Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168004.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_26, whole genome shotgun sequence
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: 16099665
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 29 of 77
Found at i:5679721 original size:34 final size:34
Alignment explanation
Indices: 5679681--5679763 Score: 105
Period size: 34 Copynumber: 2.5 Consensus size: 34
5679671 TCTAAGATTT
*
5679681 TATAATTTTTCAAAAATAAATTTTTAAAAAATCA
1 TATAATTTTTCAAAAATAAATTTTCAAAAAATCA
** *
5679715 TATAATTTTTTGAAAATAAATTTTCAAAAAATTA
1 TATAATTTTTCAAAAATAAATTTTCAAAAAATCA
* *
5679749 TA-AACTTATCAAAAA
1 TATAATTTTTCAAAAA
5679764 ATTTAACTTT
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
33 9 0.22
34 32 0.78
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (34 bp):
TATAATTTTTCAAAAATAAATTTTCAAAAAATCA
Found at i:5679779 original size:18 final size:19
Alignment explanation
Indices: 5679730--5679785 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 19
5679720 TTTTTTGAAA
5679730 ATAAA-TTTTCAAAAAATT
1 ATAAACTTTTCAAAAAATT
*
5679748 ATAAACTTATCAAAAAATT
1 ATAAACTTTTCAAAAAATT
* *
5679767 -T-AACTTTTCCAAAACTT
1 ATAAACTTTTCAAAAAATT
5679784 AT
1 AT
5679786 GTAAAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 13 0.41
18 7 0.22
19 12 0.38
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAACTTTTCAAAAAATT
Found at i:5680784 original size:39 final size:39
Alignment explanation
Indices: 5680711--5680787 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 39
5680701 AAACTTTTCA
*
5680711 AACTTCCTTTCACATCCAAAACATTAAGCAAGATCCTCC
1 AACTTCCTTTCACATCCAAAACATCAAGCAAGATCCTCC
*
5680750 AACTTCCTTTCA-AGTCCAAAACATCCAA-CCAGATCCTC
1 AACTTCCTTTCACA-TCCAAAACAT-CAAGCAAGATCCTC
5680788 TAAGCCCGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 1 0.03
39 31 0.91
40 2 0.06
ACGTcount: A:0.35, C:0.35, G:0.05, T:0.25
Consensus pattern (39 bp):
AACTTCCTTTCACATCCAAAACATCAAGCAAGATCCTCC
Found at i:5688924 original size:21 final size:20
Alignment explanation
Indices: 5688900--5688941 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5688890 ATTTGGTTTA
5688900 TTCACAAAAAAATTATTAAAT
1 TTCACAAAAAAATTA-TAAAT
* *
5688921 TTCATATAAAAATTATAAAT
1 TTCACAAAAAAATTATAAAT
5688941 T
1 T
5688942 AAATATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
TTCACAAAAAAATTATAAAT
Found at i:5688947 original size:20 final size:21
Alignment explanation
Indices: 5688907--5688948 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
5688897 TTATTCACAA
**
5688907 AAAAATTATTAAATTTCATAT
1 AAAAATTATTAAATTAAATAT
5688928 AAAAATTA-TAAATTAAATAT
1 AAAAATTATTAAATTAAATAT
5688948 A
1 A
5688949 TAACACAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
AAAAATTATTAAATTAAATAT
Found at i:5689701 original size:15 final size:16
Alignment explanation
Indices: 5689681--5689716 Score: 65
Period size: 15 Copynumber: 2.3 Consensus size: 16
5689671 CACCCTACCA
5689681 CACCCAATCCC-TCCC
1 CACCCAATCCCTTCCC
5689696 CACCCAATCCCTTCCC
1 CACCCAATCCCTTCCC
5689712 CACCC
1 CACCC
5689717 CCTACACCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.55
16 9 0.45
ACGTcount: A:0.19, C:0.67, G:0.00, T:0.14
Consensus pattern (16 bp):
CACCCAATCCCTTCCC
Found at i:5689759 original size:20 final size:19
Alignment explanation
Indices: 5689694--5689769 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 19
5689684 CCAATCCCTC
5689694 CCCACCCAATCCCTTCCCCA
1 CCCACCCAATCCC-TCCCCA
* * * *
5689714 CCC-CCTACACCCCACTCCA
1 CCCACCCA-ATCCCTCCCCA
5689733 CCCCACCCAATCCCTCCCCA
1 -CCCACCCAATCCCTCCCCA
5689753 TCCCACCCAATCCCTCC
1 -CCCACCCAATCCCTCC
5689770 TCATGTGCTT
Statistics
Matches: 44, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 7 0.16
20 34 0.77
21 3 0.07
ACGTcount: A:0.20, C:0.67, G:0.00, T:0.13
Consensus pattern (19 bp):
CCCACCCAATCCCTCCCCA
Found at i:5690240 original size:43 final size:43
Alignment explanation
Indices: 5690184--5690266 Score: 132
Period size: 43 Copynumber: 1.9 Consensus size: 43
5690174 AATAACGGTC
5690184 CGTTATTGCCGCTATTC-TCTGTTAAGCCGTTATTTACGGTGTT
1 CGTTATTGCCGCTATTCTTC-GTTAAGCCGTTATTTACGGTGTT
* *
5690227 CGTTATTGTCGCTATTCTTCGTTAAGCCGTTATTTGCGGT
1 CGTTATTGCCGCTATTCTTCGTTAAGCCGTTATTTACGGT
5690267 TGTTACACTC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
43 35 0.95
44 2 0.05
ACGTcount: A:0.13, C:0.20, G:0.22, T:0.45
Consensus pattern (43 bp):
CGTTATTGCCGCTATTCTTCGTTAAGCCGTTATTTACGGTGTT
Found at i:5699914 original size:16 final size:16
Alignment explanation
Indices: 5699895--5699925 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5699885 ATCTTCACTA
*
5699895 ATTAATGTTTTCACCG
1 ATTAATGTTATCACCG
5699911 ATTAATGTTATCACC
1 ATTAATGTTATCACC
5699926 ACATGTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.19, G:0.10, T:0.42
Consensus pattern (16 bp):
ATTAATGTTATCACCG
Found at i:5706665 original size:29 final size:30
Alignment explanation
Indices: 5706602--5706666 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
5706592 AAATAATAAT
* * * * *
5706602 TTATTTGGATATAAATCAAAGTATAAATAC
1 TTATTTGAATATAAATAAAAATATAAAAAA
5706632 TTATTTGAATAT-AATAAAAATATAAAAAA
1 TTATTTGAATATAAATAAAAATATAAAAAA
5706661 TTATTT
1 TTATTT
5706667 AACAAATGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 19 0.63
30 11 0.37
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (30 bp):
TTATTTGAATATAAATAAAAATATAAAAAA
Found at i:5710631 original size:2 final size:2
Alignment explanation
Indices: 5710622--5710651 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5710612 TTTGTCCACT
5710622 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5710652 CAACCTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5711012 original size:23 final size:22
Alignment explanation
Indices: 5710956--5711005 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
5710946 TTTAATTCTA
** *
5710956 AAAATATTAAAAGCAATTTATT
1 AAAATATTATTAGTAATTTATT
*
5710978 AAAATATTATTAGTAATTTTTT
1 AAAATATTATTAGTAATTTATT
5711000 ATAAAT
1 A-AAAT
5711006 TTAATTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
AAAATATTATTAGTAATTTATT
Found at i:5712397 original size:22 final size:23
Alignment explanation
Indices: 5712372--5712456 Score: 81
Period size: 22 Copynumber: 3.9 Consensus size: 23
5712362 AATTTTTTAG
*
5712372 AAATTAAATGATAAATTA-TTGT
1 AAATTAAATGATAAATTAGTAGT
* *
5712394 AAA-TAATTGATAATTTAGTAGT
1 AAATTAAATGATAAATTAGTAGT
*
5712416 ATATT-AATGATAAATTAGTAGT
1 AAATTAAATGATAAATTAGTAGT
*
5712438 AAA--AAATTGATAATTTAGT
1 AAATTAAA-TGATAAATTAGT
5712457 GGTTAATTCT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
21 14 0.27
22 36 0.71
23 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (23 bp):
AAATTAAATGATAAATTAGTAGT
Found at i:5712516 original size:65 final size:64
Alignment explanation
Indices: 5712430--5712550 Score: 145
Period size: 65 Copynumber: 1.9 Consensus size: 64
5712420 TAATGATAAA
* * * * *
5712430 TTAGTAGTAAAAAATTGATAATTTAGTGGTTAATTCTTGAAAACTTAA-AAGTAAATCGATAGAA
1 TTAGTAGTAAAAAATTCATAATATAATAGTTAA-TCATGAAAACTTAATAA-TAAATCGATAGAA
5712494 T
64 T
** *
5712495 TTAGTAGTAAATCATTCATAATATAATAGTTAATCATGATAACTTAATAATAAATC
1 TTAGTAGTAAAAAATTCATAATATAATAGTTAATCATGAAAACTTAATAATAAATC
5712551 ATGTATAATT
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
64 18 0.38
65 29 0.62
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.36
Consensus pattern (64 bp):
TTAGTAGTAAAAAATTCATAATATAATAGTTAATCATGAAAACTTAATAATAAATCGATAGAAT
Found at i:5712542 original size:21 final size:20
Alignment explanation
Indices: 5712526--5712581 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
5712516 TATAATAGTT
5712526 AATCATGATAACTTAATAATA
1 AATCATGATAACTTAAT-ATA
5712547 AATCATGTATAA-TTAATATA
1 AATCATG-ATAACTTAATATA
*
5712567 AATCAGTAATAACTT
1 AATCA-TGATAACTT
5712582 TGTAATGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 12 0.39
21 15 0.48
22 4 0.13
ACGTcount: A:0.50, C:0.09, G:0.05, T:0.36
Consensus pattern (20 bp):
AATCATGATAACTTAATATA
Found at i:5712742 original size:22 final size:22
Alignment explanation
Indices: 5712687--5712788 Score: 93
Period size: 22 Copynumber: 4.6 Consensus size: 22
5712677 AATATATAAA
*
5712687 AATATAATAGTAAATCATTAAT
1 AATATAATAGTAAATCACTAAT
*
5712709 AATTTAGA-AGTAAATCACTAAT
1 AATATA-ATAGTAAATCACTAAT
* *
5712731 AATATAATAGTAAATTACAAAT
1 AATATAATAGTAAATCACTAAT
* *
5712753 AACT-TAATTA-TAAATCAGTGAT
1 AA-TATAA-TAGTAAATCACTAAT
*
5712775 AATTTAATAGTAAA
1 AATATAATAGTAAA
5712789 ATAGTTAATC
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
21 4 0.06
22 57 0.88
23 4 0.06
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.34
Consensus pattern (22 bp):
AATATAATAGTAAATCACTAAT
Found at i:5712754 original size:44 final size:43
Alignment explanation
Indices: 5712687--5712788 Score: 107
Period size: 44 Copynumber: 2.3 Consensus size: 43
5712677 AATATATAAA
** *
5712687 AATATAATAGTAAATCATTAATAATTTAGA-AGTAAATCACTAAT
1 AATATAATAGTAAATCACAAATAACTTA-ATA-TAAATCACTAAT
* * *
5712731 AATATAATAGTAAATTACAAATAACTTAATTATAAATCAGTGAT
1 AATATAATAGTAAATCACAAATAACTTAA-TATAAATCACTAAT
*
5712775 AATTTAATAGTAAA
1 AATATAATAGTAAA
5712789 ATAGTTAATC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
43 1 0.02
44 47 0.96
45 1 0.02
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.34
Consensus pattern (43 bp):
AATATAATAGTAAATCACAAATAACTTAATATAAATCACTAAT
Found at i:5712949 original size:22 final size:21
Alignment explanation
Indices: 5712924--5713051 Score: 114
Period size: 22 Copynumber: 5.8 Consensus size: 21
5712914 CGTAATGATG
* *
5712924 AATCATTCATAATTTAATGGCA
1 AATCATT-ATAATTTAATAGTA
* *
5712946 AATCATTTATAAATTAGA-AATA
1 AATCA-TTATAATTTA-ATAGTA
5712968 AATCATTAATAATTTAATAGTA
1 AATCATT-ATAATTTAATAGTA
*
5712990 AATCATTACTAATTTAGTAGTA
1 AATCATTA-TAATTTAATAGTA
* *
5713012 AATCATAAATAAATTAATAGTA
1 AATCAT-TATAATTTAATAGTA
*
5713034 AATAACTTATAATTTAAT
1 AATCA-TTATAATTTAAT
5713052 TATTAATCAT
Statistics
Matches: 86, Mismatches: 13, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
21 4 0.05
22 77 0.90
23 5 0.06
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.38
Consensus pattern (21 bp):
AATCATTATAATTTAATAGTA
Found at i:5712980 original size:44 final size:44
Alignment explanation
Indices: 5712924--5713036 Score: 129
Period size: 44 Copynumber: 2.6 Consensus size: 44
5712914 CGTAATGATG
* *
5712924 AATCATTCATAATTTAATGGCAAATCATTTA-TAAATTAGAAATA
1 AATCATTAATAATTTAATAGCAAATCA-TTACTAAATTAGAAATA
* * * *
5712968 AATCATTAATAATTTAATAGTAAATCATTACTAATTTAGTAGTA
1 AATCATTAATAATTTAATAGCAAATCATTACTAAATTAGAAATA
* * *
5713012 AATCATAAATAAATTAATAGTAAAT
1 AATCATTAATAATTTAATAGCAAAT
5713037 AACTTATAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
43 3 0.05
44 57 0.95
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.37
Consensus pattern (44 bp):
AATCATTAATAATTTAATAGCAAATCATTACTAAATTAGAAATA
Found at i:5718353 original size:5 final size:5
Alignment explanation
Indices: 5718343--5718369 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
5718333 AAACAATCTT
5718343 TATTA TATTA TATTA TATTA TATTA TA
1 TATTA TATTA TATTA TATTA TATTA TA
5718370 GTATGGAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATTA
Found at i:5728177 original size:92 final size:92
Alignment explanation
Indices: 5728020--5728202 Score: 321
Period size: 92 Copynumber: 2.0 Consensus size: 92
5728010 TCTGTTCCCA
* *
5728020 TTCTACTATGCAAGTTCCCTATACTTCCAAGTTTGCAAGTATTTGAACTCCCATGAATAGATTTA
1 TTCTACCATGCAAGTTCCCTATACTTCCAAGTTTGCAAGTACTTGAACTCCCATGAATAGATTTA
*
5728085 CACTGCTTACCCCTCTTGCCTGATGCG
66 CACTGCTTACCACTCTTGCCTGATGCG
* *
5728112 TTCTACCATGCAAGTTCTCTATACTTCCAAGTTTGCAAGTACTTGAACTTCCATGAATAGATTTA
1 TTCTACCATGCAAGTTCCCTATACTTCCAAGTTTGCAAGTACTTGAACTCCCATGAATAGATTTA
5728177 CACTGCTTACCACTCTTGCCTGATGC
66 CACTGCTTACCACTCTTGCCTGATGC
5728203 AACCATTCAT
Statistics
Matches: 86, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
92 86 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.35
Consensus pattern (92 bp):
TTCTACCATGCAAGTTCCCTATACTTCCAAGTTTGCAAGTACTTGAACTCCCATGAATAGATTTA
CACTGCTTACCACTCTTGCCTGATGCG
Found at i:5732213 original size:14 final size:14
Alignment explanation
Indices: 5732194--5732251 Score: 62
Period size: 14 Copynumber: 4.0 Consensus size: 14
5732184 TTTTTAAACT
*
5732194 TTTTTTATTTTTTA
1 TTTTTTACTTTTTA
* *
5732208 TTTTTTTCATTTTTG
1 TTTTTTAC-TTTTTA
5732223 TCTTTTTACTTTTTA
1 T-TTTTTACTTTTTA
*
5732238 TATTTTACTTTTTA
1 TTTTTTACTTTTTA
5732252 AAATTTTCGC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
14 18 0.50
15 12 0.33
16 6 0.17
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.78
Consensus pattern (14 bp):
TTTTTTACTTTTTA
Found at i:5732213 original size:15 final size:15
Alignment explanation
Indices: 5732193--5732243 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
5732183 ATTTTTAAAC
5732193 TTTTTTTATTTTTTA
1 TTTTTTTATTTTTTA
*
5732208 TTTTTTTCA-TTTTTG
1 TTTTTTT-ATTTTTTA
*
5732223 TCTTTTTACTTTTTATA
1 TTTTTTTA-TTTTT-TA
5732240 TTTT
1 TTTT
5732244 ACTTTTTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 1 0.04
15 18 0.64
16 5 0.18
17 4 0.14
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTTTATTTTTTA
Found at i:5732601 original size:15 final size:15
Alignment explanation
Indices: 5732581--5732610 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5732571 CATTTAATAC
5732581 ATGACCAAAATTTAA
1 ATGACCAAAATTTAA
5732596 ATGACCAAAATTTAA
1 ATGACCAAAATTTAA
5732611 GTCACATTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (15 bp):
ATGACCAAAATTTAA
Found at i:5734057 original size:3 final size:3
Alignment explanation
Indices: 5734049--5734073 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5734039 TACTTAATAG
5734049 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
5734074 GTTGTAGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:5735318 original size:2 final size:2
Alignment explanation
Indices: 5735311--5735342 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5735301 CTTCACTCTA
5735311 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5735343 TTGAAATGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5748630 original size:51 final size:51
Alignment explanation
Indices: 5748569--5748671 Score: 129
Period size: 52 Copynumber: 2.0 Consensus size: 51
5748559 AAATTTAGTA
* * * *
5748569 TTATTCTTTTT-TATTGTATTTTTTTTTGTTTTGTATTATTATTATTATTTTT
1 TTATTCTTTTTGTATT-TATTTTTTTGTATTTCGTA-TAATATTATTATTTTT
5748621 TTATT-TTTTTGGTATTTATTTTTTTGTATTTCGTATAATATTATTATTTTT
1 TTATTCTTTTT-GTATTTATTTTTTTGTATTTCGTATAATATTATTATTTTT
5748672 ATTTTTGGGG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
51 20 0.44
52 21 0.47
53 4 0.09
ACGTcount: A:0.17, C:0.02, G:0.07, T:0.74
Consensus pattern (51 bp):
TTATTCTTTTTGTATTTATTTTTTTGTATTTCGTATAATATTATTATTTTT
Found at i:5748637 original size:48 final size:52
Alignment explanation
Indices: 5748575--5748671 Score: 132
Period size: 51 Copynumber: 1.9 Consensus size: 52
5748565 AGTATTATTC
* *
5748575 TTTTTTATTGTA-TT-TTTTTTTGT-TTT-GTATTATTATTATTATTTTTTTA
1 TTTTTTATGGTATTTATTTTTTTGTATTTCGTA-TAATATTATTATTTTTTTA
5748624 TTTTTT-TGGTATTTATTTTTTTGTATTTCGTATAATATTATTATTTTT
1 TTTTTTATGGTATTTATTTTTTTGTATTTCGTATAATATTATTATTTTT
5748672 ATTTTTGGGG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
48 4 0.10
49 8 0.19
50 9 0.21
51 18 0.43
52 3 0.07
ACGTcount: A:0.18, C:0.01, G:0.07, T:0.74
Consensus pattern (52 bp):
TTTTTTATGGTATTTATTTTTTTGTATTTCGTATAATATTATTATTTTTTTA
Found at i:5748642 original size:14 final size:15
Alignment explanation
Indices: 5748620--5748651 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5748610 TTATTATTTT
5748620 TTTATTTTTTTGGTA
1 TTTATTTTTTTGGTA
5748635 TTTATTTTTTT-GTA
1 TTTATTTTTTTGGTA
5748649 TTT
1 TTT
5748652 CGTATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.78
Consensus pattern (15 bp):
TTTATTTTTTTGGTA
Found at i:5757061 original size:18 final size:18
Alignment explanation
Indices: 5757038--5757087 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
5757028 TCTAGATTCA
5757038 CAAAGATTTCAAGTTTCG
1 CAAAGATTTCAAGTTTCG
*
5757056 CAAAGATTTCAA-TTTTG
1 CAAAGATTTCAAGTTTCG
*
5757073 CAAA-ATTTTAAGTTT
1 CAAAGATTTCAAGTTT
5757088 TGTAGGGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 6 0.21
17 11 0.38
18 12 0.41
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (18 bp):
CAAAGATTTCAAGTTTCG
Found at i:5757088 original size:17 final size:18
Alignment explanation
Indices: 5757038--5757089 Score: 72
Period size: 17 Copynumber: 3.0 Consensus size: 18
5757028 TCTAGATTCA
*
5757038 CAAAGATTTCAAGTTTCG
1 CAAAGATTTCAAGTTTTG
5757056 CAAAGATTTCAA-TTTTG
1 CAAAGATTTCAAGTTTTG
*
5757073 CAAA-ATTTTAAGTTTTG
1 CAAAGATTTCAAGTTTTG
5757090 TAGGGATTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 6 0.19
17 13 0.42
18 12 0.39
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (18 bp):
CAAAGATTTCAAGTTTTG
Found at i:5757183 original size:18 final size:17
Alignment explanation
Indices: 5757160--5757233 Score: 53
Period size: 17 Copynumber: 4.4 Consensus size: 17
5757150 TCCAAGTTTC
*
5757160 GCAAAGGTTCCAGATTT
1 GCAAAAGTTCCAGATTT
** *
5757177 GCAAAAGTTTTAAATTT
1 GCAAAAGTTCCAGATTT
* *
5757194 AGCAAAGGTTCCA-AATT
1 -GCAAAAGTTCCAGATTT
*
5757211 GCAAATA-TTCTAGATTT
1 GCAAA-AGTTCCAGATTT
5757228 GCAAAA
1 GCAAAA
5757234 ATTTCAAGCT
Statistics
Matches: 43, Mismatches: 11, Indels: 7
0.70 0.18 0.11
Matches are distributed among these distances:
16 10 0.23
17 24 0.56
18 9 0.21
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (17 bp):
GCAAAAGTTCCAGATTT
Found at i:5757441 original size:17 final size:17
Alignment explanation
Indices: 5757417--5757470 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
5757407 TTTAAATTTG
5757417 CAAGAATTTCAGTTTCA
1 CAAGAATTTCAGTTTCA
* **
5757434 CAATAATTTCAGTTTTG
1 CAAGAATTTCAGTTTCA
*
5757451 CAAGAATTTAAGTTTCA
1 CAAGAATTTCAGTTTCA
5757468 CAA
1 CAA
5757471 AAGTTTCAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (17 bp):
CAAGAATTTCAGTTTCA
Found at i:5757442 original size:34 final size:34
Alignment explanation
Indices: 5757404--5757480 Score: 102
Period size: 34 Copynumber: 2.3 Consensus size: 34
5757394 GATTATCAAG
* *
5757404 AATTTTAAATTTGCAAGAATTTCAGTTTCACAAT
1 AATTTCAAATTTGCAAGAATTTAAGTTTCACAAT
**
5757438 AATTTCAGTTTTGCAAGAATTTAAGTTTCACAA-
1 AATTTCAAATTTGCAAGAATTTAAGTTTCACAAT
5757471 AAGTTTCAAA
1 AA-TTTCAAA
5757481 AATTCTCAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 2 0.06
34 34 0.94
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (34 bp):
AATTTCAAATTTGCAAGAATTTAAGTTTCACAAT
Found at i:5757570 original size:35 final size:34
Alignment explanation
Indices: 5757520--5757586 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
5757510 TTTGATAAAG
**
5757520 TTTCAAATTGGCAAGAATTGATAGATTCACAAGGA
1 TTTCAAATTCACAAGAATT-ATAGATTCACAAGGA
* *
5757555 TTTCAAATTCACAAGAATTTTAGATTCGCAAG
1 TTTCAAATTCACAAGAATTATAGATTCACAAG
5757587 AAATAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 11 0.39
35 17 0.61
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.31
Consensus pattern (34 bp):
TTTCAAATTCACAAGAATTATAGATTCACAAGGA
Found at i:5757581 original size:17 final size:17
Alignment explanation
Indices: 5757531--5757588 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
5757521 TTCAAATTGG
*
5757531 CAAGAATTGATAGATTCA
1 CAAGAATT-TTAGATTCA
* * *
5757549 CAAGGATTTCAAATTCA
1 CAAGAATTTTAGATTCA
*
5757566 CAAGAATTTTAGATTCG
1 CAAGAATTTTAGATTCA
5757583 CAAGAA
1 CAAGAA
5757589 ATAAAAAATT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
17 25 0.78
18 7 0.22
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.28
Consensus pattern (17 bp):
CAAGAATTTTAGATTCA
Found at i:5757926 original size:26 final size:25
Alignment explanation
Indices: 5757878--5757928 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
5757868 ATTCACATCC
* *
5757878 AAAATTTCAAAATTTCACATTAAAA
1 AAAATTTCAAAAATTAACATTAAAA
* *
5757903 AAAATTTTAAAAATTAACATTTAAA
1 AAAATTTCAAAAATTAACATTAAAA
5757928 A
1 A
5757929 GTTAAAGATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (25 bp):
AAAATTTCAAAAATTAACATTAAAA
Found at i:5757971 original size:23 final size:22
Alignment explanation
Indices: 5757857--5758016 Score: 101
Period size: 22 Copynumber: 7.1 Consensus size: 22
5757847 TTTTTCCTTG
*
5757857 AAAATTTAAAAATTCACATCC-
1 AAAATTTAAAGATTCACATCCA
**
5757878 AAAATTTCAAA-ATTTCACATTAAAA
1 AAAATTT-AAAGA-TTCACA-T-CCA
* * **
5757903 AAAATTTTAAAAATTAACAT-TT
1 AAAA-TTTAAAGATTCACATCCA
* *** *
5757925 AAAAGTTAAAGATTTTTATTCA
1 AAAATTTAAAGATTCACATCCA
5757947 AAAAGTTTAAAGATTCACATCCA
1 AAAA-TTTAAAGATTCACATCCA
* *
5757970 AAGATTTCAAAGATTCACATTCA
1 AAAATTT-AAAGATTCACATCCA
*
5757993 AAAAATTAAAGATTCACATCCA
1 AAAATTTAAAGATTCACATCCA
5758015 AA
1 AA
5758017 GTTTTAAAAG
Statistics
Matches: 107, Mismatches: 22, Indels: 19
0.72 0.15 0.13
Matches are distributed among these distances:
21 18 0.17
22 36 0.34
23 36 0.34
24 1 0.01
25 12 0.11
26 4 0.04
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.31
Consensus pattern (22 bp):
AAAATTTAAAGATTCACATCCA
Found at i:5758017 original size:45 final size:44
Alignment explanation
Indices: 5757857--5758016 Score: 144
Period size: 45 Copynumber: 3.5 Consensus size: 44
5757847 TTTTTCCTTG
* *
5757857 AAAATTTAAAAATTCACATCCAAAATTTCAAA-ATTTCACATTAAA
1 AAAAATTAAAAATTCACATCCAAAATTTCAAAGA-TTCACATT-CA
* ** * ***
5757902 AAAAATTTTAAAAATTAACATTTAAAAGTT-AAAGATTTTTATTCA
1 AAAAA--TTAAAAATTCACATCCAAAATTTCAAAGATTCACATTCA
* *
5757947 AAAAGTTTAAAGATTCACATCCAAAGATTTCAAAGATTCACATTCA
1 AAAA-ATTAAAAATTCACATCCAAA-ATTTCAAAGATTCACATTCA
*
5757993 AAAAATTAAAGATTCACATCCAAA
1 AAAAATTAAAAATTCACATCCAAA
5758017 GTTTTAAAAG
Statistics
Matches: 90, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
44 15 0.17
45 31 0.34
46 24 0.27
47 20 0.22
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.31
Consensus pattern (44 bp):
AAAAATTAAAAATTCACATCCAAAATTTCAAAGATTCACATTCA
Found at i:5758212 original size:29 final size:28
Alignment explanation
Indices: 5758177--5758259 Score: 150
Period size: 29 Copynumber: 3.0 Consensus size: 28
5758167 TTTTTCTTAT
5758177 AAAAAGAAAAATCTTATCATGAAAGATAA
1 AAAAAGAAAAATCTTATCATGAAAGAT-A
5758206 AAAAAGAAAAATCTTATCATGAAAGATA
1 AAAAAGAAAAATCTTATCATGAAAGATA
5758234 AAAAA-AAAAATCTTATCATGAAAGAT
1 AAAAAGAAAAATCTTATCATGAAAGAT
5758260 CTTTCTCATT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
27 21 0.39
28 6 0.11
29 27 0.50
ACGTcount: A:0.61, C:0.07, G:0.10, T:0.22
Consensus pattern (28 bp):
AAAAAGAAAAATCTTATCATGAAAGATA
Found at i:5758244 original size:27 final size:27
Alignment explanation
Indices: 5758175--5758259 Score: 143
Period size: 27 Copynumber: 3.1 Consensus size: 27
5758165 AGTTTTTCTT
*
5758175 ATAAAAAGAAAAATCTTATCATGAAAG
1 ATAAAAAAAAAAATCTTATCATGAAAG
5758202 ATAAAAAAAGAAAAATCTTATCATGAAAG
1 AT-AAAAAA-AAAAATCTTATCATGAAAG
5758231 ATAAAAAAAAAAATCTTATCATGAAAG
1 ATAAAAAAAAAAATCTTATCATGAAAG
5758258 AT
1 AT
5758260 CTTTCTCATT
Statistics
Matches: 55, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
27 23 0.42
28 11 0.20
29 21 0.38
ACGTcount: A:0.61, C:0.07, G:0.09, T:0.22
Consensus pattern (27 bp):
ATAAAAAAAAAAATCTTATCATGAAAG
Found at i:5761981 original size:16 final size:16
Alignment explanation
Indices: 5761960--5761992 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5761950 GTTAATAAAC
*
5761960 ATAATATATGCAAAAA
1 ATAATATATACAAAAA
5761976 ATAATATATACAAAAA
1 ATAATATATACAAAAA
5761992 A
1 A
5761993 CAACATAAAG
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:0.67, C:0.06, G:0.03, T:0.24
Consensus pattern (16 bp):
ATAATATATACAAAAA
Found at i:5770495 original size:81 final size:81
Alignment explanation
Indices: 5770391--5770539 Score: 280
Period size: 81 Copynumber: 1.8 Consensus size: 81
5770381 CTACTCTCAT
*
5770391 TATATTATATTATGAAATTAGATTAGTTTTGAGGAATTTTCCTTTTCAAAAGAGTACCAAACAGT
1 TATATTATATTATGAAATAAGATTAGTTTTGAGGAATTTTCCTTTTCAAAAGAGTACCAAACAGT
5770456 CTTTATTAGTTTATAG
66 CTTTATTAGTTTATAG
*
5770472 TATATTATATTATGAAATAAGATTAGTTTTGAGGAATTTTCCTTTTCAAAAGAGTACCAGACAGT
1 TATATTATATTATGAAATAAGATTAGTTTTGAGGAATTTTCCTTTTCAAAAGAGTACCAAACAGT
5770537 CTT
66 CTT
5770540 AATTTCCTAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (81 bp):
TATATTATATTATGAAATAAGATTAGTTTTGAGGAATTTTCCTTTTCAAAAGAGTACCAAACAGT
CTTTATTAGTTTATAG
Found at i:5772838 original size:29 final size:29
Alignment explanation
Indices: 5772801--5772859 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
5772791 TTGCTGTTAT
* * **
5772801 TAATTAATTTCAAAAAGTTCTAAATGTAA
1 TAATTAATTTAAAAAACTAATAAATGTAA
5772830 TAATTAATTTAAAAAACTAATAAATGTAA
1 TAATTAATTTAAAAAACTAATAAATGTAA
5772859 T
1 T
5772860 TGTTATGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (29 bp):
TAATTAATTTAAAAAACTAATAAATGTAA
Found at i:5773698 original size:23 final size:24
Alignment explanation
Indices: 5773658--5773707 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
5773648 TTGGATTACG
* *
5773658 TTTAGGGTTTAGAGTTTATGG-TT
1 TTTAGGGTTAAGAGTTTAGGGCTT
**
5773681 TTTAGGGTTAAGCTTTTAGGGCTT
1 TTTAGGGTTAAGAGTTTAGGGCTT
5773705 TTT
1 TTT
5773708 TGTTAATTTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.16, C:0.04, G:0.28, T:0.52
Consensus pattern (24 bp):
TTTAGGGTTAAGAGTTTAGGGCTT
Found at i:5778951 original size:2 final size:2
Alignment explanation
Indices: 5778946--5778972 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5778936 TCTAATTTTT
5778946 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5778973 TACCCAGTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5783474 original size:14 final size:14
Alignment explanation
Indices: 5783451--5783479 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5783441 AGTAAAACGC
5783451 TTTCTGTTTTTTTT
1 TTTCTGTTTTTTTT
5783465 TTTCT-TTTTTTTT
1 TTTCTGTTTTTTTT
5783478 TT
1 TT
5783480 GTAACAAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.00, C:0.07, G:0.03, T:0.90
Consensus pattern (14 bp):
TTTCTGTTTTTTTT
Found at i:5787424 original size:17 final size:17
Alignment explanation
Indices: 5787398--5787432 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
5787388 ATGATTTTAC
*
5787398 ATTAAGAAGAAATGAGA
1 ATTAAAAAGAAATGAGA
*
5787415 ATTAAAAAGAAATTAGA
1 ATTAAAAAGAAATGAGA
5787432 A
1 A
5787433 ACAATTATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (17 bp):
ATTAAAAAGAAATGAGA
Found at i:5789350 original size:32 final size:32
Alignment explanation
Indices: 5789314--5789378 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
5789304 GTGTTATCAA
5789314 AAACAGACCCAAACTTAATCAAATATTGAACC
1 AAACAGACCCAAACTTAATCAAATATTGAACC
5789346 AAACAGACCCAAACTTAATCAAATATTGAACC
1 AAACAGACCCAAACTTAATCAAATATTGAACC
5789378 A
1 A
5789379 TCTTCTTTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.51, C:0.25, G:0.06, T:0.18
Consensus pattern (32 bp):
AAACAGACCCAAACTTAATCAAATATTGAACC
Found at i:5791035 original size:3 final size:3
Alignment explanation
Indices: 5791027--5791052 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5791017 ACGTGCACTC
5791027 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
5791053 ATGCCAATCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:5797880 original size:81 final size:81
Alignment explanation
Indices: 5797752--5797900 Score: 271
Period size: 81 Copynumber: 1.8 Consensus size: 81
5797742 CTACTCTCAT
* *
5797752 TATATTATATTATGAAATTAGATTAGTTTTGAGGAATTTTCCTTTTCAAAAGAGTACTAAACAGT
1 TATATTATATTATGAAATAAGATTAGTTTTGAGGAATTTTCCTTTTCAAAAGAGTACCAAACAGT
5797817 CTTTATTAGTTTATAG
66 CTTTATTAGTTTATAG
*
5797833 TATATTATATTATGAAATAAGATTAGTTTTGAGGAATTTTCCTTTTCAAAAGAGTACCAGACAGT
1 TATATTATATTATGAAATAAGATTAGTTTTGAGGAATTTTCCTTTTCAAAAGAGTACCAAACAGT
5797898 CTT
66 CTT
5797901 AATTTTCTAT
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (81 bp):
TATATTATATTATGAAATAAGATTAGTTTTGAGGAATTTTCCTTTTCAAAAGAGTACCAAACAGT
CTTTATTAGTTTATAG
Found at i:5800202 original size:29 final size:29
Alignment explanation
Indices: 5800165--5800223 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
5800155 TTGCTGTTAT
* * **
5800165 TAATTAATTTCAAAAAGTTCTAAATGTAA
1 TAATTAATTTAAAAAACTAATAAATGTAA
5800194 TAATTAATTTAAAAAACTAATAAATGTAA
1 TAATTAATTTAAAAAACTAATAAATGTAA
5800223 T
1 T
5800224 TGTTATGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (29 bp):
TAATTAATTTAAAAAACTAATAAATGTAA
Found at i:5809911 original size:5 final size:5
Alignment explanation
Indices: 5809903--5809932 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
5809893 ATCTAATTTC
*
5809903 ATAAT ATAAT ATAAT ATGAT ATAAT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
5809933 GAAGACTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:5811543 original size:2 final size:2
Alignment explanation
Indices: 5811538--5811564 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5811528 GAAGAAACAA
5811538 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
5811565 ACAAGGGCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5812020 original size:91 final size:91
Alignment explanation
Indices: 5811863--5812045 Score: 276
Period size: 91 Copynumber: 2.0 Consensus size: 91
5811853 TTGCAACTTC
* * * * * * *
5811863 CATGAACTCGAAACACATTCCTTTACCTGAAGAACAGCAAAGCAAAGATCTTCCAGGTCTGTTTT
1 CATGAACTCCAAACACACTCCTTTACCTCAACAACAGCAAAGCAAAGATCTTCCAGCTCAGCTTT
*
5811928 CAGTGCCCACAGACCCAATCTAGAAG
66 CAGTGCCCACAAACCCAATCTAGAAG
**
5811954 CATGAACTCCAAACACACTCCTTTACCTCAACAACAGTGAAGCAAAGATCTTCCAGCTCAGCTTT
1 CATGAACTCCAAACACACTCCTTTACCTCAACAACAGCAAAGCAAAGATCTTCCAGCTCAGCTTT
5812019 CAGTGCCCACAAACCCAATCTAGAAG
66 CAGTGCCCACAAACCCAATCTAGAAG
5812045 C
1 C
5812046 TAGGGAACAC
Statistics
Matches: 82, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 82 1.00
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (91 bp):
CATGAACTCCAAACACACTCCTTTACCTCAACAACAGCAAAGCAAAGATCTTCCAGCTCAGCTTT
CAGTGCCCACAAACCCAATCTAGAAG
Found at i:5821274 original size:22 final size:23
Alignment explanation
Indices: 5821249--5821291 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
5821239 AAAAAATATG
* *
5821249 AAAATT-TATAAAAGAATTCTTT
1 AAAATTGTAAAAAAAAATTCTTT
5821271 AAAATTGTAAAAAAAAATTCT
1 AAAATTGTAAAAAAAAATTCT
5821292 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.35
Consensus pattern (23 bp):
AAAATTGTAAAAAAAAATTCTTT
Found at i:5821297 original size:23 final size:22
Alignment explanation
Indices: 5821249--5821303 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
5821239 AAAAAATATG
* * **
5821249 AAAATTTATAAAAGAATTCTTT
1 AAAATTTAAAAAAAAATTCTAA
5821271 AAAATTGTAAAAAAAAATTCTAA
1 AAAATT-TAAAAAAAAATTCTAA
5821294 AAAA-TTAAAA
1 AAAATTTAAAA
5821304 TTTTTCATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 5 0.18
22 7 0.25
23 16 0.57
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (22 bp):
AAAATTTAAAAAAAAATTCTAA
Found at i:5821336 original size:19 final size:19
Alignment explanation
Indices: 5821282--5821337 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 19
5821272 AAATTGTAAA
*
5821282 AAAAAATTCTAAAAAAT-T
1 AAAATATTCTAAAAAATAT
* * *
5821300 AAAAT-TTTTCATAAATAT
1 AAAATATTCTAAAAAATAT
5821318 AAAATATTCTAAAAAATAT
1 AAAATATTCTAAAAAATAT
5821337 A
1 A
5821338 CAAAATAAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
17 8 0.28
18 10 0.34
19 11 0.38
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATATTCTAAAAAATAT
Found at i:5821647 original size:2 final size:2
Alignment explanation
Indices: 5821637--5821673 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
5821627 TCTTGTGTGC
*
5821637 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5821674 GGGAGAAATC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5822018 original size:26 final size:25
Alignment explanation
Indices: 5821989--5822038 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
5821979 GAAATATTCT
*
5821989 AAACATTAAAAAATTTTTGAAAAATA
1 AAACATCAAAAAATTTTT-AAAAATA
*
5822015 AAACATCCAAAAATTTTTAAAAAT
1 AAACATCAAAAAATTTTTAAAAAT
5822039 TTAAAAGTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.60, C:0.08, G:0.02, T:0.30
Consensus pattern (25 bp):
AAACATCAAAAAATTTTTAAAAATA
Found at i:5823449 original size:2 final size:2
Alignment explanation
Indices: 5823442--5823474 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5823432 GTTCCCATAC
5823442 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5823475 TTTAATTTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5823976 original size:26 final size:25
Alignment explanation
Indices: 5823928--5823977 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
5823918 AAAAAACGAA
*
5823928 TTTAATTTTTATATTCGACTTTAAG
1 TTTAATTTTTATATTCGAATTTAAG
* *
5823953 TTTAATTATTTGTGTTCGAATTTAA
1 TTTAATT-TTTATATTCGAATTTAA
5823978 ATTCGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.28, C:0.06, G:0.10, T:0.56
Consensus pattern (25 bp):
TTTAATTTTTATATTCGAATTTAAG
Found at i:5824612 original size:30 final size:30
Alignment explanation
Indices: 5824556--5824612 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
5824546 TTTAAATTTC
* **
5824556 ACATTTTCTTTAAATTTTTATGTTTTTGGG
1 ACATTTTCTTTAAAATTAAATGTTTTTGGG
*
5824586 ACATTTTCTTTAAAATTAAATTTTTTT
1 ACATTTTCTTTAAAATTAAATGTTTTT
5824613 AAAATTTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.60
Consensus pattern (30 bp):
ACATTTTCTTTAAAATTAAATGTTTTTGGG
Found at i:5833488 original size:14 final size:15
Alignment explanation
Indices: 5833460--5833489 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5833450 GTTATTTTCG
5833460 TTTATTTTCTTAATT
1 TTTATTTTCTTAATT
5833475 TTTATTTT-TTAATT
1 TTTATTTTCTTAATT
5833489 T
1 T
5833490 ACACTTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTATTTTCTTAATT
Found at i:5835733 original size:3 final size:3
Alignment explanation
Indices: 5835725--5835789 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
5835715 AATGTACACA
5835725 TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5835772 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
5835790 GTTCACTTGT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:5842856 original size:38 final size:38
Alignment explanation
Indices: 5842814--5842891 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
5842804 GGGAAGACAC
*
5842814 AATACACCCTAAATTTAACTATAATACCACTGAAAAAT
1 AATACACCCTAAATTTAACTACAATACCACTGAAAAAT
*
5842852 AATACACCCTAAATTTAACTACAATACCACTTAAAAAT
1 AATACACCCTAAATTTAACTACAATACCACTGAAAAAT
5842890 AA
1 AA
5842892 CATTACCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.51, C:0.22, G:0.01, T:0.26
Consensus pattern (38 bp):
AATACACCCTAAATTTAACTACAATACCACTGAAAAAT
Found at i:5843201 original size:91 final size:91
Alignment explanation
Indices: 5843044--5843226 Score: 312
Period size: 91 Copynumber: 2.0 Consensus size: 91
5843034 TTGCAACTTC
* * * *
5843044 CATGAACTCGAAACACACTCCTTTACCTGAAGAACAGCGAAGCAAAGATCTTCCAGGTCTGTTTT
1 CATGAACTCCAAACACACTCCCTTACCTGAAGAACAGCGAAGCAAAGATCTTCCAGCTCTGCTTT
*
5843109 CAGTGCCCACAGACCCAATCTAGAAG
66 CAGTGCCCACAAACCCAATCTAGAAG
*
5843135 CATGAACTCCAAACACACTCCCTTACCTGAAGAACAGTGAAGCAAAGATCTTCCAGCTCTGCTTT
1 CATGAACTCCAAACACACTCCCTTACCTGAAGAACAGCGAAGCAAAGATCTTCCAGCTCTGCTTT
5843200 CAGTGCCCACAAACCCAATCTAGAAG
66 CAGTGCCCACAAACCCAATCTAGAAG
5843226 C
1 C
5843227 TAGGGAACAC
Statistics
Matches: 86, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
91 86 1.00
ACGTcount: A:0.33, C:0.31, G:0.16, T:0.20
Consensus pattern (91 bp):
CATGAACTCCAAACACACTCCCTTACCTGAAGAACAGCGAAGCAAAGATCTTCCAGCTCTGCTTT
CAGTGCCCACAAACCCAATCTAGAAG
Found at i:5854277 original size:131 final size:131
Alignment explanation
Indices: 5854043--5854317 Score: 514
Period size: 131 Copynumber: 2.1 Consensus size: 131
5854033 AAAGCCCGTC
* * * *
5854043 AAATTGATATAATGAAAATTTTATGCTCAACTTAAAACTCATTTTGAATTTGAGGAAATTTTAAT
1 AAATTAATTTAATGAAAAATTTATGCTCAACTTAAAACTCATTTTGAATTTGAGCAAATTTTAAT
5854108 TTTTAAATTTGAATTGATTTGAGATAAAAATTTAAACTACTTAAATTTGTTTATTTATCAAATAA
66 TTTTAAATTTGAATTGATTTGAGATAAAAATTTAAACTACTTAAATTTGTTTATTTATCAAATAA
5854173 A
131 A
5854174 AAATTAATTTAATGAAAAATTTATGCTCAACTTAAAACTCATTTTGAATTTGAGCAAATTTTAAT
1 AAATTAATTTAATGAAAAATTTATGCTCAACTTAAAACTCATTTTGAATTTGAGCAAATTTTAAT
5854239 TTTTAAATTTGAATTGATTTGAGATAAAAATTTAAACTACTTAAATTTGTTTATTTATCAAATAA
66 TTTTAAATTTGAATTGATTTGAGATAAAAATTTAAACTACTTAAATTTGTTTATTTATCAAATAA
5854304 A
131 A
5854305 AAATTAATTTAAT
1 AAATTAATTTAAT
5854318 TTTTAATATT
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
131 140 1.00
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (131 bp):
AAATTAATTTAATGAAAAATTTATGCTCAACTTAAAACTCATTTTGAATTTGAGCAAATTTTAAT
TTTTAAATTTGAATTGATTTGAGATAAAAATTTAAACTACTTAAATTTGTTTATTTATCAAATAA
A
Found at i:5854486 original size:21 final size:22
Alignment explanation
Indices: 5854445--5854496 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
5854435 AAAAAAATTG
5854445 ATTAAATTTACAAATTATTTAA
1 ATTAAATTTACAAATTATTTAA
5854467 ATTAAATATTA-AAA-TATTTAA
1 ATTAAAT-TTACAAATTATTTAA
5854488 ATT-AATTTA
1 ATTAAATTTA
5854497 TTTAATAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.10
20 3 0.10
21 10 0.34
22 10 0.34
23 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTAAATTTACAAATTATTTAA
Found at i:5854507 original size:17 final size:16
Alignment explanation
Indices: 5854485--5854517 Score: 57
Period size: 16 Copynumber: 2.0 Consensus size: 16
5854475 TTAAAATATT
5854485 TAAATTAATTTATTTAA
1 TAAATTAA-TTATTTAA
5854502 TAAATTAATTATTTAA
1 TAAATTAATTATTTAA
5854518 ACTTAACTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAATTAATTATTTAA
Found at i:5856402 original size:18 final size:19
Alignment explanation
Indices: 5856379--5856422 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 19
5856369 GAGGTGAGAA
5856379 TTTAATAATTTTTTA-TTT
1 TTTAATAATTTTTTATTTT
5856397 TTTAATAATTTTTTATTTT
1 TTTAATAATTTTTTATTTT
5856416 TTTAATA
1 TTTAATA
5856423 TCTTAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTAATAATTTTTTATTTT
Found at i:5856783 original size:14 final size:15
Alignment explanation
Indices: 5856754--5856784 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
5856744 TTATTTTATT
5856754 AAAAATTATAATTAA
1 AAAAATTATAATTAA
5856769 AAAAATTATAA-TAA
1 AAAAATTATAATTAA
5856783 AA
1 AA
5856785 TATATCTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATTATAATTAA
Found at i:5864779 original size:25 final size:23
Alignment explanation
Indices: 5864734--5864780 Score: 58
Period size: 25 Copynumber: 2.0 Consensus size: 23
5864724 AGAAACGCTA
* *
5864734 AGAAAAGAAACAAATTGAGAAAT
1 AGAAAAGAAACAAAGTAAGAAAT
5864757 AGAACAAGAAAACAAAGTAAGAAA
1 AGAA-AAG-AAACAAAGTAAGAAA
5864781 ATAATTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 3 0.15
25 13 0.65
ACGTcount: A:0.68, C:0.06, G:0.17, T:0.09
Consensus pattern (23 bp):
AGAAAAGAAACAAAGTAAGAAAT
Found at i:5866254 original size:23 final size:23
Alignment explanation
Indices: 5866228--5866278 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
5866218 TATTTAGTTT
*
5866228 TAATTGGTAAATGAATAAAAAAA
1 TAATCGGTAAATGAATAAAAAAA
5866251 TAATCGGTAAATGAATAAAAAAA
1 TAATCGGTAAATGAATAAAAAAA
5866274 TAATC
1 TAATC
5866279 ATCAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.59, C:0.04, G:0.12, T:0.25
Consensus pattern (23 bp):
TAATCGGTAAATGAATAAAAAAA
Found at i:5866653 original size:25 final size:24
Alignment explanation
Indices: 5866608--5866655 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
5866598 TATTCCTAAA
5866608 ATTTTATTTATTTTTTGAAATATT
1 ATTTTATTTATTTTTTGAAATATT
5866632 ATTTTCATATTATTTTTT-AAATAT
1 ATTTT-AT-TTATTTTTTGAAATAT
5866656 AACATTTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 5 0.23
25 8 0.36
26 9 0.41
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (24 bp):
ATTTTATTTATTTTTTGAAATATT
Found at i:5873214 original size:14 final size:14
Alignment explanation
Indices: 5873195--5873249 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
5873185 GCAGTGATCC
5873195 ATAAACATAAAGCT
1 ATAAACATAAAGCT
*
5873209 ATAAACATAAACGAGT
1 ATAAACATAAA-G-CT
* *
5873225 ATAATC-TGAAGCT
1 ATAAACATAAAGCT
5873238 ATAAACATAAAG
1 ATAAACATAAAG
5873250 ATTTTAGTGT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
13 6 0.19
14 16 0.50
15 4 0.12
16 6 0.19
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.22
Consensus pattern (14 bp):
ATAAACATAAAGCT
Found at i:5878210 original size:2 final size:2
Alignment explanation
Indices: 5878203--5878231 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5878193 CAAAAACATA
5878203 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5878232 AGGTTATGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5882278 original size:18 final size:19
Alignment explanation
Indices: 5882245--5882283 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
5882235 TTGTGTATGT
*
5882245 ATATATAAGATCTAGATAG
1 ATATATAAGATATAGATAG
5882264 ATATAT-AGATATAGATAG
1 ATATATAAGATATAGATAG
5882282 AT
1 AT
5882284 TTTACCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.49, C:0.03, G:0.15, T:0.33
Consensus pattern (19 bp):
ATATATAAGATATAGATAG
Found at i:5882355 original size:3 final size:3
Alignment explanation
Indices: 5882347--5882389 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
5882337 ACAAGTGAAC
5882347 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5882390 AGGGATATAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5892103 original size:2 final size:2
Alignment explanation
Indices: 5892096--5892124 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5892086 GTATGATTGG
5892096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5892125 AATAAAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5894779 original size:26 final size:25
Alignment explanation
Indices: 5894741--5894795 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
5894731 TCGATCTCAG
* * *
5894741 TTTAAATTTGAATACAAATAATTGAA
1 TTTAAAGTCGAATACAAA-AATTAAA
*
5894767 TTTAAAGTCGAATATAAAAATTAAA
1 TTTAAAGTCGAATACAAAAATTAAA
5894792 TTTA
1 TTTA
5894796 TTTTTTATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 10 0.40
26 15 0.60
ACGTcount: A:0.51, C:0.04, G:0.07, T:0.38
Consensus pattern (25 bp):
TTTAAAGTCGAATACAAAAATTAAA
Found at i:5895242 original size:2 final size:2
Alignment explanation
Indices: 5895235--5895267 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5895225 CCAAATTAAA
5895235 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5895268 GTATGGGAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5901806 original size:177 final size:176
Alignment explanation
Indices: 5901479--5901807 Score: 391
Period size: 180 Copynumber: 1.9 Consensus size: 176
5901469 TTATTTTTCG
* * * *
5901479 TGAAATTTTATTTAAATTCTTCCACCATTTGGGACAAATTTAAAGAAATTTCTCACCTAGAGATT
1 TGAAATTTTATCTAAATTATTCCACCATTTGGGACAAATTTAAAAAAAATTCTCACCTAGAGATT
* * * * * * * **
5901544 TCTTAGTAATTTATCATTTGAAATTTCTAAGAATCTTATCCTTGGATAATTGTTGAATATTTTCA
66 TCATAGAAATTTACCATTTGAAACTTCTAAAAATCTCATCATTGGATAATTAATGAATATTTTCA
*
5901609 ACTAAAAAGTTTTTTTTTGTTTGAAAATAAATATTAATTATTGTTAT
131 AC-AAAAAGTTTTATTTTGTTTGAAAATAAATATTAATTATTGTTAT
5901656 TGAAATTTTATCTAAATTATTCCACCATTTGGGACAAATTTAGAAAAAAAAATTCTCACCTAG-G
1 TGAAATTTTATCTAAATTATTCCACCATTTGGGACAAATTT---AAAAAAAATTCTCACCTAGAG
*
5901720 CAATTT-ATAGAAATTTACCATTTGAAACTTCTAAAAAT-TACATCATTGGATAATTAAT-ATTT
63 --ATTTCATAGAAATTTACCATTTGAAACTTCTAAAAATCT-CATCATTGGATAATTAATGA-AT
* *
5901782 ATTTTTAA-AAATA-TTTTATTTTGTTT
124 ATTTTCAACAAAAAGTTTTATTTTGTTT
5901808 TATATTTTTT
Statistics
Matches: 128, Mismatches: 17, Indels: 14
0.81 0.11 0.09
Matches are distributed among these distances:
177 51 0.40
178 4 0.03
179 3 0.02
180 66 0.52
181 4 0.03
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (176 bp):
TGAAATTTTATCTAAATTATTCCACCATTTGGGACAAATTTAAAAAAAATTCTCACCTAGAGATT
TCATAGAAATTTACCATTTGAAACTTCTAAAAATCTCATCATTGGATAATTAATGAATATTTTCA
ACAAAAAGTTTTATTTTGTTTGAAAATAAATATTAATTATTGTTAT
Found at i:5902829 original size:14 final size:14
Alignment explanation
Indices: 5902783--5902849 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 14
5902773 CACAAAAAAT
*
5902783 CAAATAAATAAAAA
1 CAAATAAATAATAA
* * *
5902797 CAGATAAACAACCAA
1 CAAATAAATAA-TAA
*
5902812 CAAATAAATAGTAA
1 CAAATAAATAATAA
5902826 CAAA-ATAATAATAA
1 CAAATA-AATAATAA
5902840 -AAATAAATAA
1 CAAATAAATAA
5902850 ATAAATAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
13 9 0.21
14 23 0.55
15 10 0.24
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.16
Consensus pattern (14 bp):
CAAATAAATAATAA
Found at i:5903269 original size:131 final size:131
Alignment explanation
Indices: 5903116--5903356 Score: 335
Period size: 131 Copynumber: 1.8 Consensus size: 131
5903106 AACTTTTTTA
* * *
5903116 AAAAATAAATACAGCTTCTCTAAACAGAGACTCAACAA-TTTTAGAAAATAAATAAAGCTCCTCT
1 AAAAATAAATAAAGCTTCTCTAAACAGAGACTCAACAACTTTAAAAAAATAAATAAA-CTCCTCT
* * * *
5903180 AA-TAAGAGGTTTAACAACTTTGGAAAAATAAATAAAGCTTCTCTAATTAGAGGCTTAACAACTT
65 AAGT-AGAGGCTAAACAACTTTGAAAAAATAAATAAAGCTTATCTAATTAGAGGCTTAACAACTT
5903244 TGG
129 TGG
* * *
5903247 AAAAATAAATAAAGC-TCTTCTAAGCAGAGGCTCAACAACTTTAAAAAAATAAATAAACTCCTTT
1 AAAAATAAATAAAGCTTC-TCTAAACAGAGACTCAACAACTTTAAAAAAATAAATAAACTCCTCT
*
5903311 AAGTAGAGGCTAAACAACTTTGAAAAAATAAATAAAGTTTATCTAA
65 AAGTAGAGGCTAAACAACTTTGAAAAAATAAATAAAGCTTATCTAA
5903357 GCAGAGGAAT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
130 2 0.02
131 77 0.80
132 17 0.18
ACGTcount: A:0.48, C:0.15, G:0.11, T:0.27
Consensus pattern (131 bp):
AAAAATAAATAAAGCTTCTCTAAACAGAGACTCAACAACTTTAAAAAAATAAATAAACTCCTCTA
AGTAGAGGCTAAACAACTTTGAAAAAATAAATAAAGCTTATCTAATTAGAGGCTTAACAACTTTG
G
Found at i:5903356 original size:87 final size:86
Alignment explanation
Indices: 5903090--5903363 Score: 273
Period size: 87 Copynumber: 3.1 Consensus size: 86
5903080 CAAGACTCTC
* * * * *
5903090 CTAAGCAGAGGTTC-ACAACTTTTTTAAAAAATAAATACAGCTTCTCTAAACAGAGACTCAACAA
1 CTAAGCAGAGGTTCAACAAC--TTTAAAAAAATAAATA-AACTTCTCTAAATAGAGGCTAAACAA
* * **
5903154 -TTTTAGAAAATAAATAAAGCTCCT
63 CTTTGAAAAAATAAATAAAG-TTTT
** * ** * *
5903178 CTAATAAGAGGTTTAACAACTTTGGAAAAATAAATAAAGCTTCTCTAATTAGAGGCTTAACAACT
1 CTAAGCAGAGGTTCAACAACTTTAAAAAAATAAATAAA-CTTCTCTAAATAGAGGCTAAACAACT
* *
5903243 TTGGAAAAATAAATAAAGCTCTT
65 TTGAAAAAATAAATAAAG-TTTT
* * * *
5903266 CTAAGCAGAGGCTCAACAACTTTAAAAAAATAAATAAACTCCTTTAAGTAGAGGCTAAACAACTT
1 CTAAGCAGAGGTTCAACAACTTTAAAAAAATAAATAAACTTCTCTAAATAGAGGCTAAACAACTT
5903331 TGAAAAAATAAATAAAGTTTAT
66 TGAAAAAATAAATAAAGTTT-T
5903353 CTAAGCAGAGG
1 CTAAGCAGAGG
5903364 AATCATAGAT
Statistics
Matches: 156, Mismatches: 26, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
86 3 0.02
87 85 0.54
88 63 0.40
89 5 0.03
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (86 bp):
CTAAGCAGAGGTTCAACAACTTTAAAAAAATAAATAAACTTCTCTAAATAGAGGCTAAACAACTT
TGAAAAAATAAATAAAGTTTT
Found at i:5903363 original size:44 final size:44
Alignment explanation
Indices: 5903090--5903363 Score: 277
Period size: 44 Copynumber: 6.2 Consensus size: 44
5903080 CAAGACTCTC
* * *
5903090 CTAAGCAGAGGTTC-ACAACTTTTTTAAAAAATAAATACAGCTTCT
1 CTAAGCAGAGGCTCAACAAC--TTTGAAAAAATAAATAAAGCTTCT
* * * * *
5903135 CTAAACAGAGACTCAACAA-TTTTAGAAAATAAATAAAGCTCCT
1 CTAAGCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTTCT
** * * *
5903178 CTAATAAGAGGTTTAACAACTTTGGAAAAATAAATAAAGCTTCT
1 CTAAGCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTTCT
** * *
5903222 CTAATTAGAGGCTTAACAACTTTGGAAAAATAAATAAAGC-TCTT
1 CTAAGCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTTC-T
* *
5903266 CTAAGCAGAGGCTCAACAACTTTAAAAAAATAAATAAA-CTCCT
1 CTAAGCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTTCT
* * * * *
5903309 TTAAGTAGAGGCTAAACAACTTTGAAAAAATAAATAAAGTTTAT
1 CTAAGCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTTCT
5903353 CTAAGCAGAGG
1 CTAAGCAGAGG
5903364 AATCATAGAT
Statistics
Matches: 192, Mismatches: 32, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
43 73 0.38
44 104 0.54
45 11 0.06
46 4 0.02
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (44 bp):
CTAAGCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTTCT
Found at i:5903363 original size:131 final size:131
Alignment explanation
Indices: 5903090--5903363 Score: 331
Period size: 131 Copynumber: 2.1 Consensus size: 131
5903080 CAAGACTCTC
* * *
5903090 CTAAGCAGAGGTTCACAACTTTTTTAAAAAATAAATACAGCTTCTCTAAACAGAGACTCAACAAT
1 CTAAGCAGAGGTTAACAAC-TTTTGAAAAAATAAATAAAGCTTCTCTAAACAGAGACTCAACAAT
* * * * *
5903155 TTTAGAAAATAAATAAAGCTCCTCTAATAAGAGGTTTAACAACTTTGGAAAAATAAATAAAGCTT
65 TTAAAAAAATAAATAAAGCTCCTCTAATAAGAGGCTAAACAACTTTGAAAAAATAAATAAAGCTT
*
5903220 CT
130 AT
** * * *
5903222 CTAATTAGAGGCTTAACAAC-TTTGGAAAAATAAATAAAGC-TCTTCTAAGCAGAGGCTCAACAA
1 CTAAGCAGAGG-TTAACAACTTTTGAAAAAATAAATAAAGCTTC-TCTAAACAGAGACTCAACAA
*
5903285 CTTTAAAAAAATAAATAAA-CTCCTTTAAGT-AGAGGCTAAACAACTTTGAAAAAATAAATAAAG
64 -TTTAAAAAAATAAATAAAGCTCCTCTAA-TAAGAGGCTAAACAACTTTGAAAAAATAAATAAAG
*
5903348 TTTAT
127 CTTAT
5903353 CTAAGCAGAGG
1 CTAAGCAGAGG
5903364 AATCATAGAT
Statistics
Matches: 120, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
130 2 0.02
131 85 0.71
132 26 0.22
133 7 0.06
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.27
Consensus pattern (131 bp):
CTAAGCAGAGGTTAACAACTTTTGAAAAAATAAATAAAGCTTCTCTAAACAGAGACTCAACAATT
TAAAAAAATAAATAAAGCTCCTCTAATAAGAGGCTAAACAACTTTGAAAAAATAAATAAAGCTTA
T
Found at i:5916702 original size:15 final size:15
Alignment explanation
Indices: 5916673--5916723 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 15
5916663 AGCTTACACA
5916673 ATAAGAATAATTTTT
1 ATAAGAATAATTTTT
5916688 ATAAGTAATAATTTTTCAT
1 ATAAG-AATAA-TTTT--T
5916707 ATAAGAATAAATTTTT
1 ATAAGAAT-AATTTTT
5916723 A
1 A
5916724 CCGAATATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
15 5 0.16
16 7 0.23
17 4 0.13
18 7 0.23
19 8 0.26
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAAGAATAATTTTT
Found at i:5917575 original size:37 final size:37
Alignment explanation
Indices: 5917480--5917562 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
5917470 CGGATTGACC
* * *
5917480 TTACATTTTAT-T-AAATAATATTAAATAAATATATT
1 TTACATTTTATATGTAATAATATTAAATAAAGACATT
*
5917515 TTATATTTTATATGTAATAATATTAAATAAAGACATT
1 TTACATTTTATATGTAATAATATTAAATAAAGACATT
5917552 TTACATTTTAT
1 TTACATTTTAT
5917563 TTTGTTTCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
35 10 0.24
36 1 0.02
37 30 0.73
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (37 bp):
TTACATTTTATATGTAATAATATTAAATAAAGACATT
Found at i:5929111 original size:2 final size:2
Alignment explanation
Indices: 5929104--5929130 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5929094 TACATAACCT
5929104 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5929131 TATGTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5930686 original size:14 final size:14
Alignment explanation
Indices: 5930637--5930691 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
5930627 ACACTAAAAT
5930637 CTTTATGTTTATAG
1 CTTTATGTTTATAG
* * *
5930651 CTTCA-GATTATACT
1 CTTTATGTTTATA-G
5930665 CGTTTATGTTTATAG
1 C-TTTATGTTTATAG
5930680 CTTTATGTTTAT
1 CTTTATGTTTAT
5930692 GGATCACTGC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
13 6 0.19
14 16 0.50
15 4 0.12
16 6 0.19
ACGTcount: A:0.22, C:0.11, G:0.13, T:0.55
Consensus pattern (14 bp):
CTTTATGTTTATAG
Found at i:5941987 original size:3 final size:3
Alignment explanation
Indices: 5941979--5942036 Score: 86
Period size: 3 Copynumber: 20.0 Consensus size: 3
5941969 ACAGTGAACC
5941979 ATA ATA ATA AT- ATA ATA ATA ATA A-A ATA AT- ATA ATAA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA
5942022 ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA
5942037 TGTGTACATT
Statistics
Matches: 51, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.12
3 42 0.82
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5944759 original size:28 final size:27
Alignment explanation
Indices: 5944731--5944782 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
5944721 CCAAAAACCA
* * *
5944731 AAACTCTTTTTTTTTTTTGTTTTCTCC
1 AAACTATTTTCTTATTTTGTTTTCTCC
*
5944758 AAATTATTTTCTTATTTTGTTTTCT
1 AAACTATTTTCTTATTTTGTTTTCT
5944783 TGTTCTCTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.15, C:0.13, G:0.04, T:0.67
Consensus pattern (27 bp):
AAACTATTTTCTTATTTTGTTTTCTCC
Found at i:5953839 original size:26 final size:25
Alignment explanation
Indices: 5953801--5953850 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
5953791 ATTCGATCTC
*
5953801 AGTTTAAATTTGAATACAAATAATTG
1 AGTTTAAAGTTGAATACAAA-AATTG
*
5953827 AGTTTAAAGTTGAATATAAAAATT
1 AGTTTAAAGTTGAATACAAAAATT
5953851 AAATTTATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (25 bp):
AGTTTAAAGTTGAATACAAAAATTG
Found at i:5960306 original size:11 final size:11
Alignment explanation
Indices: 5960290--5960316 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5960280 ATCTGATAGA
5960290 ATTCTTAAAAT
1 ATTCTTAAAAT
5960301 ATTCTTAAAAT
1 ATTCTTAAAAT
5960312 ATTCT
1 ATTCT
5960317 CTAACCTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (11 bp):
ATTCTTAAAAT
Found at i:5960638 original size:25 final size:24
Alignment explanation
Indices: 5960609--5960655 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
5960599 TCACCTAGAG
*
5960609 ATTTCTTAGTAAT-TTATCATTTGAA
1 ATTTCTAAG-AATCTTATC-TTTGAA
5960634 ATTTCTAAGAATCTTATCTTTG
1 ATTTCTAAGAATCTTATCTTTG
5960656 GATAATTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (24 bp):
ATTTCTAAGAATCTTATCTTTGAA
Found at i:5961812 original size:17 final size:17
Alignment explanation
Indices: 5961773--5961816 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
5961763 ACGGCAGAAT
5961773 CTATTAT-TTTTTATTA
1 CTATTATCTTTTTATTA
* * *
5961789 TTTTTATCTTTTTTTTA
1 CTATTATCTTTTTATTA
5961806 CTATTATCTTT
1 CTATTATCTTT
5961817 ATACCTAATT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (17 bp):
CTATTATCTTTTTATTA
Found at i:5961907 original size:14 final size:14
Alignment explanation
Indices: 5961861--5961927 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 14
5961851 CACAAAAAAT
*
5961861 CAAATAAATAAAAA
1 CAAATAAATAATAA
* * *
5961875 CAGATAAACAACCAA
1 CAAATAAATAA-TAA
*
5961890 CAAATAAATAGTAA
1 CAAATAAATAATAA
5961904 CAAA-ATAATAATAA
1 CAAATA-AATAATAA
5961918 -AAATAAATAA
1 CAAATAAATAA
5961928 ATAAATAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 7
0.74 0.14 0.12
Matches are distributed among these distances:
13 9 0.21
14 23 0.55
15 10 0.24
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.16
Consensus pattern (14 bp):
CAAATAAATAATAA
Found at i:5962445 original size:44 final size:44
Alignment explanation
Indices: 5962171--5962445 Score: 304
Period size: 44 Copynumber: 6.2 Consensus size: 44
5962161 CAAGACTCTC
* *
5962171 CTAAGCAGAGGCTC-ACAACTTTTTTAAAAAATAAATACAGCTTCT
1 CTAAGCAGAGGCTCAACAAC--TTTGAAAAAATAAATAAAGCTTCT
* * * * *
5962216 CTAAACAGAGACTCAACAA-TTTTAGAAAATAAATAAAGCTCCT
1 CTAAGCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTTCT
** * *
5962259 CTAATAAGAGGTTCAACAACTTTGGAAAAATAAATAAAGCTTCT
1 CTAAGCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTTCT
** *
5962303 CTAATTAGAGGCTCAACAACTTTGGAAAAATAAATAAAGC-TCTT
1 CTAAGCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTTC-T
* * *
5962347 CTAAGCAGAGGCTCAACAACTTTAAAAAAATAAATAAAACTCCT
1 CTAAGCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTTCT
* * * * *
5962391 TTAAGTAGAGGCTAAACAACTTTGAAAAAATAAATAAAGTTTAT
1 CTAAGCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTTCT
5962435 CTAAGCAGAGG
1 CTAAGCAGAGG
5962446 AATCATAGAT
Statistics
Matches: 195, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
43 38 0.19
44 140 0.72
45 13 0.07
46 4 0.02
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (44 bp):
CTAAGCAGAGGCTCAACAACTTTGAAAAAATAAATAAAGCTTCT
Found at i:5962445 original size:132 final size:131
Alignment explanation
Indices: 5962171--5962445 Score: 340
Period size: 132 Copynumber: 2.1 Consensus size: 131
5962161 CAAGACTCTC
* *
5962171 CTAAGCAGAGGCTCACAACTTTTTTAAAAAATAAATACAGCTTCTCTAAACAGAGACTCAACAAT
1 CTAAGCAGAGGCTCACAAC-TTTTGAAAAAATAAATAAAGCTTCTCTAAACAGAGACTCAACAAT
* * * * * *
5962236 TTTAGAAAATAAATAAAGCTCCTCTAATAAGAGGTTCAACAACTTTGGAAAAATAAATAAAGCTT
65 TTAAAAAAATAAATAAAACTCCTCTAATAAGAGGCTAAACAACTTTGAAAAAATAAATAAAGCTT
*
5962301 CT
130 AT
** * * *
5962303 CTAATTAGAGGCTCAACAAC-TTTGGAAAAATAAATAAAGC-TCTTCTAAGCAGAGGCTCAACAA
1 CTAAGCAGAGGCTC-ACAACTTTTGAAAAAATAAATAAAGCTTC-TCTAAACAGAGACTCAACAA
*
5962366 CTTTAAAAAAATAAATAAAACTCCTTTAAGT-AGAGGCTAAACAACTTTGAAAAAATAAATAAAG
64 -TTTAAAAAAATAAATAAAACTCCTCTAA-TAAGAGGCTAAACAACTTTGAAAAAATAAATAAAG
*
5962430 TTTAT
127 CTTAT
5962435 CTAAGCAGAGG
1 CTAAGCAGAGG
5962446 AATCATAGAT
Statistics
Matches: 121, Mismatches: 18, Indels: 8
0.82 0.12 0.05
Matches are distributed among these distances:
130 2 0.02
131 35 0.29
132 78 0.64
133 6 0.05
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (131 bp):
CTAAGCAGAGGCTCACAACTTTTGAAAAAATAAATAAAGCTTCTCTAAACAGAGACTCAACAATT
TAAAAAAATAAATAAAACTCCTCTAATAAGAGGCTAAACAACTTTGAAAAAATAAATAAAGCTTA
T
Found at i:5966649 original size:2 final size:2
Alignment explanation
Indices: 5966642--5966666 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5966632 TCTTTAGCGC
5966642 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5966667 AACCAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5967282 original size:2 final size:2
Alignment explanation
Indices: 5967275--5967304 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5967265 AAAAACATAG
5967275 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5967305 AGGTTATGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5967817 original size:24 final size:24
Alignment explanation
Indices: 5967787--5967835 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
5967777 ATTTTTGGAG
5967787 TTTGGTTTTTCTTTTGCTTGGGTA
1 TTTGGTTTTTCTTTTGCTTGGGTA
*
5967811 TTTGGTTTTTGTTTTGCTTGGGTA
1 TTTGGTTTTTCTTTTGCTTGGGTA
5967835 T
1 T
5967836 GGGAAGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.04, C:0.06, G:0.27, T:0.63
Consensus pattern (24 bp):
TTTGGTTTTTCTTTTGCTTGGGTA
Found at i:5970837 original size:18 final size:18
Alignment explanation
Indices: 5970816--5970850 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5970806 TAAATATATT
5970816 TATGTATATAAGGTTATG
1 TATGTATATAAGGTTATG
* *
5970834 TATGTATGTGAGGTTAT
1 TATGTATATAAGGTTAT
5970851 TATTGGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.26, T:0.46
Consensus pattern (18 bp):
TATGTATATAAGGTTATG
Found at i:5978126 original size:24 final size:24
Alignment explanation
Indices: 5978094--5978139 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5978084 ATAGAATTCC
* * *
5978094 ACCGCGCCATCATGTCGTTTTGGA
1 ACCGAGCCATCACGTCCTTTTGGA
5978118 ACCGAGCCATCACGTCCTTTTG
1 ACCGAGCCATCACGTCCTTTTG
5978140 AAACTGGATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.17, C:0.33, G:0.22, T:0.28
Consensus pattern (24 bp):
ACCGAGCCATCACGTCCTTTTGGA
Found at i:5986961 original size:19 final size:19
Alignment explanation
Indices: 5986913--5986962 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 19
5986903 TCCTTTCGCC
*
5986913 TTTT-TTTTTTTTTTGAAA
1 TTTTATTTTTTTTTTCAAA
** *
5986931 TTTTATAATTTTTTTCAGA
1 TTTTATTTTTTTTTTCAAA
5986950 TTTTATTTTTTTT
1 TTTTATTTTTTTT
5986963 AAAAATCAGA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (19 bp):
TTTTATTTTTTTTTTCAAA
Found at i:5987684 original size:11 final size:11
Alignment explanation
Indices: 5987659--5987704 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
5987649 ATTTATTTTT
*
5987659 TTTTATATATTA
1 TTTTA-ATATAA
5987671 TTTTAATATAA
1 TTTTAATATAA
5987682 TTTTAATAT-A
1 TTTTAATATAA
*
5987692 TTTAAATA-AA
1 TTTTAATATAA
5987702 TTT
1 TTT
5987705 ATTTATAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
10 12 0.39
11 14 0.45
12 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAATATAA
Found at i:5987753 original size:19 final size:21
Alignment explanation
Indices: 5987731--5987769 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5987721 TTTTATTTTA
5987731 TAAAAATT-T-AAAATATATC
1 TAAAAATTATAAAAATATATC
5987750 TAAAAATTATAAAAATATAT
1 TAAAAATTATAAAAATATAT
5987770 AATTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAAAATTATAAAAATATATC
Found at i:5989344 original size:13 final size:13
Alignment explanation
Indices: 5989326--5989364 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5989316 TCTATGATTT
5989326 TTTTTTTTTTGTC
1 TTTTTTTTTTGTC
*
5989339 TTTTTTTTTTCTC
1 TTTTTTTTTTGTC
*
5989352 TTGTGTTTTTTGT
1 TT-TTTTTTTTGT
5989365 AAAATTGTCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 14 0.64
14 8 0.36
ACGTcount: A:0.00, C:0.08, G:0.10, T:0.82
Consensus pattern (13 bp):
TTTTTTTTTTGTC
Found at i:5989346 original size:18 final size:18
Alignment explanation
Indices: 5989323--5989362 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
5989313 TGGTCTATGA
5989323 TTTTTTTTTT-T-TTGTC
1 TTTTTTTTTTCTCTTGTC
*
5989339 TTTTTTTTTTCTCTTGTG
1 TTTTTTTTTTCTCTTGTC
5989357 TTTTTT
1 TTTTTT
5989363 GTAAAATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 1 0.05
18 10 0.48
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (18 bp):
TTTTTTTTTTCTCTTGTC
Found at i:5989554 original size:19 final size:20
Alignment explanation
Indices: 5989532--5989574 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
5989522 GTTTTACTAT
* *
5989532 TTTTAGA-TTTTCATTGTTG
1 TTTTAGACTTTGCATTGATG
5989551 TTTTAGACTTTGCATTGATG
1 TTTTAGACTTTGCATTGATG
5989571 TTTT
1 TTTT
5989575 TAGGTAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.07, G:0.16, T:0.60
Consensus pattern (20 bp):
TTTTAGACTTTGCATTGATG
Found at i:5991359 original size:13 final size:14
Alignment explanation
Indices: 5991341--5991371 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5991331 ATACAAATTG
5991341 ATTTTTAG-AAAAT
1 ATTTTTAGAAAAAT
5991354 ATTTTTAGAAAAAT
1 ATTTTTAGAAAAAT
5991368 ATTT
1 ATTT
5991372 ATATTTTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (14 bp):
ATTTTTAGAAAAAT
Found at i:5991515 original size:25 final size:23
Alignment explanation
Indices: 5991485--5991552 Score: 73
Period size: 26 Copynumber: 2.7 Consensus size: 23
5991475 TATTAATATA
*
5991485 ATTATTAAAATATTAAATTTTATTT
1 ATTATTAAAATATTAAA--CTATTT
5991510 ATTATTAAAGTATATTGAAACTATTT
1 ATTATTAAA--ATATT-AAACTATTT
5991536 ATTATTAAAATTATTAA
1 ATTATTAAAA-TATTAA
5991553 TATTGAAGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
24 3 0.08
25 13 0.34
26 14 0.37
27 5 0.13
28 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (23 bp):
ATTATTAAAATATTAAACTATTT
Found at i:5991559 original size:31 final size:33
Alignment explanation
Indices: 5991521--5991641 Score: 85
Period size: 33 Copynumber: 3.7 Consensus size: 33
5991511 TTATTAAAGT
5991521 ATATTGAAACTATT-TATTATTAAAATTA-TTA
1 ATATTGAAACTATTATATTATTAAAATTACTTA
* *
5991552 ATATTGAAGAATAATTATATT-TTAATAATAATATTTA
1 ATATTGAA-ACT-ATTATATTATTAA-AAT--TACTTA
*
5991589 ATATT-AAA-TATTATATTAATATAAAAATACTTA
1 ATATTGAAACTATTATATT-AT-TAAAATTACTTA
* *
5991622 A-AATAAAACTATT-TATTATT
1 ATATTGAAACTATTATATTATT
5991642 CTTTATATTA
Statistics
Matches: 74, Mismatches: 4, Indels: 24
0.73 0.04 0.24
Matches are distributed among these distances:
31 9 0.12
32 6 0.08
33 28 0.38
34 12 0.16
35 4 0.05
36 7 0.09
37 8 0.11
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.45
Consensus pattern (33 bp):
ATATTGAAACTATTATATTATTAAAATTACTTA
Found at i:5991738 original size:15 final size:16
Alignment explanation
Indices: 5991718--5991766 Score: 64
Period size: 17 Copynumber: 3.1 Consensus size: 16
5991708 ATTAAAATAT
5991718 TAATATTTAT-TATTA
1 TAATATTTATATATTA
5991733 TAATATTTATACTATTA
1 TAATATTTATA-TATTA
* *
5991750 AAATATTTATATTTTA
1 TAATATTTATATATTA
5991766 T
1 T
5991767 GTTGAAAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 10 0.34
16 4 0.14
17 15 0.52
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TAATATTTATATATTA
Found at i:5993943 original size:34 final size:33
Alignment explanation
Indices: 5993891--5993956 Score: 87
Period size: 34 Copynumber: 2.0 Consensus size: 33
5993881 TTTTACAAAG
*
5993891 TATTGCAAATATCCAAAAATACATTTTCGAAAAA
1 TATTACAAATATCCAAAAATACATTTTC-AAAAA
* * *
5993925 TATTACAATTATCTAAAAATATATTTTCAAAA
1 TATTACAAATATCCAAAAATACATTTTCAAAA
5993957 GTAATTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.50, C:0.12, G:0.03, T:0.35
Consensus pattern (33 bp):
TATTACAAATATCCAAAAATACATTTTCAAAAA
Found at i:5995442 original size:25 final size:25
Alignment explanation
Indices: 5995414--5995476 Score: 108
Period size: 25 Copynumber: 2.5 Consensus size: 25
5995404 AATTAACTAA
*
5995414 AATTATTATAATATTTTTTTATTAT
1 AATTATTAAAATATTTTTTTATTAT
5995439 AATTATTAAAATATTTTTTTATTAT
1 AATTATTAAAATATTTTTTTATTAT
5995464 AATTGATTAAAAT
1 AATT-ATTAAAAT
5995477 TATTATAATA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
25 28 0.78
26 8 0.22
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (25 bp):
AATTATTAAAATATTTTTTTATTAT
Found at i:5999354 original size:114 final size:114
Alignment explanation
Indices: 5999154--5999382 Score: 458
Period size: 114 Copynumber: 2.0 Consensus size: 114
5999144 CATCACCTAG
5999154 GTTGGTTGTTGCTTCATTTGTTATTTCTTAATTGTTTCTTGTTTCCCTATTTGTTATTCACATGG
1 GTTGGTTGTTGCTTCATTTGTTATTTCTTAATTGTTTCTTGTTTCCCTATTTGTTATTCACATGG
5999219 TGGGCCGTTTGTTTCAGTTGATAGTCTTTCATATACATAGGGTGCTTTA
66 TGGGCCGTTTGTTTCAGTTGATAGTCTTTCATATACATAGGGTGCTTTA
5999268 GTTGGTTGTTGCTTCATTTGTTATTTCTTAATTGTTTCTTGTTTCCCTATTTGTTATTCACATGG
1 GTTGGTTGTTGCTTCATTTGTTATTTCTTAATTGTTTCTTGTTTCCCTATTTGTTATTCACATGG
5999333 TGGGCCGTTTGTTTCAGTTGATAGTCTTTCATATACATAGGGTGCTTTA
66 TGGGCCGTTTGTTTCAGTTGATAGTCTTTCATATACATAGGGTGCTTTA
5999382 G
1 G
5999383 AGTTGTTATC
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 115 1.00
ACGTcount: A:0.15, C:0.14, G:0.21, T:0.51
Consensus pattern (114 bp):
GTTGGTTGTTGCTTCATTTGTTATTTCTTAATTGTTTCTTGTTTCCCTATTTGTTATTCACATGG
TGGGCCGTTTGTTTCAGTTGATAGTCTTTCATATACATAGGGTGCTTTA
Found at i:5999586 original size:78 final size:83
Alignment explanation
Indices: 5999492--5999661 Score: 251
Period size: 88 Copynumber: 2.0 Consensus size: 83
5999482 AAATTTGACA
5999492 TAGTGTAATGCTGGTGCTATAAATA-TT-TTA-TTTT-TT-AATTGATTTTTGGAAATTGAAATT
1 TAGTGTAATGCTGGTGCTATAAATACTTCTTATTTTTATTAAATTGATTTTTGGAAATTGAAATT
5999552 TGAAAATACTCTATCAAC
66 TGAAAATACTCTATCAAC
5999570 TAGTGTAATGCTGGTGCTATAAATACTTCTTATTTTTTCAAATTAAAATTGATTTTTGGAAATTG
1 TAGTGTAATGCTGGTGCTATAAATACTTCTTA-TTTTT---ATT-AAATTGATTTTTGGAAATTG
*
5999635 AAATTTGAAAATACTCTATCTAC
61 AAATTTGAAAATACTCTATCAAC
5999658 TAGT
1 TAGT
5999662 TCTCTATTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
78 25 0.31
79 2 0.02
80 3 0.04
82 4 0.05
86 2 0.02
88 45 0.56
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.44
Consensus pattern (83 bp):
TAGTGTAATGCTGGTGCTATAAATACTTCTTATTTTTATTAAATTGATTTTTGGAAATTGAAATT
TGAAAATACTCTATCAAC
Done.