Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 93 of 150
Found at i:29253828 original size:219 final size:218
Alignment explanation
Indices: 29253574--29253996 Score: 630
Period size: 219 Copynumber: 1.9 Consensus size: 218
29253564 ACCGAAGAAG
* * *
29253574 CAGATCTTATCTCCCTAAGCAGTAGTTGTGCAGATCAAAGTCTCCAGCCTTGTCTCCCTGAGCAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGTCCCCAGCCTTGTCTCCCTGAGCAG
* * * *
29253639 TAGTGGAGTAGGTTGAAAATTACAGATATTATCTCCCTAAGCAGTAGTGGAGCGGATCGAAGATG
66 CAGTGGAGTAGGTTGAAAATTACAGATATTATCTCCCTAAGAAGTAGTGGAGCAGATCGAAG-TC
* * * * * ** * *
29253704 GCAAGCCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATTGTAGACCTTATCTCCCTGAGC
130 CCAAGCCATACCTCCCTGAGCAGCAGTGGAGTAAGTTGAAAATTACAAACCTTATCTCCCTAAGC
29253769 AGTAGTGGAGTAGGTTGAAAATTA
195 AGTAGTGGAGTAGGTTGAAAATTA
*
29253793 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGTCCCCAGCCTTGTCTCCCTGAGCAG
1 CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGTCCCCAGCCTTGTCTCCCTGAGCAG
* *
29253858 CAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGAAGTAGTGGAGCATATCGAAGTCC
66 CAGTGGAGTAGGTTGAAAATTACAGATATTATCTCCCTAAGAAGTAGTGGAGCAGATCGAAGTCC
* * * *
29253923 CCAGCCATGCCTCTCTGAGCAGCAGTGGAGTAAGTTGAAAATTACAAATCTTATCTCCCTAAGCA
131 CAAGCCATACCTCCCTGAGCAGCAGTGGAGTAAGTTGAAAATTACAAACCTTATCTCCCTAAGCA
29253988 GTAGTGGAG
196 GTAGTGGAG
29253997 CAGATCGAAC
Statistics
Matches: 181, Mismatches: 23, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
218 63 0.35
219 118 0.65
ACGTcount: A:0.28, C:0.22, G:0.25, T:0.26
Consensus pattern (218 bp):
CAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGTCCCCAGCCTTGTCTCCCTGAGCAG
CAGTGGAGTAGGTTGAAAATTACAGATATTATCTCCCTAAGAAGTAGTGGAGCAGATCGAAGTCC
CAAGCCATACCTCCCTGAGCAGCAGTGGAGTAAGTTGAAAATTACAAACCTTATCTCCCTAAGCA
GTAGTGGAGTAGGTTGAAAATTA
Found at i:29253868 original size:87 final size:87
Alignment explanation
Indices: 29253753--29254039 Score: 430
Period size: 87 Copynumber: 3.3 Consensus size: 87
29253743 AGATTGTAGA
*
29253753 CCTTATCTCCCTGAGCAGTAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAG
1 CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAG
29253818 TGGAGCAGATCGAAGTCCCCAG
66 TGGAGCAGATCGAAGTCCCCAG
* *
29253840 CCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGAAGTAG
1 CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAG
*
29253905 TGGAGCATATCGAAGTCCCCAG
66 TGGAGCAGATCGAAGTCCCCAG
* ** * * *
29253927 CCATGCCTCTCTGAGCAGCAGTGGAGTAAGTTGAAAATTACAAATCTTATCTCCCTAAGCAGTAG
1 CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAG
** *
29253992 TGGAGCAGATCGAACACCCAAG
66 TGGAGCAGATCGAAGTCCCCAG
* **
29254014 TCTTATCTCCCTGAGTTGCAGTGGAG
1 CCTTATCTCCCTGAGCAGCAGTGGAG
29254040 CAGACTAAAG
Statistics
Matches: 179, Mismatches: 21, Indels: 0
0.89 0.10 0.00
Matches are distributed among these distances:
87 179 1.00
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (87 bp):
CCTTATCTCCCTGAGCAGCAGTGGAGTAGGTTGAAAATTACAGATCTTATCTCCCTAAGCAGTAG
TGGAGCAGATCGAAGTCCCCAG
Found at i:29255913 original size:20 final size:21
Alignment explanation
Indices: 29255864--29255919 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
29255854 AAAAATACAT
*
29255864 TATTTTTTTAAATTATTATCAA
1 TATTGTTTTAAA-TATTATCAA
29255886 TA-TGTTTTAAAT-TTATCAA
1 TATTGTTTTAAATATTATCAA
29255905 TATTGTTTTAAATAT
1 TATTGTTTTAAATAT
29255920 ATATATATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
19 9 0.29
20 11 0.35
21 9 0.29
22 2 0.06
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.57
Consensus pattern (21 bp):
TATTGTTTTAAATATTATCAA
Found at i:29258377 original size:21 final size:21
Alignment explanation
Indices: 29258346--29258394 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
29258336 ATGTTTGATT
29258346 ACAAGCACCTTAAGTATTGAAA
1 ACAA-CACCTTAAGTATTGAAA
29258368 ACAACACCTTAAGTATTGAAA
1 ACAACACCTTAAGTATTGAAA
29258389 ACAACA
1 ACAACA
29258395 GATCAACTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.20
Consensus pattern (21 bp):
ACAACACCTTAAGTATTGAAA
Found at i:29266461 original size:23 final size:23
Alignment explanation
Indices: 29266431--29266508 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
29266421 AGAAAGCTTC
29266431 CAAGCCCAAAATCAATTTAAGCT
1 CAAGCCCAAAATCAATTTAAGCT
* *
29266454 CAAGCCCAAGAT-AA-ATAAGCTTT
1 CAAGCCCAAAATCAATTTAAGC--T
*
29266477 CAAGCCCAAAATCAATTTGAGCT
1 CAAGCCCAAAATCAATTTAAGCT
29266500 CAAGCCCAA
1 CAAGCCCAA
29266509 GATAAATATG
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
21 5 0.11
22 2 0.04
23 33 0.72
24 2 0.04
25 4 0.09
ACGTcount: A:0.42, C:0.27, G:0.12, T:0.19
Consensus pattern (23 bp):
CAAGCCCAAAATCAATTTAAGCT
Found at i:29266481 original size:46 final size:46
Alignment explanation
Indices: 29266424--29266516 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
29266414 AAACTCGAGA
29266424 AAGCTTCCAAGCCCAAAATCAATTTAAGCTCAAGCCCAAGATAAAT
1 AAGCTTCCAAGCCCAAAATCAATTTAAGCTCAAGCCCAAGATAAAT
* *
29266470 AAGCTTTCAAGCCCAAAATCAATTTGAGCTCAAGCCCAAGATAAAT
1 AAGCTTCCAAGCCCAAAATCAATTTAAGCTCAAGCCCAAGATAAAT
29266516 A
1 A
29266517 TGATTAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.43, C:0.25, G:0.12, T:0.20
Consensus pattern (46 bp):
AAGCTTCCAAGCCCAAAATCAATTTAAGCTCAAGCCCAAGATAAAT
Found at i:29268133 original size:8 final size:8
Alignment explanation
Indices: 29268120--29268147 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
29268110 GCATGCATGT
29268120 TTGAATGG
1 TTGAATGG
29268128 TTGAATGG
1 TTGAATGG
29268136 TTGAATGG
1 TTGAATGG
29268144 TTGA
1 TTGA
29268148 TGATTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (8 bp):
TTGAATGG
Found at i:29272728 original size:5 final size:5
Alignment explanation
Indices: 29272718--29272750 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
29272708 GGTAGTTTGA
29272718 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAA
29272751 GCAACAGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAAAT
Found at i:29274504 original size:20 final size:20
Alignment explanation
Indices: 29274479--29274527 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
29274469 AAGCTTATAC
*
29274479 TAAGTAAATGGAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
29274499 TAAGTAAATGAAATGGAAAG
1 TAAGTAAATGAAATGGAAAG
29274519 TAAGTAAAT
1 TAAGTAAAT
29274528 TGAGTGGTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.22
Consensus pattern (20 bp):
TAAGTAAATGAAATGGAAAG
Found at i:29281641 original size:40 final size:42
Alignment explanation
Indices: 29281554--29281641 Score: 108
Period size: 42 Copynumber: 2.1 Consensus size: 42
29281544 ACACGGTTTG
* * *
29281554 TGACACGGTCGTGTGTATCAAGTTAGTGAGTCACACGGTCTA
1 TGACACGGTCGTGTGTATCAAGTCAGAGAGTCACACGGACTA
* * *
29281596 CGACACGGTTGTGTGTATCAAGTCAGAGAGTTACAC-GACT-
1 TGACACGGTCGTGTGTATCAAGTCAGAGAGTCACACGGACTA
29281636 TGACAC
1 TGACAC
29281642 ACGGCCTACG
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
40 5 0.13
41 3 0.08
42 31 0.79
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (42 bp):
TGACACGGTCGTGTGTATCAAGTCAGAGAGTCACACGGACTA
Found at i:29282766 original size:21 final size:21
Alignment explanation
Indices: 29282742--29282786 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
29282732 AGACGGAAGA
29282742 ATCATCTACTCATTAGATGAG
1 ATCATCTACTCATTAGATGAG
29282763 ATCATCTACTCATTAGATGAG
1 ATCATCTACTCATTAGATGAG
29282784 ATC
1 ATC
29282787 TTAGTCTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.33
Consensus pattern (21 bp):
ATCATCTACTCATTAGATGAG
Found at i:29287380 original size:14 final size:14
Alignment explanation
Indices: 29287358--29287387 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
29287348 CCTCAAATGC
29287358 AACCAGGACTCATT
1 AACCAGGACTCATT
*
29287372 AACCGGGACTCATT
1 AACCAGGACTCATT
29287386 AA
1 AA
29287388 TCGTCATAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.27, G:0.17, T:0.20
Consensus pattern (14 bp):
AACCAGGACTCATT
Found at i:29287743 original size:55 final size:55
Alignment explanation
Indices: 29287683--29287791 Score: 182
Period size: 55 Copynumber: 2.0 Consensus size: 55
29287673 TAACTTTCAA
*
29287683 AATTTAATCATGAAACTCATAAATTGAAATCTAAGCATTTTCATCATTTTCTCAC
1 AATTTAATCATGAAACTCATAAATTGAAATCTAAGCATATTCATCATTTTCTCAC
* * *
29287738 AATTTAATCCTTAAACTCATAAATTGAAATCTAAGCATATTCATCCTTTTCTCA
1 AATTTAATCATGAAACTCATAAATTGAAATCTAAGCATATTCATCATTTTCTCA
29287792 AGCTAGTCGA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 50 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.39
Consensus pattern (55 bp):
AATTTAATCATGAAACTCATAAATTGAAATCTAAGCATATTCATCATTTTCTCAC
Found at i:29294186 original size:16 final size:16
Alignment explanation
Indices: 29294165--29294196 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29294155 GAAATTAAAG
*
29294165 AAAAATATTATAGAAT
1 AAAAATATTAAAGAAT
29294181 AAAAATATTAAAGAAT
1 AAAAATATTAAAGAAT
29294197 GTATATATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.28
Consensus pattern (16 bp):
AAAAATATTAAAGAAT
Found at i:29295567 original size:13 final size:13
Alignment explanation
Indices: 29295549--29295579 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29295539 AAACTGGAGA
*
29295549 TTTATTTTTTTAT
1 TTTATTTTATTAT
29295562 TTTATTTTATTAT
1 TTTATTTTATTAT
29295575 TTTAT
1 TTTAT
29295580 GTATGTGGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTATTTTATTAT
Found at i:29298859 original size:16 final size:16
Alignment explanation
Indices: 29298838--29298870 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29298828 ATGAGAATGG
*
29298838 TTTATTGAGTCTAGTT
1 TTTATTGACTCTAGTT
29298854 TTTATTGACTCTAGTT
1 TTTATTGACTCTAGTT
29298870 T
1 T
29298871 CATCAGAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.09, G:0.15, T:0.58
Consensus pattern (16 bp):
TTTATTGACTCTAGTT
Found at i:29300648 original size:26 final size:26
Alignment explanation
Indices: 29300619--29300681 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
29300609 CCTATAAATG
29300619 TTCTGAAACTAATACATGCTATGATA
1 TTCTGAAACTAATACATGCTATGATA
* * *
29300645 TTCTGAAACTGATATATGTTATGATA
1 TTCTGAAACTAATACATGCTATGATA
29300671 TTCTGAAACTA
1 TTCTGAAACTA
29300682 CTGTAGGTAG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.38
Consensus pattern (26 bp):
TTCTGAAACTAATACATGCTATGATA
Found at i:29304885 original size:52 final size:51
Alignment explanation
Indices: 29304761--29304939 Score: 224
Period size: 52 Copynumber: 3.5 Consensus size: 51
29304751 ACTAGTGACT
*
29304761 CAAGTGTGGTACTATGTGAAGGCCAC-TTTG-AGAAGAGATAGC-TTGATCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTTGAAGAA-AGATAGCTTTGGTCA
*
29304810 CAAGTGTGGTACTATGTGAAGGCCACTTTCTGAAGAAAGATAACTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTT-TGAAGAAAGATAGCTTTGGTCA
* * *
29304862 CAAGTGTGGTACCATGTGAAGGCCACTTTGTGAAG-AAGGTAGCTTT-GACTA
1 CAAGTGTGGTACTATGTGAAGGCCACTTT-TGAAGAAAGATAGCTTTGGTC-A
* *
29304913 CAAGGGTGGTACTATGTGCAGGCCACT
1 CAAGTGTGGTACTATGTGAAGGCCACT
29304940 AGGTATCCGT
Statistics
Matches: 115, Mismatches: 10, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
49 26 0.23
50 4 0.03
51 42 0.37
52 43 0.37
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (51 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTTGAAGAAAGATAGCTTTGGTCA
Found at i:29304930 original size:51 final size:52
Alignment explanation
Indices: 29304761--29304939 Score: 242
Period size: 51 Copynumber: 3.5 Consensus size: 52
29304751 ACTAGTGACT
*
29304761 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AGATAGC-TTGA-TCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGACTCA
* * *
29304810 CAAGTGTGGTACTATGTGAAGGCCACTTTCTGAAGAAAGATAACTTTG-GTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAG-AAGATAGCTTTGACTCA
* *
29304862 CAAGTGTGGTACCATGTGAAGGCCACTTTGTGAAGAAGGTAGCTTTGACT-A
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGACTCA
* *
29304913 CAAGGGTGGTACTATGTGCAGGCCACT
1 CAAGTGTGGTACTATGTGAAGGCCACT
29304940 AGGTATCCGT
Statistics
Matches: 114, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
49 33 0.29
51 41 0.36
52 40 0.35
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.27
Consensus pattern (52 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGTGAAGAAGATAGCTTTGACTCA
Found at i:29311394 original size:13 final size:12
Alignment explanation
Indices: 29311376--29311420 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
29311366 TCCCAACATT
29311376 AAAAAAATCAAGA
1 AAAAAAATCAA-A
29311389 AAAAAAATTCAAA
1 AAAAAAA-TCAAA
*
29311402 AAAAAATTCAAA
1 AAAAAAATCAAA
29311414 AAAAAAA
1 AAAAAAA
29311421 GTGGGAGTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.38
13 14 0.48
14 4 0.14
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.11
Consensus pattern (12 bp):
AAAAAAATCAAA
Found at i:29311402 original size:11 final size:12
Alignment explanation
Indices: 29311388--29311419 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
29311378 AAAAATCAAG
29311388 AAAAAAAATTCA
1 AAAAAAAATTCA
29311400 AAAAAAAATTCA
1 AAAAAAAATTCA
29311412 AAAAAAAA
1 AAAAAAAA
29311420 AGTGGGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.81, C:0.06, G:0.00, T:0.12
Consensus pattern (12 bp):
AAAAAAAATTCA
Found at i:29312459 original size:13 final size:12
Alignment explanation
Indices: 29312441--29312482 Score: 54
Period size: 10 Copynumber: 3.7 Consensus size: 12
29312431 TGTGAGTGAG
29312441 AAAAGAACATTGA
1 AAAAGAA-ATTGA
29312454 AAAAGAAATTG-
1 AAAAGAAATTGA
29312465 -AAAGAAA-TGA
1 AAAAGAAATTGA
29312475 AAAAGAAA
1 AAAAGAAA
29312483 AAGATGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.07
10 7 0.26
11 7 0.26
12 4 0.15
13 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.17, T:0.12
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:29312542 original size:12 final size:12
Alignment explanation
Indices: 29312525--29312603 Score: 56
Period size: 12 Copynumber: 6.6 Consensus size: 12
29312515 AGTGAAAAGC
29312525 AAAAAGAGATTG
1 AAAAAGAGATTG
*
29312537 AAAAAGAAATTG
1 AAAAAGAGATTG
*
29312549 --AAAGAGA-AG
1 AAAAAGAGATTG
*
29312558 AAAAAGAAAGAGTGG
1 AAAAAG--AGA-TTG
*
29312573 AAAAAGAAATTG
1 AAAAAGAGATTG
*
29312585 AAAAAGAGTTTG
1 AAAAAGAGATTG
*
29312597 TAAAAGA
1 AAAAAGA
29312604 AACGAGTGAA
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
9 1 0.02
10 6 0.12
11 4 0.08
12 29 0.56
13 5 0.10
15 7 0.13
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.14
Consensus pattern (12 bp):
AAAAAGAGATTG
Found at i:29312566 original size:15 final size:15
Alignment explanation
Indices: 29312548--29312581 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
29312538 AAAAGAAATT
29312548 GAAAGAGAAGAAAAA
1 GAAAGAGAAGAAAAA
**
29312563 GAAAGAGTGGAAAAA
1 GAAAGAGAAGAAAAA
29312578 GAAA
1 GAAA
29312582 TTGAAAAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.68, C:0.00, G:0.29, T:0.03
Consensus pattern (15 bp):
GAAAGAGAAGAAAAA
Found at i:29312587 original size:21 final size:20
Alignment explanation
Indices: 29312535--29312587 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 20
29312525 AAAAAGAGAT
29312535 TGAAAAAGAAATTGAAAGA-
1 TGAAAAAGAAATTGAAAGAG
*
29312554 -GAAGAA-AAA--GAAAGAG
1 TGAAAAAGAAATTGAAAGAG
29312570 TGGAAAAAGAAATTGAAA
1 T-GAAAAAGAAATTGAAA
29312588 AAGAGTTTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 10
0.68 0.05 0.26
Matches are distributed among these distances:
15 6 0.23
17 3 0.12
18 10 0.38
19 3 0.12
21 4 0.15
ACGTcount: A:0.64, C:0.00, G:0.25, T:0.11
Consensus pattern (20 bp):
TGAAAAAGAAATTGAAAGAG
Found at i:29321300 original size:25 final size:25
Alignment explanation
Indices: 29321223--29321375 Score: 150
Period size: 25 Copynumber: 6.1 Consensus size: 25
29321213 TCATTAGGGT
* *
29321223 TACCAATTTATAACTCGTAAGAGCA
1 TACCGATTTATAGCTCGTAAGAGCA
* * *
29321248 TAACGATTTAAAGATCGTAAGAGCA
1 TACCGATTTATAGCTCGTAAGAGCA
29321273 TACCGATTTATAGCTCGTAAGAGCA
1 TACCGATTTATAGCTCGTAAGAGCA
* *
29321298 TA-CTAGTTTATAGCTCGTGAGAGCA
1 TACCGA-TTTATAGCTCGTAAGAGCA
* *
29321323 TACCGATCTT-CAGCTC-AAATGAGCA
1 TACCGAT-TTATAGCTCGTAA-GAGCA
* * *
29321348 TACCGATTCACAGCTCGTATGAGCA
1 TACCGATTTATAGCTCGTAAGAGCA
29321373 TAC
1 TAC
29321376 ATGTACATGA
Statistics
Matches: 105, Mismatches: 17, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
24 4 0.04
25 96 0.91
26 5 0.05
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (25 bp):
TACCGATTTATAGCTCGTAAGAGCA
Found at i:29324252 original size:26 final size:26
Alignment explanation
Indices: 29324205--29324277 Score: 78
Period size: 26 Copynumber: 2.8 Consensus size: 26
29324195 GAATTTTCTC
* *
29324205 AAAATTTTATCAATGGTGAAATCGT-A
1 AAAATTTTATC-AGGGTAAAATCGTCA
*
29324231 AAAATTTTATTCAGGGTAAAATTGTCA
1 AAAATTTTA-TCAGGGTAAAATCGTCA
*
29324258 AAAATTTTCT-AGGGTAAAAT
1 AAAATTTTATCAGGGTAAAAT
29324278 TGGGGTGAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 10 0.24
26 20 0.49
27 11 0.27
ACGTcount: A:0.42, C:0.07, G:0.15, T:0.36
Consensus pattern (26 bp):
AAAATTTTATCAGGGTAAAATCGTCA
Found at i:29326672 original size:21 final size:21
Alignment explanation
Indices: 29326633--29326673 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29326623 TGTTTTAAGG
*
29326633 TTATTTTGATATCTTTAAAAT
1 TTATTTTGATATCTCTAAAAT
29326654 TTATATTTGATAT-TCTAAAA
1 TTAT-TTTGATATCTCTAAAA
29326674 AGTCATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (21 bp):
TTATTTTGATATCTCTAAAAT
Found at i:29326674 original size:22 final size:21
Alignment explanation
Indices: 29326633--29326674 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
29326623 TGTTTTAAGG
*
29326633 TTATTTTGATATCTTTAAAAT
1 TTATTTTGATATCTTAAAAAT
29326654 TTATATTTGATAT-TCTAAAAA
1 TTAT-TTTGATATCT-TAAAAA
29326675 GTCATTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (21 bp):
TTATTTTGATATCTTAAAAAT
Found at i:29329569 original size:20 final size:20
Alignment explanation
Indices: 29329501--29329571 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
29329491 ATTGCACTTT
* *
29329501 GGTGCATCTGCTTGCACTAC
1 GGTGCCTCTGTTTGCACTAC
* * ** *
29329521 AGTGCCTCTATTCACACTTC
1 GGTGCCTCTGTTTGCACTAC
* *
29329541 GATGTCTCTGTTTGCACTAC
1 GGTGCCTCTGTTTGCACTAC
29329561 GGTGCCTCTGT
1 GGTGCCTCTGT
29329572 ACAGGTTACG
Statistics
Matches: 35, Mismatches: 16, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.14, C:0.30, G:0.21, T:0.35
Consensus pattern (20 bp):
GGTGCCTCTGTTTGCACTAC
Found at i:29336053 original size:45 final size:45
Alignment explanation
Indices: 29336000--29336158 Score: 164
Period size: 45 Copynumber: 3.6 Consensus size: 45
29335990 ATTAATGAAA
*
29336000 ATAAAGGTGGTTGCTATGTGCTGATTTC-GCAGGATACCAATG-GTT
1 ATAAAGGTGGTTGCTATGTGCTGATTTCACCAGG-TACCAATGAG-T
* * * *
29336045 ATATAGGTGGTTGCTATGTACTGATTTCACCTGGTACCATTGAGT
1 ATAAAGGTGGTTGCTATGTGCTGATTTCACCAGGTACCAATGAGT
* * * *
29336090 ATAAAGGTGGTTGTTATGTGCTGATTTCACC-GAGTACTATTGACT
1 ATAAAGGTGGTTGCTATGTGCTGATTTCACCAG-GTACCAATGAGT
* *
29336135 ATAAGGGTGG-TGCTGTGTGCTGAT
1 ATAAAGGTGGTTGCTATGTGCTGAT
29336159 CCACCATGTA
Statistics
Matches: 98, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
44 13 0.13
45 81 0.83
46 4 0.04
ACGTcount: A:0.23, C:0.13, G:0.28, T:0.36
Consensus pattern (45 bp):
ATAAAGGTGGTTGCTATGTGCTGATTTCACCAGGTACCAATGAGT
Found at i:29346328 original size:29 final size:29
Alignment explanation
Indices: 29346295--29346354 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
29346285 AACATCCAAA
29346295 ATCTACAAAACATAATAACCCGAGTAAGT
1 ATCTACAAAACATAATAACCCGAGTAAGT
29346324 ATCTACAAAACATAATAACCCGAGTAAGT
1 ATCTACAAAACATAATAACCCGAGTAAGT
29346353 AT
1 AT
29346355 ATAAAATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.22
Consensus pattern (29 bp):
ATCTACAAAACATAATAACCCGAGTAAGT
Found at i:29354487 original size:138 final size:138
Alignment explanation
Indices: 29354234--29354678 Score: 701
Period size: 138 Copynumber: 3.2 Consensus size: 138
29354224 AAAGAACATA
* *
29354234 AATAGAATTAATATATGAATTTGATTCATACTAAATATTAATTGTATATATTTTACCGAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTAT
* *
29354299 TAATATCAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGGCATGGAAATTAATATTCTT
66 TAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
29354364 TTGGAAAT
131 TTGGAAAT
* * *
29354372 AATATAATTATTATATGAATTTGATTCATACAAAATATGAATTGTAAATATTTTACCGAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTAT
* * *
29354437 TAATATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATGGAAATTAATGTTATT
66 TAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
*
29354502 TTGGAAAG
131 TTGGAAAT
* * **
29354510 AATTTAATTAATATATGAATTTGATCCATACAAAATATTAATTGTATATATTTTACTAAATTTAT
1 AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTAT
* * * *
29354575 TAATATAAATAGTTATATTAATTAATTTCGATCAAAATATACAAGACATGGAAATTAATATTCTT
66 TAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
*
29354640 TTGAAAAT
131 TTGGAAAT
*
29354648 AATACAATTAATATATGAATTTGATTCATAC
1 AATATAATTAATATATGAATTTGATTCATAC
29354679 TTTACCGAAT
Statistics
Matches: 277, Mismatches: 30, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
138 277 1.00
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.41
Consensus pattern (138 bp):
AATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTAT
TAATATAAACAATTATATTAATTAATTTCGGTCAAAATATAAAAGACATGGAAATTAATATTCTT
TTGGAAAT
Found at i:29354717 original size:118 final size:118
Alignment explanation
Indices: 29354568--29354792 Score: 364
Period size: 118 Copynumber: 1.9 Consensus size: 118
29354558 TATTTTACTA
* *
29354568 AATTTATTAATATAAATAGTTATATTAATTAATTTCGATCAAAATATACA-AGACATGGAAATTA
1 AATTTATTAATATAAACAATTATATTAATTAATTTCGATCAAAATATA-ATAGACATGGAAATTA
*
29354632 ATATTC-TTTTGAAAATAATACAATTAATATATGAATTTGATTCATACTTTACCG
65 ATATTCTTTTTG-AAAGAATACAATTAATATATGAATTTGATTCATACTTTACCG
* *
29354686 AATTTATTAATCTAAACAATTATATTAATTAATTTTGATCAAAATATAATAGACATGGAAATTAA
1 AATTTATTAATATAAACAATTATATTAATTAATTTCGATCAAAATATAATAGACATGGAAATTAA
*
29354751 TATTCTTTTTGAAAGAATATAATTAATATATGAATTTGATTC
66 TATTCTTTTTGAAAGAATACAATTAATATATGAATTTGATTC
29354793 GTACAGAATA
Statistics
Matches: 99, Mismatches: 6, Indels: 4
0.91 0.06 0.04
Matches are distributed among these distances:
117 1 0.01
118 93 0.94
119 5 0.05
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (118 bp):
AATTTATTAATATAAACAATTATATTAATTAATTTCGATCAAAATATAATAGACATGGAAATTAA
TATTCTTTTTGAAAGAATACAATTAATATATGAATTTGATTCATACTTTACCG
Found at i:29354879 original size:256 final size:256
Alignment explanation
Indices: 29354423--29354912 Score: 793
Period size: 256 Copynumber: 1.9 Consensus size: 256
29354413 TTGTAAATAT
*
29354423 TTTACCGAATTTATTAATATAAACAATTATATTAATTAATTTTGGTCAAAATATAAAAGACATGG
1 TTTACCGAATTTATTAATATAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGG
* *
29354488 AAATTAATGTTATTTTGGAAAGAATTTAATTAATATATGAATTTGATCCATACAAAATATTAATT
66 AAATTAATATTATTTTGGAAAGAATATAATTAATATATGAATTTGATCCATACAAAATATTAATT
* * *
29354553 GTATATATTTTACTAAATTTATTAATATAAATAGTTATATTAATTAATTTCGATCAAAATATACA
131 GTATATATTTTACTAAATTTATTAATATAAACAGTTATATTAACTAATTTCGATCAAAATATAAA
*
29354618 AGACATGGAAATTAATATTCTTTTGAAAATAATACAATTAATATATGAATTTGATTCATAC
196 AGACATGGAAATTAATATTCTTTTGAAAAGAATACAATTAATATATGAATTTGATTCATAC
* *
29354679 TTTACCGAATTTATTAATCTAAACAATTATATTAATTAATTTTGATCAAAATATAATAGACATGG
1 TTTACCGAATTTATTAATATAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGG
* * * * *
29354744 AAATTAATATTCTTTTTGAAAGAATATAATTAATATATGAATTTGATTCGTACAGAATATTAATT
66 AAATTAATATTATTTTGGAAAGAATATAATTAATATATGAATTTGATCCATACAAAATATTAATT
* *
29354809 GTATATATTTTA-TCAAATTTATTAATATAAACAGTTATATTAACTAATTTTGGTCAAAATATAA
131 GTATATATTTTACT-AAATTTATTAATATAAACAGTTATATTAACTAATTTCGATCAAAATATAA
* * *
29354873 AAGACATGTAAATTAATATTCTTTTGGAAAGAATATAATT
195 AAGACATGGAAATTAATATTCTTTTGAAAAGAATACAATT
29354913 TATTTTCCTA
Statistics
Matches: 214, Mismatches: 19, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
255 1 0.00
256 213 1.00
ACGTcount: A:0.44, C:0.07, G:0.08, T:0.41
Consensus pattern (256 bp):
TTTACCGAATTTATTAATATAAACAATTATATTAATTAATTTTGATCAAAATATAAAAGACATGG
AAATTAATATTATTTTGGAAAGAATATAATTAATATATGAATTTGATCCATACAAAATATTAATT
GTATATATTTTACTAAATTTATTAATATAAACAGTTATATTAACTAATTTCGATCAAAATATAAA
AGACATGGAAATTAATATTCTTTTGAAAAGAATACAATTAATATATGAATTTGATTCATAC
Found at i:29356226 original size:41 final size:41
Alignment explanation
Indices: 29356128--29356318 Score: 228
Period size: 41 Copynumber: 4.7 Consensus size: 41
29356118 AAATCGAGCA
* *
29356128 TTAGCGGCGTTTTTGAAAAAGTGCCGCTAATGCTC-GGGTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGGTT
* * *
29356168 TTAGCGGTGTTTTTGAGAAACCGCCTCTAATGCTCGGGGTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGGTT
* **
29356209 TTAGCGGCGTTTATGAGAAAGCGCCGCTAATGCTCGCAGTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGGTT
*
29356250 TTAGCGGCGTTTTTGAGAAAGCGCCAC--ATGCTCGGGGTT
1 TTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGGTT
* * * *
29356289 TTGGCAGCGCTTTTTCA-AAAACGCCGCTAA
1 TTAGCGGCG-TTTTTGAGAAAGCGCCGCTAA
29356319 AAGTTTTTTA
Statistics
Matches: 127, Mismatches: 20, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
39 25 0.20
40 36 0.28
41 66 0.52
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAGAAAGCGCCGCTAATGCTCGGGGTT
Found at i:29356317 original size:80 final size:80
Alignment explanation
Indices: 29356150--29356318 Score: 216
Period size: 80 Copynumber: 2.1 Consensus size: 80
29356140 TTGAAAAAGT
* * * *
29356150 GCCGCTAATGCTCGGGTTTTAGCGGTGTTTTTGAGAAACCGCCTCTAATGCTCGGGGTTTTAGCG
1 GCCGCTAATGCTCGAGTTTTAGCGGCGTTTTTGAGAAACCGCCAC-AATGCTCGGGGTTTTAGCA
* *
29356215 GCGTTTATGAGAAAGC
65 GCGTTTATCAGAAAAC
* *
29356231 GCCGCTAATGCTCGCAGTTTTAGCGGCGTTTTTGAGAAAGCGCCAC-ATGCTCGGGGTTTTGGCA
1 GCCGCTAATGCTCG-AGTTTTAGCGGCGTTTTTGAGAAACCGCCACAATGCTCGGGGTTTTAGCA
*
29356295 GCGCTTTTTCA-AAAAC
65 GCG-TTTATCAGAAAAC
29356311 GCCGCTAA
1 GCCGCTAA
29356319 AAGTTTTTTA
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
80 31 0.40
81 19 0.25
82 27 0.35
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (80 bp):
GCCGCTAATGCTCGAGTTTTAGCGGCGTTTTTGAGAAACCGCCACAATGCTCGGGGTTTTAGCAG
CGTTTATCAGAAAAC
Found at i:29356352 original size:18 final size:17
Alignment explanation
Indices: 29356321--29356354 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29356311 GCCGCTAAAA
*
29356321 GTTTTTTATCTTAATTG
1 GTTTTTTATATTAATTG
29356338 GTTTATTTATATTAATT
1 GTTT-TTTATATTAATT
29356355 AAATAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.65
Consensus pattern (17 bp):
GTTTTTTATATTAATTG
Found at i:29356456 original size:23 final size:26
Alignment explanation
Indices: 29356403--29356457 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
29356393 TCTTCAGAAA
*
29356403 AAAATAATAACACGTAGAAATAATTT
1 AAAATAATAACACATAGAAATAATTT
* *
29356429 GAAATAA-AACACATGGAAA-AA-TT
1 AAAATAATAACACATAGAAATAATTT
29356452 AAAATA
1 AAAATA
29356458 CTATTATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 7 0.28
24 2 0.08
25 10 0.40
26 6 0.24
ACGTcount: A:0.62, C:0.07, G:0.09, T:0.22
Consensus pattern (26 bp):
AAAATAATAACACATAGAAATAATTT
Found at i:29356695 original size:15 final size:15
Alignment explanation
Indices: 29356667--29356718 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
29356657 CTAGTTTAAA
* *
29356667 ATTTAAGGAGTATGG
1 ATTTAGGGATTATGG
29356682 ATTTAGGGATTATGG
1 ATTTAGGGATTATGG
*
29356697 A-TTAGGGATTAGGG
1 ATTTAGGGATTATGG
*
29356711 ATTAAGGG
1 ATTTAGGG
29356719 TTGGGATTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
14 13 0.41
15 19 0.59
ACGTcount: A:0.31, C:0.00, G:0.37, T:0.33
Consensus pattern (15 bp):
ATTTAGGGATTATGG
Found at i:29356750 original size:14 final size:14
Alignment explanation
Indices: 29356684--29356791 Score: 67
Period size: 14 Copynumber: 7.6 Consensus size: 14
29356674 GAGTATGGAT
* *
29356684 TTAGGGATTATGGA
1 TTAGGGATTAGGGG
*
29356698 TTAGGGATTAGGGA
1 TTAGGGATTAGGGG
*
29356712 TTAAGGG-TT-GGGAT
1 TT-AGGGATTAGGG-G
* *
29356726 TTAAGGTTTAGGGG
1 TTAGGGATTAGGGG
29356740 TTAGGGATTAGGGG
1 TTAGGGATTAGGGG
* ***
29356754 TTAGGGGTTAATAG
1 TTAGGGATTAGGGG
*
29356768 TTAGGGATTTAGGGT
1 TTAGGGA-TTAGGGG
*
29356783 TTAAGGATT
1 TTAGGGATT
29356792 CATGGGTCAG
Statistics
Matches: 73, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
13 6 0.08
14 51 0.70
15 16 0.22
ACGTcount: A:0.25, C:0.00, G:0.40, T:0.35
Consensus pattern (14 bp):
TTAGGGATTAGGGG
Found at i:29356763 original size:7 final size:7
Alignment explanation
Indices: 29356684--29356759 Score: 75
Period size: 7 Copynumber: 10.9 Consensus size: 7
29356674 GAGTATGGAT
29356684 TTAGGGA
1 TTAGGGA
*
29356691 TTATGGA
1 TTAGGGA
29356698 TTAGGGA
1 TTAGGGA
29356705 TTAGGGA
1 TTAGGGA
29356712 TTAAGGG-
1 TT-AGGGA
29356719 TT-GGGA
1 TTAGGGA
* *
29356725 TTTAAGGT
1 -TTAGGGA
*
29356733 TTAGGGG
1 TTAGGGA
29356740 TTAGGGA
1 TTAGGGA
*
29356747 TTAGGGG
1 TTAGGGA
29356754 TTAGGG
1 TTAGGG
29356760 GTTAATAGTT
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
5 3 0.05
7 48 0.84
8 6 0.11
ACGTcount: A:0.24, C:0.00, G:0.43, T:0.33
Consensus pattern (7 bp):
TTAGGGA
Found at i:29356772 original size:35 final size:35
Alignment explanation
Indices: 29356698--29356788 Score: 96
Period size: 35 Copynumber: 2.6 Consensus size: 35
29356688 GGATTATGGA
* *
29356698 TTAGGGATTAGGGATTAAGGGTTGGGATTTAAGGT
1 TTAGGGATTAGGGATTAAGGGTTGGGAGTTAAAGT
* *
29356733 TTAGGGGTTAGGGATTAGGGGTTAGGG-GTTAATAG-
1 TTAGGGATTAGGGATTAAGGGTT-GGGAGTTAA-AGT
*
29356768 TTAGGGATTTAGGGTTTAAGG
1 TTAGGGA-TTAGGGATTAAGG
29356789 ATTCATGGGT
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
35 31 0.67
36 15 0.33
ACGTcount: A:0.24, C:0.00, G:0.42, T:0.34
Consensus pattern (35 bp):
TTAGGGATTAGGGATTAAGGGTTGGGAGTTAAAGT
Found at i:29356861 original size:25 final size:25
Alignment explanation
Indices: 29356829--29356876 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
29356819 AGATTAATTA
*
29356829 TTTTTTAATTTATATTTTAAATATG
1 TTTTTTAATTTATATATTAAATATG
29356854 TTTTTTAATTTATATATTAAATA
1 TTTTTTAATTTATATATTAAATA
29356877 ATTTCATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTTTAATTTATATATTAAATATG
Found at i:29357084 original size:7 final size:7
Alignment explanation
Indices: 29357074--29357111 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
29357064 GATTTAAAGT
29357074 TTAGGGG
1 TTAGGGG
*
29357081 TTAGGAG
1 TTAGGGG
29357088 TTAGGGG
1 TTAGGGG
29357095 TTAGGGG
1 TTAGGGG
29357102 TCT-GGGG
1 T-TAGGGG
29357109 TTA
1 TTA
29357112 AGAGTTAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 1 0.04
7 25 0.93
8 1 0.04
ACGTcount: A:0.16, C:0.03, G:0.50, T:0.32
Consensus pattern (7 bp):
TTAGGGG
Found at i:29357093 original size:14 final size:14
Alignment explanation
Indices: 29357074--29357118 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
29357064 GATTTAAAGT
29357074 TTAGGGGTTAGGAG
1 TTAGGGGTTAGGAG
*
29357088 TTAGGGGTTAGGGG
1 TTAGGGGTTAGGAG
*
29357102 TCT-GGGGTTAAGAG
1 T-TAGGGGTTAGGAG
29357116 TTA
1 TTA
29357119 AGAATTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 1 0.04
14 24 0.92
15 1 0.04
ACGTcount: A:0.20, C:0.02, G:0.47, T:0.31
Consensus pattern (14 bp):
TTAGGGGTTAGGAG
Found at i:29357142 original size:341 final size:342
Alignment explanation
Indices: 29356508--29357204 Score: 840
Period size: 341 Copynumber: 2.0 Consensus size: 342
29356498 TTACTGATTT
* * * *
29356508 TTTTTTAATTTATTTATTAAAAAATTTCTTATATAATCGTAAAAGAGGTAGTATTAATTTTAAAA
1 TTTTTTAATTTATATATTAAAAAATTTCATATATAATCGAAAAAGAGATAGTATTAATTTTAAAA
* * *
29356573 TATTGAATTAATTATCACTATAGTTTAGGATTTTTGGTTTAATGTATATAATTTATTTAAGATTT
66 TATTGAATTAATTATCACTATAGTTTAGGATTTTTGGTTTAAGGTATATAATTAATTTAAGATAT
* *
29356638 AAGGCCGGTTTAGGAGTTACTAGTTTAAAATTTAAGGAGTATGGATTTAGGGATTATGGATTAGG
131 AAGGCCAGTTTAGGAGTTACTAGTTTAAAATTT-A-GAG--TGGATTTA-GGATTATGGATTAAG
* *
29356703 GATTAGGGATTAAGGGTTGGGATTTAAGGTTTAGGGGTTAGGGATTAGGGGTTAGGGGTTAATAG
191 GATTAGGGATTAAGGGTTGGGATTTAAAGTTTAGGGGTTAGGGATTAGGGGTTAGGGGTTAAGAG
* * ** * * * *
29356768 TTAGGGATTTAGGGTTTAAGGATTCATGGGTCAGGTTAGGGTTTTGGGTTTAGATTAATTA-TTT
256 TTAGAGATTAAGAATTTAAGGATTCAAGGGTCAGGTTAAGGTCTAGGGTTTAGATTAATTAGTTT
*
29356832 TTTAATTTATATTTTAAATATG
321 TTTAATTTATATATTAAATATG
* *
29356854 TTTTTTAATTTATATATTAAATAATTTCATATATAATTGAAAAAGATAAGATAGTATTAATTTTA
1 TTTTTTAATTTATATATTAAAAAATTTCATATATAATCGAAAAAG---AGATAGTATTAATTTTA
* * * **
29356919 AAATATTTAATTAATTATCATTATAGTTTATGG-TTTATATGGTTTACGGTATATGGTTAATTTA
63 AAATATTGAATTAATTATCACTATAGTTTA-GGATTT-T-TGGTTTAAGGTATATAATTAATTTA
* ** *
29356983 AGATATAAGGCCAGTTTAGGAGTTACTATTTTAAGGTTT-G-G-GGA-TTA-TA-TATGGATTTA
125 AGATATAAGGCCAGTTTAGGAGTTACTAGTTTAAAATTTAGAGTGGATTTAGGATTATGGA-TTA
* *
29357042 AGGATTATGGTTTAAGGGTTGGGATTTAAAGTTTAGGGGTTA-GGAGTTAGGGGTTAGGGGTCT-
189 AGGATTAGGGATTAAGGGTTGGGATTTAAAGTTTAGGGGTTAGGGA-TTAGGGGTTAGGGGT-TA
* * *
29357105 GGGGTTA-AGAGTTAAGAATTTAAGGTTTCAAGGGTCAGGTTAAGGTCTAGGGTTTAGATTAATT
252 AGAGTTAGAGA-TTAAGAATTTAAGGATTCAAGGGTCAGGTTAAGGTCTAGGGTTTAGATTAATT
29357169 AGTTTTTTTAATTTATATATTAAATATG
316 AG-TTTTTTAATTTATATATTAAATATG
29357197 TTCTTTTA
1 TT-TTTTA
29357205 TAATTGTAAA
Statistics
Matches: 302, Mismatches: 36, Indels: 28
0.83 0.10 0.08
Matches are distributed among these distances:
340 11 0.04
341 107 0.35
342 1 0.00
343 29 0.10
344 8 0.03
346 40 0.13
347 1 0.00
348 1 0.00
349 47 0.16
350 3 0.01
351 54 0.18
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.43
Consensus pattern (342 bp):
TTTTTTAATTTATATATTAAAAAATTTCATATATAATCGAAAAAGAGATAGTATTAATTTTAAAA
TATTGAATTAATTATCACTATAGTTTAGGATTTTTGGTTTAAGGTATATAATTAATTTAAGATAT
AAGGCCAGTTTAGGAGTTACTAGTTTAAAATTTAGAGTGGATTTAGGATTATGGATTAAGGATTA
GGGATTAAGGGTTGGGATTTAAAGTTTAGGGGTTAGGGATTAGGGGTTAGGGGTTAAGAGTTAGA
GATTAAGAATTTAAGGATTCAAGGGTCAGGTTAAGGTCTAGGGTTTAGATTAATTAGTTTTTTAA
TTTATATATTAAATATG
Found at i:29359490 original size:23 final size:21
Alignment explanation
Indices: 29359458--29359499 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
29359448 TATTTTAACC
*
29359458 CTATTTATAAAATCTAAAAACT
1 CTATTTAT-AAATCAAAAAACT
29359480 CTATTATATAAATCAAAAAA
1 CTATT-TATAAATCAAAAAA
29359500 TGCCCCTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (21 bp):
CTATTTATAAATCAAAAAACT
Found at i:29361594 original size:43 final size:43
Alignment explanation
Indices: 29361543--29361853 Score: 374
Period size: 43 Copynumber: 7.3 Consensus size: 43
29361533 ATGGCACTTT
* *
29361543 TAGCGGCGTTTGTGAAAAAAGCGCCACTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATCTA
* * * *
29361586 TAGTGGCGTTTGTGGGAGAAGCGCCGCTAAAAGTCATGATTTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATCTA
* * *
29361629 TAGCGGTGTTTG-GGCAAAAAGTGCTGCTAAAAGTCATGATCTA
1 TAGCGGCGTTTGTGG-AAAAAGCGCCGCTAAAAGTCATGATCTA
* * * * *
29361672 TAGCGGCGTTTGTGGGAAAAGAGCCGCTAAAGGTCTTGAGCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATCTA
* * * *
29361715 TAGCGGCATTTGT-GTAAAAGCGTCGCTAAAAGTCTTGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATCTA
* * * *
29361757 TAGCGGCGTTTGTGGAAAAAGCACCGCTAAAGGTCCTGATATA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATCTA
* * *
29361800 TAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTA
1 TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATCTA
29361843 TAGCGGCGTTT
1 TAGCGGCGTTT
29361854 ATTTCTAAAA
Statistics
Matches: 226, Mismatches: 39, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
42 38 0.17
43 186 0.82
44 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.29, T:0.26
Consensus pattern (43 bp):
TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAAGTCATGATCTA
Found at i:29361786 original size:128 final size:129
Alignment explanation
Indices: 29361543--29361849 Score: 393
Period size: 128 Copynumber: 2.4 Consensus size: 129
29361533 ATGGCACTTT
** * * * * *
29361543 TAGCGGCGTTTGTGAAAAAAGCGCCACTAAAAGTCATGATCTATAGTGGCGTTTGTGGGAGAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCATTTGTGGGAAAAGC
* * ** * *
29361608 GCCGCTAAAAGTCATGATTTATAGCGGTGTTTGGGCAAAAAGTGCTGCTAAAAGTCATGATCTA
66 GCCGCTAAAAGTCATGATCTATAGCGGCGTTTGGGCAAAAAGCACCGCTAAAAGTCATGATATA
* * * *
29361672 TAGCGGCGTTTGTGGGAAAAGAGCCGCTAAAGGTCTTGAGCTATAGCGGCATTTGT-GTAAAAGC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCATTTGTGGGAAAAGC
* * * *
29361736 GTCGCTAAAAGTCTTGATCTATAGCGGCGTTTGTGG-AAAAAGCACCGCTAAAGGTCCTGATATA
66 GCCGCTAAAAGTCATGATCTATAGCGGCGTTTG-GGCAAAAAGCACCGCTAAAAGTCATGATATA
*
29361800 TAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGC
1 TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGC
29361850 GTTTATTTCT
Statistics
Matches: 152, Mismatches: 25, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
128 103 0.68
129 49 0.32
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (129 bp):
TAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTATAGCGGCATTTGTGGGAAAAGC
GCCGCTAAAAGTCATGATCTATAGCGGCGTTTGGGCAAAAAGCACCGCTAAAAGTCATGATATA
Found at i:29367902 original size:23 final size:23
Alignment explanation
Indices: 29367876--29368055 Score: 215
Period size: 23 Copynumber: 8.0 Consensus size: 23
29367866 GCTATGCCGA
*
29367876 TCAGGCACTTTACGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
29367899 TCAGGCACTTTATGTGTCGTAATT
1 TCAGGCACTTTATGTGTCGT-ATT
* **
29367923 T-AGGCACCTCGTGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
29367945 TCAGGCACTTTATGTGTCGTAAT
1 TCAGGCACTTTATGTGTCGTATT
* **
29367968 TCAGGCACCTCGTGTGTCGTATT
1 TCAGGCACTTTATGTGTCGTATT
*
29367991 TCAGGCACTTTATGTGTCGTAAT
1 TCAGGCACTTTATGTGTCGTATT
* **
29368014 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACTTTATGTGTCGTATT
29368035 TCAGGCAC-TTATGTGTCGTAT
1 TCAGGCACTTTATGTGTCGTAT
29368056 ACTGATTAGG
Statistics
Matches: 133, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
20 10 0.08
21 8 0.06
22 4 0.03
23 107 0.80
24 4 0.03
ACGTcount: A:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (23 bp):
TCAGGCACTTTATGTGTCGTATT
Found at i:29367939 original size:46 final size:46
Alignment explanation
Indices: 29367889--29368054 Score: 302
Period size: 46 Copynumber: 3.7 Consensus size: 46
29367879 GGCACTTTAC
*
29367889 GTGTCGTATTTCAGGCACTTTATGTGTCGTAATTTAGGCACCTCGT
1 GTGTCGTATTTCAGGCACTTTATGTGTCGTAATTCAGGCACCTCGT
29367935 GTGTCGTATTTCAGGCACTTTATGTGTCGTAATTCAGGCACCTCGT
1 GTGTCGTATTTCAGGCACTTTATGTGTCGTAATTCAGGCACCTCGT
29367981 GTGTCGTATTTCAGGCACTTTATGTGTCGTAATTCAGGCACCTCGT
1 GTGTCGTATTTCAGGCACTTTATGTGTCGTAATTCAGGCACCTCGT
29368027 GTGTCGTA--TCAGGCAC-TTATGTGTCGTA
1 GTGTCGTATTTCAGGCACTTTATGTGTCGTA
29368055 TACTGATTAG
Statistics
Matches: 119, Mismatches: 1, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
43 12 0.10
44 8 0.07
46 99 0.83
ACGTcount: A:0.17, C:0.20, G:0.25, T:0.37
Consensus pattern (46 bp):
GTGTCGTATTTCAGGCACTTTATGTGTCGTAATTCAGGCACCTCGT
Found at i:29373268 original size:41 final size:41
Alignment explanation
Indices: 29373178--29373328 Score: 268
Period size: 41 Copynumber: 3.7 Consensus size: 41
29373168 GACCTTTTGG
*
29373178 GGCTTTTAGCGGCGTTTTTGAGAAAGCGCCGCT-ATGCTCA
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
*
29373218 GGCTTTTAGCGGCGTTTTTGAAAAAGCACCGCTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
*
29373259 GGCTTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
29373300 GGCTTTTAGCGGCGTTTTTGAAAAAGCGC
1 GGCTTTTAGCGGCGTTTTTGAAAAAGCGC
29373329 TGCAAAAACA
Statistics
Matches: 105, Mismatches: 5, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
40 31 0.30
41 74 0.70
ACGTcount: A:0.22, C:0.21, G:0.27, T:0.30
Consensus pattern (41 bp):
GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA
Found at i:29373815 original size:20 final size:20
Alignment explanation
Indices: 29373768--29373833 Score: 71
Period size: 20 Copynumber: 3.2 Consensus size: 20
29373758 AGGGTTGTGA
*
29373768 TTTAGGGGTTAAGGGTTAGGG
1 TTTA-GGGTTTAGGGTTAGGG
* *
29373789 GTCAGGGATTT-GGGTTAGGG
1 TTTAGGG-TTTAGGGTTAGGG
29373809 TTTAGGGTTTAGGGTTTAGGG
1 TTTAGGGTTTAGGG-TTAGGG
29373830 TTTA
1 TTTA
29373834 AATTAAATAG
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
19 3 0.08
20 20 0.54
21 14 0.38
ACGTcount: A:0.17, C:0.02, G:0.44, T:0.38
Consensus pattern (20 bp):
TTTAGGGTTTAGGGTTAGGG
Found at i:29373822 original size:27 final size:27
Alignment explanation
Indices: 29373768--29373831 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
29373758 AGGGTTGTGA
29373768 TTTAGGGGTTAAGGGTTAGGGGTCAGGG
1 TTTA-GGGTTAAGGGTTAGGGGTCAGGG
* *
29373796 ATTT-GGGTT-AGGGTTTAGGGTTTAGGG
1 -TTTAGGGTTAAGGG-TTAGGGGTCAGGG
29373823 TTTAGGGTT
1 TTTAGGGTT
29373832 TAAATTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
26 7 0.23
27 21 0.68
29 3 0.10
ACGTcount: A:0.16, C:0.02, G:0.45, T:0.38
Consensus pattern (27 bp):
TTTAGGGTTAAGGGTTAGGGGTCAGGG
Found at i:29373832 original size:7 final size:7
Alignment explanation
Indices: 29373768--29373833 Score: 66
Period size: 7 Copynumber: 9.6 Consensus size: 7
29373758 AGGGTTGTGA
29373768 TTTAGGGG
1 TTTA-GGG
*
29373776 TTAAGGG
1 TTTAGGG
29373783 -TTAGGG
1 TTTAGGG
* *
29373789 GTCAGGG
1 TTTAGGG
29373796 ATTT-GGG
1 -TTTAGGG
29373803 -TTAGGG
1 TTTAGGG
29373809 TTTAGGG
1 TTTAGGG
29373816 TTTAGGG
1 TTTAGGG
29373823 TTTAGGG
1 TTTAGGG
29373830 TTTA
1 TTTA
29373834 AATTAAATAG
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
5 2 0.04
6 8 0.16
7 35 0.71
8 4 0.08
ACGTcount: A:0.17, C:0.02, G:0.44, T:0.38
Consensus pattern (7 bp):
TTTAGGG
Found at i:29378456 original size:24 final size:23
Alignment explanation
Indices: 29378428--29378475 Score: 62
Period size: 22 Copynumber: 2.0 Consensus size: 23
29378418 AATTTAAAAA
29378428 ATAAAACATAATATAATATTT-ATT
1 ATAAAA-ATAA-ATAATATTTGATT
*
29378452 ATAAAAATAAATATTATTTGATT
1 ATAAAAATAAATAATATTTGATT
29378475 A
1 A
29378476 AAATATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 8 0.36
24 6 0.27
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAAAATAAATAATATTTGATT
Found at i:29378597 original size:43 final size:43
Alignment explanation
Indices: 29378525--29378638 Score: 185
Period size: 43 Copynumber: 2.7 Consensus size: 43
29378515 TGCTAGAAGT
* *
29378525 GCCGCTAAAGGT-TTGTTCTTTAGCGGCGTTTGTGGAAAAAGC
1 GCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAAAAGC
* *
29378567 GTCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGGAAAAGC
1 GCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAAAAGC
29378610 GCCGCTAAAGGTCGTGGTCTTTAGCGGCG
1 GCCGCTAAAGGTCGTGGTCTTTAGCGGCG
29378639 CTGTCATTAA
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
42 11 0.17
43 55 0.83
ACGTcount: A:0.18, C:0.18, G:0.35, T:0.28
Consensus pattern (43 bp):
GCCGCTAAAGGTCGTGGTCTTTAGCGGCGTTTGTGGAAAAAGC
Found at i:29378689 original size:31 final size:31
Alignment explanation
Indices: 29378651--29378722 Score: 126
Period size: 31 Copynumber: 2.3 Consensus size: 31
29378641 GTCATTAACG
*
29378651 GCGCCGCTAATGCTTATAGCGGCGCTAAAAA
1 GCGCCGCTAATGCTTATAGCAGCGCTAAAAA
*
29378682 GCGCCGCTAATGCTTATAGCAGCGCTAAGAA
1 GCGCCGCTAATGCTTATAGCAGCGCTAAAAA
29378713 GCGCCGCTAA
1 GCGCCGCTAA
29378723 AGACCCTGAC
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (31 bp):
GCGCCGCTAATGCTTATAGCAGCGCTAAAAA
Found at i:29378870 original size:22 final size:22
Alignment explanation
Indices: 29378838--29378881 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
29378828 TAGCGGTGCT
* *
29378838 AAAAAGTGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
29378860 AAAAAGCGCCGCTAAAAGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
29378882 TTTTGGTGTA
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:0.43, C:0.25, G:0.20, T:0.11
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:29383186 original size:81 final size:81
Alignment explanation
Indices: 29383051--29383285 Score: 348
Period size: 81 Copynumber: 2.9 Consensus size: 81
29383041 ATTGGTGGCT
*
29383051 TAGGTTGAAGAAGGACGTAGCTGATTTTATTAGTAGATGTTTAGTTTACCAAAGGGTTAAAGCTA
1 TAGGTTGAAGAAGGACGTAGCTGATTTTGTTAGTAGATGTTTAGTTTACCAAAGGGTTAAAGCTA
29383116 AGCATCAATGT-CTGCC
66 AGCATCAATGTGC-GCC
* * * * * *
29383132 TAGGTTAAAGAAGGATGTAGCTAATTTTGTTAGTAAATTTTTAGTTTTCCAAAGGGTTAAAGCTA
1 TAGGTTGAAGAAGGACGTAGCTGATTTTGTTAGTAGATGTTTAGTTTACCAAAGGGTTAAAGCTA
29383197 AGCATCAATGTGCGCC
66 AGCATCAATGTGCGCC
* * *
29383213 T-GGATTGAAGAAGGACGTAGTTGATTTTGTTGGTAGATGTTTAGTTTGCCAAAGGGTTAAAGCT
1 TAGG-TTGAAGAAGGACGTAGCTGATTTTGTTAGTAGATGTTTAGTTTACCAAAGGGTTAAAGCT
29383277 AAGCATCAA
65 AAGCATCAA
29383286 CGTTCACCTG
Statistics
Matches: 137, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
80 2 0.01
81 134 0.98
82 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.25, T:0.33
Consensus pattern (81 bp):
TAGGTTGAAGAAGGACGTAGCTGATTTTGTTAGTAGATGTTTAGTTTACCAAAGGGTTAAAGCTA
AGCATCAATGTGCGCC
Found at i:29410306 original size:12 final size:12
Alignment explanation
Indices: 29410284--29410318 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
29410274 CTTTACTTAC
29410284 TCACTTACTTGT
1 TCACTTACTTGT
29410296 TCACTTACTTGT
1 TCACTTACTTGT
*
29410308 TTACTTACTTG
1 TCACTTACTTG
29410319 CTTACTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.17, C:0.23, G:0.09, T:0.51
Consensus pattern (12 bp):
TCACTTACTTGT
Found at i:29410323 original size:12 final size:12
Alignment explanation
Indices: 29410276--29410326 Score: 59
Period size: 12 Copynumber: 4.2 Consensus size: 12
29410266 ACCCGCTTCT
* *
29410276 TTACTTACTCAC
1 TTACTTGCTTAC
29410288 TTACTTG-TTCAC
1 TTACTTGCTT-AC
*
29410300 TTACTTGTTTAC
1 TTACTTGCTTAC
29410312 TTACTTGCTTAC
1 TTACTTGCTTAC
29410324 TTA
1 TTA
29410327 AATAACTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
11 1 0.03
12 31 0.91
13 2 0.06
ACGTcount: A:0.20, C:0.24, G:0.06, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:29410650 original size:50 final size:50
Alignment explanation
Indices: 29410578--29410799 Score: 246
Period size: 50 Copynumber: 4.3 Consensus size: 50
29410568 TACCCCATAT
** * *
29410578 ATGGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
** * *
29410628 ATGGTCTTACGGGGGACCTCTCATCTCAGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
* * *
29410678 ATTGCCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
* * * * *
29410728 ATGGTCTTACATGGGACCTCCCATAATCTCAATGATGCCAATGTCATGTCCCAGAA
1 ATGGTCTTACATGGGACCTCTCAT-A--TC---GGTGCCAACGCCATGTCCCAGAC
29410784 ATGGTCTTACATGGGA
1 ATGGTCTTACATGGGA
29410800 TCTCATTCCC
Statistics
Matches: 145, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
50 108 0.74
53 2 0.01
56 35 0.24
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.26
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATGTCCCAGAC
Found at i:29418741 original size:20 final size:21
Alignment explanation
Indices: 29418718--29418759 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
29418708 AAAAAAATTG
29418718 AAATATT-AAAAATTAGAAAA
1 AAATATTAAAAAATTAGAAAA
*
29418738 AAATATTAAAAAATTATAAAA
1 AAATATTAAAAAATTAGAAAA
29418759 A
1 A
29418760 TCGTAAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (21 bp):
AAATATTAAAAAATTAGAAAA
Found at i:29418757 original size:10 final size:10
Alignment explanation
Indices: 29418725--29418842 Score: 52
Period size: 10 Copynumber: 12.3 Consensus size: 10
29418715 TTGAAATATT
*
29418725 AAAAATTAGA
1 AAAAATTATA
*
29418735 AAAAAATATTA
1 AAAAATTA-TA
29418746 AAAAATTAT-
1 AAAAATTATA
**
29418755 AAAAATCGTA
1 AAAAATTATA
* *
29418765 AAAAGTAAT-
1 AAAAATTATA
*
29418774 AAAAATTGTA
1 AAAAATTATA
**
29418784 AAATTTTAT-
1 AAAAATTATA
* *
29418793 AAAAACTGTA
1 AAAAATTATA
*
29418803 AAATA-TAT-
1 AAAAATTATA
*
29418811 AGAAA-TATTA
1 AAAAATTA-TA
29418821 AAAAATTAT-
1 AAAAATTATA
29418830 AAAAATTATA
1 AAAAATTATA
29418840 AAA
1 AAA
29418843 TTTTATAAAG
Statistics
Matches: 77, Mismatches: 23, Indels: 16
0.66 0.20 0.14
Matches are distributed among these distances:
8 5 0.06
9 30 0.39
10 32 0.42
11 10 0.13
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (10 bp):
AAAAATTATA
Found at i:29418758 original size:19 final size:19
Alignment explanation
Indices: 29418718--29418835 Score: 82
Period size: 19 Copynumber: 6.2 Consensus size: 19
29418708 AAAAAAATTG
*
29418718 AAATATT-AAAAATTAGAAAA
1 AAATATTAAAAAATT--ATAA
29418738 AAATATTAAAAAATTATAA
1 AAATATTAAAAAATTATAA
** * *
29418757 AAATCGTAAAAAGTAATAA
1 AAATATTAAAAAATTATAA
**
29418776 AAAT-TGTAAAATTTTATAA
1 AAATAT-TAAAAAATTATAA
* * *
29418795 AAACT-GTAAAATA-TATAG
1 AAA-TATTAAAAAATTATAA
29418813 AAATATTAAAAAATTATAA
1 AAATATTAAAAAATTATAA
29418832 AAAT
1 AAAT
29418836 TATAAAATTT
Statistics
Matches: 78, Mismatches: 15, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
17 1 0.01
18 13 0.17
19 49 0.63
20 8 0.10
21 7 0.09
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (19 bp):
AAATATTAAAAAATTATAA
Found at i:29418778 original size:38 final size:38
Alignment explanation
Indices: 29418736--29418890 Score: 119
Period size: 37 Copynumber: 4.1 Consensus size: 38
29418726 AAAATTAGAA
29418736 AAAAATATTAAAAAATTATAAAAATC-GTAAAA-AGTAAT
1 AAAAATATTAAAAAATTATAAAAATCTGTAAAATA-T-AT
**
29418774 AAAAAT-TGTAAAATTTTATAAAAA-CTGTAAAATATAT
1 AAAAATAT-TAAAAAATTATAAAAATCTGTAAAATATAT
* * *
29418811 AGAAATATTAAAAAATTATAAAAAT-TATAAAAT-TTT
1 AAAAATATTAAAAAATTATAAAAATCTGTAAAATATAT
* *
29418847 ATAAAGTAGTAAGAAAAATTATACAAAA--TGTAAAGATATAT
1 A-AAAATA-TTA-AAAAATTATA-AAAATCTGTAAA-ATATAT
29418888 AAA
1 AAA
29418891 TTTCGTAAAA
Statistics
Matches: 94, Mismatches: 12, Indels: 20
0.75 0.10 0.16
Matches are distributed among these distances:
36 3 0.03
37 34 0.36
38 30 0.32
39 16 0.17
40 8 0.09
41 3 0.03
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.30
Consensus pattern (38 bp):
AAAAATATTAAAAAATTATAAAAATCTGTAAAATATAT
Found at i:29418848 original size:19 final size:18
Alignment explanation
Indices: 29418737--29418851 Score: 74
Period size: 19 Copynumber: 6.2 Consensus size: 18
29418727 AAATTAGAAA
*
29418737 AAAATATTA-AAAAATTAT
1 AAAA-ATTATAAAATTTAT
* *
29418755 AAAAATCGTA-AAAAGTAAT
1 AAAAAT--TATAAAATTTAT
*
29418774 AAAAATTGTAAAATTTTAT
1 AAAAATTATAAAA-TTTAT
* * *
29418793 AAAAACTGTAAAATATAT
1 AAAAATTATAAAATTTAT
*
29418811 AGAAATATTA-AAAAATTAT
1 A-AAA-ATTATAAAATTTAT
29418830 AAAAATTATAAAATTTTAT
1 AAAAATTATAAAA-TTTAT
29418849 AAA
1 AAA
29418852 GTAGTAAGAA
Statistics
Matches: 77, Mismatches: 12, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
17 7 0.09
18 20 0.26
19 48 0.62
20 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (18 bp):
AAAAATTATAAAATTTAT
Found at i:29418851 original size:10 final size:9
Alignment explanation
Indices: 29418737--29418842 Score: 74
Period size: 9 Copynumber: 11.4 Consensus size: 9
29418727 AAATTAGAAA
29418737 AAAATATTA-
1 AAAA-ATTAT
29418746 AAAAATTAT
1 AAAAATTAT
**
29418755 AAAAATCGT
1 AAAAATTAT
*
29418764 AAAAAGTAAT
1 AAAAA-TTAT
*
29418774 AAAAATTGT
1 AAAAATTAT
*
29418783 AAAATTTTAT
1 AAAA-ATTAT
* *
29418793 AAAAACTGT
1 AAAAATTAT
29418802 -AAAATATAT
1 AAAAAT-TAT
29418811 AGAAATATTA-
1 A-AAA-ATTAT
29418821 AAAAATTAT
1 AAAAATTAT
29418830 AAAAATTAT
1 AAAAATTAT
29418839 AAAA
1 AAAA
29418843 TTTTATAAAG
Statistics
Matches: 76, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
8 12 0.16
9 42 0.55
10 15 0.20
11 5 0.07
12 2 0.03
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:29418889 original size:39 final size:36
Alignment explanation
Indices: 29418737--29418911 Score: 124
Period size: 38 Copynumber: 4.6 Consensus size: 36
29418727 AAATTAGAAA
*
29418737 AAAATA-TTAAAAAATTATAAAAATCGTAAAA-AGTAAT
1 AAAATAGTAAAAAAATTATAAAAAT-GTAAAATA-T-AT
* **
29418774 AAAAATTGT-AAAATTTTATAAAAACTGTAAAATATAT
1 -AAAATAGTAAAAAAATTATAAAAA-TGTAAAATATAT
* * *
29418811 AGAAATA-TTAAAAAATTATAAAAATTATAAAATTTTAT
1 A-AAATAGTAAAAAAATTATAAAAA-TGTAAAA-TATAT
*
29418849 AAAGTAGTAAGAAAAATTATACAAAATGTAAAGATATAT
1 AAAATAGTAA-AAAAATTATA-AAAATGTAAA-ATATAT
* *
29418888 AAATTTCGTAAAAAAATTATAAAA
1 AAA-ATAGTAAAAAAATTATAAAA
29418912 CTTATCGTAC
Statistics
Matches: 111, Mismatches: 15, Indels: 22
0.75 0.10 0.15
Matches are distributed among these distances:
36 2 0.02
37 29 0.26
38 35 0.32
39 35 0.32
40 10 0.09
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (36 bp):
AAAATAGTAAAAAAATTATAAAAATGTAAAATATAT
Found at i:29419375 original size:88 final size:85
Alignment explanation
Indices: 29419193--29419377 Score: 237
Period size: 88 Copynumber: 2.1 Consensus size: 85
29419183 AATAAGAGTA
* * *
29419193 AGGGCTTATTTGCTTTTTTGAAAAATTTTGAGTCTTTTTTATGCATTTTGAAAGTTCAAATGCTC
1 AGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGCCTTTTTTATGCATTTTGAAAGTTCAAATGCTC
** *
29419258 AATTGAGTGGAAACAAAAGC
66 AATTGAGTAAAAAAAAAAGC
* * *
29419278 AGTGTCTTAATTGCTTTTTTGAAGAAGTTTGATAGCCTTTTTTATGCATTTTGAAAGTTCAAGTG
1 AG-GGCTTAATTGCTTTTTTGAAAAAGTTTG--AGCCTTTTTTATGCATTTTGAAAGTTCAAATG
29419343 CTCAATTGAGTAAAAAAAAAAAG-
63 CTCAATTGAGT-AAAAAAAAAAGC
29419366 AGGGACTTAATT
1 AGGG-CTTAATT
29419378 TTTTATTTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
85 2 0.02
86 24 0.28
87 1 0.01
88 50 0.59
89 8 0.09
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (85 bp):
AGGGCTTAATTGCTTTTTTGAAAAAGTTTGAGCCTTTTTTATGCATTTTGAAAGTTCAAATGCTC
AATTGAGTAAAAAAAAAAGC
Found at i:29420899 original size:31 final size:31
Alignment explanation
Indices: 29420862--29420923 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
29420852 AGATAATTTT
*
29420862 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTCATTAGGATTCAATTACTCTTG
29420893 AAAGAGTTTCATTAGGATTCAATTACTCTTG
1 AAAGAGTTTCATTAGGATTCAATTACTCTTG
29420924 TAATTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (31 bp):
AAAGAGTTTCATTAGGATTCAATTACTCTTG
Found at i:29427086 original size:31 final size:31
Alignment explanation
Indices: 29427048--29427109 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
29427038 AGATAATTTT
*
29427048 AAAGAGTTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTCATTAGGATTCAATTACTCTTG
29427079 AAAGAGTTTCATTAGGATTCAATTACTCTTG
1 AAAGAGTTTCATTAGGATTCAATTACTCTTG
29427110 TAATTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (31 bp):
AAAGAGTTTCATTAGGATTCAATTACTCTTG
Found at i:29434263 original size:43 final size:42
Alignment explanation
Indices: 29434193--29434341 Score: 158
Period size: 43 Copynumber: 3.5 Consensus size: 42
29434183 TATGTATTTT
* *
29434193 CGTGTAAGACCACGTCTGGGACGTTGGCATCGAATTGTGTATA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGAATTGTG-ATA
* * * *
29434236 CGTGTAAGACCATGGCTTGGACATTGGCATCGTATT-TGATT
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGAATTGTGATA
* * **
29434277 TGTGTAAGACCCTGTCTGGGACCGTGGCATC-AATATGTGATTA
1 CGTGTAAGACCATGTCTGGGACATTGGCATCGAAT-TGTGA-TA
*
29434320 CATGTAAGACCATGTCTGGGAC
1 CGTGTAAGACCATGTCTGGGAC
29434342 GTTGTACGAG
Statistics
Matches: 86, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
40 2 0.02
41 28 0.33
42 5 0.06
43 51 0.59
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (42 bp):
CGTGTAAGACCATGTCTGGGACATTGGCATCGAATTGTGATA
Found at i:29448591 original size:33 final size:33
Alignment explanation
Indices: 29448549--29448622 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
29448539 ACAGTTGTAG
*
29448549 TAATAAGACCGCTGATTTACTGTGTAATTTAGA
1 TAATAAGACCGCTGATTTACTGGGTAATTTAGA
* *
29448582 TAATAAGACCGCTGATTTTCTGGGTAATTTAGC
1 TAATAAGACCGCTGATTTACTGGGTAATTTAGA
*
29448615 TATTAAGA
1 TAATAAGA
29448623 AAAAGTGTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.36
Consensus pattern (33 bp):
TAATAAGACCGCTGATTTACTGGGTAATTTAGA
Found at i:29448943 original size:39 final size:41
Alignment explanation
Indices: 29448867--29448960 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 41
29448857 CGCTTTATGG
*
29448867 AAAAA-GCCGCTAAAGATCGAGCATTTACGGCGCTTTT-CA
1 AAAAACGCCGCTAAAAATCGAGCATTTACGGCGCTTTTCCA
* * *
29448906 AAACACGCCGCTAAAAAT-GAGCA-TTAGTGGCGTTTTTCCA
1 AAAAACGCCGCTAAAAATCGAGCATTTA-CGGCGCTTTTCCA
29448946 AAAAACGCCGC-AAAA
1 AAAAACGCCGCTAAAA
29448961 GACCTAAGCC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
38 3 0.06
39 21 0.45
40 23 0.49
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (41 bp):
AAAAACGCCGCTAAAAATCGAGCATTTACGGCGCTTTTCCA
Found at i:29449056 original size:41 final size:41
Alignment explanation
Indices: 29448994--29449200 Score: 299
Period size: 41 Copynumber: 5.0 Consensus size: 41
29448984 TTCTGACATT
* *
29448994 TCGGGGCTTTAGCTGCGTTTTTGAAAAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
29449035 TCGGGGCTTTAGCGGCATTTTTG-AAAAGCCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCATTTTTGAAAAAG-CGCCGCTAATGC
* *
29449076 TCGAGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAAAGC
1 TCGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
*
29449117 TCGGTGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
1 TCGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
* * * * * *
29449158 TCAGTGCTATAGTGGCGTTTTTGAAAAAGCGTCGCTAATGC
1 TCGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
29449199 TC
1 TC
29449201 TATGCTTTAA
Statistics
Matches: 152, Mismatches: 12, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
40 5 0.03
41 142 0.93
42 5 0.03
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.29
Consensus pattern (41 bp):
TCGGGGCTTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGC
Found at i:29449559 original size:15 final size:14
Alignment explanation
Indices: 29449539--29449586 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
29449529 ACTATCTTAA
29449539 GGTTTATGGATTATG
1 GGTTTATGGATTA-G
* *
29449554 GGTTTAGGGATTAC
1 GGTTTATGGATTAG
*
29449568 GGTTTATGGTTTAAG
1 GGTTTATGGATT-AG
29449583 GGTT
1 GGTT
29449587 GGGGTTTAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 10 0.37
15 17 0.63
ACGTcount: A:0.19, C:0.02, G:0.35, T:0.44
Consensus pattern (14 bp):
GGTTTATGGATTAG
Found at i:29449580 original size:7 final size:7
Alignment explanation
Indices: 29449539--29449667 Score: 89
Period size: 7 Copynumber: 18.0 Consensus size: 7
29449529 ACTATCTTAA
*
29449539 GGTTTAT
1 GGTTTAG
*
29449546 GGATTATG
1 GGTTTA-G
29449554 GGTTTAG
1 GGTTTAG
* *
29449561 GGATTAC
1 GGTTTAG
*
29449568 GGTTTAT
1 GGTTTAG
29449575 GGTTTAAG
1 GGTTT-AG
*
29449583 GG-TTGG
1 GGTTTAG
*
29449589 GGTTTAA
1 GGTTTAG
29449596 GGTTTAG
1 GGTTTAG
*
29449603 GGGTTAG
1 GGTTTAG
*
29449610 GTGTTAAG
1 G-GTTTAG
*
29449618 GGTTAAG
1 GGTTTAG
*
29449625 GGTTTAT
1 GGTTTAG
* *
29449632 GATTTAT
1 GGTTTAG
29449639 GGTTTAG
1 GGTTTAG
*
29449646 GGGTTAGG
1 GGTTTA-G
29449654 GGTTTAG
1 GGTTTAG
29449661 GGTTTAG
1 GGTTTAG
29449668 ATTAATTAGT
Statistics
Matches: 95, Mismatches: 22, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
6 3 0.03
7 73 0.77
8 19 0.20
ACGTcount: A:0.19, C:0.01, G:0.40, T:0.41
Consensus pattern (7 bp):
GGTTTAG
Found at i:29449580 original size:21 final size:21
Alignment explanation
Indices: 29449549--29449667 Score: 103
Period size: 21 Copynumber: 5.5 Consensus size: 21
29449539 GGTTTATGGA
* *
29449549 TTATGGGTTTAGGGATTACGGT
1 TTAT-GGTTTAGGGGTTAGGGT
* *
29449571 TTATGGTTTAAGGGTTGGGGT
1 TTATGGTTTAGGGGTTAGGGT
*
29449592 TTAAGGTTTAGGGGTTAGGTGT
1 TTATGGTTTAGGGGTTAGG-GT
* * * * * *
29449614 TAAGGGTTAAGGGTTTATGAT
1 TTATGGTTTAGGGGTTAGGGT
29449635 TTATGGTTTAGGGGTTAGGGGT
1 TTATGGTTTAGGGGTTA-GGGT
*
29449657 TTAGGGTTTAG
1 TTATGGTTTAG
29449668 ATTAATTAGT
Statistics
Matches: 75, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
21 43 0.57
22 32 0.43
ACGTcount: A:0.18, C:0.01, G:0.39, T:0.41
Consensus pattern (21 bp):
TTATGGTTTAGGGGTTAGGGT
Found at i:29449666 original size:29 final size:28
Alignment explanation
Indices: 29449539--29449666 Score: 98
Period size: 29 Copynumber: 4.5 Consensus size: 28
29449529 ACTATCTTAA
* * *
29449539 GGTTTATGGATTATGGGTTTAGGGATTAC
1 GGTTTATGGTTTAT-GGTTTAGGGGTTAG
* * *
29449568 GGTTTATGGTTTAAGGGTT-GGGGTTTAA
1 GGTTTATGGTTTATGGTTTAGGGG-TTAG
* * *
29449596 GGTTTAGGGGTTA-GGTGTTAAGGGTTAAG
1 GGTTTATGGTTTATGGT-TTAGGGGTT-AG
*
29449625 GGTTTATGATTTATGGTTTAGGGGTTAGG
1 GGTTTATGGTTTATGGTTTAGGGGTTA-G
*
29449654 GGTTTAGGGTTTA
1 GGTTTATGGTTTA
29449667 GATTAATTAG
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
27 5 0.06
28 23 0.30
29 46 0.60
30 3 0.04
ACGTcount: A:0.19, C:0.01, G:0.39, T:0.41
Consensus pattern (28 bp):
GGTTTATGGTTTATGGTTTAGGGGTTAG
Found at i:29449835 original size:14 final size:15
Alignment explanation
Indices: 29449818--29449850 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
29449808 TATGGTTTAT
29449818 GGTTTAAGGGTT-GG
1 GGTTTAAGGGTTAGG
*
29449832 GGTTTAAGGTTTAGG
1 GGTTTAAGGGTTAGG
29449847 GGTT
1 GGTT
29449851 AGGGGTACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.15, C:0.00, G:0.45, T:0.39
Consensus pattern (15 bp):
GGTTTAAGGGTTAGG
Found at i:29449835 original size:21 final size:22
Alignment explanation
Indices: 29449811--29449903 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 22
29449801 TAGGGATTAT
*
29449811 GGTTTATGGTTTAAGGGTT-GG
1 GGTTTAAGGTTTAAGGGTTAGG
*
29449832 GGTTTAAGGTTTAGGGGTTAGG
1 GGTTTAAGGTTTAAGGGTTAGG
* * *
29449854 GGTACTTAAGGGTTAGGGGTTTA-T
1 GGT--TTAAGGTTTAAGGG-TTAGG
* * *
29449878 GATTTAAGGTTTAGGGGATAGG
1 GGTTTAAGGTTTAAGGGTTAGG
29449900 GGTT
1 GGTT
29449904 AGTGGTTTAG
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
21 19 0.33
22 21 0.36
24 15 0.26
25 3 0.05
ACGTcount: A:0.19, C:0.01, G:0.42, T:0.38
Consensus pattern (22 bp):
GGTTTAAGGTTTAAGGGTTAGG
Found at i:29449892 original size:39 final size:38
Alignment explanation
Indices: 29449821--29449894 Score: 103
Period size: 39 Copynumber: 1.9 Consensus size: 38
29449811 GGTTTATGGT
* *
29449821 TTAAGGGTTGGGGTTTAAGGTTTAGGGGTTAGGGGTAC
1 TTAAGGGTTGGGGTTTAAGATTTAAGGGTTAGGGGTAC
* *
29449859 TTAAGGGTTAGGGGTTTATGATTTAAGGTTTAGGGG
1 TTAAGGGTT-GGGGTTTAAGATTTAAGGGTTAGGGG
29449895 ATAGGGGTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 9 0.29
39 22 0.71
ACGTcount: A:0.20, C:0.01, G:0.42, T:0.36
Consensus pattern (38 bp):
TTAAGGGTTGGGGTTTAAGATTTAAGGGTTAGGGGTAC
Found at i:29450701 original size:40 final size:40
Alignment explanation
Indices: 29450656--29450781 Score: 125
Period size: 40 Copynumber: 3.2 Consensus size: 40
29450646 TTTTCCCCAT
29450656 TTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCC
1 TTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCC
* * * ** * * *
29450696 TTTATTTTTCCC--CCCAATT-TCCCCAAATCGGCA-GCTCT
1 TTTATTTTTCCCAAACCATTTCTCCCCTACCCCG-ATTC-CC
*
29450734 TTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCAC
1 TTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCC
29450774 TTTATTTT
1 TTTATTTT
29450782 CCCCCCTAAT
Statistics
Matches: 63, Mismatches: 17, Indels: 12
0.68 0.18 0.13
Matches are distributed among these distances:
37 9 0.14
38 19 0.30
40 26 0.41
41 9 0.14
ACGTcount: A:0.18, C:0.37, G:0.04, T:0.40
Consensus pattern (40 bp):
TTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCC
Found at i:29450747 original size:78 final size:78
Alignment explanation
Indices: 29450655--29450806 Score: 279
Period size: 78 Copynumber: 1.9 Consensus size: 78
29450645 TTTTTCCCCA
*
29450655 TTTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCCCTTTATTTTTCCCCCC-AATTTCCC
1 TTTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCACTTTA-TTTTCCCCCCTAATTTCCC
29450719 CAAATCGGCAGCTC
65 CAAATCGGCAGCTC
29450733 TTTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCACTTTATTTTCCCCCCTAATTTCCCC
1 TTTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCACTTTATTTTCCCCCCTAATTTCCCC
29450798 AAATCGGCA
66 AAATCGGCA
29450807 ACCCTCTACA
Statistics
Matches: 72, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
77 10 0.14
78 62 0.86
ACGTcount: A:0.19, C:0.39, G:0.05, T:0.38
Consensus pattern (78 bp):
TTTTATTTTTCCCAAACCATTTCTCCCCTACCCCGATTCACTTTATTTTCCCCCCTAATTTCCCC
AAATCGGCAGCTC
Found at i:29451385 original size:43 final size:43
Alignment explanation
Indices: 29451337--29451642 Score: 350
Period size: 43 Copynumber: 7.2 Consensus size: 43
29451327 TGCTAAAAAT
* * * * *
29451337 GCCGCTATAGGTCATGACCTTTAGCGGCGCTTATACAACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
** *
29451380 GCCGCTATAGATCGGGACCTTTAGCGGCGCTTTTTCCACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
* * * *
29451423 GCCGCTGTAGATCAAGACCTTTAGCGACAG-TTTT-TCACAAGC
1 GCCGCTATAGATCAAGACCTTTAGCGGC-GCTTTTCCCACAAAC
** *
29451465 GCCGCTATAGATC-AGAACCTTTAGCGGCGCTTTTTACAAAAAC
1 GCCGCTATAGATCAAG-ACCTTTAGCGGCGCTTTTCCCACAAAC
* * **
29451508 GCCGCTATAGCTCAAGATCTTTAGCGGC-AATTTCCCACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
* *
29451550 GCCGCTATAAATCAAGACCTTTAGCGGCGCATTTCCCACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
* * *
29451593 GCCACTATAGATCAAAACCTTTAGCGACGCTTTTCCCACAAAC
1 GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
29451636 GCCGCTA
1 GCCGCTA
29451643 AAAACATATC
Statistics
Matches: 223, Mismatches: 34, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
41 3 0.01
42 67 0.30
43 150 0.67
44 3 0.01
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.24
Consensus pattern (43 bp):
GCCGCTATAGATCAAGACCTTTAGCGGCGCTTTTCCCACAAAC
Found at i:29451485 original size:85 final size:85
Alignment explanation
Indices: 29451337--29451642 Score: 348
Period size: 85 Copynumber: 3.6 Consensus size: 85
29451327 TGCTAAAAAT
* * * * * * *
29451337 GCCGCTATAGGTCATGACCTTTAGCGGC-GCTTATACAACAAACGCCGCTATAGATCGGGACCTT
1 GCCGCTATAGATCAAGACCTTTAGCGACAG-TT-TTCCACAAACGCCGCTATAGATCAGAACCTT
29451401 TAGCGGCGCTTTTTCCACAAAC
64 TAGCGGCGCTTTTTCCACAAAC
* * *
29451423 GCCGCTGTAGATCAAGACCTTTAGCGACAGTTTTTCACAAGCGCCGCTATAGATCAGAACCTTTA
1 GCCGCTATAGATCAAGACCTTTAGCGACAGTTTTCCACAAACGCCGCTATAGATCAGAACCTTTA
* *
29451488 GCGGCGCTTTTTACAAAAAC
66 GCGGCGCTTTTTCCACAAAC
* * * * * *
29451508 GCCGCTATAGCTCAAGATCTTTAGCGGCAATTTCCCACAAACGCCGCTATAAATCA-AGACCTTT
1 GCCGCTATAGATCAAGACCTTTAGCGACAGTTTTCCACAAACGCCGCTATAGATCAGA-ACCTTT
* *
29451572 AGCGGCGCATTTCCCACAAAC
65 AGCGGCGCTTTTTCCACAAAC
* *
29451593 GCCACTATAGATCAAAACCTTTAGCGAC-GCTTTTCCCACAAACGCCGCTA
1 GCCGCTATAGATCAAGACCTTTAGCGACAG-TTTT-CCACAAACGCCGCTA
29451643 AAAACATATC
Statistics
Matches: 184, Mismatches: 32, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
84 1 0.01
85 141 0.77
86 41 0.22
87 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.24
Consensus pattern (85 bp):
GCCGCTATAGATCAAGACCTTTAGCGACAGTTTTCCACAAACGCCGCTATAGATCAGAACCTTTA
GCGGCGCTTTTTCCACAAAC
Found at i:29451590 original size:128 final size:128
Alignment explanation
Indices: 29451337--29451642 Score: 359
Period size: 128 Copynumber: 2.4 Consensus size: 128
29451327 TGCTAAAAAT
* * **
29451337 GCCGCTATAGGTCATG-ACCTTTAGCGGCGC-TTATACAACAAACGCCGCTATAGATCGGGACCT
1 GCCGCTATAGATCA-GAACCTTTAGCGGCGCTTTTTACAA-AAACGCCGCTATAGATCAAGACCT
** * * * ** *
29451400 TTAGCGGCGCTTTTTCCACAAACGCCGCTGTAGATCAAGACCTTTAGCGACAGTTTTTCACAAGC
64 TTAGCGGCGAATTTCCCACAAACGCCGCTATAAATCAAGACCTTTAGCGACAGTTTCCCACAAAC
* *
29451465 GCCGCTATAGATCAGAACCTTTAGCGGCGCTTTTTACAAAAACGCCGCTATAGCTCAAGATCTTT
1 GCCGCTATAGATCAGAACCTTTAGCGGCGCTTTTTACAAAAACGCCGCTATAGATCAAGACCTTT
*
29451530 AGCGGC-AATTTCCCACAAACGCCGCTATAAATCAAGACCTTTAGCGGC-GCATTTCCCACAAAC
66 AGCGGCGAATTTCCCACAAACGCCGCTATAAATCAAGACCTTTAGCGACAG--TTTCCCACAAAC
* * * ** *
29451593 GCCACTATAGATCAAAACCTTTAGCGACGCTTTTCCCACAAACGCCGCTA
1 GCCGCTATAGATCAGAACCTTTAGCGGCGCTTTTTACAAAAACGCCGCTA
29451643 AAAACATATC
Statistics
Matches: 153, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
126 1 0.01
127 37 0.24
128 108 0.71
129 7 0.05
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.24
Consensus pattern (128 bp):
GCCGCTATAGATCAGAACCTTTAGCGGCGCTTTTTACAAAAACGCCGCTATAGATCAAGACCTTT
AGCGGCGAATTTCCCACAAACGCCGCTATAAATCAAGACCTTTAGCGACAGTTTCCCACAAAC
Found at i:29451677 original size:14 final size:14
Alignment explanation
Indices: 29451660--29451686 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
29451650 ATCTTTAAAA
29451660 AAATAATTTTTATC
1 AAATAATTTTTATC
29451674 AAATAATTTTTAT
1 AAATAATTTTTAT
29451687 TTCTATGATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (14 bp):
AAATAATTTTTATC
Found at i:29453260 original size:114 final size:113
Alignment explanation
Indices: 29453012--29453276 Score: 307
Period size: 114 Copynumber: 2.3 Consensus size: 113
29453002 AGAATAAGAA
* * * *
29453012 TTAGCGGCGTTTTATAGAAAGCGCCGTAAAAAACCTAATCCGAACGACGTCGTTTGCCGAGCTTT
1 TTAGCGGCGTTTTAGAGAAAGCGCCGCAAAAAACCTAATCCCAACGACGCCGTTTGCCGAGCTTT
* *
29453077 CGGGGATTTAACGGCATTTCTAATAAAGCGTCGTTAATGCTCAGGGAT
66 CGGGGATTTAACGGCATTTCTAATAAAGCGCCGCTAATGCTCAGGGAT
* * * * *
29453125 TTAGCGGCGTTTTTGAGAAAGCGCCGCAAAAAGCCTAATCCCAACGATGCCGTTTTTCTGAGCTT
1 TTAGCGGCGTTTTAGAGAAAGCGCCGCAAAAAACCTAATCCCAACGACGCCG-TTTGCCGAGCTT
* ** * * * * *
29453190 TCGAGTGA-TTAGTGGCGTTTTTAATAAAGCGCCGCTAATTCTTAGGGCT
65 TCG-GGGATTTAACGGCATTTCTAATAAAGCGCCGCTAATGCTCAGGGAT
* * *
29453239 TTAGCGGCGTTTTCGAAAAAGCGCCACAAAAAACCTAA
1 TTAGCGGCGTTTTAGAGAAAGCGCCGCAAAAAACCTAA
29453277 GTACAACGAC
Statistics
Matches: 127, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
113 45 0.35
114 79 0.62
115 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (113 bp):
TTAGCGGCGTTTTAGAGAAAGCGCCGCAAAAAACCTAATCCCAACGACGCCGTTTGCCGAGCTTT
CGGGGATTTAACGGCATTTCTAATAAAGCGCCGCTAATGCTCAGGGAT
Found at i:29453721 original size:15 final size:15
Alignment explanation
Indices: 29453683--29453736 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
29453673 GGTGTTATGC
29453683 TTTAGGGGTTAGGGAG
1 TTTAGGGGTTAGGG-G
29453699 ATTTAGGGGTTAGGGG
1 -TTTAGGGGTTAGGGG
* * *
29453715 GTTAGGGATTTGGGG
1 TTTAGGGGTTAGGGG
29453730 TTTAGGG
1 TTTAGGG
29453737 TTTGAACGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
15 18 0.55
16 1 0.03
17 14 0.42
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (15 bp):
TTTAGGGGTTAGGGG
Found at i:29465680 original size:29 final size:27
Alignment explanation
Indices: 29465647--29465708 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
29465637 AATTAAAGAG
29465647 TATATAAAAAGTATAGAATTACGTATATA
1 TATATAAAAAGTA-AGAA-TACGTATATA
* * *
29465676 TATATGAAAATTAAGAATATGTATATA
1 TATATAAAAAGTAAGAATACGTATATA
*
29465703 AATATA
1 TATATA
29465709 TATATATATG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 13 0.46
28 4 0.14
29 11 0.39
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.35
Consensus pattern (27 bp):
TATATAAAAAGTAAGAATACGTATATA
Found at i:29465916 original size:3 final size:3
Alignment explanation
Indices: 29465908--29465941 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
29465898 AAGGGAAAAT
29465908 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
29465942 CATCAAATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29468390 original size:100 final size:100
Alignment explanation
Indices: 29468159--29469460 Score: 1025
Period size: 100 Copynumber: 13.2 Consensus size: 100
29468149 GGATTGGCTT
* * ** * *
29468159 CTTCAATATGTTT-AATTGCAATGTCGAGGAAGTAAGATTCGCTGTCGTAGCTTCAATCTATTCC
1 CTTCAATCT-TTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCC
** * * * * *
29468223 ATTACACCGCCAGGGAAAGTAAGATTCGTCGTTGTGG
65 GCTGCATCGCCTGGG-AAGTAAGATTCGCCGTTGTAG
* * * * **
29468260 CCTCAATCTATTTAACCA-T--AATGTCAGGGAAACAAGATTCGCCGTTTTAGCTTCAATCTGTT
1 CTTCAATCT-TTTAA--ATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTT
* * * * * *
29468322 CCGTTGCACCGCTTGGAAAGTAAGATTCGCCATTGCAG
63 CCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * *
29468360 CTTCAATCTTTTAAATTGCAATG-CTGGGGAAACGAGATTCACCGTCGTAGCTTCAATCTGTTCT
1 CTTCAATCTTTTAAATTGCAATGTC-GGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCC
* * *
29468424 G-TCGCATCTCCTGGG-AGTAAGATTCGTCGTTGTGG
65 GCT-GCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * *
29468459 CCTCAATCTTTTAAATTGCAATGTTGGGGAAGC-ATGATTCGCCGTTGTAGCTTCAATCTGTTCC
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGA-GATTCGCCGTCGTAGCTTCAATCTGTTCC
* * *
29468523 GCTGCACCGCCT-GAAAGGTAAGATTCGCTGTTGTAG
65 GCTGCATCGCCTGGGAA-GTAAGATTCGCCGTTGTAG
* * * * * * * *
29468559 CTTCAATCTTTGAAACTGCAATGTCGAGGAAGCAAGATACACCGTCGTAGCTTTAATCTGTTCTG
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
* * * * *
29468624 TTGCATCGTCT-GGAAGTAGGATTCACCGTTGTGG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
* *
29468658 CTTCAATCTTTT-AATTGCAATGTCGGGGAAGTGAGATTCGCTGTCGTAGCTTCAATCTGTTCCG
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
* * * *
29468722 CTGTATCACCTGGGAAGTAAGATTCACCGTTGTTG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * * * * *
29468757 CTTCGATCTTTTGAATTGCAATGTCGAGGAAGGGAGATTCGCTGTCGTAGCTTCAATCTATTCCA
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
* * *
29468822 CTGCATCGCCTGGGAAGTAAGATTCACCGTTATGG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * ** *
29468857 CTTCGATCTTTTGAATTGCAATGTCGGGGAAGTGAGATTCGATGTCGTAGCTTTAATCTGTTCCG
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
*
29468922 CTGCATCTCCTGGGAAGTAAGATTCGCCGTTGTAG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
* * * * *
29468957 CCTCAATCTTTTAAATTGCAATGTTGGGGAAGC-AGGATTCGTCGTTGTAGCTTCAATCTATTCC
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGA-GATTCGCCGTCGTAGCTTCAATCTGTTCC
* * * * **
29469021 GTTACACCGCCT-GAAAGGTAAGATTCGCTATTGTAG
65 GCTGCATCGCCTGGGAA-GTAAGATTCGCCGTTGTAG
* * * * * * * *
29469057 CTTCAATCTTTGAAACTACAATGTCGAGGAAGTGAGATTCGCCGTCGTAGCTTTAATCTATTTCG
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
*
29469122 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGG
66 CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
** * * * * * * *
29469157 CTTTGATCTTTTGAATTGC-----CAGAGAAGCAAGA-TCTGCTG-CTGTAGCTTCAATCCGTTT
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTC-GCCGTC-GTAGCTTCAATCTGTTC
* * * * * *
29469215 CACTGCAAC-ACTAGGAAAATAAGA-TCTGCTGTTGTAG
64 CGCTGCATCGCCT-GGGAAGTAAGATTC-GCCGTTGTAG
* * * * * *
29469252 CTTCAATCTTTTTAA---C--TGTCGGGGAAGCAAGATCCGCTGTTGTAGCTTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
* * * * *
29469312 CTGCAAC-ACTAGGAAAGTAAGATCCGCTGTTGTAG
66 CTGCATCGCCT-GGGAAGTAAGATTCGCCGTTGTAG
* * * * * * *
29469347 CTTCAATCTTTTTAA---C--TGTCGGGGAAGCAAGATCCGCTGTTGTAGCCTCAATCTGTTCCA
1 CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
* * * * *
29469407 CTGCAACG-ATAGGAAAGTAAGATCCGCTGTTGTAG
66 CTGCATCGCCT-GGGAAGTAAGATTCGCCGTTGTAG
*
29469442 CTTCAATCTTTTTAATTGC
1 CTTCAATCTTTTAAATTGC
29469461 CATCTATGGT
Statistics
Matches: 997, Mismatches: 170, Indels: 71
0.81 0.14 0.06
Matches are distributed among these distances:
92 1 0.00
94 7 0.01
95 231 0.23
96 2 0.00
97 1 0.00
98 54 0.05
99 149 0.15
100 487 0.49
101 62 0.06
102 1 0.00
103 1 0.00
104 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (100 bp):
CTTCAATCTTTTAAATTGCAATGTCGGGGAAGCGAGATTCGCCGTCGTAGCTTCAATCTGTTCCG
CTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTAG
Found at i:29469106 original size:498 final size:499
Alignment explanation
Indices: 29468159--29469175 Score: 1321
Period size: 498 Copynumber: 2.0 Consensus size: 499
29468149 GGATTGGCTT
*
29468159 CTTCAATATGTTTAATTGCAATGTCGAGGAAGTAAGATTCGCTGTCGTAGCTTCAATCTATTCCA
1 CTTCAATCT-TTTAATTGCAATGTCGAGGAAGTAAGATTCGCTGTCGTAGCTTCAATCTATTCCA
* * ** *
29468224 TTACACCGCCAGGGAAAGTAAGATTCGTCGTTGTGGCCTCAATCTATTTAACCATAATGTCAGGG
65 CTACACCACCAGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTATTTAACCACAATGTCAGGG
** * ** * *
29468289 AAACAAGATTCGCCGTTTTAGCTTCAATCTGTTCCGTTGCACCGCTTGGAAAGTAAGATTCGCCA
130 AAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCTGGAAAGTAAGATTCACCA
*
29468354 TTGCAGCTTCAATCTTTTAAATTGCAATGCTGGGGAAACGAGATTCACCGTCGTAGCTTCAATCT
195 TTACAGCTTCAATCTTTTAAATTGCAATGCTGGGGAAACGAGATTCACCGTCGTAGCTTCAATCT
* * *
29468419 GTTCTGTCGCATCTCCTGGGAGTAAGATTCGTCGTTGTGGCCTCAATCTTTTAAATTGCAATGTT
260 GTTCCGTCGCATCTCCTGGGAGTAAGATTCGCCGTTGTAGCCTCAATCTTTTAAATTGCAATGTT
* * *
29468484 GGGGAAGCATGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCCTGAAAGGTAAGATTC
325 GGGGAAGCAGGATTCGCCGTTGTAGCTTCAATCTATTCCGCTACACCGCCTGAAAGGTAAGATTC
* *
29468549 GCTGTTGTAGCTTCAATCTTTGAAACTGCAATGTCGAGGAAGCAAGATACACCGTCGTAGCTTTA
390 GCTATTGTAGCTTCAATCTTTGAAACTACAATGTCGAGGAAGCAAGATACACCGTCGTAGCTTTA
* * * *
29468614 ATCT-GTTCTGTTGCATCGTCT-GGAAGTAGGATTCACCGTTGTGG
455 ATCTATTTC-GCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGG
* * * *
29468658 CTTCAATCTTTTAATTGCAATGTCGGGGAAGTGAGATTCGCTGTCGTAGCTTCAATCTGTTCCGC
1 CTTCAATCTTTTAATTGCAATGTCGAGGAAGTAAGATTCGCTGTCGTAGCTTCAATCTATTCCAC
** * * * * * ***
29468723 TGTATCACCTGGG-AAGTAAGATTCACCGTTGTTGCTTCGATCT-TTTGAATTGCAATGTC-GAG
66 TACACCACCAGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTATTT-AACCACAATGTCAG-G
*** * * *
29468785 GAAGGGAGATTCGCTGTCGTAGCTTCAATCTATTCCACTGCATCGCCTGGGAAGTAAGATTCACC
129 GAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCTGGAAAGTAAGATTCACC
* ** * * ** * *
29468850 GTTATGGCTTCGATCTTTTGAATTGCAATG-TCGGGGAAGTGAGATTCGA-TGTCGTAGCTTTAA
194 ATTACAGCTTCAATCTTTTAAATTGCAATGCT-GGGGAAACGAGATTC-ACCGTCGTAGCTTCAA
29468913 TCTGTTCCG-CTGCATCTCCTGGGAAGTAAGATTCGCCGTTGTAGCCTCAATCTTTTAAATTGCA
257 TCTGTTCCGTC-GCATCTCCTGGG-AGTAAGATTCGCCGTTGTAGCCTCAATCTTTTAAATTGCA
* *
29468977 ATGTTGGGGAAGCAGGATTCGTCGTTGTAGCTTCAATCTATTCCGTTACACCGCCTGAAAGGTAA
320 ATGTTGGGGAAGCAGGATTCGCCGTTGTAGCTTCAATCTATTCCGCTACACCGCCTGAAAGGTAA
** * *
29469042 GATTCGCTATTGTAGCTTCAATCTTTGAAACTACAATGTCGAGGAAGTGAGATTCGCCGTCGTAG
385 GATTCGCTATTGTAGCTTCAATCTTTGAAACTACAATGTCGAGGAAGCAAGATACACCGTCGTAG
*
29469107 CTTTAATCTATTTCGCTGCATCGCCTGGGAAGTAAGATTCGCCGTTGTGG
450 CTTTAATCTATTTCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGG
**
29469157 CTTTGATCTTTTGAATTGC
1 CTTCAATCTTTT-AATTGC
29469176 CAGAGAAGCA
Statistics
Matches: 445, Mismatches: 64, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
496 6 0.01
497 155 0.35
498 236 0.53
499 42 0.09
500 6 0.01
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.33
Consensus pattern (499 bp):
CTTCAATCTTTTAATTGCAATGTCGAGGAAGTAAGATTCGCTGTCGTAGCTTCAATCTATTCCAC
TACACCACCAGGGAAAGTAAGATTCACCGTTGTGGCCTCAATCTATTTAACCACAATGTCAGGGA
AACAAGATTCGCCGTCGTAGCTTCAATCTATTCCACTGCACCGCCTGGAAAGTAAGATTCACCAT
TACAGCTTCAATCTTTTAAATTGCAATGCTGGGGAAACGAGATTCACCGTCGTAGCTTCAATCTG
TTCCGTCGCATCTCCTGGGAGTAAGATTCGCCGTTGTAGCCTCAATCTTTTAAATTGCAATGTTG
GGGAAGCAGGATTCGCCGTTGTAGCTTCAATCTATTCCGCTACACCGCCTGAAAGGTAAGATTCG
CTATTGTAGCTTCAATCTTTGAAACTACAATGTCGAGGAAGCAAGATACACCGTCGTAGCTTTAA
TCTATTTCGCTGCATCGCCTGGGAAGTAAGATTCACCGTTGTGG
Found at i:29469160 original size:50 final size:49
Alignment explanation
Indices: 29468293--29469168 Score: 318
Period size: 50 Copynumber: 17.6 Consensus size: 49
29468283 TCAGGGAAAC
* * * * * *
29468293 AAGATTCGCCGTTTTAGCTTCAATCTGTTCCGTTGCACCGCTTGGAAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAAGT
* * *** **
29468343 AAGATTCGCCATTGCAGCTTCAATCTTTTAAATTGCAAT-G-CTGGGGAAAC
1 AAGATTCGCCGTTGTAGCTTCAATCTTTT-CGCTGC-ATCGCCT-GGGAAGT
* * * * *
29468393 GAGATTCACCGTCGTAGCTTCAATCTGTTCTG-TCGCATCTCCTGGG-AGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTTC-GCT-GCATCGCCTGGGAAGT
* * * *** * *
29468442 AAGATTCGTCGTTGTGGCCTCAATCTTTTAAATTGCAAT-G-TTGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTCAATCTTTT-CGCTGC-ATCGCCT-GGGAAGT
* * * *
29468492 ATGATTCGCCGTTGTAGCTTCAATCTGTTCCGCTGCACCGCCT-GAAAGGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAA-GT
* *** * *
29468542 AAGATTCGCTGTTGTAGCTTCAATCTTTGAAACTGCAAT-GTC-GAGGAAGC
1 AAGATTCGCCGTTGTAGCTTCAATCTTT-TCGCTGC-ATCGCCTG-GGAAGT
* * * * * * *
29468592 AAGATACACCGTCGTAGCTTTAATCTGTTCTGTTGCATCGTCT-GGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTTC-GCTGCATCGCCTGGGAAGT
* * * *** * *
29468641 AGGATTCACCGTTGTGGCTTCAATCTTTTAATTGCAAT-GTCGGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTTCGCTGC-ATCGCCTGGGAAGT
* * * * * *
29468690 GAGATTCGCTGTCGTAGCTTCAATCTGTTCCGCTGTATCACCTGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAAGT
* * * * * *
29468740 AAGATTCACCGTTGTTGCTTCGATCTTTT-GAATTGCAAT-GTC-GAGGAAGG
1 AAGATTCGCCGTTGTAGCTTCAATCTTTTCG--CTGC-ATCGCCTG-GGAAGT
* * * * *
29468790 GAGATTCGCTGTCGTAGCTTCAATCTATTCCACTGCATCGCCTGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAAGT
* * * * * * *
29468840 AAGATTCACCGTTATGGCTTCGATCTTTT-GAATTGCAAT-GTCGGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTTCG--CTGC-ATCGCCTGGGAAGT
* ** * * * *
29468890 GAGATTCGATGTCGTAGCTTTAATCTGTTCCGCTGCATCTCCTGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAAGT
* *** * *
29468940 AAGATTCGCCGTTGTAGCCTCAATCTTTTAAATTGCAAT-G-TTGGGGAAGC
1 AAGATTCGCCGTTGTAGCTTCAATCTTTT-CGCTGC-ATCGCCT-GGGAAGT
* * * * * * *
29468990 AGGATTCGTCGTTGTAGCTTCAATCTATTCCGTTACACCGCCT-GAAAGGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAA-GT
** *** * *
29469040 AAGATTCGCTATTGTAGCTTCAATCTTTGAAACTACAAT-GTC-GAGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCTTT-TCGCTGC-ATCGCCTG-GGAAGT
* * *
29469090 GAGATTCGCCGTCGTAGCTTTAATCTATTTCGCTGCATCGCCTGGGAAGT
1 AAGATTCGCCGTTGTAGCTTCAATCT-TTTCGCTGCATCGCCTGGGAAGT
* **
29469140 AAGATTCGCCGTTGTGGCTTTGATCTTTT
1 AAGATTCGCCGTTGTAGCTTCAATCTTTT
29469169 GAATTGCCAG
Statistics
Matches: 584, Mismatches: 187, Indels: 111
0.66 0.21 0.13
Matches are distributed among these distances:
48 9 0.02
49 123 0.21
50 420 0.72
51 31 0.05
52 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (49 bp):
AAGATTCGCCGTTGTAGCTTCAATCTTTTCGCTGCATCGCCTGGGAAGT
Found at i:29469238 original size:95 final size:95
Alignment explanation
Indices: 29469136--29469462 Score: 458
Period size: 95 Copynumber: 3.4 Consensus size: 95
29469126 ATCGCCTGGG
* * * ** * * * * *
29469136 AAGTAAGATTCGCCGTTGTGGCTTTGATCTTTTGAATTGCCAGAGAAGCAAGATCTGCTGCTGTA
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGCAAGATCCGCTGTTGTA
* *
29469201 GCTTCAATCCGTTTCACTGCAACACTAGGA
66 GCTTCAATCTGTTCCACTGCAACACTAGGA
* * * *
29469231 AAATAAGATCTGCTGTTGTAGCTTCAATCTTTTTAACTGTCGGGGAAGCAAGATCCGCTGTTGTA
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGCAAGATCCGCTGTTGTA
29469296 GCTTCAATCTGTTCCACTGCAACACTAGGA
66 GCTTCAATCTGTTCCACTGCAACACTAGGA
* *
29469326 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGTCGGGGAAGCAAGATCCGCTGTTGTA
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGCAAGATCCGCTGTTGTA
*
29469391 GCCTCAATCTGTTCCACTGCAACGA-TAGGA
66 GCTTCAATCTGTTCCACTGCAAC-ACTAGGA
*
29469421 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAATTGCCA
1 AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCA
29469463 TCTATGGTTT
Statistics
Matches: 209, Mismatches: 22, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
95 208 1.00
96 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (95 bp):
AAGTAAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTGCCAGGGAAGCAAGATCCGCTGTTGTA
GCTTCAATCTGTTCCACTGCAACACTAGGA
Found at i:29469348 original size:50 final size:50
Alignment explanation
Indices: 29469185--29469450 Score: 266
Period size: 50 Copynumber: 5.5 Consensus size: 50
29469175 CCAGAGAAGC
* * * *
29469185 AAGATCTGCTGCTGTAGCTTCAATCCGTTTCACTGCAACACTAGGAAAAT
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTTCACTGCAACACTAGGAAAGT
* * * * * * *
29469235 AAGATCTGCTGTTGTAGCTTCAATCTTTTTAACTG----TC-GGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTTCACTGCAACACTAGGAAAGT
*
29469280 AAGATCCGCTGTTGTAGCTTCAATCTGTTCCACTGCAACACTAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTTCACTGCAACACTAGGAAAGT
* * * * * *
29469330 AAGATCCGCTGTTGTAGCTTCAATCTTTTTAACTG----TC-GGGGAAGC
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTTCACTGCAACACTAGGAAAGT
* *
29469375 AAGATCCGCTGTTGTAGCCTCAATCTGTTCCACTGCAACGA-TAGGAAAGT
1 AAGATCCGCTGTTGTAGCTTCAATCTGTTTCACTGCAAC-ACTAGGAAAGT
29469425 AAGATCCGCTGTTGTAGCTTCAATCT
1 AAGATCCGCTGTTGTAGCTTCAATCT
29469451 TTTTAATTGC
Statistics
Matches: 172, Mismatches: 33, Indels: 22
0.76 0.15 0.10
Matches are distributed among these distances:
45 71 0.41
46 2 0.01
49 1 0.01
50 98 0.57
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (50 bp):
AAGATCCGCTGTTGTAGCTTCAATCTGTTTCACTGCAACACTAGGAAAGT
Found at i:29470820 original size:8 final size:8
Alignment explanation
Indices: 29470809--29470851 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
29470799 CCATTTTTAC
*
29470809 TTTTTCTT
1 TTTTTCAT
29470817 TTTTTCAT
1 TTTTTCAT
29470825 TTTTTCA-
1 TTTTTCAT
*
29470832 TTATTCATT
1 TTTTTCA-T
29470841 TTTTTCAT
1 TTTTTCAT
29470849 TTT
1 TTT
29470852 CATCATCATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 6 0.20
8 18 0.60
9 6 0.20
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:29470852 original size:22 final size:22
Alignment explanation
Indices: 29470815--29470865 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
29470805 TTACTTTTTC
*
29470815 TTTTTTTCATTTTTTCATTATTCA
1 TTTTTTTCA-TTTTTCATCA-TCA
29470839 TTTTTTTCA-TTTTCATCATCA
1 TTTTTTTCATTTTTCATCATCA
29470860 TTTTTT
1 TTTTTT
29470866 GACCCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 9 0.35
22 8 0.31
24 9 0.35
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTTCATTTTTCATCATCA
Found at i:29470853 original size:15 final size:15
Alignment explanation
Indices: 29470818--29470854 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
29470808 CTTTTTCTTT
29470818 TTTTCA-TTTTTTCA
1 TTTTCATTTTTTTCA
29470832 TTATTCATTTTTTTCA
1 TT-TTCATTTTTTTCA
29470848 TTTTCAT
1 TTTTCAT
29470855 CATCATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.10
15 9 0.43
16 10 0.48
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCATTTTTTTCA
Found at i:29471680 original size:5 final size:6
Alignment explanation
Indices: 29471664--29471692 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
29471654 TTGACCTCTC
29471664 CTTTTT CTTTTT CTTTTT C-TTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
29471693 TTGACTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.23
6 17 0.77
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (6 bp):
CTTTTT
Found at i:29471693 original size:12 final size:12
Alignment explanation
Indices: 29471664--29471692 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
29471654 TTGACCTCTC
29471664 CTTTTTCTTTTT
1 CTTTTTCTTTTT
29471676 CTTTTTC-TTTT
1 CTTTTTCTTTTT
29471687 CTTTTT
1 CTTTTT
29471693 TTGACTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 10 0.59
12 7 0.41
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (12 bp):
CTTTTTCTTTTT
Found at i:29471716 original size:10 final size:9
Alignment explanation
Indices: 29471702--29471763 Score: 83
Period size: 9 Copynumber: 7.0 Consensus size: 9
29471692 TTTGACTTTG
29471702 ATTTTTTTT
1 ATTTTTTTT
29471711 ATTTTTTTT
1 ATTTTTTTT
29471720 A--TTTTTT
1 ATTTTTTTT
*
29471727 ATTTTTTTG
1 ATTTTTTTT
29471736 ATTTTTTTT
1 ATTTTTTTT
*
29471745 GATTTTTTTG
1 -ATTTTTTTT
29471755 ATTTTTTTT
1 ATTTTTTTT
29471764 TAGTCTGAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
7 7 0.15
9 31 0.67
10 8 0.17
ACGTcount: A:0.11, C:0.00, G:0.05, T:0.84
Consensus pattern (9 bp):
ATTTTTTTT
Found at i:29471719 original size:25 final size:26
Alignment explanation
Indices: 29471688--29471762 Score: 82
Period size: 25 Copynumber: 2.9 Consensus size: 26
29471678 TTTTCTTTTC
*
29471688 TTTTTTTGA-CTTTGATTTTTTTTAT
1 TTTTTTTGATCTTTGATTTTTTTGAT
* *
29471713 TTTTTTT-ATTTTTTATTTTTTTGAT
1 TTTTTTTGATCTTTGATTTTTTTGAT
*
29471738 TTTTTTTGATTTTTTTGATTTTTTT
1 TTTTTTTGA--TCTTTGATTTTTTT
29471763 TTAGTCTGAA
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 1 0.02
25 27 0.64
26 1 0.02
28 13 0.31
ACGTcount: A:0.11, C:0.01, G:0.07, T:0.81
Consensus pattern (26 bp):
TTTTTTTGATCTTTGATTTTTTTGAT
Found at i:29471725 original size:19 final size:19
Alignment explanation
Indices: 29471698--29471765 Score: 90
Period size: 19 Copynumber: 3.8 Consensus size: 19
29471688 TTTTTTTGAC
29471698 TTTGA-TTTTTTTTA-TTT
1 TTTGATTTTTTTTTATTTT
*
29471715 TTT--TTATTTTTTATTTT
1 TTTGATTTTTTTTTATTTT
*
29471732 TTTGATTTTTTTTGATTTT
1 TTTGATTTTTTTTTATTTT
29471751 TTTGATTTTTTTTTA
1 TTTGATTTTTTTTTA
29471766 GTCTGAACTC
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
16 8 0.19
17 9 0.21
19 26 0.60
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (19 bp):
TTTGATTTTTTTTTATTTT
Found at i:29471725 original size:44 final size:43
Alignment explanation
Indices: 29471677--29471763 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 43
29471667 TTTCTTTTTC
* * *
29471677 TTTTTCTTTTCTTTTTTTGACTTTGATTTTTTTTATTTTTTTTAT
1 TTTTTATTTT-TTTATTT-ACTTTGATTTTTTTGATTTTTTTTAT
**
29471722 TTTTTATTTTTTTGATTTTTTTTGATTTTTTTGATTTTTTTT
1 TTTTTATTTTTTT-ATTTACTTTGATTTTTTTGATTTTTTTT
29471764 TAGTCTGAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
44 24 0.67
45 12 0.33
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (43 bp):
TTTTTATTTTTTTATTTACTTTGATTTTTTTGATTTTTTTTAT
Found at i:29473022 original size:19 final size:19
Alignment explanation
Indices: 29472998--29473038 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
29472988 TGTGAAAATC
*
29472998 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATG-AATG
29473017 TAATGCAAATGCATGAATG
1 TAATGCAAATGCATGAATG
29473036 TAA
1 TAA
29473039 AAAGAGACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (19 bp):
TAATGCAAATGCATGAATG
Found at i:29474680 original size:3 final size:3
Alignment explanation
Indices: 29474672--29474699 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29474662 AAGGGAAAAT
29474672 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
29474700 CATCAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:29475980 original size:5 final size:5
Alignment explanation
Indices: 29475972--29476052 Score: 57
Period size: 5 Copynumber: 16.6 Consensus size: 5
29475962 ATTTAAAATA
* *
29475972 TATAT TATAT TATAT TATAT T-TACT TA-AT TA-AT AAGTAT CT-TTT
1 TATAT TATAT TATAT TATAT TATA-T TATAT TATAT TA-TAT -TATAT
*
29476016 TATAT TATAT TATTAT TA-A- TATAT TATAC TATAT TAT
1 TATAT TATAT TA-TAT TATAT TATAT TATAT TATAT TAT
29476053 TATATATATA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
3 2 0.03
4 11 0.18
5 41 0.67
6 7 0.11
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (5 bp):
TATAT
Found at i:29476139 original size:35 final size:34
Alignment explanation
Indices: 29476084--29476150 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 34
29476074 AGAATAGAAA
*
29476084 TGAGAAAGAAAGAAACAAAGAAGGAAAACGAAATT
1 TGAGAAAGAAAGAAACAAAGAA-GAAAAAGAAATT
*
29476119 TGAGAAAGAAA-AAGAGAAAGAAGAAAAAGAAA
1 TGAGAAAGAAAGAA-ACAAAGAAGAAAAAGAAA
29476151 GAGAACCACG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
34 11 0.38
35 18 0.62
ACGTcount: A:0.67, C:0.03, G:0.24, T:0.06
Consensus pattern (34 bp):
TGAGAAAGAAAGAAACAAAGAAGAAAAAGAAATT
Found at i:29483775 original size:20 final size:20
Alignment explanation
Indices: 29483750--29483834 Score: 116
Period size: 20 Copynumber: 4.2 Consensus size: 20
29483740 TATTGCTGAA
29483750 CAGAGGCACCGAAGTGCAAT
1 CAGAGGCACCGAAGTGCAAT
*
29483770 CAGAGGCAACGAAGTGCAAT
1 CAGAGGCACCGAAGTGCAAT
** *
29483790 CAGAGGCGTCGAAGTACAAT
1 CAGAGGCACCGAAGTGCAAT
* *
29483810 CAAAGGCACCAAAGTGCAAT
1 CAGAGGCACCGAAGTGCAAT
29483830 CAGAG
1 CAGAG
29483835 AGTACATAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.39, C:0.22, G:0.28, T:0.11
Consensus pattern (20 bp):
CAGAGGCACCGAAGTGCAAT
Found at i:29483877 original size:22 final size:22
Alignment explanation
Indices: 29483815--29483945 Score: 85
Period size: 22 Copynumber: 6.0 Consensus size: 22
29483805 ACAATCAAAG
* *
29483815 GCACCAAAGTGC-AATCAGAGA
1 GCACAAAAGTGCAAATTAGAGA
*
29483836 GTACATAAA-TGCTAAA-TAGAGA
1 GCACA-AAAGTGC-AAATTAGAGA
29483858 GCACAAAAGTGCAAATTAGAGA
1 GCACAAAAGTGCAAATTAGAGA
* *
29483880 GC-CTAGAAGTG-ATAATTAGAAA
1 GCAC-AAAAGTGCA-AATTAGAGA
*
29483902 GCATAAAAGTGCTAAA-TAGAGA
1 GCACAAAAGTGC-AAATTAGAGA
** * *
29483924 GCACTGAAGTGCTAATCAGAGA
1 GCACAAAAGTGCAAATTAGAGA
29483946 TCCAATTTCA
Statistics
Matches: 85, Mismatches: 14, Indels: 21
0.71 0.12 0.17
Matches are distributed among these distances:
21 16 0.19
22 64 0.75
23 4 0.05
24 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.18
Consensus pattern (22 bp):
GCACAAAAGTGCAAATTAGAGA
Found at i:29483910 original size:44 final size:44
Alignment explanation
Indices: 29483852--29483939 Score: 117
Period size: 44 Copynumber: 2.0 Consensus size: 44
29483842 AAATGCTAAA
*
29483852 TAGAGAGCACAAAAGTGC-AAATTAGAGAGC-CTAGAAGTGATAAT
1 TAGAAAGCACAAAAGTGCTAAA-TAGAGAGCACT-GAAGTGATAAT
* *
29483896 TAGAAAGCATAAAAGTGCTAAATAGAGAGCACTGAAGTGCTAAT
1 TAGAAAGCACAAAAGTGCTAAATAGAGAGCACTGAAGTGATAAT
29483940 CAGAGATCCA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
44 34 0.87
45 5 0.13
ACGTcount: A:0.45, C:0.11, G:0.24, T:0.19
Consensus pattern (44 bp):
TAGAAAGCACAAAAGTGCTAAATAGAGAGCACTGAAGTGATAAT
Found at i:29485139 original size:23 final size:23
Alignment explanation
Indices: 29485095--29485139 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
29485085 TTAAAAAGTA
*
29485095 GTTAATTTCCACTTTAAACCTTG
1 GTTAATTTCCACTATAAACCTTG
*
29485118 GTTAATTTACCA-TATAAGCCTT
1 GTTAATTT-CCACTATAAACCTT
29485140 TTAACTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (23 bp):
GTTAATTTCCACTATAAACCTTG
Found at i:29496272 original size:20 final size:20
Alignment explanation
Indices: 29496202--29496272 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 20
29496192 ATACAGTGTG
* *
29496202 GATAAACCACTAATTAGTGTA
1 GATAAACCACTAA-TCGTATA
* *
29496223 GATAAAAACTACTAATACGCTATG
1 GAT--AAACCACTAAT-CG-TATA
29496247 GATAAACCACTAATCGTATA
1 GATAAACCACTAATCGTATA
29496267 GATAAA
1 GATAAA
29496273 ATCTGCTAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
20 9 0.22
21 5 0.12
22 11 0.28
23 10 0.25
24 5 0.12
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.25
Consensus pattern (20 bp):
GATAAACCACTAATCGTATA
Found at i:29496284 original size:44 final size:45
Alignment explanation
Indices: 29496177--29496303 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
29496167 TAAATGTTGC
* *
29496177 AGATAAAAGCTGCTAATACAG-TGTGGATAAACCACTAATTAGTGT
1 AGATAAAAACTGCTAATAC-GCTGTGGATAAACCACTAATTAGTAT
* * *
29496222 AGATAAAAACTACTAATACGCTATGGATAAACCACTAA-TCGTAT
1 AGATAAAAACTGCTAATACGCTGTGGATAAACCACTAATTAGTAT
* *
29496266 AGATAAAATCTGCTAATACGAC-GTGGATTAACCACTAA
1 AGATAAAAACTGCTAATACG-CTGTGGATAAACCACTAA
29496304 ACGGTGAAGA
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
44 37 0.52
45 34 0.48
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.25
Consensus pattern (45 bp):
AGATAAAAACTGCTAATACGCTGTGGATAAACCACTAATTAGTAT
Found at i:29504638 original size:7 final size:7
Alignment explanation
Indices: 29504622--29504651 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
29504612 TTTATAGGAT
29504622 ATATTAAA
1 ATATT-AA
29504630 ATATTAA
1 ATATTAA
29504637 ATATTAA
1 ATATTAA
29504644 ATATTAA
1 ATATTAA
29504651 A
1 A
29504652 AAAACACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
ATATTAA
Done.