Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 156 of 444
Found at i:42576979 original size:41 final size:41
Alignment explanation
Indices: 42576903--42576980 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
42576893 CGGAGGAAGA
* * *
42576903 AATTGAGGGTTGCATAGTTGCTTGACGACTATGGATCCACC
1 AATTGAGGATCGCATAGTTGCTTGACGACCATGGATCCACC
* * *
42576944 AATTGAGGATCGCATGGTTGCTTGATGACCGTGGATC
1 AATTGAGGATCGCATAGTTGCTTGACGACCATGGATC
42576981 TACCGGTGGC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.29
Consensus pattern (41 bp):
AATTGAGGATCGCATAGTTGCTTGACGACCATGGATCCACC
Found at i:42577179 original size:22 final size:22
Alignment explanation
Indices: 42577127--42577191 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
42577117 GCCAATTATT
**
42577127 CTGATTATGGCTTTACGCCAAC
1 CTGATTATGGCTTTGTGCCAAC
*
42577149 CT-ACATATGGCTTTGTGCCAAC
1 CTGA-TTATGGCTTTGTGCCAAC
*
42577171 CTGATTATGGCTGTGTGCCAA
1 CTGATTATGGCTTTGTGCCAA
42577192 ACGTATTTAC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 1 0.03
22 34 0.94
23 1 0.03
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.32
Consensus pattern (22 bp):
CTGATTATGGCTTTGTGCCAAC
Found at i:42582905 original size:28 final size:28
Alignment explanation
Indices: 42582859--42582927 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
42582849 TTTAAAACCC
*
42582859 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
42582886 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
42582914 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
42582928 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:42584577 original size:20 final size:20
Alignment explanation
Indices: 42584554--42584591 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42584544 CACATCCAAA
*
42584554 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
42584574 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
42584592 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:42590892 original size:28 final size:28
Alignment explanation
Indices: 42590846--42590914 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
42590836 TTTAAAACCC
*
42590846 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
42590873 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
42590901 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
42590915 TGATCTACGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 7 0.17
28 33 0.82
ACGTcount: A:0.19, C:0.10, G:0.28, T:0.43
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:42592564 original size:20 final size:20
Alignment explanation
Indices: 42592541--42592578 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42592531 CACATCCAAA
*
42592541 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
42592561 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
42592579 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:42610410 original size:52 final size:50
Alignment explanation
Indices: 42610314--42610434 Score: 125
Period size: 52 Copynumber: 2.4 Consensus size: 50
42610304 ATTGTGAGAA
* * ** **
42610314 CACATGTGTAGTACTATGTGCAGGCTACTATGTGTTTAAAATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTACAGGCTACTACATGTACAAAATGG--TTAGGT
* * *
42610366 CACGTGTGTAGTACTAAGTACAGGCTACTACATGTACCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTACAGGCTACTACATGTACAAAATGGTTAGGT
* *
42610416 CGCATGAGTAGTACTAAGT
1 CACATGTGTAGTACTAAGT
42610435 GCAAGGTACT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
50 22 0.39
52 35 0.61
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTACAGGCTACTACATGTACAAAATGGTTAGGT
Found at i:42610563 original size:51 final size:51
Alignment explanation
Indices: 42610472--42610596 Score: 155
Period size: 51 Copynumber: 2.5 Consensus size: 51
42610462 TCGATCATAT
* *
42610472 GTGTGGTACTAAGTGCAGGCCACTATGTGTAAAAGATAGCTTTG-GTCACAA
1 GTGTGGTACTATGTGCAGGCCACTATGTGTAAAAGATAGCTTTGACT-ACAA
* * * *
42610523 GTGTGGTACTATGTGAAGGCCACTTTTTG-AAGAAGGTAGCTTTGACTACAA
1 GTGTGGTACTATGTGCAGGCCACTATGTGTAA-AAGATAGCTTTGACTACAA
*
42610574 GGGTGGTACTATGTGCAGGCCAC
1 GTGTGGTACTATGTGCAGGCCAC
42610597 CGGGAATCCG
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
50 2 0.03
51 61 0.95
52 1 0.02
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (51 bp):
GTGTGGTACTATGTGCAGGCCACTATGTGTAAAAGATAGCTTTGACTACAA
Found at i:42615979 original size:2 final size:2
Alignment explanation
Indices: 42615972--42616010 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
42615962 TATAACCAAG
42615972 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42616011 AACCATAAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42619661 original size:50 final size:51
Alignment explanation
Indices: 42619586--42619710 Score: 153
Period size: 50 Copynumber: 2.5 Consensus size: 51
42619576 TTATGCGAAA
* * * * *
42619586 ACATGTGTGGTACTATGTGCAGGCTACTACGTGTACTAGAT-GGTTAGGTC
1 ACATGTGTGGTACTAAGTGCAGGCTACTACGCGTACCAGATAGCTTAGATC
* * * *
42619636 ACATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGCTTCGATC
1 ACATGTGTGGTACTAAGTGCAGGCTACTACGCGTACCAGATAGCTTAGATC
*
42619687 ATATGTGTGGTACTAAGTGCAGGC
1 ACATGTGTGGTACTAAGTGCAGGC
42619711 CACTTTGTGA
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 35 0.56
51 28 0.44
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (51 bp):
ACATGTGTGGTACTAAGTGCAGGCTACTACGCGTACCAGATAGCTTAGATC
Found at i:42621519 original size:40 final size:41
Alignment explanation
Indices: 42621474--42621640 Score: 164
Period size: 40 Copynumber: 4.2 Consensus size: 41
42621464 CGGAATATAA
*
42621474 CCGGATATAATCAAGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
42621514 CCGGATAGAAT-AACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
42621554 CCGGATGT-AGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
42621594 CCGGATATAAT-TTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
42621633 CCGGATAT
1 CCGGATAT
42621641 CATTCAATTT
Statistics
Matches: 105, Mismatches: 19, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
39 17 0.16
40 87 0.83
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (41 bp):
CCGGATATAATCAACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42622489 original size:17 final size:19
Alignment explanation
Indices: 42622466--42622511 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
42622456 AAGAAGCATG
42622466 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
42622484 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
42622502 AATCATGCTC
1 AATCATGCTC
42622512 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:42629764 original size:13 final size:13
Alignment explanation
Indices: 42629746--42629780 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
42629736 GTGTAGACTT
42629746 CACACGCCCAAGG
1 CACACGCCCAAGG
* *
42629759 CACACGCCTAGGG
1 CACACGCCCAAGG
42629772 CACACGCCC
1 CACACGCCC
42629781 GTGCCTGAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.26, C:0.49, G:0.23, T:0.03
Consensus pattern (13 bp):
CACACGCCCAAGG
Found at i:42630825 original size:42 final size:41
Alignment explanation
Indices: 42630757--42630902 Score: 152
Period size: 42 Copynumber: 3.5 Consensus size: 41
42630747 TACCATACCA
*
42630757 ATGCCATATCCTAGATATGGTTTTACATGTAATCTCATATCG
1 ATGCCATATCCTAGATATGGTCTTACATG-AATCTCATATCG
* * ** *
42630799 ATGCCAATAGCCTAGCTAT-GTCTTACACAAAATCTCACATCG
1 ATGCC-ATATCCTAGATATGGTCTTACA-TGAATCTCATATCG
* *
42630841 ATGCCATATCCCAGATATGGTCTTACATGAAGTCTCATATTG
1 ATGCCATATCCTAGATATGGTCTTACATGAA-TCTCATATCG
*
42630883 ATGTCATATTCC-AGATATGG
1 ATGCCATA-TCCTAGATATGG
42630903 CTTTACACAT
Statistics
Matches: 85, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
41 12 0.14
42 59 0.69
43 14 0.16
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (41 bp):
ATGCCATATCCTAGATATGGTCTTACATGAATCTCATATCG
Found at i:42630917 original size:42 final size:41
Alignment explanation
Indices: 42630757--42630919 Score: 125
Period size: 42 Copynumber: 3.9 Consensus size: 41
42630747 TACCATACCA
* * * *
42630757 ATGCCATATCCTAGATATGGTTTTACATGTAA-TCTCATATCG
1 ATGCCATATCCCAGATATGGTCTTACA--CAAGTCTCACATCG
* * * *
42630799 ATGCCAATAGCCTAGCTAT-GTCTTACACAAAATCTCACATCG
1 ATGCC-ATATCCCAGATATGGTCTTACAC-AAGTCTCACATCG
* * *
42630841 ATGCCATATCCCAGATATGGTCTTACATGAAGTCTCATATTG
1 ATGCCATATCCCAGATATGGTCTTACA-CAAGTCTCACATCG
* *
42630883 ATGTCATATTCCAGATATGG-CTTTACACATAGTCTCA
1 ATGCCATATCCCAGATATGGTC-TTACACA-AGTCTCA
42630920 GTAGCCCTAA
Statistics
Matches: 99, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
41 14 0.14
42 74 0.75
43 11 0.11
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (41 bp):
ATGCCATATCCCAGATATGGTCTTACACAAGTCTCACATCG
Found at i:42630919 original size:84 final size:84
Alignment explanation
Indices: 42630757--42630911 Score: 199
Period size: 84 Copynumber: 1.8 Consensus size: 84
42630747 TACCATACCA
* * * *
42630757 ATGCCATATCCTAGATATGGTTTTACATGTAATCTCATATCGATGCCAATAGCCTAGCTATGTCT
1 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCATATCGATGCCAATAGCCTAGATATGGCT
42630822 TACACAAAATCTCACATCG
66 TACACAAAATCTCACATCG
* * *
42630841 ATGCCATATCCCAGATATGGTCTTACATG-AAGTCTCATATTGATGTC-ATATTCC-AGATATGG
1 ATGCCATATCCCAGATATGGTCTTACATGTAA-TCTCATATCGATGCCAATA-GCCTAGATATGG
42630903 CTTTACACA
64 C-TTACACA
42630912 TAGTCTCAGT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
83 12 0.20
84 49 0.80
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (84 bp):
ATGCCATATCCCAGATATGGTCTTACATGTAATCTCATATCGATGCCAATAGCCTAGATATGGCT
TACACAAAATCTCACATCG
Found at i:42638242 original size:42 final size:42
Alignment explanation
Indices: 42638195--42638302 Score: 117
Period size: 43 Copynumber: 2.5 Consensus size: 42
42638185 TACCTTACTA
* * * **
42638195 ATGCCATATCCCAGATATGGTCTTACATGTAATCTCGTATCG
1 ATGCCATATCACAGATATGGTCTTACACGAAATCTCACATCG
* * * *
42638237 ATGCCAATAGCACAGCTACGGTCTTACACGAAATCTCACATTG
1 ATGCC-ATATCACAGATATGGTCTTACACGAAATCTCACATCG
*
42638280 ATGCCATATCATAGATATGGTCT
1 ATGCCATATCACAGATATGGTCT
42638303 CGTATTGATG
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
42 19 0.37
43 33 0.63
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.30
Consensus pattern (42 bp):
ATGCCATATCACAGATATGGTCTTACACGAAATCTCACATCG
Found at i:42638312 original size:30 final size:30
Alignment explanation
Indices: 42638276--42638332 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
42638266 GAAATCTCAC
*
42638276 ATTGATGCCATATCATAGATATGGTCTCGT
1 ATTGATGCCATATCACAGATATGGTCTCGT
*
42638306 ATTGATGCCATATCCCAGATATGGTCT
1 ATTGATGCCATATCACAGATATGGTCT
42638333 TACACATAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (30 bp):
ATTGATGCCATATCACAGATATGGTCTCGT
Found at i:42640382 original size:26 final size:27
Alignment explanation
Indices: 42640353--42640476 Score: 119
Period size: 27 Copynumber: 4.6 Consensus size: 27
42640343 TTAGTTTACC
*
42640353 AAATTACTGAAATACCCCCAG-TTGTA
1 AAATTACCGAAATACCCCCAGTTTGTA
* * *
42640379 AAATTACC-AAAGTACCCTCGGTTTATA
1 AAATTACCGAAA-TACCCCCAGTTTGTA
* * *
42640406 AAATTACCCAAATATCCTC-GATTTGTA
1 AAATTACCGAAATACCCCCAG-TTTGTA
* *
42640433 AAATTACCGAAATACCCTCAGTTTGCA
1 AAATTACCGAAATACCCCCAGTTTGTA
*
42640460 AAATTACTGAAATACCC
1 AAATTACCGAAATACCC
42640477 TCGACATGTA
Statistics
Matches: 83, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
25 3 0.04
26 15 0.18
27 61 0.73
28 4 0.05
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.28
Consensus pattern (27 bp):
AAATTACCGAAATACCCCCAGTTTGTA
Found at i:42640411 original size:27 final size:26
Alignment explanation
Indices: 42640374--42640507 Score: 135
Period size: 27 Copynumber: 5.0 Consensus size: 26
42640364 ATACCCCCAG
*
42640374 TTGTAAAATTACCAAAGTACCCTCGGT
1 TTGTAAAATTACCAAA-TACCCTCGAT
* *
42640401 TTATAAAATTACCCAAATATCCTCGAT
1 TTGTAAAATTA-CCAAATACCCTCGAT
42640428 TTGTAAAATTACCGAAATACCCTC-AGT
1 TTGTAAAATTACC-AAATACCCTCGA-T
* * *
42640455 TTGCAAAATTACTGAAATACCCTCGAC
1 TTGTAAAATTAC-CAAATACCCTCGAT
* *
42640482 ATGTAAAATTATCAAAGTACCCTCGA
1 TTGTAAAATTACCAAA-TACCCTCGA
42640508 ATTAAAAAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 12
0.79 0.11 0.11
Matches are distributed among these distances:
26 6 0.07
27 77 0.87
28 6 0.07
ACGTcount: A:0.38, C:0.22, G:0.10, T:0.29
Consensus pattern (26 bp):
TTGTAAAATTACCAAATACCCTCGAT
Found at i:42640506 original size:81 final size:80
Alignment explanation
Indices: 42640353--42640507 Score: 179
Period size: 81 Copynumber: 1.9 Consensus size: 80
42640343 TTAGTTTACC
* * ***
42640353 AAATTACTGAAATACCCCCAGTTGTAAAATTACCAAAGTACCCTCGGTTTATAAAATTACCCAAA
1 AAATTACCGAAATACCCCCAGTTGCAAAATTACCAAAGTACCCTCGACATATAAAATTACCCAAA
*
42640418 TATCCTCGATTTGTA
66 TACCCTCGATTTGTA
* * * *
42640433 AAATTACCGAAATACCCTCAGTTTGCAAAATTACTGAAA-TACCCTCGACATGTAAAATTA-TCA
1 AAATTACCGAAATACCCCCAG-TTGCAAAATTAC-CAAAGTACCCTCGACATATAAAATTACCCA
42640496 AAGTACCCTCGA
64 AA-TACCCTCGA
42640508 ATTAAAAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
80 23 0.37
81 36 0.58
82 3 0.05
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.28
Consensus pattern (80 bp):
AAATTACCGAAATACCCCCAGTTGCAAAATTACCAAAGTACCCTCGACATATAAAATTACCCAAA
TACCCTCGATTTGTA
Found at i:42640521 original size:54 final size:54
Alignment explanation
Indices: 42640353--42640522 Score: 184
Period size: 54 Copynumber: 3.2 Consensus size: 54
42640343 TTAGTTTACC
* * * *
42640353 AAATTACTGAAATACCC-CCAGTTGTAAAATTACCAAAGTACCCTCGGTTTATA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTAAA
** * * **
42640406 AAATTACCCAAATATCCTCGATTTGTAAAATTACCGAAA-TACCCTC-AGTTTGCA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACC-AAAGTACCCTCGA-TTTAAA
* * *
42640460 AAATTACTGAAATACCCTCGACATGTAAAATTATCAAAGTACCCTCGAATTAAA
1 AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTAAA
42640514 AAATTACTG
1 AAATTACTG
42640523 TTTTACCCTC
Statistics
Matches: 95, Mismatches: 17, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
53 17 0.18
54 74 0.78
55 4 0.04
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.28
Consensus pattern (54 bp):
AAATTACTGAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTAAA
Found at i:42640529 original size:27 final size:27
Alignment explanation
Indices: 42640499--42641044 Score: 668
Period size: 27 Copynumber: 20.2 Consensus size: 27
42640489 ATTATCAAAG
* *
42640499 TACCCTCGAATTAAAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
42640526 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
42640553 TACCCTCGATTTACAAAATTA-TCGTTT
1 TACCCTCGATTTACAAAATTACT-GTTT
** *
42640580 TACCCTTAATTTACAAAATTATTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
42640607 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
42640634 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
42640661 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * * * *
42640688 TACCCTTGTTTTACAGAGTTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
42640715 TACCCTTGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
42640742 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * * *
42640769 TACCCTCGAATAATAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
42640796 TACCCTTGATTTACAAAATTATTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
42640823 TAGCCTCTATTTA-AAGAATTACAGTTT
1 TACCCTCGATTTACAA-AATTACTGTTT
* *
42640850 TACCCTTGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
42640877 TACCCTCGATTTACAAAATTA-TCGTTT
1 TACCCTCGATTTACAAAATTACT-GTTT
* * *
42640904 TACCCTCGATTGATAGAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
42640931 TACCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
42640958 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
42640985 TACCCTCAATTTAAAAAATTA-TCGTTT
1 TACCCTCGATTTACAAAATTACT-GTTT
* *
42641012 TACCCTCGATTTATAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
42641039 TACCCT
1 TACCCT
42641045 TAGGGTGTTA
Statistics
Matches: 450, Mismatches: 61, Indels: 16
0.85 0.12 0.03
Matches are distributed among these distances:
26 3 0.01
27 443 0.98
28 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTGTTT
Found at i:42641594 original size:12 final size:12
Alignment explanation
Indices: 42641579--42641672 Score: 57
Period size: 12 Copynumber: 7.7 Consensus size: 12
42641569 CCTGATACTT
42641579 ATTCTGATTCTA
1 ATTCTGATTCTA
*
42641591 ATTCTG-TCACCTA
1 ATTCTGAT--TCTA
*
42641604 ATTCTGATTCTG
1 ATTCTGATTCTA
*
42641616 ATTTTGATTCT-
1 ATTCTGATTCTA
* * *
42641627 GTCACCTGATTCTG
1 AT--TCTGATTCTA
*
42641641 ATTCTGATTCTC
1 ATTCTGATTCTA
*
42641653 ATTTTGATTCTA
1 ATTCTGATTCTA
*
42641665 GTTCTGAT
1 ATTCTGAT
42641673 AATGTTTCTT
Statistics
Matches: 62, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
11 2 0.03
12 42 0.68
13 16 0.26
14 2 0.03
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (12 bp):
ATTCTGATTCTA
Found at i:42641613 original size:6 final size:6
Alignment explanation
Indices: 42641604--42641672 Score: 61
Period size: 6 Copynumber: 11.3 Consensus size: 6
42641594 CTGTCACCTA
* * *
42641604 ATTCTG ATTCTG ATTTTG ATTCTG -TCACCTG ATTCTG ATTCTG ATTCTC
1 ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG ATTCTG ATTCTG
*
42641653 ATTTTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG A-TTCTG AT
42641673 AATGTTTCTT
Statistics
Matches: 50, Mismatches: 8, Indels: 10
0.74 0.12 0.15
Matches are distributed among these distances:
5 2 0.04
6 43 0.86
7 4 0.08
8 1 0.02
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.51
Consensus pattern (6 bp):
ATTCTG
Found at i:42641613 original size:19 final size:18
Alignment explanation
Indices: 42641585--42641646 Score: 55
Period size: 19 Copynumber: 3.7 Consensus size: 18
42641575 ACTTATTCTG
*
42641585 ATTCTAATTCTGTCACCT
1 ATTCTGATTCTGTCACCT
42641603 AATTCTGATTCTG--A--T
1 -ATTCTGATTCTGTCACCT
42641618 -TT-TGATTCTGTCACCT
1 ATTCTGATTCTGTCACCT
42641634 GATTCTGATTCTG
1 -ATTCTGATTCTG
42641647 ATTCTCATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 14
0.70 0.02 0.28
Matches are distributed among these distances:
12 8 0.23
13 2 0.06
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 2 0.06
19 19 0.54
ACGTcount: A:0.19, C:0.21, G:0.13, T:0.47
Consensus pattern (18 bp):
ATTCTGATTCTGTCACCT
Found at i:42641614 original size:31 final size:31
Alignment explanation
Indices: 42641579--42641651 Score: 119
Period size: 31 Copynumber: 2.4 Consensus size: 31
42641569 CCTGATACTT
42641579 ATTCTGATTCTAATTCTGTCACCTAATTCTG
1 ATTCTGATTCTAATTCTGTCACCTAATTCTG
* * *
42641610 ATTCTGATTTTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTAATTCTGTCACCTAATTCTG
42641641 ATTCTGATTCT
1 ATTCTGATTCT
42641652 CATTTTGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTAATTCTGTCACCTAATTCTG
Found at i:42643754 original size:27 final size:27
Alignment explanation
Indices: 42643650--42643775 Score: 91
Period size: 27 Copynumber: 4.7 Consensus size: 27
42643640 TTAGTTTACT
* *
42643650 AAATTACTGAAATAGCC-CCAG-TTGTA
1 AAATTACCGAAATA-CCTTCAGTTTGTA
** * *
42643676 AAATTACC-AAAGTACCCCCGGTTTATA
1 AAATTACCGAAA-TACCTTCAGTTTGTA
* *
42643703 AAATTACCCAAATA--TTCTCGATTTGTA
1 AAATTACCGAAATACCTTC-AG-TTTGTA
*
42643730 AAATTACCGAAATACCTTCAGTTTGCA
1 AAATTACCGAAATACCTTCAGTTTGTA
*
42643757 AAATTACTGAAATACCTTC
1 AAATTACCGAAATACCTTC
42643776 GACATGTAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 15
0.76 0.10 0.14
Matches are distributed among these distances:
25 6 0.07
26 13 0.16
27 55 0.68
28 4 0.05
29 3 0.04
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.30
Consensus pattern (27 bp):
AAATTACCGAAATACCTTCAGTTTGTA
Found at i:42643786 original size:27 final size:27
Alignment explanation
Indices: 42643726--42643789 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
42643716 ATTCTCGATT
**
42643726 TGTAAAATTACCGAAATACCTTCAGTT
1 TGTAAAATTACCGAAATACCTTCAGCA
* *
42643753 TGCAAAATTACTGAAATACCTTC-GACA
1 TGTAAAATTACCGAAATACCTTCAG-CA
42643780 TGTAAAATTA
1 TGTAAAATTA
42643790 TCAAAGTACC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
26 1 0.03
27 30 0.97
ACGTcount: A:0.41, C:0.17, G:0.11, T:0.31
Consensus pattern (27 bp):
TGTAAAATTACCGAAATACCTTCAGCA
Found at i:42643826 original size:27 final size:27
Alignment explanation
Indices: 42643796--42644286 Score: 599
Period size: 27 Copynumber: 18.2 Consensus size: 27
42643786 ATTATCAAAG
* * *
42643796 TACCCTCGAATTACAAAATTATTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
*
42643823 TACCCTCGATTTACAGAAGTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
42643850 TACCCTCGATTTAAAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* **
42643877 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
42643904 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
42643931 TACCCTCGATTTACAGAGTTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
42643958 TACCCTCGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
42643985 TACTCTCGATTTATAGAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
*
42644012 TACCCTCGATTGACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
42644039 TAGCCTCGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
42644066 TACCCTCAATTTACATAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
42644093 TACCCTCAATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
42644120 TACTCTCGATTTACAAAATTAGTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* **
42644147 TACCCTCGATTTACAAAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
42644174 TACCCTCGATTGACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
42644201 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
42644228 TA-CCTCGATTTAAAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
**
42644254 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACTGTTT
42644281 TACCCT
1 TACCCT
42644287 TAGGGTGTTA
Statistics
Matches: 408, Mismatches: 53, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
26 24 0.06
27 383 0.94
28 1 0.00
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:42644825 original size:31 final size:31
Alignment explanation
Indices: 42644790--42644893 Score: 122
Period size: 31 Copynumber: 3.4 Consensus size: 31
42644780 TTGCATTCAC
* * *
42644790 ATTCTGATTTTTATTCTGTTACCTGATAT-TG
1 ATTCTGATTCTAATTCTGTCACCTGAT-TCTG
*
42644821 ATTCTGATTCTAATTC-GATCACCTAATTCTG
1 ATTCTGATTCTAATTCTG-TCACCTGATTCTG
*
42644852 ATTCTGATTCTGATTCTGTCACCTGATTCTG
1 ATTCTGATTCTAATTCTGTCACCTGATTCTG
*
42644883 ATTCTAATTCT
1 ATTCTGATTCT
42644894 CATTTTGATT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
30 2 0.03
31 60 0.95
32 1 0.02
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTAATTCTGTCACCTGATTCTG
Found at i:42644828 original size:6 final size:6
Alignment explanation
Indices: 42644819--42644905 Score: 61
Period size: 6 Copynumber: 14.2 Consensus size: 6
42644809 TACCTGATAT
* * *
42644819 TGATTC TGATTC TAATTC -GATCACC TAATTC TGATTC TGATTC TGATTC
1 TGATTC TGATTC TGATTC TGAT--TC TGATTC TGATTC TGATTC TGATTC
* * * *
42644868 TG-TCACC TGATTC TGATTC TAATTC TCATTT TGATTC T
1 TGAT--TC TGATTC TGATTC TGATTC TGATTC TGATTC T
42644906 AGTTCTAATA
Statistics
Matches: 62, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
5 3 0.05
6 52 0.84
7 4 0.06
8 3 0.05
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (6 bp):
TGATTC
Found at i:42648572 original size:16 final size:16
Alignment explanation
Indices: 42648551--42648585 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
42648541 TCGATGATCC
42648551 CGAATCCGATAGCTAA
1 CGAATCCGATAGCTAA
42648567 CGAATCCGATAGCTAA
1 CGAATCCGATAGCTAA
42648583 CGA
1 CGA
42648586 GCAAAATCTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.26, G:0.20, T:0.17
Consensus pattern (16 bp):
CGAATCCGATAGCTAA
Found at i:42649059 original size:40 final size:40
Alignment explanation
Indices: 42648936--42649155 Score: 329
Period size: 40 Copynumber: 5.5 Consensus size: 40
42648926 ACCCAAGTTT
* * * *
42648936 CTTCGGGAT-TTAG-CCGGATATAACCACACGCCCAATTGC
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAATGC
* * *
42648975 CTTCGGGTCTTAACCCGGACATAGCAACT-GCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
42649014 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
42649054 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
*
42649094 CTTCGGGTCTTAACCCGGATATAACAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
*
42649134 CTTCGGGGCTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
42649156 CATTCAAATG
Statistics
Matches: 165, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
38 1 0.01
39 44 0.27
40 120 0.73
ACGTcount: A:0.26, C:0.30, G:0.21, T:0.23
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAATGC
Found at i:42652862 original size:29 final size:29
Alignment explanation
Indices: 42652851--42652952 Score: 186
Period size: 29 Copynumber: 3.5 Consensus size: 29
42652841 TTTCCAGTTT
* *
42652851 GCACACTTAGTGCCAAATATTTCCAGTAC
1 GCACACTTAGTGCCATATATTTCCAGCAC
42652880 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACTTAGTGCCATATATTTCCAGCAC
42652909 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACTTAGTGCCATATATTTCCAGCAC
42652938 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
42652953 ATCTCGTCAC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 71 1.00
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAC
Found at i:42652883 original size:58 final size:58
Alignment explanation
Indices: 42652821--42652952 Score: 165
Period size: 58 Copynumber: 2.3 Consensus size: 58
42652811 CCTCCGAACT
* * *** *
42652821 CGCACACCCAGTGCCGTATTTTTCCAGTTTGCACACTTAGTGCCAAATATTTCCAGTA
1 CGCACACCCAGTGCCATATATTTCCAGCACGCACACTTAGTGCCAAATATTTCCAGCA
** *
42652879 CGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACCCAGTGCCATATATTTCCAGCACGCACACTTAGTGCCAAATATTTCCAGCA
**
42652937 CGCACACTTAGTGCCA
1 CGCACACCCAGTGCCA
42652953 ATCTCGTCAC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 65 1.00
ACGTcount: A:0.26, C:0.31, G:0.15, T:0.28
Consensus pattern (58 bp):
CGCACACCCAGTGCCATATATTTCCAGCACGCACACTTAGTGCCAAATATTTCCAGCA
Found at i:42660126 original size:29 final size:29
Alignment explanation
Indices: 42660066--42660163 Score: 159
Period size: 29 Copynumber: 3.5 Consensus size: 29
42660056 TTTTTCAGTT
*
42660066 GCACACTTAGTGCC--A-ATTTCCAG-TC
1 GCACACTTAGTGCCATATATTTCCAGCAC
42660091 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACTTAGTGCCATATATTTCCAGCAC
42660120 GCACACTTAGTGCCATATATTTCCAGCAC
1 GCACACTTAGTGCCATATATTTCCAGCAC
42660149 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
42660164 ATCTCGTCAC
Statistics
Matches: 68, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
25 14 0.21
27 1 0.01
28 8 0.12
29 45 0.66
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.27
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAC
Found at i:42664960 original size:40 final size:40
Alignment explanation
Indices: 42664903--42665086 Score: 243
Period size: 40 Copynumber: 4.7 Consensus size: 40
42664893 TCGAATGATG
* *
42664903 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* *
42664943 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42664983 TCCGGGCTAAG-CCCGAAGGCA-TTGTGCGAGTTATTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
42665021 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
42665062 -CCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42665087 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
38 25 0.20
39 19 0.15
40 73 0.57
41 10 0.08
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:42665039 original size:78 final size:80
Alignment explanation
Indices: 42664903--42665084 Score: 246
Period size: 78 Copynumber: 2.3 Consensus size: 80
42664893 TCGAATGATG
*
42664903 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
42664968 GTGCGAGTTACTA-A
66 GTGCGAGTTACTATA
* * * **
42664982 TTCCGGGCTAAG-CCCGAAGGCATTGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 -TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAATCCGGACTAAGAT-CCGAAGGCAT
42665044 TTGTGCGAGTTACTATA
64 TTGTGCGAGTTACTATA
* *
42665061 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
42665085 TGAACGAGTA
Statistics
Matches: 91, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
77 1 0.01
78 51 0.56
79 28 0.31
80 11 0.12
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTGTGCTAAGTGACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGTTACTATA
Found at i:42667009 original size:46 final size:46
Alignment explanation
Indices: 42666959--42667134 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
42666949 TGGTTGAGCA
42666959 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42667005 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
42667050 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42667098 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42667135 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:42667115 original size:93 final size:93
Alignment explanation
Indices: 42666956--42667127 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42666946 GGATGGTTGA
* *
42666956 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42667021 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
42667049 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42667114 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
42667128 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42674548 original size:46 final size:46
Alignment explanation
Indices: 42674498--42674673 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
42674488 TGGTTGAGCA
42674498 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42674544 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
42674589 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42674637 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42674674 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:42674654 original size:93 final size:93
Alignment explanation
Indices: 42674495--42674666 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42674485 GGATGGTTGA
* *
42674495 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42674560 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
42674588 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42674653 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
42674667 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42677189 original size:39 final size:39
Alignment explanation
Indices: 42677135--42677260 Score: 180
Period size: 39 Copynumber: 3.2 Consensus size: 39
42677125 TTCAGTGATG
* *
42677135 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCAGGAAT
1 TATATCCGGACTTAGGGTCCGTAGGCTATGTGCTGGAAT
* *
42677174 TATATCCGGACTTAGGGTTCGTAAGCTATGTGCTGGAAT
1 TATATCCGGACTTAGGGTCCGTAGGCTATGTGCTGGAAT
* * *
42677213 TATATCCGGACTTAAGGTCCGTAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAGGGTCCGTAGGCTATGTGCTGGAAT
*
42677252 TATGTCCGG
1 TATATCCGG
42677261 GCTAAAGTCC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (39 bp):
TATATCCGGACTTAGGGTCCGTAGGCTATGTGCTGGAAT
Found at i:42677278 original size:39 final size:39
Alignment explanation
Indices: 42677135--42677278 Score: 128
Period size: 39 Copynumber: 3.7 Consensus size: 39
42677125 TTCAGTGATG
** * * *
42677135 TATATCCGGACTTAGGGTCCGCAGGCTATGTGCAGGAAT
1 TATATCCGGACTTAAAGTCCGCAGGCTACGTGCTGGAAA
** * * * * *
42677174 TATATCCGGACTTAGGGTTCGTAAGCTATGTGCTGGAAT
1 TATATCCGGACTTAAAGTCCGCAGGCTACGTGCTGGAAA
* *
42677213 TATATCCGGACTTAAGGTCCGTAGGCTACGTGCTGGAAA
1 TATATCCGGACTTAAAGTCCGCAGGCTACGTGCTGGAAA
* *
42677252 TATGTCCGGGC-TAAAGTCCCGCAGGCT
1 TATATCCGGACTTAAAGT-CCGCAGGCT
42677279 TCGAGTTGGT
Statistics
Matches: 91, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
38 5 0.05
39 86 0.95
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (39 bp):
TATATCCGGACTTAAAGTCCGCAGGCTACGTGCTGGAAA
Found at i:42678105 original size:2 final size:2
Alignment explanation
Indices: 42678098--42678125 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42678088 ACATACATGC
42678098 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
42678126 GAGCTTACAG
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:42682416 original size:22 final size:22
Alignment explanation
Indices: 42682390--42682433 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42682380 GAAAATAATC
* *
42682390 AAAATTAATCAAAATTTATTAT
1 AAAATCAATCAAAATTCATTAT
*
42682412 AAAATCAATTAAAATTCATTAT
1 AAAATCAATCAAAATTCATTAT
42682434 GTTAATAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.39
Consensus pattern (22 bp):
AAAATCAATCAAAATTCATTAT
Found at i:42685825 original size:28 final size:28
Alignment explanation
Indices: 42685792--42685850 Score: 109
Period size: 28 Copynumber: 2.1 Consensus size: 28
42685782 TTCCTCTTTT
*
42685792 CCTTGAGCTACAATATGCTTATCTTCAA
1 CCTTGAGCTACAAAATGCTTATCTTCAA
42685820 CCTTGAGCTACAAAATGCTTATCTTCAA
1 CCTTGAGCTACAAAATGCTTATCTTCAA
42685848 CCT
1 CCT
42685851 CGACAGCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.27, G:0.10, T:0.34
Consensus pattern (28 bp):
CCTTGAGCTACAAAATGCTTATCTTCAA
Found at i:42688104 original size:13 final size:13
Alignment explanation
Indices: 42688086--42688110 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42688076 CACGCCGGTG
42688086 TGGCTAGACCGTA
1 TGGCTAGACCGTA
42688099 TGGCTAGACCGT
1 TGGCTAGACCGT
42688111 GTGGTCAATT
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:0.20, C:0.24, G:0.32, T:0.24
Consensus pattern (13 bp):
TGGCTAGACCGTA
Found at i:42689582 original size:42 final size:42
Alignment explanation
Indices: 42689476--42689584 Score: 164
Period size: 42 Copynumber: 2.6 Consensus size: 42
42689466 CATCCATTAT
* * * *
42689476 GAACTCGGACCACTCAACGAGCTCGGATGCCATATATATCAT
1 GAACCCGGACCACTCAACGAGTTCGGATGCCACATATATCAC
42689518 GAACCCGGACCACTCAACGAGTTCGGATGCCACATATATCAC
1 GAACCCGGACCACTCAACGAGTTCGGATGCCACATATATCAC
* *
42689560 GAACCTGGACCACTCAAGGAGTTCG
1 GAACCCGGACCACTCAACGAGTTCG
42689585 AACTTCTTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 61 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.18
Consensus pattern (42 bp):
GAACCCGGACCACTCAACGAGTTCGGATGCCACATATATCAC
Found at i:42696592 original size:39 final size:39
Alignment explanation
Indices: 42696538--42696711 Score: 190
Period size: 40 Copynumber: 4.4 Consensus size: 39
42696528 AAACCAAGTA
* * * * *
42696538 CCTTCGGAATTTAGCCAGATATAGCT-ACTTGCTCAAATG
1 CCTTCGGGACTTAGCCGGATATAG-TAACTCGCACAAATG
* *
42696577 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAGTG
1 CCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATG
*
42696617 CCTTCGGGACTTAGCCCGGTTATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAG-CCGGATATAGTAACTCGCACAAATG
* * * *
42696657 CCTTCGGG-CTTAGCCCGAAATTAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCGGATA-TAGTAACTCGCACAAATG
42696696 CCTTCGGGACTTAGCC
1 CCTTCGGGACTTAGCC
42696712 CAGTTATCAT
Statistics
Matches: 118, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
38 4 0.03
39 42 0.36
40 72 0.61
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCGGATATAGTAACTCGCACAAATG
Found at i:42696619 original size:40 final size:40
Alignment explanation
Indices: 42696571--42696718 Score: 219
Period size: 40 Copynumber: 3.7 Consensus size: 40
42696561 GCTACTTGCT
42696571 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
42696611 CAAGTGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
** * *
42696651 CAAATGCCTTCGGG-CTTAGCCC-GAAATTAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTA-TAGTAACTCGCA
*
42696690 CAAATGCCTTCGGGACTTAGCCCAGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
42696719 CATCCGAATA
Statistics
Matches: 97, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
38 2 0.02
39 32 0.33
40 61 0.63
41 2 0.02
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:42696669 original size:79 final size:80
Alignment explanation
Indices: 42696571--42696718 Score: 219
Period size: 79 Copynumber: 1.9 Consensus size: 80
42696561 GCTACTTGCT
** * * *
42696571 CAAATGCCTTCGGGACTTAGCCCG-GTTATAGTAACTCGCACAAGTGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGAAAT-TAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCA
42696635 GTTATAGTAACTCGCA
65 GTTATAGTAACTCGCA
*
42696651 CAAATGCCTTCGGG-CTTAGCCCGAAATTAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCAG
1 CAAATGCCTTCGGGACTTAGCCCGAAATTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCAG
42696715 TTAT
66 TTAT
42696719 CATCCGAATA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
79 46 0.75
80 15 0.25
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAGCCCGAAATTAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCAG
TTATAGTAACTCGCA
Found at i:42703664 original size:14 final size:14
Alignment explanation
Indices: 42703647--42703676 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
42703637 TGATGATTTC
42703647 TACAAAAAGATTGT
1 TACAAAAAGATTGT
42703661 TACAAAAAGATTGT
1 TACAAAAAGATTGT
42703675 TA
1 TA
42703677 AACCTATGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (14 bp):
TACAAAAAGATTGT
Found at i:42710496 original size:63 final size:63
Alignment explanation
Indices: 42710418--42710545 Score: 238
Period size: 63 Copynumber: 2.0 Consensus size: 63
42710408 GTAATTATAA
*
42710418 GTTAAGAAATGTAATTAATCTATCACAATTATGTCATCCTGATTAAAGTCAGCTTTTGAAATC
1 GTTAAGAAATGTAATTAATCTATCACAATTATGTCATCCTGATTAAAATCAGCTTTTGAAATC
*
42710481 GTTAAGAAATGTAATTAATCTATCACAATTATGTCATCTTGATTAAAATCAGCTTTTGAAATC
1 GTTAAGAAATGTAATTAATCTATCACAATTATGTCATCCTGATTAAAATCAGCTTTTGAAATC
42710544 GT
1 GT
42710546 GTATTAGAAC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 63 1.00
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (63 bp):
GTTAAGAAATGTAATTAATCTATCACAATTATGTCATCCTGATTAAAATCAGCTTTTGAAATC
Found at i:42714769 original size:26 final size:26
Alignment explanation
Indices: 42714739--42714790 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
42714729 TAAAGATAAT
42714739 GTATTATTTACATACAAACTTACATA
1 GTATTATTTACATACAAACTTACATA
42714765 GTATTATTTACATACAAACTTACATA
1 GTATTATTTACATACAAACTTACATA
42714791 CTTTCTCATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.15, G:0.04, T:0.38
Consensus pattern (26 bp):
GTATTATTTACATACAAACTTACATA
Found at i:42719951 original size:41 final size:41
Alignment explanation
Indices: 42719867--42720163 Score: 447
Period size: 41 Copynumber: 7.3 Consensus size: 41
42719857 AATTATACAT
* *
42719867 TAGCGGCGTTTTTGACAAAGCGCCG-TTAAAAACAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
42719907 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
*
42719948 TAGCGGCGTTTTTGACAAAGCGCCGCT-AAAAACAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
* * * * *
42719988 TAGCGACATTTTTGGAAAAGCACTGCT-AAAAACAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
42720028 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
* * * *
42720069 TACCGGCGTTTTTGTCAAAGTGCCGCTAAAAAATAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
42720110 TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAAACAGAGCAA
1 TAGCGGCGTTTTTGGCAAAGCGCCGCT-AAAAAACAGAGCAA
*
42720152 TAACGGCGTTTT
1 TAGCGGCGTTTT
42720164 ACCAAAAACG
Statistics
Matches: 231, Mismatches: 23, Indels: 4
0.90 0.09 0.02
Matches are distributed among these distances:
40 93 0.40
41 114 0.49
42 24 0.10
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.20
Consensus pattern (41 bp):
TAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAACAGAGCAA
Found at i:42720041 original size:121 final size:122
Alignment explanation
Indices: 42719875--42720163 Score: 429
Period size: 121 Copynumber: 2.4 Consensus size: 122
42719865 ATTAGCGGCG
* *
42719875 TTTTT-GACAAAGCGCCGTTAAAAACAGAGCAATAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAA
1 TTTTTGGA-AAAGCACCGCTAAAAACAGAGCAATAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAA
*
42719939 ACAGAGCAATAGCGGCGTTTTTGACAAAGCGCCGCT-AAAAACAGAGCAATAGCGACA
65 ACAGAGCAATACCGGCGTTTTTGACAAAGCGCCGCTAAAAAACAGAGCAATAGCGACA
*
42719996 TTTTTGGAAAAGCACTGCTAAAAACAGAGCAATAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAA
1 TTTTTGGAAAAGCACCGCTAAAAACAGAGCAATAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAA
* * * * *
42720061 CAGAGCAATACCGGCGTTTTTGTCAAAGTGCCGCTAAAAAATAGAGCAATAGCGGCG
66 CAGAGCAATACCGGCGTTTTTGACAAAGCGCCGCTAAAAAACAGAGCAATAGCGACA
* * *
42720118 TTTTTGGCAAAGCGCCGCTAAAAAAACAGAGCAATAACGGCGTTTT
1 TTTTTGGAAAAGCACCGCT--AAAAACAGAGCAATAGCGGCGTTTT
42720164 ACCAAAAACG
Statistics
Matches: 151, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
121 91 0.60
122 36 0.24
124 24 0.16
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (122 bp):
TTTTTGGAAAAGCACCGCTAAAAACAGAGCAATAGCGGCGTTTTTGGCAAAGCGCCGCTAAAAAA
CAGAGCAATACCGGCGTTTTTGACAAAGCGCCGCTAAAAAACAGAGCAATAGCGACA
Found at i:42720279 original size:38 final size:39
Alignment explanation
Indices: 42720210--42720287 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 39
42720200 ACCTTAAACC
* * *
42720210 CCCAAAAAAATCATAGACACTAGTCTATATAACCCCTAAA
1 CCCAAAAAAACCATAAACACTAATC-ATATAACCCCTAAA
*
42720250 CCCAAAAAAACCTTAAACACTAATC-TATAACCCCTAAA
1 CCCAAAAAAACCATAAACACTAATCATATAACCCCTAAA
42720288 ACCTTAAACC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 13 0.38
40 21 0.62
ACGTcount: A:0.49, C:0.29, G:0.03, T:0.19
Consensus pattern (39 bp):
CCCAAAAAAACCATAAACACTAATCATATAACCCCTAAA
Found at i:42721162 original size:6 final size:6
Alignment explanation
Indices: 42721146--42721176 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
42721136 ACCCATATGA
*
42721146 TCCCTT CCCCTT TCCCTT TCCCTT TCCCTT T
1 TCCCTT TCCCTT TCCCTT TCCCTT TCCCTT T
42721177 GGTTTTGAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
TCCCTT
Found at i:42721340 original size:2 final size:2
Alignment explanation
Indices: 42721335--42721360 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42721325 TTATTTAAAA
42721335 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
42721361 CAAAATGGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42721843 original size:7 final size:7
Alignment explanation
Indices: 42721831--42721897 Score: 134
Period size: 7 Copynumber: 9.6 Consensus size: 7
42721821 AATCTTTAAA
42721831 AAAATTG
1 AAAATTG
42721838 AAAATTG
1 AAAATTG
42721845 AAAATTG
1 AAAATTG
42721852 AAAATTG
1 AAAATTG
42721859 AAAATTG
1 AAAATTG
42721866 AAAATTG
1 AAAATTG
42721873 AAAATTG
1 AAAATTG
42721880 AAAATTG
1 AAAATTG
42721887 AAAATTG
1 AAAATTG
42721894 AAAA
1 AAAA
42721898 ATAAAAAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 60 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (7 bp):
AAAATTG
Found at i:42721912 original size:22 final size:22
Alignment explanation
Indices: 42721880--42721936 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 22
42721870 TTGAAAATTG
42721880 AAAATTGAAAATTGAAAAA-TAAA
1 AAAATT-AAAATT-AAAAACTAAA
*
42721903 AAAATTAAAATTAAAAACTTAA
1 AAAATTAAAATTAAAAACTAAA
*
42721925 AAACTTAAAATT
1 AAAATTAAAATT
42721937 TTAATATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 5 0.16
22 20 0.65
23 6 0.19
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.26
Consensus pattern (22 bp):
AAAATTAAAATTAAAAACTAAA
Found at i:42722005 original size:16 final size:17
Alignment explanation
Indices: 42721986--42722019 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42721976 ATCAATATTT
42721986 AAAATTT-AAAAAAATA
1 AAAATTTCAAAAAAATA
*
42722002 AAAATTTCAAAAATATA
1 AAAATTTCAAAAAAATA
42722019 A
1 A
42722020 TCTCAGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (17 bp):
AAAATTTCAAAAAAATA
Found at i:42722133 original size:41 final size:41
Alignment explanation
Indices: 42722083--42722207 Score: 155
Period size: 41 Copynumber: 3.1 Consensus size: 41
42722073 ACAAAAAAAT
*
42722083 AAAGTTGAGCAATAGTGGCGTTTTTAGTGAAAACGCCACAA
1 AAAGTTGAGCAATAGTGGCGTTTTTAGTAAAAACGCCACAA
* *
42722124 AAAGTTGAGCTATAGTGGCGTTTTTAGTAAAAACGCTACAA
1 AAAGTTGAGCAATAGTGGCGTTTTTAGTAAAAACGCCACAA
* * * * *
42722165 AAAATTAAG-ATACAGTGGCGTTTTT-GTAAAAATGCCGCAA
1 AAAGTTGAGCA-ATAGTGGCGTTTTTAGTAAAAACGCCACAA
42722205 AAA
1 AAA
42722208 ACTCTACATC
Statistics
Matches: 73, Mismatches: 10, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
40 15 0.21
41 58 0.79
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (41 bp):
AAAGTTGAGCAATAGTGGCGTTTTTAGTAAAAACGCCACAA
Found at i:42727071 original size:19 final size:19
Alignment explanation
Indices: 42727043--42727087 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
42727033 TTATGATATC
42727043 TTTA-TATTTAATTTAATT
1 TTTATTATTTAATTTAATT
* *
42727061 TTTATTATTTATTTTAGTT
1 TTTATTATTTAATTTAATT
*
42727080 TTGATTAT
1 TTTATTAT
42727088 AAATTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (19 bp):
TTTATTATTTAATTTAATT
Found at i:42728921 original size:48 final size:47
Alignment explanation
Indices: 42728859--42729182 Score: 280
Period size: 48 Copynumber: 6.7 Consensus size: 47
42728849 GCTACAAGAT
*
42728859 GTGTCAGTGCAAGACCATGTCTGGGACATGGCATCAGCACGTATAGAG
1 GTGTCAGTGTAAGACCATGTCTGGGACATGGCATC-GCACGTATAGAG
*
42728907 GTGTCAGTGTAAGACCGA-GTTTGGGACATGGCATCGACACGTATAGAG
1 GTGTCAGTGTAAGACC-ATGTCTGGGACATGGCATCG-CACGTATAGAG
*
42728955 GTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATATAG
1 GTGTCAGTGTAAGACCATGTCTGGGACATGGCATC-GCACGTATAGAG
* * * * * *
42729003 GTGTTAGCGTAAGACCATGTCTGAGACATGACATCAGCACGGATATGTG
1 GTGTCAGTGTAAGACCATGTCTGGGACATGGCATC-GCACGTATA-GAG
* * * * * * *
42729052 AGAG-CTAGTGTAAGATCATGCCTGGGACATGGCGTCGGCCTCGATTTTGA-
1 -GTGTC-AGTGTAAGACCATGTCTGGGACATGGCATC-G-CACG-TATAGAG
* * * * *
42729102 -TAGTCAATGTAAGACCATGTTTGGGACATGGCATCG-ACTTGATGGAT
1 GT-GTCAGTGTAAGACCATGTCTGGGACATGGCATCGCACGT-ATAGAG
* * *
42729149 GAGCCAGTGTAAGACCATGTCTAGGACATGGCAT
1 GTGTCAGTGTAAGACCATGTCTGGGACATGGCAT
42729183 TTGGCATTAT
Statistics
Matches: 221, Mismatches: 41, Indels: 29
0.76 0.14 0.10
Matches are distributed among these distances:
45 1 0.00
46 4 0.02
47 30 0.14
48 124 0.56
49 29 0.13
50 28 0.13
51 4 0.02
52 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.24
Consensus pattern (47 bp):
GTGTCAGTGTAAGACCATGTCTGGGACATGGCATCGCACGTATAGAG
Found at i:42728976 original size:96 final size:95
Alignment explanation
Indices: 42728861--42729182 Score: 312
Period size: 96 Copynumber: 3.3 Consensus size: 95
42728851 TACAAGATGT
* *
42728861 GTCAGTGCAAGACCATGTCTGGGACATGGCATCAGCACGTATAGAGGTGTCAGTGTAAGACCGA-
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTCAGTGTAAGACC-AT
*
42728925 GTTTGGGACATGGCATCGACACGTATAGAGGT
65 GTTTGGGACATGGCATCGACACG-ATAGAGGA
* * *
42728957 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATATAGGTGTTAGCGTAAGACCATG
1 GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTCAGTGTAAGACCATG
* * * *
42729022 TCTGAGACATGACATC-AGCACGGATATGTGAGA
66 TTTGGGACATGGCATCGA-CAC-GATA-GAG-GA
* * * * * * *
42729055 G-CTAGTGTAAGATCATGCCTGGGACATGGCGTCGGCCTCGATTTTGA--TAGTCAATGTAAGAC
1 GTC-AGTGTAAGACCATGTCTGGGACATGGCATCGG-CACG-TATAGAGGT-GTCAGTGTAAGAC
** * *
42729117 CATGTTTGGGACATGGCATCGACTTGATGGATGA
62 CATGTTTGGGACATGGCATCGACACGATAGAGGA
* *
42729151 GCCAGTGTAAGACCATGTCTAGGACATGGCAT
1 GTCAGTGTAAGACCATGTCTGGGACATGGCAT
42729183 TTGGCATTAT
Statistics
Matches: 183, Mismatches: 32, Indels: 22
0.77 0.14 0.09
Matches are distributed among these distances:
95 2 0.01
96 105 0.57
97 6 0.03
98 35 0.19
99 31 0.17
100 4 0.02
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (95 bp):
GTCAGTGTAAGACCATGTCTGGGACATGGCATCGGCACGTATAGAGGTGTCAGTGTAAGACCATG
TTTGGGACATGGCATCGACACGATAGAGGA
Found at i:42731260 original size:30 final size:30
Alignment explanation
Indices: 42731205--42731335 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
42731195 ATAGTGAATC
*
42731205 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
42731234 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
42731264 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * * *
42731292 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
42731322 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42731336 CAATCTTGTC
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 19 0.21
30 48 0.52
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:42731315 original size:58 final size:58
Alignment explanation
Indices: 42731204--42731335 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 58
42731194 TATAGTGAAT
* * * * *
42731204 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
* *
42731263 TCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAAC
42731321 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
42731336 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 2 0.03
58 42 0.66
59 20 0.31
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
Found at i:42739201 original size:30 final size:30
Alignment explanation
Indices: 42739146--42739276 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
42739136 ATAGTGAATC
*
42739146 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
*
42739175 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAACT
42739205 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AACT
* * * *
42739233 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAACT
42739263 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42739277 CAATCTTGTC
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 19 0.21
30 48 0.52
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.32
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAACT
Found at i:42739256 original size:58 final size:58
Alignment explanation
Indices: 42739145--42739276 Score: 176
Period size: 58 Copynumber: 2.3 Consensus size: 58
42739135 TATAGTGAAT
* * * * *
42739145 CCGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTCAGC
1 CCGCACACTTAGTGCTATATA-TATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
* *
42739204 TCGCACACTTAGTGCTATATA-ATCAAACTCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATATATC-AACTCGCACACTTAGTGCTATACAATTTTAAAC
42739262 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
42739277 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 2 0.03
58 42 0.66
59 20 0.31
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (58 bp):
CCGCACACTTAGTGCTATATATATCAACTCGCACACTTAGTGCTATACAATTTTAAAC
Found at i:42742428 original size:40 final size:40
Alignment explanation
Indices: 42742384--42742570 Score: 288
Period size: 40 Copynumber: 4.7 Consensus size: 40
42742374 GCTACTTTCT
*
42742384 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
42742424 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
42742464 CAAATGCCTTCGGGACTTAGCCCGGATATAGAAAC-CGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* * * *
42742503 CAAATGCCTTCGGGACTTAGCCTGGAT-TAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
42742542 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
42742571 CATCCGAATA
Statistics
Matches: 135, Mismatches: 10, Indels: 4
0.91 0.07 0.03
Matches are distributed among these distances:
38 5 0.04
39 57 0.42
40 73 0.54
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:42750714 original size:40 final size:40
Alignment explanation
Indices: 42750670--42750818 Score: 246
Period size: 40 Copynumber: 3.7 Consensus size: 40
42750660 GCTACTTGCT
42750670 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
42750710 CAAATGCCTTTGGGACTTAGCCCAGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
42750750 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTCACTAGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TTATAGTAACTCGCA
42750790 CAAATGCCTTCGGGACTTAGCCCGGTTAT
1 CAAATGCCTTCGGGACTTAGCCCGGTTAT
42750819 CATCCGAATA
Statistics
Matches: 101, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
39 2 0.02
40 97 0.96
41 2 0.02
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:42759416 original size:46 final size:46
Alignment explanation
Indices: 42759349--42759471 Score: 167
Period size: 46 Copynumber: 2.7 Consensus size: 46
42759339 TTATTTGTAT
42759349 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTAAGACG-AGA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTAAGACGTA-A
* * * * * *
42759395 GCTAGTGTAAAACATGTCTGGGACATGCATTGGCCTTGAGATGTAA
1 GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTAAGACGTAA
*
42759441 GCCAGTGTAAGACATGTCTGGGACATGCATC
1 GCTAGTGTAAGACATGTCTGGGACATGCATC
42759472 AGCTAAGAGA
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
46 66 0.99
47 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.24
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCATCGACATTAAGACGTAA
Found at i:42759482 original size:46 final size:45
Alignment explanation
Indices: 42759352--42759518 Score: 164
Period size: 46 Copynumber: 3.6 Consensus size: 45
42759342 TTTGTATGCT
*
42759352 AGTGTAAGACATGTCTGGGACATGCATCGACATTAAGACGA-G-AGCT
1 AGTGTAAGACATGTCTGGGACATGCATCGAC--TAAGA-GATGTAGCC
* * * *
42759398 AGTGTAAAACATGTCTGGGACATGCATTGGCCT-TGAGATGTAAGCC
1 AGTGTAAGACATGTCTGGGACATGCA-TCGACTAAGAGATGT-AGCC
*
42759444 AGTGTAAGACATGTCTGGGACATGCATC-AGCTAAGAGATGT-GTC
1 AGTGTAAGACATGTCTGGGACATGCATCGA-CTAAGAGATGTAGCC
*
42759488 ACTGTAAGACCATGTCTGGGACATGGCATCG
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCG
42759519 GCGCGTATAG
Statistics
Matches: 101, Mismatches: 11, Indels: 17
0.78 0.09 0.13
Matches are distributed among these distances:
43 2 0.02
44 13 0.13
45 18 0.18
46 65 0.64
47 3 0.03
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACTAAGAGATGTAGCC
Found at i:42759546 original size:48 final size:48
Alignment explanation
Indices: 42759443--42759661 Score: 279
Period size: 48 Copynumber: 4.6 Consensus size: 48
42759433 AGATGTAAGC
*
42759443 CAGTGTAAGA-CATGTCTGGGACAT-GCATC--AGC-TA-AGAGATGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCGCGTATAGAG--GTGT
*
42759487 CACTGTAAGACCATGTCTGGGACATGGCATCGGCGCGTATAGAGGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCGCGTATAGAGGTGT
* * * *
42759535 CAGTGTAAGACCATGTTTAGGACATGGCATCGGTGCGTATAGAGATGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCGCGTATAGAGGTGT
* * *
42759583 CAGTGTAAGACCATGTTTGGGACATGGCATCGACACGTATAGAGGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGGCGCGTATAGAGGTGT
* *
42759631 TAGTGTAAGACCATGTCTAGGACATGGCATC
1 CAGTGTAAGACCATGTCTGGGACATGGCATC
42759662 AGCAGGACTA
Statistics
Matches: 154, Mismatches: 15, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
44 9 0.06
45 14 0.09
46 5 0.03
48 120 0.78
49 2 0.01
50 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.31, T:0.25
Consensus pattern (48 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGGCGCGTATAGAGGTGT
Found at i:42764741 original size:40 final size:40
Alignment explanation
Indices: 42764697--42764879 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
42764687 ACTTTTTCAA
*
42764697 ATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAG
1 ATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCACAG
* *
42764737 ATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCACAA
1 ATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAG
*
42764777 ATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCAC-G
1 ATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCACAG
* * * *
42764816 AATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACA-
1 -ATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCACAG
*
42764857 AAGCCTTCGGGACTTAGCCCGGA
1 ATGCCTTCGGGACTTAGCCCGGA
42764880 CATCATTCGA
Statistics
Matches: 126, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
39 3 0.02
40 113 0.90
41 10 0.08
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
ATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCACAG
Found at i:42764806 original size:80 final size:82
Alignment explanation
Indices: 42764694--42764879 Score: 233
Period size: 80 Copynumber: 2.3 Consensus size: 82
42764684 GCTACTTTTT
*
42764694 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCAC-AGATGCCTTCGGGA-CTTAACC
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACGA-ATGCCTTC-GGATCTTAACC
* *
42764756 CGGATTTAGTAAC-TCGCA
64 CGGATATAGTAACTTAGCA
* **
42764774 CAAATGCCTTC-GGATCTTAGTCCGGATT-TAGTAACTCGCACGAATGCCTTCGGATCTTAGTCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTATAGTAACTCGCACGAATGCCTTCGGATCTTAACCC
*
42764837 GGATATAGTCACTTAGCA
65 GGATATAGTAACTTAGCA
42764855 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42764880 CATCATTCGA
Statistics
Matches: 92, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
79 6 0.07
80 72 0.78
81 14 0.15
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (82 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACGAATGCCTTCGGATCTTAACCCG
GATATAGTAACTTAGCA
Found at i:42773656 original size:40 final size:40
Alignment explanation
Indices: 42773536--42773748 Score: 300
Period size: 40 Copynumber: 5.2 Consensus size: 40
42773526 CGGGATTTAA
* * * * *
42773536 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
42773576 CCGGATTTGAGTGAGCTTGCACAAAGAGCCTTCGGGTCTTAGC
1 CCGGATAT-A-TCAACTCGCACGAA-TGCCTTCGGGTCTTAGC
42773619 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42773659 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42773699 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42773739 CCGGATATAT
1 CCGGATATAT
42773749 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
40 113 0.74
41 11 0.07
42 8 0.05
43 21 0.14
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:42781770 original size:40 final size:40
Alignment explanation
Indices: 42781662--42781871 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
42781652 CGGGATTTAA
* * * * *
42781662 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
42781702 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42781742 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42781782 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42781822 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42781862 CCGGATATAT
1 CCGGATATAT
42781872 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:42789907 original size:40 final size:40
Alignment explanation
Indices: 42789799--42790008 Score: 305
Period size: 40 Copynumber: 5.2 Consensus size: 40
42789789 CGGGATTTAA
* * * * *
42789799 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
42789839 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42789879 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42789919 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42789959 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
42789999 CCGGATATAT
1 CCGGATATAT
42790009 TTCCAATGTT
Statistics
Matches: 153, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 152 0.99
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:42796571 original size:78 final size:80
Alignment explanation
Indices: 42796478--42796630 Score: 213
Period size: 78 Copynumber: 1.9 Consensus size: 80
42796468 AGCCCGGTTA
* *
42796478 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACAATGCCTTCA
1 TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGGATTTAATAACTTAGCACAAAGCCTTCA
42796541 GG-CTTAGCCCAGAAT
65 GGACTTAGCCCAGAAT
** * * *
42796556 TAGTAACTCGCACAAATGCCTTCGGATCTTAGTCCGGATTTAGTCACTTAGCACAAAGCCTTCGG
1 TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATTTAATAACTTAGCACAAAGCCTTCAG
42796621 GACTTAGCCC
66 GACTTAGCCC
42796631 GGACATCATT
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
77 3 0.05
78 39 0.60
79 15 0.23
80 8 0.12
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGATTTAATAACTTAGCACAAAGCCTTCAG
GACTTAGCCCAGAAT
Found at i:42796633 original size:40 final size:40
Alignment explanation
Indices: 42796450--42796633 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
42796440 GCTACTCGTT
*
42796450 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
* *
42796490 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
42796530 C-AATGCCTTCAGG-CTTAGCCCAGAATTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
42796568 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
42796609 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
42796634 CATCATTCGA
Statistics
Matches: 124, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 24 0.19
39 20 0.16
40 67 0.54
41 13 0.10
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:42799125 original size:2 final size:2
Alignment explanation
Indices: 42799118--42799153 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
42799108 GCTCTTGCAC
42799118 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42799154 GTTTGCACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42799964 original size:39 final size:40
Alignment explanation
Indices: 42799859--42800066 Score: 226
Period size: 40 Copynumber: 5.2 Consensus size: 40
42799849 TATTCGAATG
* * * *
42799859 ATATCCGGGCTAAGTCCTGAAGGCTTTTGTGCTAAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACT
* *
42799900 ATACCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACT
1 ATATCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACT
*
42799940 A-ATTCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACT
1 ATA-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * *
42799979 AAATCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGATACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
* * * *
42800019 ATAACCGGGCTATGTCCCGAAGGCATTTGAGTGAG-TAGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CT
42800059 ATATCCGG
1 ATATCCGG
42800067 TTAAATTCTG
Statistics
Matches: 142, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
39 37 0.26
40 78 0.55
41 26 0.18
42 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACT
Found at i:42800069 original size:79 final size:79
Alignment explanation
Indices: 42799916--42800070 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 79
42799906 GGACTAAGAT
* * *
42799916 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAGCGAGTTACTAA
42799981 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* * *
42799995 CCGAAGGCATTTGTGCGAGATACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAGTGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAGCGAGTTA-C
*
42800058 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
42800071 ATTCTGAAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
78 2 0.03
79 40 0.61
80 24 0.36
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTGGAGCGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:42802068 original size:20 final size:20
Alignment explanation
Indices: 42802043--42802080 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42802033 TATACATGAC
42802043 AAAAATCTT-CTAAGTTCTGT
1 AAAAAT-TTCCTAAGTTCTGT
42802063 AAAAATTTCCTAAGTTCT
1 AAAAATTTCCTAAGTTCT
42802081 CTGTTTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (20 bp):
AAAAATTTCCTAAGTTCTGT
Found at i:42802559 original size:22 final size:22
Alignment explanation
Indices: 42802533--42802576 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
42802523 GAAAATAATC
*
42802533 AAAATTAATCAAAATTTATTAT
1 AAAATTAATCAAAATTCATTAT
*
42802555 AAAATTAATTAAAATTCATTAT
1 AAAATTAATCAAAATTCATTAT
42802577 GCTAATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAATTAATCAAAATTCATTAT
Found at i:42805275 original size:19 final size:19
Alignment explanation
Indices: 42805234--42805275 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
42805224 ATTCTTGTCG
*
42805234 AAAA-AATTTAATTATTAT
1 AAAATAATTTAATTATAAT
*
42805252 AAAATAATTTAATTGTAAT
1 AAAATAATTTAATTATAAT
*
42805271 TAAAT
1 AAAAT
42805276 TATTAACATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
AAAATAATTTAATTATAAT
Found at i:42805489 original size:6 final size:6
Alignment explanation
Indices: 42805478--42805506 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
42805468 CATAATATAA
42805478 TTAATT TTAATT TTAATT TTAATT TTAAT
1 TTAATT TTAATT TTAATT TTAATT TTAAT
42805507 CCAATTTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTAATT
Found at i:42805923 original size:25 final size:25
Alignment explanation
Indices: 42805895--42805945 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
42805885 ACTCTTCTCA
*
42805895 TCTCTTCACTTCTCTTTCATTTTTC
1 TCTCTTCACTTCTCTTTCATTATTC
* *
42805920 TCTCTTCATTTCTCTTTTATTATTC
1 TCTCTTCACTTCTCTTTCATTATTC
42805945 T
1 T
42805946 TCATTCCCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.10, C:0.27, G:0.00, T:0.63
Consensus pattern (25 bp):
TCTCTTCACTTCTCTTTCATTATTC
Found at i:42806431 original size:25 final size:25
Alignment explanation
Indices: 42806403--42806454 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
42806393 ATCAGTACAT
*
42806403 GTTTGATCATCTAA-GGTAGCTAAGG
1 GTTTAATCATC-AACGGTAGCTAAGG
* *
42806428 GTTTAATTATCAACGGTATCTAAGG
1 GTTTAATCATCAACGGTAGCTAAGG
42806453 GT
1 GT
42806455 ACATTAGCCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 2 0.09
25 21 0.91
ACGTcount: A:0.29, C:0.12, G:0.25, T:0.35
Consensus pattern (25 bp):
GTTTAATCATCAACGGTAGCTAAGG
Found at i:42808995 original size:28 final size:29
Alignment explanation
Indices: 42808955--42809011 Score: 98
Period size: 28 Copynumber: 2.0 Consensus size: 29
42808945 ATGACACGTT
42808955 AAATCATCATTTCAAACAAAAAA-TTATG
1 AAATCATCATTTCAAACAAAAAACTTATG
*
42808983 AAATTATCATTTCAAACAAAAAACTTATG
1 AAATCATCATTTCAAACAAAAAACTTATG
42809012 TTAATTTATA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 22 0.81
29 5 0.19
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.30
Consensus pattern (29 bp):
AAATCATCATTTCAAACAAAAAACTTATG
Found at i:42810396 original size:25 final size:24
Alignment explanation
Indices: 42810350--42810424 Score: 60
Period size: 25 Copynumber: 3.0 Consensus size: 24
42810340 ACTATTCACA
* *
42810350 AAAAATAATAGTATATAAAATTTT
1 AAAAATAATAATAAATAAAATTTT
* *
42810374 AAAAATATATAATAAATATAATTAT
1 AAAAATA-ATAATAAATAAAATTTT
** *
42810399 ATTAATATTAAATAAAATAAAATTTT
1 AAAAATAAT-AAT-AAATAAAATTTT
42810425 CCCCACCCCT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
24 8 0.21
25 21 0.54
26 10 0.26
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (24 bp):
AAAAATAATAATAAATAAAATTTT
Found at i:42810883 original size:17 final size:17
Alignment explanation
Indices: 42810856--42810902 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
42810846 AAATTTAAAT
42810856 TTTTTAT-TATTATCAA
1 TTTTTATATATTATCAA
* *
42810872 TTTTTATATATTTTTAA
1 TTTTTATATATTATCAA
* *
42810889 ATTTTATACATTAT
1 TTTTTATATATTAT
42810903 TTTTTGTTAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 7 0.28
17 18 0.72
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTTATATATTATCAA
Found at i:42811824 original size:21 final size:20
Alignment explanation
Indices: 42811788--42811843 Score: 71
Period size: 18 Copynumber: 2.8 Consensus size: 20
42811778 TTACACCACG
42811788 TTGTGGATAAAACCACTCATCA
1 TTGTGGAT-AAACCACTC-TCA
*
42811810 TTGTGGATGAACCA--CTCA
1 TTGTGGATAAACCACTCTCA
42811828 TTGTGGATAAACCACT
1 TTGTGGATAAACCACT
42811844 AGTAATAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 16 0.53
19 1 0.03
21 5 0.17
22 8 0.27
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (20 bp):
TTGTGGATAAACCACTCTCA
Found at i:42812047 original size:35 final size:35
Alignment explanation
Indices: 42812015--42812086 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
42812005 TCAAACAGGT
*
42812015 CAATACGGTAGCATTTAATTATGATTTTAACAGAA
1 CAATACGATAGCATTTAATTATGATTTTAACAGAA
*
42812050 CAATACGATAGCATTTAATTATGCTTTTAACAGAA
1 CAATACGATAGCATTTAATTATGATTTTAACAGAA
42812085 CA
1 CA
42812087 GTACAGTAGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.33
Consensus pattern (35 bp):
CAATACGATAGCATTTAATTATGATTTTAACAGAA
Found at i:42812097 original size:35 final size:34
Alignment explanation
Indices: 42812015--42812097 Score: 121
Period size: 35 Copynumber: 2.4 Consensus size: 34
42812005 TCAAACAGGT
42812015 CAATACGGTAGCATTTAATTATGATTTTAACAGAA
1 CAATAC-GTAGCATTTAATTATGATTTTAACAGAA
*
42812050 CAATACGATAGCATTTAATTATGCTTTTAACAGAA
1 CAATACG-TAGCATTTAATTATGATTTTAACAGAA
*
42812085 CAGTACAGTAGCA
1 CAATAC-GTAGCA
42812098 ATCAATATGC
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
34 1 0.02
35 42 0.95
36 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (34 bp):
CAATACGTAGCATTTAATTATGATTTTAACAGAA
Found at i:42812126 original size:34 final size:35
Alignment explanation
Indices: 42812069--42812164 Score: 101
Period size: 34 Copynumber: 2.8 Consensus size: 35
42812059 AGCATTTAAT
* * *
42812069 TATGCTTTTAACAGAAC-AGTACAGTAGC-AATCAA
1 TATGCTTATAACAGATCAACTACAGTAGCAAAT-AA
* *
42812103 TATGCTTATAATAGTTCAA-TACAGTAGCAAATAA
1 TATGCTTATAACAGATCAACTACAGTAGCAAATAA
*
42812137 TATGTTTATAACAGATCAACT-CAGTAGC
1 TATGCTTATAACAGATCAACTACAGTAGC
42812165 CAAAAGTCAT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
34 47 0.90
35 5 0.10
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (35 bp):
TATGCTTATAACAGATCAACTACAGTAGCAAATAA
Found at i:42812477 original size:28 final size:28
Alignment explanation
Indices: 42812412--42812516 Score: 119
Period size: 28 Copynumber: 3.8 Consensus size: 28
42812402 AATTTTAGGT
*
42812412 AAAACTATAAAATCTAAAAACA-A-GGG-
1 AAAATTATAAAATCTAAAAA-ATAGGGGC
* *
42812438 AAATTTGTAAAATCTAAAAAATAGGGGC
1 AAAATTATAAAATCTAAAAAATAGGGGC
*
42812466 AAAATTATAAAATATAAAAAATAGGGGC
1 AAAATTATAAAATCTAAAAAATAGGGGC
*
42812494 AAAA-CAGTAAAATCTAAAAAATA
1 AAAATTA-TAAAATCTAAAAAATA
42812517 AGGAACACAC
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.01
26 18 0.27
27 4 0.06
28 44 0.66
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (28 bp):
AAAATTATAAAATCTAAAAAATAGGGGC
Found at i:42824163 original size:36 final size:36
Alignment explanation
Indices: 42824112--42824191 Score: 151
Period size: 36 Copynumber: 2.2 Consensus size: 36
42824102 AATGGGCCAA
42824112 GTTGGGCCGGACTCAACTAAACATTTAGGCCCATTT
1 GTTGGGCCGGACTCAACTAAACATTTAGGCCCATTT
*
42824148 GTTGGGCCGGGCTCAACTAAACATTTAGGCCCATTT
1 GTTGGGCCGGACTCAACTAAACATTTAGGCCCATTT
42824184 GTTGGGCC
1 GTTGGGCC
42824192 CGACCCGGCC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (36 bp):
GTTGGGCCGGACTCAACTAAACATTTAGGCCCATTT
Found at i:42839432 original size:19 final size:18
Alignment explanation
Indices: 42839408--42839465 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 18
42839398 TATACGGGTT
42839408 TATGCACTTTGTGTGCTAG
1 TATGCAC-TTGTGTGCTAG
*
42839427 TATGCAC-TGTGTGTTAG
1 TATGCACTTGTGTGCTAG
* *
42839444 TATGTACTATATGTGCTAG
1 TATGCACT-TGTGTGCTAG
42839463 TAT
1 TAT
42839466 ATTTGCTTCG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 15 0.45
19 18 0.55
ACGTcount: A:0.21, C:0.12, G:0.24, T:0.43
Consensus pattern (18 bp):
TATGCACTTGTGTGCTAG
Found at i:42840356 original size:28 final size:27
Alignment explanation
Indices: 42840306--42840358 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
42840296 AGACTCCATT
42840306 TTATTAGGATAATTAATATTAAGATAA
1 TTATTAGGATAATTAATATTAAGATAA
* *
42840333 TTATTAGGATTATTTAATTTTAAGAT
1 TTATTAGGA-TAATTAATATTAAGAT
42840359 TTTATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (27 bp):
TTATTAGGATAATTAATATTAAGATAA
Found at i:42840363 original size:27 final size:26
Alignment explanation
Indices: 42840303--42840364 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 26
42840293 ATAAGACTCC
42840303 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * *
42840329 ATAATTATTAGGATTATTTAATTTTAAG
1 AT-TTTATTAGGA-TAATTAATATTAAG
42840357 ATTTTATT
1 ATTTTATT
42840365 TTAATTATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 2 0.07
27 14 0.47
28 14 0.47
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.52
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:42840387 original size:20 final size:20
Alignment explanation
Indices: 42840359--42840406 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
42840349 ATTTTAAGAT
*
42840359 TTTAT-TTTAATT-ATCTTTA
1 TTTATCTTTAATTAAT-TGTA
42840378 TTTATCTTTAATTAATTGTA
1 TTTATCTTTAATTAATTGTA
42840398 TTTATCTTT
1 TTTATCTTT
42840407 TTAGAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 19 0.73
21 2 0.08
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATCTTTAATTAATTGTA
Found at i:42844065 original size:5 final size:5
Alignment explanation
Indices: 42844051--42844101 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
42844041 GCAACCCAAT
*
42844051 TTTTA TTTTTA TTTTA TTTTA TTTT- TATTTA TTTTA TCTTA --TTA TTTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTTA
42844100 TT
1 TT
42844102 ATTTATTCTT
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
3 3 0.08
4 1 0.03
5 30 0.75
6 6 0.15
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:42844067 original size:11 final size:11
Alignment explanation
Indices: 42844051--42844108 Score: 66
Period size: 10 Copynumber: 5.2 Consensus size: 11
42844041 GCAACCCAAT
42844051 TTTTATTTTTA
1 TTTTATTTTTA
42844062 TTTTA-TTTTA
1 TTTTATTTTTA
*
42844072 TTTT-TATTTA
1 TTTTATTTTTA
42844082 TTTTATCTTATTA
1 TTTTAT-TT-TTA
42844095 TTTTATTATTTA
1 TTTTATT-TTTA
42844107 TT
1 TT
42844109 CTTTTCAGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
10 17 0.43
11 6 0.15
12 7 0.17
13 10 0.25
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:42844092 original size:25 final size:25
Alignment explanation
Indices: 42844051--42844108 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 25
42844041 GCAACCCAAT
42844051 TTTTATT-TTTATTTTA--TT-TTA
1 TTTTATTATTTATTTTATCTTATTA
42844072 -TTT-TTATTTATTTTATCTTATTA
1 TTTTATTATTTATTTTATCTTATTA
42844095 TTTTATTATTTATT
1 TTTTATTATTTATT
42844109 CTTTTCAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
19 2 0.06
20 12 0.39
22 2 0.06
23 3 0.10
24 3 0.10
25 9 0.29
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTATTATTTATTTTATCTTATTA
Found at i:42844106 original size:20 final size:22
Alignment explanation
Indices: 42844049--42844107 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 22
42844039 AGGCAACCCA
*
42844049 ATTTTTATT-TTTATTTTATTTT
1 ATTTTTATTATTTATCTTA-TTT
42844071 ATTTTTATTTATTTTATCTTA-TT
1 ATTTTTA-TTA-TTTATCTTATTT
42844094 A-TTTTATTATTTAT
1 ATTTTTATTATTTAT
42844108 TCTTTTCAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 5 0.15
21 3 0.09
22 12 0.36
23 5 0.15
25 8 0.24
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (22 bp):
ATTTTTATTATTTATCTTATTT
Found at i:42845072 original size:96 final size:95
Alignment explanation
Indices: 42844897--42845076 Score: 229
Period size: 96 Copynumber: 1.9 Consensus size: 95
42844887 TCTAAGAATG
* * * *
42844897 TGTTAGGCTGAGTAACAGGGGTGAGGTGCTTGGTTGTCATCTCTCTTCATGTCAAAAGGTTCGAT
1 TGTTAGGCTGAGTAACAGGGGTGAGGTGCTTGGCTATCATCTCTCTTCACGTCAAAAGGTTCAAT
* * *
42844962 ATGTTTTTAGAAAAAATAAAAATTAGGAGTA
66 ATATTCTAAG-AAAAATAAAAATTAGGAGTA
* * *
42844993 TGTTGGGCTGAGTAACCGGGGTGGGGTGCTTGGCTATCAT-TCTCTTC-CGTCAAAAGGTTCAAT
1 TGTTAGGCTGAGTAACAGGGGTGAGGTGCTTGGCTATCATCTCTCTTCACGTCAAAAGGTTCAAT
42845056 ATATTCCTAAGTAAAAATAAA
66 ATATT-CTAAG-AAAAATAAA
42845077 TAAATAAAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
94 18 0.25
95 19 0.26
96 35 0.49
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (95 bp):
TGTTAGGCTGAGTAACAGGGGTGAGGTGCTTGGCTATCATCTCTCTTCACGTCAAAAGGTTCAAT
ATATTCTAAGAAAAATAAAAATTAGGAGTA
Found at i:42845733 original size:27 final size:26
Alignment explanation
Indices: 42845673--42845734 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
42845663 ATAAGACTCC
42845673 ATTTTATTAGGATAATTAATATTAAG
1 ATTTTATTAGGATAATTAATATTAAG
* * * *
42845699 ATAATTATTAGGATTATTTAATTTTAGG
1 AT-TTTATTAGGA-TAATTAATATTAAG
42845727 ATTTTATT
1 ATTTTATT
42845735 TTAATTATCT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 2 0.07
27 14 0.48
28 13 0.45
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (26 bp):
ATTTTATTAGGATAATTAATATTAAG
Found at i:42845757 original size:20 final size:20
Alignment explanation
Indices: 42845729--42845776 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
42845719 ATTTTAGGAT
*
42845729 TTTAT-TTTAATT-ATCTTTA
1 TTTATCTTTAATTAAT-TGTA
42845748 TTTATCTTTAATTAATTGTA
1 TTTATCTTTAATTAATTGTA
42845768 TTTATCTTT
1 TTTATCTTT
42845777 TTAGAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 19 0.73
21 2 0.08
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.67
Consensus pattern (20 bp):
TTTATCTTTAATTAATTGTA
Found at i:42854889 original size:19 final size:19
Alignment explanation
Indices: 42854865--42854902 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
42854855 ATTTAATATT
42854865 TGTAAAAGATAATTTTTCA
1 TGTAAAAGATAATTTTTCA
42854884 TGTAAAAGATAATTTTTCA
1 TGTAAAAGATAATTTTTCA
42854903 CTCTGAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.42
Consensus pattern (19 bp):
TGTAAAAGATAATTTTTCA
Found at i:42854939 original size:24 final size:24
Alignment explanation
Indices: 42854908--42854953 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
42854898 TTTCACTCTG
42854908 AGTAGCATAATTTTCGTTTTTATA
1 AGTAGCATAATTTTCGTTTTTATA
*
42854932 AGTAGCATAATTTTTGTTTTTA
1 AGTAGCATAATTTTCGTTTTTA
42854954 ATCAATTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.07, G:0.13, T:0.52
Consensus pattern (24 bp):
AGTAGCATAATTTTCGTTTTTATA
Found at i:42866482 original size:20 final size:20
Alignment explanation
Indices: 42866457--42866502 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
42866447 ATTTAACTAA
42866457 TTAACTACT-AGCTAACAACC
1 TTAACTACTGA-CTAACAACC
* *
42866477 TTAACTGCTGACTATCAACC
1 TTAACTACTGACTAACAACC
42866497 TTAACT
1 TTAACT
42866503 GTTATTCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 22 0.96
21 1 0.04
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (20 bp):
TTAACTACTGACTAACAACC
Found at i:42868797 original size:30 final size:30
Alignment explanation
Indices: 42868742--42868901 Score: 222
Period size: 29 Copynumber: 5.5 Consensus size: 30
42868732 ATAGTGAATC
42868742 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42868771 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42868801 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
42868830 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
42868858 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42868888 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42868902 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 47 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:42868834 original size:59 final size:57
Alignment explanation
Indices: 42868742--42868901 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 57
42868732 ATAGTGAATC
*
42868742 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
42868801 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
42868858 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
42868902 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 50 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Found at i:42876677 original size:30 final size:30
Alignment explanation
Indices: 42876622--42876781 Score: 222
Period size: 29 Copynumber: 5.5 Consensus size: 30
42876612 ATAGTGAATC
42876622 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42876651 CGCACACTTAGTGCTATATAATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42876681 CGCACACTTAGTGCTATAT-ATTTTCAGCT
1 CGCACACTTAGTGCTATATAATTTTCAGCT
*
42876710 CGCACACTTAGTGCTATATAA---TCAAACT
1 CGCACACTTAGTGCTATATAATTTTC-AGCT
* * * * *
42876738 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAATTTTCAGCT
42876768 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42876782 CAATCTTGTC
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.18
29 48 0.40
30 47 0.39
31 1 0.01
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (30 bp):
CGCACACTTAGTGCTATATAATTTTCAGCT
Found at i:42876714 original size:59 final size:57
Alignment explanation
Indices: 42876622--42876781 Score: 223
Period size: 59 Copynumber: 2.8 Consensus size: 57
42876612 ATAGTGAATC
*
42876622 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATTTTC-AGCT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAA---TCAAACT
42876681 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
* * * * *
42876738 CGCACACTTAGTGCTGTACAATTTTAAACCCGCACACTTAGTGC
1 CGCACACTTAGTGCTATA-TATTTTCAGCTCGCACACTTAGTGC
42876782 CAATCTTGTC
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 21 0.23
59 50 0.54
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (57 bp):
CGCACACTTAGTGCTATATATTTTCAGCTCGCACACTTAGTGCTATATAATCAAACT
Done.