Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 76 of 129
Found at i:12029973 original size:16 final size:16
Alignment explanation
Indices: 12029952--12030032 Score: 64
Period size: 16 Copynumber: 5.2 Consensus size: 16
12029942 AACAATTAAT
12029952 AAATAAATAAAAAAGA
1 AAATAAATAAAAAAGA
*
12029968 AAATAAAT-AAAAAGC
1 AAATAAATAAAAAAGA
*
12029983 AAA-AATTAAAATATA-A
1 AAATAAATAAAA-A-AGA
* *
12029999 AAACAAATCAAATAA-A
1 AAATAAAT-AAAAAAGA
12030015 AAATAAA-AAAAAAGA
1 AAATAAATAAAAAAGA
12030030 AAA
1 AAA
12030033 ACTTGCAATC
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
14 8 0.15
15 16 0.31
16 20 0.38
17 5 0.10
18 3 0.06
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.14
Consensus pattern (16 bp):
AAATAAATAAAAAAGA
Found at i:12030964 original size:19 final size:19
Alignment explanation
Indices: 12030933--12030984 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 19
12030923 AAGTAATAAT
* *
12030933 AATA-AAAACAAAAAATAA
1 AATAGAAAATAAAAAAGAA
* * *
12030951 GATAGAAATTAAAATAGAA
1 AATAGAAAATAAAAAAGAA
12030970 AATAGAAAATAAAAA
1 AATAGAAAATAAAAA
12030985 TAAAATAACA
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
18 3 0.12
19 22 0.88
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.15
Consensus pattern (19 bp):
AATAGAAAATAAAAAAGAA
Found at i:12031016 original size:6 final size:6
Alignment explanation
Indices: 12030916--12030989 Score: 51
Period size: 6 Copynumber: 11.7 Consensus size: 6
12030906 CCAAAAAACC
* * * * *
12030916 AAAAAT AAAGTAAT AATAAT AAAAAC AAAAA- ATAAGAT AGAAAT TAAAAT
1 AAAAAT AAA--AAT AAAAAT AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT
12030966 AGAAAAT AGAAAAT AAAAAT AAAA
1 A-AAAAT A-AAAAT AAAAAT AAAA
12030990 TAACAAAAAT
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
5 1 0.02
6 34 0.63
7 14 0.26
8 5 0.09
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (6 bp):
AAAAAT
Found at i:12034210 original size:17 final size:18
Alignment explanation
Indices: 12034172--12034210 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
12034162 TTAAATTGTT
12034172 TATTTTGAGTTATGTCATA
1 TATTTTGAGTTATG-CATA
12034191 TATTTTGAGTTATG-ATA
1 TATTTTGAGTTATGCATA
12034208 TAT
1 TAT
12034211 ATAAGTGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 6 0.30
19 14 0.70
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (18 bp):
TATTTTGAGTTATGCATA
Found at i:12035824 original size:284 final size:284
Alignment explanation
Indices: 12035304--12035856 Score: 1007
Period size: 284 Copynumber: 1.9 Consensus size: 284
12035294 TTGGCTTAAA
* * *
12035304 CATTGAGCACAGTTTAGTGTCTACTCAATTTTTATTCAACCATGTTAAGTCTTGTCCTTGACATT
1 CATTAAGCACAGTTTAGTATCTACTCAATTTTTATTCAACCATGTTAAGTCTTGTCATTGACATT
*
12035369 AACTTACAAATAAGCTTTAGAACAATTCTAAACTCTTATTTCACTTTGGCCAAAGATTTTTTAAG
66 AACTTACAAATAAGCTTTAGAACAATTCTAAACTCTTATTTCACTTTAGCCAAAGATTTTTTAAG
* *
12035434 TTAATTCAATCAAGACTAATCAAGATACTTTTTTAATCACACAAGGTGATGAATCTCATCTTGAT
131 TTAATTCAATCAAGACTAATCAAGATACTCTTTTAATCACACAAGGTGATGAATCCCATCTTGAT
* *
12035499 TATTTCATTATGCCTCATGTTATACCCAAAAATACTCAACTAGAGTGTTCATGGTTAGAATCATA
196 TATTTCATTATGCCTCATGTTATACCAAAAAATACTCAACTAGAGTGTTCATGGTTAGAACCATA
12035564 AGAAAGTAACTCAATGGTTAAAAC
261 AGAAAGTAACTCAATGGTTAAAAC
*
12035588 CATTAAGCATAGTTTAGTATCTACTCAATTTTTATTCAACCATGTTAAGTCTTGTCATTGACATT
1 CATTAAGCACAGTTTAGTATCTACTCAATTTTTATTCAACCATGTTAAGTCTTGTCATTGACATT
12035653 AACTTACAAATAAGCTTTAGAACAATTCTAAACTCTTATTTCACTTTAGCCAAAGATTTTTTAAG
66 AACTTACAAATAAGCTTTAGAACAATTCTAAACTCTTATTTCACTTTAGCCAAAGATTTTTTAAG
*
12035718 TTAATTCAATCAAGACTAATTAAGATACTCTTTTAATCACACAAGGTGATGAATCCCATCTTGAT
131 TTAATTCAATCAAGACTAATCAAGATACTCTTTTAATCACACAAGGTGATGAATCCCATCTTGAT
*
12035783 TATTTCATTATGCCTCATGTTATACTAAAAAATACTCAACTAGAGTGTTCATGGTTAGAACCATA
196 TATTTCATTATGCCTCATGTTATACCAAAAAATACTCAACTAGAGTGTTCATGGTTAGAACCATA
12035848 AGAAAGTAA
261 AGAAAGTAA
12035857 AGTCAAAGTA
Statistics
Matches: 258, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
284 258 1.00
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.36
Consensus pattern (284 bp):
CATTAAGCACAGTTTAGTATCTACTCAATTTTTATTCAACCATGTTAAGTCTTGTCATTGACATT
AACTTACAAATAAGCTTTAGAACAATTCTAAACTCTTATTTCACTTTAGCCAAAGATTTTTTAAG
TTAATTCAATCAAGACTAATCAAGATACTCTTTTAATCACACAAGGTGATGAATCCCATCTTGAT
TATTTCATTATGCCTCATGTTATACCAAAAAATACTCAACTAGAGTGTTCATGGTTAGAACCATA
AGAAAGTAACTCAATGGTTAAAAC
Found at i:12037778 original size:16 final size:17
Alignment explanation
Indices: 12037759--12037793 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
12037749 ATTCAAAATT
12037759 TAATTT-TTATAAAAAA
1 TAATTTATTATAAAAAA
*
12037775 TAATTTATTTTAAAAAA
1 TAATTTATTATAAAAAA
12037792 TA
1 TA
12037794 GTTTCTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TAATTTATTATAAAAAA
Found at i:12038121 original size:22 final size:22
Alignment explanation
Indices: 12038079--12038123 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12038069 TTCAATCAGT
* *
12038079 AACAATATATTAAAAATATAAA
1 AACAATATATAAAAAAAATAAA
12038101 AACAATATA-AAAAACAAATAAA
1 AACAATATATAAAAA-AAATAAA
12038123 A
1 A
12038124 TAAAAATCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 4 0.20
22 16 0.80
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (22 bp):
AACAATATATAAAAAAAATAAA
Found at i:12039769 original size:44 final size:43
Alignment explanation
Indices: 12039721--12039856 Score: 118
Period size: 44 Copynumber: 3.2 Consensus size: 43
12039711 CAAAAGACTA
*
12039721 ACAAATTTTGCCTAGAAAATTTAGAGATTATGCCCAAAGGTCTT
1 ACAAATTTTGCCTAGAAAA-TTAGAGATTATGCTCAAAGGTCTT
* * * ** * *
12039765 ACAAATCTCGACTCTAAAA-TA-A-ATT-TAGCTCAAAAGACTT
1 ACAAATTTTGCCTAGAAAATTAGAGATTAT-GCTCAAAGGTCTT
** *
12039805 ATGAATTTTGCCTAGAGAACTTAGAGATTATGCTCAAAGGTCTT
1 ACAAATTTTGCCTAGA-AAATTAGAGATTATGCTCAAAGGTCTT
12039849 ACAAATTT
1 ACAAATTT
12039857 CACTCTAAAA
Statistics
Matches: 66, Mismatches: 20, Indels: 12
0.67 0.20 0.12
Matches are distributed among these distances:
39 1 0.02
40 22 0.33
41 3 0.05
42 4 0.06
43 1 0.02
44 34 0.52
45 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (43 bp):
ACAAATTTTGCCTAGAAAATTAGAGATTATGCTCAAAGGTCTT
Found at i:12039918 original size:83 final size:84
Alignment explanation
Indices: 12039672--12040053 Score: 338
Period size: 84 Copynumber: 4.7 Consensus size: 84
12039662 AATTATATTT
* * * **
12039672 AAAGGTCTTATAAATTTCAACTCTAAAATAGATTTATCTCAAAAGACTAACAAATTTTGCCTAGA
1 AAAGGTCTTACAAATTTCAACTCTAAAATAGATTTAGCTCAAAAGACTTATGAATTTTGCCTAGA
* *
12039737 AAATTTAGAGATTATGCCC
66 GAACTTAGAGATTATGCCC
* * *
12039756 AAAGGTCTTACAAATCTCGACTCTAAAATAAATTTAGCTCAAAAGACTTATGAATTTTGCCTAGA
1 AAAGGTCTTACAAATTTCAACTCTAAAATAGATTTAGCTCAAAAGACTTATGAATTTTGCCTAGA
*
12039821 GAACTTAGAGATTATGCTC
66 GAACTTAGAGATTATGCCC
* * * * * *
12039840 AAAGGTCTTACAAATTTC-ACTCTAAAATAGATTAAGCTAAAAAAACTTATGAATCTTACCTATA
1 AAAGGTCTTACAAATTTCAACTCTAAAATAGATTTAGCTCAAAAGACTTATGAATTTTGCCTAGA
* *
12039904 GGACTTGGAGATTATGCCC
66 GAACTTAGAGATTATGCCC
* ** * * * * ** * *
12039923 ATATATTTTACAAA--T---CT-TGACA-A-ATTCAGCTCAAAAGACTTACAAATCTTGCTTAGA
1 AAAGGTCTTACAAATTTCAACTCTAAAATAGATTTAGCTCAAAAGACTTATGAATTTTGCCTAGA
* *
12039980 GGACTT-GAAGATTATGCCT
66 GAACTTAG-AGATTATGCCC
* * *
12039999 AGAA-GTCTTACAAATCTCAACTTTAAAATAGATTTAGCT-AAGAAGACTTAGGAAT
1 A-AAGGTCTTACAAATTTCAACTCTAAAATAGATTTAGCTCAA-AAGACTTATGAAT
12040054 CTTACTTGAA
Statistics
Matches: 242, Mismatches: 45, Indels: 22
0.78 0.15 0.07
Matches are distributed among these distances:
75 1 0.00
76 51 0.21
77 2 0.01
78 4 0.02
79 2 0.01
81 3 0.01
82 3 0.01
83 68 0.28
84 108 0.45
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (84 bp):
AAAGGTCTTACAAATTTCAACTCTAAAATAGATTTAGCTCAAAAGACTTATGAATTTTGCCTAGA
GAACTTAGAGATTATGCCC
Found at i:12040109 original size:84 final size:84
Alignment explanation
Indices: 12039942--12040143 Score: 221
Period size: 84 Copynumber: 2.4 Consensus size: 84
12039932 ACAAATCTTG
* * * * * *
12039942 ACAAATTCAGCTCAAAAGACTTACAAATCTTGCTT-AGAGGACTTGAAGATTATGCCTAGAAGTC
1 ACAAATTTAACTCAAAAGACTTAGAAATCTTACTTGA-AAGACTTAAAGATTATGCCTAGAAGTC
*
12040006 TTACAAATCTCAACTTTAAA
65 TTACAAATCTCAACATTAAA
* * * *
12040026 ATAGATTTAGCT-AAGAAGACTTAGGAATCTTACTTGAAAGACTTAAAGATTATGCCT-GAAGAT
1 ACAAATTTAACTCAA-AAGACTTAGAAATCTTACTTGAAAGACTTAAAGATTATGCCTAGAAG-T
* **
12040089 CTTATAAATCTCTTCATTAAA
64 CTTACAAATCTCAACATTAAA
*
12040110 ACAAATTTAACTCAAAAGACTTATAAATCTTACT
1 ACAAATTTAACTCAAAAGACTTAGAAATCTTACT
12040144 CAGAGAACAT
Statistics
Matches: 97, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
83 6 0.06
84 88 0.91
85 3 0.03
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (84 bp):
ACAAATTTAACTCAAAAGACTTAGAAATCTTACTTGAAAGACTTAAAGATTATGCCTAGAAGTCT
TACAAATCTCAACATTAAA
Found at i:12040161 original size:84 final size:81
Alignment explanation
Indices: 12039942--12040182 Score: 214
Period size: 84 Copynumber: 2.9 Consensus size: 81
12039932 ACAAATCTTG
* * * *
12039942 ACAAATTCAGCTCAAAAGACTTACAAATCTTGCTTAGAGGACTTGAAGATTATGCCTAGAAGTCT
1 ACAAATTTAGCTCAAAAGACTTACAAATCTTAC-TAGAGAACTAG-AGATTATGCCT-GAAGTCT
*
12040007 TACAAATCTCAACTTTAAA
63 TACAAATCTCAACATTAAA
* * ** * * *
12040026 ATAGATTTAGCT-AAGAAGACTTAGGAATCTTACTTGAAAGACTTAAAGATTATGCCTGAAGATC
1 ACAAATTTAGCTCAA-AAGACTTACAAATCTTACTAGAGA-AC-TAGAGATTATGCCTGAAG-TC
* **
12040090 TTATAAATCTCTTCATTAAA
62 TTACAAATCTCAACATTAAA
* * * *
12040110 ACAAATTTAACTCAAAAGACTTATAAATCTTACTCAGAGAACATAGGGATTATGCCTGAAAGTTT
1 ACAAATTTAGCTCAAAAGACTTACAAATCTTACT-AGAGAAC-TAGAGATTATGCCTG-AAGTCT
12040175 TACAAATC
63 TACAAATC
12040183 AAGTGTTAAA
Statistics
Matches: 123, Mismatches: 27, Indels: 14
0.75 0.16 0.09
Matches are distributed among these distances:
83 9 0.07
84 105 0.85
85 9 0.07
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.30
Consensus pattern (81 bp):
ACAAATTTAGCTCAAAAGACTTACAAATCTTACTAGAGAACTAGAGATTATGCCTGAAGTCTTAC
AAATCTCAACATTAAA
Found at i:12043139 original size:19 final size:20
Alignment explanation
Indices: 12043117--12043169 Score: 74
Period size: 21 Copynumber: 2.7 Consensus size: 20
12043107 CTAATTCATT
*
12043117 CTAAA-CCCAAAACTTCAAA
1 CTAAATCCCAAAAATTCAAA
12043136 CTAAATGCCCAAAAATTCAAA
1 CTAAAT-CCCAAAAATTCAAA
12043157 C-AAATCCCAAAAA
1 CTAAATCCCAAAAA
12043170 CCATCCTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 13 0.42
20 4 0.13
21 14 0.45
ACGTcount: A:0.55, C:0.28, G:0.02, T:0.15
Consensus pattern (20 bp):
CTAAATCCCAAAAATTCAAA
Found at i:12053539 original size:12 final size:13
Alignment explanation
Indices: 12053503--12053541 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
12053493 GGGAGGACTG
12053503 TGTTTTTGTTT-T
1 TGTTTTTGTTTGT
12053515 TGTCTTTTGTTTGT
1 TGT-TTTTGTTTGT
12053529 TGTTTTT-TTTGT
1 TGTTTTTGTTTGT
12053541 T
1 T
12053542 ATTATTTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.36
13 12 0.48
14 4 0.16
ACGTcount: A:0.00, C:0.03, G:0.18, T:0.79
Consensus pattern (13 bp):
TGTTTTTGTTTGT
Found at i:12054310 original size:22 final size:22
Alignment explanation
Indices: 12054279--12054321 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
12054269 ACCAGTCAAA
12054279 ATTATACCCGAAGGTCTTAAAG
1 ATTATACCCGAAGGTCTTAAAG
* * *
12054301 ATTATGCCCGGATGTCTTAAA
1 ATTATACCCGAAGGTCTTAAA
12054322 AATCATGCAT
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:0.33, C:0.19, G:0.19, T:0.30
Consensus pattern (22 bp):
ATTATACCCGAAGGTCTTAAAG
Found at i:12054496 original size:110 final size:106
Alignment explanation
Indices: 12054301--12054743 Score: 343
Period size: 110 Copynumber: 4.0 Consensus size: 106
12054291 GGTCTTAAAG
* * * * *
12054301 ATTATGCCCGGATGTCTTAAAAATCATGCATTG-AGGTTTTACAAAATCGACTAGGATAATACCG
1 ATTATGCCCGGAGGTCTTAAAAATCATGC-TCGAAGGTCTTACAGAATCGACTA-G-TAACA-CG
* * * * *
12054365 TAAGTCAAAAAATAAGGAATCGATCGGGACAACACCGTGAATTAAA
62 CAAGTTAAAAAATAA-AAATCGATCGGGACAACACCGCGAATCAAA
* * *
12054411 ATTATGCCCGGGGGTCTTAAAAATCATGTTCGAAGGTCTTACAGAATCGACTAGTACGACATCAC
1 ATTATGCCCGGAGGTCTTAAAAATCATGCTCGAAGGTCTTACAGAATCGACTAGTA--ACA-CGC
* * * *
12054476 AAGTTAAAAAATAAATAATCGATCAGGCCAACATCGCGAATCGAA
63 AAGTTAAAAAATAAA-AATCGATCGGGACAACACCGCGAATCAAA
* * * * * * **
12054521 ATTATGCCAGGAGGACTTAGAAGTCATGCCCGAAAGTCTTACAGAATCGATCGGGATAACACTGC
1 ATTATGCCCGGAGGTCTTAAAAATCATGCTCGAAGGTCTTACAGAATCGA-CTAG-TAACAC-GC
* * *
12054586 AAG-TCAAAAATAAAAATCGATTGGGACAACACCGCGAATCGAA
63 AAGTTAAAAAATAAAAATCGATCGGGACAACACCGCGAATCAAA
** * * * * ** *
12054629 ATTATGTTCGAAGGTCTTAGAAATCATGCTCGGAGATCTTACAGAATCGATCGGGATAACACCGT
1 ATTATGCCCGGAGGTCTTAAAAATCATGCTCGAAGGTCTTACAGAATCGA-CTAG-TAACA-CGC
* * * *
12054694 AAGTCAAAAAATTAAAAATTGATCGAGACAACACTGCGAAT-AGAA
63 AAGTTAAAAAA-TAAAAATCGATCGGGACAACACCGCGAATCA-AA
12054739 ATTAT
1 ATTAT
12054744 ATTCGAAGGT
Statistics
Matches: 270, Mismatches: 52, Indels: 22
0.78 0.15 0.06
Matches are distributed among these distances:
108 82 0.30
109 20 0.07
110 164 0.61
111 2 0.01
112 2 0.01
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (106 bp):
ATTATGCCCGGAGGTCTTAAAAATCATGCTCGAAGGTCTTACAGAATCGACTAGTAACACGCAAG
TTAAAAAATAAAAATCGATCGGGACAACACCGCGAATCAAA
Found at i:12054648 original size:108 final size:109
Alignment explanation
Indices: 12054354--12054757 Score: 386
Period size: 110 Copynumber: 3.7 Consensus size: 109
12054344 AAATCGACTA
* * * * ** **
12054354 GGATAATACCGTAAGTCAAAAAATAAGGAATCGATCGGGACAACACCGTGAATTAAAATTATGCC
1 GGATAACACCGCAAGTCAAAAAATAA-AAATCGATCGGGACAACACCGCGAATCGAAATTATGTT
** * ** * *
12054419 CGGGGGTCTTAAAAATCATGTTCGAAGGTCTTACAGAATCGA-CT
65 CGAAGGTCTTAGAAATCATGCCCGAAGATCTTACAGAATCGATCG
* * * * * * *
12054463 AG-TACGACATCACAAGTTAAAAAATAAATAATCGATCAGGCCAACATCGCGAATCGAAATTATG
1 GGATA--ACACCGCAAGTCAAAAAATAAA-AATCGATCGGGACAACACCGCGAATCGAAATTATG
* * * *
12054527 -CCAGGAGGACTTAGAAGTCATGCCCGAA-AGTCTTACAGAATCGATCG
63 TTC-GAAGGTCTTAGAAATCATGCCCGAAGA-TCTTACAGAATCGATCG
* *
12054574 GGATAACACTGCAAGTC-AAAAATAAAAATCGATTGGGACAACACCGCGAATCGAAATTATGTTC
1 GGATAACACCGCAAGTCAAAAAATAAAAATCGATCGGGACAACACCGCGAATCGAAATTATGTTC
* *
12054638 GAAGGTCTTAGAAATCATGCTCGGAGATCTTACAGAATCGATCG
66 GAAGGTCTTAGAAATCATGCCCGAAGATCTTACAGAATCGATCG
* * * * * *
12054682 GGATAACACCGTAAGTCAAAAAATTAAAAATTGATCGAGACAACACTGCGAATAGAAATTATATT
1 GGATAACACCGCAAGTCAAAAAA-TAAAAATCGATCGGGACAACACCGCGAATCGAAATTATGTT
12054747 CGAAGGTCTTA
65 CGAAGGTCTTA
12054758 AAGATTATAC
Statistics
Matches: 240, Mismatches: 44, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
108 85 0.35
109 19 0.08
110 132 0.55
111 2 0.01
112 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (109 bp):
GGATAACACCGCAAGTCAAAAAATAAAAATCGATCGGGACAACACCGCGAATCGAAATTATGTTC
GAAGGTCTTAGAAATCATGCCCGAAGATCTTACAGAATCGATCG
Found at i:12054773 original size:110 final size:108
Alignment explanation
Indices: 12054482--12054773 Score: 304
Period size: 108 Copynumber: 2.7 Consensus size: 108
12054472 TCACAAGTTA
* * * ** * * *
12054482 AAAAATAAATAATCGATC-AGGCCAACATCGCGAATCGAAATTAT-GCCAGGAGGACTTAGAAGT
1 AAAAATAAA-AATCGATCGA-GACAACACCGCGAATAGAAATTATATTC-GAAGGTCTTAGAAAT
* * *
12054545 CATGCCC-GAAAGTCTTACAGAATCGATCGGGATAACACTGCAAGTC
63 CATACCCGGAGA-TCTTACAGAATCGATCGGGATAACACCGCAAGTC
* * * *
12054591 AAAAATAAAAATCGATTGGGACAACACCGCGAATCGAAATTATGTTCGAAGGTCTTAGAAATCAT
1 AAAAATAAAAATCGATCGAGACAACACCGCGAATAGAAATTATATTCGAAGGTCTTAGAAATCAT
* * *
12054656 GCTCGGAGATCTTACAGAATCGATCGGGATAACACCGTAAGTC
66 ACCCGGAGATCTTACAGAATCGATCGGGATAACACCGCAAGTC
* *
12054699 AAAAAATTAAAAATTGATCGAGACAACACTGCGAATAGAAATTATATTCGAAGGTCTTA-AAGAT
1 -AAAAA-TAAAAATCGATCGAGACAACACCGCGAATAGAAATTATATTCGAAGGTCTTAGAA-AT
*
12054763 TATACCCGGAG
63 CATACCCGGAG
12054774 GAGTTAGAAA
Statistics
Matches: 155, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
108 79 0.51
109 20 0.13
110 56 0.36
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (108 bp):
AAAAATAAAAATCGATCGAGACAACACCGCGAATAGAAATTATATTCGAAGGTCTTAGAAATCAT
ACCCGGAGATCTTACAGAATCGATCGGGATAACACCGCAAGTC
Found at i:12056558 original size:1 final size:1
Alignment explanation
Indices: 12056552--12056617 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
12056542 TCCTTTCTTG
* * * * ** * * *
12056552 TTTTTTTTTTTTTTTATCTTTTTGTCTTTTTACTTTTTTGTTTTTTTTTTTTGTTTTTTTTGTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12056617 T
1 T
12056618 GTGATGCCCC
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.03, C:0.05, G:0.06, T:0.86
Consensus pattern (1 bp):
T
Found at i:12057199 original size:9 final size:9
Alignment explanation
Indices: 12057185--12057224 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
12057175 AAAAAAAACC
12057185 TTTTTTCTT
1 TTTTTTCTT
12057194 TTTTTTC--
1 TTTTTTCTT
12057201 TTTTTTCTT
1 TTTTTTCTT
*
12057210 TTTTTTATT
1 TTTTTTCTT
12057219 TTTTTT
1 TTTTTT
12057225 TATCTTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
7 7 0.25
9 21 0.75
ACGTcount: A:0.03, C:0.07, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:12057205 original size:16 final size:16
Alignment explanation
Indices: 12057184--12057222 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
12057174 AAAAAAAAAC
12057184 CTTTTTTCTTTTTTTT
1 CTTTTTTCTTTTTTTT
12057200 CTTTTTTCTTTTTTTT
1 CTTTTTTCTTTTTTTT
*
12057216 ATTTTTT
1 CTTTTTT
12057223 TTTATCTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.03, C:0.10, G:0.00, T:0.87
Consensus pattern (16 bp):
CTTTTTTCTTTTTTTT
Found at i:12063364 original size:15 final size:14
Alignment explanation
Indices: 12063327--12063377 Score: 66
Period size: 14 Copynumber: 3.6 Consensus size: 14
12063317 TGTCATTTTG
*
12063327 GATTTTAAGGTTTC
1 GATTTTAGGGTTTC
* *
12063341 AATTTTAGGGTTTG
1 GATTTTAGGGTTTC
12063355 GATGTTTAGGGTTTC
1 GAT-TTTAGGGTTTC
12063370 GATTTTAG
1 GATTTTAG
12063378 AACTTGGAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
14 18 0.58
15 13 0.42
ACGTcount: A:0.20, C:0.04, G:0.27, T:0.49
Consensus pattern (14 bp):
GATTTTAGGGTTTC
Found at i:12063367 original size:29 final size:28
Alignment explanation
Indices: 12063323--12063377 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
12063313 GGTTTGTCAT
12063323 TTTGGATTTTAAGGTTTCAATTTTAGGG
1 TTTGGATTTTAAGGTTTCAATTTTAGGG
* *
12063351 TTTGGATGTTTAGGGTTTCGATTTTAG
1 TTTGGAT-TTTAAGGTTTCAATTTTAG
12063378 AACTTGGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.18, C:0.04, G:0.27, T:0.51
Consensus pattern (28 bp):
TTTGGATTTTAAGGTTTCAATTTTAGGG
Found at i:12063384 original size:29 final size:28
Alignment explanation
Indices: 12063324--12063385 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
12063314 GTTTGTCATT
***
12063324 TTGGATTTTAAGGTTTCAATTTTAGGGT
1 TTGGATTTTAAGGTTTCAATTTTAGAAC
* *
12063352 TTGGATGTTTAGGGTTTCGATTTTAGAAC
1 TTGGAT-TTTAAGGTTTCAATTTTAGAAC
12063381 TTGGA
1 TTGGA
12063386 AGGATTAGGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 6 0.21
29 22 0.79
ACGTcount: A:0.21, C:0.05, G:0.27, T:0.47
Consensus pattern (28 bp):
TTGGATTTTAAGGTTTCAATTTTAGAAC
Found at i:12063462 original size:14 final size:14
Alignment explanation
Indices: 12063443--12063473 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12063433 TTGAATTTTT
12063443 GGGTTTCAAATTTA
1 GGGTTTCAAATTTA
*
12063457 GGGTTTCAATTTTA
1 GGGTTTCAAATTTA
12063471 GGG
1 GGG
12063474 ATTTGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.06, G:0.29, T:0.42
Consensus pattern (14 bp):
GGGTTTCAAATTTA
Found at i:12063491 original size:21 final size:21
Alignment explanation
Indices: 12063467--12063511 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
12063457 GGGTTTCAAT
*
12063467 TTTAGGG-ATTTGATTTTAGGG
1 TTTAGGGAATTT-ATTTTAAGG
12063488 TTTAGGGAATTTATTTTAAGG
1 TTTAGGGAATTTATTTTAAGG
12063509 TTT
1 TTT
12063512 GGAAGGTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (21 bp):
TTTAGGGAATTTATTTTAAGG
Found at i:12064008 original size:17 final size:19
Alignment explanation
Indices: 12063961--12064010 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
12063951 ATCATGCATA
*
12063961 AATATATAAAAAAAAACTC
1 AATATATAAAAAATAACTC
*
12063980 AAAATA-ACAAAAATAA-T-
1 AATATATA-AAAAATAACTC
12063997 AATATATAAAAAAT
1 AATATATAAAAAAT
12064011 TCAAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 11 0.42
18 3 0.12
19 12 0.46
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AATATATAAAAAATAACTC
Found at i:12068134 original size:21 final size:22
Alignment explanation
Indices: 12068087--12068141 Score: 76
Period size: 21 Copynumber: 2.5 Consensus size: 22
12068077 AAAAAATTGT
12068087 TTTTTCTTAAACACCCTTAAAA
1 TTTTTCTTAAACACCCTTAAAA
* *
12068109 TTTTT-TTGAACACCTTTAAAA
1 TTTTTCTTAAACACCCTTAAAA
12068130 TTTTTACTTAAA
1 TTTTT-CTTAAA
12068142 TACCAAAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 19 0.68
22 5 0.18
23 4 0.14
ACGTcount: A:0.35, C:0.16, G:0.02, T:0.47
Consensus pattern (22 bp):
TTTTTCTTAAACACCCTTAAAA
Found at i:12070434 original size:19 final size:19
Alignment explanation
Indices: 12070412--12070448 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
12070402 TATAGATTTA
*
12070412 TGGTTGTTTTGTGGGTTTG
1 TGGTTATTTTGTGGGTTTG
12070431 TGGTTATTTTGTGGGTTT
1 TGGTTATTTTGTGGGTTT
12070449 ACTATATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.03, C:0.00, G:0.38, T:0.59
Consensus pattern (19 bp):
TGGTTATTTTGTGGGTTTG
Found at i:12071607 original size:20 final size:21
Alignment explanation
Indices: 12071566--12071611 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
12071556 CCCGAAATTA
12071566 ATAAAATATTATTTTTAAAAT
1 ATAAAATATTATTTTTAAAAT
*
12071587 ATAAAATATTATTTTT-CAAT
1 ATAAAATATTATTTTTAAAAT
12071607 ATAAA
1 ATAAA
12071612 TATAAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:12071631 original size:8 final size:8
Alignment explanation
Indices: 12071605--12071667 Score: 65
Period size: 8 Copynumber: 7.6 Consensus size: 8
12071595 TTATTTTTCA
12071605 ATATAAAT
1 ATATAAAT
12071613 ATA-AAATT
1 ATATAAA-T
12071621 ATATAAAT
1 ATATAAAT
*
12071629 ATATAAAG
1 ATATAAAT
12071637 ATATAAAGAT
1 ATAT-AA-AT
12071647 ATATAAAT
1 ATATAAAT
* *
12071655 AAATAATT
1 ATATAAAT
12071663 ATATA
1 ATATA
12071668 TTTTTCTTAC
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
7 3 0.07
8 31 0.67
9 7 0.15
10 5 0.11
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (8 bp):
ATATAAAT
Found at i:12071667 original size:26 final size:26
Alignment explanation
Indices: 12071611--12071660 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
12071601 TTCAATATAA
*
12071611 ATATAAAATTATATAAATATATAAAG
1 ATATAAAATTATATAAATAAATAAAG
12071637 ATATAAAGA-TATATAAATAAATAA
1 ATATAAA-ATTATATAAATAAATAA
12071661 TTATATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (26 bp):
ATATAAAATTATATAAATAAATAAAG
Found at i:12081034 original size:39 final size:39
Alignment explanation
Indices: 12080971--12081073 Score: 115
Period size: 39 Copynumber: 2.7 Consensus size: 39
12080961 TATTTTAATC
* * * *
12080971 TAATATAATAAAT--AAATTTTTATTA-ATTATTATATAA
1 TAATTTAATAAATAAAAATTATTATTATACTA-TAAATAA
12081008 TAATTTAATAAATAAAAATTATTATTATACTATAAATAA
1 TAATTTAATAAATAAAAATTATTATTATACTATAAATAA
* *
12081047 TAAATTAATAAATAAATATTATT-TTAT
1 TAATTTAATAAATAAAAATTATTATTAT
12081074 GAATTAAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
37 12 0.21
38 4 0.07
39 38 0.67
40 3 0.05
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (39 bp):
TAATTTAATAAATAAAAATTATTATTATACTATAAATAA
Found at i:12081260 original size:19 final size:19
Alignment explanation
Indices: 12081228--12081282 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
12081218 AAAGTTTAAT
* *
12081228 ATTTTTTAAGTATTTATTA
1 ATTTTATAAATATTTATTA
* *
12081247 ATTTTATAAATATTAAATA
1 ATTTTATAAATATTTATTA
12081266 ATTTTA-AAAT-TTTATTA
1 ATTTTATAAATATTTATTA
12081283 TATATAAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
17 5 0.17
18 4 0.13
19 21 0.70
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
ATTTTATAAATATTTATTA
Found at i:12082013 original size:20 final size:19
Alignment explanation
Indices: 12081993--12082043 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 19
12081983 TTATAAAATA
*
12081993 AAATAATTATTTTATATAT
1 AAATAATTATTTAATATAT
12082012 AAAT--TTATTTAATATATT
1 AAATAATTATTTAATATA-T
12082030 AAA-AATTATATTAA
1 AAATAATTAT-TTAA
12082044 AAAATTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
17 11 0.41
18 4 0.15
19 8 0.30
20 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATAATTATTTAATATAT
Found at i:12082344 original size:32 final size:32
Alignment explanation
Indices: 12082301--12082371 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
12082291 TTGCTCAAGT
*
12082301 TTTAAAAAAATTTAAATAAAATATTAAAATTCA
1 TTTAAATAAATTTAAAT-AAATATTAAAATTCA
* * * *
12082334 -TTAAATAAATTTTAATTAATTTTTAAATTCA
1 TTTAAATAAATTTAAATAAATATTAAAATTCA
12082365 TTTAAAT
1 TTTAAAT
12082372 TTTAGATCGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
31 12 0.38
32 20 0.62
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (32 bp):
TTTAAATAAATTTAAATAAATATTAAAATTCA
Found at i:12082445 original size:15 final size:15
Alignment explanation
Indices: 12082425--12082481 Score: 60
Period size: 15 Copynumber: 3.7 Consensus size: 15
12082415 TCACATTCAC
12082425 ATATATATAAATTAT
1 ATATATATAAATTAT
* *
12082440 ATATATGTGAATTAT
1 ATATATATAAATTAT
* * *
12082455 ATATAAATTAATTTGT
1 ATATATA-TAAATTAT
12082471 ATATATATAAA
1 ATATATATAAA
12082482 AATAAAAAAT
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 21 0.66
16 11 0.34
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (15 bp):
ATATATATAAATTAT
Found at i:12082850 original size:41 final size:43
Alignment explanation
Indices: 12082788--12082872 Score: 138
Period size: 41 Copynumber: 2.0 Consensus size: 43
12082778 TAACAAAAAC
*
12082788 TAATCTCATCTCAAATAAAAC-A-GTTTAATCTTTGATGTGAT
1 TAATCTCATCTCAAATAAAACAATCTTTAATCTTTGATGTGAT
*
12082829 TAATTTCATCTCAAATAAAACAATCTTTAATCTTTGATGTGAT
1 TAATCTCATCTCAAATAAAACAATCTTTAATCTTTGATGTGAT
12082872 T
1 T
12082873 TTTCCTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
41 20 0.50
42 1 0.03
43 19 0.47
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.41
Consensus pattern (43 bp):
TAATCTCATCTCAAATAAAACAATCTTTAATCTTTGATGTGAT
Found at i:12092759 original size:11 final size:11
Alignment explanation
Indices: 12092726--12092763 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12092716 TGACTTAAAT
12092726 TTTAATAAAAA
1 TTTAATAAAAA
*
12092737 -TTATATACAAA
1 TTTA-ATAAAAA
12092748 TTTAATAAAAA
1 TTTAATAAAAA
12092759 TTTAA
1 TTTAA
12092764 AACTACATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 3 0.13
11 17 0.74
12 3 0.13
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
TTTAATAAAAA
Found at i:12095844 original size:5 final size:5
Alignment explanation
Indices: 12095834--12095860 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12095824 GATTCTTTTT
12095834 ATAAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA AT
12095861 TAGGCACATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:12095927 original size:6 final size:7
Alignment explanation
Indices: 12095910--12095935 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
12095900 GGGATTTTGA
12095910 AAAAAAT
1 AAAAAAT
12095917 AAAAAAT
1 AAAAAAT
12095924 AAAAAAT
1 AAAAAAT
12095931 AAAAA
1 AAAAA
12095936 GCTCTCCACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:12097761 original size:15 final size:16
Alignment explanation
Indices: 12097743--12097777 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12097733 ACATATGTTT
12097743 ATAAA-TATTTATTAA
1 ATAAATTATTTATTAA
*
12097758 ATAAATTTTTTATTAA
1 ATAAATTATTTATTAA
12097774 ATAA
1 ATAA
12097778 TATAAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAAATTATTTATTAA
Found at i:12098856 original size:12 final size:12
Alignment explanation
Indices: 12098815--12098903 Score: 67
Period size: 13 Copynumber: 7.2 Consensus size: 12
12098805 AAATTAAAAG
12098815 ATTTTGTTATATAA
1 ATTTT-TTA-ATAA
*
12098829 TTTTTTTAA-AA
1 ATTTTTTAATAA
*
12098840 A--TTTTAATAT
1 ATTTTTTAATAA
12098850 ATTTTTTAAATAA
1 ATTTTTT-AATAA
12098863 ATATTTTTAATAA
1 AT-TTTTTAATAA
* *
12098876 AATTTTTGATAA
1 ATTTTTTAATAA
12098888 ATTTTTATTAATAA
1 A-TTTT-TTAATAA
12098902 AT
1 AT
12098904 AAATACCATA
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
9 6 0.10
10 2 0.03
11 2 0.03
12 15 0.25
13 19 0.32
14 16 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
ATTTTTTAATAA
Found at i:12098871 original size:14 final size:13
Alignment explanation
Indices: 12098841--12098904 Score: 69
Period size: 12 Copynumber: 4.9 Consensus size: 13
12098831 TTTTTAAAAA
*
12098841 TTTTAATATAT-T
1 TTTTAATAAATAT
12098853 TTTTAAATAAATAT
1 TTTT-AATAAATAT
12098867 TTTTAATAAA-AT
1 TTTTAATAAATAT
* *
12098879 TTTTGATAAATTT
1 TTTTAATAAATAT
12098892 TTATTAATAAATA
1 TT-TTAATAAATA
12098905 AATACCATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
12 15 0.35
13 15 0.35
14 13 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
TTTTAATAAATAT
Found at i:12099760 original size:13 final size:13
Alignment explanation
Indices: 12099743--12099778 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
12099733 AAATATTTTT
12099743 AAATTATTTTAAA
1 AAATTATTTTAAA
* *
12099756 GAATTTTTTTAAA
1 AAATTATTTTAAA
12099769 AAATTATTTT
1 AAATTATTTT
12099779 GTCTTTAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
AAATTATTTTAAA
Found at i:12103826 original size:31 final size:30
Alignment explanation
Indices: 12103779--12103840 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 30
12103769 TTGGCAATGA
*
12103779 TAAATAGTATAACATTAAGGTGAAAAACTAG
1 TAAAGAGTATAACATTAAGGTGAAAAA-TAG
*
12103810 TAAAGAGTATATCATTAAGGTGAAAAATAG
1 TAAAGAGTATAACATTAAGGTGAAAAATAG
12103840 T
1 T
12103841 TATTCTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 4 0.14
31 25 0.86
ACGTcount: A:0.50, C:0.05, G:0.18, T:0.27
Consensus pattern (30 bp):
TAAAGAGTATAACATTAAGGTGAAAAATAG
Found at i:12104899 original size:16 final size:16
Alignment explanation
Indices: 12104878--12104916 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12104868 ACATGTGCAC
12104878 ATGTATATATATATAT
1 ATGTATATATATATAT
*
12104894 ATGTATATGTATATAT
1 ATGTATATATATATAT
12104910 ATG-ATAT
1 ATGTATAT
12104917 GATTTGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (16 bp):
ATGTATATATATATAT
Found at i:12112190 original size:19 final size:17
Alignment explanation
Indices: 12112134--12112178 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
12112124 TTTAAAGATA
12112134 TTTTCTCTTTTAT-TCAT
1 TTTTCTCTTTTATCT-AT
12112151 TTTTCTCTTTTATCTAT
1 TTTTCTCTTTTATCTAT
*
12112168 TTTTTTCTTTT
1 TTTTCTCTTTT
12112179 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 25 0.96
18 1 0.04
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTCTCTTTTATCTAT
Found at i:12115746 original size:11 final size:11
Alignment explanation
Indices: 12115730--12115771 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
12115720 GCGATTACAC
12115730 AATATAAAAAT
1 AATATAAAAAT
*
12115741 AATATAAATAAAA
1 AATAT-AA-AAAT
12115754 AATATAAAAAT
1 AATATAAAAAT
12115765 AATATAA
1 AATATAA
12115772 TTTAAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 15 0.56
12 4 0.15
13 8 0.30
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:12124562 original size:510 final size:512
Alignment explanation
Indices: 12123559--12124581 Score: 1644
Period size: 510 Copynumber: 2.0 Consensus size: 512
12123549 CCTAACAGCT
* *
12123559 CAACACTCTTAACATTTTTTTATCTCTCATTTTCTTTCACAGCTTCACTGTTGCACTATTTCTAT
1 CAACACTCTTAACATTTTCTTATCTCTCATTTTCTTTCACAGCTTCACTGTTGCACTATCTCTAT
*
12123624 CTTCTCCCTCAAATTTTTCACAATTTTTTATCTCTAATCTGCCACACATCGATCTCACATCTCAA
66 CTTCTCCCTCAAATTTTTCACAATTTTCTATCTCTAATCTGCCACACATCGATCTCACATCTCAA
* *
12123689 CACTCTGATTTACCGCATATCCTCTTCCTCTCTTTCTTGTCACTCAAATCTCACTCTCATCTCAT
131 CACTCTAATCTACCGCATATCCTCTT-CTCTCTTTCTTGTCACTCAAATCTCACTCTCATCTCAT
* * * * *
12123754 AGTCCTTTTGCCTTTCACCCTTATCTTGTGCGCTATTGTCGTGTCCTTCTGTCACACCACTCTGC
195 AGTCCATTTGCCTTTCACCCTCATCTTATGCGCTATCGTCGTGTCCTTCTATCACACCACTCTGC
12123819 ACATTTGCCTCCTTTATTCTTCAGTTCATCTCACAGAGTCATGGTCTTTTAGGATCTTTCAATTT
260 ACATTTGCCTCCTTTATTCTTCAGTTCATCTCACAGAGTCATGGTCTTTTAGGATCTTTCAATTT
* * * *
12123884 TTCTTGCAGTGTCACCTTATTTCTTTTTTAGTTTTTCTCGTAAAGTTGAGGTCAGTAGCTTTGTT
325 TTCTTGCAGTGTCACCTTATTCCTTTTTTAATTTCTCTCGTAAAGTTGAGGTCAGTAGCGTTGTT
* * * * *
12123949 TTCATCCTTGTTTCTTAGGATTTTAAAGCACCTTCACTAAAATATTTTGAAAGGAAACCTACCTT
390 TTCATCCTTGTTTCTTAAGATTTTAAAGCACATTCACTAAAAAATTTTGAAAGGAAACCCACATT
* *
12124014 CACTAAAAGATCCATGTACTAACTAGCTATAGCACATAGAAATATGGGGTTTAACAAC
455 CACTAAAAGATCCATGTACTAACTAGCTATAACACATAGAAATATGAGGTTTAACAAC
12124072 CAACACTCTTAACATTTTCTTATCTCTCATTTT-TCTTCACAGCTTCACTGTTGCACTATCTCTA
1 CAACACTCTTAACATTTTCTTATCTCTCATTTTCT-TTCACAGCTTCACTGTTGCACTATCTCTA
* *
12124136 TCTTTTCCCTCAGATTTTTCACAATTTTCTATCTCTAATCTGCCACACATCGATCTCACATCTCA
65 TCTTCTCCCTCAAATTTTTCACAATTTTCTATCTCTAATCTGCCACACATCGATCTCACATCTCA
* *
12124201 ACACTCTAATCTACCGCATATCCTCTT-T-T-TTTTTTGTCACTCAAATCTCACTCTCATTTCAT
130 ACACTCTAATCTACCGCATATCCTCTTCTCTCTTTCTTGTCACTCAAATCTCACTCTCATCTCAT
* *
12124263 AGTCCATTTGCCTTTCACCCTCATCTTATGCGCTATCGTCGTGTCTTTCTATCGCACCACTCTGC
195 AGTCCATTTGCCTTTCACCCTCATCTTATGCGCTATCGTCGTGTCCTTCTATCACACCACTCTGC
* * *
12124328 ACCTTTGCCT-CTTTCATTCTTCAGTTCCTCTCACAGCGTCATGGT-TTTTCAGGATCTTTCAAT
260 ACATTTGCCTCCTTT-ATTCTTCAGTTCATCTCACAGAGTCATGGTCTTTT-AGGATCTTTCAA-
*
12124391 TTTTTCTTGCAGTGTCACTTTATTCCTTTTTTAATTTCTCTCGTAAAGTTGAGGTCAGTAGCGTT
322 TTTTTCTTGCAGTGTCACCTTATTCCTTTTTTAATTTCTCTCGTAAAGTTGAGGTCAGTAGCGTT
* *
12124456 GTTTTCATCCTTGTTTCTTAAGATTTTAAAGCACATTTACTAAAAAATTTTGAAAGGAAACCCAT
387 GTTTTCATCCTTGTTTCTTAAGATTTTAAAGCACATTCACTAAAAAATTTTGAAAGGAAACCCAC
* *
12124521 ATTCACTAAAAGATCCATGTACTAGCTAGCTATAACACATAGAAATATGAGGTTTAGCAAC
452 ATTCACTAAAAGATCCATGTACTAACTAGCTATAACACATAGAAATATGAGGTTTAACAAC
12124582 TAACCACGTG
Statistics
Matches: 471, Mismatches: 35, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
508 8 0.02
509 138 0.29
510 176 0.37
511 1 0.00
512 1 0.00
513 147 0.31
ACGTcount: A:0.23, C:0.26, G:0.10, T:0.40
Consensus pattern (512 bp):
CAACACTCTTAACATTTTCTTATCTCTCATTTTCTTTCACAGCTTCACTGTTGCACTATCTCTAT
CTTCTCCCTCAAATTTTTCACAATTTTCTATCTCTAATCTGCCACACATCGATCTCACATCTCAA
CACTCTAATCTACCGCATATCCTCTTCTCTCTTTCTTGTCACTCAAATCTCACTCTCATCTCATA
GTCCATTTGCCTTTCACCCTCATCTTATGCGCTATCGTCGTGTCCTTCTATCACACCACTCTGCA
CATTTGCCTCCTTTATTCTTCAGTTCATCTCACAGAGTCATGGTCTTTTAGGATCTTTCAATTTT
TCTTGCAGTGTCACCTTATTCCTTTTTTAATTTCTCTCGTAAAGTTGAGGTCAGTAGCGTTGTTT
TCATCCTTGTTTCTTAAGATTTTAAAGCACATTCACTAAAAAATTTTGAAAGGAAACCCACATTC
ACTAAAAGATCCATGTACTAACTAGCTATAACACATAGAAATATGAGGTTTAACAAC
Found at i:12124923 original size:48 final size:47
Alignment explanation
Indices: 12124830--12124955 Score: 154
Period size: 48 Copynumber: 2.7 Consensus size: 47
12124820 TTAAATAAGA
* *
12124830 ATTACAATTTGTCTCA-TATATATAATA-TTTGTTTTTTAATATATTT
1 ATTACAATTTGTCCCACTATATATAATATTTTG-TTTGTAATATATTT
* * *
12124876 ATTACAATTTATCCCACTTATATATAATATTTTGTTTGTAGTTTATTT
1 ATTACAATTTGTCCCAC-TATATATAATATTTTGTTTGTAATATATTT
12124924 ATTACAATTTGT-CC-C-ATATATAATATTTTGTT
1 ATTACAATTTGTCCCACTATATATAATATTTTGTT
12124956 CTTTAATTTA
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
44 17 0.24
46 15 0.21
47 2 0.03
48 33 0.46
49 4 0.06
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.54
Consensus pattern (47 bp):
ATTACAATTTGTCCCACTATATATAATATTTTGTTTGTAATATATTT
Found at i:12125605 original size:23 final size:23
Alignment explanation
Indices: 12125575--12125619 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
12125565 CTAATTTTAA
*
12125575 ATCCAATTAAATGAAAAAATCAG
1 ATCCAATTAAAAGAAAAAATCAG
*
12125598 ATCCAATTAAAAGAAAAGATCA
1 ATCCAATTAAAAGAAAAAATCA
12125620 TATTAGCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.58, C:0.13, G:0.09, T:0.20
Consensus pattern (23 bp):
ATCCAATTAAAAGAAAAAATCAG
Found at i:12125655 original size:22 final size:22
Alignment explanation
Indices: 12125630--12125672 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
12125620 TATTAGCATC
12125630 TTTACACA-TTCATTTCCTTATG
1 TTTACACATTTCATTT-CTTATG
* *
12125652 TTTATATATTTCATTTCTTAT
1 TTTACACATTTCATTTCTTAT
12125673 TTTCTTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.23, C:0.16, G:0.02, T:0.58
Consensus pattern (22 bp):
TTTACACATTTCATTTCTTATG
Found at i:12133055 original size:26 final size:27
Alignment explanation
Indices: 12133026--12133084 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
12133016 TATATATGAT
*
12133026 ATTTGTTAAATTA-ATA-AATAATTAAA
1 ATTTATTAAATTATATATAATAA-TAAA
*
12133052 ATTTATTAATTTATTATATAATAATAAA
1 ATTTATTAAATTA-TATATAATAATAAA
12133080 ATTTA
1 ATTTA
12133085 ATTATTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 11 0.39
28 12 0.43
29 5 0.18
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
ATTTATTAAATTATATATAATAATAAA
Found at i:12133091 original size:28 final size:29
Alignment explanation
Indices: 12133042--12133106 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
12133032 TAAATTAATA
12133042 AATAATTAAAATTTATTAATTTATTATAT
1 AATAATTAAAATTTATTAATTTATTATAT
12133071 AATAA-TAAAATTTAATT-ATTTATTATAT
1 AATAATTAAAATTT-ATTAATTTATTATAT
*
12133099 TA-AATTAA
1 AATAATTAA
12133107 GTTAATTATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
27 2 0.06
28 23 0.70
29 8 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AATAATTAAAATTTATTAATTTATTATAT
Found at i:12133115 original size:22 final size:20
Alignment explanation
Indices: 12133082--12133125 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
12133072 ATAATAAAAT
*
12133082 TTAATTATTTATTATATTAAA
1 TTAATTAATTATTATA-TAAA
*
12133103 TTAAGTTAATTATTTTATAAA
1 TTAA-TTAATTATTATATAAA
12133124 TT
1 TT
12133126 TTTAATACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTAATTAATTATTATATAAA
Found at i:12136658 original size:9 final size:9
Alignment explanation
Indices: 12136644--12136669 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12136634 CCTTTCCAAT
12136644 ACTCCCCAG
1 ACTCCCCAG
12136653 ACTCCCCAG
1 ACTCCCCAG
12136662 ACTCCCCA
1 ACTCCCCA
12136670 TTCCAGCAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.58, G:0.08, T:0.12
Consensus pattern (9 bp):
ACTCCCCAG
Found at i:12138554 original size:22 final size:22
Alignment explanation
Indices: 12138529--12138573 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
12138519 TTGATAATTG
*
12138529 AATTTATTAAATATATTTAACT
1 AATTTATTAAATATATCTAACT
* **
12138551 AATTTTTTATTTATATCTAACT
1 AATTTATTAAATATATCTAACT
12138573 A
1 A
12138574 TTTTTGTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTTATTAAATATATCTAACT
Found at i:12143745 original size:2 final size:2
Alignment explanation
Indices: 12143738--12143771 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12143728 TTCGTACTTC
12143738 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
12143772 GTGGTATGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:12145560 original size:21 final size:22
Alignment explanation
Indices: 12145529--12145581 Score: 90
Period size: 22 Copynumber: 2.4 Consensus size: 22
12145519 ATATATAATT
12145529 ATATATTTATA-TTTAAAAAATA
1 ATAT-TTTATATTTTAAAAAATA
12145551 ATATTTTATATTTTAAAAAATA
1 ATATTTTATATTTTAAAAAATA
12145573 ATATTTTAT
1 ATATTTTAT
12145582 TAATTTTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATTTTATATTTTAAAAAATA
Found at i:12153386 original size:29 final size:26
Alignment explanation
Indices: 12153338--12153410 Score: 62
Period size: 24 Copynumber: 2.8 Consensus size: 26
12153328 TAAACATAAA
**
12153338 ATATATATTTTTTATTTTATTAAATTT
1 ATATATATTTTTTAAATTA-TAAATTT
*
12153365 ATATATAATTTTTTAAAATTATAAA-TC
1 ATATAT-ATTTTTT-AAATTATAAATTT
12153392 ATAT-TA-TTTTTATAATTAT
1 ATATATATTTTTTA-AATTAT
12153411 TTTTATAATT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
23 1 0.03
24 11 0.28
25 1 0.03
26 1 0.03
27 11 0.28
28 11 0.28
29 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (26 bp):
ATATATATTTTTTAAATTATAAATTT
Found at i:12153409 original size:12 final size:12
Alignment explanation
Indices: 12153394--12153420 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
12153384 TATAAATCAT
12153394 ATTATTTTTATA
1 ATTATTTTTATA
12153406 ATTATTTTTATA
1 ATTATTTTTATA
12153418 ATT
1 ATT
12153421 TTATCATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTATTTTTATA
Found at i:12154099 original size:6 final size:6
Alignment explanation
Indices: 12154089--12154119 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
12154079 GGGGTAAAGA
*
12154089 AAAAAA AAAAAC AAAAAC AAAAAC AAAAAC A
1 AAAAAC AAAAAC AAAAAC AAAAAC AAAAAC A
12154120 GGAAGAAGCC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:12155317 original size:23 final size:23
Alignment explanation
Indices: 12155264--12155317 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
12155254 ATACCATACT
*
12155264 ATAATAAAACAATATATCATGTA
1 ATAATAATACAATATATCATGTA
* * *
12155287 ATAATAATATAATATTTTATGTA
1 ATAATAATACAATATATCATGTA
12155310 ATAATAAT
1 ATAATAAT
12155318 CATGTAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (23 bp):
ATAATAATACAATATATCATGTA
Found at i:12155361 original size:19 final size:19
Alignment explanation
Indices: 12155310--12155372 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
12155300 ATTTTATGTA
*
12155310 ATAATAATCATGTAATAAT
1 ATAATAATCATGCAATAAT
12155329 ATAATATATCATGCAATTAAT
1 ATAATA-ATCATGCAA-TAAT
*
12155350 -TAATAATCATGCAAAAAT
1 ATAATAATCATGCAATAAT
12155368 A-AATA
1 ATAATA
12155373 TCACAAATAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.18
19 15 0.38
20 13 0.33
21 4 0.10
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (19 bp):
ATAATAATCATGCAATAAT
Found at i:12155534 original size:14 final size:14
Alignment explanation
Indices: 12155517--12155568 Score: 70
Period size: 14 Copynumber: 3.8 Consensus size: 14
12155507 AGAGAATAAA
*
12155517 AAAAGAAAAAAATC
1 AAAATAAAAAAATC
*
12155531 AAAATAATAAAATC
1 AAAATAAAAAAATC
*
12155545 AAAATTAAAAAA-C
1 AAAATAAAAAAATC
12155558 AAAATAAAAAA
1 AAAATAAAAAA
12155569 GAAAAACATA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
13 11 0.33
14 22 0.67
ACGTcount: A:0.79, C:0.06, G:0.02, T:0.13
Consensus pattern (14 bp):
AAAATAAAAAAATC
Found at i:12157449 original size:20 final size:21
Alignment explanation
Indices: 12157424--12157464 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
12157414 ACCTGTTCAA
12157424 AATAT-ATGTAAAATAT-AAAT
1 AATATAAT-TAAAATATCAAAT
12157444 AATATAATTAAAATATCAAAT
1 AATATAATTAAAATATCAAAT
12157465 CATAATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (21 bp):
AATATAATTAAAATATCAAAT
Found at i:12162980 original size:21 final size:21
Alignment explanation
Indices: 12162935--12162987 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
12162925 TATATAAGGG
12162935 TAAAATAAT--AAATTTTAAT
1 TAAAATAATAAAAATTTTAAT
*
12162954 TGAAATAATAAAAATATTT-AT
1 TAAAATAATAAAAAT-TTTAAT
12162975 TAAAAT-ATAAAAA
1 TAAAATAATAAAAA
12162988 CTTGATTAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 8 0.28
20 7 0.24
21 11 0.38
22 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TAAAATAATAAAAATTTTAAT
Found at i:12165534 original size:18 final size:17
Alignment explanation
Indices: 12165508--12165557 Score: 57
Period size: 18 Copynumber: 2.9 Consensus size: 17
12165498 GATCACAAGG
12165508 TTTTATTTTAATTTTTC
1 TTTTATTTTAATTTTTC
* *
12165525 TTTCTATTTTAGGTTTTTG
1 TTT-TATTTTA-ATTTTTC
12165544 TTTTA-TTTAATTTT
1 TTTTATTTTAATTTT
12165558 CTAATTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 4 0.14
17 7 0.25
18 9 0.32
19 8 0.29
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTATTTTAATTTTTC
Found at i:12165690 original size:17 final size:18
Alignment explanation
Indices: 12165656--12165690 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
12165646 TGCATTATGT
12165656 TTATTTAGTTTTTACATG
1 TTATTTAGTTTTTACATG
*
12165674 TTATTTA-TTTTTTCATG
1 TTATTTAGTTTTTACATG
12165691 AATTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.20, C:0.06, G:0.09, T:0.66
Consensus pattern (18 bp):
TTATTTAGTTTTTACATG
Found at i:12166145 original size:69 final size:69
Alignment explanation
Indices: 12166053--12166189 Score: 168
Period size: 69 Copynumber: 2.0 Consensus size: 69
12166043 GAGGATAATT
* * *
12166053 TTCAATAAAAAATCTTATCAATAGATTAAAGGATATTATGACTATAAACTT-GGTTTATAGGTAT
1 TTCAATAAAAAATCTTATCAATAGATTAAAGAATATTATGACTA-AAAATTAGGTTTATAGATAT
12166117 TTATG
65 TTATG
* * * ** * *
12166122 TTCAATAGAAAGTCTTATTAATAGATTGGAGAATATTTTGACTAAAAATTATGTTTATAGATATT
1 TTCAATAAAAAATCTTATCAATAGATTAAAGAATATTATGACTAAAAATTAGGTTTATAGATATT
12166187 TAT
66 TAT
12166190 TTTTGGAAGC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
68 5 0.09
69 52 0.91
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.41
Consensus pattern (69 bp):
TTCAATAAAAAATCTTATCAATAGATTAAAGAATATTATGACTAAAAATTAGGTTTATAGATATT
TATG
Found at i:12171032 original size:22 final size:22
Alignment explanation
Indices: 12171002--12171118 Score: 99
Period size: 22 Copynumber: 5.1 Consensus size: 22
12170992 CCTTTGAAAC
*
12171002 TTTGGATGTGAATTTTTAAAAT
1 TTTGCATGTGAATTTTTAAAAT
**
12171024 TTTGCATGTGAACCTTTAAAAGTT
1 TTTGCATGTGAATTTTTAAAA--T
** *
12171048 TTTAAATGTGAACTTTTAAAAT
1 TTTGCATGTGAATTTTTAAAAT
* * * *
12171070 TTTGGATATGAATCTCTAAAAT
1 TTTGCATGTGAATTTTTAAAAT
*
12171092 TTTTCAAATGTGAATTTTTAAAAT
1 TTTGC--ATGTGAATTTTTAAAAT
12171116 TTT
1 TTT
12171119 AGATGCGAGT
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
22 38 0.51
24 36 0.49
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (22 bp):
TTTGCATGTGAATTTTTAAAAT
Found at i:12171065 original size:46 final size:46
Alignment explanation
Indices: 12171007--12171118 Score: 163
Period size: 46 Copynumber: 2.4 Consensus size: 46
12170997 GAAACTTTGG
* *
12171007 ATGTGAATTTTTAAAATTTTGCATGTGAACCTTTAAAAGTTTTT-AA
1 ATGTGAATTTTTAAAATTTTGCATATGAACCTCTAAAA-TTTTTCAA
* * *
12171053 ATGTGAACTTTTAAAATTTTGGATATGAATCTCTAAAATTTTTCAA
1 ATGTGAATTTTTAAAATTTTGCATATGAACCTCTAAAATTTTTCAA
12171099 ATGTGAATTTTTAAAATTTT
1 ATGTGAATTTTTAAAATTTT
12171119 AGATGCGAGT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
45 5 0.08
46 54 0.92
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (46 bp):
ATGTGAATTTTTAAAATTTTGCATATGAACCTCTAAAATTTTTCAA
Found at i:12171113 original size:24 final size:23
Alignment explanation
Indices: 12171007--12171118 Score: 102
Period size: 24 Copynumber: 4.9 Consensus size: 23
12170997 GAAACTTTGG
**
12171007 ATGTGAATTTTTAAAA-TTTTGC
1 ATGTGAATTTTTAAAATTTTTAA
**
12171029 ATGTGAACCTTTAAAAGTTTTTAA
1 ATGTGAATTTTTAAAA-TTTTTAA
* **
12171053 ATGTGAACTTTTAAAA-TTTTGG
1 ATGTGAATTTTTAAAATTTTTAA
* * *
12171075 ATATGAATCTCTAAAATTTTTCAA
1 ATGTGAATTTTTAAAATTTTT-AA
12171099 ATGTGAATTTTTAAAATTTT
1 ATGTGAATTTTTAAAATTTT
12171119 AGATGCGAGT
Statistics
Matches: 70, Mismatches: 16, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
22 30 0.43
23 4 0.06
24 36 0.51
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (23 bp):
ATGTGAATTTTTAAAATTTTTAA
Found at i:12171420 original size:17 final size:17
Alignment explanation
Indices: 12171400--12171437 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
12171390 TCTTCCTTTT
*
12171400 TTGCGAAATTGAAATTC
1 TTGCGAAATTAAAATTC
12171417 TTGCGAAATTAAAATTC
1 TTGCGAAATTAAAATTC
12171434 TTGC
1 TTGC
12171438 AAACCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (17 bp):
TTGCGAAATTAAAATTC
Found at i:12171448 original size:17 final size:16
Alignment explanation
Indices: 12171400--12171458 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 16
12171390 TCTTCCTTTT
*
12171400 TTGCGAAATTGAAATTC
1 TTGC-AAATTAAAATTC
12171417 TTGCGAAATTAAAATTC
1 TTGC-AAATTAAAATTC
12171434 TTGCAAACCTT-AAATTC
1 TTGCAAA--TTAAAATTC
*
12171451 TTACAAAT
1 TTGCAAAT
12171459 GTGAAGTTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
15 1 0.03
16 3 0.08
17 32 0.84
18 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.36
Consensus pattern (16 bp):
TTGCAAATTAAAATTC
Found at i:12171497 original size:16 final size:17
Alignment explanation
Indices: 12171465--12171528 Score: 67
Period size: 17 Copynumber: 3.8 Consensus size: 17
12171455 AAATGTGAAG
12171465 TTCTTATGAACCTTAAA
1 TTCTTATGAACCTTAAA
12171482 TTCTTATGAA-CTTAAA
1 TTCTTATGAACCTTAAA
* * * *
12171498 GTTCATGTGAGCCTGAAA
1 -TTCTTATGAACCTTAAA
*
12171516 TTCTTAAGAACCT
1 TTCTTATGAACCT
12171529 AAAACTCTTG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
16 6 0.16
17 26 0.70
18 5 0.14
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (17 bp):
TTCTTATGAACCTTAAA
Found at i:12171500 original size:34 final size:33
Alignment explanation
Indices: 12171439--12171531 Score: 87
Period size: 34 Copynumber: 2.7 Consensus size: 33
12171429 AATTCTTGCA
* * * *
12171439 AACCTTAAATTCTTACAAATGTGAAGTTCTTATG
1 AACCTTAAATTCTTAGAACT-TAAAGTTCATATG
*
12171473 AACCTTAAATTCTTATGAACTTAAAGTTCATGTG
1 AACCTTAAATTCTTA-GAACTTAAAGTTCATATG
* * *
12171507 AGCCTGAAATTCTTAAGAACCTAAA
1 AACCTTAAATTCTT-AGAACTTAAA
12171532 ACTCTTGCAA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
34 45 0.92
35 4 0.08
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (33 bp):
AACCTTAAATTCTTAGAACTTAAAGTTCATATG
Found at i:12171554 original size:17 final size:17
Alignment explanation
Indices: 12171534--12171568 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12171524 AACCTAAAAC
12171534 TCTTGCAAACCTGAAGT
1 TCTTGCAAACCTGAAGT
* *
12171551 TCTTGCGAATCTGAAGT
1 TCTTGCAAACCTGAAGT
12171568 T
1 T
12171569 TTGTGAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (17 bp):
TCTTGCAAACCTGAAGT
Found at i:12171694 original size:17 final size:17
Alignment explanation
Indices: 12171623--12171701 Score: 68
Period size: 17 Copynumber: 4.6 Consensus size: 17
12171613 TAAAAAAATG
* * *
12171623 TTGTGATTCTAAAACTT
1 TTGTGAATCTAGAACCT
*
12171640 TTATGAATCTAGAACCT
1 TTGTGAATCTAGAACCT
** * *
12171657 TTACGAAACTTAGAATCT
1 TTGTGAATC-TAGAACCT
12171675 TTGTGAATCTAGAACCT
1 TTGTGAATCTAGAACCT
*
12171692 TTGAGAATCT
1 TTGTGAATCT
12171702 TGAATCATTT
Statistics
Matches: 49, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
17 36 0.73
18 13 0.27
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (17 bp):
TTGTGAATCTAGAACCT
Found at i:12173623 original size:30 final size:30
Alignment explanation
Indices: 12173587--12173646 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
12173577 AATATAATTC
*
12173587 ATATTA-TTGCATGATAGTTTATGTTATATT
1 ATATTATTTGCATGATAATTTATGTT-TATT
* *
12173617 ATATTATTTGTATGATAATTTTTGTTTATT
1 ATATTATTTGCATGATAATTTATGTTTATT
12173647 TTAATTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.28, C:0.02, G:0.12, T:0.58
Consensus pattern (30 bp):
ATATTATTTGCATGATAATTTATGTTTATT
Found at i:12175915 original size:15 final size:15
Alignment explanation
Indices: 12175895--12175928 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12175885 CGTTCAAGTA
12175895 AAATAATCCAAAATC
1 AAATAATCCAAAATC
* *
12175910 AAATAATTCAAAATG
1 AAATAATCCAAAATC
12175925 AAAT
1 AAAT
12175929 CCAAACAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.12, G:0.03, T:0.24
Consensus pattern (15 bp):
AAATAATCCAAAATC
Found at i:12176761 original size:13 final size:13
Alignment explanation
Indices: 12176735--12176770 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
12176725 AGTTTGACAC
12176735 GAAATATC--AAA
1 GAAATATCAAAAA
12176746 GAAATATCAAAAA
1 GAAATATCAAAAA
12176759 GAAATAT-AAAAA
1 GAAATATCAAAAA
12176771 AATTACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 8 0.35
12 5 0.22
13 10 0.43
ACGTcount: A:0.69, C:0.06, G:0.08, T:0.17
Consensus pattern (13 bp):
GAAATATCAAAAA
Found at i:12176953 original size:22 final size:24
Alignment explanation
Indices: 12176929--12176973 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
12176919 TGAACTTAAA
*
12176929 TTTT-ATTTTTATATAATTTTTAT
1 TTTTAATTTATATATAATTTTTAT
*
12176952 TTTTAATTTATATATATTTTTT
1 TTTTAATTTATATATAATTTTT
12176974 TAAAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTAATTTATATATAATTTTTAT
Found at i:12176997 original size:33 final size:34
Alignment explanation
Indices: 12176932--12176997 Score: 80
Period size: 34 Copynumber: 2.0 Consensus size: 34
12176922 ACTTAAATTT
* * * *
12176932 TATTTTTATATAATTTTTATTTTTAATTTATATA
1 TATTTTTATAAAATTTTAAATTTTAATATATATA
*
12176966 TATTTTTTTAAAATTTTAAATTTT-ATATATAT
1 TATTTTTATAAAATTTTAAATTTTAATATATAT
12176998 GTGTGAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 7 0.26
34 20 0.74
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (34 bp):
TATTTTTATAAAATTTTAAATTTTAATATATATA
Found at i:12177138 original size:132 final size:134
Alignment explanation
Indices: 12176977--12177242 Score: 405
Period size: 133 Copynumber: 2.0 Consensus size: 134
12176967 ATTTTTTTAA
* * *
12176977 AATTTTAAATTTTATATATATGTGTGAATTAATATAATTACATTAAACTTAACTTAAT-A-TCTT
1 AATTTTAAATTTTATATATATATATGAATTAATATAATTACATTAAACTTAACTTAATCACACTT
*
12177040 TTTTAAAATTTTTTATTATATAAATTAAGTTTAATGGGT-GTATTTGAAATTTATTTTTTTAATT
66 TTTT-AAATTTTTTATTATATAAATTAAGTTTAATGGGTAG-ATTTGAAATTTAATTTTTTAATT
12177104 TGGATT
129 TGGATT
* * *
12177110 AATTTTAATTTTTA-ATATATATATGAATTAATATAATTATATTAAACTTAATTTAATCACACTT
1 AATTTTAAATTTTATATATATATATGAATTAATATAATTACATTAAACTTAACTTAATCACACTT
* *
12177174 TTTTTAATTTTTTATTATATAAATTAAGTTTAATTGGTAGATTTGAAATTTAATTTTTTAATTTG
66 TTTTAAATTTTTTATTATATAAATTAAGTTTAATGGGTAGATTTGAAATTTAATTTTTTAATTTG
12177239 GATT
131 GATT
12177243 GGGATTGAAA
Statistics
Matches: 121, Mismatches: 9, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
132 39 0.32
133 74 0.61
134 8 0.07
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (134 bp):
AATTTTAAATTTTATATATATATATGAATTAATATAATTACATTAAACTTAACTTAATCACACTT
TTTTAAATTTTTTATTATATAAATTAAGTTTAATGGGTAGATTTGAAATTTAATTTTTTAATTTG
GATT
Found at i:12177442 original size:2 final size:2
Alignment explanation
Indices: 12177399--12177423 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12177389 AGGATCATAA
12177399 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
12177424 AAACAACTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12178299 original size:26 final size:25
Alignment explanation
Indices: 12178270--12178327 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
12178260 TATTTTTAAT
*
12178270 TATTTATTTAATTTTATATT-TATATA
1 TATTTATTT-A-TTTAAATTATATATA
*
12178296 TATTTTATTTATTTAAATTATATTTA
1 TA-TTTATTTATTTAAATTATATATA
12178322 TATTTA
1 TATTTA
12178328 AAAATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
25 11 0.39
26 10 0.36
27 7 0.25
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
TATTTATTTATTTAAATTATATATA
Found at i:12178306 original size:15 final size:15
Alignment explanation
Indices: 12178283--12178324 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
12178273 TTATTTAATT
*
12178283 TTATATTTATATATA
1 TTATATTTATATAAA
* *
12178298 TTTTATTTATTTAAA
1 TTATATTTATATAAA
12178313 TTATATTTATAT
1 TTATATTTATAT
12178325 TTAAAAATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTATATTTATATAAA
Found at i:12183954 original size:18 final size:18
Alignment explanation
Indices: 12183931--12183980 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
12183921 ATTTACATGT
12183931 TTAAAATATAAAATATA-A
1 TTAAAATATAAAAT-TACA
*
12183949 TTAAAATATCAAATTACA
1 TTAAAATATAAAATTACA
*
12183967 ATAAAA-ATAAAATT
1 TTAAAATATAAAATT
12183981 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 9 0.32
18 19 0.68
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (18 bp):
TTAAAATATAAAATTACA
Found at i:12183975 original size:19 final size:18
Alignment explanation
Indices: 12183933--12183975 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
12183923 TTACATGTTT
* *
12183933 AAAATATAAAATATAATT
1 AAAATATAAAATACAATA
*
12183951 AAAATATCAAATTACAATA
1 AAAATAT-AAAATACAATA
12183970 AAAATA
1 AAAATA
12183976 AAATTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (18 bp):
AAAATATAAAATACAATA
Found at i:12197906 original size:25 final size:24
Alignment explanation
Indices: 12197860--12197927 Score: 66
Period size: 25 Copynumber: 2.7 Consensus size: 24
12197850 ATGTTGATAT
* *
12197860 ATTAAAAAATTTTATTTAATTTC-AA
1 ATTAAAATATTTTA-AT-ATTTCAAA
12197885 ATCTAAAATATATTTAATATTTCAAA
1 AT-TAAAATAT-TTTAATATTTCAAA
*
12197911 ATTTAAATATTTTAATA
1 ATTAAAATATTTTAATA
12197928 ATAAATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
24 7 0.19
25 14 0.38
26 12 0.32
27 4 0.11
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTAAAATATTTTAATATTTCAAA
Found at i:12200692 original size:12 final size:12
Alignment explanation
Indices: 12200675--12200699 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12200665 TACAAAATAT
12200675 ATATTATATTTA
1 ATATTATATTTA
12200687 ATATTATATTTA
1 ATATTATATTTA
12200699 A
1 A
12200700 ATCATAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTATATTTA
Found at i:12202076 original size:128 final size:125
Alignment explanation
Indices: 12201890--12202123 Score: 276
Period size: 128 Copynumber: 1.8 Consensus size: 125
12201880 GTCAAAAATA
* * *
12201890 CCTTCAATAATCTCCTTATAAATTTTTGTAAGATGATTATTCAATACATTTTTAGACAAAAA-CC
1 CCTTCAATAATCTCCTTATAAAATTTTATAAGATGATTATTCAATACAATTTTAGACAAAAAGCC
12201954 TATTGAATAATCCCAAAAAATTTTTTTTAATAAGGTTATTAAAGACATTTTTTTACCAAAAAGG
66 --TTGAATAATCCCAAAAAA--TTTTTTAATAAGGTTATTAAAGACATTTTTTTACCAAAAAGG
* * * * *
12202018 CCTTTAATAATC-CCATTATAAAATTTTATGAGGTGATTACTT-AATATAATTTTGGACAAAAAT
1 CCTTCAATAATCTCC-TTATAAAATTTTATAAGATGATTA-TTCAATACAATTTTAGACAAAAA-
** * *
12202081 GCCTTGAATAATTTCAAAAAATTTTTTAGTAGGGTTATTAAAG
63 GCCTTGAATAATCCCAAAAAATTTTTTAATAAGGTTATTAAAG
12202124 GTGTTTCTAG
Statistics
Matches: 90, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
126 20 0.22
127 2 0.02
128 64 0.71
129 2 0.02
130 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (125 bp):
CCTTCAATAATCTCCTTATAAAATTTTATAAGATGATTATTCAATACAATTTTAGACAAAAAGCC
TTGAATAATCCCAAAAAATTTTTTAATAAGGTTATTAAAGACATTTTTTTACCAAAAAGG
Found at i:12202265 original size:125 final size:124
Alignment explanation
Indices: 12201833--12202265 Score: 343
Period size: 125 Copynumber: 3.4 Consensus size: 124
12201823 AAGGCCTTAA
* * * *
12201833 AATAATCTCAAACTAAATTTTTAATAGGGA-TATTAAAGGCGTTTTTGGTCAAAAATACCTTCAA
1 AATAATCTCAAA-AAAATTTTTAATA-GGATTATTAAAGGCATTTTTGATCAAAAACACCTTCAA
* * * ** *
12201897 TAATCTCCTTATAAATTTTTGTAAGATGATTATTCAATACATTTTTAGACAAAAACCTATTG
64 TAATCTCATTATAAATTTTTATAAG-TGATTACTCAATACATTTTTAGACAAAAATATCTTG
* * * * * ** *
12201959 AATAATCCCAAAAAATTTTTTTTAATAAGG-TTATTAAAGACATTTTTTTACCAAAAAGGCCTTT
1 AATAATCTCAAAAAA--ATTTTTAAT-AGGATTATTAAAGGCA-TTTTTGATCAAAAACACCTTC
* * * * * * * **
12202023 AATAATCCCATTATAAAATTTTATGAGGTGATTACTTAATATAATTTTGGACAAAAATGCCTTG
62 AATAATCTCATTATAAATTTTTAT-AAGTGATTACTCAATACATTTTTAGACAAAAATATCTTG
* * * * ** * *
12202087 AATAATTTCAAAAAATTTTTTAGTAGGGTTATTAAAGGTGTTTCTAGGA--AAAAACACATTCAA
1 AATAATCTCAAAAAAATTTTTAATAGGATTATTAAAGGCATTT-T-TGATCAAAAACACCTTCAA
* * * * * *
12202150 TAATCTCATCATAAATTTTTCTAACGTGATTACTCAATGCGTTTTTTGATAAAAATATCTTG
64 TAATCTCATTATAAATTTTTATAA-GTGATTACTCAATACATTTTTAGACAAAAATATCTTG
* * *
12202212 AATAATCTCAAAAAAAATTTTAATAGGATTATTGAAGGTATTTTTGATCAAAAA
1 AATAATCTCAAAAAAATTTTTAATAGGATTATTAAAGGCATTTTTGATCAAAAA
12202266 TGTATTTAAT
Statistics
Matches: 236, Mismatches: 59, Indels: 25
0.74 0.18 0.08
Matches are distributed among these distances:
123 2 0.01
124 2 0.01
125 105 0.44
126 29 0.12
127 20 0.08
128 76 0.32
129 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.38
Consensus pattern (124 bp):
AATAATCTCAAAAAAATTTTTAATAGGATTATTAAAGGCATTTTTGATCAAAAACACCTTCAATA
ATCTCATTATAAATTTTTATAAGTGATTACTCAATACATTTTTAGACAAAAATATCTTG
Found at i:12203187 original size:16 final size:17
Alignment explanation
Indices: 12203158--12203190 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
12203148 AATATATTTA
12203158 TTAAATATATAAAAAAG
1 TTAAATATATAAAAAAG
12203175 TTAAATA-ATAAAAAAG
1 TTAAATATATAAAAAAG
12203191 AAAAAAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (17 bp):
TTAAATATATAAAAAAG
Found at i:12203359 original size:2 final size:2
Alignment explanation
Indices: 12203342--12203389 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
12203332 AAAAATTTAA
* *
12203342 AT AT TT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12203384 AT AT AT
1 AT AT AT
12203390 CTAAAATGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12205543 original size:20 final size:20
Alignment explanation
Indices: 12205520--12205559 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12205510 ATTAAACAAA
*
12205520 TACTTAAATTATTAAATCAG
1 TACTGAAATTATTAAATCAG
* *
12205540 TACTGGAATTATTAGATCAG
1 TACTGAAATTATTAAATCAG
12205560 GGATATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (20 bp):
TACTGAAATTATTAAATCAG
Found at i:12209214 original size:20 final size:20
Alignment explanation
Indices: 12209191--12209228 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12209181 GTTATATAAA
12209191 ATATAAAATTTTATATATTT
1 ATATAAAATTTTATATATTT
* *
12209211 ATATTATATTTTATATAT
1 ATATAAAATTTTATATAT
12209229 AAATTATATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
ATATAAAATTTTATATATTT
Found at i:12209227 original size:32 final size:33
Alignment explanation
Indices: 12209168--12209233 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 33
12209158 GATGTGATAA
*
12209168 TTTATATATTTATGTTATATAAAATATA-AAAT
1 TTTATATATTTATATTATATAAAATATATAAAT
***
12209200 TTTATATATTTATATTATATTTTATATATAAAT
1 TTTATATATTTATATTATATAAAATATATAAAT
12209233 T
1 T
12209234 ATATGTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 24 0.83
33 5 0.17
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (33 bp):
TTTATATATTTATATTATATAAAATATATAAAT
Found at i:12209234 original size:18 final size:19
Alignment explanation
Indices: 12209198--12209237 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
12209188 AAAATATAAA
*
12209198 ATTTTATATATTTATATTAT
1 ATTTTATATA-TTAAATTAT
12209218 ATTTTATATA-TAAATTAT
1 ATTTTATATATTAAATTAT
12209236 AT
1 AT
12209238 GTTAAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
20 10 0.53
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTATATATTAAATTAT
Found at i:12210109 original size:6 final size:6
Alignment explanation
Indices: 12210098--12210128 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
12210088 TAATGAATGT
12210098 CTTTAA CTTTAA CTTTAA CTTTAA CTTTAA C
1 CTTTAA CTTTAA CTTTAA CTTTAA CTTTAA C
12210129 CGTAAGGAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.48
Consensus pattern (6 bp):
CTTTAA
Found at i:12210488 original size:22 final size:23
Alignment explanation
Indices: 12210452--12210494 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
12210442 TAATTTTTTT
* *
12210452 ATTTTTTATATTATTTTAATATA
1 ATTTTTAATATTATTTAAATATA
12210475 ATTTTTAATA-TATTTAAATA
1 ATTTTTAATATTATTTAAATA
12210495 CATTTAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTTTAATATTATTTAAATATA
Found at i:12212807 original size:26 final size:25
Alignment explanation
Indices: 12212792--12212856 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 25
12212782 GATTGTTTCT
12212792 AAAATTAGTAGAATAAATTATTCAAA
1 AAAATTAGTAGAATAAATTATTC-AA
*
12212818 AAAATTAGTAGAATAAATTTATAATAAA
1 AAAATTAGTAGAATAAA-TTAT--TCAA
12212846 AAAATTAGTAG
1 AAAATTAGTAG
12212857 TAATTAAAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
26 17 0.49
27 4 0.11
28 13 0.37
29 1 0.03
ACGTcount: A:0.58, C:0.02, G:0.09, T:0.31
Consensus pattern (25 bp):
AAAATTAGTAGAATAAATTATTCAA
Found at i:12212811 original size:13 final size:13
Alignment explanation
Indices: 12212793--12212836 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
12212783 ATTGTTTCTA
12212793 AAATTAGTAGAAT
1 AAATTAGTAGAAT
* *
12212806 AAATTATTCA-AAA
1 AAATTAGT-AGAAT
12212819 AAATTAGTAGAAT
1 AAATTAGTAGAAT
12212832 AAATT
1 AAATT
12212837 TATAATAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
12 1 0.04
13 23 0.92
14 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.09, T:0.32
Consensus pattern (13 bp):
AAATTAGTAGAAT
Found at i:12213694 original size:338 final size:340
Alignment explanation
Indices: 12213075--12213696 Score: 813
Period size: 338 Copynumber: 1.8 Consensus size: 340
12213065 CTGTCTAATT
* * * **
12213075 TATATAATATATTAAAGTTATTCCCACTCATTTACACAATGTTAACTAAGATTTGATATAAAATA
1 TATATAATATATTAAAGTTATTCCCAATAATGTACACAATGCCAACTAAGATTTGATATAAAATA
* * * * * *
12213140 TGATTTGAAGGGTAATTGGGGTCTTTAATTATATAATTTAATATCACTTTTGATTTTTGACATAT
66 TGAATTAAAGGGTAACTAGGGTCTTTAATTATACAATTTAATATCACTTTTGACTTTTGA-ATAT
* * *
12213205 ATTTTTGGATTAATTGGACTATTCTGTTTTATAGGGGTTTTTTAGAACTTCAATTAAATTTAATT
130 ATTTTTAGATTAATTGGACTATTCTGTTTTATAGGGGTTGTTTAGAACTTAAATTAAATTTAATT
* * * * * *
12213270 GATGTATTTGAGTTATTCCAACTTAGCATAGTGAAGCCATTTGGGATTTTGATGCATAATTTTAT
195 GATGTATTTGAGTTATTCCAACATAACATAGTGAAGCCATTTGAGAATTTCATACATAATTTTAT
*
12213335 AGCAATTAAGATGTGGTATAAAATATGATTTTAAAAATAATTGAAGTTTTTGATTATAATAATTT
260 AGCAACTAAGATGTGGTATAAAATATGATTTTAAAAATAATTGAAGTTTTTGATTATAATAATTT
12213400 GGAATCACTTTTAACC
325 GGAATCACTTTTAACC
* * *
12213416 TATATAATATATTAAAGTTATT-CCAATAATGTATATAATGCCAATTAAGATTTGATATAAAATA
1 TATATAATATATTAAAGTTATTCCCAATAATGTACACAATGCCAACTAAGATTTGATATAAAATA
* * * *
12213480 TGAATTAAAGGGTAACTAGGGTCTTTAATTATACAATTTACTATCACTTTTGACTTTTG-TTTTT
66 TGAATTAAAGGGTAACTAGGGTCTTTAATTATACAATTTAATATCACTTTTGACTTTTGAATATA
* * * *
12213544 TTTTTAGATTAATTGGATTATTTTGTTTGT-TAGGGGTTGTTTATAACTTAAATTTAATTTAATT
131 TTTTTAGATTAATTGGACTATTCTGTTT-TATAGGGGTTGTTTAGAACTTAAATTAAATTTAATT
* * * * * *
12213608 GATGTGTTTGAGTTATTCCAACATAATATA-TGGGAGTCGTTTGAGAATTTCATACATAATTTTG
195 GATGTATTTGAGTTATTCCAACATAACATAGT-GAAGCCATTTGAGAATTTCATACATAATTTTA
**
12213672 T-GCTAACTACTATGTGGTATAAAAT
259 TAGC-AACTAAGATGTGGTATAAAAT
12213697 TTGTTTTTGG
Statistics
Matches: 238, Mismatches: 40, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
337 3 0.01
338 126 0.53
339 1 0.00
340 86 0.36
341 22 0.09
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (340 bp):
TATATAATATATTAAAGTTATTCCCAATAATGTACACAATGCCAACTAAGATTTGATATAAAATA
TGAATTAAAGGGTAACTAGGGTCTTTAATTATACAATTTAATATCACTTTTGACTTTTGAATATA
TTTTTAGATTAATTGGACTATTCTGTTTTATAGGGGTTGTTTAGAACTTAAATTAAATTTAATTG
ATGTATTTGAGTTATTCCAACATAACATAGTGAAGCCATTTGAGAATTTCATACATAATTTTATA
GCAACTAAGATGTGGTATAAAATATGATTTTAAAAATAATTGAAGTTTTTGATTATAATAATTTG
GAATCACTTTTAACC
Found at i:12214589 original size:5 final size:6
Alignment explanation
Indices: 12214575--12214697 Score: 61
Period size: 6 Copynumber: 18.3 Consensus size: 6
12214565 CCCAATGGGC
* * *
12214575 TTTTAT TTTTAT TTTCAT TATTTAAT ATATAT TTTTAT TTTTAT TATTT-T
1 TTTTAT TTTTAT TTTTAT T-TTT-AT TTTTAT TTTTAT TTTTAT T-TTTAT
*
12214625 TTTTAT CTATTAATAT TTTTAT TATTTATCT GCTTTTATT TTTTAT TATTATT
1 TTTTAT -T-TT--TAT TTTTAT T-TTTA--T --TTTTA-T TTTTAT TTTTA-T
12214678 TTTTAT TTGTT-T TTTTAT TT
1 TTTTAT TT-TTAT TTTTAT TT
12214698 ATCTAATTAT
Statistics
Matches: 92, Mismatches: 9, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
5 5 0.05
6 46 0.50
7 24 0.26
8 6 0.07
9 3 0.03
10 7 0.08
11 1 0.01
ACGTcount: A:0.21, C:0.03, G:0.02, T:0.74
Consensus pattern (6 bp):
TTTTAT
Found at i:12214641 original size:19 final size:18
Alignment explanation
Indices: 12214581--12214650 Score: 59
Period size: 19 Copynumber: 3.6 Consensus size: 18
12214571 GGGCTTTTAT
12214581 TTTTATTTTCATTATTTAATA
1 TTTT-TTTT-ATTA-TTAATA
* * *
12214602 TATATTTTTATTTTTATTA
1 T-TTTTTTTATTATTAATA
12214621 TTTTTTTTATCTATTAATA
1 TTTTTTTTAT-TATTAATA
*
12214640 TTTTTATTATT
1 TTTTTTTTATT
12214651 TATCTGCTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
18 9 0.22
19 21 0.52
20 3 0.08
21 5 0.12
22 2 0.05
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTTTTTTATTATTAATA
Found at i:12214679 original size:36 final size:33
Alignment explanation
Indices: 12214575--12214724 Score: 96
Period size: 34 Copynumber: 4.5 Consensus size: 33
12214565 CCCAATGGGC
* * *
12214575 TTTTATTTTTA-T-TTTCATTATTTAATATATAT
1 TTTTATTTTTATTATTTTATTTTTTATTAT-TAT
*
12214607 TTTTATTTTTATTATTTT-TTTTATCTATTAATAT
1 TTTTATTTTTATTATTTTATTTT-T-TATTATTAT
*
12214641 TTTTATTATTTATCTGCTTTTATTTTTTATTATTATT
1 TTTTATT-TTTAT-T-ATTTTATTTTTTATTATTA-T
* *
12214678 TTTTATTTGT-TT-TTTTATTTATCTAATTATTAT
1 TTTTATTTTTATTATTTTATTT-T-TTATTATTAT
* *
12214711 TATT-TTTTTGTTAT
1 TTTTATTTTTATTAT
12214725 CTATTAATAT
Statistics
Matches: 95, Mismatches: 10, Indels: 24
0.74 0.08 0.19
Matches are distributed among these distances:
32 23 0.24
33 11 0.12
34 24 0.25
35 10 0.11
36 10 0.11
37 13 0.14
38 4 0.04
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (33 bp):
TTTTATTTTTATTATTTTATTTTTTATTATTAT
Found at i:12214683 original size:30 final size:29
Alignment explanation
Indices: 12214638--12214746 Score: 86
Period size: 30 Copynumber: 3.8 Consensus size: 29
12214628 TATCTATTAA
*
12214638 TATTTTTATTATTTATCTGCTTTTATTT-TT
1 TATTATTATTATTTATCTG-TTTT-TTTATT
* *
12214668 TATTATTATTTTTTATTTGTTTTTTTATT
1 TATTATTATTATTTATCTGTTTTTTTATT
*
12214697 TATCTAATTATTA-TTAT-T-TTTTTGTTATC
1 TAT-T-ATTATTATTTATCTGTTTTT-TTATT
*
12214726 TATTAATA-TATTTATCT-TTTT
1 TATTATTATTATTTATCTGTTTT
12214747 ATTTTGATTA
Statistics
Matches: 67, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
26 2 0.03
27 7 0.10
28 14 0.21
29 17 0.25
30 21 0.31
31 6 0.09
ACGTcount: A:0.21, C:0.05, G:0.03, T:0.72
Consensus pattern (29 bp):
TATTATTATTATTTATCTGTTTTTTTATT
Found at i:12214710 original size:27 final size:27
Alignment explanation
Indices: 12214659--12214750 Score: 79
Period size: 27 Copynumber: 3.6 Consensus size: 27
12214649 TTTATCTGCT
* *
12214659 TTTA-TTTTTTA-TTAT-TATTTTTTA
1 TTTATTTTTTTATTTATCTAATTATTA
*
12214683 TTTGTTTTTTTATTTATCTAATTATTA
1 TTTATTTTTTTATTTATCTAATTATTA
*
12214710 -TTATTTTTTT-GTTATCT-ATTAATATA
1 TTTATTTTTTTATTTATCTAATT-AT-TA
*
12214736 TTTATCTTTTTATTT
1 TTTATTTTTTTATTT
12214751 TGATTAATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
24 6 0.11
25 15 0.28
26 15 0.28
27 16 0.30
28 2 0.04
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (27 bp):
TTTATTTTTTTATTTATCTAATTATTA
Found at i:12215600 original size:3 final size:3
Alignment explanation
Indices: 12215592--12215625 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
12215582 ATTTATTTAT
*
12215592 TTA TTA TTA TTA TTA TTA TTTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
12215626 GATTAGATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:12215612 original size:19 final size:19
Alignment explanation
Indices: 12215588--12215625 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
12215578 TTTTATTTAT
*
12215588 TTATTTATTATTATTATTA
1 TTATTTATTACTATTATTA
12215607 TTATTTATTACTATTATTA
1 TTATTTATTACTATTATTA
12215626 GATTAGATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTTATTACTATTATTA
Found at i:12215614 original size:16 final size:16
Alignment explanation
Indices: 12215595--12215625 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12215585 TATTTATTTA
*
12215595 TTATTATTATTATTAT
1 TTATTACTATTATTAT
12215611 TTATTACTATTATTA
1 TTATTACTATTATTA
12215626 GATTAGATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (16 bp):
TTATTACTATTATTAT
Found at i:12215744 original size:30 final size:30
Alignment explanation
Indices: 12215705--12215778 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 30
12215695 AAAAATATTT
*
12215705 TTGAGGAAAAGTTGAAAGTATCAATTTTCC
1 TTGAAGAAAAGTTGAAAGTATCAATTTTCC
*
12215735 TTGAAGAAAAGTTGAAAGTATCAATTTTTC
1 TTGAAGAAAAGTTGAAAGTATCAATTTTCC
*
12215765 TTGAAAATAAAGTT
1 TTGAAGA-AAAGTT
12215779 TCTAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 34 0.85
31 6 0.15
ACGTcount: A:0.41, C:0.07, G:0.18, T:0.35
Consensus pattern (30 bp):
TTGAAGAAAAGTTGAAAGTATCAATTTTCC
Found at i:12215933 original size:117 final size:114
Alignment explanation
Indices: 12215740--12215992 Score: 323
Period size: 117 Copynumber: 2.2 Consensus size: 114
12215730 TTTCCTTGAA
* * * *
12215740 GAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAGTTTCTAAAAAATATTTTTGAGAAAAAGT
1 GAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAAGTTTCTAAAAAAGATTTTTGAGAAAAAGT
* * **
12215805 TGAAAGTATCAATTTTTCTTGAAA-ATAAGCTTTCTAAAAAAAATATTTTTTTG
66 TGAAAGTATCAATTTTCCTCGAAATA-AAG-TTT-T-AAAAAAATA-TTTTGGG
* *
12215858 GAAAAGTTGAAAGTATCAATTCTCCTTAAAAAT-AAGTTT-TCAAAATAGATTTTTGAGGAAAAG
1 GAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAAGTTTCT-AAAAAAGATTTTTGAGAAAAAG
*
12215921 TTGAAAGTATCAATTTTCCTCGAAATGAAAGTTTTCAAAAAATATTTTGGG
65 TTGAAAGTATCAATTTTCCTCGAAAT-AAAGTTTTAAAAAAATATTTTGGG
12215972 GAAAAGTTGAAAGTATCAATT
1 GAAAAGTTGAAAGTATCAATT
12215993 TTTCCTGTAC
Statistics
Matches: 121, Mismatches: 11, Indels: 10
0.85 0.08 0.07
Matches are distributed among these distances:
114 26 0.21
115 8 0.07
116 2 0.02
117 51 0.42
118 33 0.27
119 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.36
Consensus pattern (114 bp):
GAAAAGTTGAAAGTATCAATTCTCCTTAAAAATAAAGTTTCTAAAAAAGATTTTTGAGAAAAAGT
TGAAAGTATCAATTTTCCTCGAAATAAAGTTTTAAAAAAATATTTTGGG
Found at i:12215935 original size:57 final size:58
Alignment explanation
Indices: 12215735--12215994 Score: 323
Period size: 57 Copynumber: 4.5 Consensus size: 58
12215725 TCAATTTTCC
* *
12215735 TTGAAGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATAAAG-TTTCTAAAAAATATTT
1 TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTC-AAAAAATATTT
* * *
12215793 TTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAAAT-AAGCTTTCTAAAAAAAATATTT
1 TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAG-TTT-T-CAAAAAATATTT
** * * * *
12215853 TTTTGGAAAAGTTGAAAGTATCAATTCTCCTTAAAAAT-AAGTTTTCAAAATAGATTT
1 TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTCAAAAAATATTT
*
12215910 TTGAGGAAAAGTTGAAAGTATCAATTTTCCTCG-AAATGAAAGTTTTCAAAAAATA-TT
1 TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAGTTTTCAAAAAATATTT
*
12215967 TTGGGGAAAAGTTGAAAGTATCAATTTT
1 TTGAGGAAAAGTTGAAAGTATCAATTTT
12215995 TCCTGTACAA
Statistics
Matches: 176, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
56 4 0.02
57 69 0.39
58 51 0.29
59 5 0.03
60 47 0.27
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (58 bp):
TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTTCAAAAAATATTT
Found at i:12216183 original size:98 final size:97
Alignment explanation
Indices: 12215972--12216166 Score: 243
Period size: 99 Copynumber: 2.0 Consensus size: 97
12215962 ATATTTTGGG
* *
12215972 GAAAAGTTGAAAGTATCAATTTTTCCTGTACAAAAGCAATCATTTTTTTCTTCTTTTTTTTATTG
1 GAAAACTTAAAAGTATCAATTTTTCCTGTACAAAAGCAATCATTTTTTTCTTCTTTTTTTTATTG
****
12216037 AATTTTCTTTAATGTTAAATAATCTTTTTTTGAA
66 AATTTTCTTTAATGTTAAATAATC--TCGACGAA
* * *
12216071 GAAAAGTTAAAAGTATCAATTTTT-TTGTACAAAAGCAATCATTTTTTTCTTTCTTTTTATTTTC
1 GAAAACTTAAAAGTATCAATTTTTCCTGTACAAAAGCAATCATTTTTTTC-TTC-TTTT-TTTTA
12216135 TTGAATTTT-TTTAATGTTAAATAATC-CGACGA
63 TTGAATTTTCTTTAATGTTAAATAATCTCGACGA
12216167 CGGAGTCTCT
Statistics
Matches: 86, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
97 2 0.02
98 24 0.28
99 26 0.30
100 21 0.24
101 13 0.15
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.49
Consensus pattern (97 bp):
GAAAACTTAAAAGTATCAATTTTTCCTGTACAAAAGCAATCATTTTTTTCTTCTTTTTTTTATTG
AATTTTCTTTAATGTTAAATAATCTCGACGAA
Found at i:12220060 original size:12 final size:12
Alignment explanation
Indices: 12220045--12220075 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
12220035 GAAAAAATTT
12220045 AAAAAAAATAGA
1 AAAAAAAATAGA
*
12220057 AAAAAAAATGGA
1 AAAAAAAATAGA
12220069 AAAAAAA
1 AAAAAAA
12220076 GAGATTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.84, C:0.00, G:0.10, T:0.06
Consensus pattern (12 bp):
AAAAAAAATAGA
Found at i:12221822 original size:41 final size:40
Alignment explanation
Indices: 12221759--12222029 Score: 205
Period size: 41 Copynumber: 6.6 Consensus size: 40
12221749 ATGATTGTCA
12221759 AGGAGCAATTTACTTTTT-AAAGTCATAGTGCCTCTATTTAG
1 AGGAGCAATTTA-TTTTTCAAAGTC-TAGTGCCTCTATTTAG
* *
12221800 AGGAGCAATTTATTTTTCAAAGTTGTGGTGCCTCTATTTAG
1 AGGAGCAATTTATTTTTCAAAG-TCTAGTGCCTCTATTTAG
* * *
12221841 AGGAGCAATTTACTTTCTAAAAGT-TGAGGTGCCTCTGTTTAG
1 AGGAGCAATTTA-TTTTTCAAAGTCT-A-GTGCCTCTATTTAG
* * * * *
12221883 ATGAGCAATTTACTTTTCAAAGTTGTGGTGCCTCTATTTAT
1 AGGAGCAATTTATTTTTCAAAG-TCTAGTGCCTCTATTTAG
* * *
12221924 AGGAGCAATTTACTTTCCAAAAGT-TAAT-CCTCTGA-TTAG
1 AGGAGCAATTTATTTTTC-AAAGTCTAGTGCCTCT-ATTTAG
* * *
12221963 -GAGAGCCATTTACTTTTCAAAAGTCATTGTGCCTCTGA-TTAG
1 AG-GAGCAATTTATTTTTC-AAAGTC-TAGTGCCTCT-ATTTAG
* *
12222005 AAGAGCCATTTATTTTTCTAAAGTC
1 AGGAGCAATTTATTTTTC-AAAGTC
12222030 GTTGAGCCTC
Statistics
Matches: 191, Mismatches: 25, Indels: 27
0.79 0.10 0.11
Matches are distributed among these distances:
38 1 0.01
39 28 0.15
40 9 0.05
41 82 0.43
42 70 0.37
43 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (40 bp):
AGGAGCAATTTATTTTTCAAAGTCTAGTGCCTCTATTTAG
Found at i:12221900 original size:83 final size:80
Alignment explanation
Indices: 12221759--12221983 Score: 301
Period size: 83 Copynumber: 2.8 Consensus size: 80
12221749 ATGATTGTCA
* * *
12221759 AGGAGCAATTTACTTT-TTAAAGTCATAGTGCCTCTATTTAGAGGAGCAATTTATTTTTCAAAGT
1 AGGAGCAATTTACTTTCTAAAAGT--TAGTGCCTCTGTTTAGA-GAGCAATTTACTTTTCAAAGT
12221823 TGTGGTGCCTCTATTTAG
63 TGTGGTGCCTCTATTTAG
12221841 AGGAGCAATTTACTTTCTAAAAGTTGAGGTGCCTCTGTTTAGATGAGCAATTTACTTTTCAAAGT
1 AGGAGCAATTTACTTTCTAAAAGTT-A-GTGCCTCTGTTTAGA-GAGCAATTTACTTTTCAAAGT
*
12221906 TGTGGTGCCTCTATTTAT
63 TGTGGTGCCTCTATTTAG
* * * *
12221924 AGGAGCAATTTACTTTCCAAAAGTTAAT-CCTCTGATTAGGAGAGCCATTTACTTTTCAAA
1 AGGAGCAATTTACTTTCTAAAAGTTAGTGCCTCTGTTTA-GAGAGCAATTTACTTTTCAAA
12221984 AGTCATTGTG
Statistics
Matches: 130, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
80 27 0.21
81 4 0.03
82 18 0.14
83 81 0.62
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (80 bp):
AGGAGCAATTTACTTTCTAAAAGTTAGTGCCTCTGTTTAGAGAGCAATTTACTTTTCAAAGTTGT
GGTGCCTCTATTTAG
Done.