Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 140 of 325
Found at i:42674458 original size:17 final size:17
Alignment explanation
Indices: 42674433--42674468 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
42674423 AGGGGACACA
*
42674433 CGGCGAAACTATACCCC
1 CGGCCAAACTATACCCC
42674450 CGGCCAAACTATACCCC
1 CGGCCAAACTATACCCC
42674467 CG
1 CG
42674469 TACATATGGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.44, G:0.17, T:0.11
Consensus pattern (17 bp):
CGGCCAAACTATACCCC
Found at i:42678736 original size:20 final size:20
Alignment explanation
Indices: 42678711--42678749 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42678701 TTAATTTATA
*
42678711 TTTTTAAATTTTTTAAAATG
1 TTTTTAAATATTTTAAAATG
*
42678731 TTTTTATATATTTTAAAAT
1 TTTTTAAATATTTTAAAAT
42678750 TTTAAAATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
TTTTTAAATATTTTAAAATG
Found at i:42689865 original size:11 final size:12
Alignment explanation
Indices: 42689840--42689867 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
42689830 TGAGTGTAGT
42689840 AAAATATTTTAA
1 AAAATATTTTAA
42689852 AAAATATTTTAA
1 AAAATATTTTAA
42689864 AAAA
1 AAAA
42689868 AAGATATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAATATTTTAA
Found at i:42690932 original size:21 final size:21
Alignment explanation
Indices: 42690907--42690955 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
42690897 AAATTTTCCA
42690907 ATACATTTGTTTAAAAATATT
1 ATACATTTGTTTAAAAATATT
*
42690928 ATACACTTGTTTAAAAATATT
1 ATACATTTGTTTAAAAATATT
42690949 ATA-ATTT
1 ATACATTT
42690956 TATTTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.47
Consensus pattern (21 bp):
ATACATTTGTTTAAAAATATT
Found at i:42692993 original size:66 final size:68
Alignment explanation
Indices: 42692917--42693103 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
42692907 TAGTACCACT
*
42692917 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
42692979 CACG
65 CACG
42692983 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
42693048 ATCACG
63 ATCACG
42693054 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
42693104 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:42693028 original size:71 final size:71
Alignment explanation
Indices: 42692940--42693103 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
42692930 CGATTTGTCT
42692940 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42693005 CTTTCA
66 CTTTCA
42693011 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42693076 CTTTCA
66 CTTTCA
42693082 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
42693104 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:42693141 original size:71 final size:70
Alignment explanation
Indices: 42692940--42693137 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
42692930 CGATTTGTCT
* * *
42692940 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
42693005 CTTTCA
65 CTTTCA
* * *
42693011 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
42693076 CTTTCA
65 CTTTCA
* *
42693082 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
42693138 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:42700559 original size:66 final size:68
Alignment explanation
Indices: 42700483--42700669 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
42700473 TAGTACCACT
*
42700483 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
42700545 CACG
65 CACG
42700549 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
42700614 ATCACG
63 ATCACG
42700620 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
42700670 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:42700594 original size:71 final size:71
Alignment explanation
Indices: 42700506--42700669 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
42700496 CGATTTGTCT
42700506 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42700571 CTTTCA
66 CTTTCA
42700577 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42700642 CTTTCA
66 CTTTCA
42700648 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
42700670 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:42700707 original size:71 final size:70
Alignment explanation
Indices: 42700506--42700703 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
42700496 CGATTTGTCT
* * *
42700506 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
42700571 CTTTCA
65 CTTTCA
* * *
42700577 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
42700642 CTTTCA
65 CTTTCA
* *
42700648 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
42700704 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:42703321 original size:51 final size:52
Alignment explanation
Indices: 42703200--42703325 Score: 186
Period size: 52 Copynumber: 2.5 Consensus size: 52
42703190 ATGTCACTAG
42703200 TGACT-CAAGTGTGGTACTATGTGAAGGCCACTTTGTAAAGAAAGATAGCTT
1 TGACTACAAGTGTGGTACTATGTGAAGGCCACTTTGTAAAGAAAGATAGCTT
* * *
42703251 TG-GTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTT
1 TGACT-ACAAGTGTGGTACTATGTGAAGGCCACTTTGTAAAGAAAGATAGCTT
*
42703302 TGACTACAAGGGTGGTACTATGTG
1 TGACTACAAGTGTGGTACTATGTG
42703326 CAGCCCACCG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
50 1 0.01
51 31 0.46
52 35 0.52
ACGTcount: A:0.28, C:0.13, G:0.29, T:0.29
Consensus pattern (52 bp):
TGACTACAAGTGTGGTACTATGTGAAGGCCACTTTGTAAAGAAAGATAGCTT
Found at i:42705565 original size:44 final size:44
Alignment explanation
Indices: 42705502--42705674 Score: 208
Period size: 44 Copynumber: 3.8 Consensus size: 44
42705492 TGTAACCCGC
* *
42705502 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGCGTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATCGCAT
42705546 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG-AT-GCCTAGTT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATCG-C-A--T
* * *
42705592 ACATCTCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCA--TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-CA-TCGCAT
42705639 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
42705675 ATGCTCAACC
Statistics
Matches: 110, Mismatches: 8, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
42 1 0.01
43 2 0.02
44 36 0.33
45 2 0.02
46 31 0.28
47 31 0.28
48 2 0.02
49 2 0.02
50 2 0.02
51 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (44 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGCATCGCAT
Found at i:42705667 original size:93 final size:91
Alignment explanation
Indices: 42705510--42705678 Score: 302
Period size: 93 Copynumber: 1.8 Consensus size: 91
42705500 GCCCATAAGT
42705510 GAACTCGGACTCAACTCAACGAGCTCGGCGTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
1 GAACTCGGACTCAACTCAACGAGCTCGGCGTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
42705575 AGTTCGGATGCCTAGTTACATCTCAC
66 AGTTCGGATGCCTAGTTACATCTCAC
* *
42705601 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGG-C-GTCGCATCCATAAGTGAACTCGGACTCAACTCAA
42705666 CGAGTTCGGATGC
64 CGAGTTCGGATGC
42705679 TCAACCATCC
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 27 0.36
92 1 0.01
93 46 0.62
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCGTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCAC
Found at i:42708229 original size:46 final size:46
Alignment explanation
Indices: 42708162--42708334 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
42708152 TGTAACCCGC
*
42708162 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
42708208 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * *
42708258 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGAC--TCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
42708299 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
42708335 ATGCCAATAT
Statistics
Matches: 110, Mismatches: 8, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 1 0.01
43 2 0.02
44 29 0.26
46 35 0.32
47 28 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:42708327 original size:91 final size:92
Alignment explanation
Indices: 42708170--42708339 Score: 306
Period size: 91 Copynumber: 1.8 Consensus size: 92
42708160 GCCCATAAGT
*
42708170 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACG-TCGCATCCATAAGTGAACTCGGACTCAACTCAA
42708235 CGAGTTCGGATGCCTAGTTACATCTCAC
65 CGAGTTCGGATGCCTAGTTACATCTCAC
*
42708263 GAACTCGGACTCAACTCAACGAGTTCGGAC-TCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACGTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
42708327 GAGTTCGGATGCC
66 GAGTTCGGATGCC
42708340 AATATCCTAG
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 47 0.63
93 28 0.37
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:42710743 original size:29 final size:29
Alignment explanation
Indices: 42710704--42710791 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
42710694 CAAAGATAAC
*
42710704 AAGAAAACCGAATAAAGAAATCCAAGATA
1 AAGAAACCCGAATAAAGAAATCCAAGATA
*
42710733 GAGAAACCCGAATAAAGAAATCC-AGAATA
1 AAGAAACCCGAATAAAGAAATCCAAG-ATA
* * * *
42710762 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGA-AACCCGAATAAAGAAATCCAAGATA
42710792 CGATACTATG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
28 2 0.04
29 27 0.55
30 18 0.37
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (29 bp):
AAGAAACCCGAATAAAGAAATCCAAGATA
Found at i:42710762 original size:15 final size:15
Alignment explanation
Indices: 42710704--42710782 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
42710694 CAAAGATAAC
*
42710704 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
42710718 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
42710733 GAGAAA-CCCGAATA
1 AAGAAATCCAGAATA
42710747 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
42710762 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
42710777 AAGAAA
1 AAGAAA
42710783 CCCAAGATAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
14 19 0.36
15 34 0.64
ACGTcount: A:0.58, C:0.14, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:42710791 original size:15 final size:15
Alignment explanation
Indices: 42710715--42710791 Score: 77
Period size: 15 Copynumber: 5.2 Consensus size: 15
42710705 AGAAAACCGA
42710715 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* * *
42710730 ATAGAGAAACCCGA-
1 ATAAAGAAATCCAAG
42710744 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
42710758 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
42710774 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
42710789 ATA
1 ATA
42710792 CGATACTATG
Statistics
Matches: 49, Mismatches: 10, Indels: 6
0.75 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 10 0.20
15 37 0.76
16 1 0.02
ACGTcount: A:0.56, C:0.16, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:42713796 original size:46 final size:46
Alignment explanation
Indices: 42713729--42713901 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
42713719 TGTAACCCGC
*
42713729 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
*
42713775 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCAT
* * *
42713825 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGAC--TCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
42713866 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGG
42713902 ATGCCAACCA
Statistics
Matches: 110, Mismatches: 8, Indels: 20
0.80 0.06 0.14
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 1 0.01
43 2 0.02
44 29 0.26
46 35 0.32
47 28 0.25
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCAT
Found at i:42713894 original size:91 final size:92
Alignment explanation
Indices: 42713737--42713906 Score: 306
Period size: 91 Copynumber: 1.8 Consensus size: 92
42713727 GCCCATAAGT
*
42713737 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACG-TCGCATCCATAAGTGAACTCGGACTCAACTCAA
42713802 CGAGTTCGGATGCCTAGTTACATCTCAC
65 CGAGTTCGGATGCCTAGTTACATCTCAC
*
42713830 GAACTCGGACTCAACTCAACGAGTTCGGAC-TCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGACGTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
42713894 GAGTTCGGATGCC
66 GAGTTCGGATGCC
42713907 AACCATCCTA
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 47 0.63
93 28 0.37
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.21
Consensus pattern (92 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGTTCGGATGCCTAGTTACATCTCAC
Found at i:42716667 original size:24 final size:24
Alignment explanation
Indices: 42716615--42716673 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
42716605 GGAGATGGAA
* **
42716615 ATGAAGACGAAAACGGGGGTGGAG
1 ATGAAGATGAAAACGGGGGTCAAG
* *
42716639 GTGAAGATGAAGACGGGGGTCAAG
1 ATGAAGATGAAAACGGGGGTCAAG
42716663 ATGAAGATGAA
1 ATGAAGATGAA
42716674 TATGGGAGTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.39, C:0.07, G:0.42, T:0.12
Consensus pattern (24 bp):
ATGAAGATGAAAACGGGGGTCAAG
Found at i:42721323 original size:39 final size:39
Alignment explanation
Indices: 42721236--42721349 Score: 156
Period size: 39 Copynumber: 2.9 Consensus size: 39
42721226 TATGGTAACC
** * *
42721236 CGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
* *
42721276 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
42721315 CGCCCAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
42721350 TCGAACATTC
Statistics
Matches: 65, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
39 50 0.77
40 15 0.23
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:42725531 original size:21 final size:21
Alignment explanation
Indices: 42725505--42725546 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42725495 AATTAGATTA
* *
42725505 CAAAAAGTATCGATACCTTTT
1 CAAAAAATATCGATACATTTT
42725526 CAAAAAATATCGATACATTTT
1 CAAAAAATATCGATACATTTT
42725547 ACCAAGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (21 bp):
CAAAAAATATCGATACATTTT
Found at i:42729978 original size:13 final size:13
Alignment explanation
Indices: 42729960--42729984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42729950 AAGTAATCAC
42729960 ACACGGGCGTGTT
1 ACACGGGCGTGTT
42729973 ACACGGGCGTGT
1 ACACGGGCGTGT
42729985 CCCTACCGAG
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:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
ACACGGGCGTGTT
Found at i:42741541 original size:46 final size:46
Alignment explanation
Indices: 42741472--42741647 Score: 173
Period size: 46 Copynumber: 3.8 Consensus size: 46
42741462 TATTTGGGCA
42741472 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
* *
42741518 TTCGAACTCGTTGAGTTGAGTCCGAGTT--C-GA-GAGATGT-AACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGTGAA-T--G
* * * *
42741563 CATCCGAGCTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
* * * *
42741611 CCCGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42741648 GCGGGTTACA
Statistics
Matches: 107, Mismatches: 12, Indels: 22
0.76 0.09 0.16
Matches are distributed among these distances:
42 3 0.03
43 7 0.07
44 1 0.01
45 1 0.01
46 60 0.56
47 25 0.23
48 1 0.01
49 1 0.01
50 5 0.05
51 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
Found at i:42741627 original size:93 final size:93
Alignment explanation
Indices: 42741468--42741640 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
42741458 GGGATATTTG
* * * ** *
42741468 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATGTTCGAACTCGTTGAG
1 GGCATCCGAACTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
42741533 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
42741561 GGCATCCGAGCTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG
1 GGCATCCGAACTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
42741626 TTGAGTCCGAGTTCG
66 TTGAGTCCGAGTTCG
42741641 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTAGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:42742311 original size:44 final size:44
Alignment explanation
Indices: 42742248--42742335 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
42742238 AATTACTAGC
42742248 TAATCCATGGAAAACCATGAAATAGGTAAAATTTACCATAAAAT
1 TAATCCATGGAAAACCATGAAATAGGTAAAATTTACCATAAAAT
42742292 TAATCCATGGAAAACCATGAAATAGGTAAAATTTACCATAAAAT
1 TAATCCATGGAAAACCATGAAATAGGTAAAATTTACCATAAAAT
42742336 AGATTCAGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (44 bp):
TAATCCATGGAAAACCATGAAATAGGTAAAATTTACCATAAAAT
Found at i:42744656 original size:15 final size:15
Alignment explanation
Indices: 42744617--42744687 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
42744607 GTATCTTGGG
*
42744617 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
42744632 TATCTTTATTCTGGA
1 TTTCTTTATTCTGGA
* *
42744647 TTTCTTTATTCCGGG
1 TTTCTTTATTCTGGA
*
42744662 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
42744677 TTTCTTTATTC
1 TTTCTTTATTC
42744688 AGTTTTCTTG
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
14 2 0.04
15 41 0.91
16 2 0.04
ACGTcount: A:0.13, C:0.18, G:0.13, T:0.56
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:42744686 original size:30 final size:31
Alignment explanation
Indices: 42744608--42744687 Score: 94
Period size: 30 Copynumber: 2.6 Consensus size: 31
42744598 CATAGTATCG
* *
42744608 TATCTTGGGTTTCTTTA-TCCTGGATATCTT
1 TATCTTGGATTTCTTTATTCCTGGATATCTC
* *
42744638 TAT-TCTGGATTTCTTTATTCC-GGGTTTCTC
1 TATCT-TGGATTTCTTTATTCCTGGATATCTC
42744668 TATCTTGGATTTCTTTATTC
1 TATCTTGGATTTCTTTATTC
42744688 AGTTTTCTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
29 1 0.02
30 38 0.88
31 4 0.09
ACGTcount: A:0.12, C:0.17, G:0.15, T:0.55
Consensus pattern (31 bp):
TATCTTGGATTTCTTTATTCCTGGATATCTC
Found at i:42747230 original size:46 final size:46
Alignment explanation
Indices: 42747071--42747244 Score: 201
Period size: 46 Copynumber: 3.8 Consensus size: 46
42747061 ATTTGGGCAT
*
42747071 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG-
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *** * * * *
42747116 TCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-AC-TAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGAACGC
*
42747161 ATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
*
42747209 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42747245 GCGGGTTACA
Statistics
Matches: 106, Mismatches: 17, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
44 2 0.02
45 28 0.26
46 46 0.43
47 27 0.25
48 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:42748622 original size:18 final size:17
Alignment explanation
Indices: 42748595--42748629 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42748585 AAATTCTTGC
42748595 AAGATAAATGATTGAATT
1 AAGATAAATGA-TGAATT
*
42748613 AAGATGAATGATGAATT
1 AAGATAAATGATGAATT
42748630 GAGTATAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (17 bp):
AAGATAAATGATGAATT
Found at i:42750649 original size:20 final size:19
Alignment explanation
Indices: 42750613--42750663 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
42750603 TAGGGCTATT
*
42750613 TTGTAAA-GTTGTAAAATAA
1 TTGTAAATG-TGTGAAATAA
42750632 GTTGTAAATGTGTGAAATAA
1 -TTGTAAATGTGTGAAATAA
42750652 TTG-AAAT-TGTGA
1 TTGTAAATGTGTGA
42750664 GTTGCTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.14
19 3 0.10
20 16 0.55
21 1 0.03
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.37
Consensus pattern (19 bp):
TTGTAAATGTGTGAAATAA
Found at i:42751430 original size:11 final size:11
Alignment explanation
Indices: 42751414--42751441 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
42751404 GCTAGTGTAA
42751414 GACATGTATGG
1 GACATGTATGG
42751425 GACATGTATGG
1 GACATGTATGG
42751436 GACATG
1 GACATG
42751442 CATCAGCCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.36, T:0.25
Consensus pattern (11 bp):
GACATGTATGG
Found at i:42751535 original size:48 final size:49
Alignment explanation
Indices: 42751461--42751593 Score: 144
Period size: 48 Copynumber: 2.7 Consensus size: 49
42751451 CGAGATATAC
* *
42751461 AAGCTAGTGTAAGACCTGTCTGGGACATGGCATC-GACACAGATAGATTA
1 AAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGACAC-GATAGATAA
* * * * * *
42751510 GAGCCAGTGTAAGACCTGTCT-GGACACGACATCGGGCTCGATATATAA
1 AAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGACACGATAGATAA
* * *
42751558 AAGTCAGTGTAAGACCTATCTGGGACATGGCGTCGG
1 AAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGG
42751594 CATCTTATCC
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
48 35 0.51
49 33 0.49
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (49 bp):
AAGCCAGTGTAAGACCTGTCTGGGACATGGCATCGGACACGATAGATAA
Found at i:42756822 original size:15 final size:15
Alignment explanation
Indices: 42756804--42756842 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
42756794 TGTTATATAT
42756804 ATATATAATATAATA
1 ATATATAATATAATA
* *
42756819 ATATATTATATTATA
1 ATATATAATATAATA
42756834 ATAT-TAATA
1 ATATATAATA
42756843 CCTAAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATATAATATAATA
Found at i:42764144 original size:40 final size:39
Alignment explanation
Indices: 42763979--42764162 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
42763969 AAATTGAATG
* * *
42763979 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
42764019 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
42764059 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
42764099 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
42764138 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
42764163 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:42764187 original size:80 final size:81
Alignment explanation
Indices: 42764019--42764207 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
42764009 GCTGGAAATT
* * * *
42764019 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
42764084 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
42764100 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
42764163 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
42764179 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
42764208 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:42772259 original size:40 final size:39
Alignment explanation
Indices: 42772094--42772277 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
42772084 AAATTGAATG
* * *
42772094 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
42772134 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
42772174 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
42772214 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
42772253 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
42772278 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:42772302 original size:80 final size:81
Alignment explanation
Indices: 42772134--42772322 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
42772124 GCTGGAAATT
* * * *
42772134 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
42772199 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
42772215 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
42772278 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
42772294 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
42772323 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:42775227 original size:21 final size:22
Alignment explanation
Indices: 42775188--42775228 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
42775178 AACATATTCA
*
42775188 CATACTTCTAATCTATACATGC
1 CATACTTCTAATATATACATGC
42775210 CATACTTC-AATATATACAT
1 CATACTTCTAATATATACAT
42775229 TTTCAAAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (22 bp):
CATACTTCTAATATATACATGC
Found at i:42775808 original size:43 final size:44
Alignment explanation
Indices: 42775688--42775809 Score: 142
Period size: 43 Copynumber: 2.8 Consensus size: 44
42775678 AGCTCATACA
* *
42775688 ATGCCAACGTCCTAGACATGGTCTTACATGT-GATCAAATATTG
1 ATGCCAATGTCCTAGACATGGTCTTACATGTAAATCAAATATTG
* * * * * * *
42775731 ATGCCATTTTCCCAAATAGGGTCTTACACG-AAATCAAATA-TG
1 ATGCCAATGTCCTAGACATGGTCTTACATGTAAATCAAATATTG
42775773 ATGCCAATGTCCTAGACATGGTCTTACATGTAAATCA
1 ATGCCAATGTCCTAGACATGGTCTTACATGTAAATCA
42775810 TAAGTCGATG
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
42 25 0.41
43 36 0.59
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (44 bp):
ATGCCAATGTCCTAGACATGGTCTTACATGTAAATCAAATATTG
Found at i:42780558 original size:23 final size:23
Alignment explanation
Indices: 42780528--42780573 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
42780518 TTGGAGTGCT
42780528 ATTGGGCTATTTGCACACTTTCG
1 ATTGGGCTATTTGCACACTTTCG
42780551 ATTGGGCTATTTGCACACTTTCG
1 ATTGGGCTATTTGCACACTTTCG
42780574 CAGACAAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (23 bp):
ATTGGGCTATTTGCACACTTTCG
Found at i:42781034 original size:26 final size:27
Alignment explanation
Indices: 42780996--42781061 Score: 82
Period size: 26 Copynumber: 2.5 Consensus size: 27
42780986 TTTACCTAGA
*
42780996 GCCCCTA-ATTGATAAAATGACT-TTAT
1 GCCCCTATA-TGATAAAATAACTGTTAT
* *
42781022 GCCCTTATGTGATAAAATAACTGTTAT
1 GCCCCTATATGATAAAATAACTGTTAT
42781049 GCCCCTATATGAT
1 GCCCCTATATGAT
42781062 GTATGATTGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
26 18 0.55
27 15 0.45
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.35
Consensus pattern (27 bp):
GCCCCTATATGATAAAATAACTGTTAT
Found at i:42781700 original size:20 final size:20
Alignment explanation
Indices: 42781675--42781722 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
42781665 CCTCTTTGGA
42781675 TTTTATTTTTAATTTGGGAT
1 TTTTATTTTTAATTTGGGAT
42781695 TTTTATTTTTAATTTGGGAT
1 TTTTATTTTTAATTTGGGAT
42781715 TTTTATTT
1 TTTTATTT
42781723 GCTTCGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (20 bp):
TTTTATTTTTAATTTGGGAT
Found at i:42782105 original size:44 final size:42
Alignment explanation
Indices: 42782055--42782190 Score: 125
Period size: 43 Copynumber: 3.2 Consensus size: 42
42782045 GTGTTACACT
* *
42782055 ACGTCTGGGATGTTGGTATCG-ACTTATGATTTACGTGTAAGACC
1 ACGTCTGGGATGTTGGCATCGTAC-T-TGATTT-CATGTAAGACC
42782099 ACGTCTGGGATGTTGGCATCGTACTTGATTTCATGTAAGACC
1 ACGTCTGGGATGTTGGCATCGTACTTGATTTCATGTAAGACC
* * * * *
42782141 -CTGTCTGGGACAG-TGGCATCAATATTTGATTACATATAAGACC
1 AC-GTCTGGGA-TGTTGGCATC-GTACTTGATTTCATGTAAGACC
*
42782184 ACATCTG
1 ACGTCTG
42782191 AGACATTGGC
Statistics
Matches: 79, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
41 1 0.01
42 25 0.32
43 29 0.37
44 22 0.28
45 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (42 bp):
ACGTCTGGGATGTTGGCATCGTACTTGATTTCATGTAAGACC
Found at i:42782149 original size:42 final size:44
Alignment explanation
Indices: 42782055--42782150 Score: 128
Period size: 44 Copynumber: 2.2 Consensus size: 44
42782045 GTGTTACACT
* *
42782055 ACGTCTGGGATGTTGGTATCGACTTATGATTTACGTGTAAGACC
1 ACGTCTGGGATGTTGGCATCGACTTATGATTTACATGTAAGACC
42782099 ACGTCTGGGATGTTGGCATCGTAC-T-TGATTT-CATGTAAGACC
1 ACGTCTGGGATGTTGGCATCG-ACTTATGATTTACATGTAAGACC
42782141 -CTGTCTGGGA
1 AC-GTCTGGGA
42782151 CAGTGGCATC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
41 1 0.02
42 18 0.38
43 6 0.12
44 21 0.44
45 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.28, T:0.33
Consensus pattern (44 bp):
ACGTCTGGGATGTTGGCATCGACTTATGATTTACATGTAAGACC
Found at i:42786094 original size:40 final size:40
Alignment explanation
Indices: 42786039--42786139 Score: 130
Period size: 40 Copynumber: 2.5 Consensus size: 40
42786029 TGAATGATAC
* * ** *
42786039 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAAT
* *
42786079 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAAT
*
42786119 CCGGGTTAAGACCCGAAGGCA
1 CCGGGCTAAGACCCGAAGGCA
42786140 ATTGTGCTTA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.22
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCAAGTGACCAAAT
Found at i:42796158 original size:21 final size:23
Alignment explanation
Indices: 42796129--42796177 Score: 62
Period size: 26 Copynumber: 2.0 Consensus size: 23
42796119 AACCAAATGC
*
42796129 ACAAGATAATGGCACATTTGCAT
1 ACAACATAATGGCACATTTGCAT
42796152 CACATAACATAATGGCACATTTGCAT
1 -AC--AACATAATGGCACATTTGCAT
42796178 CACATATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.09
26 20 0.91
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (23 bp):
ACAACATAATGGCACATTTGCAT
Found at i:42796165 original size:26 final size:26
Alignment explanation
Indices: 42796134--42796188 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
42796124 AATGCACAAG
42796134 ATAATGGCACATTTGCATCACATAAC
1 ATAATGGCACATTTGCATCACATAAC
*
42796160 ATAATGGCACATTTGCATCACATATC
1 ATAATGGCACATTTGCATCACATAAC
42796186 ATA
1 ATA
42796189 TATCAAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.29
Consensus pattern (26 bp):
ATAATGGCACATTTGCATCACATAAC
Found at i:42796860 original size:42 final size:42
Alignment explanation
Indices: 42796768--42796909 Score: 126
Period size: 44 Copynumber: 3.3 Consensus size: 42
42796758 GTCCCAGACT
* * *
42796768 TGGTCTTACATGTAATCAAATATCGATGCCACTGTCCCAAACAG
1 TGGTCTTACACGAAATCAAATAT-GATGCCACCGTCCCAAA-AG
* * * *
42796812 -GTTCTTACACGAAATCAAATATGATGCCACCATCCCATATG
1 TGGTCTTACACGAAATCAAATATGATGCCACCGTCCCAAAAG
* * * *
42796853 TGGTCTTACACGTAAATCATAAGT-CGATGCCAACGTCCCACACG
1 TGGTCTTACACG-AAATCA-AA-TATGATGCCACCGTCCCAAAAG
42796897 TGGTCTTACACGA
1 TGGTCTTACACGA
42796910 TAACACATAT
Statistics
Matches: 81, Mismatches: 13, Indels: 9
0.79 0.13 0.09
Matches are distributed among these distances:
41 1 0.01
42 24 0.30
43 26 0.32
44 29 0.36
45 1 0.01
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (42 bp):
TGGTCTTACACGAAATCAAATATGATGCCACCGTCCCAAAAG
Found at i:42796892 original size:44 final size:42
Alignment explanation
Indices: 42796750--42796909 Score: 119
Period size: 43 Copynumber: 3.7 Consensus size: 42
42796740 AGCTCGTACA
** * * * *
42796750 ATGCCAATGTCCCAGACTTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACATCCCACACGTGGTCTTACACGAAATCAAATA-CG
* * * *
42796793 ATGCC-ACTGTCCCAAACAG-GTTCTTACACGAAATCAAATATG
1 ATGCCAAC-ATCCCACAC-GTGGTCTTACACGAAATCAAATACG
* * *
42796835 ATGCCACCATCCCATATGTGGTCTTACACGTAAATCATAAGT-CG
1 ATGCCAACATCCCACACGTGGTCTTACACG-AAATCA-AA-TACG
*
42796879 ATGCCAACGTCCCACACGTGGTCTTACACGA
1 ATGCCAACATCCCACACGTGGTCTTACACGA
42796910 TAACACATAT
Statistics
Matches: 93, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
41 1 0.01
42 23 0.25
43 39 0.42
44 29 0.31
45 1 0.01
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.26
Consensus pattern (42 bp):
ATGCCAACATCCCACACGTGGTCTTACACGAAATCAAATACG
Found at i:42798821 original size:93 final size:93
Alignment explanation
Indices: 42798714--42798884 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
42798704 GCCCCTAAGT
* *
42798714 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
*
42798779 TGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCGGATGCCTAGTTACATTTCAC
* *
42798807 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
42798872 CGAGTTCGGATGC
66 CGAGTTCGGATGC
42798885 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCACATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATTTCAC
Found at i:42798881 original size:46 final size:46
Alignment explanation
Indices: 42798709--42798881 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
42798699 AACCCGCCCC
* * *
42798709 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCACATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCA
* *
42798755 TAAGTGAACTCGGACTCAACTCAATGAGTTCGGATGCCTAGTT-ACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCACATCCA
* * *
42798803 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCA
42798848 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
42798882 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 1 0.01
45 2 0.02
46 60 0.57
47 28 0.26
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCACATCCA
Found at i:42801424 original size:48 final size:48
Alignment explanation
Indices: 42801348--42802210 Score: 1330
Period size: 48 Copynumber: 18.0 Consensus size: 48
42801338 GTTACAACAC
* * *
42801348 TCACATTAGCCATTCGGCTTTACCACATATTCTTATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* **
42801396 TCACATTCGCCATTCGGCTTTATGACATATACATATCTCATATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
42801444 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
42801492 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
42801540 TCACATTAGCCATTCGGCTTTGCCACATATACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
42801588 TCACATTCGCCATTCGGCTTTACGACATATACATATCTCATATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
42801636 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
42801684 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
*
42801732 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* * * * * *
42801780 TCACATTCGCCATTCGGCTTAACCACATACACACATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
42801828 TCACATTAGCCATTCGGTTTTACCACATATACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
*
42801876 TCACATTAGCCATTCGGCTTTACCACATATACATATCTTATATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
42801924 TCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
42801972 TCACATTAACCATTCGGCTTTACCACATATACATATCTCATACATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* * * *
42802020 TCACATTCGCCATTCGGCTTTACCACATCTACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* *
42802068 TCACATTAGCCTTTCGGCTTTACCACATATACATATCTTATATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* * *
42802116 TCACATTAGCCATTCGGCTTTACCACATACACATATCACACATATATT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
* * *
42802164 TCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATAT
42802211 ATATTTATCT
Statistics
Matches: 745, Mismatches: 70, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 745 1.00
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.35
Consensus pattern (48 bp):
TCACATTAGCCATTCGGCTTTACCACATATACATATCTCATATATATT
Found at i:42803405 original size:2 final size:2
Alignment explanation
Indices: 42803398--42803425 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42803388 CCATTGCCGA
42803398 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
42803426 CATCAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42805082 original size:19 final size:19
Alignment explanation
Indices: 42805050--42805124 Score: 59
Period size: 19 Copynumber: 4.1 Consensus size: 19
42805040 GATTTTTTTG
*
42805050 TTAAAATATGTATTAATATA
1 TTAAATTAT-TATTAATATA
* *
42805070 TTAAATTAATATTTAA-GTA
1 TTAAATTATTA-TTAATATA
42805089 TT-AATT-TTA-TAATATA
1 TTAAATTATTATTAATATA
* *
42805105 TTATATTATTATTTATATA
1 TTAAATTATTATTAATATA
42805124 T
1 T
42805125 AACATAAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 11
0.70 0.11 0.18
Matches are distributed among these distances:
15 3 0.07
16 4 0.09
17 5 0.12
18 7 0.16
19 13 0.30
20 11 0.26
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTAAATTATTATTAATATA
Found at i:42808914 original size:43 final size:43
Alignment explanation
Indices: 42808767--42808917 Score: 155
Period size: 43 Copynumber: 3.5 Consensus size: 43
42808757 TATGTGTTTT
* * *
42808767 CATGTAAGACGACATCTGGGACATTGGCATCGACT-TATAATTTA
1 CATGTAAGACCACATCTGGGACATTGGCATCGA-TATTTGA-TTA
** * *
42808811 CATGTAAGACCATGTCTGGGACATTGGCCTC-ATATTTGATTT
1 CATGTAAGACCACATCTGGGACATTGGCATCGATATTTGATTA
* * *
42808853 CGTGTAAGACC-CTATCTGGGACAGTGGCATCGATATTTGATCA
1 CATGTAAGACCAC-ATCTGGGACATTGGCATCGATATTTGATTA
*
42808896 CATGTAAGACCACGTCTGGGAC
1 CATGTAAGACCACATCTGGGAC
42808918 GTTCGCGTTG
Statistics
Matches: 87, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
42 28 0.32
43 31 0.36
44 28 0.32
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (43 bp):
CATGTAAGACCACATCTGGGACATTGGCATCGATATTTGATTA
Found at i:42823949 original size:40 final size:40
Alignment explanation
Indices: 42823894--42824057 Score: 195
Period size: 40 Copynumber: 4.1 Consensus size: 40
42823884 TGAATGATAC
* *
42823894 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* *
42823934 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * ** *
42823974 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * * *
42824014 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
42824054 CCGG
1 CCGG
42824058 CTAGATTCCG
Statistics
Matches: 103, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
39 1 0.01
40 100 0.97
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:42827918 original size:24 final size:24
Alignment explanation
Indices: 42827885--42827938 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
42827875 AAGGCTATCA
42827885 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
42827909 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAAGATTTAGGAGCTGATAAG
42827933 GGAGAA
1 GGAGAA
42827939 CGGTGTTGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.04, G:0.41, T:0.20
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:42829469 original size:26 final size:26
Alignment explanation
Indices: 42829362--42829472 Score: 150
Period size: 27 Copynumber: 4.2 Consensus size: 26
42829352 AGGAAGTGTC
* * *
42829362 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGACTCTGCCAC-ATTATCTGTT
*
42829389 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGACTCTGCCACAT-TATCTGTT
42829416 CTGGTGACTCTGCCACGATTATCTGTT
1 CTGGTGACTCTGCCAC-ATTATCTGTT
*
42829443 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGACTCTGCCACATTATCTGTT
42829469 CTGG
1 CTGG
42829473 CAGCCATGCT
Statistics
Matches: 78, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
26 16 0.21
27 60 0.77
28 2 0.03
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGACTCTGCCACATTATCTGTT
Found at i:42831937 original size:30 final size:30
Alignment explanation
Indices: 42831901--42832031 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
42831891 GACAAGATTG
* * * * *
42831901 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
42831931 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
42831959 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42831989 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42832018 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42832032 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:42831992 original size:58 final size:58
Alignment explanation
Indices: 42831901--42832031 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
42831891 GACAAGATTG
* * * * * *
42831901 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
42831959 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
42832018 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42832032 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:42834248 original size:40 final size:39
Alignment explanation
Indices: 42834203--42834332 Score: 136
Period size: 40 Copynumber: 3.3 Consensus size: 39
42834193 CGGAATATAA
42834203 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
42834243 CCGGATAGAATGTC-TCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
42834283 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
42834323 CCGGATATAA
1 CCGGATATAA
42834333 TTTCCAGCAT
Statistics
Matches: 72, Mismatches: 14, Indels: 8
0.77 0.15 0.09
Matches are distributed among these distances:
38 1 0.01
40 69 0.96
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:42834347 original size:40 final size:40
Alignment explanation
Indices: 42834219--42834370 Score: 148
Period size: 40 Copynumber: 3.8 Consensus size: 40
42834209 ATAACCATGT
* * *
42834219 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
42834259 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
42834299 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
42834339 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
42834371 CATTCAATTT
Statistics
Matches: 91, Mismatches: 17, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.02
40 86 0.95
41 3 0.03
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:42834353 original size:80 final size:80
Alignment explanation
Indices: 42834219--42834368 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
42834209 ATAACCATGT
*
42834219 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGAT-TTAGC
42834283 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
42834299 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTC-GCACGAA-TGCCTTCGGGATTTAG
42834362 CCCGGAT
64 CCCGGAT
42834369 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGTCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:42842932 original size:30 final size:30
Alignment explanation
Indices: 42842896--42843026 Score: 162
Period size: 30 Copynumber: 4.5 Consensus size: 30
42842886 GACAAGATTG
* *
42842896 GCACTAAGTGTGC-AGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGA-GTTTAAAATTATATA
*
42842926 GCACTAAGTGTGCGAGTTT--GATTATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
42842954 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* *
42842984 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
42843013 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42843027 GATTCACTAT
Statistics
Matches: 92, Mismatches: 6, Indels: 7
0.88 0.06 0.07
Matches are distributed among these distances:
28 23 0.25
29 20 0.22
30 48 0.52
31 1 0.01
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:42842987 original size:58 final size:59
Alignment explanation
Indices: 42842896--42843026 Score: 169
Period size: 58 Copynumber: 2.2 Consensus size: 59
42842886 GACAAGATTG
* * * * *
42842896 GCACTAAGTGTGC-AGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
42842954 GCACTAAGTGTGCGA-GCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
42843013 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42843027 GATTCACTAT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
57 2 0.03
58 40 0.62
59 22 0.34
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (59 bp):
GCACTAAGTGTGCGAGGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:42845284 original size:24 final size:24
Alignment explanation
Indices: 42845257--42845485 Score: 363
Period size: 24 Copynumber: 9.6 Consensus size: 24
42845247 CTTATTATGT
* * **
42845257 TCGCACACATAGAGCTATAGCAAA
1 TCGCACACATAGTGCCATAGTGAA
* * *
42845281 TCGCACACGTAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTGAA
* *
42845305 TCGCACACTTAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTGAA
42845329 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTGAA
42845353 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTGAA
42845377 TCGCACACATAGTGCCATAGT-AA
1 TCGCACACATAGTGCCATAGTGAA
42845400 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTGAA
42845424 TCGCACACATAGTGCCATAGT-AA
1 TCGCACACATAGTGCCATAGTGAA
42845447 TCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTGAA
42845471 TCGCACACATAGTGC
1 TCGCACACATAGTGC
42845486 ATTTGAGATA
Statistics
Matches: 196, Mismatches: 7, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
23 46 0.23
24 150 0.77
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.21
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTGAA
Found at i:42845420 original size:47 final size:48
Alignment explanation
Indices: 42845257--42845485 Score: 363
Period size: 47 Copynumber: 4.8 Consensus size: 48
42845247 CTTATTATGT
* * ** * *
42845257 TCGCACACATAGAGCTATAGCAAATCGCACACGTAGTGCTATAGTAAA
1 TCGCACACATAGTGCCATAGTGAATCGCACACATAGTGCCATAGTAAA
* * *
42845305 TCGCACACTTAGTGCCATAGTAAATCGCACACATAGTGCCATAGTGAA
1 TCGCACACATAGTGCCATAGTGAATCGCACACATAGTGCCATAGTAAA
42845353 TCGCACACATAGTGCCATAGTGAATCGCACACATAGTGCCATAGT-AA
1 TCGCACACATAGTGCCATAGTGAATCGCACACATAGTGCCATAGTAAA
42845400 TCGCACACATAGTGCCATAGTGAATCGCACACATAGTGCCATAGT-AA
1 TCGCACACATAGTGCCATAGTGAATCGCACACATAGTGCCATAGTAAA
42845447 TCGCACACATAGTGCCATAGTGAATCGCACACATAGTGC
1 TCGCACACATAGTGCCATAGTGAATCGCACACATAGTGC
42845486 ATTTGAGATA
Statistics
Matches: 172, Mismatches: 9, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
47 88 0.51
48 84 0.49
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.21
Consensus pattern (48 bp):
TCGCACACATAGTGCCATAGTGAATCGCACACATAGTGCCATAGTAAA
Found at i:42845942 original size:2 final size:2
Alignment explanation
Indices: 42845935--42845962 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42845925 ATGGGCATAC
42845935 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42845963 CATACCCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42852476 original size:39 final size:39
Alignment explanation
Indices: 42852370--42852528 Score: 153
Period size: 40 Copynumber: 4.1 Consensus size: 39
42852360 TCGGATTCAA
* * *
42852370 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTAGCACAATTGCCTTCGGGTCTT-AG
* *** *
42852410 CCGGATTTGGTAACTTGCACAATTGCCTTCGGGTCTTAG
1 CCGGATATAACAACTAGCACAATTGCCTTCGGGTCTTAG
*
42852449 CCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAG
1 CCGGATATAACAACTAGCAC-AATTGCCTTCGGGTCTTAG
* * *
42852488 CCCGGATATAATC-ACTAGCATAAATGCCTTC-GGACTTAG
1 -CCGGATATAA-CAACTAGCACAATTGCCTTCGGGTCTTAG
42852527 CC
1 CC
42852529 CGGGTATCAT
Statistics
Matches: 99, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
38 2 0.02
39 41 0.41
40 55 0.56
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCGGATATAACAACTAGCACAATTGCCTTCGGGTCTTAG
Found at i:42852516 original size:79 final size:78
Alignment explanation
Indices: 42852357--42852528 Score: 186
Period size: 79 Copynumber: 2.2 Consensus size: 78
42852347 GAGTCACGTA
* * * **
42852357 CCTTCGGA-TTCAACCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGGT
1 CCTTCGGACTT-AGCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAAT
* *
42852421 AACTTGCACAATTG
65 AACTAGCACAAATG
* ** *
42852435 CCTTCGGGTCTTAGCCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAA
1 CCTTC-GGACTTAGCCGGATATAACAACAAGCAC-AATTGCCTTCGGGTCTTAACCCGGATATAA
* *
42852499 TCACTAGCATAAATG
64 TAACTAGCACAAATG
42852514 CCTTCGGACTTAGCC
1 CCTTCGGACTTAGCC
42852529 CGGGTATCAT
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
78 14 0.18
79 59 0.77
80 4 0.05
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.26
Consensus pattern (78 bp):
CCTTCGGACTTAGCCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATA
ACTAGCACAAATG
Found at i:42860469 original size:40 final size:40
Alignment explanation
Indices: 42860409--42860572 Score: 170
Period size: 40 Copynumber: 4.1 Consensus size: 40
42860399 CGGGATTCAA
* ** *
42860409 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC
* *** *
42860449 CCGGATTTGGTAACTTGCACAATTGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC
42860489 CCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCAC-AATTGCCTTCGGGTCTTAGC
* * * * *
42860529 CCGGATATAATC-ACTAGCATAAATGCCTTCGAGACTTAGC
1 CCGGATATAA-CAACTCGCACAATTGCCTTCGGGTCTTAGC
42860569 CCGG
1 CCGG
42860573 GTATCATTCA
Statistics
Matches: 104, Mismatches: 17, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.02
40 99 0.95
41 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CCGGATATAACAACTCGCACAATTGCCTTCGGGTCTTAGC
Found at i:42860556 original size:80 final size:80
Alignment explanation
Indices: 42860409--42860572 Score: 195
Period size: 80 Copynumber: 2.0 Consensus size: 80
42860399 CGGGATTCAA
* * ** * *
42860409 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAACCCGGATTTGGTAACTTGCACAATTG
1 CCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATAACTAGCACAAATG
* *
42860474 CCTTCGGGTCTTAGC
66 CCTTCGAGACTTAGC
** * * *
42860489 CCGGATATAACAACTCGCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAATCACTAGCATAAAT
1 CCGGATATAACAACAAGCAC-AATTGCCTTCGGGTCTTAACCCGGATATAATAACTAGCACAAAT
42860553 GCCTTCGAGACTTAGC
65 GCCTTCGAGACTTAGC
42860569 CCGG
1 CCGG
42860573 GTATCATTCA
Statistics
Matches: 70, Mismatches: 13, Indels: 2
0.82 0.15 0.02
Matches are distributed among these distances:
80 68 0.97
81 2 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (80 bp):
CCGGATATAACAACAAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATAACTAGCACAAATG
CCTTCGAGACTTAGC
Found at i:42865495 original size:40 final size:40
Alignment explanation
Indices: 42865438--42865604 Score: 178
Period size: 40 Copynumber: 4.2 Consensus size: 40
42865428 TGAATGATAC
* *
42865438 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * *
42865478 CTGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATTATAT
* * * ** *
42865518 CCGGGCTAAGACCCGAAGACATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
* * *
42865558 CCGGG-TAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
42865597 CC-GGCTAA
1 CCGGGCTAA
42865605 ATTCCGAAGA
Statistics
Matches: 102, Mismatches: 22, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
38 2 0.02
39 31 0.30
40 67 0.66
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATTATAT
Found at i:42865596 original size:79 final size:80
Alignment explanation
Indices: 42865438--42865604 Score: 196
Period size: 80 Copynumber: 2.1 Consensus size: 80
42865428 TGAATGATAC
* * * ** * *
42865438 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATATCTGGGCTAAGACCCGAAGGCATTCG
1 CCGGGCTAAGACCCGAAGACATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCATTCG
*
42865503 TGCGAGTTGTTATAT
66 TGCGAGTGGTTATAT
* *
42865518 CCGGGCTAAGACCCGAAGACATTTGTGCAAGTTACCAAATCCGGG-TAAGACCCGAAGGCAATT-
1 CCGGGCTAAGACCCGAAGACATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGC-ATTC
**
42865581 GTGCTTGTGGTTATAT
65 GTGCGAGTGGTTATAT
42865597 CC-GGCTAA
1 CCGGGCTAA
42865605 ATTCCGAAGA
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
78 6 0.08
79 29 0.39
80 39 0.53
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGACATTTATGCAAGTGACCAAATCCGGGCTAAGACCCGAAGGCATTCG
TGCGAGTGGTTATAT
Found at i:42870484 original size:14 final size:15
Alignment explanation
Indices: 42870465--42870493 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42870455 ACACATTTGG
42870465 CTTTTAATTT-TTTT
1 CTTTTAATTTATTTT
42870479 CTTTTAATTTATTTT
1 CTTTTAATTTATTTT
42870494 ACCCCTAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (15 bp):
CTTTTAATTTATTTT
Found at i:42880246 original size:19 final size:19
Alignment explanation
Indices: 42880222--42880259 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
42880212 TTGAAGTTTC
*
42880222 TGTAACGCCCCGTACCCGA
1 TGTAACACCCCGTACCCGA
*
42880241 TGTAACACCCTGTACCCGA
1 TGTAACACCCCGTACCCGA
42880260 GACCGTTGCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.39, G:0.18, T:0.18
Consensus pattern (19 bp):
TGTAACACCCCGTACCCGA
Found at i:42881671 original size:40 final size:40
Alignment explanation
Indices: 42881616--42881771 Score: 242
Period size: 40 Copynumber: 3.9 Consensus size: 40
42881606 AGACATAGCT
*
42881616 ACTCGCTCAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
*
42881656 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
* *
42881696 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-AATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTA
* *
42881736 ACTAGCACAAATGCCTTCGGGACTTAGCCCAGTTAT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTAT
42881772 CATCCGAATA
Statistics
Matches: 107, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
39 1 0.01
40 105 0.98
41 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTATAGTA
Found at i:42881722 original size:80 final size:80
Alignment explanation
Indices: 42881590--42881767 Score: 254
Period size: 80 Copynumber: 2.2 Consensus size: 80
42881580 CAACCAAGTA
* * *
42881590 CCTTCGGGATTTAG-CCAGACATAGCTACTCGCTCAAATGCCTTCGGGACTTAGCCCGG-TTATA
1 CCTTCGGGACTTAGCCCAGACATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TA
*
42881653 GTAACTCGCACAAATG
65 GTAACTAGCACAAATG
* *
42881669 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
1 CCTTCGGGACTTAGCCCAGACATAGCT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
*
42881733 GTCACTAGCACAAATG
65 GTAACTAGCACAAATG
42881749 CCTTCGGGACTTAGCCCAG
1 CCTTCGGGACTTAGCCCAG
42881768 TTATCATCCG
Statistics
Matches: 88, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
79 14 0.16
80 73 0.83
81 1 0.01
ACGTcount: A:0.25, C:0.29, G:0.22, T:0.24
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCAGACATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAG
TAACTAGCACAAATG
Found at i:42887850 original size:40 final size:40
Alignment explanation
Indices: 42887737--42887913 Score: 254
Period size: 40 Copynumber: 4.5 Consensus size: 40
42887727 CAACCAAGTA
* * *
42887737 CCTTCGGGATTTAG-CCGGACATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
*
42887776 CCTTCGGGACTTAGCCC-GTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
42887815 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* *
42887855 CCTTCGGGACTTAGCCCGGA-ATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
42887895 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
42887914 TTATCATCCG
Statistics
Matches: 127, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.01
39 48 0.38
40 78 0.61
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:42887867 original size:79 final size:80
Alignment explanation
Indices: 42887737--42887913 Score: 261
Period size: 79 Copynumber: 2.2 Consensus size: 80
42887727 CAACCAAGTA
* * **
42887737 CCTTCGGGATTTAG-CCGGACATAGCTACTCGCTCAAATGCCTTCGGGACTTAGCCCGTTA-TAG
1 CCTTCGGGACTTAGCCCGGACATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAG
*
42887800 TAACTCGCACAAATG
66 TAACTAGCACAAATG
*
42887815 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
1 CCTTCGGGACTTAGCCCGGACATAGCT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTA
*
42887879 GTCACTAGCACAAATG
65 GTAACTAGCACAAATG
42887895 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
42887914 TTATCATCCG
Statistics
Matches: 89, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
78 14 0.16
79 40 0.45
80 35 0.39
ACGTcount: A:0.24, C:0.29, G:0.23, T:0.24
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGACATAGCTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAG
TAACTAGCACAAATG
Found at i:42891022 original size:40 final size:40
Alignment explanation
Indices: 42890955--42891118 Score: 208
Period size: 40 Copynumber: 4.1 Consensus size: 40
42890945 ACCCAAGTAT
* *
42890955 CTTCGGGAT-TTAG-CCGGATATAACAACTTGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
42890994 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * *
42891034 CTTCGGGTCTTAGCCCAGATATAATC-ACTAGCATAAATGC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
42891074 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
42891114 CTTCG
1 CTTCG
42891119 AATCTTAGTC
Statistics
Matches: 108, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.12
40 92 0.85
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:42891125 original size:80 final size:80
Alignment explanation
Indices: 42890971--42891126 Score: 233
Period size: 80 Copynumber: 1.9 Consensus size: 80
42890961 GATTTAGCCG
* * *
42890971 GATATAACAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCT
1 GATATAACAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGCAACTCGCACAAATGCCT
**
42891036 TCGGGTCTTAGCCCA
66 TCGAATCTTAGCCCA
* *
42891051 GATATAATC-ACTAGCATAAATGCCTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGCC
1 GATATAA-CAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGCAACTCGCACAAATGCC
42891115 TTCGAATCTTAG
65 TTCGAATCTTAG
42891127 TCCGGTTATC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
80 67 0.99
81 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.20, T:0.24
Consensus pattern (80 bp):
GATATAACAACTAGCACAAATGCCTTCGGGACATAGCCCGGATATAGCAACTCGCACAAATGCCT
TCGAATCTTAGCCCA
Found at i:42892943 original size:15 final size:15
Alignment explanation
Indices: 42892919--42892988 Score: 54
Period size: 15 Copynumber: 4.7 Consensus size: 15
42892909 ATAAAAAAAC
*
42892919 AGAAAACCAAGATAG
1 AGAAATCCAAGATAG
*
42892934 AGAAATCCAAGATGG
1 AGAAATCCAAGATAG
* * *
42892949 AG-AAGCCCAGAATAA
1 AGAAATCCAAG-ATAG
*
42892964 AGAAATCCATGATA-
1 AGAAATCCAAGATAG
42892978 AGGAAATCCAA
1 A-GAAATCCAA
42892989 ATTACAATCC
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
14 7 0.17
15 30 0.71
16 5 0.12
ACGTcount: A:0.53, C:0.16, G:0.20, T:0.11
Consensus pattern (15 bp):
AGAAATCCAAGATAG
Found at i:42900487 original size:68 final size:69
Alignment explanation
Indices: 42900360--42900494 Score: 200
Period size: 68 Copynumber: 2.0 Consensus size: 69
42900350 TGAATGAACT
* * * * *
42900360 TAATTACTTTAATATTAAATTAATATAATATTTATCAAGATAAATATTATATTAAATTTAATATT
1 TAATCACTTTAATAATAAATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAATATT
42900425 AAGA
66 AAGA
* *
42900429 TAATCACTTTAATAATAAATTAATAAAATA-CTATCAAGATAAGTATTAAATTAGATTTAATATT
1 TAATCACTTTAATAATAAATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAATATT
42900493 AA
66 AA
42900495 AACTATTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
68 32 0.54
69 27 0.46
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (69 bp):
TAATCACTTTAATAATAAATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAATATT
AAGA
Found at i:42900510 original size:68 final size:69
Alignment explanation
Indices: 42900369--42900510 Score: 162
Period size: 68 Copynumber: 2.1 Consensus size: 69
42900359 TTAATTACTT
* * * * *
42900369 TAATATTAAATTAATATAATATTTATCAAGATAAATATTATATTAAATTTAATATTAAGATAATC
1 TAATAATAAATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAATATTAAAATAATC
***
42900434 ACTT
66 AAAA
* *
42900438 TAATAATAAATTAATAAAATA-CTATCAAGATAAGTATTAAATTAGATTTAATATTAAAACT-AT
1 TAATAATAAATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAATATTAAAA-TAAT
*
42900501 TAAAA
65 CAAAA
42900506 TAATA
1 TAATA
42900511 TTATTTTTGG
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
68 41 0.67
69 20 0.33
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.39
Consensus pattern (69 bp):
TAATAATAAATTAATAAAATATCTATCAAGATAAATATTAAATTAAATTTAATATTAAAATAATC
AAAA
Found at i:42900942 original size:19 final size:19
Alignment explanation
Indices: 42900909--42900948 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
42900899 AAAATATTAT
*
42900909 ATTAATTTTAATTTAGTTG
1 ATTAATTTTAATTTACTTG
42900928 ATTAA-TTTAATTTTACTTG
1 ATTAATTTTAA-TTTACTTG
42900947 AT
1 AT
42900949 CAAAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (19 bp):
ATTAATTTTAATTTACTTG
Found at i:42903829 original size:49 final size:49
Alignment explanation
Indices: 42903773--42904036 Score: 438
Period size: 49 Copynumber: 5.4 Consensus size: 49
42903763 TACATATATG
* * * *
42903773 TGTGATAAGGCCAAATGGCCAATGCGATGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
* * *
42903822 TGTGATAAGGCCTAAAGGCCGATATGATGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
* *
42903871 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTTAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
*
42903920 TGTGATGAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
42903969 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
1 TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
42904018 TGTGATAAGGCCTAATGGC
1 TGTGATAAGGCCTAATGGC
42904037 TAATGTAAAA
Statistics
Matches: 203, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 203 1.00
ACGTcount: A:0.30, C:0.09, G:0.31, T:0.30
Consensus pattern (49 bp):
TGTGATAAGGCCTAATGGCCGATGTGGTGAATGTGAAAGTGTATGTATA
Found at i:42904195 original size:37 final size:37
Alignment explanation
Indices: 42904138--42904221 Score: 134
Period size: 37 Copynumber: 2.3 Consensus size: 37
42904128 GGAATATGTT
*
42904138 CCGGGTGAGA-CCGATGACTACGTGTGGAGATTATGA
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
* *
42904174 CCGGGTAAGACCCGATGACTACGTGTGGGGATTATGT
1 CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
42904211 CCGGGTAAGAC
1 CCGGGTAAGAC
42904222 TTCTTTTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
36 9 0.20
37 35 0.80
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (37 bp):
CCGGGTAAGACCCGATGACTACGTGTGGAGATTATGA
Found at i:42913279 original size:40 final size:39
Alignment explanation
Indices: 42913111--42913281 Score: 159
Period size: 40 Copynumber: 4.3 Consensus size: 39
42913101 AGAAATTGAA
* *
42913111 TGATATCCGGGCTAAGCCCCGAAGACAATTATGCTG-AAAT-
1 TGATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATG
* * * * *
42913151 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTAG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
* *
42913191 CT-ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTG
1 -TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAA-ATG
* *
42913231 TTAAATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG
1 TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAAT-G
42913271 TGATATCCGGG
1 TGATATCCGGG
42913282 TAAAGTCCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 14
0.78 0.12 0.10
Matches are distributed among these distances:
37 2 0.02
38 4 0.04
39 4 0.04
40 95 0.89
41 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (39 bp):
TGATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATG
Found at i:42917279 original size:20 final size:20
Alignment explanation
Indices: 42917254--42917298 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
42917244 AGGGACTAAA
* *
42917254 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTCTAAAATTTG
*
42917274 ATGAAAAATTCTAAAATTTT
1 ATGAAAAATTCTAAAATTTG
42917294 ATGAA
1 ATGAA
42917299 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTCTAAAATTTG
Found at i:42924322 original size:66 final size:68
Alignment explanation
Indices: 42924246--42924432 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
42924236 TAGTACCACT
*
42924246 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
42924308 CACG
65 CACG
42924312 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
42924377 ATCACG
63 ATCACG
42924383 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
42924433 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:42924357 original size:71 final size:71
Alignment explanation
Indices: 42924269--42924432 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
42924259 CGATTTGTCT
42924269 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42924334 CTTTCA
66 CTTTCA
42924340 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
42924405 CTTTCA
66 CTTTCA
42924411 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
42924433 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:42924470 original size:71 final size:70
Alignment explanation
Indices: 42924269--42924466 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
42924259 CGATTTGTCT
* * *
42924269 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
42924334 CTTTCA
65 CTTTCA
* * *
42924340 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
42924405 CTTTCA
65 CTTTCA
* *
42924411 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
42924467 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:42930220 original size:40 final size:40
Alignment explanation
Indices: 42930175--42930341 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
42930165 CGGAATATAA
42930175 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
42930215 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
42930255 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
42930295 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
42930334 CCGGATAT
1 CCGGATAT
42930342 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42942433 original size:40 final size:39
Alignment explanation
Indices: 42942388--42942517 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
42942378 CGGAATACAA
42942388 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* *
42942428 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* * * *
42942468 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC
42942508 CCGGATATAA
1 CCGGATATAA
42942518 TTTCCAGCAT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (39 bp):
CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC
Found at i:42950480 original size:40 final size:39
Alignment explanation
Indices: 42950435--42950564 Score: 163
Period size: 40 Copynumber: 3.3 Consensus size: 39
42950425 CGGAATACAA
42950435 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* *
42950475 CCGGATAGAACGACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TGCACGAATGCCTTCGGGTCTTAGC
* * * *
42950515 CCGGATGTAGCCGCTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACT-GCACGAA-TGCCTTCGGGTCTTAGC
42950555 CCGGATATAA
1 CCGGATATAA
42950565 TTTCCAGCAT
Statistics
Matches: 77, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
39 3 0.04
40 74 0.96
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.23
Consensus pattern (39 bp):
CCGGATATAACCACTGCACGAATGCCTTCGGGTCTTAGC
Found at i:42957326 original size:16 final size:16
Alignment explanation
Indices: 42957307--42957337 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42957297 CTTCTTCACT
42957307 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
42957323 TACTTACTTACTTAA
1 TACTCACTTACTTAA
42957338 TCAAATTTAC
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:42957343 original size:20 final size:20
Alignment explanation
Indices: 42957304--42957343 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42957294 AAACTTCTTC
* *
42957304 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
42957324 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
42957344 TTACTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:42957718 original size:55 final size:55
Alignment explanation
Indices: 42957588--42957780 Score: 227
Period size: 55 Copynumber: 3.5 Consensus size: 55
42957578 CTTACCATTG
* *
42957588 CCATGTCTCGACATGGTCTTACATGGTATCCTTT-CCTTATG-AACTTATCAATG
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTTGCCTTATGTAACTTATCAATT
* *
42957641 CCAT-TCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATAGTAACTTATCAATT
1 CCATGT-CTTGACATGGTCTTACATGGTATCCTTTGCCTTAT-GTAACTTATCAATT
* *
42957696 CCATGTCTTGACATGGTTTTACATGGTATCC-TTGCCTTAT-TAACCTTACCAATT
1 CCATGTCTTGACATGGTCTTACATGGTATCCTTTGCCTTATGTAA-CTTATCAATT
* * *
42957750 GCCATGCCTTGGCCTGGTCTTACATGGTATC
1 -CCATGTCTTGACATGGTCTTACATGGTATC
42957781 GTTAAACCCT
Statistics
Matches: 120, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
52 6 0.05
53 32 0.27
54 10 0.08
55 69 0.57
56 3 0.03
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (55 bp):
CCATGTCTTGACATGGTCTTACATGGTATCCTTTGCCTTATGTAACTTATCAATT
Found at i:42960256 original size:21 final size:21
Alignment explanation
Indices: 42960231--42960281 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
42960221 GCAAGCTCTA
42960231 AATCATGTGTCGGATAGTTCT
1 AATCATGTGTCGGATAGTTCT
42960252 AATCATGTGTCGGATAGTTCT
1 AATCATGTGTCGGATAGTTCT
**
42960273 TCTCATGTG
1 AATCATGTG
42960282 GCTTTAGCTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.39
Consensus pattern (21 bp):
AATCATGTGTCGGATAGTTCT
Found at i:42972981 original size:217 final size:217
Alignment explanation
Indices: 42972585--42973017 Score: 776
Period size: 217 Copynumber: 2.0 Consensus size: 217
42972575 AAATTAATCG
*
42972585 TTTTTGATTTAGTTTGCTAGTAGTTATGACTAAGATTATTAATTTTAATTTATTACTTTTTCCTT
1 TTTTTGATTTAGTTTGCTAGTAGTTATGACTAAGATTATTAATTTTAATTTATTACTTTTGCCTT
42972650 TTTAAATTTGTTTTCATCTTACCTTGAACATTCATCACGACAAATTAATGGTTTTGCTTACAGGT
66 TTTAAATTTGTTTTCATCTTACCTTGAACATTCATCACGACAAATTAATGGTTTTGCTTACAGGT
* * *
42972715 ATACTATGTCGTCCTCAAGAGGAAAGAAAGTCGTCGTCCCTACTTCGAAGAACAGGAAGGGATCA
131 ATACTATGTCGTCCTCAAGAGGAAAGAAAGCCGCCATCCCTACTTCGAAGAACAGGAAGGGATCA
*
42972780 TCATCTTCCTCGGGTCCTATCA
196 TCATCTTCCTCGGGTCATATCA
*
42972802 TTTTTTATTTAGTTTGCTAGTAGTTATGACTAAGATTATTAATTTTAATTTATTACTTTTGCCTT
1 TTTTTGATTTAGTTTGCTAGTAGTTATGACTAAGATTATTAATTTTAATTTATTACTTTTGCCTT
*
42972867 TTTAAATTTGTTTTCATCTTACCTTGAACATTCATCACGGCAAATTAATGGTTTTGCTTACAGGT
66 TTTAAATTTGTTTTCATCTTACCTTGAACATTCATCACGACAAATTAATGGTTTTGCTTACAGGT
* * *
42972932 ATACTATGTCGTCTTCACGAGGAAAGAAAGCCGCCATCCCTATTTCGAAGAACAGGAAGGGATCA
131 ATACTATGTCGTCCTCAAGAGGAAAGAAAGCCGCCATCCCTACTTCGAAGAACAGGAAGGGATCA
42972997 TCATCTTCCTCGGGTCATATC
196 TCATCTTCCTCGGGTCATATC
42973018 GCAGAAATTT
Statistics
Matches: 206, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
217 206 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.40
Consensus pattern (217 bp):
TTTTTGATTTAGTTTGCTAGTAGTTATGACTAAGATTATTAATTTTAATTTATTACTTTTGCCTT
TTTAAATTTGTTTTCATCTTACCTTGAACATTCATCACGACAAATTAATGGTTTTGCTTACAGGT
ATACTATGTCGTCCTCAAGAGGAAAGAAAGCCGCCATCCCTACTTCGAAGAACAGGAAGGGATCA
TCATCTTCCTCGGGTCATATCA
Found at i:42982559 original size:46 final size:46
Alignment explanation
Indices: 42982451--42982673 Score: 159
Period size: 46 Copynumber: 4.7 Consensus size: 46
42982441 TCATTGGTTT
* *
42982451 GAGCCAGTGTAAGACTATATTTGGGACATGGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGAC-ATGTCTGGGACAT-GCATCGGCATTGAGACGA
* * * *
42982499 GTGCTAGTGTAAGACATGTCTGGGACATGCATTGGCCTTGAGACGTA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACG-A
* *
42982546 -AGCCAGTGCAAGACATGTCTGGGATATGCATCGGC--T-ACGA-GA
1 GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGA-GACGA
* * * * * * * *
42982588 TGTGTCACTGTAAGACCATGTCTGGGACGTGGCATCAGCCTCGATGATGA
1 -GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCATTGA-GACGA
* *
42982638 TAGCCAGTGTAAGACCATGTCCGGGACATGGCATCG
1 GAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCG
42982674 ATAACTTACC
Statistics
Matches: 138, Mismatches: 27, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
42 1 0.01
43 2 0.01
44 12 0.09
45 12 0.09
46 52 0.38
47 12 0.09
48 13 0.09
49 32 0.23
50 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.23
Consensus pattern (46 bp):
GAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCATTGAGACGA
Found at i:42984580 original size:23 final size:23
Alignment explanation
Indices: 42984518--42984630 Score: 95
Period size: 23 Copynumber: 4.8 Consensus size: 23
42984508 GAGCCATGAT
*
42984518 CGGTAAGCTCCTCCTGAGCTGATAA
1 CGGTAAGCT-CTACTGAGCTGA-AA
* * *
42984543 GCAGTATGCTCTATTGAGCTGAAA
1 -CGGTAAGCTCTACTGAGCTGAAA
*
42984567 CGGTAAGCTCTATTGAGCTG-AA
1 CGGTAAGCTCTACTGAGCTGAAA
*
42984589 CAGTAAGCTCATACT-AGCTGAAA
1 CGGTAAGCTC-TACTGAGCTGAAA
* * *
42984612 TGGTAAGCTCCAATGAGCT
1 CGGTAAGCTCTACTGAGCT
42984631 AAAAATAGTA
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
22 18 0.25
23 35 0.49
24 2 0.03
25 10 0.14
26 7 0.10
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (23 bp):
CGGTAAGCTCTACTGAGCTGAAA
Found at i:42984597 original size:22 final size:23
Alignment explanation
Indices: 42984532--42984656 Score: 94
Period size: 23 Copynumber: 5.3 Consensus size: 23
42984522 AAGCTCCTCC
*
42984532 TGAGCTGATAAGCAGTATGCTCTAT
1 TGAGCTGA-AA-CAGTAAGCTCTAT
*
42984557 TGAGCTGAAACGGTAAGCTCTAT
1 TGAGCTGAAACAGTAAGCTCTAT
*
42984580 TGAGCTG-AACAGTAAGCTCATAC
1 TGAGCTGAAACAGTAAGCTC-TAT
** * *
42984603 T-AGCTGAAATGGTAAGCTCCAA
1 TGAGCTGAAACAGTAAGCTCTAT
* * *
42984625 TGAGCTAAAAATAGTAAGCCCT-T
1 TGAGCT-GAAACAGTAAGCTCTAT
42984648 ATGAGCTGA
1 -TGAGCTGA
42984657 TATATCGGTA
Statistics
Matches: 81, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
22 18 0.22
23 36 0.44
24 19 0.23
25 8 0.10
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (23 bp):
TGAGCTGAAACAGTAAGCTCTAT
Found at i:42986281 original size:694 final size:694
Alignment explanation
Indices: 42984952--42986341 Score: 2681
Period size: 694 Copynumber: 2.0 Consensus size: 694
42984942 ACCGATCTAG
42984952 TTCCAAAATTTGCTTATATTGATCTTAATCAAGCCAAATATGTGCCAAAATCATGGAAGCTTCAA
1 TTCCAAAATTTGCTTATATTGATCTTAATCAAGCCAAATATGTGCCAAAATCATGGAAGCTTCAA
*
42985017 ACCCTTATTTTTCTTTCTCAATTTCGGCAATATAGATGGAAGATGATGAATAAAATGATTTTGGT
66 ACCCTTATTTTTCTTTCTCAATTTCGGCAATATAAATGGAAGATGATGAATAAAATGATTTTGGT
42985082 TTTATTTATTATTAACTTAATACATAAATTACTATATTAACCTTAGTAATAAAACATTTAAATCA
131 TTTATTTATTATTAACTTAATACATAAATTACTATATTAACCTTAGTAATAAAACATTTAAATCA
42985147 TCAAATATAAGGTTATCTATGTCAAGTTCCACTATCAATGGTCTAATAACATCTTAAGGACCTCT
196 TCAAATATAAGGTTATCTATGTCAAGTTCCACTATCAATGGTCTAATAACATCTTAAGGACCTCT
42985212 CATTTATTATGGTTTAAACACCTTTAACAATTAGAACTCAACATTTACGCATTACGCGATTTAAT
261 CATTTATTATGGTTTAAACACCTTTAACAATTAGAACTCAACATTTACGCATTACGCGATTTAAT
42985277 CCTTTTTACCGAATTAAGCATTTAAACGGTAAAATTTCTTAACGAAATTTTCATATAATAATTCT
326 CCTTTTTACCGAATTAAGCATTTAAACGGTAAAATTTCTTAACGAAATTTTCATATAATAATTCT
*
42985342 ATCATGCTGTAAACCCTAATAAAATAATAAAATAAAAAATTTAACCTCAAATTTATGATCCCAAA
391 ATCATGCTGTAAAACCTAATAAAATAATAAAATAAAAAATTTAACCTCAAATTTATGATCCCAAA
* * *
42985407 ACCACTTTTTCAATTTGACATAAAAACAGACTGTTACAGAAATGGCTGAGTAAAAGTACTCAATT
456 ACCACTTTTTCAATTTGAAAAAAAAACAGACTGTTACAGAAATGGCTCAGTAAAAGTACTCAATT
*
42985472 TTAGTAAAGGATAAAAACCTATTTGTATCTTATTTTATTTAATCAATTTGATTATCATTAAAAAA
521 TTAGTAAAGGATAAAAACCCATTTGTATCTTATTTTATTTAATCAATTTGATTATCATTAAAAAA
42985537 CTAGAGTATGTTTCTAATGAGTTCTACCAAAATCTTTATCTTTACGATTTGAAGTTGGTCTAGGG
586 CTAGAGTATGTTTCTAATGAGTTCTACCAAAATCTTTATCTTTACGATTTGAAGTTGGTCTAGGG
*
42985602 ACTACATTGCTAGGTTTTAAGCCATTTGGAAACTAAATTTATTT
651 ACTACATTGCTAGGTTTTAAGCCATTTGGAAACCAAATTTATTT
42985646 TTCCAAAATTTGCTTATATTGATCTTAATCAAGCCAAATATGTGCCAAAATCATGGAAGCTTCAA
1 TTCCAAAATTTGCTTATATTGATCTTAATCAAGCCAAATATGTGCCAAAATCATGGAAGCTTCAA
42985711 ACCCTTATTTTTCTTTCTCAATTTCGGCAATATAAATGGAAGATGATGAATAAAATGATTTTGGT
66 ACCCTTATTTTTCTTTCTCAATTTCGGCAATATAAATGGAAGATGATGAATAAAATGATTTTGGT
42985776 TTTATTTATTATTAACTTAATACATAAATTACTATATTAACCTTAGTAATAAAACATTTAAATCA
131 TTTATTTATTATTAACTTAATACATAAATTACTATATTAACCTTAGTAATAAAACATTTAAATCA
42985841 TCAAATATAAGGTTATCTATGTCAAGTTCCACTATCAATGGTCTAATAACATCTTAAGGACCTCT
196 TCAAATATAAGGTTATCTATGTCAAGTTCCACTATCAATGGTCTAATAACATCTTAAGGACCTCT
*
42985906 CATTTATTATGGTTTAAACACCTTTAACAATTAGAACTCAACATTTACGCATTACGCGATTTAGT
261 CATTTATTATGGTTTAAACACCTTTAACAATTAGAACTCAACATTTACGCATTACGCGATTTAAT
42985971 CCTTTTTACCGAATTAAGCATTTAAACGGTAAAATTTCTTAACGAAATTTTCATATAATAATTCT
326 CCTTTTTACCGAATTAAGCATTTAAACGGTAAAATTTCTTAACGAAATTTTCATATAATAATTCT
*
42986036 ATCATGCTGTAAAACCTATTAAAATAATAAAATAAAAAATTTAACCTCAAATTTATGATCCCAAA
391 ATCATGCTGTAAAACCTAATAAAATAATAAAATAAAAAATTTAACCTCAAATTTATGATCCCAAA
*
42986101 ACTACTTTTTCAATTTGAAAAAAAAACAGACTGTTACAGAAATGGCTCAGTAAAAGTACTCAATT
456 ACCACTTTTTCAATTTGAAAAAAAAACAGACTGTTACAGAAATGGCTCAGTAAAAGTACTCAATT
*
42986166 TTAGTAAAGGATAAAAACCCATTTGTATCTTATTTTATTTAATCAATTTGATTGTCATTAAAAAA
521 TTAGTAAAGGATAAAAACCCATTTGTATCTTATTTTATTTAATCAATTTGATTATCATTAAAAAA
42986231 CTAGAGTATGTTTCTAATGAGTTCTACCAAAATCTTTATCTTTACGATTTGAAGTTGGTCTAGGG
586 CTAGAGTATGTTTCTAATGAGTTCTACCAAAATCTTTATCTTTACGATTTGAAGTTGGTCTAGGG
42986296 ACTACATTGCTAGGTTTTAAGCCATTTGGAAACCAAATTTATTT
651 ACTACATTGCTAGGTTTTAAGCCATTTGGAAACCAAATTTATTT
42986340 TT
1 TT
42986342 TAGTTGAAAT
Statistics
Matches: 685, Mismatches: 11, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
694 685 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (694 bp):
TTCCAAAATTTGCTTATATTGATCTTAATCAAGCCAAATATGTGCCAAAATCATGGAAGCTTCAA
ACCCTTATTTTTCTTTCTCAATTTCGGCAATATAAATGGAAGATGATGAATAAAATGATTTTGGT
TTTATTTATTATTAACTTAATACATAAATTACTATATTAACCTTAGTAATAAAACATTTAAATCA
TCAAATATAAGGTTATCTATGTCAAGTTCCACTATCAATGGTCTAATAACATCTTAAGGACCTCT
CATTTATTATGGTTTAAACACCTTTAACAATTAGAACTCAACATTTACGCATTACGCGATTTAAT
CCTTTTTACCGAATTAAGCATTTAAACGGTAAAATTTCTTAACGAAATTTTCATATAATAATTCT
ATCATGCTGTAAAACCTAATAAAATAATAAAATAAAAAATTTAACCTCAAATTTATGATCCCAAA
ACCACTTTTTCAATTTGAAAAAAAAACAGACTGTTACAGAAATGGCTCAGTAAAAGTACTCAATT
TTAGTAAAGGATAAAAACCCATTTGTATCTTATTTTATTTAATCAATTTGATTATCATTAAAAAA
CTAGAGTATGTTTCTAATGAGTTCTACCAAAATCTTTATCTTTACGATTTGAAGTTGGTCTAGGG
ACTACATTGCTAGGTTTTAAGCCATTTGGAAACCAAATTTATTT
Found at i:42989011 original size:139 final size:140
Alignment explanation
Indices: 42988745--42989162 Score: 784
Period size: 139 Copynumber: 3.0 Consensus size: 140
42988735 TAAATTGTGA
42988745 CCTTGGGTTAGGCTCAAAAATAATAAAAGGGGGTGAATTGGTATCTTAGAAATATTTGGAAACTT
1 CCTTGGGTTAGGCTCAAAAATAATAAAAGGGGGTGAATTGGTATCTTAGAAATATTTGGAAACTT
*
42988810 TTCCAAATGATAAGGAAACGGAAGAAAAATTTGGACAATTCGTTTTTTAGTGGTTTGGCTCCAAT
66 TTCCAAATGATAAGGAAACGGAAGAAAAATTTGGACAATTCGATTTTTAGTGGTTTGGCTCCAAT
42988875 TGTCTACCTC
131 TGTCTACCTC
42988885 CCTTGGGTTAGGCTCAAAAATAATAAAAGGGGGTGAATTGGTATCTTAGAAATATTTGG-AACTT
1 CCTTGGGTTAGGCTCAAAAATAATAAAAGGGGGTGAATTGGTATCTTAGAAATATTTGGAAACTT
*
42988949 TTCCAAATGATAAGGAAACGAAAGAAAAATTTGGACAATTCGATTTTTAGTGGTTTGGCTCCAAT
66 TTCCAAATGATAAGGAAACGGAAGAAAAATTTGGACAATTCGATTTTTAGTGGTTTGGCTCCAAT
42989014 TGTCTACCTC
131 TGTCTACCTC
*
42989024 CCTTGGGTTAGGCTCAAAAATAATAAAATGGGGTGAATTGGTATCTTAGAAATATTTGGAAACTT
1 CCTTGGGTTAGGCTCAAAAATAATAAAAGGGGGTGAATTGGTATCTTAGAAATATTTGGAAACTT
*
42989089 TTCCAAATGATAAGGAAACGGAAGAAAAATTTGGACAATCCGATTTTTAGTGGTTTGGCTCCAAT
66 TTCCAAATGATAAGGAAACGGAAGAAAAATTTGGACAATTCGATTTTTAGTGGTTTGGCTCCAAT
*
42989154 TCTCTACCT
131 TGTCTACCT
42989163 TTACTACATT
Statistics
Matches: 271, Mismatches: 6, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
139 136 0.50
140 135 0.50
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.32
Consensus pattern (140 bp):
CCTTGGGTTAGGCTCAAAAATAATAAAAGGGGGTGAATTGGTATCTTAGAAATATTTGGAAACTT
TTCCAAATGATAAGGAAACGGAAGAAAAATTTGGACAATTCGATTTTTAGTGGTTTGGCTCCAAT
TGTCTACCTC
Found at i:42994833 original size:37 final size:37
Alignment explanation
Indices: 42994774--42994856 Score: 130
Period size: 37 Copynumber: 2.2 Consensus size: 37
42994764 AGCTCAGATG
* *
42994774 AAATCTCCACATGAAGTTATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
*
42994811 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
*
42994848 TAATCTCCA
1 AAATCTCCA
42994857 AGTTTCATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.29, C:0.30, G:0.17, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGAAGTCATCGGGTCTTACCCGGACA
Found at i:42995047 original size:48 final size:48
Alignment explanation
Indices: 42994992--42995236 Score: 436
Period size: 48 Copynumber: 5.1 Consensus size: 48
42994982 ACACATCGCC
* *
42994992 TACATATTTCATACTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
42995040 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
*
42995088 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACTTATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
42995136 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
* * *
42995184 TACATATTTCACATTATCCATTCGGCTTTACAACATATACATATCTTA
1 TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
42995232 TACAT
1 TACAT
42995237 CAATTTCAGC
Statistics
Matches: 190, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
48 190 1.00
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (48 bp):
TACATATTTCACATTAGCCATTCGGCTTTACCACATATACATATCTCA
Found at i:42997861 original size:87 final size:87
Alignment explanation
Indices: 42997715--42997956 Score: 295
Period size: 87 Copynumber: 2.8 Consensus size: 87
42997705 ATGATGTATC
* * *
42997715 GACGACCATCGAATATGAAAAGGGATAGTTTCAACTACAGGCTATGGAAAGGGATGGTGACGACC
1 GACGACCATCGAATATGAAAAGGGATAGTTTCAACTATAGACTATGAAAAGGGATGGTGACGACC
*
42997780 ATCAACTACGAAAAGGGATGGT
66 ATCAACTACGAAAAAGGATGGT
* * * *
42997802 GACGACCATCGAATATGAAAAAGGATAGTTTCGACTATTGACTATGAAAAGGGATGGTGACAACC
1 GACGACCATCGAATATGAAAAGGGATAGTTTCAACTATAGACTATGAAAAGGGATGGTGACGACC
*
42997867 ATCAACTATGAAAAAGGATGGT
66 ATCAACTACGAAAAAGGATGGT
* * ** * ** * * * * *
42997889 GACAACAATTAAATATGAAAAGGGATGGTGACAACCATCGAATACGAAAAGGGATGGTTACGACC
1 GACGACCATCGAATATGAAAAGGGATAGTTTCAACTATAGACTATGAAAAGGGATGGTGACGACC
42997954 ATC
66 ATC
42997957 GTTAGCACAT
Statistics
Matches: 131, Mismatches: 24, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
87 131 1.00
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (87 bp):
GACGACCATCGAATATGAAAAGGGATAGTTTCAACTATAGACTATGAAAAGGGATGGTGACGACC
ATCAACTACGAAAAAGGATGGT
Found at i:42997957 original size:29 final size:29
Alignment explanation
Indices: 42997715--42997957 Score: 213
Period size: 29 Copynumber: 8.4 Consensus size: 29
42997705 ATGATGTATC
*
42997715 GACGACCATCGAATATGAAAAGGGATAGT
1 GACGACCATCGAATATGAAAAGGGATGGT
** * * ** *
42997744 TTCAACTA-CAGGCTATGGAAAGGGATGGT
1 GACGACCATC-GAATATGAAAAGGGATGGT
*
42997773 GACGACCATC-AACTACGAAAAGGGATGGT
1 GACGACCATCGAA-TATGAAAAGGGATGGT
* *
42997802 GACGACCATCGAATATGAAAAAGGATAGT
1 GACGACCATCGAATATGAAAAGGGATGGT
** * * *
42997831 TTCGACTATTGACTATGAAAAGGGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
* *
42997860 GACAACCATC-AACTATGAAAAAGGATGGT
1 GACGACCATCGAA-TATGAAAAGGGATGGT
* * **
42997889 GACAACAATTAAATATGAAAAGGGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
* *
42997918 GACAACCATCGAATACGAAAAGGGATGGT
1 GACGACCATCGAATATGAAAAGGGATGGT
*
42997947 TACGACCATCG
1 GACGACCATCG
42997958 TTAGCACATT
Statistics
Matches: 166, Mismatches: 42, Indels: 12
0.75 0.19 0.05
Matches are distributed among these distances:
28 2 0.01
29 159 0.96
30 5 0.03
ACGTcount: A:0.40, C:0.15, G:0.26, T:0.19
Consensus pattern (29 bp):
GACGACCATCGAATATGAAAAGGGATGGT
Found at i:42999512 original size:23 final size:23
Alignment explanation
Indices: 42999476--42999537 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
42999466 TATTTGGGAG
* * * *
42999476 AAGAGGCAACCAAGGGAACTACC
1 AAGAGGAAATCAAGGAAACCACC
*
42999499 AAGAGGAAATCAAGGAAACCACT
1 AAGAGGAAATCAAGGAAACCACC
*
42999522 AGGAGGAAATCAAGGA
1 AAGAGGAAATCAAGGA
42999538 TACATGGGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.48, C:0.18, G:0.27, T:0.06
Consensus pattern (23 bp):
AAGAGGAAATCAAGGAAACCACC
Found at i:43007521 original size:49 final size:49
Alignment explanation
Indices: 43007359--43007596 Score: 271
Period size: 49 Copynumber: 4.8 Consensus size: 49
43007349 TGAGGTCGCA
* * * *
43007359 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAAACTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAA-T-TGGTCACG
* * * **
43007410 TGTGTCGTACTAAGTGCAGGCTACTACT-TGTATCAAATGGTTAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTA-TGTGTACCAGATAATT-GGTCACG
* *
43007460 TGTGTAGTACTAAGTGCAGGTTACTATGTGTACCGGATAATTGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACG
* * * * *
43007509 TTTGTAGTACTAAGTGCAGGCTACTACGTGTAGCAGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACG
* *
43007558 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATA
43007597 GCTTTGGTTA
Statistics
Matches: 156, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
49 85 0.54
50 40 0.26
51 30 0.19
52 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAATTGGTCACG
Found at i:43016738 original size:125 final size:125
Alignment explanation
Indices: 43016516--43016763 Score: 399
Period size: 125 Copynumber: 2.0 Consensus size: 125
43016506 AAGGCAATGC
*
43016516 TTTTGTTTCTCAATTGTTTAACTTCTCGTGCCAAAATCTTAACTTGCTCCTCACCATAAGTCATA
1 TTTTGTTTCTCAATTGTTTAACTTCTCGTGCCAAAATCTTAACCTGCTCCTCACCATAAGTCATA
*
43016581 TCCGGTCGAATCTCAACTGCTGTCAATGAAATCACATGTGAAGGATCTGATGTATATCGG
66 TCCGGTCGAATCTCAACTGCTGTCAATGAAATCACATGTGAAGGATCTGATCTATATCGG
*
43016641 TTTTGTTTCTCAATTGTTTAACTTCTCGCT-CCAAAATCTTAACCTGTTCCTCACCATAAGTCAT
1 TTTTGTTTCTCAATTGTTTAACTTCTCG-TGCCAAAATCTTAACCTGCTCCTCACCATAAGTCAT
* * * * **
43016705 ATCTGGTTGAATCTTAACTTCTGTCGGTGAAATCACATGTGAAGGATCTGATCTATATC
65 ATCCGGTCGAATCTCAACTGCTGTCAATGAAATCACATGTGAAGGATCTGATCTATATC
43016764 CGCGCAACAT
Statistics
Matches: 113, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
125 112 0.99
126 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (125 bp):
TTTTGTTTCTCAATTGTTTAACTTCTCGTGCCAAAATCTTAACCTGCTCCTCACCATAAGTCATA
TCCGGTCGAATCTCAACTGCTGTCAATGAAATCACATGTGAAGGATCTGATCTATATCGG
Found at i:43017609 original size:9 final size:9
Alignment explanation
Indices: 43017595--43017622 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
43017585 AGGAAAGAAT
43017595 CAACAAAAA
1 CAACAAAAA
43017604 CAACAAAAA
1 CAACAAAAA
43017613 CAACAAAAA
1 CAACAAAAA
43017622 C
1 C
43017623 CAAGAGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.75, C:0.25, G:0.00, T:0.00
Consensus pattern (9 bp):
CAACAAAAA
Found at i:43018901 original size:21 final size:21
Alignment explanation
Indices: 43018833--43018901 Score: 59
Period size: 21 Copynumber: 3.1 Consensus size: 21
43018823 AACTCACTGA
43018833 GTTGTGGTCTGAGTTCATGAT
1 GTTGTGGTCTGAGTTCATGAT
* * *
43018854 ATATGTGACATCTGAGCTCATTG-T
1 GT-TGTG--GTCTGAGTTCA-TGAT
*
43018878 GTTGTGGTTTGAGTTCATGAT
1 GTTGTGGTCTGAGTTCATGAT
43018899 GTT
1 GTT
43018902 TGTTGCACAA
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
20 2 0.06
21 13 0.36
22 4 0.11
23 4 0.11
24 11 0.31
25 2 0.06
ACGTcount: A:0.17, C:0.10, G:0.29, T:0.43
Consensus pattern (21 bp):
GTTGTGGTCTGAGTTCATGAT
Found at i:43023198 original size:40 final size:40
Alignment explanation
Indices: 43023143--43023318 Score: 259
Period size: 40 Copynumber: 4.4 Consensus size: 40
43023133 GATGATAACT
* *
43023143 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-ATTCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATA-TCC
43023183 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* *
43023223 GGGCTAAGTCCCAAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
*
43023263 GGGCTAAGTCCCGAAGGCATTTGAGCGAG-TAGCTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
*
43023303 -GGCTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
43023319 TACTTGGTTT
Statistics
Matches: 126, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
39 17 0.13
40 108 0.86
41 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:43028676 original size:27 final size:27
Alignment explanation
Indices: 43028619--43028676 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
43028609 ACCCCTAATC
* * *
43028619 GATAAAATGATTATTATGCCCCTGCGT
1 GATAAAATGACTATTATGCCCCTACGA
* * *
43028646 GATAAAATGACTGTTATGCGCCTATGA
1 GATAAAATGACTATTATGCCCCTACGA
43028673 GATA
1 GATA
43028677 TATAATTATA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (27 bp):
GATAAAATGACTATTATGCCCCTACGA
Found at i:43029378 original size:18 final size:19
Alignment explanation
Indices: 43029355--43029390 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
43029345 TAGGAACTCG
43029355 TGTTTTAAAAAG-AAACAA
1 TGTTTTAAAAAGTAAACAA
*
43029373 TGTTTTACAAAGTAAACA
1 TGTTTTAAAAAGTAAACA
43029391 CAAGAACGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.50, C:0.08, G:0.11, T:0.31
Consensus pattern (19 bp):
TGTTTTAAAAAGTAAACAA
Done.