGTTACAAAGATCTTTATGACCTCTGGATAG
675246 GTCCTTCGGA
Statistics
Matches: 93, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
58 44 0.47
59 49 0.53
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (59 bp):
GACCTCTGGATAGTTACAAAGATCTTTATGACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:676374 original size:38 final size:38
Alignment explanation
Indices: 676332--676404 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
676322 GTAGTGCTAC
*
676332 ACATAAGGTCGTGCCCACCATATACACCGAAGTGTATT
1 ACATAAGGTCGTGCCCACCATATACACCAAAGTGTATT
676370 ACATAAGGTCGTGCCCACCATATACACCAAAGTGT
1 ACATAAGGTCGTGCCCACCATATACACCAAAGTGT
676405 GTTATAAACC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (38 bp):
ACATAAGGTCGTGCCCACCATATACACCAAAGTGTATT
Found at i:679850 original size:31 final size:31
Alignment explanation
Indices: 679815--679880 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
679805 AAACTGATTC
**
679815 GTTACAAAT-AGATAATGTTAGTGATTAATTT
1 GTTACAAATCA-ATAACATTAGTGATTAATTT
679846 GTTACAAATCAATAACATTAGTGATTAATTT
1 GTTACAAATCAATAACATTAGTGATTAATTT
679877 GTTA
1 GTTA
679881 TTTTTAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (31 bp):
GTTACAAATCAATAACATTAGTGATTAATTT
Found at i:681598 original size:193 final size:191
Alignment explanation
Indices: 681243--681626 Score: 718
Period size: 193 Copynumber: 2.0 Consensus size: 191
681233 TTGTCAGCGT
681243 GAGAGGCAAGCAGGAAAGAATAGCGCTTTGGACCAAGAATGCTGTCAATGAAAACTGCACAGGAG
1 GAGAGGCAAGCAGGAAAGAATAGCGCTTTGGACCAAGAATGCTGTCAATGAAAACTGCACAGGAG
681308 TCAGTTGCTTTGTTCGAAAAATGATTAGTGCAATTCCAAAACCGTTGAAACCTATTTTGTTGGTT
66 TCAGTTGCTTTGTTCGAAAAATGATTAGTGCAATTCCAAAACCGTTGAAACCTATTTTGTTGGTT
681373 TTTGTTGTTGATGCAGATAACATCGGGAAACAGTGGAAAGAGTTGCTTGATTACAACGAAA
131 TTTGTTGTTGATGCAGATAACATCGGGAAACAGTGGAAAGAGTTGCTTGATTACAACGAAA
681434 GAGAGGCAAGCA-GAAAGAATAGCGCTTTGGACCAAGAATGCTGTCAATG-AAACTGCACAGGTG
1 GAGAGGCAAGCAGGAAAGAATAGCGCTTTGGACCAAGAATGCTGTCAATGAAAACTGCACA-G-G
681497 AGTCAGTTGCTTTGTTACGAAAAATGATTAGTGCAATTCCAAAACCGTTGAAACCTATTTTTGTT
64 AGTCAGTTGCTTTGTT-CGAAAAATGATTAGTGCAATTCCAAAACCGTTGAAACCTA-TTTTGTT
681562 GGTTTTTGTTGTTGATGCAGATAACATCGGGAAACAGTGGAAAGAGTTGCTTGATTACAACGAAA
127 GGTTTTTGTTGTTGATGCAGATAACATCGGGAAACAGTGGAAAGAGTTGCTTGATTACAACGAAA
681627 CTATTGGGTT
Statistics
Matches: 189, Mismatches: 0, Indels: 6
0.97 0.00 0.03
Matches are distributed among these distances:
189 10 0.05
190 38 0.20
191 29 0.15
192 40 0.21
193 72 0.38
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.27
Consensus pattern (191 bp):
GAGAGGCAAGCAGGAAAGAATAGCGCTTTGGACCAAGAATGCTGTCAATGAAAACTGCACAGGAG
TCAGTTGCTTTGTTCGAAAAATGATTAGTGCAATTCCAAAACCGTTGAAACCTATTTTGTTGGTT
TTTGTTGTTGATGCAGATAACATCGGGAAACAGTGGAAAGAGTTGCTTGATTACAACGAAA
Found at i:687248 original size:13 final size:13
Alignment explanation
Indices: 687230--687256 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
687220 TATAATCTAG
687230 GAAAAAGAACATT
1 GAAAAAGAACATT
687243 GAAAAAGAACATT
1 GAAAAAGAACATT
687256 G
1 G
687257 CGAAGTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.07, G:0.19, T:0.15
Consensus pattern (13 bp):
GAAAAAGAACATT
Found at i:696332 original size:31 final size:31
Alignment explanation
Indices: 696297--696362 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
696287 AAACTGATTC
**
696297 GTTACAAAT-AGATAATGTTAGTGATTAATTT
1 GTTACAAATCA-ATAACATTAGTGATTAATTT
696328 GTTACAAATCAATAACATTAGTGATTAATTT
1 GTTACAAATCAATAACATTAGTGATTAATTT
696359 GTTA
1 GTTA
696363 TTTTTAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.14, T:0.41
Consensus pattern (31 bp):
GTTACAAATCAATAACATTAGTGATTAATTT
Found at i:724851 original size:40 final size:39
Alignment explanation
Indices: 724802--724927 Score: 128
Period size: 40 Copynumber: 3.1 Consensus size: 39
724792 AATAAATTTA
*
724802 CAACACGAACTCCTATTTCGCAACATAATTTCCAAATTCG
1 CAACACGAACT-CTATTTCGCAACACAATTTCCAAATTCG
* ** * *
724842 CAACTCGAACATGGAAATTTTCGCAACGCGATTT-CAAATTCG
1 CAACACGAAC-T--CTA-TTTCGCAACACAATTTCCAAATTCG
*
724884 CAACACGAACTCTAATTTCGCAACACAGTTTCCAAATTCG
1 CAACACGAACTCT-ATTTCGCAACACAATTTCCAAATTCG
724924 CAAC
1 CAAC
724928 GCTAATTTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
39 13 0.19
40 22 0.32
41 2 0.03
42 18 0.26
43 13 0.19
ACGTcount: A:0.35, C:0.29, G:0.11, T:0.25
Consensus pattern (39 bp):
CAACACGAACTCTATTTCGCAACACAATTTCCAAATTCG
Found at i:724885 original size:19 final size:19
Alignment explanation
Indices: 724861--724927 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 19
724851 CATGGAAATT
*
724861 TTCGCAACGCGATTTCAAA
1 TTCGCAACACGATTTCAAA
** *
724880 TTCGCAACACGAACTCTAAT
1 TTCGCAACACGATTTC-AAA
724900 TTCGCAACAC-AGTTTCCAAA
1 TTCGCAACACGA-TTT-CAAA
724920 TTCGCAAC
1 TTCGCAAC
724928 GCTAATTTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 14 0.37
20 23 0.61
21 1 0.03
ACGTcount: A:0.33, C:0.30, G:0.12, T:0.25
Consensus pattern (19 bp):
TTCGCAACACGATTTCAAA
Found at i:729223 original size:16 final size:15
Alignment explanation
Indices: 729200--729238 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
729190 TTATTAATAA
*
729200 TTTAATTTTATATTT
1 TTTAATTTTACATTT
729215 TTATAATTTTACATTT
1 TT-TAATTTTACATTT
729231 TTTAATTT
1 TTTAATTT
729239 ATAATATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTAATTTTACATTT
Found at i:730080 original size:280 final size:279
Alignment explanation
Indices: 729574--730109 Score: 1004
Period size: 280 Copynumber: 1.9 Consensus size: 279
729564 AAATAATTAT
*
729574 AAATCTTATATTTTTAAATATTTATTAATTATTTACACCTATTTTTCAAAATTCTAGATTCTTTC
1 AAATATTATATTTTTAAATATTTATTAATTATTTACACCTATTTTTCAAAATTCTAGATTCTTTC
729639 TATTGGATTTATATTTTTTTAAAAATATAAAATGAATATAAAATATTTTTTATTTATTAACAATG
66 TATTGGATTTATATTTTTTTAAAAATATAAAATGAATATAAAATATTTTTTATTTATTAACAATG
729704 TATATACATTTTATAAATATAATTATTCGAATTTAAAGTCGCTAAAGAGAAAAATACTCTATTTT
131 TATATACATTTTATAAATATAATTATTCGAATTTAAAGTCGCTAAAGAGAAAAATACTCTATTTT
729769 ATTAATGAAACCACTTAATAATTACATAAATTTATATTTTTAAAGTATATAACTTATCGGTTATG
196 ATTAATGAAACCACTTAATAATTACATAAATTTATATTTTTAAAGTATATAACTTAT-GGTTATG
729834 TAAGTTCACCCACGTCATTG
260 TAAGTTCACCCACGTCATTG
729854 AAATATTATATTTTTAAATATTTTATTAATTATTTACA-CTATTTTTCAAAATTCTAGATTCTTT
1 AAATATTATATTTTTAAATA-TTTATTAATTATTTACACCTATTTTTCAAAATTCTAGATTCTTT
* *
729918 CTATTGGATTTATATATTTTTT-ATAATATAAAATGATTATAAAATATTTTTTATTTATTAACAA
65 CTATTGGATTTATAT-TTTTTTAAAAATATAAAATGAATATAAAATATTTTTTATTTATTAACAA
729982 TGTATATACATTTTATAAATATAATTATTCGAATTTAAAGTCGCTAAAGAGAAAAATACTCTATT
129 TGTATATACATTTTATAAATATAATTATTCGAATTTAAAGTCGCTAAAGAGAAAAATACTCTATT
730047 TTATTAATGAAACCACTTAATAATTACATAAATTTATATTTTTAAAGTATATAACTTATGGTT
194 TTATTAATGAAACCACTTAATAATTACATAAATTTATATTTTTAAAGTATATAACTTATGGTT
730110 TGTTGAACAA
Statistics
Matches: 251, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
279 4 0.02
280 224 0.89
281 23 0.09
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (279 bp):
AAATATTATATTTTTAAATATTTATTAATTATTTACACCTATTTTTCAAAATTCTAGATTCTTTC
TATTGGATTTATATTTTTTTAAAAATATAAAATGAATATAAAATATTTTTTATTTATTAACAATG
TATATACATTTTATAAATATAATTATTCGAATTTAAAGTCGCTAAAGAGAAAAATACTCTATTTT
ATTAATGAAACCACTTAATAATTACATAAATTTATATTTTTAAAGTATATAACTTATGGTTATGT
AAGTTCACCCACGTCATTG
Found at i:731738 original size:10 final size:10
Alignment explanation
Indices: 731723--731749 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
731713 ATAACCACTT
731723 TTCTTTGTTA
1 TTCTTTGTTA
731733 TTCTTTGTTA
1 TTCTTTGTTA
731743 TTCTTTG
1 TTCTTTG
731750 AGGATCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.07, C:0.11, G:0.11, T:0.70
Consensus pattern (10 bp):
TTCTTTGTTA
Found at i:734084 original size:24 final size:24
Alignment explanation
Indices: 734052--734098 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
734042 AGAAACTGTT
734052 GCTGGAGCCGGAGCTGGTACCGAC
1 GCTGGAGCCGGAGCTGGTACCGAC
* *
734076 GCTGGAGCCGGGGCTGGTGCCGA
1 GCTGGAGCCGGAGCTGGTACCGA
734099 TGATGGTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.28, G:0.47, T:0.13
Consensus pattern (24 bp):
GCTGGAGCCGGAGCTGGTACCGAC
Found at i:735754 original size:106 final size:105
Alignment explanation
Indices: 735536--736255 Score: 1203
Period size: 106 Copynumber: 6.8 Consensus size: 105
735526 GAATTGGATA
*
735536 TCCC-TCGTCGTGAAGTTGAACATGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
* *
735600 TTGGCTCTGAAATTGGGAAGTTGTTTATGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTTGTGACAACCAGCGG
* * *
735640 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTTTAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG-TTGAA
735705 ATTGGCTCTGAAATTGAGAAGTTGTTTGTGACAACCAGCGG
65 ATTGGCTCTGAAATTGAGAAGTTGTTTGTGACAACCAGCGG
735746 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
735811 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTTG-TGACAACCAGCGG
735852 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAG-TGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
735916 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTTG-TGACAACCAGCGG
* * *
735957 TCCCTTCGTCGTGAAGTTGAACATGTGTTGTCTGGATTCCAATATCCTTCGCTGTAAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
* *
736022 TTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTT-GTGACAACCAGCGG
* *
736063 TCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG-TGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
* *
736127 TTGGCTCTAAAATTGAGAAGTTGTTTATTGACAACCAGCGG
66 TTGGCTCTGAAATTGAGAAGTTGTTT-GTGACAACCAGCGG
* * * *
736168 TCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCACTATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
736233 TTGGCTCTGAAATTGAGAAGTTG
66 TTGGCTCTGAAATTGAGAAGTTG
736256 ATTGAGGTGT
Statistics
Matches: 586, Mismatches: 24, Indels: 10
0.95 0.04 0.02
Matches are distributed among these distances:
104 4 0.01
105 286 0.49
106 296 0.51
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
TTGGCTCTGAAATTGAGAAGTTGTTTGTGACAACCAGCGG
Found at i:735950 original size:211 final size:210
Alignment explanation
Indices: 735536--736255 Score: 1246
Period size: 211 Copynumber: 3.4 Consensus size: 210
735526 GAATTGGATA
*
735536 TCCC-TCGTCGTGAAGTTGAACATGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
* *
735600 TTGGCTCTGAAATTGGGAAGTTGTTTATGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
66 TTGGCTCTGAAATTGAGAAGTTGTTTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
*
735665 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTTTAAATTGGCTCTGAAATTGAGAAGTTGT
131 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAG--TGAAATTGGCTCTGAAATTGAGAAGTTGT
735730 TTG-TGACAACCAGCGG
194 TTGTTGACAACCAGCGG
735746 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
*
735811 TTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACAT
66 TTGGCTCTGAAATTGAGAAGTTGTTT-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
*
735876 GCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTGAAATTGGCTCTGAAATTGAGAAGTTGTT
130 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTGAAATTGGCTCTGAAATTGAGAAGTTGTT
735941 TGTTGACAACCAGCGG
195 TGTTGACAACCAGCGG
* * *
735957 TCCCTTCGTCGTGAAGTTGAACATGTGTTGTCTGGATTCCAATATCCTTCGCTGTAAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
*
736022 TTGGCTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
66 TTGGCTCTGAAATTGAGAAGTTGTTT-TTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
*
736087 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTGAAATTGGCTCTAAAATTGAGAAGTTGTT
130 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTGAAATTGGCTCTGAAATTGAGAAGTTGTT
*
736152 TATTGACAACCAGCGG
195 TGTTGACAACCAGCGG
* * * *
736168 TCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTGGAGTCCACTATCCTTCGTTGTGAAGTTGAAA
1 TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
736233 TTGGCTCTGAAATTGAGAAGTTG
66 TTGGCTCTGAAATTGAGAAGTTG
736256 ATTGAGGTGT
Statistics
Matches: 486, Mismatches: 21, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
210 35 0.07
211 381 0.78
212 70 0.14
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (210 bp):
TCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAA
TTGGCTCTGAAATTGAGAAGTTGTTTTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTGAAATTGGCTCTGAAATTGAGAAGTTGTTT
GTTGACAACCAGCGG
Found at i:741020 original size:24 final size:24
Alignment explanation
Indices: 740988--741034 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
740978 AGAAACTGTT
740988 GCTGGAGCCGGAGCTGGTACCGAC
1 GCTGGAGCCGGAGCTGGTACCGAC
* *
741012 GCTGGAGCCGGGGCTGGTGCCGA
1 GCTGGAGCCGGAGCTGGTACCGA
741035 TGATGGTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.13, C:0.28, G:0.47, T:0.13
Consensus pattern (24 bp):
GCTGGAGCCGGAGCTGGTACCGAC
Found at i:742256 original size:23 final size:22
Alignment explanation
Indices: 742222--742283 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 22
742212 CTTCTTCTTC
742222 CTTCTTTCCTTCCTTCCAACTTT
1 CTTC-TTCCTTCCTTCCAACTTT
**
742245 CTTTCTTCCTTCCTTCCTTCTTT
1 C-TTCTTCCTTCCTTCCAACTTT
*
742268 CTTCTTCTTCTCCTTC
1 CTTCTTCCT-TCCTTC
742284 TCCTTCTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 7 0.21
23 24 0.71
24 3 0.09
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.56
Consensus pattern (22 bp):
CTTCTTCCTTCCTTCCAACTTT
Found at i:742281 original size:19 final size:19
Alignment explanation
Indices: 742218--742284 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
742208 CCATCTTCTT
742218 CTTCCTTCTTTCCTTCCTTC
1 CTTCCTTCTTT-CTTCCTTC
** *
742238 CAACTTTCTTTCTTCCTTC
1 CTTCCTTCTTTCTTCCTTC
742257 CTTCCTTCTTTCTT-CTTC
1 CTTCCTTCTTTCTTCCTTC
*
742275 TTCTCCTTCT
1 CT-TCCTTCT
742285 CCTTCTCACA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 5 0.13
19 26 0.67
20 8 0.21
ACGTcount: A:0.03, C:0.40, G:0.00, T:0.57
Consensus pattern (19 bp):
CTTCCTTCTTTCTTCCTTC
Found at i:760750 original size:31 final size:31
Alignment explanation
Indices: 760705--760788 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
760695 TGAGCTATAT
760705 ATAAAATA-CTAATTTAATCATTAAACTTTTG
1 ATAAAATATC-AATTTAATCATTAAACTTTTG
* * *
760736 ATAGAATATCAATTTAACCCTTAAACTTTTG
1 ATAAAATATCAATTTAATCATTAAACTTTTG
760767 ATAAAATATCAATTTAACTCAT
1 ATAAAATATCAATTTAA-TCAT
760789 GAATTTGATC
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 42 0.93
32 3 0.07
ACGTcount: A:0.44, C:0.13, G:0.04, T:0.39
Consensus pattern (31 bp):
ATAAAATATCAATTTAATCATTAAACTTTTG
Found at i:764990 original size:31 final size:31
Alignment explanation
Indices: 764955--765062 Score: 164
Period size: 31 Copynumber: 3.5 Consensus size: 31
764945 TGTAAATTAA
764955 ATTCAAACTACTTTCGGATTGAATAAATCAG
1 ATTCAAACTACTTTCGGATTGAATAAATCAG
764986 ATTCAAACTACTTTCGGATTGAATAAATCAG
1 ATTCAAACTACTTTCGGATTGAATAAATCAG
* * * *
765017 ATTCACACTACTTTC-AATCTGAGTAAATTAG
1 ATTCAAACTACTTTCGGAT-TGAATAAATCAG
765048 ATTCAAACTACTTTC
1 ATTCAAACTACTTTC
765063 AGTTTGAGTT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
30 2 0.03
31 69 0.97
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (31 bp):
ATTCAAACTACTTTCGGATTGAATAAATCAG
Found at i:765071 original size:31 final size:31
Alignment explanation
Indices: 764946--765071 Score: 155
Period size: 31 Copynumber: 4.1 Consensus size: 31
764936 TCCAACACGT
* * *
764946 GTAAATTAAATTCAAACTACTTTCGGATTGA
1 GTAAATCAGATTCAAACTACTTTCAGATTGA
* *
764977 ATAAATCAGATTCAAACTACTTTCGGATTGA
1 GTAAATCAGATTCAAACTACTTTCAGATTGA
* *
765008 ATAAATCAGATTCACACTACTTTCA-ATCTGA
1 GTAAATCAGATTCAAACTACTTTCAGAT-TGA
* *
765039 GTAAATTAGATTCAAACTACTTTCAGTTTGA
1 GTAAATCAGATTCAAACTACTTTCAGATTGA
765070 GT
1 GT
765072 TGATTTCATT
Statistics
Matches: 84, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
30 2 0.02
31 81 0.96
32 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (31 bp):
GTAAATCAGATTCAAACTACTTTCAGATTGA
Found at i:773250 original size:163 final size:167
Alignment explanation
Indices: 772943--773250 Score: 380
Period size: 167 Copynumber: 1.9 Consensus size: 167
772933 ATTTATTAAT
* *
772943 TAAAATCTATGATTATCTGTTTCAGCTGATGAATTTTTCTTTCCATTATCTGTTTTTTAGTGTAC
1 TAAAATCTATGATTATCTGTGTCAGCTGATGAATTTTTCTTTCCATTATCTGTTATTTAGTGTAC
* * * * * *
773008 TATTTGTTGTTTTTTCAGATGTGCTCTTGATATTGACCCCCAATTCTTGGGTTTATGAAGTAAAG
66 TATTTGTTGTTTTTTCAGATGTGCTATCGACATTAACCCCAAATTCATGGGTTTATGAAGTAAAG
*
773073 TCTGTTATTGAAGACTTGAGGGTAAAAAGATATGAAG
131 TCTATTATTGAAGACTTGAGGGTAAAAAGATATGAAG
* * * *
773110 TAAAATTTATTATTATCTGTGTCGGCT-ATGGAATTTTTCTTTTCA-T-TCT-TTAATTTAGTGT
1 TAAAATCTATGATTATCTGTGTCAGCTGAT-GAATTTTTCTTTCCATTATCTGTT-ATTTAGTGT
* * *
773171 ATTATTTGTTG-TTTTTGAGATGTGCTATCGGCATTAACTCCCAAATT-AT-GGTTTATGAAGTT
64 ACTATTTGTTGTTTTTTCAGATGTGCTATCGACATTAAC-CCCAAATTCATGGGTTTATGAAG-T
773233 AAA-TCTATTATTGAAGAC
127 AAAGTCTATTATTGAAGAC
773251 CTGATCAATT
Statistics
Matches: 121, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
163 25 0.21
164 28 0.23
165 28 0.23
166 3 0.02
167 37 0.31
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.45
Consensus pattern (167 bp):
TAAAATCTATGATTATCTGTGTCAGCTGATGAATTTTTCTTTCCATTATCTGTTATTTAGTGTAC
TATTTGTTGTTTTTTCAGATGTGCTATCGACATTAACCCCAAATTCATGGGTTTATGAAGTAAAG
TCTATTATTGAAGACTTGAGGGTAAAAAGATATGAAG
Found at i:774401 original size:20 final size:20
Alignment explanation
Indices: 774376--774415 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
774366 AGCAACAGAA
*
774376 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
774396 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
774416 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:774444 original size:53 final size:51
Alignment explanation
Indices: 774372--774520 Score: 264
Period size: 53 Copynumber: 2.9 Consensus size: 51
774362 AATTAGCAAC
774372 AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
774423 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
774476 AGAATAAAAATTGATTCTATCTAATT-AAAATGATCCTATCTAATA
1 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATA
774521 TTTAATTTAG
Statistics
Matches: 95, Mismatches: 1, Indels: 4
0.95 0.01 0.04
Matches are distributed among these distances:
51 24 0.25
52 25 0.26
53 46 0.48
ACGTcount: A:0.48, C:0.12, G:0.06, T:0.34
Consensus pattern (51 bp):
AGAATAAAAATGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:774458 original size:20 final size:21
Alignment explanation
Indices: 774429--774468 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
774419 TAATAGAATA
*
774429 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
774450 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
774469 AACTAATAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:774514 original size:19 final size:20
Alignment explanation
Indices: 774482--774519 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
774472 TAATAGAATA
*
774482 AAAATTGATTCTATCTAATT
1 AAAATTGATCCTATCTAATT
774502 AAAA-TGATCCTATCTAAT
1 AAAATTGATCCTATCTAAT
774520 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.39
Consensus pattern (20 bp):
AAAATTGATCCTATCTAATT
Found at i:779116 original size:19 final size:20
Alignment explanation
Indices: 779089--779133 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
779079 ATTAGCAACA
*
779089 GAAT-AAAAATGATTCTATC
1 GAATAAAAAATGATCCTATC
*
779108 GAATTAAAAATGATCCTATC
1 GAATAAAAAATGATCCTATC
*
779128 TAATAA
1 GAATAA
779134 CTAATAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (20 bp):
GAATAAAAAATGATCCTATC
Found at i:779169 original size:53 final size:52
Alignment explanation
Indices: 779090--779237 Score: 217
Period size: 52 Copynumber: 2.8 Consensus size: 52
779080 TTAGCAACAG
* *
779090 AATAAAAA-TGATTCTATCGAATTAAAAATGATCCTATCTAATAACTAATAA
1 AATAAAAACTAATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAA
* *
779141 AATAAAAAACTAATTTTATCTAATTAAAAATGATCCTATCTAATAACTAATAG
1 AAT-AAAAACTAATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAA
* * *
779194 AATAAAAACTGATTCTATCTAATTAAAATTGATCATATCTAATA
1 AATAAAAACTAATTCTATCTAATTAAAAATGATCCTATCTAATA
779238 TTTAATTTAG
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
51 3 0.03
52 42 0.48
53 42 0.48
ACGTcount: A:0.50, C:0.11, G:0.05, T:0.34
Consensus pattern (52 bp):
AATAAAAACTAATTCTATCTAATTAAAAATGATCCTATCTAATAACTAATAA
Found at i:779226 original size:20 final size:20
Alignment explanation
Indices: 779198--779236 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
779188 TAATAGAATA
779198 AAAACTGATTC-TATCTAATT
1 AAAACTGA-TCATATCTAATT
*
779218 AAAATTGATCATATCTAAT
1 AAAACTGATCATATCTAAT
779237 ATTTAATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.44, C:0.13, G:0.05, T:0.38
Consensus pattern (20 bp):
AAAACTGATCATATCTAATT
Done.