Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 92 of 318
Found at i:27857825 original size:20 final size:20
Alignment explanation
Indices: 27857800--27857837 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
27857790 ACCATTGACA
27857800 ATAAAAATT-AAAACAAAAAC
1 ATAAAAATTGAAAA-AAAAAC
27857820 ATAAAAATTGAAAAAAAA
1 ATAAAAATTGAAAAAAAA
27857838 TTCCTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (20 bp):
ATAAAAATTGAAAAAAAAAC
Found at i:27862707 original size:14 final size:14
Alignment explanation
Indices: 27862688--27862719 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
27862678 CCTTTATGGT
*
27862688 GTATTCTGTAAATC
1 GTATTCTATAAATC
27862702 GTATTCTATAAATC
1 GTATTCTATAAATC
27862716 GTAT
1 GTAT
27862720 GTTTTCTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (14 bp):
GTATTCTATAAATC
Found at i:27874647 original size:3 final size:3
Alignment explanation
Indices: 27874632--27874702 Score: 126
Period size: 3 Copynumber: 24.0 Consensus size: 3
27874622 CTTTAAACAC
*
27874632 AAT AAT AA- CAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
27874679 AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT
27874703 GTCTTTCAAA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 1 0.02
3 64 0.98
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:27881581 original size:33 final size:33
Alignment explanation
Indices: 27881539--27881605 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
27881529 AATTAGTTAG
*
27881539 TCCAGCTGTTACTTGCCAAATGACACATTGTCC
1 TCCACCTGTTACTTGCCAAATGACACATTGTCC
*
27881572 TCCACCTGTTACTTGCCAAATGACGCATTGTCC
1 TCCACCTGTTACTTGCCAAATGACACATTGTCC
27881605 T
1 T
27881606 TGCTCCCTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.22, C:0.31, G:0.15, T:0.31
Consensus pattern (33 bp):
TCCACCTGTTACTTGCCAAATGACACATTGTCC
Found at i:27890760 original size:64 final size:65
Alignment explanation
Indices: 27890600--27890916 Score: 270
Period size: 64 Copynumber: 4.8 Consensus size: 65
27890590 ATACAGATGG
* * * ** * *
27890600 TATGTAGCTAGGTCACATGTGTAATA-TGGGATGTATACCATGT-GTACAAGAGAGCTACGAGAC
1 TATGTAGCTAGGTCGCATGGGTGATACTATG-TGTACACCATGTAG-ACAAGAGAGCTAC-AGAG
27890663 ATTA
63 A-TA
* *
27890667 TGAGGTAGCTAGGTGGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACAG-GAT
1 T-ATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACAGAGAT
27890731 A
65 A
*
27890732 TATGTAGTTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTAC-GAGATA
1 TATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACAGAGATA
* * * * * * * * * *
27890796 AATGTAGCTAGGTTGCATGTGTGGTTCCAGGTGAAGGACACCATGTAAACAAGAGAGCTA-TGAG
1 TATGTAGCTAGGTCGCATGGGTGATACTA--TG-TGTACACCATGTAGACAAGAGAGCTACAGAG
27890860 ATA
63 ATA
* * * * * *
27890863 -AAGTGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGT-GTACAAGAGAGC
1 TATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGC
27890917 CAAAATTATG
Statistics
Matches: 207, Mismatches: 34, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
63 20 0.10
64 81 0.39
65 3 0.01
66 24 0.12
67 32 0.15
68 44 0.21
69 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.25
Consensus pattern (65 bp):
TATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAGACAAGAGAGCTACAGAGATA
Found at i:27896937 original size:48 final size:46
Alignment explanation
Indices: 27896775--27896993 Score: 165
Period size: 49 Copynumber: 4.6 Consensus size: 46
27896765 ATGCCGACGC
* * * * *
27896775 CATGTCCGAGACAAGTCTTACACT-GACTTTCATATGTTGAGGCCAATG
1 CATGTCCTAGACATGTCTTACACTAG-CTCTCATA--ATGAGGCCGATG
* * * * * *
27896823 ACATGTCCCAGATAGGTCTTACACTGGCTCTCATCCATTG-GTGTCGATG
1 -CATGTCCTAGACATGTCTTACACTAGCTCTCAT--AATGAG-GCCGATG
* * *
27896872 CCATGTCCTAAACATGTCTTACACTAGCT-TGTATATCTCGAGGCCGATG
1 -CATGTCCTAGACATGTCTTACACTAGCTCT-CATA-AT-GAGGCCGATG
* *
27896921 CATGTCCTAGACATGTCTTACATTAGCTCTCATAATGTGGCCGATG
1 CATGTCCTAGACATGTCTTACACTAGCTCTCATAATGAGGCCGATG
*
27896967 CATGTCCCAGACATGTCTTACACTAGC
1 CATGTCCTAGACATGTCTTACACTAGC
27896994 ACACATATCA
Statistics
Matches: 139, Mismatches: 22, Indels: 21
0.76 0.12 0.12
Matches are distributed among these distances:
46 34 0.24
47 2 0.01
48 32 0.23
49 68 0.49
50 2 0.01
51 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (46 bp):
CATGTCCTAGACATGTCTTACACTAGCTCTCATAATGAGGCCGATG
Found at i:27901149 original size:43 final size:42
Alignment explanation
Indices: 27901102--27901209 Score: 126
Period size: 43 Copynumber: 2.5 Consensus size: 42
27901092 GCAACACGGC
* *
27901102 CGTGTGAACCTATTTCAAATTGCACACGGTCTGGTGAAATGG
1 CGTGTGACCCTATTTCAAATTGCACACGGTCTAGTGAAATGG
* ** *
27901144 TCGTGTGACCCTATTTCGAATCACACACGGTCTAGTGACATGG
1 -CGTGTGACCCTATTTCAAATTGCACACGGTCTAGTGAAATGG
* *
27901187 CTGTATGACCCTATTTTAAATTG
1 C-GTGTGACCCTATTTCAAATTG
27901210 TACATGTTCT
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 1 0.02
43 52 0.98
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (42 bp):
CGTGTGACCCTATTTCAAATTGCACACGGTCTAGTGAAATGG
Found at i:27904398 original size:23 final size:23
Alignment explanation
Indices: 27904366--27904409 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
27904356 ACTACCATTT
27904366 TCTAAATAAAATAATAATAAATA
1 TCTAAATAAAATAATAATAAATA
* *
27904389 TCTAAGTAAAATATTAATAAA
1 TCTAAATAAAATAATAATAAA
27904410 ATGATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (23 bp):
TCTAAATAAAATAATAATAAATA
Found at i:27904402 original size:13 final size:11
Alignment explanation
Indices: 27904370--27904411 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
27904360 CCATTTTCTA
*
27904370 AATAAAATAAT
1 AATAAAATATT
27904381 AAT-AAATATCT
1 AATAAAATAT-T
27904392 AAGTAAAATATT
1 AA-TAAAATATT
27904404 AATAAAAT
1 AATAAAAT
27904412 GATATTTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 5 0.19
11 12 0.44
12 4 0.15
13 6 0.22
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (11 bp):
AATAAAATATT
Found at i:27904792 original size:3 final size:3
Alignment explanation
Indices: 27904784--27904827 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
27904774 CTACTTCTTA
27904784 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
27904828 GATGATCATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:27909296 original size:94 final size:93
Alignment explanation
Indices: 27909143--27909484 Score: 275
Period size: 94 Copynumber: 3.6 Consensus size: 93
27909133 ACGTGCTTAG
* * * * * * * *
27909143 GACATGCTTCGGCCACATTATGAGAGCCAGTGTAAAACCATGTCTGGGGCATGGCATCGGCATCC
1 GACATGCATCAGCCTCA-TATGATAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGC-TCA
27909208 AA-ACGAGGGCTAGTGTAAGACATGTCTAA
64 AAGACGAGGGCTAGTGTAAGACATGTCTAA
* * *
27909237 GATATGCATCAGCCAT-ACTATGATAGCCAGTGTAAGACCATGTCTAGGATATGGTATCGGCTCA
1 GACATGCATCAGCC-TCA-TATGATAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCTCA
* * * **
27909301 AAGATGAGTGTTAGTGTAAGACATGTCTGG
64 AAGACGAGGGCTAGTGTAAGACATGTCTAA
* * * * *
27909331 GACATGCATCGGCCTCGATAGAGATAGCCAGTGTAAGA-CGTGTCTAGGACA-CGCATTGGCT--
1 GACATGCATCAGCCTC-ATA-TGATAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCTCA
* ** * **
27909392 AAGA-GTTGTTCTAGTGTAAGACATGTTTGG
64 AAGACG-AGGGCTAGTGTAAGACATGTCTAA
* * *
27909422 GACATGCATCAGCACATGTATATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 GACATGCATCAGC-C-T-CATATGATAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGC
27909485 AATATATCCC
Statistics
Matches: 200, Mismatches: 37, Indels: 22
0.77 0.14 0.08
Matches are distributed among these distances:
90 1 0.00
91 36 0.18
92 16 0.08
93 27 0.14
94 103 0.51
95 17 0.09
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.24
Consensus pattern (93 bp):
GACATGCATCAGCCTCATATGATAGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCTCAAA
GACGAGGGCTAGTGTAAGACATGTCTAA
Found at i:27909364 original size:47 final size:45
Alignment explanation
Indices: 27909313--27909484 Score: 154
Period size: 47 Copynumber: 3.7 Consensus size: 45
27909303 GATGAGTGTT
27909313 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGATAGAGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-GATAGAG-TAGCC
* * * * * *
27909360 AGTGTAAGACGTGTCTAGGACACGCATTGG-CT-A-AGAGTTGTTCT
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTGATAGAGTAG--CC
* *
27909404 AGTGTAAGACATGTTTGGGACATGCATCAGCACATGTATATGAG-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGC-C-TG-ATA-GAGTAGCC
27909452 AGTGTAAGACCATGTCTGGGACATGGCATCGGC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC
27909485 AATATATCCC
Statistics
Matches: 98, Mismatches: 16, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 26 0.27
46 3 0.03
47 27 0.28
48 10 0.10
49 14 0.14
50 9 0.09
51 3 0.03
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTGATAGAGTAGCC
Found at i:27918442 original size:46 final size:46
Alignment explanation
Indices: 27918388--27918706 Score: 424
Period size: 46 Copynumber: 6.9 Consensus size: 46
27918378 GTGTGCTCTT
*
27918388 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
* * *
27918434 TCATATGAAATGTGTAAGACAATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
*
27918480 TGATATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACC
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
* *
27918526 TGATATGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
*** * * *
27918572 TGACGGGAAATGAATAAGACCATGGTTGAAAGATACCATGGCAGCG
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
* * * *
27918618 TGACATGAAATGAATAAGACCATGGTTGAAAGATAACATGGCAACA
1 TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
* * * * *
27918664 TGACA-GAAAATGAGTAAGACCATAGATGAAAGACACTATGGCA
1 TGATATG-AAATGAGTAAGACCATGGTTGAAAGATACCATGGCA
27918707 TCATGTCAAA
Statistics
Matches: 249, Mismatches: 23, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
45 1 0.00
46 248 1.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.21
Consensus pattern (46 bp):
TGATATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACC
Found at i:27919011 original size:16 final size:17
Alignment explanation
Indices: 27918990--27919022 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
27918980 ATTATGGTGC
27918990 ATGAAAT-ATTGATATA
1 ATGAAATGATTGATATA
27919006 ATGAAATGATTGATATA
1 ATGAAATGATTGATATA
27919023 TACTTATGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGAAATGATTGATATA
Found at i:27920625 original size:47 final size:45
Alignment explanation
Indices: 27920514--27920823 Score: 220
Period size: 47 Copynumber: 6.7 Consensus size: 45
27920504 TGATTTGTGC
* * *
27920514 GCTAGTGTAAGACTTGTCTGGGACATGCTTCGGC--CACATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATC-CA-GA-GAGA
* * * *
27920560 GCCAGTGTAAAACTATGTCTGGGGCATGGCATCGGCATCCAGACGAGG
1 GCTAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCATCCAGA-GAGA
** * * * *
27920608 GCTAGTGTAAGACATGTCTAAGACATGCATCAGCCATACTA-TGATA
1 GCTAGTGTAAGACATGTCTGGGACATGCATC-GGCAT-CCAGAGAGA
*
27920654 GCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCA--CAGAGATGA
1 GCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATCCAGAGA-GA
* * *
27920700 GTGCTAGTGTAAGACATGTCTGGGACATGCATAGGCCTCGACAGAGATA
1 --GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATC--CAGAGAGA
* * * * * *
27920749 GCCAGTGTAAGACGTGTCTGGGACACGCATCGGC-T-AAGAGTTGT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCCAGAG-AGA
27920793 GCTAGTGTAAGACATGTCTGGGACATGCATC
1 GCTAGTGTAAGACATGTCTGGGACATGCATC
27920824 AGCACACGTA
Statistics
Matches: 207, Mismatches: 40, Indels: 36
0.73 0.14 0.13
Matches are distributed among these distances:
43 4 0.02
44 29 0.14
45 2 0.01
46 38 0.18
47 84 0.41
48 40 0.19
49 3 0.01
50 7 0.03
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (45 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGGCATCCAGAGAGA
Found at i:27920651 original size:94 final size:93
Alignment explanation
Indices: 27920514--27920877 Score: 379
Period size: 94 Copynumber: 3.9 Consensus size: 93
27920504 TGATTTGTGC
* * * * * * *
27920514 GCTAGTGTAAGACTTGTCTGGGACATGCTTCGGCCACATTATGAGAGCCAGTGTAAAACTATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATGTC
* * *
27920579 TGGGGCATGGCATCGGCATCCAGACGAGG
66 TGGGACATGGCATCGGCATCAAGA-GAGT
** *
27920608 GCTAGTGTAAGACATGTCTAAGACATGCATCAGCCATACTATGATAGCCAGTGTAAGACCATGTC
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATGTC
27920673 TGGGACATGGCATCGGCA-CAGAGATGAGT
66 TGGGACATGGCATCGGCATCA-AGA-GAGT
27920702 GCTAGTGTAAGACATGTCTGGGACATGCAT-AGGCC-TCGAC-A-GAGATAGCCAGTGTAAGA-C
1 GCTAGTGTAAGACATGTCTGGGACATGCATCA-GCCAT--ACTATGAG--AGCCAGTGTAAGACC
* * *
27920762 GTGTCTGGGACA-CGCATCGGC-T-AAGAGTTGT
61 ATGTCTGGGACATGGCATCGGCATCAAGAG-AGT
** *
27920793 GCTAGTGTAAGACATGTCTGGGACATGCATCAGCACACGTA-TATGAGAAACGGTGTAAGACCAT
1 GCTAGTGTAAGACATGTCTGGGACATGCATCAGC-CA--TACTATGAGAGCCAGTGTAAGACCAT
27920857 GTCTGGGACATGGCATCGGCA
63 GTCTGGGACATGGCATCGGCA
27920878 ATATATCCCA
Statistics
Matches: 227, Mismatches: 25, Indels: 35
0.79 0.09 0.12
Matches are distributed among these distances:
90 1 0.00
91 37 0.16
92 13 0.06
93 27 0.12
94 133 0.59
95 16 0.07
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (93 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCAGCCATACTATGAGAGCCAGTGTAAGACCATGTC
TGGGACATGGCATCGGCATCAAGAGAGT
Found at i:27927291 original size:47 final size:47
Alignment explanation
Indices: 27927182--27927292 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
27927172 CCGGGATAAG
* *
27927182 CACATAGTGCTTCATCGGAACAAATCCTGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
27927229 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
27927276 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
27927293 ACTCAATGTC
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
46 1 0.02
47 52 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.15, T:0.26
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:27931740 original size:13 final size:13
Alignment explanation
Indices: 27931718--27931751 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
27931708 GTTTGATTAA
27931718 TGATTAATTAGTT
1 TGATTAATTAGTT
*
27931731 TGATTCATTAGTT
1 TGATTAATTAGTT
*
27931744 TAATTAAT
1 TGATTAAT
27931752 CATATTTTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (13 bp):
TGATTAATTAGTT
Found at i:27931781 original size:21 final size:21
Alignment explanation
Indices: 27931741--27931781 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
27931731 TGATTCATTA
*
27931741 GTTTAATTAATCATATTTTAT
1 GTTTAATTAATCATAGTTTAT
*
27931762 GTTTAATTAATCTTAGTTTA
1 GTTTAATTAATCATAGTTTA
27931782 ATCATAGTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (21 bp):
GTTTAATTAATCATAGTTTAT
Found at i:27935756 original size:2 final size:2
Alignment explanation
Indices: 27935749--27935782 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
27935739 ATCTTTTGAG
27935749 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27935783 CTATCATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27942217 original size:28 final size:28
Alignment explanation
Indices: 27942177--27942239 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
27942167 GTCATTATCA
27942177 ACCCCATAAGTTATAAAACTCTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
* ** *
27942205 ACCCCATAAGTTATGAGTCTTTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
27942233 ACCCCAT
1 ACCCCAT
27942240 TAATATGGGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.30, C:0.30, G:0.06, T:0.33
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACTCTTCCTAT
Found at i:27947989 original size:59 final size:60
Alignment explanation
Indices: 27947893--27948025 Score: 205
Period size: 59 Copynumber: 2.2 Consensus size: 60
27947883 GACAAGATTG
* * *
27947893 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATA
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
* * *
27947953 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
27948012 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
27948026 GATTCACTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 52 0.78
60 15 0.22
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (60 bp):
GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
Found at i:27948038 original size:29 final size:29
Alignment explanation
Indices: 27947923--27948025 Score: 188
Period size: 29 Copynumber: 3.5 Consensus size: 29
27947913 AAAATTGTAC
*
27947923 AGCACTAAGTGTGCGAACTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
27947952 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT
27947982 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
27948011 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
27948026 GATTCACTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 43 0.60
30 29 0.40
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:27955984 original size:59 final size:60
Alignment explanation
Indices: 27955888--27956020 Score: 205
Period size: 59 Copynumber: 2.2 Consensus size: 60
27955878 GACAAGATTG
* * *
27955888 GCACTAAGTGTGCGGGTTTAAAAATTGTACAGCACTAAGTGTGCGAACTGAAAATATATA
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
* * *
27955948 GCACTAAGTGTGCGAG-CTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
27956007 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
27956021 GATTCACTAT
Statistics
Matches: 67, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
59 52 0.78
60 15 0.22
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (60 bp):
GCACTAAGTGTGCGAGTCTAAAAATTATACAGCACTAAGTGTGCGAACTGAAAATATATA
Found at i:27956033 original size:29 final size:29
Alignment explanation
Indices: 27955918--27956020 Score: 188
Period size: 29 Copynumber: 3.5 Consensus size: 29
27955908 AAAATTGTAC
*
27955918 AGCACTAAGTGTGCGAACTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
27955947 AGCACTAAGTGTGCGAGCTGAAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAA-TATAT
27955977 AGCACTAAGTGTGCGAGCTGAAAATATAT
1 AGCACTAAGTGTGCGAGCTGAAAATATAT
27956006 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
27956021 GATTCACTAT
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
29 43 0.60
30 29 0.40
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.24
Consensus pattern (29 bp):
AGCACTAAGTGTGCGAGCTGAAAATATAT
Found at i:27960683 original size:22 final size:21
Alignment explanation
Indices: 27960658--27960698 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
27960648 CTTAGATATG
27960658 AAAAATAATTAATTTGTAAAGT
1 AAAAATAATTAATTT-TAAAGT
**
27960680 AAAAATTGTTAATTTTAAA
1 AAAAATAATTAATTTTAAA
27960699 CATAGGAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
AAAAATAATTAATTTTAAAGT
Found at i:27961602 original size:22 final size:23
Alignment explanation
Indices: 27961575--27961623 Score: 91
Period size: 22 Copynumber: 2.2 Consensus size: 23
27961565 ATGATATTTA
27961575 TATTCCTAAAATCTTAATGAGT-
1 TATTCCTAAAATCTTAATGAGTC
27961597 TATTCCTAAAATCTTAATGAGTC
1 TATTCCTAAAATCTTAATGAGTC
27961620 TATT
1 TATT
27961624 TTCAAAGGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 22 0.85
23 4 0.15
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (23 bp):
TATTCCTAAAATCTTAATGAGTC
Found at i:27967225 original size:15 final size:16
Alignment explanation
Indices: 27967205--27967237 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
27967195 AAGTGCAGTA
27967205 ATGAAAATTTTG-GAG
1 ATGAAAATTTTGAGAG
27967220 ATGAAAATTTTGAGAG
1 ATGAAAATTTTGAGAG
27967236 AT
1 AT
27967238 AGACATTCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.33
Consensus pattern (16 bp):
ATGAAAATTTTGAGAG
Found at i:27968161 original size:25 final size:25
Alignment explanation
Indices: 27968133--27968181 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
27968123 TAACCAAAGC
*
27968133 TTTT-CTTCTCCCAGTTAAACTCTGT
1 TTTTACTT-TCCCACTTAAACTCTGT
*
27968158 TTTTAGTTTCCCACTTAAACTCTG
1 TTTTACTTTCCCACTTAAACTCTG
27968182 ATTAACCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.18, C:0.27, G:0.08, T:0.47
Consensus pattern (25 bp):
TTTTACTTTCCCACTTAAACTCTGT
Found at i:27971531 original size:16 final size:16
Alignment explanation
Indices: 27971510--27971541 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
27971500 AAGAATGGAT
27971510 GCGAAGCTGGCTTTAA
1 GCGAAGCTGGCTTTAA
27971526 GCGAAGCTGGCTTTAA
1 GCGAAGCTGGCTTTAA
27971542 ATAGAGAGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (16 bp):
GCGAAGCTGGCTTTAA
Found at i:27971594 original size:27 final size:27
Alignment explanation
Indices: 27971563--27971976 Score: 256
Period size: 27 Copynumber: 15.4 Consensus size: 27
27971553 CATGCGAAGC
* *
27971563 TACCAAAATACCC-CTGGTTTGTAAAAT
1 TACCGAAATACCCTC-GATTTGTAAAAT
* *
27971590 TACCAAAATACCC-CTGATTTGTGAAAT
1 TACCGAAATACCCTC-GATTTGTAAAAT
* **
27971617 TACTGAAATACCCTCGACCTGTAAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
** *
27971644 TATTGAAATACCCTCGACTTGTAAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
*
27971671 TACC-AAAGTACCC-CGATTTATAAAAT
1 TACCGAAA-TACCCTCGATTTGTAAAAT
* *
27971697 TACCTAAATATCCTCGATTTGTAAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
* *
27971724 TATCGAAATACCCTC-AGTTTGCAAAAT
1 TACCGAAATACCCTCGA-TTTGTAAAAT
*
27971751 TACTGAAATACCCTCGATTTGTAAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
* ** *
27971778 TACTGAAATACTCCT-G-TAAGATAGAAT
1 TACCGAAATAC-CCTCGATTTG-TAAAAT
** ** *
27971805 TACC-ATTTTACCCTCGATTTACAGAAT
1 TACCGA-AATACCCTCGATTTGTAAAAT
** * *
27971832 TACC-ATTTTACCCTCGATTTATAGAAT
1 TACCGA-AATACCCTCGATTTGTAAAAT
** **
27971859 TACC-ATTTTACCCTCGATTTACAAAAT
1 TACCGA-AATACCCTCGATTTGTAAAAT
* * * **
27971886 TACTGAAATACCCTTGGTTTACAAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
* ***
27971913 TACCAAAATACCCTCGATCAATAAAAT
1 TACCGAAATACCCTCGATTTGTAAAAT
* **
27971940 TACCAAAATACCC-CTGATTTGTGGAAT
1 TACCGAAATACCCTC-GATTTGTAAAAT
27971967 TACCGAAATA
1 TACCGAAATA
27971977 TAGGGTAGAA
Statistics
Matches: 321, Mismatches: 53, Indels: 26
0.80 0.13 0.06
Matches are distributed among these distances:
26 30 0.09
27 284 0.88
28 7 0.02
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (27 bp):
TACCGAAATACCCTCGATTTGTAAAAT
Found at i:27971773 original size:107 final size:108
Alignment explanation
Indices: 27971563--27971780 Score: 282
Period size: 107 Copynumber: 2.0 Consensus size: 108
27971553 CATGCGAAGC
* * *
27971563 TACCAAAATACCCCTGGTTTGTAAAATTACCAAAATACCCCTGATTTGTGAAATTACTGAAATAC
1 TACCAAAATACCCCTGATTTATAAAATTACCAAAATACCCCTGATTTGTAAAATTACTGAAATAC
* *
27971628 CCTCGACCTGTAAAATTATTGAAATACCCTCGACTTGTAAAAT
66 CCTCGACCTGCAAAATTACTGAAATACCCTCGACTTGTAAAAT
* * *
27971671 TACCAAAGTACCCC-GATTTATAAAATTACCTAAATA-TCCTCGATTTGTAAAATTA-TCGAAAT
1 TACCAAAATACCCCTGATTTATAAAATTACCAAAATACCCCT-GATTTGTAAAATTACT-GAAAT
** *
27971733 ACCCTC-AGTTTGCAAAATTACTGAAATACCCTCGATTTGTAAAAT
64 ACCCTCGA-CCTGCAAAATTACTGAAATACCCTCGACTTGTAAAAT
27971778 TAC
1 TAC
27971781 TGAAATACTC
Statistics
Matches: 96, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
106 5 0.05
107 78 0.81
108 13 0.14
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.31
Consensus pattern (108 bp):
TACCAAAATACCCCTGATTTATAAAATTACCAAAATACCCCTGATTTGTAAAATTACTGAAATAC
CCTCGACCTGCAAAATTACTGAAATACCCTCGACTTGTAAAAT
Found at i:27972007 original size:27 final size:27
Alignment explanation
Indices: 27971977--27972161 Score: 307
Period size: 27 Copynumber: 6.9 Consensus size: 27
27971967 TACCGAAATA
* *
27971977 TAGGGTAGAATTATCGAAATACCTCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
* *
27972004 TAGGGTAGAATTATCGCAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
27972031 TAGGGTAGAATTACCGAAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
27972058 TAGGGTAGAATTACCGAAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
27972085 TAGGGTAGAATTACCGAAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
**
27972112 TAGGGTAGAATTATTGAAATACCCCTG
1 TAGGGTAGAATTACCGAAATACCCCTG
*
27972139 TAGGGTAGAATTACCGAGATACC
1 TAGGGTAGAATTACCGAAATACC
27972162 TTGTGAGGTA
Statistics
Matches: 149, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 149 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (27 bp):
TAGGGTAGAATTACCGAAATACCCCTG
Found at i:27972859 original size:27 final size:26
Alignment explanation
Indices: 27972829--27972957 Score: 96
Period size: 27 Copynumber: 4.8 Consensus size: 26
27972819 ATTCTGTTAA
* *
27972829 GTGGCTTTGCCACATTATCTGTTTCTG
1 GTGGCTATGCCACAATATCTG-TTCTG
27972856 GTGGCTATGCCACAAATATCTGTTCTG
1 GTGGCTATGCCAC-AATATCTGTTCTG
* * * *
27972883 GTGGCTCTGCCATAATATCTGCATCTA
1 GTGGCTATGCCACAATATCTG-TTCTG
* * * * *
27972910 GTGACTCTGTCACAATATCTGCATCTA
1 GTGGCTATGCCACAATATCTG-TTCTG
* * *
27972937 GTGACTCTGTCACAATATCTG
1 GTGGCTATGCCACAATATCTG
27972958 ATAACTGAGC
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
26 8 0.09
27 76 0.84
28 7 0.08
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.36
Consensus pattern (26 bp):
GTGGCTATGCCACAATATCTGTTCTG
Found at i:27973126 original size:6 final size:6
Alignment explanation
Indices: 27973117--27973250 Score: 103
Period size: 6 Copynumber: 21.8 Consensus size: 6
27973107 TTTTTGTTAC
* * *
27973117 CTGATA CTGATT CTGATT CTGATT CTGATT CTGCTAC CTGATAT -TGATT
1 CTGATT CTGATT CTGATT CTGATT CTGATT CTGAT-T CTGAT-T CTGATT
* * * * *
27973166 CTGATT TTGATC CTG-TT ACCTGATA CTGATT CTAATT CTGATT CTG-TCAC
1 CTGATT CTGATT CTGATT --CTGATT CTGATT CTGATT CTGATT CTGAT--T
* *
27973216 CTGATT CTGATT CTGATT CTAATT CTAATT CTGAT
1 CTGATT CTGATT CTGATT CTGATT CTGATT CTGAT
27973251 AATGTTTCTT
Statistics
Matches: 103, Mismatches: 17, Indels: 16
0.76 0.12 0.12
Matches are distributed among these distances:
5 3 0.03
6 87 0.84
7 11 0.11
8 2 0.02
ACGTcount: A:0.21, C:0.19, G:0.14, T:0.46
Consensus pattern (6 bp):
CTGATT
Found at i:27973159 original size:37 final size:37
Alignment explanation
Indices: 27973114--27973250 Score: 119
Period size: 37 Copynumber: 3.9 Consensus size: 37
27973104 TTGTTTTTGT
*
27973114 TACCTGATACTGATTCTGATTCTGATTCTGATTCTGC
1 TACCTGATACTGATTCTGATTCTGATTCTGATCCTGC
* *
27973151 TACCTG--A-T-A-T-TGATTCTGATTTTGATCCTGT
1 TACCTGATACTGATTCTGATTCTGATTCTGATCCTGC
* *
27973182 TACCTGATACTGATTCTAATTCTGATTCTG-TCACCTGA
1 TACCTGATACTGATTCTGATTCTGATTCTGAT--CCTGC
* * * *
27973220 T-TCTGATTCTGATTCTAATTCTAATTCTGAT
1 TACCTGATACTGATTCTGATTCTGATTCTGAT
27973251 AATGTTTCTT
Statistics
Matches: 82, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
31 24 0.29
32 1 0.01
33 2 0.02
34 2 0.02
35 2 0.02
36 2 0.02
37 43 0.52
38 6 0.07
ACGTcount: A:0.21, C:0.20, G:0.14, T:0.45
Consensus pattern (37 bp):
TACCTGATACTGATTCTGATTCTGATTCTGATCCTGC
Found at i:27973165 original size:31 final size:30
Alignment explanation
Indices: 27973130--27973241 Score: 136
Period size: 31 Copynumber: 3.6 Consensus size: 30
27973120 ATACTGATTC
27973130 TGATTCTGATTCTGATTCTGCTACCTGATAT
1 TGATTCTGATTCTGATTCTG-TACCTGATAT
* * *
27973161 TGATTCTGATTTTGATCCTGTTACCTGATAC
1 TGATTCTGATTCTGATTCTG-TACCTGATAT
*
27973192 TGATTCTAATTCTGATTCTGTCACCTGAT-T
1 TGATTCTGATTCTGATTCTGT-ACCTGATAT
*
27973222 CTGATTCTGATTCTAATTCT
1 -TGATTCTGATTCTGATTCT
27973242 AATTCTGATA
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.01
31 68 0.99
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.46
Consensus pattern (30 bp):
TGATTCTGATTCTGATTCTGTACCTGATAT
Found at i:27973189 original size:25 final size:25
Alignment explanation
Indices: 27973129--27973198 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 25
27973119 GATACTGATT
* *
27973129 CTGATTCTGATTCTGATTCTGCTAC
1 CTGATACTGATTCTGATTCTGATAC
* *
27973154 CTGATATTGATTCTGATTTTGAT-C
1 CTGATACTGATTCTGATTCTGATAC
* *
27973178 CTGTTACCTGATACTGATTCT
1 CTGATA-CTGATTCTGATTCT
27973199 AATTCTGATT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
24 6 0.17
25 30 0.83
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.46
Consensus pattern (25 bp):
CTGATACTGATTCTGATTCTGATAC
Found at i:27973259 original size:18 final size:17
Alignment explanation
Indices: 27973238--27973271 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
27973228 CTGATTCTAA
27973238 TTCTAATTCTGATAATGT
1 TTCTAATTCTG-TAATGT
*
27973256 TTCTTATTCTGTAATG
1 TTCTAATTCTGTAATG
27973272 GGTTAAAGCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (17 bp):
TTCTAATTCTGTAATGT
Found at i:27974967 original size:6 final size:6
Alignment explanation
Indices: 27974949--27975068 Score: 77
Period size: 6 Copynumber: 19.3 Consensus size: 6
27974939 AAGAAACATT
* *
27974949 ATCAGA A-CTAGA ATCAGA ATCAGA ATCAGA ATTAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * * *
27974998 ATCAGA ATCAGT ATCAGGTA A-CCGA ATCAAA ATCAGA ATCAGT ATCAGGTA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCA-G-A
*
27975049 A-CAGA ATCAAAA ATCAGA AT
1 ATCAGA ATC-AGA ATCAGA AT
27975069 GTGAATGCAA
Statistics
Matches: 88, Mismatches: 14, Indels: 24
0.70 0.11 0.19
Matches are distributed among these distances:
5 6 0.07
6 66 0.75
7 13 0.15
8 3 0.03
ACGTcount: A:0.47, C:0.16, G:0.17, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:27974996 original size:31 final size:31
Alignment explanation
Indices: 27974933--27975068 Score: 159
Period size: 31 Copynumber: 4.4 Consensus size: 31
27974923 TAACCCATTA
* * *
27974933 CAAAATAAGAAACATTATCA-G-AACTAGAAT
1 CAAAATCAGAATCAGTATCAGGTAAC-AGAAT
* * * *
27974963 CAGAATCAGAATCAGAATTAGGTGACAGAAT
1 CAAAATCAGAATCAGTATCAGGTAACAGAAT
* *
27974994 CAGAATCAGAATCAGTATCAGGTAACCGAAT
1 CAAAATCAGAATCAGTATCAGGTAACAGAAT
27975025 CAAAATCAGAATCAGTATCAGGTAACAGAAT
1 CAAAATCAGAATCAGTATCAGGTAACAGAAT
27975056 CAAAAATCAGAAT
1 C-AAAATCAGAAT
27975069 GTGAATGCAA
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
30 14 0.16
31 63 0.70
32 13 0.14
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.19
Consensus pattern (31 bp):
CAAAATCAGAATCAGTATCAGGTAACAGAAT
Found at i:27975297 original size:27 final size:27
Alignment explanation
Indices: 27975205--27975307 Score: 109
Period size: 27 Copynumber: 3.8 Consensus size: 27
27975195 GCTCAGTTAT
* * *
27975205 CAGATATTGTGACAGAGTCACTAGATA
1 CAGATATTGTGGCAGAGCCACTAGAAA
* *
27975232 CAGATATTGTGCCAGAGCCACCAG-AA
1 CAGATATTGTGGCAGAGCCACTAGAAA
*
27975258 TAGATATTTGTGGCAGAGCCACTAGAAA
1 CAGATA-TTGTGGCAGAGCCACTAGAAA
* * *
27975286 CAGATAATGTGGTAAAGCCACT
1 CAGATATTGTGGCAGAGCCACT
27975308 TAACAGAATA
Statistics
Matches: 63, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
26 6 0.10
27 50 0.79
28 7 0.11
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.22
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACTAGAAA
Found at i:27975493 original size:22 final size:22
Alignment explanation
Indices: 27975465--27975529 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
27975455 TCAAATACGT
*
27975465 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
27975487 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
**
27975509 TTGATACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
27975530 AAGGCTTGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:27976013 original size:27 final size:27
Alignment explanation
Indices: 27975955--27976142 Score: 193
Period size: 27 Copynumber: 7.0 Consensus size: 27
27975945 AGGGGCAAAA
* * * *
27975955 TAGTAATTTTACCCCACA-AGGTATCT
1 TAGTAATTCTACCCTACAGGGGTATTT
*
27975981 TGGTAATT-TCACCCTACAGGGGTATTT
1 TAGTAATTCT-ACCCTACAGGGGTATTT
* * *
27976008 TAGTAATTCTACACTATAGAGGTATTT
1 TAGTAATTCTACCCTACAGGGGTATTT
* *
27976035 CAGTAATTCTACCCTACAAGGGTATTT
1 TAGTAATTCTACCCTACAGGGGTATTT
*
27976062 TGGTAATTCTACCCTACAGGGGTATTT
1 TAGTAATTCTACCCTACAGGGGTATTT
**
27976089 CGGTAATTCTACCCTACAGGGGTA-TT
1 TAGTAATTCTACCCTACAGGGGTATTT
* * *
27976115 TCGATATTTCTACCCTACAAGGGTATTT
1 TAG-TAATTCTACCCTACAGGGGTATTT
27976143 CGTTAATTTT
Statistics
Matches: 136, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
25 1 0.01
26 17 0.12
27 115 0.85
28 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (27 bp):
TAGTAATTCTACCCTACAGGGGTATTT
Found at i:27976095 original size:81 final size:81
Alignment explanation
Indices: 27975956--27976151 Score: 254
Period size: 81 Copynumber: 2.4 Consensus size: 81
27975946 GGGGCAAAAT
* * * *
27975956 AGTAATTTTACCCCACAA-GGTATCTTGGTAATTTCACCCTACAGGGGTATTTTAGTAATTCTAC
1 AGTAATTCTACCCTACAAGGGTATTTTGGTAATTTCACCCTACAGGGGTATTTCAGTAATTCTAC
*
27976020 ACTATAGAGGTATTTC
66 ACTACAGAGGTATTTC
*
27976036 AGTAATTCTACCCTACAAGGGTATTTTGGTAA-TTCTACCCTACAGGGGTATTTCGGTAATTCTA
1 AGTAATTCTACCCTACAAGGGTATTTTGGTAATTTC-ACCCTACAGGGGTATTTCAGTAATTCTA
* *
27976100 CCCTACAGGGGTATTTC
65 CACTACAGAGGTATTTC
* * *
27976117 -GATATTTCTACCCTACAAGGGTATTTCGTTAATTT
1 AG-TAATTCTACCCTACAAGGGTATTTTGGTAATTT
27976152 TATAAATCGA
Statistics
Matches: 101, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
80 20 0.20
81 79 0.78
82 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (81 bp):
AGTAATTCTACCCTACAAGGGTATTTTGGTAATTTCACCCTACAGGGGTATTTCAGTAATTCTAC
ACTACAGAGGTATTTC
Found at i:27976219 original size:27 final size:28
Alignment explanation
Indices: 27976182--27976556 Score: 280
Period size: 27 Copynumber: 13.9 Consensus size: 28
27976172 GTAATTCTGT
*
27976182 AAATC-AGGGGTACTTTGGTAATTTTAC
1 AAATCAAGGGGTATTTTGGTAATTTTAC
* * ***
27976209 AAGTCGA-GGGTATTTCAATAATTTTAC
1 AAATCAAGGGGTATTTTGGTAATTTTAC
** * ** *
27976236 AGGTCAA-AGGTATTTCAGTAATTTCAC
1 AAATCAAGGGGTATTTTGGTAATTTTAC
*
27976263 AAAT-TAGGGGTATTTTGGTAATTTTAC
1 AAATCAAGGGGTATTTTGGTAATTTTAC
* ** *
27976290 AAA-CCAGGGGTATTTCAGTAATTTCAC
1 AAATCAAGGGGTATTTTGGTAATTTTAC
27976317 AAATC-AGGGGTATTTTGGTAATTTTAC
1 AAATCAAGGGGTATTTTGGTAATTTTAC
* * *
27976344 TAA-CCAGGGGTATTTTGGTAATTTTAT
1 AAATCAAGGGGTATTTTGGTAATTTTAC
* *
27976371 AAAT-AAAGGGTATTTTAGTAATTTTAC
1 AAATCAAGGGGTATTTTGGTAATTTTAC
*
27976398 AAA-CTAGGGGTATTTTGGTAATTTTGTA-
1 AAATCAAGGGGTATTTTGGTAA-TTT-TAC
27976426 AAAT-AA-GGGTATTTTGGTAATTTTAC
1 AAATCAAGGGGTATTTTGGTAATTTTAC
* * * *
27976452 AAAAC-AGGGTTATTTTGGTGATTTTAT
1 AAATCAAGGGGTATTTTGGTAATTTTAC
* * * *
27976479 AAACCAA-GAGTATTCTAGTAATTTTAC
1 AAATCAAGGGGTATTTTGGTAATTTTAC
* **
27976506 AAA-CTA-GGGTATTTTTGGTAATTTTGT
1 AAATCAAGGGGTA-TTTTGGTAATTTTAC
* *
27976533 AAACCAA-GGGTATTTTGATAATTT
1 AAATCAAGGGGTATTTTGGTAATTT
27976557 GGTAAACTAA
Statistics
Matches: 278, Mismatches: 54, Indels: 32
0.76 0.15 0.09
Matches are distributed among these distances:
25 2 0.01
26 15 0.05
27 242 0.87
28 17 0.06
29 2 0.01
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (28 bp):
AAATCAAGGGGTATTTTGGTAATTTTAC
Found at i:27976255 original size:81 final size:78
Alignment explanation
Indices: 27976132--27976547 Score: 236
Period size: 81 Copynumber: 5.1 Consensus size: 78
27976122 TTCTACCCTA
* * * *** *
27976132 CAAGGGTATTTC-GTTAATTTTATAAATCGAGGGTAAAACAGTAATTCTGTAAATCAGGGGTACT
1 CAAGGGTATTTCAG-TAATTTTACAAATCAAAGGTATTTCAGTAATT-T-TAAATCAGGGGTATT
27976196 TTGGTAATTTTACAAGT
63 TTGGTAATTTTACAA-T
* * ** * *
27976213 CGAGGGTATTTCAATAATTTTACAGGTCAAAGGTATTTCAGTAATTTCACAAATTAGGGGTATTT
1 CAAGGGTATTTCAGTAATTTTACAAATCAAAGGTATTTCAGTAATTT--TAAATCAGGGGTATTT
*
27976278 TGGTAATTTTACAAAC
64 TGGTAATTTTAC-AAT
* * ** ** *
27976294 CAGGGGTATTTCAGTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACTAACCAGGGGTATTT
1 CAAGGGTATTTCAGTAATTTTACAAATCAAAGGTATTTCAGTAATTTTA--AATCAGGGGTATTT
*
27976359 TGGTAATTTTATAAAT
64 TGGTAATTTTA-CAAT
* * ** ** *
27976375 AAAGGGTATTTTAGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTGTAAAAT-AAGGGTAT
1 CAAGGGTATTTCAGTAATTTTACAAATC-AAAGGTATTTCAGTAA-TTT-T-AAATCAGGGGTAT
27976438 TTTGGTAATTTTACAA-
62 TTTGGTAATTTTACAAT
* ** * * * *
27976454 AACAGGGTTATTTTGGTGATTTTATAAA-CCAAGAGTA-TTCTAGTAATTTTACAAACTA-GGGT
1 CA-AGGG-TATTTCAGTAATTTTACAAATCAAAG-GTATTTC-AGTAATTTTA-AATC-AGGGGT
*
27976516 ATTTTTGGTAATTTTGTA-AAC
60 A-TTTTGGTAA-TTT-TACAAT
27976537 CAAGGGTATTT
1 CAAGGGTATTT
27976548 TGATAATTTG
Statistics
Matches: 267, Mismatches: 47, Indels: 42
0.75 0.13 0.12
Matches are distributed among these distances:
78 1 0.00
79 6 0.02
80 19 0.07
81 220 0.82
82 16 0.06
83 4 0.01
84 1 0.00
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (78 bp):
CAAGGGTATTTCAGTAATTTTACAAATCAAAGGTATTTCAGTAATTTTAAATCAGGGGTATTTTG
GTAATTTTACAAT
Found at i:27976407 original size:54 final size:54
Alignment explanation
Indices: 27976270--27976556 Score: 351
Period size: 54 Copynumber: 5.3 Consensus size: 54
27976260 CACAAATTAG
** * * * *
27976270 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTCAGTAATTTCACAAATCAG
1 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCAA
* **
27976324 GGGTATTTTGGTAATTTTACTAACCAGGGGTATTTTGGTAATTTTATAAATAAA
1 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCAA
* * * **
27976378 GGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTGTAAAATAA
1 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCAA
* * *
27976432 GGGTATTTTGGTAATTTTACAAAACAGGGTTATTTTGGTGATTTTATAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCAA
* * * * *
27976486 GAGTATTCTAGTAATTTTACAAACTA-GGGTATTTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAGGGGTA-TTTTGGTAATTTTATAAACCAA
*
27976540 GGGTATTTTGATAATTT
1 GGGTATTTTGGTAATTT
27976557 GGTAAACTAA
Statistics
Matches: 199, Mismatches: 33, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
53 4 0.02
54 195 0.98
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (54 bp):
GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTATAAACCAA
Found at i:27977864 original size:57 final size:59
Alignment explanation
Indices: 27977771--27977890 Score: 138
Period size: 57 Copynumber: 2.1 Consensus size: 59
27977761 CAACACAACT
** * * * *
27977771 TTACTCAATTATACAAATTATTACAACTTTTGTAATGTTTTGTAAAATTATACAAAATA
1 TTACTCAATTATACAAATTATTACAACTTTCCTAATGTGTTATAAAATTACACAAAACA
* *
27977830 TTACTCAA-T-TACACATTATTACAA-TGTTCCTAATGTGTTATATAATTACACAAAACA
1 TTACTCAATTATACAAATTATTACAACT-TTCCTAATGTGTTATAAAATTACACAAAACA
27977887 TTAC
1 TTAC
27977891 CAAATTCAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
56 1 0.02
57 42 0.81
58 1 0.02
59 8 0.15
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.40
Consensus pattern (59 bp):
TTACTCAATTATACAAATTATTACAACTTTCCTAATGTGTTATAAAATTACACAAAACA
Found at i:27978297 original size:15 final size:15
Alignment explanation
Indices: 27978247--27978299 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
27978237 AAAATATAAA
27978247 ATAAAATA-TTTAAT
1 ATAAAATATTTTAAT
* *
27978261 TTCAAAATATAATTTAAA
1 AT-AAAATAT--TTTAAT
27978279 ATAAAATATTTTAAT
1 ATAAAATATTTTAAT
27978294 ATAAAA
1 ATAAAA
27978300 ACAATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
14 1 0.03
15 17 0.55
17 7 0.23
18 6 0.19
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (15 bp):
ATAAAATATTTTAAT
Found at i:27982560 original size:17 final size:17
Alignment explanation
Indices: 27982537--27982585 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
27982527 TATATTATAA
*
27982537 AAAATTAAATTAAATTT
1 AAAATTAAATTAAAATT
*
27982554 TAAATTAAA-TAAAATT
1 AAAATTAAATTAAAATT
*
27982570 AAAATTTAATTAAAAT
1 AAAATTAAATTAAAAT
27982586 AATTATAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 13 0.48
17 14 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATTAAATTAAAATT
Found at i:27982568 original size:22 final size:21
Alignment explanation
Indices: 27982538--27982597 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
27982528 ATATTATAAA
*
27982538 AAATTAAATTAAATTTTAAATT
1 AAATAAAATTAAATTTT-AATT
*
27982560 AAATAAAATTAAAATTTAATT
1 AAATAAAATTAAATTTTAATT
*
27982581 AAA-ATAATTATAATTTT
1 AAATAAAATTA-AATTTT
27982598 TTAATTTGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
20 6 0.18
21 12 0.36
22 15 0.45
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AAATAAAATTAAATTTTAATT
Found at i:27982928 original size:28 final size:28
Alignment explanation
Indices: 27982884--27982939 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
27982874 AAACCTTATA
*
27982884 TTATTTAGATTTGAACGTAACACTTGAG
1 TTATTTAGATTTAAACGTAACACTTGAG
*
27982912 TTATTTAGATTTAAACGTAACATTTGAG
1 TTATTTAGATTTAAACGTAACACTTGAG
27982940 CTTTGTTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.41
Consensus pattern (28 bp):
TTATTTAGATTTAAACGTAACACTTGAG
Found at i:27983364 original size:12 final size:12
Alignment explanation
Indices: 27983347--27983371 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27983337 CCATTTATCA
27983347 TTACACTAATGG
1 TTACACTAATGG
27983359 TTACACTAATGG
1 TTACACTAATGG
27983371 T
1 T
27983372 AAAGTAACAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TTACACTAATGG
Found at i:27984465 original size:19 final size:19
Alignment explanation
Indices: 27984443--27984480 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
27984433 GGGGAAGAAG
*
27984443 AAAAGGAAAATAAAG-AAAT
1 AAAAAGAAAA-AAAGTAAAT
27984462 AAAAAGAAAAAAAGTAAAT
1 AAAAAGAAAAAAAGTAAAT
27984481 TATTTTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (19 bp):
AAAAAGAAAAAAAGTAAAT
Found at i:27990679 original size:1 final size:1
Alignment explanation
Indices: 27990673--27990707 Score: 70
Period size: 1 Copynumber: 35.0 Consensus size: 1
27990663 CCATGGTGGG
27990673 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
27990708 AATATTATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:27994598 original size:6 final size:6
Alignment explanation
Indices: 27994589--27994640 Score: 104
Period size: 6 Copynumber: 8.7 Consensus size: 6
27994579 TTAAAAATTA
27994589 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT
27994637 AAAT
1 AAAT
27994641 TAATTTTAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATAT
Found at i:27998326 original size:24 final size:24
Alignment explanation
Indices: 27998299--27998348 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
27998289 AATGATGTAT
* * *
27998299 AATGTCTCTCTTGTATGTAACCGA
1 AATGTCCCCCTTGAATGTAACCGA
27998323 AATGTCCCCCTTGAATGTAACCGA
1 AATGTCCCCCTTGAATGTAACCGA
27998347 AA
1 AA
27998349 ACCACTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (24 bp):
AATGTCCCCCTTGAATGTAACCGA
Found at i:27999174 original size:44 final size:44
Alignment explanation
Indices: 27999099--27999189 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
27999089 ACTTTGTTTT
27999099 TTAGTTTCCCACTTAAACTCTAATTAATGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTAATTAATGTAGGTTATTTTAATA
* * *
27999143 TTAGTTTCCCACTTAAACTTTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTAATTAATGTAGGTTATTTTAATA
27999187 TTA
1 TTA
27999190 TTTAACCTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.30, C:0.12, G:0.11, T:0.47
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACTCTAATTAATGTAGGTTATTTTAATA
Found at i:28007476 original size:24 final size:23
Alignment explanation
Indices: 28007442--28007528 Score: 77
Period size: 23 Copynumber: 3.6 Consensus size: 23
28007432 TCCGGGCTAT
28007442 ATAACGGGAAGCTCATAAGAGCC
1 ATAACGGGAAGCTCATAAGAGCC
*
28007465 ATAATCGGGAAGCTCACAAAGAGCC
1 ATAA-CGGGAAGCTCA-TAAGAGCC
* * * *
28007490 -TATCAGGAAGCTCCTAAAGAGCA
1 ATAACGGGAAGCTCAT-AAGAGCC
28007513 ATGTAACGGGAAGCTC
1 A--TAACGGGAAGCTC
28007529 TGAATAGCCA
Statistics
Matches: 50, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
23 19 0.38
24 13 0.26
25 7 0.14
26 11 0.22
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.15
Consensus pattern (23 bp):
ATAACGGGAAGCTCATAAGAGCC
Found at i:28024469 original size:26 final size:26
Alignment explanation
Indices: 28024438--28024491 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
28024428 TGAAATTCCC
28024438 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
28024464 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
28024490 AT
1 AT
28024492 GTGACAGCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:28026240 original size:40 final size:40
Alignment explanation
Indices: 28026167--28026374 Score: 184
Period size: 40 Copynumber: 5.2 Consensus size: 40
28026157 CAATTGAATG
* * ** *
28026167 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAATT
* * * * **
28026207 ATACCCGGGTTAAGACCCGAAGGCCATT-GTGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGG-CATTCGTGCAAGTAATT
* **
28026247 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAATT
* * * **
28026287 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAATT
* * * **
28026327 CTATTCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAATT
28026367 ATATCCGG
1 ATATCCGG
28026375 TTGTATTCCG
Statistics
Matches: 137, Mismatches: 29, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
39 4 0.03
40 129 0.94
41 4 0.03
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAATT
Found at i:28026305 original size:80 final size:80
Alignment explanation
Indices: 28026169--28026374 Score: 218
Period size: 80 Copynumber: 2.6 Consensus size: 80
28026159 ATTGAATGAT
* * ** * * * *
28026169 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATACCCGGGTTAAGACCCGAAGGCCA-
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGG-CAT
*
28026233 TTGTGCTAGT-GACCAC
65 TTGTGCAAGTCGACC-C
* * *
28026249 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
** *
28026314 TGTGCAAGTCGTTCT
66 TGTGCAAGTCGACCC
* * *
28026329 ATTCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
28026375 TTGTATTCCG
Statistics
Matches: 105, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
79 2 0.02
80 101 0.96
81 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
TGTGCAAGTCGACCC
Found at i:28027773 original size:26 final size:26
Alignment explanation
Indices: 28027737--28027796 Score: 102
Period size: 26 Copynumber: 2.3 Consensus size: 26
28027727 GGGTGTTACA
* *
28027737 CATTATCATGGAATATTTACCTAATC
1 CATTATCATGGAACATTTACCTAACC
28027763 CATTATCATGGAACATTTACCTAACC
1 CATTATCATGGAACATTTACCTAACC
28027789 CATTATCA
1 CATTATCA
28027797 ATTTGTATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.35, C:0.23, G:0.07, T:0.35
Consensus pattern (26 bp):
CATTATCATGGAACATTTACCTAACC
Found at i:28030256 original size:27 final size:26
Alignment explanation
Indices: 28030219--28030333 Score: 149
Period size: 27 Copynumber: 4.3 Consensus size: 26
28030209 AGCATGACTG
* *
28030219 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
28030245 CCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
28030273 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* * *
28030300 CCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
28030327 CCAGAAC
1 CCAGAAC
28030334 GCTTCCTCCA
Statistics
Matches: 80, Mismatches: 6, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
26 5 0.06
27 58 0.73
28 17 0.21
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:28030278 original size:54 final size:54
Alignment explanation
Indices: 28030219--28030333 Score: 169
Period size: 54 Copynumber: 2.1 Consensus size: 54
28030209 AGCATGACTG
*
28030219 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAGCCA
* * * *
28030273 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATATTTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
28030327 CCAGAAC
1 CCAGAAC
28030334 GCTTCCTCCA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
54 37 0.67
55 18 0.33
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.17
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAGCCA
Found at i:28030497 original size:28 final size:26
Alignment explanation
Indices: 28030436--28030509 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
28030426 AAATTAACCC
* * * *
28030436 TAGGGGTATAGCGGTAATTTTGCACC
1 TAGGGGTATAACAGTAATTTTCCACA
28030462 TAGGGGTATAACAGTAATTTTCCATACA
1 TAGGGGTATAACAGTAATTTTCC--ACA
* *
28030490 TAGGGGTATTATAGTAATTT
1 TAGGGGTATAACAGTAATTT
28030510 AGCTACTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
26 20 0.50
28 20 0.50
ACGTcount: A:0.30, C:0.11, G:0.24, T:0.35
Consensus pattern (26 bp):
TAGGGGTATAACAGTAATTTTCCACA
Found at i:28032558 original size:28 final size:28
Alignment explanation
Indices: 28032493--28032593 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
28032483 ATAGTGAATC
*
28032493 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
28032522 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
28032550 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
28032580 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28032594 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28040515 original size:28 final size:28
Alignment explanation
Indices: 28040450--28040550 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
28040440 ATAGTGAATC
*
28040450 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
28040479 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
28040507 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
28040537 CGCACACTTAGTGC
1 CGCACACTTAGTGC
28040551 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:28043089 original size:26 final size:26
Alignment explanation
Indices: 28043060--28043169 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
28043050 CATGAAATTC
*
28043060 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
28043086 TTATCATGGAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCCA
*
28043112 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
* *
28043138 TTATCATTGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCCA
28043164 TTATCA
1 TTATCA
28043170 ATTTGTATCA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCCA
Found at i:28045530 original size:18 final size:19
Alignment explanation
Indices: 28045509--28045546 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
28045499 TAATTTTAAT
28045509 ATTATG-TAATATTATAAA
1 ATTATGATAATATTATAAA
*
28045527 ATTATGATAATTTTATAAA
1 ATTATGATAATATTATAAA
28045546 A
1 A
28045547 AAATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
ATTATGATAATATTATAAA
Found at i:28047339 original size:22 final size:22
Alignment explanation
Indices: 28047304--28047357 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
28047294 ACACGTTAGT
*
28047304 AAAT-AAA-ATATTTAAATAT-
1 AAATAAAATATATTTAAACATG
*
28047323 AAATAAACATATATTTATACATG
1 AAATAAA-ATATATTTAAACATG
28047346 AAATAAAATATA
1 AAATAAAATATA
28047358 AATAGAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 4 0.14
20 2 0.07
21 1 0.03
22 15 0.52
23 7 0.24
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (22 bp):
AAATAAAATATATTTAAACATG
Found at i:28051393 original size:2 final size:2
Alignment explanation
Indices: 28051381--28051412 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
28051371 AAAGTTTATT
*
28051381 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28051413 CATGACTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:28052302 original size:131 final size:132
Alignment explanation
Indices: 28052088--28052329 Score: 369
Period size: 131 Copynumber: 1.8 Consensus size: 132
28052078 AAACAGGATT
* * * *
28052088 CGATGTTTGGCAATTCGAGGAATCGTGCCCTAACATGTTGGGTTGCAATTCCGCGTTTGCTCGAA
1 CGATATTTAGCAATTCGAGGAATCGTGCCCTAACATGTTGGGTTGCAATTCCGCATTTGCTCAAA
* *
28052153 ATAATCGAATATCACTTCAAAATTTCACTCATGTC-TCTCAAAATTCTTCAAAACTAGGACGAGA
66 ATAATCGAATATCACTTCAAAATTTCACTCATATCTTCTAAAAATTCTTCAAAACTAGGACGAGA
28052217 TC
131 TC
* * *
28052219 CGATATTTAGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAATTTCGCATTTGCTCAAA
1 CGATATTTAGCAATTCGAGGAATCGTGCCCTAACATGTTGGGTTGCAATTCCGCATTTGCTCAAA
* * *
28052284 ATAATCGAGTATCCCTTCAAAATTTCATTCATATCTTCTAAAAATT
66 ATAATCGAATATCACTTCAAAATTTCACTCATATCTTCTAAAAATT
28052330 ATTTGGCGTT
Statistics
Matches: 98, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
131 89 0.91
132 9 0.09
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (132 bp):
CGATATTTAGCAATTCGAGGAATCGTGCCCTAACATGTTGGGTTGCAATTCCGCATTTGCTCAAA
ATAATCGAATATCACTTCAAAATTTCACTCATATCTTCTAAAAATTCTTCAAAACTAGGACGAGA
TC
Found at i:28056784 original size:43 final size:43
Alignment explanation
Indices: 28056736--28056892 Score: 144
Period size: 43 Copynumber: 3.7 Consensus size: 43
28056726 AGCTCGTATA
* *
28056736 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAGCAAATATCG
1 ATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAATATCG
* *** *
28056779 ATGCC-ACTGTCTC-GA-ATAGGGTCTTACACAAAATCAAATA-CA
1 ATGCCAAC-GTCCCAGACAT--GGTCTTACATGTAATCAAATATCG
* *
28056821 ATGCCAATGTCCCAGACATGGTCTTACATGTAAATCATAA-GTCG
1 ATGCCAACGTCCCAGACATGGTCTTACATGT-AATCA-AATATCG
*
28056865 ATGCCAACGTCCCAGACGTGGTCTTACA
1 ATGCCAACGTCCCAGACATGGTCTTACA
28056893 CGATAACACA
Statistics
Matches: 89, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
41 1 0.01
42 23 0.26
43 34 0.38
44 31 0.35
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACATGGTCTTACATGTAATCAAATATCG
Found at i:28067916 original size:29 final size:29
Alignment explanation
Indices: 28067874--28067930 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
28067864 TACCTGGAGG
*
28067874 AGCAAGTTGATAAATGCTTATTATTTTTT
1 AGCAAGTTGATAAATGCGTATTATTTTTT
28067903 AGCAAGTTGATAAATGCGTATTATTTTT
1 AGCAAGTTGATAAATGCGTATTATTTTT
28067931 CATACGGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.46
Consensus pattern (29 bp):
AGCAAGTTGATAAATGCGTATTATTTTTT
Found at i:28072462 original size:70 final size:70
Alignment explanation
Indices: 28072377--28072534 Score: 307
Period size: 70 Copynumber: 2.3 Consensus size: 70
28072367 AAACAAATAA
*
28072377 ATTGATTAAAAATGAATCAAGTATTAATAGTTAAATTTGGGTTTTACCCCAACTTCAAGATTGGG
1 ATTGATTAAAAATGAATCAAGTATTAATAGTTAAATTTGGGTTTGACCCCAACTTCAAGATTGGG
28072442 AAAAG
66 AAAAG
28072447 ATTGATTAAAAATGAATCAAGTATTAATAGTTAAATTTGGGTTTGACCCCAACTTCAAGATTGGG
1 ATTGATTAAAAATGAATCAAGTATTAATAGTTAAATTTGGGTTTGACCCCAACTTCAAGATTGGG
28072512 AAAAG
66 AAAAG
28072517 ATTGATTAAAAATGAATC
1 ATTGATTAAAAATGAATC
28072535 GAGACAGTTG
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 87 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.32
Consensus pattern (70 bp):
ATTGATTAAAAATGAATCAAGTATTAATAGTTAAATTTGGGTTTGACCCCAACTTCAAGATTGGG
AAAAG
Found at i:28078411 original size:23 final size:23
Alignment explanation
Indices: 28078368--28078412 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
28078358 AATAATTATT
*
28078368 GTATATTTTGTATTATTAATCTG
1 GTATATTTTGTATTATCAATCTG
*
28078391 GTATATTTATGTGTT-TCAATCT
1 GTATATTT-TGTATTATCAATCT
28078413 TATTTTACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.24, C:0.07, G:0.13, T:0.56
Consensus pattern (23 bp):
GTATATTTTGTATTATCAATCTG
Found at i:28081793 original size:39 final size:40
Alignment explanation
Indices: 28081693--28081874 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
28081683 TCGAATGATG
* * *
28081693 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
28081733 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
28081773 TCCGGGCTAAG-CCCGAAGGCATT-GTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * **
28081811 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
**
28081852 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28081875 TGAGCGAGTC
Statistics
Matches: 117, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 22 0.19
39 23 0.20
40 63 0.54
41 9 0.08
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:28081838 original size:78 final size:80
Alignment explanation
Indices: 28081693--28081874 Score: 210
Period size: 78 Copynumber: 2.3 Consensus size: 80
28081683 TCGAATGATG
* * * *
28081693 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
28081758 GTGCGAGTTAATAAA
66 GTGCGAGTTAATAAA
* **
28081773 TCCGGGCTAAG-CCCGAAGGCATTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
***
28081835 CGTGCGAGTCGCTATAA
65 CGTGCGAGTTAATA-AA
**
28081852 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28081875 TGAGCGAGTC
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
77 1 0.01
78 46 0.53
79 29 0.33
80 11 0.13
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTTAATAAA
Found at i:28083707 original size:11 final size:11
Alignment explanation
Indices: 28083691--28083725 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
28083681 TAATGTTAGT
28083691 AAAAGAAAAAG
1 AAAAGAAAAAG
*
28083702 AAAAGAAAAAA
1 AAAAGAAAAAG
*
28083713 AAAAAAAAAAG
1 AAAAGAAAAAG
28083724 AA
1 AA
28083726 TGCTCATCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAG
Found at i:28085034 original size:29 final size:29
Alignment explanation
Indices: 28085001--28085132 Score: 201
Period size: 29 Copynumber: 4.6 Consensus size: 29
28084991 GTGACGAGAT
28085001 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
28085030 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
28085059 TGGCACTAAGTGTGCGTGCTGGAAATATT
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
** *
28085088 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* **
28085117 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
28085133 AGTTCGGAGG
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 94 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:28093093 original size:39 final size:40
Alignment explanation
Indices: 28092993--28093174 Score: 176
Period size: 40 Copynumber: 4.6 Consensus size: 40
28092983 TCGAATGATG
* * *
28092993 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
28093033 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
28093073 TCCGGGCTAAG-CCCGAAGGCATT-GTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * **
28093111 CCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTCGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
**
28093152 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28093175 TGAGCGAGTC
Statistics
Matches: 117, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
38 22 0.19
39 23 0.20
40 63 0.54
41 9 0.08
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:28093138 original size:78 final size:80
Alignment explanation
Indices: 28092993--28093174 Score: 210
Period size: 78 Copynumber: 2.3 Consensus size: 80
28092983 TCGAATGATG
* * * *
28092993 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
28093058 GTGCGAGTTAATAAA
66 GTGCGAGTTAATAAA
* **
28093073 TCCGGGCTAAG-CCCGAAGGCATTGTGC-AAGTTACTAAACCCGGGTTAAG-TCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCGAAGGCATT
***
28093135 CGTGCGAGTCGCTATAA
65 CGTGCGAGTTAATA-AA
**
28093152 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28093175 TGAGCGAGTC
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
77 1 0.01
78 46 0.53
79 29 0.33
80 11 0.13
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAACCCGGACTAAGATCCGAAGGCATTC
GTGCGAGTTAATAAA
Found at i:28095838 original size:7 final size:7
Alignment explanation
Indices: 28095828--28095942 Score: 81
Period size: 7 Copynumber: 17.1 Consensus size: 7
28095818 TTTTTATTTT
28095828 TATATTA
1 TATATTA
28095835 TATATTA
1 TATATTA
28095842 TATAATTA
1 TAT-ATTA
28095850 T-T-TTA
1 TATATTA
28095855 TATATTA
1 TATATTA
28095862 CTCATATTA
1 -T-ATATTA
*
28095871 TTTA-TA
1 TATATTA
28095877 TATATTA
1 TATATTA
28095884 TATATTA
1 TATATTA
28095891 T-T-TTCA
1 TATATT-A
*
28095897 CATA-TA
1 TATATTA
28095903 TACT-TT-
1 TA-TATTA
28095909 TATATTA
1 TATATTA
28095916 TATATTA
1 TATATTA
28095923 TAT-TTA
1 TATATTA
28095929 T-T-TTA
1 TATATTA
28095934 TATTATTA
1 TA-TATTA
28095942 T
1 T
28095943 GTCATTTTAT
Statistics
Matches: 88, Mismatches: 4, Indels: 31
0.72 0.03 0.25
Matches are distributed among these distances:
5 12 0.14
6 18 0.20
7 41 0.47
8 11 0.12
9 6 0.07
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (7 bp):
TATATTA
Found at i:28095855 original size:20 final size:19
Alignment explanation
Indices: 28095827--28095942 Score: 119
Period size: 20 Copynumber: 5.8 Consensus size: 19
28095817 ATTTTTATTT
*
28095827 TTATATTATATATTATATAA
1 TTATTTTATATATTATAT-A
28095847 TTATTTTATATATTACTCATA
1 TTATTTTATATATTA-T-ATA
28095868 TTATTTATATATATTATATA
1 TTATTT-TATATATTATATA
* *
28095888 TTATTTTCACATA-TATACTT
1 TTATTTT-ATATATTATA-TA
*
28095908 TTATATTATATATTATAT-
1 TTATTTTATATATTATATA
28095926 TTATTTTATATTATTAT
1 TTATTTTATA-TATTAT
28095943 GTCATTTTAT
Statistics
Matches: 83, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
18 9 0.11
19 16 0.19
20 38 0.46
21 9 0.11
22 11 0.13
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTTTATATATTATATA
Found at i:28095871 original size:29 final size:26
Alignment explanation
Indices: 28095821--28095942 Score: 85
Period size: 26 Copynumber: 4.6 Consensus size: 26
28095811 TGCTTTATTT
28095821 TTATTTT-TATATTATATATTATATAA
1 TTATTTTATATATTATATATTAT-TAA
*
28095847 TTATTTTATATATTACTCATATTATTTA
1 TTATTTTATATATTA-T-ATATTATTAA
* *
28095875 TATATATTATATATTAT-T-TTCA-CATA
1 T-TATTTTATATATTATATATT-ATTA-A
* *
28095901 TATACTTT-TATATTATATATTA-TAT
1 T-TATTTTATATATTATATATTATTAA
28095926 TTATTTTATATTATTAT
1 TTATTTTATA-TATTAT
28095943 GTCATTTTAT
Statistics
Matches: 77, Mismatches: 9, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
24 5 0.06
25 13 0.17
26 25 0.32
27 9 0.12
28 5 0.06
29 20 0.26
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
TTATTTTATATATTATATATTATTAA
Found at i:28095934 original size:18 final size:18
Alignment explanation
Indices: 28095821--28095979 Score: 106
Period size: 20 Copynumber: 8.1 Consensus size: 18
28095811 TGCTTTATTT
* *
28095821 TTATTTTTATATTATATA
1 TTATATTTATTTTATATA
28095839 TTATATAATTATTTTATATA
1 TTATAT--TTATTTTATATA
28095859 TTACTCATATTATTTATATATA
1 TTA-T-AT-TTATTT-TATATA
*
28095881 TTATATATTATTTTCACATA
1 TTATAT-TTATTTT-ATATA
*
28095901 -TATACTTTTATATTATATA
1 TTATA--TTTATTTTATATA
28095920 TTATATTTATTTTATATTA
1 TTATATTTATTTTATA-TA
* *
28095939 TTAT-GTCATTTTATACTA
1 TTATATTTATTTTATA-TA
*
28095957 TTAAATATTTTTATTTATATA
1 TT--ATATTTAT-TTTATATA
28095978 TT
1 TT
28095980 GTTATCATTA
Statistics
Matches: 115, Mismatches: 12, Indels: 25
0.76 0.08 0.16
Matches are distributed among these distances:
18 28 0.24
19 15 0.13
20 39 0.34
21 16 0.14
22 17 0.15
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.60
Consensus pattern (18 bp):
TTATATTTATTTTATATA
Found at i:28096293 original size:17 final size:17
Alignment explanation
Indices: 28096236--28096293 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
28096226 TCTAAACCAT
*
28096236 TATATTTTATATTTTTA
1 TATATTATATATTTTTA
*
28096253 TATAATTAT-TATTCTTA
1 TAT-ATTATATATTTTTA
28096270 TA-A--ATATATTTTTA
1 TATATTATATATTTTTA
28096284 TATATTATAT
1 TATATTATAT
28096294 CATTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 2 0.06
14 9 0.27
15 2 0.06
17 16 0.48
18 4 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTATATATTTTTA
Found at i:28108491 original size:205 final size:205
Alignment explanation
Indices: 28108134--28108507 Score: 651
Period size: 205 Copynumber: 1.8 Consensus size: 205
28108124 TAGGCCGCAG
* *
28108134 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGAAGATTCAAGATGATTTTGCATCCTTGTG
1 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGTG
* *
28108199 CTTACAAGGAGCGAATCGAAGACATAGCTGATTTGGCTTTCACGTGTTTACGATGAAGCAAATCT
66 CTTACAAGGAGCGAATCGAAGACATAGCTGATTTGACTTTCACGTGTTCACGATGAAGCAAATCT
* *
28108264 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGG
131 AAGATGATTTGGCATATCTGTATTGTCAAAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGG
28108329 GGAGCAGATA
196 GGAGCAGATA
*
28108339 CATAGCAGATCTCACCATT-AGATGTTTATACTGAAGGAGATCCAAGATGATTTGGCATCCTTGT
1 CATAGCAGATCTCACC-TTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGT
*
28108403 GCTTACAAGGAGCGAATCGAAGACATAGCTGATTTGACTTTCACGTGTTCACGATGAAGTAAATC
65 GCTTACAAGGAGCGAATCGAAGACATAGCTGATTTGACTTTCACGTGTTCACGATGAAGCAAATC
*
28108468 TAAGATGATTTGGTATATCTGTATTGTCAAAGAACAAATC
130 TAAGATGATTTGGCATATCTGTATTGTCAAAGAACAAATC
28108508 GAAGAAGCAG
Statistics
Matches: 159, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
205 157 0.99
206 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.29
Consensus pattern (205 bp):
CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGTG
CTTACAAGGAGCGAATCGAAGACATAGCTGATTTGACTTTCACGTGTTCACGATGAAGCAAATCT
AAGATGATTTGGCATATCTGTATTGTCAAAGAACAAATCAAAGTCTGGCATCTCCACTTCGACGG
GGAGCAGATA
Found at i:28110141 original size:20 final size:19
Alignment explanation
Indices: 28110113--28110228 Score: 110
Period size: 20 Copynumber: 5.8 Consensus size: 19
28110103 ATTTTTATTT
*
28110113 TTATATTATATATTATATAA
1 TTATTTTATATATTATAT-A
28110133 TTATTTTATATATTACTCATA
1 TTATTTTATATATTA-T-ATA
28110154 TTATTTATATATATTATATA
1 TTATTT-TATATATTATATA
* * *
28110174 CTATTTTCACATA-TATACTT
1 TTATTTT-ATATATTATA-TA
*
28110194 TTATATTATATATTATAT-
1 TTATTTTATATATTATATA
28110212 TTATTTTATATTATTAT
1 TTATTTTATA-TATTAT
28110229 GTCATTTTAT
Statistics
Matches: 81, Mismatches: 8, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
18 9 0.11
19 16 0.20
20 36 0.44
21 9 0.11
22 11 0.14
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTTTATATATTATATA
Found at i:28110221 original size:16 final size:18
Alignment explanation
Indices: 28110197--28110245 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
28110187 TATACTTTTA
*
28110197 TATTATATATTA-TAT-T
1 TATTTTATATTATTATGT
28110213 TATTTTATATTATTATGT
1 TATTTTATATTATTATGT
* *
28110231 CATTTTATACTATTA
1 TATTTTATATTATTA
28110246 AATATTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
16 11 0.39
17 3 0.11
18 14 0.50
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (18 bp):
TATTTTATATTATTATGT
Found at i:28110579 original size:17 final size:17
Alignment explanation
Indices: 28110522--28110579 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
28110512 TCTAAACCAT
*
28110522 TATATTTTATATTTTTA
1 TATATTATATATTTTTA
*
28110539 TATAATTAT-TATTCTTA
1 TAT-ATTATATATTTTTA
28110556 TA-A--ATATATTTTTA
1 TATATTATATATTTTTA
28110570 TATATTATAT
1 TATATTATAT
28110580 CATTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 2 0.06
14 9 0.27
15 2 0.06
17 16 0.48
18 4 0.12
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATTATATATTTTTA
Found at i:28116074 original size:26 final size:27
Alignment explanation
Indices: 28116045--28116126 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 27
28116035 GCCCGTTGAA
*
28116045 TCATTCGC-TATTTCACACACTAAGTG
1 TCATTCGCATATCTCACACACTAAGTG
* *
28116071 TCATTCTCAATATCTCTCACACTAAGTG
1 TCATTCGC-ATATCTCACACACTAAGTG
* * *
28116099 TCATTCTCAATATCTCGCACAGTAAGTG
1 TCATTCGC-ATATCTCACACACTAAGTG
28116127 CCATATTTGA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
26 7 0.14
28 42 0.86
ACGTcount: A:0.28, C:0.27, G:0.11, T:0.34
Consensus pattern (27 bp):
TCATTCGCATATCTCACACACTAAGTG
Found at i:28116093 original size:28 final size:28
Alignment explanation
Indices: 28116060--28116126 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
28116050 CGCTATTTCA
*
28116060 CACACTAAGTGTCATTCTCAATATCTCT
1 CACACTAAGTGTCATTCTCAATATCTCG
28116088 CACACTAAGTGTCATTCTCAATATCTCG
1 CACACTAAGTGTCATTCTCAATATCTCG
*
28116116 CACAGTAAGTG
1 CACACTAAGTG
28116127 CCATATTTGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (28 bp):
CACACTAAGTGTCATTCTCAATATCTCG
Found at i:28116200 original size:40 final size:40
Alignment explanation
Indices: 28116141--28116235 Score: 172
Period size: 40 Copynumber: 2.4 Consensus size: 40
28116131 ATTTGATGTC
*
28116141 TCGCACACTAAATGCTGTACATAGTCGAAACTATCTCAAA
1 TCGCACACTAAGTGCTGTACATAGTCGAAACTATCTCAAA
*
28116181 TCGCACACTAAGTGTTGTACATAGTCGAAACTATCTCAAA
1 TCGCACACTAAGTGCTGTACATAGTCGAAACTATCTCAAA
28116221 TCGCACACTAAGTGC
1 TCGCACACTAAGTGC
28116236 CAAATTTAGC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (40 bp):
TCGCACACTAAGTGCTGTACATAGTCGAAACTATCTCAAA
Found at i:28136025 original size:19 final size:19
Alignment explanation
Indices: 28136001--28136038 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28135991 ACAGCTGTGT
28136001 ACCCTGGCCATGTGTCACA
1 ACCCTGGCCATGTGTCACA
*
28136020 ACCCTGGCTATGTGTCACA
1 ACCCTGGCCATGTGTCACA
28136039 CACGGCTGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.21, C:0.34, G:0.21, T:0.24
Consensus pattern (19 bp):
ACCCTGGCCATGTGTCACA
Found at i:28137075 original size:33 final size:33
Alignment explanation
Indices: 28137022--28137099 Score: 104
Period size: 33 Copynumber: 2.4 Consensus size: 33
28137012 GTGAATCTCC
* *
28137022 ATGGTCTTACATTCTTAATGCCATAACCCAATT
1 ATGGTCTTACATTCTGAATGCCATAACCCAACT
* *
28137055 ATGGTCTTATCATT-TGAATGCCATAGCCCAGCT
1 ATGGTCTTA-CATTCTGAATGCCATAACCCAACT
28137088 ATGGTCTTACAT
1 ATGGTCTTACAT
28137100 ACGAATACTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
32 3 0.08
33 33 0.82
34 4 0.10
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (33 bp):
ATGGTCTTACATTCTGAATGCCATAACCCAACT
Found at i:28148587 original size:25 final size:25
Alignment explanation
Indices: 28148559--28148606 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
28148549 TTTATTATTT
*
28148559 TTATTAAATATTT-TTAATAATAATC
1 TTATTAAA-ATTTAATAATAATAATC
28148584 TTATTAAAATTTAATAATAATAA
1 TTATTAAAATTTAATAATAATAA
28148607 CAATAATCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (25 bp):
TTATTAAAATTTAATAATAATAATC
Found at i:28148791 original size:12 final size:11
Alignment explanation
Indices: 28148727--28148792 Score: 57
Period size: 12 Copynumber: 5.7 Consensus size: 11
28148717 AATAATAATT
28148727 TTATATTAAAA
1 TTATATTAAAA
28148738 TTATTATT-AAA
1 TTA-TATTAAAA
28148749 -TATTATTAATAA
1 TTA-TATTAA-AA
28148761 TTATATTAATAA
1 TTATATTAA-AA
28148773 TGT-TATTAAAA
1 T-TATATTAAAA
28148784 TATATATTA
1 T-TATATTA
28148793 TTTTATTAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
10 7 0.15
11 11 0.23
12 27 0.56
13 3 0.06
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
TTATATTAAAA
Found at i:28148905 original size:25 final size:26
Alignment explanation
Indices: 28148856--28148906 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
28148846 ATTTTTATTT
*
28148856 TTATTAAAATATATTTAACAATAATC
1 TTATTAAAATATATATAACAATAATC
*
28148882 TTATTAAAATTTA-ATAACAATAATC
1 TTATTAAAATATATATAACAATAATC
28148907 ATCTACCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (26 bp):
TTATTAAAATATATATAACAATAATC
Found at i:28149047 original size:44 final size:46
Alignment explanation
Indices: 28148977--28149070 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 46
28148967 ATTACAACAT
*
28148977 CATTCCATTCAACCAAACACAAGAATT-CT-ATTATAGCTCTATTC
1 CATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTC
*** * *
28149021 CATTCCATTCAACCAAACAGTTGAATTACTGATTACAGTTCTATTT
1 CATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTC
28149067 CATT
1 CATT
28149071 ACAGCTCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 24 0.57
45 2 0.05
46 16 0.38
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.35
Consensus pattern (46 bp):
CATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTC
Found at i:28149073 original size:16 final size:16
Alignment explanation
Indices: 28149052--28149106 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
28149042 TGAATTACTG
*
28149052 ATTACAGTTCTATTTC
1 ATTACAGCTCTATTTC
28149068 ATTACAGCTCTA-TTC
1 ATTACAGCTCTATTTC
* *
28149083 AATTACAGCCCTATTCC
1 -ATTACAGCTCTATTTC
28149100 ATTACAG
1 ATTACAG
28149107 TGAACCAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.09
16 29 0.85
17 2 0.06
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTTC
Found at i:28150803 original size:31 final size:31
Alignment explanation
Indices: 28150768--28150831 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
28150758 CCTTTTCATA
*
28150768 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCATATTTCACAACACTGGGCCGAAGCCT
**
28150799 TTTCATATTTCACATTACTGGGCCGAAGCCT
1 TTTCATATTTCACAACACTGGGCCGAAGCCT
28150830 TT
1 TT
28150832 ACTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATATTTCACAACACTGGGCCGAAGCCT
Found at i:28151133 original size:25 final size:24
Alignment explanation
Indices: 28151039--28151170 Score: 185
Period size: 25 Copynumber: 5.4 Consensus size: 24
28151029 CTGGAGGCCT
* *
28151039 AGCCTCTTTTAACAACTAGGGCA-A
1 AGCC-CTTTTAATAACTGGGGCATA
28151063 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
28151087 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
* *
28151111 AGCCCTTTATCATAACTGAGGCATA
1 AGCCCTTT-TAATAACTGGGGCATA
*
28151136 AGCCCTTTATCATAACTGGGGCATA
1 AGCCCTTT-TAATAACTGGGGCATA
28151161 AGCCCTTTTA
1 AGCCCTTTTA
28151171 CACTTCCTCC
Statistics
Matches: 100, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
23 16 0.16
24 38 0.38
25 46 0.46
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:28151244 original size:20 final size:20
Alignment explanation
Indices: 28151219--28151285 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
28151209 TTATGAATAC
28151219 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
28151239 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
* *
28151259 GTCATGCGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
28151279 ACCATGT
1 ATCATGT
28151286 TTATCAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:28151354 original size:25 final size:25
Alignment explanation
Indices: 28151322--28151369 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
28151312 ATCTATAAAC
* *
28151322 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
28151347 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
28151370 CATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:28153836 original size:27 final size:26
Alignment explanation
Indices: 28153801--28153912 Score: 143
Period size: 27 Copynumber: 4.2 Consensus size: 26
28153791 AGCATGGCTG
* *
28153801 CCAGAACAGATAATGTGACAGAGTCA
1 CCAGAACAGATAATGTGGCAGAGCCA
*
28153827 CCAGATACAGATAATCGTGGCAGAACCA
1 CCAGA-ACAGATAAT-GTGGCAGAGCCA
28153855 CCAGAACAGATATATGTGGCAGAGCCA
1 CCAGAACAGATA-ATGTGGCAGAGCCA
* *
28153882 CCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATAA-TGTGGCAGAGCCA
28153909 CCAG
1 CCAG
28153913 GACGCTTCCT
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 6 0.08
27 54 0.71
28 16 0.21
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (26 bp):
CCAGAACAGATAATGTGGCAGAGCCA
Found at i:28153865 original size:54 final size:54
Alignment explanation
Indices: 28153801--28153912 Score: 163
Period size: 54 Copynumber: 2.1 Consensus size: 54
28153791 AGCATGGCTG
*
28153801 CCAGAACAGATA-ATGTGACAGAGTCACCAGATACAGATAATCGTGGCAGAACCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGAT-CAGATAATCGTGGCAGAACCA
* * * *
28153855 CCAGAACAGATATATGTGGCAGAGCCACCAGATCAGATAATTGTGGCATAGCCA
1 CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCA
28153909 CCAG
1 CCAG
28153913 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
54 34 0.65
55 18 0.35
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (54 bp):
CCAGAACAGATATATGTGACAGAGCCACCAGATCAGATAATCGTGGCAGAACCA
Found at i:28155357 original size:24 final size:24
Alignment explanation
Indices: 28155330--28155400 Score: 124
Period size: 24 Copynumber: 3.0 Consensus size: 24
28155320 CTAGATTTCC
**
28155330 TCCCTTATCTGCTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
28155354 TCCCTTATCAACTCCTAAATCCTA
1 TCCCTTATCAACTCCTAAATCCTA
28155378 TCCCTTATCAACTCCTAAATCCT
1 TCCCTTATCAACTCCTAAATCCT
28155401 CTCCTGACAG
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.25, C:0.38, G:0.01, T:0.35
Consensus pattern (24 bp):
TCCCTTATCAACTCCTAAATCCTA
Found at i:28157747 original size:24 final size:24
Alignment explanation
Indices: 28157715--28157785 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
28157705 CTGTCAGGAG
28157715 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
*
28157739 AGGATTTAGGAGTTGATAAGGAAT
1 AGGATTTAGGAGTTGATAAGGGAT
**
28157763 AGGATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
28157786 GGAAATCTAG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 43 1.00
ACGTcount: A:0.37, C:0.01, G:0.37, T:0.25
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:28157797 original size:48 final size:48
Alignment explanation
Indices: 28157715--28157810 Score: 115
Period size: 48 Copynumber: 2.0 Consensus size: 48
28157705 CTGTCAGGAG
** * *
28157715 AGGATTTAGGAGTTGATAAGGGATAGGATTTAGGAGTTGAT-AAGGAAT
1 AGGATTTAGGAGCAGATAAGGGA-AGGATCTAGGAGCTGATCAAGGAAT
28157763 AGGATTTAGGAGCAGATAAGGG-AGGAAATCTAGGAGCTGATCAAGGAA
1 AGGATTTAGGAGCAGATAAGGGAAGG--ATCTAGGAGCTGATCAAGGAA
28157811 CAAGAGGTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
46 3 0.07
48 32 0.78
49 6 0.15
ACGTcount: A:0.38, C:0.04, G:0.35, T:0.23
Consensus pattern (48 bp):
AGGATTTAGGAGCAGATAAGGGAAGGATCTAGGAGCTGATCAAGGAAT
Found at i:28159243 original size:27 final size:26
Alignment explanation
Indices: 28159203--28159314 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
28159193 AGGAAGCGTC
* *
28159203 CTGGTGGCTATGCCACAATTATATGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
28159230 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
28159257 CTGGTGGTTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* * *
28159285 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGAT
28159311 CTGG
1 CTGG
28159315 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
26 7 0.10
27 50 0.68
28 16 0.22
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:28159307 original size:54 final size:54
Alignment explanation
Indices: 28159203--28159314 Score: 154
Period size: 54 Copynumber: 2.1 Consensus size: 54
28159193 AGGAAGCGTC
*
28159203 CTGGTGGCTATGCCACAATTATATGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATATGATCTGGTGACTCTGCCACATATATCTGTT
* * * * *
28159257 CTGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATATG-ATCTGGTGACTCTGCCACATATATCTGTT
28159311 CTGG
1 CTGG
28159315 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
54 33 0.65
55 18 0.35
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATATGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:28163983 original size:18 final size:18
Alignment explanation
Indices: 28163962--28163996 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28163952 AAGAAACATT
*
28163962 ATCAGAACTAGAATCAGA
1 ATCAAAACTAGAATCAGA
*
28163980 ATCAAAATTAGAATCAG
1 ATCAAAACTAGAATCAG
28163997 GTGACAGAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.14, G:0.14, T:0.20
Consensus pattern (18 bp):
ATCAAAACTAGAATCAGA
Found at i:28164033 original size:19 final size:19
Alignment explanation
Indices: 28163991--28164034 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28163981 TCAAAATTAG
* *
28163991 AATCAGGTGACAGAATCAG
1 AATCAGGTAACAGAATCAA
*
28164010 TATCAGGTAACAGAATCAA
1 AATCAGGTAACAGAATCAA
28164029 AATCAG
1 AATCAG
28164035 AATGTGAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.20, T:0.18
Consensus pattern (19 bp):
AATCAGGTAACAGAATCAA
Found at i:28164462 original size:27 final size:27
Alignment explanation
Indices: 28164432--28164654 Score: 313
Period size: 27 Copynumber: 8.3 Consensus size: 27
28164422 GGGGCAATAT
* * *
28164432 GGTAATTTTACCCCACAAGGGTATCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
28164459 GGTAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAAGGGTATTTC
*
28164486 GGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
28164513 GGTCATTCTACCCTAC-AGGGCTATTTC
1 GGTAATTCTACCCTACAAGGG-TATTTC
* *
28164540 GGTAATTCTACCCTACAGGGGCATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
28164567 GGTAATTCCACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
28164594 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
28164621 AGTAATTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
28164648 GGTAATT
1 GGTAATT
28164655 TCACAAAGCA
Statistics
Matches: 175, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
26 4 0.02
27 168 0.96
28 3 0.02
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:28164680 original size:81 final size:81
Alignment explanation
Indices: 28164432--28164681 Score: 326
Period size: 81 Copynumber: 3.1 Consensus size: 81
28164422 GGGGCAATAT
* * * *
28164432 GGTAATTTTACCCCACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTTGGT-ATTTCTA
1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTC-A
*
28164496 CCCTACAAGGGTATTTC
65 CCCTACAGGGGTATTTC
* * *
28164513 GGTCATTCTACCCTAC-AGGGCTATTTCGGTAATTCTACCCTACAGGGGCATTTCGGTAATTCCA
1 GGTAATTCTACCCTACAAGGG-TATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTCA
28164577 CCCTACAGGGGTATTTC
65 CCCTACAGGGGTATTTC
* * *
28164594 AGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCTACAAGGGTATTTCGGTAATTTCA-
1 GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTCAC
** *
28164658 CAAAGCAGGGGTATTTT
66 CCTA-CAGGGGTATTTC
28164675 GGTAATT
1 GGTAATT
28164682 TTACAAACTA
Statistics
Matches: 147, Mismatches: 18, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
80 6 0.04
81 133 0.90
82 8 0.05
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (81 bp):
GGTAATTCTACCCTACAAGGGTATTTCGGTAATTCTACCCTACAGGGGTATTTCGGTAATTTCAC
CCTACAGGGGTATTTC
Found at i:28164697 original size:27 final size:27
Alignment explanation
Indices: 28164636--28164764 Score: 116
Period size: 27 Copynumber: 4.8 Consensus size: 27
28164626 TTCTACCCTA
* *
28164636 CAAGGGTATTTCGGTAATTTCACAAAG
1 CAAGGGTATTTTGGTAATTTTACAAAG
*
28164663 CAGGGGTATTTTGGTAATTTTACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAAG
* *** *
28164689 CTAATGGTATTTTGGTAATTTTATTGAT
1 C-AAGGGTATTTTGGTAATTTTACAAAG
* ** *
28164717 CGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAAG
**
28164744 CAAGGGTATTTCAGTAATTTT
1 CAAGGGTATTTTGGTAATTTT
28164765 TTACATTGAG
Statistics
Matches: 83, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.01
27 81 0.98
28 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.41
Consensus pattern (27 bp):
CAAGGGTATTTTGGTAATTTTACAAAG
Found at i:28164698 original size:54 final size:54
Alignment explanation
Indices: 28164636--28164763 Score: 141
Period size: 54 Copynumber: 2.4 Consensus size: 54
28164626 TTCTACCCTA
28164636 CAAGGGTATTTCGGTAATTTCACAAAGC-AGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTCGGTAATTTCACAAAGCGA-GGGTATTTTGGTAATTTTACAAAC
* * * * *** * **
28164690 TAATGGTATTTTGGTAATTTTATTGATCGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTCGGTAATTTCACAAAGCGAGGGTATTTTGGTAATTTTACAAAC
*
28164744 CAAGGGTATTTCAGTAATTT
1 CAAGGGTATTTCGGTAATTT
28164764 TTTACATTGA
Statistics
Matches: 59, Mismatches: 14, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
54 58 0.98
55 1 0.02
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.41
Consensus pattern (54 bp):
CAAGGGTATTTCGGTAATTTCACAAAGCGAGGGTATTTTGGTAATTTTACAAAC
Done.