Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 28 of 125
Found at i:5318677 original size:23 final size:23
Alignment explanation
Indices: 5318650--5318696 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
5318640 ATCCTGAAAC
5318650 CTAGTATTCAAGTCAAAGTTATT
1 CTAGTATTCAAGTCAAAGTTATT
*
5318673 CTAGTATTCTAGTCAAAGTTATT
1 CTAGTATTCAAGTCAAAGTTATT
5318696 C
1 C
5318697 ATGAACGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (23 bp):
CTAGTATTCAAGTCAAAGTTATT
Found at i:5321433 original size:35 final size:33
Alignment explanation
Indices: 5321394--5321460 Score: 89
Period size: 35 Copynumber: 2.0 Consensus size: 33
5321384 ATTATAAATT
* *
5321394 TTTAAAATTTAATTCGATTATGAATCGATTTTTAC
1 TTTAAAAATTAATTCGATT-T-AATCGAATTTTAC
*
5321429 TTTAAAAATTAATTTGATTTAATCGAATTTTA
1 TTTAAAAATTAATTCGATTTAATCGAATTTTA
5321461 TTAATTCAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 11 0.38
34 1 0.03
35 17 0.59
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.49
Consensus pattern (33 bp):
TTTAAAAATTAATTCGATTTAATCGAATTTTAC
Found at i:5321517 original size:12 final size:12
Alignment explanation
Indices: 5321502--5321526 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5321492 TTATATATTA
5321502 TTTTAATAAAAT
1 TTTTAATAAAAT
5321514 TTTTAATAAAAT
1 TTTTAATAAAAT
5321526 T
1 T
5321527 AAATAAATTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTTTAATAAAAT
Found at i:5322443 original size:3 final size:3
Alignment explanation
Indices: 5322437--5322496 Score: 56
Period size: 3 Copynumber: 21.0 Consensus size: 3
5322427 TTTTTTAGTT
* **
5322437 TAA TAA TAA TAA TAA TAA TAA -AA TATA TAT TTT TAA -AA -AA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA
5322479 TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA
5322497 AAAAGAGACA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 8 0.16
3 38 0.78
4 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:5323481 original size:20 final size:19
Alignment explanation
Indices: 5323456--5323508 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
5323446 AATTTTCTAA
5323456 TTTATTTATTTATTATTATT
1 TTTATTTATTTATTATT-TT
*
5323476 TTTA-TTATTTTAAGTATTTT
1 TTTATTTA-TTT-ATTATTTT
*
5323496 TTTATATATTTAT
1 TTTATTTATTTAT
5323509 GCATGATAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
19 4 0.15
20 16 0.59
21 7 0.26
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
TTTATTTATTTATTATTTT
Found at i:5323951 original size:15 final size:15
Alignment explanation
Indices: 5323915--5323963 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
5323905 TTCAAAAACC
*
5323915 CCTAAAATCTAAAATTT
1 CCTAAAATCCAAAA--T
5323932 CCTAAAATCCAAAAT
1 CCTAAAATCCAAAAT
*
5323947 CCTAAAATCCAAGAT
1 CCTAAAATCCAAAAT
5323962 CC
1 CC
5323964 GTTAAATTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 17 0.57
17 13 0.43
ACGTcount: A:0.47, C:0.27, G:0.02, T:0.24
Consensus pattern (15 bp):
CCTAAAATCCAAAAT
Found at i:5324051 original size:21 final size:21
Alignment explanation
Indices: 5324025--5324065 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5324015 CCAAATCCTA
5324025 AAACTCTCAAAA-CTTAAATCC
1 AAACTCTCAAAATC-TAAATCC
*
5324046 AAACTCTTAAAATCTAAATC
1 AAACTCTCAAAATCTAAATC
5324066 TTCAAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (21 bp):
AAACTCTCAAAATCTAAATCC
Found at i:5324076 original size:23 final size:23
Alignment explanation
Indices: 5324011--5324095 Score: 61
Period size: 23 Copynumber: 3.8 Consensus size: 23
5324001 TCATACCTTA
* *
5324011 AAAACC-AAATCCT-AAAACTCTC
1 AAAACCTAAATCTTCAAAA-TCTT
* *
5324033 AAAACTTAAATC--CAAACTCTT
1 AAAACCTAAATCTTCAAAATCTT
*
5324054 AAAATCTAAATCTTCAAAATCTT
1 AAAACCTAAATCTTCAAAATCTT
* * *
5324077 GAAACCTTAATCTTTAAAA
1 AAAACCTAAATCTTCAAAA
5324096 CCTTTACTCA
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
21 13 0.27
22 8 0.16
23 28 0.57
ACGTcount: A:0.48, C:0.22, G:0.01, T:0.28
Consensus pattern (23 bp):
AAAACCTAAATCTTCAAAATCTT
Found at i:5331551 original size:110 final size:108
Alignment explanation
Indices: 5331437--5331729 Score: 313
Period size: 110 Copynumber: 2.7 Consensus size: 108
5331427 TTATCCCGTT
* * *
5331437 GATTCTGTAAGACTTCCAGACATGATTCTGTAAGACTTCTGGGCATAATTTTGATTCGCGATGTT
1 GATTCTGTAAGACCTCC-GACATGATT-TATAAGACTTCTGGGCATAATTTTGATTCGCGATATT
* * *
5331502 ATCTCGATCAATTTCTT-CTTTTCGACTTGCGGTATTGTCTCAATC
64 ATCCCGATCAATTTCTTCCTTTT-GACTTACGGTATTGTCCCAATC
* * **
5331547 GATTCTGTAAGACCTCCGGATATGATTATATAAGACCTTC-GAGCATAATTTTGATTTACGATAT
1 GATTCTGTAAGACCTCC-GACATGATT-TATAAGA-CTTCTGGGCATAATTTTGATTCGCGATAT
* * *
5331611 TATCCCGATCGATTTCTTCCTTTTGACTTACGGTGTTGTCCCAGTC
63 TATCCCGATCAATTTCTTCCTTTTGACTTACGGTATTGTCCCAATC
* * * * * * *
5331657 AATTCTGTAAGGCCTCCGAACATTATTTCTAAGA-TCTCTGGGTATAAATTTGATTCGCGGTATT
1 GATTCTGTAAGACCTCCG-ACATGATTTATAAGACT-TCTGGGCATAATTTTGATTCGCGATATT
5331721 ATCCCGATC
64 ATCCCGATC
5331730 GATTCTTGAT
Statistics
Matches: 152, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
107 1 0.01
108 2 0.01
109 35 0.23
110 105 0.69
111 9 0.06
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (108 bp):
GATTCTGTAAGACCTCCGACATGATTTATAAGACTTCTGGGCATAATTTTGATTCGCGATATTAT
CCCGATCAATTTCTTCCTTTTGACTTACGGTATTGTCCCAATC
Found at i:5331891 original size:193 final size:195
Alignment explanation
Indices: 5331588--5331952 Score: 461
Period size: 193 Copynumber: 1.9 Consensus size: 195
5331578 AAGACCTTCG
* *
5331588 AGCATAATTTTGATTTACGATATTATCCCGATCGATTTCTTCCTTTTGACTTACGGTGTTGTCCC
1 AGCATAATTTTGATTTACGATATTATCCCAATCGATTTCTT-CTTTTGACTTACGGTGTTATCCC
* * * * * *
5331653 AGTCAATTCTGTAAGGCCTCCGAACATTATTTCTAAGATCTCTGGGTATAAATTTGATTCGCGGT
65 AATCAATTCTGTAAGACCTCCGAACATGATTTCTAAGACCTCTGGGCATAAATTCGATTCGCGGT
5331718 ATTATCCCGATCGA-TTCTTGATTTTTTGACTTACGGTGTTGTTTCAGTCTATTTTTAAGACCTC
130 ATTATCCCGATCGATTTCTT-ATTTTTTGACTTACGGTGTTGTTTCAGTCTATTTTTAAGACCTC
5331782 TA
194 TA
* * * *
5331784 AGCATAATTTTGA-TT-CGTTATGTTATCCCAATTGATTT-TT-TTTTTACTTACGGTGTTATCT
1 AGCATAATTTTGATTTACG--ATATTATCCCAATCGATTTCTTCTTTTGACTTACGGTGTTATCC
* * ** * *
5331845 CAATCGATTCTGTAAGACCTTCGGGCATGATTTCTAAGACCTCTGGGCATAAATTCGATTTGTGG
64 CAATCAATTCTGTAAGACCTCCGAACATGATTTCTAAGACCTCTGGGCATAAATTCGATTCGCGG
* * * *
5331910 TGTTATCCTGATTGATTTCTTATTTTTTGACTTGCGGTGTTGT
129 TATTATCCCGATCGATTTCTTATTTTTTGACTTACGGTGTTGT
5331953 CCCAGTCAAT
Statistics
Matches: 144, Mismatches: 22, Indels: 9
0.82 0.13 0.05
Matches are distributed among these distances:
193 104 0.72
194 7 0.05
195 4 0.03
196 29 0.20
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (195 bp):
AGCATAATTTTGATTTACGATATTATCCCAATCGATTTCTTCTTTTGACTTACGGTGTTATCCCA
ATCAATTCTGTAAGACCTCCGAACATGATTTCTAAGACCTCTGGGCATAAATTCGATTCGCGGTA
TTATCCCGATCGATTTCTTATTTTTTGACTTACGGTGTTGTTTCAGTCTATTTTTAAGACCTCTA
Found at i:5332069 original size:110 final size:110
Alignment explanation
Indices: 5331804--5332069 Score: 310
Period size: 110 Copynumber: 2.5 Consensus size: 110
5331794 TGATTCGTTA
* * * *
5331804 TGTTATCCCAATTGATT-TT-TTTTTT-ACTTACGGTGTTA-TCTCAATCGATTCTGTAAGACCT
1 TGTTATCCCAATTGATTCTTATTTTTTGACTTGCGGTGTTAGTCTCAGTCAATTCTATAAGACCT
* ** * *
5331865 TCGGGCATGATTTCTAAGACCTCTGGGCATAAATTCGATTTGTGG
66 TCGAGCATGATTTCTAAGACCTCCAGACATAAATTCGATTTGCGG
** * **
5331910 TGTTATCCTGATTGATTTCTTATTTTTTGACTTGCGGTGTT-GTCCCAGTCAATTCTATAAGATT
1 TGTTATCCCAATTGA-TTCTTATTTTTTGACTTGCGGTGTTAGTCTCAGTCAATTCTATAAGACC
* * *
5331974 TTCGAGCATGATTTCTAAGACCTCCAGATATAATTTTGATTTGCGG
65 TTCGAGCATGATTTCTAAGACCTCCAGACATAAATTCGATTTGCGG
*
5332020 TGTTCTCCCAATTGATTCTTAATTTTTTGACTTGCGGT-TTAGTCTCAGTC
1 TGTTATCCCAATTGATTCTT-ATTTTTTGACTTGCGGTGTTAGTCTCAGTC
5332070 GTCGTATTTT
Statistics
Matches: 132, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
106 13 0.10
107 2 0.02
108 2 0.02
109 13 0.10
110 102 0.77
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (110 bp):
TGTTATCCCAATTGATTCTTATTTTTTGACTTGCGGTGTTAGTCTCAGTCAATTCTATAAGACCT
TCGAGCATGATTTCTAAGACCTCCAGACATAAATTCGATTTGCGG
Found at i:5332475 original size:33 final size:34
Alignment explanation
Indices: 5332335--5332478 Score: 107
Period size: 34 Copynumber: 4.3 Consensus size: 34
5332325 TTCATCATTC
* * * *
5332335 AATCCCGATTTCTTTA-ATTCAAAATCACAGTTT
1 AATCTCGATCTCTTTATATTTAAAATCGCAGTTT
* * * * *
5332368 AATCTCGAT-TATTGTTATTTTTTAACTCG-TGATTT
1 AATCTCGATCT-CT-TTATATTTAAAATCGCAG-TTT
* * * * *
5332403 AATCTCGATCTTTTTATTTTTCAATTCGCGGTTT
1 AATCTCGATCTCTTTATATTTAAAATCGCAGTTT
5332437 AATCTCGATCTCTTTA-ATTTAAAATCGCAGTTT
1 AATCTCGATCTCTTTATATTTAAAATCGCAGTTT
5332470 AATCTCGAT
1 AATCTCGAT
5332479 TGTTGTTATT
Statistics
Matches: 89, Mismatches: 16, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
32 1 0.01
33 31 0.35
34 35 0.39
35 21 0.24
36 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.10, T:0.47
Consensus pattern (34 bp):
AATCTCGATCTCTTTATATTTAAAATCGCAGTTT
Found at i:5332478 original size:102 final size:102
Alignment explanation
Indices: 5332246--5332962 Score: 818
Period size: 102 Copynumber: 7.0 Consensus size: 102
5332236 TCCCAATTTT
* * ** *
5332246 TTTAATTCAAAATCGTAGTTTAATCTCGATTATTGTTATTTTTTAACTTACGATTTAATCTCGGT
1 TTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGAT
* * * * *
5332311 CTC-TTA-TTCTCTGATTCATC-ATTCAATCCCGATTTC
66 CTCTTTATTTTTC-GATTC-GCGGTTCAATCTCGATCTC
* * *
5332347 TTTAATTCAAAATCACAGTTTAATCTCGATTATTGTTATTTTTTAACTCGTGATTTAATCTCGAT
1 TTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGAT
* * *
5332412 CTTTTTATTTTTCAATTCGCGGTTTAATCTCGATCTC
66 CTCTTTATTTTTCGATTCGCGGTTCAATCTCGATCTC
* * * * *
5332449 TTTAATTTAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTCTGACTCGTGATTTAATCTTGAT
1 TTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGAT
* * *
5332514 CTCTTTATTCTTCGATTCGTGGTTCAATCTTGATCTC
66 CTCTTTATTTTTCGATTCGCGGTTCAATCTCGATCTC
* * * *
5332551 TTTAATTCAAAATCGTAGTTTAATCTCGATTATTGTTATTTTTTGACTCGTGATTTAATCTCGAT
1 TTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGAT
* *
5332616 CTTTTTATTCTTT-GATTCGCGGTTCAATCTCAATCTC
66 CTCTTTATT-TTTCGATTCGCGGTTCAATCTCGATCTC
* *
5332653 TTTAACTT-AAAATCGTAGTTTAATCTCGATTGTTGTTATTTTTTGACTCGCGATTTAATCTCGA
1 TTTAA-TTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGA
* * * *
5332717 TCTCTTTA-TTCTCTGATTCGTGGTTTAATCTCGATCTT
65 TCTCTTTATTTTTC-GATTCGCGGTTCAATCTCGATCTC
* ** * * * * * *
5332755 TTTAATTCAAACTTACAGTTTAATCTCGATTGTTATTTTTTTTTTACTCACGATTTAATCCCGGT
1 TTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGAT
* * ** *
5332820 CTCTTTATTCTCCGATTCGCCATTCAATCTCGATCTT
66 CTCTTTATTTTTCGATTCGCGGTTCAATCTCGATCTC
** *
5332857 TTTAATTCAAAATTACAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCCCGAT
1 TTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGAT
* * * *
5332922 CTCTTTATTTTTTGATTCGTGATTTAAT-TCCGATCTC
66 CTCTTTATTTTTCGATTCGCGGTTCAATCT-CGATCTC
5332959 TTTA
1 TTTA
5332963 TTCTTCGATT
Statistics
Matches: 532, Mismatches: 74, Indels: 19
0.85 0.12 0.03
Matches are distributed among these distances:
100 2 0.00
101 66 0.12
102 454 0.85
103 10 0.02
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.49
Consensus pattern (102 bp):
TTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGAT
CTCTTTATTTTTCGATTCGCGGTTCAATCTCGATCTC
Found at i:5332592 original size:204 final size:204
Alignment explanation
Indices: 5332246--5332962 Score: 922
Period size: 204 Copynumber: 3.5 Consensus size: 204
5332236 TCCCAATTTT
* * ** *
5332246 TTTAATTCAAAATCGTAGTTTAATCTCGATTATTGTTATTTTTTAACTTACGATTTAATCTCGGT
1 TTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGAT
* ** * *
5332311 CTC-TTATTCTCTGATTCATCATTCAATCCCGATTTCTTTAATTCAAAATCACAGTTTAATCTCG
66 CTCTTTATTCTCTGATTCGTGGTTCAATCTCGATCTCTTTAATTCAAAATCACAGTTTAATCTCG
* *
5332375 ATTATTGTTATTTTTTAACTCGTGATTTAATCTCGATCTTTTTATTTTTCAATTCGCGGTTTAAT
131 ATTATTGTTATTTTTTAACTCGTGATTTAATCTCGATCTTTTTATTTTTCGATTCGCGGTTCAAT
5332440 CTCGATCTC
196 CTCGATCTC
* * * * *
5332449 TTTAATTTAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTCTGACTCGTGATTTAATCTTGAT
1 TTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGAT
* **
5332514 CTCTTTATTCT-TCGATTCGTGGTTCAATCTTGATCTCTTTAATTCAAAATCGTAGTTTAATCTC
66 CTCTTTATTCTCT-GATTCGTGGTTCAATCTCGATCTCTTTAATTCAAAATCACAGTTTAATCTC
*
5332578 GATTATTGTTATTTTTTGACTCGTGATTTAATCTCGATCTTTTTATTCTTT-GATTCGCGGTTCA
130 GATTATTGTTATTTTTTAACTCGTGATTTAATCTCGATCTTTTTATT-TTTCGATTCGCGGTTCA
*
5332642 ATCTCAATCTC
194 ATCTCGATCTC
* *
5332653 TTTAACTT-AAAATCGTAGTTTAATCTCGATTGTTGTTATTTTTTGACTCGCGATTTAATCTCGA
1 TTTAA-TTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGA
* * * *
5332717 TCTCTTTATTCTCTGATTCGTGGTTTAATCTCGATCTTTTTAATTCAAACTTACAGTTTAATCTC
65 TCTCTTTATTCTCTGATTCGTGGTTCAATCTCGATCTCTTTAATTCAAAATCACAGTTTAATCTC
* * * * ** * * * * * **
5332782 GATTGTTATTTTTTTTTTACTCACGATTTAATCCCGGTCTCTTTATTCTCCGATTCGCCATTCAA
130 GATTATTGTTATTTTTTAACTCGTGATTTAATCTCGATCTTTTTATTTTTCGATTCGCGGTTCAA
*
5332847 TCTCGATCTT
195 TCTCGATCTC
** *
5332857 TTTAATTCAAAATTACAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCCCGAT
1 TTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGAT
* * * *
5332922 CTCTTTATTTTTTGATTCGTGATTTAAT-TCCGATCTCTTTA
66 CTCTTTATTCTCTGATTCGTGGTTCAATCT-CGATCTCTTTA
5332963 TTCTTCGATT
Statistics
Matches: 449, Mismatches: 57, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
203 63 0.14
204 380 0.85
205 6 0.01
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.49
Consensus pattern (204 bp):
TTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCTCGAT
CTCTTTATTCTCTGATTCGTGGTTCAATCTCGATCTCTTTAATTCAAAATCACAGTTTAATCTCG
ATTATTGTTATTTTTTAACTCGTGATTTAATCTCGATCTTTTTATTTTTCGATTCGCGGTTCAAT
CTCGATCTC
Found at i:5332948 original size:238 final size:237
Alignment explanation
Indices: 5332688--5333175 Score: 588
Period size: 238 Copynumber: 2.1 Consensus size: 237
5332678 TCGATTGTTG
*
5332688 TTATTTTTTGACTCGCGATTTAA-TCTCGATCTCTTTATTC-TCTGATTCGTGGTTTAATCTCGA
1 TTATTTTTTGACTCGCGATTTAATTC-CGATCTCTTTATTCTTC-GATTCGTGGTTCAATCTCGA
* * * * *
5332751 TCTTTTTAATTCAAACTTACAGTTTAATCTCGATTGTTATTTTTTTTTTACTCACGATTTAATCC
64 TCTCTTTAATTCAAAATCACAGTTTAATCTCGATTGTTATTATTTTTTGACTCACGATTTAATCC
* * * * *
5332816 CGGTCTCTTTATTCTCCGA-TTCGCCATTCAATCTCGATCTTTTTAATTCAAAATTACAGTTTAA
129 CGATCTCTTTATTCTCCGATTTCG--ATTCAATCCCAATCTCTTTAATTCAAAATCACAGTTTAA
5332880 TCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCCCGATCTCT
192 TCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCCCGATCTCT
* * *
5332926 TTATTTTTTGATTCGTGATTTAATTCCGATCTCTTTATTCTTCGATTCGTGGTTCAATCTTGATC
1 TTATTTTTTGACTCGCGATTTAATTCCGATCTCTTTATTCTTCGATTCGTGGTTCAATCTCGATC
* * * *** *
5332991 TCTTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTGATTTGTGGTTTAATCCCG
66 TCTTTAATTCAAAATCACAGTTTAATCTCGATTGTTATTATTTTTTGACTCACGATTTAATCCCG
* * * * * *
5333056 ATCTCTTTATTCTCTGATTTTGGTTTAATCCCAATCTCTTTAATTTAAAATCATAGTTTAATCTC
131 ATCTCTTTATTCTCCGATTTCGATTCAATCCCAATCTCTTTAATTCAAAATCACAGTTTAATCTC
*** * * * * *
5333121 GATTGTTGTTAACCTTTGACTCG-TAGTTTATTCTCGATCTTT
196 GATTGTTGTTATTTTTTAACTCGCGA-TTTAATCCCGATCTCT
5333163 TTATTTTTTGACT
1 TTATTTTTTGACT
5333176 TATGATTCAA
Statistics
Matches: 210, Mismatches: 36, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
236 1 0.00
237 79 0.38
238 123 0.59
239 7 0.03
ACGTcount: A:0.21, C:0.18, G:0.11, T:0.50
Consensus pattern (237 bp):
TTATTTTTTGACTCGCGATTTAATTCCGATCTCTTTATTCTTCGATTCGTGGTTCAATCTCGATC
TCTTTAATTCAAAATCACAGTTTAATCTCGATTGTTATTATTTTTTGACTCACGATTTAATCCCG
ATCTCTTTATTCTCCGATTTCGATTCAATCCCAATCTCTTTAATTCAAAATCACAGTTTAATCTC
GATTGTTGTTATTTTTTAACTCGCGATTTAATCCCGATCTCT
Found at i:5332960 original size:306 final size:306
Alignment explanation
Indices: 5332244--5332962 Score: 933
Period size: 306 Copynumber: 2.4 Consensus size: 306
5332234 AATCCCAATT
**
5332244 TTTTTAATTCAAAATCGTAGTTTAATCTCGATTATTGTTATTTTTTAACTTACGATTTAATCTCG
1 TTTTTAATTCAAAATCGTAGTTTAATCTCGATTATTGTTATTTTTTAACTCGCGATTTAATCTCG
* * * * * *
5332309 GTCTC-TTATTCTCTGATTCATCATTCAATCCCGATTTCTTTAATTCAAAATCACAGTTTAATCT
66 ATCTCTTTATTCTTTGATTCGTGATTCAATTCCGATCTCTTTAATTCAAAATCACAGTTTAATCT
* * *
5332373 CGATTATTGTTATTTTTTAACTCGTGATTTAATCTCGATCTTTTTATTTTTCAATTCGCGGTTTA
131 CGATTATTGTTATTTTTTAACTCGCGATTTAATCTCGATCTCTTTATTTCTCAATTCGCGGTTTA
* * * **
5332438 ATCTCGATCTCTTTAATTTAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTCTGACTCGTGAT
196 ATCTCGATCTCTTTAATTCAAAATCACAGTTTAATCTCGATTGTTATTATTTTCTGACTCACGAT
** * *** *
5332503 TTAATCTTGATCTCTTTATTCTTCGATTCGTGGTTCAATCTTGATC
261 TTAATCCCGATCTCTTTATTCTCCGATTCGCCATTCAATCTCGATC
* * *
5332549 TCTTTAATTCAAAATCGTAGTTTAATCTCGATTATTGTTATTTTTTGACTCGTGATTTAATCTCG
1 TTTTTAATTCAAAATCGTAGTTTAATCTCGATTATTGTTATTTTTTAACTCGCGATTTAATCTCG
* * * * **
5332614 ATCTTTTTATTCTTTGATTCGCGGTTCAA-TCTCAATCTCTTTAACTT-AAAATCGTAGTTTAAT
66 ATCTCTTTATTCTTTGATTCGTGATTCAATTC-CGATCTCTTTAA-TTCAAAATCACAGTTTAAT
* * * *
5332677 CTCGATTGTTGTTATTTTTTGACTCGCGATTTAATCTCGATCTCTTTA-TTCTCTGATTCGTGGT
129 CTCGATTATTGTTATTTTTTAACTCGCGATTTAATCTCGATCTCTTTATTTCTC-AATTCGCGGT
* * * * * *
5332741 TTAATCTCGATCTTTTTAATTCAAACTTACAGTTTAATCTCGATTGTTATTTTTTTTTTACTCAC
193 TTAATCTCGATCTCTTTAATTCAAAATCACAGTTTAATCTCGATTGTTATTATTTTCTGACTCAC
*
5332806 GATTTAATCCCGGTCTCTTTATTCTCCGATTCGCCATTCAATCTCGATC
258 GATTTAATCCCGATCTCTTTATTCTCCGATTCGCCATTCAATCTCGATC
*** * *
5332855 TTTTTAATTCAAAATTACAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCCCG
1 TTTTTAATTCAAAATCGTAGTTTAATCTCGATTATTGTTATTTTTTAACTCGCGATTTAATCTCG
* *
5332920 ATCTCTTTATTTTTTGATTCGTGATTTAATTCCGATCTCTTTA
66 ATCTCTTTATTCTTTGATTCGTGATTCAATTCCGATCTCTTTA
5332963 TTCTTCGATT
Statistics
Matches: 352, Mismatches: 57, Indels: 9
0.84 0.14 0.02
Matches are distributed among these distances:
305 68 0.19
306 280 0.80
307 4 0.01
ACGTcount: A:0.23, C:0.18, G:0.11, T:0.49
Consensus pattern (306 bp):
TTTTTAATTCAAAATCGTAGTTTAATCTCGATTATTGTTATTTTTTAACTCGCGATTTAATCTCG
ATCTCTTTATTCTTTGATTCGTGATTCAATTCCGATCTCTTTAATTCAAAATCACAGTTTAATCT
CGATTATTGTTATTTTTTAACTCGCGATTTAATCTCGATCTCTTTATTTCTCAATTCGCGGTTTA
ATCTCGATCTCTTTAATTCAAAATCACAGTTTAATCTCGATTGTTATTATTTTCTGACTCACGAT
TTAATCCCGATCTCTTTATTCTCCGATTCGCCATTCAATCTCGATC
Found at i:5333048 original size:306 final size:306
Alignment explanation
Indices: 5332246--5333064 Score: 828
Period size: 306 Copynumber: 2.7 Consensus size: 306
5332236 TCCCAATTTT
** ** * *
5332246 TTTAATTCAAAATCGTAGTTTAATCTCGATTATTGTTATTTTTTAACTTACGATTTAATCTCGGT
1 TTTAATTCAAAATCACAGTTTAATCTCGATTATTGTTATTTTTTAACTCGCGATTTAATCCCGAT
* * * * * ** *
5332311 CTC-TTATTCTCTGATTCATC-ATTCAATCCCGATTTCTTTAA-TTCAAAATCACAGTTTAATCT
66 CTCTTTATTCTTTGATTC-GCGATTCAATCTCAATCTCTTTAACTT-AAAATCGTAGTTCAATCT
** * ** * * ** *
5332373 CGATTATTGTTATTTTTTAACTCGTGATTTAATCTCGATCTTTTTATTTTTCAATTCGCGGTTTA
129 CGATTGCTGTTATATTCAAAATCGCGATTTAATCTCGATCTTTTTATTTTTTGATTCGTGGTTTA
* * * **
5332438 ATCTCGATCTCTTTAATTTAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTCTGACTCGTGAT
194 ATCTCGATCTCTTTAATTCAAAATCACAGTTTAATCTCGATTGTTATTATTTTCTGACTCACGAT
** * *** *
5332503 TTAATCTTGATCTCTTTATTCTTCGATTCGTGGTTCAATCTTGATCTC
259 TTAATCCCGATCTCTTTATTCTCCGATTCGCCATTCAATCTCGATCTC
** * * *
5332551 TTTAATTCAAAATCGTAGTTTAATCTCGATTATTGTTATTTTTTGACTCGTGATTTAATCTCGAT
1 TTTAATTCAAAATCACAGTTTAATCTCGATTATTGTTATTTTTTAACTCGCGATTTAATCCCGAT
* * *
5332616 CTTTTTATTCTTTGATTCGCGGTTCAATCTCAATCTCTTTAACTTAAAATCGTAGTTTAATCTCG
66 CTCTTTATTCTTTGATTCGCGATTCAATCTCAATCTCTTTAACTTAAAATCGTAGTTCAATCTCG
* * *** * * * *
5332681 ATTGTTGTTATTTTTTGACTCGCGATTTAATCTCGATCTCTTTATTCTCTGATTCGTGGTTTAAT
131 ATTGCTGTTATATTCAAAATCGCGATTTAATCTCGATCTTTTTATTTTTTGATTCGTGGTTTAAT
* * * * * *
5332746 CTCGATCTTTTTAATTCAAACTTACAGTTTAATCTCGATTGTTATTTTTTTTTTACTCACGATTT
196 CTCGATCTCTTTAATTCAAAATCACAGTTTAATCTCGATTGTTATTATTTTCTGACTCACGATTT
* *
5332811 AATCCCGGTCTCTTTATTCTCCGATTCGCCATTCAATCTCGATCTT
261 AATCCCGATCTCTTTATTCTCCGATTCGCCATTCAATCTCGATCTC
* *
5332857 TTTAATTCAAAATTACAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCCCGAT
1 TTTAATTCAAAATCACAGTTTAATCTCGATTATTGTTATTTTTTAACTCGCGATTTAATCCCGAT
* * * * * ** * *
5332922 CTCTTTATTTTTTGATTCGTGATTTAAT-TCCGATCTCTTTATTCTTCGATTCGTGGTTCAATCT
66 CTCTTTATTCTTTGATTCGCGATTCAATCT-CAATCTCTTTA-ACTTAAAATCGTAGTTCAATCT
* *
5332986 TGATCT-CT-TTA-ATTCAAAATCGC-AGTTTAATCTCGAT-TGTTGTTATTTTTTGATTTGTGG
129 CGAT-TGCTGTTATATTCAAAATCGCGA-TTTAATCTCGATCT-TT-TTATTTTTTGATTCGTGG
*
5333046 TTTAATCCCGATCTCTTTA
190 TTTAATCTCGATCTCTTTA
5333065 TTCTCTGATT
Statistics
Matches: 430, Mismatches: 75, Indels: 17
0.82 0.14 0.03
Matches are distributed among these distances:
304 2 0.00
305 84 0.20
306 321 0.75
307 22 0.05
308 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.11, T:0.49
Consensus pattern (306 bp):
TTTAATTCAAAATCACAGTTTAATCTCGATTATTGTTATTTTTTAACTCGCGATTTAATCCCGAT
CTCTTTATTCTTTGATTCGCGATTCAATCTCAATCTCTTTAACTTAAAATCGTAGTTCAATCTCG
ATTGCTGTTATATTCAAAATCGCGATTTAATCTCGATCTTTTTATTTTTTGATTCGTGGTTTAAT
CTCGATCTCTTTAATTCAAAATCACAGTTTAATCTCGATTGTTATTATTTTCTGACTCACGATTT
AATCCCGATCTCTTTATTCTCCGATTCGCCATTCAATCTCGATCTC
Found at i:5333059 original size:68 final size:68
Alignment explanation
Indices: 5332845--5333064 Score: 187
Period size: 68 Copynumber: 3.2 Consensus size: 68
5332835 TTCGCCATTC
* * ** * * * *
5332845 AATCTCGATCTTTTTAATTCAAAATTACAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGA
1 AATCCCGATCTCTTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTGATTCGTGG
5332910 TTT
66 TTT
* *** * * * * *
5332913 AATCCCGATCTCTTTATTTTTTGATTCG-TGATTTAAT-TCCGATCT-CT-TTATTCTTCGATTC
1 AATCCCGATCTCTTTA-ATTCAAAATCGCAG-TTTAATCT-CGAT-TGTTGTTATTTTTTGATTC
*
5332974 GTGGTTC
62 GTGGTTT
** *
5332981 AATCTTGATCTCTTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTGATTTGTGG
1 AATCCCGATCTCTTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTGATTCGTGG
5333046 TTT
66 TTT
5333049 AATCCCGATCTCTTTA
1 AATCCCGATCTCTTTA
5333065 TTCTCTGATT
Statistics
Matches: 111, Mismatches: 33, Indels: 16
0.69 0.21 0.10
Matches are distributed among these distances:
66 1 0.01
67 17 0.15
68 77 0.69
69 15 0.14
70 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.12, T:0.49
Consensus pattern (68 bp):
AATCCCGATCTCTTTAATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTTTTTGATTCGTGG
TTT
Found at i:5333074 original size:34 final size:34
Alignment explanation
Indices: 5332910--5333097 Score: 141
Period size: 34 Copynumber: 5.6 Consensus size: 34
5332900 TAACTCGCGA
* * *
5332910 TTTAATCCCGATCTCTTTATTTTTTGATTCGTGA
1 TTTAATCCCGATCTCTTTATTCTCTGATTCGTGG
*
5332944 TTTAATTCCGATCTCTTTATTCT-TCGATTCGTGG
1 TTTAATCCCGATCTCTTTATTCTCT-GATTCGTGG
* ** * ** * **
5332978 TTCAATCTTGATCTCTTTAAT-TCAAAATCGCAG
1 TTTAATCCCGATCTCTTTATTCTCTGATTCGTGG
* * * * *
5333011 TTTAATCTCGAT-TGTTGTTATTTTTTGATTTGTGG
1 TTTAATCCCGATCT-CT-TTATTCTCTGATTCGTGG
*
5333046 TTTAATCCCGATCTCTTTATTCTCTGATT-TTGG
1 TTTAATCCCGATCTCTTTATTCTCTGATTCGTGG
*
5333079 TTTAATCCCAATCTCTTTA
1 TTTAATCCCGATCTCTTTA
5333098 ATTTAAAATC
Statistics
Matches: 118, Mismatches: 30, Indels: 13
0.73 0.19 0.08
Matches are distributed among these distances:
32 1 0.01
33 39 0.33
34 60 0.51
35 17 0.14
36 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.12, T:0.51
Consensus pattern (34 bp):
TTTAATCCCGATCTCTTTATTCTCTGATTCGTGG
Found at i:5333074 original size:136 final size:135
Alignment explanation
Indices: 5332806--5333097 Score: 395
Period size: 136 Copynumber: 2.2 Consensus size: 135
5332796 TTTTACTCAC
* * *
5332806 GATTTAATCCCGGTCTCTTTATTCTCCGATTCGCCATTCAATCTCGATCTTTTTAATTCAAAATT
1 GATTTAATCCCGATCTCTTTATTCTCCGATTCGCCATTCAATCTCGATCTCTTTAATTCAAAATC
* *
5332871 ACAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCCCGATCTCTTTATTTTTTG
66 ACAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCCCGATCTCTTTATTCTCTG
5332936 ATTCGT
131 ATT-GT
* * *** *
5332942 GATTTAATTCCGATCTCTTTATTCTTCGATTCGTGGTTCAATCTTGATCTCTTTAATTCAAAATC
1 GATTTAATCCCGATCTCTTTATTCTCCGATTCGCCATTCAATCTCGATCTCTTTAATTCAAAATC
* * * * * *
5333007 GCAGTTTAATCTCGATTGTTGTTATTTTTTGATTTGTGGTTTAATCCCGATCTCTTTATTCTCTG
66 ACAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCCCGATCTCTTTATTCTCTG
*
5333072 ATTTT
131 ATTGT
* *
5333077 GGTTTAATCCCAATCTCTTTA
1 GATTTAATCCCGATCTCTTTA
5333098 ATTTAAAATC
Statistics
Matches: 135, Mismatches: 21, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
135 19 0.14
136 116 0.86
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (135 bp):
GATTTAATCCCGATCTCTTTATTCTCCGATTCGCCATTCAATCTCGATCTCTTTAATTCAAAATC
ACAGTTTAATCTCGATTGTTGTTATTTTTTAACTCGCGATTTAATCCCGATCTCTTTATTCTCTG
ATTGT
Found at i:5333107 original size:101 final size:102
Alignment explanation
Indices: 5332926--5333131 Score: 290
Period size: 101 Copynumber: 2.0 Consensus size: 102
5332916 CCCGATCTCT
* ***
5332926 TTATTTTTTGATTCGTGATTTAATTCCGATCTCTTTATTCTTCGATTCGTGGTTCAATCTTGATC
1 TTATTTTTTGATTCGTGATTTAATCCCGATCTCTTTATTCTTCGATTCGTGGTTCAATCCCAATC
*
5332991 TCTTTAATTCAAAATCGCAGTTTAATCTCGATTGTTG
66 TCTTTAATTCAAAATCACAGTTTAATCTCGATTGTTG
* * * *
5333028 TTATTTTTTGATTTGTGGTTTAATCCCGATCTCTTTATTC-TCTGATT-TTGGTTTAATCCCAAT
1 TTATTTTTTGATTCGTGATTTAATCCCGATCTCTTTATTCTTC-GATTCGTGGTTCAATCCCAAT
* *
5333091 CTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTG
65 CTCTTTAATTCAAAATCACAGTTTAATCTCGATTGTTG
5333129 TTA
1 TTA
5333132 ACCTTTGACT
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
101 51 0.55
102 41 0.45
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.50
Consensus pattern (102 bp):
TTATTTTTTGATTCGTGATTTAATCCCGATCTCTTTATTCTTCGATTCGTGGTTCAATCCCAATC
TCTTTAATTCAAAATCACAGTTTAATCTCGATTGTTG
Found at i:5333139 original size:101 final size:102
Alignment explanation
Indices: 5332932--5333167 Score: 278
Period size: 101 Copynumber: 2.3 Consensus size: 102
5332922 CTCTTTATTT
* * ***
5332932 TTTGATTCGTGATTTAATTCCGATCTCTTTATTCTTCGATTCGTGGTTCAATCTTGATCTCTTTA
1 TTTGATTCGTGGTTTAATCCCGATCTCTTTATTCTTCGATTCGTGGTTCAATCCCAATCTCTTTA
* ***
5332997 ATTCAAAATCGCAGTTTAATCTCGATTGTTGTTATTT
66 ATTCAAAATCACAGTTTAATCTCGATTGTTGTTAACC
* * *
5333034 TTTGATTTGTGGTTTAATCCCGATCTCTTTATTC-TCTGATT-TTGGTTTAATCCCAATCTCTTT
1 TTTGATTCGTGGTTTAATCCCGATCTCTTTATTCTTC-GATTCGTGGTTCAATCCCAATCTCTTT
* *
5333097 AATTTAAAATCATAGTTTAATCTCGATTGTTGTTAACC
65 AATTCAAAATCACAGTTTAATCTCGATTGTTGTTAACC
* * * * *
5333135 TTTGACTCGTAGTTTATTCTCGATCTTTTTATT
1 TTTGATTCGTGGTTTAATCCCGATCTCTTTATT
5333168 TTTTGACTTA
Statistics
Matches: 113, Mismatches: 20, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
101 78 0.69
102 35 0.31
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.50
Consensus pattern (102 bp):
TTTGATTCGTGGTTTAATCCCGATCTCTTTATTCTTCGATTCGTGGTTCAATCCCAATCTCTTTA
ATTCAAAATCACAGTTTAATCTCGATTGTTGTTAACC
Found at i:5333514 original size:345 final size:341
Alignment explanation
Indices: 5333030--5333780 Score: 1017
Period size: 345 Copynumber: 2.2 Consensus size: 341
5333020 GATTGTTGTT
* * ** *
5333030 ATTTTTTGATTTGTGGTTTAATCCCGATCTCTTTATTCTCTGATT-TTGGTTTAATCCCAATCTC
1 ATTTTTTGA-TTGCGGTTTAATCCAG-TCTCTTTATTCTCTGATTCAAGGTTTAATCCCGATCTC
* * *
5333094 TTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTAACCTTTGACTCGTAGTTTATTCTCGAT
64 TTTAATTTAAAATCACAGTTTAATCTCGATTGTTGTTAACCTTTGACTCATAGTTTATTCCCGAT
*
5333159 CTTTTTATTTTTTGACTTATGATTCAATCCAAGTTAACGCCATTTTCTGACTCGCGATTTAATCT
129 CTTCTTATTTTTTGACTTATGATTCAATCCAAGTTAACGCCATTTTCTGACTCGCGATTTAAT-T
* * * ** *
5333224 T-GGTCAT-TTTATTTTTTGATTTGCAGTTCAAT-CTCGATCTCTTTAATTTAAAATCGTAGTTT
193 TCAGTC-TCTTTATTCTTCGATTCACAGTTCAATCCT-GATCTCTTTAATTTAAAATCATAGTTT
* * *
5333286 AATCTCGA-TTGTTGTTAACCTCTAACTCTTGGTTTATTCCCGGTCTTCTTATTTTTTGACTTGT
256 AATCTCGATTTGTTGTTAACCTCTAACTCGTGATTTATTCCCGGTCTTCTTATTTTTTGACTTAT
5333350 GATTCAATCCAAGTTAACGTC
321 GATTCAATCCAAGTTAACGTC
* * *
5333371 ATTTTTTGACTTGCGGTTTAGTCACAGTCTTTTTATTCTCTGATTCAAGGTTCAATCCCGATCTC
1 ATTTTTTGA-TTGCGGTTTAATC-CAGTCTCTTTATTCTCTGATTCAAGGTTTAATCCCGATCTC
*
5333436 TTTAATTTAAAATCACAGTTTAATCTCGATTGTTGTTGTTAACCTTTGACTCATGGTTTATTCCC
64 TTTAATTTAAAATCACAGTTTAATCTCGA---TTGTTGTTAACCTTTGACTCATAGTTTATTCCC
* * *
5333501 GATCTTCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACGTCATTTTCTGACTCGCGGTTTAA
126 GATCTTCTTATTTTTTGACTTATGATTCAATCCAAGTTAACGCCATTTTCTGACTCGCGATTTAA
* * *
5333566 TTTCAGTCTCTTTATTCTTCGATTCACGGTTCAATCCTGATCTTTTTAATTTAAAATTATAGTTT
191 TTTCAGTCTCTTTATTCTTCGATTCACAGTTCAATCCTGATCTCTTTAATTTAAAATCATAGTTT
* **
5333631 AATCTCGATTGTTGTTGTTAACCTCTGACTCGTGATTTATTCTTGGTCTTCTTATTTTTTGACTT
256 AATCTCGA-T-TTGTTGTTAACCTCTAACTCGTGATTTATTCCCGGTCTTCTTATTTTTTGACTT
5333696 ATGATTCAATCCAAGTTAACGTC
319 ATGATTCAATCCAAGTTAACGTC
* * * * *
5333719 ATTTTTTGATTCGCGGTTTAATGTCAGTATCTTTATTCTTTGATTCAAAGTTTAATCTCGAT
1 ATTTTTTGATT-GCGGTTTAAT-CCAGTCTCTTTATTCTCTGATTCAAGGTTTAATCCCGAT
5333781 ATTTTTATTC
Statistics
Matches: 357, Mismatches: 40, Indels: 19
0.86 0.10 0.05
Matches are distributed among these distances:
341 37 0.10
342 45 0.13
344 3 0.01
345 147 0.41
346 2 0.01
347 2 0.01
348 121 0.34
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.48
Consensus pattern (341 bp):
ATTTTTTGATTGCGGTTTAATCCAGTCTCTTTATTCTCTGATTCAAGGTTTAATCCCGATCTCTT
TAATTTAAAATCACAGTTTAATCTCGATTGTTGTTAACCTTTGACTCATAGTTTATTCCCGATCT
TCTTATTTTTTGACTTATGATTCAATCCAAGTTAACGCCATTTTCTGACTCGCGATTTAATTTCA
GTCTCTTTATTCTTCGATTCACAGTTCAATCCTGATCTCTTTAATTTAAAATCATAGTTTAATCT
CGATTTGTTGTTAACCTCTAACTCGTGATTTATTCCCGGTCTTCTTATTTTTTGACTTATGATTC
AATCCAAGTTAACGTC
Found at i:5333539 original size:174 final size:171
Alignment explanation
Indices: 5333030--5333780 Score: 904
Period size: 174 Copynumber: 4.4 Consensus size: 171
5333020 GATTGTTGTT
* * * ** * *
5333030 ATTTTTTGATTTGTGGTTTAATC-CCGATCTCTTTATTCTCTGATT-TTGGTTTAATCCCAATCT
1 ATTTTTTGACTTGCGGTTTAATCTCAG-TCTCTTTATTCTCTGATTCAAGGTTCAATCCCGATCT
* * *
5333093 CTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTAACCTTTGACTCGTAGTTTATTCTCGA
65 CTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTAACCTCTGACTCGTGGTTTATTCCCGA
* *
5333158 TCTTTTTATTTTTTGACTTATGATTCAATCCAAGTTAACGCC
130 TCTTCTTATTTTTTGACTTATGATTCAATCCAAGTTAACGTC
* * * ** * * *
5333200 ATTTTCTGACTCGCGATTTAATCTTGGTCAT-TTTATTTTTTGATTTGC-A-GTTCAATCTCGAT
1 ATTTTTTGACTTGCGGTTTAATCTCAGTC-TCTTTATTCTCTGA-TT-CAAGGTTCAATCCCGAT
* * *
5333262 CTCTTTAATTTAAAATCGTAGTTTAATCTCGATTGTTGTTAACCTCTAACTCTTGGTTTATTCCC
63 CTCTTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTAACCTCTGACTCGTGGTTTATTCCC
* *
5333327 GGTCTTCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACGTC
128 GATCTTCTTATTTTTTGACTTATGATTCAATCCAAGTTAACGTC
* * *
5333371 ATTTTTTGACTTGCGGTTTAGTCACAGTCTTTTTATTCTCTGATTCAAGGTTCAATCCCGATCTC
1 ATTTTTTGACTTGCGGTTTAATCTCAGTCTCTTTATTCTCTGATTCAAGGTTCAATCCCGATCTC
* * *
5333436 TTTAATTTAAAATCACAGTTTAATCTCGATTGTTGTTGTTAACCTTTGACTCATGGTTTATTCCC
66 TTTAATTTAAAATCATAGTTTAATCTCGA---TTGTTGTTAACCTCTGACTCGTGGTTTATTCCC
*
5333501 GATCTTCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACGTC
128 GATCTTCTTATTTTTTGACTTATGATTCAATCCAAGTTAACGTC
* * * * *
5333545 ATTTTCTGACTCGCGGTTTAATTTCAGTCTCTTTATTCT-TCGATTCACGGTTCAATCCTGATCT
1 ATTTTTTGACTTGCGGTTTAATCTCAGTCTCTTTATTCTCT-GATTCAAGGTTCAATCCCGATCT
* * * *
5333609 TTTTAATTTAAAATTATAGTTTAATCTCGATTGTTGTTGTTAACCTCTGACTCGTGATTTATTCT
65 CTTTAATTTAAAATCATAGTTTAATCTCGA---TTGTTGTTAACCTCTGACTCGTGGTTTATTCC
* *
5333674 TGGTCTTCTTATTTTTTGACTTATGATTCAATCCAAGTTAACGTC
127 CGATCTTCTTATTTTTTGACTTATGATTCAATCCAAGTTAACGTC
* * * * * *
5333719 ATTTTTTGA-TTCGCGGTTTAATGTCAGTATCTTTATTCTTTGATTCAAAGTTTAATCTCGAT
1 ATTTTTTGACTT-GCGGTTTAATCTCAGTCTCTTTATTCTCTGATTCAAGGTTCAATCCCGAT
5333781 ATTTTTATTC
Statistics
Matches: 501, Mismatches: 66, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
169 1 0.00
170 34 0.07
171 187 0.37
173 2 0.00
174 276 0.55
175 1 0.00
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.48
Consensus pattern (171 bp):
ATTTTTTGACTTGCGGTTTAATCTCAGTCTCTTTATTCTCTGATTCAAGGTTCAATCCCGATCTC
TTTAATTTAAAATCATAGTTTAATCTCGATTGTTGTTAACCTCTGACTCGTGGTTTATTCCCGAT
CTTCTTATTTTTTGACTTATGATTCAATCCAAGTTAACGTC
Found at i:5333882 original size:345 final size:341
Alignment explanation
Indices: 5333030--5333883 Score: 937
Period size: 345 Copynumber: 2.5 Consensus size: 341
5333020 GATTGTTGTT
* * * * *** * * *
5333030 ATTTTTTGATTTGTGGTTTAATC-CCGATCTCTTTATTCTCTGATT-TTGGTTTAATCCCAATCT
1 ATTTTTTGACTTGCGGTTTAATCACAG-TATCTTTATTCTCTGATTCAAAGTTCAATCCCGATAT
* *
5333093 CTTTAATTTAAAATCATAGTTTAATCTCGA---TTGTTGTTAACCTTTGACTCGTAGTTTATTCT
65 CTTTAATTTAAAATCACAGTTTAATCTCGATCCTTGTTGTT-A--TTTGACTCGTGGTTTATTCT
*
5333155 CGATCTTTTTATTTTTTGACTTATGATTCAATCCAAGTTAACGCCATTTTCTGACTCGCGATTTA
127 CGATC-TTTTATTTTTTGACTTGTGATTCAATCCAAGTTAACGCCATTTTCTGACTCGCGATTTA
* * * ** *
5333220 ATCTTGGTCATTTTATTTTTTGATTTGCAGTTCAATCTCGATCTCTTTAATTTAAAATCGTAGTT
191 ATCTTAGTCATTTTATTCTTCGATTCACAGTTCAATCTCGATCTCTTTAATTTAAAATCATAGTT
* * *
5333285 TAATCTCGATTGTTGTTAACCTCTAACTCTTGGTTTATTCCCGGTCTTCTTATTTTTTGACTTGT
256 TAATCTCGATTGTTGTTAACCTCTAACTCGTGATTTATTCCCGGTCTTCTTATTTTTTGACTTAT
5333350 GATTCAATCCAAGTTAACGTC
321 GATTCAATCCAAGTTAACGTC
* * * * *
5333371 ATTTTTTGACTTGCGGTTTAGTCACAGTCTTTTTATTCTCTGATTCAAGGTTCAATCCCGATCTC
1 ATTTTTTGACTTGCGGTTTAATCACAGTATCTTTATTCTCTGATTCAAAGTTCAATCCCGATATC
** * *
5333436 TTTAATTTAAAATCACAGTTTAATCTCGATTGTTGTTGTTAACCTTTGACTCATGGTTTATTCCC
66 TTTAATTTAAAATCACAGTTTAATCTCGATCCTTGTTGTT-A--TTTGACTCGTGGTTTATTCTC
* *
5333501 GATCTTCTTATTTTTTGACTTGTGATTCAATCCAAGTTAACGTCATTTTCTGACTCGCGGTTTAA
128 GATCTT-TTATTTTTTGACTTGTGATTCAATCCAAGTTAACGCCATTTTCTGACTCGCGATTTAA
* * *
5333566 T-TTCAGTC-TCTTTATTCTTCGATTCACGGTTCAATC-CTGATCTTTTTAATTTAAAATTATAG
192 TCTT-AGTCAT-TTTATTCTTCGATTCACAGTTCAATCTC-GATCTCTTTAATTTAAAATCATAG
* **
5333628 TTTAATCTCGATTGTTGTTGTTAACCTCTGACTCGTGATTTATTCTTGGTCTTCTTATTTTTTGA
254 TTTAATCTCGA---TTGTTGTTAACCTCTAACTCGTGATTTATTCCCGGTCTTCTTATTTTTTGA
5333693 CTTATGATTCAATCCAAGTTAACGTC
316 CTTATGATTCAATCCAAGTTAACGTC
** * * *
5333719 ATTTTTTGA-TTCGCGGTTTAATGTCAGTATCTTTATTCTTTGATTCAAAGTTTAATCTCGATAT
1 ATTTTTTGACTT-GCGGTTTAATCACAGTATCTTTATTCTCTGATTCAAAGTTCAATCCCGATAT
* ** * * *
5333783 -TTTTATTCTCTGATTCAC-GATTTAATC-CTGATCCTTAGTAT-TT-TTTTACTCGTGGTTTAA
65 CTTTAATT-T-AAAATCACAG-TTTAATCTC-GATCCTT-GT-TGTTATTTGACTCGTGGTTTAT
*
5333843 TCTCGATCTCTTTATTTTTT-ACTTGTGATTTAATCCAAGTT
124 TCTCGATCT-TTTATTTTTTGACTTGTGATTCAATCCAAGTT
5333884 CAATCCTGAT
Statistics
Matches: 441, Mismatches: 52, Indels: 36
0.83 0.10 0.07
Matches are distributed among these distances:
341 37 0.08
342 45 0.10
344 6 0.01
345 166 0.38
346 31 0.07
347 9 0.02
348 125 0.28
349 17 0.04
350 4 0.01
351 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.13, T:0.48
Consensus pattern (341 bp):
ATTTTTTGACTTGCGGTTTAATCACAGTATCTTTATTCTCTGATTCAAAGTTCAATCCCGATATC
TTTAATTTAAAATCACAGTTTAATCTCGATCCTTGTTGTTATTTGACTCGTGGTTTATTCTCGAT
CTTTTATTTTTTGACTTGTGATTCAATCCAAGTTAACGCCATTTTCTGACTCGCGATTTAATCTT
AGTCATTTTATTCTTCGATTCACAGTTCAATCTCGATCTCTTTAATTTAAAATCATAGTTTAATC
TCGATTGTTGTTAACCTCTAACTCGTGATTTATTCCCGGTCTTCTTATTTTTTGACTTATGATTC
AATCCAAGTTAACGTC
Found at i:5334175 original size:15 final size:15
Alignment explanation
Indices: 5334155--5334184 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5334145 TTCTTTTCAG
*
5334155 TTTAATATTAATAAT
1 TTTAATAATAATAAT
5334170 TTTAATAATAATAAT
1 TTTAATAATAATAAT
5334185 AAAAAAATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTAATAATAATAAT
Found at i:5334896 original size:14 final size:15
Alignment explanation
Indices: 5334871--5334900 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
5334861 TTTTTTTTTG
5334871 AAACAGAAAAAAAAT
1 AAACAGAAAAAAAAT
*
5334886 AAACAAAAAAAAAAT
1 AAACAGAAAAAAAAT
5334901 TTAGTTGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.07, G:0.03, T:0.07
Consensus pattern (15 bp):
AAACAGAAAAAAAAT
Found at i:5335384 original size:3 final size:3
Alignment explanation
Indices: 5335343--5335376 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
5335333 AATTACTTAA
5335343 AAT AAT AAT AAT AAT AAT AA- AATT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT A
5335377 GAATAATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 25 0.86
4 2 0.07
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5341372 original size:24 final size:24
Alignment explanation
Indices: 5341345--5341408 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
5341335 TTCAATTGAC
* *
5341345 ATATATAAAGTAAAAATAAGAATT
1 ATATATAAAATAAAAATAAAAATT
*
5341369 ATATATAAATTAAAAATAAAAATT
1 ATATATAAAATAAAAATAAAAATT
5341393 ATATA-AAAATAAAAAT
1 ATATATAAAATAAAAAT
5341409 TAAGTTTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 10 0.27
24 27 0.73
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (24 bp):
ATATATAAAATAAAAATAAAAATT
Found at i:5344927 original size:12 final size:13
Alignment explanation
Indices: 5344902--5344934 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5344892 TTCCTCTTGT
5344902 TATTATTAGTTTG
1 TATTATTAGTTTG
*
5344915 TGTTATT-GTTTG
1 TATTATTAGTTTG
5344927 TATTATTA
1 TATTATTA
5344935 CTAGCATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 2
0.81 0.10 0.10
Matches are distributed among these distances:
12 11 0.65
13 6 0.35
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (13 bp):
TATTATTAGTTTG
Found at i:5348970 original size:58 final size:58
Alignment explanation
Indices: 5348904--5349125 Score: 250
Period size: 58 Copynumber: 3.8 Consensus size: 58
5348894 TCTTGTGTAG
* * *
5348904 GGAAAATTGATACTTTCAACTTTTTCCTAAAAATATTCTTTTGAAACTTTAATTTTGA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAACTTTAATTTTAA
* * *
5348962 GAAAAATTGATACTTTCAA-TTTTTCCTCAAAAATTGATTTTTTTTTAAACTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTTCC-CAAAAA-T-A-TTTTTTTGAAACTTTAATTTT-AA
* * *** * *
5349024 GGAAATTTGATACTTTCTAACTTTTCCCCAAAAA-CCCTTTTTGAAATTTTATTTTTAA
1 GGAAAATTGATACTTTC-AACTTTTTCCCAAAAATATTTTTTTGAAACTTTAATTTTAA
*
5349082 GGAAAATTGATATTTTCAACTTTTTCCCAAAAATATTTTTTTGA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGA
5349126 TTTTTATTTA
Statistics
Matches: 134, Mismatches: 22, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
57 22 0.16
58 47 0.35
59 16 0.12
60 1 0.01
61 18 0.13
62 16 0.12
63 8 0.06
64 6 0.04
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTGAAACTTTAATTTTAA
Found at i:5349088 original size:120 final size:118
Alignment explanation
Indices: 5348904--5349123 Score: 291
Period size: 120 Copynumber: 1.8 Consensus size: 118
5348894 TCTTGTGTAG
* * * * *
5348904 GGAAAATTGATACTTTCAACTTTTTCCTAAAAATATTCTTTTGAAACTTTAATTTTGAGAAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAACACTCTTTTGAAACTTTAATTTTAAGAAAAAT
5348969 TGATACTTTCAA-TTTTTCCTCAAAAATTGATTTTTTTTTAAACTTTGATTTTCAA
66 TGATACTTTCAACTTTTTCC-CAAAAA-T-ATTTTTTTTTAAACTTTGATTTTCAA
* * * * *
5349024 GGAAATTTGATACTTTCTAACTTTTCCCCAAAAACCCT-TTTTGAAATTTTATTTTTAAGGAAAA
1 GGAAAATTGATACTTTC-AACTTTTCCCCAAAAACACTCTTTTGAAACTTTAATTTTAAGAAAAA
*
5349088 TTGATATTTTCAACTTTTTCCCAAAAATATTTTTTT
65 TTGATACTTTCAACTTTTTCCCAAAAATATTTTTTT
5349124 GATTTTTATT
Statistics
Matches: 87, Mismatches: 11, Indels: 6
0.84 0.11 0.06
Matches are distributed among these distances:
118 8 0.09
119 1 0.01
120 56 0.64
121 22 0.25
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.46
Consensus pattern (118 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAACACTCTTTTGAAACTTTAATTTTAAGAAAAAT
TGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTTAAACTTTGATTTTCAA
Found at i:5349224 original size:12 final size:12
Alignment explanation
Indices: 5349169--5349234 Score: 53
Period size: 12 Copynumber: 5.1 Consensus size: 12
5349159 AATAAAAGTG
5349169 AAAATAATAATAA
1 AAAATAA-AATAA
5349182 TAATAATAAAATAA
1 -AA-AATAAAATAA
*
5349196 AATAAGGAAAAGTAA
1 AA-AA-TAAAA-TAA
*
5349211 AACA-AAAATAA
1 AAAATAAAATAA
5349222 AAAATAAAATAA
1 AAAATAAAATAA
5349234 A
1 A
5349235 GGTAAAAAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
11 6 0.13
12 12 0.27
13 5 0.11
14 12 0.27
15 10 0.22
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.18
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:5349240 original size:18 final size:18
Alignment explanation
Indices: 5349189--5349242 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 18
5349179 TAATAATAAT
5349189 AAAATAAAAT-AAGG--A
1 AAAATAAAATAAAGGTAA
* * **
5349204 AAAGTAAAACAAAAATAA
1 AAAATAAAATAAAGGTAA
5349222 AAAATAAAATAAAGGTAA
1 AAAATAAAATAAAGGTAA
5349240 AAA
1 AAA
5349243 GAATACTAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
15 8 0.29
16 2 0.07
18 18 0.64
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.13
Consensus pattern (18 bp):
AAAATAAAATAAAGGTAA
Found at i:5350129 original size:4 final size:4
Alignment explanation
Indices: 5350122--5350146 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5350112 AAAAACAAAG
5350122 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
5350147 AGAAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:5350173 original size:15 final size:15
Alignment explanation
Indices: 5350136--5350173 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5350126 ATAAATAAAT
5350136 AAATAAAT-AAAAGA
1 AAATAAATCAAAAGA
*
5350150 AAA-AAATCAAACGA
1 AAATAAATCAAAAGA
5350164 AAATAAATCA
1 AAATAAATCA
5350174 GATAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 4 0.19
14 11 0.52
15 6 0.29
ACGTcount: A:0.74, C:0.08, G:0.05, T:0.13
Consensus pattern (15 bp):
AAATAAATCAAAAGA
Found at i:5350189 original size:12 final size:12
Alignment explanation
Indices: 5350172--5350212 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
5350162 GAAAATAAAT
5350172 CAGATAAATTAA
1 CAGATAAATTAA
5350184 CAGATAAATTAA
1 CAGATAAATTAA
5350196 -A-ATTAAA-TAA
1 CAGA-TAAATTAA
5350206 CAGATAA
1 CAGATAA
5350213 TTACATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 4 0.15
11 9 0.35
12 13 0.50
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.24
Consensus pattern (12 bp):
CAGATAAATTAA
Found at i:5350370 original size:25 final size:25
Alignment explanation
Indices: 5350296--5350424 Score: 83
Period size: 24 Copynumber: 5.2 Consensus size: 25
5350286 CATAAATCCC
* *
5350296 TAAAAAAATAATAATA-AAAGAAAA
1 TAAAATAATAATAATAAAAATAAAA
* * * *
5350320 GAAAA-AAT-ATATATATACAT-ATA
1 TAAAATAATAATA-ATAAAAATAAAA
5350343 TAAAATAATAATAATAAAAATAAAA
1 TAAAATAATAATAATAAAAATAAAA
* *
5350368 TAAAATAAAAAT-GTAAAAATACAAAA
1 TAAAATAATAATAATAAAAAT--AAAA
*
5350394 TAAAAATAA-ATTAA-AAAAATAAAAA
1 T-AAAATAATAATAATAAAAAT-AAAA
5350419 TAAAAT
1 TAAAAT
5350425 GAAGAGAACA
Statistics
Matches: 83, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
22 3 0.04
23 12 0.14
24 27 0.33
25 21 0.25
26 13 0.16
27 7 0.08
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (25 bp):
TAAAATAATAATAATAAAAATAAAA
Found at i:5350393 original size:7 final size:6
Alignment explanation
Indices: 5350349--5350423 Score: 75
Period size: 6 Copynumber: 12.2 Consensus size: 6
5350339 TATATAAAAT
*
5350349 AATAAT AATAAA AAT-AA AAT-AA AATAAA AATGTAAA AATACAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AA--TAAA AATA-AA AATAAA
5350398 AATAAA TTAA-AAA AATAAA AATAAA A
1 AATAAA --AATAAA AATAAA AATAAA A
5350424 TGAAGAGAAC
Statistics
Matches: 61, Mismatches: 1, Indels: 14
0.80 0.01 0.18
Matches are distributed among these distances:
5 12 0.20
6 32 0.52
7 9 0.15
8 8 0.13
ACGTcount: A:0.77, C:0.01, G:0.01, T:0.20
Consensus pattern (6 bp):
AATAAA
Found at i:5350409 original size:32 final size:30
Alignment explanation
Indices: 5350299--5350423 Score: 76
Period size: 30 Copynumber: 4.1 Consensus size: 30
5350289 AAATCCCTAA
* * *
5350299 AAAAATAATAATAAAAGAAAA-GAAAAAAT
1 AAAAATAAAAATAAAATAAAATAAAAAAAT
* * * * * *
5350328 ATATATATACAT-ATATAAAATAATAATAAT
1 AAAAATAAAAATAAAATAAAATAA-AAAAAT
**
5350358 AAAAAT-AAAATAAAATAAAAATGTAAAAAT
1 AAAAATAAAAATAAAAT-AAAATAAAAAAAT
* *
5350388 ACAAAATAAAAATAAATTAAAAAAATAAAAAT
1 A-AAAATAAAAATAAAATAAAATAA-AAAAAT
5350420 AAAA
1 AAAA
5350424 TGAAGAGAAC
Statistics
Matches: 68, Mismatches: 21, Indels: 12
0.67 0.21 0.12
Matches are distributed among these distances:
28 6 0.09
29 11 0.16
30 18 0.26
31 17 0.25
32 16 0.24
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (30 bp):
AAAAATAAAAATAAAATAAAATAAAAAAAT
Found at i:5350752 original size:42 final size:41
Alignment explanation
Indices: 5350621--5351125 Score: 679
Period size: 42 Copynumber: 12.1 Consensus size: 41
5350611 TTTGATCAAA
* ** * * *
5350621 GCTCCTCTGAACAGAGGTTCAACGACTTTGGAAAAATAAACT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
*
5350663 GCTCCTCT-AACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
5350703 ACTCTTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
* * *
5350745 GCTCTTCTAAACAGAGGCGCCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
5350786 GTTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
5350827 GCTCCTCTAAACAGAGGCACCACAACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
5350869 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
*
5350911 GCTCCTCTAAACAGAGGTACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
* * *
5350953 GTTCCTCTAAACAAAGGCATCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
* * *
5350995 GCTTCTCTAAATAGAGGCACCATGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAAGTAAATT
* * *
5351037 GCTCATCTAAACAGAGGCACCACAACTTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
* * *
5351079 GCTCCTCTAAACAGAGGCATCATGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
5351120 ACTCCT
1 GCTCCT
5351126 TGACAATCAT
Statistics
Matches: 414, Mismatches: 43, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
40 15 0.04
41 137 0.33
42 253 0.61
43 9 0.02
ACGTcount: A:0.36, C:0.22, G:0.17, T:0.25
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:5351426 original size:44 final size:44
Alignment explanation
Indices: 5351365--5351469 Score: 108
Period size: 43 Copynumber: 2.4 Consensus size: 44
5351355 GTTTAAAGTT
* *
5351365 TTTAAAGGTTCTT-ATTTGGCAAACTTGGA-ATTCATATCCAAAAA
1 TTTAAAGCTT-TTCATTTGG-AAACTTGGAGATTCACATCCAAAAA
** *
5351409 TTTAAAGCTTTTCATTT-GAATTTTGGAGATTCACATCCAAAAG
1 TTTAAAGCTTTTCATTTGGAAACTTGGAGATTCACATCCAAAAA
* *
5351452 TTCAAAACTTTTCATTTG
1 TTTAAAGCTTTTCATTTG
5351470 TTCGACGATT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
42 7 0.14
43 31 0.61
44 13 0.25
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (44 bp):
TTTAAAGCTTTTCATTTGGAAACTTGGAGATTCACATCCAAAAA
Found at i:5351449 original size:43 final size:42
Alignment explanation
Indices: 5351389--5351469 Score: 117
Period size: 43 Copynumber: 1.9 Consensus size: 42
5351379 TTTGGCAAAC
* * *
5351389 TTGGAATTCATATCCAAAAATTTAAAGCTTTTCATTTGAATT
1 TTGGAATTCACATCCAAAAATTCAAAACTTTTCATTTGAATT
*
5351431 TTGGAGATTCACATCCAAAAGTTCAAAACTTTTCATTTG
1 TTGGA-ATTCACATCCAAAAATTCAAAACTTTTCATTTG
5351470 TTCGACGATT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
42 5 0.15
43 29 0.85
ACGTcount: A:0.35, C:0.15, G:0.11, T:0.40
Consensus pattern (42 bp):
TTGGAATTCACATCCAAAAATTCAAAACTTTTCATTTGAATT
Found at i:5351557 original size:21 final size:20
Alignment explanation
Indices: 5351509--5351548 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
5351499 GGTTTCACTC
5351509 TTCAAAGATTCTCATTTTGAAA
1 TTCAAAG-TTCTCA-TTTGAAA
5351531 TTCAAAGTTCTCATTTGA
1 TTCAAAGTTCTCATTTGA
5351549 GTTCTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (20 bp):
TTCAAAGTTCTCATTTGAAA
Found at i:5352692 original size:14 final size:14
Alignment explanation
Indices: 5352663--5352700 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
5352653 CTTTTTCTCA
*
5352663 TTTTTTATTCTTTC
1 TTTTTTTTTCTTTC
5352677 TTTCTTTTTT-TTTC
1 TTT-TTTTTTCTTTC
5352691 TTTTTTTTTC
1 TTTTTTTTTC
5352701 ATCATCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 6 0.29
14 10 0.48
15 5 0.24
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTTTTTTCTTTC
Found at i:5352698 original size:31 final size:33
Alignment explanation
Indices: 5352654--5352720 Score: 84
Period size: 34 Copynumber: 2.1 Consensus size: 33
5352644 TTTGAATCTC
5352654 TTTTTCTCATTTTTT-AT-TCTTTCTTTCTTTT
1 TTTTTCTCATTTTTTCATATCTTTCTTTCTTTT
** *
5352685 TTTTTCTTTTTTTTTCATCATCTTTTTTTCTTTT
1 TTTTTCTCATTTTTTCAT-ATCTTTCTTTCTTTT
5352719 TT
1 TT
5352721 CTCATTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 13 0.43
32 2 0.07
34 15 0.50
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (33 bp):
TTTTTCTCATTTTTTCATATCTTTCTTTCTTTT
Found at i:5352729 original size:30 final size:30
Alignment explanation
Indices: 5352654--5352733 Score: 81
Period size: 30 Copynumber: 2.6 Consensus size: 30
5352644 TTTGAATCTC
* *
5352654 TTTTTCTCATTTTTTATTCTTTCTTTCTTTT
1 TTTTTCTCATTTTTCA-TCTATCTTTCTTTT
** *
5352685 TTTTTCTTTTTTTTTCATC-ATCTTTTTTTCT
1 TTTTTC-TCATTTTTCATCTATCTTTCTTT-T
5352716 TTTTTCTCATTTTTCATC
1 TTTTTCTCATTTTTCATC
5352734 CATTGTTGAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
30 18 0.45
31 15 0.38
32 7 0.17
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (30 bp):
TTTTTCTCATTTTTCATCTATCTTTCTTTT
Found at i:5352729 original size:31 final size:31
Alignment explanation
Indices: 5352654--5352733 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
5352644 TTTGAATCTC
*
5352654 TTTTTCTCATTTTTT-ATTCTTTCTTTCTTTT
1 TTTTTCTCATTTTTTCA-TCTATCTTTCTTTT
** *
5352685 TTTTTCTTTTTTTTTCATC-ATCTTTTTTTCT
1 TTTTTCTCATTTTTTCATCTATCTTTCTTT-T
5352716 TTTTTCTCA-TTTTTCATC
1 TTTTTCTCATTTTTTCATC
5352734 CATTGTTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
30 17 0.41
31 23 0.56
32 1 0.02
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (31 bp):
TTTTTCTCATTTTTTCATCTATCTTTCTTTT
Found at i:5356745 original size:62 final size:59
Alignment explanation
Indices: 5356612--5356772 Score: 209
Period size: 62 Copynumber: 2.7 Consensus size: 59
5356602 CTTGTGTAGA
* * *
5356612 AAAAATTGATACTTTTAACTTTT-TCCTAAAAATA-TTCTTTTGAAACTTTAATTTCGAG
1 AAAAATTGATACTTTCAACTTTTCTCC-AAAAATATTTTTTTTGAAACTTTAATTTCAAG
* *
5356670 AAAAATTGATACTTTCAACTTTTCTTCAAAAATTTATTTTTTTTGAAACTTTGATTTTCAAG
1 AAAAATTGATACTTTCAACTTTTCTCCAAAAA--TATTTTTTTTGAAACTTT-AATTTCAAG
* *
5356732 GAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTT
1 AAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTT
5356773 GATTTTTATT
Statistics
Matches: 90, Mismatches: 8, Indels: 8
0.85 0.08 0.08
Matches are distributed among these distances:
58 27 0.30
59 2 0.02
60 11 0.12
61 14 0.16
62 36 0.40
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (59 bp):
AAAAATTGATACTTTCAACTTTTCTCCAAAAATATTTTTTTTGAAACTTTAATTTCAAG
Found at i:5356839 original size:5 final size:5
Alignment explanation
Indices: 5356799--5356877 Score: 58
Period size: 5 Copynumber: 16.0 Consensus size: 5
5356789 AAATAAAATG
* *
5356799 ATAAA ACAAA ATAAA AGTGAA A-AAA ATAATA ATAAA ATAAA ATAAGA
1 ATAAA ATAAA ATAAA A-TAAA ATAAA ATAA-A ATAAA ATAAA ATAA-A
* * *
5356846 A-AAA GTAAA ACAAA A-ATA A-AAA ATAAA ATAAA
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA
5356878 GGTAAAAAGA
Statistics
Matches: 59, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
4 10 0.17
5 38 0.64
6 11 0.19
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (5 bp):
ATAAA
Found at i:5356848 original size:26 final size:26
Alignment explanation
Indices: 5356799--5356866 Score: 70
Period size: 26 Copynumber: 2.7 Consensus size: 26
5356789 AAATAAAATG
*
5356799 ATAAAAC-AAAATAAAAGTGAAAAAA
1 ATAAAACAAAAATAAAAGTAAAAAAA
*
5356824 ATAATAA-TAAAATAAAA-TAAGAAAAA
1 ATAA-AACAAAAATAAAAGTAA-AAAAA
*
5356850 GTAAAACAAAAATAAAA
1 ATAAAACAAAAATAAAA
5356867 AATAAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
25 8 0.22
26 28 0.78
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (26 bp):
ATAAAACAAAAATAAAAGTAAAAAAA
Found at i:5356867 original size:12 final size:12
Alignment explanation
Indices: 5356806--5356877 Score: 53
Period size: 11 Copynumber: 6.1 Consensus size: 12
5356796 ATGATAAAAC
5356806 AAAATAAAAGTGAA
1 AAAATAAAA-T-AA
*
5356820 AAAA-ATAATAA
1 AAAATAAAATAA
5356831 TAAAATAAAAT-A
1 -AAAATAAAATAA
* *
5356843 AGAA-AAAGTAA
1 AAAATAAAATAA
*
5356854 AACA-AAAATAA
1 AAAATAAAATAA
5356865 AAAATAAAATAA
1 AAAATAAAATAA
5356877 A
1 A
5356878 GGTAAAAAGA
Statistics
Matches: 46, Mismatches: 8, Indels: 10
0.72 0.12 0.16
Matches are distributed among these distances:
10 4 0.09
11 17 0.37
12 14 0.30
13 7 0.15
14 4 0.09
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:5356897 original size:34 final size:33
Alignment explanation
Indices: 5356788--5356876 Score: 99
Period size: 36 Copynumber: 2.6 Consensus size: 33
5356778 TTATTTAAAG
* * *
5356788 AAAATAAAATGATAAAACAAAATAAAAGTGAAAA-A
1 AAAATAAAA-AATAAAATAAGA-AAAAGT-AAAACA
5356823 AATAATAATAAAATAAAATAAGAAAAAGTAAAACA
1 AA-AATAA-AAAATAAAATAAGAAAAAGTAAAACA
5356858 AAAATAAAAAATAAAATAA
1 AAAATAAAAAATAAAATAA
5356877 AGGTAAAAAG
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
33 12 0.25
34 9 0.19
35 11 0.23
36 14 0.29
37 2 0.04
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (33 bp):
AAAATAAAAAATAAAATAAGAAAAAGTAAAACA
Found at i:5357284 original size:20 final size:20
Alignment explanation
Indices: 5357245--5357284 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
5357235 GCTTTTCTCT
*
5357245 AAAAATTTCACCGGATTCTG
1 AAAAATTTCACCGGAATCTG
*
5357265 AAAAATTTCACTGGAATCTG
1 AAAAATTTCACCGGAATCTG
5357285 GGTTTTTTCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
AAAAATTTCACCGGAATCTG
Found at i:5357455 original size:13 final size:14
Alignment explanation
Indices: 5357428--5357457 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5357418 GAATTTTTCC
5357428 AAAAATTCCCAAAA
1 AAAAATTCCCAAAA
*
5357442 AAAAATTGCCAAAA
1 AAAAATTCCCAAAA
5357456 AA
1 AA
5357458 TCTCCAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.17, G:0.03, T:0.13
Consensus pattern (14 bp):
AAAAATTCCCAAAA
Found at i:5357790 original size:12 final size:12
Alignment explanation
Indices: 5357773--5357813 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
5357763 TCAGATAAAT
5357773 CAGATAAATTAA
1 CAGATAAATTAA
5357785 CAGATAAATTAA
1 CAGATAAATTAA
5357797 -A-ATTAAA-TAA
1 CAGA-TAAATTAA
5357807 CAGATAA
1 CAGATAA
5357814 TTACATAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
10 4 0.15
11 9 0.35
12 13 0.50
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.24
Consensus pattern (12 bp):
CAGATAAATTAA
Found at i:5357846 original size:11 final size:11
Alignment explanation
Indices: 5357832--5357869 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
5357822 ATATTAACAG
5357832 AAAAAG-AAAA
1 AAAAAGAAAAA
*
5357842 AAAAAGAAGAA
1 AAAAAGAAAAA
5357853 AAAAAGAAGAAA
1 AAAAAGAA-AAA
5357865 AAAAA
1 AAAAA
5357870 TAATAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 6 0.25
11 11 0.46
12 7 0.29
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAA
Found at i:5357874 original size:3 final size:3
Alignment explanation
Indices: 5357868--5358016 Score: 80
Period size: 3 Copynumber: 48.7 Consensus size: 3
5357858 GAAGAAAAAA
5357868 AAT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
* ** *
5357912 ATAT ACAT ATT AAT AAAT ACAT AAAT CCCT AA- AAA AAT AAT AAT AA-
1 A-AT A-AT AAT AAT -AAT A-AT -AAT -AAT AAT AAT AAT AAT AAT AAT
* * *
5357958 AAG AA- AAA AAT ATAT ATAT ACAT ATAT AA- AAT AAT AAT AAT AAA AAT
1 AAT AAT AAT AAT A-AT A-AT A-AT A-AT AAT AAT AAT AAT AAT AAT AAT
5358005 AA- AAT AA- AAT AA
1 AAT AAT AAT AAT AA
5358017 AAATGTAAAA
Statistics
Matches: 118, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
2 15 0.13
3 74 0.63
4 28 0.24
5 1 0.01
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:5357930 original size:59 final size:53
Alignment explanation
Indices: 5357867--5358020 Score: 131
Period size: 52 Copynumber: 2.8 Consensus size: 53
5357857 AGAAGAAAAA
5357867 AAATA-ATAAAATAATAATAATAATAATAATAATAATAATAAAGATATATACATATTAAT
1 AAATACATAAAATAATAATAATAATAATAATAATAA-AATAAA-A-ATAT--ATA-T-AT
** *
5357926 AAATACAT-AAATCCCTAA-AAAAATAATAATAA-AAGAA-AAAAATATATATAT
1 AAATACATAAAAT-AATAATAATAATAATAATAATAA-AATAAAAATATATATAT
* * *
5357977 ACATATATAAAATAATAATAATAAAAATAA-AATAAAATAAAAAT
1 AAATACATAAAATAATAATAATAATAATAATAATAAAATAAAAAT
5358021 GTAAAATTAC
Statistics
Matches: 79, Mismatches: 10, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
51 15 0.19
52 22 0.28
53 3 0.04
55 4 0.05
56 1 0.01
57 3 0.04
58 4 0.05
59 22 0.28
60 5 0.06
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (53 bp):
AAATACATAAAATAATAATAATAATAATAATAATAAAATAAAAATATATATAT
Found at i:5358019 original size:6 final size:6
Alignment explanation
Indices: 5357990--5358071 Score: 71
Period size: 6 Copynumber: 13.3 Consensus size: 6
5357980 TATATAAAAT
* *
5357990 AATAAT AATAAA AAT-AA AAT-AA AATAAA AATGTAAA ATTACAA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AA--TAAA AATA-AA AATAAA
*
5358039 AATAAA TTAA-AAA ATTAAA AATAAA AATAAA AA
1 AATAAA --AATAAA AATAAA AATAAA AATAAA AA
5358072 ATATATATAT
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
5 11 0.17
6 38 0.59
7 8 0.12
8 7 0.11
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.22
Consensus pattern (6 bp):
AATAAA
Found at i:5358038 original size:13 final size:12
Alignment explanation
Indices: 5357990--5358071 Score: 71
Period size: 13 Copynumber: 6.7 Consensus size: 12
5357980 TATATAAAAT
*
5357990 AATAATAATAAA
1 AATAAAAATAAA
5358002 AAT-AAAAT-AA
1 AATAAAAATAAA
5358012 AATAAAAATGTAAA
1 AATAAAAA--TAAA
*
5358026 ATTACAAAATAAA
1 AATA-AAAATAAA
5358039 AATAAATTAA-AAA
1 AATAAA--AATAAA
*
5358052 ATTAAAAATAAA
1 AATAAAAATAAA
5358064 AATAAAAA
1 AATAAAAA
5358072 ATATATATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 16
0.73 0.06 0.21
Matches are distributed among these distances:
10 5 0.09
11 10 0.18
12 15 0.26
13 16 0.28
14 7 0.12
15 4 0.07
ACGTcount: A:0.76, C:0.01, G:0.01, T:0.22
Consensus pattern (12 bp):
AATAAAAATAAA
Found at i:5358050 original size:32 final size:31
Alignment explanation
Indices: 5357983--5358071 Score: 103
Period size: 32 Copynumber: 2.9 Consensus size: 31
5357973 ATATACATAT
*
5357983 ATAAAATAA-TAATAATAAAAAT-AAAATAAA
1 ATAAAA-AATTAAAAATAAAAATAAAAATAAA
*
5358013 AT-AAAAATGTAAAATTACAAAATAAAAATAAA
1 ATAAAAAAT-TAAAAATA-AAAATAAAAATAAA
*
5358045 TTAAAAAATTAAAAATAAAAATAAAAA
1 ATAAAAAATTAAAAATAAAAATAAAAA
5358072 ATATATATAT
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
28 2 0.04
29 3 0.06
30 8 0.16
31 15 0.30
32 16 0.32
33 6 0.12
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.22
Consensus pattern (31 bp):
ATAAAAAATTAAAAATAAAAATAAAAATAAA
Found at i:5358074 original size:105 final size:109
Alignment explanation
Indices: 5357872--5358083 Score: 260
Period size: 105 Copynumber: 2.0 Consensus size: 109
5357862 AAAAAAAATA
* * *
5357872 ATAAAATAATAATAATAATAATAATAATAATAATAAAGATATATACATATTAATAAATACATAAA
1 ATAAAATAATAATAATAAAAATAATAATAATAATAAAGATATATACAAATTAATAAATAAATAAA
*
5357937 TCCCTAAAAAAATAATAATAAAAGAAAAAAATATATATATACATAT
66 T--CTAAAAAAATAAAAATAAAAGAAAAAAATATATATATACATAT
*
5357983 ATAAAATAATAATAATAAAAATAA-AATAA-AATAAA-A-ATGTA-AAATTACA-AAATAAAAAT
1 ATAAAATAATAATAATAAAAATAATAATAATAATAAAGATATATACAAATTA-ATAAAT--AAAT
*
5358042 AAAT-TAAAAAATTAAAAATAAAA-ATAAAAAATATATATATAC
63 AAATCTAAAAAAATAAAAATAAAAGA-AAAAAATATATATATAC
5358084 TTACCCATTT
Statistics
Matches: 91, Mismatches: 6, Indels: 14
0.82 0.05 0.13
Matches are distributed among these distances:
104 1 0.01
105 34 0.37
106 9 0.10
107 5 0.05
108 8 0.09
109 6 0.07
110 5 0.05
111 23 0.25
ACGTcount: A:0.68, C:0.04, G:0.01, T:0.27
Consensus pattern (109 bp):
ATAAAATAATAATAATAAAAATAATAATAATAATAAAGATATATACAAATTAATAAATAAATAAA
TCTAAAAAAATAAAAATAAAAGAAAAAAATATATATATACATAT
Found at i:5367294 original size:2 final size:2
Alignment explanation
Indices: 5367287--5367325 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
5367277 TAATTCATGC
5367287 TA TA TA TA TA TA TA T- TA T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5367326 GCTGTTGGCA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:5372959 original size:2 final size:2
Alignment explanation
Indices: 5372952--5372985 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
5372942 CAGAAGGATA
* *
5372952 AT AT AT AT AT AT AT AT AT AT AT TT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5372986 TTCACAGTGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
AT
Found at i:5389954 original size:26 final size:24
Alignment explanation
Indices: 5389920--5389970 Score: 75
Period size: 24 Copynumber: 2.0 Consensus size: 24
5389910 TTACGTATAC
5389920 ACTAAAATTATATATATAAAAAAAAA
1 ACTAAAATTAT-TAT-TAAAAAAAAA
*
5389946 ACTACAATTATTATTAAAAAAAAA
1 ACTAAAATTATTATTAAAAAAAAA
5389970 A
1 A
5389971 AAAGCATTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 11 0.46
25 3 0.12
26 10 0.42
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (24 bp):
ACTAAAATTATTATTAAAAAAAAA
Found at i:5389971 original size:26 final size:26
Alignment explanation
Indices: 5389920--5389972 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
5389910 TTACGTATAC
*
5389920 ACTAAAATTATATATATAAAAAAAAA
1 ACTAAAATTATATATAAAAAAAAAAA
*
5389946 ACTACAATTAT-TATTAAAAAAAAAAA
1 ACTAAAATTATATA-TAAAAAAAAAAA
5389972 A
1 A
5389973 AGCATTGTCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 2 0.08
26 22 0.92
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (26 bp):
ACTAAAATTATATATAAAAAAAAAAA
Found at i:5391517 original size:11 final size:12
Alignment explanation
Indices: 5391499--5391524 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5391489 TATCAATTTT
5391499 AAATTTTTATTA
1 AAATTTTTATTA
5391511 AAATTTTTATTA
1 AAATTTTTATTA
5391523 AA
1 AA
5391525 TCATTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
AAATTTTTATTA
Found at i:5392227 original size:2 final size:2
Alignment explanation
Indices: 5392222--5392267 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
5392212 TGTATGTGTG
5392222 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5392264 TA TA
1 TA TA
5392268 CTTTAAAGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5396419 original size:22 final size:22
Alignment explanation
Indices: 5396391--5396434 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
5396381 GCTATTAGTT
*
5396391 ACTTTTCCATTGGTATCCTGAC
1 ACTTTTCCATTGGCATCCTGAC
5396413 ACTTTTCCATTGGCATCCTGAC
1 ACTTTTCCATTGGCATCCTGAC
5396435 CACATCCTGG
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:0.18, C:0.30, G:0.14, T:0.39
Consensus pattern (22 bp):
ACTTTTCCATTGGCATCCTGAC
Found at i:5398517 original size:19 final size:19
Alignment explanation
Indices: 5398489--5398531 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
5398479 AATTTTATTG
*
5398489 ATAAAATTTTTTAAAAATTT
1 ATAAAA-TTTTAAAAAATTT
*
5398509 -TAAAGTTTTAAAAAATTT
1 ATAAAATTTTAAAAAATTT
5398527 ATAAA
1 ATAAA
5398532 TACGCTACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
ATAAAATTTTAAAAAATTT
Found at i:5398522 original size:18 final size:19
Alignment explanation
Indices: 5398496--5398531 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
5398486 TTGATAAAAT
*
5398496 TTTTTAAAAATTT-TAAAG
1 TTTTAAAAAATTTATAAAG
5398514 TTTTAAAAAATTTATAAA
1 TTTTAAAAAATTTATAAA
5398532 TACGCTACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TTTTAAAAAATTTATAAAG
Found at i:5400927 original size:2 final size:2
Alignment explanation
Indices: 5400920--5400945 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5400910 TACGTATTAT
5400920 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5400946 GACACATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5403537 original size:5 final size:5
Alignment explanation
Indices: 5403527--5403556 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
5403517 TCCTAGCTTA
5403527 AAGAC AAGAC AAGAC AAGAC AAGAC AAGAC
1 AAGAC AAGAC AAGAC AAGAC AAGAC AAGAC
5403557 TTTCAGTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAC
Found at i:5416431 original size:27 final size:25
Alignment explanation
Indices: 5416361--5416439 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
5416351 TATACATGAA
* *
5416361 TATATTTTTTAAATAAAAATATATT
1 TATATTATTTAATTAAAAATATATT
* * *
5416386 AATTTTAATTAATCT-AAAATAATAATT
1 TATATTATTTAAT-TAAAAAT-AT-ATT
*
5416413 TATATTATTTAATTAAAAATTTATT
1 TATATTATTTAATTAAAAATATATT
5416438 TA
1 TA
5416440 GTAAATATAT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
25 18 0.44
26 5 0.12
27 18 0.44
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (25 bp):
TATATTATTTAATTAAAAATATATT
Found at i:5417304 original size:12 final size:12
Alignment explanation
Indices: 5417268--5417304 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
5417258 AATAAATTTT
5417268 ATAA-AAAATAA
1 ATAATAAAATAA
5417279 ATAATAATAA-AA
1 ATAATAA-AATAA
5417291 ATAATAAAATAA
1 ATAATAAAATAA
5417303 AT
1 AT
5417305 CATATTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.26
12 15 0.65
13 2 0.09
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAATAAAATAA
Found at i:5417818 original size:18 final size:15
Alignment explanation
Indices: 5417785--5417823 Score: 51
Period size: 18 Copynumber: 2.4 Consensus size: 15
5417775 TTTTTTGTTT
5417785 TTTTATTTTTAAAAA
1 TTTTATTTTTAAAAA
5417800 TTTTATTTATTAAATAAA
1 TTTTATTT-TT-AA-AAA
5417818 TTTTAT
1 TTTTAT
5417824 AAAAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 8 0.38
16 2 0.10
17 2 0.10
18 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTATTTTTAAAAA
Found at i:5418048 original size:21 final size:23
Alignment explanation
Indices: 5417999--5418049 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
5417989 AATATATAAA
* *
5417999 AATATATATATTATTATTTATTT
1 AATATATATATTATTATATATGT
5418022 AATATATAT-TTA-TATATATGT
1 AATATATATATTATTATATATGT
*
5418043 ATTATAT
1 AATATAT
5418050 TAATAAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 13 0.52
22 3 0.12
23 9 0.36
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
AATATATATATTATTATATATGT
Found at i:5418662 original size:4 final size:4
Alignment explanation
Indices: 5418645--5418689 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
5418635 TGTAAAAAGT
* * * *
5418645 ATAC AGAC AGAC ATAC ATAT ATAC ATAC ATAC ATAC GTAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
5418690 CAATATGAGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.22
Consensus pattern (4 bp):
ATAC
Found at i:5420098 original size:30 final size:30
Alignment explanation
Indices: 5420064--5420142 Score: 151
Period size: 30 Copynumber: 2.7 Consensus size: 30
5420054 TTTTAACTTG
5420064 TACAATTGAACAATGACACAACACACTTAT
1 TACAATTGAACAATGACACAACACACTTAT
5420094 TACAATTGAACAATGACACAACACACTTAT
1 TACAATTGAACAATGACACAACACACTTAT
5420124 TACAATTGAAC-ATGACACA
1 TACAATTGAACAATGACACA
5420143 TTACATGGAC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 8 0.16
30 41 0.84
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.23
Consensus pattern (30 bp):
TACAATTGAACAATGACACAACACACTTAT
Found at i:5423768 original size:336 final size:336
Alignment explanation
Indices: 5423155--5423823 Score: 1088
Period size: 336 Copynumber: 2.0 Consensus size: 336
5423145 AAAGAATTTT
* * * * * *
5423155 AAACTCATATACATATTGAAGTAAAAAATCGTGTAAGAGATGCACTCTTTCTTAGAGGTTCTAAT
1 AAACTCACATACAGATTGAAGTAAAAAACCATGCAAGAGATGCACTCTTCCTTAGAGGTTCTAAT
* * *
5423220 GTGAATTACGTGAGTGAACAAAATTATGAAAAAACTCACAAGTCTTTTGGTAAATTTCAAAATAA
66 GTGAATTACGTGAGTAAACAAAATTATGAAAAAACTCACAAGTCTTTTAGTAAATTTCAAAACAA
* * *
5423285 TTTTAAAGTCAAGAAGAATAGATTTAAGAAGTCTAAATTTAACAAGGACAAAATGTGTTTCCATT
131 TTTTAAAGTCAAGAAAAATAGATTTAAGAAGTCCAAATTTAACAAGAACAAAATGTGTTTCCATT
* *
5423350 ATGAAAAGAAATGACATTTGATTAAAGATTATAGATTTAAAAACGCTGAAATTAAGATTGGTTCT
196 ATGAAAAGAAAGGACATTTGATTAAAGATTACAGATTTAAAAACGCTGAAATTAAGATTGGTTCT
* * *
5423415 AGTTCTGAAAGCAAGGCAAATTTGGTTGAGCAAAAAATTAATAAACTTGTTGTAATGGTGACTGA
261 AGTTCTGAAAGCAAGGCAAATCTGGTTGAGCAAAAAATTAATAAACTTATTGCAATGGTGACTGA
5423480 CATGCAAATTC
326 CATGCAAATTC
5423491 AAACTCACATACAGATTGAAGTAAAAAACCATGCAAGAGATGCACTCTTCCTTAGAGGTT-TCAA
1 AAACTCACATACAGATTGAAGTAAAAAACCATGCAAGAGATGCACTCTTCCTTAGAGGTTCT-AA
*
5423555 TGTGAATTACGTGAGTAAACAAAATTTTGAAAAAACTCACAAGTCTTTTAGTAAATTTCAAAACA
65 TGTGAATTACGTGAGTAAACAAAATTATGAAAAAACTCACAAGTCTTTTAGTAAATTTCAAAACA
*
5423620 ATTTTAAAGTCAAGAAAAATGGATTTAAGAAGTCCAAATTTAACAAGAACAAAATGTGTTTCCAT
130 ATTTTAAAGTCAAGAAAAATAGATTTAAGAAGTCCAAATTTAACAAGAACAAAATGTGTTTCCAT
* * *
5423685 TGTGAAAAGAAAGGACATTTGATTAAAGATTACAGATTTAAAAATGTTGAAATTAAGATTGGTTC
195 TATGAAAAGAAAGGACATTTGATTAAAGATTACAGATTTAAAAACGCTGAAATTAAGATTGGTTC
* * * *
5423750 TAGTTTTGAAAGCAAGGCAAATCTGGTTGAGTAAGAAATTAATGAACTTATTGCAATGGTGACTG
260 TAGTTCTGAAAGCAAGGCAAATCTGGTTGAGCAAAAAATTAATAAACTTATTGCAATGGTGACTG
5423815 ACATGCAAA
325 ACATGCAAA
5423824 CTAAAATGAT
Statistics
Matches: 306, Mismatches: 26, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
335 1 0.00
336 305 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (336 bp):
AAACTCACATACAGATTGAAGTAAAAAACCATGCAAGAGATGCACTCTTCCTTAGAGGTTCTAAT
GTGAATTACGTGAGTAAACAAAATTATGAAAAAACTCACAAGTCTTTTAGTAAATTTCAAAACAA
TTTTAAAGTCAAGAAAAATAGATTTAAGAAGTCCAAATTTAACAAGAACAAAATGTGTTTCCATT
ATGAAAAGAAAGGACATTTGATTAAAGATTACAGATTTAAAAACGCTGAAATTAAGATTGGTTCT
AGTTCTGAAAGCAAGGCAAATCTGGTTGAGCAAAAAATTAATAAACTTATTGCAATGGTGACTGA
CATGCAAATTC
Found at i:5428385 original size:3 final size:3
Alignment explanation
Indices: 5428377--5428402 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5428367 TCTATAGATT
5428377 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5428403 TCTTTACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5429281 original size:16 final size:17
Alignment explanation
Indices: 5429254--5429302 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 17
5429244 TAAATACGTG
5429254 AAAAATTAATTTTT-ATA
1 AAAAATT-ATTTTTAATA
5429271 AAAAATTATTTATTAATA
1 AAAAATTATTT-TTAATA
5429289 AAATAATTTATTTT
1 AAA-AA-TTATTTT
5429303 ATTTTATTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.14
17 9 0.32
18 6 0.21
19 3 0.11
20 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAAATTATTTTTAATA
Found at i:5429921 original size:19 final size:20
Alignment explanation
Indices: 5429881--5429921 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
5429871 TTGAAGCTTT
*
5429881 ATATATTATTAAAGTTATAA
1 ATATATTATTAAAGTGATAA
5429901 ATATA-TATTCAAAGTGA-AA
1 ATATATTATT-AAAGTGATAA
5429920 AT
1 AT
5429922 TAGTAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.39
Consensus pattern (20 bp):
ATATATTATTAAAGTGATAA
Found at i:5430225 original size:41 final size:43
Alignment explanation
Indices: 5430135--5430225 Score: 102
Period size: 41 Copynumber: 2.2 Consensus size: 43
5430125 TAGATTTGAT
5430135 AATTTAA-AATATGATATAAAATTTATAAAAAATAAAAAATAC
1 AATTTAATAATATGATATAAAATTTATAAAAAATAAAAAATAC
* * ***
5430177 AA--AAATAATATGATTTAAAATTT-TAAAAAATTGTAAATA-
1 AATTTAATAATATGATATAAAATTTATAAAAAATAAAAAATAC
5430216 AATTTAATAA
1 AATTTAATAA
5430226 AATTAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
39 2 0.05
40 15 0.38
41 21 0.52
42 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (43 bp):
AATTTAATAATATGATATAAAATTTATAAAAAATAAAAAATAC
Found at i:5430542 original size:22 final size:22
Alignment explanation
Indices: 5430503--5430555 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 22
5430493 CTGAAATTAA
5430503 AAAATATTTATTTTTTTAAAATAT
1 AAAATA-TTATTTTTTT-AAATAT
5430527 AAAATATTA-TTTTTTAAATAT
1 AAAATATTATTTTTTTAAATAT
5430548 AAATATAT
1 AAA-ATAT
5430556 AAATAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
21 9 0.32
22 10 0.36
23 3 0.11
24 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AAAATATTATTTTTTTAAATAT
Found at i:5430596 original size:24 final size:24
Alignment explanation
Indices: 5430496--5430601 Score: 70
Period size: 24 Copynumber: 4.2 Consensus size: 24
5430486 ACTTGATCTG
***
5430496 AAATTAAAAAATATTTATTTTTTTA
1 AAATTAAAAAATATTT-TTTAAATA
*
5430521 AAATATAAAATATTATTTTTTAAATA
1 AAAT-TAAAA-AATATTTTTTAAATA
* ** *
5430547 TAAA-TATATAAATAAATTTAAAATA
1 -AAATTA-AAAAATATTTTTTAAATA
*
5430572 AAATTAAAAAATATTTTTTATATA
1 AAATTAAAAAATATTTTTTAAATA
*
5430596 ATATTA
1 AAATTA
5430602 GATCGAGTTT
Statistics
Matches: 61, Mismatches: 15, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
24 21 0.34
25 19 0.31
26 12 0.20
27 9 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AAATTAAAAAATATTTTTTAAATA
Found at i:5430963 original size:11 final size:11
Alignment explanation
Indices: 5430932--5430964 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
5430922 ATCAATTCGG
*
5430932 ATATTAAATAT
1 ATATTAAATTT
5430943 ATATTAAATTT
1 ATATTAAATTT
5430954 ATATTAAATTT
1 ATATTAAATTT
5430965 CAAATCAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATTAAATTT
Found at i:5431033 original size:18 final size:19
Alignment explanation
Indices: 5431010--5431050 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
5431000 TTAAATCAAA
*
5431010 TTATATATATT-TTAATTT
1 TTATATATATTCTAAATTT
*
5431028 TTATATATCTTCTAAATTT
1 TTATATATATTCTAAATTT
5431047 TTAT
1 TTAT
5431051 CAAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
TTATATATATTCTAAATTT
Found at i:5431101 original size:32 final size:32
Alignment explanation
Indices: 5431054--5431130 Score: 97
Period size: 32 Copynumber: 2.4 Consensus size: 32
5431044 TTTTTATCAA
5431054 ATAAAAA-TAATAATTTTATA-TCAAAT-ATAT
1 ATAAAAATTAA-AATTTTATATTCAAATAATAT
*
5431084 TTAAATATATTAAAATTTTATATTCAAATAATAT
1 ATAAA-A-ATTAAAATTTTATATTCAAATAATAT
5431118 ATAAAAATTAAAA
1 ATAAAAATTAAAA
5431131 AATTAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
30 4 0.10
31 1 0.03
32 17 0.43
33 10 0.25
34 8 0.20
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (32 bp):
ATAAAAATTAAAATTTTATATTCAAATAATAT
Found at i:5431147 original size:22 final size:22
Alignment explanation
Indices: 5431119--5431161 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5431109 AAATAATATA
*
5431119 TAAAAATTAAAAAATTAAATTT
1 TAAAAATCAAAAAATTAAATTT
*
5431141 TAAAAATCAATAAATTAAATT
1 TAAAAATCAAAAAATTAAATT
5431162 GAATAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (22 bp):
TAAAAATCAAAAAATTAAATTT
Found at i:5431597 original size:36 final size:36
Alignment explanation
Indices: 5431527--5431597 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 36
5431517 CAGAAAAAGA
* * *
5431527 TTTACTTAAAATTTCATAAATAAAATTTATAAAATT
1 TTTACTTAAAAATTAATAAATAAAATTGATAAAATT
5431563 TTTA-TTAAAAATTAATAAATTAAAAATTGA-AAAAT
1 TTTACTTAAAAATTAATAAA-T-AAAATTGATAAAAT
5431598 CTTATCATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
35 13 0.43
36 10 0.33
37 7 0.23
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (36 bp):
TTTACTTAAAAATTAATAAATAAAATTGATAAAATT
Found at i:5440977 original size:20 final size:22
Alignment explanation
Indices: 5440948--5440998 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
5440938 GATATTTTTA
5440948 AATA-TTTATA-TTT-AAAAAT
1 AATATTTTATATTTTAAAAAAT
5440967 AATATTTTATATTTTAAAAAAT
1 AATATTTTATATTTTAAAAAAT
5440989 AATATTTTAT
1 AATATTTTAT
5440999 TAATTTTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.14
20 6 0.21
21 3 0.10
22 16 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATTTTATATTTTAAAAAAT
Found at i:5443199 original size:8 final size:8
Alignment explanation
Indices: 5443179--5443223 Score: 65
Period size: 8 Copynumber: 5.8 Consensus size: 8
5443169 ATATTATTTT
5443179 TAAA-ATA
1 TAAATATA
*
5443186 TAAATATT
1 TAAATATA
5443194 TAAATATA
1 TAAATATA
*
5443202 TAATTATA
1 TAAATATA
5443210 TAAATATA
1 TAAATATA
5443218 TAAATA
1 TAAATA
5443224 AAAAAATAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
7 4 0.12
8 29 0.88
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAAATATA
Found at i:5445671 original size:12 final size:12
Alignment explanation
Indices: 5445654--5445685 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
5445644 ATTATAAAAT
5445654 TTTAAATTTGAA
1 TTTAAATTTGAA
5445666 TTTAAATTTGAA
1 TTTAAATTTGAA
*
5445678 TTTGAATT
1 TTTAAATT
5445686 GATTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (12 bp):
TTTAAATTTGAA
Found at i:5445819 original size:17 final size:19
Alignment explanation
Indices: 5445781--5445821 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
5445771 TTATTTTAAC
*
5445781 TAATTTTAATATAATTAAA
1 TAATTTTAATATAATAAAA
5445800 TAATTTT-ATAT-ATAAAA
1 TAATTTTAATATAATAAAA
5445817 TAATT
1 TAATT
5445822 ATTTTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 4 0.19
19 7 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATTTTAATATAATAAAA
Found at i:5445853 original size:17 final size:18
Alignment explanation
Indices: 5445831--5445867 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
5445821 TATTTTATTT
*
5445831 TATAAAAATTTA-AAATA
1 TATAAAAATTAATAAATA
5445848 TATAAAAATTAATAAATA
1 TATAAAAATTAATAAATA
5445866 TA
1 TA
5445868 CATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (18 bp):
TATAAAAATTAATAAATA
Found at i:5447785 original size:24 final size:22
Alignment explanation
Indices: 5447757--5447801 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
5447747 AATTCAGTTA
5447757 TATCATTATTATATTTCATAAATT
1 TATCATT-TTATATTT-ATAAATT
*
5447781 TATCATTTTTTATTTATAAAT
1 TATCATTTTATATTTATAAAT
5447802 AGAATCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 6 0.30
23 7 0.35
24 7 0.35
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.58
Consensus pattern (22 bp):
TATCATTTTATATTTATAAATT
Found at i:5449466 original size:39 final size:37
Alignment explanation
Indices: 5449423--5449498 Score: 89
Period size: 39 Copynumber: 2.0 Consensus size: 37
5449413 TTAATAAAAT
*
5449423 TTTTAATATATATAAAAATAAAATTATATATAATAATTA
1 TTTTAATATATATAAAAATAAAA--ATATATAAAAATTA
* * **
5449462 TTTTATTTTATATAAATTTAAAAATATATAAAAATTA
1 TTTTAATATATATAAAAATAAAAATATATAAAAATTA
5449499 ATAAAATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 13 0.41
39 19 0.59
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (37 bp):
TTTTAATATATATAAAAATAAAAATATATAAAAATTA
Found at i:5456150 original size:31 final size:30
Alignment explanation
Indices: 5456107--5456168 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 30
5456097 CGCAATATGA
*
5456107 TAATATAAT-AAAATGATATA-TTTATAATTT
1 TAATAAAATAAAAAT-ATATATTTTAT-ATTT
5456137 TAATAAAATTAAAAATATATATTTTATATTT
1 TAATAAAA-TAAAAATATATATTTTATATTT
5456168 T
1 T
5456169 CGTATCAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
30 7 0.25
31 11 0.39
32 10 0.36
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
TAATAAAATAAAAATATATATTTTATATTT
Found at i:5456507 original size:16 final size:17
Alignment explanation
Indices: 5456471--5456511 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
5456461 GTTTGTTGCC
5456471 TTTGCTTTGCTTTCCAT
1 TTTGCTTTGCTTTCCAT
5456488 TTTGCTTTG-TTTCCCA-
1 TTTGCTTTGCTTT-CCAT
5456504 TTTGCTTT
1 TTTGCTTT
5456512 TCATTATTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.05, C:0.22, G:0.12, T:0.61
Consensus pattern (17 bp):
TTTGCTTTGCTTTCCAT
Found at i:5456967 original size:22 final size:23
Alignment explanation
Indices: 5456942--5457001 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
5456932 CATTAATTTT
5456942 TAATTTTTATATAT-TA-TTATAA
1 TAATTTTTATATATATATTTA-AA
*
5456964 TAATATTTATA-ATATATTTAAA
1 TAATTTTTATATATATATTTAAA
*
5456986 TAGATTTATATATATA
1 TA-ATTTTTATATATA
5457002 AATAATTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
21 2 0.06
22 16 0.52
23 10 0.32
24 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TAATTTTTATATATATATTTAAA
Found at i:5460461 original size:6 final size:6
Alignment explanation
Indices: 5460450--5460474 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5460440 TATTTGTGTC
5460450 AGAGCA AGAGCA AGAGCA AGAGCA A
1 AGAGCA AGAGCA AGAGCA AGAGCA A
5460475 AACATTCAGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.16, G:0.32, T:0.00
Consensus pattern (6 bp):
AGAGCA
Found at i:5467338 original size:10 final size:9
Alignment explanation
Indices: 5467305--5467337 Score: 50
Period size: 10 Copynumber: 3.7 Consensus size: 9
5467295 TATGCCCATC
5467305 TTTTTCTTT
1 TTTTTCTTT
5467314 TTTTT-TTT
1 TTTTTCTTT
5467322 TTTTTCATTT
1 TTTTTC-TTT
5467332 TTTTTC
1 TTTTTC
5467338 AAACGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 5 0.23
10 9 0.41
ACGTcount: A:0.03, C:0.09, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTCTTT
Found at i:5467419 original size:6 final size:6
Alignment explanation
Indices: 5467408--5467453 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
5467398 TACAAATCAT
* * *
5467408 ATAAAA ATAAAA A-AGAA ATAAAT ATAAAA AT-AAA ATAATA ATAAAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA
5467454 GATTAACTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (6 bp):
ATAAAA
Found at i:5467443 original size:17 final size:17
Alignment explanation
Indices: 5467408--5467453 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
5467398 TACAAATCAT
5467408 ATAAAAATAAAAAAGAA
1 ATAAAAATAAAAAAGAA
*
5467425 ATAAATATAAAAATA-AA
1 ATAAAAATAAAAA-AGAA
*
5467442 ATAATAATAAAA
1 ATAAAAATAAAA
5467454 GATTAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 24 0.96
18 1 0.04
ACGTcount: A:0.78, C:0.00, G:0.02, T:0.20
Consensus pattern (17 bp):
ATAAAAATAAAAAAGAA
Found at i:5469695 original size:22 final size:22
Alignment explanation
Indices: 5469668--5469719 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
5469658 TATCATTTTT
* *
5469668 AATTATAGTTATAATTAAA-AA
1 AATTATAATTACAATTAAATAA
*
5469689 ATATTATAATTACGATTAAATAA
1 A-ATTATAATTACAATTAAATAA
5469712 AATTATAA
1 AATTATAA
5469720 AAAAATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 22 0.85
23 3 0.12
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (22 bp):
AATTATAATTACAATTAAATAA
Found at i:5469750 original size:26 final size:27
Alignment explanation
Indices: 5469703--5469763 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
5469693 TATAATTACG
5469703 ATTAAATAAAATTATAAAAAAATTAAT
1 ATTAAATAAAATTATAAAAAAATTAAT
* **
5469730 ATTAAAT-AAATTTTATTAAAATTAAT
1 ATTAAATAAAATTATAAAAAAATTAAT
5469756 ATTTAAAT
1 A-TTAAAT
5469764 TTAATTACAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 17 0.57
27 13 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTAAATAAAATTATAAAAAAATTAAT
Found at i:5471451 original size:30 final size:29
Alignment explanation
Indices: 5471386--5471468 Score: 78
Period size: 31 Copynumber: 2.7 Consensus size: 29
5471376 TATTAATGAT
***
5471386 TTATTTAAGTACAAATTAAAAATTTAAGAAC
1 TTATTTAAGT--AAATTAAAAACCAAAGAAC
5471417 TTATTTAAGTATATATTAAAAACCAAAG-AC
1 TTATTTAAGTA-A-ATTAAAAACCAAAGAAC
5471447 TTATTTCAATGTAAATTAAAAA
1 TTATTT-AA-GTAAATTAAAAA
5471469 TTAAAATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
29 1 0.02
30 17 0.38
31 24 0.53
32 3 0.07
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (29 bp):
TTATTTAAGTAAATTAAAAACCAAAGAAC
Found at i:5471491 original size:29 final size:30
Alignment explanation
Indices: 5471459--5471522 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 30
5471449 ATTTCAATGT
* * * *
5471459 AAATTAAAAAT-TAAAATTTTTTTTGAATA
1 AAATTAAAAATATAAAAATTTATATAAATA
*
5471488 AAA-TAAAAGTATAAAAATTTATATAAATA
1 AAATTAAAAATATAAAAATTTATATAAATA
5471517 AAATTA
1 AAATTA
5471523 TACAATTCAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
28 6 0.21
29 20 0.71
30 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (30 bp):
AAATTAAAAATATAAAAATTTATATAAATA
Found at i:5483617 original size:18 final size:18
Alignment explanation
Indices: 5483594--5483631 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5483584 CGAACTAAAT
**
5483594 TATATTTTTTTATTTTTA
1 TATATTTTTAAATTTTTA
5483612 TATATTTTTAAATTTTTA
1 TATATTTTTAAATTTTTA
5483630 TA
1 TA
5483632 AAATAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TATATTTTTAAATTTTTA
Found at i:5483720 original size:25 final size:24
Alignment explanation
Indices: 5483675--5483729 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 24
5483665 TAAATATGTT
*
5483675 AAAATTTTATATTAAAAAAATATAA
1 AAAATTTTAAATTAAAAAAAT-TAA
5483700 AAAATTTTAAA-TATAAAAAATTAA
1 AAAATTTTAAATTA-AAAAAATTAA
*
5483724 TAAATT
1 AAAATT
5483730 GAACCGAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
AAAATTTTAAATTAAAAAAATTAA
Found at i:5483727 original size:17 final size:16
Alignment explanation
Indices: 5483692--5483728 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
5483682 TATATTAAAA
*
5483692 AAATATAAAAAATTTT
1 AAATATAAAAAATTAT
5483708 AAATATAAAAAATTAAT
1 AAATATAAAAAATT-AT
5483725 AAAT
1 AAAT
5483729 TGAACCGAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATATAAAAAATTAT
Found at i:5485937 original size:24 final size:24
Alignment explanation
Indices: 5485892--5485938 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5485882 CTAAAGTATT
*
5485892 TAAAATTAAATTTTAAATTTTTTA
1 TAAAATTAAATGTTAAATTTTTTA
*
5485916 TAAAATTAAA-GTTATATGTTTTT
1 TAAAATTAAATGTTAAAT-TTTTT
5485939 TAATAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (24 bp):
TAAAATTAAATGTTAAATTTTTTA
Found at i:5489262 original size:22 final size:24
Alignment explanation
Indices: 5489230--5489273 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
5489220 TATACATAAA
*
5489230 TTTATTTAAAT-ATAT-TAAAATT
1 TTTATTAAAATAATATATAAAATT
5489252 TTTATTAAAATAATATATAAAA
1 TTTATTAAAATAATATATAAAA
5489274 AATAACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 4 0.21
24 5 0.26
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATTAAAATAATATATAAAATT
Found at i:5494075 original size:30 final size:30
Alignment explanation
Indices: 5494033--5494106 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
5494023 CTGTCCGATC
5494033 AAGGGCTT-AATTGAGTGAAAATAGA-TGTAT
1 AAGGG-TTCAATTGAGTGAAAATA-ATTGTAT
* *
5494063 AAGGGTTCAATTGGGTGAAAATAATTGTTT
1 AAGGGTTCAATTGAGTGAAAATAATTGTAT
*
5494093 GAGGGTTCAATTGA
1 AAGGGTTCAATTGA
5494107 TTTGAAATAG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 3 0.08
30 35 0.92
ACGTcount: A:0.35, C:0.04, G:0.28, T:0.32
Consensus pattern (30 bp):
AAGGGTTCAATTGAGTGAAAATAATTGTAT
Found at i:5506976 original size:27 final size:28
Alignment explanation
Indices: 5506945--5507008 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
5506935 TTTAATTCTT
* *
5506945 TAAATTAAATAA-AATACATCATA-ATA
1 TAAAATAAATAATAATAAATCATATATA
* *
5506971 TAAAATAAATAATTATAAATCATATATT
1 TAAAATAAATAATAATAAATCATATATA
5506999 TAAAATAAAT
1 TAAAATAAAT
5507009 TCAATAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 11 0.34
27 9 0.28
28 12 0.38
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (28 bp):
TAAAATAAATAATAATAAATCATATATA
Found at i:5507946 original size:23 final size:23
Alignment explanation
Indices: 5507893--5507946 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
5507883 TTTATACAAT
*
5507893 CAATTTCTAAAATATAATATTTA
1 CAATTTTTAAAATATAATATTTA
* * *
5507916 -ATAATTTTAAATTTTAATATTTA
1 CA-ATTTTTAAAATATAATATTTA
5507939 CAATTTTT
1 CAATTTTT
5507947 TTATTAATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
22 1 0.04
23 22 0.92
24 1 0.04
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.52
Consensus pattern (23 bp):
CAATTTTTAAAATATAATATTTA
Found at i:5512954 original size:2 final size:2
Alignment explanation
Indices: 5512947--5512976 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5512937 CAAAAGAAAA
5512947 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5512977 CAATCGACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5513980 original size:5 final size:5
Alignment explanation
Indices: 5513964--5514074 Score: 51
Period size: 5 Copynumber: 23.6 Consensus size: 5
5513954 ATATAAAAAT
* * * *
5513964 TTTAA TTTTAA TTTAA TTTAA -ATAT TTTTA -TT-A TTCAA -TTAA TTTAA
1 TTTAA -TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
* * ** *
5514011 ATTAA -TAAA TTTAA TTTAA -TTAA TAAAA ATT-- TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA TTTAA
*
5514057 TTTTAA -ATAA TTTAA TTT
1 -TTTAA TTTAA TTTAA TTT
5514075 GAAATTGATG
Statistics
Matches: 77, Mismatches: 18, Indels: 21
0.66 0.16 0.18
Matches are distributed among these distances:
3 3 0.04
4 18 0.23
5 46 0.60
6 10 0.13
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (5 bp):
TTTAA
Done.