Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 45 of 135
Found at i:16488759 original size:15 final size:15
Alignment explanation
Indices: 16488719--16488761 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
16488709 TTCTTAAAAT
16488719 AATTAAAGAATATAAA
1 AATTAAA-AATATAAA
*
16488735 AATTATAAATAT-AA
1 AATTAAAAATATAAA
16488749 AATATAAAAATAT
1 AAT-TAAAAATAT
16488762 GTATTATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 5 0.21
15 13 0.54
16 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (15 bp):
AATTAAAAATATAAA
Found at i:16491838 original size:2 final size:2
Alignment explanation
Indices: 16491833--16491857 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
16491823 TTAATTTTTT
16491833 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
16491858 TCATTCCTTT
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:16491936 original size:31 final size:30
Alignment explanation
Indices: 16491898--16491955 Score: 80
Period size: 31 Copynumber: 1.9 Consensus size: 30
16491888 AAGTTAATGG
*
16491898 TTAAATTTTAGTTTCAATCCCCATATTTCGC
1 TTAAATTTGAGTTT-AATCCCCATATTTCGC
* *
16491929 TTAAATTTGAGTTTAATCTCTATATTT
1 TTAAATTTGAGTTTAATCCCCATATTT
16491956 TAATTTGACA
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:0.28, C:0.16, G:0.07, T:0.50
Consensus pattern (30 bp):
TTAAATTTGAGTTTAATCCCCATATTTCGC
Found at i:16505457 original size:15 final size:15
Alignment explanation
Indices: 16505434--16505463 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
16505424 AAAACACAAA
16505434 TTTTACGGGAAAAAT
1 TTTTACGGGAAAAAT
*
16505449 TTTTTCGGGAAAAAT
1 TTTTACGGGAAAAAT
16505464 CACAAACAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (15 bp):
TTTTACGGGAAAAAT
Found at i:16508302 original size:3 final size:3
Alignment explanation
Indices: 16508294--16508330 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
16508284 GATATTTGAA
16508294 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
16508331 GAATTTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:16509887 original size:30 final size:30
Alignment explanation
Indices: 16509851--16509911 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 30
16509841 TTTCAATCTC
16509851 TCAACTTTGAAAATGA-GACAAAACAGTCCT
1 TCAACTTTGAAAAT-ATGACAAAACAGTCCT
16509881 TCAACTTTGAAAATATGACAAAACAGTCCT
1 TCAACTTTGAAAATATGACAAAACAGTCCT
16509911 T
1 T
16509912 TTCCGTCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (30 bp):
TCAACTTTGAAAATATGACAAAACAGTCCT
Found at i:16511277 original size:24 final size:23
Alignment explanation
Indices: 16511248--16511292 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
16511238 CGTAAAGTTC
16511248 AAAATTAGTATAAATATGAAATCA
1 AAAATTAGTATAAATAT-AAATCA
*
16511272 AAAATTAGTTTAAATATAAAT
1 AAAATTAGTATAAATATAAAT
16511293 AAATCACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.58, C:0.02, G:0.07, T:0.33
Consensus pattern (23 bp):
AAAATTAGTATAAATATAAATCA
Found at i:16516102 original size:23 final size:23
Alignment explanation
Indices: 16516072--16516118 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
16516062 TTAGGCTCTG
16516072 ATTAATTCATATATTCACTTCTA
1 ATTAATTCATATATTCACTTCTA
16516095 ATTAATTCATATATTCACTTCTA
1 ATTAATTCATATATTCACTTCTA
16516118 A
1 A
16516119 AAAAGTGACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTAATTCATATATTCACTTCTA
Found at i:16533954 original size:28 final size:28
Alignment explanation
Indices: 16533918--16534005 Score: 79
Period size: 28 Copynumber: 3.1 Consensus size: 28
16533908 TTAAGACGAC
*
16533918 TATATAAAAAAATTCAATAAATAAAA-AA
1 TATATAAAAAAATTAAAT-AATAAAATAA
* *
16533946 TATATAAAAATATTAAATATTAAAATAA
1 TATATAAAAAAATTAAATAATAAAATAA
* * * * *
16533974 TATAATATAATATTTAAAAAATAAAAAAA
1 TAT-ATAAAAAAATTAAATAATAAAATAA
16534003 TAT
1 TAT
16534006 GGACGGACCT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
27 6 0.12
28 21 0.44
29 21 0.44
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (28 bp):
TATATAAAAAAATTAAATAATAAAATAA
Found at i:16544768 original size:24 final size:25
Alignment explanation
Indices: 16544738--16544797 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 25
16544728 TAAAAGTCCT
* *
16544738 GCATTAAAA-CCCTATCAATGATCG
1 GCATTAAAACCCCGATCAATGACCG
*
16544762 GCATTAATAGACCCCGATCAATGGCCG
1 GCATTAA-A-ACCCCGATCAATGACCG
16544789 GCATTAAAA
1 GCATTAAAA
16544798 GTCCACTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 7 0.23
25 2 0.07
26 2 0.07
27 19 0.63
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.22
Consensus pattern (25 bp):
GCATTAAAACCCCGATCAATGACCG
Found at i:16554556 original size:30 final size:29
Alignment explanation
Indices: 16554522--16554801 Score: 155
Period size: 30 Copynumber: 9.5 Consensus size: 29
16554512 GTTTAGCGCT
16554522 AAAATGGTAATTTTTGAGAAGTTCGAGGGC
1 AAAAT-GTAATTTTTGAGAAGTTCGAGGGC
* * *
16554552 AAAATGGTAATTTTTGGAAAAATT-GAGGTC
1 AAAAT-GTAATTTTT-GAGAAGTTCGAGGGC
* * * *
16554582 AAAAATGAAATTTTTG-GAAGTCCGAAGGT
1 -AAAATGTAATTTTTGAGAAGTTCGAGGGC
*
16554611 AAAATGGTAATTTTT-AGAAAGTTTG-GGGTC
1 AAAAT-GTAATTTTTGAG-AAGTTCGAGGG-C
* * * *
16554641 AAAAATGAAATTTTTGA-AAGTTTGGGGGTA
1 -AAAATGTAATTTTTGAGAAGTTCGAGGG-C
* * * *
16554671 AAAATGTAGTTTTTGAAAAGTTTGGAGGTC
1 AAAATGTAATTTTTGAGAAG-TTCGAGGGC
* * *
16554701 AAAATGAAATTTCTTGA-AAGTTTGGAGGTC
1 AAAATGTAATTT-TTGAGAAG-TTCGAGGGC
*
16554731 AAAATGTAATTTTTG-GAAGTTCG-GGGTT
1 AAAATGTAATTTTTGAGAAGTTCGAGGG-C
* *
16554759 AAAATGTAATTTTTTAAAAGTTCG-GGGTC
1 AAAATGTAATTTTTGAGAAGTTCGAGGG-C
* *
16554788 AAAATATGATTTTT
1 AAAATGTAATTTTT
16554802 AGACAATTTA
Statistics
Matches: 200, Mismatches: 34, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
27 2 0.01
28 25 0.12
29 65 0.32
30 82 0.41
31 26 0.13
ACGTcount: A:0.36, C:0.04, G:0.25, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGAGAAGTTCGAGGGC
Found at i:16554644 original size:89 final size:88
Alignment explanation
Indices: 16554521--16554748 Score: 232
Period size: 89 Copynumber: 2.5 Consensus size: 88
16554511 AGTTTAGCGC
*
16554521 TAAAATGGTAATTTTTGAGAAGTTCGAGGG-CAAAATGGTAATTTTTGGAAAAATT-GAGGTCAA
1 TAAAATGGTAATTTTTGA-AAGTTTG-GGGTCAAAAT-GTAATTTTTGGAAAAATTGGAGGT-AA
*
16554584 AAATGAAATTTTTG-GAAGTCCGAAGG
62 AAATGAAATTTTTGAAAAGTCCGAAGG
* ** *
16554610 TAAAATGGTAATTTTTAGAAAGTTTGGGGTCAAAAATGAAATTTTT-GAAAGTTTGGGGGTAAAA
1 TAAAATGGTAATTTTT-GAAAGTTTGGGGTC-AAAATGTAATTTTTGGAAAAATTGGAGGTAAAA
* * ** *
16554674 ATGTAGTTTTTGAAAAGTTTGGAGG
64 ATGAAATTTTTGAAAAGTCCGAAGG
*
16554699 TCAAAAT-GAAATTTCTTGAAAGTTTGGAGGTCAAAATGTAATTTTTGGAA
1 T-AAAATGGTAATTT-TTGAAAGTTTGG-GGTCAAAATGTAATTTTTGGAA
16554749 GTTCGGGGTT
Statistics
Matches: 117, Mismatches: 13, Indels: 17
0.80 0.09 0.12
Matches are distributed among these distances:
88 23 0.20
89 73 0.62
90 21 0.18
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (88 bp):
TAAAATGGTAATTTTTGAAAGTTTGGGGTCAAAATGTAATTTTTGGAAAAATTGGAGGTAAAAAT
GAAATTTTTGAAAAGTCCGAAGG
Found at i:16554751 original size:59 final size:58
Alignment explanation
Indices: 16554487--16554801 Score: 248
Period size: 59 Copynumber: 5.3 Consensus size: 58
16554477 TGGACACTTC
* * * * * *
16554487 GAGGTCAAAAAT-TGAATCTTTGAAAGTTTAGCG-CTAAAATGGTAATTTTTGAGAAG-TTC
1 GAGGTC-AAAATGT-AATTTTTGAAAGTTTGGGGTCAAAAAT-GAAATTTTTGA-AAGTTTG
* ** * * **
16554546 GAGGGCAAAATGGTAATTTTTGGAAAAATTGAGGTCAAAAATGAAATTTTTGGAAGTCCG
1 GAGGTCAAAAT-GTAATTTTT-GAAAGTTTGGGGTCAAAAATGAAATTTTTGAAAGTTTG
*
16554606 AAGGT-AAAATGGTAATTTTTAGAAAGTTTGGGGTCAAAAATGAAATTTTTGAAAGTTTG
1 GAGGTCAAAAT-GTAATTTTT-GAAAGTTTGGGGTCAAAAATGAAATTTTTGAAAGTTTG
* * *
16554665 GGGGTAAAAATGTAGTTTTTGAAAAGTTTGGAGGTC-AAAATGAAATTTCTTGAAAGTTTG
1 GAGGTCAAAATGTAATTTTTG-AAAGTTTGG-GGTCAAAAATGAAATTT-TTGAAAGTTTG
* * * * * *
16554725 GAGGTCAAAATGTAATTTTTGGAAGTTCGGGGT-TAAAATGTAATTTTTTAAAAGTTCG
1 GAGGTCAAAATGTAATTTTTGAAAGTTTGGGGTCAAAAATG-AAATTTTTGAAAGTTTG
* *
16554783 G-GGTCAAAATATGATTTTT
1 GAGGTCAAAATGTAATTTTT
16554802 AGACAATTTA
Statistics
Matches: 210, Mismatches: 35, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
57 16 0.08
58 25 0.12
59 105 0.50
60 58 0.28
61 6 0.03
ACGTcount: A:0.36, C:0.05, G:0.24, T:0.35
Consensus pattern (58 bp):
GAGGTCAAAATGTAATTTTTGAAAGTTTGGGGTCAAAAATGAAATTTTTGAAAGTTTG
Found at i:16554751 original size:89 final size:87
Alignment explanation
Indices: 16554619--16554792 Score: 235
Period size: 89 Copynumber: 2.0 Consensus size: 87
16554609 GTAAAATGGT
* *
16554619 AATTTTTAGAAAGTTTGGGGTCAAAAATGAAATTTTTGAAAGTTTGGGGGTAAAAATGTAGTTTT
1 AATTTTTAGAAAGTTTGGGGTCAAAAATGAAATTTTTGAAAG-TTCGGGGTAAAAATGTAATTTT
*
16554684 TGAAAAGTTTGGAGGTCAAAATGA
65 TGAAAAGTTCGG-GGTCAAAATGA
* * *
16554708 AATTTCTT-GAAAGTTTGGAGGTC-AAAATGTAATTTTTGGAAGTTCGGGGTTAAAATGTAATTT
1 AATTT-TTAGAAAGTTTGG-GGTCAAAAATGAAATTTTTGAAAGTTCGGGGTAAAAATGTAATTT
*
16554771 TTTAAAAGTTCGGGGTCAAAAT
64 TTGAAAAGTTCGGGGTCAAAAT
16554793 ATGATTTTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
87 9 0.12
88 29 0.38
89 32 0.42
90 6 0.08
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (87 bp):
AATTTTTAGAAAGTTTGGGGTCAAAAATGAAATTTTTGAAAGTTCGGGGTAAAAATGTAATTTTT
GAAAAGTTCGGGGTCAAAATGA
Found at i:16554799 original size:29 final size:29
Alignment explanation
Indices: 16554621--16554801 Score: 120
Period size: 29 Copynumber: 6.1 Consensus size: 29
16554611 AAAATGGTAA
*
16554621 TTTTTAGAAAGTTTGGGGTCAAAA-ATGAAA
1 TTTTTA-AAAGTTTGGGGTCAAAATATG-AT
*
16554651 TTTTTGAAAGTTTGGGGGT-AAAA-ATGTAGT
1 TTTTTAAAAGTTT-GGGGTCAAAATATG-A-T
* *
16554681 TTTTGAAAAGTTTGGAGGTCAAAATGA-AAT
1 TTTTTAAAAGTTTGG-GGTCAAAAT-ATGAT
* * * *
16554711 TTCTTGAAAGTTTGGAGGTCAAAATGT-AA
1 TTTTTAAAAGTTTGG-GGTCAAAATATGAT
** * * * *
16554740 TTTTTGGAAGTTCGGGGTTAAAATGTAAT
1 TTTTTAAAAGTTTGGGGTCAAAATATGAT
*
16554769 TTTTTAAAAGTTCGGGGTCAAAATATGAT
1 TTTTTAAAAGTTTGGGGTCAAAATATGAT
16554798 TTTT
1 TTTT
16554802 AGACAATTTA
Statistics
Matches: 122, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
28 10 0.08
29 59 0.48
30 47 0.39
31 5 0.04
33 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (29 bp):
TTTTTAAAAGTTTGGGGTCAAAATATGAT
Found at i:16556348 original size:14 final size:13
Alignment explanation
Indices: 16556329--16556367 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
16556319 TACACCAAAA
16556329 CTCTGTTTCTTTGC
1 CTCTG-TTCTTTGC
16556343 CTCTGTT-TTTGC
1 CTCTGTTCTTTGC
*
16556355 CTATGTTCTTTGC
1 CTCTGTTCTTTGC
16556368 TCCTTTTTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 11 0.48
13 7 0.30
14 5 0.22
ACGTcount: A:0.03, C:0.26, G:0.15, T:0.56
Consensus pattern (13 bp):
CTCTGTTCTTTGC
Found at i:16556701 original size:17 final size:16
Alignment explanation
Indices: 16556673--16556744 Score: 90
Period size: 17 Copynumber: 4.3 Consensus size: 16
16556663 TGGACTTTTT
16556673 AATTTAAATAAATTTA
1 AATTTAAATAAATTTA
16556689 AATTTATAATAAATTTA
1 AATTTA-AATAAATTTA
*
16556706 AATTTCAAATGAATTTA
1 AATTT-AAATAAATTTA
* *
16556723 AACCTAAAATAAATTTA
1 AA-TTTAAATAAATTTA
16556740 AATTT
1 AATTT
16556745 TGTTGGGTTC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
16 7 0.15
17 38 0.81
18 2 0.04
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.42
Consensus pattern (16 bp):
AATTTAAATAAATTTA
Found at i:16557107 original size:242 final size:244
Alignment explanation
Indices: 16556775--16557290 Score: 752
Period size: 242 Copynumber: 2.1 Consensus size: 244
16556765 GGCTTCAACA
* * *
16556775 GACTAAATAACAAATCTACCAATTTGGAAGGTCAAATTTAACTTAAAAAAAGATTAATAATCAAA
1 GACTAAATAACAAATCTATCATTTTGGGAGGTCAAATTTAACTTAAAAAAAGATTAATAATCAAA
* * *
16556840 TTGACAAAATATGTAAACTTTAAGAACTAAATCTGTCATTATCCCTATTGATTTATACAACCTTC
66 TTCACAAAATATGTAAACTTTAAGAACTAAATCTGTAATTACCCCTATTGATTTATACAACCTTC
* * * ** *
16556905 TGTTTAAGACTTGAAAATTAATAAATTTATCGTATCTTAACATCAGTAATT-CTGTCTCTT-GGG
131 TATTTAAGACTTGAAAATTAATAAATTTATAGTATCTCAACATCAACAATTCCT-T-TCTTAGGA
*
16556968 TGAAGTGCAATTTATCATTATACTAATATATAATATCATTAAAATTTAAGG
194 CGAAGTGCAATTTATCATTATACTAATATATAATATCATTAAAATTTAAGG
* * * * *
16557019 GATTAAATAATAAATCTATCATTTTGGGAGGTCAAATTTAGCTT-TAAAAA-TTTAATAATCAAA
1 GACTAAATAACAAATCTATCATTTTGGGAGGTCAAATTTAACTTAAAAAAAGATTAATAATCAAA
**
16557082 TTCATGAAATATGTAAACTTTAAGAACTAAATCTGTAATTACCCCTATTGATTTATACAACCTTC
66 TTCACAAAATATGTAAACTTTAAGAACTAAATCTGTAATTACCCCTATTGATTTATACAACCTTC
* *
16557147 TATTTAAGACTTGAAATTTAATAAATTTATAGTATCTCAACATCAACAATTCCTTTTTTAGGACG
131 TATTTAAGACTTGAAAATTAATAAATTTATAGTATCTCAACATCAACAATTCCTTTCTTAGGACG
* * *
16557212 AAGTGCAATTTATCTTTATATTAATATATAATATCATTAAATTTTAAGG
196 AAGTGCAATTTATCATTATACTAATATATAATATCATTAAAATTTAAGG
*
16557261 GACTAAATAACAAATCTATTATTTTGGGAG
1 GACTAAATAACAAATCTATCATTTTGGGAG
16557291 ACAAAATTAT
Statistics
Matches: 242, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
241 3 0.01
242 194 0.80
243 7 0.03
244 38 0.16
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.37
Consensus pattern (244 bp):
GACTAAATAACAAATCTATCATTTTGGGAGGTCAAATTTAACTTAAAAAAAGATTAATAATCAAA
TTCACAAAATATGTAAACTTTAAGAACTAAATCTGTAATTACCCCTATTGATTTATACAACCTTC
TATTTAAGACTTGAAAATTAATAAATTTATAGTATCTCAACATCAACAATTCCTTTCTTAGGACG
AAGTGCAATTTATCATTATACTAATATATAATATCATTAAAATTTAAGG
Found at i:16558835 original size:21 final size:22
Alignment explanation
Indices: 16558811--16558869 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
16558801 TGGAAATGGT
*
16558811 GGTGGAGGTGGCGGTGGG-GGA
1 GGTGGAGGTGGCGGGGGGAGGA
* *
16558832 GGTGGTGGAGGCAGTGGGGGAGGA
1 GGTGGAGGTGGC-G-GGGGGAGGA
16558856 GGTGGAGGTGGCGG
1 GGTGGAGGTGGCGG
16558870 AGGAAACGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
21 10 0.33
22 2 0.07
23 5 0.17
24 13 0.43
ACGTcount: A:0.12, C:0.05, G:0.69, T:0.14
Consensus pattern (22 bp):
GGTGGAGGTGGCGGGGGGAGGA
Found at i:16559006 original size:33 final size:33
Alignment explanation
Indices: 16558957--16559039 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
16558947 GAATGGTGGA
* * * *
16558957 GGAGGAGGAGGAGGTGGAGGCAATGTTGGCGGG
1 GGAGGAGGTGGGGGTGGAGGCAACGGTGGCGGG
* *
16558990 GGAGGGGGTGGGGGTGGAGGCAACGGTGGTGGG
1 GGAGGAGGTGGGGGTGGAGGCAACGGTGGCGGG
*
16559023 GGAGGAGGTGGTGGTGG
1 GGAGGAGGTGGGGGTGG
16559040 TGGTGGAGGA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.16, C:0.05, G:0.66, T:0.13
Consensus pattern (33 bp):
GGAGGAGGTGGGGGTGGAGGCAACGGTGGCGGG
Found at i:16567455 original size:16 final size:17
Alignment explanation
Indices: 16567419--16567454 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
16567409 ATCCTTCTAG
16567419 TTTTCTATCCTTTCAAA
1 TTTTCTATCCTTTCAAA
16567436 TTTTC-ATCCTTTC-AA
1 TTTTCTATCCTTTCAAA
16567451 TTTT
1 TTTT
16567455 TTTCCACTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 8 0.42
17 5 0.26
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTCTATCCTTTCAAA
Found at i:16582730 original size:3 final size:3
Alignment explanation
Indices: 16582706--16582743 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
16582696 TTCCCTTGTT
* *
16582706 TTA TT- TTA TTT TTA TGA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
16582744 AAACCAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.07
3 28 0.93
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:16588185 original size:6 final size:6
Alignment explanation
Indices: 16588149--16588269 Score: 85
Period size: 6 Copynumber: 20.7 Consensus size: 6
16588139 ATCGGGCCCT
* * *
16588149 TTTAAA TTT-AT TTTAAGA -TTAAA TTT-GA TTTAAA TTTAGA TTT--A
1 TTTAAA TTTAAA TTTAA-A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * *
16588193 TTTCAAA TTTAAA TTTAAA ATTAAA CTTTAAA TTTGAA TTT-AA TTTAAG
1 TTT-AAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA
* *
16588242 TCTAAA TTT-AT TTTAAA TTTAAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTA
16588270 TTATAAATTG
Statistics
Matches: 90, Mismatches: 14, Indels: 22
0.71 0.11 0.17
Matches are distributed among these distances:
4 4 0.04
5 18 0.20
6 53 0.59
7 15 0.17
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (6 bp):
TTTAAA
Found at i:16588192 original size:12 final size:12
Alignment explanation
Indices: 16588149--16588269 Score: 85
Period size: 11 Copynumber: 10.3 Consensus size: 12
16588139 ATCGGGCCCT
*
16588149 TTTAAATTT-AT
1 TTTAAATTTAAA
16588160 TTTAAGA-TTAAA
1 TTTAA-ATTTAAA
*
16588172 TTT-GATTTAAA
1 TTTAAATTTAAA
*
16588183 TTTAGATTT--A
1 TTTAAATTTAAA
16588193 TTTCAAATTTAAA
1 TTT-AAATTTAAA
*
16588206 TTTAAAATTAAA
1 TTTAAATTTAAA
*
16588218 CTTTAAATTTGAA
1 -TTTAAATTTAAA
*
16588231 TTT-AATTTAAG
1 TTTAAATTTAAA
* *
16588242 TCTAAATTT-AT
1 TTTAAATTTAAA
16588253 TTTAAATTTAAAA
1 TTTAAATTT-AAA
16588266 TTTA
1 TTTA
16588270 TTATAAATTG
Statistics
Matches: 87, Mismatches: 12, Indels: 20
0.73 0.10 0.17
Matches are distributed among these distances:
10 5 0.06
11 37 0.43
12 26 0.30
13 19 0.22
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.51
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:16588268 original size:18 final size:17
Alignment explanation
Indices: 16588149--16588278 Score: 84
Period size: 17 Copynumber: 8.1 Consensus size: 17
16588139 ATCGGGCCCT
16588149 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
16588167 -TTAAATTTGA-TTTAAA
1 TTTAAATTT-ATTTTAAA
* *
16588183 TTTAGATTTATTTCAAA
1 TTTAAATTTATTTTAAA
16588200 TTTAAATTTA----AAA
1 TTTAAATTTATTTTAAA
*
16588213 -TT-AA---ACTTTAAA
1 TTTAAATTTATTTTAAA
* * *
16588225 TTTGAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
*
16588242 TCTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
16588259 TTTAAAATTTATTATAAA
1 TTT-AAATTTATTTTAAA
16588277 TT
1 TT
16588279 GAAACCCAAT
Statistics
Matches: 88, Mismatches: 11, Indels: 26
0.70 0.09 0.21
Matches are distributed among these distances:
8 1 0.01
11 2 0.02
12 5 0.06
13 5 0.06
14 2 0.02
16 2 0.02
17 55 0.62
18 16 0.18
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:16589137 original size:22 final size:22
Alignment explanation
Indices: 16589082--16589137 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
16589072 AAATACCTAT
16589082 TTAAT-GTATTAAATAGTTTTA
1 TTAATAGTATTAAATAGTTTTA
*
16589103 TTAATAATATTAAATA-TTTTCA
1 TTAATAGTATTAAATAGTTTT-A
*
16589125 TTAATAGTTTTAA
1 TTAATAGTATTAA
16589138 TAAGTTTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 9 0.30
22 21 0.70
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
TTAATAGTATTAAATAGTTTTA
Found at i:16590251 original size:30 final size:29
Alignment explanation
Indices: 16590162--16590308 Score: 81
Period size: 30 Copynumber: 5.0 Consensus size: 29
16590152 CTCTAGTCCC
* *
16590162 CAAACTTTCCAAAATTCTATTTTTGA-CCT
1 CAAACTTTCAAAAATTCCATTTTT-ACCCT
* *
16590191 CGAAACTTCCAAAAAATTACC-GTTTTACCCT
1 C-AAACTTTC-AAAAATT-CCATTTTTACCCT
*
16590222 CAAACTTTCTAAAATTCCATTTTTAACCCT
1 CAAACTTTCAAAAATTCCATTTTT-ACCCT
* * *
16590252 --AA-TTTCACCCAAAATTACCA-ATCTACCCC
1 CAAACTTTCA---AAAATT-CCATTTTTACCCT
* *
16590281 CAAACTTTCTAAAACTCCATTTTTACCC
1 CAAACTTTCAAAAATTCCATTTTTACCC
16590309 CGATTTCACC
Statistics
Matches: 89, Mismatches: 15, Indels: 28
0.67 0.11 0.21
Matches are distributed among these distances:
27 4 0.04
28 7 0.08
29 26 0.29
30 28 0.31
31 19 0.21
32 5 0.06
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (29 bp):
CAAACTTTCAAAAATTCCATTTTTACCCT
Found at i:16590288 original size:59 final size:59
Alignment explanation
Indices: 16590159--16590502 Score: 311
Period size: 58 Copynumber: 5.9 Consensus size: 59
16590149 ACTCTCTAGT
* * * * * * **
16590159 CCCCAAACTTTCCAAAATTCTATTTTTGACCTCGAAACTTC-CAAAAAATTACCGTTTTAC
1 CCCCAAACTTTCTAAAATTCCATTTTTAACC-C-CAATTTCACCAAAAATTACCAATTTAC
* * * *
16590219 CCTCAAACTTTCTAAAATTCCATTTTTAACCCTAATTTCACCCAAAATTACCAATCTAC
1 CCCCAAACTTTCTAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCAATTTAC
* * * * *
16590278 CCCCAAACTTTCTAAAACTCCATTTTT-ACCCCGATTTCACCCAAGATTACCATTTTAC
1 CCCCAAACTTTCTAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCAATTTAC
* * * * * * * * * *
16590336 CCTCGAACCTTCCAAAATCCCATTTTTACCCCCGATTTCACCAAAAAATACTATTTTAC
1 CCCCAAACTTTCTAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCAATTTAC
* * * *
16590395 CCCCGAACTTT-TCAAAATCCCA-TTTTGACCCCATTTTCACCAAAAATTACC-ATTTAC
1 CCCCAAACTTTCT-AAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCAATTTAC
* * * *
16590452 CCCTAAACTTTCCAAAATTTCATTTTTGACCCCAATTTCACCAAAAATTAC
1 CCCCAAACTTTCTAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTAC
16590503 ATTTTTACCC
Statistics
Matches: 234, Mismatches: 45, Indels: 12
0.80 0.15 0.04
Matches are distributed among these distances:
57 21 0.09
58 102 0.44
59 84 0.36
60 27 0.12
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.33
Consensus pattern (59 bp):
CCCCAAACTTTCTAAAATTCCATTTTTAACCCCAATTTCACCAAAAATTACCAATTTAC
Found at i:16590359 original size:58 final size:58
Alignment explanation
Indices: 16590162--16590514 Score: 329
Period size: 59 Copynumber: 6.0 Consensus size: 58
16590152 CTCTAGTCCC
* * * * * *
16590162 CAAACTTTCCAAAATTCTATTTTTGACCTCGAAACTTC-CAAAAAATTACCGTTTTACCCT
1 CAAACTTTCCAAAATCCCATTTTT-ACC-C-CAATTTCACCAAAAATTACCATTTTACCCT
* * * * * * *
16590222 CAAACTTTCTAAAATTCCATTTTTAACCCTAATTTCACCCAAAATTACCAATCTACCCC
1 CAAACTTTCCAAAATCCCATTTTT-ACCCCAATTTCACCAAAAATTACCATTTTACCCT
* * * *
16590281 CAAACTTTCTAAAA-CTCCATTTTTACCCCGATTTCACCCAAGATTACCATTTTACCCT
1 CAAACTTTCCAAAATC-CCATTTTTACCCCAATTTCACCAAAAATTACCATTTTACCCT
* * * * * *
16590339 CGAACCTTCCAAAATCCCATTTTTACCCCCGATTTCACCAAAAAATACTATTTTACCCC
1 CAAACTTTCCAAAATCCCATTTTTA-CCCCAATTTCACCAAAAATTACCATTTTACCCT
* * * *
16590398 CGAACTTTTCAAAATCCCATTTTGACCCCATTTTCACCAAAAATTACCA-TTTACCC-
1 CAAACTTTCCAAAATCCCATTTTTACCCCAATTTCACCAAAAATTACCATTTTACCCT
**
16590454 CTAAACTTTCCAAAATTTCATTTTTGACCCCAATTTCACCAAAAATTA-CATTTTTACCCT
1 C-AAACTTTCCAAAATCCCATTTTT-ACCCCAATTTCACCAAAAATTACCA-TTTTACCCT
16590514 C
1 C
16590515 TGAAGTCAAA
Statistics
Matches: 245, Mismatches: 39, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
56 1 0.00
57 27 0.11
58 94 0.38
59 97 0.40
60 26 0.11
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.33
Consensus pattern (58 bp):
CAAACTTTCCAAAATCCCATTTTTACCCCAATTTCACCAAAAATTACCATTTTACCCT
Found at i:16590359 original size:117 final size:117
Alignment explanation
Indices: 16590202--16590502 Score: 360
Period size: 117 Copynumber: 2.6 Consensus size: 117
16590192 GAAACTTCCA
* * * *
16590202 AAAAATTACCGTTTTACCCTCAAACTTTCTAAAATTCCATTTTTAACCCTAATTTCACCCAAAAT
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAAT
*
16590267 TACCAATCTACCCCCAAAC-TTTCTAAAA-CTCCATTTTTACCCCGA-TTTCACC
66 TACCAATCTACCCCCAAACTTTTC-AAAATC-CCATTTTGACCCC-ATTTTCACC
* * * * * * * *
16590319 CAAGATTACCATTTTACCCTCGAACCTTCCAAAATCCCATTTTTACCCCCGATTTCACCAAAAAA
1 AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAAT
* * * *
16590384 TACTATTTTACCCCCGAACTTTTCAAAATCCCATTTTGACCCCATTTTCACC
66 TACCAATCTACCCCCAAACTTTTCAAAATCCCATTTTGACCCCATTTTCACC
* *
16590436 AAAAATTACCA-TTTACCC-CTAAACTTTCCAAAATTTCATTTTTGACCCCAATTTCACCAAAAA
1 AAAAATTACCATTTTACCCTC-AAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAA
16590499 TTAC
65 TTAC
16590503 ATTTTTACCC
Statistics
Matches: 153, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
115 1 0.01
116 47 0.31
117 100 0.65
118 5 0.03
ACGTcount: A:0.33, C:0.32, G:0.03, T:0.33
Consensus pattern (117 bp):
AAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCAATTTCACCAAAAAT
TACCAATCTACCCCCAAACTTTTCAAAATCCCATTTTGACCCCATTTTCACC
Found at i:16590379 original size:29 final size:30
Alignment explanation
Indices: 16590297--16590449 Score: 76
Period size: 29 Copynumber: 5.2 Consensus size: 30
16590287 TTCTAAAACT
*
16590297 CCATTTTTA-CCCCGA-TTTCACCCAAGATTA
1 CCATTTTTACCCCCGACTTTCA-CCAA-AATA
* * *
16590327 CCA-TTTTACCCTCGAACCTT--CCAAAATC
1 CCATTTTTACCCCCG-ACTTTCACCAAAATA
16590355 CCATTTTTACCCCCGA-TTTCACCAAAAAATA
1 CCATTTTTACCCCCGACTTTCACC--AAAATA
* * *
16590386 CTA-TTTTACCCCCGAACTTT--TCAAAATC
1 CCATTTTTACCCCCG-ACTTTCACCAAAATA
* *
16590414 CCATTTTGA-CCCC-ATTTTCACCAAAAATTA
1 CCATTTTTACCCCCGACTTTCACC-AAAA-TA
16590444 CCATTT
1 CCATTT
16590450 ACCCCTAAAC
Statistics
Matches: 93, Mismatches: 15, Indels: 30
0.67 0.11 0.22
Matches are distributed among these distances:
26 4 0.04
27 2 0.02
28 18 0.19
29 29 0.31
30 26 0.28
31 9 0.10
32 5 0.05
ACGTcount: A:0.30, C:0.33, G:0.04, T:0.33
Consensus pattern (30 bp):
CCATTTTTACCCCCGACTTTCACCAAAATA
Found at i:16591303 original size:153 final size:153
Alignment explanation
Indices: 16591025--16591303 Score: 468
Period size: 153 Copynumber: 1.8 Consensus size: 153
16591015 TTCTCAAAAC
* * * *
16591025 ATATATCTATATTACAAATAATTTTAAAGCGAGGCAATGTCCTGTCGTGTGAAAACTTCGAAAGA
1 ATATATCTACATCACAAATAATTTTAAAACGAGGCAATGTCCTGTCGTGTGAAAACTTCGAAAAA
*
16591090 TCGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCAAATCGAATATCCTCTTCAAAAGT
66 CCGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCAAATCGAATATCCTCTTCAAAAGT
16591155 TCCCGAAACATCCTTCAATTTTT
131 TCCCGAAACATCCTTCAATTTTT
*
16591178 ATATATCTACATCACAAATAATTTTAAAACGAGGCAATGTCCTTTCGTGTGAAAACTTCGAAAAA
1 ATATATCTACATCACAAATAATTTTAAAACGAGGCAATGTCCTGTCGTGTGAAAACTTCGAAAAA
* * * *
16591243 CCGCGCTTTAACGTGTTAAGTGTGATTTTCGTGATTCATGCCAATCGGATATCCTTTTCAA
66 CCGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCAAATCGAATATCCTCTTCAA
16591304 GAGCTTTCAA
Statistics
Matches: 116, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
153 116 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (153 bp):
ATATATCTACATCACAAATAATTTTAAAACGAGGCAATGTCCTGTCGTGTGAAAACTTCGAAAAA
CCGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCAAATCGAATATCCTCTTCAAAAGT
TCCCGAAACATCCTTCAATTTTT
Found at i:16591317 original size:153 final size:152
Alignment explanation
Indices: 16591025--16591335 Score: 455
Period size: 153 Copynumber: 2.0 Consensus size: 152
16591015 TTCTCAAAAC
* * * *
16591025 ATATATCTATATTACAAATAATTTTAAAGCGAGGCAATGTCCTGTCGTGTGAAAACTTCGAAAGA
1 ATATATCTACATCACAAATAATTTTAAAACGAGGCAATGTCCTGTCGTGTGAAAACTTCGAAAAA
*
16591090 TCGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCAAATCGAATATCCTCTTCAAAAGT
66 CCGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCAAATCGAATATCCTCTTCAAAAGT
* *
16591155 TCCCGAAACA-TCCTTCAATTTTT
131 TCCCAAAACACT-CTTCAA-TCTT
*
16591178 ATATATCTACATCACAAATAATTTTAAAACGAGGCAATGTCCTTTCGTGTGAAAACTTCGAAAAA
1 ATATATCTACATCACAAATAATTTTAAAACGAGGCAATGTCCTGTCGTGTGAAAACTTCGAAAAA
* * * * *
16591243 CCGCGCTTTAACGTGTTAAGTGTGATTTTCGTGATTCATGCCAATCGGATATCCTTTTCAAGAGC
66 CCGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCAAATCGAATATCCTCTTCAAAAG-
*
16591308 TT-TCAAAACACTCTTCAATCTT
130 TTCCCAAAACACTCTTCAATCTT
16591330 ATATAT
1 ATATAT
16591336 TTATATACAA
Statistics
Matches: 142, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
152 9 0.06
153 130 0.92
154 3 0.02
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (152 bp):
ATATATCTACATCACAAATAATTTTAAAACGAGGCAATGTCCTGTCGTGTGAAAACTTCGAAAAA
CCGCGCTTTAACGTGTTAAGTGTGATTTTCGTAATTCATGCAAATCGAATATCCTCTTCAAAAGT
TCCCAAAACACTCTTCAATCTT
Found at i:16595302 original size:5 final size:5
Alignment explanation
Indices: 16595294--16595330 Score: 65
Period size: 5 Copynumber: 7.4 Consensus size: 5
16595284 AAAGGGAGGG
*
16595294 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGG GAAGA GA
1 GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GAAGA GA
16595331 GCTTTAGAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (5 bp):
GAAGA
Found at i:16597179 original size:27 final size:28
Alignment explanation
Indices: 16597136--16597188 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
16597126 GAAGTACAAG
*
16597136 CATCCTTTAAAATGAAA-AATTTTATTT
1 CATCCTTTAAAATGAAATAATATTATTT
16597163 CATCTCTTTAAAA-GAAATAATATTAT
1 CATC-CTTTAAAATGAAATAATATTAT
16597189 AAATTAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.42
Consensus pattern (28 bp):
CATCCTTTAAAATGAAATAATATTATTT
Found at i:16599419 original size:27 final size:27
Alignment explanation
Indices: 16599384--16599440 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 27
16599374 TCTTTTTGAA
16599384 TTAATAAAA-TTCTCTTTAAGTTTTTCTT
1 TTAATAAAATTTCTC-TTAAG-TTTTCTT
*
16599412 TTAA-AAAATTTCTCTTGAGTTTTCTT
1 TTAATAAAATTTCTCTTAAGTTTTCTT
16599438 TTA
1 TTA
16599441 GATGAGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 10 0.37
27 8 0.30
28 9 0.33
ACGTcount: A:0.28, C:0.11, G:0.05, T:0.56
Consensus pattern (27 bp):
TTAATAAAATTTCTCTTAAGTTTTCTT
Found at i:16601321 original size:11 final size:11
Alignment explanation
Indices: 16601303--16601340 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
16601293 ATAATAACAA
16601303 CAAAATAATAG
1 CAAAATAATAG
*
16601314 CAATATAATAG
1 CAAAATAATAG
*
16601325 CAAAATGATAG
1 CAAAATAATAG
16601336 CAAAA
1 CAAAA
16601341 CAATGAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.18
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:16601321 original size:22 final size:22
Alignment explanation
Indices: 16601296--16601338 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
16601286 TATCCAAATA
16601296 ATAACAACAAAATAATAGCAAT
1 ATAACAACAAAATAATAGCAAT
* * *
16601318 ATAATAGCAAAATGATAGCAA
1 ATAACAACAAAATAATAGCAA
16601339 AACAATGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAATAGCAAT
Found at i:16632182 original size:23 final size:24
Alignment explanation
Indices: 16632149--16632193 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
16632139 TATATGAAAT
*
16632149 ATAAATTTTAAATATTT-TAAACA
1 ATAAATATTAAATATTTATAAACA
16632172 ATAAATATTAAATATTTATAAA
1 ATAAATATTAAATATTTATAAA
16632194 ATTTAATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:16632593 original size:16 final size:17
Alignment explanation
Indices: 16632562--16632594 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
16632552 TAGATGACAC
16632562 CAATAAGATTAAAAACA
1 CAATAAGATTAAAAACA
*
16632579 CAATAA-ATTATAAACA
1 CAATAAGATTAAAAACA
16632595 ATTTTAAGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.64, C:0.12, G:0.03, T:0.21
Consensus pattern (17 bp):
CAATAAGATTAAAAACA
Found at i:16640745 original size:17 final size:17
Alignment explanation
Indices: 16640723--16640784 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
16640713 TCCAACTTTT
*
16640723 TTTAAATTTATTTTAAG
1 TTTAAATTTATTTTAAA
**
16640740 TTTAAATTGGTTTTAAA
1 TTTAAATTTATTTTAAA
*
16640757 TTTGAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
16640774 TTTAAAATTTA
1 TTT-AAATTTA
16640785 AAATGGTTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 31 0.84
18 6 0.16
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.56
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:16640771 original size:28 final size:28
Alignment explanation
Indices: 16640722--16640775 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
16640712 ATCCAACTTT
*
16640722 TTTTAAATTTATTTTAAGTTTAAATTGG
1 TTTTAAATTTAATTTAAGTTTAAATTGG
*
16640750 TTTTAAATTTGAATTT-ATTTTAAATT
1 TTTTAAATTT-AATTTAAGTTTAAATT
16640776 TAAAATTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (28 bp):
TTTTAAATTTAATTTAAGTTTAAATTGG
Found at i:16642547 original size:29 final size:29
Alignment explanation
Indices: 16642514--16643036 Score: 369
Period size: 29 Copynumber: 17.9 Consensus size: 29
16642504 TTGAAACCCA
* * *
16642514 AACTTTCCAAAAATTA-TATTTTGCCCCTG
1 AACTGTCCAAAAATTACCATTTT-ACCCTG
* * *
16642543 AACTTTCCAAAAGTTACCTTTTTACCCTCG
1 AACTGTCCAAAAATTACCATTTTACCCT-G
* **
16642573 GA-TGTCCAAAAATTA-CATTTTTTACTTTG
1 AACTGTCCAAAAATTACCA--TTTTACCCTG
*
16642602 AACTTTCCAAAAATTACCATTTTACCCTCG
1 AACTGTCCAAAAATTACCATTTTACCCT-G
*
16642632 -AGTGTCCAAAAATTACCATTTTACCCTCG
1 AACTGTCCAAAAATTACCATTTTACCCT-G
*
16642661 AA-TGTCCAAAAATTA-CATTTTTGACCCTA
1 AACTGTCCAAAAATTACCA-TTTT-ACCCTG
* * *
16642690 AACTTTCCAAAAATTAGCATTTTACCCCCG
1 AACTGTCCAAAAATTACCATTTTA-CCCTG
* ** *
16642720 AAC-ATAAAAAAAATACCATTTTACCCTCG
1 AACTGTCCAAAAATTACCATTTTACCCT-G
* *
16642749 AAC-ATCCAAAAATTACCATTTTA-CCTT
1 AACTGTCCAAAAATTACCATTTTACCCTG
* * *
16642776 AAATGTCTAAAAATTA-TATTTTTGACCCTG
1 AACTGTCCAAAAATTACCA-TTTT-ACCCTG
*
16642806 AACTGTCCAAAAATTATCATTTTACCCTCG
1 AACTGTCCAAAAATTACCATTTTACCCT-G
* * **
16642836 AAC-ATCAAAAAATTACCATTTTACCCCCA
1 AACTGTCCAAAAATTACCATTTTA-CCCTG
* *
16642865 AAC-ATCCAAAAATTACCATTTTACCCCG
1 AACTGTCCAAAAATTACCATTTTACCCTG
* *
16642893 AA-TGTCTAAAAATTACCATTTTTGCCCTTG
1 AACTGTCCAAAAATTACCA-TTTTACCC-TG
*
16642923 AACTTTCCAAAAATTACCA-TTTACCCTCG
1 AACTGTCCAAAAATTACCATTTTACCCT-G
* *
16642952 AA-TGTTCAAAAATTA-CATTTTTTGACCCCG
1 AACTGTCCAAAAATTACCA--TTTT-ACCCTG
* * * *
16642982 AGCTTTCCAATAATTACAATTTTACCCTTG
1 AACTGTCCAAAAATTACCATTTTACCC-TG
*
16643012 AAC-ATCCAAAAATTACCATTTTACC
1 AACTGTCCAAAAATTACCATTTTACC
16643037 TCCAGGTGTC
Statistics
Matches: 396, Mismatches: 65, Indels: 66
0.75 0.12 0.13
Matches are distributed among these distances:
27 5 0.01
28 54 0.14
29 206 0.52
30 97 0.24
31 33 0.08
32 1 0.00
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (29 bp):
AACTGTCCAAAAATTACCATTTTACCCTG
Found at i:16642640 original size:88 final size:88
Alignment explanation
Indices: 16642509--16643033 Score: 395
Period size: 88 Copynumber: 6.0 Consensus size: 88
16642499 ATATTTTGAA
* * * * *
16642509 ACCC-AAACTTTCCAAAAATTATATTTTGCCCCTGAACTTTCCAAAAGTTACCTTTTTACCCTCG
1 ACCCTAAACTTTCCAAAAATTACATTTTACCCCTGAACTGTCCAAAAATTACCATTTTACCCTCG
* *
16642573 GATGTCCAAAAATTACATTTTTT
66 AATGTCCAAAAATTACATTTTTG
** * *
16642596 ACTTTGAACTTTCCAAAAATTACCATTTTA-CCCTCG-AGTGTCCAAAAATTACCATTTTACCCT
1 ACCCTAAACTTTCCAAAAATTA-CATTTTACCCCT-GAACTGTCCAAAAATTACCATTTTACCCT
16642659 CGAATGTCCAAAAATTACATTTTTG
64 CGAATGTCCAAAAATTACATTTTTG
* * ** *
16642684 ACCCTAAACTTTCCAAAAATTAGCATTTTACCCCCGAAC-ATAAAAAAAATACCATTTTACCCTC
1 ACCCTAAACTTTCCAAAAATTA-CATTTTACCCCTGAACTGTCCAAAAATTACCATTTTACCCTC
**
16642748 GAACATCCAAAAATTACCA-TTTT-
65 GAATGTCCAAAAATTA-CATTTTTG
* * * * *
16642771 ACCTTAAA-TGTCTAAAAATTATATTTTTGA-CCCTGAACTGTCCAAAAATTATCATTTTACCCT
1 ACCCTAAACTTTCCAAAAATTACA-TTTT-ACCCCTGAACTGTCCAAAAATTACCATTTTACCCT
** *
16642834 CGAACATCAAAAAATTACCA-TTTT-
64 CGAATGTCCAAAAATTA-CATTTTTG
* * * *
16642858 ACCCCCAAAC-ATCCAAAAATTACCATTTTACCCC-GAA-TGTCTAAAAATTACCATTTTTGCCC
1 A-CCCTAAACTTTCCAAAAATTA-CATTTTACCCCTGAACTGTCCAAAAATTACCA-TTTTACCC
* *
16642920 TTGAACTTTCCAAAAATTACCA--TTT-
63 TCGAA-TGTCCAAAAATTA-CATTTTTG
* * * * *
16642945 ACCCTCGAA-TGTT-CAAAAATTACATTTTTTGACCCC-GAGCTTTCCAATAATTACAATTTTAC
1 ACCCT-AAACT-TTCCAAAAATTACA--TTTT-ACCCCTGAACTGTCCAAAAATTACCATTTTAC
* **
16643007 CCTTGAACATCCAAAAATTACCATTTT
61 CCTCGAATGTCCAAAAATTA-CATTTT
16643034 ACCTCCAGGT
Statistics
Matches: 357, Mismatches: 57, Indels: 45
0.78 0.12 0.10
Matches are distributed among these distances:
85 1 0.00
86 41 0.11
87 83 0.23
88 186 0.52
89 32 0.09
90 14 0.04
ACGTcount: A:0.35, C:0.25, G:0.06, T:0.34
Consensus pattern (88 bp):
ACCCTAAACTTTCCAAAAATTACATTTTACCCCTGAACTGTCCAAAAATTACCATTTTACCCTCG
AATGTCCAAAAATTACATTTTTG
Found at i:16642688 original size:59 final size:59
Alignment explanation
Indices: 16642548--16643091 Score: 402
Period size: 59 Copynumber: 9.3 Consensus size: 59
16642538 CCCTGAACTT
* * * *
16642548 TCCAAAAGTTACC-TTTTTACCCTCG-GATGTCCAAAAATTA-CATTTTTTA-CTTTGAACTT
1 TCCAAAAATTACCATTTTTACCCTCGAG-TGTCCAAAAATTACCA--TTTTACCCTCGAA-TG
16642607 TCCAAAAATTACCA-TTTTACCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATG
1 TCCAAAAATTACCATTTTTACCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATG
** * * * * **
16642665 TCCAAAAATTA-CATTTTTGACCCTAAACTTTCCAAAAATTAGCATTTTACCCCCGAACA
1 TCCAAAAATTACCATTTTT-ACCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATG
** * *** **
16642724 TAAAAAAAATACCA-TTTTACCCTCGAACATCCAAAAATTACCATTTTA-CCTTAAATG
1 TCCAAAAATTACCATTTTTACCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATG
* * * * **
16642781 TCTAAAAATTA-TATTTTTGACCCT-GAACTGTCCAAAAATTATCATTTTACCCTCGAACA
1 TCCAAAAATTACCATTTTT-ACCCTCG-AGTGTCCAAAAATTACCATTTTACCCTCGAATG
* * * ***
16642840 TCAAAAAATTACCA-TTTTACCCCCAAACATCCAAAAATTACCATTTTACCC-CGAATG
1 TCCAAAAATTACCATTTTTACCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATG
* * * * *
16642897 TCTAAAAATTACCATTTTTGCCCTTGAACTTTCCAAAAATTACCA-TTTACCCTCGAATG
1 TCCAAAAATTACCATTTTTACCCTCG-AGTGTCCAAAAATTACCATTTTACCCTCGAATG
* * * * * **
16642956 TTCAAAAATTA-CATTTTTTGACCC-CGAGCTTTCCAATAATTACAATTTTACCCTTGAACA
1 TCCAAAAATTACCA-TTTTT-ACCCTCGAG-TGTCCAAAAATTACCATTTTACCCTCGAATG
* * * * * *
16643016 TCCAAAAATTACCA-TTTTA-CCTCCAGGTGTCCAAAAACTATCGTTTTACCCCCGGATG
1 TCCAAAAATTACCATTTTTACCCTCGA-GTGTCCAAAAATTACCATTTTACCCTCGAATG
*
16643074 TCCAAAAATTACCGTTTT
1 TCCAAAAATTACCATTTT
16643092 GCCTCTGAGC
Statistics
Matches: 381, Mismatches: 80, Indels: 48
0.75 0.16 0.09
Matches are distributed among these distances:
56 1 0.00
57 38 0.10
58 148 0.39
59 162 0.43
60 30 0.08
61 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.07, T:0.33
Consensus pattern (59 bp):
TCCAAAAATTACCATTTTTACCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATG
Found at i:16642827 original size:116 final size:116
Alignment explanation
Indices: 16642610--16642953 Score: 494
Period size: 116 Copynumber: 3.0 Consensus size: 116
16642600 TGAACTTTCC
*** *
16642610 AAAAATTACCATTTTACCCTCGAGTGTCCAAAAATTACCATTTTACCCTCGAATGTCCAAAAATT
1 AAAAATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTA-CCTCGAATGTCTAAAAATT
* * *
16642675 ACATTTTTGACCCTAAACTTTCCAAAAATTAGCATTTTACCCCCGAACATAA
65 ACATTTTTGACCCTGAACTTTCCAAAAATTACCATTTTACCCTCGAACATAA
* **
16642727 AAAAAATACCATTTTACCCTCGAACATCCAAAAATTACCATTTTACCTTAAATGTCTAAAAATTA
1 AAAAATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTACCTCGAATGTCTAAAAATTA
* * * *
16642792 TATTTTTGACCCTGAACTGTCCAAAAATTATCATTTTACCCTCGAACATCA
66 CATTTTTGACCCTGAACTTTCCAAAAATTACCATTTTACCCTCGAACATAA
* * *
16642843 AAAAATTACCATTTTACCCCCAAACATCCAAAAATTACCATTTTACCCCGAATGTCTAAAAATTA
1 AAAAATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTACCTCGAATGTCTAAAAATTA
16642908 CCATTTTTG-CCCTTGAACTTTCCAAAAATTACCA-TTTACCCTCGAA
66 -CATTTTTGACCC-TGAACTTTCCAAAAATTACCATTTTACCCTCGAA
16642954 TGTTCAAAAA
Statistics
Matches: 203, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
116 136 0.67
117 67 0.33
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.31
Consensus pattern (116 bp):
AAAAATTACCATTTTACCCTCGAACATCCAAAAATTACCATTTTACCTCGAATGTCTAAAAATTA
CATTTTTGACCCTGAACTTTCCAAAAATTACCATTTTACCCTCGAACATAA
Found at i:16643048 original size:29 final size:30
Alignment explanation
Indices: 16643016--16643096 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 30
16643006 CCCTTGAACA
*
16643016 TCCAAAAATTACCATTTTACCTCCAGG-TG
1 TCCAAAAATTACCGTTTTACCTCCAGGATG
* * *
16643045 TCCAAAAACTATCGTTTTACC-CCCGGATG
1 TCCAAAAATTACCGTTTTACCTCCAGGATG
*
16643074 TCCAAAAATTACCGTTTTGCCTC
1 TCCAAAAATTACCGTTTTACCTC
16643097 TGAGCATCCA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
28 4 0.09
29 38 0.88
30 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.31
Consensus pattern (30 bp):
TCCAAAAATTACCGTTTTACCTCCAGGATG
Found at i:16648341 original size:5 final size:5
Alignment explanation
Indices: 16648331--16648396 Score: 61
Period size: 5 Copynumber: 13.8 Consensus size: 5
16648321 AATAATTAAA
*
16648331 AAAAG AAAAG AAAGAA AAAAG AATAA- AAAAG -AAAG AAAAG AAAA- AAAA-
1 AAAAG AAAAG AAA-AG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAAG AAAAG
*
16648379 AAAA- AAAAG AAAGG AAAA
1 AAAAG AAAAG AAAAG AAAA
16648397 AAGAAATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
4 18 0.35
5 28 0.54
6 6 0.12
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:16648346 original size:4 final size:4
Alignment explanation
Indices: 16648332--16648417 Score: 62
Period size: 4 Copynumber: 22.8 Consensus size: 4
16648322 ATAATTAAAA
*
16648332 AAAG AAAAG AAAG AAA- AAAG -AAT AAA- AAAG AAAG AAAAG AAA- AAA-
1 AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG -AAAG AAAG AAAG
* *
16648377 AAA- AAAA AAAG AAAGG AAA- AAAG AAAT AAAG AAA- AAAG AAA
1 AAAG AAAG AAAG AAA-G AAAG AAAG AAAG AAAG AAAG AAAG AAA
16648418 ATAAAAAAAG
Statistics
Matches: 69, Mismatches: 4, Indels: 17
0.77 0.04 0.19
Matches are distributed among these distances:
3 23 0.33
4 34 0.49
5 12 0.17
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:16648348 original size:16 final size:16
Alignment explanation
Indices: 16648329--16648418 Score: 96
Period size: 16 Copynumber: 5.7 Consensus size: 16
16648319 ATAATAATTA
16648329 AAAAAAGAAAAGAAAG
1 AAAAAAGAAAAGAAAG
*
16648345 AAAAAAGAATA-AAA-
1 AAAAAAGAAAAGAAAG
* *
16648359 AAGAAAGAAAAGAAAAA
1 AAAAAAGAAAAG-AAAG
*
16648376 AAAAAAAAAAAGAAAGG
1 AAAAAAGAAAAGAAA-G
*
16648393 AAAAAAG-AAATAAAG
1 AAAAAAGAAAAGAAAG
16648408 AAAAAAGAAAA
1 AAAAAAGAAAA
16648419 TAAAAAAAGG
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
14 9 0.15
15 11 0.18
16 25 0.41
17 16 0.26
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (16 bp):
AAAAAAGAAAAGAAAG
Found at i:16648348 original size:30 final size:29
Alignment explanation
Indices: 16648312--16648417 Score: 107
Period size: 26 Copynumber: 3.8 Consensus size: 29
16648302 GGATTCAATG
*
16648312 AAGAAAAATAATAATTAAAA-AAAGAAAAGA
1 AAGAAAAAGAATAA--AAAAGAAAGAAAAGA
16648342 AAGAAAAAAGAATAAAAAAGAAAGAAAAGA
1 AAG-AAAAAGAATAAAAAAGAAAGAAAAGA
*
16648372 AA-AAAAA-AA-AAAAAAGAAAGGAAA-A
1 AAGAAAAAGAATAAAAAAGAAAGAAAAGA
* *
16648397 AAGAAATA-AAGAAAAAAGAAA
1 AAGAAAAAGAATAAAAAAGAAA
16648418 ATAAAAAAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
25 3 0.04
26 20 0.29
27 12 0.17
28 5 0.07
29 4 0.06
30 15 0.22
31 10 0.14
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (29 bp):
AAGAAAAAGAATAAAAAAGAAAGAAAAGA
Found at i:16648358 original size:10 final size:9
Alignment explanation
Indices: 16648328--16648427 Score: 82
Period size: 9 Copynumber: 10.9 Consensus size: 9
16648318 AATAATAATT
16648328 AAAAAAAGA
1 AAAAAAAGA
*
16648337 AAAGAAAG-
1 AAAAAAAGA
16648345 -AAAAAAGA
1 AAAAAAAGA
16648353 ATAAAAAAGA
1 A-AAAAAAGA
*
16648363 AAGAAAAGA
1 AAAAAAAGA
16648372 AAAAAAA-A
1 AAAAAAAGA
16648380 AAAAAAAGA
1 AAAAAAAGA
16648389 AAGGAAAAA-A
1 AA--AAAAAGA
*
16648399 GAAATAAAGA
1 -AAAAAAAGA
*
16648409 AAAAAGAAAA
1 AAAAA-AAGA
16648419 TAAAAAAAG
1 -AAAAAAAG
16648428 GGAAAAAGAA
Statistics
Matches: 73, Mismatches: 8, Indels: 19
0.73 0.08 0.19
Matches are distributed among these distances:
7 6 0.08
8 8 0.11
9 31 0.42
10 16 0.22
11 12 0.16
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:16648358 original size:26 final size:25
Alignment explanation
Indices: 16648329--16648417 Score: 103
Period size: 22 Copynumber: 3.6 Consensus size: 25
16648319 ATAATAATTA
16648329 AAAAAAGAAAAGAAAGAAAAAAGAAT
1 AAAAAA-AAAAGAAAGAAAAAAGAAT
* *
16648355 AAAAAAGAAAGAAA-AGAAAA-AA-
1 AAAAAAAAAAGAAAGAAAAAAGAAT
16648377 AAAAAAAAAAGAAAGGAAAAAAGAAAT
1 AAAAAAAAAAGAAA-GAAAAAAG-AAT
*
16648404 AAAGAAAAAAGAAA
1 AAAAAAAAAAGAAA
16648418 ATAAAAAAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
22 13 0.25
23 2 0.04
24 10 0.19
25 7 0.13
26 8 0.15
27 13 0.25
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAAGAAAGAAAAAAGAAT
Found at i:16648362 original size:21 final size:19
Alignment explanation
Indices: 16648331--16648439 Score: 87
Period size: 21 Copynumber: 5.2 Consensus size: 19
16648321 AATAATTAAA
16648331 AAAAGAAAAGAAAGAAAAAAG
1 AAAA-AAAA-AAAGAAAAAAG
16648352 AATAAAAAAGAAAGAAAAGAA-
1 AA-AAAAAA-AAAGAAAA-AAG
16648373 AAAAAAAAAAA-AAAGAAAGG
1 AAAAAAAAAAAGAAA-AAA-G
16648393 AAAAAAGAAATAAAGAAAAAAG
1 -AAAAA-AAA-AAAGAAAAAAG
*
16648415 AAAATAAAAAAAGGGAAAAAG
1 AAAA-AAAAAAA-GAAAAAAG
16648436 AAAA
1 AAAA
16648440 GGAGAGGTCG
Statistics
Matches: 76, Mismatches: 1, Indels: 22
0.77 0.01 0.22
Matches are distributed among these distances:
18 5 0.07
19 4 0.05
20 9 0.12
21 40 0.53
22 9 0.12
23 6 0.08
24 3 0.04
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.03
Consensus pattern (19 bp):
AAAAAAAAAAAGAAAAAAG
Found at i:16648405 original size:49 final size:47
Alignment explanation
Indices: 16648328--16648426 Score: 146
Period size: 49 Copynumber: 2.1 Consensus size: 47
16648318 AATAATAATT
*
16648328 AAAAAAAGAAAAGAAAGAAAAAAGAATAAA-AAAGAAAGAAAAGAAAA
1 AAAAAAAAAAAAGAAAGAAAAAAGAATAAAGAAA-AAAGAAAAGAAAA
*
16648375 AAAAAAAAAAAAGAAAGGAAAAAAGAAATAAAGAAAAAAGAAAATAAAA
1 AAAAAAAAAAAAGAAA-GAAAAAAG-AATAAAGAAAAAAGAAAAGAAAA
16648424 AAA
1 AAA
16648427 GGGAAAAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
47 15 0.32
48 8 0.17
49 21 0.45
50 3 0.06
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (47 bp):
AAAAAAAAAAAAGAAAGAAAAAAGAATAAAGAAAAAAGAAAAGAAAA
Found at i:16648419 original size:16 final size:15
Alignment explanation
Indices: 16648329--16648439 Score: 95
Period size: 15 Copynumber: 7.3 Consensus size: 15
16648319 ATAATAATTA
16648329 AAAAAAGAAAAGAAAG
1 AAAAAAGAAAA-AAAG
16648345 AAAAAAGAATAAAAAAG
1 AAAAAAG-A-AAAAAAG
16648362 AAAGAAAAGAAAAAAA-
1 -AA-AAAAGAAAAAAAG
*
16648378 AAAAAA-AAAGAAAGG
1 AAAAAAGAAA-AAAAG
*
16648393 AAAAAAGAAATAAAG
1 AAAAAAGAAAAAAAG
*
16648408 AAAAAAG-AAAATA-
1 AAAAAAGAAAAAAAG
**
16648421 AAAAAAGGGAAAAAG
1 AAAAAAGAAAAAAAG
16648436 AAAA
1 AAAA
16648440 GGAGAGGTCG
Statistics
Matches: 79, Mismatches: 7, Indels: 19
0.75 0.07 0.18
Matches are distributed among these distances:
13 10 0.13
14 15 0.19
15 22 0.28
16 10 0.13
17 11 0.14
18 6 0.08
19 5 0.06
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:16648424 original size:26 final size:25
Alignment explanation
Indices: 16648330--16648417 Score: 103
Period size: 25 Copynumber: 3.5 Consensus size: 25
16648320 TAATAATTAA
16648330 AAAAAGAAAAGAAAGAAAAAAG-AAT
1 AAAAA-AAAAGAAAGAAAAAAGAAAT
*
16648355 AAAAAAGAAAGAAA-AGAAAA-AAA-
1 AAAAAA-AAAGAAAGAAAAAAGAAAT
16648378 AAAAAAAAAGAAAGGAAAAAAGAAAT
1 AAAAAAAAAGAAA-GAAAAAAGAAAT
16648404 AAAGAAAAAAGAAA
1 AAA-AAAAAAGAAA
16648418 ATAAAAAAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
22 7 0.13
23 6 0.11
24 13 0.24
25 15 0.28
26 3 0.06
27 10 0.19
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAGAAAGAAAAAAGAAAT
Found at i:16648432 original size:37 final size:38
Alignment explanation
Indices: 16648331--16648438 Score: 118
Period size: 36 Copynumber: 3.0 Consensus size: 38
16648321 AATAATTAAA
* * *
16648331 AAAAG-AAAAGAAAGAAAAAAG-AA-TAAAAAAGAAAG
1 AAAAGAAAAAAAAAAAAAAAAGAAAGGAAAAAAGAAAG
16648366 AAAAGAAAAAAAAAAAAAAAAGAAAGGAAAAAAGAAA-
1 AAAAGAAAAAAAAAAAAAAAAGAAAGGAAAAAAGAAAG
* * * *
16648403 TAAAGAAAAAAGAAAATAAAA-AAAGGGAAAAAGAAA
1 AAAAGAAAAAAAAAAAAAAAAGAAAGGAAAAAAGAAA
16648439 AGGAGAGGTC
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
35 5 0.08
36 28 0.44
37 20 0.32
38 10 0.16
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (38 bp):
AAAAGAAAAAAAAAAAAAAAAGAAAGGAAAAAAGAAAG
Found at i:16648434 original size:1 final size:1
Alignment explanation
Indices: 16648328--16648426 Score: 54
Period size: 1 Copynumber: 99.0 Consensus size: 1
16648318 AATAATAATT
* * * * * * * * * **
16648328 AAAAAAAGAAAAGAAAGAAAAAAGAATAAAAAAGAAAGAAAAGAAAAAAAAAAAAAAAAGAAAGG
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * *
16648393 AAAAAAGAAATAAAGAAAAAAGAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16648427 GGGAAAAAGA
Statistics
Matches: 68, Mismatches: 30, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
1 68 1.00
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (1 bp):
A
Found at i:16650094 original size:210 final size:211
Alignment explanation
Indices: 16649726--16650186 Score: 590
Period size: 210 Copynumber: 2.2 Consensus size: 211
16649716 ATGCGGTCGC
* *
16649726 CTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCAGCTTCTTGATGAGATACT
1 CTTCCTGATGAGATACTGAGAAACAGGTCGAAACAATAAAATGGTCAGCTTCTTGATGAGATACT
* * * * * * *
16649791 AAGAATTGGACCAAATTCTTCTTCCTGATGAGATACAAAGAAGAGGATTGAAACAAGTGAGGCAG
66 AAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAAAGAAGAGGATTAAAACAAATGAGGCAC
* **
16649856 TCATCTTCTTAATGAGATACTGAGAAGTAGACCAAATCAA-TGAAACTAAAGCTCGATGTGAGGA
131 TCATCTTCCTAATGAGATACCAAGAAGTAGACCAAATCAAGTGAAACTAAAGCTCGATGTGAGGA
16649920 AAACTTCGAACCCCAG
196 AAACTTCGAACCCCAG
* *
16649936 CTTCTTGATGAGGTACTGAGAAACAGGTCGAAACAATAAAATGGTC-GTCTTCTTGATGAGATAC
1 CTTCCTGATGAGATACTGAGAAACAGGTCGAAACAATAAAATGGTCAG-CTTCTTGATGAGATAC
*
16650000 -AGAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAAAGAAGTGGATTAAAACAAATGAGGC
65 TA-AGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAAAGAAGAGGATTAAAACAAATGAGGC
* * * *
16650064 ACTCATCTTCCTGATGAGATACCAAGAAGTAGACCAAATCAAGTGAAGC-AAAGTTCAAATGTGA
129 ACTCATCTTCCTAATGAGATACCAAGAAGTAGACCAAATCAAGTGAAACTAAAGCTC-GATGTGA
* * * *
16650128 GTG-AAGCTTCAAACTCCTAT
193 G-GAAAACTTCGAAC-CCCAG
** ** *
16650148 CTTCCTGATGAGATACAAAGAAGTAGGTCGAAGCAATAA
1 CTTCCTGATGAGATACTGAGAAACAGGTCGAAACAATAA
16650187 CGCAGTCATC
Statistics
Matches: 215, Mismatches: 30, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
209 2 0.01
210 156 0.73
211 21 0.10
212 36 0.17
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (211 bp):
CTTCCTGATGAGATACTGAGAAACAGGTCGAAACAATAAAATGGTCAGCTTCTTGATGAGATACT
AAGAAGTGAACCAAATCCGTCTTCCTGATGAGATACAAAGAAGAGGATTAAAACAAATGAGGCAC
TCATCTTCCTAATGAGATACCAAGAAGTAGACCAAATCAAGTGAAACTAAAGCTCGATGTGAGGA
AAACTTCGAACCCCAG
Found at i:16650626 original size:17 final size:17
Alignment explanation
Indices: 16650604--16650643 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
16650594 TCCAACATTT
* *
16650604 TTTAAATTTATTTTAAG
1 TTTAAATTGATTTTAAA
*
16650621 TTTAAATTGGTTTTAAA
1 TTTAAATTGATTTTAAA
16650638 TTTAAA
1 TTTAAA
16650644 ATTTGAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (17 bp):
TTTAAATTGATTTTAAA
Found at i:16651051 original size:22 final size:22
Alignment explanation
Indices: 16651026--16651075 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
16651016 AGTTTGGGAG
* * *
16651026 AAATCAATACAAACACATTTCA
1 AAATCAATACAAAAAAAATTCA
*
16651048 AAATCAGTACAAAAAAAATTCA
1 AAATCAATACAAAAAAAATTCA
16651070 AAATCA
1 AAATCA
16651076 CCAGACAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.60, C:0.18, G:0.02, T:0.20
Consensus pattern (22 bp):
AAATCAATACAAAAAAAATTCA
Found at i:16652530 original size:29 final size:29
Alignment explanation
Indices: 16652487--16652742 Score: 148
Period size: 29 Copynumber: 8.8 Consensus size: 29
16652477 TTAACCCCTA
16652487 AACTTTCCAAAAATTACATTTTGACCTTG
1 AACTTTCCAAAAATTACATTTTGACCTTG
* * * * *
16652516 AATTTTCAAAAAATTACATTTTGCCCCTA
1 AACTTTCCAAAAATTACATTTTGACCTTG
* * **
16652545 AACTTTCCAAAAA-TACCTTTTTACCCCCG
1 AACTTTCCAAAAATTACATTTTGA-CCTTG
* *
16652574 AA-TGTCCAAAAATTACATTTTTAACCTTG
1 AACTTTCCAAAAATTACA-TTTTGACCTTG
16652603 AACTTTCCAAAAATTACCATTTT-ACCTTCG
1 AACTTTCCAAAAATTA-CATTTTGACCTT-G
* * * *
16652633 AAC-ATCTAAAAATTACCATTTT-ACCCTC
1 AACTTTCCAAAAATTA-CATTTTGACCTTG
** * * **
16652661 AGGTGTCCAAAAATTATCGTTTT-ACCCCCG
1 AACTTTCCAAAAATTA-CATTTTGA-CCTTG
* * *
16652691 AA-TGTCCAAAAATTACATTTTTAACCCTG
1 AACTTTCCAAAAATTACA-TTTTGACCTTG
* *
16652720 AAGTTTTCAAAAATTACCATTTT
1 AACTTTCCAAAAATTA-CATTTT
16652743 ACCCCTGGGT
Statistics
Matches: 180, Mismatches: 35, Indels: 23
0.76 0.15 0.10
Matches are distributed among these distances:
28 18 0.10
29 113 0.63
30 45 0.25
31 4 0.02
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.36
Consensus pattern (29 bp):
AACTTTCCAAAAATTACATTTTGACCTTG
Found at i:16652554 original size:58 final size:57
Alignment explanation
Indices: 16652465--16652745 Score: 201
Period size: 58 Copynumber: 4.8 Consensus size: 57
16652455 TAAACTCTCC
* * * *
16652465 AAAAATCATATTTTAACCCCTAAACTTTCCAAAAATTACATTTTGACCTTGAATTTTCA
1 AAAAATTACATTTTTACCCCTAAACTTTCCAAAAATTACATTTT-ACCTTGAA-TGTCA
* * ** *
16652524 AAAAATTACA-TTTTGCCCCTAAACTTTCCAAAAA-TACCTTTTTACCCCCGAATGTCC
1 AAAAATTACATTTTTACCCCTAAACTTTCCAAAAATTA-CATTTTA-CCTTGAATGTCA
* * * ** *
16652581 AAAAATTACATTTTTAACCTTGAACTTTCCAAAAATTACCATTTTACCTTCGAACATCT
1 AAAAATTACATTTTTACCCCTAAACTTTCCAAAAATTA-CATTTTACCTT-GAATGTCA
* ** * * ** *
16652640 AAAAATTACCA-TTTTA-CCCTCAGGTGTCCAAAAATTATCGTTTTACCCCCGAATGTCC
1 AAAAATTA-CATTTTTACCCCTAAACTTTCCAAAAATTA-CATTTTA-CCTTGAATGTCA
* * * *
16652698 AAAAATTACATTTTTAACCCTGAAGTTTTCAAAAATTACCATTTTACC
1 AAAAATTACATTTTTACCCCTAAACTTTCCAAAAATTA-CATTTTACC
16652746 CCTGGGTGTC
Statistics
Matches: 176, Mismatches: 37, Indels: 19
0.76 0.16 0.08
Matches are distributed among these distances:
57 18 0.10
58 96 0.55
59 60 0.34
60 2 0.01
ACGTcount: A:0.36, C:0.24, G:0.05, T:0.35
Consensus pattern (57 bp):
AAAAATTACATTTTTACCCCTAAACTTTCCAAAAATTACATTTTACCTTGAATGTCA
Found at i:16652668 original size:88 final size:85
Alignment explanation
Indices: 16652492--16652922 Score: 252
Period size: 88 Copynumber: 4.9 Consensus size: 85
16652482 CCCTAAACTT
* * * * * *
16652492 TCCAAAAATTA-CA-TTTTGACCTTGAATTTTCAAAAAATTACATTTTGCCCCTAAACTTTCCAA
1 TCCAAAAATTACCATTTTTAACCTTGAA-TTTCCAAAAATTACATTTTACCTC-GAAC-TTCTAA
* * *
16652555 AAA-TACCTTTTTACCCCCGAATG
63 AAATTACCATTTTACCCCAG-GTG
*
16652578 TCCAAAAATTA-CATTTTTAACCTTGAACTTTCCAAAAATTACCATTTTACCTTCGAACATCTAA
1 TCCAAAAATTACCATTTTTAACCTTGAA-TTTCCAAAAATTA-CATTTTACC-TCGAACTTCTAA
16652642 AAATTACCATTTTACCCTCAGGTG
63 AAATTACCATTTTACCC-CAGGTG
* * * ** * * *
16652666 TCCAAAAATTATC-GTTTTACCCCCGAATGTCCAAAAATTACATTTTTAACC-CTGAAGTTTTCA
1 TCCAAAAATTACCATTTTTAACCTTGAATTTCCAAAAATTACA-TTTT-ACCTC-GAACTTCT-A
*
16652729 AAAATTACCATTTTACCCCTGGGTG
62 AAAATTACCATTTTACCCC-AGGTG
*** ** * * * *
16652754 TCCAAAAATTACCA-TTTT-ACCCACAGACGTCTAAAAATTACATTTTTGAACTCGAGCTTTTCA
1 TCCAAAAATTACCATTTTTAACCTTGA-ATTTCCAAAAATTACA-TTTT-ACCTCGAACTTCT-A
* *
16652817 AAAATTATCATTTTACCCCCGAGTG
62 AAAATTACCATTTTACCCCAG-GTG
* * ** * * * *
16652842 TCCAAAAATTCCCA-TTTTACCCACGAATGTCCAAAAATTACCATTTTACCCCCGGA-TGTCCAA
1 TCCAAAAATTACCATTTTTAACCTTGAATTTCCAAAAATTA-CATTTTA-CCTCGAACT-TCTAA
*
16652905 AAATTACAATTTTACCCC
63 AAATTACCATTTTACCCC
16652923 CGGGCATCCA
Statistics
Matches: 279, Mismatches: 47, Indels: 37
0.77 0.13 0.10
Matches are distributed among these distances:
86 16 0.06
87 78 0.28
88 175 0.63
89 10 0.04
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.33
Consensus pattern (85 bp):
TCCAAAAATTACCATTTTTAACCTTGAATTTCCAAAAATTACATTTTACCTCGAACTTCTAAAAA
TTACCATTTTACCCCAGGTG
Found at i:16652761 original size:117 final size:116
Alignment explanation
Indices: 16652462--16652924 Score: 401
Period size: 117 Copynumber: 4.0 Consensus size: 116
16652452 CCCTAAACTC
* * * *
16652462 TCCAAAAA-T-CATATTTTAACCCCTAAACTTTCCAAAAATTA-CATTTTGA-CCTTGAATTTTC
1 TCCAAAAATTACAT-TTTTAA-CCCTGAAGTTTCCAAAAATTACCATTTT-ACCCCTGAA-TGTC
* * ** * *
16652523 AAAAAATTA-CATTTTGCCCCTAAACTTTCCAAAAA-TACCTTTTTACCCCCGAATG
62 CAAAAATTACCATTTTACCCC--AGGTGTCCAAAAATTACATTTTTACCCCCGAATG
* * * ** *
16652578 TCCAAAAATTACATTTTTAACCTTGAACTTTCCAAAAATTACCATTTTA-CCTTCGAACATCTAA
1 TCCAAAAATTACATTTTTAACCCTGAAGTTTCCAAAAATTACCATTTTACCCCT-GAATGTCCAA
*
16652642 AAATTACCATTTTACCCTCAGGTGTCCAAAAATTATC-GTTTTACCCCCGAATG
65 AAATTACCATTTTACCC-CAGGTGTCCAAAAATTA-CATTTTTACCCCCGAATG
* **
16652695 TCCAAAAATTACATTTTTAACCCTGAAGTTTTCAAAAATTACCATTTTACCCCTGGGTGTCCAAA
1 TCCAAAAATTACATTTTTAACCCTGAAGTTTCCAAAAATTACCATTTTACCCCTGAATGTCCAAA
** * * * * *
16652760 AATTACCATTTTACCCACAGACGTCTAAAAATTACATTTTTGA-ACTCGAGCTT
66 AATTACCATTTTACCC-CAGGTGTCCAAAAATTACATTTTT-ACCCCCGA-ATG
* * * * *
16652813 TTCAAAAATTATCA-TTTTACCCCCG-AGTGTCCAAAAATTCCCATTTTACCCAC-GAATGTCCA
1 TCCAAAAATTA-CATTTTTAACCCTGAAGTTTCCAAAAATTACCATTTTACCC-CTGAATGTCCA
* *
16652875 AAAATTACCATTTTACCCCCGGATGTCCAAAAATTACAATTTTACCCCCG
64 AAAATTACCATTTTACCCCAGG-TGTCCAAAAATTACATTTTTACCCCCG
16652925 GGCATCCAAA
Statistics
Matches: 288, Mismatches: 43, Indels: 31
0.80 0.12 0.09
Matches are distributed among these distances:
116 56 0.19
117 200 0.69
118 30 0.10
119 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.07, T:0.33
Consensus pattern (116 bp):
TCCAAAAATTACATTTTTAACCCTGAAGTTTCCAAAAATTACCATTTTACCCCTGAATGTCCAAA
AATTACCATTTTACCCCAGGTGTCCAAAAATTACATTTTTACCCCCGAATG
Found at i:16652935 original size:29 final size:29
Alignment explanation
Indices: 16652550--16652924 Score: 289
Period size: 29 Copynumber: 12.9 Consensus size: 29
16652540 CCCTAAACTT
* *
16652550 TCCAAAAA-TACCTTTTTACCCCCGAATG
1 TCCAAAAATTACCATTTTACCCCCGAGTG
* ** * *
16652578 TCCAAAAATTA-CATTTTTAACCTTGAACTT
1 TCCAAAAATTACCA-TTTTACCCCCG-AGTG
** ***
16652608 TCCAAAAATTACCATTTTACCTTCGAACA
1 TCCAAAAATTACCATTTTACCCCCGAGTG
* *
16652637 TCTAAAAATTACCATTTTACCCTC-AGGTG
1 TCCAAAAATTACCATTTTACCCCCGA-GTG
* * *
16652666 TCCAAAAATTATCGTTTTACCCCCGAATG
1 TCCAAAAATTACCATTTTACCCCCGAGTG
* * *
16652695 TCCAAAAATTA-CATTTTTAACCCTGAAGTT
1 TCCAAAAATTACCA-TTTTACCCCCG-AGTG
* * *
16652725 TTCAAAAATTACCATTTTACCCCTGGGTG
1 TCCAAAAATTACCATTTTACCCCCGAGTG
* *
16652754 TCCAAAAATTACCATTTTACCCAC-AGACG
1 TCCAAAAATTACCATTTTACCCCCGAG-TG
* * * *
16652783 TCTAAAAATTA-CATTTTTGA-ACTCGAGCTT
1 TCCAAAAATTACCA-TTTT-ACCCCCGAG-TG
* *
16652813 TTCAAAAATTATCATTTTACCCCCGAGTG
1 TCCAAAAATTACCATTTTACCCCCGAGTG
* * *
16652842 TCCAAAAATTCCCATTTTACCCACGAATG
1 TCCAAAAATTACCATTTTACCCCCGAGTG
16652871 TCCAAAAATTACCATTTTACCCCCG-GATG
1 TCCAAAAATTACCATTTTACCCCCGAG-TG
*
16652900 TCCAAAAATTACAATTTTACCCCCG
1 TCCAAAAATTACCATTTTACCCCCG
16652925 GGCATCCAAA
Statistics
Matches: 275, Mismatches: 56, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
28 14 0.05
29 190 0.69
30 65 0.24
31 6 0.02
ACGTcount: A:0.34, C:0.26, G:0.08, T:0.32
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCGAGTG
Found at i:16662146 original size:30 final size:30
Alignment explanation
Indices: 16662110--16662170 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
16662100 CATAGCTAAC
16662110 CAAATCACTTAGCAAATAGCAATCCATGAA
1 CAAATCACTTAGCAAATAGCAATCCATGAA
16662140 CAAATCACTTAGCAAATAGCAATCCATGAA
1 CAAATCACTTAGCAAATAGCAATCCATGAA
16662170 C
1 C
16662171 TACAGACCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.46, C:0.25, G:0.10, T:0.20
Consensus pattern (30 bp):
CAAATCACTTAGCAAATAGCAATCCATGAA
Found at i:16664099 original size:31 final size:31
Alignment explanation
Indices: 16664064--16664122 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
16664054 TTAGCATTTG
*
16664064 TATTTTTTAAAATTTGAAAATTTGGTCTCTA
1 TATTTTTTAAAATTTGAAAATTTAGTCTCTA
* * *
16664095 TATTTTTTGAATTTTGAAATTTTAGTCT
1 TATTTTTTAAAATTTGAAAATTTAGTCT
16664123 TAAAGTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (31 bp):
TATTTTTTAAAATTTGAAAATTTAGTCTCTA
Found at i:16669627 original size:18 final size:19
Alignment explanation
Indices: 16669588--16669633 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
16669578 TCAGTATTAA
*
16669588 TAATAATAATAAATGTTTT
1 TAATAATAATAAATGATTT
16669607 TAATAATAATAAAT-ATTT
1 TAATAATAATAAATGATTT
16669625 TAATAATAA
1 TAATAATAA
16669634 AGTAATAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 12 0.46
19 14 0.54
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TAATAATAATAAATGATTT
Found at i:16670981 original size:29 final size:29
Alignment explanation
Indices: 16670723--16671039 Score: 259
Period size: 29 Copynumber: 10.8 Consensus size: 29
16670713 TAGAAGTCTT
** *
16670723 TAAACTGTCCAAAAATTATATTTTGACCCC
1 TAAACT-TCCAAAAATTCCATTTTAACCCC
* * * *
16670753 TAAACTTCTCTAAAATTTCATTTTTGA-CCT
1 TAAACTTC-CAAAAATTCCA-TTTTAACCCC
* *
16670783 TGAAACTTCTAAAAATTACATTTTAA-CCC
1 T-AAACTTCCAAAAATTCCATTTTAACCCC
* *
16670812 TAAAACTCCCAAAAATTCCATTTTAACCCT
1 T-AAACTTCCAAAAATTCCATTTTAACCCC
*
16670842 TAAACTTTCAAAAATTCCATTTTAACCCC
1 TAAACTTCCAAAAATTCCATTTTAACCCC
* *
16670871 AAAACTTTCAAAAATTCCATTTTAA-CCC
1 TAAACTTCCAAAAATTCCATTTTAACCCC
* *
16670899 TCGAACTTCTAAAAATTCCATTTTAACCCC
1 T-AAACTTCCAAAAATTCCATTTTAACCCC
* *
16670929 TAAA-TATCCAAAAATTACATTTTTACCCC
1 TAAACT-TCCAAAAATTCCATTTTAACCCC
* * *
16670958 CAAACTTCCAAAAATTCCATTTTTGACCTC
1 TAAACTTCCAAAAATTCCA-TTTTAACCCC
* * * *
16670988 AAAACTTTCTAAAATTACC-TTTTTACCCC
1 TAAACTTCCAAAAATT-CCATTTTAACCCC
* *
16671017 TATA-TGTCCAAAAATTCCGTTTT
1 TAAACT-TCCAAAAATTCCATTTT
16671040 TGATCCTGAT
Statistics
Matches: 236, Mismatches: 39, Indels: 25
0.79 0.13 0.08
Matches are distributed among these distances:
28 7 0.03
29 160 0.68
30 54 0.23
31 15 0.06
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.36
Consensus pattern (29 bp):
TAAACTTCCAAAAATTCCATTTTAACCCC
Found at i:16671651 original size:115 final size:118
Alignment explanation
Indices: 16671436--16671727 Score: 343
Period size: 115 Copynumber: 2.5 Consensus size: 118
16671426 GAAAGTCCTT
* ** **
16671436 AAACTATCCAAAAATT--ATATTTTGACCCCTGAACTTCTCTAAAATTCCATTTTTGA-CCTTGA
1 AAACT-TCCAAAAATTCCAT-TTTTGACCTCAAAACTT-TCTAAAATTCCA-TTTTGACCCCCGA
*
16671498 AACTTCTAAAAATTACATTTTAACCCTAAAACTCCCAAAAATTCCA-TTTTACCCCTC
62 AACTTCTAAAAATTACATTTTAACCCTAAAACTCCCAAAAATTACATTTTTACCCC-C
* *
16671555 AAACTTTCAAAAATTCCA-TTTTGA-CTCAAAACTTTCAAAAATTCCATTTTGACCCCCG-AACT
1 AAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTTCTAAAATTCCATTTTGACCCCCGAAACT
*
16671617 TCTAAAAATTCCATTTTAACCCCTAAATA-T-CCAAAAATTACATTTTTACCCCC
66 TCTAAAAATTACATTTTAA-CCCTAAA-ACTCCCAAAAATTACATTTTTACCCCC
* *
16671670 AAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTTCTAAAATTACC-TTTTTACCCC
1 AAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTTCTAAAATT-CCATTTTGACCCC
16671728 TATATGTCCA
Statistics
Matches: 151, Mismatches: 13, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
115 57 0.38
116 37 0.25
117 34 0.23
118 17 0.11
119 5 0.03
120 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.03, T:0.34
Consensus pattern (118 bp):
AAACTTCCAAAAATTCCATTTTTGACCTCAAAACTTTCTAAAATTCCATTTTGACCCCCGAAACT
TCTAAAAATTACATTTTAACCCTAAAACTCCCAAAAATTACATTTTTACCCCC
Found at i:16671742 original size:29 final size:29
Alignment explanation
Indices: 16671435--16671751 Score: 243
Period size: 29 Copynumber: 10.8 Consensus size: 29
16671425 TGAAAGTCCT
** *
16671435 TAAACTATCCAAAAATTATATTTTGACCCC
1 TAAACT-TCCAAAAATTCCATTTTTACCCC
* * *
16671465 TGAACTTCTCTAAAATTCCATTTTTGA-CCT
1 TAAACTTC-CAAAAATTCCATTTTT-ACCCC
* * *
16671495 TGAAACTTCTAAAAATTACA-TTTTAACCC
1 T-AAACTTCCAAAAATTCCATTTTTACCCC
*
16671524 TAAAACTCCCAAAAATTCCA-TTTTACCCC
1 T-AAACTTCCAAAAATTCCATTTTTACCCC
* * *
16671553 TCAAACTTTCAAAAATTCCATTTTGA-CTC
1 T-AAACTTCCAAAAATTCCATTTTTACCCC
* * *
16671582 AAAACTTTCAAAAATTCCATTTTGACCCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
** * *
16671611 CGAACTTCTAAAAATTCCATTTTAACCCC
1 TAAACTTCCAAAAATTCCATTTTTACCCC
*
16671640 TAAA-TATCCAAAAATTACATTTTTACCCC
1 TAAACT-TCCAAAAATTCCATTTTTACCCC
* *
16671669 CAAACTTCCAAAAATTCCATTTTTGACCTC
1 TAAACTTCCAAAAATTCCATTTTT-ACCCC
* * *
16671699 GAAACTTTCTAAAATTACC-TTTTTACCCC
1 TAAACTTCCAAAAATT-CCATTTTTACCCC
* *
16671728 TATA-TGTCCAAAAATTCCGTTTTT
1 TAAACT-TCCAAAAATTCCATTTTT
16671752 GATCCTGATT
Statistics
Matches: 231, Mismatches: 44, Indels: 25
0.77 0.15 0.08
Matches are distributed among these distances:
28 29 0.13
29 138 0.60
30 55 0.24
31 9 0.04
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (29 bp):
TAAACTTCCAAAAATTCCATTTTTACCCC
Found at i:16671782 original size:59 final size:58
Alignment explanation
Indices: 16671535--16671785 Score: 210
Period size: 59 Copynumber: 4.3 Consensus size: 58
16671525 AAAACTCCCA
* * * *
16671535 AAAATTCCATTTTACCCCTCAAACTTTCAAAAATTCCA-TTTTGA-CTCAAAACTTTCA
1 AAAATTACATTTTACCCC-CAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTTCT
* * * * * * * *
16671592 AAAATTCCATTTTGACCCCCGAACTTCTAAAAATTCCA-TTTTAACCCCTAAA-TATCCA
1 AAAATTACATTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGAAACT-TTCT
16671650 AAAATTACATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTTCT
1 AAAATTACA-TTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTTCT
* * * * **
16671709 AAAATTACCTTTTTACCCCTATA-TGTCCAAAAATTCCGTTTTTGATCCT-G-ATTTTTCTT
1 AAAATTA-CATTTTACCCCCAAACT-TCCAAAAATTCCATTTTTGA-CCTCGAAACTTTC-T
16671768 AAAATTATCATTTTACCC
1 AAAATTA-CATTTTACCC
16671786 TTGGATGTCT
Statistics
Matches: 161, Mismatches: 23, Indels: 18
0.80 0.11 0.09
Matches are distributed among these distances:
57 35 0.22
58 49 0.30
59 72 0.45
60 5 0.03
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (58 bp):
AAAATTACATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTTCT
Found at i:16671794 original size:59 final size:59
Alignment explanation
Indices: 16671535--16671844 Score: 157
Period size: 59 Copynumber: 5.3 Consensus size: 59
16671525 AAAACTCCCA
* * * *
16671535 AAAATT-CCATTTTACCCCTCAAACT-TTCAAAAATTCCA-TTTTGA-CTCAAAACTTTCA
1 AAAATTACCATTTTACCCCT-AGA-TGTCCAAAAATTCCATTTTTGACCTCGAAACTTTCT
* * * * * * *
16671592 AAAATT-CCATTTTGACCCC-CGAACT-TCTAAAAATTCCA-TTTTAACCCCTAAA-TATCCA
1 AAAATTACCATTTT-ACCCCTAG-A-TGTCCAAAAATTCCATTTTTGACCTCGAAACT-TTCT
* *
16671650 AAAATTA-CATTTTTACCCCCAAACT-TCCAAAAATTCCATTTTTGACCTCGAAACTTTCT
1 AAAATTACCA-TTTTACCCCTAGA-TGTCCAAAAATTCCATTTTTGACCTCGAAACTTTCT
* * * **
16671709 AAAATTACCTTTTTACCCCTATATGTCCAAAAATTCCGTTTTTGATCCT-G-ATTTTTCTT
1 AAAATTACCATTTTACCCCTAGATGTCCAAAAATTCCATTTTTGA-CCTCGAAACTTTC-T
* * * * * * * *
16671768 AAAATTATCATTTTACCCTTGGATGT-CTAAAATGT-CATTTTTTACC-CTAAATTTTTCC
1 AAAATTACCATTTTACCCCTAGATGTCCAAAAAT-TCCATTTTTGACCTCGAAA-CTTTCT
*
16671826 AAAATTACCATTTTCCCCC
1 AAAATTACCATTTTACCCC
16671845 GAGAGTTTAA
Statistics
Matches: 200, Mismatches: 36, Indels: 33
0.74 0.13 0.12
Matches are distributed among these distances:
57 35 0.17
58 77 0.38
59 83 0.41
60 5 0.03
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.38
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAGATGTCCAAAAATTCCATTTTTGACCTCGAAACTTTCT
Found at i:16684095 original size:14 final size:13
Alignment explanation
Indices: 16684068--16684102 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
16684058 GATGTGGCGA
16684068 TGACGTGG-ATGC
1 TGACGTGGTATGC
16684080 TGACGTGGTAATGC
1 TGACGTGGT-ATGC
16684094 TGACGTGGT
1 TGACGTGGT
16684103 GGTGGCGGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.38
14 13 0.62
ACGTcount: A:0.17, C:0.14, G:0.40, T:0.29
Consensus pattern (13 bp):
TGACGTGGTATGC
Found at i:16685449 original size:58 final size:58
Alignment explanation
Indices: 16685359--16685522 Score: 165
Period size: 57 Copynumber: 2.8 Consensus size: 58
16685349 AGACATCCGC
* * * ** * * *
16685359 GGGTAAAAAGGTAATTTTTGAAAGTTTCGAGGTCAAAAATAGATTTTTGG-AAGTTTG-
1 GGGTAAAATGATAATTTTGGAAAAATT-GAGGTCAAAAATAAAATTTTGGAAAGTTCGA
16685416 GGAGTAAAATGATAAATTTTGGAAAAATTGAGGTC-AAAATAAAATTTTGGAAAGTTCGA
1 GG-GTAAAATGAT-AATTTTGGAAAAATTGAGGTCAAAAATAAAATTTTGGAAAGTTCGA
* *
16685475 GGGTAAAATGGTAATTTTGGAAAAATTG-GCGTCAAAAATGGAAATTTT
1 GGGTAAAATGATAATTTTGGAAAAATTGAG-GTCAAAAAT-AAAATTTT
16685523 TAAAGTTTAA
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
56 1 0.01
57 34 0.38
58 34 0.38
59 21 0.23
ACGTcount: A:0.40, C:0.04, G:0.24, T:0.32
Consensus pattern (58 bp):
GGGTAAAATGATAATTTTGGAAAAATTGAGGTCAAAAATAAAATTTTGGAAAGTTCGA
Found at i:16685496 original size:29 final size:29
Alignment explanation
Indices: 16685359--16685497 Score: 85
Period size: 29 Copynumber: 4.8 Consensus size: 29
16685349 AGACATCCGC
* *
16685359 GGGTAAAAAGGTAATTTTTGAAAGTTTCGA
1 GGGTAAAATGGTAATTTTGGAAAG-TTCGA
* * *
16685389 -GGTCAAAAATAG-ATTTTTGG-AAGTTTG-
1 GGGT--AAAATGGTAATTTTGGAAAGTTCGA
* *
16685416 GGAGTAAAATGATAAATTTTGGAAAAATT-GA
1 GG-GTAAAATGGT-AATTTTGG-AAAGTTCGA
**
16685447 -GGTCAAAAT-AAAATTTTGGAAAGTTCGA
1 GGGT-AAAATGGTAATTTTGGAAAGTTCGA
16685475 GGGTAAAATGGTAATTTTGGAAA
1 GGGTAAAATGGTAATTTTGGAAA
16685498 AATTGGCGTC
Statistics
Matches: 83, Mismatches: 13, Indels: 27
0.67 0.11 0.22
Matches are distributed among these distances:
27 10 0.12
28 19 0.23
29 32 0.39
30 13 0.16
31 9 0.11
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (29 bp):
GGGTAAAATGGTAATTTTGGAAAGTTCGA
Found at i:16685511 original size:29 final size:29
Alignment explanation
Indices: 16685421--16685522 Score: 95
Period size: 30 Copynumber: 3.5 Consensus size: 29
16685411 GTTTGGGAGT
16685421 AAAATGATAAATTTTGGAAAAATTGAGGTC
1 AAAATGA-AAATTTTGGAAAAATTGAGGTC
*
16685451 AAAAT-AAAATTTTGG-AAAGTTCGAGGGT-
1 AAAATGAAAATTTTGGAAAAATT-GA-GGTC
**
16685479 AAAATGGTAATTTTGGAAAAATTG-GCGTC
1 AAAATGAAAATTTTGGAAAAATTGAG-GTC
*
16685508 AAAAATGGAAATTTT
1 -AAAATGAAAATTTT
16685523 TAAAGTTTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
27 6 0.10
28 18 0.30
29 13 0.22
30 23 0.38
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.30
Consensus pattern (29 bp):
AAAATGAAAATTTTGGAAAAATTGAGGTC
Found at i:16685528 original size:58 final size:58
Alignment explanation
Indices: 16685359--16685612 Score: 161
Period size: 57 Copynumber: 4.4 Consensus size: 58
16685349 AGACATCCGC
* * ** * * **
16685359 GGGTAAAAAGGTAATTTTTGAAAGTTTCGAGGTCAAAAATAG-ATTTTTGG-AAGTT-TG
1 GGGTAAAATGGTAATTTTGGAAAAATT-G-GGTCAAAAATGGAAATTTTGGAAAGTTCAA
* * *
16685416 GGAGTAAAATGATAAATTTTGGAAAAATTGAGGTC-AAAAT-AAAATTTTGGAAAGTTCGA
1 GG-GTAAAATGGT-AATTTTGGAAAAATTG-GGTCAAAAATGGAAATTTTGGAAAGTTCAA
* *
16685475 GGGTAAAATGGTAATTTTGGAAAAATTGGCGTCAAAAATGGAAATTTT-TAAAGTTTAA
1 GGGTAAAATGGTAATTTTGGAAAAATTGG-GTCAAAAATGGAAATTTTGGAAAGTTCAA
*** * * *
16685533 GTCAAAAAT-GTAATTTTTGGATAAATTAGGGT-AAAAATGGAAATTTAGG-AAGTTTAA
1 GGGTAAAATGGTAA-TTTTGGAAAAATT-GGGTCAAAAATGGAAATTTTGGAAAGTTCAA
*
16685590 -GATAAAAAT-GTAATTTTTGGAAA
1 GGGT-AAAATGGTAA-TTTTGGAAA
16685613 GTTTAGGGAC
Statistics
Matches: 161, Mismatches: 24, Indels: 24
0.77 0.11 0.11
Matches are distributed among these distances:
56 1 0.01
57 77 0.48
58 60 0.37
59 23 0.14
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (58 bp):
GGGTAAAATGGTAATTTTGGAAAAATTGGGTCAAAAATGGAAATTTTGGAAAGTTCAA
Found at i:16685546 original size:57 final size:57
Alignment explanation
Indices: 16685479--16685612 Score: 175
Period size: 57 Copynumber: 2.3 Consensus size: 57
16685469 GTTCGAGGGT
**
16685479 AAAATGGTAA-TTTTGGAAAAATT-GGCGTCAAAAATGGAAATTTTTAAAGTTTAAG-TCA
1 AAAAT-GTAATTTTTGGAAAAATTAGG-GT-AAAAATGGAAATTTAGAAAGTTTAAGAT-A
* *
16685537 AAAATGTAATTTTTGGATAAATTAGGGTAAAAATGGAAATTTAGGAAGTTTAAGATA
1 AAAATGTAATTTTTGGAAAAATTAGGGTAAAAATGGAAATTTAGAAAGTTTAAGATA
16685594 AAAATGTAATTTTTGGAAA
1 AAAATGTAATTTTTGGAAA
16685613 GTTTAGGGAC
Statistics
Matches: 68, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
57 46 0.68
58 20 0.29
59 2 0.03
ACGTcount: A:0.45, C:0.02, G:0.19, T:0.34
Consensus pattern (57 bp):
AAAATGTAATTTTTGGAAAAATTAGGGTAAAAATGGAAATTTAGAAAGTTTAAGATA
Found at i:16685615 original size:29 final size:28
Alignment explanation
Indices: 16685508--16685617 Score: 93
Period size: 29 Copynumber: 3.9 Consensus size: 28
16685498 AATTGGCGTC
*
16685508 AAAAATGGAAATTTTT--AAAGTTTAAGT
1 AAAAAT-GTAATTTTTGGAAAGTTTAAGT
* *
16685535 CAAAAATGTAATTTTTGGATAA-ATTAGGGT
1 -AAAAATGTAATTTTTGGA-AAGTTTA-AGT
* * *
16685565 AAAAATGGAAATTTAGG-AAGTTTAAGAT
1 AAAAATGTAATTTTTGGAAAGTTTAAG-T
16685593 AAAAATGTAATTTTTGGAAAGTTTA
1 AAAAATGTAATTTTTGGAAAGTTTA
16685618 GGGACCTTCA
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
27 11 0.17
28 24 0.38
29 25 0.39
30 4 0.06
ACGTcount: A:0.45, C:0.01, G:0.18, T:0.35
Consensus pattern (28 bp):
AAAAATGTAATTTTTGGAAAGTTTAAGT
Found at i:16687332 original size:35 final size:35
Alignment explanation
Indices: 16687284--16687364 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
16687274 AATTTTTTTT
* * *
16687284 AATTT-AAAATAAATTTAAACTCAAAATGAATTTA
1 AATTTAAAAATAAATTCAAACTCAAAATAAATTAA
* *
16687318 AATTTAAAAATAAATTCAAATTTAAAATAAATTAA
1 AATTTAAAAATAAATTCAAACTCAAAATAAATTAA
16687353 AATTTTAAAAAT
1 AA-TTTAAAAAT
16687365 TAAAAGTTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
34 5 0.12
35 26 0.65
36 9 0.22
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.36
Consensus pattern (35 bp):
AATTTAAAAATAAATTCAAACTCAAAATAAATTAA
Found at i:16687333 original size:18 final size:17
Alignment explanation
Indices: 16687284--16687362 Score: 95
Period size: 17 Copynumber: 4.5 Consensus size: 17
16687274 AATTTTTTTT
16687284 AATTTAAAATAAATTTA
1 AATTTAAAATAAATTTA
* * *
16687301 AACTCAAAATGAATTTA
1 AATTTAAAATAAATTTA
*
16687318 AATTTAAAAATAAATTCA
1 AATTT-AAAATAAATTTA
*
16687336 AATTTAAAATAAATTAA
1 AATTTAAAATAAATTTA
16687353 AATTTTAAAA
1 AA-TTTAAAA
16687363 ATTAAAAGTT
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
17 30 0.58
18 22 0.42
ACGTcount: A:0.59, C:0.04, G:0.01, T:0.35
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:16688160 original size:194 final size:194
Alignment explanation
Indices: 16687680--16688496 Score: 1014
Period size: 194 Copynumber: 4.1 Consensus size: 194
16687670 TGGTTTCGTC
* * * **
16687680 TACTTCTCAGTATCTTATCAGGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTGTACCTC
1 TACTTCTCTGTATCTCATCAGGAAGATAACCGCCCCGCTTGTTTCAATCCGCTTCTCTGTACCTC
* * * * *
16687745 ATCAGGAAGACGAATTTGGTCTACTTCTTAGTATTTCATTAGAAAGCTAA-CTATTTTATTGCTT
66 ATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAG-AAGCTAACCT-TTTTATTGCTT
* * * * * ** *
16687809 TGACCTACTTCTCAGTATCTCATCAGAAAGCTGGGATTCGAAGATTTGATCACATCGAGCCCTAA
129 CGCCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTG-T----TC-TGCATTGA
16687874 GTTGGTA
188 GTTGGTA
* * * *
16687881 TACTTCTCTGTATCTCATCAAGAAGATAACCGCCCAGTTTGTTTCAATCCACTTCTCTGTACCTC
1 TACTTCTCTGTATCTCATCAGGAAGATAACCGCCCCGCTTGTTTCAATCCGCTTCTCTGTACCTC
*
16687946 ATCA-AGAAGACGAATTTGGTCCACTTCTCAGTGTCTCATCATGAAGCTAACCTTTTTATTGCTT
66 ATCAGA-AAGACGAATTTGGTCCACTTCTCAGTATCTCATCA-GAAGCTAACCTTTTTATTGCTT
*
16688010 CGCCCTTCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGTTC-GCATTGAGTTGGT
129 CGCCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGTTCTGCATTGAGTTGGT
16688074 A
194 A
* * * *
16688075 TACTTCTCTGTATCTCATCAGAAAGATAACCGCCCCGTTTGTTTTAATCCGCCTCTCTGTACCTC
1 TACTTCTCTGTATCTCATCAGGAAGATAACCGCCCCGCTTGTTTCAATCCGCTTCTCTGTACCTC
* * * *
16688140 ATCAGAAAGATGAATTTGGTCCACTTCTCAATGTCTCAGCAAGAAGCTAACCTTTTTATTGCTTC
66 ATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATC-AGAAGCTAACCTTTTTATTGCTTC
* * * *
16688205 GCCCTGCTTCTCAGTATCTCATCAAGAAGTTGGGGTTCGAAGATTTGCTC-GCATTGAGTTGGTA
130 GCCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGTTCTGCATTGAGTTGGTA
* * * * *
16688269 TACTTCTCTGTATCTCATCAGGAATATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGTACCTC
1 TACTTCTCTGTATCTCATCAGGAAGATAACCGCCCCGCTTGTTTCAATCCGCTTCTCTGTACCTC
*
16688334 ATCAGAAAGACGAATTTGGTCCACTTTTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTC
66 ATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCA-GAAGCTAACCTTTTTATTGCTTC
* * *
16688399 GCCCTGCTTCTCAGTATCTCATCAGGAAGCTTGTG-TTCGAAGATTTACTTACTTTGAACCTTGA
130 GCCCTGCTTCTCAGTATCTCATCAGGAAGC-TGGGATTCGAAGATTT-GTT-C--TG--CATTGA
16688463 GTTGGTA
188 GTTGGTA
*
16688470 TACTTCTCTGTATCTTATCAGGAAGAT
1 TACTTCTCTGTATCTCATCAGGAAGAT
16688497 GACTGCCTCA
Statistics
Matches: 544, Mismatches: 58, Indels: 28
0.86 0.09 0.04
Matches are distributed among these distances:
193 1 0.00
194 340 0.62
195 6 0.01
196 3 0.01
199 1 0.00
200 1 0.00
201 189 0.35
202 3 0.01
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.35
Consensus pattern (194 bp):
TACTTCTCTGTATCTCATCAGGAAGATAACCGCCCCGCTTGTTTCAATCCGCTTCTCTGTACCTC
ATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGAAGCTAACCTTTTTATTGCTTCG
CCCTGCTTCTCAGTATCTCATCAGGAAGCTGGGATTCGAAGATTTGTTCTGCATTGAGTTGGTA
Found at i:16700655 original size:414 final size:412
Alignment explanation
Indices: 16699653--16700639 Score: 1284
Period size: 412 Copynumber: 2.4 Consensus size: 412
16699643 TAAGAACTGA
* * * * * * * * * * *
16699653 AAGTCGTGTCCAACACGTTAGGGCACTATGTTCTCAGATTTTCAAAATTGAAGGACGTTTTGAAA
1 AAGTCATGACCAACACATTAGGGCACGACGTTCTCGGAATCTCAAAATTAAAAGACGTATTGAAA
* * ** * * * *
16699718 GATTTTTAAGAGGATATACAATTGCATGAAGTACGAAAAATCACACCCCGCACGTTAGGGCACGA
66 AACTTGGAAAAGGATATCCAATTGCATGAATTACAAAAAATCACACCCCGCACGTTAGGGCACGA
* * * *
16699783 TTTTTCGGAGTTTCCACACGAAAAGGACATTGCCTCATTTTTAAAACAATTTTGAAAACAAATAT
131 TTTTTCGAAGTTTCCACACGAAAAGGACATTGCCTCAGTTTTAAAATAATTTTCAAAACAAATAT
* * *
16699848 GAAATTTCGAAGTTTCCACACGAAAATCACACCTCGCACATTAGGTCATGGTTTTCGAGGTTTTC
196 GAAATTTCGAAGTTCCCACACGAAAATCACACCCCGCACATTAGGGCATGGTTTTCGAGGTTTTC
* *
16699913 ACATGGAAAGACATTGCGTCGTTTTACTTTAAATTTATATATATTTGAAAACTTGAAATTTCGTA
261 ACACGAAAAGACATTGCGTCGTTTTACTTTAAATTTATATATATTTGAAAACTTGAAATTTCGTA
* *
16699978 TTGAGTTTTAAAATACGATCTTCGGACACATTACTTAAAGGGCCTGAAGATAAAATGGCAGTTTA
326 TTGAGTTTTAAAATACGATCCTCGAACACATTACTTAAAGGGCCTGAAGATAAAATGGCAGTTTA
16700043 CTTCGATTTTCGAGAAAAATTG
391 CTTCGATTTTCGAGAAAAATTG
* * * * * * * * *
16700065 AAGTCATGACCAACACGTTAGGGTACTATGTTCTCGGATTTTCAAAATTGAAGGACGTTTTGAAA
1 AAGTCATGACCAACACATTAGGGCACGACGTTCTCGGAATCTCAAAATTAAAAGACGTATTGAAA
* * ** * *
16700130 GATTTTTAAGAGGATATCCAATTGCATGAATTACGAAAAATCACACCCCGCACGTTAGGGCACGA
66 AACTTGGAAAAGGATATCCAATTGCATGAATTACAAAAAATCACACCCCGCACGTTAGGGCACGA
*
16700195 TTTTTCGAAGTTTCTACACGAAAAGGACATTGCCTCAGTTTTAAAATAATTTTCAAAACAAATAT
131 TTTTTCGAAGTTTCCACACGAAAAGGACATTGCCTCAGTTTTAAAATAATTTTCAAAACAAATAT
16700260 GAAATTTCGAAGTTCCCACACGAAAATCACACCCCGCACATTAGGGCATGGTTTTCGAGGTTTTC
196 GAAATTTCGAAGTTCCCACACGAAAATCACACCCCGCACATTAGGGCATGGTTTTCGAGGTTTTC
* * *
16700325 GCACGAAAAGACATTGCGTCGTTTTGCTTTTAATTTATATATATATTTGAAAACTTGAAATTTCG
261 ACACGAAAAGACATTGCGTCGTTTTAC-TTTAAATT-TATATATATTTGAAAACTTGAAATTTCG
* *
16700390 TATTGAGTTTTAAAATACGATCCTCGAACACATTACTTAAAGGGTCTGAAGATAGAATGGCAGTT
324 TATTGAGTTTTAAAATACGATCCTCGAACACATTACTTAAAGGGCCTGAAGATAAAATGGCAGTT
*
16700455 TACTTCGATTTGT-GAGAAGAATTG
389 TACTTCGATTT-TCGAGAAAAATTG
* * * *
16700479 AAGTCGTGACCAACACATTAGGGCACGACGTTCTTGGAATCTCGAAGTTAAAAGA-G-ATT-AAA
1 AAGTCATGACCAACACATTAGGGCACGACGTTCTCGGAATCTCAAAATTAAAAGACGTATTGAAA
* * * *
16700541 AACTTGGAAAATGATATTCGATT-CGAGTGAGTTATACAAAAAATCACA-CCCGACACGTTAGGG
66 AACTTGGAAAAGGATATCCAATTGC-A-TGA-AT-TACAAAAAATCACACCCCG-CACGTTAGGG
* ** *
16700604 CATGATTTCCCGAAGTTTCCACACGAAAAGAACATT
126 CACGATTTTTCGAAGTTTCCACACGAAAAGGACATT
16700640 ATCTTGATTT
Statistics
Matches: 515, Mismatches: 52, Indels: 14
0.89 0.09 0.02
Matches are distributed among these distances:
410 1 0.00
411 19 0.04
412 274 0.53
413 13 0.03
414 207 0.40
415 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.30
Consensus pattern (412 bp):
AAGTCATGACCAACACATTAGGGCACGACGTTCTCGGAATCTCAAAATTAAAAGACGTATTGAAA
AACTTGGAAAAGGATATCCAATTGCATGAATTACAAAAAATCACACCCCGCACGTTAGGGCACGA
TTTTTCGAAGTTTCCACACGAAAAGGACATTGCCTCAGTTTTAAAATAATTTTCAAAACAAATAT
GAAATTTCGAAGTTCCCACACGAAAATCACACCCCGCACATTAGGGCATGGTTTTCGAGGTTTTC
ACACGAAAAGACATTGCGTCGTTTTACTTTAAATTTATATATATTTGAAAACTTGAAATTTCGTA
TTGAGTTTTAAAATACGATCCTCGAACACATTACTTAAAGGGCCTGAAGATAAAATGGCAGTTTA
CTTCGATTTTCGAGAAAAATTG
Found at i:16700942 original size:59 final size:57
Alignment explanation
Indices: 16700843--16701066 Score: 184
Period size: 59 Copynumber: 3.8 Consensus size: 57
16700833 TCGGAGTTGG
* * * * * *
16700843 AAAATGTGATTTTTGGATA-CTCGAGGGCAAAACGGTAATTTTTGGAAGGTTCGGGATCA
1 AAAATG-GATTTTTGGA-AGTTCAAGGGTAAAATGGTAATTTTTGGAA-GTTAGAGATCA
* * ** *
16700902 AAAATGGAGTTTTTAGACA-TTCAAGGGTAAAATGGTAATTTTTAGAAGTTTTAGATTCG
1 AAAATGGA-TTTTTGGA-AGTTCAAGGGTAAAATGGTAATTTTTGGAAGTTAGAGA-TCA
* * **
16700961 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGTAAATTTTGGAAAAATAGAGATCA
1 AAAATGG-ATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGG-AAGTTAGAGATCA
* *
16701020 AAAATGGAATTTTGGAAAGTTCGAA-GGTAAAATGGTAATTTTGGGAA
1 AAAATGGATTTTTGG-AAGTTC-AAGGGTAAAATGGTAATTTTTGGAA
16701067 AATCGGAGTA
Statistics
Matches: 134, Mismatches: 24, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
58 17 0.13
59 109 0.81
60 8 0.06
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.32
Consensus pattern (57 bp):
AAAATGGATTTTTGGAAGTTCAAGGGTAAAATGGTAATTTTTGGAAGTTAGAGATCA
Found at i:16701002 original size:30 final size:29
Alignment explanation
Indices: 16700863--16701066 Score: 107
Period size: 29 Copynumber: 6.9 Consensus size: 29
16700853 TTTTGGATAC
* *
16700863 TCGAGGGCAAAACGGTAATTTTTGGAAGGT
1 TCGAGGGTAAAATGGTAATTTTTGGAA-GT
* * *
16700893 TCG-GGATCAAAAATGG-AGTTTTTAGACA-T
1 TCGAGGGT--AAAATGGTAATTTTTGGA-AGT
* *
16700922 TCAAGGGTAAAATGGTAATTTTTAGAAGT
1 TCGAGGGTAAAATGGTAATTTTTGGAAGT
** **
16700951 TTTAGATTCGAAAATGG-AATTTTTGGAAGT
1 TCGAGGGT--AAAATGGTAATTTTTGGAAGT
* **
16700981 TCGAGGGTAAAATGGTAAATTTTGGAAAAA
1 TCGAGGGTAAAATGGTAATTTTTGG-AAGT
* *
16701011 TAGA-GATCAAAAATGG-AA-TTTTGGAAAGT
1 TCGAGGGT--AAAATGGTAATTTTTGG-AAGT
* *
16701040 TCGAAGGTAAAATGGTAATTTTGGGAA
1 TCGAGGGTAAAATGGTAATTTTTGGAA
16701067 AATCGGAGTA
Statistics
Matches: 132, Mismatches: 27, Indels: 31
0.69 0.14 0.16
Matches are distributed among these distances:
28 22 0.17
29 45 0.34
30 44 0.33
31 21 0.16
ACGTcount: A:0.37, C:0.05, G:0.26, T:0.31
Consensus pattern (29 bp):
TCGAGGGTAAAATGGTAATTTTTGGAAGT
Found at i:16701283 original size:29 final size:29
Alignment explanation
Indices: 16700961--16701297 Score: 175
Period size: 29 Copynumber: 11.6 Consensus size: 29
16700951 TTTAGATTCG
* *
16700961 AAAATGGAATTTTTGG-AAGTTCGAGGGT-
1 AAAATAGAA-TTTTGGAAAATTCGAGGGTA
* * * *
16700989 AAAATGGTAAATTTTGGAAAAATAGA-GATCA
1 AAAATAG--AATTTTGGAAAATTCGAGGGT-A
* * *
16701020 AAAATGGAATTTTGGAAAGTTCGAAGGT-
1 AAAATAGAATTTTGGAAAATTCGAGGGTA
* *
16701048 AAAATGGTAATTTTGGGAAAA-TCG-GAGTA
1 AAAATAG-AATTTT-GGAAAATTCGAGGGTA
16701077 AAAAT-GAAATTTTGGAAAATTC-AGGGGTA
1 AAAATAG-AATTTTGGAAAATTCGA-GGGTA
* ** * *
16701106 AAAATGTGCTTTTTGGAAAAATC-AAGGTCA
1 AAAAT-AGAATTTTGGAAAATTCGAGGGT-A
*
16701136 AAAATAGAATTTTGGAAAGTTCG-GGGTA
1 AAAATAGAATTTTGGAAAATTCGAGGGTA
*
16701164 AAAACGTA-ATTTTTGGAAAAATT--AGGGTCA
1 AAAA--TAGAATTTTGG-AAAATTCGAGGGT-A
* *
16701194 AAAATGGAATTTT-GAAAAGTTCGAGCGTA
1 AAAATAGAATTTTGGAAAA-TTCGAGGGTA
* *
16701223 AAAATATAATTTTTGGAAAAATT-TAGGG-A
1 AAAATAGAA-TTTTGG-AAAATTCGAGGGTA
* *
16701252 AAAATAGAATTTTGGGAAGTTCGAGGGTA
1 AAAATAGAATTTTGGAAAATTCGAGGGTA
*
16701281 AAAATATAATATTTGGA
1 AAAATAGAAT-TTTGGA
16701298 CAGTTTAGGG
Statistics
Matches: 240, Mismatches: 38, Indels: 60
0.71 0.11 0.18
Matches are distributed among these distances:
27 14 0.06
28 44 0.18
29 106 0.44
30 61 0.25
31 11 0.05
32 4 0.02
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.29
Consensus pattern (29 bp):
AAAATAGAATTTTGGAAAATTCGAGGGTA
Found at i:16701284 original size:58 final size:58
Alignment explanation
Indices: 16700961--16701297 Score: 305
Period size: 58 Copynumber: 5.8 Consensus size: 58
16700951 TTTAGATTCG
* ** **
16700961 AAAATGGAATTTTTGG-AAGTTCGAGGGT-AAAATGGTAAATTTTGGAAAAATAGAGATCA
1 AAAATGGAA-TTTTGGAAAGTTCGAGGGTAAAAAT-GTAATTTTTGGAAAAATTTAG-GGA
* * *
16701020 AAAATGGAATTTTGGAAAGTTCGAAGGT-AAAATGGTAA-TTTTGGGAAAA--TCGGAGTA
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAAAT-GTAATTTTTGGAAAAATTTAGG-G-A
* * ** ** *
16701077 AAAATGAAATTTTGGAAAATTC-AGGGGTAAAAATGTGCTTTTTGGAAAAATCAAGGTCA
1 AAAATGGAATTTTGGAAAGTTCGA-GGGTAAAAATGTAATTTTTGGAAAAATTTAGG-GA
* *
16701136 AAAATAGAATTTTGGAAAGTTCG-GGGTAAAAACGTAATTTTTGGAAAAA-TTAGGGTCA
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAAATTTAGGG--A
* * *
16701194 AAAATGGAATTTTGAAAAGTTCGAGCGTAAAAATATAATTTTTGGAAAAATTTAGGGA
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAAATTTAGGGA
* * * *
16701252 AAAATAGAATTTTGGGAAGTTCGAGGGTAAAAATATAATATTTGGA
1 AAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGA
16701298 CAGTTTAGGG
Statistics
Matches: 230, Mismatches: 35, Indels: 27
0.79 0.12 0.09
Matches are distributed among these distances:
56 2 0.01
57 29 0.13
58 118 0.51
59 73 0.32
60 8 0.03
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.29
Consensus pattern (58 bp):
AAAATGGAATTTTGGAAAGTTCGAGGGTAAAAATGTAATTTTTGGAAAAATTTAGGGA
Found at i:16703220 original size:17 final size:17
Alignment explanation
Indices: 16703178--16703235 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
16703168 TATTTTTTTT
*
16703178 AATTTAAAGTAAATTTA
1 AATTTAAAATAAATTTA
* * *
16703195 AACTCAAAATGAATTTA
1 AATTTAAAATAAATTTA
*
16703212 AATTTAAAAATAAATTCA
1 AATTT-AAAATAAATTTA
16703230 AATTTA
1 AATTTA
16703236 TTATAAATTA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
17 17 0.53
18 15 0.47
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.36
Consensus pattern (17 bp):
AATTTAAAATAAATTTA
Found at i:16703227 original size:18 final size:18
Alignment explanation
Indices: 16703178--16703235 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
16703168 TATTTTTTTT
*
16703178 AATTT-AAAGTAAATTTA
1 AATTTAAAAATAAATTTA
* * *
16703195 AA-CTCAAAATGAATTTA
1 AATTTAAAAATAAATTTA
*
16703212 AATTTAAAAATAAATTCA
1 AATTTAAAAATAAATTTA
16703230 AATTTA
1 AATTTA
16703236 TTATAAATTA
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
16 1 0.03
17 14 0.44
18 17 0.53
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.36
Consensus pattern (18 bp):
AATTTAAAAATAAATTTA
Found at i:16707541 original size:101 final size:101
Alignment explanation
Indices: 16707360--16707562 Score: 271
Period size: 101 Copynumber: 2.0 Consensus size: 101
16707350 TTTATACGGT
* * * * * * *
16707360 GTGCAGCATTATCTGTACTGCAGGGGCCTCGACCCTTGGCCTTAAACCCTACACAGATCCTCTTA
1 GTGCAGCATGATCCGTACTGCAGGAGCCTCAACCCTCGGCCTTAAACCCTACACAGATCATATTA
* * * *
16707425 TTTTGTCACTGTATTTTATTTATTTAACTAGGATTC
66 TTTTATCACTATATTTTATTTATTTAACAAGAATTC
* * *
16707461 GTGCAGCATGGTCCGTACTGCTGGAGCCTCAACCCTCGGCCTTAAACCCTACACATATCATATTA
1 GTGCAGCATGATCCGTACTGCAGGAGCCTCAACCCTCGGCCTTAAACCCTACACAGATCATATTA
*
16707526 TTTTATCATTATATTTTATTTATTTAACAAGAATTC
66 TTTTATCACTATATTTTATTTATTTAACAAGAATTC
16707562 G
1 G
16707563 AATCACAAAA
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
101 87 1.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (101 bp):
GTGCAGCATGATCCGTACTGCAGGAGCCTCAACCCTCGGCCTTAAACCCTACACAGATCATATTA
TTTTATCACTATATTTTATTTATTTAACAAGAATTC
Found at i:16715838 original size:18 final size:17
Alignment explanation
Indices: 16715814--16715851 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
16715804 TTATTTTTAA
*
16715814 AAAATTATAAAAAT-AT
1 AAAATTATTAAAATAAT
16715830 -AAATTATTAAAATAAT
1 AAAATTATTAAAATAAT
16715846 AAAATT
1 AAAATT
16715852 TCACTATAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 12 0.63
16 2 0.11
17 5 0.26
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATTAAAATAAT
Found at i:16715875 original size:11 final size:11
Alignment explanation
Indices: 16715859--16715886 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
16715849 ATTTCACTAT
16715859 AACTATCATAA
1 AACTATCATAA
16715870 AACTATCATAA
1 AACTATCATAA
16715881 AACTAT
1 AACTAT
16715887 ACAAATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.54, C:0.18, G:0.00, T:0.29
Consensus pattern (11 bp):
AACTATCATAA
Found at i:16716997 original size:15 final size:15
Alignment explanation
Indices: 16716966--16716995 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16716956 TTAATAAATT
16716966 ATTACATATTCTAAA
1 ATTACATATTCTAAA
16716981 ATTACATATT-TAAA
1 ATTACATATTCTAAA
16716995 A
1 A
16716996 ATAGTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (15 bp):
ATTACATATTCTAAA
Found at i:16719776 original size:14 final size:15
Alignment explanation
Indices: 16719748--16719790 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
16719738 AAATTCAAAT
16719748 TTTAATTTTTCAATA
1 TTTAATTTTTCAATA
*
16719763 TTTACTTTTT-AATA
1 TTTAATTTTTCAATA
* *
16719777 CTTAAATTTTCAAT
1 TTTAATTTTTCAAT
16719791 TTATTAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAATTTTTCAATA
Found at i:16731874 original size:24 final size:24
Alignment explanation
Indices: 16731853--16732024 Score: 212
Period size: 24 Copynumber: 7.4 Consensus size: 24
16731843 TTATGCTCAT
16731853 CAGCTAATATGCGTTTACGCTCGC
1 CAGCTAATATGCGTTTACGCTCGC
16731877 CAGCTAATA------TACGCTCGC
1 CAGCTAATATGCGTTTACGCTCGC
* * *
16731895 CAGCTAGTATGCTTTTACGCTCTC
1 CAGCTAATATGCGTTTACGCTCGC
* * *
16731919 CAGCTAATATACGTTTACACTCGT
1 CAGCTAATATGCGTTTACGCTCGC
*
16731943 CAGCTAATATGGGTTTACGCTCGC
1 CAGCTAATATGCGTTTACGCTCGC
* *
16731967 CAGCTGATATACGTTTACGCTCGC
1 CAGCTAATATGCGTTTACGCTCGC
*
16731991 CAGCTAATATGCTTTTACGCTCGC
1 CAGCTAATATGCGTTTACGCTCGC
16732015 CAGCTAATAT
1 CAGCTAATAT
16732025 AATAAAAGCA
Statistics
Matches: 124, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
18 17 0.14
24 107 0.86
ACGTcount: A:0.23, C:0.28, G:0.18, T:0.31
Consensus pattern (24 bp):
CAGCTAATATGCGTTTACGCTCGC
Found at i:16732456 original size:21 final size:20
Alignment explanation
Indices: 16732422--16732461 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
16732412 AACTTAAACA
*
16732422 TCATCACCAATTATTTCAAC
1 TCATCACCAATTATCTCAAC
*
16732442 TCATCACATAATTATCTCAA
1 TCATCAC-CAATTATCTCAA
16732462 ATGATCAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.35
Consensus pattern (20 bp):
TCATCACCAATTATCTCAAC
Found at i:16743001 original size:51 final size:52
Alignment explanation
Indices: 16742847--16743001 Score: 154
Period size: 51 Copynumber: 2.9 Consensus size: 52
16742837 ATATATTATA
* *
16742847 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATTACAT
1 ATTTTTATTAAATT-ATA-TTTAATAATAA-T-TATT-AAAAT-TTAATAAATTACAT
* * *
16742904 ATTATTTTATTAAATTGTATTTAATAATAATTATGT-TAATTAAATAAATTA-AT
1 A-T-TTTTATTAAATTATATTTAATAATAATTAT-TAAAATTTAATAAATTACAT
*
16742957 ATTTTTATTAAATTATATTTAATAATAATCATTAAAATTTAATAA
1 ATTTTTATTAAATTATATTTAATAATAATTATTAAAATTTAATAA
16743002 CAATAATCAT
Statistics
Matches: 84, Mismatches: 9, Indels: 16
0.77 0.08 0.15
Matches are distributed among these distances:
50 1 0.01
51 37 0.44
52 1 0.01
53 3 0.04
54 9 0.11
55 3 0.04
56 3 0.04
57 3 0.04
58 12 0.14
59 8 0.10
60 4 0.05
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (52 bp):
ATTTTTATTAAATTATATTTAATAATAATTATTAAAATTTAATAAATTACAT
Found at i:16743124 original size:39 final size:43
Alignment explanation
Indices: 16743069--16743173 Score: 121
Period size: 46 Copynumber: 2.5 Consensus size: 43
16743059 TTTCTTATGC
*
16743069 TATTACAGCATC-ATTCCATT-CAACCAA-ACACAA-GAA-TAT
1 TATTACAGC-TCTATTCCATTGCAACCAACAAACAATGAATTAT
*
16743108 TATTACAGCTCTATTCCATTGCAATCAACCAAACAATTGAATTAT
1 TATTACAGCTCTATTCCATTGCAACCAA-CAAACAA-TGAATTAT
16743153 TGATTACAGCTCTATTCCATT
1 T-ATTACAGCTCTATTCCATT
16743174 ACAGCTCTAT
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
38 2 0.04
39 17 0.30
40 6 0.11
42 5 0.09
44 3 0.05
45 4 0.07
46 19 0.34
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (43 bp):
TATTACAGCTCTATTCCATTGCAACCAACAAACAATGAATTAT
Found at i:16743165 original size:46 final size:44
Alignment explanation
Indices: 16743088--16743173 Score: 129
Period size: 46 Copynumber: 1.9 Consensus size: 44
16743078 ATCATTCCAT
16743088 TCAACCAAACACAAGAATATTATTACAGCTCTATTCCATTGCAA
1 TCAACCAAACACAAGAATATTATTACAGCTCTATTCCATTGCAA
*
16743132 TCAACCAAACA-ATTGAATTATTGATTACAGCTCTATTCCATT
1 TCAACCAAACACA-AGAA-TATT-ATTACAGCTCTATTCCATT
16743174 ACAGCTCTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
43 1 0.03
44 14 0.37
45 4 0.11
46 19 0.50
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.31
Consensus pattern (44 bp):
TCAACCAAACACAAGAATATTATTACAGCTCTATTCCATTGCAA
Found at i:16743176 original size:16 final size:16
Alignment explanation
Indices: 16743155--16743226 Score: 117
Period size: 16 Copynumber: 4.5 Consensus size: 16
16743145 TGAATTATTG
16743155 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
16743171 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
* *
16743187 ATTACAGTTCTATTAC
1 ATTACAGCTCTATTCC
*
16743203 ATTACACCTCTATTCC
1 ATTACAGCTCTATTCC
16743219 ATTACAGC
1 ATTACAGC
16743227 GAACCAAACG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.28, C:0.29, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:16744644 original size:20 final size:20
Alignment explanation
Indices: 16744596--16744646 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
16744586 GGAGTTTGGG
* *
16744596 GGAAGTAAAAGATTTGCGGA
1 GGAAGTAAGAGATTTGAGGA
16744616 GGAAGTAAGAGATTTGAGGA
1 GGAAGTAAGAGATTTGAGGA
16744636 GGAAGTAAGAG
1 GGAAGTAAGAG
16744647 GAAAAAAGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.41, C:0.02, G:0.39, T:0.18
Consensus pattern (20 bp):
GGAAGTAAGAGATTTGAGGA
Found at i:16747759 original size:24 final size:24
Alignment explanation
Indices: 16747718--16747773 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
16747708 CATCATTAAA
* * *
16747718 TTTTTTTCCGACACTTAATTCTTAT
1 TTTTTTTTCGACACTTAA-TATGAT
*
16747743 TTTTTTTTCGA-ATTTAATATGAT
1 TTTTTTTTCGACACTTAATATGAT
16747766 TTTTTTTT
1 TTTTTTTT
16747774 ACTGGACTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 12 0.44
24 5 0.19
25 10 0.37
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.64
Consensus pattern (24 bp):
TTTTTTTTCGACACTTAATATGAT
Found at i:16749194 original size:30 final size:28
Alignment explanation
Indices: 16749056--16749194 Score: 86
Period size: 30 Copynumber: 4.7 Consensus size: 28
16749046 TTTAAGAAAC
*
16749056 AAAAATGAAAGGG-TAATTTTAAAAGGAA
1 AAAAAT-AAAGGGTTAAATTTAAAAGGAA
* * * *
16749084 CAAAAATAAGAGGGTTGAATTTTAACGAAAA
1 -AAAAATAA-AGGGTTAAATTTAAAAG-GAA
* *
16749115 TAAAAATAAAGGATTTAATTTAAAA--AA
1 -AAAAATAAAGGGTTAAATTTAAAAGGAA
*
16749142 AATCAGAATAAATGGGTAAAATTTAAAAGGAA
1 AA--A-AATAAA-GGGTTAAATTTAAAAGGAA
16749174 AAATAATGAAAGGGTTAAATT
1 AAA-AAT-AAAGGGTTAAATT
16749195 CGAATTAAAG
Statistics
Matches: 85, Mismatches: 15, Indels: 19
0.71 0.13 0.16
Matches are distributed among these distances:
26 2 0.02
27 2 0.02
28 3 0.04
29 16 0.19
30 45 0.53
31 13 0.15
32 4 0.05
ACGTcount: A:0.56, C:0.02, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAAATAAAGGGTTAAATTTAAAAGGAA
Found at i:16751617 original size:13 final size:13
Alignment explanation
Indices: 16751596--16751629 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
16751586 CTTGAAAACC
16751596 AAGGCAAAAAAAAA
1 AAGG-AAAAAAAAA
*
16751610 AAGGAAAAAAAGA
1 AAGGAAAAAAAAA
16751623 AAGGAAA
1 AAGGAAA
16751630 GTAAAGACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (13 bp):
AAGGAAAAAAAAA
Found at i:16752491 original size:14 final size:14
Alignment explanation
Indices: 16752474--16752540 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 14
16752464 ATAAATAAAT
16752474 AAAAAAGAAAG-AA
1 AAAAAAGAAAGAAA
16752487 AAAAAAGAAAAGAAA
1 AAAAAAG-AAAGAAA
16752502 AAAAGAA-ATAAGGAAA
1 AAAA-AAGA-AA-GAAA
*
16752518 AAGAAA-AAAGAAA
1 AAAAAAGAAAGAAA
16752531 AAAAAAGAAA
1 AAAAAAGAAA
16752541 ATGAGAGGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
13 16 0.35
14 10 0.22
15 11 0.24
16 9 0.20
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (14 bp):
AAAAAAGAAAGAAA
Found at i:16752509 original size:22 final size:21
Alignment explanation
Indices: 16752474--16752541 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
16752464 ATAAATAAAT
*
16752474 AAAAAAGAAAGAAAAAAAAGA
1 AAAAAAAAAAGAAAAAAAAGA
* *
16752495 AAAGAAAAAAAG-AAATAAGGA
1 AAA-AAAAAAAGAAAAAAAAGA
16752516 AAAAGAAAAAAGAAAAAAAAAGA
1 AAAA-AAAAAAG-AAAAAAAAGA
16752539 AAA
1 AAA
16752542 TGAGAGGTCG
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 20 0.53
22 7 0.18
23 10 0.26
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.01
Consensus pattern (21 bp):
AAAAAAAAAAGAAAAAAAAGA
Found at i:16752541 original size:7 final size:7
Alignment explanation
Indices: 16752474--16752533 Score: 70
Period size: 7 Copynumber: 8.9 Consensus size: 7
16752464 ATAAATAAAT
16752474 AAAAAAG
1 AAAAAAG
*
16752481 AAAGAA-
1 AAAAAAG
16752487 AAAAAAG
1 AAAAAAG
*
16752494 AAAAGA-
1 AAAAAAG
16752500 AAAAAAG
1 AAAAAAG
*
16752507 AAATAAG
1 AAAAAAG
*
16752514 GAAAAAG
1 AAAAAAG
16752521 AAAAAAG
1 AAAAAAG
16752528 AAAAAA
1 AAAAAA
16752534 AAAGAAAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
6 10 0.23
7 33 0.77
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAAG
Found at i:16753559 original size:50 final size:50
Alignment explanation
Indices: 16753484--16753869 Score: 345
Period size: 50 Copynumber: 7.8 Consensus size: 50
16753474 AGAAAAACAT
*
16753484 GAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTTA
1 GAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCTTA
* * * *
16753534 GAAGATGTGACGGGAAAGGTTGAGGTCGCAACGGTGAACCCGATACCAT-
1 GAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCTTA
* ** * * *
16753583 GAAGATTTGAAGGG-AAGGATTGAGGTCGCGACGGTAAATCCGGTACCTCA
1 GAAGATTTGAAGGGAAAGG-TTGAGGTCGCAACGGCGAACCCGATACCTTA
* * * * *
16753633 AAATATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGATACCTCA
1 GAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCTTA
* * * * * * * * * * * *
16753683 AAAGATATGATGGAAAAGATTTAGATTGTAACGACGAATCCGATACCAT-
1 GAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCTTA
* * *
16753732 GAA-ATATGATA-GGAAAGGTTGAGGTCGCAATGGCGAACCCGATACCAT-
1 GAAGATTTGA-AGGGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCTTA
* * * **
16753780 GAAGATTTTAAGGGAAAGGTTGAGGCCGCAACAGCGAA-CTTAGTACCTTA
1 GAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGA-TACCTTA
* * *
16753830 GAAGATATGAAGGGAAAGGTTGCGGCCGCAACGGCGAACC
1 GAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAACC
16753870 TGGTACAATA
Statistics
Matches: 269, Mismatches: 58, Indels: 17
0.78 0.17 0.05
Matches are distributed among these distances:
48 44 0.16
49 70 0.26
50 150 0.56
51 5 0.02
ACGTcount: A:0.34, C:0.17, G:0.31, T:0.19
Consensus pattern (50 bp):
GAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCTTA
Found at i:16753652 original size:99 final size:97
Alignment explanation
Indices: 16753481--16753869 Score: 349
Period size: 99 Copynumber: 3.9 Consensus size: 97
16753471 CTGAGAAAAA
* * * *
16753481 CATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAACCCGGTACCTTAGAAGATGTGACG
1 CATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAATCCGGTACC-TAAAATAT-TGAAG
16753546 GGAAAGGTTGAGGTCGCAACGGTGAACCCGATAC
64 GGAAAGGTTGAGGTCGCAACGGTGAACCCGATAC
* **
16753580 CATGAAGATTTGAAGGG-AAGGATTGAGGTCGCGACGGTAAATCCGGTACCTCAAAATATTTGAA
1 CATGAAGATTTGAAGGGAAAGG-TTGAGGTCGCAACGGCGAATCCGGTACCT-AAAATA-TTGAA
*
16753644 GGGAAAGGTTGAGGCCGCAACGGTGAACCCGATAC
63 GGGAAAGGTTGAGGTCGCAACGGTGAACCCGATAC
* * * * * * * * * * * *
16753679 C-TCAAAAGATATGATGGAAAAGATTTAGATTGTAACGACGAATCCGATACCATGAAATA-TGAT
1 CAT--GAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAATCCGGTACC-TAAAATATTGA-
* *
16753742 A-GGAAAGGTTGAGGTCGCAATGGCGAACCCGATAC
62 AGGGAAAGGTTGAGGTCGCAACGGTGAACCCGATAC
* * * **
16753777 CATGAAGATTTTAAGGGAAAGGTTGAGGCCGCAACAGCGAA-CTTAGTACCTTAGAAGATA-TGA
1 CATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAATC-CGGTACC-TA-AA-ATATTGA
* * *
16753840 AGGGAAAGGTTGCGGCCGCAACGGCGAACC
62 AGGGAAAGGTTGAGGTCGCAACGGTGAACC
16753870 TGGTACAATA
Statistics
Matches: 230, Mismatches: 47, Indels: 26
0.76 0.16 0.09
Matches are distributed among these distances:
96 1 0.00
97 30 0.13
98 44 0.19
99 116 0.50
100 35 0.15
101 4 0.02
ACGTcount: A:0.34, C:0.17, G:0.30, T:0.19
Consensus pattern (97 bp):
CATGAAGATTTGAAGGGAAAGGTTGAGGTCGCAACGGCGAATCCGGTACCTAAAATATTGAAGGG
AAAGGTTGAGGTCGCAACGGTGAACCCGATAC
Found at i:16753894 original size:197 final size:197
Alignment explanation
Indices: 16753546--16753900 Score: 459
Period size: 197 Copynumber: 1.8 Consensus size: 197
16753536 AGATGTGACG
* *
16753546 GGAAAGGTTGAGGTCGCAACGGTGAACCCGATACCATGAAGATTTGAAGGGAAGGATTGAGGTCG
1 GGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCATGAAGATTTGAAGGGAAGGATTGAGGCCG
* * * * *
16753611 CGACGGTAAATCCGGTACCTCAAAATATTTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGA
66 CAACGGTAAATCCAGTACCTCAAAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGA
* * *
16753676 TACCTCAAAAGATATGATGGAAAAGATTTAGATTGTAACGACGAATCCGATACCATGAAATATGA
131 TACATCAAAAGACAAGATGGAAAAGATTTAGATTGTAACGACGAATCCGATACCATGAAATATGA
16753741 TA
196 TA
* *
16753743 GGAAAGGTTGAGGTCGCAATGGCGAACCCGATACCATGAAGATTTTAAGGGAAAGG-TTGAGGCC
1 GGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCATGAAGATTTGAAGGG-AAGGATTGAGGCC
* * * * *
16753807 GCAACAGCG-AACT-TAGTACCTTAGAAGATATGAAGGGAAAGGTTGCGGCCGCAACGGCGAACC
65 GCAAC-G-GTAAATCCAGTACCTCAAAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACC
* *
16753870 TGGTACAAT-AGAAA-ACAAGATGGAAAAGATT
128 CGATAC-ATCA-AAAGACAAGATGGAAAAGATT
16753901 GAAGCCGCAA
Statistics
Matches: 134, Mismatches: 19, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
197 121 0.90
198 12 0.09
199 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.19
Consensus pattern (197 bp):
GGAAAGGTTGAGGTCGCAACGGCGAACCCGATACCATGAAGATTTGAAGGGAAGGATTGAGGCCG
CAACGGTAAATCCAGTACCTCAAAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCCGA
TACATCAAAAGACAAGATGGAAAAGATTTAGATTGTAACGACGAATCCGATACCATGAAATATGA
TA
Found at i:16754297 original size:39 final size:39
Alignment explanation
Indices: 16754238--16754643 Score: 205
Period size: 39 Copynumber: 10.4 Consensus size: 39
16754228 CAGCCATCCG
* *
16754238 ATCTTTTACCCCAAGCTTGGGGCAGATCACCACCAGTCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCACCAGTCA
* * *
16754277 ATCTCTTACCCCGAGCTTGGGGTAGATTA-CAGCCA-TCCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCA-CCAGT-CA
* * *
16754316 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCACCAGTCA
** * * *
16754355 ATCTCTTACCTCAAAGC-TGGGGTAGATCACCATCAGCCA
1 ATCTCTTACC-CCGAGCTTGGGGCAGATCACCACCAGTCA
* * * * * *
16754394 ATCTCTTACCTCGAGCTTAGGGTAGATTACAACCA-TCCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCACCAGT-CA
* * * * * *
16754433 ATCTTTTACCCTGAACTTGGGACAGATTACCATCAG-CTA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCACCAGTC-A
* * * ** *
16754472 ATGTCTTACCTCAAGCTTGGGGCAGAT-AGTAACCA-TCCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCA-CCACCAGT-CA
* ** * ** * * *
16754511 ATCTTTTACCCTAAGCCTAAGGCAGATCATCATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCACCAGTCA
* * * **** * *
16754550 ATCTCTTACCCCGAGCCTGAGGTAGATTGTAACCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCACCAGTCA
* * ** * *
16754589 ATCTTTTACCCCAAGCTTAAGACAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATCACCACCAGTCA
16754628 ATCTCTTACCCCGAGC
1 ATCTCTTACCCCGAGC
16754644 CAGGGCGGAT
Statistics
Matches: 271, Mismatches: 82, Indels: 28
0.71 0.22 0.07
Matches are distributed among these distances:
38 8 0.03
39 255 0.94
40 8 0.03
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATCACCACCAGTCA
Found at i:16754310 original size:78 final size:78
Alignment explanation
Indices: 16754223--16754381 Score: 230
Period size: 78 Copynumber: 2.0 Consensus size: 78
16754213 GCCTGAGACC
* * * *
16754223 GATTGCAGCCATCCGATCTTTTACCCCAAGCTTGGGGCAGATCACCACCAGTCAATCTCTTACC-
1 GATTACAGCCATCCGATCTCTTACCCCAAGCCTGGGGCAGATCACCACCAGCCAATCTCTTACCT
**
16754287 CCGAGCTTGGGGTA
66 CAAAGC-TGGGGTA
* *
16754301 GATTACAGCCATCCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCAATCTCTTACCT
1 GATTACAGCCATCCGATCTCTTACCCCAAGCCTGGGGCAGATCACCACCAGCCAATCTCTTACCT
16754366 CAAAGCTGGGGTA
66 CAAAGCTGGGGTA
16754379 GAT
1 GAT
16754382 CACCATCAGC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
78 68 0.94
79 4 0.06
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.23
Consensus pattern (78 bp):
GATTACAGCCATCCGATCTCTTACCCCAAGCCTGGGGCAGATCACCACCAGCCAATCTCTTACCT
CAAAGCTGGGGTA
Found at i:16754364 original size:117 final size:117
Alignment explanation
Indices: 16754238--16754498 Score: 353
Period size: 117 Copynumber: 2.2 Consensus size: 117
16754228 CAGCCATCCG
* * *
16754238 ATCTTTTACCCCAAGCTTGGGGCAGATCACCACCAGTCAATCTCTTACCCCGAGCTTGGGGTAGA
1 ATCTCTTACCCCAAGCTTGGGGCAGATCACCACCAGCCAATCTCTTACCCCGAGCTTAGGGTAGA
* * *
16754303 TTACAGCCATCCGATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
66 TTACAACCATCCGATCTCTTACCCCGAACCTGGGACAGATCACCATCAGCCA
* * * *
16754355 ATCTCTTACCTCAAAGC-TGGGGTAGATCACCATCAGCCAATCTCTTACCTCGAGCTTAGGGTAG
1 ATCTCTTACC-CCAAGCTTGGGGCAGATCACCACCAGCCAATCTCTTACCCCGAGCTTAGGGTAG
* * * * *
16754419 ATTACAACCATCCGATCTTTTACCCTGAACTTGGGACAGATTACCATCAGCTA
65 ATTACAACCATCCGATCTCTTACCCCGAACCTGGGACAGATCACCATCAGCCA
* *
16754472 ATGTCTTACCTCAAGCTTGGGGCAGAT
1 ATCTCTTACCCCAAGCTTGGGGCAGAT
16754499 AGTAACCATC
Statistics
Matches: 123, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
116 4 0.03
117 114 0.93
118 5 0.04
ACGTcount: A:0.25, C:0.30, G:0.20, T:0.25
Consensus pattern (117 bp):
ATCTCTTACCCCAAGCTTGGGGCAGATCACCACCAGCCAATCTCTTACCCCGAGCTTAGGGTAGA
TTACAACCATCCGATCTCTTACCCCGAACCTGGGACAGATCACCATCAGCCA
Found at i:16754442 original size:78 final size:77
Alignment explanation
Indices: 16754378--16754679 Score: 293
Period size: 78 Copynumber: 3.9 Consensus size: 77
16754368 AAGCTGGGGT
* *
16754378 AGATCACCATCAGCCAATCTCTTACCTCGAGCTTAGGGTAGATTACAACCATCCGATCTTTTACC
1 AGATCACCATCAGCCAATCTCTTACCCCGAGCTT-GGGTAGATTATAACCATCCGATCTTTTACC
* **
16754443 CTGAA-CTTGGGAC
65 C-AAAGCTTAAGAC
* * * * * *
16754456 AGATTACCATCAGCTAATGTCTTACCTCAAGCTTGGGGCAGA-TAGTAACCATCCGATCTTTTAC
1 AGATCACCATCAGCCAATCTCTTACCCCGAGCTT-GGGTAGATTA-TAACCATCCGATCTTTTAC
* * *
16754520 CCTAAGCCTAAGGC
64 CCAAAGCTTAAGAC
* * * *
16754534 AGATCATCATCAGCCAATCTCTTACCCCGAGCCTGAGGTAGATTGTAACCATTCGATCTTTTACC
1 AGATCACCATCAGCCAATCTCTTACCCCGAGCTTG-GGTAGATTATAACCATCCGATCTTTTACC
*
16754599 CCAAGCTTAAGAC
65 CAAAGCTTAAGAC
* ** ** * * * *
16754612 AGATCACCATCAGTCAATCTCTTACCCCGAGCCAGGGCGGATTGTAACCATCCAATATCTTACCC
1 AGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGTAGATTATAACCATCCGATCTTTTACCC
16754677 AAA
66 AAA
16754680 AAAAATTCTT
Statistics
Matches: 185, Mismatches: 35, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
77 31 0.17
78 153 0.83
79 1 0.01
ACGTcount: A:0.28, C:0.29, G:0.16, T:0.26
Consensus pattern (77 bp):
AGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGTAGATTATAACCATCCGATCTTTTACCC
AAAGCTTAAGAC
Found at i:16754479 original size:156 final size:156
Alignment explanation
Indices: 16754316--16754679 Score: 371
Period size: 156 Copynumber: 2.3 Consensus size: 156
16754306 CAGCCATCCG
* * ** *
16754316 ATCTCTTACCCCGAGCCTGGGGCAGATCA-CCATCAGCCAATCTCTTACCTCAAAG-CTGGGGTA
1 ATCTCTTACCCCGAGCCTGGGGCAGAT-AGCAACCAGCCAATCTCTTACC-CAAAGCCTAAGGCA
* *
16754379 GATCACCATCAGCCAATCTCTTACCTCGAG-CTTAGGGTAGATTACAACCATCCGATCTTTTACC
64 GATCACCATCAGCCAATCTCTTACCCCGAGCCTGA-GGTAGATTACAACCATCCGATCTTTTACC
* ** *
16754443 CTGAA-CTTGGGACAGATTACCATCAG-CTA
128 C-CAAGCTTAAGACAGATCACCATCAGTC-A
* * * * * * * * *
16754472 ATGTCTTACCTCAAGCTTGGGGCAGATAGTAACCATCCGATCTTTTACCCTAAGCCTAAGGCAGA
1 ATCTCTTACCCCGAGCCTGGGGCAGATAGCAACCAGCCAATCTCTTACCCAAAGCCTAAGGCAGA
* ** *
16754537 TCATCATCAGCCAATCTCTTACCCCGAGCCTGAGGTAGATTGTAACCATTCGATCTTTTACCCCA
66 TCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGTAGATTACAACCATCCGATCTTTTACCCCA
16754602 AGCTTAAGACAGATCACCATCAGTCA
131 AGCTTAAGACAGATCACCATCAGTCA
* * * * * *
16754628 ATCTCTTACCCCGAGCC-AGGGCGGATTGTAACCATCCAATATCTTACCCAAA
1 ATCTCTTACCCCGAGCCTGGGGCAGATAGCAACCAGCCAATCTCTTACCCAAA
16754680 AAAAATTCTT
Statistics
Matches: 168, Mismatches: 35, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
155 35 0.21
156 129 0.77
157 4 0.02
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.25
Consensus pattern (156 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATAGCAACCAGCCAATCTCTTACCCAAAGCCTAAGGCAGA
TCACCATCAGCCAATCTCTTACCCCGAGCCTGAGGTAGATTACAACCATCCGATCTTTTACCCCA
AGCTTAAGACAGATCACCATCAGTCA
Found at i:16754962 original size:50 final size:50
Alignment explanation
Indices: 16754908--16755059 Score: 189
Period size: 50 Copynumber: 3.0 Consensus size: 50
16754898 ATTTAAAAAG
* * *
16754908 AAAGGTTGAGACCACAACGACGAACCCGATACCTTAAAAGATGTGA-CGAA
1 AAAGGTTGAGGCCACAACGATGAACCCGATACCTCAAAAGATGTGATCG-A
* * ** *
16754958 AAAGGTTGTGGTCGTAACGATGAACCCGATACCTCAAAAGATGTGATTGA
1 AAAGGTTGAGGCCACAACGATGAACCCGATACCTCAAAAGATGTGATCGA
* * *
16755008 AAAGGTTGAGGCCACAACGGTGAACCCAATACCTCAAAAGATGTGATGGA
1 AAAGGTTGAGGCCACAACGATGAACCCGATACCTCAAAAGATGTGATCGA
16755058 AA
1 AA
16755060 TTATTGAGGT
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
50 85 0.99
51 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (50 bp):
AAAGGTTGAGGCCACAACGATGAACCCGATACCTCAAAAGATGTGATCGA
Found at i:16755486 original size:41 final size:41
Alignment explanation
Indices: 16755429--16755523 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
16755419 CATCATCATT
*
16755429 CAATCTTTTACCCTTAATCAAGAAGGGCAGATTGAAGATTC
1 CAATCTTTTACCCTTAATCAAGAAGGGCAGAATGAAGATTC
16755470 CAATCTTTTACCCTTAATCAAGAAGGGCAGAATGAAGATTC
1 CAATCTTTTACCCTTAATCAAGAAGGGCAGAATGAAGATTC
*
16755511 CGATCTTTTACCC
1 CAATCTTTTACCC
16755524 CGAGCCTGTG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (41 bp):
CAATCTTTTACCCTTAATCAAGAAGGGCAGAATGAAGATTC
Done.