Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008428.1 Hibiscus syriacus cultivar Beakdansim tig00111213_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 6915314
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 30
Found at i:4724239 original size:19 final size:19
Alignment explanation
Indices: 4724199--4724241 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
4724189 TCTTTTCAAA
*
4724199 ATTTTTATATATACTTATT
1 ATTTTCATATATACTTATT
*
4724218 ATTTTCATA-ATATTTATAT
1 ATTTTCATATATACTTAT-T
4724237 ATTTT
1 ATTTT
4724242 TTTATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (19 bp):
ATTTTCATATATACTTATT
Found at i:4724239 original size:22 final size:22
Alignment explanation
Indices: 4724213--4724274 Score: 60
Period size: 22 Copynumber: 2.9 Consensus size: 22
4724203 TTATATATAC
4724213 TTATTATTTTCATAATATTT-A
1 TTATTATTTTCATAATATTTCA
*
4724234 TATATT-TTTTTATTAATATTTCA
1 T-TATTATTTTCA-TAATATTTCA
*
4724257 TT-TTATTTGCA-AATATTT
1 TTATTATTTTCATAATATTT
4724275 TATTTCATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
20 7 0.21
21 8 0.24
22 17 0.50
23 2 0.06
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.63
Consensus pattern (22 bp):
TTATTATTTTCATAATATTTCA
Found at i:4725654 original size:17 final size:17
Alignment explanation
Indices: 4725619--4725655 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 17
4725609 TACATTCATA
4725619 TTTTTATATTTGCATTT
1 TTTTTATATTTGCATTT
4725636 TTTTTCATATTTGCATTT
1 TTTTT-ATATTTGCATTT
4725654 TT
1 TT
4725656 ACGTTCGTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.16, C:0.08, G:0.05, T:0.70
Consensus pattern (17 bp):
TTTTTATATTTGCATTT
Found at i:4729090 original size:18 final size:16
Alignment explanation
Indices: 4729067--4729109 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
4729057 CTCATCCAGC
4729067 AAAGAAAGAAGAAAAAAA
1 AAAGAAA-AA-AAAAAAA
4729085 AAAGAAAAAAAAAGAAA
1 AAAGAAAAAAAAA-AAA
*
4729102 AAGGAAAA
1 AAAGAAAA
4729110 TTGAATCAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
16 4 0.17
17 12 0.52
18 7 0.30
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAAAAAAA
Found at i:4729091 original size:11 final size:11
Alignment explanation
Indices: 4729075--4729103 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
4729065 GCAAAGAAAG
4729075 AAGAAAAAAAA
1 AAGAAAAAAAA
4729086 AAG-AAAAAAA
1 AAGAAAAAAAA
4729096 AAGAAAAA
1 AAGAAAAA
4729104 GGAAAATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (11 bp):
AAGAAAAAAAA
Found at i:4734044 original size:22 final size:22
Alignment explanation
Indices: 4734015--4734069 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
4734005 ATCTACACTC
* *
4734015 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGACAAATTCTCTT
*
4734037 TTTAAAGATGACAAATTCTCTT
1 TTCAAAGATGACAAATTCTCTT
4734059 TTCAAAGATGA
1 TTCAAAGATGA
4734070 AAACTTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAAATTCTCTT
Found at i:4734633 original size:113 final size:111
Alignment explanation
Indices: 4734509--4735337 Score: 916
Period size: 113 Copynumber: 7.7 Consensus size: 111
4734499 TACCAGTTCG
*
4734509 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* * *
4734574 AACCTTTTGCTCAAATCCATCTCTTGATGGATCAGCTTTTCCAGAAAA
66 AACCTTTTGTTC-AAT-CATCTCTTGATGGATCAACTTTTCCAGAGAA
* *
4734622 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* *
4734687 AACCTTTT-TTC-ATCA--T-TTGATGGATCAAC-ATTACAGAGAA
66 AACCTTTTGTTCAATCATCTCTTGATGGATCAACTTTTCCAGAGAA
* *
4734727 AGTTCATAATGAGAAGAACTCATCTGAAGAA-G-AG--GAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* * * * * *
4734788 AA-CTTTTCGTTCGAATTTATCACTCGAGGGATCAGCTTTTCCAGAAAA
66 AACCTTTT-GTTC-AA-TCATCTCTTGATGGATCAACTTTTCCAGAGAA
* *
4734836 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* * *
4734901 AACCTTTT-TTC-ATC--GT-TTGATGGATCAAC-ATTACAGAGAA
66 AACCTTTTGTTCAATCATCTCTTGATGGATCAACTTTTCCAGAGAA
* *
4734941 AGTTCATAATGAGAAGAACTCATCTGAAGAA-G-AG--GAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* * * * * *
4735002 AA-CTTTTCGTTCGAATTTATCACTCGAGGGATCAGCTTTTCCAGAAAA
66 AACCTTTT-GTTC-AA-TCATCTCTTGATGGATCAACTTTTCCAGAGAA
* *
4735050 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* *
4735115 AACCTTTT-TTC-ATCA--T-TTGATGGATCAAC-ATTACAGAGAA
66 AACCTTTTGTTCAATCATCTCTTGATGGATCAACTTTTCCAGAGAA
* *
4735155 AGTTCATAATGAGAAGAACTCATCTGAAGAA-G-AG--GAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
* * * * *
4735216 AA-CTTTTCGTTCGAATTTATCACTCGAGGGATCAACTTTTCCAGAGAG
66 AACCTTTT-GTTC-AA-TCATCTCTTGATGGATCAACTTTTCCAGAGAA
* * *
4735264 AGTTCATCATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAA-AAGCTTGTT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAA-CTTGTT
*
4735328 CGACCTTTTG
65 CAACCTTTTG
4735338 CATGACTCTA
Statistics
Matches: 603, Mismatches: 70, Indels: 86
0.79 0.09 0.11
Matches are distributed among these distances:
100 15 0.02
101 75 0.12
102 9 0.01
103 6 0.01
104 6 0.01
105 122 0.20
106 32 0.05
107 1 0.00
108 31 0.05
109 121 0.20
110 7 0.01
111 6 0.01
112 10 0.02
113 147 0.24
114 15 0.02
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (111 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAACTTGTTC
AACCTTTTGTTCAATCATCTCTTGATGGATCAACTTTTCCAGAGAA
Found at i:4735336 original size:214 final size:214
Alignment explanation
Indices: 4734509--4735318 Score: 1415
Period size: 214 Copynumber: 3.8 Consensus size: 214
4734499 TACCAGTTCG
* * *
4734509 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAA-G-AG--GAAGTTCATAATAAGAAGAACTTGTTC
* * ** * * *
4734574 AACCTTTT-GCTCAAATCCATCTCTTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAG
62 AA-CTTTTCGTTCGAATTTATCACTCGAGGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAG
4734638 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTTTTCATCAT
126 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTTTTCATCAT
4734703 TTGATGGATCAACATTACAGAGAA
191 TTGATGGATCAACATTACAGAGAA
4734727 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAGGAAGTTCATAATAAGAAGAACTTGTTCAACT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAGGAAGTTCATAATAAGAAGAACTTGTTCAACT
4734792 TTTCGTTCGAATTTATCACTCGAGGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTC
66 TTTCGTTCGAATTTATCACTCGAGGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTC
*
4734857 ATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTTTTCATCGTTTGAT
131 ATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTTTTCATCATTTGAT
4734922 GGATCAACATTACAGAGAA
196 GGATCAACATTACAGAGAA
4734941 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAGGAAGTTCATAATAAGAAGAACTTGTTCAACT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAGGAAGTTCATAATAAGAAGAACTTGTTCAACT
4735006 TTTCGTTCGAATTTATCACTCGAGGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTC
66 TTTCGTTCGAATTTATCACTCGAGGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTC
4735071 ATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTTTTCATCATTTGAT
131 ATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTTTTCATCATTTGAT
4735136 GGATCAACATTACAGAGAA
196 GGATCAACATTACAGAGAA
4735155 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAGGAAGTTCATAATAAGAAGAACTTGTTCAACT
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAGGAAGTTCATAATAAGAAGAACTTGTTCAACT
* * * *
4735220 TTTCGTTCGAATTTATCACTCGAGGGATCAACTTTTCCAGAGAGAGTTCATCATGAGAAGAACTC
66 TTTCGTTCGAATTTATCACTCGAGGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTC
* *
4735285 ATCTGAAGAAAGAAGAAGAAGTTCATAATGAGAA
131 ATCTGAAGAAGGAAGAAGAAATTCATAATGAGAA
4735319 AAGCTTGTTC
Statistics
Matches: 573, Mismatches: 18, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
213 5 0.01
214 534 0.93
216 2 0.00
217 1 0.00
218 31 0.05
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (214 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGAGGAAGTTCATAATAAGAAGAACTTGTTCAACT
TTTCGTTCGAATTTATCACTCGAGGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTC
ATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTATTCAACCTTTTTTCATCATTTGAT
GGATCAACATTACAGAGAA
Found at i:4735686 original size:9 final size:10
Alignment explanation
Indices: 4735681--4735741 Score: 51
Period size: 9 Copynumber: 6.5 Consensus size: 10
4735671 CCCATTTTAT
*
4735681 TTATTTGTTTA
1 TTATTTATT-A
4735692 TTA-TTATTA
1 TTATTTATTA
4735701 TTA-TTATTA
1 TTATTTATTA
*
4735710 -TATATATTA
1 TTATTTATTA
*
4735719 TTATATA-TA
1 TTATTTATTA
4735728 TTA-TTATTA
1 TTATTTATTA
4735737 TTATT
1 TTATT
4735742 AAAAAAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
8 4 0.09
9 25 0.58
10 11 0.26
11 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
TTATTTATTA
Found at i:4735697 original size:3 final size:3
Alignment explanation
Indices: 4735689--4735742 Score: 76
Period size: 3 Copynumber: 18.0 Consensus size: 3
4735679 ATTTATTTGT
4735689 TTA TTA TTA TTA TTA TTA TTA -TA TATA TTA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA
4735734 TTA TTA TTA
1 TTA TTA TTA
4735743 AAAAAATAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.09
3 37 0.79
4 6 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:4737009 original size:13 final size:13
Alignment explanation
Indices: 4736993--4737032 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
4736983 ATATAATAAA
4736993 TAAATATTTATTT
1 TAAATATTTATTT
*
4737006 TAAATAAATTATTT
1 TAAAT-ATTTATTT
4737020 T-AATATTTATTT
1 TAAATATTTATTT
4737032 T
1 T
4737033 TCAATATCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 8 0.33
13 8 0.33
14 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAAATATTTATTT
Found at i:4738679 original size:21 final size:19
Alignment explanation
Indices: 4738652--4738698 Score: 76
Period size: 21 Copynumber: 2.4 Consensus size: 19
4738642 GATTGTAATC
4738652 AAAATAAAATAAAATTAAG
1 AAAATAAAATAAAATTAAG
4738671 TATAAATAAAATAAAATTAAG
1 -A-AAATAAAATAAAATTAAG
4738692 AAAATAA
1 AAAATAA
4738699 TTAAGGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.23
20 2 0.08
21 18 0.69
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.23
Consensus pattern (19 bp):
AAAATAAAATAAAATTAAG
Found at i:4739538 original size:13 final size:13
Alignment explanation
Indices: 4739522--4739546 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4739512 AAAAAGAAAA
4739522 TTAAAAGATAATT
1 TTAAAAGATAATT
4739535 TTAAAAGATAAT
1 TTAAAAGATAAT
4739547 CCTAATTCCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
TTAAAAGATAATT
Found at i:4744035 original size:19 final size:19
Alignment explanation
Indices: 4744013--4744052 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
4744003 TCAAAATTTC
* * *
4744013 ATTTTGTTTTTAAAATCAA
1 ATTTTGCTTTCAAAACCAA
4744032 ATTTTGCTTTCAAAACCAA
1 ATTTTGCTTTCAAAACCAA
4744051 AT
1 AT
4744053 CATTTTTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTTTGCTTTCAAAACCAA
Found at i:4747183 original size:2 final size:2
Alignment explanation
Indices: 4747176--4747201 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4747166 CAAATTTTAC
4747176 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4747202 TTTAGAATCA
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):
AT
Found at i:4748504 original size:38 final size:38
Alignment explanation
Indices: 4748453--4748532 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
4748443 CTCACATGTT
4748453 CAACAAACACAACGACGTGAGATACAAGGATACATCCA
1 CAACAAACACAACGACGTGAGATACAAGGATACATCCA
4748491 CAACAAACACAACGACGTGAGATACAAGGATACATCCA
1 CAACAAACACAACGACGTGAGATACAAGGATACATCCA
4748529 CAAC
1 CAAC
4748533 CAACCAAGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.47, C:0.28, G:0.15, T:0.10
Consensus pattern (38 bp):
CAACAAACACAACGACGTGAGATACAAGGATACATCCA
Found at i:4749724 original size:20 final size:19
Alignment explanation
Indices: 4749694--4749746 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
4749684 ACCAAACCTT
*
4749694 TATCTTTTTTTTTAATCCG
1 TATCCTTTTTTTTAATCCG
** **
4749713 TATCCCTTTTTTAAAATTTG
1 TAT-CCTTTTTTTTAATCCG
4749733 TATCCTTTTTTTTA
1 TATCCTTTTTTTTA
4749747 TTTTCGGTGG
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.19, C:0.15, G:0.04, T:0.62
Consensus pattern (19 bp):
TATCCTTTTTTTTAATCCG
Found at i:4750980 original size:10 final size:10
Alignment explanation
Indices: 4750965--4750998 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
4750955 TTCATTTACC
4750965 ATTTATTTTT
1 ATTTATTTTT
4750975 ATTTATTTTT
1 ATTTATTTTT
* *
4750985 ATCTATTTCT
1 ATTTATTTTT
4750995 ATTT
1 ATTT
4750999 TACTAACCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:4761632 original size:105 final size:105
Alignment explanation
Indices: 4761261--4761917 Score: 935
Period size: 105 Copynumber: 6.4 Consensus size: 105
4761251 TTTTACCCAA
* * *
4761261 AGCCGATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCATGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
4761326 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
* *
4761366 AGCCAATTTC-A----AC-ACGAAGGATATTGGACTCTAGACAATGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
*
4761425 AAGGGACCGCTGGTTGTCAACAAACATTTCTCGAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
*
4761465 AG------TCAACTTCACAACGAAGGATATTGGACTCTAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
4761524 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
*
4761564 AACCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* *
4761629 AAGGGACCGCTGGTTGTCAACAACCATTTCTC-AATCCCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT-TCAG
* *
4761669 AGTCAATTTCAACTTCACAACGAAGGATATTTGACTCCAGACAACGCAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
* * *
4761734 AAGGGACCGCTGGTTGTCAATAAATATTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
* * ****
4761774 AGCCAATTTCAACTTCACCACGAAGGATATTGGACTCAAGACAGTATAAGTTCAACTTCACGACG
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
** ** * *
4761839 AAGGGACCGCTGACTGTCAACCGACGACTTCTCAATTTCAG
66 AAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATTCAG
** *
4761880 AGCCAATTTCAACTTCACAGTGAATGATATTGGACTCC
1 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
4761918 GGAACAATAC
Statistics
Matches: 499, Mismatches: 38, Indels: 29
0.88 0.07 0.05
Matches are distributed among these distances:
93 2 0.00
94 1 0.00
98 2 0.00
99 170 0.34
100 2 0.00
104 4 0.01
105 269 0.54
106 49 0.10
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACG
AAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAG
Found at i:4762690 original size:38 final size:38
Alignment explanation
Indices: 4762639--4762718 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
4762629 CTCACATGTT
4762639 CAACAAACACAACGACGTGAGATACAAGGATACATCCA
1 CAACAAACACAACGACGTGAGATACAAGGATACATCCA
4762677 CAACAAACACAACGACGTGAGATACAAGGATACATCCA
1 CAACAAACACAACGACGTGAGATACAAGGATACATCCA
4762715 CAAC
1 CAAC
4762719 CAACCAAGCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.47, C:0.28, G:0.15, T:0.10
Consensus pattern (38 bp):
CAACAAACACAACGACGTGAGATACAAGGATACATCCA
Found at i:4763909 original size:20 final size:19
Alignment explanation
Indices: 4763886--4763933 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
4763876 CCTTTATCTT
4763886 TTTTTTTTAATCCGTATCCC
1 TTTTTTTTAATCCGTAT-CC
** **
4763906 TTTTTTAAAATTTGTATCC
1 TTTTTTTTAATCCGTATCC
4763925 TTTTTTTTA
1 TTTTTTTTA
4763934 TTTTCGGTGG
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.19, C:0.15, G:0.04, T:0.62
Consensus pattern (19 bp):
TTTTTTTTAATCCGTATCC
Found at i:4766438 original size:34 final size:34
Alignment explanation
Indices: 4766398--4766467 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
4766388 GTTTAGATAC
4766398 TAAATGCATAATATACCCTTTTGTTTAAGTTGTG
1 TAAATGCATAATATACCCTTTTGTTTAAGTTGTG
* * *
4766432 TAAATGCGTAATTTTCCCTTTTGTTTAAGTTGTG
1 TAAATGCATAATATACCCTTTTGTTTAAGTTGTG
4766466 TA
1 TA
4766468 TGGTGCTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (34 bp):
TAAATGCATAATATACCCTTTTGTTTAAGTTGTG
Found at i:4767088 original size:29 final size:26
Alignment explanation
Indices: 4767035--4767088 Score: 63
Period size: 29 Copynumber: 2.0 Consensus size: 26
4767025 ATATGACACC
*
4767035 ATTTTCTTCTTAATTTTTCATAATTT
1 ATTTTCTTCTTAATTTTTCAAAATTT
*
4767061 ATTTTCTTCTCTTAAATTTTTGAAAATT
1 ATTTTC-T-TCTT-AATTTTTCAAAATT
4767089 ATTCCCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 6 0.26
27 1 0.04
28 4 0.17
29 12 0.52
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.61
Consensus pattern (26 bp):
ATTTTCTTCTTAATTTTTCAAAATTT
Found at i:4772928 original size:32 final size:32
Alignment explanation
Indices: 4772892--4772955 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
4772882 CAAGCAAATC
4772892 AGCAACAACCATATATGAATTGTAATTTTGTT
1 AGCAACAACCATATATGAATTGTAATTTTGTT
4772924 AGCAACAACCATATATGAATTGTAATTTTGTT
1 AGCAACAACCATATATGAATTGTAATTTTGTT
4772956 GGAAACAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (32 bp):
AGCAACAACCATATATGAATTGTAATTTTGTT
Found at i:4772963 original size:32 final size:32
Alignment explanation
Indices: 4772895--4772963 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
4772885 GCAAATCAGC
*
4772895 AACAACCATATATGAATTGTAATTTTGTTAGC
1 AACAACCATATATGAATTGTAATTTTGTTAGA
*
4772927 AACAACCATATATGAATTGTAATTTTGTTGGA
1 AACAACCATATATGAATTGTAATTTTGTTAGA
4772959 AACAA
1 AACAA
4772964 TGGTGAACTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (32 bp):
AACAACCATATATGAATTGTAATTTTGTTAGA
Found at i:4775230 original size:29 final size:29
Alignment explanation
Indices: 4775196--4775254 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
4775186 CTTAAATTAA
*
4775196 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATAAATTTAGT
4775225 TTTGATGTCATTGCTTACATAAATTTAGT
1 TTTGATGTCATTGCTTACATAAATTTAGT
4775254 T
1 T
4775255 AGGTGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.12, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATAAATTTAGT
Found at i:4781400 original size:21 final size:23
Alignment explanation
Indices: 4781363--4781424 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 23
4781353 ACCAGAACCC
*
4781363 CAGGGGGTAT-TGATTCCC-CT-A
1 CAGGGGGAATCTG-TTCCCACTCA
*
4781384 CAGGGGGAATCTGTTCCCATTCA
1 CAGGGGGAATCTGTTCCCACTCA
* *
4781407 AAGGGGGAATCGGTTCCC
1 CAGGGGGAATCTGTTCCC
4781425 TTATGGGGGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
21 14 0.41
22 3 0.09
23 17 0.50
ACGTcount: A:0.21, C:0.24, G:0.31, T:0.24
Consensus pattern (23 bp):
CAGGGGGAATCTGTTCCCACTCA
Found at i:4791824 original size:21 final size:21
Alignment explanation
Indices: 4791774--4791826 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
4791764 TGGAGTATGG
* *
4791774 GGGGAATCAGTACCCCTTAAT
1 GGGGAATCGGTACCCCCTAAT
*
4791795 GGGGAATCGGTACCCCCTCAT
1 GGGGAATCGGTACCCCCTAAT
4791816 GGGGAATCGGT
1 GGGGAATCGGT
4791827 TCCCTAAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.25, G:0.32, T:0.21
Consensus pattern (21 bp):
GGGGAATCGGTACCCCCTAAT
Found at i:4794535 original size:4 final size:4
Alignment explanation
Indices: 4794526--4794555 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
4794516 CTTTATCTCA
4794526 ATTT ATTT ATTTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT A-TTT ATTT ATTT ATTT ATTT A
4794556 ATCTTTATCT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
ATTT
Found at i:4795064 original size:29 final size:29
Alignment explanation
Indices: 4795027--4795084 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
4795017 CGCTTCGAGA
4795027 AAAAAAGGAAAAAACAAGAAGAGCATAGT
1 AAAAAAGGAAAAAACAAGAAGAGCATAGT
4795056 AAAAAAGGAAAAAACAAGAAGAGCATAGT
1 AAAAAAGGAAAAAACAAGAAGAGCATAGT
4795085 TAATCCTTGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.66, C:0.07, G:0.21, T:0.07
Consensus pattern (29 bp):
AAAAAAGGAAAAAACAAGAAGAGCATAGT
Found at i:4802072 original size:2 final size:2
Alignment explanation
Indices: 4802065--4802131 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
4802055 TTCAAACTAG
4802065 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
4802107 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
4802132 GGTTTGTAGT
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4807107 original size:21 final size:21
Alignment explanation
Indices: 4807074--4807113 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4807064 TTCTACGTGG
*
4807074 TCCTTCGGGACATATATGTAA
1 TCCTTCGGAACATATATGTAA
*
4807095 TCCTTTGGAACATATATGT
1 TCCTTCGGAACATATATGT
4807114 GGTACTTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:4810617 original size:23 final size:23
Alignment explanation
Indices: 4810591--4810651 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
4810581 CTCATATAAA
4810591 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* *
4810614 TGCACC-ATAGTGCCGCGTAGAAT
1 TGCACCGA-AGTGCCACATAGAAT
*
4810637 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
4810652 TATAATAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:4810848 original size:101 final size:98
Alignment explanation
Indices: 4810676--4810867 Score: 321
Period size: 101 Copynumber: 1.9 Consensus size: 98
4810666 TAAGGACATA
* *
4810676 TCCTTAAGAATATACATATACTAGGGATCAAGTATGTGTTCACCAGACTTCACACATGTTCCAAA
1 TCCTTAAGAATATACATATACCAAGGATCAAGTATGTGTTCACCAGACTTCACACATGTTCCAAA
*
4810741 GAATACATATATGTCCGGAAGGACCAATATCAT
66 GAATACATATATGTCCCGAAGGACCAATATCAT
*
4810774 TCCTTAAGAATCATAACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACACATGTTCC
1 TCCTTAAGAAT-AT-ACATATACCAAGGATCAAGTATGTGT-TCACCAGACTTCACACATGTTCC
4810839 AAAGAATACATATATGTCCCGAAGGACCA
63 AAAGAATACATATATGTCCCGAAGGACCA
4810868 CATAAACCCT
Statistics
Matches: 87, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
98 11 0.13
99 2 0.02
100 23 0.26
101 51 0.59
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.26
Consensus pattern (98 bp):
TCCTTAAGAATATACATATACCAAGGATCAAGTATGTGTTCACCAGACTTCACACATGTTCCAAA
GAATACATATATGTCCCGAAGGACCAATATCAT
Found at i:4811951 original size:19 final size:20
Alignment explanation
Indices: 4811914--4811951 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4811904 TCTTTTATAT
4811914 TCATATAATTTATTATCATA
1 TCATATAATTTATTATCATA
*
4811934 TCATATGATTTA-TATCAT
1 TCATATAATTTATTATCAT
4811952 CATAACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.50
Consensus pattern (20 bp):
TCATATAATTTATTATCATA
Found at i:4811960 original size:22 final size:20
Alignment explanation
Indices: 4811915--4811961 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
4811905 CTTTTATATT
*
4811915 CATATAATTTATTATCATAT
1 CATATAATTTATTATCATAA
*
4811935 CATATGATTTATATCATCATAA
1 CATATAATTTAT-T-ATCATAA
4811957 CATAT
1 CATAT
4811962 CACACATTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 11 0.48
21 1 0.04
22 11 0.48
ACGTcount: A:0.40, C:0.13, G:0.02, T:0.45
Consensus pattern (20 bp):
CATATAATTTATTATCATAA
Found at i:4815496 original size:23 final size:23
Alignment explanation
Indices: 4815478--4815530 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
4815468 AATGCATCGA
4815478 AGTGCCACATAGAATTGCACCGT
1 AGTGCCACATAGAATTGCACCGT
* *
4815501 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCACATAGAATTGCACCGT
4815524 AGTGCCA
1 AGTGCCA
4815531 TATAATAATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
AGTGCCACATAGAATTGCACCGT
Found at i:4815729 original size:99 final size:102
Alignment explanation
Indices: 4815532--4815759 Score: 365
Period size: 99 Copynumber: 2.3 Consensus size: 102
4815522 GTAGTGCCAT
** * *
4815532 ATAATA-ATGTCCATAAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAA
1 ATAATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAA
4815596 GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
66 GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
*
4815633 AT-ATATATGTCCCGAAGGACC-CATATCATTCCTTAAGAATCATATACATATGCCAAGGATC-A
1 ATAATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAA
4815695 GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
66 GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
*
4815732 ATACATATATGTGCCGAAGGACCACATA
1 ATA-ATATATGTCCCGAAGGACCACATA
4815760 GACCCTCGAC
Statistics
Matches: 117, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
99 40 0.34
100 40 0.34
101 33 0.28
102 4 0.03
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (102 bp):
ATAATATATGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAA
GTATGTGTCTCACCAGACTTCACACATGTTCCAAAGA
Found at i:4819268 original size:74 final size:74
Alignment explanation
Indices: 4819112--4819272 Score: 218
Period size: 74 Copynumber: 2.2 Consensus size: 74
4819102 GGAGGGGTTG
* * *
4819112 TTGTCCCTTCCAAAATTTTTGGTATAATAGTATCTTAGGTCCTTTTTAGTTTAAATATTAATCAA
1 TTGTCCCTCCCAAAATTTTTGATATAATAGTATCTTAGGTCCTTTCTAGTTTAAATATTAATCAA
*
4819177 ATGAGACTT
66 ATAAGACTT
* * *
4819186 TTGCCCCTCCCAAAATTTTTGATATAATA-TCATTTTAGGTCCTTTCTAGTTTAAATATTACTCA
1 TTGTCCCTCCCAAAATTTTTGATATAATAGT-ATCTTAGGTCCTTTCTAGTTTAAATATTAATCA
*
4819250 AATAAG-GTCT
65 AATAAGACT-T
4819260 TTGTCCCTCCCAA
1 TTGTCCCTCCCAA
4819273 TTTTTAGATT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
73 2 0.03
74 74 0.97
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.42
Consensus pattern (74 bp):
TTGTCCCTCCCAAAATTTTTGATATAATAGTATCTTAGGTCCTTTCTAGTTTAAATATTAATCAA
ATAAGACTT
Found at i:4822426 original size:31 final size:31
Alignment explanation
Indices: 4822388--4822457 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
4822378 AAATTGATTT
4822388 AATTATAGTATTAAACTTTAATTTAGGCTTC
1 AATTATAGTATTAAACTTTAATTTAGGCTTC
4822419 AATTATAGTATTAAACTTTAATTTAGGCTTC
1 AATTATAGTATTAAACTTTAATTTAGGCTTC
4822450 AATTATAG
1 AATTATAG
4822458 CATTGGGTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (31 bp):
AATTATAGTATTAAACTTTAATTTAGGCTTC
Found at i:4825380 original size:32 final size:32
Alignment explanation
Indices: 4825339--4825422 Score: 168
Period size: 32 Copynumber: 2.6 Consensus size: 32
4825329 GATCTTCCTT
4825339 TAGTTTCTCTCGAACACTAAAGATCAATAACA
1 TAGTTTCTCTCGAACACTAAAGATCAATAACA
4825371 TAGTTTCTCTCGAACACTAAAGATCAATAACA
1 TAGTTTCTCTCGAACACTAAAGATCAATAACA
4825403 TAGTTTCTCTCGAACACTAA
1 TAGTTTCTCTCGAACACTAA
4825423 GTAGTATACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.30
Consensus pattern (32 bp):
TAGTTTCTCTCGAACACTAAAGATCAATAACA
Found at i:4827985 original size:27 final size:27
Alignment explanation
Indices: 4827944--4828014 Score: 72
Period size: 27 Copynumber: 2.6 Consensus size: 27
4827934 TTCAATCTTC
* *
4827944 TTATTTCATTACTTTAATTTTCTAT-TT
1 TTATTTCAATCCTTT-ATTTTCTATATT
*
4827971 TTATTTCAATCCTTTATTTTTTATAATT
1 TTATTTCAATCCTTTATTTTCTAT-ATT
*
4827999 TTAATTTCAGTCCTTT
1 TT-ATTTCAATCCTTT
4828015 GATTATTGCA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 8 0.22
27 13 0.35
28 4 0.11
29 12 0.32
ACGTcount: A:0.23, C:0.13, G:0.01, T:0.63
Consensus pattern (27 bp):
TTATTTCAATCCTTTATTTTCTATATT
Found at i:4828302 original size:27 final size:28
Alignment explanation
Indices: 4828249--4828302 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
4828239 TTAATTACTA
4828249 TTATTTTAATTTTCCCTTTAAAATTATG
1 TTATTTTAATTTTCCCTTTAAAATTATG
*
4828277 TTATTTTAATCTTT-GC-TTAAAATTAT
1 TTATTTTAAT-TTTCCCTTTAAAATTAT
4828303 TAATTGATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 10 0.42
28 11 0.46
29 3 0.12
ACGTcount: A:0.30, C:0.09, G:0.04, T:0.57
Consensus pattern (28 bp):
TTATTTTAATTTTCCCTTTAAAATTATG
Found at i:4830914 original size:3 final size:3
Alignment explanation
Indices: 4830906--4830931 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4830896 CATTCATTAA
4830906 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
4830932 GATAAGGTTT
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:4837543 original size:252 final size:252
Alignment explanation
Indices: 4837098--4837601 Score: 1008
Period size: 252 Copynumber: 2.0 Consensus size: 252
4837088 CTTTTTCTCG
4837098 AGGTTCCACTTTAATTATTCGAATTGCAATATTGATAAAAATTAATTTAAGTTAATATTAGAACC
1 AGGTTCCACTTTAATTATTCGAATTGCAATATTGATAAAAATTAATTTAAGTTAATATTAGAACC
4837163 TCCACTTTAGATTAGATTTCAACTTAGTCTCTTTAATTTAGGGAGTAATCTTAGTTGGTCCTCGC
66 TCCACTTTAGATTAGATTTCAACTTAGTCTCTTTAATTTAGGGAGTAATCTTAGTTGGTCCTCGC
4837228 CTAAATGCTCAAAGGACCATATCAATTATTCGATTCAATAACTGGTTAAAATCAAGTATGATTAA
131 CTAAATGCTCAAAGGACCATATCAATTATTCGATTCAATAACTGGTTAAAATCAAGTATGATTAA
4837293 TATTAGAGCCTACATTTTTTAGGTTTATGCCTCTAGGTTATTTAATTTTCATAATTT
196 TATTAGAGCCTACATTTTTTAGGTTTATGCCTCTAGGTTATTTAATTTTCATAATTT
4837350 AGGTTCCACTTTAATTATTCGAATTGCAATATTGATAAAAATTAATTTAAGTTAATATTAGAACC
1 AGGTTCCACTTTAATTATTCGAATTGCAATATTGATAAAAATTAATTTAAGTTAATATTAGAACC
4837415 TCCACTTTAGATTAGATTTCAACTTAGTCTCTTTAATTTAGGGAGTAATCTTAGTTGGTCCTCGC
66 TCCACTTTAGATTAGATTTCAACTTAGTCTCTTTAATTTAGGGAGTAATCTTAGTTGGTCCTCGC
4837480 CTAAATGCTCAAAGGACCATATCAATTATTCGATTCAATAACTGGTTAAAATCAAGTATGATTAA
131 CTAAATGCTCAAAGGACCATATCAATTATTCGATTCAATAACTGGTTAAAATCAAGTATGATTAA
4837545 TATTAGAGCCTACATTTTTTAGGTTTATGCCTCTAGGTTATTTAATTTTCATAATTT
196 TATTAGAGCCTACATTTTTTAGGTTTATGCCTCTAGGTTATTTAATTTTCATAATTT
4837602 GACACTTTAA
Statistics
Matches: 252, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
252 252 1.00
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (252 bp):
AGGTTCCACTTTAATTATTCGAATTGCAATATTGATAAAAATTAATTTAAGTTAATATTAGAACC
TCCACTTTAGATTAGATTTCAACTTAGTCTCTTTAATTTAGGGAGTAATCTTAGTTGGTCCTCGC
CTAAATGCTCAAAGGACCATATCAATTATTCGATTCAATAACTGGTTAAAATCAAGTATGATTAA
TATTAGAGCCTACATTTTTTAGGTTTATGCCTCTAGGTTATTTAATTTTCATAATTT
Found at i:4852771 original size:30 final size:30
Alignment explanation
Indices: 4852707--4852789 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
4852697 GAAGGGCAGA
* * *
4852707 GAAAGAGAAGAAGAGATCGAGAAAGGGAAGGG
1 GAAAGAG-A-AAGAGAGCGAGATAGGGAACGG
* * * *
4852739 GAACGGGATAGAGAGCGAGATATGGAACGG
1 GAAAGAGAAAGAGAGCGAGATAGGGAACGG
*
4852769 GAAAGAGAAAGAGAGAGAGAT
1 GAAAGAGAAAGAGAGCGAGAT
4852790 CGCTTGAGTA
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
30 34 0.85
31 1 0.03
32 5 0.12
ACGTcount: A:0.47, C:0.05, G:0.42, T:0.06
Consensus pattern (30 bp):
GAAAGAGAAAGAGAGCGAGATAGGGAACGG
Found at i:4854048 original size:26 final size:26
Alignment explanation
Indices: 4854019--4854082 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
4854009 GATATTCACA
*
4854019 TAACATGATAACGAAGGACATTTACG
1 TAACATGATAACGAACGACATTTACG
*
4854045 TAACATGATAACGAACGACATTTATG
1 TAACATGATAACGAACGACATTTACG
4854071 TAACATGATAAC
1 TAACATGATAAC
4854083 AAAGTTGACA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.25
Consensus pattern (26 bp):
TAACATGATAACGAACGACATTTACG
Found at i:4859339 original size:2 final size:2
Alignment explanation
Indices: 4859332--4859387 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
4859322 GTGAATATGA
4859332 GT GT GT GT GT GT GT GT GT GT GT GT GT G- GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
4859373 GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT G
4859388 AGAGAGAGAG
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:4859392 original size:2 final size:2
Alignment explanation
Indices: 4859387--4859423 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4859377 GTGTGTGTGT
4859387 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
4859424 TACTTGCAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:4860707 original size:193 final size:195
Alignment explanation
Indices: 4860378--4860767 Score: 766
Period size: 193 Copynumber: 2.0 Consensus size: 195
4860368 AAACCACTTC
4860378 AATATGTATCTAGAATCTTGAAGAGCTGGCCAGATGGGTGATGTGAACATGATTAATGAACTATC
1 AATATGTATCTAGAATCTTGAAGAGCTGGCCAGATGGGTGATGTGAACATGATTAATGAACTATC
4860443 AAGAGAACAAAAAAAGCATATGTATTATAGTATAGTATGGAAGAAATGAGAGAGCATTTCATGCA
66 AAGAGAACAAAAAAAGCATATGTATTATAGTATAGTATGGAAGAAATGAGAGAGCATTTCATGCA
4860508 AG-AAAA-AGAGATGATAGATAAAATAAGGCAGGTGGTATCATCCTATCCTTTGTTGGTTTGTGA
131 AGAAAAATAGAGATGATAGATAAAATAAGGCAGGTGGTATCATCCTATCCTTTGTTGGTTTGTGA
4860571 AATATGTATCTAGAATCTTGAAGAGCTGGCCAGATGGGTGATGTGAACATGATTAATGAACTATC
1 AATATGTATCTAGAATCTTGAAGAGCTGGCCAGATGGGTGATGTGAACATGATTAATGAACTATC
4860636 AAGAGAACAAAAAAAGCATATGTATTATAGTATAGTATGGAAGAAATGAGAGAGCATTTCATGCA
66 AAGAGAACAAAAAAAGCATATGTATTATAGTATAGTATGGAAGAAATGAGAGAGCATTTCATGCA
4860701 AGAAAAATAGAGATGATAGATAAAATAAGGCAGGTGGTATCATCCTATCCTTTGTTGGTTTGTGA
131 AGAAAAATAGAGATGATAGATAAAATAAGGCAGGTGGTATCATCCTATCCTTTGTTGGTTTGTGA
4860766 AA
1 AA
4860768 AATCAAGAGT
Statistics
Matches: 195, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
193 132 0.68
194 4 0.02
195 59 0.30
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (195 bp):
AATATGTATCTAGAATCTTGAAGAGCTGGCCAGATGGGTGATGTGAACATGATTAATGAACTATC
AAGAGAACAAAAAAAGCATATGTATTATAGTATAGTATGGAAGAAATGAGAGAGCATTTCATGCA
AGAAAAATAGAGATGATAGATAAAATAAGGCAGGTGGTATCATCCTATCCTTTGTTGGTTTGTGA
Found at i:4881000 original size:8 final size:7
Alignment explanation
Indices: 4880985--4881021 Score: 51
Period size: 6 Copynumber: 5.4 Consensus size: 7
4880975 TTTTAAAAAA
4880985 TATTATT
1 TATTATT
4880992 TACTTATT
1 TA-TTATT
4881000 TATTA-T
1 TATTATT
4881006 TATTA-T
1 TATTATT
4881012 TATTATT
1 TATTATT
4881019 TAT
1 TAT
4881022 AGGCCCCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 12 0.43
7 9 0.32
8 7 0.25
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (7 bp):
TATTATT
Found at i:4881789 original size:16 final size:16
Alignment explanation
Indices: 4881768--4881806 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
4881758 GAATCCGGTT
**
4881768 GATTGGTTCTCGGCCG
1 GATTGGTTCTCAACCG
4881784 GATTGG-TCTCAACCG
1 GATTGGTTCTCAACCG
4881799 GATTGGTT
1 GATTGGTT
4881807 GATGAGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.13, C:0.21, G:0.33, T:0.33
Consensus pattern (16 bp):
GATTGGTTCTCAACCG
Found at i:4883340 original size:21 final size:21
Alignment explanation
Indices: 4883303--4883342 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4883293 CACTGACTCT
*
4883303 TTTTATTTTTGTTATCTTTTA
1 TTTTATTTTTGTCATCTTTTA
4883324 TTTTATTTTT-TGCATCTTT
1 TTTTATTTTTGT-CATCTTT
4883343 CATTCAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.12, C:0.07, G:0.05, T:0.75
Consensus pattern (21 bp):
TTTTATTTTTGTCATCTTTTA
Found at i:4884974 original size:99 final size:99
Alignment explanation
Indices: 4884859--4885049 Score: 267
Period size: 99 Copynumber: 1.9 Consensus size: 99
4884849 TTATAATATT
* * *
4884859 ATATATATACAATAAAGCTTGAACTGTCCCTCT-AGAGCAATTGATTAAACGCCCTGGCTTTATG
1 ATATATATACAATAAAGCTTGAACTGTCCATCTAAG-GCAATTGATTAAACACCCCGGCTTTATG
** *
4884923 GATAAGATTTGGCTAGCCTGATAAAGGTTATTATA
65 GATAAGATTCAGCTAACCTGATAAAGGTTATTATA
* ** *
4884958 ATATTTATACAATAAAGCTTGAGTTGTCCATCTAAGGCAATTGGTTAAACACCCCGGCTTTATGG
1 ATATATATACAATAAAGCTTGAACTGTCCATCTAAGGCAATTGATTAAACACCCCGGCTTTATGG
*
4885023 ATAAGATTCAGCTAACCTTATAAAGGT
66 ATAAGATTCAGCTAACCTGATAAAGGT
4885050 ATTTATATAT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
99 78 0.98
100 2 0.03
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (99 bp):
ATATATATACAATAAAGCTTGAACTGTCCATCTAAGGCAATTGATTAAACACCCCGGCTTTATGG
ATAAGATTCAGCTAACCTGATAAAGGTTATTATA
Found at i:4886569 original size:125 final size:124
Alignment explanation
Indices: 4886344--4886799 Score: 657
Period size: 124 Copynumber: 3.7 Consensus size: 124
4886334 ACATGCAAGC
* * * *
4886344 TTGGA-TTCAACTTCACGACGAAGGACATTCAAGT-AAGGCTCAACTTCATAACGAATGGGCCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
* *
4886407 CCATGGTTTCAACTTCACGACGAAGGGAATCATGCTCACCAGCAACATTCATCTTTAGA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTTAGA
* * * * *
4886466 TTGAATTTCAACTTAACGATGAAGGATATCCAATTTAAGGCTCAACTTCACAACGAAAGGGACCA
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGG-CCA
* * *
4886531 TCCACGGTTTCAACTTCATGACGAAGGGAATCGTGCTCACTAGCAATATTCATCTTTAGA
65 TCCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTTAGA
* * *
4886591 TTGGATTTCAACTTCACGACAAATGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
*
4886656 GCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATC-TTAGGA
66 CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTTA-GA
* * *
4886715 TTGGATTTCAACTTCACGACGAAGTATATCTAATTCAAGGCTCAACTTCACAACGAATGGGTCAT
1 TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
* * *
4886780 TCACGATTTGAACTTCACGA
66 CCACGGTTTCAACTTCACGA
4886800 AGGAGGATAT
Statistics
Matches: 298, Mismatches: 32, Indels: 6
0.89 0.10 0.02
Matches are distributed among these distances:
122 4 0.01
123 27 0.09
124 155 0.52
125 112 0.38
ACGTcount: A:0.32, C:0.23, G:0.18, T:0.26
Consensus pattern (124 bp):
TTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAGGCTCAACTTCACAACGAATGGGCCAT
CCACGGTTTCAACTTCACGACGAAGGGAATCGTGCTCACCAGCAACATTCATCTTTAGA
Found at i:4887047 original size:3 final size:3
Alignment explanation
Indices: 4887041--4887066 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4887031 TAATATTTAT
4887041 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
4887067 TATTTTTTAT
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:4892202 original size:21 final size:21
Alignment explanation
Indices: 4892176--4892220 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4892166 GATTTCTGGG
* *
4892176 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4892197 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4892218 CAA
1 CAA
4892221 ACGACAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4892826 original size:18 final size:18
Alignment explanation
Indices: 4892803--4892837 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4892793 CTAGGAGATT
4892803 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
4892821 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
4892838 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:4893604 original size:30 final size:30
Alignment explanation
Indices: 4893556--4893612 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
4893546 CGTGTAAGTG
*
4893556 AACTACGTGACTATGTGATCATATGAAAAGA
1 AACTACGTGACTAAGTGAT-ATATGAAAAGA
* *
4893587 AACTATGTGA-TAAGTGATATGTGAAA
1 AACTACGTGACTAAGTGATATATGAAA
4893613 GTGAATTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 7 0.30
30 7 0.30
31 9 0.39
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (30 bp):
AACTACGTGACTAAGTGATATATGAAAAGA
Found at i:4893897 original size:149 final size:149
Alignment explanation
Indices: 4893717--4894020 Score: 590
Period size: 149 Copynumber: 2.0 Consensus size: 149
4893707 GAGTCGAGGG
4893717 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
4893782 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
*
4893847 TATGGCACTACGGTGCACT
131 TATGGCACTACGGTGCAAT
4893866 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
4893931 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
4893996 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
4894015 TCTACG
1 TCTACG
4894021 GGGCACTTCG
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 153 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:4894043 original size:23 final size:23
Alignment explanation
Indices: 4893999--4894043 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4893989 ATCATTATAT
*
4893999 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
4894022 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
4894044 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:4897326 original size:21 final size:21
Alignment explanation
Indices: 4897300--4897344 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
4897290 GATTTCTGGG
* *
4897300 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
4897321 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
4897342 CAA
1 CAA
4897345 ACGACAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:4897950 original size:18 final size:18
Alignment explanation
Indices: 4897927--4897961 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4897917 CTAGGAGATT
4897927 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
4897945 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
4897962 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:4898731 original size:30 final size:30
Alignment explanation
Indices: 4898683--4898739 Score: 71
Period size: 31 Copynumber: 1.9 Consensus size: 30
4898673 CGTGTAAGTG
*
4898683 AACTACGTGACTATGTGATCATATGAAAAGA
1 AACTACGTGACTAAGTGAT-ATATGAAAAGA
* *
4898714 AACTATGTGA-TAAGTGATATGTGAAA
1 AACTACGTGACTAAGTGATATATGAAA
4898740 GTGAATTACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 7 0.30
30 7 0.30
31 9 0.39
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (30 bp):
AACTACGTGACTAAGTGATATATGAAAAGA
Found at i:4899024 original size:149 final size:149
Alignment explanation
Indices: 4898844--4899147 Score: 581
Period size: 149 Copynumber: 2.0 Consensus size: 149
4898834 GAGTCGAGGG
4898844 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
*
4898909 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
*
4898974 TATGGCACTACGGTGCACT
131 TATGGCACTACGGTGCAAT
*
4898993 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACGCAT
1 TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
4899058 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
4899123 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
4899142 TCTACG
1 TCTACG
4899148 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.35
Consensus pattern (149 bp):
TCTACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACAT
ACTTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:4899170 original size:23 final size:23
Alignment explanation
Indices: 4899126--4899170 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4899116 ATCATTATAT
*
4899126 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
4899149 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
4899171 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:4906091 original size:18 final size:19
Alignment explanation
Indices: 4906056--4906092 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
4906046 CACGGAATGT
4906056 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
4906076 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
4906093 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:4906314 original size:36 final size:36
Alignment explanation
Indices: 4906243--4906315 Score: 96
Period size: 36 Copynumber: 2.0 Consensus size: 36
4906233 GTTGAAAAAT
* *
4906243 ATTTATATATTTTCTTTAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
4906279 ATTTATATACTTTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATATA-TTTTCTTTA-AAAATTGAAAATCATAAA
4906315 A
1 A
4906316 AGTTTTAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 19 0.58
37 14 0.42
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.47
Consensus pattern (36 bp):
ATTTATATATTTTCTTTAAAAATTGAAAATCATAAA
Found at i:4908086 original size:29 final size:28
Alignment explanation
Indices: 4908033--4908092 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
4908023 TAAAGTTATC
*
4908033 TTTTTTGTCAATATAGGTAACTAAAATAT
1 TTTTTTGTCAAAATAGGTAACTAAAAT-T
*
4908062 TTTTTTGTCAAAATAGGT-GCTTAAAATT
1 TTTTTTGTCAAAATAGGTAAC-TAAAATT
4908090 TTT
1 TTT
4908093 AATTTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 5 0.18
29 23 0.82
ACGTcount: A:0.33, C:0.07, G:0.12, T:0.48
Consensus pattern (28 bp):
TTTTTTGTCAAAATAGGTAACTAAAATT
Found at i:4911186 original size:15 final size:16
Alignment explanation
Indices: 4911168--4911205 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
4911158 ATTAGATATA
4911168 AATAAATATTTC-TTG
1 AATAAATATTTCATTG
4911183 AATAAA-ATTTCATTG
1 AATAAATATTTCATTG
4911198 AGATAAAT
1 A-ATAAAT
4911206 TCATCGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.25
15 10 0.50
16 5 0.25
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.39
Consensus pattern (16 bp):
AATAAATATTTCATTG
Found at i:4914778 original size:21 final size:21
Alignment explanation
Indices: 4914749--4914795 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
4914739 ATTCTGACTA
4914749 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
4914770 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
4914791 TCGCA
1 TCGCA
4914796 ACGCGATTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:4914819 original size:20 final size:20
Alignment explanation
Indices: 4914791--4914878 Score: 115
Period size: 20 Copynumber: 4.4 Consensus size: 20
4914781 TTTTCCTAAT
*
4914791 TCGCAACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
* *
4914811 TCGCCACGCGATTACGTAAA
1 TCGCAACGCGAATACGTAAA
* *
4914831 TCGCCACGCAAATACGTAAA
1 TCGCAACGCGAATACGTAAA
4914851 TCGCAACGCGAAT-CTGTAAA
1 TCGCAACGCGAATAC-GTAAA
4914871 TCGCAACG
1 TCGCAACG
4914879 AGATTCTGAC
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
19 1 0.02
20 61 0.98
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.18
Consensus pattern (20 bp):
TCGCAACGCGAATACGTAAA
Found at i:4915776 original size:23 final size:24
Alignment explanation
Indices: 4915738--4915790 Score: 81
Period size: 23 Copynumber: 2.2 Consensus size: 24
4915728 GTATTCGAAA
4915738 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
4915762 TTTGATC-TGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
4915785 TTTGAT
1 TTTGAT
4915791 GATTTTTCAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 20 0.74
24 7 0.26
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.40
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:4918139 original size:20 final size:20
Alignment explanation
Indices: 4918114--4918207 Score: 109
Period size: 20 Copynumber: 4.7 Consensus size: 20
4918104 GACATTCATT
*
4918114 TGACTATCACAACGC-GAATA
1 TGACTATCGCAACGCGGAA-A
*
4918134 TGACTATCGCAACACGGAAA
1 TGACTATCGCAACGCGGAAA
* * * *
4918154 TTACTATCGCAATGTGGAAT
1 TGACTATCGCAACGCGGAAA
4918174 TGACTATCGCAACGCGGAAA
1 TGACTATCGCAACGCGGAAA
*
4918194 TGACTATCGTAACG
1 TGACTATCGCAACG
4918208 AGAGAATCGC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 58 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGGAAA
Found at i:4918229 original size:33 final size:33
Alignment explanation
Indices: 4918179--4918274 Score: 120
Period size: 33 Copynumber: 2.8 Consensus size: 33
4918169 GGAATTGACT
* ** *
4918179 ATCGCAACGCGGAAATGACTATCGTAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
4918213 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
4918246 ATCACAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
4918275 CAAAATTAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 29 0.53
34 26 0.47
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:4918346 original size:33 final size:33
Alignment explanation
Indices: 4918289--4918384 Score: 138
Period size: 33 Copynumber: 2.8 Consensus size: 33
4918279 ATTAGTTTCG
4918289 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
4918323 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
** *
4918356 CGTTGCGATAGTCATTTCTGCGTTGCGAT
1 CGTTGCGATTTTCATTTC-GCATTGCGAT
4918385 AGTCTGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
33 34 0.60
34 23 0.40
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:4918505 original size:14 final size:14
Alignment explanation
Indices: 4918486--4918522 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
4918476 CATCAATTAA
4918486 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
4918500 ACAAATCATCTTTT
1 ACAAATCAACATTT
4918514 ACAAATCAA
1 ACAAATCAA
4918523 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:4918659 original size:81 final size:83
Alignment explanation
Indices: 4918533--4918700 Score: 288
Period size: 81 Copynumber: 2.0 Consensus size: 83
4918523 TTAAACAATC
4918533 AAAAATAATAATGAATCAACTTTTGCACCAATACATCTATTTCA-C-GCTCACTTCAGGATTAAC
1 AAAAATAATAATGAATCAACTTTTGCACCAATACATCTATTTCACCAGCTCACTTCAGGATTAAC
4918596 CTGC-AAACCAAACATTG
66 CTGCAAAACCAAACATTG
4918613 AAAAATAATAATGAAATCAACTTTTGCACCAATACATCTATTTCACGCAGCTCACTTCAGGATTA
1 AAAAATAATAATG-AATCAACTTTTGCACCAATACATCTATTTCAC-CAGCTCACTTCAGGATTA
4918678 ACCTGCAGAAACCAAACATTG
64 ACCTGCA-AAACCAAACATTG
4918699 AA
1 AA
4918701 TCAACAACAC
Statistics
Matches: 82, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
80 13 0.16
81 31 0.38
83 1 0.01
84 22 0.27
86 15 0.18
ACGTcount: A:0.41, C:0.23, G:0.10, T:0.26
Consensus pattern (83 bp):
AAAAATAATAATGAATCAACTTTTGCACCAATACATCTATTTCACCAGCTCACTTCAGGATTAAC
CTGCAAAACCAAACATTG
Found at i:4920563 original size:20 final size:20
Alignment explanation
Indices: 4920549--4920679 Score: 123
Period size: 20 Copynumber: 6.9 Consensus size: 20
4920539 AATCGCAACA
4920549 CGAAAATGACTATCGCAATG
1 CGAAAATGACTATCGCAATG
* *
4920569 TGAAAATGACTATCACAATG
1 CGAAAATGACTATCGCAATG
**
4920589 CGAATTTGACTATCGCAA--
1 CGAAAATGACTATCGCAATG
*
4920607 CG-AGA-GA--ATCGCAATG
1 CGAAAATGACTATCGCAATG
** *
4920623 CG-AAATGAAAATCGCAACG
1 CGAAAATGACTATCGCAATG
4920642 CGAAAATGACTATCGCAATG
1 CGAAAATGACTATCGCAATG
**
4920662 CGAATTTGACTATCGCAA
1 CGAAAATGACTATCGCAA
4920680 CGAGAGAATC
Statistics
Matches: 90, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
17 3 0.03
18 2 0.02
19 10 0.11
20 62 0.69
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
CGAAAATGACTATCGCAATG
Found at i:4920711 original size:73 final size:73
Alignment explanation
Indices: 4920560--4920698 Score: 251
Period size: 73 Copynumber: 1.9 Consensus size: 73
4920550 GAAAATGACT
* *
4920560 ATCGCAATGTGAAAATGACTATCACAATGCGAATTTGACTATCGCAACGAGAGAATCGCAATGCG
1 ATCGCAACGCGAAAATGACTATCACAATGCGAATTTGACTATCGCAACGAGAGAATCGCAATGCG
4920625 AAATGAAA
66 AAATGAAA
*
4920633 ATCGCAACGCGAAAATGACTATCGCAATGCGAATTTGACTATCGCAACGAGAGAATCGCAATGCG
1 ATCGCAACGCGAAAATGACTATCACAATGCGAATTTGACTATCGCAACGAGAGAATCGCAATGCG
4920698 A
66 A
4920699 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
73 63 1.00
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (73 bp):
ATCGCAACGCGAAAATGACTATCACAATGCGAATTTGACTATCGCAACGAGAGAATCGCAATGCG
AAATGAAA
Found at i:4920755 original size:20 final size:20
Alignment explanation
Indices: 4920726--4920866 Score: 177
Period size: 20 Copynumber: 7.3 Consensus size: 20
4920716 GATTCTTTTG
**
4920726 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
4920746 TTGTGATAGTCATTTTTGCA
1 TTGCGATAGTCATTTTCGCA
4920766 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
4920786 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
4920806 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
* *
4920820 TTGCGATAGTCATTTTTGCG
1 TTGCGATAGTCATTTTCGCA
4920840 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
4920860 TTGCGAT
1 TTGCGAT
4920867 CGTAAACTAT
Statistics
Matches: 104, Mismatches: 11, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
14 7 0.07
16 6 0.06
18 5 0.05
20 86 0.83
ACGTcount: A:0.19, C:0.18, G:0.21, T:0.41
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:4920774 original size:40 final size:40
Alignment explanation
Indices: 4920705--4920866 Score: 186
Period size: 40 Copynumber: 4.3 Consensus size: 40
4920695 GCGATTTTCA
*
4920705 TTTCGCATTGCGAT--TC--TTTTG--TTGCGATAGTCAA
1 TTTCGCATTGCGATAGTCATTTTTGCATTGCGATAGTCAT
* *
4920739 ATTCGCATTGTGATAGTCATTTTTGCATTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCATTTTTGCATTGCGATAGTCAT
*
4920779 TTTCGCATTGCGATAGTCATTTTCGCATTGCGAT--TC--
1 TTTCGCATTGCGATAGTCATTTTTGCATTGCGATAGTCAT
* *
4920815 TCTCG--TTGCGATAGTCATTTTTGCGTTGCGATAGTCAT
1 TTTCGCATTGCGATAGTCATTTTTGCATTGCGATAGTCAT
4920853 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
4920867 CGTAAACTAT
Statistics
Matches: 106, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
34 37 0.35
36 8 0.08
38 11 0.10
40 50 0.47
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.43
Consensus pattern (40 bp):
TTTCGCATTGCGATAGTCATTTTTGCATTGCGATAGTCAT
Found at i:4922789 original size:20 final size:20
Alignment explanation
Indices: 4922744--4922831 Score: 86
Period size: 20 Copynumber: 4.4 Consensus size: 20
4922734 GAAACTTTAA
**
4922744 ATCGCAACACGAAAATGAAA
1 ATCGCAACACGAAAATGATT
* *
4922764 ACCGCAACACGAAAATGACT
1 ATCGCAACACGAAAATGATT
* **
4922784 ATCGCAACGCGAATTTGATT
1 ATCGCAACACGAAAATGATT
* **
4922804 ATCGCAACGCGAATTTGATT
1 ATCGCAACACGAAAATGATT
4922824 ATCGCAAC
1 ATCGCAAC
4922832 GCAAGAATCG
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.40, C:0.24, G:0.17, T:0.19
Consensus pattern (20 bp):
ATCGCAACACGAAAATGATT
Found at i:4922832 original size:20 final size:20
Alignment explanation
Indices: 4922783--4922833 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
4922773 CGAAAATGAC
4922783 TATCGCAACGCGAATTTGAT
1 TATCGCAACGCGAATTTGAT
4922803 TATCGCAACGCGAATTTGAT
1 TATCGCAACGCGAATTTGAT
4922823 TATCGCAACGC
1 TATCGCAACGC
4922834 AAGAATCGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (20 bp):
TATCGCAACGCGAATTTGAT
Found at i:4922902 original size:20 final size:20
Alignment explanation
Indices: 4922877--4922923 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
4922867 GATTCTCTCG
4922877 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
4922897 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
4922917 TTGCGAT
1 TTGCGAT
4922924 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:4923575 original size:20 final size:20
Alignment explanation
Indices: 4923503--4923563 Score: 122
Period size: 20 Copynumber: 3.0 Consensus size: 20
4923493 CGATAGTCAG
4923503 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
4923523 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
4923543 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
4923563 A
1 A
4923564 ATCACGTTGC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:4923598 original size:21 final size:21
Alignment explanation
Indices: 4923572--4923679 Score: 76
Period size: 21 Copynumber: 5.2 Consensus size: 21
4923562 TAATCACGTT
4923572 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * * ***
4923593 GTGAATTTGGGAAATCGCGTT
1 GCGAATTAGGAAAATCGCAAC
* * **
4923614 GC-AATTTACG-TAATCGCATT
1 GCGAA-TTAGGAAAATCGCAAC
4923634 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
4923655 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
4923676 GCGA
1 GCGA
4923680 TAGTCAGATT
Statistics
Matches: 66, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
20 16 0.24
21 50 0.76
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.23
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:4923625 original size:62 final size:62
Alignment explanation
Indices: 4923545--4923673 Score: 213
Period size: 62 Copynumber: 2.1 Consensus size: 62
4923535 ATTTACGTAT
* * *
4923545 TCGCATTGCGATTTACGTAATCACGTTGCGAATTAGGAAAATCGCAACGTGAATTTGGGAAA
1 TCGCATTGCAATTTACGTAATCACATTGCGAATTAGGAAAATCGCAACGCGAATTTGGGAAA
* *
4923607 TCGCGTTGCAATTTACGTAATCGCATTGCGAATTAGGAAAATCGCAACGCGAATTTGGGAAA
1 TCGCATTGCAATTTACGTAATCACATTGCGAATTAGGAAAATCGCAACGCGAATTTGGGAAA
4923669 TCGCA
1 TCGCA
4923674 ATGCGATAGT
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 61 1.00
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (62 bp):
TCGCATTGCAATTTACGTAATCACATTGCGAATTAGGAAAATCGCAACGCGAATTTGGGAAA
Found at i:4935147 original size:32 final size:32
Alignment explanation
Indices: 4935084--4935144 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
4935074 TTGTTGAATG
*
4935084 ATTACAAAATGGTCATTAAATCTTATCAAATT
1 ATTACAAAATGGTCACTAAATCTTATCAAATT
* *
4935116 ATTATAAAATTGTCACTAAAT-TTATCAAA
1 ATTACAAAATGGTCACTAAATCTTATCAAA
4935145 ATTTTGTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 8 0.31
32 18 0.69
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.38
Consensus pattern (32 bp):
ATTACAAAATGGTCACTAAATCTTATCAAATT
Found at i:4942837 original size:27 final size:28
Alignment explanation
Indices: 4942807--4942865 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
4942797 AGAACAAAAT
* *
4942807 ATAAACCATATGATAATGAATTATG-AG
1 ATAAACCACATGATAATGAACTATGTAG
** *
4942834 ATAAATTACATGATCATGAACTATGTAG
1 ATAAACCACATGATAATGAACTATGTAG
4942862 ATAA
1 ATAA
4942866 CAATGATTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 20 0.77
28 6 0.23
ACGTcount: A:0.47, C:0.08, G:0.14, T:0.31
Consensus pattern (28 bp):
ATAAACCACATGATAATGAACTATGTAG
Found at i:4943863 original size:21 final size:21
Alignment explanation
Indices: 4943837--4943879 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
4943827 TCGAGGGTTC
*
4943837 TATGTGGTCATTCGGGACAAA
1 TATGTGGTCATTCAGGACAAA
*
4943858 TATGTGGTCCTTCAGGACAAA
1 TATGTGGTCATTCAGGACAAA
4943879 T
1 T
4943880 TCTATGTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (21 bp):
TATGTGGTCATTCAGGACAAA
Found at i:4945163 original size:19 final size:18
Alignment explanation
Indices: 4945129--4945168 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
4945119 CTTTCAAAAA
4945129 TTTAAAATTATTATATAT
1 TTTAAAATTATTATATAT
*
4945147 TTTAAAATATTTTATATAT
1 TTTAAAAT-TATTATATAT
4945166 TTT
1 TTT
4945169 TTATTAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAAAATTATTATATAT
Found at i:4946863 original size:16 final size:17
Alignment explanation
Indices: 4946842--4946893 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
4946832 TTTTTAATTT
4946842 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
4946858 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
4946873 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
4946890 AATT
1 AATT
4946894 TTTTATTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:4950240 original size:80 final size:80
Alignment explanation
Indices: 4950080--4950244 Score: 235
Period size: 80 Copynumber: 2.1 Consensus size: 80
4950070 AATATGATCT
*
4950080 ATATTATTTATTCGAGTTTTGCACGTCCTTTTCATAATTTAATATGATTTATATTTATATTTATT
1 ATATTATTTATTCGAGTTTTGCACGTCCTTTTCATAATTTAATATGATTTATATTTATATTCATT
**
4950145 TATATTAAATCAAAA
66 TATAGCAAATCAAAA
* *
4950160 ATATTATTTATTCGAGTTTTGCACGTCCTTTTCATATTTTAATGTGATTTATATTTAT-TTACAT
1 ATATTATTTATTCGAGTTTTGCACGTCCTTTTCATAATTTAATATGATTTATATTTATATT-CAT
* *
4950224 TCTA-GGCAAATTAAAA
65 T-TATAGCAAATCAAAA
4950240 ATATT
1 ATATT
4950245 TAACCACTTT
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
79 2 0.03
80 72 0.95
81 2 0.03
ACGTcount: A:0.32, C:0.10, G:0.08, T:0.50
Consensus pattern (80 bp):
ATATTATTTATTCGAGTTTTGCACGTCCTTTTCATAATTTAATATGATTTATATTTATATTCATT
TATAGCAAATCAAAA
Found at i:4957848 original size:21 final size:21
Alignment explanation
Indices: 4957792--4957851 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
4957782 TTTGGTTTAG
* *
4957792 TCGACTATCGTAATACGAACT
1 TCGACTATCGCAATGCGAACT
4957813 TCGACTATCGCAATGCGAACT
1 TCGACTATCGCAATGCGAACT
*
4957834 TGGACTATCGCAATGCGA
1 TCGACTATCGCAATGCGA
4957852 TAGTCGAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (21 bp):
TCGACTATCGCAATGCGAACT
Found at i:4957969 original size:20 final size:19
Alignment explanation
Indices: 4957923--4957971 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 19
4957913 GATAGTCGAC
4957923 TATCGCATTGCGATTTACA
1 TATCGCATTGCGATTTACA
4957942 TATCGCATTGCGATTTACA
1 TATCGCATTGCGATTTACA
4957961 TATTCGCATTG
1 TA-TCGCATTG
4957972 TGATAGTCCA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 21 0.72
20 8 0.28
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.39
Consensus pattern (19 bp):
TATCGCATTGCGATTTACA
Found at i:4958010 original size:21 final size:21
Alignment explanation
Indices: 4957841--4958003 Score: 176
Period size: 21 Copynumber: 7.9 Consensus size: 21
4957831 ACTTGGACTA
* *
4957841 TCGCAATGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
4957862 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
4957883 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
4957904 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
4957924 ATCGCATTGCGAT-TTAC-A-T
1 -TCGCATTGCGATAGTCCAAGT
* *
4957943 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
*
4957964 TCGCATTGTGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
4957985 TCGCATTGCGATAGTCCAA
1 TCGCATTGCGATAGTCCAA
4958004 AATCGCAATG
Statistics
Matches: 127, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
19 18 0.14
20 17 0.13
21 92 0.72
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:4958230 original size:42 final size:42
Alignment explanation
Indices: 4958171--4958427 Score: 451
Period size: 42 Copynumber: 6.1 Consensus size: 42
4958161 CGTTGCGATT
*
4958171 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
4958213 TTGGACTATCGCAACGAATTTGGAATAAATCACAACTCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
4958255 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
4958297 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
4958339 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
* *
4958381 TTCGACTATCGCAACGAATTTGGAATAAATCACAACGCGAAC
1 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
4958423 TTGGA
1 TTGGA
4958428 ATAAATCACA
Statistics
Matches: 203, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 203 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
Found at i:4958440 original size:65 final size:65
Alignment explanation
Indices: 4958199--4958489 Score: 300
Period size: 65 Copynumber: 4.6 Consensus size: 65
4958189 CTTGGAATAA
* * *
4958199 ATCGCAACGCGAACTTGGACT--ATCGCAA--CGAATTTGGAATAAATCACAACTCGAACTTCGA
1 ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCACAACGCGAACTTCGA
4958260 CT
64 CT
* * * * *
4958262 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT--ATCGCAA--CGAATTTGGAAT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCACAACGCGAACTTCGACT
* * *
4958323 AAATCGCAACGCGAACTTGGACT--ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTC
1 --ATCGCAA--CGAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCACAACGCGAACTTC
4958384 GACT
62 GACT
* * * *
4958388 ATCGCAACGAATTTGGAATAAATCACAACGCGAACTTGGAATAAATCACAACGCAAACTTGGACT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCACAACGCGAACTTCGACT
*
4958453 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTT
4958490 CGACTATCGC
Statistics
Matches: 191, Mismatches: 21, Indels: 30
0.79 0.09 0.12
Matches are distributed among these distances:
61 40 0.21
63 54 0.28
65 97 0.51
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (65 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGAATAAATCACAACGCGAACTTCGACT
Found at i:4958440 original size:107 final size:107
Alignment explanation
Indices: 4958174--4958534 Score: 413
Period size: 107 Copynumber: 3.4 Consensus size: 107
4958164 TGCGATTTTG
* * * *
4958174 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACT--ATCGCAACG--AATTTG
1 GACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTGGAATAAATCACAACGCAAACTTG
* * * * * *
4958235 GAATAAATCACAACTCGAACTTCGACT--ATCGCAA--CGAACTTG
66 GACT--ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTC
* * * * * *
4958277 GAATAAATCGCAACGCGAACTTGGACT--ATCGCAA--CGAATTTGGAATAAATCGCAACGCGAA
1 GACT--ATCGCAA--CGAACTTGGAATAAATCACAACGCGAACTTGGAATAAATCACAACGCAAA
4958338 CTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
62 CTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
4958384 GACTATCGCAACGAATTTGGAATAAATCACAACGCGAACTTGGAATAAATCACAACGCAAACTTG
1 GACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTGGAATAAATCACAACGCAAACTTG
4958449 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
66 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
4958491 GACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTGGA
1 GACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTGGA
4958535 CTATCGCAAT
Statistics
Matches: 223, Mismatches: 19, Indels: 28
0.83 0.07 0.10
Matches are distributed among these distances:
103 32 0.14
105 49 0.22
107 142 0.64
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (107 bp):
GACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTGGAATAAATCACAACGCAAACTTG
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:4958440 original size:149 final size:149
Alignment explanation
Indices: 4958269--4958543 Score: 496
Period size: 149 Copynumber: 1.8 Consensus size: 149
4958259 ACTATCGCAA
* *
4958269 CGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACG
1 CGAACTTGGAATAAATCACAACGCAAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACG
* * *
4958334 CGAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAA
66 CGAACTTCGACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAA
4958399 TTTGGAATAAATCACAACG
131 TTTGGAATAAATCACAACG
4958418 CGAACTTGGAATAAATCACAACGCAAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACG
1 CGAACTTGGAATAAATCACAACGCAAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACG
*
4958483 CGAACTTCGACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTGGACTATCGCAA
66 CGAACTTCGACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTCGACTATCGCAA
4958544 TGCGAATATG
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
149 120 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (149 bp):
CGAACTTGGAATAAATCACAACGCAAACTTGGACTATCGCAACGAATTTGGAATAAATCGCAACG
CGAACTTCGACTATCGCAACGAACTTGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAA
TTTGGAATAAATCACAACG
Found at i:4958469 original size:126 final size:124
Alignment explanation
Indices: 4958171--4958469 Score: 413
Period size: 126 Copynumber: 2.4 Consensus size: 124
4958161 CGTTGCGATT
* *
4958171 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGG
1 TTGGAATATCACAACGAACTTGGAAT-AATCGCAAC-CGAACTTGGACTATCGCAACGAATTTGG
* *
4958236 AATAAATCACAACTCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
64 AATAAATCACAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCACAACGCGAAC
* * *
4958297 TTGGACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGG
1 TTGGAATATCACAACGAACTTGGAAT-AATCGCAAC-CGAACTTGGACTATCGCAACGAATTTGG
* *
4958362 AATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCACAACGCGAAC
64 AATAAATCACAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCACAACGCGAAC
* *
4958423 TTGGAATAAATCACAACGCAAACTTGGACT-ATCGCAA-CGAATTTGGA
1 TTGGAAT--ATCACAACG--AACTTGGAATAATCGCAACCGAACTTGGA
4958470 ATAAATCGCA
Statistics
Matches: 159, Mismatches: 10, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
126 136 0.86
128 15 0.09
130 8 0.05
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (124 bp):
TTGGAATATCACAACGAACTTGGAATAATCGCAACCGAACTTGGACTATCGCAACGAATTTGGAA
TAAATCACAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCACAACGCGAAC
Found at i:4958474 original size:42 final size:42
Alignment explanation
Indices: 4958418--4958543 Score: 216
Period size: 42 Copynumber: 3.0 Consensus size: 42
4958408 AATCACAACG
*
4958418 CGAACTTGGAATAAATCACAACGCAAACTTGGACTATCGCAA
1 CGAACTTGGAATAAATCACAACGCGAACTTGGACTATCGCAA
* * *
4958460 CGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAA
1 CGAACTTGGAATAAATCACAACGCGAACTTGGACTATCGCAA
4958502 CGAACTTGGAATAAATCACAACGCGAACTTGGACTATCGCAA
1 CGAACTTGGAATAAATCACAACGCGAACTTGGACTATCGCAA
4958544 TGCGAATATG
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 77 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (42 bp):
CGAACTTGGAATAAATCACAACGCGAACTTGGACTATCGCAA
Found at i:4963418 original size:2 final size:2
Alignment explanation
Indices: 4963411--4963450 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
4963401 AATATTTCGA
*
4963411 AT AT AT AT AT AT AT -T TT AT AT AT -T AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4963450 A
1 A
4963451 GTTTTGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:4963464 original size:37 final size:37
Alignment explanation
Indices: 4963434--4963703 Score: 271
Period size: 38 Copynumber: 7.1 Consensus size: 37
4963424 TTTTATATAT
4963434 TATATATATATATTATAG-TTTTGAAAAT-TTTTAAAAA
1 TATATATA-ATA-TATAGTTTTTGAAAATATTTTAAAAA
* *
4963471 CATATATAATATATAGTTTTTGAAAATGCTTTTAAAAA
1 TATATATAATATATAGTTTTTGAAAAT-ATTTTAAAAA
*
4963509 TATATATAATATATAGTTTTTGAAAATATTTTGAAAA
1 TATATATAATATATAGTTTTTGAAAATATTTTAAAAA
*
4963546 TATATATAATATATAGTTTCTTAAAAATATTTTTAAAAA
1 TATATATAATATATAGTTT-TTGAAAATA-TTTTAAAAA
* **
4963585 -ACATATCTTATATAGTTTTTGAAAACGT-TTTTAAAAA
1 TATATATAATATATAGTTTTTGAAAA--TATTTTAAAAA
* * * * * *
4963622 AACATATATTATATAGATTTT-AAAACATTTTTGAAAA
1 TATATATAATATATAGTTTTTGAAAATA-TTTTAAAAA
* *
4963659 CATATATAATATATAGTTTTTTAAAAATATTTTTTAAAAA
1 TATATATAATATATAG-TTTTTGAAAATA--TTTTAAAAA
4963699 TATAT
1 TATAT
4963704 TATTTTGAAA
Statistics
Matches: 199, Mismatches: 21, Indels: 23
0.82 0.09 0.09
Matches are distributed among these distances:
35 5 0.03
36 13 0.07
37 74 0.37
38 80 0.40
39 14 0.07
40 13 0.07
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (37 bp):
TATATATAATATATAGTTTTTGAAAATATTTTAAAAA
Found at i:4963564 original size:75 final size:72
Alignment explanation
Indices: 4963434--4963703 Score: 274
Period size: 75 Copynumber: 3.6 Consensus size: 72
4963424 TTTTATATAT
* *
4963434 TATATATATATATTATAG-TTTTGAAAATTTTTAAAAACATATATAATATATAGTTTTTGAAAAT
1 TATATATA-ATA-TATAGTTTTTGAAAATTTTTAAAAAAATATATAATATATAGTTTTTAAAAAT
4963498 GCTTTTAAAAA
64 --TTTTAAAAA
* *
4963509 TATATATAATATATAGTTTTTGAAAATATTTTGAAAATATATATAATATATAGTTTCTTAAAAAT
1 TATATATAATATATAGTTTTTGAAAAT-TTTTAAAAAAATATATAATATATAGTTT-TT-AAAA-
4963574 ATTTTTAAAAA
62 ATTTTTAAAAA
* ** * * *
4963585 -ACATATCTTATATAGTTTTTGAAAACGTTTTTAAAAAAACATATATTATATAGATTTTAAAACA
1 TATATATAATATATAGTTTTTGAAAA--TTTTTAAAAAAATATATAATATATAGTTTTTAAAA-A
*
4963649 TTTTTGAAAA
63 TTTTTAAAAA
* * **
4963659 CATATATAATATATAGTTTTTTAAAAATATTTTTTAAAAATATAT
1 TATATATAATATATAG-TTTTTGAAAAT-TTTTAAAAAAATATAT
4963704 TATTTTGAAA
Statistics
Matches: 165, Mismatches: 20, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
73 5 0.03
74 28 0.17
75 83 0.50
76 43 0.26
77 4 0.02
78 2 0.01
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (72 bp):
TATATATAATATATAGTTTTTGAAAATTTTTAAAAAAATATATAATATATAGTTTTTAAAAATTT
TTAAAAA
Found at i:4963606 original size:113 final size:113
Alignment explanation
Indices: 4963460--4963703 Score: 341
Period size: 113 Copynumber: 2.2 Consensus size: 113
4963450 AGTTTTGAAA
* * *
4963460 ATTTTTAAAAACATATATAATATATAGTTTTTGAAAATGCTTTTAAAAATATATATAATATATAG
1 ATTTTTAAAAACATATAT-ATATATAGTTTTTGAAAACGCTTTTAAAAAAACATATAATATATAG
* * *
4963525 TTTTTGAAA-ATATTTTGAAAATATATATAATATATAGTTTCTTAAAAAT
65 ATTTTAAAACAT-TTTTGAAAACATATATAATATATAGTTTCTTAAAAAT
* * *
4963574 ATTTTTAAAAAACATATCT-TATATAGTTTTTGAAAACGTTTTTAAAAAAACATATATTATATAG
1 ATTTTT-AAAAACATATATATATATAGTTTTTGAAAACGCTTTTAAAAAAACATATAATATATAG
*
4963638 ATTTTAAAACATTTTTGAAAACATATATAATATATAGTTTTTTAAAAAT
65 ATTTTAAAACATTTTTGAAAACATATATAATATATAGTTTCTTAAAAAT
*
4963687 ATTTTTTAAAA-ATATAT
1 ATTTTTAAAAACATATAT
4963704 TATTTTGAAA
Statistics
Matches: 116, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
111 5 0.04
112 4 0.03
113 88 0.76
114 8 0.07
115 11 0.09
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (113 bp):
ATTTTTAAAAACATATATATATATAGTTTTTGAAAACGCTTTTAAAAAAACATATAATATATAGA
TTTTAAAACATTTTTGAAAACATATATAATATATAGTTTCTTAAAAAT
Found at i:4963693 original size:13 final size:13
Alignment explanation
Indices: 4963675--4963701 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4963665 TAATATATAG
4963675 TTTTTTAAAAATA
1 TTTTTTAAAAATA
4963688 TTTTTTAAAAATA
1 TTTTTTAAAAATA
4963701 T
1 T
4963702 ATTATTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTTTTAAAAATA
Found at i:4963702 original size:38 final size:38
Alignment explanation
Indices: 4963435--4963703 Score: 266
Period size: 37 Copynumber: 7.2 Consensus size: 38
4963425 TTTATATATT
*
4963435 ATATATATATATTATAG-TTTT-GAAA-ATTTTTAAAAAC
1 ATATATA-ATA-TATAGTTTTTAAAAATATTTTTAAAAAC
* ** *
4963472 ATATATAATATATAGTTTTTGAAAATGCTTTTAAAAAT
1 ATATATAATATATAGTTTTTAAAAATATTTTTAAAAAC
* * *
4963510 ATATATAATATATAGTTTTTGAAAATA-TTTTGAAAAT
1 ATATATAATATATAGTTTTTAAAAATATTTTTAAAAAC
4963547 ATATATAATATATAGTTTCTTAAAAATATTTTTAAAAAAC
1 ATATATAATATATAGTTT-TTAAAAATATTTTT-AAAAAC
* * ** *
4963587 ATATCT--TATATAGTTTTTGAAAACGTTTTTAAAAAA
1 ATATATAATATATAGTTTTTAAAAATATTTTTAAAAAC
* * * * *
4963623 ACATATATTATATAGATTTT-AAAACATTTTTGAAAAC
1 ATATATAATATATAGTTTTTAAAAATATTTTTAAAAAC
*
4963660 ATATATAATATATAGTTTTTTAAAAATATTTTTTAAAA-
1 ATATATAATATATAG-TTTTTAAAAATATTTTTAAAAAC
4963698 ATATAT
1 ATATAT
4963704 TATTTTGAAA
Statistics
Matches: 197, Mismatches: 25, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
35 5 0.03
36 16 0.08
37 75 0.38
38 74 0.38
39 18 0.09
40 9 0.05
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (38 bp):
ATATATAATATATAGTTTTTAAAAATATTTTTAAAAAC
Found at i:4965018 original size:9 final size:9
Alignment explanation
Indices: 4964970--4965063 Score: 54
Period size: 9 Copynumber: 10.2 Consensus size: 9
4964960 CCTTTGCCTT
*
4964970 TTTAATTTA
1 TTTATTTTA
*
4964979 TTTTAATTTA
1 -TTTATTTTA
*
4964989 TTTAATTT-
1 TTTATTTTA
*
4964997 TTTGTGTTT-
1 TTTAT-TTTA
4965006 TTTATTTTA
1 TTTATTTTA
4965015 TTTATTATTA
1 TTTATT-TTA
4965025 -TTATTATTA
1 TTTATT-TTA
4965034 -TTACTTATCTA
1 TTTA-TT-T-TA
4965045 TTTATTTTA
1 TTTATTTTA
4965054 TTT-TTTTA
1 TTTATTTTA
4965062 TT
1 TT
4965064 ATTATTTCCT
Statistics
Matches: 75, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
8 13 0.17
9 38 0.51
10 17 0.23
11 4 0.05
12 3 0.04
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.72
Consensus pattern (9 bp):
TTTATTTTA
Found at i:4965024 original size:3 final size:3
Alignment explanation
Indices: 4965007--4965069 Score: 60
Period size: 3 Copynumber: 20.7 Consensus size: 3
4964997 TTTGTGTTTT
4965007 TTA TT- TTA TTTA TTA TTA TTA TTA TTA TTA CTTA TCTA TTTA TT- TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA -TTA T-TA -TTA TTA TTA
*
4965054 TT- TTT TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
4965070 TCCTTTCTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
2 6 0.12
3 35 0.67
4 10 0.19
5 1 0.02
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:4965837 original size:17 final size:18
Alignment explanation
Indices: 4965810--4965843 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4965800 TTCATATACC
*
4965810 TTATGTCTTCGTGTGGGT
1 TTATGTCTTCGTATGGGT
4965828 TTAT-TCTTCGTATGGG
1 TTATGTCTTCGTATGGG
4965844 CATAAGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.09, C:0.12, G:0.29, T:0.50
Consensus pattern (18 bp):
TTATGTCTTCGTATGGGT
Found at i:4969040 original size:28 final size:31
Alignment explanation
Indices: 4969009--4969069 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 31
4968999 TAATATAGTT
4969009 TAATTTTT-GCAAAT-G-TTTTTGAAAA-ATA
1 TAATTTTTAG-AAATCGATTTTTGAAAATATA
4969037 TAATTTTTAGAAATCGATTTTTGAAAATATA
1 TAATTTTTAGAAATCGATTTTTGAAAATATA
4969068 TA
1 TA
4969070 TATATACAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 12 0.41
29 2 0.07
30 10 0.34
31 5 0.17
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (31 bp):
TAATTTTTAGAAATCGATTTTTGAAAATATA
Found at i:4969075 original size:37 final size:35
Alignment explanation
Indices: 4969034--4969214 Score: 129
Period size: 38 Copynumber: 4.9 Consensus size: 35
4969024 TTTTTGAAAA
4969034 ATATA-ATTTTTAGAAATCGATTTTTGAAAATATATAT
1 ATATACATTTTT-GAAAT--ATTTTTGAAAATATATAT
* *
4969071 ATATACAGTTTTGAAA-ATATTTCGAATATATATATAT
1 ATATACATTTTTGAAATAT-TTTTGAA-A-ATATATAT
* * *
4969108 ATAATATAGTTTTGAAAT-TTTTTGAAAACATATAT
1 AT-ATACATTTTTGAAATATTTTTGAAAATATATAT
* *
4969143 AATATATAGTTTTTTAAA-ATGCTTTTGAAAATATATAT
1 -ATATACA-TTTTTGAAATAT--TTTTGAAAATATATAT
*
4969181 AATATATAGTTTTTGAAA-ATATTTTGAAAATATA
1 -ATATACA-TTTTTGAAATAT-TTTTGAAAATATA
4969215 GTTCTTTAAA
Statistics
Matches: 123, Mismatches: 10, Indels: 22
0.79 0.06 0.14
Matches are distributed among these distances:
34 2 0.02
35 18 0.15
36 12 0.10
37 38 0.31
38 53 0.43
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (35 bp):
ATATACATTTTTGAAATATTTTTGAAAATATATAT
Found at i:4969148 original size:38 final size:37
Alignment explanation
Indices: 4969055--4969214 Score: 186
Period size: 37 Copynumber: 4.4 Consensus size: 37
4969045 AGAAATCGAT
*
4969055 TTTTG-AAA-ATATATATATATACAGTTTTGAAAATA
1 TTTTGAAAATATATATATATATATAGTTTTGAAAATA
* * *
4969090 TTTCGAATATATATATATATAATATAGTTTTG-AAATT
1 TTTTGAAAATATATATATAT-ATATAGTTTTGAAAATA
* * *
4969127 TTTTGAAAACATATATA-ATATATAGTTTTTTAAAATGC
1 TTTTGAAAATATATATATATATATAG-TTTTGAAAAT-A
4969165 TTTTGAAAATATATATA-ATATATAGTTTTTGAAAATA
1 TTTTGAAAATATATATATATATATAG-TTTTGAAAATA
4969202 TTTTGAAAATATA
1 TTTTGAAAATATA
4969215 GTTCTTTAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
35 10 0.09
36 8 0.07
37 45 0.42
38 44 0.41
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (37 bp):
TTTTGAAAATATATATATATATATAGTTTTGAAAATA
Found at i:4969213 original size:26 final size:25
Alignment explanation
Indices: 4969165--4969235 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
4969155 TTTAAAATGC
* *
4969165 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATAT-TTTAAAATATAGT
4969191 TTTTGAAAATATTTTGAAAATATAGT
1 TTTTGAAAATATTTT-AAAATATAGT
*
4969217 TCTTT-AAAACATTTTAAAA
1 T-TTTGAAAATATTTTAAAA
4969236 AAACATATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
25 6 0.15
26 31 0.77
27 3 0.08
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (25 bp):
TTTTGAAAATATTTTAAAATATAGT
Found at i:4969339 original size:37 final size:37
Alignment explanation
Indices: 4969210--4969337 Score: 157
Period size: 37 Copynumber: 3.4 Consensus size: 37
4969200 TATTTTGAAA
*
4969210 ATATAGTTCTTTAAAACATTTTAAAAAAACATATATT
1 ATATAGTTTTTTAAAACATTTTAAAAAAACATATATT
* * *
4969247 ATATAGTTTTTGAAAACTTTTTTAAAAAACATATATT
1 ATATAGTTTTTTAAAACATTTTAAAAAAACATATATT
* * * * * *
4969284 ATATAGTTTTTAAAAAAATTTTGAAAACATATATAAT
1 ATATAGTTTTTTAAAACATTTTAAAAAAACATATATT
4969321 ATATAGTTTTTTTAAAA
1 ATATAG-TTTTTTAAAA
4969338 ATATTTTTTA
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
37 69 0.88
38 9 0.12
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (37 bp):
ATATAGTTTTTTAAAACATTTTAAAAAAACATATATT
Found at i:4969388 original size:15 final size:15
Alignment explanation
Indices: 4969327--4969381 Score: 78
Period size: 15 Copynumber: 3.8 Consensus size: 15
4969317 TAATATATAG
*
4969327 TTTTTTTAAAAAT-A
1 TTTTTTGAAAAATAA
4969341 TTTTTT-AAAAATAA
1 TTTTTTGAAAAATAA
*
4969355 TATTTTGAAAAATAA
1 TTTTTTGAAAAATAA
4969370 TTTTTTGAAAAA
1 TTTTTTGAAAAA
4969382 AGGTTTTGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
13 6 0.16
14 12 0.32
15 19 0.51
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (15 bp):
TTTTTTGAAAAATAA
Found at i:4969401 original size:13 final size:13
Alignment explanation
Indices: 4969327--4969401 Score: 60
Period size: 14 Copynumber: 5.5 Consensus size: 13
4969317 TAATATATAG
*
4969327 TTTTTTTAAAAATA
1 TTTTTTGAAAAA-A
*
4969341 TTTTTTAAAAATAA
1 TTTTTTGAAAA-AA
*
4969355 TATTTTGAAAAATAA
1 TTTTTTG-AAAA-AA
4969370 TTTTTTGAAAAAA
1 TTTTTTGAAAAAA
** *
4969383 GGTTTTGAAAACA
1 TTTTTTGAAAAAA
4969396 TTTTTT
1 TTTTTT
4969402 ATTTATATTA
Statistics
Matches: 50, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
13 16 0.32
14 20 0.40
15 14 0.28
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (13 bp):
TTTTTTGAAAAAA
Found at i:4969440 original size:4 final size:4
Alignment explanation
Indices: 4969431--4969474 Score: 79
Period size: 4 Copynumber: 10.8 Consensus size: 4
4969421 TTTATTACTC
4969431 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA -TTTA TTT
4969475 TGGTTTTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 35 0.90
5 4 0.10
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Done.