Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168015.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_27, 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: 15675301
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 118000 characters in sequence are not A, C, G, or T
File 35 of 93
Found at i:3867280 original size:51 final size:52
Alignment explanation
Indices: 3867223--3867327 Score: 124
Period size: 51 Copynumber: 2.0 Consensus size: 52
3867213 TTGACGTCAT
* * *
3867223 TGAGCCTCTGCTTAAAGGAGT-TTTATTTATTTTT-TAAAGTCGTTAAGCTTC
1 TGAGCCTCTGCTTAAAGGA-TCCTTATTTATTTTTAAAAAGTCGTTAAGCCTC
* * * *
3867274 TGAGCCTTTGCTTAGAGTATCCTTATTTATTTTTAAAAAGTCGTTGAGCCTC
1 TGAGCCTCTGCTTAAAGGATCCTTATTTATTTTTAAAAAGTCGTTAAGCCTC
3867326 TG
1 TG
3867328 TTTAGAGGAG
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
50 1 0.02
51 28 0.62
52 16 0.36
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (52 bp):
TGAGCCTCTGCTTAAAGGATCCTTATTTATTTTTAAAAAGTCGTTAAGCCTC
Found at i:3867400 original size:87 final size:86
Alignment explanation
Indices: 3867109--3867434 Score: 311
Period size: 87 Copynumber: 3.7 Consensus size: 86
3867099 TGATTGTCAA
* *
3867109 AGAGCTTTATTTATTTTTCAAAA-TTGTTGAGCCTCTGCTTAAATGAGCTTTATTTATTTTTTGA
1 AGAGCTTTATTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAAAGGAGCTTTATTTATTTTTTG-
* *
3867173 AAGTTGTTGAGCCTTTATTT-G
65 AAGTAGTTGAGCCTTTGTTTAG
* * * *
3867194 AAGGAGCTTTATTTAATTTTT--GACGTCATTGAGCCTCTGCTTAAAGGAGTTTTATTTATTTTT
1 -A-GAGCTTTATTT-ATTTTTCAAAAGTCGTTGAGCCTCTGCTTAAAGGAGCTTTATTTATTTTT
* *
3867257 TAAAGTCGTTAAGCTTCTGAGCCTTTGCTTAG
63 TGAA---G-T-AG--T-TGAGCCTTTGTTTAG
* * * * * *
3867289 AGTATCCTTATTTATTTTTAAAAAGTCGTTGAGCCTCTGTTTAGAGGAGCTTTATTTATTTTTCG
1 AG-AGCTTTATTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAAAGGAGCTTTATTTATTTTTTG
3867354 AAGTAGTTGAGCCTTTGTTTAG
65 AAGTAGTTGAGCCTTTGTTTAG
* * *
3867376 ATGAGCTTTATTTATTTTTCAAAAGTCCTTGAGCCTTTACTTAAAGGAG-TCTTATTTAT
1 A-GAGCTTTATTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAAAGGAGCT-TTATTTAT
3867435 GAGCCTCTGT
Statistics
Matches: 194, Mismatches: 29, Indels: 33
0.76 0.11 0.13
Matches are distributed among these distances:
86 5 0.03
87 107 0.55
88 8 0.04
89 1 0.01
90 3 0.02
91 2 0.01
92 1 0.01
93 8 0.04
94 20 0.10
95 39 0.20
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.46
Consensus pattern (86 bp):
AGAGCTTTATTTATTTTTCAAAAGTCGTTGAGCCTCTGCTTAAAGGAGCTTTATTTATTTTTTGA
AGTAGTTGAGCCTTTGTTTAG
Found at i:3867634 original size:7 final size:7
Alignment explanation
Indices: 3867622--3867659 Score: 60
Period size: 7 Copynumber: 5.4 Consensus size: 7
3867612 TAATATTGTT
3867622 AATAAAA
1 AATAAAA
3867629 AATAAAA
1 AATAAAA
3867636 AATAAAA
1 AATAAAA
3867643 AATAAATA
1 AATAAA-A
3867651 AA-AAAA
1 AATAAAA
3867657 AAT
1 AAT
3867660 TTTGGCAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 3 0.10
7 23 0.79
8 3 0.10
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (7 bp):
AATAAAA
Found at i:3869131 original size:49 final size:49
Alignment explanation
Indices: 3869078--3869187 Score: 123
Period size: 49 Copynumber: 2.2 Consensus size: 49
3869068 TCCAAAAATT
* * * * *
3869078 AAAAAAATAATTTCTAAATAGACTTAACTGGTGGAAAATGTAGAAATCAA
1 AAAAAAATAAATTCTAAATAGACCTAAATGATGAAAAATGTAGAAAT-AA
* * *
3869128 AAAAAGA-AAATTCTAAATTGACCTAAATGATGAAAAATTTAGAAATAA
1 AAAAAAATAAATTCTAAATAGACCTAAATGATGAAAAATGTAGAAATAA
3869176 AATAAAAATAAA
1 AA-AAAAATAAA
3869188 AGTAAATCGT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
48 4 0.08
49 36 0.73
50 9 0.18
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.25
Consensus pattern (49 bp):
AAAAAAATAAATTCTAAATAGACCTAAATGATGAAAAATGTAGAAATAA
Found at i:3872402 original size:50 final size:48
Alignment explanation
Indices: 3872345--3872441 Score: 158
Period size: 50 Copynumber: 2.0 Consensus size: 48
3872335 TATAATGTTT
* *
3872345 TTTAGTTTTGTTGATTTGAGGTTTTGCTTGAGGACAAGCAAAGATTCAAA
1 TTTAGTTTTGTTGATTTAAGGTTTTGCTT-ACGACAAGC-AAGATTCAAA
3872395 TTTAGTTTTGTTGATTTAAGGTTTTGCTTACGACAAGCAAGATTCAA
1 TTTAGTTTTGTTGATTTAAGGTTTTGCTTACGACAAGCAAGATTCAA
3872442 GTGAGGGGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 9 0.20
49 8 0.18
50 28 0.62
ACGTcount: A:0.28, C:0.09, G:0.22, T:0.41
Consensus pattern (48 bp):
TTTAGTTTTGTTGATTTAAGGTTTTGCTTACGACAAGCAAGATTCAAA
Found at i:3873253 original size:17 final size:17
Alignment explanation
Indices: 3873221--3873268 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
3873211 TTACTTTTCT
*
3873221 TTTCTTTTTATTTTTTAA
1 TTTC-TTTTAGTTTTTAA
*
3873239 GTTTCTTTTAGTTTTTTA
1 -TTTCTTTTAGTTTTTAA
3873257 TTTCTTTTAGTT
1 TTTCTTTTAGTT
3873269 AAGTTATTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 12 0.44
18 11 0.41
19 4 0.15
ACGTcount: A:0.12, C:0.06, G:0.06, T:0.75
Consensus pattern (17 bp):
TTTCTTTTAGTTTTTAA
Found at i:3873573 original size:24 final size:26
Alignment explanation
Indices: 3873546--3873599 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 26
3873536 TTCTCAGGGA
*
3873546 TTTTTTA-TTTGTAAT-TTTAAATTC
1 TTTTTTACTTTGAAATCTTTAAATTC
*
3873570 --TTTTACTTTGAAATCTTTTAATTC
1 TTTTTTACTTTGAAATCTTTAAATTC
3873594 TTTTTT
1 TTTTTT
3873600 TAGGATTAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
22 5 0.21
23 7 0.29
24 8 0.33
26 4 0.17
ACGTcount: A:0.22, C:0.07, G:0.04, T:0.67
Consensus pattern (26 bp):
TTTTTTACTTTGAAATCTTTAAATTC
Found at i:3875866 original size:18 final size:18
Alignment explanation
Indices: 3875843--3875881 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3875833 CATGATATGA
3875843 ATGACAAGGTATGAATGC
1 ATGACAAGGTATGAATGC
**
3875861 ATGACAATTTATGAATGC
1 ATGACAAGGTATGAATGC
3875879 ATG
1 ATG
3875882 TAATAATGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.28
Consensus pattern (18 bp):
ATGACAAGGTATGAATGC
Found at i:3875959 original size:19 final size:19
Alignment explanation
Indices: 3875935--3876165 Score: 247
Period size: 19 Copynumber: 12.2 Consensus size: 19
3875925 TTGCTTTGGC
*
3875935 TTTGGAAGGTGATTTAGGG
1 TTTGGAAGGTGGTTTAGGG
*
3875954 TTTGGAAGGTGGTTTAGGA
1 TTTGGAAGGTGGTTTAGGG
*
3875973 TTTGGAAGGTGGTTTATTGG
1 TTTGGAAGGTGGTTTA-GGG
3875993 TTTGG--GGTTTGGTTT-GGG
1 TTTGGAAGG--TGGTTTAGGG
*
3876011 TTTGGAAGGTGGTTTAGGT
1 TTTGGAAGGTGGTTTAGGG
* *
3876030 TTTGAAAGGTGGTTTATTGG
1 TTTGGAAGGTGGTTTA-GGG
*
3876050 TTTGG-GGGTTGGTTT-GGG
1 TTTGGAAGG-TGGTTTAGGG
*
3876068 TTTGGAAGGTGGTTTAGGT
1 TTTGGAAGGTGGTTTAGGG
* *
3876087 TTTGGAAGATGGTTTAGGT
1 TTTGGAAGGTGGTTTAGGG
*
3876106 TTTGGAAGGTGGTTTAGGT
1 TTTGGAAGGTGGTTTAGGG
**
3876125 TTTAAAAGGTGGTTTAGGG
1 TTTGGAAGGTGGTTTAGGG
* *
3876144 TTTGAAAGGTGGCTTAGGG
1 TTTGGAAGGTGGTTTAGGG
3876163 TTT
1 TTT
3876166 AATGGAATTT
Statistics
Matches: 181, Mismatches: 21, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
18 28 0.15
19 128 0.71
20 25 0.14
ACGTcount: A:0.16, C:0.00, G:0.42, T:0.42
Consensus pattern (19 bp):
TTTGGAAGGTGGTTTAGGG
Found at i:3876009 original size:76 final size:74
Alignment explanation
Indices: 3875912--3876140 Score: 241
Period size: 76 Copynumber: 3.0 Consensus size: 74
3875902 CAAATACATG
* * *
3875912 ATTGGTTTGGGGGTTGCTTTGGCTTTGGAAGGTGATTTAGGGTTTGGAAGGTGGTTTAGGATTTG
1 ATTGGTTT-GGGGTTGGTTTGGCTTTGGAAGGTGGTTTAGGTTTTGGAAGGTGGTTTAGG-TTTG
3875977 GAAGGTGGTTT
64 GAAGGTGGTTT
* *
3875988 ATTGGTTTGGGGTTTGGTTTGGGTTTGGAAGGTGGTTTAGGTTTTGAAAGGTGGTTTATTGGTTT
1 ATTGGTTTGGGG-TTGGTTTGGCTTTGGAAGGTGGTTTAGGTTTTGGAAGGTGGTTTA--GGTTT
*
3876053 GG-GGGTTGG-TT
63 GGAAGG-TGGTTT
* * *
3876064 -TGGGTTTGGAAGG-TGGTTTAGGTTTTGGAAGATGGTTTAGGTTTTGGAAGGTGGTTTAGGTTT
1 ATTGGTTTGG--GGTTGGTTT-GGCTTTGGAAGGTGGTTTAGGTTTTGGAAGGTGGTTTAGG-TT
**
3876127 TAAAAGGTGGTTT
62 TGGAAGGTGGTTT
3876140 A
1 A
3876141 GGGTTTGAAA
Statistics
Matches: 129, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
74 2 0.02
75 24 0.19
76 91 0.71
77 10 0.08
78 2 0.02
ACGTcount: A:0.15, C:0.01, G:0.41, T:0.43
Consensus pattern (74 bp):
ATTGGTTTGGGGTTGGTTTGGCTTTGGAAGGTGGTTTAGGTTTTGGAAGGTGGTTTAGGTTTGGA
AGGTGGTTT
Found at i:3876015 original size:57 final size:57
Alignment explanation
Indices: 3875951--3876155 Score: 272
Period size: 57 Copynumber: 3.6 Consensus size: 57
3875941 AGGTGATTTA
* *
3875951 GGGTTTGGAAGGTGGTTTAGGATTTGGAAGGTGGTTTATTGGTTTGGGGTTTGGTTT
1 GGGTTTGGAAGGTGGTTTAGGTTTTGGAAGGTGGTTTATTGGTTTGGGGGTTGGTTT
*
3876008 GGGTTTGGAAGGTGGTTTAGGTTTTGAAAGGTGGTTTATTGGTTTGGGGGTTGGTTT
1 GGGTTTGGAAGGTGGTTTAGGTTTTGGAAGGTGGTTTATTGGTTTGGGGGTTGGTTT
* *
3876065 GGGTTTGGAAGGTGGTTTAGGTTTTGGAAGATGGTTTA--GGTTTTGGAAGG-TGGTTT
1 GGGTTTGGAAGGTGGTTTAGGTTTTGGAAGGTGGTTTATTGG-TTTGG-GGGTTGGTTT
* ** * *
3876121 AGGTTTTAAAAGGTGGTTTAGGGTTTGAAAGGTGG
1 -GGGTTTGGAAGGTGGTTTAGGTTTTGGAAGGTGG
3876156 CTTAGGGTTT
Statistics
Matches: 133, Mismatches: 12, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
55 2 0.02
56 11 0.08
57 120 0.90
ACGTcount: A:0.16, C:0.00, G:0.43, T:0.41
Consensus pattern (57 bp):
GGGTTTGGAAGGTGGTTTAGGTTTTGGAAGGTGGTTTATTGGTTTGGGGGTTGGTTT
Found at i:3878432 original size:49 final size:49
Alignment explanation
Indices: 3878370--3878629 Score: 206
Period size: 49 Copynumber: 5.2 Consensus size: 49
3878360 TTTTTATTAA
* * *
3878370 AAAAG-CTATTTTTGGAAAAGGCTCTTACGAAAATAGGCAAAGAACTTT
1 AAAAGTCTCTTTTTGGAAAAGGTTCTTATGAAAATAGGCAAAGAACTTT
* * *
3878418 AAAAGTCTCTTTTTGGAAAGGGTT-TCTATGAAAATAAGC-AACAACTTCAAT
1 AAAAGTCTCTTTTTGGAAAAGGTTCT-TATGAAAATAGGCAAAGAACTT---T
* * * ** * *
3878469 AAAAAGTCTCTTTAT-AAAAAGGGTTCCTACAAAAATAGGCAACGAACCTT
1 -AAAAGTCTCTTTTTGGAAAA-GGTTCTTATGAAAATAGGCAAAGAACTTT
* * * *
3878519 AAAAATCTCTTTTTAG-AAAGCGTTTTTATGAAAATAGGCAATGAACTTT
1 AAAAGTCTCTTTTTGGAAAAG-GTTCTTATGAAAATAGGCAAAGAACTTT
* * * *
3878568 AAAAAATCTCTTTTTGGAAAAGGTTCCTATGAAAATAGGTAATGAACTTT
1 -AAAAGTCTCTTTTTGGAAAAGGTTCTTATGAAAATAGGCAAAGAACTTT
**
3878618 AAGGGTCTCTTT
1 AAAAGTCTCTTT
3878630 CCAATGCCAA
Statistics
Matches: 167, Mismatches: 32, Indels: 25
0.75 0.14 0.11
Matches are distributed among these distances:
48 14 0.08
49 72 0.43
50 41 0.25
51 8 0.05
52 27 0.16
53 5 0.03
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (49 bp):
AAAAGTCTCTTTTTGGAAAAGGTTCTTATGAAAATAGGCAAAGAACTTT
Found at i:3878507 original size:101 final size:99
Alignment explanation
Indices: 3878366--3878629 Score: 262
Period size: 101 Copynumber: 2.6 Consensus size: 99
3878356 AGATTTTTTA
* * * * * * *
3878366 TTAAAAAAGCTATTTTTGGAAAAGGCTCTTACGAAAATAGGCAAAGAACTTTAAAAGTCTCTTTT
1 TTAAAAAATCTCTTTATGAAAAAGGTTCCTACAAAAATAGGCAAAGAACTTTAAAAGTCTCTTTT
* *
3878431 TGGAAAGGGTTTCTATGAAAATAAGCAA-CAACT
66 TAGAAAGCGTTTCTATGAAAATAAGCAATCAACT
* * * *
3878464 TCAATAAAAAGTCTCTTTAT-AAAAAGGGTTCCTACAAAAATAGGCAACGAACCTTAAAAATCTC
1 T---TAAAAAATCTCTTTATGAAAAA-GGTTCCTACAAAAATAGGCAAAGAACTTTAAAAGTCTC
* * *
3878528 TTTTTAGAAAGCGTTTTTATGAAAATAGGCAATGAACT
62 TTTTTAGAAAGCGTTTCTATGAAAATAAGCAATCAACT
* * ** * * **
3878566 TTAAAAAATCTCTTTTTGGAAAAGGTTCCTATGAAAATAGGTAATGAACTTTAAGGGTCTCTTT
1 TTAAAAAATCTCTTTATGAAAAAGGTTCCTACAAAAATAGGCAAAGAACTTTAAAAGTCTCTTT
3878630 CCAATGCCAA
Statistics
Matches: 133, Mismatches: 27, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
98 1 0.01
99 47 0.35
100 8 0.06
101 72 0.54
102 5 0.04
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (99 bp):
TTAAAAAATCTCTTTATGAAAAAGGTTCCTACAAAAATAGGCAAAGAACTTTAAAAGTCTCTTTT
TAGAAAGCGTTTCTATGAAAATAAGCAATCAACT
Found at i:3879076 original size:7 final size:7
Alignment explanation
Indices: 3879064--3879121 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
3879054 CTTTCTCTTT
3879064 TTTTTTC
1 TTTTTTC
3879071 TTTTTT-
1 TTTTTTC
**
3879077 TTTTCAC
1 TTTTTTC
*
3879084 TTTTCTC
1 TTTTTTC
3879091 TCTTTTTC
1 T-TTTTTC
3879099 TTTTTTC
1 TTTTTTC
*
3879106 -TTTTCC
1 TTTTTTC
3879112 TTTTTT-
1 TTTTTTC
3879118 TTTT
1 TTTT
3879122 CCCAAATCCT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
6 13 0.31
7 23 0.55
8 6 0.14
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (7 bp):
TTTTTTC
Found at i:3879090 original size:45 final size:41
Alignment explanation
Indices: 3879040--3879122 Score: 103
Period size: 41 Copynumber: 1.9 Consensus size: 41
3879030 GACATTTTCC
* *
3879040 TTTCTCTCTTCTTGCTTTCTCTTTTTTTTTCTTTTTTTTTTCACT
1 TTTCTCTCTT-TTGC-TT-T-TTTCTTTTCCTTTTTTTTTTCACT
*
3879085 TTTCTCTCTTTTTCTTTTTTCTTTTCCTTTTTTTTTTC
1 TTTCTCTCTTTTGCTTTTTTCTTTTCCTTTTTTTTTTC
3879123 CCAAATCCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
41 19 0.54
42 1 0.03
43 2 0.06
44 3 0.09
45 10 0.29
ACGTcount: A:0.01, C:0.22, G:0.01, T:0.76
Consensus pattern (41 bp):
TTTCTCTCTTTTGCTTTTTTCTTTTCCTTTTTTTTTTCACT
Found at i:3879094 original size:22 final size:20
Alignment explanation
Indices: 3879069--3879121 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 20
3879059 TCTTTTTTTT
3879069 TCTTTTTTTTTTCACTTTTCTC
1 TCTTTTTTTTTT-ACTTTTC-C
*
3879091 TCTTTTTCTTTTTTCTTTTCC
1 TCTTTTT-TTTTTACTTTTCC
3879112 T-TTTTTTTTT
1 TCTTTTTTTTT
3879122 CCCAAATCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.14
20 5 0.17
21 2 0.07
22 13 0.45
23 5 0.17
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (20 bp):
TCTTTTTTTTTTACTTTTCC
Found at i:3879213 original size:7 final size:7
Alignment explanation
Indices: 3879191--3879229 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
3879181 AGGAGATCTA
3879191 TTTTTCT
1 TTTTTCT
*
3879198 TCTTTCT
1 TTTTTCT
3879205 TTTTTCT
1 TTTTTCT
3879212 TTTTT-T
1 TTTTTCT
*
3879218 GTTTTCT
1 TTTTTCT
3879225 TTTTT
1 TTTTT
3879230 TGTTGTTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.19
7 22 0.81
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (7 bp):
TTTTTCT
Found at i:3879222 original size:13 final size:13
Alignment explanation
Indices: 3879192--3879247 Score: 62
Period size: 13 Copynumber: 4.3 Consensus size: 13
3879182 GGAGATCTAT
3879192 TTTTCTTCTTTCTT-
1 TTTTCTT-TTT-TTG
3879206 TTTTCTTTTTTTG
1 TTTTCTTTTTTTG
3879219 TTTTCTTTTTTTG
1 TTTTCTTTTTTTG
* *
3879232 TTGT-TTTGTTTG
1 TTTTCTTTTTTTG
3879244 TTTT
1 TTTT
3879248 TCTATAACTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
12 12 0.32
13 19 0.50
14 7 0.18
ACGTcount: A:0.00, C:0.09, G:0.09, T:0.82
Consensus pattern (13 bp):
TTTTCTTTTTTTG
Found at i:3879230 original size:21 final size:20
Alignment explanation
Indices: 3879200--3879242 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
3879190 ATTTTTCTTC
*
3879200 TTTCTTTTTTCTTTTTTTGT
1 TTTCTTTTTTCTTGTTTTGT
*
3879220 TTTCTTTTTTTGTTGTTTTGT
1 TTTC-TTTTTTCTTGTTTTGT
3879241 TT
1 TT
3879243 GTTTTTCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (20 bp):
TTTCTTTTTTCTTGTTTTGT
Found at i:3885494 original size:19 final size:16
Alignment explanation
Indices: 3885455--3885487 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3885445 AACGATTTGA
3885455 ATGATAATGATGATTT
1 ATGATAATGATGATTT
3885471 ATGATAATGATGATTT
1 ATGATAATGATGATTT
3885487 A
1 A
3885488 CGATGATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (16 bp):
ATGATAATGATGATTT
Found at i:3892295 original size:28 final size:27
Alignment explanation
Indices: 3892235--3892303 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
3892225 TATTTCATAA
* *
3892235 ATTCATAAATCAATGTCAAAATATGTC
1 ATTCATAAATCATTGTCAAAATATATC
3892262 ACTTCATAAATCATTGT-AAAATACCTATC
1 A-TTCATAAATCATTGTCAAAATA--TATC
3892291 ATTCA-AATATCAT
1 ATTCATAA-ATCAT
3892304 AATCAAACCA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
27 9 0.25
28 23 0.64
29 4 0.11
ACGTcount: A:0.43, C:0.17, G:0.04, T:0.35
Consensus pattern (27 bp):
ATTCATAAATCATTGTCAAAATATATC
Found at i:3892364 original size:16 final size:16
Alignment explanation
Indices: 3892343--3892375 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3892333 AAAATCATCG
3892343 TAAATCATCATTATCA
1 TAAATCATCATTATCA
3892359 TAAATCATCATTATCA
1 TAAATCATCATTATCA
3892375 T
1 T
3892376 TCAAATCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.42, C:0.18, G:0.00, T:0.39
Consensus pattern (16 bp):
TAAATCATCATTATCA
Found at i:3894978 original size:26 final size:25
Alignment explanation
Indices: 3894949--3895004 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
3894939 TCCCCCCTTT
3894949 TTTTTATT-CTTTCCTTCATTTTTTTC
1 TTTTTATTACTTT-C-TCATTTTTTTC
*
3894975 TTTTTCTTACTTTCTCATTTTTTTC
1 TTTTTATTACTTTCTCATTTTTTTC
*
3895000 ATTTT
1 TTTTT
3895005 CATTTTTTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 15 0.56
26 8 0.30
27 4 0.15
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (25 bp):
TTTTTATTACTTTCTCATTTTTTTC
Found at i:3895352 original size:12 final size:12
Alignment explanation
Indices: 3895317--3895354 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
3895307 TGAAGAAAGT
3895317 TTTTTTTTAGG-
1 TTTTTTTTAGGA
*
3895328 TTTTTTTTTGGA
1 TTTTTTTTAGGA
3895340 TTTTTTTTAGGA
1 TTTTTTTTAGGA
3895352 TTT
1 TTT
3895355 CCTTGGACTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.11, C:0.00, G:0.16, T:0.74
Consensus pattern (12 bp):
TTTTTTTTAGGA
Found at i:3899691 original size:14 final size:14
Alignment explanation
Indices: 3899672--3899704 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
3899662 TCAATTAAAA
3899672 TTTATTATTATTAT
1 TTTATTATTATTAT
*
3899686 TTTATTTTTATTAT
1 TTTATTATTATTAT
3899700 TTTAT
1 TTTAT
3899705 AATTTCCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:3900113 original size:21 final size:22
Alignment explanation
Indices: 3900073--3900113 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
3900063 TATTATTTGG
*
3900073 ATTTTTGTATTTATTATTTATT
1 ATTTTTGTATTAATTATTTATT
*
3900095 ATTTTTGT-TTAATTCTTTA
1 ATTTTTGTATTAATTATTTA
3900114 ACATTTAGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (22 bp):
ATTTTTGTATTAATTATTTATT
Found at i:3902678 original size:59 final size:58
Alignment explanation
Indices: 3902609--3902803 Score: 146
Period size: 59 Copynumber: 3.3 Consensus size: 58
3902599 TCATTAAGCT
* *
3902609 TTTTCTTCAATGGTGATATTCAAAAACCTTACAATGGCGATATCTGAAATCATCTTACA
1 TTTTCCTCAATGGTGATATTCAAAAACCTT-TAATGGCGATATCTGAAATCATCTTACA
* * * * * * * *
3902668 TTTTCCTCAATGGCGATA-TCTAGAAACCTGTTGATGACAACATC-CAAAGTCATCTTGCA
1 TTTTCCTCAATGGTGATATTC-AAAAACCT-TTAATGGCGATATCTGAAA-TCATCTTACA
* * * * * * * *
3902727 TTCTCCTCAATGG-CATATTCGAGAACCTTTTACTGGTGATATCTGAAGTCATTTTAC-
1 TTTTCCTCAATGGTGATATTCAAAAACC-TTTAATGGCGATATCTGAAATCATCTTACA
3902784 TTTTGCCTCAATGGTGATAT
1 TTTT-CCTCAATGGTGATAT
3902804 CTGAGCTCTT
Statistics
Matches: 101, Mismatches: 27, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
57 3 0.03
58 36 0.36
59 61 0.60
60 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.36
Consensus pattern (58 bp):
TTTTCCTCAATGGTGATATTCAAAAACCTTTAATGGCGATATCTGAAATCATCTTACA
Found at i:3902953 original size:19 final size:20
Alignment explanation
Indices: 3902931--3902980 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
3902921 AAATCAAAAG
*
3902931 AAAA-CAAAAAAAATCCTAA
1 AAAATCAAAAAAAATCCCAA
*
3902950 AAAATTC-AAAAAATTCCCAA
1 AAAA-TCAAAAAAAATCCCAA
3902970 AAAATCAAAAA
1 AAAATCAAAAA
3902981 TAAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 6 0.23
20 19 0.73
21 1 0.04
ACGTcount: A:0.70, C:0.16, G:0.00, T:0.14
Consensus pattern (20 bp):
AAAATCAAAAAAAATCCCAA
Found at i:3902960 original size:20 final size:19
Alignment explanation
Indices: 3902937--3902980 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
3902927 AAAGAAAACA
*
3902937 AAAAAAATCCTAAAAAATTC
1 AAAAAAATCCCAAAAAA-TC
*
3902957 AAAAAATTCCCAAAAAATC
1 AAAAAAATCCCAAAAAATC
3902976 AAAAA
1 AAAAA
3902981 TAAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (19 bp):
AAAAAAATCCCAAAAAATC
Found at i:3908507 original size:12 final size:12
Alignment explanation
Indices: 3908490--3908514 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3908480 GCAAGCAACA
3908490 GTGATGATGATG
1 GTGATGATGATG
3908502 GTGATGATGATG
1 GTGATGATGATG
3908514 G
1 G
3908515 GCAACACTAA
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:0.24, C:0.00, G:0.44, T:0.32
Consensus pattern (12 bp):
GTGATGATGATG
Found at i:3908593 original size:19 final size:20
Alignment explanation
Indices: 3908560--3908613 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
3908550 ATCTTGAAAT
*
3908560 AAAAATAAATTAAAGGA-ATTA
1 AAAAATAAA--AAAGGACATCA
3908581 AAAAATAAAAAAGGACATCA
1 AAAAATAAAAAAGGACATCA
3908601 AAATAA-AAAAAAG
1 AAA-AATAAAAAAG
3908614 ACCATGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 6 0.20
20 13 0.43
21 11 0.37
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (20 bp):
AAAAATAAAAAAGGACATCA
Found at i:3913724 original size:36 final size:37
Alignment explanation
Indices: 3913654--3913740 Score: 122
Period size: 36 Copynumber: 2.4 Consensus size: 37
3913644 ATTAAGTAGG
* *
3913654 AATTTTGCATACCATCAATGATCATCAATGAAATAAA
1 AATTTTGCATACCACCAATGATCATCAATCAAATAAA
* *
3913691 AATTTTGCATGCCACCAA-GATCATCAGTCAAATAAA
1 AATTTTGCATACCACCAATGATCATCAATCAAATAAA
*
3913727 AATTTTTCATACCA
1 AATTTTGCATACCA
3913741 TTTCCTAGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
36 28 0.64
37 16 0.36
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.30
Consensus pattern (37 bp):
AATTTTGCATACCACCAATGATCATCAATCAAATAAA
Found at i:3913784 original size:61 final size:61
Alignment explanation
Indices: 3913689--3913804 Score: 196
Period size: 61 Copynumber: 1.9 Consensus size: 61
3913679 CAATGAAATA
* * *
3913689 AAAATTTTGCATGCCACCAAGATCATCAGTCAAATAAAAATTTTTCATACCATTTCCTAGT
1 AAAATTTTGCATACCACCAAGATAATCAATCAAATAAAAATTTTTCATACCATTTCCTAGT
*
3913750 AAAATTTTGCGTACCACCAAGATAATCAATCAAATAAAAATTTTTCATACCATTT
1 AAAATTTTGCATACCACCAAGATAATCAATCAAATAAAAATTTTTCATACCATTT
3913805 GCTTTCCTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.41, C:0.20, G:0.07, T:0.33
Consensus pattern (61 bp):
AAAATTTTGCATACCACCAAGATAATCAATCAAATAAAAATTTTTCATACCATTTCCTAGT
Found at i:3916526 original size:38 final size:38
Alignment explanation
Indices: 3916484--3916560 Score: 136
Period size: 38 Copynumber: 2.0 Consensus size: 38
3916474 ATAAGCATAT
* *
3916484 TTCCAAACAATTGACAAGTACCATAAGTGTTTTTTCTA
1 TTCCAAACAATTGACAAGTACAAGAAGTGTTTTTTCTA
3916522 TTCCAAACAATTGACAAGTACAAGAAGTGTTTTTTCTA
1 TTCCAAACAATTGACAAGTACAAGAAGTGTTTTTTCTA
3916560 T
1 T
3916561 CAATTTTGCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.36
Consensus pattern (38 bp):
TTCCAAACAATTGACAAGTACAAGAAGTGTTTTTTCTA
Found at i:3922001 original size:21 final size:20
Alignment explanation
Indices: 3921955--3922002 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
3921945 ACGTATGAAA
3921955 TTTTAGAAAAAGAAAATTTTG
1 TTTT-GAAAAAGAAAATTTTG
*
3921976 ATTTGAAAAAG-AAATTTGATG
1 TTTTGAAAAAGAAAATTT--TG
3921997 TTTTGA
1 TTTTGA
3922003 TGAATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 6 0.26
20 7 0.30
21 10 0.43
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.40
Consensus pattern (20 bp):
TTTTGAAAAAGAAAATTTTG
Found at i:3927791 original size:12 final size:12
Alignment explanation
Indices: 3927774--3927812 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
3927764 TACTTCCTCC
3927774 TCATTTGATTCA
1 TCATTTGATTCA
3927786 TCATTTGATTCA
1 TCATTTGATTCA
*
3927798 TC-TTGTAATTCA
1 TCATT-TGATTCA
3927810 TCA
1 TCA
3927813 AATGTGCATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 2 0.08
12 22 0.92
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.49
Consensus pattern (12 bp):
TCATTTGATTCA
Found at i:3927888 original size:119 final size:118
Alignment explanation
Indices: 3927677--3927910 Score: 441
Period size: 119 Copynumber: 2.0 Consensus size: 118
3927667 TCATCATAAG
3927677 CATCTTGTAATTCATCAAATGTGCATGAATTTAAATCATATGGATTAGAACCTTAGGCTCATCAA
1 CATCTTGTAATTCATCAAATGTGCATGAATTTAAATCATATGGATTAGAACCTTAGGCTCATCAA
3927742 AAGCCATGAGACATAGATTGGCTACTTCCTCCTCATTTGATTCATCATTTGATT
66 AAGCCATGAGACATAGATTGGCTACTTCCTCCTCATTTGATTCATC-TTTGATT
*
3927796 CATCTTGTAATTCATCAAATGTGCATGAATTTAAATCATATGGATTAGAACCTTGGGCTCATCAA
1 CATCTTGTAATTCATCAAATGTGCATGAATTTAAATCATATGGATTAGAACCTTAGGCTCATCAA
*
3927861 AAGCTATGAGACATAGATTGGCTACTTCCTCCTCATTTGATTCATCTTTG
66 AAGCCATGAGACATAGATTGGCTACTTCCTCCTCATTTGATTCATCTTTG
3927911 GAAAAGTCAC
Statistics
Matches: 113, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
118 4 0.04
119 109 0.96
ACGTcount: A:0.30, C:0.19, G:0.15, T:0.35
Consensus pattern (118 bp):
CATCTTGTAATTCATCAAATGTGCATGAATTTAAATCATATGGATTAGAACCTTAGGCTCATCAA
AAGCCATGAGACATAGATTGGCTACTTCCTCCTCATTTGATTCATCTTTGATT
Found at i:3929760 original size:17 final size:17
Alignment explanation
Indices: 3929738--3929771 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3929728 ACGGATCGAC
*
3929738 CCCCTCATATATGGGAT
1 CCCCTCATATAGGGGAT
3929755 CCCCTCATATAGGGGAT
1 CCCCTCATATAGGGGAT
3929772 TGATTGGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (17 bp):
CCCCTCATATAGGGGAT
Found at i:3930623 original size:18 final size:18
Alignment explanation
Indices: 3930591--3930636 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
3930581 TAAAATAGTA
* *
3930591 AGTCAAACTCTAAACCCT
1 AGTCAAACCCGAAACCCT
* *
3930609 AGTGAAACCCGAAACCTT
1 AGTCAAACCCGAAACCCT
3930627 AGTCAAACCC
1 AGTCAAACCC
3930637 TAACCTTTTG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.33, G:0.11, T:0.17
Consensus pattern (18 bp):
AGTCAAACCCGAAACCCT
Found at i:3930682 original size:32 final size:32
Alignment explanation
Indices: 3930646--3930728 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
3930636 CTAACCTTTT
*
3930646 GGTCAAACCCTAAAACCTAAACTCAATACCTA
1 GGTCAAACCCTAAAACCTAAACTCAAAACCTA
* *
3930678 GGTCACACCCTAAAATCC-AAACTTAAAACCTA
1 GGTCAAACCCTAAAA-CCTAAACTCAAAACCTA
** *
3930710 TATCAAACCC-AAAGCCTAA
1 GGTCAAACCCTAAAACCTAA
3930729 GGTCAAACCC
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
30 2 0.05
31 5 0.12
32 33 0.79
33 2 0.05
ACGTcount: A:0.45, C:0.31, G:0.06, T:0.18
Consensus pattern (32 bp):
GGTCAAACCCTAAAACCTAAACTCAAAACCTA
Found at i:3930907 original size:18 final size:18
Alignment explanation
Indices: 3930860--3930924 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
3930850 CCTTATAACT
*
3930860 AAAGTCAAACACTAAAACCC
1 AAAGTCAAACACTAAGA--C
* * *
3930880 TAGGTCAAACCCTAAGAC
1 AAAGTCAAACACTAAGAC
* *
3930898 AAATTCAAACACTAAGCC
1 AAAGTCAAACACTAAGAC
3930916 AAAGTCAAA
1 AAAGTCAAA
3930925 TTCTCAACAT
Statistics
Matches: 35, Mismatches: 10, Indels: 2
0.74 0.21 0.04
Matches are distributed among these distances:
18 22 0.63
20 13 0.37
ACGTcount: A:0.51, C:0.26, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAGTCAAACACTAAGAC
Found at i:3931911 original size:136 final size:136
Alignment explanation
Indices: 3931658--3931937 Score: 542
Period size: 136 Copynumber: 2.1 Consensus size: 136
3931648 CTTATCTATT
*
3931658 TCCTCTATCTTTGGGTCTAACCTAAACTATATTAAGTCCAACTTAATTTGTCCCAATTGTACTCT
1 TCCTTTATCTTTGGGTCTAACCTAAACTATATTAAGTCCAACTTAATTTGTCCCAATTGTACTCT
3931723 TTCACAATAGTCCCATTATGTGTGATCAATTAGGTTCCATAGCATGTTGGTAGTAAACATAAGTA
66 TTCACAATAGTCCCATTATGTGTGATCAATTAGGTTCCATAGCATGTTGGTAGTAAACATAAGTA
3931788 TTGTAA
131 TTGTAA
*
3931794 TCCTTTATGTTTGGGTCTAACCTAAACTATATTAAGTCCAACTTAATTTGTCCCAATTGTACTCT
1 TCCTTTATCTTTGGGTCTAACCTAAACTATATTAAGTCCAACTTAATTTGTCCCAATTGTACTCT
3931859 TTCACAATAGTCCCATTATGTGTGATCAATTAGGTTCCATAGCATGTTGGTAGTAAACATAAGTA
66 TTCACAATAGTCCCATTATGTGTGATCAATTAGGTTCCATAGCATGTTGGTAGTAAACATAAGTA
3931924 TTGTAA
131 TTGTAA
3931930 TCCTTTAT
1 TCCTTTAT
3931938 ATTCAGCTTA
Statistics
Matches: 142, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 142 1.00
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (136 bp):
TCCTTTATCTTTGGGTCTAACCTAAACTATATTAAGTCCAACTTAATTTGTCCCAATTGTACTCT
TTCACAATAGTCCCATTATGTGTGATCAATTAGGTTCCATAGCATGTTGGTAGTAAACATAAGTA
TTGTAA
Found at i:3935739 original size:25 final size:24
Alignment explanation
Indices: 3935711--3935769 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
3935701 ATCTTTTTCC
3935711 CTTTTTTTTTCTCT-CCTCATTTTTT
1 CTTTTTTTTTCT-TGCCT-ATTTTTT
* *
3935736 CTTTTTTCTTCTTGCCTTTTTTTT
1 CTTTTTTTTTCTTGCCTATTTTTT
*
3935760 GTTTTTTTTT
1 CTTTTTTTTT
3935770 TTGTGTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
24 15 0.52
25 14 0.48
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (24 bp):
CTTTTTTTTTCTTGCCTATTTTTT
Found at i:3938060 original size:15 final size:16
Alignment explanation
Indices: 3938041--3938082 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
3938031 AAAATTGAAG
3938041 AAAAAGAGAAAAA-AA
1 AAAAAGAGAAAAATAA
*
3938056 TAAAAGA-AAAAATAA
1 AAAAAGAGAAAAATAA
3938071 AAAAAGAGAAAA
1 AAAAAGAGAAAA
3938083 GAAAGAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.22
15 14 0.61
16 4 0.17
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (16 bp):
AAAAAGAGAAAAATAA
Found at i:3939439 original size:34 final size:32
Alignment explanation
Indices: 3939392--3939495 Score: 104
Period size: 34 Copynumber: 3.2 Consensus size: 32
3939382 GCATCCAGGT
*
3939392 TTTAAGCCCAATTTAGCTAGTACTCATGAAAATA
1 TTTAAGCCTAATTTAGCTAGTAC-CATGAAAA-A
* **
3939426 TTTAAGCCTAATTTAGCTAGCACCTAT-AGGAA
1 TTTAAGCCTAATTTAGCTAGTACC-ATGAAAAA
* *
3939458 -TTAAGCCTAGTTTAGCTAGTACCCATGAAAGA
1 TTTAAGCCTAATTTAGCTAGTA-CCATGAAAAA
3939490 TTTAAG
1 TTTAAG
3939496 GTCAGTCTAG
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
31 21 0.37
32 5 0.09
33 8 0.14
34 23 0.40
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (32 bp):
TTTAAGCCTAATTTAGCTAGTACCATGAAAAA
Found at i:3939634 original size:33 final size:32
Alignment explanation
Indices: 3939392--3939663 Score: 163
Period size: 33 Copynumber: 8.2 Consensus size: 32
3939382 GCATCCAGGT
* *
3939392 TTTAAGCCCAATTTAGCTAGTACTC-ATGAAAATA
1 TTTAAGCCCAGTTTAGCTAGCAC-CAATG-AAA-A
* * * *
3939426 TTTAAGCCTAATTTAGCTAGCACCTAT-AGGAA
1 TTTAAGCCCAGTTTAGCTAGCACCAATGA-AAA
* * *
3939458 -TTAAGCCTAGTTTAGCTAGTACCCATGAAAGA
1 TTTAAGCCCAGTTTAGCTAGCACCAATGAAA-A
** * * *
3939490 TTTAAGGTCAGTCTAGCTGGCACCTATGAAAAGA
1 TTTAAGCCCAGTTTAGCTAGCACCAATG-AAA-A
* * * * * * *
3939524 TTCAAGCCTAGATTAGTTAGTACCTGATGCAAA
1 TTTAAGCCCAGTTTAGCTAGCACC-AATGAAAA
* * * *
3939557 TTTAAGCCCAGATTAGCTACCACCCCATAAAAAGA
1 TTTAAGCCCAGTTTAGCTAGCA-CCAAT-GAAA-A
*
3939592 TTTAAGCCCAGTTTAGCTAGCAACCAATGAAAT
1 TTTAAGCCCAGTTTAGCTAGC-ACCAATGAAAA
**
3939625 TTTAAGCCCAGTTTAGCTAGCATTAATGAAAA
1 TTTAAGCCCAGTTTAGCTAGCACCAATGAAAA
3939657 TTTAAGC
1 TTTAAGC
3939664 TTAGATTATC
Statistics
Matches: 186, Mismatches: 41, Indels: 24
0.74 0.16 0.10
Matches are distributed among these distances:
31 24 0.13
32 19 0.10
33 63 0.34
34 52 0.28
35 27 0.15
36 1 0.01
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (32 bp):
TTTAAGCCCAGTTTAGCTAGCACCAATGAAAA
Found at i:3940538 original size:8 final size:8
Alignment explanation
Indices: 3940521--3940632 Score: 81
Period size: 8 Copynumber: 14.0 Consensus size: 8
3940511 CCATTAAATG
3940521 AAAA-ATA
1 AAAATATA
3940528 AAAATATA
1 AAAATATA
3940536 AAAATAT-
1 AAAATATA
* *
3940543 AAAAGACA
1 AAAATATA
3940551 AAAATATA
1 AAAATATA
*
3940559 AATATAT-
1 AAAATATA
3940566 AAAA-AT-
1 AAAATATA
3940572 AAAATATA
1 AAAATATA
*
3940580 ACAATATA
1 AAAATATA
*
3940588 ATAATAATTA
1 AAAAT-A-TA
3940598 AAAATATTA
1 AAAATA-TA
*
3940607 AAGATATTA
1 AAAATA-TA
3940616 AAAGATATA
1 AAA-ATATA
*
3940625 TAAATATA
1 AAAATATA
3940633 TAATAAAAGG
Statistics
Matches: 86, Mismatches: 12, Indels: 13
0.77 0.11 0.12
Matches are distributed among these distances:
6 6 0.07
7 14 0.16
8 38 0.44
9 19 0.22
10 9 0.10
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.27
Consensus pattern (8 bp):
AAAATATA
Found at i:3940557 original size:23 final size:21
Alignment explanation
Indices: 3940521--3940588 Score: 82
Period size: 23 Copynumber: 3.1 Consensus size: 21
3940511 CCATTAAATG
3940521 AAAAATAAAAATATAAAAATAT
1 AAAAA-AAAAATATAAAAATAT
*
3940543 AAAAGACAAAAATATAAATATAT
1 AAAA-A-AAAAATATAAAAATAT
* *
3940566 AAAAATAAAATATAACAATAT
1 AAAAAAAAAATATAAAAATAT
3940587 AA
1 AA
3940589 TAATAATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
21 15 0.38
22 5 0.12
23 20 0.50
ACGTcount: A:0.74, C:0.03, G:0.01, T:0.22
Consensus pattern (21 bp):
AAAAAAAAAATATAAAAATAT
Found at i:3940603 original size:18 final size:18
Alignment explanation
Indices: 3940569--3940635 Score: 52
Period size: 18 Copynumber: 3.7 Consensus size: 18
3940559 AATATATAAA
*
3940569 AATAAAATATAACAATAT
1 AATAAAATATAAAAATAT
3940587 AATAATAAT-TAAAAATAT
1 AATAA-AATATAAAAATAT
3940605 --TAAAGATATTAAAAGATAT
1 AATAAA-ATA-TAAAA-ATAT
3940624 -ATAAATATATAA
1 AATAAA-ATATAA
3940636 TAAAAGGGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
15 1 0.02
16 5 0.12
18 18 0.44
19 10 0.24
20 7 0.17
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (18 bp):
AATAAAATATAAAAATAT
Found at i:3942192 original size:18 final size:20
Alignment explanation
Indices: 3942163--3942199 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3942153 TAAAAATATA
3942163 AATAATAAATATG-TAAAAC
1 AATAATAAATATGATAAAAC
3942182 AATAA-AAATATGATAAAA
1 AATAATAAATATGATAAAA
3942200 GTAAAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (20 bp):
AATAATAAATATGATAAAAC
Found at i:3942703 original size:76 final size:77
Alignment explanation
Indices: 3942616--3942770 Score: 258
Period size: 77 Copynumber: 2.0 Consensus size: 77
3942606 TTTAAGCCCT
* *
3942616 AAGTTTACCCAAAACCCTAAAATCATTAT-AAATTTAAGAATCTATAAGAAAGTTTCCCATAAAG
1 AAGTTTACCCAAAACCCTAAAATCATTATAAAATTTAAAAATCTATAAGAAAGCTTCCCATAAAG
3942680 TAATATGTCCCC
66 TAATATGTCCCC
*
3942692 AAGTTTACCCAAAACCCTAAAATCATTATAAAATTTAAAAATCTATATGAAAGCTTCCCATAAAG
1 AAGTTTACCCAAAACCCTAAAATCATTATAAAATTTAAAAATCTATAAGAAAGCTTCCCATAAAG
* *
3942757 TGATATGTTCCC
66 TAATATGTCCCC
3942769 AA
1 AA
3942771 ATGCCTCCTA
Statistics
Matches: 73, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
76 29 0.40
77 44 0.60
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (77 bp):
AAGTTTACCCAAAACCCTAAAATCATTATAAAATTTAAAAATCTATAAGAAAGCTTCCCATAAAG
TAATATGTCCCC
Found at i:3943815 original size:3 final size:3
Alignment explanation
Indices: 3943807--3943848 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
3943797 TTTTTATTAA
3943807 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3943849 TCAATTCCCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3947960 original size:18 final size:20
Alignment explanation
Indices: 3947924--3947967 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
3947914 TTCTTTTATT
3947924 ATATATTTATATATCTTTTA
1 ATATATTTATATATCTTTTA
*
3947944 ATATCTTTA-ATAT-TTTTA
1 ATATATTTATATATCTTTTA
3947962 AT-TATT
1 ATATATT
3947968 CTTATATTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 7 0.32
19 4 0.18
20 8 0.36
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATATTTATATATCTTTTA
Found at i:3947967 original size:10 final size:9
Alignment explanation
Indices: 3947924--3948028 Score: 52
Period size: 8 Copynumber: 12.6 Consensus size: 9
3947914 TTCTTTTATT
*
3947924 ATATATTTA
1 ATATTTTTA
3947933 TATATCTTTTA
1 -ATAT-TTTTA
*
3947944 ATATCTTTA
1 ATATTTTTA
3947953 ATATTTTTA
1 ATATTTTTA
*
3947962 ATTATTCTT-
1 A-TATTTTTA
*
3947971 ATATTCTT-
1 ATATTTTTA
3947979 ATA-TTTT-
1 ATATTTTTA
*
3947986 AT-TTTAT-
1 ATATTTTTA
3947993 ATATTTTT-
1 ATATTTTTA
3948001 -TATTTTT-
1 ATATTTTTA
*
3948008 ATCTTTTT-
1 ATATTTTTA
3948016 ATATTTTT-
1 ATATTTTTA
3948024 ATATT
1 ATATT
3948029 ATTATTATTA
Statistics
Matches: 81, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
7 17 0.21
8 32 0.40
9 14 0.17
10 14 0.17
11 4 0.05
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (9 bp):
ATATTTTTA
Found at i:3948001 original size:16 final size:15
Alignment explanation
Indices: 3947982--3948050 Score: 68
Period size: 16 Copynumber: 4.3 Consensus size: 15
3947972 TATTCTTATA
3947982 TTTTATTTTATATATT
1 TTTTATTTT-TATATT
*
3947998 TTTTATTTTTATCTT
1 TTTTATTTTTATATT
3948013 TTTATATTTTTATATT
1 TTT-TATTTTTATATT
3948029 ATTATTATTATTT-TCATT
1 -TT-TTATT-TTTAT-ATT
3948047 TTTT
1 TTTT
3948051 GTTTAATGGC
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
15 8 0.17
16 22 0.48
17 9 0.20
18 7 0.15
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTATTTTTATATT
Found at i:3948023 original size:24 final size:25
Alignment explanation
Indices: 3947987--3948033 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
3947977 TTATATTTTA
* *
3947987 TTTTATATATTTTTTATTTTTATCT
1 TTTTATATATTTTATATTATTATCT
3948012 TTTTATAT-TTTTATATTATTAT
1 TTTTATATATTTTATATTATTAT
3948034 TATTATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTTATATATTTTATATTATTATCT
Found at i:3948797 original size:19 final size:21
Alignment explanation
Indices: 3948773--3948811 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3948763 GGGTATATCG
*
3948773 TTTCCT-ATA-AGCAGTATGT
1 TTTCCTCATATAGCACTATGT
3948792 TTTCCTCATATAGCACTATG
1 TTTCCTCATATAGCACTATG
3948812 AAAAAGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 3 0.18
21 8 0.47
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.41
Consensus pattern (21 bp):
TTTCCTCATATAGCACTATGT
Found at i:3952433 original size:16 final size:17
Alignment explanation
Indices: 3952406--3952439 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3952396 GAAATTATAT
3952406 AAAAAATCATTTTCTTA
1 AAAAAATCATTTTCTTA
*
3952423 AAAAAAT-ATTTTTTTA
1 AAAAAATCATTTTCTTA
3952439 A
1 A
3952440 CAATGTAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
AAAAAATCATTTTCTTA
Found at i:3954377 original size:24 final size:25
Alignment explanation
Indices: 3954350--3954396 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
3954340 AGAAATTCTC
3954350 ATAATAATT-TTT-TAAAAAATAAAG
1 ATAAT-ATTCTTTATAAAAAATAAAG
*
3954374 ATAATATTCTTTATGAAAAATAA
1 ATAATATTCTTTATAAAAAATAA
3954397 TTATTGAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.15
24 8 0.40
25 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (25 bp):
ATAATATTCTTTATAAAAAATAAAG
Found at i:3954622 original size:3 final size:3
Alignment explanation
Indices: 3954614--3954664 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
3954604 TATTACTACA
3954614 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
3954662 ATT
1 ATT
3954665 CACAAGTCCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:3954697 original size:20 final size:20
Alignment explanation
Indices: 3954661--3954707 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
3954651 TTATTATTAT
*
3954661 TATTCACAAGTCCTAAAACAA
1 TATTAACAAGTCCTAAAA-AA
3954682 TATTAACAAG-CCTAAAAAA
1 TATTAACAAGTCCTAAAAAA
3954701 TAGTTAA
1 TA-TTAA
3954708 GGGCTCATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 4 0.17
20 11 0.46
21 9 0.38
ACGTcount: A:0.51, C:0.17, G:0.06, T:0.26
Consensus pattern (20 bp):
TATTAACAAGTCCTAAAAAA
Found at i:3954969 original size:6 final size:6
Alignment explanation
Indices: 3954937--3954979 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
3954927 TTTTTACTCA
* * *
3954937 TTTCTT TTCCTT CTTTCTT TTTTTT TTTCTT TTTCTT CTTCTT
1 TTTCTT TTTCTT -TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
3954980 CTCCTTCCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
6 26 0.84
7 5 0.16
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:3955150 original size:14 final size:14
Alignment explanation
Indices: 3955133--3955185 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 14
3955123 TTCTTTTTTT
3955133 TTTTTTTTTCTTTC
1 TTTTTTTTTCTTTC
3955147 -TTTTTTTTCTATTC
1 TTTTTTTTTCT-TTC
*
3955161 TTTCTTTTCTCTTTC
1 TTT-TTTTTTCTTTC
3955176 TTTTTGTTTT
1 TTTTT-TTTT
3955186 TTTTTCTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
13 10 0.30
14 5 0.15
15 11 0.33
16 7 0.21
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTTTTTTTCTTTC
Found at i:3955167 original size:49 final size:49
Alignment explanation
Indices: 3955114--3955213 Score: 134
Period size: 49 Copynumber: 2.0 Consensus size: 49
3955104 ACATTCCCTC
*
3955114 TCTTTT-TATTTCTTTTTTTTTTTTTTTTCTTTCTTTT-TT-TTCTATTCTT
1 TCTTTTCTATTTC-TTTTTGTTTTTTTTTC-TTCTTTTCTTATTCT-TTCTT
*
3955163 TCTTTTCTCTTTCTTTTTGTTTTTTTTTCTTCTTTTCTTATTCTTTCTT
1 TCTTTTCTATTTCTTTTTGTTTTTTTTTCTTCTTTTCTTATTCTTTCTT
3955212 TC
1 TC
3955214 CCCCAGTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
48 7 0.15
49 30 0.65
50 9 0.20
ACGTcount: A:0.03, C:0.16, G:0.01, T:0.80
Consensus pattern (49 bp):
TCTTTTCTATTTCTTTTTGTTTTTTTTTCTTCTTTTCTTATTCTTTCTT
Found at i:3955180 original size:45 final size:44
Alignment explanation
Indices: 3955122--3955212 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 44
3955112 TCTCTTTTTA
* *
3955122 TTTCTTTT-TTTTTTTTTTTTCTTTCTT-TTTTTTCTATTCTTTCT
1 TTTCTTTTCTTTTTGTTTTTT-TTTCTTCTTTTCT-TATTCTTTCT
3955166 TTTCTCTTTCTTTTTGTTTTTTTTTCTTCTTTTCTTATTCTTTCT
1 TTTCT-TTTCTTTTTGTTTTTTTTTCTTCTTTTCTTATTCTTTCT
3955211 TT
1 TT
3955213 CCCCCAGTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
44 5 0.12
45 21 0.50
46 16 0.38
ACGTcount: A:0.02, C:0.15, G:0.01, T:0.81
Consensus pattern (44 bp):
TTTCTTTTCTTTTTGTTTTTTTTTCTTCTTTTCTTATTCTTTCT
Found at i:3968050 original size:90 final size:90
Alignment explanation
Indices: 3967897--3968079 Score: 276
Period size: 90 Copynumber: 2.0 Consensus size: 90
3967887 ATGTAGAGTC
* * * *
3967897 CTTATGCAAACACAATTCTTTCATAGCTAAGCAAAGAAAGTTCTGTAGGATTATATCTCTTTTGG
1 CTTATGCAAACACAATTCCTTCATAGCTAAGCAAAGAAAGTACTCTAAGATTATATCTCTTTTGG
* * *
3967962 CCTAACTTGTTGGAGTCCAAATGAG
66 CCGAACATGTTAGAGTCCAAATGAG
* * *
3967987 CTTATGCAAACACAATTCCTTCATGGCTAAGCAAAGGAAGTACTCTAAGATTATATCTTTTTTGG
1 CTTATGCAAACACAATTCCTTCATAGCTAAGCAAAGAAAGTACTCTAAGATTATATCTCTTTTGG
3968052 CCGAACATGTTAGAGTCCAAATGAG
66 CCGAACATGTTAGAGTCCAAATGAG
3968077 CTT
1 CTT
3968080 TGAACTTGCA
Statistics
Matches: 83, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
90 83 1.00
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (90 bp):
CTTATGCAAACACAATTCCTTCATAGCTAAGCAAAGAAAGTACTCTAAGATTATATCTCTTTTGG
CCGAACATGTTAGAGTCCAAATGAG
Found at i:3978177 original size:13 final size:14
Alignment explanation
Indices: 3978159--3978187 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3978149 CCAACTCGAA
3978159 TAAAATA-TATAAT
1 TAAAATATTATAAT
3978172 TAAAATATTATAAT
1 TAAAATATTATAAT
3978186 TA
1 TA
3978188 TACAAGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TAAAATATTATAAT
Found at i:3978560 original size:22 final size:22
Alignment explanation
Indices: 3978535--3978593 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
3978525 AAAATGAATT
3978535 TTATGTTTTGAAAAAAATAA-AA
1 TTATGTTTT-AAAAAAATAATAA
* *
3978557 TTATACATTTT-ATAAAATAATAA
1 TTAT--GTTTTAAAAAAATAATAA
3978580 TTATGTTTTAAAAA
1 TTATGTTTTAAAAA
3978594 TTAAAAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 8
0.71 0.10 0.20
Matches are distributed among these distances:
21 4 0.14
22 15 0.52
23 6 0.21
24 4 0.14
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (22 bp):
TTATGTTTTAAAAAAATAATAA
Found at i:3978602 original size:21 final size:21
Alignment explanation
Indices: 3978564--3978603 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
3978554 AAATTATACA
*
3978564 TTTTATAAAATAATAATTATG
1 TTTTATAAAATAAAAATTATG
3978585 TTTTA-AAAATTAAAAATTA
1 TTTTATAAAA-TAAAAATTA
3978604 AGAATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
TTTTATAAAATAAAAATTATG
Found at i:3982282 original size:2 final size:2
Alignment explanation
Indices: 3982275--3982306 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3982265 ATATAATCTC
3982275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3982307 GAAATAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3982354 original size:3 final size:3
Alignment explanation
Indices: 3982348--3982377 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3982338 ACTACTAGGA
3982348 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT
3982378 TGCGGACGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.67, T:0.33
Consensus pattern (3 bp):
GGT
Found at i:3984106 original size:30 final size:30
Alignment explanation
Indices: 3984070--3984128 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
3984060 TAAGAAGCAC
3984070 CTTAAGTTAGGCAAATATTCGGCAGAATGA
1 CTTAAGTTAGGCAAATATTCGGCAGAATGA
* *
3984100 CTTAAGTTGGGCAAATATTTGGCAGAATG
1 CTTAAGTTAGGCAAATATTCGGCAGAATG
3984129 TAAGCAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.12, G:0.25, T:0.29
Consensus pattern (30 bp):
CTTAAGTTAGGCAAATATTCGGCAGAATGA
Found at i:3986180 original size:61 final size:61
Alignment explanation
Indices: 3986105--3986228 Score: 221
Period size: 61 Copynumber: 2.0 Consensus size: 61
3986095 ATCAACATAC
**
3986105 AAGACAATTGTGATAATTTGGTGAACTTAAAACATCACCTATCAGTTCTACAAGGGAGACT
1 AAGACAATTGTGATAATGGGGTGAACTTAAAACATCACCTATCAGTTCTACAAGGGAGACT
*
3986166 AAGACAATTGTGATAATGGGGTGAACTTAAAACATCACCTATCAGTTCTATAAGGGAGACT
1 AAGACAATTGTGATAATGGGGTGAACTTAAAACATCACCTATCAGTTCTACAAGGGAGACT
3986227 AA
1 AA
3986229 CTTTAAGAGA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.27
Consensus pattern (61 bp):
AAGACAATTGTGATAATGGGGTGAACTTAAAACATCACCTATCAGTTCTACAAGGGAGACT
Found at i:3989147 original size:62 final size:62
Alignment explanation
Indices: 3989020--3989176 Score: 153
Period size: 63 Copynumber: 2.5 Consensus size: 62
3989010 AATTTGGTCT
* *
3989020 AAAAATATCTTAATAATGTTTATAAAAAAAAATGAGAGGATTATTTAAGATATTTTTGGATA
1 AAAAATATCTTAATAATGTTTATAAAAAAAAATCAGAGGATTATTTAAGATATTTTTGGACA
* ** *
3989082 AAAAATATCTTAAATAAT-TTTAGTTAAAAAGTATCA-AGTGATTATTTAAGGT-TATTTT-GAC
1 AAAAATATCTT-AATAATGTTTA-TAAAAAAAAATCAGAG-GATTATTTAAGATAT-TTTTGGAC
3989143 A
62 A
*
3989144 AAAAA-ATCCCTTAAGTAATGTTTTTAAAAAAAA
1 AAAAATAT--CTTAA-TAATGTTTATAAAAAAAA
3989177 TGATGAGGAT
Statistics
Matches: 77, Mismatches: 10, Indels: 15
0.75 0.10 0.15
Matches are distributed among these distances:
61 2 0.03
62 28 0.36
63 44 0.57
64 3 0.04
ACGTcount: A:0.48, C:0.04, G:0.11, T:0.37
Consensus pattern (62 bp):
AAAAATATCTTAATAATGTTTATAAAAAAAAATCAGAGGATTATTTAAGATATTTTTGGACA
Found at i:4000914 original size:439 final size:430
Alignment explanation
Indices: 4000105--4000972 Score: 1430
Period size: 439 Copynumber: 2.0 Consensus size: 430
4000095 TAAACCTTAG
4000105 CAAATAGTATTTTCTAAAACTCATTTCTATGGCATTTTATAAAAATATGAAAAATCTTTATCGAA
1 CAAATAGTATTTTCTAAAACTCATTTCTATGGCATTTTATAAAAATATGAAAAATCTTTATCGAA
4000170 AATTAATCTAAATGCTCCAATACATTTATGACATTTTAGATAGATTTTTTTACCTAAAAATTCCT
66 AATTAATCTAAATGCTCCAATACATTTATGACATTTTAGATAGATTTTTTTACCTAAAAATTCCT
4000235 AAAGCATCACTGCTTGGATTTCTTTAGGATTACATCCTAAGAGATTTTTTGTTTGTTTTGAAAAA
131 AAAGCATCACTGCTTGGATTTCTTTAGGATTACATCCTAAGAGATTTTTTGTTTGTTTTGAAAAA
4000300 TTATTAAAAGTCATGTAATAATAAAATTATCCAGAGATTTATTTTAAAAAGCATATTTTTATCTA
196 TTATTAAAAGTCATGTAATAATAAAATTATCCAGAGATTTATTTTAAAAAGCATATTTTTATCTA
4000365 AATGACTTTTCAAATTAAAGAAAATAATGATAACATAGAGGTTTTTCGTATTGAAAAAAACTTTT
261 AATGACTTTTCAAATTAAAGAAAATAATGATAACATAGAGGTTTTTCGTATTGAAAAAAACTTTT
* * *
4000430 AAATATTTCAATATTTTGGTAATTTTTTGAAAACATTTCTTACCTAAAAAATTCTCGGATATCAT
326 AAATATTCCAATACTTTGGTAATTTTTTGAAAACATTTCTTACCTAAAAAATTCTCGAATATCAT
4000495 TTCTTGAATTTTTCGGAGTCCTATCATCAAAAATTTTTAA
391 TTCTTGAATTTTTCGGAGTCCTATCATCAAAAATTTTTAA
*
4000535 CAAATAGTATTTTCTAAAACTCATTTCTATGGCA-TTTATAAAAAATTAT-TAAAATCTTCTATC
1 CAAATAGTATTTTCTAAAACTCATTTCTATGGCATTTTAT-AAAAA-TATGAAAAATCTT-TAT-
* *
4000598 CG-AAATTAATCTAAATGCTGCAATACATTTGTGACATTTTAGATAGATTTTTTTACGCTAAACA
62 CGAAAATTAATCTAAATGCTCCAATACATTTATGACATTTTAGATAGATTTTTTTAC-CTAAA-A
4000662 ATAT-CTAAAGCATCACTGGCTTGGAATTTCTTTAGGATTACATCCATAAGAGAATTTTTTTGTT
125 AT-TCCTAAAGCATCACT-GCTTGG-ATTTCTTTAGGATTACATCC-TAAGAG-A-TTTTTTGTT
* *
4000726 TG-TTTG-AAGATTATTAAAAGTCATGTAATCAATATAATTATCCAGAGATTT-TTTTAAAAAGC
184 TGTTTTGAAAAATTATTAAAAGTCATGTAAT-AATAAAATTATCCAGAGATTTATTTTAAAAAGC
4000788 ATATTTTTTTATCT-AATGACTTTCTTCAAATTAAAGAAAAT-ATGATAACATACGAGGTTTTTC
248 ATA--TTTTTATCTAAATGAC-TT-TTCAAATTAAAGAAAATAATGATAACATA-GAGGTTTTTC
*
4000851 GTATTGAAAAAAACTTTTAAATATTCCAATACTTTGGTAATTTTTTGAAAACATTTCTTACCTAT
308 GTATTGAAAAAAACTTTTAAATATTCCAATACTTTGGTAATTTTTTGAAAACATTTCTTACCTAA
4000916 AAAATTCTCGAATATCATTTCTTGAATTTTTCGGAGTCCTATCATCAAAAATTTTTA
373 AAAATTCTCGAATATCATTTCTTGAATTTTTCGGAGTCCTATCATCAAAAATTTTTA
4000973 TTATTTTAAA
Statistics
Matches: 411, Mismatches: 9, Indels: 27
0.92 0.02 0.06
Matches are distributed among these distances:
429 5 0.01
430 47 0.11
431 58 0.14
432 7 0.02
433 16 0.04
434 7 0.02
435 20 0.05
436 42 0.10
437 31 0.08
438 33 0.08
439 145 0.35
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.41
Consensus pattern (430 bp):
CAAATAGTATTTTCTAAAACTCATTTCTATGGCATTTTATAAAAATATGAAAAATCTTTATCGAA
AATTAATCTAAATGCTCCAATACATTTATGACATTTTAGATAGATTTTTTTACCTAAAAATTCCT
AAAGCATCACTGCTTGGATTTCTTTAGGATTACATCCTAAGAGATTTTTTGTTTGTTTTGAAAAA
TTATTAAAAGTCATGTAATAATAAAATTATCCAGAGATTTATTTTAAAAAGCATATTTTTATCTA
AATGACTTTTCAAATTAAAGAAAATAATGATAACATAGAGGTTTTTCGTATTGAAAAAAACTTTT
AAATATTCCAATACTTTGGTAATTTTTTGAAAACATTTCTTACCTAAAAAATTCTCGAATATCAT
TTCTTGAATTTTTCGGAGTCCTATCATCAAAAATTTTTAA
Found at i:4001654 original size:3 final size:3
Alignment explanation
Indices: 4001646--4001675 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4001636 TCAAAGAGTA
4001646 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
4001676 TTCATTTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:4001728 original size:3 final size:3
Alignment explanation
Indices: 4001720--4001747 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
4001710 TAAATTGCAT
4001720 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
4001748 TTGTGGCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:4003827 original size:137 final size:137
Alignment explanation
Indices: 4003615--4003887 Score: 537
Period size: 137 Copynumber: 2.0 Consensus size: 137
4003605 TTCTTTCCGG
4003615 TTCAATCTCCTCCTTCCCTTGTATGGTTCTCCTTTTGTTGTTATTGCCAGCCTCTTTTGTATTTT
1 TTCAATCTCCTCCTTCCCTTGTATGGTTCTCCTTTTGTTGTTATTGCCAGCCTCTTTTGTATTTT
*
4003680 TTAAAGAACTTGCCCCCAAACTACTCAAAAACCGTCCCCTTTCTCACTCTCCTTCCCCCCTTTTT
66 TTAAAGAACTTGCCCCCAAACCACTCAAAAACCGTCCCCTTTCTCACTCTCCTTCCCCCCTTTTT
4003745 ATAGTTT
131 ATAGTTT
4003752 TTCAATCTCCTCCTTCCCTTGTATGGTTCTCCTTTTGTTGTTATTGCCAGCCTCTTTTGTATTTT
1 TTCAATCTCCTCCTTCCCTTGTATGGTTCTCCTTTTGTTGTTATTGCCAGCCTCTTTTGTATTTT
4003817 TTAAAGAACTTGCCCCCAAACCACTCAAAAACCGTCCCCTTTCTCACTCTCCTTCCCCCCTTTTT
66 TTAAAGAACTTGCCCCCAAACCACTCAAAAACCGTCCCCTTTCTCACTCTCCTTCCCCCCTTTTT
4003882 ATAGTT
131 ATAGTT
4003888 CAGCTCCCTC
Statistics
Matches: 135, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.17, C:0.33, G:0.09, T:0.42
Consensus pattern (137 bp):
TTCAATCTCCTCCTTCCCTTGTATGGTTCTCCTTTTGTTGTTATTGCCAGCCTCTTTTGTATTTT
TTAAAGAACTTGCCCCCAAACCACTCAAAAACCGTCCCCTTTCTCACTCTCCTTCCCCCCTTTTT
ATAGTTT
Found at i:4007620 original size:31 final size:31
Alignment explanation
Indices: 4007573--4007640 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
4007563 AAGGTTTCAA
* * *
4007573 GGTTTTGCTTAGGGTTTGGGGTTTCACCTAG
1 GGTTTTACTTAAGGTTTGGGATTTCACCTAG
* *
4007604 GGTTTTACTTAAGGTTTTGGATTTCACTTAG
1 GGTTTTACTTAAGGTTTGGGATTTCACCTAG
4007635 GGTTTT
1 GGTTTT
4007641 GGGTTTCACC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.13, C:0.10, G:0.29, T:0.47
Consensus pattern (31 bp):
GGTTTTACTTAAGGTTTGGGATTTCACCTAG
Found at i:4007638 original size:19 final size:19
Alignment explanation
Indices: 4007610--4007654 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
4007600 CTAGGGTTTT
4007610 ACTTAAGGTTTTGGATTTC
1 ACTTAAGGTTTTGGATTTC
* *
4007629 ACTTAGGGTTTTGGGTTTC
1 ACTTAAGGTTTTGGATTTC
*
4007648 ACCTAAG
1 ACTTAAG
4007655 ATTTAGAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.13, G:0.24, T:0.42
Consensus pattern (19 bp):
ACTTAAGGTTTTGGATTTC
Found at i:4009836 original size:27 final size:27
Alignment explanation
Indices: 4009806--4009866 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 27
4009796 CAATTTAGTA
* * *
4009806 TTTATTTATTTATATATTTTTTAAATT
1 TTTATTTATTTAAAAATTTTATAAATT
* *
4009833 TTTAATTATTTAAAAATTTTATATATT
1 TTTATTTATTTAAAAATTTTATAAATT
4009860 TTTATTT
1 TTTATTT
4009867 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTATTTATTTAAAAATTTTATAAATT
Found at i:4011302 original size:17 final size:18
Alignment explanation
Indices: 4011280--4011323 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
4011270 AAAATAGAAG
*
4011280 AAAAAAGAGTGAAA-AAT
1 AAAAAAAAGTGAAATAAT
*
4011297 AAAAAAAATTGAAATAAT
1 AAAAAAAAGTGAAATAAT
4011315 AGAAAAAAA
1 A-AAAAAAA
4011324 AACAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 12 0.52
18 4 0.17
19 7 0.30
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (18 bp):
AAAAAAAAGTGAAATAAT
Found at i:4011303 original size:18 final size:19
Alignment explanation
Indices: 4011278--4011323 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
4011268 CAAAAATAGA
4011278 AGAAAAAAGAGTGAAA-AAT
1 AGAAAAAA-AGTGAAATAAT
*
4011297 A-AAAAAAATTGAAATAAT
1 AGAAAAAAAGTGAAATAAT
4011315 AGAAAAAAA
1 AGAAAAAAA
4011324 AACAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.25
18 10 0.42
19 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (19 bp):
AGAAAAAAAGTGAAATAAT
Found at i:4011450 original size:19 final size:19
Alignment explanation
Indices: 4011415--4011458 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
4011405 GCATGCTGGC
*
4011415 AAAA-GTGAAAAAGAAAAG
1 AAAAGGTGAAAAAGAAAAA
* *
4011433 AAAAGGTGAACAATAAAAA
1 AAAAGGTGAAAAAGAAAAA
4011452 AAAAGGT
1 AAAAGGT
4011459 ATTCAGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 4 0.18
19 18 0.82
ACGTcount: A:0.68, C:0.02, G:0.20, T:0.09
Consensus pattern (19 bp):
AAAAGGTGAAAAAGAAAAA
Found at i:4011836 original size:40 final size:40
Alignment explanation
Indices: 4011781--4011860 Score: 142
Period size: 40 Copynumber: 2.0 Consensus size: 40
4011771 AAAAGAAAAA
4011781 AAAATGAGCTGAAAAAAAAAAGAACAAAAACAAGTAACCT
1 AAAATGAGCTGAAAAAAAAAAGAACAAAAACAAGTAACCT
**
4011821 AAAATGAGCTGAAAAATGAAAGAACAAAAACAAGTAACCT
1 AAAATGAGCTGAAAAAAAAAAGAACAAAAACAAGTAACCT
4011861 TTCTTTTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.62, C:0.12, G:0.14, T:0.11
Consensus pattern (40 bp):
AAAATGAGCTGAAAAAAAAAAGAACAAAAACAAGTAACCT
Found at i:4012570 original size:22 final size:22
Alignment explanation
Indices: 4012531--4012589 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
4012521 TAGGATTACA
* *
4012531 TGCTAGCTAAACTGGGCTTATG
1 TGCTAGTTAATCTGGGCTTATG
4012553 TG-TCAGTTAATCTGGGCTTATG
1 TGCT-AGTTAATCTGGGCTTATG
4012575 TGCTAGTTAATCTGG
1 TGCTAGTTAATCTGG
4012590 ACTTCAATCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 1 0.03
22 31 0.94
23 1 0.03
ACGTcount: A:0.20, C:0.15, G:0.27, T:0.37
Consensus pattern (22 bp):
TGCTAGTTAATCTGGGCTTATG
Found at i:4013732 original size:19 final size:19
Alignment explanation
Indices: 4013686--4013731 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
4013676 TTTTCTTTTT
4013686 TTCATTTTTCCTTATTTCA
1 TTCATTTTTCCTTATTTCA
*
4013705 TTCACTTTTCCTT-TTTCCA
1 TTCATTTTTCCTTATTT-CA
4013724 TTC-TTTTT
1 TTCATTTTT
4013732 TTTCTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.11, C:0.24, G:0.00, T:0.65
Consensus pattern (19 bp):
TTCATTTTTCCTTATTTCA
Found at i:4019177 original size:6 final size:7
Alignment explanation
Indices: 4019160--4019186 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4019150 TTTTGCTTAA
4019160 AAAAAAG
1 AAAAAAG
4019167 AAAAAAG
1 AAAAAAG
4019174 AAAAAAG
1 AAAAAAG
4019181 AAAAAA
1 AAAAAA
4019187 ATGATGACTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:4020133 original size:97 final size:95
Alignment explanation
Indices: 4019980--4020626 Score: 967
Period size: 97 Copynumber: 6.7 Consensus size: 95
4019970 TAAAGTTGAG
*
4019980 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGAATTTTAAAGTTGTTGAGCCTCTGTTGAGAAGAG
1 CCTCTGTTGAGAGGAGCTTTTTCAAG-AAAGAATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAG
*
4020045 CTTTTTCAAGAAAGAATTTTTCAAGTTGTGGAA
65 CTTTTTCAAGAAA-AA-TTTTAAAGTTGTGGAA
*
4020078 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTAGAGCCTCTGTTGAGAGGAGC
1 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGC
* * *
4020143 TTTTTCAAGAAAAGATTTTAAAGTCGTTGAG
66 TTTTTCAAGAAAA-ATTTTAAAGTTGTGGAA
*
4020174 CCTCTGTTGAGAGGAGCTTTTTCGAAGAAAGAATTTTAAAGTTGTTGAGCCTCTGTTGAGAAGAG
1 CCTCTGTTGAGAGGAGCTTTTTC-AAGAAAGAATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAG
*
4020239 CTTTTTCAAGAAAAAATTTTTAAAGTTGTGGAG
65 CTTTTTCAAG-AAAAA-TTTTAAAGTTGTGGAA
*
4020272 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTAGAGCCTCTGTTGAGAGGAGC
1 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGC
* * *
4020337 TTTTTCAAAATAAAATTTTAAAGTTATGGAG
66 TTTTTCAAGA-AAAATTTTAAAGTTGTGGAA
*
4020368 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTGGAGCCTCTGTTGAGAGGAGC
1 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGC
*
4020433 TTTTCCAAGATGAAAATTTTAAAGTTGT-GAA
66 TTTTTCAAGA--AAAATTTTAAAGTTGTGGAA
* *
4020464 GCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTGAAGTTGTTGAGCCTCTGCTGAGAGGA
1 -CCTCTGTTGAGAGGAGCTTTTTCAAGAAAG-AATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGA
*
4020529 GTTTTTTCGAA-ATAAAATTTTAAAGTTGTGGAA
64 GCTTTTTC-AAGA-AAAATTTTAAAGTTGTGGAA
* *
4020562 CCTCTGTTGAGAGGAGCTTTTTCAAG-AAGAAATTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAG
1 CCTCTGTTGAGAGGAGCTTTTTCAAGAAAG-AATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAG
4020626 C
65 C
4020627 CCTTTTCTGT
Statistics
Matches: 510, Mismatches: 29, Indels: 22
0.91 0.05 0.04
Matches are distributed among these distances:
96 162 0.32
97 239 0.47
98 107 0.21
99 2 0.00
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (95 bp):
CCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTTGAGCCTCTGTTGAGAGGAGC
TTTTTCAAGAAAAATTTTAAAGTTGTGGAA
Found at i:4020138 original size:48 final size:48
Alignment explanation
Indices: 4019977--4020626 Score: 943
Period size: 48 Copynumber: 13.4 Consensus size: 48
4019967 TTTTAAAGTT
*
4019977 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGAATTTTAAAGTTGTT
1 GAGCCTCTGTTGAGAGGAGCTTTTTCAAG-AAAGAATTTTAAAGTTGTG
* *
4020026 GAGCCTCTGTTGAGAAGAGCTTTTTCAAGAAAGAATTTTTCAAGTTGTG
1 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAA-TTTTAAAGTTGTG
* *
4020075 GAACCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTA
1 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTG
* *
4020123 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAA-AGATTTTAAAGTCGTT
1 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGA-ATTTTAAAGTTGTG
*
4020171 GAGCCTCTGTTGAGAGGAGCTTTTTCGAAGAAAGAATTTTAAAGTTGTT
1 GAGCCTCTGTTGAGAGGAGCTTTTTC-AAGAAAGAATTTTAAAGTTGTG
* *
4020220 GAGCCTCTGTTGAGAAGAGCTTTTTCAAGAAAAAATTTTTAAAGTTGTG
1 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAA-TTTTAAAGTTGTG
*
4020269 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTA
1 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTG
* *
4020317 GAGCCTCTGTTGAGAGGAGCTTTTTCAA-AATAAAATTTTAAAGTTATG
1 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAA-AGAATTTTAAAGTTGTG
4020365 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTG
1 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTG
*
4020413 GAGCCTCTGTTGAGAGGAGCTTTTCCAAGATGAA-AATTTTAAAGTTGTG
1 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGA--AAGAATTTTAAAGTTGTG
* * *
4020462 AAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTGAAGTTGTT
1 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAG-AATTTTAAAGTTGTG
* *
4020511 GAGCCTCTGCTGAGAGGAGTTTTTTCGAA-ATAA-AATTTTAAAGTTGTG
1 GAGCCTCTGTTGAGAGGAGCTTTTTC-AAGA-AAGAATTTTAAAGTTGTG
* *
4020559 GAACCTCTGTTGAGAGGAGCTTTTTCAAG-AAGAAATTTTAAAGTTGTT
1 GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAG-AATTTTAAAGTTGTG
* *
4020607 GAGCCTCTGCTAAGAGGAGC
1 GAGCCTCTGTTGAGAGGAGC
4020627 CCTTTTCTGT
Statistics
Matches: 546, Mismatches: 39, Indels: 33
0.88 0.06 0.05
Matches are distributed among these distances:
46 2 0.00
47 7 0.01
48 287 0.53
49 243 0.45
50 7 0.01
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (48 bp):
GAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTG
Found at i:4020407 original size:242 final size:240
Alignment explanation
Indices: 4019974--4020626 Score: 985
Period size: 242 Copynumber: 2.7 Consensus size: 240
4019964 GATTTTTAAA
4019974 GTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGAATTTTAAAGTTGTTGAGCCTCTGTTGA
1 GTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAA-AATTTTAAAGTTGTTGAGCCTCTGTTGA
* *
4020039 GAAGAGCTTTTTCAAGAAAGAATTTTTCAAGTTGTGGAACCTCTGTTGAGAGGAGCTTTTTCAAG
65 GAGGAGCTTTTTCAAGAAAGAA-TTTTAAAGTTGTGGAACCTCTGTTGAGAGGAGCTTTTTCAAG
*
4020104 AAAGAATTTTAAAGTTGTAGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGATTTTAAAGTCG
129 AAAAAATTTTAAAGTTGTAGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGATTTTAAAGTCG
* *
4020169 TTGAGCCTCTGTTGAGAGGAGCTTTTTCGAAGA-AAGAATTTTAAAGTT
194 TGGAGCCTCTGTTGAGAGGAGC-TTTTCCAAGAGAA-AATTTTAAAGTT
* *
4020217 GTTGAGCCTCTGTTGAGAAGAGCTTTTTCAAGAAAAAATTTTTAAAGTTGTGGAGCCTCTGTTGA
1 GTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAAA-TTTTAAAGTTGTTGAGCCTCTGTTGA
* *
4020282 GAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTAGAGCCTCTGTTGAGAGGAGCTTTTTCAA-A
65 GAGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTGGAACCTCTGTTGAGAGGAGCTTTTTCAAGA
* * *
4020346 ATAAAATTTTAAAGTTATGGAGCCTCTGTTGAGAGGAGCTTTTTCAAG-AAAGAATTTTAAAGTT
130 A-AAAATTTTAAAGTTGTAGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAG-ATTTTAAAGTC
4020410 GTGGAGCCTCTGTTGAGAGGAGCTTTTCCAAGATGAAAATTTTAAAGTT
193 GTGGAGCCTCTGTTGAGAGGAGCTTTTCCAAGA-GAAAATTTTAAAGTT
* *
4020459 G-TGAAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAGAAATTTTGAAGTTGTTGAGCCTCTGCTG
1 GTTG-AGCCTCTGTTGAGAGGAGCTTTTTCAAGAAA-AAATTTTAAAGTTGTTGAGCCTCTGTTG
*
4020523 AGAGGAGTTTTTTCGAA-ATAA-AATTTTAAAGTTGTGGAACCTCTGTTGAGAGGAGCTTTTTCA
64 AGAGGAGCTTTTTC-AAGA-AAGAATTTTAAAGTTGTGGAACCTCTGTTGAGAGGAGCTTTTTCA
* * * *
4020586 AGAAGAAATTTTAAAGTTGTTGAGCCTCTGCTAAGAGGAGC
127 AGAAAAAATTTTAAAGTTGTAGAGCCTCTGTTGAGAGGAGC
4020627 CCTTTTCTGT
Statistics
Matches: 376, Mismatches: 24, Indels: 21
0.89 0.06 0.05
Matches are distributed among these distances:
241 17 0.05
242 267 0.71
243 92 0.24
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (240 bp):
GTTGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAAATTTTAAAGTTGTTGAGCCTCTGTTGAG
AGGAGCTTTTTCAAGAAAGAATTTTAAAGTTGTGGAACCTCTGTTGAGAGGAGCTTTTTCAAGAA
AAAATTTTAAAGTTGTAGAGCCTCTGTTGAGAGGAGCTTTTTCAAGAAAAGATTTTAAAGTCGTG
GAGCCTCTGTTGAGAGGAGCTTTTCCAAGAGAAAATTTTAAAGTT
Found at i:4020804 original size:5 final size:5
Alignment explanation
Indices: 4020794--4020846 Score: 60
Period size: 5 Copynumber: 11.0 Consensus size: 5
4020784 AATAATATTT
4020794 AACAA AACAA AACAA AA-AA GAA-AA AA-AA AACAA AACAGA AA-AA AACAA
1 AACAA AACAA AACAA AACAA -AACAA AACAA AACAA AACA-A AACAA AACAA
4020842 AACAA
1 AACAA
4020847 GTAAACAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
4 11 0.25
5 30 0.68
6 3 0.07
ACGTcount: A:0.83, C:0.13, G:0.04, T:0.00
Consensus pattern (5 bp):
AACAA
Found at i:4020823 original size:18 final size:18
Alignment explanation
Indices: 4020797--4020838 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
4020787 AATATTTAAC
*
4020797 AAAACAAAACAAAAAAGA
1 AAAAAAAAACAAAAAAGA
*
4020815 AAAAAAAAACAAAACAGA
1 AAAAAAAAACAAAAAAGA
4020833 AAAAAA
1 AAAAAA
4020839 CAAAACAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.86, C:0.10, G:0.05, T:0.00
Consensus pattern (18 bp):
AAAAAAAAACAAAAAAGA
Found at i:4021875 original size:27 final size:25
Alignment explanation
Indices: 4021845--4021896 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
4021835 AACCGGTACT
*
4021845 GAACTGCCGAACCAACCAGACCGAACC
1 GAACCGCCGAACCAACC-G-CCGAACC
*
4021872 GAACCGCCGATCCAACCGCCGAACC
1 GAACCGCCGAACCAACCGCCGAACC
4021897 AGTCAGACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 1 0.04
27 15 0.65
ACGTcount: A:0.33, C:0.44, G:0.19, T:0.04
Consensus pattern (25 bp):
GAACCGCCGAACCAACCGCCGAACC
Found at i:4021890 original size:12 final size:12
Alignment explanation
Indices: 4021850--4021897 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
4021840 GTACTGAACT
4021850 GCCGAACCAACC
1 GCCGAACCAACC
4021862 AGACCGAACCGAACC
1 -G-CCGAACC-AACC
*
4021877 GCCGATCCAACC
1 GCCGAACCAACC
4021889 GCCGAACCA
1 GCCGAACCA
4021898 GTCAGACCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 12 0.39
13 7 0.23
14 8 0.26
15 4 0.13
ACGTcount: A:0.33, C:0.46, G:0.19, T:0.02
Consensus pattern (12 bp):
GCCGAACCAACC
Found at i:4022449 original size:16 final size:16
Alignment explanation
Indices: 4022392--4022449 Score: 64
Period size: 16 Copynumber: 3.6 Consensus size: 16
4022382 AAACCCTTAA
4022392 AAATCCAAAATCCATT-
1 AAATCCAAAATCC-TTG
* *
4022408 AAATCCAAAACCGCTCG
1 AAATCCAAAATC-CTTG
4022425 AAATCCAAAATCCTTG
1 AAATCCAAAATCCTTG
*
4022441 AAGTCCAAA
1 AAATCCAAA
4022450 GTCCGAAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 23 0.66
17 12 0.34
ACGTcount: A:0.47, C:0.28, G:0.07, T:0.19
Consensus pattern (16 bp):
AAATCCAAAATCCTTG
Found at i:4024655 original size:17 final size:17
Alignment explanation
Indices: 4024633--4024706 Score: 50
Period size: 17 Copynumber: 4.4 Consensus size: 17
4024623 TAAAAATAAA
4024633 AAATATATTATATATTT
1 AAATATATTATATATTT
* *
4024650 AAATATCAATATAAATTAT
1 AAATAT-ATTATATATT-T
4024669 AACATA-A-TA-ATATTT
1 AA-ATATATTATATATTT
*
4024684 -AATGT-TTATATATATT
1 AAATATATTATATAT-TT
4024700 AAATATA
1 AAATATA
4024707 AAATATATAA
Statistics
Matches: 43, Mismatches: 5, Indels: 17
0.66 0.08 0.26
Matches are distributed among these distances:
13 2 0.05
14 3 0.07
15 5 0.12
16 6 0.14
17 12 0.28
18 9 0.21
19 3 0.07
20 3 0.07
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (17 bp):
AAATATATTATATATTT
Found at i:4025391 original size:12 final size:11
Alignment explanation
Indices: 4025374--4025442 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 11
4025364 ATTATATGTG
*
4025374 TTAATTTTATAT
1 TTAATTTAAT-T
4025386 TTAATTTAAAATT
1 TTAATTT--AATT
4025399 TTATATTTAAATAT
1 TTA-ATTT-AAT-T
*
4025413 TTAATTTAATA
1 TTAATTTAATT
4025424 TTAA-TTAATT
1 TTAATTTAATT
*
4025434 TTAAATTAA
1 TTAATTTAA
4025443 ATACTTAACA
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
10 9 0.18
11 8 0.16
12 10 0.20
13 12 0.24
14 10 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
TTAATTTAATT
Found at i:4025408 original size:14 final size:14
Alignment explanation
Indices: 4025385--4025439 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
4025375 TAATTTTATA
4025385 TTTAATTTAAA-AT
1 TTTAATTTAAATAT
4025398 TTTATATTTAAATA-
1 TTTA-ATTTAAATAT
4025412 TTTAATTT-AATAT
1 TTTAATTTAAATAT
4025425 TAATTAATTTTAAAT
1 T--TTAA-TTTAAAT
4025440 TAAATACTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
12 4 0.11
13 9 0.26
14 11 0.31
15 5 0.14
16 3 0.09
17 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TTTAATTTAAATAT
Found at i:4025410 original size:13 final size:13
Alignment explanation
Indices: 4025382--4025450 Score: 60
Period size: 13 Copynumber: 5.6 Consensus size: 13
4025372 TGTTAATTTT
4025382 ATATTTAATTTAA
1 ATATTTAATTTAA
4025395 A-ATTTTATATTTAA
1 ATA-TTTA-ATTTAA
4025409 ATATTTAATTT-A
1 ATATTTAATTTAA
4025421 ATA-TTAA-TT-A
1 ATATTTAATTTAA
*
4025431 AT-TTTAAATTAA
1 ATATTTAATTTAA
*
4025443 ATACTTAA
1 ATATTTAA
4025451 CATAACATGA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
10 9 0.19
11 6 0.12
12 8 0.17
13 13 0.27
14 11 0.23
15 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (13 bp):
ATATTTAATTTAA
Found at i:4036005 original size:22 final size:22
Alignment explanation
Indices: 4035980--4036029 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
4035970 TCTCAAATTA
4035980 ATAAATTATTATT-TTTTAAAAT
1 ATAAATTATTATTATTTT-AAAT
*
4036002 ATAAAATATTATTATTTTAAAT
1 ATAAATTATTATTATTTTAAAT
4036024 ATAAAT
1 ATAAAT
4036030 ATTTAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAAATTATTATTATTTTAAAT
Found at i:4036025 original size:15 final size:15
Alignment explanation
Indices: 4036003--4036057 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
4035993 TTTTAAAATA
*
4036003 TAAAATATTATTATT
1 TAAAATATAATTATT
* *
4036018 TTAAATATAAATATT
1 TAAAATATAATTATT
*
4036033 TAAAAATATCATTATT
1 T-AAAATATAATTATT
4036049 TAAAATATA
1 TAAAATATA
4036058 TATAAATAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
15 20 0.62
16 12 0.38
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAAATATAATTATT
Found at i:4036039 original size:16 final size:16
Alignment explanation
Indices: 4036020--4036059 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
4036010 TTATTATTTT
4036020 AAATATAAATATTTAA
1 AAATATAAATATTTAA
* *
4036036 AAATATCATTATTTAA
1 AAATATAAATATTTAA
4036052 AATATATA
1 AA-ATATA
4036060 TAAATAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATAAATATTTAA
Found at i:4036068 original size:31 final size:31
Alignment explanation
Indices: 4035998--4036069 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
4035988 TTATTTTTTA
* *
4035998 AAATATAAAATATTATTATTTTAAATATAAAT
1 AAATA-AAAATATCATTATTTAAAATATAAAT
** *
4036030 ATTTAAAAATATCATTATTTAAAATATATAT
1 AAATAAAAATATCATTATTTAAAATATAAAT
4036061 AAATAAAAA
1 AAATAAAAA
4036070 ATTAAATAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 30 0.91
32 3 0.09
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (31 bp):
AAATAAAAATATCATTATTTAAAATATAAAT
Found at i:4038998 original size:24 final size:24
Alignment explanation
Indices: 4038971--4039018 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
4038961 CACTACGATT
*
4038971 AAATTA-ATAATTTTAAATATGATA
1 AAATTATATAATATTAAA-ATGATA
4038995 AAATTATATAATATTAAAATGATA
1 AAATTATATAATATTAAAATGATA
4039019 TAAAAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATTATATAATATTAAAATGATA
Found at i:4039072 original size:23 final size:23
Alignment explanation
Indices: 4039046--4039101 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
4039036 TGTGATTTAA
*
4039046 AATTTTAATAAAAATTATATATT
1 AATTTTAATAAAAAATATATATT
*
4039069 AA-TTTAATTAAAAAATATATCTT
1 AATTTTAA-TAAAAAATATATATT
4039092 -ATGTTTAATA
1 AAT-TTTAATA
4039102 TATTGATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 6 0.21
23 17 0.61
24 5 0.18
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (23 bp):
AATTTTAATAAAAAATATATATT
Found at i:4041574 original size:16 final size:17
Alignment explanation
Indices: 4041553--4041588 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
4041543 GGTCATTTCG
*
4041553 TTTCGGTT-TAGTCGAT
1 TTTCGGTTATAATCGAT
4041569 TTTCGGTTATAATCGAT
1 TTTCGGTTATAATCGAT
4041586 TTT
1 TTT
4041589 AAAATAGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.17, C:0.11, G:0.19, T:0.53
Consensus pattern (17 bp):
TTTCGGTTATAATCGAT
Found at i:4043520 original size:33 final size:33
Alignment explanation
Indices: 4043482--4043586 Score: 101
Period size: 33 Copynumber: 3.3 Consensus size: 33
4043472 TATTACTTTA
4043482 TTATTTTTTCATTATTTGAATATAA-TT--TTAT
1 TTATTTTTT-ATTATTTGAATATAATTTAATTAT
* * *
4043513 TT-TTATTTATTATTTTAATATAATATAATTAT
1 TTATTTTTTATTATTTGAATATAATTTAATTAT
* * * * *
4043545 TTATTTTTTATTGTTTGGATATAATTTGATCAC
1 TTATTTTTTATTATTTGAATATAATTTAATTAT
4043578 TTATTTTTT
1 TTATTTTTT
4043587 TTTTCTTTGA
Statistics
Matches: 59, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 14 0.24
30 6 0.10
31 2 0.03
32 6 0.10
33 31 0.53
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.64
Consensus pattern (33 bp):
TTATTTTTTATTATTTGAATATAATTTAATTAT
Found at i:4043532 original size:29 final size:30
Alignment explanation
Indices: 4043478--4043556 Score: 99
Period size: 29 Copynumber: 2.7 Consensus size: 30
4043468 TGACTATTAC
4043478 TTTATTATTT-TTTCATTATTTGAATATAAT
1 TTTATTATTTATTT-ATTATTTGAATATAAT
*
4043508 TTTATT-TTTATTTATTATTTTAATATAAT
1 TTTATTATTTATTTATTATTTGAATATAAT
* * *
4043537 ATAATTATTTATTTTTTATT
1 TTTATTATTTATTTATTATT
4043557 GTTTGGATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 22 0.51
30 21 0.49
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (30 bp):
TTTATTATTTATTTATTATTTGAATATAAT
Found at i:4046736 original size:14 final size:15
Alignment explanation
Indices: 4046708--4046740 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4046698 GACATCAATT
4046708 AAAGAGGAAACTATG
1 AAAGAGGAAACTATG
*
4046723 AAAGA-GAAAGTATG
1 AAAGAGGAAACTATG
4046737 AAAG
1 AAAG
4046741 TAAAAAAAAA
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:0.58, C:0.03, G:0.27, T:0.12
Consensus pattern (15 bp):
AAAGAGGAAACTATG
Found at i:4049382 original size:27 final size:27
Alignment explanation
Indices: 4049352--4049403 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
4049342 TAAGAAAAAA
*
4049352 TAAAACCAAAA-AATAATAAAAATAAGT
1 TAAAAACAAAATAA-AATAAAAATAAGT
*
4049379 TAAAAATAAAATAAAATAAAAATAA
1 TAAAAACAAAATAAAATAAAAATAA
4049404 AAAGAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (27 bp):
TAAAAACAAAATAAAATAAAAATAAGT
Found at i:4049389 original size:16 final size:16
Alignment explanation
Indices: 4049347--4049405 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
4049337 TTTTTTAAGA
*
4049347 AAAAATAAAACCAAAA-
1 AAAAATAAAA-TAAAAT
* **
4049363 AATAATAAAAATAAGTT
1 AAAAAT-AAAATAAAAT
4049380 AAAAATAAAATAAAAT
1 AAAAATAAAATAAAAT
4049396 AAAAATAAAA
1 AAAAATAAAA
4049406 AGAAAAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
16 25 0.74
17 9 0.26
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (16 bp):
AAAAATAAAATAAAAT
Found at i:4049415 original size:16 final size:15
Alignment explanation
Indices: 4049346--4049420 Score: 51
Period size: 16 Copynumber: 4.7 Consensus size: 15
4049336 TTTTTTTAAG
*
4049346 AAAAAATAAAACCAAA
1 AAAAAATAAAA-AAAA
* *
4049362 AAATAATAAAAATAAGT
1 AAAAAATAAAAA-AA-A
*
4049379 TAAAAATAAAATAAAA
1 AAAAAATAAAA-AAAA
* *
4049395 TAAAAATAAAAAGAA
1 AAAAAATAAAAAAAA
*
4049410 AAAAAAGAAAA
1 AAAAAATAAAA
4049421 CGTGTGATCG
Statistics
Matches: 47, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
15 12 0.26
16 23 0.49
17 11 0.23
18 1 0.02
ACGTcount: A:0.80, C:0.03, G:0.04, T:0.13
Consensus pattern (15 bp):
AAAAAATAAAAAAAA
Found at i:4050451 original size:26 final size:26
Alignment explanation
Indices: 4050404--4050461 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
4050394 CACAAATGGA
*
4050404 CCTAATCAGGCTCGAACTTCAATAGG
1 CCTAATCAGGCTCGAAATTCAATAGG
* *
4050430 CCTAATCAGGCT-TAAATGTCAATTGG
1 CCTAATCAGGCTCGAAAT-TCAATAGG
4050456 CCTAAT
1 CCTAAT
4050462 AGGGCCAGAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (26 bp):
CCTAATCAGGCTCGAAATTCAATAGG
Found at i:4050875 original size:89 final size:89
Alignment explanation
Indices: 4050768--4051473 Score: 533
Period size: 89 Copynumber: 7.9 Consensus size: 89
4050758 AAATGATCGA
* * ** * * *
4050768 GATAAAATCACAAGTCAAAATAAAGTGACCAAGATTGAGTTGAGGTCGAAAATAAATGATCGGGG
1 GATAAAACCACAAGTCAAAATAAAGTGACCAGGACCGAGTTGAGGTCAAAAATAAATGATCAGGA
* **
4050833 TAAAACCATGAATCATGTGACTAG
66 TGAAACCATGAATCATAAGACTAG
* * *
4050857 GATAAAACCACAAGTCAAAATAAAGCGACCAGGATCGAGTCGAGGTCAAAAATAAATGATCAGGA
1 GATAAAACCACAAGTCAAAATAAAGTGACCAGGACCGAGTTGAGGTCAAAAATAAATGATCAGGA
*
4050922 TGAAACCATGAAATCATAAGAC-CG
66 TGAAACCATG-AATCATAAGACTAG
* ** ** * *
4050946 AGATCAAACCATGAGTCAAAATAAAGTGACCAGGATTGAGTTGAGGTAAAAAATAAATGATCGGG
1 -GATAAAACCACAAGTCAAAATAAAGTGACCAGGACCGAGTTGAGGTCAAAAATAAATGATCAGG
* * *
4051011 ATAAAACCATGATTCATAAGAC-CG
65 ATGAAACCATGAATCATAAGACTAG
* * ** * * * * *
4051035 CGATGAAATCATGAGTCAAAATAAAGCGACAAAGACCGAGTTGAGGTCGAAAGTAAATGATCAGG
1 -GATAAAACCACAAGTCAAAATAAAGTGACCAGGACCGAGTTGAGGTCAAAAATAAATGATCAGG
* * *
4051100 ACGAAACCATGGATTATAAGACTAG
65 ATGAAACCATGAATCATAAGACTAG
* * * * * * ** * *
4051125 GACAAAACTACGAGTCAAAATAAAGTGACCAAGACCAAGTCGAGGTTGAAAGTAAATGATCGGGA
1 GATAAAACCACAAGTCAAAATAAAGTGACCAGGACCGAGTTGAGGTCAAAAATAAATGATCAGGA
* *
4051190 TGAAACCACGAATCATAAGA-TCAA
66 TGAAACCATGAATCATAAGACT-AG
* * * * ** * * * *
4051214 GATGAAACTA-AGAGTAAAAACAAAGTGACTGGGACCAAGTTGAAGTTAAAAATAAATAATCAGG
1 GATAAAACCACA-AGTCAAAATAAAGTGACCAGGACCGAGTTGAGGTCAAAAATAAATGATCAGG
* ** * *
4051278 ATGAAACCACGAATCATGTGACCAT
65 ATGAAACCATGAATCATAAGACTAG
* * ** * * * *
4051303 GATGAAACTATGAGTTAAAATAAAATGACTAGGACTGAGTTGAGGTCAAAAATAAATGATCAGGA
1 GATAAAACCACAAGTCAAAATAAAGTGACCAGGACCGAGTTGAGGTCAAAAATAAATGATCAGGA
* **
4051368 TGAAACCACGAATCATGTGA-TCAG
66 TGAAACCATGAATCATAAGACT-AG
* ** * ** * * * * ** *
4051392 AACCAAATCACAA-TCAAAATAAAACGATCAGGATCAAGTCGAGGTTGAAAATAAATGATCATGA
1 GATAAAACCACAAGTCAAAATAAAGTGACCAGGACCGAGTTGAGGTCAAAAATAAATGATCAGGA
4051456 TGAAACCATGAATCATAA
66 TGAAACCATGAATCATAA
4051474 AACCATGACA
Statistics
Matches: 502, Mismatches: 107, Indels: 17
0.80 0.17 0.03
Matches are distributed among these distances:
88 56 0.11
89 370 0.74
90 76 0.15
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (89 bp):
GATAAAACCACAAGTCAAAATAAAGTGACCAGGACCGAGTTGAGGTCAAAAATAAATGATCAGGA
TGAAACCATGAATCATAAGACTAG
Found at i:4051094 original size:179 final size:176
Alignment explanation
Indices: 4050780--4051478 Score: 609
Period size: 178 Copynumber: 3.9 Consensus size: 176
4050770 TAAAATCACA
* * *
4050780 AGTCAAAATAAAGTGACCAAGATTGAGTTGAGGTCGAAAATAAATGATCGGGGTAAAACCATGAA
1 AGTCAAAATAAAGTGACCAAGACTGAGTTGAGGTCAAAAATAAATGATCGGGATAAAACCATGAA
** * * * * *
4050845 TCATGTGACTAGGATAAAACCACA-AGTCAAAATAAAGCGACCAGGATCGAGTCGAGGTCAAAAA
66 TCATAAGAC-CGGATGAAA-CA-AGAGTCAAAATAAAGCGACAAGGACCGAGTTGAGGTCAAAAA
*
4050909 TAAATGATCAGGATGAAACCATGAAATCATAAGACC-GAGATCAAACCATG
128 TAAATGATCAGGATGAAACCATG-AATCATAAGACCAG-GATCAAACTATG
* * * *
4050959 AGTCAAAATAAAGTGACCAGGATTGAGTTGAGGTAAAAAATAAATGATCGGGATAAAACCATGAT
1 AGTCAAAATAAAGTGACCAAGACTGAGTTGAGGTCAAAAATAAATGATCGGGATAAAACCATGAA
* * * *
4051024 TCATAAGACCGCGATGAAATCATGAGTCAAAATAAAGCGACAAAGACCGAGTTGAGGTCGAAAGT
66 TCATAAGACCG-GATGAAA-CAAGAGTCAAAATAAAGCGACAAGGACCGAGTTGAGGTCAAAAAT
* * * * *
4051089 AAATGATCAGGACGAAACCATGGATTATAAGACTAGGA-CAAAACTACG
129 AAATGATCAGGATGAAACCATGAATCATAAGACCAGGATC-AAACTATG
** * ** * * *
4051137 AGTCAAAATAAAGTGACCAAGACCAAGTCGAGGTTGAAAGTAAATGATCGGGATGAAACCACGAA
1 AGTCAAAATAAAGTGACCAAGACTGAGTTGAGGTCAAAAATAAATGATCGGGATAAAACCATGAA
** * * * ** * * *
4051202 TCATAAGATCAAGATGAAACTAAGAGTAAAAACAAAGTGACTGGGACCAAGTTGAAGTTAAAAAT
66 TCATAAGA-CCGGATGAAAC-AAGAGTCAAAATAAAGCGACAAGGACCGAGTTGAGGTCAAAAAT
* * ** * *
4051267 AAATAATCAGGATGAAACCACGAATCATGTGACCATGATGAAACTATG
129 AAATGATCAGGATGAAACCATGAATCATAAGACCAGGATCAAACTATG
* * * * * * *
4051315 AGTTAAAATAAAATGACTAGGACTGAGTTGAGGTCAAAAATAAATGATCAGGATGAAACCACGAA
1 AGTCAAAATAAAGTGACCAAGACTGAGTTGAGGTCAAAAATAAATGATCGGGATAAAACCATGAA
** * * ** * * * * **
4051380 TCATGTGATCAGAACCAAATCACA-A-TCAAAATAAAACGATC-AGGATCAAGTCGAGGTTGAAA
66 TCATAAGA-CCGGATGAAA-CA-AGAGTCAAAATAAAGCGA-CAAGGACCGAGTTGAGGTCAAAA
* *
4051442 ATAAATGATCATGATGAAACCATGAATCATAAAACCA
127 ATAAATGATCAGGATGAAACCATGAATCATAAGACCA
4051479 TGACAAAATC
Statistics
Matches: 419, Mismatches: 91, Indels: 22
0.79 0.17 0.04
Matches are distributed among these distances:
177 59 0.14
178 225 0.54
179 135 0.32
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.19
Consensus pattern (176 bp):
AGTCAAAATAAAGTGACCAAGACTGAGTTGAGGTCAAAAATAAATGATCGGGATAAAACCATGAA
TCATAAGACCGGATGAAACAAGAGTCAAAATAAAGCGACAAGGACCGAGTTGAGGTCAAAAATAA
ATGATCAGGATGAAACCATGAATCATAAGACCAGGATCAAACTATG
Found at i:4051364 original size:267 final size:266
Alignment explanation
Indices: 4050780--4051478 Score: 783
Period size: 267 Copynumber: 2.6 Consensus size: 266
4050770 TAAAATCACA
* * * * *
4050780 AGTCAAAATAAAGTGACCAAGATTGAGTTGAGGTCGAAAATAAATGATCGGGGTAAAACCATGAA
1 AGTCAAAATAAAGTGACAAAGACTGAGTTGAGGTCGAAAATAAATGATCAGGATGAAACCATGAA
* * * **
4050845 TCATGTGACTAGGATAAAACCACAAGTCAAAATAAAGCGACCAGGATCGAGTCGAGGTCAAAAAT
66 TCATGTGACTAGGACAAAACTAC-AGTCAAAATAAAGCGACCAGGATCAAGTCGAGGTTGAAAAT
* * * *
4050910 AAATGATCAGGATGAAACCATGAAATCATAAGACCGAGATCAAACCATGAGTCAAAATAAAGTGA
130 AAATGATCAGGATGAAACCATG-AATCATAAGACCAAGATCAAACCAAGAGTAAAAACAAAGTGA
*** * * * * * *
4050975 CCAGGATTGAGTTGAGGTAAAAAATAAATGATCGGGATAAAACCATGATTCATAAGACCGCGATG
194 CCAGGACCAAGTTGAAGTAAAAAATAAATAATCAGGATAAAACCACGAATCATAAGACCACGATG
4051040 AAATCATG
259 AAATCATG
* * * * *
4051048 AGTCAAAATAAAGCGACAAAGACCGAGTTGAGGTCGAAAGTAAATGATCAGGACGAAACCATGGA
1 AGTCAAAATAAAGTGACAAAGACTGAGTTGAGGTCGAAAATAAATGATCAGGATGAAACCATGAA
* ** * * * *
4051113 TTATAAGACTAGGACAAAACTACGAGTCAAAATAAAGTGACCAAGACCAAGTCGAGGTTGAAAGT
66 TCATGTGACTAGGACAAAACTAC-AGTCAAAATAAAGCGACCAGGATCAAGTCGAGGTTGAAAAT
* * * * *
4051178 AAATGATCGGGATGAAACCACGAATCATAAGATCAAGATGAAACTAAGAGTAAAAACAAAGTGAC
130 AAATGATCAGGATGAAACCATGAATCATAAGACCAAGATCAAACCAAGAGTAAAAACAAAGTGAC
** * * ** *
4051243 TGGGACCAAGTTGAAGTTAAAAATAAATAATCAGGATGAAACCACGAATCATGTGACCATGATGA
195 CAGGACCAAGTTGAAGTAAAAAATAAATAATCAGGATAAAACCACGAATCATAAGACCACGATGA
4051308 AA-CTATG
260 AATC-ATG
* * * * * *
4051315 AGTTAAAATAAAATGACTAGGACTGAGTTGAGGTCAAAAATAAATGATCAGGATGAAACCACGAA
1 AGTCAAAATAAAGTGACAAAGACTGAGTTGAGGTCGAAAATAAATGATCAGGATGAAACCATGAA
* * * * *
4051380 TCATGTGA-TCAGAACCAAA-TCACAATCAAAATAAAACGATCAGGATCAAGTCGAGGTTGAAAA
66 TCATGTGACT-AGGACAAAACT-ACAGTCAAAATAAAGCGACCAGGATCAAGTCGAGGTTGAAAA
* *
4051443 TAAATGATCATGATGAAACCATGAATCATAAAACCA
129 TAAATGATCAGGATGAAACCATGAATCATAAGACCA
4051479 TGACAAAATC
Statistics
Matches: 352, Mismatches: 76, Indels: 8
0.81 0.17 0.02
Matches are distributed among these distances:
266 67 0.19
267 158 0.45
268 127 0.36
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.19
Consensus pattern (266 bp):
AGTCAAAATAAAGTGACAAAGACTGAGTTGAGGTCGAAAATAAATGATCAGGATGAAACCATGAA
TCATGTGACTAGGACAAAACTACAGTCAAAATAAAGCGACCAGGATCAAGTCGAGGTTGAAAATA
AATGATCAGGATGAAACCATGAATCATAAGACCAAGATCAAACCAAGAGTAAAAACAAAGTGACC
AGGACCAAGTTGAAGTAAAAAATAAATAATCAGGATAAAACCACGAATCATAAGACCACGATGAA
ATCATG
Found at i:4051845 original size:41 final size:41
Alignment explanation
Indices: 4051800--4051943 Score: 216
Period size: 41 Copynumber: 3.5 Consensus size: 41
4051790 ATTTATCTTC
* * *
4051800 CCTGAATGCACTTCTTTAGCAAAGAAACCATTTTTCATTAA
1 CCTGAATGCACATCTTTGGCAAAGAAACCATCTTTCATTAA
* *
4051841 CCTGAATGCACGTATTTGGCAAAGAAACCATCTTTCATTAA
1 CCTGAATGCACATCTTTGGCAAAGAAACCATCTTTCATTAA
* * *
4051882 CTTGAATGTACATCTTTGGCAAAGAAACCATCTTTCATCAA
1 CCTGAATGCACATCTTTGGCAAAGAAACCATCTTTCATTAA
4051923 CCTGAATGCACATCTTTGGCA
1 CCTGAATGCACATCTTTGGCA
4051944 TTAGCCTGAA
Statistics
Matches: 92, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 92 1.00
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (41 bp):
CCTGAATGCACATCTTTGGCAAAGAAACCATCTTTCATTAA
Found at i:4053359 original size:29 final size:29
Alignment explanation
Indices: 4053326--4053383 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
4053316 TTAGATAGAG
4053326 AAAGTGTATTTCATTATTTGACCATGAAT
1 AAAGTGTATTTCATTATTTGACCATGAAT
4053355 AAAGTGTATTTCATTATTTGACCATGAAT
1 AAAGTGTATTTCATTATTTGACCATGAAT
4053384 CTTTTCTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (29 bp):
AAAGTGTATTTCATTATTTGACCATGAAT
Found at i:4063134 original size:15 final size:16
Alignment explanation
Indices: 4063109--4063150 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
4063099 TTTTGGTAAT
*
4063109 TTATAAAATAAAATTA
1 TTATTAAATAAAATTA
*
4063125 -TATTAAATAAATTTA
1 TTATTAAATAAAATTA
4063140 TTTATTAAATA
1 -TTATTAAATA
4063151 TTTAAATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 13 0.59
17 9 0.41
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTATTAAATAAAATTA
Done.