Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, 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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 83 of 105
Found at i:14568717 original size:57 final size:56
Alignment explanation
Indices: 14568599--14568719 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 56
14568589 TATTTTTAGG
* * *
14568599 AAAAAGTTGAAAGTATCAATTTTTCTTAAAATTAAAATTTCAAAAAAAAATTTTGAG
1 AAAAAGTTAAAAGTATCAATTTTTCTTAAAAGTAAAATTTCAAAAAAAAATTTT-AC
* * *
14568656 AAAAAGTTAAAAGTATCAATTTTTCTTGAAAGTAAACTTTCTAAAATAAATATTTT-C
1 AAAAAGTTAAAAGTATCAATTTTTCTTAAAAGTAAAATTTC-AAAA-AAAAATTTTAC
14568713 AAAAAGT
1 AAAAAGT
14568720 ATTTTGAGGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
57 44 0.79
58 4 0.07
59 8 0.14
ACGTcount: A:0.50, C:0.07, G:0.08, T:0.36
Consensus pattern (56 bp):
AAAAAGTTAAAAGTATCAATTTTTCTTAAAAGTAAAATTTCAAAAAAAAATTTTAC
Found at i:14568869 original size:60 final size:61
Alignment explanation
Indices: 14568720--14568876 Score: 217
Period size: 61 Copynumber: 2.6 Consensus size: 61
14568710 TTCAAAAAGT
* * * * *
14568720 ATTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTGAAATTAAAATTTTTAGAAAAAAAAC
1 ATTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAATTATACAAAAAAAAC
* * * *
14568781 ATTTTGAGGAAAAATTAGAAGTACCAATTTTTCTTAAAAATAAAAATTAT-CAAGAAAAAC
1 ATTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAATTATACAAAAAAAAC
*
14568841 ATTTTAAGGAAAAGTTAAAAGTATCAATTTTTCTTA
1 ATTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTA
14568877 TACAAAAGCA
Statistics
Matches: 83, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
60 40 0.48
61 43 0.52
ACGTcount: A:0.48, C:0.06, G:0.11, T:0.35
Consensus pattern (61 bp):
ATTTTGAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAAATTATACAAAAAAAAC
Found at i:14571718 original size:22 final size:23
Alignment explanation
Indices: 14571690--14571732 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
14571680 AAAAAAAATC
**
14571690 TAAAACCTTAAACC-TGAAACTT
1 TAAAACCCAAAACCTTGAAACTT
14571712 TAAAACCCAAAACCTTGAAAC
1 TAAAACCCAAAACCTTGAAAC
14571733 CCTAAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.49, C:0.26, G:0.05, T:0.21
Consensus pattern (23 bp):
TAAAACCCAAAACCTTGAAACTT
Found at i:14571724 original size:15 final size:15
Alignment explanation
Indices: 14571706--14571754 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
14571696 CTTAAACCTG
*
14571706 AAACTTTAAAACCCA
1 AAACTTTGAAACCCA
*
14571721 AAACCTTGAAACCCTA
1 AAACTTTGAAACCC-A
* *
14571737 AAATTTTGAAACCTA
1 AAACTTTGAAACCCA
14571752 AAA
1 AAA
14571755 ACTCGAAACC
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
15 16 0.57
16 12 0.43
ACGTcount: A:0.51, C:0.22, G:0.04, T:0.22
Consensus pattern (15 bp):
AAACTTTGAAACCCA
Found at i:14571786 original size:23 final size:23
Alignment explanation
Indices: 14571742--14571789 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
14571732 CCCTAAAATT
*
14571742 TTGAAACCTAAAAACTCGAAACC
1 TTGAAACCTAAAAACTCAAAACC
* **
14571765 TTGAAACTTAAAATGTCAAAACC
1 TTGAAACCTAAAAACTCAAAACC
14571788 TT
1 TT
14571790 AAAATACTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.21, G:0.08, T:0.25
Consensus pattern (23 bp):
TTGAAACCTAAAAACTCAAAACC
Found at i:14571802 original size:17 final size:16
Alignment explanation
Indices: 14571771--14571818 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 16
14571761 AACCTTGAAA
*
14571771 CTTAAAATGTCAAAAC
1 CTTAAAATCTCAAAAC
14571787 CTTAAAATACTCAAAAC
1 CTTAAAAT-CTCAAAAC
*
14571804 CCTAAAATCT-AAAAC
1 CTTAAAATCTCAAAAC
14571819 TTCAAAACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 5 0.17
16 10 0.34
17 14 0.48
ACGTcount: A:0.52, C:0.23, G:0.02, T:0.23
Consensus pattern (16 bp):
CTTAAAATCTCAAAAC
Found at i:14571827 original size:23 final size:24
Alignment explanation
Indices: 14571797--14571842 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
14571787 CTTAAAATAC
*
14571797 TCAAAACCCTAAAA-TCTAAAACT
1 TCAAAACCCTAAAACTCCAAAACT
*
14571820 TCAAAACCTTAAAACTCCAAAAC
1 TCAAAACCCTAAAACTCCAAAAC
14571843 CCTAAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.52, C:0.28, G:0.00, T:0.20
Consensus pattern (24 bp):
TCAAAACCCTAAAACTCCAAAACT
Found at i:14571834 original size:16 final size:16
Alignment explanation
Indices: 14571812--14571849 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
14571802 ACCCTAAAAT
*
14571812 CTAAAACTTCAAAACC
1 CTAAAACTCCAAAACC
*
14571828 TTAAAACTCCAAAACC
1 CTAAAACTCCAAAACC
14571844 CTAAAA
1 CTAAAA
14571850 TGAGACCCTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.53, C:0.29, G:0.00, T:0.18
Consensus pattern (16 bp):
CTAAAACTCCAAAACC
Found at i:14576967 original size:21 final size:23
Alignment explanation
Indices: 14576920--14576968 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
14576910 ATTTATTCGT
* *
14576920 TTTTTTTTTTTGTGAGTTTGGAG
1 TTTTTTTTTTTGTGACTTTGGAA
14576943 TTTTTTTTTTTG-GACTTT-GAA
1 TTTTTTTTTTTGTGACTTTGGAA
14576964 TTTTT
1 TTTTT
14576969 GGTTTTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.29
22 5 0.21
23 12 0.50
ACGTcount: A:0.10, C:0.02, G:0.18, T:0.69
Consensus pattern (23 bp):
TTTTTTTTTTTGTGACTTTGGAA
Found at i:14578066 original size:103 final size:102
Alignment explanation
Indices: 14577887--14578079 Score: 228
Period size: 103 Copynumber: 1.9 Consensus size: 102
14577877 TATTTTTTAA
* * ** * * *
14577887 AATCCTACTAAGATATTGGAGGATAATTCTTGATGGAAGATTTTACCAACATATTGAAAGTTATT
1 AATCCTACCAACATATTGGAGGATAATTCTTGACAGAAAATCTTACCAACATATTGAAAG-TATC
* ** *
14577952 TTTGGAAATAAATTATTTTCACAAACAAATAGAATTTC
65 TCTAAAAATAAATTATTTCCACAAACAAATAGAATTTC
14577990 AATCCTACCAACATATTGGAGGATAA-TCTTTGACAGAAAATCTTACCAACATATTAGAATA-TA
1 AATCCTACCAACATATTGGAGGATAATTC-TTGACAGAAAATCTTACCAACATATT-GAA-AGTA
*
14578053 TCTCTAAAAATAAATTGTTTCCACAAA
63 TCTCTAAAAATAAATTATTTCCACAAA
14578080 AAAAAAAGTT
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
102 2 0.03
103 69 0.92
104 3 0.04
105 1 0.01
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.33
Consensus pattern (102 bp):
AATCCTACCAACATATTGGAGGATAATTCTTGACAGAAAATCTTACCAACATATTGAAAGTATCT
CTAAAAATAAATTATTTCCACAAACAAATAGAATTTC
Found at i:14581805 original size:15 final size:15
Alignment explanation
Indices: 14581772--14581804 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
14581762 GCCAAAATTC
14581772 TTTTCATTATTTCTT
1 TTTTCATTATTTCTT
*
14581787 TTTTC-TTATTTATT
1 TTTTCATTATTTCTT
14581801 TTTT
1 TTTT
14581805 TAATAGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCATTATTTCTT
Found at i:14581952 original size:2 final size:2
Alignment explanation
Indices: 14581947--14581975 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
14581937 TGTGTGTGTG
14581947 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
14581976 CTTTTTAAAT
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:14583593 original size:32 final size:31
Alignment explanation
Indices: 14583527--14583646 Score: 114
Period size: 32 Copynumber: 3.8 Consensus size: 31
14583517 TATTTTTGTT
* *
14583527 AAAATTTCATATCATTTTAAAAAATTAAGCA
1 AAAATTTTATATCATTTTAAAAAATTAAGTA
* *
14583558 AAAATTTTTATATCAGTTTAAAAAATTAAATA
1 AAAA-TTTTATATCATTTTAAAAAATTAAGTA
* * * * *
14583590 AAAACTTTACATCATGTTAAAATATTATGTA
1 AAAATTTTATATCATTTTAAAAAATTAAGTA
* *
14583621 AAATTTTTTAGATCATTTTCAAAAAA
1 AAA-ATTTTATATCATTTT-AAAAAA
14583647 AGATCTATTA
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
31 27 0.39
32 38 0.54
33 5 0.07
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.39
Consensus pattern (31 bp):
AAAATTTTATATCATTTTAAAAAATTAAGTA
Found at i:14584591 original size:26 final size:27
Alignment explanation
Indices: 14584562--14584615 Score: 76
Period size: 26 Copynumber: 2.0 Consensus size: 27
14584552 ATATTTTTTT
14584562 ATTAAAATAATATAAAAAT-T-ATAAAA
1 ATTAAAATAATA-AAAAATATAATAAAA
*
14584588 ATTAAAATTATAAAAAATATAATAAAA
1 ATTAAAATAATAAAAAATATAATAAAA
14584615 A
1 A
14584616 ATCTGTCTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 6 0.24
26 12 0.48
27 7 0.28
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (27 bp):
ATTAAAATAATAAAAAATATAATAAAA
Found at i:14588649 original size:2 final size:2
Alignment explanation
Indices: 14588642--14588672 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
14588632 GATCGTAAAC
14588642 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
14588673 AACTCAAAAC
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:14590082 original size:9 final size:9
Alignment explanation
Indices: 14590068--14590199 Score: 54
Period size: 9 Copynumber: 14.1 Consensus size: 9
14590058 TGAATGCCCT
14590068 TTTAAAAAA
1 TTTAAAAAA
*
14590077 TTTAAAAAT
1 TTTAAAAAA
* *
14590086 TTTGAAAAT
1 TTTAAAAAA
*
14590095 TTTAGAAAGA
1 TTTA-AAAAA
*
14590105 TTCTAGAAAA
1 TT-TAAAAAA
*
14590115 TTT-TAAAA
1 TTTAAAAAA
14590123 TTTCAAAAGGAA
1 TTT-AAAA--AA
*
14590135 -TTAAGGAAA
1 TTTAA-AAAA
14590144 TTTAAAAAA
1 TTTAAAAAA
**
14590153 TTT-TCAAA
1 TTTAAAAAA
14590161 TTTAAAAAAAA
1 TTT--AAAAAA
**
14590172 TCCAAAAAA
1 TTTAAAAAA
*
14590181 TTAAAAAAA
1 TTTAAAAAA
*
14590190 ATTAAAAAA
1 TTTAAAAAA
14590199 T
1 T
14590200 GGCGAATTTA
Statistics
Matches: 90, Mismatches: 22, Indels: 22
0.67 0.16 0.16
Matches are distributed among these distances:
8 13 0.14
9 48 0.53
10 18 0.20
11 9 0.10
12 2 0.02
ACGTcount: A:0.58, C:0.04, G:0.06, T:0.32
Consensus pattern (9 bp):
TTTAAAAAA
Found at i:14590093 original size:10 final size:9
Alignment explanation
Indices: 14590067--14590122 Score: 58
Period size: 9 Copynumber: 5.9 Consensus size: 9
14590057 GTGAATGCCC
14590067 TTTTAAAAA
1 TTTTAAAAA
*
14590076 ATTTAAAAA
1 TTTTAAAAA
*
14590085 TTTTGAAAA
1 TTTTAAAAA
14590094 TTTTAGAAAGA
1 TTTTA-AAA-A
*
14590105 TTCTAGAAAA
1 TTTTA-AAAA
14590115 TTTTAAAA
1 TTTTAAAA
14590123 TTTCAAAAGG
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
9 22 0.56
10 8 0.21
11 9 0.23
ACGTcount: A:0.52, C:0.02, G:0.07, T:0.39
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:14590197 original size:19 final size:19
Alignment explanation
Indices: 14590162--14590198 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
14590152 ATTTTCAAAT
*
14590162 TTAAAAAAAATCCAAAAAA
1 TTAAAAAAAATCAAAAAAA
*
14590181 TTAAAAAAAATTAAAAAA
1 TTAAAAAAAATCAAAAAA
14590199 TGGCGAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.76, C:0.05, G:0.00, T:0.19
Consensus pattern (19 bp):
TTAAAAAAAATCAAAAAAA
Found at i:14590346 original size:39 final size:40
Alignment explanation
Indices: 14590286--14590361 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
14590276 ATAAAAACTT
* *
14590286 TTTTGAAAAAATATAATAATTTTTAA-ATTTTTTTTAAAAA
1 TTTTAAAAAAATATAATAA-TTTTAACATATTTTTTAAAAA
*
14590326 TTTTAAAAAAATCTAA-AATTTTAACATATTTTTTAA
1 TTTTAAAAAAATATAATAATTTTAACATATTTTTTAA
14590362 TCTTACAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 6 0.19
39 12 0.38
40 14 0.44
ACGTcount: A:0.47, C:0.03, G:0.01, T:0.49
Consensus pattern (40 bp):
TTTTAAAAAAATATAATAATTTTAACATATTTTTTAAAAA
Found at i:14590638 original size:19 final size:19
Alignment explanation
Indices: 14590549--14590688 Score: 60
Period size: 19 Copynumber: 7.2 Consensus size: 19
14590539 TTTTTAATTT
* * *
14590549 TTTTAAAAATTTTCATAAT
1 TTTTATAAATTTTTATAAA
14590568 TTTTA-AAATTCTCTTATGATAA
1 TTTTATAAATT-T-TTAT-A-AA
* *
14590590 TTTTAT-AATTTATAAAAA
1 TTTTATAAATTTTTATAAA
14590608 TATTTCAT--ATTTTTATAAA
1 T-TTT-ATAAATTTTTATAAA
*
14590627 TTTTATAAATTTTTA-GAA
1 TTTTATAAATTTTTATAAA
* *
14590645 TTTTTTAGAATTGTTT-TAAT
1 TTTTATA-AATT-TTTATAAA
*
14590665 TTTTTTAGAATTTTTCA-AAA
1 TTTTATA-AATTTTT-ATAAA
14590685 TTTT
1 TTTT
14590689 TAAGAAATTA
Statistics
Matches: 96, Mismatches: 11, Indels: 27
0.72 0.08 0.20
Matches are distributed among these distances:
17 2 0.02
18 19 0.20
19 34 0.35
20 29 0.30
21 2 0.02
22 10 0.10
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (19 bp):
TTTTATAAATTTTTATAAA
Found at i:14590694 original size:20 final size:19
Alignment explanation
Indices: 14590616--14590694 Score: 79
Period size: 20 Copynumber: 4.1 Consensus size: 19
14590606 AATATTTCAT
*
14590616 ATTTTTATAAATTTTATA-A
1 ATTTTTA-AAATTTTTTAGA
*
14590635 ATTTTTAGAATTTTTTAGA
1 ATTTTTAAAATTTTTTAGA
* *
14590654 ATTGTTTTAATTTTTTTAGA
1 ATT-TTTAAAATTTTTTAGA
*
14590674 ATTTTTCAAAATTTTTAAGA
1 ATTTTT-AAAATTTTTTAGA
14590694 A
1 A
14590695 ATTAAAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
18 8 0.16
19 14 0.29
20 27 0.55
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.57
Consensus pattern (19 bp):
ATTTTTAAAATTTTTTAGA
Found at i:14590726 original size:22 final size:21
Alignment explanation
Indices: 14590698--14590744 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
14590688 TTAAGAAATT
14590698 AAAAAAAAGTTTGATTTAAAA
1 AAAAAAAAGTTTGATTTAAAA
**
14590719 AAAAAAAAGTTTGATTTTTAA
1 AAAAAAAAGTTTGATTTAAAA
14590740 AAAAA
1 AAAAA
14590745 TTTAAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.30
Consensus pattern (21 bp):
AAAAAAAAGTTTGATTTAAAA
Found at i:14590872 original size:19 final size:20
Alignment explanation
Indices: 14590834--14590872 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
14590824 TTTTAAAATT
* *
14590834 TTCTTAGAAATTTTATAAAA
1 TTCTTAGAAACTTTAAAAAA
14590854 TTCTTAG-AACTTTAAAAAA
1 TTCTTAGAAACTTTAAAAAA
14590873 AATTTAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (20 bp):
TTCTTAGAAACTTTAAAAAA
Found at i:14590918 original size:70 final size:70
Alignment explanation
Indices: 14590844--14590992 Score: 162
Period size: 70 Copynumber: 2.1 Consensus size: 70
14590834 TTCTTAGAAA
* * *
14590844 TTTTATAAAATTCTT-AG-AACTTTAAAAAAAATTTAAAAATTTTTTTTAATTTTTAAAAAATTT
1 TTTTATAAAATTCTTGAGAAAATTT--AAAAAATTTAAAAATTTTTTATAATTTTTAAAAAATAT
14590907 TAATATT
64 TAATATT
* ** * **
14590914 TTTTA-AGAAATTTTTGAGAAAATTTTTAAATTTTTTAAATTTTTTATAATTTTTAAAAAATATT
1 TTTTATA-AAATTCTTGAGAAAATTTAAAAAATTTAAAAATTTTTTATAATTTTTAAAAAATATT
14590978 AATATT
65 AATATT
14590984 TTTT-TAAAA
1 TTTTATAAAA
14590993 AAATTTTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
69 4 0.06
70 55 0.83
71 2 0.03
72 5 0.08
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (70 bp):
TTTTATAAAATTCTTGAGAAAATTTAAAAAATTTAAAAATTTTTTATAATTTTTAAAAAATATTA
ATATT
Found at i:14590939 original size:32 final size:31
Alignment explanation
Indices: 14590891--14591018 Score: 88
Period size: 31 Copynumber: 4.2 Consensus size: 31
14590881 AATTTTTTTT
14590891 AATTTTTAAAAAA-TTTTAATATTTTTTAAGA
1 AATTTTTAAAAAATTTTTAA-ATTTTTTAAGA
*
14590922 AATTTTTGAGAAAATTTTTAAATTTTTT---A
1 AATTTTT-AAAAAATTTTTAAATTTTTTAAGA
* * ** * *
14590951 AATTTTT-TATAATTTTTAAAAAATATTAATA
1 AATTTTTAAAAAATTTTT-AAATTTTTTAAGA
** *
14590982 TTTTTTTAAAAAAATTTTAAAATTTTTT-AGA
1 AATTTTT-AAAAAATTTTTAAATTTTTTAAGA
14591013 AATTTT
1 AATTTT
14591019 CTTTTAAATA
Statistics
Matches: 72, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
27 8 0.11
28 6 0.08
29 8 0.11
31 19 0.26
32 18 0.25
33 13 0.18
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (31 bp):
AATTTTTAAAAAATTTTTAAATTTTTTAAGA
Found at i:14590957 original size:10 final size:9
Alignment explanation
Indices: 14590936--14590967 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
14590926 TTTGAGAAAA
14590936 TTTTTAAAT
1 TTTTTAAAT
14590945 TTTTTAAAT
1 TTTTTAAAT
14590954 TTTTTATAAT
1 TTTTTA-AAT
14590964 TTTT
1 TTTT
14590968 AAAAAATATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 15 0.68
10 7 0.32
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:14590993 original size:22 final size:21
Alignment explanation
Indices: 14590963--14591009 Score: 67
Period size: 22 Copynumber: 2.2 Consensus size: 21
14590953 TTTTTTATAA
*
14590963 TTTTTAAAAAATATTAATATT
1 TTTTTAAAAAATATTAAAATT
*
14590984 TTTTTAAAAAAATTTTAAAATT
1 TTTTT-AAAAAATATTAAAATT
14591006 TTTT
1 TTTT
14591010 AGAAATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTTTAAAAAATATTAAAATT
Found at i:14591015 original size:11 final size:10
Alignment explanation
Indices: 14590792--14591018 Score: 95
Period size: 10 Copynumber: 22.3 Consensus size: 10
14590782 TTATTTTGAA
*
14590792 TTTTTATAAGT
1 TTTTTA-AAAT
14590803 TTTTTAAAAT
1 TTTTTAAAAT
** *
14590813 TTTTTTGAAG
1 TTTTTAAAAT
14590823 TTTTTAAAAT
1 TTTTTAAAAT
14590833 TTTCTTAGAAAT
1 TTT-TTA-AAAT
*
14590845 TTTATAAAA-
1 TTTTTAAAAT
* * *
14590854 TTCTTAGAAC
1 TTTTTAAAAT
** *
14590864 TTTAAAAAAA
1 TTTTTAAAAT
* *
14590874 ATTTAAAAAT
1 TTTTTAAAAT
**
14590884 TTTTTTTAA-
1 TTTTTAAAAT
*
14590893 TTTTTAAAAA
1 TTTTTAAAAT
* *
14590903 ATTTTAATAT
1 TTTTTAAAAT
14590913 TTTTTAAGAAAT
1 TTTTT-A-AAAT
* *
14590925 TTTTGAGAAAA
1 TTTTTA-AAAT
14590936 TTTTT-AAAT
1 TTTTTAAAAT
14590945 TTTTT-AAAT
1 TTTTTAAAAT
*
14590954 TTTTTATAA-
1 TTTTTAAAAT
*
14590963 TTTTTAAAAA
1 TTTTTAAAAT
* * *
14590973 ATATTAATATT
1 TTTTTAA-AAT
*
14590984 TTTTTAAAAAA
1 TTTTT-AAAAT
*
14590995 ATTTTAAAAT
1 TTTTTAAAAT
14591005 TTTTTAGAAAT
1 TTTTTA-AAAT
14591016 TTT
1 TTT
14591019 CTTTTAAATA
Statistics
Matches: 158, Mismatches: 47, Indels: 22
0.70 0.21 0.10
Matches are distributed among these distances:
9 38 0.24
10 67 0.42
11 37 0.23
12 16 0.10
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (10 bp):
TTTTTAAAAT
Found at i:14592266 original size:28 final size:29
Alignment explanation
Indices: 14592224--14592278 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
14592214 AATAAAAAAT
* * *
14592224 AAAAAATTTATGAAAATTTA-AAAATTCA
1 AAAAAATCTAAGAAAATTAATAAAATTCA
14592252 AAAAAATCTAAGAAAATTAATAAAATT
1 AAAAAATCTAAGAAAATTAATAAAATT
14592279 ATGAAAAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 17 0.74
29 6 0.26
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (29 bp):
AAAAAATCTAAGAAAATTAATAAAATTCA
Found at i:14592425 original size:18 final size:18
Alignment explanation
Indices: 14592402--14592463 Score: 81
Period size: 18 Copynumber: 3.4 Consensus size: 18
14592392 CTAAAAATTT
*
14592402 TTTTAAAAAGTTTT-AATA
1 TTTTAAAAA-TTTTGAAAA
14592420 TTTTAAAAATTTTGAAAA
1 TTTTAAAAATTTTGAAAA
**
14592438 AATTAAAAATTTTGAAAA
1 TTTTAAAAATTTTGAAAA
14592456 TTTTAAAA
1 TTTTAAAA
14592464 TTATAAAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
17 4 0.11
18 34 0.89
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
TTTTAAAAATTTTGAAAA
Found at i:14592534 original size:8 final size:8
Alignment explanation
Indices: 14592402--14592514 Score: 64
Period size: 8 Copynumber: 13.0 Consensus size: 8
14592392 CTAAAAATTT
14592402 TTTTAAAAA
1 TTTT-AAAA
*
14592411 GTTTTAATA
1 -TTTTAAAA
14592420 TTTTAAAAA
1 TTTT-AAAA
14592429 TTTTGAAAAA
1 TTTT--AAAA
* *
14592439 ATTAAAAA
1 TTTTAAAA
14592447 TTTTGAAAA
1 TTTT-AAAA
14592456 TTTTAAAA
1 TTTTAAAA
*
14592464 TTATAAAAAA
1 TT-T-TAAAA
*
14592474 TTATAAAA
1 TTTTAAAA
* *
14592482 CTTCAAAA
1 TTTTAAAA
*
14592490 CTTTGAAAA
1 -TTTTAAAA
14592499 TTTTAAAA
1 TTTTAAAA
*
14592507 TTTCAAAA
1 TTTTAAAA
14592515 AAATCCAAAA
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
8 39 0.48
9 25 0.31
10 17 0.21
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.40
Consensus pattern (8 bp):
TTTTAAAA
Found at i:14592534 original size:9 final size:9
Alignment explanation
Indices: 14592402--14592547 Score: 70
Period size: 9 Copynumber: 16.2 Consensus size: 9
14592392 CTAAAAATTT
14592402 TTTTAAAAA
1 TTTTAAAAA
*
14592411 GTTTT-AATA
1 -TTTTAAAAA
14592420 TTTTAAAAA
1 TTTTAAAAA
14592429 TTTTGAAAAA
1 TTTT-AAAAA
*
14592439 -ATTAAAAA
1 TTTTAAAAA
*
14592447 TTTTGAAAA
1 TTTTAAAAA
14592456 TTTT-AAAA
1 TTTTAAAAA
*
14592464 TTATAAAAA
1 TTTTAAAAA
*
14592473 -ATTATAAAA
1 TTTTA-AAAA
* *
14592482 -CTTCAAAA
1 TTTTAAAAA
* *
14592490 CTTTGAAAA
1 TTTTAAAAA
14592499 TTTT-AAAA
1 TTTTAAAAA
*
14592507 TTTCAAAAAAA
1 TTT--TAAAAA
***
14592518 TCCAAAAAA
1 TTTTAAAAA
14592527 TTTTAAAAAA
1 TTTT-AAAAA
*
14592537 TATTAAAAA
1 TTTTAAAAA
14592546 TT
1 TT
14592548 CAACTATATA
Statistics
Matches: 105, Mismatches: 21, Indels: 21
0.71 0.14 0.14
Matches are distributed among these distances:
8 29 0.28
9 54 0.51
10 17 0.16
11 5 0.05
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.38
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:14592649 original size:21 final size:20
Alignment explanation
Indices: 14592624--14592668 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
14592614 TTTTTTTACA
* *
14592624 ATTTTTGCA-AAATTTTTAG
1 ATTTTTTCATAAAATTTTAG
14592643 ATTTTTTCATAAAATTTTAG
1 ATTTTTTCATAAAATTTTAG
14592663 ATTTTT
1 ATTTTT
14592669 ATTTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.31, C:0.04, G:0.07, T:0.58
Consensus pattern (20 bp):
ATTTTTTCATAAAATTTTAG
Found at i:14592703 original size:16 final size:17
Alignment explanation
Indices: 14592684--14592720 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
14592674 TTAAAGTTTT
*
14592684 TTTTATGAAAA-TTTAA
1 TTTTATCAAAATTTTAA
14592700 TTTTATCAAAATTTTAA
1 TTTTATCAAAATTTTAA
14592717 TTTT
1 TTTT
14592721 TAATTTTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (17 bp):
TTTTATCAAAATTTTAA
Found at i:14595378 original size:20 final size:20
Alignment explanation
Indices: 14595353--14595393 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
14595343 TCATTATATG
14595353 CCTATTTTACGAGGTATTGT
1 CCTATTTTACGAGGTATTGT
14595373 CCTATTTTACGAGGTATTGT
1 CCTATTTTACGAGGTATTGT
14595393 C
1 C
14595394 TTATATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.44
Consensus pattern (20 bp):
CCTATTTTACGAGGTATTGT
Found at i:14600622 original size:104 final size:104
Alignment explanation
Indices: 14600442--14600649 Score: 407
Period size: 104 Copynumber: 2.0 Consensus size: 104
14600432 TCATGTTTCC
*
14600442 AAACTTAACCATTGTTATCTCAATTTCTTTGCATTATTTAAAACCACATTTTCCTTTTACAAGAA
1 AAACTTAACCATTGTTATCTCAATTTCTTTGCATTATTCAAAACCACATTTTCCTTTTACAAGAA
14600507 TGTATGGATATGTTTGTTAATCTATTAAATTGATTACAG
66 TGTATGGATATGTTTGTTAATCTATTAAATTGATTACAG
14600546 AAACTTAACCATTGTTATCTCAATTTCTTTGCATTATTCAAAACCACATTTTCCTTTTACAAGAA
1 AAACTTAACCATTGTTATCTCAATTTCTTTGCATTATTCAAAACCACATTTTCCTTTTACAAGAA
14600611 TGTATGGATATGTTTGTTAATCTATTAAATTGATTACAG
66 TGTATGGATATGTTTGTTAATCTATTAAATTGATTACAG
14600650 TACCAGGTCT
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (104 bp):
AAACTTAACCATTGTTATCTCAATTTCTTTGCATTATTCAAAACCACATTTTCCTTTTACAAGAA
TGTATGGATATGTTTGTTAATCTATTAAATTGATTACAG
Found at i:14603264 original size:89 final size:89
Alignment explanation
Indices: 14603121--14603299 Score: 304
Period size: 89 Copynumber: 2.0 Consensus size: 89
14603111 TGGGTAAACA
* **
14603121 TAAACCTGATTTATTTATGAAAAATTCTGGTTTATGCATTTCACATTTTCTTCAATGTTTTGATA
1 TAAACCCGATTTATTTATGAAAAAAGCTGGTTTATGCATTTCACATTTTCTTCAATGTTTTGATA
*
14603186 TTTTAGCTTTTCAATTAACATACT
66 TTGTAGCTTTTCAATTAACATACT
**
14603210 TAAACCCGATTTATTTATGAAAAAAGCTGGTTTATGCATTTGTCATTTTCTTCAATGTTTTGATA
1 TAAACCCGATTTATTTATGAAAAAAGCTGGTTTATGCATTTCACATTTTCTTCAATGTTTTGATA
14603275 TTGTAGCTTTTCAATTAACATACT
66 TTGTAGCTTTTCAATTAACATACT
14603299 T
1 T
14603300 CTTGCTTGCA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
89 84 1.00
ACGTcount: A:0.29, C:0.13, G:0.11, T:0.47
Consensus pattern (89 bp):
TAAACCCGATTTATTTATGAAAAAAGCTGGTTTATGCATTTCACATTTTCTTCAATGTTTTGATA
TTGTAGCTTTTCAATTAACATACT
Found at i:14610704 original size:29 final size:30
Alignment explanation
Indices: 14610658--14610714 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
14610648 ATTAAAAGAG
* * * *
14610658 TAAAGATTTATTTGAATACAAT-ATAAATA
1 TAAAAATTTATCTAAATAAAATAATAAATA
14610687 TAAAAATTTATCTAAATAAAATAATAAA
1 TAAAAATTTATCTAAATAAAATAATAAA
14610715 ATTTAAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (30 bp):
TAAAAATTTATCTAAATAAAATAATAAATA
Found at i:14613260 original size:29 final size:28
Alignment explanation
Indices: 14613195--14613262 Score: 75
Period size: 29 Copynumber: 2.4 Consensus size: 28
14613185 CTTTTTTAAT
* *
14613195 TAAGTTTTTATTTTTTTATTATATCCGTA
1 TAAG-TTTTATCTTTTTATTATATCCGAA
*
14613224 TAAATTTTATCTTTTTATTTATATCC-AA
1 TAAGTTTTATCTTTTTA-TTATATCCGAA
14613252 GTAAGTTTTAT
1 -TAAGTTTTAT
14613263 TTTAATGAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 13 0.39
29 20 0.61
ACGTcount: A:0.28, C:0.07, G:0.06, T:0.59
Consensus pattern (28 bp):
TAAGTTTTATCTTTTTATTATATCCGAA
Found at i:14613470 original size:30 final size:30
Alignment explanation
Indices: 14613396--14613473 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
14613386 ATGTTTTATG
* * *
14613396 TTAAGGGTTTATTTAAATATAAATTAAAGG
1 TTAAGAGTTTATTTGAATATAAATTAAAGA
* * * *
14613426 TTAATAGCTCATTTGGATATAAATTAACA-A
1 TTAAGAGTTTATTTGAATATAAATTAA-AGA
14613456 TTAAGAGTTTATTTGAAT
1 TTAAGAGTTTATTTGAAT
14613474 GTAATAAAAA
Statistics
Matches: 36, Mismatches: 11, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
30 35 0.97
31 1 0.03
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (30 bp):
TTAAGAGTTTATTTGAATATAAATTAAAGA
Found at i:14614924 original size:28 final size:27
Alignment explanation
Indices: 14614852--14614936 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 27
14614842 TATTTTATTT
*
14614852 AAAATAAAAATTTA-TTAAGACACAAATCAA
1 AAAATAAAAACTTATTTAA-A-A-AAAT-AA
*
14614882 AAAATAAAAATTTATTTAAATAAAATAA
1 AAAATAAAAACTTATTTAAA-AAAATAA
* *
14614910 AATATAAAAACTTATTTTAAAAAATAA
1 AAAATAAAAACTTATTTAAAAAAATAA
14614937 TGCAACTTTT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
27 7 0.14
28 19 0.38
29 4 0.08
30 16 0.32
31 4 0.08
ACGTcount: A:0.65, C:0.05, G:0.01, T:0.29
Consensus pattern (27 bp):
AAAATAAAAACTTATTTAAAAAAATAA
Found at i:14615924 original size:15 final size:15
Alignment explanation
Indices: 14615904--14615936 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
14615894 AATATAAAAA
14615904 TTTTTAATT-TTACAT
1 TTTTTAATTATTA-AT
14615919 TTTTTAATTATTAAT
1 TTTTTAATTATTAAT
14615934 TTT
1 TTT
14615937 AATAAGTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTAATTATTAAT
Found at i:14616822 original size:36 final size:36
Alignment explanation
Indices: 14616737--14616831 Score: 111
Period size: 37 Copynumber: 2.6 Consensus size: 36
14616727 AAAATACAAC
* *
14616737 AATACCTCTATTCCCATAATTAGTTCAAATGATTAT
1 AATACCTCTCTTACCATAATTAGTTCAAATGATTAT
* * *
14616773 AATGCCCTTTCTTACCATAATTAG-TCAAAATTATTAT
1 AAT-ACCTCTCTTACCATAATTAGTTC-AAATGATTAT
*
14616810 AATACCTCTCTTATCATAATTA
1 AATACCTCTCTTACCATAATTA
14616832 TGAAAATATC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
36 21 0.43
37 28 0.57
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (36 bp):
AATACCTCTCTTACCATAATTAGTTCAAATGATTAT
Found at i:14616830 original size:26 final size:26
Alignment explanation
Indices: 14616801--14616857 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
14616791 AATTAGTCAA
* *
14616801 AATTATTATAATACCTCTCTTATCAT
1 AATTATGAAAATACCTCTCTTATCAT
* * *
14616827 AATTATGAAAATATCTTTTTTATCAT
1 AATTATGAAAATACCTCTCTTATCAT
14616853 AATTA
1 AATTA
14616858 ATCAAAATTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.39, C:0.12, G:0.02, T:0.47
Consensus pattern (26 bp):
AATTATGAAAATACCTCTCTTATCAT
Found at i:14624349 original size:28 final size:29
Alignment explanation
Indices: 14624317--14624378 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 29
14624307 AGTTAAATCT
*
14624317 CAAATTCA-AAACATAATAAT-AATATTTA
1 CAAATTCATAAA-ATAAAAATAAATATTTA
*
14624345 CAAATTGATAAAATAAAAATACAATATTTA
1 CAAATTCATAAAATAAAAATA-AATATTTA
14624375 CAAA
1 CAAA
14624379 ATAGAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 14 0.48
29 3 0.10
30 12 0.41
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.29
Consensus pattern (29 bp):
CAAATTCATAAAATAAAAATAAATATTTA
Found at i:14625299 original size:15 final size:15
Alignment explanation
Indices: 14625266--14625325 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
14625256 ATAAATTTGG
*
14625266 TTTTTTTAATA-TTC
1 TTTTTTTATTATTTC
*
14625280 ATTTTTTATTATTTC
1 TTTTTTTATTATTTC
*
14625295 TTTTTTTACTAAATTTTC
1 TTTTTTTA-T-TA-TTTC
*
14625313 TCTTTTTATTATT
1 TTTTTTTATTATT
14625326 ATTATTATGA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
14 9 0.25
15 12 0.33
16 2 0.06
17 2 0.06
18 11 0.31
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTTTTATTATTTC
Found at i:14626708 original size:12 final size:14
Alignment explanation
Indices: 14626683--14626715 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
14626673 GATATGCATA
14626683 TTGGTTTTTATG-T
1 TTGGTTTTTATGTT
14626696 TTGGTTTTT-TGTT
1 TTGGTTTTTATGTT
14626709 TTGGTTT
1 TTGGTTT
14626716 AGGCTAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 2 0.11
13 17 0.89
ACGTcount: A:0.03, C:0.00, G:0.24, T:0.73
Consensus pattern (14 bp):
TTGGTTTTTATGTT
Found at i:14628643 original size:17 final size:18
Alignment explanation
Indices: 14628621--14628654 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
14628611 TTGAAACGCA
*
14628621 TTATTTGTC-AATTATTT
1 TTATTTGACAAATTATTT
14628638 TTATTTGACAAATTATT
1 TTATTTGACAAATTATT
14628655 GTTTTTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.59
Consensus pattern (18 bp):
TTATTTGACAAATTATTT
Found at i:14629279 original size:19 final size:19
Alignment explanation
Indices: 14629255--14629296 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
14629245 AAATTACATT
14629255 ACTTTAATAATGTAATGGC
1 ACTTTAATAATGTAATGGC
14629274 ACTTTAATAATGTAATGGC
1 ACTTTAATAATGTAATGGC
14629293 ACTT
1 ACTT
14629297 GAAAGTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (19 bp):
ACTTTAATAATGTAATGGC
Found at i:14636743 original size:6 final size:7
Alignment explanation
Indices: 14636721--14636750 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
14636711 CATTAACTTC
14636721 AAATCAA
1 AAATCAA
14636728 AAATCAA
1 AAATCAA
14636735 AAATCAA
1 AAATCAA
*
14636742 AAATTAA
1 AAATCAA
14636749 AA
1 AA
14636751 TTTGATAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (7 bp):
AAATCAA
Found at i:14636938 original size:21 final size:21
Alignment explanation
Indices: 14636894--14636938 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
14636884 GTCTACATTT
* *
14636894 TCAAAATCTCTATTGTCATTC
1 TCAAAATCACTATTGTCATAC
14636915 TCAAAATCACTACTT-TCATAC
1 TCAAAATCACTA-TTGTCATAC
14636936 TCA
1 TCA
14636939 TTCCTAATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 19 0.90
22 2 0.10
ACGTcount: A:0.33, C:0.27, G:0.02, T:0.38
Consensus pattern (21 bp):
TCAAAATCACTATTGTCATAC
Found at i:14639370 original size:17 final size:17
Alignment explanation
Indices: 14639344--14639378 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
14639334 ACAAGAAAAT
14639344 ATAAGCAAATAAATAAA
1 ATAAGCAAATAAATAAA
*
14639361 ATAAGTAAATAAATAAA
1 ATAAGCAAATAAATAAA
14639378 A
1 A
14639379 CATGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.06, T:0.20
Consensus pattern (17 bp):
ATAAGCAAATAAATAAA
Found at i:14641892 original size:20 final size:21
Alignment explanation
Indices: 14641842--14641897 Score: 53
Period size: 20 Copynumber: 2.7 Consensus size: 21
14641832 TTTACTAAGC
14641842 TAAACACAAAAATAAAGCACAA
1 TAAAC-CAAAAATAAAGCACAA
* **
14641864 TAAA-AAAAAATAAAGTTC-A
1 TAAACCAAAAATAAAGCACAA
*
14641883 TAAACCAAAACTAAA
1 TAAACCAAAAATAAA
14641898 CTAAGTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
19 5 0.18
20 19 0.68
22 4 0.14
ACGTcount: A:0.68, C:0.14, G:0.04, T:0.14
Consensus pattern (21 bp):
TAAACCAAAAATAAAGCACAA
Found at i:14645212 original size:12 final size:12
Alignment explanation
Indices: 14645181--14645255 Score: 60
Period size: 12 Copynumber: 5.7 Consensus size: 12
14645171 CCCTTTGTCA
*
14645181 TTTTTCTTCCTTT
1 TTTTTCTT-ATTT
14645194 CTTTTTCTTATTT
1 -TTTTTCTTATTT
14645207 TTTTTCTTCCTCATTT
1 TTTTTC-T--T-ATTT
14645223 TTTTTCTTATTT
1 TTTTTCTTATTT
*
14645235 TTCTTTCTTACTT
1 TT-TTTCTTATTT
*
14645248 TCTTTCTT
1 TTTTTCTT
14645256 TGTTTTCTTT
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
12 18 0.34
13 15 0.28
14 8 0.15
15 2 0.04
16 10 0.19
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTTCTTATTT
Found at i:14645213 original size:26 final size:26
Alignment explanation
Indices: 14645181--14645252 Score: 99
Period size: 28 Copynumber: 2.7 Consensus size: 26
14645171 CCCTTTGTCA
14645181 TTTTTCTTCCTTTCTTTTTCTTATTT
1 TTTTTCTTCCTTTCTTTTTCTTATTT
*
14645207 TTTTTCTTCCTCATTTTTTTTCTTATTT
1 TTTTTCTTCCT--TTCTTTTTCTTATTT
*
14645235 TTCTTTCTTACTTTCTTT
1 TT-TTTCTTCCTTTCTTT
14645253 CTTTGTTTTC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
26 11 0.28
27 5 0.12
28 16 0.40
29 8 0.20
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (26 bp):
TTTTTCTTCCTTTCTTTTTCTTATTT
Found at i:14645253 original size:25 final size:25
Alignment explanation
Indices: 14645180--14645264 Score: 82
Period size: 25 Copynumber: 3.4 Consensus size: 25
14645170 CCCCTTTGTC
* *
14645180 ATTTTTCTTCCTTTCTTTTTCTTATT
1 ATTTTTCTTCCTTACTTTTT-TTCTT
* * *
14645206 TTTTTTCTTCCTCATTTTTTTTCTT
1 ATTTTTCTTCCTTACTTTTTTTCTT
* *
14645231 ATTTTTCTTTCTTACTTTCTTTCTT
1 ATTTTTCTTCCTTACTTTTTTTCTT
14645256 -TGTTTTCTT
1 AT-TTTTCTT
14645265 TCCCGTGCAT
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
24 1 0.02
25 31 0.65
26 16 0.33
ACGTcount: A:0.06, C:0.19, G:0.01, T:0.74
Consensus pattern (25 bp):
ATTTTTCTTCCTTACTTTTTTTCTT
Found at i:14645262 original size:13 final size:12
Alignment explanation
Indices: 14645181--14645266 Score: 59
Period size: 12 Copynumber: 6.8 Consensus size: 12
14645171 CCCTTTGTCA
*
14645181 TTTTTCTTCCTTT
1 TTTTTCTTTC-TT
14645194 CTTTTTCTTAT-TT
1 -TTTTTCTT-TCTT
* *
14645207 TTTTTCTTCCTCA
1 TTTTTCTTTCT-T
14645220 TTTTT-TTTCTT
1 TTTTTCTTTCTT
14645231 ATTTTTCTTTCTT
1 -TTTTTCTTTCTT
**
14645244 ACTTTCTTTCTT
1 TTTTTCTTTCTT
14645256 TGTTTTCTTTC
1 T-TTTTCTTTC
14645267 CCGTGCATCA
Statistics
Matches: 57, Mismatches: 9, Indels: 13
0.72 0.11 0.16
Matches are distributed among these distances:
12 28 0.49
13 21 0.37
14 8 0.14
ACGTcount: A:0.05, C:0.20, G:0.01, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCTT
Found at i:14647100 original size:57 final size:58
Alignment explanation
Indices: 14647014--14647122 Score: 166
Period size: 57 Copynumber: 1.9 Consensus size: 58
14647004 TGATTCCTTG
* * * *
14647014 GTTCTTGCCTATTCTAAAAAATACTAAACATTGAAAATATATTGAGAACATTCCATCA
1 GTTCTTGCCTATTCTAAAAAAGACTAAACATTAAAAATATACTGAAAACATTCCATCA
*
14647072 GTTCTTGCCTATTC-CAAAAAGACTAAACATTAAAAATATACTGAAAACATT
1 GTTCTTGCCTATTCTAAAAAAGACTAAACATTAAAAATATACTGAAAACATT
14647123 TGATAATGAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
57 32 0.70
58 14 0.30
ACGTcount: A:0.43, C:0.17, G:0.08, T:0.31
Consensus pattern (58 bp):
GTTCTTGCCTATTCTAAAAAAGACTAAACATTAAAAATATACTGAAAACATTCCATCA
Found at i:14647248 original size:26 final size:29
Alignment explanation
Indices: 14647190--14647249 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 29
14647180 TAATTACTAT
**
14647190 TTTTTCTTCTATTTTCTCTCTTCTTTTTT
1 TTTTTCTTCTATTTTCTCTCTTCTTTTAA
*
14647219 TTTTTCTTTTATTTTC-CT-TT-TTTTAA
1 TTTTTCTTCTATTTTCTCTCTTCTTTTAA
14647245 TTTTT
1 TTTTT
14647250 TGTGTTTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 9 0.32
27 2 0.07
28 2 0.07
29 15 0.54
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (29 bp):
TTTTTCTTCTATTTTCTCTCTTCTTTTAA
Found at i:14648495 original size:12 final size:12
Alignment explanation
Indices: 14648478--14648502 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
14648468 GTCAACTAGG
14648478 TCGTATAGGCCT
1 TCGTATAGGCCT
14648490 TCGTATAGGCCT
1 TCGTATAGGCCT
14648502 T
1 T
14648503 AAAAACCTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (12 bp):
TCGTATAGGCCT
Found at i:14648639 original size:23 final size:22
Alignment explanation
Indices: 14648613--14648664 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
14648603 ATCATTAATT
14648613 GAAAAAATTATAAAAAAATAAAA
1 GAAAAAATTAT-AAAAAATAAAA
* *
14648636 GAAAAAAATATAAAAAGTAAAA
1 GAAAAAATTATAAAAAATAAAA
14648658 -AAAAAAT
1 GAAAAAAT
14648665 AGAAAACAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 6 0.23
22 10 0.38
23 10 0.38
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (22 bp):
GAAAAAATTATAAAAAATAAAA
Found at i:14648648 original size:15 final size:16
Alignment explanation
Indices: 14648624--14648661 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
14648614 AAAAAATTAT
14648624 AAAAAAAT-AAAAG-A
1 AAAAAAATAAAAAGTA
14648638 AAAAAATATAAAAAGTA
1 AAAAAA-ATAAAAAGTA
14648655 AAAAAAA
1 AAAAAAA
14648662 AATAGAAAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.29
15 2 0.10
16 6 0.29
17 7 0.33
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (16 bp):
AAAAAAATAAAAAGTA
Found at i:14649757 original size:3 final size:3
Alignment explanation
Indices: 14649749--14649795 Score: 67
Period size: 3 Copynumber: 15.7 Consensus size: 3
14649739 TTTTCAAGAT
* * *
14649749 AAC AAC AAC AAT AAT AAC AAC AAC AAT AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
14649796 TAATAATGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.06
Consensus pattern (3 bp):
AAC
Found at i:14649767 original size:12 final size:12
Alignment explanation
Indices: 14649747--14649801 Score: 74
Period size: 12 Copynumber: 4.6 Consensus size: 12
14649737 TATTTTCAAG
*
14649747 ATAACAACAACA
1 ATAATAACAACA
14649759 ATAATAACAACA
1 ATAATAACAACA
*
14649771 ACAATAACAACA
1 ATAATAACAACA
* *
14649783 ACAACAACAACA
1 ATAATAACAACA
14649795 ATAATAA
1 ATAATAA
14649802 TGATAACTTA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.67, C:0.22, G:0.00, T:0.11
Consensus pattern (12 bp):
ATAATAACAACA
Found at i:14649767 original size:15 final size:15
Alignment explanation
Indices: 14649747--14649789 Score: 77
Period size: 15 Copynumber: 2.9 Consensus size: 15
14649737 TATTTTCAAG
14649747 ATAACAACAACAATA
1 ATAACAACAACAATA
14649762 ATAACAACAACAATA
1 ATAACAACAACAATA
*
14649777 ACAACAACAACAA
1 ATAACAACAACAA
14649790 CAACAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.67, C:0.23, G:0.00, T:0.09
Consensus pattern (15 bp):
ATAACAACAACAATA
Found at i:14649794 original size:15 final size:15
Alignment explanation
Indices: 14649749--14649795 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
14649739 TTTTCAAGAT
*
14649749 AACAACAACAATAAT
1 AACAACAACAATAAC
14649764 AACAACAACAATAAC
1 AACAACAACAATAAC
*
14649779 AACAACAACAACAAC
1 AACAACAACAATAAC
14649794 AA
1 AA
14649796 TAATAATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.68, C:0.26, G:0.00, T:0.06
Consensus pattern (15 bp):
AACAACAACAATAAC
Found at i:14653480 original size:25 final size:25
Alignment explanation
Indices: 14653446--14653499 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
14653436 TGCCCACAAT
*
14653446 ATTCATAAAGGTATTTAATTTAGGC
1 ATTCATAAAGGTATTTAATTAAGGC
14653471 ATTCATAAAGGTATTTAATTAAGGC
1 ATTCATAAAGGTATTTAATTAAGGC
14653496 ATTC
1 ATTC
14653500 TTATTTAAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.37, C:0.09, G:0.15, T:0.39
Consensus pattern (25 bp):
ATTCATAAAGGTATTTAATTAAGGC
Found at i:14653828 original size:49 final size:49
Alignment explanation
Indices: 14653696--14653829 Score: 238
Period size: 46 Copynumber: 2.8 Consensus size: 49
14653686 GAGGGATCGG
*
14653696 GTTCTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATCAG
1 GTTCTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATCAA
14653745 GTTCTGTTGAA---GCTGCAAACGTCGAATGGGTTCTGTTCAAGATCAA
1 GTTCTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATCAA
14653791 GTTCTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGT
1 GTTCTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGT
14653830 CTGCAAACGT
Statistics
Matches: 81, Mismatches: 1, Indels: 6
0.92 0.01 0.07
Matches are distributed among these distances:
46 45 0.56
49 36 0.44
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.31
Consensus pattern (49 bp):
GTTCTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATCAA
Found at i:14653838 original size:24 final size:24
Alignment explanation
Indices: 14653806--14653853 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
14653796 GTTGAAGCTG
14653806 CTGCAAACGTCGAATGGGTTCTGT
1 CTGCAAACGTCGAATGGGTTCTGT
14653830 CTGCAAACGTCGAATGGGTTCTGT
1 CTGCAAACGTCGAATGGGTTCTGT
14653854 TCAAGATCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (24 bp):
CTGCAAACGTCGAATGGGTTCTGT
Found at i:14653847 original size:73 final size:73
Alignment explanation
Indices: 14653757--14653902 Score: 283
Period size: 73 Copynumber: 2.0 Consensus size: 73
14653747 TCTGTTGAAG
14653757 CTGCAAACGTCGAATGGGTTCTGTTCAAGATCAAGTTCTGTTGAAGCTGCTGCAAACGTCGAATG
1 CTGCAAACGTCGAATGGGTTCTGTTCAAGATCAAGTTCTGTTGAAGCTGCTGCAAACGTCGAATG
14653822 GGTTCTGT
66 GGTTCTGT
*
14653830 CTGCAAACGTCGAATGGGTTCTGTTCAAGATCAGGTTCTGTTGAAGCTGCTGCAAACGTCGAATG
1 CTGCAAACGTCGAATGGGTTCTGTTCAAGATCAAGTTCTGTTGAAGCTGCTGCAAACGTCGAATG
14653895 GGTTCTGT
66 GGTTCTGT
14653903 TGAAGCTGCT
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (73 bp):
CTGCAAACGTCGAATGGGTTCTGTTCAAGATCAAGTTCTGTTGAAGCTGCTGCAAACGTCGAATG
GGTTCTGT
Found at i:14653904 original size:32 final size:32
Alignment explanation
Indices: 14653863--14653973 Score: 116
Period size: 32 Copynumber: 3.3 Consensus size: 32
14653853 TTCAAGATCA
*
14653863 GGTTCTGTTGAAGCTGCTGCAAACGTCGAATG
1 GGTTCTGTTGAAGCTGCTGTAAACGTCGAATG
*
14653895 GGTTCTGTTGAAGCTGCTGTAAACTGTTGAA-G
1 GGTTCTGTTGAAGCTGCTGTAAAC-GTCGAATG
* *
14653927 CTGTTGCAAACTGTTGAAGCTGCTGTAAAAGTCGAATG
1 -GGTT-----CTGTTGAAGCTGCTGTAAACGTCGAATG
14653965 GGTTCTGTT
1 GGTTCTGTT
14653974 CAATATCTGT
Statistics
Matches: 65, Mismatches: 6, Indels: 16
0.75 0.07 0.18
Matches are distributed among these distances:
32 29 0.45
33 8 0.12
37 8 0.12
38 20 0.31
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.32
Consensus pattern (32 bp):
GGTTCTGTTGAAGCTGCTGTAAACGTCGAATG
Found at i:14653923 original size:19 final size:19
Alignment explanation
Indices: 14653899--14653955 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
14653889 CGAATGGGTT
14653899 CTGTTGAAGCTGCTGTAAA
1 CTGTTGAAGCTGCTGTAAA
* *
14653918 CTGTTGAAGCTGTTGCAAA
1 CTGTTGAAGCTGCTGTAAA
14653937 CTGTTGAAGCTGCTGTAAA
1 CTGTTGAAGCTGCTGTAAA
14653956 AGTCGAATGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (19 bp):
CTGTTGAAGCTGCTGTAAA
Found at i:14653932 original size:9 final size:9
Alignment explanation
Indices: 14653899--14653948 Score: 55
Period size: 9 Copynumber: 5.3 Consensus size: 9
14653889 CGAATGGGTT
14653899 CTGTTGAAG
1 CTGTTGAAG
* *
14653908 CTGCTGTAAA
1 CTGTTG-AAG
14653918 CTGTTGAAG
1 CTGTTGAAG
*
14653927 CTGTTGCAAA
1 CTGTTG-AAG
14653937 CTGTTGAAG
1 CTGTTGAAG
14653946 CTG
1 CTG
14653949 CTGTAAAAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
9 18 0.55
10 15 0.45
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (9 bp):
CTGTTGAAG
Found at i:14653961 original size:119 final size:118
Alignment explanation
Indices: 14653699--14654063 Score: 402
Period size: 119 Copynumber: 3.0 Consensus size: 118
14653689 GGATCGGGTT
14653699 CTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATCAGGTTCTGTTGAA---GCTGC
1 CTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATCAGGTTCTGTTGAAGCTGCTGC
* * *
14653761 AAACGTCGAATGGGTTCTGTTCAAGATCAAGT--TCTGTTGAAGCTGCTGCAAA
66 AAACGTCGAATGGGTTCTGTTCAAGATC-TGTAAACTGTTGAAGCTGTTGCAAA
*
14653813 C-GTCGAATGGGTTCTGTCTGCAAACGTCGAATGGGTTCTGTTCAAGATCAGGTTCTGTTGAAGC
1 CTGTTGAA---G--CTG-CTGCAAACGTCGAATGGGTTCTGTTCAAGATCAGGTTCTGTTGAAGC
* *
14653877 TGCTGCAAACGTCGAATGGGTTCTGTTGAAGCTGCTGTAAACTGTTGAAGCTGTTGCAAA
60 TGCTGCAAACGTCGAATGGGTTCTGTTCAAGAT-CTGTAAACTGTTGAAGCTGTTGCAAA
* * * * *
14653937 CTGTTGAAGCTGCTGTAAAAGTCGAATGGGTTCTGTTCAATATC-TGTAAACTGTTGAAGCTGCT
1 CTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATCAGGT--TCTGTTGAA---GCT
* * *
14654001 GCAAGCTGCAAACATTGAATGGGTTCTGTTCAAGATCTGTAAACTATTGAAGCTGTTGCAAA
61 ----GCTGCAAACGTCGAATGGGTTCTGTTCAAGATCTGTAAACTGTTGAAGCTGTTGCAAA
14654063 C
1 C
14654064 ATCGAATGAG
Statistics
Matches: 212, Mismatches: 17, Indels: 32
0.81 0.07 0.12
Matches are distributed among these distances:
113 5 0.02
114 1 0.00
116 1 0.00
118 5 0.02
119 74 0.35
120 11 0.05
122 33 0.16
123 4 0.02
124 19 0.09
125 5 0.02
126 26 0.12
127 28 0.13
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.31
Consensus pattern (118 bp):
CTGTTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTCAAGATCAGGTTCTGTTGAAGCTGCTGC
AAACGTCGAATGGGTTCTGTTCAAGATCTGTAAACTGTTGAAGCTGTTGCAAA
Found at i:14654100 original size:10 final size:10
Alignment explanation
Indices: 14654085--14654119 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
14654075 TCTATTGAAG
14654085 CTGTTGCAAA
1 CTGTTGCAAA
*
14654095 CTGTTG-AAG
1 CTGTTGCAAA
14654104 CTGTTGCAAA
1 CTGTTGCAAA
14654114 CTGTTG
1 CTGTTG
14654120 AAGTTGCTGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (10 bp):
CTGTTGCAAA
Found at i:14654103 original size:19 final size:19
Alignment explanation
Indices: 14654079--14654171 Score: 123
Period size: 19 Copynumber: 4.9 Consensus size: 19
14654069 ATGAGTTCTA
*
14654079 TTGAAGCTGTTGCAAACTG
1 TTGAAGCTGCTGCAAACTG
*
14654098 TTGAAGCTGTTGCAAACTG
1 TTGAAGCTGCTGCAAACTG
* *
14654117 TTGAAGTTGCTGCAAATTG
1 TTGAAGCTGCTGCAAACTG
* *
14654136 TTGAAGCTACTGTAAACTG
1 TTGAAGCTGCTGCAAACTG
*
14654155 TTAAAGCTGCTGCAAAC
1 TTGAAGCTGCTGCAAAC
14654172 ATCGAATGGG
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 64 1.00
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.31
Consensus pattern (19 bp):
TTGAAGCTGCTGCAAACTG
Found at i:14654109 original size:9 final size:9
Alignment explanation
Indices: 14654079--14654122 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
14654069 ATGAGTTCTA
14654079 TTGAAGCTG
1 TTGAAGCTG
*
14654088 TTGCAAACTG
1 TTG-AAGCTG
14654098 TTGAAGCTG
1 TTGAAGCTG
*
14654107 TTGCAAACTG
1 TTG-AAGCTG
14654117 TTGAAG
1 TTGAAG
14654123 TTGCTGCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 13 0.45
10 16 0.55
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.32
Consensus pattern (9 bp):
TTGAAGCTG
Found at i:14654284 original size:19 final size:19
Alignment explanation
Indices: 14654260--14654316 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
14654250 ATCTGCAAAT
14654260 TGTTGAAGCTGCTGTAAAC
1 TGTTGAAGCTGCTGTAAAC
*
14654279 TGTTGAAGCTGCTGCAAAC
1 TGTTGAAGCTGCTGTAAAC
*
14654298 TATTGAAGCTGCTGTAAAC
1 TGTTGAAGCTGCTGTAAAC
14654317 ATCGAATGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (19 bp):
TGTTGAAGCTGCTGTAAAC
Found at i:14654335 original size:215 final size:209
Alignment explanation
Indices: 14653870--14654348 Score: 539
Period size: 215 Copynumber: 2.2 Consensus size: 209
14653860 TCAGGTTCTG
* **
14653870 TTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTGAAGCTGCTGTAAACTGTTGAAGCTGTTGCA
1 TTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTGAAGCTGCTGCAAACTGTTGAAGCTACTGCA
* * *
14653935 AACTGTTGAAGCTGCTGTAAAAGTCGAATGGGTTCTGTTCAATATCTGTAAACTGTTGAAGCTGC
66 AACTGTTAAAGCTGCTGCAAAAGTCGAATGGGTTCTGTTCAAGATCTGTAAACTGTTGAAGCTGC
* * * * * *
14654000 TGCAAGCTGCAAACATTGAATGGGTTCTGTTCAAGATCTGTAAACTATTGAAGCTGTTGCAAACA
131 TACAAGCTACAAACATCGAATAGGTTCTGTTCAAGATCTGCAAACTATTGAAGCTGCTGCAAACA
**
14654065 TCGAATGAGTTCTA
196 TCGAATGAGAACTA
* * * * *
14654079 TTGAAGCTGTTGCAAACTGTTGAA-GCTGTTGCAAACTGTTGAAGTTGCTGCAAATTGTTGAAGC
1 TTGAAGCTGCTGCAAAC-GTCGAATG-GGTT-----CTGTTGAAGCTGCTGCAAACTGTTGAAGC
*
14654143 TACTGTAAACTGTTAAAGCTGCTGCAAACA-TCGAATGGGTTCTGTTCAAGATCTGTAAACTGTT
59 TACTGCAAACTGTTAAAGCTGCTGCAAA-AGTCGAATGGGTTCTGTTCAAGATCTGTAAACTGTT
* * * *
14654207 GAAGCTGTTACAAGCTACAAACGTCGAATAGGTTCTGTTCAAGATCTGCAAATTGTTGAAGCTGC
123 GAAGCTGCTACAAGCTACAAACATCGAATAGGTTCTGTTCAAGATCTGCAAACTATTGAAGCTGC
* * * *
14654272 TGTAAACTGTTGAAGCTGCTGCAAACTA
188 TGCAAAC-ATCGAA--TG-AG--AACTA
* * *
14654300 TTGAAGCTGCTGTAAACATCGAATGGGTTCTGTTGAAGCTGCTACAAAC
1 TTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTGAAGCTGCTGCAAAC
14654349 GTCGAATGTG
Statistics
Matches: 219, Mismatches: 36, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
209 17 0.08
210 8 0.04
215 160 0.73
216 5 0.02
218 2 0.01
219 1 0.00
220 7 0.03
221 19 0.09
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.31
Consensus pattern (209 bp):
TTGAAGCTGCTGCAAACGTCGAATGGGTTCTGTTGAAGCTGCTGCAAACTGTTGAAGCTACTGCA
AACTGTTAAAGCTGCTGCAAAAGTCGAATGGGTTCTGTTCAAGATCTGTAAACTGTTGAAGCTGC
TACAAGCTACAAACATCGAATAGGTTCTGTTCAAGATCTGCAAACTATTGAAGCTGCTGCAAACA
TCGAATGAGAACTA
Found at i:14654341 original size:32 final size:32
Alignment explanation
Indices: 14654300--14654365 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
14654290 CTGCAAACTA
**
14654300 TTGAAGCTGCTGTAAACATCGAATGGGTTCTG
1 TTGAAGCTGCTACAAACATCGAATGGGTTCTG
* * *
14654332 TTGAAGCTGCTACAAACGTCGAATGTGTTTTG
1 TTGAAGCTGCTACAAACATCGAATGGGTTCTG
14654364 TT
1 TT
14654366 CAAGATCGGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.26, T:0.35
Consensus pattern (32 bp):
TTGAAGCTGCTACAAACATCGAATGGGTTCTG
Found at i:14655560 original size:5 final size:5
Alignment explanation
Indices: 14655552--14655598 Score: 51
Period size: 5 Copynumber: 8.8 Consensus size: 5
14655542 TTTTTCTTTA
14655552 AAAAT AAAAT AAAAAT GACAAAT AAAAT -AAAT AAAAT AATAAT AAAA
1 AAAAT AAAAT -AAAAT -A-AAAT AAAAT AAAAT AAAAT AA-AAT AAAA
14655599 ATGTAAGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
4 4 0.11
5 17 0.46
6 12 0.32
7 4 0.11
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:14655576 original size:13 final size:11
Alignment explanation
Indices: 14655550--14655600 Score: 54
Period size: 12 Copynumber: 4.6 Consensus size: 11
14655540 AATTTTTCTT
14655550 TAAAAATAAAA
1 TAAAAATAAAA
14655561 TAAAAATGACAAA
1 TAAAAAT-A-AAA
14655574 T-AAAAT-AAA
1 TAAAAATAAAA
14655583 T-AAAATAATAA
1 TAAAAATAA-AA
14655594 TAAAAAT
1 TAAAAAT
14655601 GTAAGAAAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
9 9 0.26
10 1 0.03
11 10 0.29
12 11 0.31
13 4 0.11
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:14655857 original size:174 final size:175
Alignment explanation
Indices: 14655580--14655917 Score: 431
Period size: 174 Copynumber: 1.9 Consensus size: 175
14655570 CAAATAAAAT
* *
14655580 AAATAAAATAATAATAAAAATGTAAGAAAAGAAATATTTATCTGACGATGAGATTTTAAGGTATT
1 AAATAAAATAATAATAAAAATGTAAGAAAAGAAATATTTATCTGACGATAAGATTCTAAGGTATT
* * *
14655645 TCGAGTAGCGACACCTAAGAAATCTCAAGGTAAA-TTTTTTTTTTAAAATACTACTAGCATA-TT
66 TCGAGTAGCGACACCTAAAAAATCTCAAGGTAAATTTTTTTTTTTAAAATACTACCAACATATTT
*
14655708 GAAGTATTTATAAAAGGTTTTCAATACAATAAAAAAAATTTTCTATA
131 GAA-TATTTATAAAA-ATTTTCAATACAATAAAAAAAATTTTCTATA
**
14655755 AAAT-AAA-AATAATAAAAAATG-AAGAAAAAGATAAT-TTTAT-TCGATTATAAGATTCTAAGG
1 AAATAAAATAATAAT-AAAAATGTAAG-AAAAGA-AATATTTATCT-GACGATAAGATTCTAAGG
** *
14655815 TATTTCGAGTAGCGATTCCTAAAAAATCTCTAA-GTGAATTTTTTTTTTTTAAAATACTACCAAC
62 TATTTCGAGTAGCGACACCTAAAAAATCTC-AAGGT-AAATTTTTTTTTTTAAAATACTACCAAC
* *
14655879 GTATTTGAATATTTATAAAAATTTTCAATATAATAAAAA
125 ATATTTGAATATTTATAAAAATTTTCAATACAATAAAAA
14655918 TTTCTATTTT
Statistics
Matches: 142, Mismatches: 13, Indels: 16
0.83 0.08 0.09
Matches are distributed among these distances:
173 10 0.07
174 64 0.45
175 28 0.20
176 35 0.25
177 5 0.04
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.35
Consensus pattern (175 bp):
AAATAAAATAATAATAAAAATGTAAGAAAAGAAATATTTATCTGACGATAAGATTCTAAGGTATT
TCGAGTAGCGACACCTAAAAAATCTCAAGGTAAATTTTTTTTTTTAAAATACTACCAACATATTT
GAATATTTATAAAAATTTTCAATACAATAAAAAAAATTTTCTATA
Found at i:14664529 original size:24 final size:24
Alignment explanation
Indices: 14664502--14664548 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
14664492 TTGCCATGAG
14664502 AATGAATTAATG-TTTGGATTGTAT
1 AATGAATTAATGCTTT-GATTGTAT
14664526 AATGAATTAATGCTTTGATTGTA
1 AATGAATTAATGCTTTGATTGTA
14664549 AATTTAAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.34, C:0.02, G:0.19, T:0.45
Consensus pattern (24 bp):
AATGAATTAATGCTTTGATTGTAT
Found at i:14666061 original size:3 final size:3
Alignment explanation
Indices: 14666055--14666103 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
14666045 CATGACGACG
14666055 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
14666103 A
1 A
14666104 ATTTTAAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:14667198 original size:13 final size:13
Alignment explanation
Indices: 14667180--14667204 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14667170 CCTTGATTAG
14667180 TTTTTTTCATCTC
1 TTTTTTTCATCTC
14667193 TTTTTTTCATCT
1 TTTTTTTCATCT
14667205 TAATATTTAT
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:0.20, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTTCATCTC
Found at i:14674699 original size:10 final size:10
Alignment explanation
Indices: 14674669--14674700 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
14674659 GGAAACCTTC
14674669 AACC-AAAAA
1 AACCAAAAAA
14674678 AA-CAAAAAA
1 AACCAAAAAA
14674687 AACCAAAAAA
1 AACCAAAAAA
14674697 AACC
1 AACC
14674701 CAATAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 1 0.05
9 9 0.43
10 11 0.52
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
AACCAAAAAA
Found at i:14675795 original size:15 final size:16
Alignment explanation
Indices: 14675770--14675799 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
14675760 GTATATTTTT
14675770 AATTATTTTTATTTAA
1 AATTATTTTTATTTAA
14675786 AATT-TTTTTATTTA
1 AATTATTTTTATTTA
14675800 TTAATAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
AATTATTTTTATTTAA
Found at i:14677561 original size:2 final size:2
Alignment explanation
Indices: 14677554--14677681 Score: 64
Period size: 2 Copynumber: 64.5 Consensus size: 2
14677544 TAATTTAGTA
* * * * * * * *
14677554 AT AT AT AT AT AT AT AG GT AT AT CT AT AC CT AT AT AT AC CT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
14677596 AT AT AT AT AT AT AT CT AT AT AT GT AC CT AT AT -T AT ACT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * *
14677638 AT AT AT ACT -T AT AT AG GT AT AT AT AT AG CT AT AT AT AT A- AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14677679 AT A
1 AT A
14677682 CCACCGACGA
Statistics
Matches: 89, Mismatches: 32, Indels: 10
0.68 0.24 0.08
Matches are distributed among these distances:
1 3 0.03
2 83 0.93
3 3 0.03
ACGTcount: A:0.41, C:0.09, G:0.05, T:0.45
Consensus pattern (2 bp):
AT
Found at i:14680944 original size:23 final size:23
Alignment explanation
Indices: 14680917--14680962 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
14680907 TAATAGGTAG
14680917 AAGAAGAATAAAA-AAAAAATGAA
1 AAGAAGAA-AAAAGAAAAAATGAA
*
14680940 AAGAAGAAAAAAGATAAAATGAA
1 AAGAAGAAAAAAGAAAAAATGAA
14680963 CCATTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (23 bp):
AAGAAGAAAAAAGAAAAAATGAA
Found at i:14684946 original size:120 final size:116
Alignment explanation
Indices: 14684728--14684962 Score: 285
Period size: 120 Copynumber: 2.0 Consensus size: 116
14684718 GAATCTAAAA
*
14684728 AATTCAAGAAAATAAACTGCTAAAAATGAAGTCAAATATTTAAAAAAAAAAAAGTAAAGAAAGAA
1 AATTCAAGAAAATAAACTGCTAAAAATGAAGTCAAATATTTAAAAAAAAAAAAGCAAAGAAAGAA
* * *
14684793 AGACATGCATATGGGAGATAAAAGTCTGAGGTAAAAAGTGAATAAAGCTTT
66 AGACATGCACATCGAAGATAAAAGTCTGAGGTAAAAAGTGAATAAAGCTTT
* * * * * *
14684844 AATTCAAGAAACTAGAA-TGCTATAATTGAAGTTAAATGTTTTCAAAGAAAAAAAAGGCAAAGAA
1 AATTCAAGAAAATA-AACTGCTAAAAATGAAGTCAAAT-ATTT-AAA-AAAAAAAAAGCAAAG-A
* * *
14684908 AAGAAAGACATGCACCTCGAATATGAGAA-TCTGAGGTAAAAAGTGAATAAAGCTT
61 AAGAAAGACATGCACATCGAAGAT-AAAAGTCTGAGGTAAAAAGTGAATAAAGCTT
14684963 CAGTTAAAAT
Statistics
Matches: 100, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
116 30 0.30
117 5 0.05
118 3 0.03
119 13 0.13
120 46 0.46
121 3 0.03
ACGTcount: A:0.52, C:0.09, G:0.18, T:0.21
Consensus pattern (116 bp):
AATTCAAGAAAATAAACTGCTAAAAATGAAGTCAAATATTTAAAAAAAAAAAAGCAAAGAAAGAA
AGACATGCACATCGAAGATAAAAGTCTGAGGTAAAAAGTGAATAAAGCTTT
Found at i:14687122 original size:23 final size:23
Alignment explanation
Indices: 14687090--14687166 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
14687080 TTTTTTATGG
* * *
14687090 CACTTTAAGCTTAGATTAGTTGA
1 CACTTTAAGCTCAAATTAGCTGA
14687113 C-CTTTTAAGCTCAAATTAGCTGA
1 CAC-TTTAAGCTCAAATTAGCTGA
* **
14687136 CACTTTAAGCCCAGTTTAGCTGA
1 CACTTTAAGCTCAAATTAGCTGA
14687159 CACTTTAA
1 CACTTTAA
14687167 ACTTAGTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
22 1 0.02
23 44 0.96
24 1 0.02
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (23 bp):
CACTTTAAGCTCAAATTAGCTGA
Found at i:14687978 original size:8 final size:8
Alignment explanation
Indices: 14687967--14688056 Score: 69
Period size: 8 Copynumber: 10.9 Consensus size: 8
14687957 TTCATTAATT
14687967 AAAAAATA
1 AAAAAATA
*
14687975 AAAATAA-C
1 AAAA-AATA
14687983 AAAAAATA
1 AAAAAATA
14687991 AAAAAATA
1 AAAAAATA
14687999 ATAAAAA-A
1 A-AAAAATA
* *
14688007 ATCAAAAGA
1 A-AAAAATA
*
14688016 AACAAAAGA
1 AA-AAAATA
14688025 AACAAAA-A
1 AA-AAAATA
14688033 CAAAAAATA
1 -AAAAAATA
14688042 AAAAAATA
1 AAAAAATA
14688050 AAAAAAT
1 AAAAAAT
14688057 TCTGAAAAAC
Statistics
Matches: 71, Mismatches: 4, Indels: 14
0.80 0.04 0.16
Matches are distributed among these distances:
7 2 0.03
8 44 0.62
9 25 0.35
ACGTcount: A:0.82, C:0.06, G:0.02, T:0.10
Consensus pattern (8 bp):
AAAAAATA
Found at i:14687989 original size:10 final size:9
Alignment explanation
Indices: 14687967--14688054 Score: 56
Period size: 9 Copynumber: 9.7 Consensus size: 9
14687957 TTCATTAATT
*
14687967 AAAAAATAA
1 AAAAAACAA
*
14687976 AAATAACAA
1 AAAAAACAA
14687985 AAAATAA-AA
1 AAAA-AACAA
* *
14687994 AAATAATAA
1 AAAAAACAA
*
14688003 AAAAATCAA
1 AAAAAACAA
*
14688012 AAGAAACAA
1 AAAAAACAA
*
14688021 AAGAAACAA
1 AAAAAACAA
14688030 AAACAAA-AA
1 AAA-AAACAA
14688039 ATAAAAA-AA
1 A-AAAAACAA
14688048 TAAAAAA
1 -AAAAAA
14688055 ATTCTGAAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
8 2 0.03
9 54 0.84
10 8 0.12
ACGTcount: A:0.83, C:0.06, G:0.02, T:0.09
Consensus pattern (9 bp):
AAAAAACAA
Found at i:14690784 original size:18 final size:20
Alignment explanation
Indices: 14690761--14690801 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
14690751 TACATGTATT
*
14690761 ATAAATAT-AA-TATTGAAA
1 ATAAATATGAACTATCGAAA
14690779 ATAAATATGAACTATCGAAA
1 ATAAATATGAACTATCGAAA
14690799 ATA
1 ATA
14690802 TAATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 8 0.40
19 2 0.10
20 10 0.50
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (20 bp):
ATAAATATGAACTATCGAAA
Found at i:14691329 original size:2 final size:2
Alignment explanation
Indices: 14691324--14691369 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
14691314 TCTCTCTCTC
*
14691324 TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14691365 TA TA T
1 TA TA T
14691370 CTGTTGAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14691533 original size:100 final size:100
Alignment explanation
Indices: 14691368--14691553 Score: 248
Period size: 100 Copynumber: 1.9 Consensus size: 100
14691358 TATATATTAT
* * * * * *
14691368 ATCTGTTGAAATCAATGGTTAAAAAAATGTGTAAAATTTAAAAAGTTTTACATTGTGTAAGTTGA
1 ATCTATTGAAATCAATAGTTAAAAAAATGTGTAAAATTTAAAAAGTTGTACACTGTATAAATTGA
14691433 TCCCTCATATATATATATATAATTTCTTTCCTTGG
66 TCCCTCATATATATATATATAATTTCTTTCCTTGG
* * ***
14691468 ATCTATTGAAATTAATAGTTGAAAAAATGTGTAAAACTTT-TTTAGTTGTACACTGTATAAATTG
1 ATCTATTGAAATCAATAGTTAAAAAAATGTGTAAAA-TTTAAAAAGTTGTACACTGTATAAATTG
*
14691532 ATCTCTCATATATATATATATA
65 ATCCCTCATATATATATATATA
14691554 TTTAACCATT
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
100 70 0.96
101 3 0.04
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (100 bp):
ATCTATTGAAATCAATAGTTAAAAAAATGTGTAAAATTTAAAAAGTTGTACACTGTATAAATTGA
TCCCTCATATATATATATATAATTTCTTTCCTTGG
Found at i:14691944 original size:2 final size:2
Alignment explanation
Indices: 14691933--14691971 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
14691923 TCCATTCTTC
14691933 TA TA -A TA 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 TA TA TA TA
14691972 AATTCAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:14692409 original size:24 final size:24
Alignment explanation
Indices: 14692382--14692442 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
14692372 TAATAAGAAC
*
14692382 AAATTTACTAAATAA-AATTTATAA
1 AAATTTAATAAATAACAATTT-TAA
* *
14692406 AAATTAAATAGATAACAATTTTAA
1 AAATTTAATAAATAACAATTTTAA
* *
14692430 AAATATATTAAAT
1 AAATTTAATAAAT
14692443 TCACAATAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.59, C:0.03, G:0.02, T:0.36
Consensus pattern (24 bp):
AAATTTAATAAATAACAATTTTAA
Found at i:14694429 original size:8 final size:8
Alignment explanation
Indices: 14694416--14694444 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
14694406 ACTTTTGAAA
14694416 TTAAAATT
1 TTAAAATT
14694424 TTAAAATT
1 TTAAAATT
14694432 TTAAAATT
1 TTAAAATT
14694440 TTAAA
1 TTAAA
14694445 TAGTTTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
TTAAAATT
Found at i:14698126 original size:23 final size:23
Alignment explanation
Indices: 14698100--14698147 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
14698090 AATAAACACA
*
14698100 TCCATAAGCCCAGAGAGCAACAT
1 TCCATAAGCCCAGACAGCAACAT
14698123 TCCATAAGCCCAGACAGCAACAT
1 TCCATAAGCCCAGACAGCAACAT
14698146 TC
1 TC
14698148 TTCAATGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.33, G:0.15, T:0.15
Consensus pattern (23 bp):
TCCATAAGCCCAGACAGCAACAT
Found at i:14699453 original size:7 final size:7
Alignment explanation
Indices: 14699443--14699488 Score: 92
Period size: 7 Copynumber: 6.6 Consensus size: 7
14699433 GAAAAAATCA
14699443 AAAATTG
1 AAAATTG
14699450 AAAATTG
1 AAAATTG
14699457 AAAATTG
1 AAAATTG
14699464 AAAATTG
1 AAAATTG
14699471 AAAATTG
1 AAAATTG
14699478 AAAATTG
1 AAAATTG
14699485 AAAA
1 AAAA
14699489 ACAAGAAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 39 1.00
ACGTcount: A:0.61, C:0.00, G:0.13, T:0.26
Consensus pattern (7 bp):
AAAATTG
Found at i:14704257 original size:14 final size:14
Alignment explanation
Indices: 14704234--14704265 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
14704224 AATTTCATCA
14704234 ATTAAAATTTTGAC
1 ATTAAAATTTTGAC
*
14704248 ATTAAGATTTTGAC
1 ATTAAAATTTTGAC
14704262 ATTA
1 ATTA
14704266 TAATGAGAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (14 bp):
ATTAAAATTTTGAC
Found at i:14704345 original size:2 final size:2
Alignment explanation
Indices: 14704338--14704382 Score: 54
Period size: 2 Copynumber: 21.0 Consensus size: 2
14704328 CTAAAAGCAT
*
14704338 TA TA TA TA TA TA TA TCA TA TA AA TA CTA TA TA TA TA TA TGA TA
1 TA TA TA TA TA TA TA T-A TA TA TA TA -TA TA TA TA TA TA T-A TA
14704381 TA
1 TA
14704383 AGTACTATGT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 32 0.84
3 6 0.16
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (2 bp):
TA
Found at i:14704367 original size:24 final size:24
Alignment explanation
Indices: 14704340--14704390 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
14704330 AAAAGCATTA
14704340 TATATATATATATCATATAAATAC
1 TATATATATATATCATATAAATAC
* *
14704364 TATATATATATATGATATAAGTAC
1 TATATATATATATCATATAAATAC
14704388 TAT
1 TAT
14704391 GTACATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (24 bp):
TATATATATATATCATATAAATAC
Found at i:14704398 original size:24 final size:24
Alignment explanation
Indices: 14704340--14704398 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
14704330 AAAAGCATTA
*
14704340 TATATATATATATCATATAAATAC
1 TATATACATATATCATATAAATAC
* * *
14704364 TATATATATATATGATATAAGTAC
1 TATATACATATATCATATAAATAC
*
14704388 TATGTACATAT
1 TATATACATAT
14704399 TCTATATGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (24 bp):
TATATACATATATCATATAAATAC
Found at i:14711027 original size:3 final size:3
Alignment explanation
Indices: 14711014--14711082 Score: 106
Period size: 3 Copynumber: 23.3 Consensus size: 3
14711004 TAATTTTTAA
*
14711014 ATT ATTT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT AGT ATT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
14711059 ATT ATT ATT ATT ATT ATT A-T ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
14711083 CTGATTCTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
2 4 0.07
3 54 0.89
4 3 0.05
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:14711463 original size:5 final size:5
Alignment explanation
Indices: 14711453--14711479 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
14711443 TTTTTTTCTC
14711453 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
14711480 CCTAGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:14712497 original size:15 final size:16
Alignment explanation
Indices: 14712477--14712512 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
14712467 ACAATTAGAA
14712477 TTAAATAAATAAT-TT
1 TTAAATAAATAATCTT
*
14712492 TTAAATAATTAATCTT
1 TTAAATAAATAATCTT
14712508 TTAAA
1 TTAAA
14712513 ATTTAAAATG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAATAAATAATCTT
Found at i:14713092 original size:2 final size:2
Alignment explanation
Indices: 14713083--14713118 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
14713073 TATATGTTGT
14713083 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
14713119 TAGATATCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14718171 original size:19 final size:19
Alignment explanation
Indices: 14718144--14718205 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
14718134 TCTTTTTTCC
*
14718144 TTTTCTGTAATTTAATTTT
1 TTTTTTGTAATTTAATTTT
*
14718163 TTTTTTGTAATTTAACTTT
1 TTTTTTGTAATTTAATTTT
14718182 TTTTTTGTAA-TTAATTTT
1 TTTTTTGTAATTTAATTTT
14718200 TATTTT
1 T-TTTT
14718206 ATATTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
18 8 0.21
19 31 0.79
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTTGTAATTTAATTTT
Found at i:14720834 original size:15 final size:16
Alignment explanation
Indices: 14720814--14720843 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
14720804 TTAAATTTAA
14720814 TAAATATA-TATATTT
1 TAAATATATTATATTT
14720829 TAAATATATTATATT
1 TAAATATATTATATT
14720844 ATATTATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATATATTATATTT
Found at i:14720873 original size:25 final size:23
Alignment explanation
Indices: 14720817--14720873 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 23
14720807 AATTTAATAA
*
14720817 ATATATA-TATTTTAAATATATT
1 ATATATATTATTATAAATATATT
14720839 ATAT-TA-TATTATAAATATATTT
1 ATATATATTATTATAAATATA-TT
14720861 ATTATATATTATT
1 A-TATATATTATT
14720874 TTATTTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 14 0.47
22 7 0.23
23 3 0.10
24 2 0.07
25 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATATATTATTATAAATATATT
Found at i:14720876 original size:15 final size:16
Alignment explanation
Indices: 14720832--14720878 Score: 62
Period size: 15 Copynumber: 3.0 Consensus size: 16
14720822 TATATTTTAA
14720832 ATATATTATATTATATT
1 ATATATTATATT-TATT
*
14720849 ATA-AATATATTTATT
1 ATATATTATATTTATT
14720864 ATATATTAT-TTTATT
1 ATATATTATATTTATT
14720879 TTAAATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 13 0.48
16 11 0.41
17 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATATTATATTTATT
Found at i:14720886 original size:15 final size:15
Alignment explanation
Indices: 14720840--14720886 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
14720830 AAATATATTA
*
14720840 TATTATATTATAAA-
1 TATTTTATTATAAAT
*
14720854 TATATTTATTATATAT
1 TAT-TTTATTATAAAT
*
14720870 TATTTTATTTTAAAT
1 TATTTTATTATAAAT
14720885 TA
1 TA
14720887 AATAAAGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 3 0.11
15 21 0.78
16 3 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TATTTTATTATAAAT
Found at i:14721395 original size:15 final size:16
Alignment explanation
Indices: 14721375--14721414 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 16
14721365 ATTATAAATA
14721375 ATAAATTTTAAAATTT
1 ATAAATTTTAAAATTT
14721391 A-AAA-TTT-AAATTT
1 ATAAATTTTAAAATTT
14721404 ATTAAATTTTA
1 A-TAAATTTTA
14721415 TCTTTATGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 7
0.74 0.00 0.26
Matches are distributed among these distances:
13 7 0.35
14 3 0.15
15 6 0.30
16 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
ATAAATTTTAAAATTT
Found at i:14722173 original size:2 final size:2
Alignment explanation
Indices: 14722166--14722201 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
14722156 ACAGTCCATT
14722166 TC TC TC TC TC TC 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
14722202 GCCATTCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:14725212 original size:14 final size:16
Alignment explanation
Indices: 14725183--14725212 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14725173 TTAATAAAGA
14725183 TTATATATACATTTTT
1 TTATATATACATTTTT
14725199 TTATATATA-ATTTT
1 TTATATATACATTTT
14725213 ATACATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATATATACATTTTT
Found at i:14728227 original size:16 final size:16
Alignment explanation
Indices: 14728206--14728239 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
14728196 AATTTTTTGA
14728206 TTTGTT-TTTGAATATT
1 TTTGTTATTTGAAT-TT
14728222 TTTGTTATTTGAATTT
1 TTTGTTATTTGAATTT
14728238 TT
1 TT
14728240 ATCATTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.18, C:0.00, G:0.12, T:0.71
Consensus pattern (16 bp):
TTTGTTATTTGAATTT
Found at i:14729202 original size:3 final size:3
Alignment explanation
Indices: 14729196--14729220 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
14729186 AACAACAACT
14729196 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
14729221 ATAAAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Done.