Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D03
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: 50986338
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 218898 characters in sequence are not A, C, G, or T
File 55 of 170
Found at i:16189975 original size:27 final size:26
Alignment explanation
Indices: 16189945--16190043 Score: 110
Period size: 26 Copynumber: 3.7 Consensus size: 26
16189935 AGGCCCATTC
*
16189945 TTTCAGAGAATGCCATGAAA-GCTTTCA
1 TTTCAGA-AATGCCA-CAAAGGCTTTCA
* *
16189972 TTTCAGATATGCCACAAAGGCTTCCA
1 TTTCAGAAATGCCACAAAGGCTTTCA
*
16189998 TTTCAGATATGCCACAAAGGCTTTCA
1 TTTCAGAAATGCCACAAAGGCTTTCA
* *
16190024 TTTCATAGATTGCCACAAAG
1 TTTCAGA-AATGCCACAAAG
16190044 ATATCCATTT
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
25 3 0.05
26 43 0.68
27 17 0.27
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.29
Consensus pattern (26 bp):
TTTCAGAAATGCCACAAAGGCTTTCA
Found at i:16189994 original size:26 final size:26
Alignment explanation
Indices: 16189965--16190043 Score: 124
Period size: 26 Copynumber: 3.0 Consensus size: 26
16189955 TGCCATGAAA
16189965 GCTTTCATTTCAGATATGCCACAAAG
1 GCTTTCATTTCAGATATGCCACAAAG
*
16189991 GCTTCCATTTCAGATATGCCACAAAG
1 GCTTTCATTTCAGATATGCCACAAAG
16190017 GCTTTCATTTCATAGAT-TGCCACAAAG
1 GCTTTCATTTC--AGATATGCCACAAAG
16190044 ATATCCATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
26 35 0.71
27 10 0.20
28 4 0.08
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.30
Consensus pattern (26 bp):
GCTTTCATTTCAGATATGCCACAAAG
Found at i:16190052 original size:27 final size:28
Alignment explanation
Indices: 16189976--16190080 Score: 139
Period size: 27 Copynumber: 3.9 Consensus size: 28
16189966 CTTTCATTTC
16189976 AGATATGCCACAAAGGCTTCCATTTC--
1 AGATATGCCACAAAGGCTTCCATTTCAT
*
16190002 AGATATGCCACAAAGGCTTTCATTTCAT
1 AGATATGCCACAAAGGCTTCCATTTCAT
*
16190030 AGAT-TGCCACAAA-GATATCCATTTCAT
1 AGATATGCCACAAAGGCT-TCCATTTCAT
*
16190057 AGATA-GCCACAAGGGCTTCCATTT
1 AGATATGCCACAAAGGCTTCCATTT
16190081 TTTGGTGTGT
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
26 27 0.39
27 36 0.52
28 6 0.09
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (28 bp):
AGATATGCCACAAAGGCTTCCATTTCAT
Found at i:16191449 original size:7 final size:7
Alignment explanation
Indices: 16191437--16191509 Score: 119
Period size: 7 Copynumber: 10.4 Consensus size: 7
16191427 ATATAACTCT
16191437 TTTCTTC
1 TTTCTTC
16191444 TTTCTTC
1 TTTCTTC
16191451 TTTCTTC
1 TTTCTTC
16191458 TTTCTTC
1 TTTCTTC
*
16191465 TCTCTTC
1 TTTCTTC
*
16191472 TCTCTTC
1 TTTCTTC
16191479 TTTCTTC
1 TTTCTTC
16191486 TTTCTTC
1 TTTCTTC
16191493 TTTCTTC
1 TTTCTTC
*
16191500 TTTCATC
1 TTTCTTC
16191507 TTT
1 TTT
16191510 TAACCTTTAA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 63 1.00
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.68
Consensus pattern (7 bp):
TTTCTTC
Found at i:16193229 original size:15 final size:16
Alignment explanation
Indices: 16193201--16193230 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
16193191 AACGACATGT
16193201 AAAATATCAAATGAAC
1 AAAATATCAAATGAAC
16193217 AAAATAT-AAATGAA
1 AAAATATCAAATGAA
16193231 AACATAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (16 bp):
AAAATATCAAATGAAC
Found at i:16194240 original size:23 final size:22
Alignment explanation
Indices: 16194197--16194292 Score: 71
Period size: 19 Copynumber: 4.6 Consensus size: 22
16194187 AAAAGGTATC
* *
16194197 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
16194218 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
16194241 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
* *
16194260 TACATAT--TAT-ATCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
16194279 TACATATCATATCT
1 TACAAATCATATCT
16194293 AAGACTGCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
17 2 0.03
19 29 0.47
21 6 0.10
22 15 0.24
23 10 0.16
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:16194257 original size:19 final size:19
Alignment explanation
Indices: 16194233--16194324 Score: 130
Period size: 19 Copynumber: 4.8 Consensus size: 19
16194223 AATCATATCT
16194233 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
16194252 TCTAAGATTACATATTATA
1 TCTAAGATTGCATATCATA
*
16194271 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
*
16194290 TCTAAGACTGCATATCATA
1 TCTAAGATTGCATATCATA
* *
16194309 GCTAAGACTGCATATC
1 TCTAAGATTGCATATC
16194325 CTTGAAGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 67 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:16194323 original size:57 final size:59
Alignment explanation
Indices: 16194210--16194323 Score: 151
Period size: 57 Copynumber: 1.9 Consensus size: 59
16194200 AAATTAAATC
* * *
16194210 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATATCTAAGATTACATATTATA
1 TCTAAGATTACAAAATCATA--TTCTAAGACTGCATATCATAGCTAAGACTACATATTATA
* *
16194271 TCTAAGATTAC-ATATCATA-TCTAAGACTGCATATCATAGCTAAGACTGCATAT
1 TCTAAGATTACAAAATCATATTCTAAGACTGCATATCATAGCTAAGACTACATAT
16194324 CCTTGAAGAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
57 30 0.62
60 7 0.15
61 11 0.23
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (59 bp):
TCTAAGATTACAAAATCATATTCTAAGACTGCATATCATAGCTAAGACTACATATTATA
Found at i:16194931 original size:45 final size:45
Alignment explanation
Indices: 16194874--16195297 Score: 192
Period size: 44 Copynumber: 9.7 Consensus size: 45
16194864 TTGTTTATTT
* * *
16194874 AGTCTGCCCCACTGCAATTTCAGGGGGATAAGACTTGATTTCTTG
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCGATTTCTTG
* * *
16194919 AGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTCGCTTTCTTG
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCGATTTCTTG
* * **
16194964 GGTCTGCTCCACTGCAACTTT-AGGGAGATAAGACCCGA---CGCG
1 AGTCTGCTCCACTGCAA-TTTCAGGGAGATAAGACTCGATTTCTTG
* * ** * *
16195006 A-TCTGCT-CTCTGCAACTTCAGAAAGATAAGA-TCTATGAT-TTG
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCGAT-TTCTTG
* ** * * ** *
16195048 AATCCACTCCACTGCAACTTCAGGGAGATAAGATTC-ACCATCTTC
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCGA-TTTCTTG
* * * * * *
16195093 AGTCTGC-CTCACTACAACTTCA-GGAGGATAAGGCTTGCTTACTT-
1 AGTCTGCTC-CACTGCAATTTCAGGGA-GATAAGACTCGATTTCTTG
* * * *
16195137 AGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAGA-TGC--G
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCGATTTCTTG
* * *
16195179 A-TCTGCT-CTCTGCAACTTT-AGAGAGATAAGATCTGTGA-TT-TT-
1 AGTCTGCTCCACTGCAA-TTTCAGGGAGATAAGA-CT-CGATTTCTTG
* * * * * * *
16195221 AATCCGCTCCACTGCGACTTCAGGGAGATAAGA-T-TATTCGCTTT
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCGATT-TCTTG
* *
16195265 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 AGTCTGCTCCACTGCAATTTCAGGGAGATAAGA
16195298 TTCGTCATCT
Statistics
Matches: 291, Mismatches: 59, Indels: 59
0.71 0.14 0.14
Matches are distributed among these distances:
39 4 0.01
40 35 0.12
41 17 0.06
42 10 0.03
43 15 0.05
44 105 0.36
45 103 0.35
46 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (45 bp):
AGTCTGCTCCACTGCAATTTCAGGGAGATAAGACTCGATTTCTTG
Found at i:16195073 original size:84 final size:83
Alignment explanation
Indices: 16194969--16195253 Score: 279
Period size: 84 Copynumber: 3.3 Consensus size: 83
16194959 TCTTGGGTCT
*
16194969 GCTCCACTGCAACTTTAGGGAGATAAGACCCGACGCGATCTGCTCTCTGCAACTTCAGAAAGATA
1 GCTCCACTGCAACTTCAGGGAGATAAGACCCGACGCGATCTGCTCTCTGCAACTTCAGAAAGATA
*
16195034 AGATCTATGATTTGAATCC
66 AGATCT-TGATTTTAATCC
* * * *
16195053 ACTCCACTGCAACTTCAGGGAGATAAGATTCACC-ATCTTC-AGTCTGCCTCACTACAACTTCAG
1 GCTCCACTGCAACTTCAGGGAGATAAGA--C-CCGA-C-GCGA-TCTG-CTCTCTGCAACTTCAG
* * * * * *
16195116 GAGGATAAG-GCTTGCTTACTTAGTCT
59 AAAGATAAGATCTTGATT--TTAATCC
* ** * * *
16195142 GCTCCACTACAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTTAGAGAGATA
1 GCTCCACTGCAACTTCAGGGAGATAAGACCCGACGCGATCTGCTCTCTGCAACTTCAGAAAGATA
16195207 AGATCTGTGATTTTAATCC
66 AGATCT-TGATTTTAATCC
*
16195226 GCTCCACTGCGACTTCAGGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
16195254 TTATTCGCTT
Statistics
Matches: 158, Mismatches: 30, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
84 76 0.48
85 7 0.04
86 7 0.04
87 10 0.06
88 7 0.04
89 51 0.32
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.26
Consensus pattern (83 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACCCGACGCGATCTGCTCTCTGCAACTTCAGAAAGATA
AGATCTTGATTTTAATCC
Found at i:16195208 original size:173 final size:173
Alignment explanation
Indices: 16194882--16195297 Score: 500
Period size: 173 Copynumber: 2.4 Consensus size: 173
16194872 TTAGTCTGCC
* * * ** * **
16194882 CCACTGCAATTTCAGGGGGATAAGACTTGATTTCTTGAGTCTGCTCCACTGTAACTTCAGGGAGA
1 CCACTGCAACTTCAGGGAGATAAGA-TTCACATCTTCAGTCTGCTCCACTACAACTTCAGGGAGA
* * * * *
16194947 TAAGACTCGCTTTCTTGGGTCTGCTCCACTGCAACTTTAGGGAGATAAGACCCGACGCGATCTGC
65 TAAGACTCGCTTACTTGAGTCTGCTCCACTACAACTTCAGGGAGATAAGACCAGACGCGATCTGC
16195012 TCTCTGCAACTTCAGAAAGATAAGATCTATGATTTGAATCCACT
130 TCTCTGCAACTTCAGAAAGATAAGATCTATGATTTGAATCCACT
16195056 CCACTGCAACTTCAGGGAGATAAGATTCACCATCTTCAGTCTGC-CTCACTACAACTTCA-GGAG
1 CCACTGCAACTTCAGGGAGATAAGATTCA-CATCTTCAGTCTGCTC-CACTACAACTTCAGGGA-
* * * *
16195119 GATAAGGCTTGCTTACTT-AGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAGATGCGATCT
63 GATAAGACTCGCTTACTTGAGTCTGCTCCACTACAACTTCAGGGAGATAAGACCAGACGCGATCT
* * * * *
16195183 GCTCTCTGCAACTTTAGAGAGATAAGATCTGTGATTTTAATCCGCT
128 GCTCTCTGCAACTTCAGAAAGATAAGATCTATGATTTGAATCCACT
* * * * *
16195229 CCACTGCGACTTCAGGGAGATAAGATT-ATTC-GCTTTAATCTGCTCCACTGCAACTTCAGGGAG
1 CCACTGCAACTTCAGGGAGATAAGATTCA--CATCTTCAGTCTGCTCCACTACAACTTCAGGGAG
16195292 ATAAGA
64 ATAAGA
16195298 TTCGTCATCT
Statistics
Matches: 207, Mismatches: 29, Indels: 14
0.83 0.12 0.06
Matches are distributed among these distances:
172 28 0.14
173 119 0.57
174 60 0.29
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (173 bp):
CCACTGCAACTTCAGGGAGATAAGATTCACATCTTCAGTCTGCTCCACTACAACTTCAGGGAGAT
AAGACTCGCTTACTTGAGTCTGCTCCACTACAACTTCAGGGAGATAAGACCAGACGCGATCTGCT
CTCTGCAACTTCAGAAAGATAAGATCTATGATTTGAATCCACT
Found at i:16195593 original size:50 final size:50
Alignment explanation
Indices: 16195490--16195593 Score: 127
Period size: 50 Copynumber: 2.1 Consensus size: 50
16195480 TCCAAGCCTT
* *
16195490 AACGCCAGGGAGATAAGATTCACCGTCATGGCTTCAATCTGCTCCGTTAC
1 AACGCCAGGGAAATAAGATTCACCGTCATGGCTTCAATCTGCTCCATTAC
* * ** ** *
16195540 AACGCCAGGGAAATAAGATTCGCCTTTGTGGCTTCAATCTTTTCCATTGC
1 AACGCCAGGGAAATAAGATTCACCGTCATGGCTTCAATCTGCTCCATTAC
16195590 AACG
1 AACG
16195594 TCAAGGCGAT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (50 bp):
AACGCCAGGGAAATAAGATTCACCGTCATGGCTTCAATCTGCTCCATTAC
Found at i:16195711 original size:44 final size:44
Alignment explanation
Indices: 16195661--16195780 Score: 165
Period size: 44 Copynumber: 2.7 Consensus size: 44
16195651 ATCTGTTATT
* *
16195661 TTCAACCTACTCCACTGTTGCTCAGGGAGATAGGA-TTCACAATC
1 TTCAACCTATTCCACTGATGCTCAGGGAGATAGGACTT-ACAATC
*
16195705 TTCAACCTATTCCACTGCTGACT-AGGGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTGATG-CTCAGGGAGATAGGACTTACAATC
16195749 TTCAACCTATTCCACTGATG-TCGAGGGAGATA
1 TTCAACCTATTCCACTGATGCTC-AGGGAGATA
16195781 AGGCTGGGGT
Statistics
Matches: 69, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
42 1 0.01
44 64 0.93
45 4 0.06
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
TTCAACCTATTCCACTGATGCTCAGGGAGATAGGACTTACAATC
Found at i:16195844 original size:88 final size:88
Alignment explanation
Indices: 16195780--16196068 Score: 377
Period size: 88 Copynumber: 3.3 Consensus size: 88
16195770 CGAGGGAGAT
* * * *
16195780 AAGGCTGGGGTCATCGATCTGCTTTGCTGTCGGTGCAAGAAGGCAAGATCTGCTATTTTTAACCT
1 AAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCT
*
16195845 GCTCCGCTG-TAACCCAGGGAGGC
66 ACTCCGCTGAT-ACCCAGGGAGGC
* *
16195868 AAGACTGGTGTCTTCGATCTACTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCT
1 AAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCT
* * *
16195933 GCTCTGCT-ACAACCCAGGGAGGC
66 ACTCCGCTGA-TACCCAGGGAGGC
* *
16195956 AAGGTTGGTGTCTTCGTTCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCT
1 AAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCT
* * * *
16196021 ACTACACT-ACAACCCCGGGAGGC
66 ACTCCGCTGA-TACCCAGGGAGGC
*
16196044 AAGGCTGGTGTCTTCGATCTACTTC
1 AAGGCTGGTGTCTTCGATCTGCTTC
16196069 TGTAACACCC
Statistics
Matches: 179, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
88 179 1.00
ACGTcount: A:0.20, C:0.25, G:0.27, T:0.28
Consensus pattern (88 bp):
AAGGCTGGTGTCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCT
ACTCCGCTGATACCCAGGGAGGC
Found at i:16197945 original size:47 final size:47
Alignment explanation
Indices: 16197870--16198130 Score: 414
Period size: 47 Copynumber: 5.5 Consensus size: 47
16197860 TTCGGGACTC
* * * * * * * *
16197870 ATCACATTTATACACGTTCACATCCATCACGTTGGCCACTCGGCCCT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
16197917 GTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
16197964 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
16198011 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
16198058 ATCACATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTT
1 ATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
16198107 ATCACATATATACACTTTCACATT
1 ATCACATATATACACTTTCACATT
16198131 TATTCAAATA
Statistics
Matches: 201, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
47 155 0.77
49 46 0.23
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
Found at i:16201363 original size:40 final size:40
Alignment explanation
Indices: 16201318--16201558 Score: 342
Period size: 40 Copynumber: 6.1 Consensus size: 40
16201308 CGAATACACG
* * * *
16201318 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * * *
16201358 ACACCAGCACGAATGCTCTTCAGAACTTAGCCCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
*
16201398 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATATA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
* * * *
16201438 GCACTAGCACGAATGCTCTTCGGAACTTAGCCTGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
16201478 TCACTAGCATGAATGCTCTTCGGGACTTAG-CCGGATACA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
16201517 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT-CA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
16201556 TCA
1 TCA
16201559 TCGAGACCTT
Statistics
Matches: 178, Mismatches: 22, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
39 43 0.24
40 135 0.76
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACA
Found at i:16201680 original size:38 final size:38
Alignment explanation
Indices: 16201611--16201685 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
16201601 GAATTTTAAT
*
16201611 CCGGACATAATCTCTGTACATAGCCATCGGGTCTTTAC
1 CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
* *
16201649 CCGGACATAATCTCT-TCATATAGTCAGCGGGTCTTTA
1 CCGGACATAATCTCTGT-ACATAGCCAGCGGGTCTTTA
16201686 AACTCGGATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 1 0.03
38 32 0.97
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (38 bp):
CCGGACATAATCTCTGTACATAGCCAGCGGGTCTTTAC
Found at i:16204276 original size:49 final size:47
Alignment explanation
Indices: 16204106--16204318 Score: 320
Period size: 47 Copynumber: 4.5 Consensus size: 47
16204096 TTCGGGACTC
* * * * * * *
16204106 ATCACATTTATACACGTTCACATCCATCACGTTGGCCACTCGGCC-T
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
16204152 GTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
16204199 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
*
16204246 ATCACATATATATACACTTTCACATTCATCACGTCGGCCATTAGGCCTT
1 ATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
16204295 ATCACATATATACACTTTCACATT
1 ATCACATATATACACTTTCACATT
16204319 TATTCAAATA
Statistics
Matches: 154, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
46 37 0.24
47 71 0.46
49 46 0.30
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTT
Found at i:16204290 original size:96 final size:93
Alignment explanation
Indices: 16204106--16204318 Score: 318
Period size: 96 Copynumber: 2.3 Consensus size: 93
16204096 TTCGGGACTC
* * * * * * *
16204106 ATCACATTTATACACGTTCACATCCATCACGTTGGCCACTCGGCCTGTCACATATATACACTTTC
1 ATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCTATCACATATATACACTTTC
16204171 ACATTCATCACATCGGCCATTAGGCCTT
66 ACATTCATCACATCGGCCATTAGGCCTT
*
16204199 ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACT
1 ATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCC-TATCAC--ATATATACACT
*
16204264 TTCACATTCATCACGTCGGCCATTAGGCCTT
63 TTCACATTCATCACATCGGCCATTAGGCCTT
16204295 ATCACATATATACACTTTCACATT
1 ATCACATATATACACTTTCACATT
16204319 TATTCAAATA
Statistics
Matches: 108, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
93 38 0.35
94 5 0.05
96 65 0.60
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (93 bp):
ATCACATATATACACTTTCACATTCATCACATCGGCCACTAGGCCTATCACATATATACACTTTC
ACATTCATCACATCGGCCATTAGGCCTT
Found at i:16206980 original size:27 final size:27
Alignment explanation
Indices: 16206950--16207127 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
16206940 ATATTGAGTC
* * * *
16206950 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
16206977 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16207004 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
16207032 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
16207059 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
16207086 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
16207113 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
16207128 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:16207089 original size:82 final size:81
Alignment explanation
Indices: 16206971--16207126 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
16206961 TGCTATATAA
* *
16206971 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
16207036 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
16207053 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
16207117 CACTTAGTGC
65 CACTTAGTGC
16207127 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:16210011 original size:88 final size:88
Alignment explanation
Indices: 16209862--16210065 Score: 318
Period size: 88 Copynumber: 2.3 Consensus size: 88
16209852 GGTGTCACAA
* * * ** *
16209862 CTTCGCTGTCGGTATAGGAAGGAAAGATCTGCAATTTTTAACCTGCTCCGTTGCAACCCAGGGAG
1 CTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCAATTTTTAACCTACTCCACTACAACCCAGGGAG
16209927 GCAAGGCTGGTATCTTCGATCTG
66 GCAAGGCTGGTATCTTCGATCTG
*
16209950 CTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTACAACCCAGGGAG
1 CTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCAATTTTTAACCTACTCCACTACAACCCAGGGAG
*
16210015 GCAAGGCTGGTGTCTTCGATCTG
66 GCAAGGCTGGTATCTTCGATCTG
* *
16210038 CTTCGCTTTCGGTGCAGGAAGGCAAGAT
1 CTTCGCTGTCGGTGTAGGAAGGCAAGAT
16210066 GTGTTATCTT
Statistics
Matches: 106, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 106 1.00
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (88 bp):
CTTCGCTGTCGGTGTAGGAAGGCAAGATCTGCAATTTTTAACCTACTCCACTACAACCCAGGGAG
GCAAGGCTGGTATCTTCGATCTG
Found at i:16211420 original size:14 final size:15
Alignment explanation
Indices: 16211397--16211429 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16211387 ATCAACGTTT
16211397 TTCCAAATAAGG-CC
1 TTCCAAATAAGGTCC
*
16211411 TTCCACATAAGGTCC
1 TTCCAAATAAGGTCC
16211426 TTCC
1 TTCC
16211430 CAGCTTGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.27
Consensus pattern (15 bp):
TTCCAAATAAGGTCC
Found at i:16212304 original size:25 final size:26
Alignment explanation
Indices: 16212253--16212307 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
16212243 AAGAAAATCC
* **
16212253 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
*
16212279 AAAAGAATGAAAAAAT-ATTGGCTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
16212304 AAAA
1 AAAA
16212308 TGAAAGCAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.60, C:0.05, G:0.13, T:0.22
Consensus pattern (26 bp):
AAAAGAATGAAAAAATAATTAGCTCA
Found at i:16218340 original size:16 final size:15
Alignment explanation
Indices: 16218315--16218347 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
16218305 ACGCATGAAT
16218315 ATAAAAATAATAATA
1 ATAAAAATAATAATA
16218330 ATAATAAATAATAATA
1 ATAA-AAATAATAATA
16218346 AT
1 AT
16218348 GATACAAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
ATAAAAATAATAATA
Found at i:16218341 original size:13 final size:13
Alignment explanation
Indices: 16218323--16218347 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16218313 ATATAAAAAT
16218323 AATAATAATAATA
1 AATAATAATAATA
16218336 AATAATAATAAT
1 AATAATAATAAT
16218348 GATACAAGAT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:16218835 original size:23 final size:22
Alignment explanation
Indices: 16218792--16218887 Score: 71
Period size: 19 Copynumber: 4.6 Consensus size: 22
16218782 AAAAGGTATC
* *
16218792 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
16218813 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
* *
16218836 TGCATATCATA---TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
* *
16218855 TACATAT--TAT-ATCTAAGAT
1 TACAAATCATATCTTCTAAGAT
*
16218874 TACATATCATATCT
1 TACAAATCATATCT
16218888 AAGACTGCAT
Statistics
Matches: 62, Mismatches: 6, Indels: 13
0.77 0.07 0.16
Matches are distributed among these distances:
17 2 0.03
19 29 0.47
21 6 0.10
22 15 0.24
23 10 0.16
ACGTcount: A:0.42, C:0.16, G:0.05, T:0.38
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:16218900 original size:19 final size:19
Alignment explanation
Indices: 16218805--16218891 Score: 111
Period size: 19 Copynumber: 4.4 Consensus size: 19
16218795 AAATTAAATC
*
16218805 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
*
16218825 TCTTCTAAGATTGCATATCATA
1 ---TCTAAGATTACATATCATA
*
16218847 TCTAAGATTACATATTATA
1 TCTAAGATTACATATCATA
16218866 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
16218885 TCTAAGA
1 TCTAAGA
16218892 CTGCATATCC
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
19 42 0.71
22 7 0.12
23 10 0.17
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:16219506 original size:45 final size:45
Alignment explanation
Indices: 16219411--16219872 Score: 270
Period size: 44 Copynumber: 10.6 Consensus size: 45
16219401 TTCTAATCCA
* * * * * * *
16219411 CTCCACTACAACTTTAGGGAGATGAGATTTG-TTTATTTAGTCTGG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTCT-G
* * *
16219456 C-CCACTGCAATTTCAGGGGGATAAGACTTGATTTCTTGAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTCTG
* *
16219500 CTCCACTGCAACTTCAGGGAGATAAGACTCGCTTTCTTGGGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTCTG
* * *
16219545 CTCCACTGTAACTTCAGGGAGATAAGACCCGA-TGC--GA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTCTG
* ** * * **
16219586 CT-CTCTGCAACTTCAGAAAGATAAGA-TCTG-TGAT-TTGAATCCA
1 CTCCACTGCAACTTCAGGGAGATAAGACTC-GAT-TTCTTGAGTCTG
* *** *
16219629 CTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTCTG
* * * *
16219674 C-CTCACTACAACTTCA-GGAGGATAA-AGCTTGCTTACTT-AGTCTG
1 CTC-CACTGCAACTTCAGGGA-GATAAGA-CTCGATTTCTTGAGTCTG
* * *
16219718 CTCCACTACAACTTCAGGGAGATAAGACTAGA-TGC--GA-TCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTCTG
* * * * * *
16219759 CT-CTCTGCAACTTTAGAGAGATAAGATCTGTGA-TT-TT-AATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGA-CT-CGATTTCTTGAGTCTG
* * * * *
16219802 CTCCACTGCGACTTCAGGGAGATAAGA-T-TATTCGCTTTAATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGACTCGATT-TCTTGAGTCTG
16219846 CTCCACTGCAACTTCAGGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
16219873 TTCGTCATCT
Statistics
Matches: 329, Mismatches: 59, Indels: 59
0.74 0.13 0.13
Matches are distributed among these distances:
39 1 0.00
40 42 0.13
41 15 0.05
42 9 0.03
43 13 0.04
44 135 0.41
45 114 0.35
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTCGATTTCTTGAGTCTG
Found at i:16219649 original size:84 final size:84
Alignment explanation
Indices: 16219544--16219828 Score: 299
Period size: 84 Copynumber: 3.3 Consensus size: 84
16219534 TCTTGGGTCT
*
16219544 GCTCCACTGTAACTTCAGGGAGATAAGACCCGATGCGATCTGCTCTCTGCAACTTCAGAAAGATA
1 GCTCCACTGCAACTTCAGGGAGATAAGACCCGATGCGATCTGCTCTCTGCAACTTCAGAAAGATA
*
16219609 AGATCTGTGATTTGAATCC
66 AGATCTGTGATTTTAATCC
* * * *
16219628 ACTCCACTGCAACTTCAGGGAGATAAGATTCGCC-AT-CTTCAGTCTGCCTCACTACAACTTCAG
1 GCTCCACTGCAACTTCAGGGAGATAAGA--C-CCGATGC--GA-TCTG-CTCTCTGCAACTTCAG
* * * * * *
16219691 GAGGATAA-AGCT-TGCTTACTTAGTCT
59 AAAGATAAGATCTGTGATT--TTAATCC
* ** * *
16219717 GCTCCACTACAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTTAGAGAGATA
1 GCTCCACTGCAACTTCAGGGAGATAAGACCCGATGCGATCTGCTCTCTGCAACTTCAGAAAGATA
16219782 AGATCTGTGATTTTAATCC
66 AGATCTGTGATTTTAATCC
*
16219801 GCTCCACTGCGACTTCAGGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
16219829 TTATTCGCTT
Statistics
Matches: 159, Mismatches: 29, Indels: 26
0.74 0.14 0.12
Matches are distributed among these distances:
84 75 0.47
85 8 0.05
86 8 0.05
87 10 0.06
88 8 0.05
89 50 0.31
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.27
Consensus pattern (84 bp):
GCTCCACTGCAACTTCAGGGAGATAAGACCCGATGCGATCTGCTCTCTGCAACTTCAGAAAGATA
AGATCTGTGATTTTAATCC
Found at i:16219756 original size:173 final size:173
Alignment explanation
Indices: 16219457--16219872 Score: 520
Period size: 173 Copynumber: 2.4 Consensus size: 173
16219447 TTAGTCTGGC
* * ** * *
16219457 CCACTGCAATTTCAGGGGGATAAGACTTGATTTCTTGAGTCTGCTCCACTGCAACTTCAGGGAGA
1 CCACTGCAACTTCAGGGAGATAAGA-TTGACATCTTCAGTCTGCTCCACTACAACTTCAGGGAGA
* * ** *
16219522 TAAGACTCGCTTTCTTGGGTCTGCTCCACTGTAACTTCAGGGAGATAAGACCCGATGCGATCTGC
65 TAAGACTCGCTTACTTGAGTCTGCTCCACTACAACTTCAGGGAGATAAGACCAGATGCGATCTGC
16219587 TCTCTGCAACTTCAGAAAGATAAGATCTGTGATTTGAATCCACT
130 TCTCTGCAACTTCAGAAAGATAAGATCTGTGATTTGAATCCACT
*
16219631 CCACTGCAACTTCAGGGAGATAAGATTCGCCATCTTCAGTCTGC-CTCACTACAACTTCA-GGAG
1 CCACTGCAACTTCAGGGAGATAAGATT-GACATCTTCAGTCTGCTC-CACTACAACTTCAGGGA-
* *
16219694 GATAA-AGCTTGCTTACTT-AGTCTGCTCCACTACAACTTCAGGGAGATAAGACTAGATGCGATC
63 GATAAGA-CTCGCTTACTTGAGTCTGCTCCACTACAACTTCAGGGAGATAAGACCAGATGCGATC
* * * *
16219757 TGCTCTCTGCAACTTTAGAGAGATAAGATCTGTGATTTTAATCCGCT
127 TGCTCTCTGCAACTTCAGAAAGATAAGATCTGTGATTTGAATCCACT
* * * * *
16219804 CCACTGCGACTTCAGGGAGATAAGATT-ATTC-GCTTTAATCTGCTCCACTGCAACTTCAGGGAG
1 CCACTGCAACTTCAGGGAGATAAGATTGA--CATCTTCAGTCTGCTCCACTACAACTTCAGGGAG
16219867 ATAAGA
64 ATAAGA
16219873 TTCGTCATCT
Statistics
Matches: 209, Mismatches: 24, Indels: 19
0.83 0.10 0.08
Matches are distributed among these distances:
172 26 0.12
173 122 0.58
174 61 0.29
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (173 bp):
CCACTGCAACTTCAGGGAGATAAGATTGACATCTTCAGTCTGCTCCACTACAACTTCAGGGAGAT
AAGACTCGCTTACTTGAGTCTGCTCCACTACAACTTCAGGGAGATAAGACCAGATGCGATCTGCT
CTCTGCAACTTCAGAAAGATAAGATCTGTGATTTGAATCCACT
Found at i:16220124 original size:50 final size:50
Alignment explanation
Indices: 16220065--16220159 Score: 127
Period size: 50 Copynumber: 1.9 Consensus size: 50
16220055 TCCAAGCCTT
* * *
16220065 AACGCCAGGGAGATCATATTCACCGTCGTGGCTTCAATCTTTTCCGCTAC
1 AACGCCAGGGAAATAAGATTCACCGTCGTGGCTTCAATCTTTTCCGCTAC
** * *
16220115 AACGCCAGGGAAATAAGATTCGGCTTTGTGGCTTCAATCTTTTCC
1 AACGCCAGGGAAATAAGATTCACCGTCGTGGCTTCAATCTTTTCC
16220160 ATTGCAACGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 38 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.29
Consensus pattern (50 bp):
AACGCCAGGGAAATAAGATTCACCGTCGTGGCTTCAATCTTTTCCGCTAC
Found at i:16220351 original size:44 final size:43
Alignment explanation
Indices: 16220236--16220357 Score: 156
Period size: 44 Copynumber: 2.8 Consensus size: 43
16220226 ATCTGCTATT
* *
16220236 TTCAACCTACTCCACTATTGCTTAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGTTGC-TAGGGAGATAGGATTCACAATC
*
16220280 TTCAACCTATTCCACTGCTGACTAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGTTG-CTAGGGAGATAGGA-TTCACAATC
* *
16220324 TTCAACCTATTCCACTGTTGTCAAGGGAAATAGG
1 TTCAACCTATTCCACTGTTG-CTAGGGAGATAGG
16220358 GCTGGGATCA
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
44 66 0.96
45 3 0.04
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.29
Consensus pattern (43 bp):
TTCAACCTATTCCACTGTTGCTAGGGAGATAGGATTCACAATC
Found at i:16220507 original size:88 final size:87
Alignment explanation
Indices: 16220371--16220669 Score: 499
Period size: 88 Copynumber: 3.4 Consensus size: 87
16220361 GGGATCATCA
**
16220371 ATCTGCTTCGCTGTCGGTGAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGTAACCCAG
1 ATCTGCTTCGCTGTCGGTGAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCAG
16220436 GGAGGCAAGGCTGGTGTCTTCG
66 GGAGGCAAGGCTGGTGTCTTCG
* * * *
16220458 ATCTACTTCGCTGTCGGTGAAGGAAGGCAAGATATGTTATTTTTAACCTGCTCAGCTACAACCCA
1 ATCTGCTTCGCTGTCGGTG-AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCA
16220523 GGGAGGCAAGGCTGGTGTCTTCG
65 GGGAGGCAAGGCTGGTGTCTTCG
*
16220546 ATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCA
1 ATCTGCTTCGCTGTCGGTG-AGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCA
*
16220611 GGGAGGCAAGGCTGGTGTCTTCA
65 GGGAGGCAAGGCTGGTGTCTTCG
16220634 ATCTGCTTCGCTGTCGGTGTAGGAAGGCAAGATCTG
1 ATCTGCTTCGCTGTCGGTG-AGGAAGGCAAGATCTG
16220670 TTATCTTCAC
Statistics
Matches: 196, Mismatches: 15, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
87 18 0.09
88 178 0.91
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (87 bp):
ATCTGCTTCGCTGTCGGTGAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCAG
GGAGGCAAGGCTGGTGTCTTCG
Found at i:16220664 original size:44 final size:44
Alignment explanation
Indices: 16220368--16220664 Score: 127
Period size: 44 Copynumber: 6.8 Consensus size: 44
16220358 GCTGGGATCA
* * * *
16220368 TCAATCTGCTTCGCTGTCGGTG-AGGAAGGCAAGATCTGCTATTT
1 TCAATCTGCTTCGCTGTCGGTGCAGGAAGGCAAG-GCTGGTGTCT
* * * **** *
16220412 TTAACCTGCTCCGCTGT-AACCCAGGGAGGCAAGGCTGGTGTCT
1 TCAATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGGCTGGTGTCT
* * * ** * * *
16220455 TCGATCTACTTCGCTGTCGGTGAAGGAAGGCAAGATATGTTATTT
1 TCAATCTGCTTCGCTGTCGGTGCAGGAAGGCAAG-GCTGGTGTCT
* * * **** *
16220500 TTAACCTGC-TCAGCT-ACAACCCAGGGAGGCAAGGCTGGTGTCT
1 TCAATCTGCTTC-GCTGTCGGTGCAGGAAGGCAAGGCTGGTGTCT
* * * * * *
16220543 TCGATCTGCTTCGCTGTCGGTGCAGGAAGGTAAGATCTGCTATTT
1 TCAATCTGCTTCGCTGTCGGTGCAGGAAGGCAAG-GCTGGTGTCT
* * * * **** *
16220588 TTAACCTGCTCCGCT-ACAACCCAGGGAGGCAAGGCTGGTGTCT
1 TCAATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGGCTGGTGTCT
*
16220631 TCAATCTGCTTCGCTGTCGGTGTAGGAAGGCAAG
1 TCAATCTGCTTCGCTGTCGGTGCAGGAAGGCAAG
16220665 ATCTGTTATC
Statistics
Matches: 162, Mismatches: 83, Indels: 16
0.62 0.32 0.06
Matches are distributed among these distances:
43 50 0.31
44 82 0.51
45 30 0.19
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (44 bp):
TCAATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGGCTGGTGTCT
Found at i:16220960 original size:23 final size:22
Alignment explanation
Indices: 16220906--16220956 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
16220896 AATAAAAATA
*
16220906 AAAACATATGTATAGAATATAT
1 AAAACATATGTATACAATATAT
* *
16220928 ATAAGCATATGTATACTATATAT
1 A-AAACATATGTATACAATATAT
16220951 AAAACA
1 AAAACA
16220957 ATATATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 5 0.21
23 19 0.79
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (22 bp):
AAAACATATGTATACAATATAT
Found at i:16221557 original size:38 final size:38
Alignment explanation
Indices: 16221485--16221628 Score: 225
Period size: 38 Copynumber: 3.7 Consensus size: 38
16221475 AAATTAAATC
*
16221485 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATA
16221527 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
* *
16221565 TCTAAGATTGCATATCATATCTAAGACTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATA
16221603 TCTAAGATTACATATCATATCTAAGA
1 TCTAAGATTACATATCATATCTAAGA
16221629 CTGTATATAC
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
38 80 0.82
41 7 0.07
42 11 0.11
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (38 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATA
Found at i:16221571 original size:57 final size:57
Alignment explanation
Indices: 16221485--16221628 Score: 216
Period size: 57 Copynumber: 2.5 Consensus size: 57
16221475 AAATTAAATC
* *
16221485 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATATCTAAGATTACATATCATA
1 TCTAAGATTAC-ATATCATA---TCTAAGATTGCATATCATATCTAAGACTACATATCATA
* *
16221546 TCTAAGATTGCATATCATATCTAAGATTGCATATCATATCTAAGACTGCATATCATA
1 TCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAGACTACATATCATA
16221603 TCTAAGATTACATATCATATCTAAGA
1 TCTAAGATTACATATCATATCTAAGA
16221629 CTGTATATAC
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
57 61 0.78
60 7 0.09
61 10 0.13
ACGTcount: A:0.40, C:0.17, G:0.08, T:0.35
Consensus pattern (57 bp):
TCTAAGATTACATATCATATCTAAGATTGCATATCATATCTAAGACTACATATCATA
Found at i:16221636 original size:19 final size:19
Alignment explanation
Indices: 16221508--16221628 Score: 215
Period size: 19 Copynumber: 6.4 Consensus size: 19
16221498 AATCATATCT
16221508 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
16221527 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
16221546 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
16221565 TCTAAGATTGCATATCATA
1 TCTAAGATTGCATATCATA
*
16221584 TCTAAGACTGCATATCATA
1 TCTAAGATTGCATATCATA
*
16221603 TCTAAGATTACATATCATA
1 TCTAAGATTGCATATCATA
16221622 TCTAAGA
1 TCTAAGA
16221629 CTGTATATAC
Statistics
Matches: 97, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 97 1.00
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.36
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:16224611 original size:26 final size:26
Alignment explanation
Indices: 16224582--16224648 Score: 80
Period size: 26 Copynumber: 2.6 Consensus size: 26
16224572 GGTTTCCATG
* * *
16224582 AAGGCTTCCATTTCGGATACGCCACA
1 AAGGCTTCCATTTCAGATACACCAAA
* *
16224608 AAGGCTTCCCTTTTAGATACACCAAA
1 AAGGCTTCCATTTCAGATACACCAAA
*
16224634 AAGGCTTCAATTTCA
1 AAGGCTTCCATTTCA
16224649 TAGATTGCCA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (26 bp):
AAGGCTTCCATTTCAGATACACCAAA
Found at i:16239210 original size:56 final size:55
Alignment explanation
Indices: 16239124--16239280 Score: 224
Period size: 56 Copynumber: 2.8 Consensus size: 55
16239114 TAAAGTTACA
* * *
16239124 TAAGAATCAAATTGTTTAAAGATAATATCTCATCATAATATCCTATAATATCTCAT
1 TAAGAATCAAATTG-TTAAAGATAATATCTCATAATAATATCCTATAACATCCCAT
* *
16239180 TAAGAATCAAATTGCTAAGAGATAATATCTCATAATAATATCTTATAACATCCCAT
1 TAAGAATCAAATTGTTAA-AGATAATATCTCATAATAATATCCTATAACATCCCAT
* *
16239236 TAGGAATCAAATTGTTAAAAGATAATATCTCATAATTATATCCTA
1 TAAGAATCAAATTGTT-AAAGATAATATCTCATAATAATATCCTA
16239281 ACACTTTTAC
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
55 3 0.03
56 85 0.94
57 2 0.02
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.35
Consensus pattern (55 bp):
TAAGAATCAAATTGTTAAAGATAATATCTCATAATAATATCCTATAACATCCCAT
Found at i:16239509 original size:8 final size:8
Alignment explanation
Indices: 16239496--16239532 Score: 58
Period size: 8 Copynumber: 4.6 Consensus size: 8
16239486 TTTCTTTTTC
16239496 TTTTTCTT
1 TTTTTCTT
16239504 TTTTTCTT
1 TTTTTCTT
16239512 TTCTTTCTT
1 TT-TTTCTT
16239521 TTTTT-TT
1 TTTTTCTT
16239528 TTTTT
1 TTTTT
16239533 TGGTACAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.25
8 13 0.46
9 8 0.29
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTCTT
Found at i:16239513 original size:25 final size:25
Alignment explanation
Indices: 16239485--16239533 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
16239475 TGTTTACTGT
16239485 TTTTCTTT-TTCTTTTTCTTTTTTTC
1 TTTTCTTTCTT-TTTTTCTTTTTTTC
*
16239510 TTTTCTTTCTTTTTTTTTTTTTTT
1 TTTTCTTTCTTTTTTTCTTTTTTT
16239534 GGTACAAAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.91
26 2 0.09
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (25 bp):
TTTTCTTTCTTTTTTTCTTTTTTTC
Found at i:16239533 original size:20 final size:19
Alignment explanation
Indices: 16239484--16239532 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
16239474 ATGTTTACTG
16239484 TTTTTCTTTTTCTTTTTCTT
1 TTTTTCTTTTTCTTTTT-TT
16239504 TTTTTC-TTTTCTTTCTTTT
1 TTTTTCTTTTTCTTT-TTTT
16239523 TTTTT-TTTTT
1 TTTTTCTTTTT
16239533 TGGTACAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (19 bp):
TTTTTCTTTTTCTTTTTTT
Found at i:16244615 original size:30 final size:29
Alignment explanation
Indices: 16244581--16244637 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
16244571 TTTAAACTAC
* **
16244581 AATTAGAGTTTCACGTGTATAATTGCACCA
1 AATTAAAG-TTCACGTAAATAATTGCACCA
*
16244611 AATTAAAGTTCATGTAAATAATTGCAC
1 AATTAAAGTTCACGTAAATAATTGCAC
16244638 ATTAAGGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 16 0.70
30 7 0.30
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (29 bp):
AATTAAAGTTCACGTAAATAATTGCACCA
Found at i:16244713 original size:34 final size:35
Alignment explanation
Indices: 16244669--16244735 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
16244659 TAGTAAAATA
*
16244669 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
16244703 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
16244736 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:16257380 original size:20 final size:20
Alignment explanation
Indices: 16257357--16257407 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
16257347 TTATAACGAC
**
16257357 AAAAAAATATTTTTAAATTA
1 AAAAAAATAAATTTAAATTA
* *
16257377 AAAAAATTAAATTTAACTTA
1 AAAAAAATAAATTTAAATTA
16257397 ATAAAAAATAA
1 A-AAAAAATAA
16257408 CGAAAATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAAATAAATTTAAATTA
Found at i:16257880 original size:29 final size:29
Alignment explanation
Indices: 16257832--16257889 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
16257822 CTAAATTTTC
*
16257832 AAAAAAAAAAGAGGCTTATAAGCCTAATT
1 AAAAAAAAAAGAGGCATATAAGCCTAATT
* * * *
16257861 AAAAAAAACAGTGGCATATATGGCTAATT
1 AAAAAAAAAAGAGGCATATAAGCCTAATT
16257890 TAGCCCTCCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.52, C:0.10, G:0.16, T:0.22
Consensus pattern (29 bp):
AAAAAAAAAAGAGGCATATAAGCCTAATT
Found at i:16258973 original size:16 final size:16
Alignment explanation
Indices: 16258952--16258982 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16258942 TTTTGCATTG
*
16258952 TTTTAATATTAAATAT
1 TTTTAAAATTAAATAT
16258968 TTTTAAAATTAAATA
1 TTTTAAAATTAAATA
16258983 ACATTAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAAATTAAATAT
Found at i:16259117 original size:11 final size:11
Alignment explanation
Indices: 16259101--16259125 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
16259091 AATACCCTAA
16259101 ACTATATATAT
1 ACTATATATAT
16259112 ACTATATATAT
1 ACTATATATAT
16259123 ACT
1 ACT
16259126 TATTTTCGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (11 bp):
ACTATATATAT
Found at i:16271434 original size:17 final size:17
Alignment explanation
Indices: 16271412--16271446 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
16271402 TAATTTTTAA
16271412 TAAAAAATTTATAACTT
1 TAAAAAATTTATAACTT
*
16271429 TAAAAATTTTATAACTT
1 TAAAAAATTTATAACTT
16271446 T
1 T
16271447 TGTTTTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAAAATTTATAACTT
Found at i:16272151 original size:4 final size:4
Alignment explanation
Indices: 16272142--16272269 Score: 95
Period size: 4 Copynumber: 31.0 Consensus size: 4
16272132 GAAGGAGAGG
* * *
16272142 GAAA GAAA GAAA GGAAG GAGAG GAAA GAAA G-AA -AAA GAAG GAAA GAAAA
1 GAAA GAAA GAAA -GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA
*
16272191 GGAAA G-GA GAAGA GAAA GAAA GAAA GAAA GAAA G-AA GAAAA GGAAA
1 -GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA
*
16272237 GGAGAA GAAA -AAA GAAA GAAA GAAG GAAA GAAA
1 -GA-AA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
16272270 AGGAAAGGAG
Statistics
Matches: 103, Mismatches: 8, Indels: 26
0.75 0.06 0.19
Matches are distributed among these distances:
3 12 0.12
4 60 0.58
5 27 0.26
6 4 0.04
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:16272167 original size:18 final size:19
Alignment explanation
Indices: 16272133--16272287 Score: 97
Period size: 18 Copynumber: 7.9 Consensus size: 19
16272123 GGGGGGGCAG
*
16272133 AAGGAGAGG-GAAAGAAAGA
1 AAGGA-AGGAGAAGGAAAGA
16272152 AAGGAAGGAG-AGGAAAGA
1 AAGGAAGGAGAAGGAAAGA
**
16272170 AA-GAAAAAGAAGGAAAGAA
1 AAGGAAGGAGAAGGAAAG-A
16272189 AAGGAAAGGAGAAGAGAAAGA
1 AAGG-AAGGAGAAG-GAAAGA
* * *
16272210 AAGAAAGAAAGAAAG-AAGAA
1 AAGGAAG-GAGAAGGAAAG-A
16272230 AAGGAAAGGAGAA-GAAA-A
1 AAGG-AAGGAGAAGGAAAGA
* *
16272248 AAGAAAGAAAGAAGGAAAGAA
1 AAGGAAG-GAGAAGGAAAG-A
16272269 AAGGAAAGGAGAAGAGAAA
1 AAGG-AAGGAGAAG-GAAA
16272288 AAAAAAAGAG
Statistics
Matches: 106, Mismatches: 14, Indels: 29
0.71 0.09 0.19
Matches are distributed among these distances:
17 8 0.08
18 27 0.25
19 17 0.16
20 15 0.14
21 27 0.25
22 12 0.11
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (19 bp):
AAGGAAGGAGAAGGAAAGA
Found at i:16272196 original size:5 final size:5
Alignment explanation
Indices: 16272141--16272278 Score: 70
Period size: 5 Copynumber: 29.6 Consensus size: 5
16272131 AGAAGGAGAG
* * *
16272141 GGAAA -GAAA -GAAA GG-AA GGAGA GGAAA -GAAA GAAAA AG-AA GGAAA
1 GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
* *
16272186 GAAAA GGAAA GGAGAA GAGAAA -GAAA -GAAA -GAAA -GAAA -G-AA GAAAA
1 GGAAA GGAAA GGA-AA G-GAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA
* * *
16272232 GGAAA GGAGAA GAAAAA AGAAA -GAAA -G-AA GGAAA GAAAA GGAAA GGA
1 GGAAA GGA-AA G-GAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGAAA GGA
16272279 GAAGAGAAAA
Statistics
Matches: 106, Mismatches: 15, Indels: 24
0.73 0.10 0.17
Matches are distributed among these distances:
3 4 0.04
4 42 0.40
5 47 0.44
6 10 0.09
7 3 0.03
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (5 bp):
GGAAA
Found at i:16272295 original size:29 final size:28
Alignment explanation
Indices: 16272263--16272328 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 28
16272253 AGAAAGAAGG
16272263 AAAGAAAAGGAA-AGGAGAAGAGAA-AAAAA
1 AAAGAAAA-GAAGAGG-GAAG-GAAGAAAAA
*
16272292 AAAGAGAAGAAGAGGGAAGGAAGGAAAAA
1 AAAGAAAAGAAGAGGGAAGGAA-GAAAAA
16272321 AAAGAAAA
1 AAAGAAAA
16272329 AAAAGTAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 3 0.09
28 7 0.22
29 22 0.69
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (28 bp):
AAAGAAAAGAAGAGGGAAGGAAGAAAAA
Found at i:16272313 original size:39 final size:39
Alignment explanation
Indices: 16272144--16272305 Score: 157
Period size: 39 Copynumber: 4.2 Consensus size: 39
16272134 AGGAGAGGGA
16272144 AAGAA-AG-AAAGG-AAGGAG-AG-GAAAGAAAGAAAA-AG
1 AAGAAGAGAAAAGGAAAGGAGAAGAGAAA-AAA-AAAAGAG
*
16272179 AAGGAA-AGAAAAGGAAAGGAGAAGAGAAAGAAAGAAAGA-
1 AA-GAAGAGAAAAGGAAAGGAGAAGAGAAA-AAAAAAAGAG
16272218 AAGAAAGAAGAAAAGGAAAGGAGAAGA-AAAAAGAAAGAA-AG
1 AAG-AAG-AGAAAAGGAAAGGAGAAGAGAAAAA-AAA-AAGAG
16272259 AAGGAA-AGAAAAGGAAAGGAGAAGAGAAAAAAAAAAGAG
1 AA-GAAGAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAGAG
16272298 AAGAAGAG
1 AAGAAGAG
16272306 GGAAGGAAGG
Statistics
Matches: 109, Mismatches: 2, Indels: 28
0.78 0.01 0.20
Matches are distributed among these distances:
35 2 0.02
36 5 0.05
37 5 0.05
38 12 0.11
39 39 0.36
40 20 0.18
41 25 0.23
42 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (39 bp):
AAGAAGAGAAAAGGAAAGGAGAAGAGAAAAAAAAAAGAG
Found at i:16272329 original size:80 final size:81
Alignment explanation
Indices: 16272165--16272330 Score: 223
Period size: 80 Copynumber: 2.0 Consensus size: 81
16272155 GAAGGAGAGG
*
16272165 AAAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAGAAAGAAAGAAAGAAAGAAGAA
1 AAAGAAAG-AAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAGAAAAAAAGAAAGAAAGAAGAA
* *
16272230 AAGGAAAGGAGAAGAAA
65 AAGGAAAGAAAAAGAAA
16272247 AAAGAAAG-AAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAA-AAAAAAAGAGAAGAAGAGGGAA
1 AAAGAAAGAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAGAAAAAAAGA-AAGAA-A--GAA
*
16272310 G-GAAGGAAA-AAAAAGAAA
62 GAAAAGGAAAGAAAAAGAAA
16272328 AAA
1 AAA
16272331 AAGTAATTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 9
0.85 0.04 0.10
Matches are distributed among these distances:
79 8 0.11
80 38 0.50
81 11 0.14
82 15 0.20
83 4 0.05
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (81 bp):
AAAGAAAGAAAAGAAGGAAAGAAAAGGAAAGGAGAAGAGAAAGAAAAAAAGAAAGAAAGAAGAAA
AGGAAAGAAAAAGAAA
Found at i:16278990 original size:3 final size:3
Alignment explanation
Indices: 16278982--16279016 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
16278972 TCTTAATACT
16278982 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
16279017 TAATAATAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:16279157 original size:11 final size:11
Alignment explanation
Indices: 16279137--16279176 Score: 64
Period size: 11 Copynumber: 3.7 Consensus size: 11
16279127 TAAAAAATAC
16279137 CTTCTTTTTCT
1 CTTCTTTTTCT
*
16279148 CTTCTCTTTCT
1 CTTCTTTTTCT
16279159 C-TCTTTTTCT
1 CTTCTTTTTCT
16279169 CTTCTTTT
1 CTTCTTTT
16279177 CCGCAACACC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (11 bp):
CTTCTTTTTCT
Found at i:16279163 original size:21 final size:20
Alignment explanation
Indices: 16279139--16279177 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
16279129 AAAAATACCT
16279139 TCTTTTTCTCTTCTCTTTCTC
1 TCTTTTTCTCTTCT-TTTCTC
16279160 TCTTTTTCTCTTCTTTTC
1 TCTTTTTCTCTTCTTTTC
16279178 CGCAACACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (20 bp):
TCTTTTTCTCTTCTTTTCTC
Found at i:16279304 original size:27 final size:27
Alignment explanation
Indices: 16279261--16279333 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
16279251 ACTCAAGTAA
**
16279261 TGCCGCCAATGCCTTTGGCACCATTGG
1 TGCCGCCAATGGTTTTGGCACCATTGG
* * *
16279288 TGCTGCCAATGGTTTTGGCATCTTTGG
1 TGCCGCCAATGGTTTTGGCACCATTGG
*
16279315 TGCCGCCAATCGTTTTGGC
1 TGCCGCCAATGGTTTTGGC
16279334 GTGACCAAGG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.12, C:0.27, G:0.27, T:0.33
Consensus pattern (27 bp):
TGCCGCCAATGGTTTTGGCACCATTGG
Found at i:16279444 original size:27 final size:25
Alignment explanation
Indices: 16279383--16279450 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 25
16279373 CAGGTTTTTT
*
16279383 TTAT-ATATTTTGGTAAATAAAATA
1 TTATAATATTTTGGTAAATAAAAAA
16279407 TATATATATATTTTGGTAAATAAAAAAA
1 T-TATA-ATATTTTGGTAAAT-AAAAAA
16279435 GTTATAATATTTTGGT
1 -TTATAATATTTTGGT
16279451 TATTTTTTAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
24 1 0.03
25 3 0.08
27 24 0.63
28 9 0.24
29 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (25 bp):
TTATAATATTTTGGTAAATAAAAAA
Found at i:16281901 original size:3 final size:3
Alignment explanation
Indices: 16281893--16281932 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
16281883 AGATGTAGGT
*
16281893 ATA ATA ATA ATA TATA AT- ATA ATA ATA AAA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA A
16281933 AAAAATTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16281932 original size:12 final size:12
Alignment explanation
Indices: 16281895--16281946 Score: 61
Period size: 12 Copynumber: 4.1 Consensus size: 12
16281885 ATGTAGGTAT
16281895 AATAATAATATATA
1 AATAATAATA-A-A
16281909 ATATAATAATAAA
1 A-ATAATAATAAA
16281922 AATAATAATAAA
1 AATAATAATAAA
16281934 AA-AATTAATAAA
1 AATAA-TAATAAA
16281946 A
1 A
16281947 TAGACTAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.06
12 21 0.58
13 2 0.06
14 2 0.06
15 9 0.25
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:16282193 original size:19 final size:21
Alignment explanation
Indices: 16282155--16282193 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
16282145 CCTTTTTTAA
*
16282155 AATCGTAAATAAGTAAAAAAT
1 AATCGTAAATAAGAAAAAAAT
16282176 AATCG-AAA-AAGAAAAAAA
1 AATCGTAAATAAGAAAAAAA
16282194 AAGAAAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.69, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AATCGTAAATAAGAAAAAAAT
Found at i:16282281 original size:45 final size:45
Alignment explanation
Indices: 16282217--16282306 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
16282207 GCCACATTTA
16282217 AAAAACTGCCAATCATTCTCCCTTTTTTACTGATTCTTTTTTTTT
1 AAAAACTGCCAATCATTCTCCCTTTTTTACTGATTCTTTTTTTTT
* *
16282262 AAAAACTGCCAATCGTTCTCCCTTTTTTATTGATTCTTTTTTTTT
1 AAAAACTGCCAATCATTCTCCCTTTTTTACTGATTCTTTTTTTTT
16282307 GACAATGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.21, C:0.21, G:0.06, T:0.52
Consensus pattern (45 bp):
AAAAACTGCCAATCATTCTCCCTTTTTTACTGATTCTTTTTTTTT
Found at i:16282462 original size:21 final size:21
Alignment explanation
Indices: 16282436--16282511 Score: 111
Period size: 21 Copynumber: 3.7 Consensus size: 21
16282426 AATCATATCT
*
16282436 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
*
16282457 TCTAAGATTGCATATATCATT
1 TCTAAGATTGCATATATCATA
16282478 TCTAAGATTGCATAT-T-ATA
1 TCTAAGATTGCATATATCATA
*
16282497 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
16282512 CCTCGAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.31
20 1 0.02
21 34 0.67
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:16282471 original size:19 final size:19
Alignment explanation
Indices: 16282449--16282512 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
16282439 AAGATTGTAT
16282449 ATATCATATCTAAGATTGC
1 ATATCATATCTAAGATTGC
*
16282468 ATATATCATTTCTAAGATTGC
1 --ATATCATATCTAAGATTGC
* *
16282489 ATATTATATCTAAGATTGT
1 ATATCATATCTAAGATTGC
16282508 ATATC
1 ATATC
16282513 CTCGAAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 20 0.53
21 18 0.47
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.42
Consensus pattern (19 bp):
ATATCATATCTAAGATTGC
Found at i:16293130 original size:32 final size:31
Alignment explanation
Indices: 16293085--16293180 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
16293075 CTTAGATAAT
16293085 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
16293116 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
16293148 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
16293179 TT
1 TT
16293181 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:16293741 original size:19 final size:19
Alignment explanation
Indices: 16293719--16293759 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
16293709 AAATAAAAGC
*
16293719 AAAAA-AAAAACAGAAAAA
1 AAAAACAAAAAAAGAAAAA
16293737 AAAAACAAAAAAAGAAAAA
1 AAAAACAAAAAAAGAAAAA
16293756 AAAA
1 AAAA
16293760 GCGCAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.90, C:0.05, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAAAAGAAAAA
Found at i:16293757 original size:21 final size:21
Alignment explanation
Indices: 16293722--16293777 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
16293712 TAAAAGCAAA
* *
16293722 AAAAAAACAGAAAAAAAAAAC
1 AAAAAAAGAAAAAAAAAAAAC
***
16293743 AAAAAAAGAAAAAAAAAGCGC
1 AAAAAAAGAAAAAAAAAAAAC
*
16293764 AAAAAAAGTAAAAA
1 AAAAAAAGAAAAAA
16293778 GCGCAAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.82, C:0.07, G:0.09, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAAAAAAAAAAAAC
Found at i:16293767 original size:18 final size:17
Alignment explanation
Indices: 16293746--16293792 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 17
16293736 AAAAAACAAA
16293746 AAAAGAAAAAAAAAGCGC
1 AAAA-AAAAAAAAAGCGC
*
16293764 AAAAAAAGTAAAAAGCGC
1 AAAAAAA-AAAAAAGCGC
16293782 AAAAAAAAAAA
1 AAAAAAAAAAA
16293793 CAAAAAAGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 6 0.23
18 20 0.77
ACGTcount: A:0.77, C:0.09, G:0.13, T:0.02
Consensus pattern (17 bp):
AAAAAAAAAAAAAGCGC
Found at i:16293788 original size:21 final size:21
Alignment explanation
Indices: 16293764--16293809 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
16293754 AAAAAAGCGC
**
16293764 AAAAAAAGTAAAAAGCGCAAAA
1 AAAAAAACAAAAAAG-GCAAAA
16293786 AAAAAAACAAAAAAGGCAAAA
1 AAAAAAACAAAAAAGGCAAAA
16293807 AAA
1 AAA
16293810 CGCAAAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.41
22 13 0.59
ACGTcount: A:0.78, C:0.09, G:0.11, T:0.02
Consensus pattern (21 bp):
AAAAAAACAAAAAAGGCAAAA
Found at i:16293788 original size:39 final size:40
Alignment explanation
Indices: 16293742--16293818 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 40
16293732 AAAAAAAAAA
* *
16293742 CAAAAAAAGAAA-AAAAAAGCGCAAAAAAA-GTAAAAAGCG
1 CAAAAAAAAAAACAAAAAAG-GCAAAAAAACGCAAAAAGCG
16293781 CAAAAAAAAAAACAAAAAAGGCAAAAAAACGCAAAAAG
1 CAAAAAAAAAAACAAAAAAGGCAAAAAAACGCAAAAAG
16293819 AAAAGAGTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 20 0.59
40 14 0.41
ACGTcount: A:0.74, C:0.12, G:0.13, T:0.01
Consensus pattern (40 bp):
CAAAAAAAAAAACAAAAAAGGCAAAAAAACGCAAAAAGCG
Found at i:16293799 original size:13 final size:13
Alignment explanation
Indices: 16293719--16293759 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
16293709 AAATAAAAGC
*
16293719 AAAAAAAAAACAG
1 AAAAAAAAAACAA
16293732 AAAAAAAAAACAA
1 AAAAAAAAAACAA
16293745 AAAAAGAAAAA-AA
1 AAAAA-AAAAACAA
16293758 AA
1 AA
16293760 GCGCAAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
13 21 0.81
14 5 0.19
ACGTcount: A:0.90, C:0.05, G:0.05, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:16293843 original size:21 final size:23
Alignment explanation
Indices: 16293804--16293872 Score: 75
Period size: 23 Copynumber: 2.9 Consensus size: 23
16293794 AAAAAAGGCA
16293804 AAAAAACGCAAAAAGAAAAGAGT
1 AAAAAACGCAAAAAGAAAAGAGT
* * *
16293827 AAAAAGCGCAAAAAAAAGAAGAAGC
1 AAAAAACGCAAAAAGAA-AAG-AGT
*
16293852 AAAAAAGCGCAAAAAAAAAAG
1 AAAAAA-CGCAAAAAGAAAAG
16293873 TTGCCTACCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.38
24 3 0.08
25 10 0.26
26 11 0.28
ACGTcount: A:0.71, C:0.10, G:0.17, T:0.01
Consensus pattern (23 bp):
AAAAAACGCAAAAAGAAAAGAGT
Found at i:16293872 original size:54 final size:51
Alignment explanation
Indices: 16293732--16293871 Score: 133
Period size: 51 Copynumber: 2.6 Consensus size: 51
16293722 AAAAAAACAG
* **
16293732 AAAAAAAAAACAAAAAAAG-AAAAAA-AAAGCGCAAAAAAAGTAAAAAGCGCA
1 AAAAAAAAAACAAAAAAGGCAAAAAACAAAAAG--AAAAAAGTAAAAAGCGCA
*
16293783 AAAAAAAAAACAAAAAAGGCAAAAAAACGCAAAAAGAAAAGAGTAAAAAGCGCAA
1 AAAAAAAAAACAAAAAAGGC-AAAAAA--CAAAAAGAAAAAAGTAAAAAGCGC-A
16293838 AAAAAAGAAGAAGCAAAAAAGCGCAAAAAA-AAAA
1 AAAAAA-AA-AA-CAAAAAAG-GCAAAAAACAAAA
16293872 GTTGCCTACC
Statistics
Matches: 75, Mismatches: 4, Indels: 16
0.79 0.04 0.17
Matches are distributed among these distances:
51 18 0.24
53 6 0.08
54 16 0.21
55 11 0.15
56 6 0.08
57 2 0.03
58 14 0.19
59 2 0.03
ACGTcount: A:0.75, C:0.10, G:0.14, T:0.01
Consensus pattern (51 bp):
AAAAAAAAAACAAAAAAGGCAAAAAACAAAAAGAAAAAAGTAAAAAGCGCA
Found at i:16295984 original size:32 final size:31
Alignment explanation
Indices: 16295939--16296034 Score: 174
Period size: 31 Copynumber: 3.1 Consensus size: 31
16295929 CTTAGATAAT
16295939 TTTAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
16295970 TTTAAAGAGTTTTTATTAGGATTCAATTACTC
1 TTTAAAGAG-TTTTATTAGGATTCAATTACTC
*
16296002 TTGAAAGAGTTTTATTAGGATTCAATTACTC
1 TTTAAAGAGTTTTATTAGGATTCAATTACTC
16296033 TT
1 TT
16296035 GTAATTTGCC
Statistics
Matches: 63, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
31 33 0.52
32 30 0.48
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.46
Consensus pattern (31 bp):
TTTAAAGAGTTTTATTAGGATTCAATTACTC
Found at i:16300744 original size:41 final size:41
Alignment explanation
Indices: 16300642--16300750 Score: 128
Period size: 41 Copynumber: 2.7 Consensus size: 41
16300632 ATCGGCTTTT
* * * * * *
16300642 AGCCTGCTAGACCTATAGTCCGAAATGTATCACCGGCATTA
1 AGCCTGCTAGACGTAAAGTCTGAATTATATCACCGGCATCA
* * *
16300683 AGCCTGCTAGATGTAAAGTCTGAATTATTTCACTGGCATCA
1 AGCCTGCTAGACGTAAAGTCTGAATTATATCACCGGCATCA
*
16300724 AGCCTGCTAGACGTAAAGTCTGTATTA
1 AGCCTGCTAGACGTAAAGTCTGAATTA
16300751 CATTCGATCA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.28
Consensus pattern (41 bp):
AGCCTGCTAGACGTAAAGTCTGAATTATATCACCGGCATCA
Found at i:16304315 original size:21 final size:22
Alignment explanation
Indices: 16304289--16304333 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
16304279 ATACATATTT
*
16304289 TTATATAATAAA-AAAAATTAA
1 TTATATAATAAATAAAAATAAA
*
16304310 TTATATATTAAATAAAAATAAA
1 TTATATAATAAATAAAAATAAA
16304332 TT
1 TT
16304334 TTAATTTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TTATATAATAAATAAAAATAAA
Found at i:16304342 original size:22 final size:22
Alignment explanation
Indices: 16304266--16304342 Score: 59
Period size: 25 Copynumber: 3.3 Consensus size: 22
16304256 TTTTTTCACT
*
16304266 ATTTAAATATAAAATACATATTTTT
1 ATTTAAATA-AAAATA-A-ATTTTA
*
16304291 ATAT-AATAAAAA-AAATTAATTA
1 ATTTAAATAAAAATAAATT--TTA
16304313 TATATTAAATAAAAATAAATTTTA
1 -AT-TTAAATAAAAATAAATTTTA
16304337 ATTTAA
1 ATTTAA
16304343 TTTCAAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 15
0.70 0.05 0.25
Matches are distributed among these distances:
20 3 0.07
21 1 0.02
22 7 0.16
23 8 0.19
24 8 0.19
25 11 0.26
26 5 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTTAAATAAAAATAAATTTTA
Found at i:16304680 original size:41 final size:41
Alignment explanation
Indices: 16304623--16304841 Score: 269
Period size: 41 Copynumber: 5.3 Consensus size: 41
16304613 ATTTTTAAAC
* *
16304623 CTTTAACGGCGTTTTTGTGTAAGCGCCGCTAATGCTCAGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCAGAT
** * *
16304664 CTTTAGCGGCGTTTTTGTGAAAGCGCCGCTAATGCCCCGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCAGAT
* * * *
16304705 CTTTAGCAGCGATTTCGTCTAAGCGCCGCTAATGCTCGGAT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCAGAT
* * * *
16304746 CTTTAGCGGCGTTTTTGTCTATGCGCCGCTAGTGCTCGGGT
1 CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCAGAT
* * *
16304787 CTTTAGCGGCGTTTTTATAC-AAACGCCGCTAATTCTCAGAT
1 CTTTAGCGGCGTTTTTGT-CTAAGCGCCGCTAATGCTCAGAT
16304828 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
16304842 CTAACTGTGC
Statistics
Matches: 153, Mismatches: 24, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
41 152 0.99
42 1 0.01
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (41 bp):
CTTTAGCGGCGTTTTTGTCTAAGCGCCGCTAATGCTCAGAT
Found at i:16304871 original size:82 final size:82
Alignment explanation
Indices: 16304728--16304882 Score: 184
Period size: 82 Copynumber: 1.9 Consensus size: 82
16304718 TTCGTCTAAG
* * ** * * * * *
16304728 CGCCGCTAATGCTCGGATCTTTAGCGGCGTTTTTGTCTATGCGCCGCTAGTGCTCGGGTCTTTAG
1 CGCCGCTAATGCTCAGATCTTTAGCGGCGTTTCTAACTATGCGCCACTAATGCGCGGGTCTTCAA
16304793 CGGCGTTTTTATACAAA
66 CGGCGTTTTTATACAAA
* * * **
16304810 CGCCGCTAATTCTCAGATCTTTAGCGGCGTTTCTAACTGTGCGCCACTAATTCGCTTGTCTTCAA
1 CGCCGCTAATGCTCAGATCTTTAGCGGCGTTTCTAACTATGCGCCACTAATGCGCGGGTCTTCAA
16304875 CGGCGTTT
66 CGGCGTTT
16304883 GTATTTAGGC
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
82 59 1.00
ACGTcount: A:0.15, C:0.26, G:0.24, T:0.34
Consensus pattern (82 bp):
CGCCGCTAATGCTCAGATCTTTAGCGGCGTTTCTAACTATGCGCCACTAATGCGCGGGTCTTCAA
CGGCGTTTTTATACAAA
Found at i:16304879 original size:123 final size:123
Alignment explanation
Indices: 16304627--16304902 Score: 283
Period size: 123 Copynumber: 2.2 Consensus size: 123
16304617 TTAAACCTTT
* * *
16304627 AACGGCGTTTTTGTGTAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTGTGAAAGCGCCG
1 AACGGCGTTTTTGTCTAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATGAAAACGCCG
* * *
16304692 CTAATGCCCCGATCTTTAGCAGCGATTTCGTCTAAGCGCCGCTAATGCTCGGATCTTT
66 CTAATGCCCAGATCTTTAGCAGCGATTTCGTCTAAGCGCCACTAATGCTCGGATCTTC
* * * * *
16304750 AGCGGCGTTTTTGTCTATGCGCCGCTAGTGCTCGGGTCTTTAGCGGCGTTTTTAT-ACAAACGCC
1 AACGGCGTTTTTGTCTAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATGA-AAACGCC
* * * ** *
16304814 GCTAATTCTCAGATCTTTAGCGGCG-TTTC-TAACTGTGCGCCACTAATTCGCT-TG-TCTTC
65 GCTAATGCCCAGATCTTTAGCAGCGATTTCGT--CTAAGCGCCACTAA-T-GCTCGGATCTTC
* * * *
16304873 AACGGCGTTTGTATTTAGGCGCCGCTAATG
1 AACGGCGTTTTTGTCTAAGCGCCGCTAATG
16304903 TATTTACCTT
Statistics
Matches: 125, Mismatches: 23, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
121 1 0.01
122 5 0.04
123 114 0.91
124 2 0.02
125 3 0.02
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (123 bp):
AACGGCGTTTTTGTCTAAGCGCCGCTAATGCTCAGATCTTTAGCGGCGTTTTTATGAAAACGCCG
CTAATGCCCAGATCTTTAGCAGCGATTTCGTCTAAGCGCCACTAATGCTCGGATCTTC
Found at i:16305444 original size:15 final size:15
Alignment explanation
Indices: 16305423--16305460 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
16305413 ATTTAGGTTA
16305423 ATTTAGGGGTTAGAG
1 ATTTAGGGGTTAGAG
* *
16305438 GTTTAGGGGTTTGAG
1 ATTTAGGGGTTAGAG
16305453 ATTTAGGG
1 ATTTAGGG
16305461 TTAATTTCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.21, C:0.00, G:0.42, T:0.37
Consensus pattern (15 bp):
ATTTAGGGGTTAGAG
Found at i:16305744 original size:14 final size:14
Alignment explanation
Indices: 16305727--16305753 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16305717 TTGATATATA
16305727 TATATATATATGGC
1 TATATATATATGGC
16305741 TATATATATATGG
1 TATATATATATGG
16305754 TTAATTAGTA
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:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (14 bp):
TATATATATATGGC
Found at i:16307455 original size:66 final size:66
Alignment explanation
Indices: 16307372--16307518 Score: 190
Period size: 66 Copynumber: 2.2 Consensus size: 66
16307362 GAGGCAACAT
* *
16307372 CGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCTAGCTA-CAACTGAAAGCAGATGTAG
1 CGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-AGCAACTGAAAGCAGATGCAG
16307435 CAG
64 CAG
* * * *
16307438 CGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGCAGCTTAAAGCAGATGCGGCA
1 CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTGAAAGCAGATGCAGCA
16307503 G
66 G
* *
16307504 CAAGAGAAGCAGAGG
1 CGAGAGAAGCTGAGG
16307519 CGGCAGCGAG
Statistics
Matches: 71, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
65 1 0.01
66 66 0.93
67 4 0.06
ACGTcount: A:0.40, C:0.17, G:0.29, T:0.14
Consensus pattern (66 bp):
CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTGAAAGCAGATGCAGCA
G
Found at i:16307515 original size:21 final size:21
Alignment explanation
Indices: 16307489--16307559 Score: 79
Period size: 21 Copynumber: 3.4 Consensus size: 21
16307479 CAGCAGCTTA
*
16307489 AAGCAGATGCGGCAGCAAGAG
1 AAGCAGAGGCGGCAGCAAGAG
*
16307510 AAGCAGAGGCGGCAGCGAGAG
1 AAGCAGAGGCGGCAGCAAGAG
* * * * *
16307531 AAGTACAGGCTGCAGCGAGGG
1 AAGCAGAGGCGGCAGCAAGAG
16307552 AAGCAGAG
1 AAGCAGAG
16307560 CAGCGTCAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.35, C:0.18, G:0.42, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCAAGAG
Found at i:16307969 original size:43 final size:43
Alignment explanation
Indices: 16307915--16308095 Score: 161
Period size: 43 Copynumber: 4.2 Consensus size: 43
16307905 TGGTGGCCGT
* *
16307915 TTTAGTGGCGTTTTTGGTCAAAGTGCCGCTAAAGATAAGGGTC
1 TTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTC
* * ** * * * *
16307958 TTTAGTGGCGTTTGTGGAAAAAGTGCCGCTACAGATCAGAGTC
1 TTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTC
* ** *
16308001 TATT-GCGGCGTTTTAGGGGAAAGCGCCACTAAAGA-ATA-GGTC
1 T-TTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATA-AGGGTC
* * * *
16308043 TTTAGGGGCGTTTATGGTCAAAGCACCGCTAAAGATCAGGGTC
1 TTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTC
16308086 TTTAGCGGCG
1 TTTAGCGGCG
16308096 CTTCCACTAA
Statistics
Matches: 108, Mismatches: 25, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
41 2 0.02
42 29 0.27
43 75 0.69
44 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.28
Consensus pattern (43 bp):
TTTAGCGGCGTTTTTGGTCAAAGCGCCGCTAAAGATAAGGGTC
Found at i:16308302 original size:128 final size:128
Alignment explanation
Indices: 16308068--16308333 Score: 325
Period size: 128 Copynumber: 2.1 Consensus size: 128
16308058 GGTCAAAGCA
* *
16308068 CCGCTAAAGATCAGGGTCTTTAGCGGCGCTTCCACTAAAGCGCCGCTAAAGGTCTTACTCTTCAG
1 CCGCTAAAGATCAAGGTCTTTAGCGGCACTTCCACTAAAGCGCCGCTAAAGGTCTTACTCTTCAG
* * * *** *
16308133 CGGCGTTTGGGATAAAAATGTCGCTAAAGACCCTGATCTTTAGCGGCGCTTCTACCAAAAACG
66 CGGCGTTTGGGATAAAAACGCCCCTAAAGACCAACACCTTTAGCGGCGCTTCTACCAAAAACG
* * *
16308196 CCGCTACAGATCAAGGTCTTTAGCGGCACTTCCACTAAAGCTCCGCTAGAGGTCTTACTCTTCAG
1 CCGCTAAAGATCAAGGTCTTTAGCGGCACTTCCACTAAAGCGCCGCTAAAGGTCTTACTCTTCAG
* * ** * * * * * *
16308261 CGGCGTTTGTGCTAGTAGCGCCCCTATAGACCAACACCTTTAGCGGCGTTTATTTCTAAAAACG
66 CGGCGTTTGGGATAAAAACGCCCCTAAAGACCAACACCTTTAGCGGCGCTT-CTACCAAAAACG
16308325 CCGCTAAAG
1 CCGCTAAAG
16308334 TTAGCGGCGC
Statistics
Matches: 114, Mismatches: 23, Indels: 1
0.83 0.17 0.01
Matches are distributed among these distances:
128 97 0.85
129 17 0.15
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (128 bp):
CCGCTAAAGATCAAGGTCTTTAGCGGCACTTCCACTAAAGCGCCGCTAAAGGTCTTACTCTTCAG
CGGCGTTTGGGATAAAAACGCCCCTAAAGACCAACACCTTTAGCGGCGCTTCTACCAAAAACG
Found at i:16312847 original size:1 final size:1
Alignment explanation
Indices: 16312841--16312870 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
16312831 GATGTTTTCG
16312841 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
16312871 GCTTGGTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:16314743 original size:17 final size:18
Alignment explanation
Indices: 16314721--16314756 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
16314711 TTTAATTATA
*
16314721 AAATAATGAAA-TTAATT
1 AAATAATAAAATTTAATT
16314738 AAATAATAAAATTTAATT
1 AAATAATAAAATTTAATT
16314756 A
1 A
16314757 CATATTGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AAATAATAAAATTTAATT
Found at i:16315551 original size:21 final size:23
Alignment explanation
Indices: 16315527--16315575 Score: 57
Period size: 21 Copynumber: 2.2 Consensus size: 23
16315517 TAAAATGATT
16315527 TTATAGCTAATT-AAAAT-TTTA
1 TTATAGCTAATTGAAAATATTTA
**
16315548 TTATATTTAATTGAAAATATTTA
1 TTATAGCTAATTGAAAATATTTA
*
16315571 ATATA
1 TTATA
16315576 AAAATTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 10 0.43
22 5 0.22
23 8 0.35
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (23 bp):
TTATAGCTAATTGAAAATATTTA
Found at i:16315575 original size:23 final size:21
Alignment explanation
Indices: 16315534--16315575 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
16315524 ATTTTATAGC
*
16315534 TAATTAAAATTTTATTATATT
1 TAATTAAAATTTTAATATATT
16315555 TAATTGAAAATATTTAATATA
1 TAATT-AAAAT-TTTAATATA
16315576 AAAATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 5 0.28
23 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
TAATTAAAATTTTAATATATT
Found at i:16315840 original size:21 final size:22
Alignment explanation
Indices: 16315813--16315860 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
16315803 CCGGATGTAA
*
16315813 ATAAAAAATTATTAAAA-ATTAT
1 ATAAAAAATT-GTAAAATATTAT
16315835 -TAAAAAATTGTAAAATATTAT
1 ATAAAAAATTGTAAAATATTAT
16315856 ATAAA
1 ATAAA
16315861 CTTATAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 5 0.22
21 14 0.61
22 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (22 bp):
ATAAAAAATTGTAAAATATTAT
Found at i:16315848 original size:10 final size:10
Alignment explanation
Indices: 16315813--16315899 Score: 68
Period size: 10 Copynumber: 8.4 Consensus size: 10
16315803 CCGGATGTAA
16315813 ATAAAAAATT
1 ATAAAAAATT
*
16315823 ATTAAAAATT
1 ATAAAAAATT
16315833 ATTAAAAAATT
1 A-TAAAAAATT
* *
16315844 GTAAAATATT
1 ATAAAAAATT
* *
16315854 ATATAAACTT
1 ATAAAAAATT
*
16315864 ATAACAAATTGT
1 ATAA-AAAAT-T
*
16315876 AGAAAAAAATT
1 A-TAAAAAATT
16315887 AT-AAAAATT
1 ATAAAAAATT
16315896 ATAA
1 ATAA
16315900 TTGGGCAGAA
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
9 9 0.15
10 28 0.47
11 14 0.24
12 6 0.10
13 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.33
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:16315855 original size:31 final size:30
Alignment explanation
Indices: 16315814--16315899 Score: 86
Period size: 31 Copynumber: 2.8 Consensus size: 30
16315804 CGGATGTAAA
16315814 TAAAAAATTAT-TAAAAATTATTAAAAAATTG
1 TAAAAAATTATAT-AAAATTA-TAAAAAATTG
* * *
16315845 TAAAATATTATATAAACTTATAACAAATTG
1 TAAAAAATTATATAAAATTATAAAAAATTG
16315875 TAGAAAAAAATTATA-AAAATTATAA
1 T---AAAAAATTATATAAAATTATAA
16315900 TTGGGCAGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
30 10 0.22
31 16 0.35
32 10 0.22
33 10 0.22
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.34
Consensus pattern (30 bp):
TAAAAAATTATATAAAATTATAAAAAATTG
Found at i:16317971 original size:27 final size:26
Alignment explanation
Indices: 16317910--16317967 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
16317900 ATATATCTTC
*
16317910 TCAAAATTTTACCAGGGGAAAAATCG
1 TCAAAATTTTACCAAGGGAAAAATCG
* *
16317936 TCAAAATTTTACCAAGGGTAAAATTG
1 TCAAAATTTTACCAAGGGAAAAATCG
16317962 TCAAAA
1 TCAAAA
16317968 ATTTGTTGGG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.26
Consensus pattern (26 bp):
TCAAAATTTTACCAAGGGAAAAATCG
Found at i:16328163 original size:110 final size:110
Alignment explanation
Indices: 16327963--16328293 Score: 608
Period size: 110 Copynumber: 3.0 Consensus size: 110
16327953 TAATCTCATA
16327963 AAAGAATCAAAGTGAGCATTTGATTCAAATACTGAGAAGGATTATTATGTTGTCTACAATTCCAA
1 AAAGAATCAAAGTGAGCATTTGATTCAAATACTGAGAAGGATTATTATGTTGTCTACAATTCCAA
* * *
16328028 TTGAGGAGATCACTAGTTTTAGCTATAAGAGTAGTTGACTCCATG
66 TTGAGGAGATCGCTAGTCTTGGCTATAAGAGTAGTTGACTCCATG
*
16328073 AAAGAATCAAAGTGAGCATTTGATTCAAATACTGAGAAAGATTATTATGTTGTCTACAATTCCAA
1 AAAGAATCAAAGTGAGCATTTGATTCAAATACTGAGAAGGATTATTATGTTGTCTACAATTCCAA
16328138 TTGAGGAGATCGCTAGTCTTGGCTATAAGAGTAGTTGACTCCATG
66 TTGAGGAGATCGCTAGTCTTGGCTATAAGAGTAGTTGACTCCATG
* *
16328183 AAAGAATCAAAGTGAGCATTTGATTCAAATACTAAGAAGGATTATTATGTCGTCTACAATTCCAA
1 AAAGAATCAAAGTGAGCATTTGATTCAAATACTGAGAAGGATTATTATGTTGTCTACAATTCCAA
16328248 TTGAGGAGATCGCTAGTCTTGGCTATAAGAGTAGTTGACTCCATG
66 TTGAGGAGATCGCTAGTCTTGGCTATAAGAGTAGTTGACTCCATG
16328293 A
1 A
16328294 GTAGAGACAT
Statistics
Matches: 214, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
110 214 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.31
Consensus pattern (110 bp):
AAAGAATCAAAGTGAGCATTTGATTCAAATACTGAGAAGGATTATTATGTTGTCTACAATTCCAA
TTGAGGAGATCGCTAGTCTTGGCTATAAGAGTAGTTGACTCCATG
Found at i:16330424 original size:94 final size:94
Alignment explanation
Indices: 16330263--16330442 Score: 360
Period size: 94 Copynumber: 1.9 Consensus size: 94
16330253 AACCATCTAG
16330263 CTCCTTTCCAAAATTCATGGTCAACCAAGAGTAAGAAAAACCTAAGGGAATTTCAAACTATTTTT
1 CTCCTTTCCAAAATTCATGGTCAACCAAGAGTAAGAAAAACCTAAGGGAATTTCAAACTATTTTT
16330328 AGTAAACCTATTAGCCATACCAACAACCT
66 AGTAAACCTATTAGCCATACCAACAACCT
16330357 CTCCTTTCCAAAATTCATGGTCAACCAAGAGTAAGAAAAACCTAAGGGAATTTCAAACTATTTTT
1 CTCCTTTCCAAAATTCATGGTCAACCAAGAGTAAGAAAAACCTAAGGGAATTTCAAACTATTTTT
16330422 AGTAAACCTATTAGCCATACC
66 AGTAAACCTATTAGCCATACC
16330443 TCAAGTATAA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 86 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (94 bp):
CTCCTTTCCAAAATTCATGGTCAACCAAGAGTAAGAAAAACCTAAGGGAATTTCAAACTATTTTT
AGTAAACCTATTAGCCATACCAACAACCT
Found at i:16348140 original size:51 final size:51
Alignment explanation
Indices: 16348076--16348368 Score: 297
Period size: 51 Copynumber: 5.8 Consensus size: 51
16348066 TATCGATGAA
* **
16348076 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATCTTGGT
* * * ** * *
16348127 CACATGTGTAGTACTAAGTGAAGGCTACAATATGTA-CCA-AGAAGCTTTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATA-AATC-TTGGT
* * **
16348178 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATCTTGGT
* * * * * *
16348229 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTA-CCATAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATCTTGGT
* * * *
16348279 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATCTTGGT
* * *
16348329 CACGTGTGTAGTACCATATGAAGGCTACTATGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
16348369 ATGATAAAAG
Statistics
Matches: 195, Mismatches: 41, Indels: 12
0.79 0.17 0.05
Matches are distributed among these distances:
49 1 0.01
50 90 0.46
51 99 0.51
52 4 0.02
53 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATCTTGGT
Found at i:16348252 original size:102 final size:101
Alignment explanation
Indices: 16348076--16348314 Score: 399
Period size: 102 Copynumber: 2.4 Consensus size: 101
16348066 TATCGATGAA
*
16348076 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* *
16348141 TAAGTGAAGGCTACAATATGTACCA-AGAAGCTTTGGT
66 TAAGTGAAGGCTACAATATGTACCATA-AAAC-TTGAT
16348178 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
* *
16348243 TAAGTGAAGGCTACTATGTGTACCATAAAACTTGAT
66 TAAGTGAAGGCTACAATATGTACCATAAAACTTGAT
*
16348279 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAA
16348315 CCGTAAAACT
Statistics
Matches: 130, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
101 39 0.30
102 90 0.69
103 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (101 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACAATATGTACCATAAAACTTGAT
Found at i:16348391 original size:101 final size:100
Alignment explanation
Indices: 16348083--16348401 Score: 270
Period size: 102 Copynumber: 3.1 Consensus size: 100
16348073 GAACACGTGT
* * ** * *
16348083 GTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACCAAGTGA
* * * * * * * * *
16348148 AGGCTACAATATGTACCAA-GAAGCTTTGGTCACGTGT
66 AGGCTACTATGTGTA-CAATAAAAC--AGATAACATGG
* ** * *
16348185 GTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTACTAAGTGA
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACCAAGTGA
* * * * *
16348250 AGGCTACTATGTGTACCATAAAACTTGATCACGTGT
66 AGGCTACTATGTGTACAATAAAAC-AGATAACATGG
* * *
16348286 GTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAAACTTGATCACGTGTGTAGTACCATA-TG
1 GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACCA-AGTG
16348349 AAGGCTACTATGTGTATCGAATGATAAA-AG-TAACATGG
65 AAGGCTACTATGTGTA-C-AAT-A-AAACAGATAACATGG
16348387 GTAGTACTGTGTGAA
1 GTAGTACTGTGTGAA
16348402 AAACCCCAAA
Statistics
Matches: 190, Mismatches: 21, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
100 39 0.21
101 64 0.34
102 83 0.44
103 1 0.01
104 3 0.02
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (100 bp):
GTAGTACTGTGTGAAGGCTACTACGTGAACCGATAAAACATGATCACATGTGTAGTACCAAGTGA
AGGCTACTATGTGTACAATAAAACAGATAACATGG
Found at i:16349679 original size:17 final size:17
Alignment explanation
Indices: 16349657--16349690 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
16349647 CCTAATTCAT
16349657 CCCTGTTACTTCACATA
1 CCCTGTTACTTCACATA
16349674 CCCTGTTACTTCACATA
1 CCCTGTTACTTCACATA
16349691 AATTCTAAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.35, G:0.06, T:0.35
Consensus pattern (17 bp):
CCCTGTTACTTCACATA
Found at i:16353358 original size:19 final size:18
Alignment explanation
Indices: 16353332--16353370 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
16353322 GTGCGAAAAA
16353332 TTTGATTTTAAACCCGAT
1 TTTGATTTTAAACCCGAT
*
16353350 TTTGAATTTTAAACCTGAT
1 TTTG-ATTTTAAACCCGAT
16353369 TT
1 TT
16353371 AGCTACAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (18 bp):
TTTGATTTTAAACCCGAT
Found at i:16354351 original size:23 final size:23
Alignment explanation
Indices: 16354325--16354371 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
16354315 TCACAAATCC
16354325 TATGGCATGCCAACTATATCCAA
1 TATGGCATGCCAACTATATCCAA
16354348 TATGGCATGCCAACTATATCCAA
1 TATGGCATGCCAACTATATCCAA
16354371 T
1 T
16354372 GGATCTACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (23 bp):
TATGGCATGCCAACTATATCCAA
Found at i:16357348 original size:30 final size:30
Alignment explanation
Indices: 16357312--16357380 Score: 129
Period size: 30 Copynumber: 2.3 Consensus size: 30
16357302 AATTTCTATT
16357312 AAGAAGAGAGAATTTTTGTTTTCAACCCAA
1 AAGAAGAGAGAATTTTTGTTTTCAACCCAA
*
16357342 AAGAAGAGAGAATTTTTGTTTTCACCCCAA
1 AAGAAGAGAGAATTTTTGTTTTCAACCCAA
16357372 AAGAAGAGA
1 AAGAAGAGA
16357381 AATCTCTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (30 bp):
AAGAAGAGAGAATTTTTGTTTTCAACCCAA
Found at i:16361848 original size:19 final size:19
Alignment explanation
Indices: 16361824--16361869 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
16361814 GACAATGGAC
* *
16361824 TTTATTTGTTGTTTTTTTA
1 TTTATTTGTTGGTTTTATA
*
16361843 TTTATTTTTTGGTTTTATA
1 TTTATTTGTTGGTTTTATA
16361862 TTTGATTT
1 TTT-ATTT
16361870 ATTTTCTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.13, C:0.00, G:0.11, T:0.76
Consensus pattern (19 bp):
TTTATTTGTTGGTTTTATA
Found at i:16365216 original size:236 final size:236
Alignment explanation
Indices: 16364764--16365238 Score: 923
Period size: 236 Copynumber: 2.0 Consensus size: 236
16364754 TCCTATAAGG
16364764 GTATAGTAAAATATTTTTAAAAACTAATATATATATTGATTTGGGCCTAGAAGCGGAAGATCGGG
1 GTATAGTAAAATATTTTTAAAAACTAATATATATATTGATTTGGGCCTAGAAGCGGAAGATCGGG
*
16364829 TAACCTGTGAATCCAACGAGTTGGTTTATAATAATTCATGAAGGAAATTACCATATTTCCGCAAG
66 TAACCTGTGAATCCAACGAGTTGGTTTATAATAATTCATGAAGGAAATTACCATACTTCCGCAAG
16364894 TCAATTAGATGTGAAATATAAAAATTGACTTTTTTTTTCATAGTCGCACAAGAGGTTTTGTTTTT
131 TCAATTAGATGTGAAATATAAAAATTGACTTTTTTTTTCATAGTCGCACAAGAGGTTTTGTTTTT
16364959 TGTTGGAAGCCCTCTTTTTTTTTTTAAGGAATTGCTTAGTC
196 TGTTGGAAGCCCTCTTTTTTTTTTTAAGGAATTGCTTAGTC
16365000 GTATAGTAAAATATTTTTAAAAACTAATATATATATTGATTTGGGCCTAGAAGCGGAAGATCGGG
1 GTATAGTAAAATATTTTTAAAAACTAATATATATATTGATTTGGGCCTAGAAGCGGAAGATCGGG
16365065 TAACCTGTGAATCCAACGAGTTGGTTTATAATAATTCATGAAGGAAATTACCATACTTCCGCAAG
66 TAACCTGTGAATCCAACGAGTTGGTTTATAATAATTCATGAAGGAAATTACCATACTTCCGCAAG
16365130 TCAATTAGATGTGAAATATAAAAATTGACTTTTTTTTTTCATAGTCGCACAAGAGGTTTTGTTTT
131 TCAATTAGATGTGAAATATAAAAATTGAC-TTTTTTTTTCATAGTCGCACAAGAGGTTTTGTTTT
16365195 TTGTTGGAAGCCCTCTTTTTTTTTTTTAAGGAATTGCTTAGTC
195 TTGTTGGAAGCCCTC-TTTTTTTTTTTAAGGAATTGCTTAGTC
16365238 G
1 G
16365239 CCTAGTAACA
Statistics
Matches: 236, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
236 158 0.67
237 50 0.21
238 28 0.12
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (236 bp):
GTATAGTAAAATATTTTTAAAAACTAATATATATATTGATTTGGGCCTAGAAGCGGAAGATCGGG
TAACCTGTGAATCCAACGAGTTGGTTTATAATAATTCATGAAGGAAATTACCATACTTCCGCAAG
TCAATTAGATGTGAAATATAAAAATTGACTTTTTTTTTCATAGTCGCACAAGAGGTTTTGTTTTT
TGTTGGAAGCCCTCTTTTTTTTTTTAAGGAATTGCTTAGTC
Found at i:16374967 original size:19 final size:18
Alignment explanation
Indices: 16374922--16374973 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
16374912 ATTATTGAGA
*
16374922 ATTATAAATAATTATTAAT
1 ATTATAAA-AATTATAAAT
* *
16374941 TTTGTAAAAATTAGTAAAT
1 ATTATAAAAATTA-TAAAT
16374960 ATTATAAAAATTAT
1 ATTATAAAAATTAT
16374974 TTATGAATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
ATTATAAAAATTATAAAT
Found at i:16375151 original size:20 final size:20
Alignment explanation
Indices: 16375123--16375191 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
16375113 TTATTAATTC
* *
16375123 TTTAAAATTTTAAAAAAATA
1 TTTATAATTTTATAAAAATA
*
16375143 TTTATAATTTCT-TATAAATA
1 TTTATAATTT-TATAAAAATA
* *
16375163 TTAATATTTTTATAAAAA-A
1 TTTATAATTTTATAAAAATA
16375182 -TTATAATTTT
1 TTTATAATTTT
16375192 GTATATTTTT
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
18 8 0.21
19 2 0.05
20 28 0.72
21 1 0.03
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTATAATTTTATAAAAATA
Found at i:16375184 original size:19 final size:20
Alignment explanation
Indices: 16375130--16375196 Score: 59
Period size: 19 Copynumber: 3.4 Consensus size: 20
16375120 TTCTTTAAAA
* *
16375130 TTTTAAAAAAATATTTATAAT
1 TTTTATAAAAA-ATTAATAAT
*
16375151 TTCTTAT-AAATATTAAT-AT
1 TT-TTATAAAAAATTAATAAT
16375170 TTTTATAAAAAATT-ATAAT
1 TTTTATAAAAAATTAATAAT
16375189 TTTGTATA
1 TTT-TATA
16375197 TTTTTATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
18 6 0.16
19 15 0.39
20 9 0.24
21 5 0.13
22 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (20 bp):
TTTTATAAAAAATTAATAAT
Found at i:16376857 original size:18 final size:19
Alignment explanation
Indices: 16376831--16376867 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
16376821 ATCAATTTAT
*
16376831 TATTTGAGTT-ATTCAAAA
1 TATTCGAGTTGATTCAAAA
16376849 TATTCGAGTTGATTCAAAA
1 TATTCGAGTTGATTCAAAA
16376868 GGAATCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (19 bp):
TATTCGAGTTGATTCAAAA
Found at i:16382551 original size:7 final size:7
Alignment explanation
Indices: 16382535--16382564 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
16382525 TAAATGTGTA
16382535 AAAACTT
1 AAAACTT
*
16382542 AAAACCT
1 AAAACTT
16382549 AAAACTT
1 AAAACTT
16382556 AAAACTT
1 AAAACTT
16382563 AA
1 AA
16382565 TTTATTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAACTT
Found at i:16383851 original size:21 final size:21
Alignment explanation
Indices: 16383808--16383851 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
16383798 ACACACTTAG
*
16383808 CTTAATTGAGCTATTAATTAA
1 CTTAATTGAGCTATTAATAAA
16383829 CTTAATTGAGCTAATTAA-AAA
1 CTTAATTGAGCT-ATTAATAAA
16383850 CT
1 CT
16383852 ACAAAACCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.41, C:0.11, G:0.09, T:0.39
Consensus pattern (21 bp):
CTTAATTGAGCTATTAATAAA
Found at i:16384506 original size:18 final size:18
Alignment explanation
Indices: 16384463--16384508 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
16384453 TTAATGCCGA
*
16384463 AAATACTT-AGACATATT
1 AAATACTTAAGACACATT
16384480 AAATAACTTAAGACACATT
1 AAAT-ACTTAAGACACATT
*
16384499 TAATACTTAA
1 AAATACTTAA
16384509 ACTAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 10 0.40
19 11 0.44
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (18 bp):
AAATACTTAAGACACATT
Found at i:16386869 original size:16 final size:16
Alignment explanation
Indices: 16386830--16386905 Score: 64
Period size: 18 Copynumber: 4.6 Consensus size: 16
16386820 TCTTCACACG
*
16386830 TTTCTTTTTCAATCTCT
1 TTTCTTTTTCAATC-AT
* *
16386847 TTCTCTTTTTCACTTAT
1 TT-TCTTTTTCAATCAT
*
16386864 TTTC-TTTTCAAGCACT
1 TTTCTTTTTCAATCA-T
*
16386880 CTTTCTTTTTCACTCAT
1 -TTTCTTTTTCAATCAT
16386897 TTTCTTTTT
1 TTTCTTTTT
16386906 GAGCTCTCTT
Statistics
Matches: 47, Mismatches: 8, Indels: 9
0.73 0.12 0.14
Matches are distributed among these distances:
15 7 0.15
16 12 0.26
17 10 0.21
18 18 0.38
ACGTcount: A:0.12, C:0.24, G:0.01, T:0.63
Consensus pattern (16 bp):
TTTCTTTTTCAATCAT
Found at i:16386872 original size:33 final size:33
Alignment explanation
Indices: 16386807--16386927 Score: 111
Period size: 33 Copynumber: 3.6 Consensus size: 33
16386797 CTTGTGTTTG
* * *
16386807 AGCACTCTCTTCTTCTTCACAC-GTTTCTTTTTCA
1 AGCACTCT-TTCTTTTTCACTCATTTTC-TTTTCA
* * *
16386841 ATCTCT-TTCTCTTTTTCACTTATTTTCTTTTCA
1 AGCACTCTT-TCTTTTTCACTCATTTTCTTTTCA
**
16386874 AGCACTCTTTCTTTTTCACTCATTTTCTTTTTG
1 AGCACTCTTTCTTTTTCACTCATTTTCTTTTCA
* *
16386907 AGCTCTCTTTCTTTTGCACTC
1 AGCACTCTTTCTTTTTCACTC
16386928 GTTTCATTCA
Statistics
Matches: 71, Mismatches: 13, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
32 1 0.01
33 60 0.85
34 10 0.14
ACGTcount: A:0.12, C:0.28, G:0.05, T:0.55
Consensus pattern (33 bp):
AGCACTCTTTCTTTTTCACTCATTTTCTTTTCA
Found at i:16386917 original size:17 final size:17
Alignment explanation
Indices: 16386864--16386921 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
16386854 TTTCACTTAT
* *
16386864 TTTCTTTTCAAGCACTC
1 TTTCTTTTTAAGCTCTC
*
16386881 TTTCTTTTTCA-CTCAT-
1 TTTCTTTTTAAGCTC-TC
*
16386897 TTTCTTTTTGAGCTCTC
1 TTTCTTTTTAAGCTCTC
16386914 TTTCTTTT
1 TTTCTTTT
16386922 GCACTCGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
16 13 0.38
17 21 0.62
ACGTcount: A:0.10, C:0.24, G:0.05, T:0.60
Consensus pattern (17 bp):
TTTCTTTTTAAGCTCTC
Found at i:16392475 original size:18 final size:18
Alignment explanation
Indices: 16392432--16392477 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 18
16392422 TTAATGCCGA
*
16392432 AAATACTT-AGACATATT
1 AAATACTTAAGACACATT
16392449 AAATAACTTAAGACACATT
1 AAAT-ACTTAAGACACATT
*
16392468 TAATACTTAA
1 AAATACTTAA
16392478 ACTAATTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 4 0.16
18 10 0.40
19 11 0.44
ACGTcount: A:0.50, C:0.13, G:0.04, T:0.33
Consensus pattern (18 bp):
AAATACTTAAGACACATT
Done.