Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, 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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 14 of 20
Found at i:5352827 original size:23 final size:23
Alignment explanation
Indices: 5352800--5352876 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
5352790 ATTAGTTGAT
* *
5352800 AGGCATTGCGTGACTTGTTAGTA
1 AGGCATTGCATGACTAGTTAGTA
* *
5352823 AGGCATTGTATGACTAGTTAGCA
1 AGGCATTGCATGACTAGTTAGTA
**
5352846 AGATATTGCATGACTAGTTAGTA
1 AGGCATTGCATGACTAGTTAGTA
5352869 AGGCATTG
1 AGGCATTG
5352877 TGTAACTTAG
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (23 bp):
AGGCATTGCATGACTAGTTAGTA
Found at i:5352943 original size:22 final size:22
Alignment explanation
Indices: 5352918--5352963 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
5352908 TGCAAAATCA
*
5352918 AAAAATCAATCACGTAATACTT
1 AAAAATCAATCACGTAATAATT
5352940 AAAAATCAATCACGTAATAATT
1 AAAAATCAATCACGTAATAATT
5352962 AA
1 AA
5352964 GTCACATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.54, C:0.15, G:0.04, T:0.26
Consensus pattern (22 bp):
AAAAATCAATCACGTAATAATT
Found at i:5353022 original size:22 final size:22
Alignment explanation
Indices: 5352978--5353023 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5352968 CATAATGCCT
* *
5352978 AAAAACCTATCTCATAATATTC
1 AAAAACCAATCTAATAATATTC
5353000 AAAAACCAATCTAATCAAT-TTC
1 AAAAACCAATCTAAT-AATATTC
5353022 AA
1 AA
5353024 CTCTTCAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.50, C:0.22, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAAACCAATCTAATAATATTC
Found at i:5368649 original size:22 final size:20
Alignment explanation
Indices: 5368601--5368646 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
5368591 TGTGGATATG
5368601 TATATAATAGTACTTTATTA
1 TATATAATAGTACTTTATTA
* *
5368621 TATATAATATTGCTTTATTA
1 TATATAATAGTACTTTATTA
5368641 TATATA
1 TATATA
5368647 TAAAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.52
Consensus pattern (20 bp):
TATATAATAGTACTTTATTA
Found at i:5375448 original size:25 final size:27
Alignment explanation
Indices: 5375388--5375448 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 27
5375378 AAAAATTATT
*
5375388 TTTTATAATT-AACTATTAATTAATTAA
1 TTTTAT-ATTAAAATATTAATTAATTAA
*
5375415 TATTA-ATTAAAATATT-ATTAATT-A
1 TTTTATATTAAAATATTAATTAATTAA
5375439 TTTTATATTA
1 TTTTATATTA
5375449 TATAGTATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 5 0.17
25 14 0.48
26 6 0.21
27 4 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTTATATTAAAATATTAATTAATTAA
Found at i:5378465 original size:2 final size:2
Alignment explanation
Indices: 5378458--5378519 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
5378448 TTCAATTGAG
5378458 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
5378500 CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA
5378520 TATATATCAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5378918 original size:4 final size:4
Alignment explanation
Indices: 5378911--5378952 Score: 84
Period size: 4 Copynumber: 10.5 Consensus size: 4
5378901 ATAATAAAAT
5378911 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
5378953 GCACTGTGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:5385006 original size:71 final size:71
Alignment explanation
Indices: 5384923--5385057 Score: 202
Period size: 71 Copynumber: 1.9 Consensus size: 71
5384913 CAGTTTTACC
* *
5384923 TTATCATATTTTAAAAA-TAAAATCAATCAGTTTTATCTTAACA-CATTTAAAAGAAAAGCAATC
1 TTATCATATTTTAAAAAGAAAAAT-AATCAATTTTATCTTAACACCATTT-AAAGAAAAGCAATC
5384986 ACCTAATT
64 ACCTAATT
* *
5384994 TTATCATGTTTTAAAAAGAAAAATAATCAATTTTATCTTAGCACCATTTAAAGAAAAGCAATCA
1 TTATCATATTTTAAAAAGAAAAATAATCAATTTTATCTTAACACCATTTAAAGAAAAGCAATCA
5385058 GTTGAAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
71 48 0.83
72 10 0.17
ACGTcount: A:0.47, C:0.13, G:0.06, T:0.34
Consensus pattern (71 bp):
TTATCATATTTTAAAAAGAAAAATAATCAATTTTATCTTAACACCATTTAAAGAAAAGCAATCAC
CTAATT
Found at i:5387696 original size:19 final size:19
Alignment explanation
Indices: 5387674--5387744 Score: 70
Period size: 19 Copynumber: 3.4 Consensus size: 19
5387664 TAATAACTAA
5387674 AATTATAATTAATTTAAAT
1 AATTATAATTAATTTAAAT
*
5387693 AATTATAAATTTAATTAATTTAAT
1 AATTAT-AA-TTAA-T--TTAAAT
*
5387717 AAAATATAATTAATTTAAAT
1 -AATTATAATTAATTTAAAT
5387737 AATTATAA
1 AATTATAA
5387745 ATTTTACTAA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
19 13 0.31
20 7 0.17
21 4 0.10
22 2 0.05
23 4 0.10
24 7 0.17
25 5 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATTATAATTAATTTAAAT
Found at i:5387707 original size:25 final size:24
Alignment explanation
Indices: 5387648--5387748 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 24
5387638 CAATATTACT
* *
5387648 AATTTAATTAATTGATTAATAACTAA
1 AATTTAATTAATT--TAAATAATTAA
5387674 AATTATAATTAATTTAAATAATTATA
1 AATT-TAATTAATTTAAATAATTA-A
5387700 AATTTAATTAA-TT---TAA-TAA
1 AATTTAATTAATTTAAATAATTAA
*
5387719 AATATAATTAATTTAAATAATTATA
1 AATTTAATTAATTTAAATAATTA-A
5387744 AATTT
1 AATTT
5387749 TACTAAATTT
Statistics
Matches: 63, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
19 11 0.17
20 4 0.06
21 3 0.05
23 3 0.05
24 4 0.06
25 20 0.32
26 9 0.14
27 9 0.14
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
AATTTAATTAATTTAAATAATTAA
Found at i:5387712 original size:9 final size:9
Alignment explanation
Indices: 5387674--5387740 Score: 57
Period size: 9 Copynumber: 7.4 Consensus size: 9
5387664 TAATAACTAA
5387674 AATTATAATT
1 AATT-TAATT
*
5387684 AATTTAAAT
1 AATTTAATT
*
5387693 AA-TT-ATA
1 AATTTAATT
5387700 AATTTAATT
1 AATTTAATT
*
5387709 AATTTAATAA
1 AATTTAAT-T
*
5387719 AATATAATT
1 AATTTAATT
*
5387728 AATTTAAAT
1 AATTTAATT
5387737 AATT
1 AATT
5387741 ATAAATTTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
7 3 0.07
8 4 0.09
9 27 0.60
10 11 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
AATTTAATT
Found at i:5387764 original size:25 final size:25
Alignment explanation
Indices: 5387736--5387790 Score: 60
Period size: 24 Copynumber: 2.2 Consensus size: 25
5387726 TTAATTTAAA
5387736 TAATTATAAAT-TTTACTAAATTTAC
1 TAATTATAAATATTTACTAAA-TTAC
* * *
5387761 TAA-TCTAATTATTTACTTAATTAC
1 TAATTATAAATATTTACTAAATTAC
5387785 TAATTA
1 TAATTA
5387791 ATACATGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (25 bp):
TAATTATAAATATTTACTAAATTAC
Found at i:5390207 original size:39 final size:39
Alignment explanation
Indices: 5390145--5390231 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
5390135 CAATAAATTG
*
5390145 CATGCAAGCACCACATGCCCTTGAAGAAAGGAAAAGAAA
1 CATGCAAGGACCACATGCCCTTGAAGAAAGGAAAAGAAA
* **
5390184 CATGCAAGGACCACGTGTGCTTGAAGAAAGGAAAAGAAA
1 CATGCAAGGACCACATGCCCTTGAAGAAAGGAAAAGAAA
*
5390223 CATACAAGG
1 CATGCAAGG
5390232 GACAATGAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (39 bp):
CATGCAAGGACCACATGCCCTTGAAGAAAGGAAAAGAAA
Found at i:5398676 original size:52 final size:50
Alignment explanation
Indices: 5398620--5398760 Score: 162
Period size: 49 Copynumber: 2.8 Consensus size: 50
5398610 TTCTAACAAG
*
5398620 AAGCGATAACCCTTACACAATCCACAACAGGATCTTTAG-TTTTTGCGAGATC
1 AAGCGATAACCCTT-CACAATCCACAA-AGGAT-TTTAGCTTTTTACGAGATC
* * * *
5398672 AAGCGATAA-CCTTTACAATCCACAAAAGATTTTGGCTTTTTACGGGATC
1 AAGCGATAACCCTTCACAATCCACAAAGGATTTTAGCTTTTTACGAGATC
* * *
5398721 AAGCGGTAACCC-TCACAATACACAAAGGATTTTTGCTTTT
1 AAGCGATAACCCTTCACAATCCACAAAGGATTTTAGCTTTT
5398761 GGATAGAAAG
Statistics
Matches: 77, Mismatches: 10, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
48 4 0.05
49 47 0.61
50 13 0.17
51 4 0.05
52 9 0.12
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (50 bp):
AAGCGATAACCCTTCACAATCCACAAAGGATTTTAGCTTTTTACGAGATC
Found at i:5415369 original size:35 final size:35
Alignment explanation
Indices: 5415320--5415421 Score: 93
Period size: 35 Copynumber: 2.9 Consensus size: 35
5415310 TTGTTTTACG
* *
5415320 TGAAGCAATGCTTCACTTGTTTTAATTGTTCTG-T
1 TGAAGTAATACTTCACTTGTTTTAATTGTTCTGCT
* *
5415354 GTGAAGTAGTACTTCA--TGTATTCTATTTGTTCTGCT
1 -TGAAGTAATACTTCACTTGT-TT-TAATTGTTCTGCT
* * *
5415390 TTAAGTAATACTTCACTTGTTCTAGTTGTTCT
1 TGAAGTAATACTTCACTTGTTTTAATTGTTCT
5415422 CATTATTTTC
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
33 3 0.06
34 2 0.04
35 44 0.81
36 2 0.04
37 3 0.06
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.48
Consensus pattern (35 bp):
TGAAGTAATACTTCACTTGTTTTAATTGTTCTGCT
Found at i:5417139 original size:19 final size:17
Alignment explanation
Indices: 5417112--5417150 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
5417102 GCAAATTTTC
*
5417112 ATTGTATGTTTATATGTTA
1 ATTGAATGTTT-TAT-TTA
5417131 ATTGAATGTTTTATTTA
1 ATTGAATGTTTTATTTA
5417148 ATT
1 ATT
5417151 TATTATTATG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 3 0.16
19 10 0.53
ACGTcount: A:0.28, C:0.00, G:0.13, T:0.59
Consensus pattern (17 bp):
ATTGAATGTTTTATTTA
Found at i:5420182 original size:2 final size:2
Alignment explanation
Indices: 5420169--5420213 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
5420159 TAATGTTTGA
* * * *
5420169 TG TG TG TT TG TG TG TG TG TG TG TA TA TA TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
5420211 TG T
1 TG T
5420214 CATTAACAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.07, C:0.00, G:0.40, T:0.53
Consensus pattern (2 bp):
TG
Found at i:5424436 original size:2 final size:2
Alignment explanation
Indices: 5424429--5424456 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5424419 TGGTGGAGAA
5424429 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
5424457 CTCCCTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5432910 original size:55 final size:55
Alignment explanation
Indices: 5432832--5432939 Score: 130
Period size: 55 Copynumber: 2.0 Consensus size: 55
5432822 GATTGGACTT
* **
5432832 TGTTAGGTGCCTTAGCTCTTTTGGCTATTATTAGATGCA-TTAGCATCTTTGGAAA
1 TGTTAGGTGCCTTAGCTCCTTTGGAAATTATTAGATG-ATTTAGCATCTTTGGAAA
* * *
5432887 TGTTAGGTGCCTTA-TTACCTTTGGAAATTGTTGGATGATTTAGCATCTTTGGA
1 TGTTAGGTGCCTTAGCT-CCTTTGGAAATTATTAGATGATTTAGCATCTTTGGA
5432940 TTGGGTAGGT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 2 0.04
55 43 0.96
ACGTcount: A:0.21, C:0.13, G:0.23, T:0.43
Consensus pattern (55 bp):
TGTTAGGTGCCTTAGCTCCTTTGGAAATTATTAGATGATTTAGCATCTTTGGAAA
Found at i:5432937 original size:28 final size:27
Alignment explanation
Indices: 5432871--5433002 Score: 72
Period size: 27 Copynumber: 4.8 Consensus size: 27
5432861 ATTAGATGCA
*
5432871 TTAGCATCTTTGGAAATGTTAGGTGCC
1 TTAGCATCTTTGGAAATGTTAGGTGAC
** * *
5432898 TTATTACCTTTGGAAATTGTT-GGATGAT
1 TTAGCATCTTTGGAAA-TGTTAGG-TGAC
* * *
5432926 TTAGCATCTTTGG-ATTGGGTAGGTGCC
1 TTAGCATCTTTGGAAAT-GTTAGGTGAC
* * * * *
5432953 CTGGCACCTTT-GAGATTGTTAGGTGCC
1 TTAGCATCTTTGGA-AATGTTAGGTGAC
*
5432980 TTAGCACCTTTGGATAATGTTAG
1 TTAGCATCTTTGGA-AATGTTAG
5433003 ACCATGGTAC
Statistics
Matches: 78, Mismatches: 20, Indels: 13
0.70 0.18 0.12
Matches are distributed among these distances:
26 2 0.03
27 46 0.59
28 30 0.38
ACGTcount: A:0.20, C:0.14, G:0.27, T:0.39
Consensus pattern (27 bp):
TTAGCATCTTTGGAAATGTTAGGTGAC
Found at i:5433150 original size:85 final size:82
Alignment explanation
Indices: 5432978--5433153 Score: 244
Period size: 85 Copynumber: 2.1 Consensus size: 82
5432968 TTGTTAGGTG
* * *
5432978 CCTTAGCACCTTTGGATAATGTTAGACCATGGTACCTATGGATTTGGTTAGGTGTCATACACCTT
1 CCTTAGCACCTTTGAATAATGTTAGACCATAGTACCTATGGATTTGGTTAGGTGTCATACACCAT
5433043 TGGATTTACGCCATGGA
66 TGGATTTACGCCATGGA
* * * **
5433060 CCTTAGCACCTTTGAATAGTGTTAGGTACCATAGTACCTTTGGATTTGGTTATGTGTTGTAGCAC
1 CCTTAGCACCTTTGAATAATGTTA-G-ACCATAGTACCTATGGATTTGGTTAGGTGTCATA-CAC
*
5433125 CATTGGATTTAGGCCATGGA
63 CATTGGATTTACGCCATGGA
5433145 CCTTAGCAC
1 CCTTAGCAC
5433154 GAACAAACTC
Statistics
Matches: 82, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
82 22 0.27
83 1 0.01
84 29 0.35
85 30 0.37
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (82 bp):
CCTTAGCACCTTTGAATAATGTTAGACCATAGTACCTATGGATTTGGTTAGGTGTCATACACCAT
TGGATTTACGCCATGGA
Found at i:5435019 original size:81 final size:78
Alignment explanation
Indices: 5434934--5435129 Score: 221
Period size: 80 Copynumber: 2.4 Consensus size: 78
5434924 ACAATAATAT
** * *
5434934 TTTTTTCAACATGACACGTAACATGTTTTTATATATGGTGTGTAACAACAATTTTTTTTTTCAAC
1 TTTTTT-AACATGACGTGTAACATGTTTTTATACATAGTGTGTAACAACAA-TTTTTTTTTCAAC
* ***
5434999 GTGTTGTGTAACAATC
64 ATGGCATGTAACAA-C
* * *
5435015 TTTTTTAACCATAACGTGTAACATGTTTTTGTACGTAGTGTGTAACAACAATTTTTTTTTCAACA
1 TTTTTTAA-CATGACGTGTAACATGTTTTTATACATAGTGTGTAACAACAATTTTTTTTTCAACA
5435080 TGGCATGTAACAAC
65 TGGCATGTAACAAC
* *
5435094 TTTTTTTAACTATGACGTATAACATATTTTTATACA
1 -TTTTTTAAC-ATGACGTGTAACATGTTTTTATACA
5435130 CGACGTAAAA
Statistics
Matches: 96, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
79 2 0.02
80 53 0.55
81 41 0.43
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.44
Consensus pattern (78 bp):
TTTTTTAACATGACGTGTAACATGTTTTTATACATAGTGTGTAACAACAATTTTTTTTTCAACAT
GGCATGTAACAAC
Found at i:5435865 original size:44 final size:44
Alignment explanation
Indices: 5435778--5435866 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
5435768 CTGCAGGATC
* ***
5435778 TAGCCATGCCTTTGAAAGACTAAAGTATGCCGTTTTTTTTTTTT
1 TAGCCATGACTTTGAAAGACTAAAGTATGCCGTTTTCCCTTTTT
5435822 TAGCCATGACTTTGAAAGACTAAAGTATGCCGTTTTCCCTTTTT
1 TAGCCATGACTTTGAAAGACTAAAGTATGCCGTTTTCCCTTTTT
5435866 T
1 T
5435867 TTCGTGTGTA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.43
Consensus pattern (44 bp):
TAGCCATGACTTTGAAAGACTAAAGTATGCCGTTTTCCCTTTTT
Found at i:5442829 original size:40 final size:40
Alignment explanation
Indices: 5442774--5442853 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
5442764 TAATTTGGTC
5442774 AGTATAATATTTCCACTGTTAAACTATAAATCAGAAATCA
1 AGTATAATATTTCCACTGTTAAACTATAAATCAGAAATCA
5442814 AGTATAATATTTCCACTGTTAAACTATAAATCAGAAATCA
1 AGTATAATATTTCCACTGTTAAACTATAAATCAGAAATCA
5442854 GGTACGTTCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (40 bp):
AGTATAATATTTCCACTGTTAAACTATAAATCAGAAATCA
Found at i:5453560 original size:29 final size:28
Alignment explanation
Indices: 5453505--5453626 Score: 99
Period size: 29 Copynumber: 4.3 Consensus size: 28
5453495 ATGCATTAAA
* * *
5453505 GTGTAACAA-AATGTTTTTGAATATGAC
1 GTGTAACAACAATATTTTTTAACATGAC
5453532 GTGTAACAACAATATTTTTTCAACATGAC
1 GTGTAACAACAATATTTTTT-AACATGAC
* * *
5453561 GTGTAATAATGATATATTTTTTTTAACATGGC
1 GTGTAACAA-CA-ATA--TTTTTTAACATGAC
*
5453593 ATGTAACAAC---ATTTTTTAACTATGAC
1 GTGTAACAACAATATTTTTTAAC-ATGAC
5453619 GTGTAACA
1 GTGTAACA
5453627 TGTTTTTGTA
Statistics
Matches: 77, Mismatches: 11, Indels: 15
0.75 0.11 0.15
Matches are distributed among these distances:
25 9 0.12
26 11 0.14
27 10 0.13
28 8 0.10
29 15 0.19
30 1 0.01
31 3 0.04
32 14 0.18
33 6 0.08
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (28 bp):
GTGTAACAACAATATTTTTTAACATGAC
Found at i:5453633 original size:26 final size:25
Alignment explanation
Indices: 5453578--5453626 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
5453568 AATGATATAT
*
5453578 TTTTTTTAACATGGCATGTAACAAC
1 TTTTTTTAACATGACATGTAACAAC
* *
5453603 ATTTTTTAACTATGACGTGTAACA
1 TTTTTTTAAC-ATGACATGTAACA
5453627 TGTTTTTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 9 0.45
26 11 0.55
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (25 bp):
TTTTTTTAACATGACATGTAACAAC
Found at i:5453813 original size:45 final size:45
Alignment explanation
Indices: 5453660--5453813 Score: 159
Period size: 45 Copynumber: 3.4 Consensus size: 45
5453650 AAAAGTATTT
* * * * * *
5453660 TTTTTG-ACATGGCATGTAACAATTTAACTATGATGGGTAACATA
1 TTTTTGTACATAGCATGTAACAACTTAACCATGACGTGTAACATG
* * * *
5453704 TTTTTGTACAT-GACGTATAACAACTTAACCATGACATGTCACATG
1 TTTTTGTACATAG-CATGTAACAACTTAACCATGACGTGTAACATG
* **
5453749 TTTTTATACATAGTGTGTAACAACTTAACCATGACGTGTAACATG
1 TTTTTGTACATAGCATGTAACAACTTAACCATGACGTGTAACATG
*
5453794 TTTCTGTACATAGCATGTAA
1 TTTTTGTACATAGCATGTAA
5453814 TTTCATTAAA
Statistics
Matches: 89, Mismatches: 18, Indels: 5
0.79 0.16 0.04
Matches are distributed among these distances:
44 7 0.08
45 81 0.91
46 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (45 bp):
TTTTTGTACATAGCATGTAACAACTTAACCATGACGTGTAACATG
Found at i:5463844 original size:2 final size:2
Alignment explanation
Indices: 5463837--5463868 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5463827 TGCTACAGTT
5463837 TA 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 TA
5463869 CGAGGCTTAG
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):
TA
Found at i:5467319 original size:45 final size:45
Alignment explanation
Indices: 5467188--5467333 Score: 154
Period size: 45 Copynumber: 3.3 Consensus size: 45
5467178 AATTACACAA
** * *
5467188 CATGTACAAAAATATATTGCACATCATGGTTAGGCTGTTACACG-
1 CATGTACAAAAATATATTATACATCATGGTTAAGTTGTTACACGT
** * *
5467232 CTATGTACAAAAATAT-TTGATATGTCATAGTTAAGTTATTACACGT
1 C-ATGTACAAAAATATATT-ATACATCATGGTTAAGTTGTTACACGT
* *
5467278 CATGTACAAAAATATATTATACATCATGGTTAAATTGTTACACAT
1 CATGTACAAAAATATATTATACATCATGGTTAAGTTGTTACACGT
*
5467323 CACGT-CAAAAA
1 CATGTACAAAAA
5467334 AAATACTTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
44 9 0.11
45 71 0.86
46 3 0.04
ACGTcount: A:0.39, C:0.15, G:0.13, T:0.33
Consensus pattern (45 bp):
CATGTACAAAAATATATTATACATCATGGTTAAGTTGTTACACGT
Found at i:5467474 original size:29 final size:29
Alignment explanation
Indices: 5467413--5467475 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
5467403 TATATTGAAA
* * * * *
5467413 AAAAAATATTGTTATTACATGTCGTGTTG
1 AAAAAATATTATTATTACACGTCATATTC
*
5467442 AAAAAATATTATTGTTACACGTCATATTC
1 AAAAAATATTATTATTACACGTCATATTC
5467471 AAAAA
1 AAAAA
5467476 CATTTCGTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.37
Consensus pattern (29 bp):
AAAAAATATTATTATTACACGTCATATTC
Found at i:5470441 original size:30 final size:30
Alignment explanation
Indices: 5470398--5470473 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
5470388 GGATACTTTC
* *
5470398 AAGAGAGGAGAGCATCA-ATTGGTGCTCTTCA
1 AAGAAAGG-GAGCATCAGATCGGTGCTC-TCA
* *
5470429 AAGCAAGGGAGCATTAGATCGGTGCTCTCA
1 AAGAAAGGGAGCATCAGATCGGTGCTCTCA
*
5470459 AGGAAAGGGAGCATC
1 AAGAAAGGGAGCATC
5470474 GGTGCTTCTC
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
30 22 0.59
31 15 0.41
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.18
Consensus pattern (30 bp):
AAGAAAGGGAGCATCAGATCGGTGCTCTCA
Found at i:5487106 original size:156 final size:156
Alignment explanation
Indices: 5486846--5487160 Score: 481
Period size: 156 Copynumber: 2.0 Consensus size: 156
5486836 ATATTCATCA
* * *
5486846 CCAGGGCCAGCATACTCTCCCAAGCATCATGGCCCTGTTGCAAAACCTCCTAAAGCATCATCTCC
1 CCAGGGCCAGCAAACTCTCCCAAGCATCATGGCCCTGTTGCAAAACCCCCCAAAGCATCATCTCC
* * * * *
5486911 AGGTCCAGCTTTGGCTCCTACTTCTCCATTCCCTGTTGCTGGACCTCCCCA-AGAATCATCTCCA
66 AGGGCCAGCTTTGGCTCCCACATCTCCATTCCCTGTTGCTGAACCT-CCCAGAGAATCATCCCCA
5486975 ACACCAGCACCATCTTCCCATATTTAT
130 ACACCAGCACCATCTTCCCATATTTAT
5487002 CCAGGGCCAGCAAACTCTCCCAAGCATCATGGCCCTGTTGCAAAACCCCCCAAAGCATCATCTCC
1 CCAGGGCCAGCAAACTCTCCCAAGCATCATGGCCCTGTTGCAAAACCCCCCAAAGCATCATCTCC
* * *
5487067 AGGGCCAGCTTTGGCTCCCACATC-CCCTTCCCCTGTTGCTGAATCTCCCAGTGAATCATCCCCA
66 AGGGCCAGCTTTGGCTCCCACATCTCCATT-CCCTGTTGCTGAACCTCCCAGAGAATCATCCCCA
* *
5487131 ACGCCAGCACCATCTTCCCATATTTCT
130 ACACCAGCACCATCTTCCCATATTTAT
5487158 CCA
1 CCA
5487161 TCTCTAGGAC
Statistics
Matches: 144, Mismatches: 13, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
155 8 0.06
156 136 0.94
ACGTcount: A:0.23, C:0.40, G:0.14, T:0.23
Consensus pattern (156 bp):
CCAGGGCCAGCAAACTCTCCCAAGCATCATGGCCCTGTTGCAAAACCCCCCAAAGCATCATCTCC
AGGGCCAGCTTTGGCTCCCACATCTCCATTCCCTGTTGCTGAACCTCCCAGAGAATCATCCCCAA
CACCAGCACCATCTTCCCATATTTAT
Found at i:5488588 original size:26 final size:26
Alignment explanation
Indices: 5488536--5488588 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
5488526 AGAGTTCGGA
* **
5488536 TACCCTATTAAATAATAGGATTAGAG
1 TACCCTATCAAATAATAAAATTAGAG
*
5488562 TACCCTATCAAATAATAAAATTCGAG
1 TACCCTATCAAATAATAAAATTAGAG
5488588 T
1 T
5488589 TCAAGTATCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.30
Consensus pattern (26 bp):
TACCCTATCAAATAATAAAATTAGAG
Found at i:5489617 original size:21 final size:19
Alignment explanation
Indices: 5489579--5489617 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
5489569 TTTTTAAATT
*
5489579 AAAAATATAAATTTAAAAC
1 AAAAATATAAATTGAAAAC
5489598 AAAAATATCAAAATTGAAAA
1 AAAAATAT--AAATTGAAAA
5489618 AGACCTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (19 bp):
AAAAATATAAATTGAAAAC
Found at i:5506182 original size:31 final size:31
Alignment explanation
Indices: 5506147--5506253 Score: 115
Period size: 31 Copynumber: 3.5 Consensus size: 31
5506137 ATTCATTCTG
* * *
5506147 ATTCACGAAACCCTTAAACCAATTCAATCCA
1 ATTCACAAAACTCTAAAACCAATTCAATCCA
* **
5506178 ATTCACAAAACTCTAAAACTAATTCAATTTA
1 ATTCACAAAACTCTAAAACCAATTCAATCCA
* ** *
5506209 ATTCATAAAACTCTAAAACCAATTTGATTCA
1 ATTCACAAAACTCTAAAACCAATTCAATCCA
*
5506240 ATTTACAAAACTCT
1 ATTCACAAAACTCT
5506254 TCCTAAAACC
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (31 bp):
ATTCACAAAACTCTAAAACCAATTCAATCCA
Found at i:5506330 original size:31 final size:31
Alignment explanation
Indices: 5506295--5506372 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
5506285 TCAAAGAATG
* * **
5506295 CTAAAACTGATTTAATTTTATTCAAGACAAC
1 CTAAAACTAATTCAATCCTATTCAAGACAAC
*
5506326 CTAAAACTAATTCAATCCTATTCAAGGCAAC
1 CTAAAACTAATTCAATCCTATTCAAGACAAC
* *
5506357 CTCAAACCAATTCAAT
1 CTAAAACTAATTCAAT
5506373 TTGATTTAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.42, C:0.23, G:0.05, T:0.29
Consensus pattern (31 bp):
CTAAAACTAATTCAATCCTATTCAAGACAAC
Found at i:5517411 original size:3 final size:3
Alignment explanation
Indices: 5517403--5517431 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
5517393 TGGTGGATCT
5517403 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
1 TGC TGC TGC TGC TGC TGC TGC TGC TGC TG
5517432 ATGATGATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.34, T:0.34
Consensus pattern (3 bp):
TGC
Found at i:5517769 original size:2 final size:2
Alignment explanation
Indices: 5517762--5517794 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5517752 CCACAATCAA
5517762 AG AG AG 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 AG AG AG A
5517795 AAAGGAAGGA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5517970 original size:2 final size:2
Alignment explanation
Indices: 5517963--5517987 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5517953 GTTAGTGTAT
5517963 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
5517988 TGTTAGTTTC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5520960 original size:24 final size:24
Alignment explanation
Indices: 5520911--5520960 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
5520901 TGTTTAGGGT
*
5520911 TTAATTATATTTAATTAAATTTTA
1 TTAATTATATTTAATTAAATTATA
**
5520935 TTAATTAT-TTTATATTTTATTATA
1 TTAATTATATTTA-ATTAAATTATA
5520959 TT
1 TT
5520961 GACATAACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTAATTATATTTAATTAAATTATA
Found at i:5521755 original size:21 final size:21
Alignment explanation
Indices: 5521677--5521743 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
5521667 TACTTTGTCT
5521677 TATATTAATTAATAATATAAT-A
1 TATATTAA-T-ATAATATAATGA
* * *
5521699 TTTATTCA-ATAATA-ACGTGA
1 TATATTAATATAATATA-ATGA
5521719 TATATTAATATAATATAATGA
1 TATATTAATATAATATAATGA
5521740 TATA
1 TATA
5521744 ATTATATGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
18 1 0.03
19 7 0.20
20 7 0.20
21 13 0.37
22 7 0.20
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (21 bp):
TATATTAATATAATATAATGA
Found at i:5524917 original size:2 final size:2
Alignment explanation
Indices: 5524912--5524940 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5524902 AATAAAAAAT
5524912 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 T
5524941 CCAAAACTCA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5527230 original size:13 final size:13
Alignment explanation
Indices: 5527212--5527240 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5527202 CAAAAACATC
5527212 TGATGTCTAAATT
1 TGATGTCTAAATT
5527225 TGATGTCTAAATT
1 TGATGTCTAAATT
5527238 TGA
1 TGA
5527241 GAGCTTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.31, C:0.07, G:0.17, T:0.45
Consensus pattern (13 bp):
TGATGTCTAAATT
Found at i:5530890 original size:21 final size:20
Alignment explanation
Indices: 5530844--5530888 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
5530834 TGGTTTAACG
*
5530844 TTTTAAAAAACTTTTAAATTA
1 TTTTAAAAAAC-TTTAAATAA
5530865 TTTTAAAAAA-TTTAAATAAA
1 TTTTAAAAAACTTTAAAT-AA
5530885 TTTT
1 TTTT
5530889 TATTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 7 0.32
20 5 0.23
21 10 0.45
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTAAAAAACTTTAAATAA
Found at i:5531663 original size:31 final size:28
Alignment explanation
Indices: 5531615--5531694 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 28
5531605 AATTGTTAAT
*
5531615 TATAAAAATTTATTAAATCTAAAATAAAAA
1 TATAAAATTTTATTAAA--TAAAATAAAAA
*
5531645 TATAAAATTTTAATTAAATACAATAAAAA
1 TATAAAATTTT-ATTAAATAAAATAAAAA
* *
5531674 AATAAAATTTTTCTTAAATAA
1 TATAAAA-TTTTATTAAATAA
5531695 TACAGTGACC
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
29 23 0.53
30 14 0.33
31 6 0.14
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (28 bp):
TATAAAATTTTATTAAATAAAATAAAAA
Found at i:5542954 original size:15 final size:15
Alignment explanation
Indices: 5542924--5542990 Score: 80
Period size: 15 Copynumber: 4.4 Consensus size: 15
5542914 CGTTTGGTAC
*
5542924 ATTACAATGCAATGTG
1 ATTACAA-GTAATGTG
*
5542940 ATTACAGGTAATGTG
1 ATTACAAGTAATGTG
*
5542955 ATTGCAAGTAATGTG
1 ATTACAAGTAATGTG
* *
5542970 ATTGCAAGTAATGTA
1 ATTACAAGTAATGTG
5542985 ATTACA
1 ATTACA
5542991 GGGAAAATAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
15 39 0.87
16 6 0.13
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (15 bp):
ATTACAAGTAATGTG
Found at i:5543181 original size:16 final size:15
Alignment explanation
Indices: 5543162--5543294 Score: 58
Period size: 13 Copynumber: 9.3 Consensus size: 15
5543152 ATTATTATTA
5543162 ATTTTTATATAATAT
1 ATTTTTATATAATAT
*
5543177 CATTTCT-TA-AATAT
1 -ATTTTTATATAATAT
*
5543191 ATTTTTAATATCATAT
1 ATTTTT-ATATAATAT
*
5543207 A-TTTTAT-T--TTT
1 ATTTTTATATAATAT
5543218 ATTTATTAT-T-ATA-
1 ATTT-TTATATAATAT
*
5543231 ATATTTTATAT--TTT
1 AT-TTTTATATAATAT
* *
5543245 ATTTTAATATATTTAT
1 ATTTTTATATA-ATAT
*
5543261 ATTTTTAT-TATTA-
1 ATTTTTATATAATAT
5543274 ATTTTTATATAATAT
1 ATTTTTATATAATAT
5543289 CATTTT
1 -ATTTT
5543295 AAATATATTT
Statistics
Matches: 92, Mismatches: 10, Indels: 30
0.70 0.08 0.23
Matches are distributed among these distances:
11 3 0.03
12 2 0.02
13 33 0.36
14 20 0.22
15 10 0.11
16 24 0.26
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTTTTATATAATAT
Found at i:5543239 original size:20 final size:21
Alignment explanation
Indices: 5543214--5543462 Score: 119
Period size: 21 Copynumber: 11.7 Consensus size: 21
5543204 TATATTTTAT
5543214 TTTTAT-TTATTATTATAATA
1 TTTTATATTATTATTATAATA
*
5543234 TTTTATATT-TTATTTTAATA
1 TTTTATATTATTATTATAATA
*
5543254 TATTTATATTTTTATTATTAAT-
1 T-TTTATATTATTATTA-TAATA
* *
5543276 TTTTATATAATATCATTTTAAATA
1 TTTTATAT--TATTATTAT-AATA
* * * * *
5543300 TATTTTTAATGTCA-TATATTTA
1 T-TTTATATTATTATTATA-ATA
5543322 TTTT-TATTTATTATTATAATA
1 TTTTATA-TTATTATTATAATA
*
5543343 TTTTATATT-TTATTTTAATA
1 TTTTATATTATTATTATAATA
*
5543363 TATTTATATTTTTATTATTAAT-
1 T-TTTATATTATTATTA-TAATA
* *
5543385 TTTATATAATATCATATTTAAATATA
1 TTT-TATATTAT--TA-TTATA-ATA
* *
5543411 TTTTATGTCATATATT-T--TA
1 TTTTATATTAT-TATTATAATA
5543430 TTTTAT-TTATTATTATAAT-
1 TTTTATATTATTATTATAATA
*
5543449 TTATATATT-TTATT
1 TTTTATATTATTATT
5543463 TTCATTTCTT
Statistics
Matches: 178, Mismatches: 25, Indels: 53
0.70 0.10 0.21
Matches are distributed among these distances:
17 4 0.02
18 4 0.02
19 18 0.10
20 33 0.19
21 42 0.24
22 30 0.17
23 22 0.12
24 7 0.04
25 15 0.08
26 3 0.02
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.64
Consensus pattern (21 bp):
TTTTATATTATTATTATAATA
Found at i:5543243 original size:28 final size:27
Alignment explanation
Indices: 5543190--5543448 Score: 116
Period size: 28 Copynumber: 9.6 Consensus size: 27
5543180 TTCTTAAATA
* *
5543190 TATTT-TTAATATCATATATTTTATTTT
1 TATTTATTATTATAATAT-TTTTATTTT
5543217 TATTTATTATTATAATA-TTTTATATTT
1 TATTTATTATTATAATATTTTTAT-TTT
5543244 TATTTTAATATATT-T-ATATTTTTATTATT
1 TA-TTT-AT-TATTATAATATTTTTATT-TT
* ** *
5543273 AATTT-TTA-TATAATATCATTTTAAATA
1 TATTTATTATTATAATAT--TTTTATTTT
* * * *
5543300 TATTT-TTAATGTCATATATTTATTTT
1 TATTTATTATTATAATATTTTTATTTT
5543326 TATTTATTATTATAATA-TTTTATATTT
1 TATTTATTATTATAATATTTTTAT-TTT
*
5543353 TATTTTAATATATT-T-ATATTTTTATTAT
1 TA-TTT-AT-TATTATAATATTTTTATTTT
* ** *
5543381 TAATT-TTA-TATAATA-TCATATTTA
1 TATTTATTATTATAATATTTTTATTTT
* * *
5543405 AATATATT-TTATGTCATATATTTTA-TTT
1 TATTTATTATTA--TAATAT-TTTTATTTT
5543433 TATTTATTATTATAAT
1 TATTTATTATTATAAT
5543449 TTATATATTT
Statistics
Matches: 172, Mismatches: 33, Indels: 54
0.66 0.13 0.21
Matches are distributed among these distances:
23 1 0.01
24 11 0.06
25 11 0.06
26 26 0.15
27 40 0.23
28 48 0.28
29 27 0.16
30 8 0.05
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (27 bp):
TATTTATTATTATAATATTTTTATTTT
Found at i:5543458 original size:31 final size:32
Alignment explanation
Indices: 5543420--5543502 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 32
5543410 ATTTTATGTC
*
5543420 ATATATTTTATTTTATTT-ATTATTATAATTT
1 ATATATTTTATTTTATTTCATTAATATAATTT
* *
5543451 ATATATTTTATTTTCATTTCTTTAATATATTTT
1 ATATATTTTATTTT-ATTTCATTAATATAATTT
* *
5543484 TTATATTATATATTTATTT
1 ATATATTTTAT-TTTATTT
5543503 TTAATTTATT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
31 14 0.32
32 4 0.09
33 23 0.52
34 3 0.07
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (32 bp):
ATATATTTTATTTTATTTCATTAATATAATTT
Found at i:5543491 original size:109 final size:110
Alignment explanation
Indices: 5543148--5543464 Score: 538
Period size: 109 Copynumber: 2.9 Consensus size: 110
5543138 TTAATCTATT
* *
5543148 TATTATTATTATTAATTTTTATATAATATCATTTCTTAAATATATTTTTAATATCATATATTTTA
1 TATTTTTATTATTAATTTTTATATAATATCA-TT-TTAAATATATTTTTAATGTCATATATTTTA
5543213 TTTTTATTTATTATTATAATATTTTATATTTTATTTTAATATATTTA
64 TTTTTATTTATTATTATAATATTTTATATTTTATTTTAATATATTTA
5543260 TATTTTTATTATTAATTTTTATATAATATCATTTTAAATATATTTTTAATGTCATATA-TTTATT
1 TATTTTTATTATTAATTTTTATATAATATCATTTTAAATATATTTTTAATGTCATATATTTTATT
5543324 TTTATTTATTATTATAATATTTTATATTTTATTTTAATATATTTA
66 TTTATTTATTATTATAATATTTTATATTTTATTTTAATATATTTA
5543369 TATTTTTATTATTAA-TTTTATATAATATCATATTTAAATATA-TTTT-ATGTCATATATTTTA-
1 TATTTTTATTATTAATTTTTATATAATATCAT-TTTAAATATATTTTTAATGTCATATATTTTAT
*
5543430 TTTTATTTATTATTATAAT-TTATATATTTTATTTT
65 TTTTATTTATTATTATAATATTTTATATTTTATTTT
5543465 CATTTCTTTA
Statistics
Matches: 200, Mismatches: 3, Indels: 10
0.94 0.01 0.05
Matches are distributed among these distances:
106 15 0.08
107 29 0.14
108 24 0.12
109 76 0.38
110 24 0.12
111 2 0.01
112 30 0.15
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (110 bp):
TATTTTTATTATTAATTTTTATATAATATCATTTTAAATATATTTTTAATGTCATATATTTTATT
TTTATTTATTATTATAATATTTTATATTTTATTTTAATATATTTA
Found at i:5546000 original size:21 final size:21
Alignment explanation
Indices: 5545976--5546022 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5545966 ATCATAACTG
5545976 AATTTAATTTAACTTTATATT
1 AATTTAATTTAACTTTATATT
* * * *
5545997 AATTTTATTTGATTTTTTATT
1 AATTTAATTTAACTTTATATT
5546018 AATTT
1 AATTT
5546023 CTTCCGTGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (21 bp):
AATTTAATTTAACTTTATATT
Found at i:5548547 original size:10 final size:10
Alignment explanation
Indices: 5548532--5548559 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
5548522 TTTTTTGAAT
5548532 GTCGGTTTCG
1 GTCGGTTTCG
5548542 GTCGGTTTCG
1 GTCGGTTTCG
5548552 GTCGGTTT
1 GTCGGTTT
5548560 TGGTGATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.18, G:0.39, T:0.43
Consensus pattern (10 bp):
GTCGGTTTCG
Found at i:5548646 original size:31 final size:32
Alignment explanation
Indices: 5548602--5548667 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
5548592 ACTTGGACTA
* * *
5548602 AAATGGGTTAATTGGGCTATAATTTAT-GGCT
1 AAATAGGTAAATTGGACTATAATTTATGGGCT
*
5548633 AAATAGGTAAATTGGACTATGATTTATGGGCT
1 AAATAGGTAAATTGGACTATAATTTATGGGCT
5548665 AAA
1 AAA
5548668 ATGGTTAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 23 0.77
32 7 0.23
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (32 bp):
AAATAGGTAAATTGGACTATAATTTATGGGCT
Found at i:5549039 original size:28 final size:27
Alignment explanation
Indices: 5549000--5549058 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
5548990 TGGACTTGAT
* **
5549000 GGGGGGGCGGAATCGGGACTCGTGGGA
1 GGGGGGCCGGAATCACGACTCGTGGGA
*
5549027 GGGGGGCCGGGAATCACGAGTCGTGGGA
1 GGGGGGCC-GGAATCACGACTCGTGGGA
5549055 GGGG
1 GGGG
5549059 ACCCGTGGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 7 0.26
28 20 0.74
ACGTcount: A:0.15, C:0.15, G:0.59, T:0.10
Consensus pattern (27 bp):
GGGGGGCCGGAATCACGACTCGTGGGA
Found at i:5549907 original size:22 final size:21
Alignment explanation
Indices: 5549881--5549938 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
5549871 ATTGTATATG
5549881 CATATGTT-AAAAAAAATAAATT
1 CATAT-TTCAAAAAAAA-AAATT
**
5549903 CATATTTCAAAAATCAAAATT
1 CATATTTCAAAAAAAAAAATT
*
5549924 CATATTTCACAAAAA
1 CATATTTCAAAAAAA
5549939 TTTACATTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.31
Consensus pattern (21 bp):
CATATTTCAAAAAAAAAAATT
Found at i:5551855 original size:23 final size:23
Alignment explanation
Indices: 5551812--5551880 Score: 68
Period size: 25 Copynumber: 2.9 Consensus size: 23
5551802 TAAAAAAATT
* *
5551812 AAAAATTCTA-TATATAATTTTTA
1 AAAAATT-TACTATTTACTTTTTA
*
5551835 AAAAATTTACTATTTACTTTTTTTT
1 AAAAATTTACTATTTAC--TTTTTA
*
5551860 GAAAATTTACTATTTACTTTT
1 AAAAATTTACTATTTACTTTT
5551881 GTATCTAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 2 0.05
23 16 0.41
25 21 0.54
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (23 bp):
AAAAATTTACTATTTACTTTTTA
Found at i:5551857 original size:25 final size:25
Alignment explanation
Indices: 5551829--5551880 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
5551819 CTATATATAA
5551829 TTTTTAAAAAATTTACTATTTACTT
1 TTTTTAAAAAATTTACTATTTACTT
**
5551854 TTTTTTGAAAATTTACTATTTACTT
1 TTTTTAAAAAATTTACTATTTACTT
5551879 TT
1 TT
5551881 GTATCTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTTAAAAAATTTACTATTTACTT
Found at i:5551890 original size:25 final size:25
Alignment explanation
Indices: 5551836--5551890 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
5551826 TAATTTTTAA
* * *
5551836 AAAATTTACTATTTACTTTTTTTTG
1 AAAATTTACTATTTACTTTTGTATC
5551861 AAAATTTACTATTTACTTTTGTATC
1 AAAATTTACTATTTACTTTTGTATC
*
5551886 TAAAT
1 AAAAT
5551891 ATTTTTTATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.55
Consensus pattern (25 bp):
AAAATTTACTATTTACTTTTGTATC
Found at i:5555030 original size:71 final size:71
Alignment explanation
Indices: 5554913--5555048 Score: 236
Period size: 71 Copynumber: 1.9 Consensus size: 71
5554903 TGCACAAACT
5554913 TGGAGCTGTTAGGAGATCAATAGATGTAACCCGTTATTCAGATTATGATGAGCTCAAAAAAGATA
1 TGGAGCTGTTAGGAGATCAATAGATGTAACCCGTTATTCAGATTATGATGAGCTCAAAAAAGATA
5554978 TGGCCA
66 TGGCCA
* * * *
5554984 TGGAGCTGTTAGGAGATCAATAGATGTAACCTGTTTTTCAGGTTATGATGAGCTCAAACAAGATA
1 TGGAGCTGTTAGGAGATCAATAGATGTAACCCGTTATTCAGATTATGATGAGCTCAAAAAAGATA
5555049 CGGCTCGTAG
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (71 bp):
TGGAGCTGTTAGGAGATCAATAGATGTAACCCGTTATTCAGATTATGATGAGCTCAAAAAAGATA
TGGCCA
Found at i:5557344 original size:168 final size:168
Alignment explanation
Indices: 5557035--5557350 Score: 515
Period size: 168 Copynumber: 1.9 Consensus size: 168
5557025 TTTTGAACGT
* * * * *
5557035 AAACCATGTGAACTAGGATTGTTATATAGGTCTTAACAATCACATTCATATCCGATGTGGGATAT
1 AAACCACGTGAACTAAGATTGTTATATAAGTCTTAACAATCACATTCATATCAGATGTGGAATAT
* * * *
5557100 TGGGTATCACAATCTCACCCACTCAAATCCTTGATGTCCTCATCAAGGCCACACATCACATTCAC
66 TAGGTATCACAATCCCACCCACTCAAATCCTTAATGTCCTCATCAAGGCCACACATCACATCCAC
*
5557165 AGGATCAAATCACGTGGACAAAAATTATCCACAAGACC
131 AGGACCAAATCACGTGGACAAAAATTATCCACAAGACC
* *
5557203 AAACCACGTGGACTAAGATTGTTATATAAGTCTTAACAATCACATTCATATCAGATGTGGAATGT
1 AAACCACGTGAACTAAGATTGTTATATAAGTCTTAACAATCACATTCATATCAGATGTGGAATAT
*
5557268 TAGGTATCACAATCCCACCCACTCAAATCCTTAATGTCCTCATCAAGGCCACACATCACATCCAT
66 TAGGTATCACAATCCCACCCACTCAAATCCTTAATGTCCTCATCAAGGCCACACATCACATCCAC
5557333 AGGACCAAATCACGTGGA
131 AGGACCAAATCACGTGGA
5557351 TTAGGATTGT
Statistics
Matches: 135, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
168 135 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (168 bp):
AAACCACGTGAACTAAGATTGTTATATAAGTCTTAACAATCACATTCATATCAGATGTGGAATAT
TAGGTATCACAATCCCACCCACTCAAATCCTTAATGTCCTCATCAAGGCCACACATCACATCCAC
AGGACCAAATCACGTGGACAAAAATTATCCACAAGACC
Found at i:5557524 original size:107 final size:107
Alignment explanation
Indices: 5557338--5557546 Score: 400
Period size: 107 Copynumber: 2.0 Consensus size: 107
5557328 TCCATAGGAC
*
5557338 CAAATCACGTGGATTAGGATTGTTATATAAGTCTTGACAATCACATTCATATCAGATGTGAGATG
1 CAAATCACGTGGATTAGGATTGTTATATAAGTCTTGACAATCACATTCATATCAGATGTGAGATA
5557403 TTAGGTATCACAATCCCACCACTCAAATCCTTGATGTGTGAT
66 TTAGGTATCACAATCCCACCACTCAAATCCTTGATGTGTGAT
5557445 CAAATCACGTGGATTAGGATTGTTATATAAGTCTTGACAATCACATTCATATCAGATGTGAGATA
1 CAAATCACGTGGATTAGGATTGTTATATAAGTCTTGACAATCACATTCATATCAGATGTGAGATA
*
5557510 TTAGGTATCACAATCCCACTACTCAAATCCTTGATGT
66 TTAGGTATCACAATCCCACCACTCAAATCCTTGATGT
5557547 CCTCATCAAG
Statistics
Matches: 100, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 100 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (107 bp):
CAAATCACGTGGATTAGGATTGTTATATAAGTCTTGACAATCACATTCATATCAGATGTGAGATA
TTAGGTATCACAATCCCACCACTCAAATCCTTGATGTGTGAT
Found at i:5557574 original size:21 final size:21
Alignment explanation
Indices: 5557549--5557592 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
5557539 CTTGATGTCC
5557549 TCATCAAGGCCACACATCACA
1 TCATCAAGGCCACACATCACA
5557570 TCATCAAGGCCACACATCACA
1 TCATCAAGGCCACACATCACA
5557591 TC
1 TC
5557593 CATAAGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.39, G:0.09, T:0.16
Consensus pattern (21 bp):
TCATCAAGGCCACACATCACA
Found at i:5557763 original size:92 final size:92
Alignment explanation
Indices: 5557596--5557776 Score: 292
Period size: 92 Copynumber: 2.0 Consensus size: 92
5557586 TCACATCCAT
* *
5557596 AAGACCAAATCACGTGAATTAGGATTGTTATAAAGGTCTTAACAATCACATTCATATCAGATGTG
1 AAGACCAAACCACGTGAATTAAGATTGTTATAAAGGTCTTAACAATCACATTCATATCAGATGTG
5557661 AGATGTTAGGTACCACAATCCCACCAC
66 AGATGTTAGGTACCACAATCCCACCAC
* *
5557688 AAGATCAAACCACGTGCATTAAGATTGTTATATAA-GTCTTAACAATCACATTCATATCAGATGT
1 AAGACCAAACCACGTGAATTAAGATTGTTATA-AAGGTCTTAACAATCACATTCATATCAGATGT
* *
5557752 GGGATGTTAGGTATCACAATCCCAC
65 GAGATGTTAGGTACCACAATCCCAC
5557777 TTAAATCCTT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
92 80 0.98
93 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (92 bp):
AAGACCAAACCACGTGAATTAAGATTGTTATAAAGGTCTTAACAATCACATTCATATCAGATGTG
AGATGTTAGGTACCACAATCCCACCAC
Found at i:5585137 original size:22 final size:21
Alignment explanation
Indices: 5585103--5585145 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5585093 GATCACCGTA
5585103 CAAGCAGCCAAATATT-CAAACT
1 CAAGCAG-CAAA-ATTGCAAACT
*
5585125 CAAGCATCAAAATTGCAAACT
1 CAAGCAGCAAAATTGCAAACT
5585146 ATAACTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 10 0.53
22 6 0.32
ACGTcount: A:0.47, C:0.26, G:0.09, T:0.19
Consensus pattern (21 bp):
CAAGCAGCAAAATTGCAAACT
Found at i:5589438 original size:17 final size:17
Alignment explanation
Indices: 5589416--5589449 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
5589406 AAATAAATTC
5589416 TAAGATAAAAATGATAT
1 TAAGATAAAAATGATAT
5589433 TAAGATAAAAATGATAT
1 TAAGATAAAAATGATAT
5589450 AGTCAAGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.12, T:0.29
Consensus pattern (17 bp):
TAAGATAAAAATGATAT
Found at i:5592980 original size:16 final size:16
Alignment explanation
Indices: 5592940--5592999 Score: 59
Period size: 16 Copynumber: 3.6 Consensus size: 16
5592930 GATTTATATA
* *
5592940 AATATTAATATTTTTAT
1 AATATTAAAATTTAT-T
5592957 AATAATTAAAATTTATT
1 AAT-ATTAAAATTTATT
*
5592974 AATATTAAATTTTATT
1 AATATTAAAATTTATT
5592990 -ATATTTAAAA
1 AATA-TTAAAA
5593000 AATATTATGA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 3 0.08
16 17 0.46
17 7 0.19
18 10 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
AATATTAAAATTTATT
Found at i:5593013 original size:34 final size:34
Alignment explanation
Indices: 5592935--5593006 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 34
5592925 TTATTGATTT
* *
5592935 ATATAAATATTAATATTTTTATAATAATTAAAAT
1 ATATTAATATTAATATTTTTATAATAATTAAAAA
* * *
5592969 TTATTAATATTAA-A-TTTTATTATATTTAAAAA
1 ATATTAATATTAATATTTTTATAATAATTAAAAA
5593001 ATATTA
1 ATATTA
5593007 TGATATTTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
32 20 0.62
33 1 0.03
34 11 0.34
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (34 bp):
ATATTAATATTAATATTTTTATAATAATTAAAAA
Found at i:5594657 original size:9 final size:9
Alignment explanation
Indices: 5594643--5594670 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
5594633 TTTTATATGC
5594643 AAAAAAGAA
1 AAAAAAGAA
5594652 AAAAAAGAA
1 AAAAAAGAA
5594661 AAAAAAGAA
1 AAAAAAGAA
5594670 A
1 A
5594671 GCAAGTACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:5605523 original size:2 final size:2
Alignment explanation
Indices: 5605516--5605558 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
5605506 AGAAAAACGG
*
5605516 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
5605558 G
1 G
5605559 GCACCAGTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:5605724 original size:18 final size:18
Alignment explanation
Indices: 5605701--5605736 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
5605691 TCATAACCAA
5605701 AAAAAC-AAACAAGAATCG
1 AAAAACAAAACAA-AATCG
5605719 AAAAACAAAACAAAATCG
1 AAAAACAAAACAAAATCG
5605737 TCCCAACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.69, C:0.17, G:0.08, T:0.06
Consensus pattern (18 bp):
AAAAACAAAACAAAATCG
Found at i:5607355 original size:41 final size:41
Alignment explanation
Indices: 5607310--5607393 Score: 116
Period size: 41 Copynumber: 2.0 Consensus size: 41
5607300 TAGTTTGTAG
* * *
5607310 TAGCCGTTGATACTTCCTATCATGCTGTATA-GAGTAGGTTT
1 TAGCCATTGATACTACCTATCATGCTATATACGA-TAGGTTT
*
5607351 TAGCCATTGATACTACCTATCATGCTATGTACGATAGGTTT
1 TAGCCATTGATACTACCTATCATGCTATATACGATAGGTTT
5607392 TA
1 TA
5607394 AGTGCTCCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 36 0.95
42 2 0.05
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (41 bp):
TAGCCATTGATACTACCTATCATGCTATATACGATAGGTTT
Found at i:5616406 original size:14 final size:15
Alignment explanation
Indices: 5616388--5616431 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
5616378 CTAAATAAAA
*
5616388 AAAAAAAAAACTTCC
1 AAAAAACAAACTTCC
*
5616403 AAAAAACAAGCTTCC
1 AAAAAACAAACTTCC
5616418 AAGATAAACAAACT
1 AA-A-AAACAAACT
5616432 AATATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 15 0.62
16 1 0.04
17 8 0.33
ACGTcount: A:0.61, C:0.20, G:0.05, T:0.14
Consensus pattern (15 bp):
AAAAAACAAACTTCC
Found at i:5617103 original size:16 final size:15
Alignment explanation
Indices: 5617082--5617112 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5617072 CAATGATAAG
5617082 TTTTCTTTTTTGCTTT
1 TTTTCTTTTTT-CTTT
5617098 TTTTCTTTTTTCTTT
1 TTTTCTTTTTTCTTT
5617113 AATAATGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.84
Consensus pattern (15 bp):
TTTTCTTTTTTCTTT
Found at i:5621631 original size:22 final size:22
Alignment explanation
Indices: 5621603--5621645 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5621593 AGTACCATTA
5621603 TGCAATTATCCAATAAATGATT
1 TGCAATTATCCAATAAATGATT
**
5621625 TGCAATTATCCTCTAAATGAT
1 TGCAATTATCCAATAAATGAT
5621646 AATGATCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (22 bp):
TGCAATTATCCAATAAATGATT
Found at i:5622740 original size:20 final size:22
Alignment explanation
Indices: 5622690--5622741 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
5622680 CCACAATTTT
5622690 AATTTAAAATATATATTTGATA
1 AATTTAAAATATATATTTGATA
* *
5622712 AA-TAAAAAAATATATTT-ATA
1 AATTTAAAATATATATTTGATA
5622732 AATTTAAAAT
1 AATTTAAAAT
5622742 TTATCTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 5 0.20
21 18 0.72
22 2 0.08
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (22 bp):
AATTTAAAATATATATTTGATA
Found at i:5624904 original size:17 final size:17
Alignment explanation
Indices: 5624882--5624916 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5624872 TACTTAGTCT
5624882 TTTGCTGGCTCACTTAC
1 TTTGCTGGCTCACTTAC
5624899 TTTGCTGGCTCACTTAC
1 TTTGCTGGCTCACTTAC
5624916 T
1 T
5624917 GCTTACTGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.17, T:0.43
Consensus pattern (17 bp):
TTTGCTGGCTCACTTAC
Found at i:5633999 original size:2 final size:2
Alignment explanation
Indices: 5633988--5634034 Score: 78
Period size: 2 Copynumber: 24.0 Consensus size: 2
5633978 GTTTCTGGTA
*
5633988 TC TC TC -C TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5634029 TC TC TC
1 TC TC TC
5634035 ACAGTATCTT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5636101 original size:2 final size:2
Alignment explanation
Indices: 5636094--5636124 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5636084 TCTTAGCAGC
5636094 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 A
5636125 AAAGGAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5637692 original size:4 final size:4
Alignment explanation
Indices: 5637683--5637713 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
5637673 ATATAAACAT
*
5637683 ATAA ATAA ATAA ATAA ATAA ATAG ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATA
5637714 GAGCTTACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:5637767 original size:16 final size:15
Alignment explanation
Indices: 5637745--5637789 Score: 65
Period size: 14 Copynumber: 3.0 Consensus size: 15
5637735 TTGTATATGA
5637745 TATTATCTCAAAAAT
1 TATTATCTCAAAAAT
*
5637760 TAATTATCCCAAAAA-
1 T-ATTATCTCAAAAAT
5637775 TATTATCTCAAAAAT
1 TATTATCTCAAAAAT
5637790 CCCATAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 12 0.46
15 2 0.08
16 12 0.46
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (15 bp):
TATTATCTCAAAAAT
Found at i:5637987 original size:2 final size:2
Alignment explanation
Indices: 5637973--5638009 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
5637963 CTTTGGGCTC
5637973 AT AT AT ACT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5638010 AATTCCTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 31 0.94
3 1 0.03
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5639640 original size:15 final size:15
Alignment explanation
Indices: 5639620--5639657 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
5639610 ATTTCACTAG
5639620 TTTCTTTCTTT-TTTT
1 TTTCTTT-TTTCTTTT
5639635 TTTCTTTTTTCTTTT
1 TTTCTTTTTTCTTTT
5639650 TTT-TTTTT
1 TTTCTTTTT
5639658 GAGTTCAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (15 bp):
TTTCTTTTTTCTTTT
Found at i:5639644 original size:7 final size:7
Alignment explanation
Indices: 5639620--5639657 Score: 51
Period size: 7 Copynumber: 5.4 Consensus size: 7
5639610 ATTTCACTAG
5639620 TTTCTTT
1 TTTCTTT
*
5639627 CTTTTTTT
1 -TTTCTTT
5639635 TTTCTTT
1 TTTCTTT
5639642 TTTCTTT
1 TTTCTTT
5639649 TTT-TTT
1 TTTCTTT
5639655 TTT
1 TTT
5639658 GAGTTCAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.21
7 16 0.57
8 6 0.21
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (7 bp):
TTTCTTT
Found at i:5640069 original size:30 final size:29
Alignment explanation
Indices: 5640033--5640104 Score: 92
Period size: 30 Copynumber: 2.5 Consensus size: 29
5640023 AATTATTAAT
*
5640033 TATAAAAATATATTTGATTTAAAATAAAAA
1 TATAAAAATATATTTAATTT-AAATAAAAA
* *
5640063 TATAAAAATATAATTAATTTTAATAAAAA
1 TATAAAAATATATTTAATTTAAATAAAAA
*
5640092 -ATAAAAATTTATT
1 TATAAAAATATATT
5640105 GAAATTTTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 11 0.30
29 8 0.22
30 18 0.49
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (29 bp):
TATAAAAATATATTTAATTTAAATAAAAA
Found at i:5641653 original size:13 final size:13
Alignment explanation
Indices: 5641635--5641659 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5641625 ATGACTTTTC
5641635 TCTCACTTTCTCT
1 TCTCACTTTCTCT
5641648 TCTCACTTTCTC
1 TCTCACTTTCTC
5641660 ACTGTCCAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.40, G:0.00, T:0.52
Consensus pattern (13 bp):
TCTCACTTTCTCT
Found at i:5664153 original size:20 final size:21
Alignment explanation
Indices: 5664128--5664166 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5664118 AGAATAGGAG
5664128 AAAGGGT-AAAAACAAAAAAA
1 AAAGGGTGAAAAACAAAAAAA
*
5664148 AAAGGGTGAAAACCAAAAA
1 AAAGGGTGAAAAACAAAAA
5664167 TATAAGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.69, C:0.08, G:0.18, T:0.05
Consensus pattern (21 bp):
AAAGGGTGAAAAACAAAAAAA
Found at i:5664343 original size:65 final size:64
Alignment explanation
Indices: 5664265--5664387 Score: 192
Period size: 65 Copynumber: 1.9 Consensus size: 64
5664255 GTTGATAACT
** *
5664265 AAAAAAAAGAGATGAAAGGTAAACACCTGAGAGAAATGATGAAAACCAAAAAAAAAAATTAAAAA
1 AAAAAAAAGAGATGAAAGGTAAACACCCAAGAGAAAGGATGAAAA-CAAAAAAAAAAATTAAAAA
* *
5664330 AAAAAAAAGAGATGAAGGGTAAACACCCAAGAGAAAGGGTGAAAACAAAAAAAAAAAT
1 AAAAAAAAGAGATGAAAGGTAAACACCCAAGAGAAAGGATGAAAACAAAAAAAAAAAT
5664388 GAAGGGTGAA
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
64 13 0.25
65 40 0.75
ACGTcount: A:0.65, C:0.08, G:0.18, T:0.09
Consensus pattern (64 bp):
AAAAAAAAGAGATGAAAGGTAAACACCCAAGAGAAAGGATGAAAACAAAAAAAAAAATTAAAAA
Found at i:5664393 original size:25 final size:26
Alignment explanation
Indices: 5664364--5664412 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
5664354 ACCCAAGAGA
5664364 AAGGGTGAAAACAAAAAA-AAAAATG
1 AAGGGTGAAAACAAAAAAGAAAAATG
*
5664389 AAGGGTGAAACCAAAAAAGAAAAA
1 AAGGGTGAAAACAAAAAAGAAAAA
5664413 ACAGCAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.67, C:0.06, G:0.20, T:0.06
Consensus pattern (26 bp):
AAGGGTGAAAACAAAAAAGAAAAATG
Found at i:5664712 original size:87 final size:87
Alignment explanation
Indices: 5664550--5664711 Score: 245
Period size: 87 Copynumber: 1.9 Consensus size: 87
5664540 TTCACATTAA
* * * *
5664550 TTCATTTGATTTATTTTAGGGTGGTAAAGTTATATATTTTGAATTTTATACACATAAAAATAAAA
1 TTCATTTGATTTATTTAAAGGTGGTAAAGCTATATATTTTAAATTTTATACACATAAAAATAAAA
5664615 AAAAATAAAAATTAAAAGATGG
66 AAAAATAAAAATTAAAAGATGG
* * * *
5664637 TTCATTTGGTTTATTTAAAGGTGGTAAGGCTATATATTTTAAATTTTATATACATAAAAAT-TAA
1 TTCATTTGATTTATTTAAAGGTGGTAAAGCTATATATTTTAAATTTTATACACATAAAAATAAAA
5664701 AAAAATAAAAA
66 AAAAATAAAAA
5664712 ACTGAGCCTC
Statistics
Matches: 67, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
86 13 0.19
87 54 0.81
ACGTcount: A:0.46, C:0.04, G:0.12, T:0.39
Consensus pattern (87 bp):
TTCATTTGATTTATTTAAAGGTGGTAAAGCTATATATTTTAAATTTTATACACATAAAAATAAAA
AAAAATAAAAATTAAAAGATGG
Found at i:5665175 original size:12 final size:12
Alignment explanation
Indices: 5665160--5665209 Score: 59
Period size: 12 Copynumber: 4.3 Consensus size: 12
5665150 TAAATTTAAA
*
5665160 AATAATGTATAT
1 AATAATATATAT
*
5665172 AATATTATATAT
1 AATAATATATAT
*
5665184 ACTAATATATAT
1 AATAATATATAT
5665196 -AT-ATATATAT
1 AATAATATATAT
5665206 AATA
1 AATA
5665210 TTAATTTGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
10 8 0.26
11 3 0.10
12 20 0.65
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (12 bp):
AATAATATATAT
Found at i:5665182 original size:2 final size:2
Alignment explanation
Indices: 5665167--5665210 Score: 51
Period size: 2 Copynumber: 23.5 Consensus size: 2
5665157 AAAAATAATG
5665167 TA TA TA -A TA T- TA TA TA TA CTA -A TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
5665207 -A TA T
1 TA TA T
5665211 TAATTTGGTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
1 4 0.11
2 31 0.84
3 2 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:5665182 original size:10 final size:11
Alignment explanation
Indices: 5665136--5665212 Score: 54
Period size: 10 Copynumber: 7.1 Consensus size: 11
5665126 AATAATAAAA
*
5665136 ATATATATTTT
1 ATATATATATT
*
5665147 ATATAAAT-TT
1 ATATATATATT
* *
5665157 AAAAATA-ATGT
1 ATATATATAT-T
5665168 ATATA-ATATT
1 ATATATATATT
*
5665178 ATATATACTAAT
1 ATATATA-TATT
5665190 ATATATATA-T
1 ATATATATATT
5665200 ATATATAATATT
1 ATATAT-ATATT
5665212 A
1 A
5665213 ATTTGGTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
10 21 0.40
11 19 0.37
12 12 0.23
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (11 bp):
ATATATATATT
Found at i:5670412 original size:28 final size:27
Alignment explanation
Indices: 5670380--5670433 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 27
5670370 AGATTGAAAC
5670380 TTTATACATGTTTGATGTAATTTATTTG
1 TTTATACATGTTTGATGTAA-TTATTTG
**
5670408 TTTATTTATGTTTGATGTAATTATTT
1 TTTATACATGTTTGATGTAATTATTT
5670434 ATTTGTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.24, C:0.02, G:0.13, T:0.61
Consensus pattern (27 bp):
TTTATACATGTTTGATGTAATTATTTG
Found at i:5671384 original size:26 final size:26
Alignment explanation
Indices: 5671339--5671391 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
5671329 ACCCTCATAA
*
5671339 AAAAATATTATACTTAATTATGTTAT
1 AAAAATATTATACTTAATTAAGTTAT
*
5671365 AAAAATATTTATA-TTTATTAAGTTAT
1 AAAAATA-TTATACTTAATTAAGTTAT
5671391 A
1 A
5671392 GTTTTTATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.79
27 5 0.21
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (26 bp):
AAAAATATTATACTTAATTAAGTTAT
Found at i:5672736 original size:20 final size:20
Alignment explanation
Indices: 5672693--5672736 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
5672683 TATTAACTCG
*
5672693 TAAAATATTTTTCATTTGAAA
1 TAAAATATTTTT-ATTTCAAA
5672714 TAAAATATTTATT-TTTCAAA
1 TAAAATATTT-TTATTTCAAA
5672734 TAA
1 TAA
5672737 GTATAAATCT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
21 10 0.48
22 2 0.10
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (20 bp):
TAAAATATTTTTATTTCAAA
Found at i:5690044 original size:25 final size:23
Alignment explanation
Indices: 5689996--5690049 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
5689986 TAAAATTGGA
*
5689996 CTAATTATTAAAAAATGGTTACT
1 CTAATTATTAAAAAATGGTCACT
*
5690019 CTAATTATTGAAAAATGGCCTCACT
1 CTAATTATTAAAAAATGG--TCACT
5690044 CTAATT
1 CTAATT
5690050 TAATTTCAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 17 0.63
25 10 0.37
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (23 bp):
CTAATTATTAAAAAATGGTCACT
Found at i:5696547 original size:48 final size:47
Alignment explanation
Indices: 5696491--5696583 Score: 168
Period size: 48 Copynumber: 2.0 Consensus size: 47
5696481 AGAAAAGAAG
*
5696491 AATTCAAAAGATAAAAAGAAAAGATAGCGTAATAAAAATTAGATTACA
1 AATTCAAAAGATAAAAAGAAAAGATAAC-TAATAAAAATTAGATTACA
5696539 AATTCAAAAGATAAAAAGAAAAGATAACTAATAAAAATTAGATTA
1 AATTCAAAAGATAAAAAGAAAAGATAACTAATAAAAATTAGATTA
5696584 GGGTGTAATC
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 17 0.39
48 27 0.61
ACGTcount: A:0.62, C:0.05, G:0.11, T:0.22
Consensus pattern (47 bp):
AATTCAAAAGATAAAAAGAAAAGATAACTAATAAAAATTAGATTACA
Found at i:5696784 original size:66 final size:66
Alignment explanation
Indices: 5696678--5696805 Score: 238
Period size: 66 Copynumber: 1.9 Consensus size: 66
5696668 ATAGGGGTCC
5696678 CTTTTCGCAAGGTATTCAATACTATTGTGAACAGAGCAAAGTAAGGAATAAAGAATTAGGATCTT
1 CTTTTCGCAAGGTATTCAATACTATTGTGAACAGAGCAAAGTAAGGAATAAAGAATTAGGATCTT
5696743 A
66 A
* *
5696744 CTTTTCGCAAGGTATTCAATACTATTTTGAACAGAGCAAAGTAAGGAATAAATAATTAGGAT
1 CTTTTCGCAAGGTATTCAATACTATTGTGAACAGAGCAAAGTAAGGAATAAAGAATTAGGAT
5696806 GTAATCTTAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.30
Consensus pattern (66 bp):
CTTTTCGCAAGGTATTCAATACTATTGTGAACAGAGCAAAGTAAGGAATAAAGAATTAGGATCTT
A
Found at i:5698456 original size:20 final size:19
Alignment explanation
Indices: 5698396--5698456 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
5698386 TATATGCATT
5698396 TTTACGAAATACATT-TTTA
1 TTTACGAAAT-CATTATTTA
*
5698415 TTTAC-AAATTATTTATTGTA
1 TTTACGAAATCA-TTATT-TA
5698435 TTTACGAACATCATTATTTA
1 TTTACGAA-ATCATTATTTA
5698455 TT
1 TT
5698457 CAAAATCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 1 0.03
18 6 0.17
19 7 0.20
20 11 0.31
21 7 0.20
22 3 0.09
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (19 bp):
TTTACGAAATCATTATTTA
Found at i:5700665 original size:24 final size:24
Alignment explanation
Indices: 5700631--5700691 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
5700621 TAGCAAAAAA
5700631 AAAAAAAAGAAAAACATAACAAGT
1 AAAAAAAAGAAAAACATAACAAGT
* ** **
5700655 AAAAAATAGAACTACATAACAAAA
1 AAAAAAAAGAAAAACATAACAAGT
5700679 AAGAAAAAAGAAA
1 AA-AAAAAAGAAA
5700692 GAATATAGTT
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 21 0.72
25 8 0.28
ACGTcount: A:0.75, C:0.08, G:0.08, T:0.08
Consensus pattern (24 bp):
AAAAAAAAGAAAAACATAACAAGT
Found at i:5701579 original size:3 final size:3
Alignment explanation
Indices: 5701571--5701605 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
5701561 CTCTTCGTCC
*
5701571 TCT TCT TCT TCT TCT TCT TCT TCT TCG TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
5701606 AACAGCTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.00, C:0.34, G:0.03, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:5703897 original size:24 final size:26
Alignment explanation
Indices: 5703864--5703911 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
5703854 ACACGGGCCG
* *
5703864 CTTTCTACCT-GTTTTTTTCTTTCTC
1 CTTTCTACCTCCTCTTTTTCTTTCTC
5703889 CTTT-TACCTCCTCTTTTTCTTTC
1 CTTTCTACCTCCTCTTTTTCTTTC
5703912 CTTTTTCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.04, C:0.31, G:0.02, T:0.62
Consensus pattern (26 bp):
CTTTCTACCTCCTCTTTTTCTTTCTC
Found at i:5718109 original size:42 final size:42
Alignment explanation
Indices: 5718050--5718132 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
5718040 ACTAATGGTT
*
5718050 GCCATAGTCACTATGCCACTTGTTATTTTATGCCATATGCAC
1 GCCATAGTCACTATGCCACTTGTCATTTTATGCCATATGCAC
5718092 GCCATAGTCACTATGCCACTTGTCATTTTATGCCATATGCA
1 GCCATAGTCACTATGCCACTTGTCATTTTATGCCATATGCA
5718133 TTGGCGTGGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (42 bp):
GCCATAGTCACTATGCCACTTGTCATTTTATGCCATATGCAC
Found at i:5739600 original size:18 final size:19
Alignment explanation
Indices: 5739577--5739622 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
5739567 TTCGGCTAAA
*
5739577 TTAATTTGTT-TTCTGTTT
1 TTAATTTGTTATTCTATTT
*
5739595 TTAATTTTGTTATTGTATTT
1 TTAA-TTTGTTATTCTATTT
5739615 TTAATTTG
1 TTAATTTG
5739623 ATTGTTTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 10 0.42
ACGTcount: A:0.17, C:0.02, G:0.11, T:0.70
Consensus pattern (19 bp):
TTAATTTGTTATTCTATTT
Found at i:5741268 original size:15 final size:16
Alignment explanation
Indices: 5741242--5741282 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
5741232 ATTGAATAAT
*
5741242 AAAAATATATTACA-A
1 AAAAATAAATTACATA
*
5741257 ACAAATAAATTACATA
1 AAAAATAAATTACATA
5741273 AAAAATAAAT
1 AAAAATAAAT
5741283 AAAATTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAAATAAATTACATA
Found at i:5741595 original size:22 final size:22
Alignment explanation
Indices: 5741565--5741633 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 22
5741555 AATAATATTG
* *
5741565 ATAACTAAATTATTAATTTTAT
1 ATAATTAAATTATTAATTTTAA
*
5741587 ATAATTAAATATATAAAATTATTAA
1 ATAATTAAAT-TAT-TAATT-TTAA
5741612 ATTAATTAAAATTATTAATTTT
1 A-TAATT-AAATTATTAATTTT
5741634 TTTTTTTTAC
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 9 0.24
23 3 0.08
24 6 0.16
25 8 0.21
26 8 0.21
27 4 0.11
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAATTAAATTATTAATTTTAA
Found at i:5741613 original size:8 final size:8
Alignment explanation
Indices: 5741570--5741629 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
5741560 TATTGATAAC
5741570 TAAATTAT
1 TAAATTAT
5741578 T-AATT-T
1 TAAATTAT
* *
5741584 TATATAAT
1 TAAATTAT
5741592 TAAATATAT
1 TAAAT-TAT
*
5741601 AAAATTAT
1 TAAATTAT
5741609 TAAATTAAT
1 TAAATT-AT
5741618 TAAAATTAT
1 T-AAATTAT
5741627 TAA
1 TAA
5741630 TTTTTTTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
6 2 0.05
7 6 0.15
8 16 0.39
9 12 0.29
10 5 0.12
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TAAATTAT
Found at i:5743327 original size:2 final size:2
Alignment explanation
Indices: 5743320--5743369 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
5743310 AGAGTATGAA
5743320 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5743362 AT AT AT AT
1 AT AT AT AT
5743370 GAAGCCAAGT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5744970 original size:25 final size:25
Alignment explanation
Indices: 5744942--5744995 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
5744932 ATCTCTCATA
* *
5744942 TTTATAGATGTAGGTTACA-TGACTT
1 TTTATAGACGTAGGTTA-AGTGACAT
*
5744967 TTTA-AGACGTGGGTTAAGTGACAT
1 TTTATAGACGTAGGTTAAGTGACAT
5744991 TTTAT
1 TTTAT
5744996 CCAATCATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.04
24 19 0.79
25 4 0.17
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (25 bp):
TTTATAGACGTAGGTTAAGTGACAT
Found at i:5745329 original size:52 final size:51
Alignment explanation
Indices: 5745205--5745452 Score: 177
Period size: 52 Copynumber: 4.9 Consensus size: 51
5745195 TCTTATAAGC
* * * * ***
5745205 CTAAAACCCATCTTATATGTTATTGACGAGAATACACGACAAC-ATATG-T
1 CTAAAACTCATCTTATTTGTTATTGATGTGAATATGTGACAACAATATGCT
* * * * * *
5745254 CTAAAGCCCATAC-TATCTATTATTGATTTGAATATGTGACAATAATATGTCT
1 CTAAAACTCAT-CTTATTTGTTATTGATGTGAATATGTGACAACAATATG-CT
* * * *
5745306 CTAAAACTCATCTTATTTGTTATTAATGTGGATATCG-GATAACAAT-TAGCC
1 CTAAAACTCATCTTATTTGTTATTGATGTGAATAT-GTGACAACAATAT-GCT
* * * *
5745357 CTTAAAACTCATCTTATTTGTTATTGACGTGGATATGTGACAGCAATATACCT
1 C-TAAAACTCATCTTATTTGTTATTGATGTGAATATGTGACAACAATAT-GCT
* *
5745410 TTAAAACTCATCTTATCT-TTATTGATGT-AGATATGTGACAACA
1 CTAAAACTCATCTTATTTGTTATTGATGTGA-ATATGTGACAACA
5745453 TACATTTAAA
Statistics
Matches: 157, Mismatches: 31, Indels: 20
0.75 0.15 0.10
Matches are distributed among these distances:
49 31 0.20
50 6 0.04
51 26 0.17
52 90 0.57
53 4 0.03
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (51 bp):
CTAAAACTCATCTTATTTGTTATTGATGTGAATATGTGACAACAATATGCT
Found at i:5745515 original size:52 final size:51
Alignment explanation
Indices: 5745400--5745525 Score: 134
Period size: 49 Copynumber: 2.5 Consensus size: 51
5745390 TATGTGACAG
* * * * * *
5745400 CAATATACCTTTAAAA-CTCATCTTATCTTTATTGATGTAGATATGTGACAA
1 CAATACACCTTTAAAACCT-ATTTTATCTTTACTGATATAGATATATAACAA
*
5745451 C-ATACA--TTTAAAACCTATTTTATCTATTACTGATATAGATATATAATAA
1 CAATACACCTTTAAAACCTATTTTATCT-TTACTGATATAGATATATAACAA
*
5745500 CAATACACCTTTAAAACTTATTTTAT
1 CAATACACCTTTAAAACCTATTTTAT
5745526 TTGTTATTAA
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
48 15 0.24
49 21 0.34
50 9 0.15
51 1 0.02
52 16 0.26
ACGTcount: A:0.39, C:0.15, G:0.06, T:0.40
Consensus pattern (51 bp):
CAATACACCTTTAAAACCTATTTTATCTTTACTGATATAGATATATAACAA
Found at i:5745544 original size:52 final size:52
Alignment explanation
Indices: 5745273--5745550 Score: 230
Period size: 52 Copynumber: 5.4 Consensus size: 52
5745263 ATACTATCTA
* * * *** *
5745273 TTATTGATTTGAATATGTGACAATAATATGTCTCTAAAACTCATCTTATTTG
1 TTATTGATGTGGATATGTGACAACAATACACCTTTAAAACTCATCTTATTTG
* *
5745325 TTATTAATGTGGATATCG-GATAACAATTAGC-CC-TTAAAACTCATCTTATTTG
1 TTATTGATGTGGATAT-GTGACAACAA-TA-CACCTTTAAAACTCATCTTATTTG
* * * *
5745377 TTATTGACGTGGATATGTGACAGCAATATACCTTTAAAACTCATCTTATCT-
1 TTATTGATGTGGATATGTGACAACAATACACCTTTAAAACTCATCTTATTTG
* * * *
5745428 TTATTGATGTAGATATGTGACAAC-ATACA--TTTAAAAC-CTATTTTATCTA
1 TTATTGATGTGGATATGTGACAACAATACACCTTTAAAACTC-ATCTTATTTG
* * * * * * * *
5745477 TTACTGATATAGATATATAATAACAATACACCTTTAAAACTTATTTTATTTG
1 TTATTGATGTGGATATGTGACAACAATACACCTTTAAAACTCATCTTATTTG
*
5745529 TTATTAATGTGGATATGTGACA
1 TTATTGATGTGGATATGTGACA
5745551 GTAATGCTTT
Statistics
Matches: 180, Mismatches: 34, Indels: 24
0.76 0.14 0.10
Matches are distributed among these distances:
47 1 0.01
48 16 0.09
49 19 0.11
50 9 0.05
51 26 0.14
52 105 0.58
53 4 0.02
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.41
Consensus pattern (52 bp):
TTATTGATGTGGATATGTGACAACAATACACCTTTAAAACTCATCTTATTTG
Found at i:5745587 original size:102 final size:100
Alignment explanation
Indices: 5745400--5745601 Score: 264
Period size: 102 Copynumber: 2.0 Consensus size: 100
5745390 TATGTGACAG
* *
5745400 CAATATACCTTTAAAACTCATCTTATCTTTATTGATGTAGATATGTGACAACATACATTTAAAAC
1 CAATACACCTTTAAAACTCATCTTATCTTTATTAATGTAGATATGTGACAACATACATTTAAAAC
5745465 CTATTTTATCTATTACTGATATAGATATATAATAA
66 CTATTTTATCTATTACTGATATAGATATATAATAA
* * * * * *
5745500 CAATACACCTTTAAAACTTATTTTATTTGTTATTAATGTGGATATGTGACAGTA-ATGCTTTTAA
1 CAATACACCTTTAAAACTCATCTTATCT-TTATTAATGTAGATATGTGACA--ACATACATTTAA
* *
5745564 AA-CTCATTTTATCTATTATTGATATAGATATATGATAA
63 AACCT-ATTTTATCTATTACTGATATAGATATATAATAA
5745602 TAATTTGTTT
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
100 24 0.27
101 22 0.25
102 41 0.47
103 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (100 bp):
CAATACACCTTTAAAACTCATCTTATCTTTATTAATGTAGATATGTGACAACATACATTTAAAAC
CTATTTTATCTATTACTGATATAGATATATAATAA
Found at i:5745652 original size:152 final size:152
Alignment explanation
Indices: 5745267--5745653 Score: 376
Period size: 152 Copynumber: 2.5 Consensus size: 152
5745257 AAGCCCATAC
* * * *
5745267 TATCTATTATTGATTTGAATATGTGACAATAATATGTCTCTAAAACTCATCTTATT-TGTTATTA
1 TATCTATTATTGATTAG-ATATGTGACAATAATATGT-T-TAAAACTCAT-TTTTTCTGTTAATG
* *
5745331 ATGTGGATATCGGATAACAATTAGCCCTTAAAACTCATCTTATTTGTTATTGACGTGGATATGTG
62 ATATGGATATC-GATAACAATTAGCCCTTAAAACTCATCTTATTTGTTATTAACGTGGATATGTG
5745396 ACAGCAATATACCTTTAAAACTCATCT
126 ACAGCAATATACCTTTAAAACTCATCT
* ** * * *
5745423 TATCT-TTATTGATGTAGATATGTGACAA-CATACATTTAAAAC-CTATTTTATCTATTACTGAT
1 TATCTATTATTGAT-TAGATATGTGACAATAATATGTTTAAAACTC-ATTTTTTCTGTTAATGAT
* ** * * *
5745485 ATAGATATATAATAACAA-TA-CACCTTTAAAACTTATTTTATTTGTTATTAATGTGGATATGTG
64 ATGGATAT-CGATAACAATTAGC-CC-TTAAAACTCATCTTATTTGTTATTAACGTGGATATGTG
* * * *
5745548 ACAG-TA-ATGCTTTTAAAACTCATTT
126 ACAGCAATATACCTTTAAAACTCATCT
* * * *
5745573 TATCTATTATTGATATAGATATATGATAATAATTTGTTTAAAACTCATTTTTTCTGTTAATGATC
1 TATCTATTATTGAT-TAGATATGTGACAATAATATGTTTAAAACTCATTTTTTCTGTTAATGATA
5745638 TGGATATGCGATAACA
65 TGGATAT-CGATAACA
5745654 TATTTATTTT
Statistics
Matches: 186, Mismatches: 36, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
150 22 0.12
151 29 0.16
152 103 0.55
153 2 0.01
154 4 0.02
155 19 0.10
156 7 0.04
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.42
Consensus pattern (152 bp):
TATCTATTATTGATTAGATATGTGACAATAATATGTTTAAAACTCATTTTTTCTGTTAATGATAT
GGATATCGATAACAATTAGCCCTTAAAACTCATCTTATTTGTTATTAACGTGGATATGTGACAGC
AATATACCTTTAAAACTCATCT
Found at i:5752705 original size:2 final size:2
Alignment explanation
Indices: 5752688--5752731 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
5752678 AACTAGAAAG
* * *
5752688 AT AT AT AC AT AC AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5752730 AT
1 AT
5752732 CACTAAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:5759471 original size:30 final size:30
Alignment explanation
Indices: 5759437--5759507 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
5759427 AATCATTAAT
* * *
5759437 TATAAAAGCTTATTT-GATTGAAATTAAAAG
1 TATAAGAGCTTATTTAG-CTGAAAATAAAAG
*
5759467 TATAAGGGCTTATTTAGCTGAAAATAAAAG
1 TATAAGAGCTTATTTAGCTGAAAATAAAAG
*
5759497 TACAAGAGCTT
1 TATAAGAGCTT
5759508 GATTAAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 33 0.97
31 1 0.03
ACGTcount: A:0.44, C:0.07, G:0.17, T:0.32
Consensus pattern (30 bp):
TATAAGAGCTTATTTAGCTGAAAATAAAAG
Found at i:5764337 original size:21 final size:21
Alignment explanation
Indices: 5764311--5764352 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5764301 AATATTTATA
5764311 AATGCTATTGA-AGTTGAAATG
1 AATGCTATTGAGA-TTGAAATG
5764332 AATGCTATTGAGATTGAAATG
1 AATGCTATTGAGATTGAAATG
5764353 TCTTTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.38, C:0.05, G:0.24, T:0.33
Consensus pattern (21 bp):
AATGCTATTGAGATTGAAATG
Found at i:5765246 original size:23 final size:23
Alignment explanation
Indices: 5765202--5765247 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
5765192 TTACAATTTT
**
5765202 AACATTTTGTTATTATTTATTAA
1 AACATTTTGTTATTATACATTAA
5765225 AACATTTTGTTATGTA-ACATTAA
1 AACATTTTGTTAT-TATACATTAA
5765248 TGTCTCCACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (23 bp):
AACATTTTGTTATTATACATTAA
Found at i:5766868 original size:34 final size:34
Alignment explanation
Indices: 5766830--5766901 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
5766820 TATATTATTT
5766830 TTGTTAACAATAGTATTTACTAGTTCAATTAAAA
1 TTGTTAACAATAGTATTTACTAGTTCAATTAAAA
* * *
5766864 TTGTTCATAATAGTATTTACTAGTTCCATTAAAA
1 TTGTTAACAATAGTATTTACTAGTTCAATTAAAA
5766898 TTGT
1 TTGT
5766902 GTAGATTAGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (34 bp):
TTGTTAACAATAGTATTTACTAGTTCAATTAAAA
Done.