Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 120 of 210
Found at i:36118240 original size:27 final size:25
Alignment explanation
Indices: 36118210--36118259 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
36118200 GAGAGTTCGA
36118210 AAAAAAAATTCAAAATCGAAAAAAATC
1 AAAAAAAATTCAAAA--GAAAAAAATC
*
36118237 AAAAAAAATTGAAAAGAAAAAAA
1 AAAAAAAATTCAAAAGAAAAAAA
36118260 AATTGCATAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.36
27 14 0.64
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.12
Consensus pattern (25 bp):
AAAAAAAATTCAAAAGAAAAAAATC
Found at i:36122766 original size:23 final size:23
Alignment explanation
Indices: 36122734--36122845 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
36122724 CTTTTTGAAC
* *
36122734 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
36122757 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
36122780 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
36122803 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
36122826 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
36122846 CCCAAAACCG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:36122810 original size:46 final size:46
Alignment explanation
Indices: 36122734--36122845 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
36122724 CTTTTTGAAC
* *
36122734 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
36122780 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
36122826 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
36122846 CCCAAAACCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:36125715 original size:14 final size:14
Alignment explanation
Indices: 36125684--36125728 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
36125674 TTATTTTCTT
*
36125684 TCTTTTTCTTTTCAC
1 TCTTTTTCTTTT-TC
*
36125699 TCTTTTTGTTTTTC
1 TCTTTTTCTTTTTC
36125713 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTC
36125727 TC
1 TC
36125729 GCTCAATAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.73
Consensus pattern (14 bp):
TCTTTTTCTTTTTC
Found at i:36127844 original size:11 final size:11
Alignment explanation
Indices: 36127828--36127867 Score: 59
Period size: 10 Copynumber: 3.9 Consensus size: 11
36127818 ATAATAATAA
36127828 GATTTTTTTTC
1 GATTTTTTTTC
36127839 GA-TTTTTTTC
1 GATTTTTTTTC
36127849 GATTTTTTTT-
1 GATTTTTTTTC
36127859 -ATTTTTTTT
1 GATTTTTTTT
36127868 ACAATCTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.32
10 10 0.36
11 9 0.32
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (11 bp):
GATTTTTTTTC
Found at i:36127867 original size:10 final size:10
Alignment explanation
Indices: 36127828--36127867 Score: 55
Period size: 9 Copynumber: 4.0 Consensus size: 10
36127818 ATAATAATAA
36127828 GATTTTTTTT
1 GATTTTTTTT
*
36127838 CGATTTTTTTC
1 -GATTTTTTTT
36127849 GATTTTTTTT
1 GATTTTTTTT
36127859 -ATTTTTTTT
1 GATTTTTTTT
36127868 ACAATCTCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 9 0.33
10 9 0.33
11 9 0.33
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (10 bp):
GATTTTTTTT
Found at i:36128707 original size:23 final size:24
Alignment explanation
Indices: 36128667--36128713 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
36128657 AAACCTATAC
* *
36128667 CATTTCGTACCTATACCAA-ACCA
1 CATTTCGTACCAAAACCAATACCA
36128690 CATTTCGTACCAAAACCAATACCA
1 CATTTCGTACCAAAACCAATACCA
36128714 TTCCCTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.38, C:0.34, G:0.04, T:0.23
Consensus pattern (24 bp):
CATTTCGTACCAAAACCAATACCA
Found at i:36128972 original size:20 final size:17
Alignment explanation
Indices: 36128933--36128976 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
36128923 AAATCGAAAA
*
36128933 AAATTCAAAAAAAATTG
1 AAATTAAAAAAAAATTG
36128950 AAATTAAAAAAAATATTACG
1 AAATTAAAAAAAA-ATT--G
36128970 AAATTAA
1 AAATTAA
36128977 TTAGAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
20 8 0.35
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (17 bp):
AAATTAAAAAAAAATTG
Found at i:36129780 original size:52 final size:51
Alignment explanation
Indices: 36129698--36129803 Score: 167
Period size: 52 Copynumber: 2.1 Consensus size: 51
36129688 TACCATAAGG
* * *
36129698 AAACATAATGGACAGCAACTTAAGATCTCATTTCTAGCTCGGTTGAAGCTC
1 AAACATAATAGACAACAACTTAAGACCTCATTTCTAGCTCGGTTGAAGCTC
*
36129749 AAACAATAATAGACAACAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTC
1 AAAC-ATAATAGACAACAACTTAAGACCTCATTTCTAGCTCGGTTGAAGCTC
36129801 AAA
1 AAA
36129804 TATGTGCATG
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
51 4 0.08
52 46 0.92
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (51 bp):
AAACATAATAGACAACAACTTAAGACCTCATTTCTAGCTCGGTTGAAGCTC
Found at i:36130884 original size:8 final size:9
Alignment explanation
Indices: 36130866--36130892 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
36130856 AATCTGATTC
36130866 AAAAATAAA
1 AAAAATAAA
36130875 AAAAATAAA
1 AAAAATAAA
36130884 AAAAATAAA
1 AAAAATAAA
36130893 GGAGGAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAATAAA
Found at i:36133142 original size:23 final size:23
Alignment explanation
Indices: 36133107--36133218 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
36133097 CGGTTTTGGG
* *
36133107 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
36133130 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
36133153 TTTGGTACGAATTGGTAAGGTGA
1 TTTGGTACGAAATGGTAATGCGA
* *
36133176 TTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
*
36133199 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
36133219 GTTCAAAAAG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATGCGA
Found at i:36133169 original size:46 final size:46
Alignment explanation
Indices: 36133107--36133218 Score: 179
Period size: 46 Copynumber: 2.4 Consensus size: 46
36133097 CGGTTTTGGG
*
36133107 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
* * *
36133153 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
*
36133199 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
36133219 GTTCAAAAAG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
Found at i:36136468 original size:27 final size:27
Alignment explanation
Indices: 36136438--36136492 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
36136428 CGATCAATTT
36136438 CACTTTTTGCTGGAGTTCGACAATTAG
1 CACTTTTTGCTGGAGTTCGACAATTAG
36136465 CACTTTTTGCTGGAGTTCGACAATTAG
1 CACTTTTTGCTGGAGTTCGACAATTAG
36136492 C
1 C
36136493 CCTAAATCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (27 bp):
CACTTTTTGCTGGAGTTCGACAATTAG
Found at i:36139773 original size:23 final size:23
Alignment explanation
Indices: 36139741--36139852 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
36139731 CTTTCTGAAC
* *
36139741 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
36139764 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
36139787 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
36139810 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
36139833 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
36139853 CCCAAAACCG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:36139817 original size:46 final size:46
Alignment explanation
Indices: 36139741--36139852 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
36139731 CTTTCTGAAC
* *
36139741 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
36139787 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
36139833 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
36139853 CCCAAAACCG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:36142722 original size:14 final size:14
Alignment explanation
Indices: 36142691--36142735 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
36142681 TTATTTTCTT
*
36142691 TCTTTTTCTTTTCAC
1 TCTTTTTCTTTT-TC
*
36142706 TCTTTTTGTTTTTC
1 TCTTTTTCTTTTTC
36142720 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTC
36142734 TC
1 TC
36142736 GCTCAATAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 16 0.59
15 11 0.41
ACGTcount: A:0.02, C:0.22, G:0.02, T:0.73
Consensus pattern (14 bp):
TCTTTTTCTTTTTC
Found at i:36144852 original size:11 final size:11
Alignment explanation
Indices: 36144836--36144875 Score: 59
Period size: 10 Copynumber: 3.9 Consensus size: 11
36144826 ATAATAATAA
36144836 GATTTTTTTTC
1 GATTTTTTTTC
36144847 GA-TTTTTTTC
1 GATTTTTTTTC
36144857 GATTTTTTTT-
1 GATTTTTTTTC
36144867 -ATTTTTTTT
1 GATTTTTTTT
36144876 ACAATCTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.32
10 10 0.36
11 9 0.32
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (11 bp):
GATTTTTTTTC
Found at i:36144875 original size:10 final size:10
Alignment explanation
Indices: 36144836--36144875 Score: 55
Period size: 9 Copynumber: 4.0 Consensus size: 10
36144826 ATAATAATAA
36144836 GATTTTTTTT
1 GATTTTTTTT
*
36144846 CGATTTTTTTC
1 -GATTTTTTTT
36144857 GATTTTTTTT
1 GATTTTTTTT
36144867 -ATTTTTTTT
1 GATTTTTTTT
36144876 ACAATCTCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 9 0.33
10 9 0.33
11 9 0.33
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (10 bp):
GATTTTTTTT
Found at i:36149821 original size:52 final size:52
Alignment explanation
Indices: 36149734--36149834 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
36149724 TAAGGAAACG
* * *
36149734 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAACAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
36149786 TAATAGACAACAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAACAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
36149835 TATGTGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (52 bp):
TAATAGACAACAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:36156868 original size:20 final size:20
Alignment explanation
Indices: 36156832--36156873 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
36156822 ACAAACTGAC
36156832 AAATAAAAACCAGAATT-AT
1 AAATAAAAACCAGAATTGAT
*
36156851 AAATAAAAACCATTAATTGAT
1 AAATAAAAACCA-GAATTGAT
36156872 AA
1 AA
36156874 GTTTAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 4 0.20
21 4 0.20
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (20 bp):
AAATAAAAACCAGAATTGAT
Found at i:36157347 original size:19 final size:19
Alignment explanation
Indices: 36157323--36157359 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
36157313 CCCACCCCAA
36157323 ATACAG-ATACAAAATACAT
1 ATACAGTATAC-AAATACAT
36157342 ATACAGTATACAAATACA
1 ATACAGTATACAAATACA
36157360 GAAATAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.57, C:0.16, G:0.05, T:0.22
Consensus pattern (19 bp):
ATACAGTATACAAATACAT
Found at i:36158756 original size:20 final size:20
Alignment explanation
Indices: 36158733--36158779 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
36158723 GGGTTAAAAT
*
36158733 TGAGCTGAATTGATCTCAAA
1 TGAGCTGAATTGAGCTCAAA
* *
36158753 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAA
36158773 TGAGCTG
1 TGAGCTG
36158780 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAA
Found at i:36160683 original size:12 final size:12
Alignment explanation
Indices: 36160650--36160730 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
36160640 TTTCCACTCG
36160650 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
36160661 AGCTCTCTTTCA
1 ATTTCTTTTTCA
36160673 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
36160686 CCCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
36160699 --TTCTCTTTCA
1 ATTTCTTTTTCA
36160709 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
36160721 ATCTCTTTTT
1 ATTTCTTTTT
36160731 GCTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.26, G:0.01, T:0.60
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:36160783 original size:15 final size:15
Alignment explanation
Indices: 36160760--36160806 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
36160750 TTTTGAAATC
36160760 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
36160775 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
36160790 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
36160806 T
1 T
36160807 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:36161869 original size:14 final size:15
Alignment explanation
Indices: 36161852--36161891 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
36161842 CTTTTCACTT
36161852 CTTTTTTTTTACTC-
1 CTTTTTTTTTACTCA
*
36161866 CTTTTTTTTTGCTCA
1 CTTTTTTTTTACTCA
36161881 CTTCTTTTTTT
1 CTT-TTTTTTT
36161892 TTCGAATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 3 0.13
16 7 0.30
ACGTcount: A:0.05, C:0.20, G:0.03, T:0.72
Consensus pattern (15 bp):
CTTTTTTTTTACTCA
Found at i:36161887 original size:18 final size:16
Alignment explanation
Indices: 36161843--36161893 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 16
36161833 CTCGCAAGAC
36161843 TTTTCACTTC-TTTTT
1 TTTTCACTTCTTTTTT
*
36161858 TTTT-ACTCCTTTTTT
1 TTTTCACTTCTTTTTT
36161873 TTTGCTCACTTCTTTTTT
1 TTT--TCACTTCTTTTTT
36161891 TTT
1 TTT
36161894 CGAATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
14 4 0.13
15 12 0.40
17 1 0.03
18 13 0.43
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.73
Consensus pattern (16 bp):
TTTTCACTTCTTTTTT
Found at i:36161903 original size:32 final size:31
Alignment explanation
Indices: 36161846--36161909 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 31
36161836 GCAAGACTTT
*
36161846 TCACTTCTTTTTTTTTACTCCTTTTTTTTTGC
1 TCACTTCTTTTTTTTTAAT-CTTTTTTTTTGC
*
36161878 TCACTTCTTTTTTTTTCGAATTTTTTTTTTTG
1 TCACTTCTTTTTTTTT--AATCTTTTTTTTTG
36161910 AATTTTGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 16 0.57
33 10 0.36
34 2 0.07
ACGTcount: A:0.08, C:0.17, G:0.05, T:0.70
Consensus pattern (31 bp):
TCACTTCTTTTTTTTTAATCTTTTTTTTTGC
Found at i:36161921 original size:16 final size:14
Alignment explanation
Indices: 36161885--36161925 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
36161875 TGCTCACTTC
*
36161885 TTTTTTTTTCGAAT
1 TTTTTTTTTTGAAT
36161899 TTTTTTTTTTGAAT
1 TTTTTTTTTTGAAT
36161913 TTTGATTTTTTTG
1 TTT--TTTTTTTG
36161926 TGATACTCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 16 0.67
16 8 0.33
ACGTcount: A:0.12, C:0.02, G:0.10, T:0.76
Consensus pattern (14 bp):
TTTTTTTTTTGAAT
Found at i:36179879 original size:20 final size:20
Alignment explanation
Indices: 36179854--36179891 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
36179844 AAATTAAACC
*
36179854 AAGCTAGGTTTGAGCTTATT
1 AAGCTAAGTTTGAGCTTATT
36179874 AAGCTAAGTTTGAGCTTA
1 AAGCTAAGTTTGAGCTTA
36179892 GTTCAGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (20 bp):
AAGCTAAGTTTGAGCTTATT
Found at i:36180487 original size:39 final size:39
Alignment explanation
Indices: 36180438--36180563 Score: 200
Period size: 39 Copynumber: 3.3 Consensus size: 39
36180428 TTTGGTTTGA
* * *
36180438 GTCTATAATTATGTCTTAGTTTGAAAATCATTAATATAT
1 GTCTTTAATTATGTCTTAGTTTGAACATCATTAATATGT
*
36180477 GTCTTTAATTATGTCTTATTTTGAACATCATTAATATGT
1 GTCTTTAATTATGTCTTAGTTTGAACATCATTAATATGT
*
36180516 GTCTTTAATTATGTCATAGTTTGAACATCATTAATATGT
1 GTCTTTAATTATGTCTTAGTTTGAACATCATTAATATGT
36180555 GT-TTTAATT
1 GTCTTTAATT
36180564 GTGTGTCTTA
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
38 7 0.09
39 74 0.91
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.49
Consensus pattern (39 bp):
GTCTTTAATTATGTCTTAGTTTGAACATCATTAATATGT
Found at i:36181638 original size:20 final size:20
Alignment explanation
Indices: 36181613--36181668 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
36181603 TCTATGCGGT
36181613 TCAGCTCATTCGAGCTCAAG
1 TCAGCTCATTCGAGCTCAAG
** **
36181633 TCAGCTCACACGAGCTCATT
1 TCAGCTCATTCGAGCTCAAG
36181653 TCAGCTCATT-GAGCTC
1 TCAGCTCATTCGAGCTC
36181669 GTTATTAGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 6 0.20
20 24 0.80
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (20 bp):
TCAGCTCATTCGAGCTCAAG
Found at i:36183082 original size:20 final size:20
Alignment explanation
Indices: 36183054--36183098 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
36183044 TAATGTGTCT
36183054 TGTCCTAACCGAATTAATTG
1 TGTCCTAACCGAATTAATTG
* **
36183074 TGTCTTAACTTAATTAATTG
1 TGTCCTAACCGAATTAATTG
36183094 TGTCC
1 TGTCC
36183099 AATTTTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (20 bp):
TGTCCTAACCGAATTAATTG
Found at i:36184050 original size:23 final size:24
Alignment explanation
Indices: 36184010--36184056 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
36184000 AAACCTATAC
* *
36184010 CATTTCGTACCTATACCAA-ACCA
1 CATTTCGTACCAAAACCAATACCA
36184033 CATTTCGTACCAAAACCAATACCA
1 CATTTCGTACCAAAACCAATACCA
36184057 TTCCCTAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.38, C:0.34, G:0.04, T:0.23
Consensus pattern (24 bp):
CATTTCGTACCAAAACCAATACCA
Found at i:36184315 original size:20 final size:17
Alignment explanation
Indices: 36184276--36184319 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
36184266 AAATCGAAAA
*
36184276 AAATTCAAAAAAAATTG
1 AAATTAAAAAAAAATTG
36184293 AAATTAAAAAAAATATTACG
1 AAATTAAAAAAAA-ATT--G
36184313 AAATTAA
1 AAATTAA
36184320 TTAGAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 12 0.52
18 3 0.13
20 8 0.35
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (17 bp):
AAATTAAAAAAAAATTG
Found at i:36186303 original size:9 final size:9
Alignment explanation
Indices: 36186289--36186317 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
36186279 TACTGAATTC
36186289 AAAAAATAA
1 AAAAAATAA
36186298 AAAAAATAA
1 AAAAAATAA
36186307 AAAAAATAA
1 AAAAAATAA
36186316 AA
1 AA
36186318 GGAAGGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.90, C:0.00, G:0.00, T:0.10
Consensus pattern (9 bp):
AAAAAATAA
Found at i:36196579 original size:15 final size:14
Alignment explanation
Indices: 36196559--36196608 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
36196549 ATAGGTACGT
36196559 AAAAAAAAAGTTCG
1 AAAAAAAAAGTTCG
* *
36196573 AAAAAAAAATTTTG
1 AAAAAAAAAGTTCG
36196587 AAAAAAAAA--TCG
1 AAAAAAAAAGTTCG
36196599 AAAGAAAAAA
1 AAA-AAAAAA
36196609 AAAGAAGAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
12 5 0.16
13 6 0.19
14 21 0.66
ACGTcount: A:0.72, C:0.04, G:0.10, T:0.14
Consensus pattern (14 bp):
AAAAAAAAAGTTCG
Found at i:36200991 original size:22 final size:22
Alignment explanation
Indices: 36200966--36201118 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
36200956 TTTCGATAGT
*
36200966 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
36200988 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
36201010 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
36201032 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
36201054 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
36201076 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
36201098 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
36201119 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:36203180 original size:11 final size:11
Alignment explanation
Indices: 36203164--36203203 Score: 59
Period size: 10 Copynumber: 3.9 Consensus size: 11
36203154 ATAATAATAA
36203164 GATTTTTTTTC
1 GATTTTTTTTC
36203175 GA-TTTTTTTC
1 GATTTTTTTTC
36203185 GATTTTTTTT-
1 GATTTTTTTTC
36203195 -ATTTTTTTT
1 GATTTTTTTT
36203204 ACAATCTCGT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.32
10 10 0.36
11 9 0.32
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (11 bp):
GATTTTTTTTC
Found at i:36203203 original size:10 final size:10
Alignment explanation
Indices: 36203164--36203203 Score: 55
Period size: 9 Copynumber: 4.0 Consensus size: 10
36203154 ATAATAATAA
36203164 GATTTTTTTT
1 GATTTTTTTT
*
36203174 CGATTTTTTTC
1 -GATTTTTTTT
36203185 GATTTTTTTT
1 GATTTTTTTT
36203195 -ATTTTTTTT
1 GATTTTTTTT
36203204 ACAATCTCGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
9 9 0.33
10 9 0.33
11 9 0.33
ACGTcount: A:0.10, C:0.05, G:0.07, T:0.78
Consensus pattern (10 bp):
GATTTTTTTT
Found at i:36208144 original size:52 final size:52
Alignment explanation
Indices: 36208057--36208157 Score: 175
Period size: 52 Copynumber: 1.9 Consensus size: 52
36208047 TAAGGAAACG
* * *
36208057 TAATGGACAGCAGCTTAAGATCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
1 TAATAGACAACAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
36208109 TAATAGACAACAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
1 TAATAGACAACAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAA
36208158 TATGTGCATG
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.27
Consensus pattern (52 bp):
TAATAGACAACAGCTTAAGACCTCATTTCTAGCTCGGTTGAAGCTCAAACAA
Found at i:36215196 original size:20 final size:20
Alignment explanation
Indices: 36215160--36215201 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
36215150 ACAAACTGAC
36215160 AAATAAAAACCAGAATT-AT
1 AAATAAAAACCAGAATTGAT
*
36215179 AAATAAAAACCATTAATTGAT
1 AAATAAAAACCA-GAATTGAT
36215200 AA
1 AA
36215202 GTTTAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 4 0.20
21 4 0.20
ACGTcount: A:0.62, C:0.10, G:0.05, T:0.24
Consensus pattern (20 bp):
AAATAAAAACCAGAATTGAT
Found at i:36215675 original size:19 final size:19
Alignment explanation
Indices: 36215651--36215687 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
36215641 CCCACCCCAA
36215651 ATACAG-ATACAAAATACAT
1 ATACAGTATAC-AAATACAT
36215670 ATACAGTATACAAATACA
1 ATACAGTATACAAATACA
36215688 GAAATAACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.57, C:0.16, G:0.05, T:0.22
Consensus pattern (19 bp):
ATACAGTATACAAATACAT
Found at i:36217084 original size:20 final size:20
Alignment explanation
Indices: 36217061--36217107 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
36217051 GGGTTAAAAT
*
36217061 TGAGCTGAATTGATCTCAAA
1 TGAGCTGAATTGAGCTCAAA
* *
36217081 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAA
36217101 TGAGCTG
1 TGAGCTG
36217108 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAA
Found at i:36219012 original size:12 final size:12
Alignment explanation
Indices: 36218979--36219059 Score: 53
Period size: 12 Copynumber: 6.8 Consensus size: 12
36218969 TTTCCACTCG
36218979 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
36218990 AGCTCTCTTTCA
1 ATTTCTTTTTCA
36219002 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
*
36219015 CCCTTTCTTTTTC-
1 --ATTTCTTTTTCA
*
36219028 --TTCTCTTTCA
1 ATTTCTTTTTCA
36219038 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
36219050 ATCTCTTTTT
1 ATTTCTTTTT
36219060 GCTTTTCACT
Statistics
Matches: 53, Mismatches: 10, Indels: 13
0.70 0.13 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.57
13 2 0.04
14 1 0.02
15 9 0.17
ACGTcount: A:0.12, C:0.26, G:0.01, T:0.60
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:36219112 original size:15 final size:15
Alignment explanation
Indices: 36219089--36219135 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
36219079 TTTTGAAATC
36219089 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
36219104 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
36219119 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
36219135 T
1 T
36219136 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:36240846 original size:14 final size:14
Alignment explanation
Indices: 36240827--36240881 Score: 56
Period size: 14 Copynumber: 3.8 Consensus size: 14
36240817 TCTATTGAGC
36240827 GAGAAAAAGAAAAA
1 GAGAAAAAGAAAAA
*
36240841 GAGAAAAACAAAAA
1 GAGAAAAAGAAAAA
* *
36240855 GAGTGAAATGAAAAA
1 GAG-AAAAAGAAAAA
*
36240870 GAAAGAAAAGAA
1 GAGA-AAAAGAA
36240882 TGATGAGAGT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
14 16 0.50
15 16 0.50
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.04
Consensus pattern (14 bp):
GAGAAAAAGAAAAA
Found at i:36247098 original size:22 final size:22
Alignment explanation
Indices: 36247036--36247107 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
36247026 TCTGTTCAAA
* **
36247036 CATGAGAGCTTAGTACGTGAAA
1 CATGAGAGCTTAGTACGTTAGC
36247058 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
36247080 CATGAGAGCTTAGTACGTTAGC
1 CATGAGAGCTTAGTACGTTAGC
36247102 CATGAG
1 CATGAG
36247108 GGTTTACCTC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.25
Consensus pattern (22 bp):
CATGAGAGCTTAGTACGTTAGC
Found at i:36260722 original size:26 final size:26
Alignment explanation
Indices: 36260676--36260728 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
36260666 CTCATTTGAG
36260676 TTAATAAATTCTCTTTAAGTTTTCTTT
1 TTAATAAATTCTCTTTAAG-TTTCTTT
* *
36260703 TTAATAATTTCTC-TTGAGTTTCTTT
1 TTAATAAATTCTCTTTAAGTTTCTTT
36260728 T
1 T
36260729 AGAAGAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 8 0.33
26 4 0.17
27 12 0.50
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (26 bp):
TTAATAAATTCTCTTTAAGTTTCTTT
Found at i:36266574 original size:14 final size:13
Alignment explanation
Indices: 36266556--36266591 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
36266546 AAAGTGAGAG
36266556 AAAAAGAAAATAA
1 AAAAAGAAAATAA
*
36266569 AGAAAAGAAAATTA
1 A-AAAAGAAAATAA
36266583 AAAAAGAAA
1 AAAAAGAAA
36266592 TTGAGATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 9 0.43
14 12 0.57
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (13 bp):
AAAAAGAAAATAA
Found at i:36266621 original size:18 final size:18
Alignment explanation
Indices: 36266585--36266623 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
36266575 GAAAATTAAA
* **
36266585 AAAGAAATTGAGATTGAG
1 AAAGAAATTGAAAAAGAG
36266603 AAAGAAATTGAAAAAGAG
1 AAAGAAATTGAAAAAGAG
36266621 AAA
1 AAA
36266624 ATCGAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (18 bp):
AAAGAAATTGAAAAAGAG
Found at i:36270894 original size:20 final size:20
Alignment explanation
Indices: 36270863--36270998 Score: 175
Period size: 20 Copynumber: 6.8 Consensus size: 20
36270853 AGCTAATAAC
*
36270863 GAGCTC-AATGAGCTGAATT
1 GAGCTCGAATGAGCTGACTT
* ** *
36270882 GAGCTTGTGTGAGGTGACTT
1 GAGCTCGAATGAGCTGACTT
36270902 GAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTGACTT
*
36270922 GAGCTCGAATAAGCTGACTT
1 GAGCTCGAATGAGCTGACTT
* * *
36270942 GAGCTTGAATGAGTTGGCTT
1 GAGCTCGAATGAGCTGACTT
36270962 GAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTGACTT
*
36270982 GAGCTCGAGTGAGCTGA
1 GAGCTCGAATGAGCTGA
36270999 ACCGCATGGA
Statistics
Matches: 98, Mismatches: 18, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
19 5 0.05
20 93 0.95
ACGTcount: A:0.24, C:0.16, G:0.32, T:0.27
Consensus pattern (20 bp):
GAGCTCGAATGAGCTGACTT
Found at i:36270945 original size:60 final size:60
Alignment explanation
Indices: 36270863--36270999 Score: 204
Period size: 60 Copynumber: 2.3 Consensus size: 60
36270853 AGCTAATAAC
**
36270863 GAGCTC-AATGAGCTGAATTGAGCTTGTGTGAGGTGACTTGAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTGAATTGAGCTTGAATGAGGTGACTTGAGCTCGAATGAGCTGACTT
* * * *
36270922 GAGCTCGAATAAGCTGACTTGAGCTTGAATGAGTTGGCTTGAGCTCGAATGAGCTGACTT
1 GAGCTCGAATGAGCTGAATTGAGCTTGAATGAGGTGACTTGAGCTCGAATGAGCTGACTT
*
36270982 GAGCTCGAGTGAGCTGAA
1 GAGCTCGAATGAGCTGAA
36271000 CCGCATGGAA
Statistics
Matches: 68, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
59 6 0.09
60 62 0.91
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.27
Consensus pattern (60 bp):
GAGCTCGAATGAGCTGAATTGAGCTTGAATGAGGTGACTTGAGCTCGAATGAGCTGACTT
Found at i:36271024 original size:60 final size:59
Alignment explanation
Indices: 36270900--36271024 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 59
36270890 GTGAGGTGAC
* * * *
36270900 TTGAGCTCGAATGAGCTGACTTGAGCTCGAATAAGCTGACTTGAGCTTGAATGAGTTGGC
1 TTGAGCTCGAATGAGCTGACTTGAGCTCGAATAAGCTGACTCGA-CTGGAATAAGTTGGA
* * *
36270960 TTGAGCTCGAATGAGCTGACTTGAGCTCGAGTGAGCTGAAC-CG-CATGGAAATAAGTTTGA
1 TTGAGCTCGAATGAGCTGACTTGAGCTCGAATAAGCTG-ACTCGAC-TGG-AATAAGTTGGA
36271020 TTGAG
1 TTGAG
36271025 TTGAAAATGA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
58 1 0.02
59 2 0.04
60 50 0.91
61 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.27
Consensus pattern (59 bp):
TTGAGCTCGAATGAGCTGACTTGAGCTCGAATAAGCTGACTCGACTGGAATAAGTTGGA
Found at i:36295157 original size:22 final size:22
Alignment explanation
Indices: 36295095--36295158 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
36295085 TATTTAGGAA
*
36295095 TTGGTACGAAATGGTATGGAAG
1 TTGGTACGAAATGGTATGGTAG
*
36295117 TTGGTACGAAATGGTATGGTAT
1 TTGGTACGAAATGGTATGGTAG
*
36295139 TTGGTA-GAATTGGTAATGGT
1 TTGGTACGAAATGGT-ATGGT
36295159 TCAAAAAGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 7 0.18
22 31 0.82
ACGTcount: A:0.28, C:0.03, G:0.34, T:0.34
Consensus pattern (22 bp):
TTGGTACGAAATGGTATGGTAG
Found at i:36296248 original size:10 final size:10
Alignment explanation
Indices: 36296233--36296274 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
36296223 TTTGCAAGTT
36296233 TTGAGCTAAA
1 TTGAGCTAAA
* *
36296243 TTGAGCTGAT
1 TTGAGCTAAA
*
36296253 TTGAGCT-CA
1 TTGAGCTAAA
36296262 TTGAGCTAAA
1 TTGAGCTAAA
36296272 TTG
1 TTG
36296275 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:36297347 original size:21 final size:21
Alignment explanation
Indices: 36297321--36297383 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
36297311 TTGGTATTTG
36297321 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
36297342 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* * *
36297363 GGTATTTGGCACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
36297384 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 22 0.61
22 14 0.39
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:36297352 original size:11 final size:11
Alignment explanation
Indices: 36297332--36297364 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
36297322 GAATTGGTAC
36297332 GAAATGGTATG
1 GAAATGGTATG
*
36297343 GAATTGGTAT-
1 GAAATGGTATG
36297353 GAAATGGTATG
1 GAAATGGTATG
36297364 G
1 G
36297365 TATTTGGCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:36298574 original size:30 final size:30
Alignment explanation
Indices: 36298516--36298574 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
36298506 TTGAAAAGGT
* *
36298516 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
36298546 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
36298575 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:36305171 original size:13 final size:13
Alignment explanation
Indices: 36305153--36305177 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36305143 ATGAAAATAA
36305153 AAAACCTCACAAC
1 AAAACCTCACAAC
36305166 AAAACCTCACAA
1 AAAACCTCACAA
36305178 ATCTCTCGAA
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:0.56, C:0.36, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAACCTCACAAC
Found at i:36305653 original size:18 final size:18
Alignment explanation
Indices: 36305630--36305669 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
36305620 CCGTATACAA
36305630 TTTTTTCTTTC-AATTTT
1 TTTTTTCTTTCGAATTTT
36305647 GTTTTTTCTTTCGAATTTT
1 -TTTTTTCTTTCGAATTTT
36305666 TTTT
1 TTTT
36305670 GTTTTTGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.75
Consensus pattern (18 bp):
TTTTTTCTTTCGAATTTT
Found at i:36305680 original size:28 final size:28
Alignment explanation
Indices: 36305643--36305696 Score: 92
Period size: 29 Copynumber: 1.9 Consensus size: 28
36305633 TTTCTTTCAA
36305643 TTTTGTTTTTTCTTTCGAATTTTTTTTGT
1 TTTTGTTTTTTCTTTC-AATTTTTTTTGT
36305672 TTTTGTTTTTT-TTTCAATTTTTTTT
1 TTTTGTTTTTTCTTTCAATTTTTTTT
36305697 CGAACTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 10 0.40
28 4 0.16
29 11 0.44
ACGTcount: A:0.07, C:0.06, G:0.07, T:0.80
Consensus pattern (28 bp):
TTTTGTTTTTTCTTTCAATTTTTTTTGT
Found at i:36305692 original size:11 final size:13
Alignment explanation
Indices: 36305678--36305709 Score: 50
Period size: 11 Copynumber: 2.6 Consensus size: 13
36305668 TTGTTTTTGT
36305678 TTTTTTTTC-AA-
1 TTTTTTTTCGAAC
36305689 TTTTTTTTCGAAC
1 TTTTTTTTCGAAC
36305702 TTTTTTTT
1 TTTTTTTT
36305710 ACGTACCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.12, C:0.09, G:0.03, T:0.75
Consensus pattern (13 bp):
TTTTTTTTCGAAC
Found at i:36306034 original size:21 final size:21
Alignment explanation
Indices: 36306008--36306070 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
36305998 TTGGTATTTG
36306008 GGAATTGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
*
36306029 GGAATTGGTATGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* * *
36306050 GGTATTTGGCACGAATTGGTA
1 GG-AATTGGTACGAAATGGTA
36306071 ATGGTTCAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
21 22 0.61
22 14 0.39
ACGTcount: A:0.30, C:0.05, G:0.33, T:0.32
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:36306039 original size:11 final size:11
Alignment explanation
Indices: 36306019--36306051 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
36306009 GAATTGGTAC
36306019 GAAATGGTATG
1 GAAATGGTATG
*
36306030 GAATTGGTAT-
1 GAAATGGTATG
36306040 GAAATGGTATG
1 GAAATGGTATG
36306051 G
1 G
36306052 TATTTGGCAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (11 bp):
GAAATGGTATG
Found at i:36307263 original size:30 final size:30
Alignment explanation
Indices: 36307205--36307263 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
36307195 TTGAAAAGGT
* *
36307205 TTGAGCTGAAGTTGAGCTAATTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
*
36307235 TTGAGCTGAAATGGAAGTTAATTC-AGCTC
1 TTGAGCTGAAATGG-AGCTAATTCGAGCTC
36307264 GTATTAAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:36308182 original size:20 final size:19
Alignment explanation
Indices: 36308139--36308186 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
36308129 TTTCTTTTCA
*
36308139 CTTTCTTTTTTTGAATTTT
1 CTTTCTTTTTTTCAATTTT
*
36308158 CTTTCTTTTTTTCATTTTT
1 CTTTCTTTTTTTCAATTTT
36308177 CTTTTCTTTT
1 C-TTTCTTTT
36308187 GTATTTTCGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 18 0.69
20 8 0.31
ACGTcount: A:0.06, C:0.15, G:0.02, T:0.77
Consensus pattern (19 bp):
CTTTCTTTTTTTCAATTTT
Found at i:36310289 original size:9 final size:9
Alignment explanation
Indices: 36310277--36310329 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
36310267 AAAAATTGAA
36310277 AAAAAAATC
1 AAAAAAATC
36310286 AAAAAAATC
1 AAAAAAATC
**
36310295 AAAAAAAGA
1 AAAAAAATC
*
36310304 AAAATAAATT
1 AAAA-AAATC
*
36310314 AAAAAAA-G
1 AAAAAAATC
36310322 AAAAAAAT
1 AAAAAAAT
36310330 TGTATACGGT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
8 7 0.19
9 23 0.62
10 7 0.19
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.11
Consensus pattern (9 bp):
AAAAAAATC
Found at i:36310312 original size:19 final size:18
Alignment explanation
Indices: 36310286--36310328 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
36310276 AAAAAAAATC
36310286 AAAAAAATCAAAAAAAGA
1 AAAAAAATCAAAAAAAGA
*
36310304 AAAATAAATTAAAAAAAGA
1 AAAA-AAATCAAAAAAAGA
36310323 AAAAAA
1 AAAAAA
36310329 TTGTATACGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.84, C:0.02, G:0.05, T:0.09
Consensus pattern (18 bp):
AAAAAAATCAAAAAAAGA
Found at i:36312652 original size:20 final size:20
Alignment explanation
Indices: 36312627--36312669 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
36312617 AAAAGAAAAG
36312627 AAAGAAGAGAGATTGAGAGA
1 AAAGAAGAGAGATTGAGAGA
** *
36312647 AAAGAATCGAGATTGTGAGA
1 AAAGAAGAGAGATTGAGAGA
36312667 AAA
1 AAA
36312670 ACAAGAACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.30, T:0.14
Consensus pattern (20 bp):
AAAGAAGAGAGATTGAGAGA
Found at i:36313802 original size:57 final size:57
Alignment explanation
Indices: 36313709--36313820 Score: 197
Period size: 57 Copynumber: 2.0 Consensus size: 57
36313699 AGGGAGGGGA
*
36313709 TGATACGACCCGCCCCCGGGAACGGCCATTGTTTCAGCCTACAAGCGAGGCTCGTCG
1 TGATACGACCCGCCCCCGGGAACGGCCATTGCTTCAGCCTACAAGCGAGGCTCGTCG
**
36313766 TGATACGACCCGCCCTTGGGAACGGCCATTGCTTCAGCCTACAAGCGAGGCTCGT
1 TGATACGACCCGCCCCCGGGAACGGCCATTGCTTCAGCCTACAAGCGAGGCTCGT
36313821 TGTGTTTACA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.20, C:0.34, G:0.28, T:0.19
Consensus pattern (57 bp):
TGATACGACCCGCCCCCGGGAACGGCCATTGCTTCAGCCTACAAGCGAGGCTCGTCG
Found at i:36315220 original size:46 final size:46
Alignment explanation
Indices: 36315148--36315246 Score: 162
Period size: 46 Copynumber: 2.2 Consensus size: 46
36315138 TAACATTTCA
*
36315148 TACCAAATCGTATTACCATTTCGAACCAAATCACCTTACCAATTCG
1 TACCAAATCGTATTACCATTTCGAACCAAATCACATTACCAATTCG
* *
36315194 TACCAAATCGTATTACCATTTTGAACCAAATCACATTACCATTTCG
1 TACCAAATCGTATTACCATTTCGAACCAAATCACATTACCAATTCG
*
36315240 TAACAAA
1 TACCAAA
36315247 CCCAAAATCG
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 49 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.29
Consensus pattern (46 bp):
TACCAAATCGTATTACCATTTCGAACCAAATCACATTACCAATTCG
Found at i:36315246 original size:23 final size:23
Alignment explanation
Indices: 36315135--36315246 Score: 93
Period size: 23 Copynumber: 4.9 Consensus size: 23
36315125 CTTTTTGAAC
* * * *
36315135 CATTAACATTTCATACCAAATCG
1 CATTACCATTTCGTAACAAATCA
*
36315158 TATTACCATTTCG-AACCAAATCA
1 CATTACCATTTCGTAA-CAAATCA
* * * *
36315181 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTAACAAATCA
* *
36315204 TATTACCATTTTG-AACCAAATCA
1 CATTACCATTTCGTAA-CAAATCA
36315227 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTAACAAA
36315247 CCCAAAATCG
Statistics
Matches: 67, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
22 2 0.03
23 62 0.93
24 3 0.04
ACGTcount: A:0.38, C:0.27, G:0.05, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTAACAAATCA
Found at i:36325672 original size:17 final size:17
Alignment explanation
Indices: 36325652--36325692 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
36325642 AAAAAAAATC
36325652 AAGAAAAAAAAATCGAA
1 AAGAAAAAAAAATCGAA
* *
36325669 AAGAAAAAAAATTTGAA
1 AAGAAAAAAAAATCGAA
36325686 AA-AAAAA
1 AAGAAAAA
36325693 TTGCATACGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.78, C:0.02, G:0.10, T:0.10
Consensus pattern (17 bp):
AAGAAAAAAAAATCGAA
Found at i:36325691 original size:16 final size:15
Alignment explanation
Indices: 36325642--36325692 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
36325632 TGTAGTTTCG
*
36325642 AAAAAAAATC-AAGA
1 AAAAAAAATCGAAAA
36325656 AAAAAAAATCGAAAA
1 AAAAAAAATCGAAAA
*
36325671 GAAAAAAAATTTGAAAA
1 -AAAAAAAA-TCGAAAA
36325688 AAAAA
1 AAAAA
36325693 TTGCATACGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 10 0.31
15 3 0.09
16 13 0.41
17 6 0.19
ACGTcount: A:0.78, C:0.04, G:0.08, T:0.10
Consensus pattern (15 bp):
AAAAAAAATCGAAAA
Found at i:36325855 original size:19 final size:19
Alignment explanation
Indices: 36325831--36325874 Score: 72
Period size: 19 Copynumber: 2.3 Consensus size: 19
36325821 CACGCAATTG
36325831 AAAAAA-AAAATTCGAAAGA
1 AAAAAACAAAATT-GAAAGA
36325850 AAAAAACAAAATTGAAAGA
1 AAAAAACAAAATTGAAAGA
36325869 AAAAAA
1 AAAAAA
36325875 TTGTATACGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.77, C:0.05, G:0.09, T:0.09
Consensus pattern (19 bp):
AAAAAACAAAATTGAAAGA
Found at i:36325955 original size:182 final size:178
Alignment explanation
Indices: 36325655--36326039 Score: 621
Period size: 182 Copynumber: 2.1 Consensus size: 178
36325645 AAAAATCAAG
* *
36325655 AAAAAAAAA-TCGAAAAGAAAAAAAATTTGAAAAAAAAATTGCATACGGTCTAGGTGCAGACGAA
1 AAAAAAAAATTCGAAAAAAAAAAAAAATTGAAAAAAAAATTGCATACGGTCTAGGTGCAGACGAA
*
36325719 AAGACGTGAAAGATCCGTAAAAAAAAGAGTCTGGAGACATTTCAATAGAAATTTTTCCAAAATCT
66 AAGACGTGAAAGATCCGTAAAAAAAAGAGTCTGGAGACACTTCAATAGAAATTTTTCCAAAATCT
36325784 CATCCTACACTCTTTTATATCCCCCGTAGTGAAATTTCACGCAATTGA
131 CATCCTACACTCTTTTATATCCCCCGTAGTGAAATTTCACGCAATTGA
* * **
36325832 AAAAAAAAATTCGAAAGAAAAAAACAAAATTGAAAGAAAAAAATTGTATACGGTTTAGGTGTGGA
1 AAAAAAAAATTCGAAA-AAAAAAA-AAAATTG-AA-AAAAAAATTGCATACGGTCTAGGTGCAGA
36325897 CGAAAAGAACGTGAAAGATCCGTAAAAAAAA-AGTCTGGAGACACTTCAATAGAAATTTTTCCAA
62 CGAAAAG-ACGTGAAAGATCCGTAAAAAAAAGAGTCTGGAGACACTTCAATAGAAATTTTTCCAA
36325961 AATCTCATCCTACACTCTTTTATATCCCCCGTAGTGAAATTTCACGCAATTGA
126 AATCTCATCCTACACTCTTTTATATCCCCCGTAGTGAAATTTCACGCAATTGA
* * *
36326014 AAAAAAAATTTCGATATAAAAAAAAA
1 AAAAAAAAATTCGAAAAAAAAAAAAA
36326040 GTCTTACGCA
Statistics
Matches: 192, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
177 9 0.05
178 6 0.03
179 6 0.03
180 9 0.05
181 8 0.04
182 131 0.68
183 23 0.12
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.24
Consensus pattern (178 bp):
AAAAAAAAATTCGAAAAAAAAAAAAAATTGAAAAAAAAATTGCATACGGTCTAGGTGCAGACGAA
AAGACGTGAAAGATCCGTAAAAAAAAGAGTCTGGAGACACTTCAATAGAAATTTTTCCAAAATCT
CATCCTACACTCTTTTATATCCCCCGTAGTGAAATTTCACGCAATTGA
Found at i:36327021 original size:10 final size:10
Alignment explanation
Indices: 36327006--36327047 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
36326996 TTTGCAAGTT
36327006 TTGAGCTAAA
1 TTGAGCTAAA
* *
36327016 TTGAGCTGAT
1 TTGAGCTAAA
*
36327026 TTGAGCT-CA
1 TTGAGCTAAA
36327035 TTGAGCTAAA
1 TTGAGCTAAA
36327045 TTG
1 TTG
36327048 GAAGTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
9 7 0.27
10 19 0.73
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (10 bp):
TTGAGCTAAA
Found at i:36330106 original size:19 final size:20
Alignment explanation
Indices: 36330077--36330130 Score: 74
Period size: 19 Copynumber: 2.7 Consensus size: 20
36330067 TCTCGCTTTC
*
36330077 TTTTCATTTTCTTTTTTTGAA
1 TTTTC-TTTTCTTTTTTTCAA
*
36330098 TTTTC-TTTCTTTTTTTCAT
1 TTTTCTTTTCTTTTTTTCAA
36330117 TTTTCTTTTCTTTT
1 TTTTCTTTTCTTTT
36330131 GTATTTTCGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 17 0.57
20 8 0.27
21 5 0.17
ACGTcount: A:0.07, C:0.13, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTCTTTTCTTTTTTTCAA
Found at i:36336302 original size:20 final size:20
Alignment explanation
Indices: 36336279--36336325 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
36336269 GGGTTAAAAT
*
36336279 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
36336299 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
36336319 TGAGCTG
1 TGAGCTG
36336326 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:36338231 original size:12 final size:12
Alignment explanation
Indices: 36338198--36338278 Score: 62
Period size: 12 Copynumber: 6.8 Consensus size: 12
36338188 TTTCCACTCG
36338198 ATTTC-TTTTCA
1 ATTTCTTTTTCA
** *
36338209 AGCTCTCTTTCA
1 ATTTCTTTTTCA
36338221 ATTTCTTTTTCCA
1 ATTTCTTTTT-CA
36338234 CTATTTCTTTTTC-
1 --ATTTCTTTTTCA
*
36338247 --TTCTCTTTCA
1 ATTTCTTTTTCA
36338257 ATTTCTTTTTCA
1 ATTTCTTTTTCA
*
36338269 ATCTCTTTTT
1 ATTTCTTTTT
36338279 GCTTTTCACT
Statistics
Matches: 54, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
9 8 0.15
11 3 0.06
12 30 0.56
13 2 0.04
14 1 0.02
15 10 0.19
ACGTcount: A:0.14, C:0.23, G:0.01, T:0.62
Consensus pattern (12 bp):
ATTTCTTTTTCA
Found at i:36338260 original size:21 final size:22
Alignment explanation
Indices: 36338236--36338276 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
36338226 TTTTTCCACT
*
36338236 ATTTCTTTTTC-TTCTCTTTCA
1 ATTTCTTTTTCAATCTCTTTCA
36338257 ATTTCTTTTTCAATCTCTTT
1 ATTTCTTTTTCAATCTCTTT
36338277 TTGCTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.12, C:0.22, G:0.00, T:0.66
Consensus pattern (22 bp):
ATTTCTTTTTCAATCTCTTTCA
Found at i:36338331 original size:15 final size:15
Alignment explanation
Indices: 36338308--36338354 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
36338298 TTTTGAAATC
36338308 TCATTTTCATATT-TT
1 TCATTTTCAT-TTCTT
*
36338323 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
36338338 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
36338354 T
1 T
36338355 ATTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.13, C:0.17, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:36339437 original size:16 final size:15
Alignment explanation
Indices: 36339395--36339442 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 15
36339385 GCAAGACTTT
*
36339395 TCACTTCTTTTTTTT
1 TCACTTCTTTTTTTC
* *
36339410 TACTCTTTTTTTTTTGC
1 T-CACTTCTTTTTTT-C
36339427 TCACTTCTTTTTTTC
1 TCACTTCTTTTTTTC
36339442 T
1 T
36339443 TTTTTTTTTC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
15 3 0.12
16 22 0.85
17 1 0.04
ACGTcount: A:0.06, C:0.21, G:0.02, T:0.71
Consensus pattern (15 bp):
TCACTTCTTTTTTTC
Found at i:36362813 original size:31 final size:32
Alignment explanation
Indices: 36362752--36362813 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
36362742 TTTCAGTTTA
*
36362752 ATAAGTTTGCATCTTTAATAATGGCTTGCATT
1 ATAAGTTTGCATCTTTAATAATGGCATGCATT
* *
36362784 ATAAGTTTGCAT-TTTAATTATGTCATGCAT
1 ATAAGTTTGCATCTTTAATAATGGCATGCAT
36362814 AATATTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.45
Consensus pattern (32 bp):
ATAAGTTTGCATCTTTAATAATGGCATGCATT
Found at i:36370996 original size:6 final size:6
Alignment explanation
Indices: 36370987--36371012 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
36370977 ATTAAAATAA
36370987 TTAGTT TTAGTT TTAGTT TTAGTT TT
1 TTAGTT TTAGTT TTAGTT TTAGTT TT
36371013 CTAATTAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (6 bp):
TTAGTT
Found at i:36376802 original size:18 final size:17
Alignment explanation
Indices: 36376762--36376802 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
36376752 AAGAAGAAAA
36376762 ACAAAAAGATGAGTGAT
1 ACAAAAAGATGAGTGAT
*
36376779 AAAAAAAGATAGAGTGAT
1 ACAAAAAGAT-GAGTGAT
*
36376797 TCAAAA
1 ACAAAA
36376803 GAAAAAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.59, C:0.05, G:0.20, T:0.17
Consensus pattern (17 bp):
ACAAAAAGATGAGTGAT
Found at i:36377456 original size:20 final size:20
Alignment explanation
Indices: 36377431--36377477 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
36377421 AGCTCGTTTC
36377431 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCGAGCTCAAGT
* * * *
36377451 CAGCTCATTCGAGTTGAATT
1 CAGCTCACTCGAGCTCAAGT
36377471 CAGCTCA
1 CAGCTCA
36377478 ACCTCAACCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (20 bp):
CAGCTCACTCGAGCTCAAGT
Found at i:36383489 original size:18 final size:18
Alignment explanation
Indices: 36383468--36383512 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
36383458 GAAGGTTACT
36383468 AATTTTGAGACTTTGATC
1 AATTTTGAGACTTTGATC
* *
36383486 AATTATGA-ACTTTGTTC
1 AATTTTGAGACTTTGATC
36383503 AATTTGTGAG
1 AATTT-TGAG
36383513 TATTTCAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 12 0.55
18 10 0.45
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (18 bp):
AATTTTGAGACTTTGATC
Found at i:36394362 original size:15 final size:15
Alignment explanation
Indices: 36394344--36394374 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
36394334 TTGAAAAATC
*
36394344 GAAAAATAAAAATTA
1 GAAAAAGAAAAATTA
36394359 GAAAAAGAAAAATTA
1 GAAAAAGAAAAATTA
36394374 G
1 G
36394375 TATACGGTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (15 bp):
GAAAAAGAAAAATTA
Found at i:36394362 original size:23 final size:21
Alignment explanation
Indices: 36394324--36394371 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
36394314 TAGACTCGTG
*
36394324 AAAA-AAAAATTTGAAAAATCGA
1 AAAATAAAAATTAGAAAAA--GA
36394346 AAAATAAAAATTAGAAAAAGA
1 AAAATAAAAATTAGAAAAAGA
36394367 AAAAT
1 AAAAT
36394372 TAGTATACGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 7 0.29
22 4 0.17
23 13 0.54
ACGTcount: A:0.73, C:0.02, G:0.08, T:0.17
Consensus pattern (21 bp):
AAAATAAAAATTAGAAAAAGA
Found at i:36402941 original size:12 final size:12
Alignment explanation
Indices: 36402926--36402988 Score: 60
Period size: 12 Copynumber: 5.2 Consensus size: 12
36402916 TCAGGCTCTC
36402926 TTTCAATTTCTT
1 TTTCAATTTCTT
*
36402938 TTTCCACTCTTTCTT
1 TTT-CA--ATTTCTT
36402953 TTTC---TTCTT
1 TTTCAATTTCTT
36402962 TTTCAATTTCTT
1 TTTCAATTTCTT
*
36402974 TTTCAATCTCTT
1 TTTCAATTTCTT
36402986 TTT
1 TTT
36402989 TCTTTTCACT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
9 9 0.21
12 22 0.51
13 2 0.05
14 1 0.02
15 9 0.21
ACGTcount: A:0.11, C:0.22, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTCAATTTCTT
Found at i:36402996 original size:18 final size:19
Alignment explanation
Indices: 36402968--36403005 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
36402958 TCTTTTTCAA
36402968 TTTCTTTTTCAATCTCTTT
1 TTTCTTTTTCAATCTCTTT
*
36402987 TTTC-TTTTCACTCTCTTT
1 TTTCTTTTTCAATCTCTTT
36403005 T
1 T
36403006 GTTTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCTTTTTCAATCTCTTT
Found at i:36403041 original size:15 final size:15
Alignment explanation
Indices: 36403018--36403064 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
36403008 TTTTGAAATC
36403018 TCATTTTCATCTT-TT
1 TCATTTTCAT-TTCTT
*
36403033 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
36403048 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
36403064 T
1 T
36403065 GTTCTTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 2 0.07
15 19 0.68
16 7 0.25
ACGTcount: A:0.11, C:0.19, G:0.00, T:0.70
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:36406904 original size:20 final size:20
Alignment explanation
Indices: 36406879--36406933 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
36406869 ACACAAATAC
*
36406879 AAAAGAAAAGAAAAATGAAA
1 AAAAGAAAAGAAAAATCAAA
*
36406899 AAAAG-AAAGAAAATTCAAA
1 AAAAGAAAAGAAAAATCAAA
*
36406918 AAAAGAGAATGAAAAA
1 AAAAGA-AAAGAAAAA
36406934 AAATGAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 17 0.59
20 5 0.17
21 7 0.24
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAGAAAAATCAAA
Found at i:36406944 original size:26 final size:28
Alignment explanation
Indices: 36406915--36406969 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 28
36406905 AAGAAAATTC
36406915 AAAA-AAAGAGAATGAAAAA-AAAT-GAG
1 AAAAGAAAGAG-ATGAAAAAGAAATAGAG
*
36406941 AAAAGCAAGAGATGAAAAAGAAATAGAG
1 AAAAGAAAGAGATGAAAAAGAAATAGAG
36406969 A
1 A
36406970 GTGAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 12 0.48
27 9 0.36
28 4 0.16
ACGTcount: A:0.69, C:0.02, G:0.22, T:0.07
Consensus pattern (28 bp):
AAAAGAAAGAGATGAAAAAGAAATAGAG
Found at i:36409740 original size:20 final size:20
Alignment explanation
Indices: 36409717--36409763 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
36409707 GGGTTAAAAT
*
36409717 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
36409737 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
36409757 TGAGCTG
1 TGAGCTG
36409764 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:36412615 original size:22 final size:22
Alignment explanation
Indices: 36412590--36412649 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
36412580 TTTGAACCAT
36412590 TACCAATTCGTACCAACTTCC-A
1 TACCAATTCGTACCAA-TTCCAA
*
36412612 TACCATTTCGTACCAATTCCTAAA
1 TACCAATTCGTACCAATTCC--AA
*
36412636 TACCAAATCGTACC
1 TACCAATTCGTACC
36412650 TAAACCAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 4 0.12
22 15 0.47
24 13 0.41
ACGTcount: A:0.33, C:0.33, G:0.05, T:0.28
Consensus pattern (22 bp):
TACCAATTCGTACCAATTCCAA
Found at i:36417294 original size:8 final size:9
Alignment explanation
Indices: 36417276--36417302 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
36417266 CAATTTCTCC
36417276 TTTATTTTT
1 TTTATTTTT
36417285 TTTATTTTT
1 TTTATTTTT
36417294 TTTATTTTT
1 TTTATTTTT
36417303 GAATCTGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTATTTTT
Found at i:36432516 original size:20 final size:22
Alignment explanation
Indices: 36432482--36432525 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
36432472 NNNNNNNNNN
*
36432482 TCTTTTTCTTTTTCTCTC-ATT
1 TCTTTTTCTTCTTCTCTCAATT
36432503 TCTTTTT-TTCTTCTCTCAATT
1 TCTTTTTCTTCTTCTCTCAATT
36432524 TC
1 TC
36432526 ATTCAAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.07, C:0.25, G:0.00, T:0.68
Consensus pattern (22 bp):
TCTTTTTCTTCTTCTCTCAATT
Found at i:36438973 original size:14 final size:15
Alignment explanation
Indices: 36438937--36438977 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
36438927 GAATATTTAC
36438937 ATAAAAATTAAACTAA
1 ATAAAAA-TAAACTAA
*
36438953 GTAAAAATAAA-TAA
1 ATAAAAATAAACTAA
36438967 ATAAAAATAAA
1 ATAAAAATAAA
36438978 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
ATAAAAATAAACTAA
Found at i:36439529 original size:23 final size:22
Alignment explanation
Indices: 36439478--36439529 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
36439468 CCTCGTCTTT
*
36439478 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
36439500 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
36439523 TTCTTTT
1 TTCTTTT
36439530 TCAATTTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:36442618 original size:33 final size:33
Alignment explanation
Indices: 36442550--36442629 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 33
36442540 TGTTTGAGCA
* *
36442550 CTCTCT-TTTCTTCACTCATTTCTTGTTGAAGCT
1 CTCTCTCTTT-TTCACTCATTTCTTGTTCAAACT
36442583 CTCTCTCTTTTTCACTCAATTTCTT-TTCAAACT
1 CTCTCTCTTTTTCACTC-ATTTCTTGTTCAAACT
*
36442616 CTCTTTCTTTTTCA
1 CTCTCTCTTTTTCA
36442630 ATCTCTTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
33 32 0.76
34 10 0.24
ACGTcount: A:0.14, C:0.29, G:0.04, T:0.54
Consensus pattern (33 bp):
CTCTCTCTTTTTCACTCATTTCTTGTTCAAACT
Found at i:36442629 original size:18 final size:18
Alignment explanation
Indices: 36442581--36442645 Score: 55
Period size: 18 Copynumber: 3.7 Consensus size: 18
36442571 CTTGTTGAAG
*
36442581 CTCTCTCTCTTTTTC--A
1 CTCTCTTTCTTTTTCAAA
**
36442597 CTCAATTTC-TTTTCAAA
1 CTCTCTTTCTTTTTCAAA
*
36442614 CTCTCTTTCTTTTTCAAT
1 CTCTCTTTCTTTTTCAAA
*
36442632 CTCTTTTTGCTTTT
1 CTCTCTTT-CTTTT
36442646 CACTCTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
15 5 0.13
16 6 0.16
17 8 0.21
18 14 0.37
19 5 0.13
ACGTcount: A:0.12, C:0.28, G:0.02, T:0.58
Consensus pattern (18 bp):
CTCTCTTTCTTTTTCAAA
Found at i:36442636 original size:16 final size:16
Alignment explanation
Indices: 36442582--36442637 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
36442572 TTGTTGAAGC
* *
36442582 TCTCTCTCTTTTTCAC
1 TCTCTTTCTTTTTCAA
**
36442598 TCAATTTC-TTTTCAAA
1 TCTCTTTCTTTTTC-AA
36442614 CTCTCTTTCTTTTTCAA
1 -TCTCTTTCTTTTTCAA
36442631 TCTCTTT
1 TCTCTTT
36442638 TTGCTTTTCA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 5 0.16
16 13 0.42
17 8 0.26
18 5 0.16
ACGTcount: A:0.14, C:0.29, G:0.00, T:0.57
Consensus pattern (16 bp):
TCTCTTTCTTTTTCAA
Found at i:36442661 original size:16 final size:17
Alignment explanation
Indices: 36442588--36442660 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 17
36442578 AAGCTCTCTC
**
36442588 TCTTTTTC-ACTCAATT
1 TCTTTTTCAACTCTTTT
*
36442604 TC-TTTTCAAACTCTCTT
1 TCTTTTTC-AACTCTTTT
36442621 TCTTTTTCAATCTCTTTT
1 TCTTTTTCAA-CTCTTTT
36442639 TGC-TTTTC-ACTCTTTT
1 T-CTTTTTCAACTCTTTT
36442655 T-TTTTT
1 TCTTTTT
36442661 TGAAATCTCA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
15 9 0.19
16 10 0.21
17 11 0.23
18 17 0.35
19 1 0.02
ACGTcount: A:0.12, C:0.23, G:0.01, T:0.63
Consensus pattern (17 bp):
TCTTTTTCAACTCTTTT
Found at i:36442708 original size:15 final size:15
Alignment explanation
Indices: 36442668--36442714 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
36442658 TTTTGAAATC
* *
36442668 TCATTTTCATATATT
1 TCATTTTCATTTCTT
*
36442683 TCTTTTTCATTTCTT
1 TCATTTTCATTTCTT
36442698 TCATTTTCATTTTCTT
1 TCATTTTCA-TTTCTT
36442714 T
1 T
36442715 ATTCTTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
15 20 0.74
16 7 0.26
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.68
Consensus pattern (15 bp):
TCATTTTCATTTCTT
Found at i:36448231 original size:14 final size:14
Alignment explanation
Indices: 36448212--36448241 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
36448202 TCTATTGAGC
*
36448212 GAGAAAAAGAAAAA
1 GAGAAAAACAAAAA
36448226 GAGAAAAACAAAAA
1 GAGAAAAACAAAAA
36448240 GA
1 GA
36448242 ATGAAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (14 bp):
GAGAAAAACAAAAA
Found at i:36456177 original size:14 final size:15
Alignment explanation
Indices: 36456141--36456181 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
36456131 GAATATTTAC
36456141 ATAAAAATTAAACTAA
1 ATAAAAA-TAAACTAA
*
36456157 GTAAAAATAAA-TAA
1 ATAAAAATAAACTAA
36456171 ATAAAAATAAA
1 ATAAAAATAAA
36456182 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
ATAAAAATAAACTAA
Found at i:36456664 original size:15 final size:15
Alignment explanation
Indices: 36456644--36456694 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
36456634 ACTCTCGTCC
*
36456644 TTCTTTTCTTTCTTT
1 TTCTTTTCTCTCTTT
*
36456659 TTCTTTTCACTCTTT
1 TTCTTTTCTCTCTTT
*
36456674 TTGTTTT-TCTCTTT
1 TTCTTTTCTCTCTTT
*
36456688 TTATTTT
1 TTCTTTT
36456695 TCTTGCTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
14 12 0.39
15 19 0.61
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (15 bp):
TTCTTTTCTCTCTTT
Found at i:36456685 original size:14 final size:14
Alignment explanation
Indices: 36456654--36456697 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
36456644 TTCTTTTCTT
* *
36456654 TCTTTTTCTTTTCAC
1 TCTTTTTATTTT-TC
*
36456669 TCTTTTTGTTTTTC
1 TCTTTTTATTTTTC
36456683 TCTTTTTATTTTTC
1 TCTTTTTATTTTTC
36456697 T
1 T
36456698 TGCTCAATGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.05, C:0.18, G:0.02, T:0.75
Consensus pattern (14 bp):
TCTTTTTATTTTTC
Found at i:36459935 original size:12 final size:11
Alignment explanation
Indices: 36459909--36459942 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
36459899 ACGAAATAAT
*
36459909 ATTTTTTT-GA
1 ATTTTTTTCAA
36459919 ATTTTTTTCAA
1 ATTTTTTTCAA
36459930 ATTTTTTTCAA
1 ATTTTTTTCAA
36459941 AT
1 AT
36459943 ACTTACTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (11 bp):
ATTTTTTTCAA
Found at i:36461315 original size:19 final size:19
Alignment explanation
Indices: 36461291--36461342 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
36461281 AGAAACCTAT
36461291 TTAACTAAGATGAGCTCAA
1 TTAACTAAGATGAGCTCAA
*
36461310 TTAACTAAGATGAACTCAA
1 TTAACTAAGATGAGCTCAA
*
36461329 TTAAATAAGATGAG
1 TTAACTAAGATGAG
36461343 TAATTTATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (19 bp):
TTAACTAAGATGAGCTCAA
Found at i:36464290 original size:21 final size:21
Alignment explanation
Indices: 36464266--36464305 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
36464256 TCTCTCTCGC
*
36464266 TTTCTTTTTCGCCTTTTTCAT
1 TTTCATTTTCGCCTTTTTCAT
**
36464287 TTTCATTTTCTTCTTTTTC
1 TTTCATTTTCGCCTTTTTC
36464306 CCTTGTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.05, C:0.23, G:0.03, T:0.70
Consensus pattern (21 bp):
TTTCATTTTCGCCTTTTTCAT
Found at i:36466099 original size:27 final size:27
Alignment explanation
Indices: 36466069--36466122 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
36466059 TTCAGGGAGA
36466069 TTTGAAAAACAAGATCATGAGAATAGG
1 TTTGAAAAACAAGATCATGAGAATAGG
36466096 TTTGAAAAACAAGATCATGAGAATAGG
1 TTTGAAAAACAAGATCATGAGAATAGG
36466123 CTCCCAAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (27 bp):
TTTGAAAAACAAGATCATGAGAATAGG
Found at i:36480321 original size:47 final size:48
Alignment explanation
Indices: 36480232--36480330 Score: 146
Period size: 47 Copynumber: 2.1 Consensus size: 48
36480222 AAAATCAGCT
* * * * *
36480232 GCAGCAAAGACAAGTTTAATGTCTAGATTCGGCTGGACAAATTAAATA
1 GCAGCAAAGACAAGATTAATGACTAAATTCAGCTGAACAAATTAAATA
36480280 GCAGCAAAGACAA-ATTAATGACTAAATTCAGCTGAACAAATTAAATA
1 GCAGCAAAGACAAGATTAATGACTAAATTCAGCTGAACAAATTAAATA
36480327 GCAG
1 GCAG
36480331 TAGCTAATAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
47 33 0.72
48 13 0.28
ACGTcount: A:0.44, C:0.15, G:0.18, T:0.22
Consensus pattern (48 bp):
GCAGCAAAGACAAGATTAATGACTAAATTCAGCTGAACAAATTAAATA
Found at i:36483164 original size:18 final size:19
Alignment explanation
Indices: 36483129--36483166 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
36483119 AAAAAAGAGT
36483129 TCGAAAAAAAAATTTCAAAA
1 TCGAAAAAAAAA-TTCAAAA
36483149 TCGAAAAAAAAA-TCAAAA
1 TCGAAAAAAAAATTCAAAA
36483167 AAAATTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.68, C:0.11, G:0.05, T:0.16
Consensus pattern (19 bp):
TCGAAAAAAAAATTCAAAA
Found at i:36483177 original size:29 final size:28
Alignment explanation
Indices: 36483133--36483188 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
36483123 AAGAGTTCGA
36483133 AAAAAAAATTTCAAAATCGAAAAAAAAATC
1 AAAAAAAATTTCAAAA--GAAAAAAAAATC
*
36483163 AAAAAAAA-TTGAAAAGAAAAAAAAAT
1 AAAAAAAATTTCAAAAGAAAAAAAAAT
36483189 TGCATACGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
27 11 0.44
29 6 0.24
30 8 0.32
ACGTcount: A:0.75, C:0.05, G:0.05, T:0.14
Consensus pattern (28 bp):
AAAAAAAATTTCAAAAGAAAAAAAAATC
Found at i:36487680 original size:23 final size:23
Alignment explanation
Indices: 36487648--36487759 Score: 125
Period size: 23 Copynumber: 4.9 Consensus size: 23
36487638 CTTTTTGAAC
* *
36487648 CATTAACATTTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* *
36487671 TATTACCATTTCGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
* * *
36487694 CCTTACCAATTCGTACCAAATCG
1 CATTACCATTTCGTACCAAATCA
* * *
36487717 TATTACCATTTTGAACCAAATCA
1 CATTACCATTTCGTACCAAATCA
*
36487740 CATTACCATTTCGTAACAAA
1 CATTACCATTTCGTACCAAA
36487760 CCCAAAACTG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 70 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (23 bp):
CATTACCATTTCGTACCAAATCA
Found at i:36487724 original size:46 final size:46
Alignment explanation
Indices: 36487648--36487759 Score: 170
Period size: 46 Copynumber: 2.4 Consensus size: 46
36487638 CTTTTTGAAC
* *
36487648 CATTAACATTTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
36487694 CCTTACCAATTCGTACCAAATCGTATTACCATTTTGAACCAAATCA
1 CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
* *
36487740 CATTACCATTTCGTAACAAA
1 CATTACCAATTCGTACCAAA
36487760 CCCAAAACTG
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 59 1.00
ACGTcount: A:0.37, C:0.27, G:0.06, T:0.30
Consensus pattern (46 bp):
CATTACCAATTCGTACCAAATCGTATTACCATTTCGAACCAAATCA
Found at i:36490204 original size:14 final size:13
Alignment explanation
Indices: 36490173--36490206 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
36490163 TACACCTTGG
36490173 ATTTTTTTTTCAA
1 ATTTTTTTTTCAA
*
36490186 ATTTTTATTTCAA
1 ATTTTTTTTTCAA
36490199 ATTTTTTT
1 ATTTTTTT
36490207 ACAATCACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTTTTTTTCAA
Done.