Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008017.1 Hibiscus syriacus cultivar Beakdansim tig00110483_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3132588
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 15
Found at i:282469 original size:33 final size:33
Alignment explanation
Indices: 282427--282542 Score: 160
Period size: 33 Copynumber: 3.4 Consensus size: 33
282417 ACAATCAATA
*
282427 TCGCGTTGCGATTTTGTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCTCGTTGCGATTTTCATT
282460 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTC---T--CGTTGCGATTTTCATT
*
282498 TCGCGTTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCTCGTTGCGATTTTCATT
*
282531 TCGCATTGCGAT
1 TCGCGTTGCGAT
282543 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 3, Indels: 10
0.85 0.03 0.11
Matches are distributed among these distances:
33 42 0.56
35 1 0.01
36 1 0.01
38 31 0.41
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.46
Consensus pattern (33 bp):
TCGCGTTGCGATTTTCTCGTTGCGATTTTCATT
Found at i:282550 original size:19 final size:19
Alignment explanation
Indices: 282444--282542 Score: 145
Period size: 19 Copynumber: 5.5 Consensus size: 19
282434 GCGATTTTGT
282444 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
282463 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
282482 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
282501 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
282515 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
282534 CATTGCGAT
1 CGTTGCGAT
282543 AGTCATTTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 10
0.85 0.04 0.12
Matches are distributed among these distances:
14 10 0.14
16 3 0.04
17 3 0.04
19 56 0.78
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:284043 original size:21 final size:21
Alignment explanation
Indices: 284019--284092 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
284009 GTGGGAGGGA
284019 CCTCTTCAACGATGATAGTGG
1 CCTCTTCAACGATGATAGTGG
* * **
284040 CCTCTTGAACGGTGGGAG-GG
1 CCTCTTCAACGATGATAGTGG
284060 ACCTCTTCAACGATGATAGTGG
1 -CCTCTTCAACGATGATAGTGG
*
284082 CCTCTTGAACG
1 CCTCTTCAACG
284093 GTGGGAGGGG
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.22, C:0.24, G:0.28, T:0.26
Consensus pattern (21 bp):
CCTCTTCAACGATGATAGTGG
Found at i:284107 original size:21 final size:21
Alignment explanation
Indices: 283999--284107 Score: 69
Period size: 21 Copynumber: 5.2 Consensus size: 21
283989 GTGAATCGGG
*
283999 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
284019 CCTCTTCAACGATGATAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
284041 CTCTTGAACGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
284061 CCTCTTCAACGATGATAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
284083 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
284104 CTCT
1 CTCT
284108 CGAGGAATGA
Statistics
Matches: 60, Mismatches: 25, Indels: 6
0.66 0.27 0.07
Matches are distributed among these distances:
20 2 0.03
21 54 0.90
22 4 0.07
ACGTcount: A:0.20, C:0.20, G:0.35, T:0.25
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:284129 original size:42 final size:42
Alignment explanation
Indices: 283999--284101 Score: 197
Period size: 42 Copynumber: 2.5 Consensus size: 42
283989 GTGAATCGGG
*
283999 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGATAGTGGC
284041 CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGATAGTGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGATAGTGGC
284083 CTCTTGAACGGTGGGAGGG
1 CTCTTGAACGGTGGGAGGG
284102 GACTCTCGAG
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 60 1.00
ACGTcount: A:0.20, C:0.19, G:0.36, T:0.24
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTCAACGATGATAGTGGC
Found at i:284147 original size:42 final size:42
Alignment explanation
Indices: 284072--284159 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 42
284062 CTCTTCAACG
* * * *
284072 ATGATAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGA
1 ATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGGA
* * * *
284114 ATGATAGGGGCCTCTTCAATGATAGGAGTGGACTCTTGAGGG
1 ATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGGA
284156 ATGA
1 ATGA
284160 CAGGCGAGTC
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.24, C:0.15, G:0.38, T:0.24
Consensus pattern (42 bp):
ATGATAGGGGCCTCTTCAACGATAGGAGGGGACTCTCGAGGA
Found at i:284616 original size:20 final size:19
Alignment explanation
Indices: 284579--284632 Score: 81
Period size: 20 Copynumber: 2.8 Consensus size: 19
284569 AAAAATGACT
*
284579 ATCGCAACGTGAAATGAAA
1 ATCGCAACGAGAAATGAAA
284598 ATCGCAACGAGAGAATGAAA
1 ATCGCAACGAGA-AATGAAA
*
284618 ATCGCAACGCGAAAT
1 ATCGCAACGAGAAAT
284633 TTGGTTTCAC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 14 0.44
20 18 0.56
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (19 bp):
ATCGCAACGAGAAATGAAA
Found at i:284655 original size:20 final size:20
Alignment explanation
Indices: 284632--284673 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
284622 CAACGCGAAA
284632 TTTGGTTTCACGTTGCGATT
1 TTTGGTTTCACGTTGCGATT
*
284652 TTTGGTTTCGCGTTGCGATT
1 TTTGGTTTCACGTTGCGATT
284672 TT
1 TT
284674 GTCGTTGCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.07, C:0.14, G:0.26, T:0.52
Consensus pattern (20 bp):
TTTGGTTTCACGTTGCGATT
Found at i:284699 original size:33 final size:33
Alignment explanation
Indices: 284637--284741 Score: 120
Period size: 33 Copynumber: 3.1 Consensus size: 33
284627 CGAAATTTGG
* **
284637 TTTCACGTTGCGATTTTTGGTTTCGCGTTGCGAT
1 TTTCTCGTTGCGA-TTTTCATTTCGCGTTGCGAT
*
284671 TTTGTCGTTGCGATTTTCATTTCGCGTTGCGAT
1 TTTCTCGTTGCGATTTTCATTTCGCGTTGCGAT
* * * *
284704 TCTCTCATTACGATTTTCATTCTCTCGTTGCGAT
1 TTTCTCGTTGCGATTTTCATT-TCGCGTTGCGAT
284738 TTTC
1 TTTC
284742 ATTTCAACCA
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
33 35 0.58
34 25 0.42
ACGTcount: A:0.10, C:0.21, G:0.20, T:0.49
Consensus pattern (33 bp):
TTTCTCGTTGCGATTTTCATTTCGCGTTGCGAT
Found at i:284727 original size:20 final size:20
Alignment explanation
Indices: 284702--284744 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
284692 TCGCGTTGCG
284702 ATTCTCTCATTACGATTTTC
1 ATTCTCTCATTACGATTTTC
* *
284722 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCATTACGATTTTC
284742 ATT
1 ATT
284745 TCAACCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.23, G:0.09, T:0.51
Consensus pattern (20 bp):
ATTCTCTCATTACGATTTTC
Found at i:284955 original size:94 final size:93
Alignment explanation
Indices: 284837--285118 Score: 437
Period size: 94 Copynumber: 3.1 Consensus size: 93
284827 ATGGATTGCA
* * *
284837 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTTAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
284902 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAATAAAT
*
284930 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
284995 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAATAAAT
*
285024 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
285085 TTAGCAGTATTGGCAGTAACCAAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAATAAAT
285114 TTACT
1 TTACT
285119 AAGCAATCTA
Statistics
Matches: 177, Mismatches: 10, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
90 40 0.23
93 22 0.12
94 115 0.65
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAATAAAT
Found at i:285897 original size:21 final size:22
Alignment explanation
Indices: 285855--285897 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
285845 AATAACAAAC
*
285855 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
285877 ATTA-TAATT-TTAAAAACATTA
1 ATTAGTAATTGTTAAAAA-ATTA
285898 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:286770 original size:20 final size:20
Alignment explanation
Indices: 286745--286807 Score: 74
Period size: 20 Copynumber: 3.1 Consensus size: 20
286735 TTTTGGTTGA
286745 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
* *
286765 AATGAAATTCGCAACGCG-G
1 AATGAAAATCGCAACGAGAG
**
286784 AAATGACTATCGCAACGAGAG
1 -AATGAAAATCGCAACGAGAG
286805 AAT
1 AAT
286808 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 1 0.03
20 33 0.94
21 1 0.03
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.14
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:286880 original size:33 final size:33
Alignment explanation
Indices: 286832--286924 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
286822 AAAATCGCAA
**
286832 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
286865 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
* **
286898 TGCAATAGTCATTTCCGCGTTGCGATT
1 TGCGATTTTCATTT-CGCGTTGCGATT
286925 TTCATTCTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 41 0.77
34 12 0.23
ACGTcount: A:0.12, C:0.22, G:0.24, T:0.43
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:287494 original size:20 final size:20
Alignment explanation
Indices: 287471--287564 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
287461 CGATAGTCAG
287471 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
287491 ATTCGCATTGCGATTTTCCT
1 ATTCGCATTGCGATTTACGT
287511 AATTCGCATTGCGATTTACGT
1 -ATTCGCATTGCGATTTACGT
* * *
287532 AATCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
287552 ATTCGCATTGCGA
1 ATTCGCATTGCGA
287565 ATTAGGAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 46 0.72
21 18 0.28
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:287523 original size:41 final size:40
Alignment explanation
Indices: 287451--287564 Score: 149
Period size: 41 Copynumber: 2.8 Consensus size: 40
287441 GCGCTATGTA
* *
287451 AATCGCATTGCGATAGT-CAGATTCGCATTGCGATTTACGT
1 AATCGCATTGCGAT-TTACATATTCGCATTGCGATTTACGT
* * *
287491 ATTCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACGT
1 AATCGCATTGCGATTTACAT-ATTCGCATTGCGATTTACGT
*
287532 AATCGCGTTGCGATTTACATATTCGCATTGCGA
1 AATCGCATTGCGATTTACATATTCGCATTGCGA
287565 ATTAGGAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
39 1 0.02
40 27 0.42
41 36 0.56
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (40 bp):
AATCGCATTGCGATTTACATATTCGCATTGCGATTTACGT
Found at i:287585 original size:21 final size:21
Alignment explanation
Indices: 287561--287606 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
287551 TATTCGCATT
287561 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
287582 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
287603 GCGA
1 GCGA
287607 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:287644 original size:47 final size:47
Alignment explanation
Indices: 287575--287666 Score: 184
Period size: 47 Copynumber: 2.0 Consensus size: 47
287565 ATTAGGAAAA
287575 TCGCAACGCGAATTTGGGAAATCGCAATGCGATAGTCAGAATCGCAT
1 TCGCAACGCGAATTTGGGAAATCGCAATGCGATAGTCAGAATCGCAT
287622 TCGCAACGCGAATTTGGGAAATCGCAATGCGATAGTCAGAATCGC
1 TCGCAACGCGAATTTGGGAAATCGCAATGCGATAGTCAGAATCGC
287667 GTTGCGAATC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.21
Consensus pattern (47 bp):
TCGCAACGCGAATTTGGGAAATCGCAATGCGATAGTCAGAATCGCAT
Found at i:293072 original size:22 final size:22
Alignment explanation
Indices: 293045--293097 Score: 106
Period size: 22 Copynumber: 2.4 Consensus size: 22
293035 TATGGAATAT
293045 TTCTATAAAAGTTTTCATCAAG
1 TTCTATAAAAGTTTTCATCAAG
293067 TTCTATAAAAGTTTTCATCAAG
1 TTCTATAAAAGTTTTCATCAAG
293089 TTCTATAAA
1 TTCTATAAA
293098 TGATTTTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (22 bp):
TTCTATAAAAGTTTTCATCAAG
Found at i:294018 original size:34 final size:34
Alignment explanation
Indices: 293978--294097 Score: 168
Period size: 34 Copynumber: 3.3 Consensus size: 34
293968 TAATGGTGTT
293978 ATGGTGTTATTTATTTTAGACTTATTGAGACTTAA
1 ATGGTGTTATTTATTTTAGACTTATTGAGACTT-A
294013 TGGTGTTATGGTGTTATTTATTTTAGACTTATTGAGACTTA
1 -------ATGGTGTTATTTATTTTAGACTTATTGAGACTTA
294054 ATGGTGTTATTTATTTTAGACTTATTGAGACTTA
1 ATGGTGTTATTTATTTTAGACTTATTGAGACTTA
294088 ATGGTGTTAT
1 ATGGTGTTAT
294098 GGTGTTATTT
Statistics
Matches: 78, Mismatches: 0, Indels: 8
0.91 0.00 0.09
Matches are distributed among these distances:
34 44 0.56
41 1 0.01
42 33 0.42
ACGTcount: A:0.25, C:0.05, G:0.20, T:0.50
Consensus pattern (34 bp):
ATGGTGTTATTTATTTTAGACTTATTGAGACTTA
Found at i:294022 original size:42 final size:42
Alignment explanation
Indices: 293963--294111 Score: 242
Period size: 42 Copynumber: 3.7 Consensus size: 42
293953 ATTTACTCTC
293963 AGACTTAATGGTGTTATGGTGTTATTTATTTTAGACTTATTG
1 AGACTTAATGGTGTTATGGTGTTATTTATTTTAGACTTATTG
294005 AGACTTAATGGTGTTATGGTGTTATTTATTTTAGACTTATTG
1 AGACTTAATGGTGTTATGGTGTTATTTATTTTAGACTTATTG
294047 AGACTT-A-------ATGGTGTTATTTATTTTAGACTTATTG
1 AGACTTAATGGTGTTATGGTGTTATTTATTTTAGACTTATTG
294081 AGACTTAATGGTGTTATGGTGTTATTTATTT
1 AGACTTAATGGTGTTATGGTGTTATTTATTT
294112 ACTTGTTTAT
Statistics
Matches: 99, Mismatches: 0, Indels: 16
0.86 0.00 0.14
Matches are distributed among these distances:
34 33 0.33
35 1 0.01
41 1 0.01
42 64 0.65
ACGTcount: A:0.24, C:0.05, G:0.21, T:0.50
Consensus pattern (42 bp):
AGACTTAATGGTGTTATGGTGTTATTTATTTTAGACTTATTG
Found at i:297920 original size:21 final size:20
Alignment explanation
Indices: 297869--297932 Score: 67
Period size: 21 Copynumber: 3.1 Consensus size: 20
297859 AATTATAAAC
*
297869 TTTA-ATTTAGAGTTTAGGG
1 TTTAGATTTATAGTTTAGGG
*
297888 TTTAGAGGTTATAGTTTAGGG
1 TTTAGA-TTTATAGTTTAGGG
* *
297909 TTTAAGATTTATAATTTAAGG
1 TTT-AGATTTATAGTTTAGGG
297930 TTT
1 TTT
297933 TAAGTTAGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 29 0.78
22 3 0.08
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.48
Consensus pattern (20 bp):
TTTAGATTTATAGTTTAGGG
Found at i:304337 original size:25 final size:26
Alignment explanation
Indices: 304295--304343 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
304285 CATGAACCAT
*
304295 TTTGTAACAGAAAGCTCAC-TGCAGC
1 TTTGTAACAGAAACCTCACATGCAGC
304320 TTTGTAACTA-AAACCTCACATGCA
1 TTTGTAAC-AGAAACCTCACATGCA
304344 ATGTATTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.35, C:0.24, G:0.14, T:0.27
Consensus pattern (26 bp):
TTTGTAACAGAAACCTCACATGCAGC
Found at i:319916 original size:3 final size:3
Alignment explanation
Indices: 319908--319932 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
319898 GGTGTATACC
319908 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
319933 TGTATTGGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:320554 original size:4 final size:4
Alignment explanation
Indices: 320545--320569 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
320535 CCAAAACAAA
320545 GAGG GAGG GAGG GAGG GAGG GAGG G
1 GAGG GAGG GAGG GAGG GAGG GAGG G
320570 GGAGGAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.76, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:321697 original size:31 final size:32
Alignment explanation
Indices: 321661--321725 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
321651 TTTTTACCAA
* * *
321661 TAAATTTATTA-ATATTTATTTTTAA-TTATTT
1 TAAATTT-TTATATATATATATATAATTTATTT
321692 TAAATTTTTATATATATATATATAATTTATTT
1 TAAATTTTTATATATATATATATAATTTATTT
321724 TA
1 TA
321726 TCATTATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
30 3 0.10
31 18 0.62
32 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (32 bp):
TAAATTTTTATATATATATATATAATTTATTT
Found at i:323961 original size:29 final size:29
Alignment explanation
Indices: 323926--324007 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
323916 AAACTAAATT
*
323926 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
323955 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
323984 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
324008 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:328727 original size:29 final size:29
Alignment explanation
Indices: 328692--328773 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
328682 AAACTAAATT
*
328692 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
328721 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
328750 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
328774 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:330200 original size:206 final size:206
Alignment explanation
Indices: 329840--330219 Score: 654
Period size: 206 Copynumber: 1.8 Consensus size: 206
329830 ACTGATTCTT
* *
329840 AAATCAACTATATAAAGGGGTTATGGTATCAAGAAATAGATAATCTCGTATTTACTTTTATCCCC
1 AAATCAACTATATAAAGGGGGTATGGTACCAAGAAATAGATAATCTCGTATTTACTTTTATCCCC
* *
329905 GTTAGAGAGTTTATATTTAAGAGAACTCTATCTTCTTAGAAGAACACAACCAAAGAGATATACTC
66 ATTAGAGAGTTTATATCTAAGAGAACTCTATCTTCTTAGAAGAACACAACCAAAGAGATATACTC
* *
329970 AAGGATTTCACCCTATCGATTAATTCATATATACTCAATGATTTTAACTTTTTGATTAATTTAGG
131 AAGGATTTCACCCTATCAATTAATTCAGATATACTCAATGATTTTAACTTTTTGATTAATTTAGG
330035 TACGCTTCCTG
196 TACGCTTCCTG
* * *
330046 AAATCAACTATATAAAGGGGGTATGGTCCCAAGAAATATATAATCTCGTATTTACTTTTATCTCC
1 AAATCAACTATATAAAGGGGGTATGGTACCAAGAAATAGATAATCTCGTATTTACTTTTATCCCC
*
330111 ATTAGAGAGTTTATACTCT-AGAGAACTCTATCTTCTTAGAAGATCACAACCAAAGAGATATACT
66 ATTAGAGAGTTTATA-TCTAAGAGAACTCTATCTTCTTAGAAGAACACAACCAAAGAGATATACT
330175 CAAGGATTTCACCCTATCAATTAATTCAGATATACTCAATGATTT
130 CAAGGATTTCACCCTATCAATTAATTCAGATATACTCAATGATTT
330220 CAACCTATCA
Statistics
Matches: 163, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
206 161 0.99
207 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.34
Consensus pattern (206 bp):
AAATCAACTATATAAAGGGGGTATGGTACCAAGAAATAGATAATCTCGTATTTACTTTTATCCCC
ATTAGAGAGTTTATATCTAAGAGAACTCTATCTTCTTAGAAGAACACAACCAAAGAGATATACTC
AAGGATTTCACCCTATCAATTAATTCAGATATACTCAATGATTTTAACTTTTTGATTAATTTAGG
TACGCTTCCTG
Found at i:330213 original size:36 final size:36
Alignment explanation
Indices: 330166--330239 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
330156 ACAACCAAAG
*
330166 AGATATACTCAAGGATTTCACCCTATCAATTAATTC
1 AGATATACTCAAGGATTTCAACCTATCAATTAATTC
*
330202 AGATATACTCAATGATTTCAACCTATCAATTAATTC
1 AGATATACTCAAGGATTTCAACCTATCAATTAATTC
330238 AG
1 AG
330240 GTACACTTCC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.38, C:0.20, G:0.08, T:0.34
Consensus pattern (36 bp):
AGATATACTCAAGGATTTCAACCTATCAATTAATTC
Found at i:330238 original size:17 final size:17
Alignment explanation
Indices: 330182--330238 Score: 51
Period size: 17 Copynumber: 3.2 Consensus size: 17
330172 ACTCAAGGAT
*
330182 TTCACCCTATCAATTAA
1 TTCAACCTATCAATTAA
** * *
330199 TTCAGATATACTCAATGAT
1 TTCA-ACCTA-TCAATTAA
330218 TTCAACCTATCAATTAA
1 TTCAACCTATCAATTAA
330235 TTCA
1 TTCA
330239 GGTACACTTC
Statistics
Matches: 29, Mismatches: 9, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
17 14 0.48
18 5 0.17
19 10 0.34
ACGTcount: A:0.37, C:0.23, G:0.04, T:0.37
Consensus pattern (17 bp):
TTCAACCTATCAATTAA
Found at i:330605 original size:21 final size:21
Alignment explanation
Indices: 330554--330606 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
330544 ATTATGACTA
*
330554 TCGCAATGAGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
330575 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
330596 TCGCAATGCGA
1 TCGCAATGCGA
330607 ATAAGTAAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:330639 original size:21 final size:21
Alignment explanation
Indices: 330596--330668 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
330586 TTTTCCCAAT
** *
330596 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTTGGAAAA
*
330616 TCGCAATGTGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
330637 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTTGGAAAA
*
330658 TCGCAACGCGA
1 TCGCAATGCGA
330669 TACTGACTAT
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
20 11 0.24
21 35 0.76
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGAAAA
Found at i:330681 original size:41 final size:39
Alignment explanation
Indices: 330636--330766 Score: 136
Period size: 41 Copynumber: 3.2 Consensus size: 39
330626 AATTTGGAAA
*
330636 ATCGCAATGCGAATTTGGAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCGAATTT--AAAATCGCAACGCGATACTGACT
**
330677 ATCGCAACGCGATAATACAAAATCGCAACGCGATACTGACT
1 ATCGCAACGCG--AATTTAAAATCGCAACGCGATACTGACT
* * ***
330718 TTCGCAACGCGATACTTACTTTCGCAACGCGATACTGACT
1 ATCGCAACGCGA-ATTTAAAATCGCAACGCGATACTGACT
*
330758 TTCGCAACG
1 ATCGCAACG
330767 AGATAATACA
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 30 0.39
41 43 0.56
43 3 0.04
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (39 bp):
ATCGCAACGCGAATTTAAAATCGCAACGCGATACTGACT
Found at i:330682 original size:20 final size:20
Alignment explanation
Indices: 330657--330771 Score: 142
Period size: 20 Copynumber: 5.7 Consensus size: 20
330647 AATTTGGAAA
330657 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
330677 ATCGCAACGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
330698 ATCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
330718 TTCGCAACGCGATACTTACT
1 ATCGCAACGCGATACTGACT
*
330738 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
330758 TTCGCAACGAGATA
1 ATCGCAACGCGATA
330772 ATACATAATC
Statistics
Matches: 84, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
19 2 0.02
20 65 0.77
21 15 0.18
22 2 0.02
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:330984 original size:21 final size:21
Alignment explanation
Indices: 330958--331000 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
330948 CACTCTCTCA
330958 CCCATCTCCGACGAAATCCGT
1 CCCATCTCCGACGAAATCCGT
*
330979 CCCATCTCCGGCGAAATCCGT
1 CCCATCTCCGACGAAATCCGT
331000 C
1 C
331001 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.44, G:0.16, T:0.19
Consensus pattern (21 bp):
CCCATCTCCGACGAAATCCGT
Found at i:331833 original size:18 final size:18
Alignment explanation
Indices: 331812--331859 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
331802 TCCACTTCGG
331812 GAGCCATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
331830 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
331848 GAGCCATCACCT
1 GAGCCATCACCT
331860 GATCGACTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.46, G:0.12, T:0.15
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:332431 original size:19 final size:20
Alignment explanation
Indices: 332388--332432 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
332378 CGCAACACGA
332388 AAATGACTATCGCAATGCAG
1 AAATGACTATCGCAATGCAG
*
332408 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAATGCAG
332427 AAATGA
1 AAATGA
332433 AAATCGCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (20 bp):
AAATGACTATCGCAATGCAG
Found at i:332438 original size:19 final size:19
Alignment explanation
Indices: 332396--332498 Score: 117
Period size: 19 Copynumber: 5.6 Consensus size: 19
332386 GAAAATGACT
***
332396 ATCGCAATGCAGAAATGGCT
1 ATCGCAATGC-GAAATGAAA
332416 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
332435 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
332449 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
332468 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
332487 ATCGCAATGCGA
1 ATCGCAATGCGA
332499 TTTGTGTTTC
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 45 0.63
20 10 0.14
ACGTcount: A:0.44, C:0.20, G:0.21, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:332529 original size:14 final size:14
Alignment explanation
Indices: 332510--332568 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
332500 TTGTGTTTCG
332510 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
332524 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
332541 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
332557 CGTTGCGATTTT
1 CGTTGCGATTTT
332569 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 18 0.47
15 3 0.08
16 4 0.11
17 4 0.11
18 3 0.08
19 6 0.16
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:332542 original size:33 final size:33
Alignment explanation
Indices: 332505--332584 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
332495 GCGATTTGTG
*
332505 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
332538 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
332571 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
332585 AGCCATTTCC
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:332550 original size:19 final size:19
Alignment explanation
Indices: 332526--332584 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
332516 GATTTTGTCG
332526 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
332545 TTGCGA-TTT--TGTCG--
1 TTGCGATTTTCATTTCGCA
332559 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
332578 TTGCGAT
1 TTGCGAT
332585 AGCCATTTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 6 0.18
15 3 0.09
16 4 0.12
17 4 0.12
18 3 0.09
19 13 0.39
ACGTcount: A:0.14, C:0.19, G:0.20, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:332638 original size:20 final size:20
Alignment explanation
Indices: 332557--332663 Score: 90
Period size: 20 Copynumber: 5.4 Consensus size: 20
332547 GCGATTTTGT
**
332557 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATAGTCATTTTCG
* * *
332576 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTTCG
* * * *
332596 CGATACGATAGCCATTTCCG
1 CGTTGCGATAGTCATTTTCG
332616 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* * *
332636 CGTTGCGAAAGTAAGTTTCG
1 CGTTGCGATAGTCATTTTCG
*
332656 TGTTGCGA
1 CGTTGCGA
332664 AAGTAAACTA
Statistics
Matches: 71, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
19 10 0.14
20 61 0.86
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:332664 original size:20 final size:20
Alignment explanation
Indices: 332614--332669 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
332604 TAGCCATTTC
* * *
332614 CGCGTTGCGATAGTCATTTT
1 CGCGTTGCGAAAGTAAGTTT
332634 CGCGTTGCGAAAGTAAGTTT
1 CGCGTTGCGAAAGTAAGTTT
*
332654 CGTGTTGCGAAAGTAA
1 CGCGTTGCGAAAGTAA
332670 ACTATTCTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (20 bp):
CGCGTTGCGAAAGTAAGTTT
Found at i:334717 original size:20 final size:20
Alignment explanation
Indices: 334692--334767 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
334682 TCGCAATGCG
* **
334692 ATTTTCTCGTTGATATAGCC
1 ATTTTCGCGTTGCGATAGCC
334712 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
*
334732 ATTTTCGCGTTGCGATAGTC
1 ATTTTCGCGTTGCGATAGCC
334752 ATTTTCGCGTTGCGAT
1 ATTTTCGCGTTGCGAT
334768 TTCCCCGTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.16, C:0.21, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:334998 original size:20 final size:20
Alignment explanation
Indices: 334982--335063 Score: 128
Period size: 20 Copynumber: 4.1 Consensus size: 20
334972 ATTGCGATTT
*
334982 TCAGAATCTCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
335002 TCAGAATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
*
335022 TCAGTATCGCGTTGCGAAAG
1 TCAGAATCGCGTTGCGAAAG
* *
335042 TCAGTATCGCGTTGCGATAG
1 TCAGAATCGCGTTGCGAAAG
335062 TC
1 TC
335064 TGTATCGCAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.26
Consensus pattern (20 bp):
TCAGAATCGCGTTGCGAAAG
Found at i:335068 original size:20 final size:20
Alignment explanation
Indices: 334991--335071 Score: 135
Period size: 20 Copynumber: 4.0 Consensus size: 20
334981 TTCAGAATCT
*
334991 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGTATCG
335011 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
335031 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGTATCG
* *
335051 CGTTGCGATAGTCTGTATCG
1 CGTTGCGAAAGTCAGTATCG
335071 C
1 C
335072 ATTACGATTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGTATCG
Found at i:335161 original size:21 final size:22
Alignment explanation
Indices: 335109--335161 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
335099 ATTTACTTAT
335109 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
** *
335130 TCGCAACGCGAAATT-GTAAAA
1 TCGCATTGCGAAATTGGGAAAA
335151 TCGCATTGCGA
1 TCGCATTGCGA
335162 TAGTCATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:337154 original size:16 final size:16
Alignment explanation
Indices: 337114--337145 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
337104 GATGTAAAAT
337114 AAAGACAAAATCAAAG
1 AAAGACAAAATCAAAG
337130 AAAGACAAAATCAAAG
1 AAAGACAAAATCAAAG
337146 GAAGTCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.12, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAGACAAAATCAAAG
Found at i:340298 original size:19 final size:20
Alignment explanation
Indices: 340274--340312 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
340264 ACTCATGAGT
340274 TGATGAT-AA-AAGAAGAAAA
1 TGATGATGAATAA-AAGAAAA
340293 TGATGATGAATAAAAGAAAA
1 TGATGATGAATAAAAGAAAA
340313 AACAACAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 9 0.50
21 2 0.11
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (20 bp):
TGATGATGAATAAAAGAAAA
Found at i:342744 original size:21 final size:21
Alignment explanation
Indices: 342720--342764 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
342710 GCCGATACCG
*
342720 TAGGAGGAGCACAAGAAGATC
1 TAGGAGGAGCACAAGAAGAGC
* * *
342741 TAGGAGTAGCTCATGAAGAGC
1 TAGGAGGAGCACAAGAAGAGC
342762 TAG
1 TAG
342765 CTCCCGGGGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.13, G:0.33, T:0.16
Consensus pattern (21 bp):
TAGGAGGAGCACAAGAAGAGC
Found at i:343293 original size:22 final size:22
Alignment explanation
Indices: 343265--343312 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
343255 ATTAATATAT
343265 TGGCCTAAAAGATAGGATCTAA
1 TGGCCTAAAAGATAGGATCTAA
343287 TGGCCTAAAAGATAGGATCTAA
1 TGGCCTAAAAGATAGGATCTAA
343309 TGGC
1 TGGC
343313 TATAGTTCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.25, T:0.23
Consensus pattern (22 bp):
TGGCCTAAAAGATAGGATCTAA
Found at i:349882 original size:65 final size:65
Alignment explanation
Indices: 349689--349883 Score: 216
Period size: 65 Copynumber: 3.0 Consensus size: 65
349679 AGAGTGAATC
* * * * * * * *
349689 GATGCATCAAGTGCATTCAATGTTTCAA-AATAGCCAGAGTGCATCGATGCATGGCTGGTGCATC
1 GATGCATCAAATGCATTCGATGTATCAATAAAATCCATAGTGCATCGATGCATGGTTGGTGCATT
* *
349753 GATGCATCAAATGCATTCGATGTATCCATAAAATCCTTAGTGCATCGATGCATGGTAT-GTGCAT
1 GATGCATCAAATGCATTCGATGTATCAATAAAATCCATAGTGCATCGATGCATGGT-TGGTGCAT
349817 T
65 T
* ** * *
349818 GATGCATGAAATGCATTCGATGT-TCAATTTAATTCATGGTGCATCGATGCATGGATTGGTGCAT
1 GATGCATCAAATGCATTCGATGTATCAATAAAATCCATAGTGCATCGATGCATGG-TTGGTGCAT
349882 T
65 T
349883 G
1 G
349884 GTGAATCACT
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
64 50 0.45
65 59 0.54
66 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (65 bp):
GATGCATCAAATGCATTCGATGTATCAATAAAATCCATAGTGCATCGATGCATGGTTGGTGCATT
Found at i:354909 original size:6 final size:6
Alignment explanation
Indices: 354898--354950 Score: 88
Period size: 6 Copynumber: 8.8 Consensus size: 6
354888 GAAGAAGACC
* *
354898 TCCCAT TTCCAT TTCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT
1 TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT TCCCAT
354946 TCCCA
1 TCCCA
354951 GATCCTCTGG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.17, C:0.47, G:0.00, T:0.36
Consensus pattern (6 bp):
TCCCAT
Found at i:357598 original size:11 final size:11
Alignment explanation
Indices: 357582--357638 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
357572 TCATATATTT
357582 AAAATACAATA
1 AAAATACAATA
357593 AAAATACAATA
1 AAAATACAATA
* *
357604 AAAA-AGAATT
1 AAAATACAATA
*
357614 AAAATTCAAT-
1 AAAATACAATA
*
357624 AAAATTCAATA
1 AAAATACAATA
357635 AAAA
1 AAAA
357639 AAGAATGTAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
10 18 0.45
11 22 0.55
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.21
Consensus pattern (11 bp):
AAAATACAATA
Found at i:357605 original size:21 final size:21
Alignment explanation
Indices: 357581--357638 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
357571 CTCATATATT
357581 TAAAATACAATAAAAATACAA
1 TAAAATACAATAAAAATACAA
* * * *
357602 TAAAAAAGAATTAAAATTCAA
1 TAAAATACAATAAAAATACAA
*
357623 TAAAATTCAATAAAAA
1 TAAAATACAATAAAAA
357639 AAGAATGTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (21 bp):
TAAAATACAATAAAAATACAA
Found at i:357606 original size:10 final size:10
Alignment explanation
Indices: 357581--357637 Score: 60
Period size: 10 Copynumber: 5.5 Consensus size: 10
357571 CTCATATATT
357581 TAAAATACAA
1 TAAAATACAA
357591 TAAAAATACAA
1 T-AAAATACAA
* *
357602 TAAAAAAGAA
1 TAAAATACAA
*
357612 TTAAAATTCAA
1 -TAAAATACAA
*
357623 TAAAATTCAA
1 TAAAATACAA
357633 TAAAA
1 TAAAA
357638 AAAGAATGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
10 23 0.57
11 17 0.43
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.23
Consensus pattern (10 bp):
TAAAATACAA
Found at i:357624 original size:32 final size:32
Alignment explanation
Indices: 357580--357649 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 32
357570 ACTCATATAT
357580 TTAAAATACAATAAAAATACAAT-AAAAAAGAA
1 TTAAAATACAAT-AAAATACAATAAAAAAAGAA
* *
357612 TTAAAATTCAATAAAATTCAATAAAAAAAGAA
1 TTAAAATACAATAAAATACAATAAAAAAAGAA
357644 TGTAAA
1 T-TAAA
357650 GCTAAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 9 0.26
32 21 0.62
33 4 0.12
ACGTcount: A:0.67, C:0.06, G:0.04, T:0.23
Consensus pattern (32 bp):
TTAAAATACAATAAAATACAATAAAAAAAGAA
Found at i:357659 original size:31 final size:30
Alignment explanation
Indices: 357592--357660 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
357582 AAAATACAAT
*
357592 AAAAATACAATAAAAAAGAATTAAAATTCA
1 AAAAATACAATAAAAAAGAATTAAAACTCA
* *
357622 ATAAAATTCAATAAAAAAAGAATGTAAAGCT-A
1 A-AAAATACAAT-AAAAAAGAAT-TAAAACTCA
357654 AAAAATA
1 AAAAATA
357661 TCACCTCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
30 1 0.03
31 14 0.44
32 12 0.38
33 5 0.16
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.20
Consensus pattern (30 bp):
AAAAATACAATAAAAAAGAATTAAAACTCA
Found at i:365452 original size:14 final size:14
Alignment explanation
Indices: 365435--365461 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
365425 ATATTAAATA
365435 ATAAATATAATTAT
1 ATAAATATAATTAT
365449 ATAAATATAATTA
1 ATAAATATAATTA
365462 AAAAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAAATATAATTAT
Found at i:371020 original size:6 final size:6
Alignment explanation
Indices: 371009--371039 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
370999 TCGGCTCGGC
371009 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
371040 AATACGTGTC
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:0.00, C:0.16, G:0.48, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:372149 original size:47 final size:48
Alignment explanation
Indices: 372096--372194 Score: 191
Period size: 47 Copynumber: 2.1 Consensus size: 48
372086 GTCGCTGACA
372096 TCATCGTCGAAGGGATGCAAATATGCGAGGTGATGCAAGCCAATGTT-
1 TCATCGTCGAAGGGATGCAAATATGCGAGGTGATGCAAGCCAATGTTC
372143 TCATCGTCGAAGGGATGCAAATATGCGAGGTGATGCAAGCCAATGTTC
1 TCATCGTCGAAGGGATGCAAATATGCGAGGTGATGCAAGCCAATGTTC
372191 TCAT
1 TCAT
372195 TGAGAAGCTG
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 47 0.92
48 4 0.08
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (48 bp):
TCATCGTCGAAGGGATGCAAATATGCGAGGTGATGCAAGCCAATGTTC
Found at i:377586 original size:48 final size:47
Alignment explanation
Indices: 377516--377610 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 47
377506 AACAAAGAAG
377516 TAAAGAAAAAAGAGAAGAAAAGAAAATTTATTCATCTCTACCTTGAT
1 TAAAGAAAAAAGAGAAGAAAAGAAAATTTATTCATCTCTACCTTGAT
377563 TAAAGAAAAAAAGAGAAGAAAAGAAAATTTATTCATCTCTACCTTGAT
1 TAAAG-AAAAAAGAGAAGAAAAGAAAATTTATTCATCTCTACCTTGAT
377611 GAGTTTTGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 5 0.11
48 42 0.89
ACGTcount: A:0.52, C:0.11, G:0.13, T:0.25
Consensus pattern (47 bp):
TAAAGAAAAAAGAGAAGAAAAGAAAATTTATTCATCTCTACCTTGAT
Found at i:377947 original size:36 final size:36
Alignment explanation
Indices: 377900--377973 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
377890 AGGGTTTTAA
377900 GATTTTTTAACATTAATTAACGACAATAACCATAAT
1 GATTTTTTAACATTAATTAACGACAATAACCATAAT
377936 GATTTTTTAACATTAATTAACGACAATAACCATAAT
1 GATTTTTTAACATTAATTAACGACAATAACCATAAT
377972 GA
1 GA
377974 AAGTTAATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.45, C:0.14, G:0.07, T:0.35
Consensus pattern (36 bp):
GATTTTTTAACATTAATTAACGACAATAACCATAAT
Found at i:378408 original size:31 final size:31
Alignment explanation
Indices: 378370--378468 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 31
378360 TGGCAAATTG
* *
378370 GTCACTAACATTATCGATTTGTAACAAAATA
1 GTCACTAACATTACCGACTTGTAACAAAATA
* *
378401 GTCACTAACGTTACCGACTTGTACCAAAATA
1 GTCACTAACATTACCGACTTGTAACAAAATA
* * * * * * *
378432 ATTACTAACATAACCAAATTATAACAAAATG
1 GTCACTAACATTACCGACTTGTAACAAAATA
378463 GTCACT
1 GTCACT
378469 TTGAAATCCA
Statistics
Matches: 53, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.28
Consensus pattern (31 bp):
GTCACTAACATTACCGACTTGTAACAAAATA
Found at i:385891 original size:18 final size:18
Alignment explanation
Indices: 385868--385905 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
385858 GCTCTATAAA
385868 TACAAAATAACCCCTTTC
1 TACAAAATAACCCCTTTC
385886 TACAAAATAACCCCTTTC
1 TACAAAATAACCCCTTTC
385904 TA
1 TA
385906 ATTAAGGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (18 bp):
TACAAAATAACCCCTTTC
Found at i:389821 original size:29 final size:29
Alignment explanation
Indices: 389779--389835 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
389769 AGTGTTGGCC
389779 GTAGGTCGCCATGCACTCCGGGCGACCTT
1 GTAGGTCGCCATGCACTCCGGGCGACCTT
389808 GTAGGTCGCCATGCACTCCGGGCGACCT
1 GTAGGTCGCCATGCACTCCGGGCGACCT
389836 ACCCTTGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.14, C:0.35, G:0.32, T:0.19
Consensus pattern (29 bp):
GTAGGTCGCCATGCACTCCGGGCGACCTT
Found at i:389984 original size:24 final size:24
Alignment explanation
Indices: 389955--390029 Score: 97
Period size: 24 Copynumber: 3.3 Consensus size: 24
389945 CATAGCTCGG
389955 TCGGATGGCCTCGGTCGGATGGCC
1 TCGGATGGCCTCGGTCGGATGGCC
389979 TCGGATGG-C-C--TCGGAT-GCTC
1 TCGGATGGCCTCGGTCGGATGGC-C
*
389999 TCGGATGGCCTCGGTCGGATGACC
1 TCGGATGGCCTCGGTCGGATGGCC
390023 TCGGATG
1 TCGGATG
390030 CCCAGTGTGT
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
19 2 0.05
20 15 0.34
21 1 0.02
22 2 0.05
23 1 0.02
24 22 0.50
25 1 0.02
ACGTcount: A:0.11, C:0.28, G:0.39, T:0.23
Consensus pattern (24 bp):
TCGGATGGCCTCGGTCGGATGGCC
Found at i:390019 original size:14 final size:14
Alignment explanation
Indices: 389950--389982 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
389940 CCTCGCATAG
389950 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
389964 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
389978 CTCGG
1 CTCGG
389983 ATGGCCTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.06, C:0.30, G:0.42, T:0.21
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:390029 original size:10 final size:10
Alignment explanation
Indices: 389969--390012 Score: 72
Period size: 10 Copynumber: 4.4 Consensus size: 10
389959 ATGGCCTCGG
389969 TCGGATGGCC
1 TCGGATGGCC
389979 TCGGATGGCC
1 TCGGATGGCC
389989 TCGGAT-GCTC
1 TCGGATGGC-C
389999 TCGGATGGCC
1 TCGGATGGCC
390009 TCGG
1 TCGG
390013 TCGGATGACC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 2 0.06
10 28 0.88
11 2 0.06
ACGTcount: A:0.09, C:0.30, G:0.39, T:0.23
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:399890 original size:44 final size:44
Alignment explanation
Indices: 399775--399927 Score: 213
Period size: 44 Copynumber: 3.5 Consensus size: 44
399765 CTTGTCTGGA
*
399775 TTTGGA-TTAGGTCT-AGTATGCGCTAAAGTTGCATTTCATTG-T
1 TTTGGATTTAGGT-TGAGTATGCGCTAAAGTTTCATTTCATTGTT
* *
399817 TTCGGATTTAGGTTGAGTATGTGCTAAAGTTTCATTTCATTGTT
1 TTTGGATTTAGGTTGAGTATGCGCTAAAGTTTCATTTCATTGTT
* * *
399861 TTTGGATCTACGTTGAGTATGCGCTAAAGTCTCATTTCATTGTT
1 TTTGGATTTAGGTTGAGTATGCGCTAAAGTTTCATTTCATTGTT
399905 TTTAGGATTTAGGTTGAGTATGC
1 TTT-GGATTTAGGTTGAGTATGC
399928 TAAATTTTTT
Statistics
Matches: 97, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
42 6 0.06
43 31 0.32
44 43 0.44
45 17 0.18
ACGTcount: A:0.21, C:0.11, G:0.24, T:0.44
Consensus pattern (44 bp):
TTTGGATTTAGGTTGAGTATGCGCTAAAGTTTCATTTCATTGTT
Found at i:406407 original size:17 final size:16
Alignment explanation
Indices: 406381--406426 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 16
406371 TACATCCTTC
*
406381 TAATTTTAAAATAATA
1 TAATTATAAAATAATA
406397 TTAATTATAAAA-AA-A
1 -TAATTATAAAATAATA
*
406412 TAATTATAAAGTAAT
1 TAATTATAAAATAAT
406427 TATCAATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 10 0.40
15 3 0.12
16 2 0.08
17 10 0.40
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (16 bp):
TAATTATAAAATAATA
Found at i:407169 original size:2 final size:2
Alignment explanation
Indices: 407162--407234 Score: 128
Period size: 2 Copynumber: 36.5 Consensus size: 2
407152 TTTTGATTAA
* *
407162 AT AT AT AT AC AT AT AC 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
407204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
407235 AAATATTTAA
Statistics
Matches: 67, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 67 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:412335 original size:21 final size:21
Alignment explanation
Indices: 412310--412349 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
412300 CCGCTACACA
*
412310 GGGGGAAATCGGTACCCTCTG
1 GGGGGAAATCAGTACCCTCTG
* *
412331 GGGGGGAATCAGTTCCCTC
1 GGGGGAAATCAGTACCCTC
412350 CGAGCAATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.25, G:0.38, T:0.20
Consensus pattern (21 bp):
GGGGGAAATCAGTACCCTCTG
Found at i:413299 original size:213 final size:219
Alignment explanation
Indices: 412995--413428 Score: 790
Period size: 213 Copynumber: 2.0 Consensus size: 219
412985 TTTTAATAAA
412995 AATTCAAAAAGACCAAAAATATATAATAAGTTAAAACCATTCAAAAACATCTAAAACATAAAAAT
1 AATTCAAAAAGACCAAAAATATATAATAAGTTAAAACCATTCAAAAACATCTAAAACATAAAAAT
413060 CCAATATTCATATCAAATTCAAACATCC-AACC-CAAAATGTTAAAACAATAAGTTCTAAGTCCC
66 CCAATATTCATATCAAATTCAAACATCCAAACCTCAAAATGTTAAAACAATAAGTTCTAAGTCCC
413123 ATCT-A-AGAACTAAAGCTCGACAATAATCAAGC-TCTGTAGGAGGATCGGGAGGAG-AAAAAGA
131 ATCTAAGAGAACTAAAGCTCGACAATAATCAAGCATCTGTAGGAGGATCGGGAGGAGAAAAAAGA
413184 GCTTGCATTGCAGCTATCTCATGT
196 GCTTGCATTGCAGCTATCTCATGT
*
413208 AATTCAAAAAGACCAAAAATATATAATAAGTTCAAACCATTCAAAAACATCTAAAACATAAAAAT
1 AATTCAAAAAGACCAAAAATATATAATAAGTTAAAACCATTCAAAAACATCTAAAACATAAAAAT
*
413273 CCAATATTCATATCAAATTCAAACATCCAAACCATTTAAAATGTTAAAACAATAAGTTCTAAGTC
66 CCAATATTCATATCAAATTCAAACATCCAAACC--TCAAAATGTTAAAACAATAAGTTCTAAGTC
413338 CCATCTAAGAGAACTAAAGCTCGACAATAATCAAGCATCTGTAGGAGGATCGGGAGGAGAAAAAA
129 CCATCTAAGAGAACTAAAGCTCGACAATAATCAAGCATCTGTAGGAGGATCGGGAGGAGAAAAAA
413403 GAGCTTGCATTGCAGCTATCTCATGT
194 GAGCTTGCATTGCAGCTATCTCATGT
413429 GTGAGCGCAT
Statistics
Matches: 211, Mismatches: 2, Indels: 8
0.95 0.01 0.04
Matches are distributed among these distances:
213 92 0.44
214 4 0.02
217 34 0.16
218 1 0.00
219 27 0.13
220 22 0.10
221 31 0.15
ACGTcount: A:0.46, C:0.18, G:0.12, T:0.23
Consensus pattern (219 bp):
AATTCAAAAAGACCAAAAATATATAATAAGTTAAAACCATTCAAAAACATCTAAAACATAAAAAT
CCAATATTCATATCAAATTCAAACATCCAAACCTCAAAATGTTAAAACAATAAGTTCTAAGTCCC
ATCTAAGAGAACTAAAGCTCGACAATAATCAAGCATCTGTAGGAGGATCGGGAGGAGAAAAAAGA
GCTTGCATTGCAGCTATCTCATGT
Found at i:414724 original size:13 final size:13
Alignment explanation
Indices: 414706--414738 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
414696 AATGGGGAAA
414706 TTTGAAAACTAA-G
1 TTTGAAAAC-AAGG
414719 TTTGAAAACAAGG
1 TTTGAAAACAAGG
414732 TTTGAAA
1 TTTGAAA
414739 GTCAATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 2 0.11
13 17 0.89
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.30
Consensus pattern (13 bp):
TTTGAAAACAAGG
Found at i:419140 original size:22 final size:21
Alignment explanation
Indices: 419098--419137 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
419088 AAGACTATTT
419098 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTGAAATA
419119 TCATTTTTGT-ATTTTGAAA
1 TCATTTTT-TAATTTTGAAA
419138 ATAGAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATA
Found at i:419300 original size:18 final size:17
Alignment explanation
Indices: 419277--419315 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
419267 CAACTTCTTG
419277 TTCCTCTTCATCGGAACC
1 TTCCTC-TCATCGGAACC
419295 TT-C-CTCATCGGAACC
1 TTCCTCTCATCGGAACC
419310 TTCCTC
1 TTCCTC
419316 ATCGCTCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
15 13 0.68
16 2 0.11
17 2 0.11
18 2 0.11
ACGTcount: A:0.15, C:0.41, G:0.10, T:0.33
Consensus pattern (17 bp):
TTCCTCTCATCGGAACC
Found at i:419304 original size:15 final size:15
Alignment explanation
Indices: 419284--419319 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
419274 TTGTTCCTCT
419284 TCATCGGAACCTTCC
1 TCATCGGAACCTTCC
419299 TCATCGGAACCTTCC
1 TCATCGGAACCTTCC
419314 TCATCG
1 TCATCG
419320 CTCCATGTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.19, C:0.39, G:0.14, T:0.28
Consensus pattern (15 bp):
TCATCGGAACCTTCC
Found at i:423541 original size:52 final size:52
Alignment explanation
Indices: 423463--423567 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
423453 GGATTACTTT
423463 GCATATGGGATCCTGGTTTCTTCACTGTTTCTGATAAATATTTTGGCTCAAG
1 GCATATGGGATCCTGGTTTCTTCACTGTTTCTGATAAATATTTTGGCTCAAG
423515 GCATATGGGATCCTGGTTTCTTCACTGTTTCTGATAAATATTTTGGCTCAAG
1 GCATATGGGATCCTGGTTTCTTCACTGTTTCTGATAAATATTTTGGCTCAAG
423567 G
1 G
423568 TTAATTTCTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (52 bp):
GCATATGGGATCCTGGTTTCTTCACTGTTTCTGATAAATATTTTGGCTCAAG
Found at i:424720 original size:41 final size:40
Alignment explanation
Indices: 424675--425105 Score: 262
Period size: 41 Copynumber: 10.5 Consensus size: 40
424665 TATAGTGCCA
* *
424675 TTTTTCAACAAACGTCGCAATAGAGTAGTACTTTAGCGGCG
1 TTTTT-AACAAACGTCGCTATAGACTAGTACTTTAGCGGCG
* * ** *
424716 TTTTTTACAAACGACGCTATAGACTCCTACTTTAGTGGCG
1 TTTTTAACAAACGTCGCTATAGACTAGTACTTTAGCGGCG
* * * *
424756 TTTTTATACAAACGTCACTATAAACTAGTACTTTAGTGGCAT
1 TTTTTA-ACAAACGTCGCTATAGACTAGTACTTTAGCGGC-G
* * * * * *
424798 TTTTTTACAAATGCCGCTATAGACT-TTATCTATAGTGGCG
1 TTTTTAACAAACGTCGCTATAGACTAGTA-CTTTAGCGGCG
* * * * *
424838 TTTGTTCAACAAACGTCGCAATAGAGTTGTACTTTAACGGCTT
1 TTT-TT-AACAAACGTCGCTATAGACTAGTACTTTAGCGGC-G
* **
424881 TTTTTAA-AAACGTCGCTATAAACTCTTACTTTAGCTGG-G
1 TTTTTAACAAACGTCGCTATAGACTAGTACTTTAGC-GGCG
* * * *
424920 TTTTTATATAAACGTCGCTGTAAACTCGTACTTTAGCGGCG
1 TTTTTA-ACAAACGTCGCTATAGACTAGTACTTTAGCGGCG
* * * **
424961 TTTTTATACAAACGTCGCAACAGAATAGTACTTTAGCATCG
1 TTTTTA-ACAAACGTCGCTATAGACTAGTACTTTAGCGGCG
* * * * *
425002 TTTTGTTACAAACGCCACTATAGACT--TCATCTATAGTGGCG
1 TTTT-TAACAAACGTCGCTATAGACTAGT-A-CTTTAGCGGCG
* * * * *
425043 TTTTTTTCAAAAAATGCCGCAATAGACTAGTACTTTAGCGG-T
1 --TTTTT-AACAAACGTCGCTATAGACTAGTACTTTAGCGGCG
* *
425085 TTTTTTACAAACGCCGCTATA
1 TTTTTAACAAACGTCGCTATA
425106 AACCCTTACC
Statistics
Matches: 299, Mismatches: 72, Indels: 40
0.73 0.18 0.10
Matches are distributed among these distances:
39 19 0.06
40 69 0.23
41 147 0.49
42 31 0.10
43 31 0.10
44 1 0.00
45 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (40 bp):
TTTTTAACAAACGTCGCTATAGACTAGTACTTTAGCGGCG
Found at i:424770 original size:81 final size:81
Alignment explanation
Indices: 424596--424974 Score: 342
Period size: 81 Copynumber: 4.7 Consensus size: 81
424586 CTTTAACGTT
* * * * * * *
424596 GTTTTTATACAAATGCCGCAACAGAGTAGCACTTTAGCGGCG-TTTGT--AAATGCCTCTATAGA
1 GTTTTTATACAAACGTCGCAATAGAGTAGTACTTTAGCGGCGTTTTTTACAAACGCCGCTATAGA
*
424658 CTTTATCTATAGTGCC
66 CTTTATCTATAGTGGC
* *
424674 ATTTTTCA-ACAAACGTCGCAATAGAGTAGTACTTTAGCGGCGTTTTTTACAAACGACGCTATAG
1 GTTTTT-ATACAAACGTCGCAATAGAGTAGTACTTTAGCGGCGTTTTTTACAAACGCCGCTATAG
* *
424738 ACTCCTA-CTTTAGTGGC
65 ACT-TTATCTATAGTGGC
* * * * * * *
424755 GTTTTTATACAAACGTCACTATAAACTAGTACTTTAGTGGCATTTTTTTACAAATGCCGCTATAG
1 GTTTTTATACAAACGTCGCAATAGAGTAGTACTTTAGCGGC-GTTTTTTACAAACGCCGCTATAG
424820 ACTTTATCTATAGTGGC
65 ACTTTATCTATAGTGGC
* * * * *
424837 GTTTGTTCA-ACAAACGTCGCAATAGAGTTGTACTTTAACGGCTTTTTTTAAAAACGTCGCTATA
1 GTTT-TT-ATACAAACGTCGCAATAGAGTAGTACTTTAGCGGCGTTTTTTACAAACGCCGCTATA
* *
424901 AACTCTTA-CTTTAGCTGG-
64 GACT-TTATCTATAG-TGGC
* ** * * *
424919 GTTTTTATATAAACGTCGCTGTAAACTCGTACTTTAGCGGCGTTTTTATACAAACG
1 GTTTTTATACAAACGTCGCAATAGAGTAGTACTTTAGCGGCGTTTTT-TACAAACG
424975 TCGCAACAGA
Statistics
Matches: 243, Mismatches: 44, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
78 35 0.14
79 5 0.02
80 2 0.01
81 90 0.37
82 76 0.31
83 34 0.14
84 1 0.00
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (81 bp):
GTTTTTATACAAACGTCGCAATAGAGTAGTACTTTAGCGGCGTTTTTTACAAACGCCGCTATAGA
CTTTATCTATAGTGGC
Found at i:424886 original size:164 final size:163
Alignment explanation
Indices: 424643--424972 Score: 482
Period size: 164 Copynumber: 2.0 Consensus size: 163
424633 CGGCGTTTGT
*
424643 AAATGCCTCTATAGACTTTATCTATAGTGCCATTTTTCAACAAACGTCGCAATAGAGTAGTACTT
1 AAATGCCGCTATAGACTTTATCTATAGTGCCATTTTTCAACAAACGTCGCAATAGAGTAGTACTT
* * *
424708 TAGCGGCGTTTTTTACAAACGACGCTATAGACTCCTACTTTAG-TGGCGTTTTTATACAAACGTC
66 TAACGGCGTTTTTTAAAAACGACGCTATAAACTCCTACTTTAGCTGG-GTTTTTATACAAACGTC
* *
424772 ACTATAAACTAGTACTTTAGTGGCATTTTTTTAC
130 ACTATAAACTAGTACTTTAGCGGCATTTTTATAC
* * *
424806 AAATGCCGCTATAGACTTTATCTATAGTGGCGTTTGTTCAACAAACGTCGCAATAGAGTTGTACT
1 AAATGCCGCTATAGACTTTATCTATAGTGCCATTT-TTCAACAAACGTCGCAATAGAGTAGTACT
* * * *
424871 TTAACGGCTTTTTTTAAAAACGTCGCTATAAACTCTTACTTTAGCTGGGTTTTTATATAAACGTC
65 TTAACGGCGTTTTTTAAAAACGACGCTATAAACTCCTACTTTAGCTGGGTTTTTATACAAACGTC
* * * *
424936 GCTGTAAACTCGTACTTTAGCGGCGTTTTTATAC
130 ACTATAAACTAGTACTTTAGCGGCATTTTTATAC
424970 AAA
1 AAA
424973 CGTCGCAACA
Statistics
Matches: 148, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
163 32 0.22
164 113 0.76
165 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.36
Consensus pattern (163 bp):
AAATGCCGCTATAGACTTTATCTATAGTGCCATTTTTCAACAAACGTCGCAATAGAGTAGTACTT
TAACGGCGTTTTTTAAAAACGACGCTATAAACTCCTACTTTAGCTGGGTTTTTATACAAACGTCA
CTATAAACTAGTACTTTAGCGGCATTTTTATAC
Found at i:424969 original size:205 final size:205
Alignment explanation
Indices: 424703--425123 Score: 528
Period size: 205 Copynumber: 2.1 Consensus size: 205
424693 AATAGAGTAG
* *
424703 TACTTTAGC-GGCGTTTTTTACAAACGACGCTATAGACTCCTACTTTAGTGGCGTTTTTATACAA
1 TACTTTAGCTGGCGTTTTTTACAAACGACGCTATAAACTCCTACTTTAGCGGCGTTTTTATACAA
* * ** * * * *
424767 ACGTCACTATA-AACTAGTACTTTAGTGGCATTTTTTTACAAATGCCGCTATAGACTTTATCTAT
66 ACGTCACAACAGAA-TAGTACTTTAGCAGCATTTTGTTACAAACGCCACTATAGACTTCATCTAT
* * * * *
424831 AGTGGCG-TTTGTTCAACAAACGTCGCAATAGAGTTGTACTTTAACGGCTTTTTTTAAAAACGTC
130 AGTGGCGTTTTGTTCAAAAAACGCCGCAATAGACTAGTACTTTAACGG-TTTTTTTAAAAACGCC
*
424895 GCTATAAACTCT
194 GCTATAAACCCT
* * * *
424907 TACTTTAGCTGG-GTTTTTATATAAACGTCGCTGTAAACTCGTACTTTAGCGGCGTTTTTATACA
1 TACTTTAGCTGGCGTTTTT-TACAAACGACGCTATAAACTCCTACTTTAGCGGCGTTTTTATACA
* * *
424971 AACGTCGCAACAGAATAGTACTTTAGCATCGTTTTGTTACAAACGCCACTATAGACTTCATCTAT
65 AACGTCACAACAGAATAGTACTTTAGCAGCATTTTGTTACAAACGCCACTATAGACTTCATCTAT
* * * *
425036 AGTGGCGTTTTTTTCAAAAAATGCCGCAATAGACTAGTACTTTAGCGGTTTTTTTACAAACGCCG
130 AGTGGCGTTTTGTTCAAAAAACGCCGCAATAGACTAGTACTTTAACGGTTTTTTTAAAAACGCCG
425101 CTATAAACCCT
195 CTATAAACCCT
*
425112 TACCTTA-CTGGC
1 TACTTTAGCTGGC
425124 AAGTTTGCAG
Statistics
Matches: 184, Mismatches: 28, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
204 19 0.10
205 130 0.71
206 35 0.19
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (205 bp):
TACTTTAGCTGGCGTTTTTTACAAACGACGCTATAAACTCCTACTTTAGCGGCGTTTTTATACAA
ACGTCACAACAGAATAGTACTTTAGCAGCATTTTGTTACAAACGCCACTATAGACTTCATCTATA
GTGGCGTTTTGTTCAAAAAACGCCGCAATAGACTAGTACTTTAACGGTTTTTTTAAAAACGCCGC
TATAAACCCT
Found at i:424997 original size:82 final size:82
Alignment explanation
Indices: 424682--424996 Score: 300
Period size: 82 Copynumber: 3.9 Consensus size: 82
424672 CCATTTTTCA
* * * * * *
424682 ACAAACGTCGCAATAGAGTAGTACTTTAGCGGCG-TTTTTTACAAACGACGCTATAGACTCCTAC
1 ACAAACGTCGCTATAAACTAGTACTTTAGCGGCGTTTTTTTACAAACGTCGCTATAGAATCTTAC
424746 TTTAGTGGCGTTTTTAT
66 TTTAGTGGCGTTTTTAT
* * * * * *
424763 ACAAACGTCACTATAAACTAGTACTTTAGTGGCATTTTTTTACAAATGCCGCTATAGACT-TTAT
1 ACAAACGTCGCTATAAACTAGTACTTTAGCGGCGTTTTTTTACAAACGTCGCTATAGAATCTTA-
*
424827 CTATAGTGGCGTTTGTTCA-
65 CTTTAGTGGCGTTT-TT-AT
* * * * * *
424846 ACAAACGTCGCAATAGAGTTGTACTTTAACGGC-TTTTTTTAAAAACGTCGCTATA-AACTCTTA
1 ACAAACGTCGCTATAAACTAGTACTTTAGCGGCGTTTTTTTACAAACGTCGCTATAGAA-TCTTA
424909 CTTTAGCTGG-GTTTTTAT
65 CTTTAG-TGGCGTTTTTAT
* * * * * * **
424927 ATAAACGTCGCTGTAAACTCGTACTTTAGCGGCGTTTTTATACAAACGTCGCAACAGAATAGTAC
1 ACAAACGTCGCTATAAACTAGTACTTTAGCGGCGTTTTTTTACAAACGTCGCTATAGAATCTTAC
424992 TTTAG
66 TTTAG
424997 CATCGTTTTG
Statistics
Matches: 189, Mismatches: 35, Indels: 19
0.78 0.14 0.08
Matches are distributed among these distances:
80 1 0.01
81 59 0.31
82 92 0.49
83 36 0.19
84 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (82 bp):
ACAAACGTCGCTATAAACTAGTACTTTAGCGGCGTTTTTTTACAAACGTCGCTATAGAATCTTAC
TTTAGTGGCGTTTTTAT
Found at i:432155 original size:24 final size:24
Alignment explanation
Indices: 432119--432189 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
432109 CCACATAGTT
*
432119 TTTGTCCCAAAGGACCGCGTAGAA
1 TTTGTCCCGAAGGACCGCGTAGAA
432143 TTTGTCCCGAAGGACCGCGTAGAA
1 TTTGTCCCGAAGGACCGCGTAGAA
*
432167 -ATGTCCCGAAGGACCGCGTAGAA
1 TTTGTCCCGAAGGACCGCGTAGAA
432190 CCCTCAACTC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
23 22 0.49
24 23 0.51
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.18
Consensus pattern (24 bp):
TTTGTCCCGAAGGACCGCGTAGAA
Found at i:432175 original size:23 final size:24
Alignment explanation
Indices: 432121--432189 Score: 113
Period size: 23 Copynumber: 2.9 Consensus size: 24
432111 ACATAGTTTT
* *
432121 TGTCCCAAAGGACCGCGTAGAATT
1 TGTCCCGAAGGACCGCGTAGAATA
432145 TGTCCCGAAGGACCGCGTAGAA-A
1 TGTCCCGAAGGACCGCGTAGAATA
432168 TGTCCCGAAGGACCGCGTAGAA
1 TGTCCCGAAGGACCGCGTAGAA
432190 CCCTCAACTC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
23 22 0.51
24 21 0.49
ACGTcount: A:0.29, C:0.26, G:0.29, T:0.16
Consensus pattern (24 bp):
TGTCCCGAAGGACCGCGTAGAATA
Found at i:437240 original size:2 final size:2
Alignment explanation
Indices: 437233--437257 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
437223 TATCAATTCA
437233 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
437258 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:442699 original size:21 final size:20
Alignment explanation
Indices: 442662--442700 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
442652 TTAAATACAA
**
442662 AGTATTAAATGGTGTGATTG
1 AGTATTAAATGAAGTGATTG
442682 AGTATTGAAATGAAGTGAT
1 AGTATT-AAATGAAGTGAT
442701 ATATCACTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (20 bp):
AGTATTAAATGAAGTGATTG
Found at i:442807 original size:36 final size:35
Alignment explanation
Indices: 442766--442871 Score: 115
Period size: 36 Copynumber: 3.0 Consensus size: 35
442756 TTAAACCACA
*
442766 AAACATTACATTTAGGATATAAAAACAACGAACCAT
1 AAACATTACATTTAGGACATAAAAACAAC-AACCAT
* * * * *
442802 AAACATTACATTAAGAAGATAAAAACAACAAACTT
1 AAACATTACATTTAGGACATAAAAACAACAACCAT
*
442837 AACACATTAC-TTTAAGGACATAAATACAACAACCA
1 AA-ACATTACATTT-AGGACATAAAAACAACAACCA
442872 CACCAGTAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
35 8 0.14
36 49 0.86
ACGTcount: A:0.55, C:0.18, G:0.07, T:0.21
Consensus pattern (35 bp):
AAACATTACATTTAGGACATAAAAACAACAACCAT
Found at i:451995 original size:167 final size:166
Alignment explanation
Indices: 451719--452051 Score: 657
Period size: 167 Copynumber: 2.0 Consensus size: 166
451709 TGTCTTAATC
451719 TATTTATACCAAGATAATATACCTAGGGTTTTGTGCCAAAATGACAATATTTCCCTAGGGTACAT
1 TATTTATACCAAGATAATATACCTAGGGTTTTGTGCCAAAATGACAATATTTCCCTAGGGTACAT
451784 CCCCTACACGTGAAAAAGAAGTACAAATGTGGTAGTCGTCCCCTCCTAGGTGGCAGGCAGGAGGA
66 CCCCTACACGTGAAAAAGAAGTACAAATGTGGTAGTCGTCCCCTCCTAGGTGGCAGGCAGGAGGA
451849 ATCACATGATGGTTGGAAAACTGACTCTTTTTATAAA
131 ATCACATGATGGTTGGAAAACTGACTC-TTTTATAAA
451886 TATTTATACCAAGATAATATACCTAGGGTTTTGTGCCAAAATGACAATATTTCCCTAGGGTACAT
1 TATTTATACCAAGATAATATACCTAGGGTTTTGTGCCAAAATGACAATATTTCCCTAGGGTACAT
451951 CCCCTACACGTGAAAAAGAAGTACAAATGTGGTAGTCGTCCCCTCCTAGGTGGCAGGCAGGAGGA
66 CCCCTACACGTGAAAAAGAAGTACAAATGTGGTAGTCGTCCCCTCCTAGGTGGCAGGCAGGAGGA
452016 ATCACATGATGGTTGGAAAACTGACTCTTTTATAAA
131 ATCACATGATGGTTGGAAAACTGACTCTTTTATAAA
452052 AAATATTTTC
Statistics
Matches: 166, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
166 9 0.05
167 157 0.95
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.27
Consensus pattern (166 bp):
TATTTATACCAAGATAATATACCTAGGGTTTTGTGCCAAAATGACAATATTTCCCTAGGGTACAT
CCCCTACACGTGAAAAAGAAGTACAAATGTGGTAGTCGTCCCCTCCTAGGTGGCAGGCAGGAGGA
ATCACATGATGGTTGGAAAACTGACTCTTTTATAAA
Found at i:458308 original size:145 final size:145
Alignment explanation
Indices: 458045--458334 Score: 580
Period size: 145 Copynumber: 2.0 Consensus size: 145
458035 CATTCACAGT
458045 CACACATTGGTCAGCTACTCTTATGGTGAGTTCACCCTTTTCACAATCAATAAGGAGGTGGCCAG
1 CACACATTGGTCAGCTACTCTTATGGTGAGTTCACCCTTTTCACAATCAATAAGGAGGTGGCCAG
458110 TGGCTAGGAAATGCCTCCCCAAAATTATGGGTGCATTAGACTCTCCATTCGGGACGAACACGAGA
66 TGGCTAGGAAATGCCTCCCCAAAATTATGGGTGCATTAGACTCTCCATTCGGGACGAACACGAGA
458175 ATAGTCAGCTAGTTG
131 ATAGTCAGCTAGTTG
458190 CACACATTGGTCAGCTACTCTTATGGTGAGTTCACCCTTTTCACAATCAATAAGGAGGTGGCCAG
1 CACACATTGGTCAGCTACTCTTATGGTGAGTTCACCCTTTTCACAATCAATAAGGAGGTGGCCAG
458255 TGGCTAGGAAATGCCTCCCCAAAATTATGGGTGCATTAGACTCTCCATTCGGGACGAACACGAGA
66 TGGCTAGGAAATGCCTCCCCAAAATTATGGGTGCATTAGACTCTCCATTCGGGACGAACACGAGA
458320 ATAGTCAGCTAGTTG
131 ATAGTCAGCTAGTTG
458335 TAAAATAACG
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
145 145 1.00
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (145 bp):
CACACATTGGTCAGCTACTCTTATGGTGAGTTCACCCTTTTCACAATCAATAAGGAGGTGGCCAG
TGGCTAGGAAATGCCTCCCCAAAATTATGGGTGCATTAGACTCTCCATTCGGGACGAACACGAGA
ATAGTCAGCTAGTTG
Found at i:462857 original size:20 final size:20
Alignment explanation
Indices: 462832--462885 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
462822 CGTCAAGGGA
462832 TGCATCGATACATGGTGTAG
1 TGCATCGATACATGGTGTAG
462852 TGCATCGATACATGGTGTAG
1 TGCATCGATACATGGTGTAG
*
462872 TGCATCGATGCATG
1 TGCATCGATACATG
462886 CCTTCATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.24, C:0.17, G:0.30, T:0.30
Consensus pattern (20 bp):
TGCATCGATACATGGTGTAG
Found at i:466864 original size:30 final size:29
Alignment explanation
Indices: 466830--466917 Score: 76
Period size: 30 Copynumber: 3.1 Consensus size: 29
466820 AGAAGTAAGT
466830 TGGGATGCTCTTCTATGTTTCTTAGCCATG
1 TGGGAT-CTCTTCTATGTTTCTTAGCCATG
** ** * *
466860 TGGGAT-TGGT-T-TG-TTCTTAAACTTT
1 TGGGATCTCTTCTATGTTTCTTAGCCATG
466885 TGGGATACTCTTCTATGTTTCTTAGCCATG
1 TGGGAT-CTCTTCTATGTTTCTTAGCCATG
466915 TGG
1 TGG
466918 ATTGTTTTTT
Statistics
Matches: 41, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
25 14 0.34
26 2 0.05
27 3 0.07
28 3 0.07
29 2 0.05
30 17 0.41
ACGTcount: A:0.15, C:0.16, G:0.24, T:0.45
Consensus pattern (29 bp):
TGGGATCTCTTCTATGTTTCTTAGCCATG
Found at i:468993 original size:172 final size:174
Alignment explanation
Indices: 468707--469053 Score: 680
Period size: 172 Copynumber: 2.0 Consensus size: 174
468697 CCAAGCACGA
468707 ACCAAGGGCGTGTTACTGGACTGAAGGGGTCCCCTCTGAGAAATAAACTGGCTGTTTTGTCCAAA
1 ACCAAGGGCGTGTTACTGGACTGAAGGGGTCCCCTCTGAGAAATAAACTGGCTGTTTTGTCCAAA
468772 AGCAGGTGGCAGTGGCGGTGCCGATGGATTTCCAAAGAGGAATCCACCACT-CCGCCACTAGAAC
66 AGCAGGTGGCAGTGGCGGTGCCGATGGATTTCCAAAGAGGAATCCACCACTCCCGCCACTAGAAC
468836 CACCGCCAGTGCCACTACCAGCACCA-CATTATTCCAGGCAACC
131 CACCGCCAGTGCCACTACCAGCACCACCATTATTCCAGGCAACC
468879 ACCAAGGGCGTGTTACTGGACTGAAGGGGTCCCCTCTGAGAAATAAACTGGCTGTTTTGTCCAAA
1 ACCAAGGGCGTGTTACTGGACTGAAGGGGTCCCCTCTGAGAAATAAACTGGCTGTTTTGTCCAAA
468944 AGCAGGTGGCAGTGGCGGTGCCGATGGATTTCCAAAGAGGAATCCACCACTCCCGCCACTAGAAC
66 AGCAGGTGGCAGTGGCGGTGCCGATGGATTTCCAAAGAGGAATCCACCACTCCCGCCACTAGAAC
469009 CACCGCCAGTGCCACTACCAGCACCACCATTATTCCAGGCAACC
131 CACCGCCAGTGCCACTACCAGCACCACCATTATTCCAGGCAACC
469053 A
1 A
469054 ATCTCTGAGA
Statistics
Matches: 173, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
172 116 0.67
173 39 0.23
174 18 0.10
ACGTcount: A:0.27, C:0.30, G:0.25, T:0.18
Consensus pattern (174 bp):
ACCAAGGGCGTGTTACTGGACTGAAGGGGTCCCCTCTGAGAAATAAACTGGCTGTTTTGTCCAAA
AGCAGGTGGCAGTGGCGGTGCCGATGGATTTCCAAAGAGGAATCCACCACTCCCGCCACTAGAAC
CACCGCCAGTGCCACTACCAGCACCACCATTATTCCAGGCAACC
Found at i:475477 original size:23 final size:25
Alignment explanation
Indices: 475438--475485 Score: 82
Period size: 23 Copynumber: 2.0 Consensus size: 25
475428 TGATACAACT
475438 TGACATATATATATTGAATTAAATA
1 TGACATATATATATTGAATTAAATA
475463 TGACAT-T-TATATTGAATTAAATA
1 TGACATATATATATTGAATTAAATA
475486 AACTTAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 16 0.70
24 1 0.04
25 6 0.26
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (25 bp):
TGACATATATATATTGAATTAAATA
Found at i:475531 original size:59 final size:59
Alignment explanation
Indices: 475468--475639 Score: 160
Period size: 53 Copynumber: 3.0 Consensus size: 59
475458 AAATATGACA
475468 TTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATAACATATGATT
1 TTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATAACATATGATT
** * ** ** * * ** ** **
475527 TTTAT-TTTTATTAGATAAA-AAATTAATTAAAAAATT--TA-T-TCGAA-ATATGACA
1 TTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATAACATATGATT
475579 TTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATAACATATGATT
1 TTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATAACATATGATT
475638 TT
1 TT
475640 AATTTTTATT
Statistics
Matches: 76, Mismatches: 30, Indels: 14
0.63 0.25 0.12
Matches are distributed among these distances:
52 11 0.14
53 14 0.18
54 10 0.13
55 2 0.03
56 2 0.03
57 10 0.13
58 14 0.18
59 13 0.17
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.41
Consensus pattern (59 bp):
TTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATAACATATGATT
Found at i:475583 original size:52 final size:52
Alignment explanation
Indices: 475527--475694 Score: 122
Period size: 53 Copynumber: 3.1 Consensus size: 52
475517 ACATATGATT
475527 TTTATTTTTATTAGATAAAAAATTAATTAAAAAATTTATTCGAAATATGACA
1 TTTATTTTTATTAGATAAAAAATTAATTAAAAAATTTATTCGAAATATGACA
** * ** ** * * ** ** *
475579 TTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATAACATATGA-T
1 TTTAT-TTTTATTAGATAAA-AAATTAATTAAAAAATT--TA-T-TCGAA-ATATGACA
*
475637 TTTAATTTTTATTAGATAAAAAATTAATTAAAAAATTTATTCGAAATATGGCA
1 TTT-ATTTTTATTAGATAAAAAATTAATTAAAAAATTTATTCGAAATATGACA
475690 TTTAT
1 TTTAT
475695 ATTGAATTAA
Statistics
Matches: 78, Mismatches: 29, Indels: 18
0.62 0.23 0.14
Matches are distributed among these distances:
52 12 0.15
53 17 0.22
54 10 0.13
55 2 0.03
56 2 0.03
57 10 0.13
58 17 0.22
59 8 0.10
ACGTcount: A:0.46, C:0.04, G:0.08, T:0.42
Consensus pattern (52 bp):
TTTATTTTTATTAGATAAAAAATTAATTAAAAAATTTATTCGAAATATGACA
Found at i:475652 original size:111 final size:111
Alignment explanation
Indices: 475458--475738 Score: 535
Period size: 111 Copynumber: 2.5 Consensus size: 111
475448 ATATTGAATT
475458 AAATATGACATTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATAACATAT
1 AAATATGACATTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATAACATAT
*
475523 GATTTTTATTTTTATTAGATAAAAAATTAATTAAAAAATTTATTCG
66 GATTTTAATTTTTATTAGATAAAAAATTAATTAAAAAATTTATTCG
475569 AAATATGACATTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATAACATAT
1 AAATATGACATTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATAACATAT
475634 GATTTTAATTTTTATTAGATAAAAAATTAATTAAAAAATTTATTCG
66 GATTTTAATTTTTATTAGATAAAAAATTAATTAAAAAATTTATTCG
* *
475680 AAATATGGCATTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATGTTATATA
1 AAATATGACATTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATA
475739 CGTATCGTAC
Statistics
Matches: 167, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 167 1.00
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (111 bp):
AAATATGACATTTATATTGAATTAAATAAACTTAGAAAGTAGAACGTTGATATTATATAACATAT
GATTTTAATTTTTATTAGATAAAAAATTAATTAAAAAATTTATTCG
Found at i:476014 original size:41 final size:41
Alignment explanation
Indices: 475969--476057 Score: 160
Period size: 41 Copynumber: 2.2 Consensus size: 41
475959 AATGCAATTT
475969 GACTCGACTCGAAAACTTGCGAGCTTAAAACTTTTAAACTC
1 GACTCGACTCGAAAACTTGCGAGCTTAAAACTTTTAAACTC
* *
476010 GACTCGACTCGAAAACTTGCGAGTTTAAAATTTTTAAACTC
1 GACTCGACTCGAAAACTTGCGAGCTTAAAACTTTTAAACTC
476051 GACTCGA
1 GACTCGA
476058 ACTTAAAATC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (41 bp):
GACTCGACTCGAAAACTTGCGAGCTTAAAACTTTTAAACTC
Found at i:476359 original size:23 final size:23
Alignment explanation
Indices: 476333--476387 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
476323 GTTAAGAATT
476333 CGAGTCGAGCTCAAACTCGAGTC
1 CGAGTCGAGCTCAAACTCGAGTC
* *
476356 CGAGTCGAGCTCGAGCTCGAGTC
1 CGAGTCGAGCTCAAACTCGAGTC
*
476379 TGAGTCGAG
1 CGAGTCGAG
476388 TTCATTCGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.18
Consensus pattern (23 bp):
CGAGTCGAGCTCAAACTCGAGTC
Found at i:476368 original size:17 final size:19
Alignment explanation
Indices: 476348--476388 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
476338 CGAGCTCAAA
476348 CTCGAGTC-CGAGTC-GAG
1 CTCGAGTCTCGAGTCTGAG
476365 CTCGAG-CTCGAGTCTGAG
1 CTCGAGTCTCGAGTCTGAG
476383 -TCGAGT
1 CTCGAGT
476389 TCATTCGATC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 1 0.05
17 17 0.81
18 3 0.14
ACGTcount: A:0.17, C:0.27, G:0.34, T:0.22
Consensus pattern (19 bp):
CTCGAGTCTCGAGTCTGAG
Found at i:482242 original size:20 final size:20
Alignment explanation
Indices: 482217--482351 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
482207 AATTGGGAAA
482217 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
482237 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
482257 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
482278 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* * *
482298 TTCGCAACGCGATTCTGACT
1 ATCGCAATGCGATACTGACT
* * *
482318 TTCGCAACGCGATAAT-ACAT
1 ATCGCAATGCGATACTGAC-T
482338 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
482352 TTTCAAAGCG
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 4 0.04
20 66 0.69
21 24 0.25
22 2 0.02
ACGTcount: A:0.33, C:0.24, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:482261 original size:61 final size:61
Alignment explanation
Indices: 482214--482345 Score: 183
Period size: 61 Copynumber: 2.2 Consensus size: 61
482204 GCGAATTGGG
* * * * *
482214 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * *
482275 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
482336 ATAATCGCAA
1 AAAATCGCAA
482346 TGCGATTTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:482547 original size:22 final size:22
Alignment explanation
Indices: 482519--482562 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
482509 CACTCTCTCA
482519 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
482541 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
482563 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:482851 original size:20 final size:20
Alignment explanation
Indices: 482826--482863 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
482816 CGATTCTCTC
482826 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
482846 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
482864 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:483054 original size:25 final size:24
Alignment explanation
Indices: 483000--483054 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
482990 TGTTTATTAT
* *
483000 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
483024 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
483050 TGTTT
1 TGTTT
483055 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:484203 original size:18 final size:18
Alignment explanation
Indices: 484182--484244 Score: 99
Period size: 18 Copynumber: 3.5 Consensus size: 18
484172 TCCACTTCGG
*
484182 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
484200 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
*
484218 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
484236 GAGCCATCA
1 GAGCCATCA
484245 TCTGATCGAC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 42 1.00
ACGTcount: A:0.27, C:0.44, G:0.14, T:0.14
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:484780 original size:19 final size:20
Alignment explanation
Indices: 484737--484792 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
484727 AGCAACACGA
484737 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
484757 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
484776 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
484793 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:484800 original size:14 final size:14
Alignment explanation
Indices: 484781--484839 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
484771 ATGCGAAATG
484781 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
484795 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
484814 AAAATCGCAACGAC
1 AAAATCGCAACGAC
484828 AAAATCGCAACG
1 AAAATCGCAACG
484840 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.49, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:484807 original size:33 final size:33
Alignment explanation
Indices: 484765--484856 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
484755 GGAAATGGCT
484765 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
484798 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
484831 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
484857 TGCGATTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:484819 original size:19 final size:19
Alignment explanation
Indices: 484765--484861 Score: 97
Period size: 19 Copynumber: 5.6 Consensus size: 19
484755 GGAAATGGCT
484765 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
484784 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
484798 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
484817 ATCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
*
484831 ATCGCAACGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
484850 ATCGCAATGCGA
1 ATCGCAATGCGA
484862 TTTGTGTTTC
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
14 20 0.32
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.49
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:484952 original size:20 final size:20
Alignment explanation
Indices: 484918--484973 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
484908 TTGCGATTTT
*
484918 CATTTC-GCATTGCGATAGC
1 CATTTCTGCGTTGCGATAGC
*
484937 CATTTCTGCGTTGCGATAGT
1 CATTTCTGCGTTGCGATAGC
484957 CATTT-TCGCGTTGCGAT
1 CATTTCT-GCGTTGCGAT
484974 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 7 0.21
20 26 0.79
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (20 bp):
CATTTCTGCGTTGCGATAGC
Found at i:484984 original size:20 final size:19
Alignment explanation
Indices: 484868--484976 Score: 93
Period size: 19 Copynumber: 5.9 Consensus size: 19
484858 GCGATTTGTG
484868 TTTCGCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
*
484887 TTTCGCATTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
484903 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
484920 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
484939 TTTCTGCGTTGCGATAGTCA
1 TTTC-GCGTTGCGATTTTCA
484959 TTTTCGCGTTGCGATTTT
1 -TTTCGCGTTGCGATTTT
484977 AAGTTTCGTG
Statistics
Matches: 71, Mismatches: 12, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
14 7 0.10
15 3 0.04
16 2 0.03
17 2 0.03
18 3 0.04
19 26 0.37
20 24 0.34
21 4 0.06
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:486864 original size:14 final size:14
Alignment explanation
Indices: 486845--486880 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
486835 ATTGTTTAAT
486845 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
486859 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
486873 TGATTTGT
1 TGATTTGT
486881 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:487072 original size:19 final size:19
Alignment explanation
Indices: 487017--487065 Score: 98
Period size: 19 Copynumber: 2.6 Consensus size: 19
487007 ATCACAACGA
487017 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
487036 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
487055 GAAAATCGCAA
1 GAAAATCGCAA
487066 CGAGAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.49, C:0.16, G:0.20, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:487128 original size:20 final size:20
Alignment explanation
Indices: 487111--487198 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
487101 CGATTTTCTA
487111 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
* *** *
487131 GTTGAGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
* *
487151 ATTGCAATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
487171 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
487191 GTTGCGAT
1 GTTGCGAT
487199 TTCCCCGTTG
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
19 3 0.06
20 46 0.88
21 3 0.06
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:487533 original size:20 final size:21
Alignment explanation
Indices: 487489--487540 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
487479 ATAGTCAGTA
*
487489 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
487510 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
*
487530 TCGCATGGCGA
1 TCGCATTGCGA
487541 ATTAGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:488570 original size:12 final size:12
Alignment explanation
Indices: 488553--488589 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
488543 ATATAATCCT
488553 GAAGAAGAAAAA
1 GAAGAAGAAAAA
488565 GAAGAAGAAAAA
1 GAAGAAGAAAAA
488577 GAAGAAGAAAAA
1 GAAGAAGAAAAA
488589 G
1 G
488590 TCCCCAAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:490927 original size:33 final size:33
Alignment explanation
Indices: 490881--491007 Score: 175
Period size: 33 Copynumber: 3.8 Consensus size: 33
490871 GAAAATTACT
490881 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* **
490914 ATCGCAATACGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
490946 TTTCACAATGCGAAATAAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
490980 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
491008 CGAATTTAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
32 1 0.01
33 77 0.97
34 1 0.01
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Done.