Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 128 of 144
Found at i:39852662 original size:16 final size:16
Alignment explanation
Indices: 39852641--39852682 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
39852631 TTATTAAATT
*
39852641 ATATATTTTAATTATA
1 ATATATTTTAATAATA
39852657 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
39852672 AT-TATGTTTAA
1 ATATAT-TTTAA
39852683 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:39852667 original size:15 final size:15
Alignment explanation
Indices: 39852632--39852673 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
39852622 TTAAGAATTT
*
39852632 TATTAAATTAT-ATA
1 TATTTAATTATAATA
39852646 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
39852660 TATTTAATAATAAT
1 TATTTAATTATAAT
39852674 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:39852907 original size:45 final size:44
Alignment explanation
Indices: 39852827--39852917 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 44
39852817 ACCTCTATTC
39852827 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
* *
39852871 CATTCAACCAAACA-ATTGATTTGCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACA-AGA-TTACTATTACGCCTCTATTCCATTA
39852916 CA
1 CA
39852918 CATCTATTCC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 16 0.37
45 26 0.60
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
Found at i:39852949 original size:16 final size:16
Alignment explanation
Indices: 39852896--39852960 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
39852886 TTGATTTGCT
39852896 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
* *
39852912 ATTACACATCTATTCC
1 ATTACGCCTCTATTCC
39852928 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
39852944 ATTACGTCTCTATTCC
1 ATTACGCCTCTATTCC
39852960 A
1 A
39852961 ATACAGCGAA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.23, C:0.34, G:0.05, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:39856469 original size:90 final size:90
Alignment explanation
Indices: 39856293--39857379 Score: 1424
Period size: 90 Copynumber: 12.1 Consensus size: 90
39856283 ATAAGACTTG
* * * * * *
39856293 TATCTTCGATCTTCTTCACTGCCGATACAGAAATACTAGATCTGTTATCTTCGATCTACAT-CGC
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTAC-TCCGC
* * * * * *
39856357 TGCCAATACAGAAATACTAGATCTGT
65 TACCAACATAGGAAGACAAGATCTGT
* *
39856383 TATCTTCGATCTACATCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTCGATCTACTCCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGCT
* *
39856448 ACCAACATAGGAAGGCAAGATCTGC
66 ACCAACATAGGAAGACAAGATCTGT
* *
39856473 TATCTTCGATCTACTTCGTTGCCAATACAGGAAGACAAGATCTATTATCTTCGATCTACTCCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGCT
39856538 ACCAACATAGGAAGACAAGATCT-T
66 ACCAACATAGGAAGACAAGATCTGT
* * *
39856562 CTATCTTTGATCTACTTCGTTGCCAATACAGGAAGACAAGATCTATTATCTTCGATCTACTCCGC
1 -TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGC
39856627 TACCAACATAGGAAGACAAGATCT-T
65 TACCAACATAGGAAGACAAGATCTGT
* * *
39856652 CTATCTTTGATCTACTTCGTTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCTGC
1 -TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGC
*
39856717 TACCAACATAGGAAGACAAGATCTGC
65 TACCAACATAGGAAGACAAGATCTGT
* * * * * *
39856743 TATCTTTGATCTGCTTCGCTGCCAATACAGGAAGACAATATCTATTATTTTCGATCTACTTCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGCT
*
39856808 ACCAATATAGGAAGACAAGATCTGT
66 ACCAACATAGGAAGACAAGATCTGT
* * * * * * * * * *
39856833 TATCTTCGATCTACTTTGCTACCAACATAGGAAGAAAAAATCTGCTATATTTGATCTACTTCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGCT
* * * * *
39856898 GCCAATATAGGAAGTCAATATCTAT
66 ACCAACATAGGAAGACAAGATCTGT
* *
39856923 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGCT
39856988 ACCAACATAGGAAGACAAGATCTGT
66 ACCAACATAGGAAGACAAGATCTGT
* * ** * * *
39857013 TATTTTTGATCTACTTCATTGCCAATACAGGAAGACAAGATTTGTTATCTTCGATCTGCTCCACT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGCT
* * * *
39857078 ACCAACATAGAAAGATAAGATTTGC
66 ACCAACATAGGAAGACAAGATCTGT
* *
39857103 TATCTTCGATCTACTTCGTTGCCAATATAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGCT
*
39857168 ACCAATATAGGAAGACAAGATCTGT
66 ACCAACATAGGAAGACAAGATCTGT
* *
39857193 TATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCTGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGCT
* * *
39857258 ACCAACATAAGAAGACAAGATTTGC
66 ACCAACATAGGAAGACAAGATCTGT
* * * * **
39857283 TATCTTTGATCTGCTTCGCTGCCAATACAGGAAGACAATATCTGTTATTTTAAATCTACTCCGCT
1 TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGCT
* * * *
39857348 ACCGATATAGGAAGACAGGATCTGC
66 ACCAACATAGGAAGACAAGATCTGT
39857373 TATCTTC
1 TATCTTC
39857380 AACCTACTCC
Statistics
Matches: 885, Mismatches: 109, Indels: 6
0.88 0.11 0.01
Matches are distributed among these distances:
89 1 0.00
90 884 1.00
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (90 bp):
TATCTTCGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGTTATCTTCGATCTACTCCGCT
ACCAACATAGGAAGACAAGATCTGT
Found at i:39857389 original size:45 final size:45
Alignment explanation
Indices: 39856293--39857379 Score: 1228
Period size: 45 Copynumber: 24.2 Consensus size: 45
39856283 ATAAGACTTG
* * * * * * * *
39856293 TATCTTCGATCTTCTTCACTGCCGATACAGAAATACTAGATCTGT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* * * * * *
39856338 TATCTTCGATCTACATCGCTGCCAATACAGAAATACTAGATCTGT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* * * *
39856383 TATCTTCGATCTACATCGCTGCCAATACAGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* * * *
39856428 TATCTTCGATCTACTCCGCTACCAACATAGGAAGGCAAGATCTGC
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* * * *
39856473 TATCTTCGATCTACTTCGTTGCCAATACAGGAAGACAAGATCTAT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* *
39856518 TATCTTCGATCTACTCCGCTACCAACATAGGAAGACAAGATCT-T
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* * * * *
39856562 CTATCTTTGATCTACTTCGTTGCCAATACAGGAAGACAAGATCTAT
1 -TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* *
39856608 TATCTTCGATCTACTCCGCTACCAACATAGGAAGACAAGATCT-T
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* * * *
39856652 CTATCTTTGATCTACTTCGTTGCCAATACAGGAAGACAAGATCTGT
1 -TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* *
39856698 TATCTTCGATCTAC-TCTGCTACCAACATAGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTC-GCTACCAATATAGGAAGACAAGATCTGT
* * * * * *
39856743 TATCTTTGATCTGCTTCGCTGCCAATACAGGAAGACAATATCTAT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
*
39856788 TATTTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* * * * *
39856833 TATCTTCGATCTACTTTGCTACCAACATAGGAAGAAAAAATCTGC
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* * * * * *
39856878 TATATTTGATCTACTTCGCTGCCAATATAGGAAGTCAATATCTAT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
39856923 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* *
39856968 TATCTTCGATCTACTCCGCTACCAACATAGGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* * ** * * *
39857013 TATTTTTGATCTACTTCATTGCCAATACAGGAAGACAAGATTTGT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* * * * * * * *
39857058 TATCTTCGATCTGCTCCACTACCAACATAGAAAGATAAGATTTGC
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* *
39857103 TATCTTCGATCTACTTCGTTGCCAATATAGGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
*
39857148 TATCTTCGATCTACTCCGCTACCAATATAGGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* * *
39857193 TATCTTTGATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* * * *
39857238 TATCTTCGATCTAC-TCTGCTACCAACATAAGAAGACAAGATTTGC
1 TATCTTCGATCTACTTC-GCTACCAATATAGGAAGACAAGATCTGT
* * * * *
39857283 TATCTTTGATCTGCTTCGCTGCCAATACAGGAAGACAATATCTGT
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
* ** * * * *
39857328 TATTTTAAATCTACTCCGCTACCGATATAGGAAGACAGGATCTGC
1 TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
39857373 TATCTTC
1 TATCTTC
39857380 AACCTACTCC
Statistics
Matches: 878, Mismatches: 156, Indels: 16
0.84 0.15 0.02
Matches are distributed among these distances:
44 6 0.01
45 866 0.99
46 6 0.01
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (45 bp):
TATCTTCGATCTACTTCGCTACCAATATAGGAAGACAAGATCTGT
Found at i:39862786 original size:20 final size:20
Alignment explanation
Indices: 39862761--39862803 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
39862751 ATTAAAATAT
* *
39862761 AAAAATATATATGTTTGTAA
1 AAAAATATATATATTTATAA
*
39862781 AAAAATGTATATATTTATAA
1 AAAAATATATATATTTATAA
39862801 AAA
1 AAA
39862804 GAAAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (20 bp):
AAAAATATATATATTTATAA
Found at i:39862847 original size:18 final size:17
Alignment explanation
Indices: 39862823--39862871 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
39862813 ATGAAATTAG
39862823 AAGTATAAAGAAAATAT
1 AAGTATAAAGAAAATAT
* *
39862840 ATATTATAAA-ATAATAT
1 A-AGTATAAAGAAAATAT
39862857 AAGTATATAAGAAAA
1 AAGTATA-AAGAAAA
39862872 CAAGTTAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
16 5 0.20
17 10 0.40
18 10 0.40
ACGTcount: A:0.63, C:0.00, G:0.08, T:0.29
Consensus pattern (17 bp):
AAGTATAAAGAAAATAT
Found at i:39867582 original size:36 final size:36
Alignment explanation
Indices: 39867542--39867617 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
39867532 TGAAACATAG
*
39867542 AAAATATATAAAAGTATGT-GTATATATATAT-TTATA
1 AAAAT-TA-AAAAATATGTAGTATATATATATATTATA
* *
39867578 AAAATTAAAAAATGTGTACGTATATGTATATATTATA
1 AAAATTAAAAAATATGTA-GTATATATATATATTATA
39867615 AAA
1 AAA
39867618 CGTATGTATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 8 0.24
35 2 0.06
36 16 0.47
37 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (36 bp):
AAAATTAAAAAATATGTAGTATATATATATATTATA
Found at i:39867882 original size:15 final size:16
Alignment explanation
Indices: 39867864--39867896 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
39867854 AATGTAAACA
39867864 AATTTGAAAAT-AATG
1 AATTTGAAAATGAATG
39867879 AATTTGAAAATGAATG
1 AATTTGAAAATGAATG
39867895 AA
1 AA
39867897 AAAAGGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.55, C:0.00, G:0.15, T:0.30
Consensus pattern (16 bp):
AATTTGAAAATGAATG
Found at i:39868194 original size:23 final size:22
Alignment explanation
Indices: 39868151--39868208 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
39868141 AAAGGGTATC
* *
39868151 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
39868172 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
39868195 TGCATATCATATCT
1 TACAAATCATATCT
39868209 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:39868903 original size:44 final size:45
Alignment explanation
Indices: 39868771--39868933 Score: 154
Period size: 44 Copynumber: 3.7 Consensus size: 45
39868761 ACCTGATATG
* *
39868771 ATCTACTCTACTGCAACTTCAGAGAGATAAGATCTATTATTTT-A
1 ATCTACTCCACTGCAACTTCAGGGAGATAAGATCTATTATTTTCA
* * * * ***
39868815 ATCTGCTCAACTGCAACTTCAGGGAGATAGGA-CTACTGGCTTCA
1 ATCTACTCCACTGCAACTTCAGGGAGATAAGATCTATTATTTTCA
* * *
39868859 ATCTGCTCCACTGCAACTT-AGGGAGATAAAATCTGTTATTTTCA
1 ATCTACTCCACTGCAACTTCAGGGAGATAAGATCTATTATTTTCA
* * **
39868903 ACCTACTCCACTAC-TGTTCAGGGAGATAAGA
1 ATCTACTCCACTGCAACTTCAGGGAGATAAGA
39868934 CTAGTGGCTT
Statistics
Matches: 94, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
43 18 0.19
44 76 0.81
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (45 bp):
ATCTACTCCACTGCAACTTCAGGGAGATAAGATCTATTATTTTCA
Found at i:39869011 original size:132 final size:132
Alignment explanation
Indices: 39868854--39869194 Score: 522
Period size: 132 Copynumber: 2.6 Consensus size: 132
39868844 GGACTACTGG
* ** * * *
39868854 CTTCAATCTGCTCCACTGCAACTTAGGGAGATAAAATCTGTTATTTTCAACCTACTCCACTACTG
1 CTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
* *
39868919 TTCAGGGAGATAAGACTAGTGGCTTAAATATGCTTCCCTACTACCTTGGGAAGACAAGATTCGCC
66 TTCAGGGAGATAAGACTAGTGGCTTAAATATACTTCCCTACTACCTTGGGAAGACAAGATTCACC
39868984 GT
131 GT
* * *
39868986 CTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAACCTACTCCACTGCTG
1 CTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
* * * * *
39869051 CTCAAGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCTTGGGAAGATAAGATTCACC
66 TTCAGGGAGATAAGACTAGTGGCTTAAATATACTTCCCTACTACCTTGGGAAGACAAGATTCACC
39869116 GT
131 GT
39869118 CTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
1 CTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
39869183 CTT-AGGGAGATA
66 -TTCAGGGAGATA
39869195 GGATTCACAA
Statistics
Matches: 187, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
132 186 0.99
133 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.30
Consensus pattern (132 bp):
CTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
TTCAGGGAGATAAGACTAGTGGCTTAAATATACTTCCCTACTACCTTGGGAAGACAAGATTCACC
GT
Found at i:39869045 original size:44 final size:44
Alignment explanation
Indices: 39868997--39869354 Score: 157
Period size: 44 Copynumber: 8.1 Consensus size: 44
39868987 TTCGATCTGT
* *
39868997 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAACCTAC
1 TCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTAC
* * * * ** * *
39869041 TCCACTGCTGCTCAAGGAGATAAG-GCTAGT-GGCTTAAATCTAC
1 TCCACTACTGCTTAGGGAGATAAGATCT-GTAATCTTCAACCTAC
* * * * *
39869084 TTCC-CTACTACCTT-GGGAAGATAAGAT-T-CACCGTCTTCAATCTGC
1 -TCCACTACT-GCTTAGGG-AGATAAGATCTGTA--ATCTTCAACCTAC
*
39869129 TCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTAC
1 TCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTAC
* * ** *
39869173 TCCACTGCTGCTTAGGGAGATAGGAT-TCACAATCTTCAACCTAT
1 TCCACTACTGCTTAGGGAGATAAGATCT-GTAATCTTCAACCTAC
* * * ** *
39869217 TCCACTGCTGAC-CAGGGAGATAGGAT-TCACAATCTTCAACCTAT
1 TCCACTACTG-CTTAGGGAGATAAGATCT-GTAATCTTCAACCTAC
* * * ** *
39869261 TCCACTGCTGAC-CAGGGAGATAGGAT-TCACAATCTTCAACCTAT
1 TCCACTACTG-CTTAGGGAGATAAGATCT-GTAATCTTCAACCTAC
* * * ** *
39869305 TCCACTGCTGAC-CAGGGAGATAGGAT-TCACAATCTTCAACCTAT
1 TCCACTACTG-CTTAGGGAGATAAGATCT-GTAATCTTCAACCTAC
39869349 TCCACT
1 TCCACT
39869355 GCTAACCAGG
Statistics
Matches: 269, Mismatches: 31, Indels: 28
0.82 0.09 0.09
Matches are distributed among these distances:
43 17 0.06
44 231 0.86
45 20 0.07
46 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (44 bp):
TCCACTACTGCTTAGGGAGATAAGATCTGTAATCTTCAACCTAC
Found at i:39869238 original size:132 final size:131
Alignment explanation
Indices: 39868854--39869387 Score: 454
Period size: 132 Copynumber: 4.0 Consensus size: 131
39868844 GGACTACTGG
* ** * * *
39868854 CTTCAATCTGCTCCACTGCAACTTAGGGAGATAAAATCTGTTATTTTCAACCTACTCCACTACTG
1 CTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
* * *** ** * * * *
39868919 TTCAGGGAGATAAGACTAGTGGCTTAAATATGCTTCCCTACTACCTTGGGAAGACAAGATTCGCC
66 CTCAGGGAGATAGGACTACAAGCTTAAACCT-ATTCCCTACTACCTAGGGAAGATAAGATTCACC
39868984 GT
130 GT
* * *
39868986 CTTCGATCTGTTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTTAACCTACTCCACTGCTG
1 CTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
* *** * *
39869051 CTCAAGGAGATAAGG-CTAGTGGCTTAAATCTACTTCCCTACTACCTTGGGAAGATAAGATTCAC
66 CTCAGGGAGAT-AGGACTACAAGCTTAAACCTA-TTCCCTACTACCTAGGGAAGATAAGATTCAC
39869115 CGT
129 CGT
39869118 CTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
1 CTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
* * * * * *
39869183 CTTAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTGACC-AGGG-AGATAGGATTCA
66 CTCAGGGAGATAGGACT-ACAAGCTTAAACCTATTCC-CTACT-ACCTAGGGAAGATAAGATTCA
**
39869246 CAAT
128 CCGT
* ** * * * ** * *
39869250 CTTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGAT-TCACAATCTTCAACCTATTCCACTGC
1 CTTCAATCTGCTCCACTACTG-CTTAGGGAGATAAGATCT-GTAATTTTCAACCTACTCCACTGC
* * * * *
39869313 TGAC-CAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTAACC-AGGG-AGATAGGAT
64 TG-CTCAGGGAGATAGGACT-ACAAGCTTAAACCTATTCC-CTACT-ACCTAGGGAAGATAAGAT
*
39869375 TCACCTT
125 TCACCGT
39869382 CTTCAA
1 CTTCAA
39869388 CCTATTCCAC
Statistics
Matches: 346, Mismatches: 47, Indels: 18
0.84 0.11 0.04
Matches are distributed among these distances:
131 4 0.01
132 319 0.92
133 20 0.06
134 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (131 bp):
CTTCAATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGCTG
CTCAGGGAGATAGGACTACAAGCTTAAACCTATTCCCTACTACCTAGGGAAGATAAGATTCACCG
T
Found at i:39869355 original size:44 final size:44
Alignment explanation
Indices: 39869163--39869580 Score: 610
Period size: 44 Copynumber: 9.7 Consensus size: 44
39869153 ATCTGTAATT
* *
39869163 TTCAACCTACTCCACTGCTG-CTTAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATC
39869207 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
39869251 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
39869295 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* **
39869339 TTCAACCTATTCCACTGCTAACCAGGGAGATAGGATTCACCTTC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
39869383 TTCAACCTATTCCACTGCTAACCAGGGAGATAGGATT--C-A-C
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
39869423 -T-----TATTCCACTACTGACCAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
* *
39869461 TTCAACCTATTTCACTGCTGACCAGGGAGATAGGACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* * *
39869505 TTCAACCTATTCCACTGCTGACTAGGGAGATAAGACTT-ACAACC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
39869549 TTCAACCTATTCCACTGCTGACCAGGGAGATA
1 TTCAACCTATTCCACTGCTGACCAGGGAGATA
39869581 AAGCTTTGTG
Statistics
Matches: 344, Mismatches: 17, Indels: 26
0.89 0.04 0.07
Matches are distributed among these distances:
34 26 0.08
35 2 0.01
36 1 0.00
37 1 0.00
38 1 0.00
39 2 0.01
40 1 0.00
42 1 0.00
43 1 0.00
44 306 0.89
45 2 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
Found at i:39869519 original size:122 final size:122
Alignment explanation
Indices: 39869302--39869536 Score: 382
Period size: 122 Copynumber: 1.9 Consensus size: 122
39869292 ATCTTCAACC
*
39869302 TATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTAACCAGGGA
1 TATTCCACTACTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTAACCAGGGA
* **
39869367 GATAGGATTCACCTTCTTCAACCTATTCCACTGCTAACCAGGGAGATAGGATTCACT
66 GATAGGACTCACAATCTTCAACCTATTCCACTGCTAACCAGGGAGATAGGATTCACT
* *
39869424 TATTCCACTACTGACCAGGGAGATAGGACTT-ACAATCTTCAACCTATTTCACTGCTGACCAGGG
1 TATTCCACTACTGACCAGGGAGATAGGA-TTCACAATCTTCAACCTATTCCACTGCTAACCAGGG
* *
39869488 AGATAGGACTCACAATCTTCAACCTATTCCACTGCTGACTAGGGAGATA
65 AGATAGGACTCACAATCTTCAACCTATTCCACTGCTAACCAGGGAGATA
39869537 AGACTTACAA
Statistics
Matches: 104, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
122 102 0.98
123 2 0.02
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.26
Consensus pattern (122 bp):
TATTCCACTACTGACCAGGGAGATAGGATTCACAATCTTCAACCTATTCCACTGCTAACCAGGGA
GATAGGACTCACAATCTTCAACCTATTCCACTGCTAACCAGGGAGATAGGATTCACT
Found at i:39870904 original size:20 final size:20
Alignment explanation
Indices: 39870866--39870903 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
39870856 TCTTTTTGTC
*
39870866 ATTTTCATTTTTTAATTTTG
1 ATTTTCATTTTTGAATTTTG
*
39870886 ATTTTGATTTTTG-ATTTT
1 ATTTTCATTTTTGAATTTT
39870904 TTTGGTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.18, C:0.03, G:0.08, T:0.71
Consensus pattern (20 bp):
ATTTTCATTTTTGAATTTTG
Found at i:39870916 original size:11 final size:10
Alignment explanation
Indices: 39870900--39870938 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
39870890 TGATTTTTGA
39870900 TTTTTTTGGT
1 TTTTTTTGGT
39870910 TTTTTTTGTGT
1 TTTTTTTG-GT
*
39870921 TTTTTTGGGT
1 TTTTTTTGGT
39870931 TTTTTTTG
1 TTTTTTTG
39870939 AATTGGATCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 17 0.65
11 9 0.35
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (10 bp):
TTTTTTTGGT
Found at i:39871918 original size:31 final size:31
Alignment explanation
Indices: 39871880--39871939 Score: 120
Period size: 31 Copynumber: 1.9 Consensus size: 31
39871870 TTCTGAGTCT
39871880 GTAGCAGCGTCACTCATGTCATTGATATCCC
1 GTAGCAGCGTCACTCATGTCATTGATATCCC
39871911 GTAGCAGCGTCACTCATGTCATTGATATC
1 GTAGCAGCGTCACTCATGTCATTGATATC
39871940 TGGGTACCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (31 bp):
GTAGCAGCGTCACTCATGTCATTGATATCCC
Found at i:39876148 original size:27 final size:26
Alignment explanation
Indices: 39876082--39876152 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 26
39876072 AATAGATAAA
*
39876082 AATTATAAAATATATAAATATATATGT
1 AATTATAAAA-AAATAAATATATATGT
* *
39876109 ACA-TATAAGAAAAATATATATGTATGT
1 A-ATTATAA-AAAAATAAATATATATGT
39876136 GAATTAT-AAAAAATAAA
1 -AATTATAAAAAAATAAA
39876153 AAAATAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
26 8 0.22
27 21 0.58
28 7 0.19
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.34
Consensus pattern (26 bp):
AATTATAAAAAAATAAATATATATGT
Found at i:39876626 original size:23 final size:23
Alignment explanation
Indices: 39876600--39876648 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
39876590 AAGAGATTTG
* *
39876600 AAATCAACAATATACAAATCAAT
1 AAATAAACAATACACAAATCAAT
**
39876623 AAATAAATTATACACAAATCAAT
1 AAATAAACAATACACAAATCAAT
39876646 AAA
1 AAA
39876649 ATAAGAACAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAACAATACACAAATCAAT
Found at i:39876878 original size:23 final size:22
Alignment explanation
Indices: 39876835--39876892 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
39876825 AAAGGGTATC
* *
39876835 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
39876856 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
39876879 TGCATATCATATCT
1 TACAAATCATATCT
39876893 AAGATTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 18 0.58
23 10 0.32
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:39877546 original size:10 final size:10
Alignment explanation
Indices: 39877518--39877548 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
39877508 GAAAAGAGGC
*
39877518 ATATATATAT
1 ATATATATTT
39877528 ATATATATTT
1 ATATATATTT
39877538 ATATATATTT
1 ATATATATTT
39877548 A
1 A
39877549 ATACATGGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
ATATATATTT
Found at i:39879114 original size:39 final size:39
Alignment explanation
Indices: 39879060--39879137 Score: 129
Period size: 39 Copynumber: 2.0 Consensus size: 39
39879050 ACGAAGGTGA
* *
39879060 GCTTCTTAGAGATCACATCAGTCAATTCATTACTTTTTT
1 GCTTCTTAAAGATCACATCAGTCAATTCATTACTCTTTT
*
39879099 GCTTCTTAAAGATCACATCAGTTAATTCATTACTCTTTT
1 GCTTCTTAAAGATCACATCAGTCAATTCATTACTCTTTT
39879138 AAATGATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.44
Consensus pattern (39 bp):
GCTTCTTAAAGATCACATCAGTCAATTCATTACTCTTTT
Found at i:39896556 original size:18 final size:17
Alignment explanation
Indices: 39896528--39896562 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39896518 ATTATTAAGA
*
39896528 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39896545 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39896563 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39896700 original size:18 final size:17
Alignment explanation
Indices: 39896672--39896706 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
39896662 ATTATTAAGA
*
39896672 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
39896689 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
39896707 TAAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:39896917 original size:44 final size:45
Alignment explanation
Indices: 39896868--39896962 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
39896858 TTACACCTCT
* *
39896868 ATTACATTCAACCAAACA-CAGTTTTACTATTACGCCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
** *
39896912 ATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCC
1 ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
39896957 ATTACA
1 ATTACA
39896963 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.35
Consensus pattern (45 bp):
ATTACATTCAACCAAACAGCAGATTTACTATTACACCTCTATTCC
Found at i:39896962 original size:16 final size:16
Alignment explanation
Indices: 39896941--39896973 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
39896931 TTGATTTGCT
*
39896941 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
39896957 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
39896973 A
1 A
39896974 ATCCAATACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.36, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:39896983 original size:21 final size:21
Alignment explanation
Indices: 39896954--39896996 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
39896944 ACACCTCTAT
*
39896954 TCCATTACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
39896975 TCCAATACACCTCTAATCCAA
1 TCCAATACACCTCTAATCCAA
39896996 T
1 T
39896997 ACAGCGAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.37, G:0.00, T:0.28
Consensus pattern (21 bp):
TCCAATACACCTCTAATCCAA
Found at i:39897746 original size:62 final size:59
Alignment explanation
Indices: 39897674--39897787 Score: 158
Period size: 62 Copynumber: 1.9 Consensus size: 59
39897664 AGTGATTATC
* *
39897674 TTAATATTAAATTTAATTTAATGTTTATCTTGTAGATAAATACTT-TATTAATTTAATAAGAT
1 TTAATATTAAATTTAATCTAATATTTATC-T-T-GATAAATA-TTATATTAATTTAATAAGAT
*
39897736 TTAATGTTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTA
1 TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTA
39897788 TTACTAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
58 2 0.04
59 18 0.38
60 1 0.02
61 1 0.02
62 26 0.54
ACGTcount: A:0.40, C:0.04, G:0.05, T:0.51
Consensus pattern (59 bp):
TTAATATTAAATTTAATCTAATATTTATCTTGATAAATATTATATTAATTTAATAAGAT
Found at i:39898205 original size:19 final size:19
Alignment explanation
Indices: 39898159--39898205 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
39898149 AAATTCACAT
39898159 ATTTTAATAATTTTATAAA
1 ATTTTAATAATTTTATAAA
* **
39898178 AGTAAAATAATTTTA-AAA
1 ATTTTAATAATTTTATAAA
39898196 ACTTTTAATA
1 A-TTTTAATA
39898206 TATATCAATT
Statistics
Matches: 21, Mismatches: 6, Indels: 2
0.72 0.21 0.07
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (19 bp):
ATTTTAATAATTTTATAAA
Found at i:39900038 original size:183 final size:183
Alignment explanation
Indices: 39899695--39900088 Score: 470
Period size: 183 Copynumber: 2.1 Consensus size: 183
39899685 AATTTGAAAA
* * * * *
39899695 ATACTTATTCGGTATAAAATAAAAATTTTTAAGTACAATTTATAAAAAAACCATGTTTAAGTGTA
1 ATACTTTTTGGGTAT-AAA-AAAAATATTTAAGTACAATTTAGAAAAAAAACATGTTTAAGTGTA
* * * * * *
39899760 AAATAAAAAACTAATGCACTTCGTTGAAGAAAAGGAAAAAAAACCTATAGAAGCGTAGTTTCTAA
64 AAATAAAAAACTAATGCACTTCATTGAAGAAAAGAAAAAAAAACATACAAAAGCGTAGATTCTAA
* *
39899825 TATTATATTAAAATAGTGCCAGAATGTTTAAACGATACATTATAAAAATTTATTT
129 TATTATATTAAAATACTGCCAGAATGTTTAAACGATACATTATAAAAATTTATCT
* *
39899880 ATACTTTTTGGGTATAAAAAAACTATTTAGGTACAATTTAGAAAAAAAACATGTTTAAGTGTAAA
1 ATACTTTTTGGGTATAAAAAAAATATTTAAGTACAATTTAGAAAAAAAACATGTTTAAGTGTAAA
* * *
39899945 AT-AAAAACTAATGCACTTCATTGGAA-TAAAGAAAGAAAAAACATGCAAAAGCAG-GGATTCTA
66 ATAAAAAACTAATGCACTTCATT-GAAGAAAAGAAA-AAAAAACATACAAAAGC-GTAGATTCTA
* * * ** * *
39900007 ATATTATATTAAAATACTTCTAGAGTGTTTAAATTATACATTATAAACATTTGTCT
128 ATATTATATTAAAATACTGCCAGAATGTTTAAACGATACATTATAAAAATTTATCT
*
39900063 ATATTTTTTTGGGTATAAAATAAAAT
1 ATA-CTTTTTGGGTATAAAA-AAAAT
39900089 TTTTTTATGT
Statistics
Matches: 177, Mismatches: 27, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
182 25 0.14
183 116 0.66
184 19 0.11
185 17 0.10
ACGTcount: A:0.46, C:0.09, G:0.12, T:0.33
Consensus pattern (183 bp):
ATACTTTTTGGGTATAAAAAAAATATTTAAGTACAATTTAGAAAAAAAACATGTTTAAGTGTAAA
ATAAAAAACTAATGCACTTCATTGAAGAAAAGAAAAAAAAACATACAAAAGCGTAGATTCTAATA
TTATATTAAAATACTGCCAGAATGTTTAAACGATACATTATAAAAATTTATCT
Found at i:39912309 original size:26 final size:26
Alignment explanation
Indices: 39912254--39912318 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
39912244 CCCAACCCAT
* *
39912254 AGCTCGTGTGAGCAGGCCCATTCTAC
1 AGCTCGTGTGAGCAGGCCCATTCCAA
*
39912280 AGCTCGTGTGAGCAGGCCTATTCCAA
1 AGCTCGTGTGAGCAGGCCCATTCCAA
*
39912306 AGCTTGT-TGAGCA
1 AGCTCGTGTGAGCA
39912319 TTTACAATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
25 6 0.17
26 29 0.83
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.25
Consensus pattern (26 bp):
AGCTCGTGTGAGCAGGCCCATTCCAA
Found at i:39912452 original size:27 final size:27
Alignment explanation
Indices: 39912410--39912475 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
39912400 GAGTAAACGG
* *
39912410 AAATGGTAATAT-GAAATAGATATACA
1 AAATGGTTATATGGAAATAAATATACA
* **
39912436 AAATGTTTATATGGAAATAAATATATG
1 AAATGGTTATATGGAAATAAATATACA
39912463 AAATGGTTATATG
1 AAATGGTTATATG
39912476 AAGTGTCTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 10 0.30
27 23 0.70
ACGTcount: A:0.48, C:0.02, G:0.17, T:0.33
Consensus pattern (27 bp):
AAATGGTTATATGGAAATAAATATACA
Found at i:39913111 original size:14 final size:14
Alignment explanation
Indices: 39913089--39913121 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
39913079 TTTTAAATAC
*
39913089 ATTTTGAATGATTG
1 ATTTGGAATGATTG
39913103 ATTTGGAATGATTG
1 ATTTGGAATGATTG
39913117 ATTTG
1 ATTTG
39913122 ATACAAATGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.24, T:0.48
Consensus pattern (14 bp):
ATTTGGAATGATTG
Found at i:39917371 original size:14 final size:15
Alignment explanation
Indices: 39917354--39917387 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
39917344 TAAATGAAAC
*
39917354 AATTTTC-AGGAGAA
1 AATTTTCGAGGACAA
39917368 AATTTTCGAGGACAA
1 AATTTTCGAGGACAA
39917383 AATTT
1 AATTT
39917388 CTAAAGGAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.39
15 11 0.61
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (15 bp):
AATTTTCGAGGACAA
Found at i:39921563 original size:2 final size:2
Alignment explanation
Indices: 39921556--39921580 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
39921546 CACTAATTTC
39921556 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
39921581 CGTGTAGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:39921628 original size:19 final size:19
Alignment explanation
Indices: 39921603--39921652 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
39921593 AGGTTAATTA
39921603 ACTTAATTAAT-TATATTTT
1 ACTTAATTAATCT-TATTTT
*
39921622 TCTTAATTAATCTTATTTT
1 ACTTAATTAATCTTATTTT
39921641 ACTTAATTAATC
1 ACTTAATTAATC
39921653 AACATATATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 27 0.96
20 1 0.04
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.56
Consensus pattern (19 bp):
ACTTAATTAATCTTATTTT
Found at i:39923220 original size:19 final size:20
Alignment explanation
Indices: 39923190--39923236 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
39923180 ATTTATTGTT
39923190 TATTTATTTATATGT-TATTA
1 TATTTATTTATAT-TATATTA
39923210 TATTT-TTTATATTATATTA
1 TATTTATTTATATTATATTA
39923229 TATGTTAT
1 TAT-TTAT
39923237 ATTCATTCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.04
19 15 0.62
20 7 0.29
21 1 0.04
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (20 bp):
TATTTATTTATATTATATTA
Found at i:39926202 original size:10 final size:10
Alignment explanation
Indices: 39926162--39926203 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
39926152 AATTCGAGAG
39926162 TTATTAATAT
1 TTATTAATAT
39926172 TTATT--TAT
1 TTATTAATAT
*
39926180 TTA-TAATAG
1 TTATTAATAT
39926189 TTATTAATAT
1 TTATTAATAT
39926199 TTATT
1 TTATT
39926204 TATAACAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
7 1 0.04
8 6 0.22
9 5 0.19
10 15 0.56
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (10 bp):
TTATTAATAT
Found at i:39937516 original size:14 final size:14
Alignment explanation
Indices: 39937480--39937516 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
39937470 CAATCAAACA
*
39937480 CCAGAAAATATTTT
1 CCAGAAAACATTTT
39937494 CCAGTAAAACATTTT
1 CCAG-AAAACATTTT
39937509 CCAGAAAA
1 CCAGAAAA
39937517 GTAAAACATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.46, C:0.19, G:0.08, T:0.27
Consensus pattern (14 bp):
CCAGAAAACATTTT
Found at i:39937521 original size:20 final size:20
Alignment explanation
Indices: 39937496--39937535 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
39937486 AATATTTTCC
39937496 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTCCAGAAA
39937516 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTCCAGAAA
39937536 TTATTTTACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.10, T:0.25
Consensus pattern (20 bp):
AGTAAAACATTTTCCAGAAA
Found at i:39938589 original size:16 final size:17
Alignment explanation
Indices: 39938565--39938598 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
39938555 GGCTTGAGAT
*
39938565 GAGAGAATTAA-AGAAA
1 GAGAAAATTAAGAGAAA
39938581 GAGAAAATTAAGAGAAA
1 GAGAAAATTAAGAGAAA
39938598 G
1 G
39938599 CCATACCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (17 bp):
GAGAAAATTAAGAGAAA
Found at i:39971900 original size:14 final size:15
Alignment explanation
Indices: 39971867--39971902 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
39971857 AAAATTTTAG
39971867 AAAAATGAATATTGT
1 AAAAATGAATATTGT
*
39971882 AAAAATGAATCTTGT
1 AAAAATGAATATTGT
39971897 AAAAAT
1 AAAAAT
39971903 ATTTGTTAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.31
Consensus pattern (15 bp):
AAAAATGAATATTGT
Found at i:39972389 original size:13 final size:14
Alignment explanation
Indices: 39972373--39972401 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39972363 TTTTTACTGT
39972373 TTATATATTA-ATA
1 TTATATATTACATA
39972386 TTATATATTACATA
1 TTATATATTACATA
39972400 TT
1 TT
39972402 TTTTATAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (14 bp):
TTATATATTACATA
Found at i:39973270 original size:29 final size:28
Alignment explanation
Indices: 39973213--39973277 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
39973203 AAGTGCCCCA
*
39973213 TTTTTTTATTTTATTACTAGTATATATT
1 TTTTTTTATTGTATTACTAGTATATATT
* *
39973241 TTTATTTTATTGTATTAC-ATTTTATAATT
1 TTT-TTTTATTGTATTACTAGTATAT-ATT
39973270 TTTTTTTA
1 TTTTTTTA
39973278 AAAAGAGCCA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (28 bp):
TTTTTTTATTGTATTACTAGTATATATT
Found at i:39990985 original size:29 final size:29
Alignment explanation
Indices: 39990918--39991018 Score: 104
Period size: 29 Copynumber: 3.6 Consensus size: 29
39990908 ATTACCGTAT
*
39990918 AAGTGAGCCTTTGTGGCTAACTCTG---A
1 AAGTGAGCCTTTGTGGCTATCTCTGTTAA
39990944 AAG-GATGCCTTTGTGGCTATCT-TAGTTAA
1 AAGTGA-GCCTTTGTGGCTATCTCT-GTTAA
*
39990973 AAGTGAGCCTTTGTAGCTATCTCTGTTAA
1 AAGTGAGCCTTTGTGGCTATCTCTGTTAA
** *
39991002 AAAAGTGCCTTTGTGGC
1 AAGTGAGCCTTTGTGGC
39991019 AGTTTCCGTA
Statistics
Matches: 62, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
25 3 0.05
26 19 0.31
29 37 0.60
30 3 0.05
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.35
Consensus pattern (29 bp):
AAGTGAGCCTTTGTGGCTATCTCTGTTAA
Found at i:39991105 original size:29 final size:29
Alignment explanation
Indices: 39991073--39991206 Score: 171
Period size: 29 Copynumber: 4.6 Consensus size: 29
39991063 GCCTTTATGT
* *
39991073 CTATCTCTGTCAAAAGGATGCATTTCTGA
1 CTATCTCTGTCAAAAGGATGCATTTGTGG
* *
39991102 CTATCTTTGTCAAAAGGATACATTTGTGG
1 CTATCTCTGTCAAAAGGATGCATTTGTGG
* * * *
39991131 TTGTCTCTGTCAAAAGGATGCATTTATGC
1 CTATCTCTGTCAAAAGGATGCATTTGTGG
*
39991160 CTATCTCTGTCAAAAGGATATC-TTTGTGG
1 CTATCTCTGTCAAAAGGAT-GCATTTGTGG
39991189 CTATCTCTGTCAAAAGGA
1 CTATCTCTGTCAAAAGGA
39991207 ACACCTACAT
Statistics
Matches: 89, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
29 88 0.99
30 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (29 bp):
CTATCTCTGTCAAAAGGATGCATTTGTGG
Found at i:39991146 original size:58 final size:58
Alignment explanation
Indices: 39991073--39991206 Score: 207
Period size: 58 Copynumber: 2.3 Consensus size: 58
39991063 GCCTTTATGT
* *
39991073 CTATCTCTGTCAAAAGGATGCATTTCTGACTATCTTTGTCAAAAGGATA-CATTTGTGG
1 CTATCTCTGTCAAAAGGATGCATTTATGACTATCTCTGTCAAAAGGATATC-TTTGTGG
* * *
39991131 TTGTCTCTGTCAAAAGGATGCATTTATGCCTATCTCTGTCAAAAGGATATCTTTGTGG
1 CTATCTCTGTCAAAAGGATGCATTTATGACTATCTCTGTCAAAAGGATATCTTTGTGG
39991189 CTATCTCTGTCAAAAGGA
1 CTATCTCTGTCAAAAGGA
39991207 ACACCTACAT
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 67 0.99
59 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (58 bp):
CTATCTCTGTCAAAAGGATGCATTTATGACTATCTCTGTCAAAAGGATATCTTTGTGG
Found at i:39993757 original size:33 final size:33
Alignment explanation
Indices: 39993715--39993782 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
39993705 TTGTCCTTAG
39993715 ATGTGATCTTTGACTACATCTAATATTCTGTCA
1 ATGTGATCTTTGACTACATCTAATATTCTGTCA
39993748 ATGTGATCTTTGACTACATCTAATATTCTGTCA
1 ATGTGATCTTTGACTACATCTAATATTCTGTCA
39993781 AT
1 AT
39993783 CACTACTGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.28, C:0.18, G:0.12, T:0.43
Consensus pattern (33 bp):
ATGTGATCTTTGACTACATCTAATATTCTGTCA
Found at i:39999149 original size:26 final size:26
Alignment explanation
Indices: 39999120--39999181 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
39999110 CCTATAAGTG
*
39999120 TTCTGAAACTGATACATGCTATGATA
1 TTCTGAAACTGATACATACTATGATA
* *
39999146 TTCTGAAACTGATATATATTATGATA
1 TTCTGAAACTGATACATACTATGATA
39999172 TTCTGAAACT
1 TTCTGAAACT
39999182 ACTTTAGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (26 bp):
TTCTGAAACTGATACATACTATGATA
Found at i:40009512 original size:9 final size:9
Alignment explanation
Indices: 40009498--40009530 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
40009488 GCTTGCTATG
40009498 GAGAAATAA
1 GAGAAATAA
40009507 GAGAAATAA
1 GAGAAATAA
*
40009516 AAGAAATAA
1 GAGAAATAA
40009525 GAGAAA
1 GAGAAA
40009531 ATGATGCGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.21, T:0.09
Consensus pattern (9 bp):
GAGAAATAA
Found at i:40020311 original size:18 final size:17
Alignment explanation
Indices: 40020288--40020335 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
40020278 TGAGGGTAGG
40020288 ATTTGTATCTGTATTTGC
1 ATTTGTATCTGTATTT-C
*
40020306 ATTTGTATCTGCAATTTC
1 ATTTGTATCTG-TATTTC
40020324 ATTTGTAT-TGTA
1 ATTTGTATCTGTA
40020336 ACTAATCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 1 0.04
17 2 0.07
18 20 0.74
19 4 0.15
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (17 bp):
ATTTGTATCTGTATTTC
Found at i:40032471 original size:172 final size:172
Alignment explanation
Indices: 40032184--40032606 Score: 668
Period size: 172 Copynumber: 2.5 Consensus size: 172
40032174 AAAGATTGTG
** * *
40032184 ATGTGAAAAACTTGTCTTGGATTATTTATTTTTGGAAATTGTTTAGCTAAAAATTTATGT-CATT
1 ATGTGAATGACTTGTTTTGGATTATTTGTTTTT-GAAATTGTTTAGCTAAAAATTTAT-TCCATT
* * * *
40032248 CTGGTTTGAATATGTTTGTGTCATTTTTTATGCCAAATGAGTTTAAATATTTATTTTTAATGTTT
64 CTGATTTGAATATGTTTATGTCATGTTTTATGCCAAATGAATTTAAATATTTATTTTTAATGTTT
* * *
40032313 TGATTCATGTTGGAATGATTTGGTAATGTTTCGACATGATTTTC
129 TGATTCATGCTGGAATGATTTGATAATGTTTAGACATGATTTTC
* *
40032357 ATGTGAATGACTTGTTTTGGATTATTTGTTTTTGAAATTGTTTAGCTTAAAATTTATTCCATTCC
1 ATGTGAATGACTTGTTTTGGATTATTTGTTTTTGAAATTGTTTAGCTAAAAATTTATTCCATTCT
*
40032422 GATTTGAATATGTTTATGTCATGTTTTATTCCAAATGAATTTAAATATTTATTTTTAATGTTTTG
66 GATTTGAATATGTTTATGTCATGTTTTATGCCAAATGAATTTAAATATTTATTTTTAATGTTTTG
40032487 ATTCATGCTGGAATGATTTGATAATGTTTAGACATGATTTTC
131 ATTCATGCTGGAATGATTTGATAATGTTTAGACATGATTTTC
** *
40032529 ATACGAATGGCTTGTTTTGGATTATTTGTTTTTGAAATTGTTTAGCTAAAAATTTATTCCATTCT
1 ATGTGAATGACTTGTTTTGGATTATTTGTTTTTGAAATTGTTTAGCTAAAAATTTATTCCATTCT
40032594 GATTTGAATATGT
66 GATTTGAATATGT
40032607 GATACGACCT
Statistics
Matches: 230, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
171 1 0.00
172 200 0.87
173 29 0.13
ACGTcount: A:0.27, C:0.07, G:0.16, T:0.49
Consensus pattern (172 bp):
ATGTGAATGACTTGTTTTGGATTATTTGTTTTTGAAATTGTTTAGCTAAAAATTTATTCCATTCT
GATTTGAATATGTTTATGTCATGTTTTATGCCAAATGAATTTAAATATTTATTTTTAATGTTTTG
ATTCATGCTGGAATGATTTGATAATGTTTAGACATGATTTTC
Found at i:40039334 original size:22 final size:22
Alignment explanation
Indices: 40039285--40039334 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
40039275 GAAAGAAGAA
*
40039285 AAGAAAAAAAGAATCTCGGAGAG
1 AAGAAAAAAAGAA-CTCGGAAAG
*
40039308 AA-AAAAAATGAA-TCGGAAAG
1 AAGAAAAAAAGAACTCGGAAAG
40039328 AAGAAAA
1 AAGAAAA
40039335 GAAAAACCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 9 0.38
21 4 0.17
22 9 0.38
23 2 0.08
ACGTcount: A:0.64, C:0.06, G:0.22, T:0.08
Consensus pattern (22 bp):
AAGAAAAAAAGAACTCGGAAAG
Found at i:40039522 original size:18 final size:19
Alignment explanation
Indices: 40039482--40039523 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
40039472 ATAAAAAATC
* * *
40039482 CTCTCTTTTTTCTTATTTT
1 CTCTCTTTTCTCTGATTTG
40039501 CTCTC-TTTCTCTGATTTG
1 CTCTCTTTTCTCTGATTTG
40039519 CTCTC
1 CTCTC
40039524 GATTTCTGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.05, C:0.29, G:0.05, T:0.62
Consensus pattern (19 bp):
CTCTCTTTTCTCTGATTTG
Found at i:40041565 original size:18 final size:20
Alignment explanation
Indices: 40041542--40041581 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
40041532 TTGTATTACC
*
40041542 TTTAGT-TCACT-TATCGCA
1 TTTAGTCTCACTATATCACA
40041560 TTTAGTCTCACTATATCACA
1 TTTAGTCTCACTATATCACA
40041580 TT
1 TT
40041582 ACACCATAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 5 0.26
20 8 0.42
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (20 bp):
TTTAGTCTCACTATATCACA
Found at i:40044429 original size:18 final size:19
Alignment explanation
Indices: 40044393--40044431 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
40044383 TAAAACACTT
40044393 AAGTCAAAATTCCAAGTCA
1 AAGTCAAAATTCCAAGTCA
*
40044412 AAGTCAAAA-TCTAAGTCA
1 AAGTCAAAATTCCAAGTCA
40044430 AA
1 AA
40044432 ATTTCCAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.21
Consensus pattern (19 bp):
AAGTCAAAATTCCAAGTCA
Found at i:40045815 original size:24 final size:24
Alignment explanation
Indices: 40045781--40045829 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
40045771 TGCGTGGACT
*
40045781 TTTGGCCTAATTTAAAGAAAGAAA
1 TTTGGCCTAATCTAAAGAAAGAAA
*
40045805 TTTGGCGTAATCTAAAGAAAGAAA
1 TTTGGCCTAATCTAAAGAAAGAAA
40045829 T
1 T
40045830 ATCAGAAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (24 bp):
TTTGGCCTAATCTAAAGAAAGAAA
Found at i:40046496 original size:17 final size:18
Alignment explanation
Indices: 40046464--40046498 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
40046454 ATGATCAAAC
40046464 ATATATTTATACTTATAA
1 ATATATTTATACTTATAA
*
40046482 ATATA-TTATATTTATAA
1 ATATATTTATACTTATAA
40046499 TAAGATATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (18 bp):
ATATATTTATACTTATAA
Found at i:40047774 original size:16 final size:17
Alignment explanation
Indices: 40047748--40047781 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
40047738 TAATTTAGCT
40047748 ATTTTTATTTTATTTTA
1 ATTTTTATTTTATTTTA
*
40047765 ATTTTT-TTTTGTTTTA
1 ATTTTTATTTTATTTTA
40047781 A
1 A
40047782 ATCAAATTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (17 bp):
ATTTTTATTTTATTTTA
Found at i:40051584 original size:6 final size:6
Alignment explanation
Indices: 40051573--40051633 Score: 113
Period size: 6 Copynumber: 10.2 Consensus size: 6
40051563 ATTATCTTTT
40051573 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
1 TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG TATTAG
*
40051621 TATTAG AATTAG T
1 TATTAG TATTAG T
40051634 CATATTGGTA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.49
Consensus pattern (6 bp):
TATTAG
Found at i:40053268 original size:20 final size:21
Alignment explanation
Indices: 40053230--40053271 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
40053220 CTTTTTCGAC
*
40053230 TATTTTTCTATTTTGTTATCT
1 TATTTATCTATTTTGTTATCT
*
40053251 TATTTATCT-TTTTTTTATCT
1 TATTTATCTATTTTGTTATCT
40053271 T
1 T
40053272 CTTATTAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.14, C:0.10, G:0.02, T:0.74
Consensus pattern (21 bp):
TATTTATCTATTTTGTTATCT
Found at i:40061046 original size:18 final size:18
Alignment explanation
Indices: 40061023--40061057 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
40061013 TTGTCCCTAC
*
40061023 TGTTGTTTGTTACTGTTT
1 TGTTGTTGGTTACTGTTT
40061041 TGTTGTTGGTTACTGTT
1 TGTTGTTGGTTACTGTT
40061058 GTTTTTTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.26, T:0.63
Consensus pattern (18 bp):
TGTTGTTGGTTACTGTTT
Found at i:40066833 original size:33 final size:33
Alignment explanation
Indices: 40066786--40066921 Score: 191
Period size: 33 Copynumber: 4.1 Consensus size: 33
40066776 CTATTATGCA
* * *
40066786 AGCTCTGCTAAATTGTGAGCTATAATATGTGTG
1 AGCTCTACTGAATTGTGAGCTATAATATGTGCG
* *
40066819 AACTCTACTGAATTGTGAGCTATACTATGTGCG
1 AGCTCTACTGAATTGTGAGCTATAATATGTGCG
*
40066852 AGCTCTACTGAATTGTGAGCTATAACATGTGCG
1 AGCTCTACTGAATTGTGAGCTATAATATGTGCG
* * *
40066885 AGCTCTGCTGAATTGTGAGCTATACTATGTGTG
1 AGCTCTACTGAATTGTGAGCTATAATATGTGCG
40066918 AGCT
1 AGCT
40066922 TTGTTCACTT
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 91 1.00
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (33 bp):
AGCTCTACTGAATTGTGAGCTATAATATGTGCG
Found at i:40066860 original size:16 final size:16
Alignment explanation
Indices: 40066799--40066921 Score: 83
Period size: 16 Copynumber: 7.5 Consensus size: 16
40066789 TCTGCTAAAT
*
40066799 TGTGAGCTATAATATG
1 TGTGAGCTATACTATG
* *
40066815 TGTGAACTCTACTGAAT-
1 TGTGAGCTATACT--ATG
40066832 TGTGAGCTATACTATG
1 TGTGAGCTATACTATG
* *
40066848 TGCGAGCTCTACTGAAT-
1 TGTGAGCTATACT--ATG
40066865 TGTGAGCTATAAC-ATG
1 TGTGAGCTAT-ACTATG
* * *
40066881 TGCGAGCTCTGCTGAAT-
1 TGTGAGCTATACT--ATG
40066898 TGTGAGCTATACTATG
1 TGTGAGCTATACTATG
40066914 TGTGAGCT
1 TGTGAGCT
40066922 TTGTTCACTT
Statistics
Matches: 81, Mismatches: 15, Indels: 22
0.69 0.13 0.19
Matches are distributed among these distances:
15 7 0.09
16 37 0.46
17 29 0.36
18 8 0.10
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (16 bp):
TGTGAGCTATACTATG
Found at i:40069408 original size:83 final size:83
Alignment explanation
Indices: 40069307--40069472 Score: 296
Period size: 83 Copynumber: 2.0 Consensus size: 83
40069297 TGATAAACAC
* * *
40069307 AAGATTGGTTGTATAAGATCCTTAAAAAGGTGCAAGCAAATCATCAAAATATCTTGGTCAAACAT
1 AAGATTGGTTGCACAAGATCCTTAAAAAGGTGCAAGCAAATCACCAAAATATCTTGGTCAAACAT
40069372 GCCAACAAATAAGACAAG
66 GCCAACAAATAAGACAAG
*
40069390 AAGATTGGTTGCACAAGATCCTTAAAAAGGTTCAAGCAAATCACCAAAATATCTTGGTCAAACAT
1 AAGATTGGTTGCACAAGATCCTTAAAAAGGTGCAAGCAAATCACCAAAATATCTTGGTCAAACAT
40069455 GCCAACAAATAAGACAAG
66 GCCAACAAATAAGACAAG
40069473 TTATGTGCTT
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.45, C:0.17, G:0.16, T:0.22
Consensus pattern (83 bp):
AAGATTGGTTGCACAAGATCCTTAAAAAGGTGCAAGCAAATCACCAAAATATCTTGGTCAAACAT
GCCAACAAATAAGACAAG
Found at i:40071449 original size:27 final size:27
Alignment explanation
Indices: 40071408--40071462 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
40071398 AAACAAACAA
*
40071408 ACAAACTTTGCCTGGACCCTTATCATT
1 ACAAACTTTGACTGGACCCTTATCATT
40071435 ACAAACTTTGACTGGACCCTTATCATT
1 ACAAACTTTGACTGGACCCTTATCATT
40071462 A
1 A
40071463 TTCCAAAACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (27 bp):
ACAAACTTTGACTGGACCCTTATCATT
Found at i:40071933 original size:14 final size:14
Alignment explanation
Indices: 40071914--40071945 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
40071904 TTTCCAAATC
40071914 CCAAACTAAATTAG
1 CCAAACTAAATTAG
40071928 CCAAACTAAATTAG
1 CCAAACTAAATTAG
40071942 CCAA
1 CCAA
40071946 CCTTGCCTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (14 bp):
CCAAACTAAATTAG
Found at i:40079085 original size:25 final size:24
Alignment explanation
Indices: 40079014--40079085 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 24
40079004 AAGACTAAAC
40079014 CTAATTCTAAGTTCTTAACTTAAGT
1 CTAATTCTAAGTTC-TAACTTAAGT
* *
40079039 CTAATCCTAAGTTCCAAACTTAAG-
1 CTAATTCTAAGTT-CTAACTTAAGT
*
40079063 CTAAGTTCTACGTTCTAATCTTA
1 CTAA-TTCTAAGTTCTAA-CTTA
40079086 GTTTTATGTC
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
24 7 0.18
25 31 0.79
26 1 0.03
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.39
Consensus pattern (24 bp):
CTAATTCTAAGTTCTAACTTAAGT
Found at i:40087828 original size:14 final size:14
Alignment explanation
Indices: 40087809--40087835 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40087799 GTGCAAAACT
40087809 AATAATTTAACAAA
1 AATAATTTAACAAA
40087823 AATAATTTAACAA
1 AATAATTTAACAA
40087836 TCCAACAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (14 bp):
AATAATTTAACAAA
Found at i:40087954 original size:292 final size:291
Alignment explanation
Indices: 40087544--40088100 Score: 685
Period size: 289 Copynumber: 1.9 Consensus size: 291
40087534 TTTAAGGATT
* * * * * * * *
40087544 CAACCATTGAATTTATCAATATAATTGTATTTTTCATGTATGTAAATTTTCAAACCGATCCAATA
1 CAACAATTAAATTTATCAATATAATTGTACTTTTCATGCATGTAAAATTTCAAACCAAACCAACA
* ** *
40087609 TCTCTATCATATTGATCTAAAAAGTGCATGTATTAATATTTATTGAACGATTGAAATTTTTTTTA
66 TCTCTATCATATCGATCTAAAAAGTGCAAATATTAATATTTATTGAACGATTGAAAGTTTTTTTA
* *** ** *
40087674 CATAAAACAAATAGGT-ATTTTTTTTAATTTACATCAAATTTGGCATGCATGATCTATATAAAAT
131 CAT-AAA-AAATAGCTAAAAATTTTTAATGCACATCAAATTTGACATGCAT-ATCTATAT-AAAT
* * *
40087738 GGAATCTGATATATGA-AGACTGGATCGTTAAAATACT-GATCATACAAAAATATAC-GAAAGAG
192 GGAATATGAAATATGAGAGA-TGGATCATTAAAATACTAG-TCATACAAAAATATACAGAAA-AG
40087800 TGCAAAACTAATAATTTAACAAAAATAATTTAACAATC
254 TGCAAAACTAATAATTTAACAAAAATAATTTAACAATC
* * **
40087838 CAACAATTAAATTTATCGATATAATTGTACTTTTCATGCATGTAAAATTTCAAA-TAAACTGACA
1 CAACAATTAAATTTATCAATATAATTGTACTTTTCATGCATGTAAAATTTCAAACCAAACCAACA
* *
40087902 TCT-TATCATATCGATTTAAAAAGTGTAAATATTAATATTTATTGAACGATTGAAAGTTTTTTTA
66 TCTCTATCATATCGATCTAAAAAGTGCAAATATTAATATTTATTGAACGATTGAAAGTTTTTTTA
* * *
40087966 CATAAAAAATAGCTAAAAATTTTTAATGCACGTCAAGTTTGACATGCATATCTATGTAAATGGAA
131 CATAAAAAATAGCTAAAAATTTTTAATGCACATCAAATTTGACATGCATATCTATATAAATGGAA
* * * * *
40088031 TATGAAATATTAGAGATGGATCATTAAAATACTAGTTATACAAGAATATACAGCAAAGTGTAAAA
196 TATGAAATATGAGAGATGGATCATTAAAATACTAGTCATACAAAAATATACAGAAAAGTGCAAAA
40088096 CTAAT
261 CTAAT
40088101 TCCTCTCCTT
Statistics
Matches: 223, Mismatches: 36, Indels: 13
0.82 0.13 0.05
Matches are distributed among these distances:
289 60 0.27
290 21 0.09
291 29 0.13
292 58 0.26
293 7 0.03
294 48 0.22
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (291 bp):
CAACAATTAAATTTATCAATATAATTGTACTTTTCATGCATGTAAAATTTCAAACCAAACCAACA
TCTCTATCATATCGATCTAAAAAGTGCAAATATTAATATTTATTGAACGATTGAAAGTTTTTTTA
CATAAAAAATAGCTAAAAATTTTTAATGCACATCAAATTTGACATGCATATCTATATAAATGGAA
TATGAAATATGAGAGATGGATCATTAAAATACTAGTCATACAAAAATATACAGAAAAGTGCAAAA
CTAATAATTTAACAAAAATAATTTAACAATC
Found at i:40088437 original size:57 final size:57
Alignment explanation
Indices: 40088308--40088465 Score: 183
Period size: 57 Copynumber: 2.8 Consensus size: 57
40088298 CTATTTGGGG
* * * * * * *
40088308 CCTAAACTTGACAATTGTTTTCACATTGAGGCTTGAATTTCTTTTGTCCAAGTTAATT
1 CCTAAACTTAACAATTGTTCTCAAATTGGGGTTTGAATTT-TTTTATCCAAGTTAATC
* * * * *
40088366 CCTAAACTTCACAATTGTTCTCAAATTGGGGTTTAAACTTTTTTATTCAAGTTAGTC
1 CCTAAACTTAACAATTGTTCTCAAATTGGGGTTTGAATTTTTTTATCCAAGTTAATC
*
40088423 CCTAAACTTAACAATTGTTCTC-AATTAGGGTTTGAATTTTTTT
1 CCTAAACTTAACAATTGTTCTCAAATTGGGGTTTGAATTTTTTT
40088466 TCTTTGTCCA
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
56 18 0.21
57 34 0.40
58 33 0.39
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (57 bp):
CCTAAACTTAACAATTGTTCTCAAATTGGGGTTTGAATTTTTTTATCCAAGTTAATC
Found at i:40089216 original size:16 final size:16
Alignment explanation
Indices: 40089195--40089225 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40089185 CGTTATAATC
*
40089195 TAAAAATTTTAAAAAA
1 TAAAAATTATAAAAAA
40089211 TAAAAATTATAAAAA
1 TAAAAATTATAAAAA
40089226 TTATGAAAAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAAAATTATAAAAAA
Found at i:40089266 original size:25 final size:25
Alignment explanation
Indices: 40089238--40089286 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
40089228 ATGAAAAGCT
*
40089238 AAAATATATAATCTATAAAAAATAAA
1 AAAAT-TAAAATCTATAAAAAATAAA
*
40089264 AAAATTAAAATTTATAAAAAATA
1 AAAATTAAAATCTATAAAAAATA
40089287 TTAGAAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (25 bp):
AAAATTAAAATCTATAAAAAATAAA
Found at i:40089326 original size:19 final size:20
Alignment explanation
Indices: 40089295--40089333 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
40089285 TATTAGAAAC
40089295 ATAAAACATATATAAATATA
1 ATAAAACATATATAAATATA
*
40089315 ATAAAA-ATATATATATATA
1 ATAAAACATATATAAATATA
40089334 CGGAATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAAACATATATAAATATA
Found at i:40092162 original size:24 final size:26
Alignment explanation
Indices: 40092135--40092184 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
40092125 ACTAGGGATT
40092135 AGAG-AAC-TAGTATAG-GTGAACCCA
1 AGAGAAACATAGTAT-GTGTGAACCCA
40092159 AGAGAAACATAGTATGTGTGAACCCA
1 AGAGAAACATAGTATGTGTGAACCCA
40092185 TGTGCGAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 4 0.17
25 4 0.17
26 15 0.65
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (26 bp):
AGAGAAACATAGTATGTGTGAACCCA
Found at i:40092690 original size:34 final size:34
Alignment explanation
Indices: 40092650--40092747 Score: 101
Period size: 34 Copynumber: 2.9 Consensus size: 34
40092640 AACCCTTAGG
*
40092650 TGTGCGAGCCTATATATTATGTGAACCCTAAGTT
1 TGTGCGAGCCTATATATTATGTGAACCCTAAGTC
* * *
40092684 TGTGCGAGCCTACA-AGTTATGCGAACCCTAGGTC
1 TGTGCGAGCCTATATA-TTATGTGAACCCTAAGTC
* * *
40092718 TATGCG-GTCTTATATGTTATGTGAACCCTA
1 TGTGCGAG-CCTATATATTATGTGAACCCTA
40092748 GATGCGAACC
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
33 2 0.04
34 50 0.96
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.33
Consensus pattern (34 bp):
TGTGCGAGCCTATATATTATGTGAACCCTAAGTC
Found at i:40100043 original size:46 final size:46
Alignment explanation
Indices: 40099911--40100054 Score: 121
Period size: 46 Copynumber: 3.1 Consensus size: 46
40099901 AATATTGATG
* ** * * **
40099911 TATTGTCGAGTCCCCAACATATGCAA-GAGCTCAAAACCTAAACCTA
1 TATTCTCGAGTCTACAACATATG-AAGGAGCTTAGAACCTATTCCTA
* * * * * * *
40099957 TATTCTCTAGTTTGCAACACATGTAGGAGC-TCGAAACCTATTCCTG
1 TATTCTCGAGTCTACAACATATGAAGGAGCTTAG-AACCTATTCCTA
*
40100003 TATTCTCGAGTCTACAACATATGAAGGAGCTTAGAACCTATTCATA
1 TATTCTCGAGTCTACAACATATGAAGGAGCTTAGAACCTATTCCTA
40100049 TATTCT
1 TATTCT
40100055 TGAGCCCGGA
Statistics
Matches: 74, Mismatches: 21, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
45 1 0.01
46 71 0.96
47 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.30
Consensus pattern (46 bp):
TATTCTCGAGTCTACAACATATGAAGGAGCTTAGAACCTATTCCTA
Found at i:40102335 original size:17 final size:18
Alignment explanation
Indices: 40102310--40102346 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
40102300 TATATATCAG
40102310 ATTTAAAAATAACT-CTA
1 ATTTAAAAATAACTCCTA
*
40102327 ATTTTAAAATAACTCCTA
1 ATTTAAAAATAACTCCTA
40102345 AT
1 AT
40102347 CATATTACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.38
Consensus pattern (18 bp):
ATTTAAAAATAACTCCTA
Found at i:40102430 original size:17 final size:17
Alignment explanation
Indices: 40102393--40102436 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
40102383 CAAGTTTTTC
**
40102393 AAACCCTAATTCAAATC
1 AAACCCTAATTCAAAAA
*
40102410 AAACCCTAATTTAAAAA
1 AAACCCTAATTCAAAAA
40102427 AAACTCCTAA
1 AAAC-CCTAA
40102437 CCATATATAC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 18 0.78
18 5 0.22
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (17 bp):
AAACCCTAATTCAAAAA
Found at i:40102800 original size:28 final size:28
Alignment explanation
Indices: 40102759--40102826 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
40102749 TTGTAGATGT
40102759 GAGTCAATATATGCAAATCATTATATGC
1 GAGTCAATATATGCAAATCATTATATGC
* * *
40102787 TAGTCAATATATGCTAGTCATTATATGC
1 GAGTCAATATATGCAAATCATTATATGC
*
40102815 GATTCAATATAT
1 GAGTCAATATAT
40102827 ATCCAAGTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (28 bp):
GAGTCAATATATGCAAATCATTATATGC
Found at i:40102825 original size:14 final size:14
Alignment explanation
Indices: 40102760--40102826 Score: 80
Period size: 14 Copynumber: 4.8 Consensus size: 14
40102750 TGTAGATGTG
*
40102760 AGTCAATATATGCA
1 AGTCAATATATGCT
* *
40102774 AATCATTATATGCT
1 AGTCAATATATGCT
40102788 AGTCAATATATGCT
1 AGTCAATATATGCT
* *
40102802 AGTCATTATATGCG
1 AGTCAATATATGCT
*
40102816 ATTCAATATAT
1 AGTCAATATAT
40102827 ATCCAAGTAA
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 44 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.37
Consensus pattern (14 bp):
AGTCAATATATGCT
Found at i:40103128 original size:34 final size:34
Alignment explanation
Indices: 40103084--40103164 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
40103074 AACCTATATA
* *
40103084 TTATGCGAACCCTAGGTCTATATGAGCCTACATG
1 TTATGCGAACCCTAAGTCTATACGAGCCTACATG
* * *
40103118 TTATGTGAACCCTAAGTCTATGCGAGCCTATATG
1 TTATGCGAACCCTAAGTCTATACGAGCCTACATG
*
40103152 TTATGCAAACCCT
1 TTATGCGAACCCT
40103165 CACTTGTGAG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (34 bp):
TTATGCGAACCCTAAGTCTATACGAGCCTACATG
Found at i:40106200 original size:20 final size:19
Alignment explanation
Indices: 40106159--40106207 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
40106149 ATGCATTATG
40106159 AAATTATAAAAAAACATAAA
1 AAATT-TAAAAAAACATAAA
* *
40106179 AAATTTAAAATAATCATTAA
1 AAATTTAAAA-AAACATAAA
*
40106199 AATTTTAAA
1 AAATTTAAA
40106208 TTTTATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (19 bp):
AAATTTAAAAAAACATAAA
Found at i:40107915 original size:30 final size:29
Alignment explanation
Indices: 40107881--40107956 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 29
40107871 ATTTTGATGA
*
40107881 TATTTTATAATTATTTAATTAGATAAATAT
1 TATTTTATAATTATTTAATGAGAT-AATAT
*
40107911 TATTTTATTAA-TATTTTAATGAGATATTAT
1 TATTTTA-TAATTA-TTTAATGAGATAATAT
*
40107941 TATTATTATTATTATT
1 TATT-TTATAATTATT
40107957 ATTATTATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 21 0.54
31 18 0.46
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (29 bp):
TATTTTATAATTATTTAATGAGATAATAT
Found at i:40107936 original size:31 final size:30
Alignment explanation
Indices: 40107881--40107956 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 30
40107871 ATTTTGATGA
*
40107881 TATTTTA-TAAT-TATTTAATTAGATAAATAT
1 TATTTTATTAATAT-TTTAATGAGAT-AATAT
*
40107911 TATTTTATTAATATTTTAATGAGATATTAT
1 TATTTTATTAATATTTTAATGAGATAATAT
*
40107941 TATTATTATTATTATT
1 TATT-TTATTAATATT
40107957 ATTATTATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
30 15 0.38
31 24 0.60
32 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (30 bp):
TATTTTATTAATATTTTAATGAGATAATAT
Found at i:40107943 original size:3 final size:3
Alignment explanation
Indices: 40107935--40107967 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
40107925 TTTAATGAGA
40107935 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40107968 ATTTAGTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40111009 original size:15 final size:15
Alignment explanation
Indices: 40110991--40111019 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
40110981 TTTAAATTCT
40110991 ATTTAATTTAATTTG
1 ATTTAATTTAATTTG
40111006 ATTTAATTTAATTT
1 ATTTAATTTAATTT
40111020 TTAAAATTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTAATTTAATTTG
Found at i:40115217 original size:18 final size:20
Alignment explanation
Indices: 40115194--40115232 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
40115184 ATATTTGATA
40115194 AATTAT-TTTTTC-TAAATT
1 AATTATATTTTTCTTAAATT
40115212 AATTATATTTTTCTTAAATT
1 AATTATATTTTTCTTAAATT
40115232 A
1 A
40115233 TAAATAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 6 0.32
20 7 0.37
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (20 bp):
AATTATATTTTTCTTAAATT
Found at i:40116189 original size:27 final size:27
Alignment explanation
Indices: 40116154--40116209 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
40116144 TTTCATAATG
* **
40116154 TCAATTAAGCACAACATTGATCATTAA
1 TCAAATAAGCACAACATCAATCATTAA
*
40116181 TCAAATAAGCACAATATCAATCATTAA
1 TCAAATAAGCACAACATCAATCATTAA
40116208 TC
1 TC
40116210 CAATTATCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.46, C:0.20, G:0.05, T:0.29
Consensus pattern (27 bp):
TCAAATAAGCACAACATCAATCATTAA
Found at i:40121345 original size:41 final size:41
Alignment explanation
Indices: 40121263--40121352 Score: 108
Period size: 41 Copynumber: 2.2 Consensus size: 41
40121253 TTCTAATTCT
* * *
40121263 TGAAAAGGTTGAAAAGGTAGATATCCGAAATGGATATCAAA
1 TGAAAAGGTTGAAAAGGTAGATACCCGAAAAGGATAACAAA
* * * * *
40121304 TGAAAAGTTTGAAAAGGTTGTTACCCTAAAAGGTTAACAAA
1 TGAAAAGGTTGAAAAGGTAGATACCCGAAAAGGATAACAAA
40121345 TGAAAAGG
1 TGAAAAGG
40121353 ATGTATTGAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (41 bp):
TGAAAAGGTTGAAAAGGTAGATACCCGAAAAGGATAACAAA
Found at i:40129678 original size:35 final size:33
Alignment explanation
Indices: 40129604--40129681 Score: 86
Period size: 35 Copynumber: 2.3 Consensus size: 33
40129594 TTTAATCAAA
*
40129604 TTCCTTATTTATTTACTTTATTTACTTAATATT
1 TTCCTTATTTATTTACATTATTTACTTAATATT
* * *
40129637 TCCCTTATTTCATTTTCACATT-TTTATTTATTATT
1 TTCCTTATTT-A-TTT-ACATTATTTACTTAATATT
40129672 TTCCTTATTT
1 TTCCTTATTT
40129682 GTTTTTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
33 9 0.24
34 1 0.03
35 23 0.62
36 4 0.11
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.64
Consensus pattern (33 bp):
TTCCTTATTTATTTACATTATTTACTTAATATT
Found at i:40129757 original size:12 final size:12
Alignment explanation
Indices: 40129740--40129765 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40129730 TTGTTAGTTA
40129740 TATTATTATTGT
1 TATTATTATTGT
40129752 TATTATTATTGT
1 TATTATTATTGT
40129764 TA
1 TA
40129766 CTATATTATC
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:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (12 bp):
TATTATTATTGT
Found at i:40129978 original size:35 final size:35
Alignment explanation
Indices: 40129939--40130008 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
40129929 ACATAATCAA
40129939 ATAAACTACACATATATTATTTTTAGATATTTCAT
1 ATAAACTACACATATATTATTTTTAGATATTTCAT
40129974 ATAAACTACACATATATTATTTTTAGATATTTCAT
1 ATAAACTACACATATATTATTTTTAGATATTTCAT
40130009 CAACTTTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.11, G:0.03, T:0.46
Consensus pattern (35 bp):
ATAAACTACACATATATTATTTTTAGATATTTCAT
Found at i:40130640 original size:67 final size:67
Alignment explanation
Indices: 40130557--40130688 Score: 203
Period size: 67 Copynumber: 2.0 Consensus size: 67
40130547 AAAGGATTGG
*
40130557 TGGCGACTCCATTTTCGCTTTTAAATAAAAAAGTCAACC-CTTTTACAAAAAAATGGTTTCGACA
1 TGGCGACTCCATTTTCGCTTTTAAATAAAAAAGTCAACCTCTTTTAC-AAAAAATGGTTTCAACA
40130621 GCA
65 GCA
* * **
40130624 TGGCGACTCCATTTTCGTTTTTAAATAAAAAATTTGACCTCTTTTACAAAAAATGGTTTCAACAG
1 TGGCGACTCCATTTTCGCTTTTAAATAAAAAAGTCAACCTCTTTTACAAAAAATGGTTTCAACAG
40130689 TTTTGAAACA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 52 0.88
68 7 0.12
ACGTcount: A:0.35, C:0.19, G:0.13, T:0.33
Consensus pattern (67 bp):
TGGCGACTCCATTTTCGCTTTTAAATAAAAAAGTCAACCTCTTTTACAAAAAATGGTTTCAACAG
CA
Found at i:40136715 original size:11 final size:11
Alignment explanation
Indices: 40136696--40136735 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
40136686 TTAATTGTTA
40136696 ATTTTCTTTAT
1 ATTTTCTTTAT
*
40136707 ATATTCTTTA-
1 ATTTTCTTTAT
*
40136717 ATTTTTTTTAT
1 ATTTTCTTTAT
40136728 ATTTTCTT
1 ATTTTCTT
40136736 AAAAATATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (11 bp):
ATTTTCTTTAT
Found at i:40136719 original size:21 final size:21
Alignment explanation
Indices: 40136693--40136735 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
40136683 TTATTAATTG
40136693 TTAATTTTCTTTATATATTCT
1 TTAATTTTCTTTATATATTCT
* *
40136714 TTAATTTTTTTTATATTTTCT
1 TTAATTTTCTTTATATATTCT
40136735 T
1 T
40136736 AAAAATATAA
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:0.21, C:0.07, G:0.00, T:0.72
Consensus pattern (21 bp):
TTAATTTTCTTTATATATTCT
Found at i:40137381 original size:29 final size:30
Alignment explanation
Indices: 40137334--40137393 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
40137324 CTTTATAGGG
* *
40137334 TTTTATTTTTTTTATAAAAATTATATAATT
1 TTTTAGTTGTTTTATAAAAATTATATAATT
* *
40137364 TTTTAGTTGTTTT-TAAAATTTTTATAATT
1 TTTTAGTTGTTTTATAAAAATTATATAATT
40137393 T
1 T
40137394 ATTAAAATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (30 bp):
TTTTAGTTGTTTTATAAAAATTATATAATT
Found at i:40153949 original size:104 final size:105
Alignment explanation
Indices: 40153802--40154050 Score: 324
Period size: 104 Copynumber: 2.4 Consensus size: 105
40153792 AAAAGTACAT
* * * * *
40153802 TAAAAAAACACAAAGCACTAAACTAAAAAC-AAGTAATTTATATAACCTAATCATAAATTACTAA
1 TAAAAAATCACAAAACACTATACTAAACACTAA-CAATTTATATAACCTAATCATAAATTACTAA
* **
40153866 CAGAATAACTATAAAATTA-ATTTTAAAAAAAATACATTGC
65 CAAAATAACTATAAAATTATATTTTAAAAAAAATACATCAC
*
40153906 TAAAAAATCATAAAACAC-ATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAA
1 TAAAAAATCACAAAACACTAT-ACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAA
* * **
40153970 CAAAATAACTATAAAATTATTTTTTTTAAAAACTTACATCAC
65 CAAAATAACTATAAAATTA-TATTTTAAAAAAAATACATCAC
*
40154012 TAAAAAATCACAAAACTCTATACTAAACACTAACAATTT
1 TAAAAAATCACAAAACACTATACTAAACACTAACAATTT
40154051 GTAACCTAAC
Statistics
Matches: 125, Mismatches: 15, Indels: 8
0.84 0.10 0.05
Matches are distributed among these distances:
103 1 0.01
104 71 0.57
105 2 0.02
106 49 0.39
107 2 0.02
ACGTcount: A:0.55, C:0.16, G:0.02, T:0.28
Consensus pattern (105 bp):
TAAAAAATCACAAAACACTATACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
AAAATAACTATAAAATTATATTTTAAAAAAAATACATCAC
Found at i:40154077 original size:106 final size:104
Alignment explanation
Indices: 40153802--40154083 Score: 304
Period size: 104 Copynumber: 2.7 Consensus size: 104
40153792 AAAAGTACAT
* * * * *
40153802 TAAAAAAACACAAAGCAC-TAAACTAAAAAC-AAGTAATTTATATAACCTAATCATAAATTACTA
1 TAAAAAATCACAAAACACAT-AACTAAACACTAA-CAATTTATATAACCTAACCATAAATTACTA
* **
40153865 ACAGAATAACTATAAAATTAATTTTAAAAAAAATACATTGC
64 ACAAAATAACTATAAAATTAATTTTAAAAAAAATACATCAC
* *
40153906 TAAAAAATCATAAAACACATAACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAAC
1 TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAACCATAAATTACTAAC
* * **
40153971 AAAATAACTATAAAATTATTTTTTTTAAAAACTTACATCAC
66 AAAATAACTATAAAATTA--ATTTTAAAAAAAATACATCAC
* * **
40154012 TAAAAAATCACAAAACTC-TATACTAAACACTAACAA-TT-TGTAACCTAACCCCATAAATTGTT
1 TAAAAAATCACAAAACACATA-ACTAAACACTAACAATTTATATAACCTAA--CCATAAATTACT
40154074 AACAAAATAA
63 AACAAAATAA
40154084 ATAACTATAA
Statistics
Matches: 153, Mismatches: 18, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
104 81 0.53
105 7 0.05
106 65 0.42
ACGTcount: A:0.54, C:0.16, G:0.02, T:0.28
Consensus pattern (104 bp):
TAAAAAATCACAAAACACATAACTAAACACTAACAATTTATATAACCTAACCATAAATTACTAAC
AAAATAACTATAAAATTAATTTTAAAAAAAATACATCAC
Found at i:40154244 original size:38 final size:38
Alignment explanation
Indices: 40154197--40154391 Score: 153
Period size: 38 Copynumber: 5.3 Consensus size: 38
40154187 AAACTCACAA
*
40154197 AACACAATAATTTATAATAAATTACTAACAAAATATTT
1 AACAAAATAATTTATAATAAATTACTAACAAAATATTT
* * ***
40154235 AACAAAATAA-TT-T--TACATTACTAA-AAACTCACAA
1 AACAAAATAATTTATAATAAATTACTAACAAAAT-ATTT
*
40154269 AAC-ACATAAATTTATAATAAATTACTAACAAAATATTT
1 AACAAAAT-AATTTATAATAAATTACTAACAAAATATTT
* * ***
40154307 AACAAAATAA-TT-T--TACATTACTAA-AAACTCACAA
1 AACAAAATAATTTATAATAAATTACTAACAAAAT-ATTT
*
40154341 AAC-ACATAAATTTATAATAAATTACTAACAAAATATTT
1 AACAAAAT-AATTTATAATAAATTACTAACAAAATATTT
40154379 AACAAAATAATTT
1 AACAAAATAATTT
40154392 TACATTACTA
Statistics
Matches: 116, Mismatches: 25, Indels: 32
0.67 0.14 0.18
Matches are distributed among these distances:
33 14 0.12
34 32 0.28
35 4 0.03
36 4 0.03
37 4 0.03
38 44 0.38
39 14 0.12
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (38 bp):
AACAAAATAATTTATAATAAATTACTAACAAAATATTT
Found at i:40154250 original size:72 final size:72
Alignment explanation
Indices: 40154163--40154410 Score: 459
Period size: 72 Copynumber: 3.5 Consensus size: 72
40154153 AAAATTATTT
40154163 TTTAA-AAAA-AA-TTTACATTACTAAAAACTCACAAAACACA-ATAATTTATAATAAATTACTA
1 TTTAACAAAATAATTTTACATTACTAAAAACTCACAAAACACATA-AATTTATAATAAATTACTA
40154224 ACAAAATA
65 ACAAAATA
40154232 TTTAACAAAATAATTTTACATTACTAAAAACTCACAAAACACATAAATTTATAATAAATTACTAA
1 TTTAACAAAATAATTTTACATTACTAAAAACTCACAAAACACATAAATTTATAATAAATTACTAA
40154297 CAAAATA
66 CAAAATA
40154304 TTTAACAAAATAATTTTACATTACTAAAAACTCACAAAACACATAAATTTATAATAAATTACTAA
1 TTTAACAAAATAATTTTACATTACTAAAAACTCACAAAACACATAAATTTATAATAAATTACTAA
40154369 CAAAATA
66 CAAAATA
40154376 TTTAACAAAATAATTTTACATTACTAAAAACTCAC
1 TTTAACAAAATAATTTTACATTACTAAAAACTCAC
40154411 CAAATACTAA
Statistics
Matches: 175, Mismatches: 0, Indels: 5
0.97 0.00 0.03
Matches are distributed among these distances:
69 5 0.03
70 4 0.02
71 2 0.01
72 163 0.93
73 1 0.01
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (72 bp):
TTTAACAAAATAATTTTACATTACTAAAAACTCACAAAACACATAAATTTATAATAAATTACTAA
CAAAATA
Found at i:40154286 original size:41 final size:41
Alignment explanation
Indices: 40154241--40154358 Score: 105
Period size: 34 Copynumber: 3.1 Consensus size: 41
40154231 ATTTAACAAA
40154241 ATAATTTTACATTACTAAAAACTCACAAAACACATAAATTT
1 ATAATTTTACATTACTAAAAACTCACAAAACACATAAATTT
* * ***
40154282 ATAA---TAAATTACTAACAAAAT-A-TTTA-AC--AAA---
1 ATAATTTTACATTACTAA-AAACTCACAAAACACATAAATTT
40154313 ATAATTTTACATTACTAAAAACTCACAAAACACATAAATTT
1 ATAATTTTACATTACTAAAAACTCACAAAACACATAAATTT
40154354 ATAAT
1 ATAAT
40154359 AAATTACTAA
Statistics
Matches: 55, Mismatches: 10, Indels: 24
0.62 0.11 0.27
Matches are distributed among these distances:
31 4 0.07
33 4 0.07
34 14 0.25
35 1 0.02
36 4 0.07
37 1 0.02
38 14 0.25
39 4 0.07
41 9 0.16
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (41 bp):
ATAATTTTACATTACTAAAAACTCACAAAACACATAAATTT
Found at i:40154476 original size:144 final size:143
Alignment explanation
Indices: 40154164--40154443 Score: 401
Period size: 144 Copynumber: 2.0 Consensus size: 143
40154154 AAATTATTTT
*
40154164 TTAA-AAAA-AAT-TTACATTACTAAAAACTCACAAAACACAATAATTTATAATAAATTACTAAC
1 TTAACAAAATAATATTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAAC
* * *
40154226 AAAATATTTAACAAAATAATTTTACATTACTAAAAACTCACAAAACACATAAATTTATAATAAAT
66 AAAATATTTAACAAAATAATTTTACATTACTAAAAACTCACAAAACAAATAAA-TCACAATAAAT
*
40154291 TACTAACAAAATAT
130 TACTAACAAAATAA
*
40154305 TTAACAAAATAATTTTACATTACTAAAAACTCACAAAACACATA-AATTTATAATAAATTACTAA
1 TTAACAAAATAATATTACATTACTAAAAACTCACAAAACACA-ACAATTTATAATAAATTACTAA
40154369 CAAAATATTTAACAAAATAATTTTACATTACTAAAAACTCACCAAATACTAAACTAAA-CACAAT
65 CAAAATATTTAACAAAATAATTTTACATTACTAAAAACTCA-CAAA-AC-AAA-TAAATCACAAT
*
40154433 AATTTA-TAACA
126 AAATTACTAACA
40154444 TAATCATAAA
Statistics
Matches: 127, Mismatches: 4, Indels: 12
0.89 0.03 0.08
Matches are distributed among these distances:
141 4 0.03
142 4 0.03
143 3 0.02
144 89 0.70
145 10 0.08
146 11 0.09
147 2 0.02
148 4 0.03
ACGTcount: A:0.56, C:0.15, G:0.00, T:0.30
Consensus pattern (143 bp):
TTAACAAAATAATATTACATTACTAAAAACTCACAAAACACAACAATTTATAATAAATTACTAAC
AAAATATTTAACAAAATAATTTTACATTACTAAAAACTCACAAAACAAATAAATCACAATAAATT
ACTAACAAAATAA
Found at i:40154488 original size:144 final size:143
Alignment explanation
Indices: 40154164--40154501 Score: 385
Period size: 144 Copynumber: 2.4 Consensus size: 143
40154154 AAATTATTTT
* *
40154164 TTAA-AAAA-AAT-TTACATTACTAAAAACTCACAAAACACAATAATTTATAATAAATTACTAAC
1 TTAACAAAATAATATTACATTACTAAAAAATCACAAAACACAACAATTTATAATAAATTACTAAC
* * *
40154226 AAAATATTTAACAAAATAATTTTACATTACTAAAAACTCACAAAACACATAAATTTATAATAAAT
66 AAAATATTTAACAAAATAATTTTACATTACTAAAAACTCACAAAACAAATAAA-TCACAATAAAT
*
40154291 TACTAACAAAATAT
130 TACTAACAAAATAA
* *
40154305 TTAACAAAATAATTTTACATTACTAAAAACTCACAAAACACATA-AATTTATAATAAATTACTAA
1 TTAACAAAATAATATTACATTACTAAAAAATCACAAAACACA-ACAATTTATAATAAATTACTAA
40154369 CAAAATATTTAACAAAATAATTTTACATTACTAAAAACTCACCAAATACTAAACTAAA-CACAAT
65 CAAAATATTTAACAAAATAATTTTACATTACTAAAAACTCA-CAAA-AC-AAA-TAAATCACAAT
*
40154433 AATTTA-TAACATAATCATAAA
126 AAATTACTAACA-AA--AT-AA
* * *
40154454 TT-AC-TAATAA-ATTA-ATT-TTAAAATAATTAC-AAACACAACAATTTATAA
1 TTAACAAAATAATATTACATTACTAAAA-AATCACAAAACACAACAATTTATAA
40154502 CATAATCCTA
Statistics
Matches: 173, Mismatches: 10, Indels: 25
0.83 0.05 0.12
Matches are distributed among these distances:
141 4 0.02
142 4 0.02
143 4 0.02
144 110 0.64
145 17 0.10
146 16 0.09
147 7 0.04
148 8 0.05
149 3 0.02
ACGTcount: A:0.56, C:0.14, G:0.00, T:0.30
Consensus pattern (143 bp):
TTAACAAAATAATATTACATTACTAAAAAATCACAAAACACAACAATTTATAATAAATTACTAAC
AAAATATTTAACAAAATAATTTTACATTACTAAAAACTCACAAAACAAATAAATCACAATAAATT
ACTAACAAAATAA
Found at i:40154497 original size:60 final size:60
Alignment explanation
Indices: 40154424--40154542 Score: 211
Period size: 60 Copynumber: 2.0 Consensus size: 60
40154414 ATACTAAACT
* *
40154424 AAACACAATAATTTATAACATAATCATAAATTACTAATAAATTAATTTTAAAATAATTAC
1 AAACACAACAATTTATAACATAATCATAAATTACTAACAAATTAATTTTAAAATAATTAC
*
40154484 AAACACAACAATTTATAACATAATCCTAAATTACTAACAAATTAATTTTAAAATAATTA
1 AAACACAACAATTTATAACATAATCATAAATTACTAACAAATTAATTTTAAAATAATTA
40154543 TAAAAAAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.34
Consensus pattern (60 bp):
AAACACAACAATTTATAACATAATCATAAATTACTAACAAATTAATTTTAAAATAATTAC
Found at i:40154712 original size:4 final size:4
Alignment explanation
Indices: 40154703--40154728 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
40154693 CATTACATTT
40154703 TTTC TTTC TTTC TTTC TTTC TTTC TT
1 TTTC TTTC TTTC TTTC TTTC TTTC TT
40154729 CTTCTCCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTC
Found at i:40155099 original size:38 final size:38
Alignment explanation
Indices: 40155056--40155130 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
40155046 TCTAATATCA
*
40155056 CATCTTTAGAAAAGATAAAGTCGTTTTCTTTGAATTAC
1 CATCTTTAGAAAAGATAAAGTCATTTTCTTTGAATTAC
*
40155094 CATCTTTAGAAAAGATAGAGTCATTTTCTTTGAATTA
1 CATCTTTAGAAAAGATAAAGTCATTTTCTTTGAATTA
40155131 GTTGTGTACC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (38 bp):
CATCTTTAGAAAAGATAAAGTCATTTTCTTTGAATTAC
Found at i:40156900 original size:17 final size:18
Alignment explanation
Indices: 40156874--40156919 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
40156864 TTTTATAGAT
40156874 TTTA-ATAATTATTA-AC
1 TTTATATAATTATTATAC
40156890 TTTATATAATTATTATAC
1 TTTATATAATTATTATAC
*
40156908 -ATATATAATTAT
1 TTTATATAATTAT
40156920 AGCATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 4 0.15
17 21 0.78
18 2 0.07
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (18 bp):
TTTATATAATTATTATAC
Found at i:40158734 original size:27 final size:28
Alignment explanation
Indices: 40158698--40158754 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 28
40158688 ACCAAAATGT
40158698 TATAACTTTTTTTATTTACCAAAAAATA
1 TATAACTTTTTTTATTTACCAAAAAATA
*
40158726 TATAA-TTTTTTTATTTACCAAAATATA
1 TATAACTTTTTTTATTTACCAAAAAATA
40158753 TA
1 TA
40158755 AAAAAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 23 0.82
28 5 0.18
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (28 bp):
TATAACTTTTTTTATTTACCAAAAAATA
Found at i:40158899 original size:27 final size:27
Alignment explanation
Indices: 40158831--40158900 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
40158821 CGCCAATGGG
*
40158831 ATTGGCGGCACCAAAGGTGCCAAAGCC
1 ATTGGCGGCACCAATGGTGCCAAAGCC
40158858 ATTGGCGGCACCAATGGTGCCAATA-CC
1 ATTGGCGGCACCAATGGTGCCAA-AGCC
40158885 ATTGGCGGCACCAATG
1 ATTGGCGGCACCAATG
40158901 TATATTGGGG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 40 0.98
28 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.16
Consensus pattern (27 bp):
ATTGGCGGCACCAATGGTGCCAAAGCC
Found at i:40158951 original size:4 final size:4
Alignment explanation
Indices: 40158942--40159172 Score: 145
Period size: 4 Copynumber: 55.0 Consensus size: 4
40158932 GAAGGAGAGG
*
40158942 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GGAGAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA -GA-AA GAAA GAAA
* * * *
40158992 G-AA -AAA GAAG GAAA GAAAA GGGAA G-GA GAAGA GAAA AAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA G-AAA -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA
*
40159040 GGAGAA GAAAA GGAAA GGAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAAA
1 -GA-AA G-AAA -GAAA -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
* *
40159090 GGAAA G-GA GAAGA GAAA AAAA GAAA GAAA G-AA G-AA GAAAA GGAAA
1 -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA
* *
40159135 GGAGAA GAAA -AAA GAAA AAAA GAAG GAAA GAAAA GAAA
1 -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA GAAA
40159173 AGGAGAAAAG
Statistics
Matches: 184, Mismatches: 19, Indels: 48
0.73 0.08 0.19
Matches are distributed among these distances:
3 20 0.11
4 102 0.55
5 50 0.27
6 12 0.07
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:40158988 original size:34 final size:34
Alignment explanation
Indices: 40158950--40159172 Score: 138
Period size: 34 Copynumber: 6.4 Consensus size: 34
40158940 GGGAAAGAAA
40158950 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAG
1 GAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAG
*
40158984 GAAAGAAAG-AA-AAAGAAGGAAAGAAAAGG-GAAGG
1 GAAAGAAAGAAAGAAAGAAAGAAAG-AAAGGAG-A-G
* *
40159018 AGAAGAGAAAAAAAGAAAGAAAGGAGAAGAAAAGGAAAG
1 -GAA-AGAAAGAAAGAAAGAAA-GA-AAG-AAAGGAGAG
* * * * *
40159057 GAGA-AGAAAAAAGAAAGAAAGAAGGAAAGAAAAG
1 GAAAGA-AAGAAAGAAAGAAAGAAAGAAAGGAGAG
* * *
40159091 GAAAG-GAGAAGAGAAAAAAAGAAAGAAAGAAGAAG
1 GAAAGAAAGAA-AGAAAGAAAGAAAGAAAGGAG-AG
* *
40159126 AAAAGGAAAGGAGAAGAAA-AAAGAAA-AAAAGA-AG
1 GAAA-GAAA-GA-AAGAAAGAAAGAAAGAAAGGAGAG
40159160 GAAAGAAAAGAAA
1 GAAAG-AAAGAAA
40159173 AGGAGAAAAG
Statistics
Matches: 152, Mismatches: 18, Indels: 40
0.72 0.09 0.19
Matches are distributed among these distances:
32 14 0.09
33 14 0.09
34 47 0.31
35 10 0.07
36 13 0.09
37 25 0.16
38 15 0.10
39 4 0.03
40 10 0.07
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (34 bp):
GAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAG
Found at i:40159072 original size:45 final size:45
Alignment explanation
Indices: 40158985--40159194 Score: 207
Period size: 45 Copynumber: 5.0 Consensus size: 45
40158975 AAAGGAGAGG
* * * * *
40158985 AAAGAAAGAAA-AAGAAGGAAAGAAAAGG-GAAGGAGAAGAGAAAA
1 AAAGAAAGAAAGGAGAAGAAAAGGAAAGGAGAA-GAAAAAAGAAAA
40159029 AAAGAAAGAAAGGAGAAGAAAAGGAAAGGAGAAGAAAAAAG----
1 AAAGAAAGAAAGGAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAA
40159070 AAAGAAAG-AAGGA-AAGAAAAGGAAAGGAGAAG-----AGAAAA
1 AAAGAAAGAAAGGAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAA
*
40159108 AAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAA
1 AAAGAAAGAAAGGAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAA
* * * *
40159153 AAAGAAGGAAA-GAAAAGAAAAGGAGAA-AAGAAAAAAAAAGAA
1 AAAGAAAGAAAGGAGAAGAAAAGGA-AAGGAGAAGAAAAAAGAA
40159195 GAAGAAGAGG
Statistics
Matches: 141, Mismatches: 11, Indels: 28
0.78 0.06 0.16
Matches are distributed among these distances:
34 2 0.01
38 8 0.06
39 23 0.16
40 24 0.17
41 8 0.06
44 35 0.25
45 38 0.27
46 3 0.02
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (45 bp):
AAAGAAAGAAAGGAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAA
Found at i:40159200 original size:34 final size:33
Alignment explanation
Indices: 40159101--40159229 Score: 114
Period size: 36 Copynumber: 3.6 Consensus size: 33
40159091 GAAAGGAGAA
40159101 GAGAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAG
1 GAGAAAAAAA-AAA-AAAGAAGAAGAAAA-GAAA--AG
*
40159139 AAGAAAAAAGAAAAAAAGAAGGAAAGAAAAGAAAAG
1 GAGAAAAAA-AAAAAAAGAA-G-AAGAAAAGAAAAG
* **
40159175 GAGAAAAGAAAAAAAAAGAAGAAGAAGAGGGAAG
1 GAGAAAA-AAAAAAAAAGAAGAAGAAAAGAAAAG
*
40159209 GAAGGAAAAAAAAGAAAAGAA
1 G-A-GAAAAAAAAAAAAAGAA
40159230 AATGTAATTT
Statistics
Matches: 79, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
34 11 0.14
35 13 0.16
36 23 0.29
37 8 0.10
38 16 0.20
39 8 0.10
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (33 bp):
GAGAAAAAAAAAAAAAGAAGAAGAAAAGAAAAG
Found at i:40159217 original size:44 final size:45
Alignment explanation
Indices: 40158943--40159231 Score: 122
Period size: 45 Copynumber: 6.2 Consensus size: 45
40158933 AAGGAGAGGG
* * * * **
40158943 AAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGAAAGGAGAGGAAAG-
1 AAAGAAA-AAA-AAAGAAAAAAAGAAGGAAAGAAAAGAAAAAAAAGA
* * *
40158989 AAAGAAAAAGAAGGAAAGAAAAGGGAAGGAGAAGAGAAA-AAAAGAAAGA
1 AAAGAAAAAAAAAGAAA-AAAA--GAAGGA-AAGA-AAAGAAAAAAAAGA
* * * * ** * *
40159038 AAGGAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAGAAAGAAGGAAAGA
1 AAAGAAAAAAAAAGAAAAAAAGAAGGAAAGA-AAAGAAA-AA--AAAGA
* * * *
40159087 AAAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAG-
1 AAA-GAAA--AAAAAAGAAAAAAAGAAGGAAAGAA-AAGAAAA-AAAAGA
* * **
40159136 -GAGAAGAAAAAAGAAAAAAAGAAGGAAAGAAAAG-AAAAGGAGA
1 AAAGAAAAAAAAAGAAAAAAAGAAGGAAAGAAAAGAAAAAAAAGA
* * * *
40159179 AAAGAAAAAAAAAGAAGAAGAAG-AGGGAAGGAAGGAAAAAAAAGA
1 AAAGAAAAAAAAAGAA-AAAAAGAAGGAAAGAAAAGAAAAAAAAGA
40159224 AAAGAAAA
1 AAAGAAAA
40159232 TGTAATTTTT
Statistics
Matches: 180, Mismatches: 44, Indels: 39
0.68 0.17 0.15
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 31 0.17
45 54 0.30
46 15 0.08
47 9 0.05
48 14 0.08
49 20 0.11
50 7 0.04
51 2 0.01
52 23 0.13
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (45 bp):
AAAGAAAAAAAAAGAAAAAAAGAAGGAAAGAAAAGAAAAAAAAGA
Found at i:40159231 original size:79 final size:79
Alignment explanation
Indices: 40158933--40159202 Score: 378
Period size: 79 Copynumber: 3.5 Consensus size: 79
40158923 GGGGTACCAG
* * *
40158933 AAGGAGAGG-GAA-AGAAAGAAAGAAAGAAAGAAAGAA-AGAAA-GAAAGGAGAGGAAAGAAAG-
1 AAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAG-AAGAAGA-AAAGGAAAGGAGAAGAAA-AAAGA
40158993 -AAAAAGAAGGAAAGAA
63 AAAAAAGAAGGAAAGAA
* * *
40159009 AAGGGAAGGAGAAGAGAAAAAAAGAAAGAAAGGAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAG
1 AAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAA
40159074 AAAGAAGGAAAGAA
66 AAAGAAGGAAAGAA
40159088 AAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAA
1 AAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAA
40159153 AAAGAAGGAAAGAA
66 AAAGAAGGAAAGAA
* *
40159167 AAGAAAAGGAGAAAAG-AAAAAA-AAAG-AAGAAGAAGA
1 AAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGA
40159203 GGGAAGGAAG
Statistics
Matches: 177, Mismatches: 11, Indels: 12
0.88 0.05 0.06
Matches are distributed among these distances:
76 17 0.10
77 18 0.10
78 37 0.21
79 105 0.59
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (79 bp):
AAGGAAAGGAGAAGAGAAAAAAAGAAAGAAAGAAGAAGAAAAGGAAAGGAGAAGAAAAAAGAAAA
AAAGAAGGAAAGAA
Found at i:40160215 original size:15 final size:15
Alignment explanation
Indices: 40160195--40160226 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
40160185 TGATTGGCTA
40160195 ATAAATTTAGAAATT
1 ATAAATTTAGAAATT
40160210 ATAAATTTAGAAATT
1 ATAAATTTAGAAATT
40160225 AT
1 AT
40160227 GATATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (15 bp):
ATAAATTTAGAAATT
Done.