Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 46 of 125
Found at i:9266517 original size:2 final size:2
Alignment explanation
Indices: 9266510--9266546 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
9266500 ATGAAGCTTT
9266510 TA TA TA TA TA TA -A 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
9266547 ATTTAAACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:9269901 original size:9 final size:9
Alignment explanation
Indices: 9269880--9269909 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
9269870 TATTTAAAAT
9269880 AATATATATA
1 AATATATA-A
9269890 AATATATAA
1 AATATATAA
9269899 AATATATAA
1 AATATATAA
9269908 AA
1 AA
9269910 ATAAAACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 12 0.60
10 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AATATATAA
Found at i:9269937 original size:20 final size:21
Alignment explanation
Indices: 9269904--9269956 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
9269894 TATAAAATAT
* *
9269904 ATAAA-AATAAAACCAAAA-G
1 ATAAACAAAAAAACCAAAAAA
9269923 ATAAACAAAAAAACCAAAAAA
1 ATAAACAAAAAAACCAAAAAA
9269944 ATAAACAAAAAAA
1 ATAAACAAAAAAA
9269957 GAAAAGAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 5 0.17
20 12 0.40
21 13 0.43
ACGTcount: A:0.79, C:0.11, G:0.02, T:0.08
Consensus pattern (21 bp):
ATAAACAAAAAAACCAAAAAA
Found at i:9270899 original size:21 final size:21
Alignment explanation
Indices: 9270851--9270903 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
9270841 AGATTTTCAA
* *
9270851 ACTTTTCTTTTTTGTTTTCTG
1 ACTTTTTTTTTTTCTTTTCTG
9270872 ACTTTTTTTTTTTTACTTTT-TG
1 AC-TTTTTTTTTTT-CTTTTCTG
9270894 ACTTTTTTTT
1 ACTTTTTTTT
9270904 GGAAAAAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.36
22 14 0.50
23 4 0.14
ACGTcount: A:0.08, C:0.11, G:0.06, T:0.75
Consensus pattern (21 bp):
ACTTTTTTTTTTTCTTTTCTG
Found at i:9271339 original size:18 final size:18
Alignment explanation
Indices: 9271316--9271371 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
9271306 ATTCGTAAGA
9271316 ATTTCAAATTTCACAAAG
1 ATTTCAAATTTCACAAAG
* *
9271334 ATTTCAAAAGTTCATAAA-
1 ATTTC-AAATTTCACAAAG
*
9271352 ATTTCAAATTT-ACAAGG
1 ATTTCAAATTTCACAAAG
9271369 ATT
1 ATT
9271372 CCAAGTTTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
16 3 0.10
17 8 0.26
18 10 0.32
19 10 0.32
ACGTcount: A:0.45, C:0.12, G:0.07, T:0.36
Consensus pattern (18 bp):
ATTTCAAATTTCACAAAG
Found at i:9271448 original size:18 final size:18
Alignment explanation
Indices: 9271425--9271496 Score: 63
Period size: 18 Copynumber: 4.0 Consensus size: 18
9271415 TCACAAGATG
*
9271425 TTTCAAGCTTCGCAAAAA
1 TTTCAAGATTCGCAAAAA
* * * *
9271443 TTTCAAGATTTGTAGAGA
1 TTTCAAGATTCGCAAAAA
*
9271461 TTTCAAGATTCGCAAAAG
1 TTTCAAGATTCGCAAAAA
* * *
9271479 CTTCAAGACTCACAAAAA
1 TTTCAAGATTCGCAAAAA
9271497 AAAATTTTCA
Statistics
Matches: 40, Mismatches: 14, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 40 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (18 bp):
TTTCAAGATTCGCAAAAA
Found at i:9271516 original size:59 final size:58
Alignment explanation
Indices: 9271438--9271556 Score: 159
Period size: 59 Copynumber: 2.0 Consensus size: 58
9271428 CAAGCTTCGC
*
9271438 AAAAATTTCAAGATTTGTAG-AGATTTCAAGATTCGCAAAAGCTTCAAGACTCACAAAA
1 AAAAATTTCAAGATTTGTAGAAGA-CTCAAGATTCGCAAAAGCTTCAAGACTCACAAAA
* * * * *
9271496 AAAAATTTTCAAGATTTGTAGAAGACTCAAGATTTGCAAAGGTTTCGAGATTCACAAAA
1 AAAAA-TTTCAAGATTTGTAGAAGACTCAAGATTCGCAAAAGCTTCAAGACTCACAAAA
9271555 AA
1 AA
9271557 TCTAAGATTT
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
58 5 0.09
59 45 0.85
60 3 0.06
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.27
Consensus pattern (58 bp):
AAAAATTTCAAGATTTGTAGAAGACTCAAGATTCGCAAAAGCTTCAAGACTCACAAAA
Found at i:9271718 original size:34 final size:34
Alignment explanation
Indices: 9271652--9271718 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
9271642 AATTTTAGAT
* *
9271652 GAAAGATTCATAAGATTTTCAGATTTACAAGAAC
1 GAAAGATTCATAAAATTTTCAGATTCACAAGAAC
* *
9271686 GAAAGATTCGTAAAATTTTCAGATTCATAAGAA
1 GAAAGATTCATAAAATTTTCAGATTCACAAGAA
9271719 TTTCAAGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.45, C:0.10, G:0.15, T:0.30
Consensus pattern (34 bp):
GAAAGATTCATAAAATTTTCAGATTCACAAGAAC
Found at i:9271722 original size:17 final size:17
Alignment explanation
Indices: 9271655--9271723 Score: 50
Period size: 17 Copynumber: 4.1 Consensus size: 17
9271645 TTTAGATGAA
*
9271655 AGATTCATAAGATTTTC
1 AGATTCATAAGAATTTC
* * ****
9271672 AGATTTACAAGAACGAA
1 AGATTCATAAGAATTTC
*
9271689 AGATTCGTAA-AATTTTC
1 AGATTCATAAGAA-TTTC
9271706 AGATTCATAAGAATTTC
1 AGATTCATAAGAATTTC
9271723 A
1 A
9271724 AGTTTGTAAG
Statistics
Matches: 35, Mismatches: 15, Indels: 4
0.65 0.28 0.07
Matches are distributed among these distances:
16 2 0.06
17 31 0.89
18 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.33
Consensus pattern (17 bp):
AGATTCATAAGAATTTC
Found at i:9271975 original size:44 final size:42
Alignment explanation
Indices: 9271922--9272142 Score: 161
Period size: 44 Copynumber: 5.2 Consensus size: 42
9271912 AAAGATTTTT
* * *
9271922 ATTCGAAAATTTTGGGATTCATAGCTAAAATTTCAAAAATTCTC
1 ATTC-AAAAATTTGAGATTCATA-CCAAAATTTCAAAAATTCTC
* * *
9271966 ATTCAAAAATTTGTGATTACAT-CCAAAATTTCAAAGATTTTC
1 ATTCAAAAATTTGAGATT-CATACCAAAATTTCAAAAATTCTC
* * *
9272008 ATTCAAAAAATTAGAAATTCACATCCAAAATTTCAAAAATTCTC
1 ATTC-AAAAATTTGAGATTCATA-CCAAAATTTCAAAAATTCTC
* * *
9272052 ATTCAAAAAGTTAGAGATTTACATA-AAAAATTTTAAAAATT-TAC
1 ATTCAAAAA-TTTGAGA-TT-CATACCAAAATTTCAAAAATTCT-C
* *
9272096 ATTCAAAAATCTT-A-A-TC--ACAAAAATTTCAAAGATTCTC
1 ATTCAAAAAT-TTGAGATTCATACCAAAATTTCAAAAATTCTC
*
9272134 ATCCAAAAA
1 ATTCAAAAA
9272143 ATTTCTTTAA
Statistics
Matches: 147, Mismatches: 19, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
37 1 0.01
38 23 0.16
39 2 0.01
40 1 0.01
42 24 0.16
43 31 0.21
44 60 0.41
45 2 0.01
46 3 0.02
ACGTcount: A:0.47, C:0.14, G:0.06, T:0.33
Consensus pattern (42 bp):
ATTCAAAAATTTGAGATTCATACCAAAATTTCAAAAATTCTC
Found at i:9272038 original size:86 final size:87
Alignment explanation
Indices: 9271859--9272104 Score: 246
Period size: 86 Copynumber: 2.8 Consensus size: 87
9271849 TCAAAGATTT
* * * * * * *
9271859 CAAAATTT-AAAGATTCTTATTCAAAAAATTTCAAAGTTTTACATCCAAAAGTTAAAGATTTTTA
1 CAAAATTTCAAAAATTCTCATTC-AAAAAGTT-AGAGATTTACATCCAAAATTTAAAGATTTTCA
* * * ** *
9271923 TTCGAAAATTTTGGGATTCATAGC
64 TTCAAAAAATTAGAAATTCACAGC
* * *
9271947 TAAAATTTCAAAAATTCTCATTCAAAAA-TTTGTGA-TTACATCCAAAATTTCAAAGATTTTCAT
1 CAAAATTTCAAAAATTCTCATTCAAAAAGTTAGAGATTTACATCCAAAATTT-AAAGATTTTCAT
*
9272010 TCAAAAAATTAGAAATTCACATC
65 TCAAAAAATTAGAAATTCACAGC
** * *
9272033 CAAAATTTCAAAAATTCTCATTCAAAAAGTTAGAGATTTACATAAAAAATTTTAAAAATTTACAT
1 CAAAATTTCAAAAATTCTCATTCAAAAAGTTAGAGATTTACATCCAAAA-TTTAAAGATTTTCAT
9272098 TCAAAAA
65 TCAAAAA
9272105 TCTTAATCAC
Statistics
Matches: 130, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
85 14 0.11
86 55 0.42
87 7 0.05
88 39 0.30
89 15 0.12
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.35
Consensus pattern (87 bp):
CAAAATTTCAAAAATTCTCATTCAAAAAGTTAGAGATTTACATCCAAAATTTAAAGATTTTCATT
CAAAAAATTAGAAATTCACAGC
Found at i:9272103 original size:22 final size:22
Alignment explanation
Indices: 9271982--9272103 Score: 84
Period size: 22 Copynumber: 5.5 Consensus size: 22
9271972 AAATTTGTGA
* * *
9271982 TTACATCCAAAATTTCAAAGAT
1 TTACATTCAAAATTTTAAAAAT
* ** *
9272004 TTTCATTCAAAAAATTAGAAAT
1 TTACATTCAAAATTTTAAAAAT
* * *
9272026 TCACATCCAAAATTTCAAAAAT
1 TTACATTCAAAATTTTAAAAAT
** * *
9272048 TCT-CATTCAAAAAGTTAGAGAT
1 T-TACATTCAAAATTTTAAAAAT
**
9272070 TTACATAAAAAATTTTAAAAAT
1 TTACATTCAAAATTTTAAAAAT
9272092 TTACATTCAAAA
1 TTACATTCAAAA
9272104 ATCTTAATCA
Statistics
Matches: 69, Mismatches: 29, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
21 1 0.01
22 68 0.99
ACGTcount: A:0.49, C:0.14, G:0.04, T:0.33
Consensus pattern (22 bp):
TTACATTCAAAATTTTAAAAAT
Found at i:9273123 original size:24 final size:25
Alignment explanation
Indices: 9273096--9273147 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
9273086 GAGTTTTCAA
9273096 TTTAAGTTTTC-TTCTTTCTC-TTTT
1 TTTAAGTTTTCTTTCTTT-TCATTTT
**
9273120 TTTATTTTTTCTTTCTTTTCATTTT
1 TTTAAGTTTTCTTTCTTTTCATTTT
9273145 TTT
1 TTT
9273148 TGCACATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 11 0.46
25 13 0.54
ACGTcount: A:0.08, C:0.13, G:0.02, T:0.77
Consensus pattern (25 bp):
TTTAAGTTTTCTTTCTTTTCATTTT
Found at i:9273130 original size:17 final size:17
Alignment explanation
Indices: 9273114--9273146 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
9273104 TTCTTCTTTC
9273114 TCTTT-TTTT-ATTTTT
1 TCTTTCTTTTCATTTTT
9273129 TCTTTCTTTTCATTTTT
1 TCTTTCTTTTCATTTTT
9273146 T
1 T
9273147 TTGCACATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 4 0.25
17 7 0.44
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (17 bp):
TCTTTCTTTTCATTTTT
Found at i:9273148 original size:21 final size:20
Alignment explanation
Indices: 9273102--9273148 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 20
9273092 TCAATTTAAG
*
9273102 TTTTCTTCTTTCTCTTTTTT
1 TTTTTTTCTTTCTCTTTTTT
*
9273122 TATTTTTTCTTTCT-TTTCATT
1 T-TTTTTTCTTTCTCTTT-TTT
9273143 TTTTTT
1 TTTTTT
9273149 GCACATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTTTTCTTTCTCTTTTTT
Found at i:9277881 original size:14 final size:14
Alignment explanation
Indices: 9277862--9277892 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9277852 TTAAAATAAA
*
9277862 CAAAAATTATCATG
1 CAAAAACTATCATG
9277876 CAAAAACTATCATG
1 CAAAAACTATCATG
9277890 CAA
1 CAA
9277893 TAAAATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (14 bp):
CAAAAACTATCATG
Found at i:9278701 original size:16 final size:17
Alignment explanation
Indices: 9278682--9278714 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
9278672 AAAATCCTAG
9278682 AAATCAAAA-CCTAAAA
1 AAATCAAAACCCTAAAA
9278698 AAATCAAAACCCTAAAA
1 AAATCAAAACCCTAAAA
9278715 CTTCTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.67, C:0.21, G:0.00, T:0.12
Consensus pattern (17 bp):
AAATCAAAACCCTAAAA
Found at i:9279141 original size:28 final size:28
Alignment explanation
Indices: 9279073--9279142 Score: 72
Period size: 28 Copynumber: 2.4 Consensus size: 28
9279063 CTTTTTTTGA
9279073 AAAAAGATAAAAATAAAATAAAATAATATT
1 AAAAA-AT-AAAATAAAATAAAATAATATT
* *
9279103 AAACAAA-AAAATACAATCAAATAA-ATT
1 AAA-AAATAAAATAAAATAAAATAATATT
9279130 AAAAAATTAAAAT
1 AAAAAA-TAAAAT
9279143 TTTTCTTATT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
26 3 0.09
27 6 0.17
28 20 0.57
30 4 0.11
31 2 0.06
ACGTcount: A:0.73, C:0.04, G:0.01, T:0.21
Consensus pattern (28 bp):
AAAAAATAAAATAAAATAAAATAATATT
Found at i:9280719 original size:13 final size:13
Alignment explanation
Indices: 9280701--9280741 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
9280691 TTTATTATTG
9280701 AATATTTGATTTT
1 AATATTTGATTTT
*
9280714 AATATTTGATTTAA
1 AATATTTGATTT-T
9280728 AATAATTTGATTTT
1 AAT-ATTTGATTTT
9280742 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 12 0.50
14 3 0.12
15 9 0.38
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (13 bp):
AATATTTGATTTT
Found at i:9288874 original size:19 final size:18
Alignment explanation
Indices: 9288852--9288887 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
9288842 ATTATATGAA
9288852 ATTAAAATTATGAATTTTT
1 ATTAAAATTA-GAATTTTT
*
9288871 ATTATAATTAGAATTTT
1 ATTAAAATTAGAATTTT
9288888 AACATTATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
ATTAAAATTAGAATTTTT
Found at i:9289063 original size:25 final size:26
Alignment explanation
Indices: 9289006--9289083 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 26
9288996 TATAATTGTA
* *
9289006 ATAAAATAAAAAATTTATAATTTAATTTC
1 ATAAAATTAAAAA-TT-T-ATTTATTTTC
*
9289035 ATAAAA-TAAAAATATT-TTTATTTTT
1 ATAAAATTAAAAAT-TTATTTATTTTC
9289060 ATAAAATTTAAAAATTTATTTATT
1 ATAAAA-TTAAAAATTTATTTATT
9289084 AATAACCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
25 13 0.31
26 2 0.05
27 15 0.36
28 6 0.14
29 6 0.14
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (26 bp):
ATAAAATTAAAAATTTATTTATTTTC
Found at i:9289080 original size:29 final size:28
Alignment explanation
Indices: 9289006--9289086 Score: 78
Period size: 25 Copynumber: 2.9 Consensus size: 28
9288996 TATAATTGTA
* *
9289006 ATAAAATAAAAAATTTATAATTTAATTTC
1 ATAAAATTAAAAATTTAT-TTTTAATTTC
* *
9289035 ATAAAA-TAAAAA--TATTTTTATTTTT
1 ATAAAATTAAAAATTTATTTTTAATTTC
9289060 ATAAAATTTAAAAATTTATTTATTAAT
1 ATAAAA-TTAAAAATTTATTT-TTAAT
9289087 AACCAAATTA
Statistics
Matches: 42, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
25 13 0.31
26 3 0.07
27 6 0.14
28 5 0.12
29 11 0.26
30 4 0.10
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (28 bp):
ATAAAATTAAAAATTTATTTTTAATTTC
Found at i:9289911 original size:29 final size:28
Alignment explanation
Indices: 9289879--9289965 Score: 111
Period size: 29 Copynumber: 3.0 Consensus size: 28
9289869 CTTTGAGTTA
*
9289879 TTTTATTTTATTTAAATAAATTTTTATAT
1 TTTTATTTTATATAAATAAATTTTTAT-T
* *
9289908 TTTTATTATATCTAAATAAATTTTTATT
1 TTTTATTTTATATAAATAAATTTTTATT
* *
9289936 TTTAATTTGTATATAAATAAATTCTTATT
1 TTTTATTT-TATATAAATAAATTTTTATT
9289965 T
1 T
9289966 CAAATAAAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
28 7 0.14
29 44 0.86
ACGTcount: A:0.36, C:0.02, G:0.01, T:0.61
Consensus pattern (28 bp):
TTTTATTTTATATAAATAAATTTTTATT
Found at i:9289982 original size:17 final size:16
Alignment explanation
Indices: 9289962--9290004 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
9289952 ATAAATTCTT
9289962 ATTTCAAATAAAAATTA
1 ATTT-AAATAAAAATTA
*
9289979 ATTTATATTAAAAATTA
1 ATTTA-AATAAAAATTA
9289996 ATTTAAATA
1 ATTTAAATA
9290005 TAGGCTAAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTTAAATAAAAATTA
Found at i:9290293 original size:3 final size:3
Alignment explanation
Indices: 9290285--9290357 Score: 51
Period size: 3 Copynumber: 24.3 Consensus size: 3
9290275 TTTTTAATTT
* * * * *
9290285 TAA TAA TAA TAA TAA TAA TAA CAA CAA TAA CAA TAA -CA TCAA TCA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
* *
9290330 TAA CAA TAC TAA TAA -AGA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TA-A TAA TAA TAA T
9290358 TTATTATATT
Statistics
Matches: 54, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
2 2 0.04
3 49 0.91
4 3 0.06
ACGTcount: A:0.62, C:0.11, G:0.01, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:9291130 original size:23 final size:21
Alignment explanation
Indices: 9291091--9291133 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9291081 CATGTGTCAT
*
9291091 TATTTTTTCCTTTTTTTCTTA
1 TATTTTTTCCTTATTTTCTTA
9291112 TATTTTTTCCTTACATTTTCTT
1 TATTTTTTCCTT--ATTTTCTT
9291134 TTTTATTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
23 7 0.37
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.72
Consensus pattern (21 bp):
TATTTTTTCCTTATTTTCTTA
Found at i:9293980 original size:21 final size:23
Alignment explanation
Indices: 9293938--9293990 Score: 74
Period size: 22 Copynumber: 2.3 Consensus size: 23
9293928 GATTTTTTTT
9293938 TATTTATTTGTCAAGCTTTT-AA
1 TATTTATTTGTCAAGCTTTTAAA
*
9293960 TATTTATTTTTCAAG-TTTTAAA
1 TATTTATTTGTCAAGCTTTTAAA
9293982 TATTCTATT
1 TATT-TATT
9293991 CTCCATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.14
22 20 0.71
23 4 0.14
ACGTcount: A:0.28, C:0.08, G:0.06, T:0.58
Consensus pattern (23 bp):
TATTTATTTGTCAAGCTTTTAAA
Found at i:9298790 original size:22 final size:22
Alignment explanation
Indices: 9298740--9298790 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
9298730 ACTTTCAAGT
*
9298740 ATAATTTGCAAGGCTTTTGTGC
1 ATAATTTGCAAGACTTTTGTGC
* *
9298762 ATGATTTGTAAGACTTTTG-GAC
1 ATAATTTGCAAGACTTTTGTG-C
9298784 ATAATTT
1 ATAATTT
9298791 TTAATACCTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 1 0.04
22 23 0.96
ACGTcount: A:0.27, C:0.10, G:0.20, T:0.43
Consensus pattern (22 bp):
ATAATTTGCAAGACTTTTGTGC
Found at i:9298808 original size:22 final size:22
Alignment explanation
Indices: 9298783--9298953 Score: 100
Period size: 22 Copynumber: 7.8 Consensus size: 22
9298773 GACTTTTGGA
*
9298783 CATAATTTTTAATACCTCCGAG
1 CATAATTTTTAAGACCTCCGAG
* * *
9298805 CATAATTTATAA-AGTCTCTG-G
1 CATAATTTTTAAGA-CCTCCGAG
* *
9298826 TCATAATTTTCAAGACCT-CTAGG
1 -CATAATTTTTAAGACCTCCGA-G
* * * *
9298849 CATAATTTGTAAGGCTTCCAAG
1 CATAATTTTTAAGACCTCCGAG
* *
9298871 TATAATTTTTAATACCTCC-AGG
1 CATAATTTTTAAGACCTCCGA-G
* *
9298893 CATAATTTGTAAG-CCTTCGAG
1 CATAATTTTTAAGACCTCCGAG
* * * * *
9298914 CATAATTATCAATACCTTCGAA
1 CATAATTTTTAAGACCTCCGAG
9298936 CATAATTTTTAAGACCTC
1 CATAATTTTTAAGACCTC
9298954 TGAACATATT
Statistics
Matches: 109, Mismatches: 31, Indels: 18
0.69 0.20 0.11
Matches are distributed among these distances:
21 17 0.16
22 88 0.81
23 4 0.04
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (22 bp):
CATAATTTTTAAGACCTCCGAG
Found at i:9298831 original size:44 final size:45
Alignment explanation
Indices: 9298783--9298910 Score: 129
Period size: 44 Copynumber: 2.9 Consensus size: 45
9298773 GACTTTTGGA
* **
9298783 CATAATTTTTAATACCTCC-GAGCATAATTTATAAAG--TCTCTGGT
1 CATAATTTTTAATACCTCCAG-GCATAATTTATAAGGCTTC-CAAGT
* * * *
9298827 CATAATTTTCAAGACCTCTAGGCATAATTTGTAAGGCTTCCAAGT
1 CATAATTTTTAATACCTCCAGGCATAATTTATAAGGCTTCCAAGT
* *
9298872 -ATAATTTTTAATACCTCCAGGCATAATTTGTAAGCCTTC
1 CATAATTTTTAATACCTCCAGGCATAATTTATAAGGCTTC
9298911 GAGCATAATT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
44 64 0.91
45 4 0.06
46 2 0.03
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.37
Consensus pattern (45 bp):
CATAATTTTTAATACCTCCAGGCATAATTTATAAGGCTTCCAAGT
Found at i:9298940 original size:43 final size:44
Alignment explanation
Indices: 9298827--9298948 Score: 113
Period size: 44 Copynumber: 2.8 Consensus size: 44
9298817 AGTCTCTGGT
* * * * *
9298827 CATAATTTTCAAGACCTCTAGGCATAATTTGTAAGGCTTCCAAG
1 CATAATTATCAATACCTCCAGACATAATTTGTAAGCCTTCCAAG
* * * * *
9298871 TATAATTTTTAATACCTCCAGGCATAATTTGTAAGCCTT-CGAG
1 CATAATTATCAATACCTCCAGACATAATTTGTAAGCCTTCCAAG
* *
9298914 CATAATTATCAATACCTTC-GAACATAATTTTTAAG
1 CATAATTATCAATACCTCCAG-ACATAATTTGTAAG
9298949 ACCTCTGAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 1 0.02
43 30 0.46
44 34 0.52
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (44 bp):
CATAATTATCAATACCTCCAGACATAATTTGTAAGCCTTCCAAG
Found at i:9306716 original size:23 final size:23
Alignment explanation
Indices: 9306690--9306734 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
9306680 TCAAGTTACA
* * *
9306690 CAATCGCTTACATCGTTAAAAAG
1 CAATCACTTACACCATTAAAAAG
*
9306713 CAATTACTTACACCATTAAAAA
1 CAATCACTTACACCATTAAAAA
9306735 AAGCGCTTAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.07, T:0.27
Consensus pattern (23 bp):
CAATCACTTACACCATTAAAAAG
Found at i:9308382 original size:225 final size:228
Alignment explanation
Indices: 9307991--9308445 Score: 724
Period size: 225 Copynumber: 2.0 Consensus size: 228
9307981 TGGTGCTTTT
* *
9307991 TACACCATCCCAGTTGGCAGAAGACCATGAGCAAGAGCAAAGGCAAGATCTTGATCACCCCGAAC
1 TACACCATCCCAGTTGGCAGAAGACCATGAGCAAGAGCAAAAGCAAGATCTTGAGCACCCCGAAC
* *
9308056 CTGAATTACAGGATTCAACACAGCAGCAGAAACAGCATCAGGTTCAGGAGCCCCTTGATGAGAAT
66 CTGAATCACAGAATTCAACACAGCAGCAGAAACAGCATCAGGTTCAGGAGCCCCTTGATGAGAAT
*
9308121 TTGTTCTCTGATCTTATTGTTCAAAACCCGCTTGATCAGCCAGAACCAGAACCACGGCCTCC-T-
131 TTGTTCTCTGATCTTACTGTTCAAAACCCGCTTGATCAGCCAGAACCAGAACCACGGCCTCCTTC
* *
9308184 T-CTGCTACTGCCTTCTCTCGTCAGACTTCTTC
196 TGCTGCTACTGCCTTATCTCGTCAGACGTCTTC
* *
9308216 TACACCATCCCCGTTGGCAGAAGACCATGAGCGAGAGCAAAAGCAAGATCTTGAGCACCCC-AAG
1 TACACCATCCCAGTTGGCAGAAGACCATGAGCAAGAGCAAAAGCAAGATCTTGAGCACCCCGAA-
** * *
9308280 CCTGAATCATTGAATTTAACACAGCAGCAGCAACAGCATCAGGTTCAGGAGCCCCTTGATGAGAA
65 CCTGAATCACAGAATTCAACACAGCAGCAGAAACAGCATCAGGTTCAGGAGCCCCTTGATGAGAA
9308345 TCTT-TTCTCTGATCTTACTGTTC-AAACCCGGCTTGATCAGCCAGAACCAGAACCACGGCCTCC
130 T-TTGTTCTCTGATCTTACTGTTCAAAACCC-GCTTGATCAGCCAGAACCAGAACCACGGCCTCC
9308408 TTCTGCTGCTACTGCCTTATCTCGTCAGACGTCTTC
193 TTCTGCTGCTACTGCCTTATCTCGTCAGACGTCTTC
9308444 TA
1 TA
9308446 GCTATAGAAA
Statistics
Matches: 211, Mismatches: 13, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
224 8 0.04
225 168 0.80
226 3 0.01
227 1 0.00
228 31 0.15
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (228 bp):
TACACCATCCCAGTTGGCAGAAGACCATGAGCAAGAGCAAAAGCAAGATCTTGAGCACCCCGAAC
CTGAATCACAGAATTCAACACAGCAGCAGAAACAGCATCAGGTTCAGGAGCCCCTTGATGAGAAT
TTGTTCTCTGATCTTACTGTTCAAAACCCGCTTGATCAGCCAGAACCAGAACCACGGCCTCCTTC
TGCTGCTACTGCCTTATCTCGTCAGACGTCTTC
Found at i:9308579 original size:63 final size:63
Alignment explanation
Indices: 9308474--9308594 Score: 152
Period size: 63 Copynumber: 1.9 Consensus size: 63
9308464 GAGCTACTGG
* * **
9308474 ATTCAGGATTGGATATGGCAGAGATTATCAGAGTAACAATAATGTTGATAGTCATGATAATCA
1 ATTCAGGATTGCATATGGCAGAGATGATCAGAGTAACAATAATACTGATAGTCATGATAATCA
* * * ** *
9308537 ATTCAGGATTGCATATGGTAGAGATGATGAGATTAATGATAATACTGATGGTCATGAT
1 ATTCAGGATTGCATATGGCAGAGATGATCAGAGTAACAATAATACTGATAGTCATGAT
9308595 GATAACCATC
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
63 48 1.00
ACGTcount: A:0.36, C:0.08, G:0.24, T:0.31
Consensus pattern (63 bp):
ATTCAGGATTGCATATGGCAGAGATGATCAGAGTAACAATAATACTGATAGTCATGATAATCA
Found at i:9312538 original size:16 final size:16
Alignment explanation
Indices: 9312481--9312549 Score: 52
Period size: 17 Copynumber: 4.1 Consensus size: 16
9312471 AATTGAAATT
9312481 TTATAAAAATATATTTA
1 TTATAAAAATA-ATTTA
* *
9312498 TGATAAATAATAATTCTG
1 TTATAAA-AATAATT-TA
*
9312516 TTA-ATAAATAATTTA
1 TTATAAAAATAATTTA
9312531 TTATATAATAA-AATTTA
1 TTATA-AA-AATAATTTA
9312548 TT
1 TT
9312550 TATTTATTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
15 4 0.10
16 8 0.20
17 20 0.49
18 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (16 bp):
TTATAAAAATAATTTA
Found at i:9316593 original size:23 final size:23
Alignment explanation
Indices: 9316567--9316610 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
9316557 ATTTGACATG
9316567 TTTT-AATTATATTTATAAAATCC
1 TTTTGAATTA-ATTTATAAAATCC
* *
9316590 TTTTGAGTTAATTTATGAAAT
1 TTTTGAATTAATTTATAAAAT
9316611 ATTATGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (23 bp):
TTTTGAATTAATTTATAAAATCC
Found at i:9318441 original size:30 final size:30
Alignment explanation
Indices: 9318386--9318468 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
9318376 TTTTTATTAT
* * *
9318386 ACTCAAATAAA-CCTTAAATTCTAATTTGC
1 ACTCAAATAAATTCTTAATTTTTAATTTGC
*
9318415 ACTCAAATAAATTCTTAATTTTTAATTTGT
1 ACTCAAATAAATTCTTAATTTTTAATTTGC
*
9318445 A-TCTAAATAAATTTTTAATTTTTA
1 ACTC-AAATAAATTCTTAATTTTTA
9318469 TTTTATACAT
Statistics
Matches: 47, Mismatches: 5, Indels: 3
0.85 0.09 0.05
Matches are distributed among these distances:
29 13 0.28
30 34 0.72
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (30 bp):
ACTCAAATAAATTCTTAATTTTTAATTTGC
Found at i:9318482 original size:30 final size:30
Alignment explanation
Indices: 9318419--9318484 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
9318409 ATTTGCACTC
9318419 AAATAAATTCTTAATTTTTAATTTGTATCT
1 AAATAAATTCTTAATTTTTAATTTGTATCT
*
9318449 AAATAAATTTTTAATTTTT-ATTT-TATACAT
1 AAATAAATTCTTAATTTTTAATTTGTAT-C-T
9318479 AAATAA
1 AAATAA
9318485 GCCATTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
28 3 0.09
29 5 0.15
30 25 0.76
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (30 bp):
AAATAAATTCTTAATTTTTAATTTGTATCT
Found at i:9318749 original size:20 final size:20
Alignment explanation
Indices: 9318724--9318796 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 20
9318714 TATAATATTC
9318724 ATAAATATTAATTTTTTAAT
1 ATAAATATTAATTTTTTAAT
9318744 AT-AA-ATTACATTTTAATTATAT
1 ATAAATATTA-ATTTT--TTA-AT
*
9318766 ATAAATA-TAATATTTTAA-
1 ATAAATATTAATTTTTTAAT
9318784 ATTAAAATATTAA
1 A-T-AAATATTAA
9318797 ATAATAGTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 17
0.70 0.02 0.28
Matches are distributed among these distances:
18 5 0.12
19 9 0.21
20 10 0.23
21 6 0.14
22 8 0.19
23 4 0.09
24 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (20 bp):
ATAAATATTAATTTTTTAAT
Found at i:9319482 original size:235 final size:235
Alignment explanation
Indices: 9319062--9319532 Score: 791
Period size: 235 Copynumber: 2.0 Consensus size: 235
9319052 ATTAATCCAT
* **
9319062 ACTTAAATAAAAATCTAGTAAAAAATTTTAATAAAAATATTTGCCTAAAATTATAACAAAATTTA
1 ACTTAAATAAAAATCTAGTAAAAAATTTTAATAAAAATATTTACCTAAAAACATAACAAAATTTA
*
9319127 TTAATTTTTTCAAATTTTGCATATACAATCTATGTAATAAGACATGTAAATTTATCAATTTAAAT
66 TTAATTTTTTCAAAATTTGCATATACAATCTATGTAATAAGACATGTAAATTTATCAATTTAAAT
9319192 TTTTATTTAATCATTTTTAATATAAAACTTCATGAAATTCACTTAAAAATTTTCTTTTAAAACTT
131 TTTTATTTAATCATTTTTAATATAAAACTTCATGAAATTCACTTAAAAATTTTCTTTTAAAACTT
*
9319257 TCCCGTAATATATTTGTAATGGGTCTAAAACATATCTTTA
196 TCCCGTAATATATTAGTAATGGGTCTAAAACATATCTTTA
* * * * * *
9319297 ACTTAGATAAAAATTTCA-TAAAAATTTTTGATAAAAATATTTATCTAAAAACATATCAAAATTT
1 ACTTAAATAAAAATCT-AGTAAAAAATTTTAATAAAAATATTTACCTAAAAACATAACAAAATTT
*
9319361 ATTAATTTTTTCAAAATTTGCATATACAATCTATGTAATAAGACATGTAAATTTATTAATTTAAA
65 ATTAATTTTTTCAAAATTTGCATATACAATCTATGTAATAAGACATGTAAATTTATCAATTTAAA
* *
9319426 TTTTTATTTAATTATTTTTAATATAAAACTTCATGAAATTCACTTAAAACTTTTCTTTTAAAACT
130 TTTTTATTTAATCATTTTTAATATAAAACTTCATGAAATTCACTTAAAAATTTTCTTTTAAAACT
*
9319491 TTCCCGTAATATATTAGTGATGGGTCTAAAACATATCTTTA
195 TTCCCGTAATATATTAGTAATGGGTCTAAAACATATCTTTA
9319532 A
1 A
9319533 GCTAAGGGGA
Statistics
Matches: 220, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
235 219 1.00
236 1 0.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.42
Consensus pattern (235 bp):
ACTTAAATAAAAATCTAGTAAAAAATTTTAATAAAAATATTTACCTAAAAACATAACAAAATTTA
TTAATTTTTTCAAAATTTGCATATACAATCTATGTAATAAGACATGTAAATTTATCAATTTAAAT
TTTTATTTAATCATTTTTAATATAAAACTTCATGAAATTCACTTAAAAATTTTCTTTTAAAACTT
TCCCGTAATATATTAGTAATGGGTCTAAAACATATCTTTA
Found at i:9319697 original size:24 final size:24
Alignment explanation
Indices: 9319669--9319716 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
9319659 GATATTATTG
9319669 AATTTGGTTGAATTGGAAAATTAT
1 AATTTGGTTGAATTGGAAAATTAT
9319693 AATTTGGTTGAATTGGAAAATTAT
1 AATTTGGTTGAATTGGAAAATTAT
9319717 CAGTCGCATC
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:0.38, C:0.00, G:0.21, T:0.42
Consensus pattern (24 bp):
AATTTGGTTGAATTGGAAAATTAT
Found at i:9320344 original size:24 final size:24
Alignment explanation
Indices: 9320303--9320348 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
9320293 CAATAAGAGG
*
9320303 AGCAAAACCAACAGCAGCAGCACA
1 AGCAAAACCAACACCAGCAGCACA
* *
9320327 AGCAAAATCAAGACCAGCAGCA
1 AGCAAAACCAACACCAGCAGCA
9320349 GCAAAACCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.50, C:0.30, G:0.17, T:0.02
Consensus pattern (24 bp):
AGCAAAACCAACACCAGCAGCACA
Found at i:9328669 original size:2 final size:2
Alignment explanation
Indices: 9328662--9328693 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
9328652 GATGTAAGAT
9328662 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
9328694 ACACACACAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:9338014 original size:200 final size:200
Alignment explanation
Indices: 9337639--9338028 Score: 451
Period size: 200 Copynumber: 1.9 Consensus size: 200
9337629 AGTATTAGAA
* *
9337639 CAAGGATTTTCTTCCATTACCATTTCTAAATCTATCACGTAGTAAGCTTCTTCAATTTTTGCCTA
1 CAAGGATTTCCTTCCATTACCATTTCTAAATCTATCACGTAGTAAGCTTCTTCAATCTTTGCCTA
** * *
9337704 CACATGATGAGAGTTTGTTAAAATGAGTTATCCCATATCTAATAAAATTTTAATTTCTTATAATC
66 CACATGATGAGAGCCTGCTAAAATGAGTTATCCCACATCTAATAAAATTTTAATTTCTTATAATC
* * ** *
9337769 TTATATTCAAGTTGAGCCCTTTTACTTACTGTCAATTGGTTGTAAGTTAGTTACTTAACATGGTA
131 TTATATTCAAGTTGAGACATTTTACTTACTACCAATTGATTGTAAGTTAGTTACTTAACATGGTA
9337834 CTGAG
196 CTGAG
* * * * ** * * *
9337839 CAAGGATTTCCTTTCATTGCCCTTTCTTAATCTATCATTTAGTAGGCTTTTTCAATCTTTGCTTA
1 CAAGGATTTCCTTCCATTACCATTTCTAAATCTATCACGTAGTAAGCTTCTTCAATCTTTGCCTA
* * * * *** *
9337904 TACATGATGGGAGCCTGCTAAAGTGGGTTATTTTACATCTAAT-AAATATTTAATTTTTTATAAT
66 CACATGATGAGAGCCTGCTAAAATGAGTTATCCCACATCTAATAAAAT-TTTAATTTCTTATAAT
* * * * *
9337968 CTTATATTTAAGTTG-GACATTTTCACTTTCTACCAATTTATTGTAAGTTGGTTATTTAACA
130 CTTATATTCAAGTTGAGACATTTT-ACTTACTACCAATTGATTGTAAGTTAGTTACTTAACA
9338029 ATTGCCACAC
Statistics
Matches: 155, Mismatches: 33, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
199 10 0.06
200 145 0.94
ACGTcount: A:0.28, C:0.16, G:0.13, T:0.43
Consensus pattern (200 bp):
CAAGGATTTCCTTCCATTACCATTTCTAAATCTATCACGTAGTAAGCTTCTTCAATCTTTGCCTA
CACATGATGAGAGCCTGCTAAAATGAGTTATCCCACATCTAATAAAATTTTAATTTCTTATAATC
TTATATTCAAGTTGAGACATTTTACTTACTACCAATTGATTGTAAGTTAGTTACTTAACATGGTA
CTGAG
Found at i:9345479 original size:19 final size:19
Alignment explanation
Indices: 9345447--9345499 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 19
9345437 CTTTTATCTG
9345447 CCAAAAAA-A-AAAA-AAA
1 CCAAAAAAGAGAAAAGAAA
9345463 CCCAAAAAAGTAGAAAAGAAA
1 -CCAAAAAAG-AGAAAAGAAA
*
9345484 TCAAAAAAGAGAAAAG
1 CCAAAAAAGAGAAAAG
9345500 GTTAGATGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
17 8 0.26
19 8 0.26
20 12 0.39
21 3 0.10
ACGTcount: A:0.74, C:0.11, G:0.11, T:0.04
Consensus pattern (19 bp):
CCAAAAAAGAGAAAAGAAA
Found at i:9345976 original size:41 final size:42
Alignment explanation
Indices: 9345914--9346000 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 42
9345904 AATTATGTGT
* * * *
9345914 AAAATTTATCTCTATGTGAAAATGAGTTTTAAAATACT-GAA
1 AAAAGTTATCTATATATGAAAATGAGTTTGAAAATACTGGAA
* *
9345955 AAAAGTTATCTATATATGAAAATGCGTTTGAAAATATTGGAA
1 AAAAGTTATCTATATATGAAAATGAGTTTGAAAATACTGGAA
9345997 AAAA
1 AAAA
9346001 AATTTCACTG
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
41 32 0.82
42 7 0.18
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (42 bp):
AAAAGTTATCTATATATGAAAATGAGTTTGAAAATACTGGAA
Found at i:9365474 original size:49 final size:48
Alignment explanation
Indices: 9365413--9365516 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 48
9365403 TAAACATTCA
* *
9365413 AATTTATTCTAGATTCAATCCCATTGTACATCCTCAAAATCCTTCAAG
1 AATTTGTTCTAGATTCAATCCCATTGAACATCCTCAAAATCCTTCAAG
*
9365461 AATTTGTTCCTAGATTCAATCCCATTGAACATCCTCAAATTCCTTCAAG
1 AATTTGTT-CTAGATTCAATCCCATTGAACATCCTCAAAATCCTTCAAG
9365510 AATTTGT
1 AATTTGT
9365517 CATCTACCTC
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
48 7 0.13
49 45 0.87
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (48 bp):
AATTTGTTCTAGATTCAATCCCATTGAACATCCTCAAAATCCTTCAAG
Found at i:9367865 original size:2 final size:2
Alignment explanation
Indices: 9367858--9367884 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9367848 TATAAGTTAC
9367858 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
9367885 CAATAGTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9368356 original size:2 final size:2
Alignment explanation
Indices: 9368349--9368379 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
9368339 GATTAGTGAT
*
9368349 TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9368380 GGATACATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:9368486 original size:16 final size:16
Alignment explanation
Indices: 9368462--9368493 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9368452 TGGCTGTTGG
*
9368462 GTTACGATCATGTAAA
1 GTTAAGATCATGTAAA
9368478 GTTAAGATCATGTAAA
1 GTTAAGATCATGTAAA
9368494 CAATATGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (16 bp):
GTTAAGATCATGTAAA
Found at i:9375888 original size:22 final size:22
Alignment explanation
Indices: 9375862--9375922 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
9375852 TCGATAATAA
*
9375862 TCAAATAAAATTCGAATTTTAT
1 TCAAATAGAATTCGAATTTTAT
*
9375884 TCAAATTGAATTCGAATTTTAT
1 TCAAATAGAATTCGAATTTTAT
* *
9375906 TCTAATCGAATTCGAAT
1 TCAAATAGAATTCGAAT
9375923 AATTTATTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.41
Consensus pattern (22 bp):
TCAAATAGAATTCGAATTTTAT
Found at i:9378642 original size:21 final size:21
Alignment explanation
Indices: 9378616--9378656 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
9378606 AAGATATGAT
9378616 GTCAGTTATTAATCTATTGGG
1 GTCAGTTATTAATCTATTGGG
9378637 GTCAGTTATTAATCTATTGG
1 GTCAGTTATTAATCTATTGG
9378657 CTAAGAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (21 bp):
GTCAGTTATTAATCTATTGGG
Found at i:9385421 original size:44 final size:44
Alignment explanation
Indices: 9385358--9385446 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
9385348 AAAATATTTG
**
9385358 TAAGACATGTATTTTATATTGTTAATTTTAATTGTGTTACTTAA
1 TAAGACATGTATTTTATATTGTTAATTTTAATTGCATTACTTAA
9385402 TAAGACATGTATTTTATATTGTTAATTTTAATTGCATTACTTAA
1 TAAGACATGTATTTTATATTGTTAATTTTAATTGCATTACTTAA
9385446 T
1 T
9385447 TTTTAATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.52
Consensus pattern (44 bp):
TAAGACATGTATTTTATATTGTTAATTTTAATTGCATTACTTAA
Found at i:9388499 original size:19 final size:19
Alignment explanation
Indices: 9388471--9388511 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
9388461 CAACTGCAGG
9388471 TTTTTCATTTTCT-TTTTAT
1 TTTTTCATTTT-TATTTTAT
*
9388490 TTTTTGATTTTTATTTTAT
1 TTTTTCATTTTTATTTTAT
9388509 TTT
1 TTT
9388512 ATTTTATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.12, C:0.05, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTCATTTTTATTTTAT
Found at i:9388500 original size:6 final size:5
Alignment explanation
Indices: 9388498--9388522 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
9388488 ATTTTTTGAT
9388498 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
9388523 ATTTCAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:9390665 original size:36 final size:36
Alignment explanation
Indices: 9390625--9390697 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
9390615 GTTGCTGGTC
*
9390625 ATCCAATAAGATTGTTATGACTTCATTTTGGCCAAA
1 ATCCAATAAGATTGTTATGACTTCATCTTGGCCAAA
* * *
9390661 ATCCAATAGGTTTGTTATGATTTCATCTTGGCCAAA
1 ATCCAATAAGATTGTTATGACTTCATCTTGGCCAAA
9390697 A
1 A
9390698 GATGTTAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (36 bp):
ATCCAATAAGATTGTTATGACTTCATCTTGGCCAAA
Found at i:9392708 original size:23 final size:23
Alignment explanation
Indices: 9392679--9392725 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
9392669 TAATAAAATT
9392679 TTTTTATATATTTACATATGATA
1 TTTTTATATATTTACATATGATA
*
9392702 TTTTTATATATTTATATATGATA
1 TTTTTATATATTTACATATGATA
9392725 T
1 T
9392726 ATGATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTTATATATTTACATATGATA
Found at i:9398747 original size:19 final size:19
Alignment explanation
Indices: 9398720--9398759 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
9398710 TGAAATTAAG
9398720 TAGCACTATTGTCTAACTC
1 TAGCACTATTGTCTAACTC
*
9398739 TAGCCCTATTGTCTAACTC
1 TAGCACTATTGTCTAACTC
9398758 TA
1 TA
9398760 TTGGTTAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.25, C:0.28, G:0.10, T:0.38
Consensus pattern (19 bp):
TAGCACTATTGTCTAACTC
Found at i:9399291 original size:25 final size:25
Alignment explanation
Indices: 9399245--9399293 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
9399235 ACTATTATAA
**
9399245 ATAATAATAATAGTTCCTATAAAAG
1 ATAATAATAATAGTTAATATAAAAG
9399270 ATAATAATAATAG-TAATAATAAAA
1 ATAATAATAATAGTTAAT-ATAAAA
9399294 TCAATATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.59, C:0.04, G:0.06, T:0.31
Consensus pattern (25 bp):
ATAATAATAATAGTTAATATAAAAG
Found at i:9404253 original size:16 final size:16
Alignment explanation
Indices: 9404232--9404278 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 16
9404222 TCGATATGGC
9404232 TAATTGTATATTGAAA
1 TAATTGTATATTGAAA
9404248 TAATTGCTTATATTATGAAA
1 TAATTG--TATA-T-TGAAA
9404268 TAATTGT-TATT
1 TAATTGTATATT
9404279 TTTGGAACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
15 1 0.04
16 7 0.26
17 2 0.07
18 5 0.19
19 1 0.04
20 11 0.41
ACGTcount: A:0.38, C:0.02, G:0.11, T:0.49
Consensus pattern (16 bp):
TAATTGTATATTGAAA
Found at i:9406262 original size:18 final size:19
Alignment explanation
Indices: 9406239--9406278 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
9406229 ATATATATAT
*
9406239 AAATTATA-AAAATTTTTA
1 AAATTATATAAAATTTTGA
*
9406257 AAATTATATTAAATTTTGA
1 AAATTATATAAAATTTTGA
9406276 AAA
1 AAA
9406279 AAAAAAAAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 8 0.42
19 11 0.58
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
AAATTATATAAAATTTTGA
Found at i:9406606 original size:8 final size:7
Alignment explanation
Indices: 9406590--9406673 Score: 56
Period size: 8 Copynumber: 12.4 Consensus size: 7
9406580 AATTTTATTA
9406590 ATAATAT
1 ATAATAT
9406597 ATACATAT
1 ATA-ATAT
9406605 ATAATAT
1 ATAATAT
*
9406612 AAAAT-T
1 ATAATAT
9406618 A-AATA-
1 ATAATAT
9406623 AGTAATA-
1 A-TAATAT
9406630 A-AATAT
1 ATAATAT
* *
9406636 ATACTTT
1 ATAATAT
9406643 AT-ATAT
1 ATAATAT
9406649 AT-ATAT
1 ATAATAT
9406655 ATATATAT
1 ATA-ATAT
9406663 ATATATAT
1 ATA-ATAT
9406671 ATA
1 ATA
9406674 TCTTTAGACG
Statistics
Matches: 64, Mismatches: 5, Indels: 15
0.76 0.06 0.18
Matches are distributed among these distances:
5 8 0.12
6 13 0.20
7 21 0.33
8 22 0.34
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.42
Consensus pattern (7 bp):
ATAATAT
Found at i:9406647 original size:2 final size:2
Alignment explanation
Indices: 9406632--9406674 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
9406622 AAGTAATAAA
*
9406632 AT AT AT ACT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9406675 CTTTAGACGG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
2 37 0.97
3 1 0.03
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9407113 original size:20 final size:21
Alignment explanation
Indices: 9407090--9407128 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
9407080 TTTTTAACAA
9407090 TTTTA-AATAATT-TAAAAATT
1 TTTTAGAA-AATTCTAAAAATT
9407110 TTTTAGAAAATTCTAAAAA
1 TTTTAGAAAATTCTAAAAA
9407129 ATTAAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (21 bp):
TTTTAGAAAATTCTAAAAATT
Found at i:9407139 original size:30 final size:30
Alignment explanation
Indices: 9407080--9407161 Score: 85
Period size: 30 Copynumber: 2.8 Consensus size: 30
9407070 AATTTTTATA
* * * *
9407080 TTTTTA-ACAATTTTAAATAATTTAAAAAT
1 TTTTTAGAAAATTCTAAAAAATTAAAAAAT
9407109 TTTTTAGAAAATTCTAAAAAATTAAAAAAT
1 TTTTTAGAAAATTCTAAAAAATTAAAAAAT
****
9407139 TAAAAAGAAAATTCTAAAAAATT
1 TTTTTAGAAAATTCTAAAAAATT
9407162 CTAAATATCT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
29 6 0.14
30 38 0.86
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (30 bp):
TTTTTAGAAAATTCTAAAAAATTAAAAAAT
Found at i:9407161 original size:10 final size:10
Alignment explanation
Indices: 9407116--9407166 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
9407106 AATTTTTTAG
9407116 AAAATTCTAA
1 AAAATTCTAA
9407126 AAAA-T-TAA
1 AAAATTCTAA
**
9407134 AAAATTAAAAA
1 AAAATT-CTAA
9407145 GAAAATTCTAA
1 -AAAATTCTAA
9407156 AAAATTCTAA
1 AAAATTCTAA
9407166 A
1 A
9407167 TATCTTAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
8 7 0.21
9 2 0.06
10 15 0.44
11 4 0.12
12 6 0.18
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.25
Consensus pattern (10 bp):
AAAATTCTAA
Found at i:9407343 original size:31 final size:32
Alignment explanation
Indices: 9407289--9407348 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 32
9407279 AATGAATTCT
* *
9407289 AAATAATTCTAAATTTTTTTAAAAAAATTCCA
1 AAATAATTCTAAAATTTTCTAAAAAAATTCCA
* *
9407321 AAAT-ATTTTAAAATTTTCTAAAAGAATT
1 AAATAATTCTAAAATTTTCTAAAAAAATT
9407349 AAGGAAACCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 20 0.83
32 4 0.17
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.42
Consensus pattern (32 bp):
AAATAATTCTAAAATTTTCTAAAAAAATTCCA
Found at i:9407399 original size:18 final size:18
Alignment explanation
Indices: 9407359--9407410 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
9407349 AAGGAAACCC
*
9407359 AAAAATTTTCAAAAATCA
1 AAAAATTTTCAAAAATAA
* *
9407377 TAAAATTTTTAAAAATAA
1 AAAAATTTTCAAAAATAA
*
9407395 AAAAAATTTCAGAAAA
1 AAAAATTTTCA-AAAA
9407411 AATAAAAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAAATTTTCAAAAATAA
Found at i:9407593 original size:19 final size:20
Alignment explanation
Indices: 9407569--9407616 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
9407559 TTACAATTTC
*
9407569 AATTTTTAT-ATATTTT-TTG
1 AATTTTTATGA-ATTTTATTA
9407588 AATTTTT-TGAATTTTATTA
1 AATTTTTATGAATTTTATTA
9407607 AATTTTTATG
1 AATTTTTATG
9407617 TTTTCTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.24
19 17 0.68
20 2 0.08
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (20 bp):
AATTTTTATGAATTTTATTA
Found at i:9407602 original size:8 final size:9
Alignment explanation
Indices: 9407580--9407613 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
9407570 ATTTTTATAT
9407580 ATTTTTTGA
1 ATTTTTTGA
9407589 ATTTTTTGA
1 ATTTTTTGA
*
9407598 ATTTTATTAA
1 ATTTT-TTGA
9407608 ATTTTT
1 ATTTTT
9407614 ATGTTTTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (9 bp):
ATTTTTTGA
Found at i:9407774 original size:13 final size:13
Alignment explanation
Indices: 9407756--9407782 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9407746 GAAGAAATTT
9407756 TAATGTTTTTTTA
1 TAATGTTTTTTTA
9407769 TAATGTTTTTTTA
1 TAATGTTTTTTTA
9407782 T
1 T
9407783 TTTCATTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (13 bp):
TAATGTTTTTTTA
Found at i:9408083 original size:10 final size:9
Alignment explanation
Indices: 9408020--9408162 Score: 94
Period size: 10 Copynumber: 15.0 Consensus size: 9
9408010 TTTTTGGGAT
9408020 TTTTTTGAAA
1 TTTTTT-AAA
*
9408030 TTTTATAAA
1 TTTTTTAAA
9408039 TTTTTTTAGAA
1 -TTTTTTA-AA
*
9408050 TATTTTAGAA
1 TTTTTTA-AA
*
9408060 TTGTTTTGAA
1 TT-TTTTAAA
9408070 TTTTTTAAA
1 TTTTTTAAA
*
9408079 GTTTTTAAA
1 TTTTTTAAA
*
9408088 GTTGTTTTATTA
1 -TT-TTTTA-AA
9408100 TTTTTTACAA
1 TTTTTTA-AA
*
9408110 TTTTTTAAG
1 TTTTTTAAA
9408119 TTTTTTAAA
1 TTTTTTAAA
9408128 --TTTTAAA
1 TTTTTTAAA
9408135 -TTTTTAGAA
1 TTTTTTA-AA
*
9408144 TTTTTAGAAA
1 TTTTT-TAAA
*
9408154 ATTTTTAAA
1 TTTTTTAAA
9408163 AAATTATATA
Statistics
Matches: 107, Mismatches: 16, Indels: 21
0.74 0.11 0.15
Matches are distributed among these distances:
7 7 0.07
8 5 0.05
9 31 0.29
10 49 0.46
11 14 0.13
12 1 0.01
ACGTcount: A:0.32, C:0.01, G:0.08, T:0.59
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:9408084 original size:11 final size:10
Alignment explanation
Indices: 9408070--9408131 Score: 53
Period size: 9 Copynumber: 6.4 Consensus size: 10
9408060 TTGTTTTGAA
9408070 TTTTTTAAAG
1 TTTTTTAAAG
9408080 -TTTTTAAAG
1 TTTTTTAAAG
*
9408089 TTGTTTTATTA-
1 TT-TTTTA-AAG
9408100 TTTTTTACAA-
1 TTTTTTA-AAG
9408110 TTTTTT-AAG
1 TTTTTTAAAG
9408119 TTTTTTAAA-
1 TTTTTTAAAG
9408128 TTTT
1 TTTT
9408132 AAATTTTTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
8 2 0.05
9 19 0.43
10 15 0.34
11 7 0.16
12 1 0.02
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (10 bp):
TTTTTTAAAG
Found at i:9411658 original size:30 final size:29
Alignment explanation
Indices: 9411624--9411727 Score: 104
Period size: 30 Copynumber: 3.5 Consensus size: 29
9411614 ACTAATTTAT
* *
9411624 ATTAAAAGTTTATTTAAGTTTAAATTAAAA
1 ATTAAAAATTTATTTAAGTATAAA-TAAAA
*
9411654 ATTAAAAATTTATTTGAA-TATAAAATAAAG
1 ATTAAAAATTTATTT-AAGTAT-AAATAAAA
* * *
9411684 GTTAAGAACTTATTTAAGTAT-AATAAAA
1 ATTAAAAATTTATTTAAGTATAAATAAAA
9411712 ATATAAAAATTTATTT
1 AT-TAAAAATTTATTT
9411728 TAAAAAATGA
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
28 7 0.12
29 13 0.22
30 35 0.58
31 5 0.08
ACGTcount: A:0.52, C:0.01, G:0.07, T:0.40
Consensus pattern (29 bp):
ATTAAAAATTTATTTAAGTATAAATAAAA
Found at i:9412026 original size:28 final size:28
Alignment explanation
Indices: 9411986--9412039 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
9411976 ATTTCAACTT
*
9411986 AAGTTATTGTTTATATGTCATGCTTACG
1 AAGTTATTATTTATATGTCATGCTTACG
*
9412014 AAGTTGTTATTTATATGTCATGCTTA
1 AAGTTATTATTTATATGTCATGCTTA
9412040 TGTGGTCATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (28 bp):
AAGTTATTATTTATATGTCATGCTTACG
Found at i:9414339 original size:28 final size:28
Alignment explanation
Indices: 9414255--9414364 Score: 87
Period size: 28 Copynumber: 3.8 Consensus size: 28
9414245 TAAATTCGAA
*
9414255 TAATTA-AATAAAATATTTAAAAATTAAAT
1 TAATTATAATAAAATA-TT-AAAATTTAAT
* * * * *
9414284 TGATTCAAAAATAAAAAATTTAAGATTTGAT
1 TAATT--ATAATAAAATA-TTAAAATTTAAT
*
9414315 TTATTATAATAAAATATTAAAATTTAAT
1 TAATTATAATAAAATATTAAAATTTAAT
* *
9414343 TAATTATAATAAGATATCAAAA
1 TAATTATAATAAAATATTAAAA
9414365 AACTTAAATG
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
28 29 0.45
29 13 0.20
31 12 0.18
32 11 0.17
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (28 bp):
TAATTATAATAAAATATTAAAATTTAAT
Found at i:9419119 original size:20 final size:20
Alignment explanation
Indices: 9419080--9419131 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
9419070 GGTACTTTAT
* * *
9419080 ATTTACTTTATATATGATAA
1 ATTTACTTTTTAAATAATAA
*
9419100 TTTTACTTTTTAAATAATAA
1 ATTTACTTTTTAAATAATAA
9419120 ATTTATCTTTTT
1 ATTTA-CTTTTT
9419132 TTCCCCTGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 20 0.77
21 6 0.23
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTTACTTTTTAAATAATAA
Found at i:9423581 original size:9 final size:9
Alignment explanation
Indices: 9423567--9423592 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
9423557 GGTGGGAGTG
9423567 AGGAGGAGC
1 AGGAGGAGC
9423576 AGGAGGAGC
1 AGGAGGAGC
9423585 AGGAGGAG
1 AGGAGGAG
9423593 GGTGAACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.08, G:0.58, T:0.00
Consensus pattern (9 bp):
AGGAGGAGC
Found at i:9431833 original size:28 final size:28
Alignment explanation
Indices: 9431801--9431854 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
9431791 ACAGAAATAC
9431801 ATACCAACAAATTTTGAAAAAAAAAAAA
1 ATACCAACAAATTTTGAAAAAAAAAAAA
* ** *
9431829 ATACCAAGACGTTTTGAAAAAGAAAA
1 ATACCAACAAATTTTGAAAAAAAAAA
9431855 CCAAGGGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.61, C:0.11, G:0.09, T:0.19
Consensus pattern (28 bp):
ATACCAACAAATTTTGAAAAAAAAAAAA
Found at i:9438161 original size:32 final size:32
Alignment explanation
Indices: 9438120--9438185 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
9438110 CAAAAAATTC
9438120 GAAACTGAAATTATATCAATTATCAAAGTCTT
1 GAAACTGAAATTATATCAATTATCAAAGTCTT
9438152 GAAACTGAAATTATATCAATTATCAAAGTCTT
1 GAAACTGAAATTATATCAATTATCAAAGTCTT
9438184 GA
1 GA
9438186 TCGTACTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (32 bp):
GAAACTGAAATTATATCAATTATCAAAGTCTT
Found at i:9438462 original size:18 final size:18
Alignment explanation
Indices: 9438436--9438470 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
9438426 TTATATAAAT
9438436 TTAATTTAATATATTTTAA
1 TTAATTTAATA-ATTTTAA
9438455 TTAA-TTAATAATTTTA
1 TTAATTTAATAATTTTA
9438471 TTTATTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAATTTAATAATTTTAA
Found at i:9444753 original size:20 final size:21
Alignment explanation
Indices: 9444717--9444768 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
9444707 CCCGAAATTA
9444717 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTA-TTTTTAAAAT
*
9444739 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTAAAAT
9444760 AT-AAATATT
1 ATAAAATATT
9444769 TAAAAATATC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 7 0.24
21 11 0.38
22 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTAAAAT
Found at i:9444759 original size:21 final size:22
Alignment explanation
Indices: 9444717--9444768 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
9444707 CCCGAAATTA
9444717 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
9444739 ATAAAATATTATTTTTT-AAAT
1 ATAAAATATTATTTTTTAAAAT
9444760 AT-AAATATT
1 ATAAAATATT
9444769 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 6 0.20
22 17 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:9444776 original size:30 final size:30
Alignment explanation
Indices: 9444741--9444801 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
9444731 TTTAAAATAT
* * * *
9444741 AAAATATTATTTTTTAAATATAAATATTTA
1 AAAATATCATTATATAAATATAAATAATTA
*
9444771 AAAATATCATTATATAAATATATATAATTA
1 AAAATATCATTATATAAATATAAATAATTA
9444801 A
1 A
9444802 TTAATTAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (30 bp):
AAAATATCATTATATAAATATAAATAATTA
Found at i:9454262 original size:20 final size:19
Alignment explanation
Indices: 9454238--9454282 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
9454228 ATTTGAATTT
9454238 ATTTAATAATATTTATTTAA
1 ATTTAATAATA-TTATTTAA
* * *
9454258 GTTTAGTATTATTATTTAA
1 ATTTAATAATATTATTTAA
9454277 ATTTAA
1 ATTTAA
9454283 ATTTGTTTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (19 bp):
ATTTAATAATATTATTTAA
Found at i:9454300 original size:18 final size:18
Alignment explanation
Indices: 9454277--9454318 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
9454267 TATTATTTAA
** *
9454277 ATTTAAATTTGTTTAAAT
1 ATTTAAATTCATTAAAAT
9454295 ATTTAAATTCATTAAAAT
1 ATTTAAATTCATTAAAAT
9454313 ATTTAA
1 ATTTAA
9454319 TTTTTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTTAAATTCATTAAAAT
Found at i:9456951 original size:116 final size:117
Alignment explanation
Indices: 9456738--9456963 Score: 319
Period size: 116 Copynumber: 1.9 Consensus size: 117
9456728 AGGACAACAG
* * ** * * *
9456738 AAACAAGACAGGGATTGACAAAAGTATGAGTGATCCTAATTCGATTTTAATCGATTTAATGGATT
1 AAACAAGACAAGGATTAACAAAAGTACAAGTGATCCTAATTCAATTTTAATCGACTCAATGGATT
* * **
9456803 AAATTAATTTAATTTGATTAATTGATTGATTAA-AAAAATAATTTAATACAA
66 AAATTAATTTAATTTAATTAATTAATCAATTAATAAAAATAATTTAATACAA
* *
9456854 AAACAAGACAAGGATTAATAAAAGTACAAGTGATCGTAATTCAATTTTAATCGACTCAATGGATT
1 AAACAAGACAAGGATTAACAAAAGTACAAGTGATCCTAATTCAATTTTAATCGACTCAATGGATT
*
9456919 AAGTTAATTTAATTTAATTAATTAATCAATTAATAAAAATAATTT
66 AAATTAATTTAATTTAATTAATTAATCAATTAATAAAAATAATTT
9456964 TTAAAAAATT
Statistics
Matches: 95, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
116 84 0.88
117 11 0.12
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.35
Consensus pattern (117 bp):
AAACAAGACAAGGATTAACAAAAGTACAAGTGATCCTAATTCAATTTTAATCGACTCAATGGATT
AAATTAATTTAATTTAATTAATTAATCAATTAATAAAAATAATTTAATACAA
Found at i:9457124 original size:13 final size:14
Alignment explanation
Indices: 9457108--9457140 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
9457098 TTTAATAAAA
9457108 TATTTAAAT-ATTT
1 TATTTAAATAATTT
9457121 TA-TTAAATAATTT
1 TATTTAAATAATTT
9457134 TATTTAA
1 TATTTAA
9457141 TTTATTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.33
13 8 0.44
14 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATTTAAATAATTT
Found at i:9457156 original size:16 final size:16
Alignment explanation
Indices: 9457143--9457174 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
9457133 TTATTTAATT
9457143 TATTTAAAATTTAAAA
1 TATTTAAAATTTAAAA
9457159 TATTTAAAATTTAAAA
1 TATTTAAAATTTAAAA
9457175 CATAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TATTTAAAATTTAAAA
Found at i:9457315 original size:24 final size:25
Alignment explanation
Indices: 9457256--9457315 Score: 63
Period size: 23 Copynumber: 2.5 Consensus size: 25
9457246 ATAGTTAATT
* *
9457256 TTTAAAATTTATAAATTTGATTTAA
1 TTTAAAATTAATAAATTTAATTTAA
*
9457281 -TT-AATTATAAT-AATTTAATTTAA
1 TTTAAAAT-TAATAAATTTAATTTAA
9457304 TTTAAAATTAAT
1 TTTAAAATTAAT
9457316 TATATCCCCC
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
23 14 0.50
24 11 0.39
25 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (25 bp):
TTTAAAATTAATAAATTTAATTTAA
Found at i:9465133 original size:26 final size:26
Alignment explanation
Indices: 9465104--9465158 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
9465094 AATATATATT
**
9465104 AATAATATAATTTCCTTAATGGGTAG
1 AATAATATAATTTCCTTAAAAGGTAG
* *
9465130 AATAATATGATTTGCTTAAAAGGTAG
1 AATAATATAATTTCCTTAAAAGGTAG
9465156 AAT
1 AAT
9465159 GGTTAAGTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.36
Consensus pattern (26 bp):
AATAATATAATTTCCTTAAAAGGTAG
Found at i:9465217 original size:24 final size:25
Alignment explanation
Indices: 9465166--9465226 Score: 97
Period size: 24 Copynumber: 2.5 Consensus size: 25
9465156 AATGGTTAAG
*
9465166 TATTTTATTGGATATTTTAAAAAAA
1 TATTTTATTTGATATTTTAAAAAAA
*
9465191 TATTTTATTTGATA-TTTCAAAAAA
1 TATTTTATTTGATATTTTAAAAAAA
9465215 TATTTTATTTGA
1 TATTTTATTTGA
9465227 ATTGTTTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
24 21 0.62
25 13 0.38
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (25 bp):
TATTTTATTTGATATTTTAAAAAAA
Found at i:9465377 original size:23 final size:23
Alignment explanation
Indices: 9465319--9465387 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 23
9465309 ATATTTTTTC
9465319 ATTTTTTATATCCTAAAATTATAT
1 ATTTTTTATAT-CTAAAATTATAT
* *
9465343 ATTTTTTAATATGTAAAATTCT-T
1 ATTTTTT-ATATCTAAAATTATAT
*
9465366 ATTATTTTATATTTTAAAATTA
1 ATT-TTTTATA-TCTAAAATTA
9465388 GCATTTTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
23 7 0.18
24 27 0.71
25 4 0.11
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.57
Consensus pattern (23 bp):
ATTTTTTATATCTAAAATTATAT
Found at i:9465446 original size:15 final size:14
Alignment explanation
Indices: 9465412--9465455 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 14
9465402 TACAATATAC
9465412 AAAATTTTTT-ATT
1 AAAATTTTTTAATT
9465425 AAAATTTTTATAATTT
1 AAAATTTTT-TAA-TT
*
9465441 AAATTTTTTTAATT
1 AAAATTTTTTAATT
9465455 A
1 A
9465456 TTTATTTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 9 0.33
14 4 0.15
15 4 0.15
16 10 0.37
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
AAAATTTTTTAATT
Found at i:9465614 original size:18 final size:19
Alignment explanation
Indices: 9465585--9465620 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
9465575 TTAACAACTA
*
9465585 TAAAAATCATTTTTTTCAT
1 TAAAAATCATTTTCTTCAT
9465604 TAAAAAT-ATTTTCTTCA
1 TAAAAATCATTTTCTTCA
9465621 ATTTATTTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (19 bp):
TAAAAATCATTTTCTTCAT
Found at i:9465966 original size:19 final size:18
Alignment explanation
Indices: 9465938--9465975 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
9465928 TGCTTACAAC
9465938 TTTTTTTTTAAACATTTT
1 TTTTTTTTTAAACATTTT
*
9465956 TTTTATTTTTAATCATTTT
1 TTTT-TTTTTAAACATTTT
9465975 T
1 T
9465976 AACATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTTTTAAACATTTT
Found at i:9466776 original size:25 final size:26
Alignment explanation
Indices: 9466717--9466778 Score: 81
Period size: 26 Copynumber: 2.4 Consensus size: 26
9466707 TAGATTTTTA
9466717 TTTTAATTTAAATAATTATCTAAAAT
1 TTTTAATTTAAATAATTATCTAAAAT
* * *
9466743 ATTCAATTTAAATATTTAT-TAAAAT
1 TTTTAATTTAAATAATTATCTAAAAT
*
9466768 TTTTTATTTAA
1 TTTTAATTTAA
9466779 TAAATAAAAT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
25 14 0.47
26 16 0.53
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTTAATTTAAATAATTATCTAAAAT
Found at i:9474658 original size:12 final size:12
Alignment explanation
Indices: 9474641--9474669 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
9474631 TGTTGTGTAC
9474641 ATTATTATTGTT
1 ATTATTATTGTT
9474653 ATTATTATTGTT
1 ATTATTATTGTT
9474665 ATTAT
1 ATTAT
9474670 CTTGAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.66
Consensus pattern (12 bp):
ATTATTATTGTT
Found at i:9478915 original size:12 final size:12
Alignment explanation
Indices: 9478898--9478923 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9478888 TTTTATTCTC
9478898 CTTGTCACCTTT
1 CTTGTCACCTTT
9478910 CTTGTCACCTTT
1 CTTGTCACCTTT
9478922 CT
1 CT
9478924 CATCAGTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.35, G:0.08, T:0.50
Consensus pattern (12 bp):
CTTGTCACCTTT
Found at i:9480692 original size:12 final size:13
Alignment explanation
Indices: 9480659--9480692 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
9480649 TTTTAATTTT
9480659 AAATTATTTATAA
1 AAATTATTTATAA
9480672 AAATATATTT-TAA
1 AAAT-TATTTATAA
9480685 AAATTATT
1 AAATTATT
9480693 AAATTATCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 11 0.55
14 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATTATTTATAA
Found at i:9481034 original size:231 final size:234
Alignment explanation
Indices: 9480769--9481210 Score: 628
Period size: 231 Copynumber: 1.9 Consensus size: 234
9480759 GTACATTACC
* * *
9480769 TCATCTCAATTTAAAACTAATTTTAAAATAATTTATCTTTTTCAATTTATCTAG-AGTTAACATG
1 TCATCTCAATTTAAAACCAATTTTAAAATAATTTATCTTTTTCAATTTATAT-GCAGTTAACATA
* * * * *
9480833 AGTATTTAAATTTATCATAA-TTTTAAAAAATATTATTTAATATTTTTAATATTTTTTTATTAAT
65 AGTACTTAAATATATCACAATTTTTAAAAAA-ATTATTTAATATCTTTAA-ATTTTTTTATAAAT
* * *
9480897 AA-TCATTGCATTATCTTCAGCTTTTAAATATATTTCATATAGAAAACGTGAAA-A-A-A-ATAT
128 AATTC-TTACATTATCTTCAGCTTTTAAATATATTTCACAAAGAAAACGTGAAATATATATATAT
*
9480957 AAATACCAGAACAACTTTAAGAAAGTTTATATTATACATCATT
192 AAATACCAAAACAACTTTAAGAAAGTTTATATTATACATCATT
* * *
9481000 TCATCTCAATTTAAAACCAATTTTACAGTAATTTATCTTTTTCATTTTATATGCAGTTAACATAA
1 TCATCTCAATTTAAAACCAATTTTAAAATAATTTATCTTTTTCAATTTATATGCAGTTAACATAA
9481065 GTACTTAAATATATCACAATTTTTAAAAAAATTATTTAATATCTTTAAATTTTTTTATAAATAAT
66 GTACTTAAATATATCACAATTTTTAAAAAAATTATTTAATATCTTTAAATTTTTTTATAAATAAT
* * * *
9481130 TCTTACATTATCTTTAGTTTTTAAATATATTTCACAAATAAAATGTGAAATATATATATATAAAT
131 TCTTACATTATCTTCAGCTTTTAAATATATTTCACAAAGAAAACGTGAAATATATATATATAAAT
9481195 ACCAAAACAACTTTAA
196 ACCAAAACAACTTTAA
9481211 AAAAACCCTC
Statistics
Matches: 185, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
230 57 0.31
231 93 0.50
232 11 0.06
233 1 0.01
234 23 0.12
ACGTcount: A:0.42, C:0.10, G:0.04, T:0.44
Consensus pattern (234 bp):
TCATCTCAATTTAAAACCAATTTTAAAATAATTTATCTTTTTCAATTTATATGCAGTTAACATAA
GTACTTAAATATATCACAATTTTTAAAAAAATTATTTAATATCTTTAAATTTTTTTATAAATAAT
TCTTACATTATCTTCAGCTTTTAAATATATTTCACAAAGAAAACGTGAAATATATATATATAAAT
ACCAAAACAACTTTAAGAAAGTTTATATTATACATCATT
Found at i:9482342 original size:20 final size:18
Alignment explanation
Indices: 9482317--9482357 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
9482307 TTATTATACT
9482317 TTTAAAAATTATATCAATAA
1 TTTAAAAATTATAT-AA-AA
9482337 TTT--AAATTATATAAAA
1 TTTAAAAATTATATAAAA
9482353 TTTAA
1 TTTAA
9482358 GAAAAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
16 5 0.26
17 2 0.11
18 9 0.47
20 3 0.16
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTAAAAATTATATAAAA
Found at i:9482356 original size:16 final size:18
Alignment explanation
Indices: 9482322--9482357 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
9482312 ATACTTTTAA
9482322 AAATTATATCAATAATTT
1 AAATTATATCAATAATTT
9482340 AAATTATAT-AA-AATTT
1 AAATTATATCAATAATTT
9482356 AA
1 AA
9482358 GAAAAGATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATTATATCAATAATTT
Found at i:9482814 original size:255 final size:254
Alignment explanation
Indices: 9482359--9482873 Score: 787
Period size: 255 Copynumber: 2.0 Consensus size: 254
9482349 AAAATTTAAG
* * *
9482359 AAAAGATAATTTTGACTAATAAATAAATTATCTTATCATAATCTTTATACACGTCAACACAAGTT
1 AAAATATAATTTTAACTAATAAATAAATTATCTTATCATAATCTTTATACACATCAACACAAGTT
** *
9482424 AGGATGACATTATTTAATTTAATGCTATTTATAATATCATTTTATCATATCTTATTATAATTTTA
66 AGGATGACATTATTTAATTTAATAATATTTATAATATCATTTTATCATATCTTATCATAATTTTA
* * *
9482489 TGTACAAAACATATCCTTAATTTGATATATACAATACTCCATATATTTGTAAGTGGACCTGGCAA
131 TATACAAAACATATCCTTAATTGGATATATACAATACTCCATATATTTGTAAGTGGACCTGACAA
** * *
9482554 TTTGTGTTTCCTTGTTGTGTCTTGTGTTATGTTTAACACGTGTAATTACATGAATTATT
196 TTTGTGTTTCCTTGTCATGTCTTGTGTCATGTTTAACACGTGTAATTACACGAATTATT
* ** * * *
9482613 AAAATATAATTTTAATTAATAAATAAATTATCTTATTTTAATTTTTATGCACATCAAACATAAGT
1 AAAATATAATTTTAACTAATAAATAAATTATCTTATCATAATCTTTATACACATC-AACACAAGT
* * *
9482678 TATGATGATATTATTTAATTTAATAATATTTATAATATCATTTTATCCTATCTTATCATAATTTT
65 TAGGATGACATTATTTAATTTAATAATATTTATAATATCATTTTATCATATCTTATCATAATTTT
* *
9482743 ATATACGAAACATATCCTTAATTGGATATATACAATACTCCATATATTTGTAAGTGGACTTGACA
130 ATATACAAAACATATCCTTAATTGGATATATACAATACTCCATATATTTGTAAGTGGACCTGACA
* *
9482808 ATTTGTGTTTCCTTGTCATGTCTTGTGTCATGTTTGACACGTGTAATTATACGAATTATT
195 ATTTGTGTTTCCTTGTCATGTCTTGTGTCATGTTTAACACGTGTAATTACACGAATTATT
9482868 AAAATA
1 AAAATA
9482874 CGAACATGAT
Statistics
Matches: 234, Mismatches: 26, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
254 47 0.20
255 187 0.80
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.43
Consensus pattern (254 bp):
AAAATATAATTTTAACTAATAAATAAATTATCTTATCATAATCTTTATACACATCAACACAAGTT
AGGATGACATTATTTAATTTAATAATATTTATAATATCATTTTATCATATCTTATCATAATTTTA
TATACAAAACATATCCTTAATTGGATATATACAATACTCCATATATTTGTAAGTGGACCTGACAA
TTTGTGTTTCCTTGTCATGTCTTGTGTCATGTTTAACACGTGTAATTACACGAATTATT
Found at i:9483938 original size:21 final size:21
Alignment explanation
Indices: 9483909--9483992 Score: 66
Period size: 19 Copynumber: 4.0 Consensus size: 21
9483899 ATATTATATA
*
9483909 AAAAAATATTTTTTAATTTTT
1 AAAATATATTTTTTAATTTTT
* * *
9483930 AATATATA-TTTAT-ATTTTA
1 AAAATATATTTTTTAATTTTT
*
9483949 AAAATA-ATATTTTATATTTTT
1 AAAATATATTTTTTA-ATTTTT
9483970 AAAAATAATATTTTATTAATTTT
1 -AAAAT-ATATTTT-TTAATTTT
9483993 AGATTAAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 11
0.70 0.13 0.16
Matches are distributed among these distances:
18 1 0.02
19 13 0.28
20 4 0.09
21 11 0.23
22 5 0.11
23 1 0.02
24 9 0.19
25 3 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
AAAATATATTTTTTAATTTTT
Found at i:9483969 original size:22 final size:22
Alignment explanation
Indices: 9483907--9483985 Score: 96
Period size: 22 Copynumber: 3.8 Consensus size: 22
9483897 TGATATTATA
*
9483907 TAAAAA-AATATTTTTTAATTTT
1 TAAAAATAATATTTTAT-ATTTT
*
9483929 T-AATAT-ATA-TTTATA-TTT
1 TAAAAATAATATTTTATATTTT
9483947 TAAAAATAATATTTTATATTTT
1 TAAAAATAATATTTTATATTTT
9483969 TAAAAATAATATTTTAT
1 TAAAAATAATATTTTAT
9483986 TAATTTTAGA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
18 4 0.08
19 5 0.10
20 7 0.14
21 12 0.24
22 21 0.43
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TAAAAATAATATTTTATATTTT
Found at i:9484071 original size:22 final size:24
Alignment explanation
Indices: 9484023--9484078 Score: 73
Period size: 22 Copynumber: 2.4 Consensus size: 24
9484013 AGTACGATTT
9484023 ATATAATATAAAATTTAAATATAAA
1 ATATAA-ATAAAATTTAAATATAAA
9484048 ATATAAA-AAAATTTTAAAT-T-AA
1 ATATAAATAAAA-TTTAAATATAAA
9484070 ATATAAATA
1 ATATAAATA
9484079 CGAATATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 9 0.31
23 6 0.21
24 8 0.28
25 6 0.21
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (24 bp):
ATATAAATAAAATTTAAATATAAA
Found at i:9484916 original size:29 final size:29
Alignment explanation
Indices: 9484869--9484927 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
9484859 TAAACATGAC
*
9484869 ATAAATAAATATAAATAATA-AAATTATAT
1 ATAAATAAATACAAATAATATAAATT-TAT
* *
9484898 ATAAATAAATACGACTAATATAAATTTAT
1 ATAAATAAATACAAATAATATAAATTTAT
9484927 A
1 A
9484928 CGAATAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 21 0.81
30 5 0.19
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (29 bp):
ATAAATAAATACAAATAATATAAATTTAT
Found at i:9485966 original size:131 final size:131
Alignment explanation
Indices: 9485818--9486067 Score: 419
Period size: 131 Copynumber: 1.9 Consensus size: 131
9485808 TTTTATTAAA
* **
9485818 AAAATTTTAATTTTAATATTAAATACATTAAAATTAAATTTTTTTAAACTCCATAAAAATTGATA
1 AAAATTTTAATTTTAATATTAAATACATTAAAATTAAAATTTTTTAAACTCCATAAAAATCAATA
* *
9485883 CATATCAAATAAATTGAGACAGAGCGAGTAATAAATAATATACATACATACATATATATAATATT
66 CATATCAAATAAATTGAAACAGAACGAGTAATAAATAATATACATACATACATATATATAATATT
9485948 T
131 T
9485949 AAAATTTTAATTTTAATATTAAATACATTAAAATTAAAATTTTTTAAACTCCATAAAAATCAATA
1 AAAATTTTAATTTTAATATTAAATACATTAAAATTAAAATTTTTTAAACTCCATAAAAATCAATA
* * * *
9486014 CATATCAAATAAATTGAAACATAATGAGTAGTAGATAATATACATACATACATA
66 CATATCAAATAAATTGAAACAGAACGAGTAATAAATAATATACATACATACATA
9486068 CATACATACA
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
131 110 1.00
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.36
Consensus pattern (131 bp):
AAAATTTTAATTTTAATATTAAATACATTAAAATTAAAATTTTTTAAACTCCATAAAAATCAATA
CATATCAAATAAATTGAAACAGAACGAGTAATAAATAATATACATACATACATATATATAATATT
T
Found at i:9486062 original size:4 final size:4
Alignment explanation
Indices: 9486053--9486091 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
9486043 AGTAGATAAT
*
9486053 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAT ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
9486092 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.51, C:0.21, G:0.00, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:9486092 original size:8 final size:8
Alignment explanation
Indices: 9486051--9486108 Score: 71
Period size: 8 Copynumber: 7.2 Consensus size: 8
9486041 GTAGTAGATA
9486051 ATATACAT
1 ATATACAT
*
9486059 ACATACAT
1 ATATACAT
*
9486067 ACATACAT
1 ATATACAT
*
9486075 ACATACAT
1 ATATACAT
9486083 ATATACAT
1 ATATACAT
*
9486091 ATATATAT
1 ATATACAT
*
9486099 ATATATAT
1 ATATACAT
9486107 AT
1 AT
9486109 TTATATAGAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 47 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (8 bp):
ATATACAT
Found at i:9486094 original size:2 final size:2
Alignment explanation
Indices: 9486081--9486115 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
9486071 ACATACATAC
* *
9486081 AT AT AT AC AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9486116 GAGCATGTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9486096 original size:12 final size:12
Alignment explanation
Indices: 9486053--9486099 Score: 67
Period size: 12 Copynumber: 3.9 Consensus size: 12
9486043 AGTAGATAAT
*
9486053 ATACATACATAC
1 ATACATATATAC
*
9486065 ATACATACATAC
1 ATACATATATAC
9486077 ATACATATATAC
1 ATACATATATAC
*
9486089 ATATATATATA
1 ATACATATATA
9486100 TATATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (12 bp):
ATACATATATAC
Found at i:9488294 original size:26 final size:24
Alignment explanation
Indices: 9488248--9488305 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 24
9488238 AAATAATAAT
*
9488248 AAAAATT-ATTATAATTGTGATTGAA
1 AAAAATTAATTATAATTATGATT--A
* *
9488273 AAAAATTAATTGTGATTATGATTA
1 AAAAATTAATTATAATTATGATTA
9488297 AAAAATTAA
1 AAAAATTAA
9488306 AAAATAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 10 0.34
25 7 0.24
26 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.10, T:0.38
Consensus pattern (24 bp):
AAAAATTAATTATAATTATGATTA
Found at i:9488532 original size:23 final size:22
Alignment explanation
Indices: 9488497--9488542 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
9488487 AGTAAATATC
*
9488497 AATTTAAAAAATTTTTTATTTAT
1 AATTTAAAAAA-TTCTTATTTAT
**
9488520 AATTTAATTAATTCTTATTTAT
1 AATTTAAAAAATTCTTATTTAT
9488542 A
1 A
9488543 CTATTCTACA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTTAAAAAATTCTTATTTAT
Found at i:9488875 original size:2 final size:2
Alignment explanation
Indices: 9488825--9488855 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9488815 GCCTATTTCT
9488825 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9488856 TTCTGTCAAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9489215 original size:3 final size:3
Alignment explanation
Indices: 9489209--9489240 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
9489199 AGACCCATCT
*
9489209 TTC TTC TTC TTC TTC TTC TTC TTC TTT TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
9489241 TGAATTTGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:9498882 original size:18 final size:20
Alignment explanation
Indices: 9498846--9498882 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
9498836 ATTTGACTCT
*
9498846 TAATTAATCGAAATTTAAAG
1 TAATTAATCGAAATATAAAG
9498866 TAATT-ATC-AAATATAAA
1 TAATTAATCGAAATATAAA
9498883 AAAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 3 0.19
20 5 0.31
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (20 bp):
TAATTAATCGAAATATAAAG
Found at i:9502432 original size:21 final size:21
Alignment explanation
Indices: 9502406--9502449 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
9502396 TAGACAGCCT
*
9502406 TTTGTTTCTCCATGTATTGAG
1 TTTGTTTCTCCATGTATTAAG
9502427 TTTGTTTCTCCATGTATTAAG
1 TTTGTTTCTCCATGTATTAAG
9502448 TT
1 TT
9502450 GATCAGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.55
Consensus pattern (21 bp):
TTTGTTTCTCCATGTATTAAG
Found at i:9505061 original size:12 final size:13
Alignment explanation
Indices: 9505035--9505063 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
9505025 TGATTGACTA
9505035 AAATATTTTTAAT
1 AAATATTTTTAAT
9505048 AAATATTTTT-AT
1 AAATATTTTTAAT
9505060 AAAT
1 AAAT
9505064 TTTAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATATTTTTAAT
Done.