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 34 of 93
Found at i:3692265 original size:32 final size:32
Alignment explanation
Indices: 3692186--3692267 Score: 112
Period size: 32 Copynumber: 2.6 Consensus size: 32
3692176 TGAGCTTATG
* *
3692186 TGCTAGCTAAATTAGGCTTAAATTTTGATTAA
1 TGCTAGCTAAATTGGGCTTAAACTTTGATTAA
*
3692218 TGATAGCTAAATTGGGCTTAAACCTTT-ATTAA
1 TGCTAGCTAAATTGGGCTTAAA-CTTTGATTAA
*
3692250 TGCTAGCTAATTTGGGCT
1 TGCTAGCTAAATTGGGCT
3692268 AAAAACATTG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 41 0.93
33 3 0.07
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (32 bp):
TGCTAGCTAAATTGGGCTTAAACTTTGATTAA
Found at i:3692314 original size:28 final size:29
Alignment explanation
Indices: 3692277--3692332 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
3692267 TAAAAACATT
*
3692277 GGTGCCAGCTAGACTAGGCTTAA-ATTTG
1 GGTGCCAGCTAAACTAGGCTTAAGATTTG
*
3692305 GGTGTCAGCTAAACTAGGCTTAAGATTT
1 GGTGCCAGCTAAACTAGGCTTAAGATTT
3692333 TATTGGTGCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (29 bp):
GGTGCCAGCTAAACTAGGCTTAAGATTTG
Found at i:3693364 original size:25 final size:22
Alignment explanation
Indices: 3693330--3693375 Score: 56
Period size: 25 Copynumber: 2.0 Consensus size: 22
3693320 ATTCAACATT
3693330 AAAAAAAATTCAAGAAACAAAAAGG
1 AAAAAAAATT-AA-AAA-AAAAAGG
*
3693355 AAAAGAAATTAAAAAAAAAAG
1 AAAAAAAATTAAAAAAAAAAG
3693376 AATAATGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 2 0.10
25 9 0.45
ACGTcount: A:0.76, C:0.04, G:0.11, T:0.09
Consensus pattern (22 bp):
AAAAAAAATTAAAAAAAAAAGG
Found at i:3693745 original size:4 final size:4
Alignment explanation
Indices: 3693725--3693762 Score: 55
Period size: 4 Copynumber: 10.2 Consensus size: 4
3693715 TAATCTAATC
3693725 AATA AAT- AAT- AAT- AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA AATA A
3693763 GAAAAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 9 0.27
4 24 0.73
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:3694522 original size:5 final size:6
Alignment explanation
Indices: 3694507--3694532 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3694497 ATCAGTCGAA
3694507 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
3694533 TAGATAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:3694581 original size:21 final size:21
Alignment explanation
Indices: 3694557--3694611 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
3694547 AATAGATAAC
3694557 TAAAAAAAATAATTAGACAAA
1 TAAAAAAAATAATTAGACAAA
* *
3694578 TAAAAAATATTAA-TAGATAAA
1 TAAAAAA-AATAATTAGACAAA
* *
3694599 TAATAATAATAAT
1 TAAAAAAAATAAT
3694612 CATAATAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
20 4 0.15
21 19 0.70
22 4 0.15
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (21 bp):
TAAAAAAAATAATTAGACAAA
Found at i:3694605 original size:3 final size:3
Alignment explanation
Indices: 3694583--3694632 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
3694573 ACAAATAAAA
* * *
3694583 AAT ATT AAT AGAT AAAT AAT AAT AAT AAT CAT AAT AAT CAT AAT AAT
1 AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3694630 AAT
1 AAT
3694633 TAAAAATAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 34 0.87
4 4 0.10
5 1 0.03
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:3695024 original size:43 final size:43
Alignment explanation
Indices: 3694858--3696054 Score: 504
Period size: 43 Copynumber: 27.5 Consensus size: 43
3694848 AAATTTTGGT
*
3694858 TAAAGCTCCTCTAAGCAGAGGCTCAACAACTTTGAGTAAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGA--AAAATAAA
* * * *
3694903 CAAAGCTCTTCTAAACAGAGGCTCCACGACTTT-AAAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
* * * * *
3694945 T--GGCTCATTTAATCAAAGGCTCAACAACTTTGAAAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
* * * * *
3694986 TAAAGCTCCTCTAAACAGAGGTTTAACGACTTTCAAAAATAGA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
* * * * * *
3695029 TGAAGCTCCTCTAAATAGAGGCAACCACGACTTTTG-AAAGTAAA
1 TAAAGCTCCTCTAAACAGAGGC-TCAACAAC-TTTGAAAAATAAA
* * * * * **
3695073 CAAAACTCCTATAATCAGAGGCTCAATAACTTAAAAGAAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTT-TGA-AAAATAAA
* * **** *
3695118 TAAAGCTCCTCTAATCAAAGGCTCAGTGGCTTTGGGAATAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTT--GAAAAATAAA
* * * *
3695163 T--TGCTCATCGAAACAGAGGC-AACACAACTTTG-AAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCA-ACAACTTTGAAAAATAAA
* * *
3695203 T--GGCTCCTCTAATCAGAGGCTCAACAACTTTGGAAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
* * * * * *
3695244 T--GGCTCTTTTAATCAGAGGCTTAACGACTTTGAAAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
* *
3695285 TAAAGCTTCTCTAAATAGAGG--CAACCATGACTTTTG-AAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAA-CA--AC-TTTGAAAAATAAA
* ** * * * *
3695329 CAAAAATCCTATAATCAGAGGCTTAACGAC-TTGAAAGCAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTG-AA--AAATAAA
* * * * *
3695374 CAAAGCTTCTCTAATCAGAGGCTCAACGACTTTGGGAACAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTT--GAAAAATAAA
* *
3695419 T--TGTTCCTCTAAACAGAGGC-CAACCATGACTTTTGAAAAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAA-CA--AC-TTTG-AAAAATAAA
** * * *
3695464 -ATTTGCTCCCTCTAAAATAGAGCAGCACCAAAAACTTTGGAAAAATAAA
1 TA-AAGCT-CCTCT-AAACAGAG--GC-TCAACAACTTT-GAAAAATAAA
* * *
3695513 T--GGCCTTCCTCTAAATCAAAGGCTCAAC-GCTTTGAAAAATAAA
1 TAAAG-C-TCCTCTAAA-CAGAGGCTCAACAACTTTGAAAAATAAA
*
3695556 TAAAGCTTCCTCTAAACAGAGGGCTC-ACGACTTTG-AAAATAAAA
1 TAAAGC-TCCTCTAAACAGA-GGCTCAACAACTTTGAAAAAT-AAA
* ** * * * *
3695600 TGCAAGCTATTCTAAAACAAAGGCAACCACGACTTTTG--AAATAACA
1 T-AAAGCTCCTCT-AAACAGAGGC-TCAACAAC-TTTGAAAAATAA-A
* * **
3695646 -AAATC-CCTCTAATCAGAGGCTCAATGAC-TTGAAAGAAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTG--A-AAAATAAA
* * * * *** *
3695689 CAAAGCTCCTATAATCATAGGCTCAGTGACTTTGTGAACAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAAC-TT-TGAAAAATAAA
* *
3695734 T--GGTTCCTCTAAACAGAGG--CAACCATGACTTTTGAAAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAA-CA--AC-TTTGAAAAATAAA
* * * *
3695777 T--TGCTCCTCTAAATAGAGGCACCACAAACTTTG-AAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAAC-AACTTTGAAAAATAAA
* * ** *
3695818 T--GGCTCCTCTAATCAGAGGCTCAATGACTTTGGAAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
* * * *
3695859 T--GGCTCTTCTAATCAGAGGCTCAACGACTTTGAAAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
* *
3695900 TAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAGA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
*
3695943 TAAAGCTCCTCTAAATAGAGG--CAACCATGACTTTTG-AAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAA-CA--AC-TTTGAAAAATAAA
* * * **
3695987 CAAAACTCCTCTAATCAGAGGCTCAATGAC-TTGAAAGAAAATAAA
1 TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTG--A-AAAATAAA
* *
3696032 CAAAGCTCCTCTAATCAGAGGCT
1 TAAAGCTCCTCTAAACAGAGGCT
3696055 TAATGACTTT
Statistics
Matches: 890, Mismatches: 175, Indels: 174
0.72 0.14 0.14
Matches are distributed among these distances:
39 3 0.00
40 61 0.07
41 149 0.17
42 28 0.03
43 226 0.25
44 134 0.15
45 205 0.23
46 24 0.03
47 14 0.02
48 17 0.02
49 20 0.02
50 3 0.00
51 2 0.00
52 1 0.00
53 3 0.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (43 bp):
TAAAGCTCCTCTAAACAGAGGCTCAACAACTTTGAAAAATAAA
Found at i:3695202 original size:40 final size:41
Alignment explanation
Indices: 3695147--3695285 Score: 120
Period size: 41 Copynumber: 3.4 Consensus size: 41
3695137 GGCTCAGTGG
*
3695147 CTTTGGGAATAATAAATTGCTCATCGAAACAGAGGCA-ACACAA
1 CTTT-GGAA-AATAAATGGCTCATCGAAACAGAGGCACA-ACAA
* * * *
3695190 CTTT-GAAAATAAATGGCTCCTCTAATCAGAGGCTCAACAA
1 CTTTGGAAAATAAATGGCTCATCGAAACAGAGGCACAACAA
* ** * ** *
3695230 CTTTGGAAAATAAATGGCTCTTTTAATCAGAGGCTTAACGA
1 CTTTGGAAAATAAATGGCTCATCGAAACAGAGGCACAACAA
*
3695271 CTTTGAAAAATAAAT
1 CTTTGGAAAATAAAT
3695286 AAAGCTTCTC
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
40 30 0.36
41 50 0.60
43 4 0.05
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (41 bp):
CTTTGGAAAATAAATGGCTCATCGAAACAGAGGCACAACAA
Found at i:3695331 original size:256 final size:256
Alignment explanation
Indices: 3694859--3695598 Score: 740
Period size: 256 Copynumber: 2.8 Consensus size: 256
3694849 AATTTTGGTT
* * * * ** * *
3694859 AAAGCTCCTCTAAGCAGAGGCTCAACAACTTTGAGTAA-AATAAACAAAGCTCTTCTAAACAGAG
1 AAAGCTCCTCTAATCAAAGGCTCAACGACTTTG-GGAACAAT-AA-ATTGCTCATCGAAACAGAG
** * * * * * *
3694923 GCTCCACGACTTTAAAAATAAATGGCTCATTTAATCAAAGGCTCAACAACTTTGAAAAATAAATA
63 GCAACACAACTTTGAAAATAAATGGCTCCTCTAATCAGAGGCTCAACAACTTTGGAAAATAAAT-
* * * * * * * * *
3694988 AAGCTCCTCTAAACAGAGGTTTAACGACTTTCAAAAATAGATGAAGCTCCTCTAAATAGAGGCAA
127 -GGCTCTTTTAATCAGAGGCTTAACGACTTTGAAAAATAAATAAAGCTTCTCTAAATAGAGGCAA
* * *
3695053 CCACGACTTTTGAAAGTAAACAAAACTCCTATAATCAGAGGCTCAATAACTTAAAAGAAAATAAA
191 CCACGACTTTTGAAAATAAACAAAAATCCTATAATCAGAGGCTCAACAACTTAAAAGAAAATAAA
*
3695118 T
256 C
** * *
3695119 AAAGCTCCTCTAATCAAAGGCTCAGTGGCTTTGGGAATAATAAATTGCTCATCGAAACAGAGGCA
1 AAAGCTCCTCTAATCAAAGGCTCAACGACTTTGGGAACAATAAATTGCTCATCGAAACAGAGGCA
3695184 ACACAACTTTGAAAATAAATGGCTCCTCTAATCAGAGGCTCAACAACTTTGGAAAATAAATGGCT
66 ACACAACTTTGAAAATAAATGGCTCCTCTAATCAGAGGCTCAACAACTTTGGAAAATAAATGGCT
*
3695249 CTTTTAATCAGAGGCTTAACGACTTTGAAAAATAAATAAAGCTTCTCTAAATAGAGGCAACCATG
131 CTTTTAATCAGAGGCTTAACGACTTTGAAAAATAAATAAAGCTTCTCTAAATAGAGGCAACCACG
* * * *
3695314 ACTTTTGAAAATAAACAAAAATCCTATAATCAGAGGCTTAACGACTTGAAAGCAAATAAAC
196 ACTTTTGAAAATAAACAAAAATCCTATAATCAGAGGCTCAACAACTTAAAAGAAAATAAAC
* * * * *
3695375 AAAGCTTCTCTAATCAGAGGCTCAACGACTTTGGGAACAATAAATTGTTCCTCTAAACAGAGGCC
1 AAAGCTCCTCTAATCAAAGGCTCAACGACTTTGGGAACAATAAATTGCTCATCGAAACAGAGG-C
* * *
3695440 AAC-CATGACTTTTGAAAAAATAAAATTTGCTCCCTCTAAAAT-AGAGCAGCACCAAAAACTTTG
65 AACACA--AC-TTTG--AAAAT-AAA-TGGCT-CCTCT--AATCAGAG--GC-TCAACAACTTTG
* *
3695503 GAAAAATAAATGGC-CTTCCTCTAAATCAAAGGCTCAACG-CTTTGAAAAATAAATAAAGCTTCC
117 G-AAAATAAATGGCTCTT--T-T-AATCAGAGGCTTAACGACTTTGAAAAATAAATAAAGCTT-C
* *
3695566 TCTAAACAGAGGGC--TCACGAC-TTTGAAAATAAA
176 TCTAAATAGA-GGCAACCACGACTTTTGAAAATAAA
3695599 ATGCAAGCTA
Statistics
Matches: 404, Mismatches: 54, Indels: 34
0.82 0.11 0.07
Matches are distributed among these distances:
256 168 0.42
257 4 0.01
258 73 0.18
259 9 0.02
260 30 0.07
261 5 0.01
262 3 0.01
263 4 0.01
264 5 0.01
265 4 0.01
266 3 0.01
267 2 0.00
268 14 0.03
269 12 0.03
270 13 0.03
271 28 0.07
272 24 0.06
273 3 0.01
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.24
Consensus pattern (256 bp):
AAAGCTCCTCTAATCAAAGGCTCAACGACTTTGGGAACAATAAATTGCTCATCGAAACAGAGGCA
ACACAACTTTGAAAATAAATGGCTCCTCTAATCAGAGGCTCAACAACTTTGGAAAATAAATGGCT
CTTTTAATCAGAGGCTTAACGACTTTGAAAAATAAATAAAGCTTCTCTAAATAGAGGCAACCACG
ACTTTTGAAAATAAACAAAAATCCTATAATCAGAGGCTCAACAACTTAAAAGAAAATAAAC
Found at i:3695835 original size:84 final size:82
Alignment explanation
Indices: 3694861--3696165 Score: 356
Period size: 87 Copynumber: 15.1 Consensus size: 82
3694851 TTTTGGTTAA
* ** * * *
3694861 AGCTCCTCTAAGCAGAGGCTCAACAAC-TTTGAGTAAAATAAACAAAGCTCTTCTAAACAGAGGC
1 AGCTCCTCTAAACAGAGGCTCAATGACTTTTGA--AAAAT-AA-ATAGCTCCTCTAAATAGAGGC
* *
3694925 TCCACGACTTTAAAAATAAAT
62 ACCACGACTTTGAAAATAAAT
* * * * * ** * ***
3694946 GGCTCATTTAATCAAAGGCTCAACAAC-TTTGAAAAATAAATAAAGCTCCTCTAAACAGAGGTTT
1 AGCTCCTCTAAACAGAGGCTCAATGACTTTTGAAAAATAAAT--AGCTCCTCTAAATAGAGGCAC
* * *
3695010 AACGACTTTCAAAAATAGAT
64 CACGACTTT-GAAAATAAAT
* * * * * *
3695030 GAAGCTCCTCTAAATAGAGGCAACCACGACTTTTGAAAGTAA-ACAA-AACTCCTAT-AATCAGA
1 --AGCTCCTCTAAACAGAGGC-TCAATGACTTTTGAAA--AATA-AATAGCTCCTCTAAAT-AGA
* * ** *
3695092 GGCTCAATAACTTAAAAGAAAATAAAT
59 GGCACCACGACTT---TGAAAATAAAT
* * * * * * * * * *
3695119 AAAGCTCCTCTAATCAAAGGCTCAGTGGCTTTGGGAATAATAAATTGCTCATCGAAACAGAGGCA
1 --AGCTCCTCTAAACAGAGGCTCAATGACTTT-TGAAAAATAAATAGCTCCTCTAAATAGAGGCA
* *
3695184 ACACAACTTTGAAAATAAAT
63 CCACGACTTTGAAAATAAAT
* * ** * * * * ***
3695204 GGCTCCTCTAATCAGAGGCTCAACAAC-TTTGGAAAATAAATGGCT-CTTTTAATCAGAGGCTTA
1 AGCTCCTCTAAACAGAGGCTCAATGACTTTTGAAAAATAAATAGCTCCTCTAAAT-AGAGGCACC
3695267 ACGACTTTGAAAAATAAAT
65 ACGACTTTG-AAAATAAAT
* * * * * ** *
3695286 AAAGCTTCTCTAAATAGAGGCAACCATGACTTTTG-AAAATAAACAAAAATCCTAT-AATCAGAG
1 --AGCTCCTCTAAACAGAGGC-TCAATGACTTTTGAAAAAT-AA-ATAGCTCCTCTAAAT-AGAG
*** *
3695349 GCTTAACGAC-TTGAAAGCAAATAAACAA
60 GCACCACGACTTTG--A--AAAT-AA-AT
* * * * * * * *
3695377 AGCTTCTCTAATCAGAGGCTCAACGACTTTGGGAACAATAAATTGTTCCTCTAAACAGAGGCCAA
1 AGCTCCTCTAAACAGAGGCTCAATGACTTT-TGAAAAATAAATAGCTCCTCTAAATAGAGG-C-A
*
3695442 CCATGACTTTTGAAAAAATAAAATT
63 CCACGAC-TTTG--AAAAT-AAA-T
* * * ** * * *
3695467 TGCTCCCTCTAAAATAGAGCAGCACCAAAAACTTTGGAAAAATAAATGGCCTTCCTCTAAATCAA
1 AGCT-CCTCT-AAACAGAG--GC-TCAATGACTTTTGAAAAATAAATAG-C-TCCTCTAAAT-AG
* *
3695532 AGGCTCAACG-CTTTGAAAAATAAAT
58 AGGCACCACGACTTTG-AAAATAAAT
* ** *
3695557 AAAGCTTCCTCTAAACAGAGGGCTC-ACGAC-TTTG-AAAATAAAATGCAAGCTATTCTAAAACA
1 --AGC-TCCTCTAAACAGA-GGCTCAATGACTTTTGAAAAAT-AAAT---AGCTCCTCT-AAATA
*
3695619 AAGGCAACCACGACTTTTG-AAATAACA-
57 GAGGC-ACCACGAC-TTTGAAAATAA-AT
** * *** * * *
3695646 AAATCCCTCTAATCAGAGGCTCAATGACTTGAAAGAAAATAAACAAAGCTCCTAT-AATCATAGG
1 AGCT-CCTCTAAACAGAGGCTCAATGACTTTTGA-AAAAT-AA-ATAGCTCCTCTAAAT-AGAGG
* *
3695710 C-TCAGTGACTTTGTGAACAATAAAT
61 CACCA-CGAC-TT-TGAA-AATAAAT
* * * * *
3695735 GGTTCCTCTAAACAGAGGCAACCATGACTTTTGAAAAATAAATTGCTCCTCTAAATAGAGGCACC
1 AGCTCCTCTAAACAGAGGC-TCAATGACTTTTGAAAAATAAATAGCTCCTCTAAATAGAGGCACC
*
3695800 ACAAACTTTGAAAATAAAT
65 AC-GACTTTGAAAATAAAT
* * * * * * *
3695819 GGCTCCTCTAATCAGAGGCTCAATGAC-TTTGGAAAATAAATGGCTCTTCT-AATCAGAGGCTCA
1 AGCTCCTCTAAACAGAGGCTCAATGACTTTTGAAAAATAAATAGCTCCTCTAAAT-AGAGGCACC
3695882 ACGACTTTGAAAAATAAAT
65 ACGACTTTG-AAAATAAAT
* *
3695901 AAAGCTCCTCTAAACAGAGGCTCAACGAC-TTTGAAAAATAGATAAAGCTCCTCTAAATAGAGGC
1 --AGCTCCTCTAAACAGAGGCTCAATGACTTTTGAAAAATA-A-ATAGCTCCTCTAAATAGAGGC
* *
3695965 AACCATGACTTTTGAAAATAAACAA
62 -ACCACGAC-TTTGAAAAT-AA-AT
* * *** *
3695990 AACTCCTCTAATCAGAGGCTCAATGACTTGAAAGAAAATAAACAAAGCTCCTCT-AATCAGAGGC
1 AGCTCCTCTAAACAGAGGCTCAATGACTTTTGA-AAAAT-AA-ATAGCTCCTCTAAAT-AGAGGC
*** *
3696054 TTAATGACTTTGGGAACAATAAAT
62 ACCACGACTTT--GAA-AATAAAT
* * * * * *
3696078 TGTTCCTCTAAACAGAAG-TAACCACGACTTTTGAAAAATAAATTGCTCCT-TAAATAGAGGCAC
1 AGCTCCTCTAAACAGAGGCT--CAATGACTTTTGAAAAATAAATAGCTCCTCTAAATAGAGGCAC
* *
3696141 CACAACTTTGAAAGTAAAT
64 CACGACTTTGAAAATAAAT
3696160 -GCTCCT
1 AGCTCCT
3696166 TAACAATCAT
Statistics
Matches: 910, Mismatches: 212, Indels: 200
0.69 0.16 0.15
Matches are distributed among these distances:
80 3 0.00
81 41 0.05
82 57 0.06
83 61 0.07
84 82 0.09
85 66 0.07
86 82 0.09
87 132 0.15
88 128 0.14
89 126 0.14
90 42 0.05
91 19 0.02
92 26 0.03
93 5 0.01
94 15 0.02
95 11 0.01
96 10 0.01
97 4 0.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (82 bp):
AGCTCCTCTAAACAGAGGCTCAATGACTTTTGAAAAATAAATAGCTCCTCTAAATAGAGGCACCA
CGACTTTGAAAATAAAT
Found at i:3695917 original size:343 final size:344
Alignment explanation
Indices: 3695497--3696165 Score: 1016
Period size: 343 Copynumber: 1.9 Consensus size: 344
3695487 AGCACCAAAA
3695497 ACTTTGGAAAAATAAATGGCCTTCCTCTAAATCAAAGGCTCAACGCTTTGAAAAATAAATAAAGC
1 ACTTTGGAAAAATAAATGGCCTTCCTCTAAATCAAAGGCTCAACGCTTTGAAAAATAAATAAAGC
* *
3695562 TTCCTCTAAACAGAGGGCTC-ACGACTTTG-AAAATAAAATGCAAGCTATTCTAAAACAAAGGCA
66 TTCCTCTAAACAGA-GGCTCAACGACTTTGAAAAAT-AAAT-AAAGCTACTCT-AAACAAAGGCA
3695625 ACCACGACTTTTG-AAAT-AACAAAA-TCCCTCTAATCAGAGGCTCAATGACTTGAAAGAAAATA
127 ACCACGACTTTTGAAAATAAACAAAACT-CCTCTAATCAGAGGCTCAATGACTTGAAAGAAAATA
* * * *
3695687 AACAAAGCTCCTATAATCATAGGCTCAGTGACTTTGTGAACAATAAATGGTTCCTCTAAACAGAG
191 AACAAAGCTCCTATAATCAGAGGCTCAATGACTTTGGGAACAATAAATGGTTCCTCTAAACAGAA
*
3695752 GCAACCATGACTTTTGAAAAATAAATTGCTCCTCTAAATAGAGGCACCACAAACTTTGAAAATAA
256 GCAACCACGACTTTTGAAAAATAAATTGCTCCT-TAAATAGAGGCACCAC-AACTTTGAAAATAA
3695817 ATGGCTCCTCTAATCAGAGGCTCAATG
319 AT-GCTCCTCTAATCAGAGGCTCAATG
* *
3695844 ACTTTGG-AAAATAAATGG-C-TCTTCT-AATCAGAGGCTCAACGACTTTGAAAAATAAATAAAG
1 ACTTTGGAAAAATAAATGGCCTTCCTCTAAATCAAAGGCTCAACG-CTTTGAAAAATAAATAAAG
* * * *
3695905 C-TCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAGATAAAGCTCCTCTAAATAGAGGCAACC
65 CTTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTACTCTAAACAAAGGCAACC
*
3695969 ATGACTTTTGAAAATAAACAAAACTCCTCTAATCAGAGGCTCAATGACTTGAAAGAAAATAAACA
130 ACGACTTTTGAAAATAAACAAAACTCCTCTAATCAGAGGCTCAATGACTTGAAAGAAAATAAACA
* * * *
3696034 AAGCTCCTCTAATCAGAGGCTTAATGACTTTGGGAACAATAAATTGTTCCTCTAAACAGAAGTAA
195 AAGCTCCTATAATCAGAGGCTCAATGACTTTGGGAACAATAAATGGTTCCTCTAAACAGAAGCAA
*
3696099 CCACGACTTTTGAAAAATAAATTGCTCCTTAAATAGAGGCACCACAACTTTGAAAGTAAATGCTC
260 CCACGACTTTTGAAAAATAAATTGCTCCTTAAATAGAGGCACCACAACTTTGAAAATAAATGCTC
3696164 CT
325 CT
3696166 TAACAATCAT
Statistics
Matches: 297, Mismatches: 19, Indels: 19
0.89 0.06 0.06
Matches are distributed among these distances:
340 6 0.02
341 36 0.12
342 33 0.11
343 172 0.58
344 31 0.10
345 1 0.00
346 11 0.04
347 7 0.02
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.25
Consensus pattern (344 bp):
ACTTTGGAAAAATAAATGGCCTTCCTCTAAATCAAAGGCTCAACGCTTTGAAAAATAAATAAAGC
TTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAATAAAGCTACTCTAAACAAAGGCAACCA
CGACTTTTGAAAATAAACAAAACTCCTCTAATCAGAGGCTCAATGACTTGAAAGAAAATAAACAA
AGCTCCTATAATCAGAGGCTCAATGACTTTGGGAACAATAAATGGTTCCTCTAAACAGAAGCAAC
CACGACTTTTGAAAAATAAATTGCTCCTTAAATAGAGGCACCACAACTTTGAAAATAAATGCTCC
TCTAATCAGAGGCTCAATG
Found at i:3696085 original size:132 final size:131
Alignment explanation
Indices: 3694859--3696119 Score: 527
Period size: 132 Copynumber: 9.7 Consensus size: 131
3694849 AATTTTGGTT
* * * * * *
3694859 AAAGCTCCTCTAAGCAGAGGCTCAACAACTTTGAGTAAAATAAACAAAGCTCTTCTAAACAGAGG
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGA--AAAATAGATAAAGCTCCTCTAAACAGAAG
* *** * * * *
3694924 C-TCCACGAC-TTT-AAAAAT-AA-ATGGCTCATTTAATCAAAGGCTCAACAACTTTGAAAAATA
64 CAACCACGACTTTTGAAAAATAAACAAAACTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATA
*
3694984 AAT
129 AAC
* * * * * *
3694987 AAAGCTCCTCTAAACAGAGGTTTAACGACTTTCAAAAATAGATGAAGCTCCTCTAAATAGAGGCA
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAGATAAAGCTCCTCTAAACAGAAGCA
* * ** **
3695052 ACCACGACTTTTG-AAAGTAAACAAAACTCCTATAATCAGAGGCTCAATAACTTAAAAGAAAATA
66 ACCACGACTTTTGAAAAATAAACAAAACTCCTCTAATCAGAGGCTCAACGACTT-TGA-AAAATA
*
3695116 AAT
129 AAC
* * ** * ** * * *
3695119 AAAGCTCCTCTAATCAAAGGCTCAGTGGCTTTG-GGAATA-ATAAATTGCTCATCGAAACAGAGG
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAGATAAA--GCTCCTCTAAACAGAAG
* *** * *
3695182 CAA-CACAAC-TTTG-AAAAT-AA-ATGGCTCCTCTAATCAGAGGCTCAACAACTTTGGAAAAT-
64 CAACCACGACTTTTGAAAAATAAACAAAACTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATA
3695241 AA-
129 AAC
** * * * * * * * *
3695243 ATGGCTCTTTTAATCAGAGGCTTAACGACTTTGAAAAATAAATAAAGCTTCTCTAAATAGAGGCA
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAGATAAAGCTCCTCTAAACAGAAGCA
* * * *
3695308 ACCATGACTTTTG-AAAATAAACAAAAATCCTATAATCAGAGGCTTAACGAC-TTGAAAGCAAAT
66 ACCACGACTTTTGAAAAATAAACAAAACTCCTCTAATCAGAGGCTCAACGACTTTG-AA--AAAT
3695371 AAAC
128 AAAC
* * * ** * *
3695375 AAAGCTTCTCTAATCAGAGGCTCAACGACTTTGGGAACAATA-A-ATTGTTCCTCTAAACAGAGG
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTT--GAAAAATAGATAAAGCTCCTCTAAACAGAAG
* *** * **
3695438 CCAACCATGACTTTTGAAAAAATAAA-ATTTGCTCCCTCTAAAAT-AGAGCAGCACCAAAAACTT
64 -CAACCACGACTTTTG-AAAAATAAACA-AAACT-CCTCT--AATCAGAG--GC-TCAACGACTT
3695501 TGGAAAAAT-AA-
120 T-GAAAAATAAAC
** * *
3695512 ATGGCCTTCCTCTAAATCAAAGGCTCAACG-CTTTGAAAAATAAATAAAGCTTCCTCTAAACAGA
1 AAAG-C-TCCTCTAAA-CAGAGGCTCAACGACTTTGAAAAATAGATAAAGC-TCCTCTAAACAGA
* * * ** * * * *
3695576 GGGC--TCACGAC-TTTG-AAAATAAA-ATGCAAGCTATTCTAAAACAAAGGCAACCACGACTTT
62 -AGCAACCACGACTTTTGAAAAATAAACA---AAACTCCTCT-AATCAGAGGC-TCAACGAC-TT
3695636 TG--AAAT-AAC
120 TGAAAAATAAAC
* * * * * * * *
3695645 AAA-ATCCCTCTAATCAGAGGCTCAATGAC-TTGAAAGAAAATAAACAAAGCTCCTATAATCATA
1 AAAGCT-CCTCTAAACAGAGGCTCAACGACTTTG--A-AAAATAGATAAAGCTCCTCTAAACAGA
* * * * **** * * * *
3695708 GGC--TCAGTGACTTTGTGAACAAT-AA-ATGGTTCCTCTAAACAGAGGCAACCATGACTTTTGA
62 AGCAACCA-CGACTTT-TGAAAAATAAACAAAACTCCTCTAATCAGAGGC-TCAACGAC-TTTGA
3695769 AAAAT-AA-
123 AAAATAAAC
** * * * * ** * *
3695776 ATTGCTCCTCTAAATAGAGGCACCACAAACTTTG-AAAATA-A-ATGGCTCCTCTAATCAGAGGC
1 AAAGCTCCTCTAAACAGAGGCTCAAC-GACTTTGAAAAATAGATAAAGCTCCTCTAAACAGAAGC
* * * * *** *
3695838 -TCAATGAC-TTTGGAAAAT-AA-ATGGCTCTTCTAATCAGAGGCTCAACGACTTTGAAAAATAA
65 AACCACGACTTTTGAAAAATAAACAAAACTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAA
*
3695899 AT
130 AC
* *
3695901 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAGATAAAGCTCCTCTAAATAGAGGCA
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAGATAAAGCTCCTCTAAACAGAAGCA
* *
3695966 ACCATGACTTTTG-AAAATAAACAAAACTCCTCTAATCAGAGGCTCAATGAC-TTGAAAGAAAAT
66 ACCACGACTTTTGAAAAATAAACAAAACTCCTCTAATCAGAGGCTCAACGACTTTG--A-AAAAT
3696029 AAAC
128 AAAC
* * * * ** *
3696033 AAAGCTCCTCTAATCAGAGGCTTAATGACTTTGGGAACAATA-A-ATTGTTCCTCTAAACAGAAG
1 AAAGCTCCTCTAAACAGAGGCTCAACGACTTT--GAAAAATAGATAAAGCTCCTCTAAACAGAAG
*
3696096 TAACCACGACTTTTGAAAAATAAA
64 CAACCACGACTTTTGAAAAATAAA
3696120 TTGCTCCTTA
Statistics
Matches: 873, Mismatches: 184, Indels: 147
0.73 0.15 0.12
Matches are distributed among these distances:
123 10 0.01
124 53 0.06
125 63 0.07
126 47 0.05
127 50 0.06
128 98 0.11
129 19 0.02
130 101 0.12
131 48 0.05
132 186 0.21
133 44 0.05
134 28 0.03
135 28 0.03
136 10 0.01
137 20 0.02
138 12 0.01
139 19 0.02
140 30 0.03
141 6 0.01
142 1 0.00
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (131 bp):
AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAGATAAAGCTCCTCTAAACAGAAGCA
ACCACGACTTTTGAAAAATAAACAAAACTCCTCTAATCAGAGGCTCAACGACTTTGAAAAATAAA
C
Found at i:3697186 original size:9 final size:9
Alignment explanation
Indices: 3697169--3697216 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
3697159 TGAGTCCTCC
3697169 TTTTCATTT
1 TTTTCATTT
*
3697178 TTTTTA-TT
1 TTTTCATTT
3697186 TTTT-A-TT
1 TTTTCATTT
3697193 TTTTCATTT
1 TTTTCATTT
3697202 TTTTCATTT
1 TTTTCATTT
3697211 TTTTCA
1 TTTTCA
3697217 AGCATAGTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
7 7 0.19
8 7 0.19
9 22 0.61
ACGTcount: A:0.12, C:0.08, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCATTT
Found at i:3697187 original size:8 final size:8
Alignment explanation
Indices: 3697176--3697214 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
3697166 TCCTTTTCAT
3697176 TTTTTTTA
1 TTTTTTTA
3697184 -TTTTTTA
1 TTTTTTTA
*
3697191 TTTTTTCA
1 TTTTTTTA
3697199 TTTTTTTCA
1 TTTTTTT-A
3697208 TTTTTTT
1 TTTTTTT
3697215 CAAGCATAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
7 7 0.26
8 12 0.44
9 8 0.30
ACGTcount: A:0.10, C:0.05, G:0.00, T:0.85
Consensus pattern (8 bp):
TTTTTTTA
Found at i:3704451 original size:15 final size:15
Alignment explanation
Indices: 3704431--3704465 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
3704421 TTACTTTGTT
*
3704431 AAATGTATTGAATAA
1 AAATGTAATGAATAA
*
3704446 AAATGTAATGAATGA
1 AAATGTAATGAATAA
3704461 AAATG
1 AAATG
3704466 CATGCATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (15 bp):
AAATGTAATGAATAA
Found at i:3707996 original size:21 final size:20
Alignment explanation
Indices: 3707962--3708002 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
3707952 AATTCTAATC
*
3707962 TAATAAATAAATAATAATAA
1 TAATAAAGAAATAATAATAA
3707982 TAATAAAAGAAATAATAATAA
1 TAAT-AAAGAAATAATAATAA
3708003 AAAAATAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (20 bp):
TAATAAAGAAATAATAATAA
Found at i:3707997 original size:15 final size:14
Alignment explanation
Indices: 3707962--3708010 Score: 62
Period size: 15 Copynumber: 3.2 Consensus size: 14
3707952 AATTCTAATC
3707962 TAATAAATAAATAATAA
1 TAAT-AATAAA-AA-AA
3707979 TAATAATAAAAGAAA
1 TAATAATAAAA-AAA
3707994 TAATAATAAAAAAA
1 TAATAATAAAAAAA
3708008 TAA
1 TAA
3708011 GAAAGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
14 6 0.19
15 14 0.45
16 7 0.23
17 4 0.13
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (14 bp):
TAATAATAAAAAAA
Found at i:3708012 original size:21 final size:21
Alignment explanation
Indices: 3707970--3708014 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
3707960 TCTAATAAAT
*
3707970 AAATAATAATAATAATAAAAG
1 AAATAATAATAATAAAAAAAG
3707991 AAATAATAATAA-AAAAATAAG
1 AAATAATAATAATAAAAA-AAG
3708012 AAA
1 AAA
3708015 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (21 bp):
AAATAATAATAATAAAAAAAG
Found at i:3708723 original size:6 final size:6
Alignment explanation
Indices: 3708712--3708743 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
3708702 TCAGCTGAAA
3708712 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
3708744 TAGACAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:3708794 original size:22 final size:21
Alignment explanation
Indices: 3708711--3708821 Score: 65
Period size: 21 Copynumber: 5.5 Consensus size: 21
3708701 CTCAGCTGAA
*
3708711 AAAAAATAAAAATA-A-AAAT
1 AAAAAATAATAATAGATAAAT
* *
3708730 -AAAAATAAAAATA-ATAGA-
1 AAAAAATAATAATAGATAAAT
* * * **
3708748 CAAATATATTAATAGATAACC
1 AAAAAATAATAATAGATAAAT
3708769 AAAAGAA-AATAATTAGATAAAT
1 AAAA-AATAATAA-TAGATAAAT
*
3708791 AAAAAATATTAATAGATAAAT
1 AAAAAATAATAATAGATAAAT
*
3708812 -AATAATAATA
1 AAAAAATAATA
3708822 TAATCATAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 13
0.72 0.14 0.13
Matches are distributed among these distances:
18 14 0.20
19 12 0.17
20 11 0.15
21 18 0.25
22 16 0.23
ACGTcount: A:0.69, C:0.03, G:0.05, T:0.23
Consensus pattern (21 bp):
AAAAAATAATAATAGATAAAT
Found at i:3708808 original size:21 final size:22
Alignment explanation
Indices: 3708753--3708822 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 22
3708743 ATAGACAAAT
**
3708753 ATATTAATAGATAACCAAAAGA
1 ATATTAATAGATAAATAAAAGA
*
3708775 A-AATAATTAGATAAATAAAA-A
1 ATATTAA-TAGATAAATAAAAGA
*
3708796 ATATTAATAGATAAATAATAATA
1 ATATTAATAGATAAATAA-AAGA
3708819 ATAT
1 ATAT
3708823 AATCATAATC
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
21 17 0.43
22 18 0.45
23 5 0.12
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (22 bp):
ATATTAATAGATAAATAAAAGA
Found at i:3708809 original size:17 final size:17
Alignment explanation
Indices: 3708774--3708821 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
3708764 TAACCAAAAG
3708774 AAAATAATTAGATAAATAA
1 AAAAT-ATTA-ATAAATAA
*
3708793 AAAATATTAATAGATAA
1 AAAATATTAATAAATAA
* *
3708810 ATAATAATAATA
1 AAAATATTAATA
3708822 TAATCATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 17 0.65
18 4 0.15
19 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (17 bp):
AAAATATTAATAAATAA
Found at i:3708817 original size:3 final size:3
Alignment explanation
Indices: 3708795--3708861 Score: 55
Period size: 3 Copynumber: 21.7 Consensus size: 3
3708785 ATAAATAAAA
* * * *
3708795 AAT ATT AAT AGAT AAAT AAT AAT AAT -AT AAT CAT AAT CAT AAT CAT
1 AAT AAT AAT A-AT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
3708841 AAT AAT AAT GAAA AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AA
3708862 AATTAAATTA
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
2 2 0.04
3 41 0.82
4 6 0.12
5 1 0.02
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3709125 original size:13 final size:12
Alignment explanation
Indices: 3709104--3709174 Score: 52
Period size: 12 Copynumber: 5.2 Consensus size: 12
3709094 CACTTATTCA
3709104 TTTTTTTTCTTT
1 TTTTTTTTCTTT
3709116 TTTTTCTTTCTTTT
1 TTTTT-TTTC-TTT
3709130 ACCTTTTTTTTCATTT
1 ---TTTTTTTTC-TTT
3709146 TTCCTTTTTTCTTT
1 TT--TTTTTTCTTT
**
3709160 CATTTTTTCTTT
1 TTTTTTTTCTTT
3709172 TTT
1 TTT
3709175 CCCCACCTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
12 16 0.34
13 6 0.13
14 6 0.13
15 7 0.15
16 7 0.15
17 5 0.11
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTTTTCTTT
Found at i:3709129 original size:19 final size:19
Alignment explanation
Indices: 3709107--3709174 Score: 54
Period size: 20 Copynumber: 3.6 Consensus size: 19
3709097 TTATTCATTT
3709107 TTTTTCTTTTTTTTCTTTC
1 TTTTTCTTTTTTTTCTTTC
* *
3709126 TTTTACCTTTTTTTTC---A
1 TTTT-TCTTTTTTTTCTTTC
*
3709143 TTTTTC-CTTTTTTCTTTC
1 TTTTTCTTTTTTTTCTTTC
3709161 ATTTTTTCTTTTTT
1 --TTTTTCTTTTTT
3709175 CCCCACCTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
15 7 0.19
16 1 0.03
17 4 0.11
19 4 0.11
20 16 0.44
21 4 0.11
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCTTTTTTTTCTTTC
Found at i:3709175 original size:19 final size:19
Alignment explanation
Indices: 3709100--3709175 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
3709090 TTTCCACTTA
*
3709100 TTCATTTTTT-TTCTTTTTT
1 TTCATTTTTTCTT-TTTTCT
* *
3709119 TTCTTTCTTTTACCTTTTT-T
1 TTCATT-TTTT-CTTTTTTCT
*
3709139 TTCATTTTTCCTTTTTTCT
1 TTCATTTTTTCTTTTTTCT
3709158 TTCATTTTTTCTTTTTTC
1 TTCATTTTTTCTTTTTTC
3709176 CCCACCTTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
18 6 0.13
19 26 0.55
20 10 0.21
21 4 0.09
22 1 0.02
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (19 bp):
TTCATTTTTTCTTTTTTCT
Found at i:3709745 original size:20 final size:20
Alignment explanation
Indices: 3709710--3709764 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 20
3709700 TTTCCCCTTT
*
3709710 TTTCTTTTTTTATTTTT-TC
1 TTTCTTTTTTGATTTTTCTC
3709729 TTTCTTTTTTGATTTTTCTC
1 TTTCTTTTTTGATTTTTCTC
*
3709749 TTTTTTTTTTG-TTTTT
1 TTTCTTTTTTGATTTTT
3709765 GACATGCTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 21 0.64
20 12 0.36
ACGTcount: A:0.04, C:0.09, G:0.04, T:0.84
Consensus pattern (20 bp):
TTTCTTTTTTGATTTTTCTC
Found at i:3710726 original size:22 final size:23
Alignment explanation
Indices: 3710683--3710725 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 23
3710673 CATAAACATA
3710683 AAAATCAAAATATGAAAAAAAAT
1 AAAATCAAAATATGAAAAAAAAT
3710706 AAAAT-AAAATA-GAAAAAAAA
1 AAAATCAAAATATGAAAAAAAA
3710726 AACCTGCGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 9 0.45
22 6 0.30
23 5 0.25
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (23 bp):
AAAATCAAAATATGAAAAAAAAT
Found at i:3711548 original size:16 final size:16
Alignment explanation
Indices: 3711529--3711560 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3711519 CGGAAAGAAG
3711529 AATAAAAAGAAAATAA
1 AATAAAAAGAAAATAA
*
3711545 AATAAAATGAAAATAA
1 AATAAAAAGAAAATAA
3711561 TAAGAATAGT
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:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (16 bp):
AATAAAAAGAAAATAA
Found at i:3711652 original size:5 final size:5
Alignment explanation
Indices: 3711642--3711752 Score: 82
Period size: 5 Copynumber: 21.0 Consensus size: 5
3711632 GTACAATCTT
*
3711642 TATAA TATAA TAATAA TATAA TATGA TAGTAA TATAA TATAA TATAA TATACA
1 TATAA TATAA T-ATAA TATAA TATAA TA-TAA TATAA TATAA TATAA TATA-A
* * * * *
3711695 -ATAA TATAGTA TACTGA TATAT TATGA TATAC TAATAA T-TAT TATAA
1 TATAA TATA--A TA-TAA TATAA TATAA TATAA T-ATAA TATAA TATAA
3711742 TAATAA TATAA
1 T-ATAA TATAA
3711753 GAAATAAAAA
Statistics
Matches: 84, Mismatches: 12, Indels: 20
0.72 0.10 0.17
Matches are distributed among these distances:
4 4 0.05
5 54 0.64
6 22 0.26
7 3 0.04
8 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:3712542 original size:56 final size:56
Alignment explanation
Indices: 3712424--3712655 Score: 186
Period size: 56 Copynumber: 4.2 Consensus size: 56
3712414 GACTAAGTTG
** * **
3712424 AGGTCAAACGACCGGGATTAAATTGTAAGTCTAGAAAA-TGACCTAGAT-AGAG-CTA
1 AGGTCAAACGACTAGGATTGAACCGTAAGTCTAGAAAACTGACCTAGATCA-AGTC-A
* * * *
3712479 AGATCAAACGACTAGGATTGAACCGTGAGTTTAAAAAACTGACCTAGATCAAGTCA
1 AGGTCAAACGACTAGGATTGAACCGTAAGTCTAGAAAACTGACCTAGATCAAGTCA
* * * * * * *
3712535 AGGTCAAACGA-TTGTAATTGAACCATAAGTCTAGAAAATTGACTTGGA-CTGAGTCA
1 AGGTCAAACGACTAG-GATTGAACCGTAAGTCTAGAAAACTGACCTAGATC-AAGTCA
* * * * * * *
3712591 AGGTCAAATGACCAAGATTGAACTGCAAGTCTGGAAAACTGACCTAGATCGAGTCA
1 AGGTCAAACGACTAGGATTGAACCGTAAGTCTAGAAAACTGACCTAGATCAAGTCA
3712647 AGGTCAAAC
1 AGGTCAAAC
3712656 AAGTGATGAA
Statistics
Matches: 137, Mismatches: 33, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
55 32 0.23
56 102 0.74
57 3 0.02
ACGTcount: A:0.39, C:0.17, G:0.22, T:0.22
Consensus pattern (56 bp):
AGGTCAAACGACTAGGATTGAACCGTAAGTCTAGAAAACTGACCTAGATCAAGTCA
Found at i:3724041 original size:6 final size:6
Alignment explanation
Indices: 3724030--3724125 Score: 58
Period size: 6 Copynumber: 16.3 Consensus size: 6
3724020 TAAATCATTT
* * * *
3724030 AATAAA AATAAA TCAT-AA AA-AAA ACTAGA CATAAA AATAAA AATAAA
1 AATAAA AATAAA -AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
** * *
3724077 AATATG AA-AAA AAT-AA AAT-AA AATCAAA AATTAA AATTAA AATAGAA
1 AATAAA AATAAA AATAAA AATAAA AAT-AAA AATAAA AATAAA AATA-AA
3724124 AA
1 AA
3724126 AGGAAAACTT
Statistics
Matches: 69, Mismatches: 14, Indels: 13
0.72 0.15 0.14
Matches are distributed among these distances:
5 17 0.25
6 41 0.59
7 11 0.16
ACGTcount: A:0.74, C:0.04, G:0.03, T:0.19
Consensus pattern (6 bp):
AATAAA
Found at i:3724042 original size:18 final size:19
Alignment explanation
Indices: 3724008--3724045 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
3723998 TTGTAAAACC
*
3724008 TTTAATAAATGATAAATCA
1 TTTAATAAATAATAAATCA
3724027 TTTAATAAA-AATAAATCA
1 TTTAATAAATAATAAATCA
3724045 T
1 T
3724046 AAAAAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (19 bp):
TTTAATAAATAATAAATCA
Found at i:3724087 original size:35 final size:32
Alignment explanation
Indices: 3724030--3724118 Score: 79
Period size: 35 Copynumber: 2.6 Consensus size: 32
3724020 TAAATCATTT
* * *
3724030 AATAAAAATAAATCATAAAAAAAACTAGACATAAA
1 AATAAAAATAAA-AATAAAAAAAAATA-AAAT-AA
*
3724065 AATAAAAATAAAAATATGAAAAAAATAAAATAA
1 AATAAAAATAAAAATA-AAAAAAAATAAAATAA
* *
3724098 AATCAAAAATTAAAATTAAAA
1 AAT-AAAAATAAAAATAAAAA
3724119 TAGAAAAAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
33 8 0.18
34 17 0.38
35 20 0.44
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.19
Consensus pattern (32 bp):
AATAAAAATAAAAATAAAAAAAAATAAAATAA
Found at i:3724895 original size:86 final size:86
Alignment explanation
Indices: 3724750--3724924 Score: 323
Period size: 86 Copynumber: 2.0 Consensus size: 86
3724740 CAATCTAGGC
3724750 TTGAATCTTGGGATTGACTTATGCACGAGCATGATTTAAAGCCAGATTTCTGTTAATGTTCAAAA
1 TTGAATCTTGGGATTGACTTATGCACGAGCATGATTTAAAGCCAGATTTCTGTTAATGTTCAAAA
3724815 TCAAATTAAAAGTTCTATGAT
66 TCAAATTAAAAGTTCTATGAT
* * *
3724836 TTGAATCTTGGGATTGACTTATGCCCGAGCATGATTTAAAGCTAGATTTCTGTTAATGTTCAGAA
1 TTGAATCTTGGGATTGACTTATGCACGAGCATGATTTAAAGCCAGATTTCTGTTAATGTTCAAAA
3724901 TCAAATTAAAAGTTCTATGAT
66 TCAAATTAAAAGTTCTATGAT
3724922 TTG
1 TTG
3724925 CATTAAATCA
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
86 86 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (86 bp):
TTGAATCTTGGGATTGACTTATGCACGAGCATGATTTAAAGCCAGATTTCTGTTAATGTTCAAAA
TCAAATTAAAAGTTCTATGAT
Found at i:3725052 original size:3 final size:3
Alignment explanation
Indices: 3725034--3725101 Score: 79
Period size: 3 Copynumber: 23.7 Consensus size: 3
3725024 AAAAAAACAA
*
3725034 AAT AA- AAT AA- AAT AAT AAT AAT AAT AAT AGT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * *
3725080 AGT AAT AAT -GT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
3725102 GAGATACTAT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 5 0.09
3 51 0.91
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3725122 original size:26 final size:25
Alignment explanation
Indices: 3725040--3725122 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 25
3725030 ACAAAATAAA
* *
3725040 ATAA-AATAATAATAATAATAATAGT
1 ATAATAATAAGAATACTAATAAT-GT
* *
3725065 AATAATAATAATAATAGTAATAATGT
1 -ATAATAATAAGAATACTAATAATGT
3725091 AGTAATAATAAGAGATACT-ATAATGGT
1 A-TAATAATAAGA-ATACTAATAAT-GT
3725118 ATAAT
1 ATAAT
3725123 GTACTATAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
25 1 0.02
26 25 0.50
27 24 0.48
ACGTcount: A:0.57, C:0.01, G:0.10, T:0.33
Consensus pattern (25 bp):
ATAATAATAAGAATACTAATAATGT
Found at i:3725239 original size:5 final size:5
Alignment explanation
Indices: 3725117--3725233 Score: 80
Period size: 5 Copynumber: 23.4 Consensus size: 5
3725107 ACTATAATGG
* * * *
3725117 TATAA TGTAC TATAA TAT-A TAATAA TATAA TATGA GAGTAA TATAA TATAA
1 TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TA-TAA TATAA TATAA
* * * * *
3725168 TATAA TATAA TATACA -ATAA TATAC TAT-A T-TGA TATAT TATGA TATAC
1 TATAA TATAA TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA
*
3725216 TAACAA TATAA TATAA TA
1 T-ATAA TATAA TATAA TA
3725234 ATATAACAAA
Statistics
Matches: 85, Mismatches: 19, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
3 1 0.01
4 6 0.07
5 69 0.81
6 9 0.11
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.38
Consensus pattern (5 bp):
TATAA
Found at i:3725951 original size:11 final size:11
Alignment explanation
Indices: 3725895--3725942 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
3725885 ATTCAAAACT
3725895 TTTTTTTTCAC
1 TTTTTTTTCAC
3725906 TTTTTTTTCAC
1 TTTTTTTTCAC
3725917 TTTTTTTTC-C
1 TTTTTTTTCAC
*
3725927 TTTTTATT-AC
1 TTTTTTTTCAC
3725937 TTTTTT
1 TTTTTT
3725943 CCCTTTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
10 14 0.41
11 20 0.59
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTTTTTCAC
Found at i:3725969 original size:11 final size:10
Alignment explanation
Indices: 3725895--3725968 Score: 64
Period size: 11 Copynumber: 7.3 Consensus size: 10
3725885 ATTCAAAACT
3725895 TTTTTTTTCAC
1 TTTTTTTTC-C
3725906 TTTTTTTTCAC
1 TTTTTTTTC-C
3725917 TTTTTTTTCC
1 TTTTTTTTCC
* *
3725927 TTTTTATTAC
1 TTTTTTTTCC
*
3725937 -TTTTTTCCC
1 TTTTTTTTCC
3725946 TTTTTTCTT--
1 TTTTTT-TTCC
3725955 TTTATTTTTCC
1 TTT-TTTTTCC
3725966 TTT
1 TTT
3725969 AAGGGATTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
9 11 0.21
10 17 0.33
11 24 0.46
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (10 bp):
TTTTTTTTCC
Found at i:3730992 original size:13 final size:13
Alignment explanation
Indices: 3730954--3730992 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
3730944 GGGTTTTACC
3730954 TAGGGTTTCA-TT
1 TAGGGTTTCATTT
*
3730966 TAGGGTTTTAATTT
1 TAGGG-TTTCATTT
3730980 TAGGGTTTCATTT
1 TAGGGTTTCATTT
3730993 AAGTTTATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
12 5 0.22
13 11 0.48
14 7 0.30
ACGTcount: A:0.18, C:0.05, G:0.23, T:0.54
Consensus pattern (13 bp):
TAGGGTTTCATTT
Found at i:3731103 original size:53 final size:53
Alignment explanation
Indices: 3731044--3731147 Score: 133
Period size: 53 Copynumber: 1.9 Consensus size: 53
3731034 ACTTTTGGAG
*
3731044 CAAGCTCACTTTT-TATAA-TTT-TAAAAAATTAATTCTTATATATTTTTTCAATA
1 CAAGCTCA-TTTTATATAATTTTCTAAAAAATGAATT-TT-TATATTTTTTCAATA
3731097 CAAGCTCATTTTATATAAGTTTTTCTAAAAAATGAATTTTTATATTTTTTC
1 CAAGCTCATTTTATATAA--TTTTCTAAAAAATGAATTTTTATATTTTTTC
3731148 TTATTTTTCT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
52 4 0.09
53 13 0.29
55 11 0.24
56 5 0.11
57 12 0.27
ACGTcount: A:0.36, C:0.11, G:0.04, T:0.50
Consensus pattern (53 bp):
CAAGCTCATTTTATATAATTTTCTAAAAAATGAATTTTTATATTTTTTCAATA
Found at i:3734475 original size:16 final size:17
Alignment explanation
Indices: 3734454--3734487 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
3734444 GTTTTAAGTT
3734454 TCTACA-TTTTATTTTC
1 TCTACACTTTTATTTTC
3734470 TCTACACTTTTATTTTC
1 TCTACACTTTTATTTTC
3734487 T
1 T
3734488 TGCTTTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.62
Consensus pattern (17 bp):
TCTACACTTTTATTTTC
Found at i:3734808 original size:14 final size:15
Alignment explanation
Indices: 3734781--3734809 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3734771 ATCTGGTTCC
3734781 AATTCCATAAAAAAT
1 AATTCCATAAAAAAT
3734796 AATTCCA-AAAAAAT
1 AATTCCATAAAAAAT
3734810 CTCTAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.62, C:0.14, G:0.00, T:0.24
Consensus pattern (15 bp):
AATTCCATAAAAAAT
Found at i:3735765 original size:36 final size:36
Alignment explanation
Indices: 3735718--3735792 Score: 123
Period size: 36 Copynumber: 2.1 Consensus size: 36
3735708 AGGAATCTCT
3735718 TTAACTAATCCTCATGTAATTAACATATAGACTTTC
1 TTAACTAATCCTCATGTAATTAACATATAGACTTTC
* * *
3735754 TTAACTAATCCTCATGTGATTGACATCTAGACTTTC
1 TTAACTAATCCTCATGTAATTAACATATAGACTTTC
3735790 TTA
1 TTA
3735793 GTCTCTATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (36 bp):
TTAACTAATCCTCATGTAATTAACATATAGACTTTC
Found at i:3737272 original size:16 final size:18
Alignment explanation
Indices: 3737248--3737284 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
3737238 CTCATTTTGT
*
3737248 AAGCTTCCAT-AA-GAAA
1 AAGCATCCATGAAGGAAA
3737264 AAGCATCCATGAAGGAAA
1 AAGCATCCATGAAGGAAA
3737282 AAG
1 AAG
3737285 TGAATGATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 9 0.50
17 2 0.11
18 7 0.39
ACGTcount: A:0.51, C:0.16, G:0.19, T:0.14
Consensus pattern (18 bp):
AAGCATCCATGAAGGAAA
Found at i:3746864 original size:15 final size:15
Alignment explanation
Indices: 3746846--3746882 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
3746836 CTTCATAAAC
3746846 TTTATGCTCACTCTA
1 TTTATGCTCACTCTA
*
3746861 TTTATGCTCCCTCTA
1 TTTATGCTCACTCTA
3746876 TTTATGC
1 TTTATGC
3746883 CATTCATGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.16, C:0.27, G:0.08, T:0.49
Consensus pattern (15 bp):
TTTATGCTCACTCTA
Found at i:3756732 original size:20 final size:20
Alignment explanation
Indices: 3756709--3756805 Score: 92
Period size: 20 Copynumber: 4.9 Consensus size: 20
3756699 AACAAATTCC
3756709 AAAAAAATTTTAAAAATTAT
1 AAAAAAATTTTAAAAATTAT
* *
3756729 -AAAAAATTTTAAGAATTCT
1 AAAAAAATTTTAAAAATTAT
* ** *
3756748 AAAAAACTTACAAAAATTCT
1 AAAAAAATTTTAAAAATTAT
*
3756768 AAAAAAATTGTAAAAA-TAGCT
1 AAAAAAATTTTAAAAATTA--T
3756789 AAAAAAA-TTTAAAAATT
1 AAAAAAATTTTAAAAATT
3756806 TTCAAAAAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 7
0.77 0.14 0.09
Matches are distributed among these distances:
19 18 0.29
20 35 0.56
21 9 0.15
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (20 bp):
AAAAAAATTTTAAAAATTAT
Found at i:3756772 original size:21 final size:19
Alignment explanation
Indices: 3756702--3756854 Score: 83
Period size: 20 Copynumber: 7.7 Consensus size: 19
3756692 AATTATAAAC
* *
3756702 AAATTCCAAAAAAATTTTAA
1 AAATTCTAAAAAAA-TTCAA
* * *
3756722 AAATTATAAAAAATTTTAA
1 AAATTCTAAAAAAATTCAA
* *
3756741 GAATTCTAAAAAACTTACAA
1 AAATTCTAAAAAAATT-CAA
*
3756761 AAATTCTAAAAAAATTGTAA
1 AAATTCTAAAAAAATT-CAA
* *
3756781 AAATAGCTAAAAAAATTTAA
1 AAAT-TCTAAAAAAATTCAA
* **
3756801 AAATTTTCAAAAAACCTCAAA
1 AAATTCT-AAAAAAATTC-AA
* * *
3756822 AAATT-TCAAAACATTACCA
1 AAATTCTAAAAAAATT-CAA
*
3756841 AAATTTTAAAAAAA
1 AAATTCTAAAAAAA
3756855 ATTTAAGATT
Statistics
Matches: 103, Mismatches: 24, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
19 30 0.29
20 55 0.53
21 18 0.17
ACGTcount: A:0.60, C:0.10, G:0.02, T:0.28
Consensus pattern (19 bp):
AAATTCTAAAAAAATTCAA
Found at i:3756801 original size:10 final size:10
Alignment explanation
Indices: 3756709--3756860 Score: 55
Period size: 10 Copynumber: 15.2 Consensus size: 10
3756699 AACAAATTCC
3756709 AAAAAAATTT
1 AAAAAAATTT
*
3756719 -TAAAAA-TT
1 AAAAAAATTT
3756727 ATAAAAAATTT
1 A-AAAAAATTT
* *
3756738 -TAAGAATTCT
1 AAAAAAATT-T
*
3756748 -AAAAAACTT
1 AAAAAAATTT
*
3756757 ACAAAAATTCT
1 AAAAAAATT-T
3756768 AAAAAAATTGT
1 AAAAAAATT-T
* **
3756779 AAAAATAGCT
1 AAAAAAATTT
3756789 AAAAAAATTT
1 AAAAAAATTT
*
3756799 -AAAAATTTT
1 AAAAAAATTT
* **
3756808 CAAAAAACCT
1 AAAAAAATTT
*
3756818 CAAAAAATTT
1 AAAAAAATTT
* *
3756828 CAAAACA-TT
1 AAAAAAATTT
* *
3756837 ACCAAAATTTT
1 A-AAAAAATTT
3756848 AAAAAAAATTT
1 -AAAAAAATTT
3756859 AA
1 AA
3756861 GATTTGGATA
Statistics
Matches: 102, Mismatches: 30, Indels: 20
0.67 0.20 0.13
Matches are distributed among these distances:
8 2 0.02
9 22 0.22
10 50 0.49
11 27 0.26
12 1 0.01
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.29
Consensus pattern (10 bp):
AAAAAAATTT
Found at i:3756802 original size:9 final size:9
Alignment explanation
Indices: 3756710--3756814 Score: 66
Period size: 10 Copynumber: 10.7 Consensus size: 9
3756700 ACAAATTCCA
3756710 AAAAAATTT
1 AAAAAATTT
*
3756719 TAAAAATTAT
1 AAAAAATT-T
3756729 AAAAAATTT
1 AAAAAATTT
* *
3756738 TAAGAATTCT
1 AAAAAATT-T
*
3756748 AAAAAACTT
1 AAAAAATTT
3756757 ACAAAAATTCT
1 A-AAAAATT-T
3756768 AAAAAAATTGT
1 -AAAAAATT-T
* *
3756779 AAAAATAGCTA
1 AAAAA-A-TTT
3756790 AAAAAATTT
1 AAAAAATTT
*
3756799 AAAAATTTT
1 AAAAAATTT
3756808 CAAAAAA
1 -AAAAAA
3756815 CCTCAAAAAA
Statistics
Matches: 73, Mismatches: 15, Indels: 15
0.71 0.15 0.15
Matches are distributed among these distances:
9 25 0.34
10 31 0.42
11 15 0.21
12 2 0.03
ACGTcount: A:0.62, C:0.06, G:0.03, T:0.30
Consensus pattern (9 bp):
AAAAAATTT
Found at i:3756812 original size:29 final size:29
Alignment explanation
Indices: 3756728--3756832 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 29
3756718 TTAAAAATTA
* * * *
3756728 TAAAAAATTTTAAGAATTCT-AAAAAACT
1 TAAAAAAATTTAAAAATTGTAAAAAAACC
* * *
3756756 TACAAAAATTCTAAAAAAATTGTAAAAATAGC
1 TAAAAAAATT-T--AAAAATTGTAAAAAAACC
* *
3756788 TAAAAAAATTTAAAAATTTTCAAAAAACC
1 TAAAAAAATTTAAAAATTGTAAAAAAACC
* *
3756817 TCAAAAAATTTCAAAA
1 TAAAAAAATTTAAAAA
3756833 CATTACCAAA
Statistics
Matches: 59, Mismatches: 14, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
28 8 0.14
29 29 0.49
31 8 0.14
32 14 0.24
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.28
Consensus pattern (29 bp):
TAAAAAAATTTAAAAATTGTAAAAAAACC
Found at i:3756974 original size:10 final size:10
Alignment explanation
Indices: 3756959--3757007 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
3756949 AAAAAAATAT
3756959 AAATTTTTAA
1 AAATTTTTAA
*
3756969 AAATTTGTAA
1 AAATTTTTAA
* *
3756979 AAAATTTAAA
1 AAATTTTTAA
3756989 AAATTTTCTAA
1 AAATTTT-TAA
3757000 AAAGTTTT
1 AAA-TTTT
3757008 CATTTTTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
10 22 0.71
11 5 0.16
12 4 0.13
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (10 bp):
AAATTTTTAA
Found at i:3757043 original size:9 final size:8
Alignment explanation
Indices: 3757027--3757131 Score: 63
Period size: 8 Copynumber: 12.4 Consensus size: 8
3757017 AATCATACAA
3757027 TTTTAATT
1 TTTTAATT
3757035 TTGTTAA-T
1 TT-TTAATT
3757043 TTTTAATT
1 TTTTAATT
3757051 TTTTGAATT
1 TTTT-AATT
3757060 TTTTAAAATT
1 TTTT--AATT
* *
3757070 TTCT-AGT
1 TTTTAATT
**
3757077 TTGAAATT
1 TTTTAATT
3757085 TTTTAATT
1 TTTTAATT
3757093 TTTTAAATT
1 TTTT-AATT
*
3757102 GATTTAGATT
1 -TTTTA-ATT
3757112 TTTTAAATT
1 TTTT-AATT
3757121 ATTTT-ATT
1 -TTTTAATT
3757129 TTT
1 TTT
3757132 CAAAAAAAAA
Statistics
Matches: 77, Mismatches: 10, Indels: 21
0.71 0.09 0.19
Matches are distributed among these distances:
7 11 0.14
8 25 0.32
9 23 0.30
10 18 0.23
ACGTcount: A:0.28, C:0.01, G:0.06, T:0.66
Consensus pattern (8 bp):
TTTTAATT
Found at i:3757069 original size:10 final size:9
Alignment explanation
Indices: 3757042--3757126 Score: 54
Period size: 9 Copynumber: 9.7 Consensus size: 9
3757032 ATTTTGTTAA
3757042 TTTTT-AAT
1 TTTTTAAAT
*
3757050 TTTTTGAAT
1 TTTTTAAAT
3757059 TTTTTAAAAT
1 TTTTT-AAAT
*
3757069 TTTCT--A-
1 TTTTTAAAT
* *
3757075 GTTTGAAAT
1 TTTTTAAAT
3757084 TTTTT-AAT
1 TTTTTAAAT
3757092 TTTTTAAAT
1 TTTTTAAAT
* *
3757101 TGATTTAGAT
1 T-TTTTAAAT
3757111 TTTTTAAAT
1 TTTTTAAAT
3757120 TATTTTA
1 T-TTTTA
3757127 TTTTTCAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
6 2 0.03
7 1 0.02
8 14 0.24
9 22 0.38
10 19 0.33
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:3757114 original size:19 final size:17
Alignment explanation
Indices: 3757080--3757131 Score: 68
Period size: 19 Copynumber: 2.9 Consensus size: 17
3757070 TTCTAGTTTG
*
3757080 AAATTTTTTAATTTTTT
1 AAATTATTTAATTTTTT
3757097 AAATTGATTTAGATTTTTT
1 AAATT-ATTTA-ATTTTTT
*
3757116 AAATTATTTTATTTTT
1 AAATTATTTAATTTTT
3757132 CAAAAAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 11 0.35
18 8 0.26
19 12 0.39
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
AAATTATTTAATTTTTT
Found at i:3757298 original size:21 final size:19
Alignment explanation
Indices: 3757270--3757321 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
3757260 AATTTTTGAA
3757270 AATT-TTTTTTGAATTTATTT
1 AATTATTTTTT-AATTT-TTT
3757290 AATTATTTTTATAATTTTTT
1 AATTATTTTT-TAATTTTTT
*
3757310 CATATATTTTTT
1 AAT-TATTTTTT
3757322 TATAATTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
20 10 0.36
21 17 0.61
22 1 0.04
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
AATTATTTTTTAATTTTTT
Found at i:3757304 original size:12 final size:11
Alignment explanation
Indices: 3757289--3757332 Score: 61
Period size: 12 Copynumber: 3.8 Consensus size: 11
3757279 TGAATTTATT
3757289 TAATTATTTTTA
1 TAATT-TTTTTA
*
3757301 TAATTTTTTCA
1 TAATTTTTTTA
3757312 TATATTTTTTTA
1 TA-ATTTTTTTA
3757324 TAATTTTTT
1 TAATTTTTT
3757333 AAAAGTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 14 0.48
12 15 0.52
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:3757308 original size:10 final size:10
Alignment explanation
Indices: 3757295--3757360 Score: 69
Period size: 10 Copynumber: 6.3 Consensus size: 10
3757285 TATTTAATTA
3757295 TTTTTATAAT
1 TTTTTATAAT
3757305 TTTTTCATATATT
1 TTTTT-ATA-A-T
3757318 TTTTTATAAT
1 TTTTTATAAT
* *
3757328 TTTTTAAAAG
1 TTTTTATAAT
*
3757338 TTTTTAGAAT
1 TTTTTATAAT
*
3757348 TTTTTAGAAT
1 TTTTTATAAT
3757358 TTT
1 TTT
3757361 AAAATTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
10 35 0.71
11 4 0.08
12 4 0.08
13 6 0.12
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.65
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:3757320 original size:13 final size:12
Alignment explanation
Indices: 3757295--3757332 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 12
3757285 TATTTAATTA
3757295 TTTTTATA-ATT
1 TTTTTATATATT
*
3757306 TTTTCATATATT
1 TTTTTATATATT
3757318 TTTTTATA-ATT
1 TTTTTATATATT
3757329 TTTT
1 TTTT
3757333 AAAAGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTATATATT
Found at i:3757343 original size:20 final size:19
Alignment explanation
Indices: 3757260--3757379 Score: 80
Period size: 20 Copynumber: 5.8 Consensus size: 19
3757250 TTTAATGTAC
* *
3757260 AATTTTTGAAAATTTTTTTT
1 AATTTTTTAAAA-TTTTTAT
*
3757280 GAATTTATTTAATTATTTTTAT
1 -AATTT-TTTAA-AATTTTTAT
*
3757302 AATTTTTTCATATATTTTTTTAT
1 AATTTTTT-A-A-A-ATTTTTAT
*
3757325 AATTTTTTAAAAGTTTTTAG
1 AATTTTTTAAAA-TTTTTAT
* *
3757345 AATTTTTTAGAA-TTTTAA
1 AATTTTTTAAAATTTTTAT
3757363 AATTTTTTAGAAATTTT
1 AATTTTTTA-AAATTTT
3757380 CTTTTTATGA
Statistics
Matches: 81, Mismatches: 10, Indels: 17
0.75 0.09 0.16
Matches are distributed among these distances:
18 14 0.17
19 2 0.02
20 24 0.30
21 12 0.15
22 13 0.16
23 16 0.20
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.62
Consensus pattern (19 bp):
AATTTTTTAAAATTTTTAT
Found at i:3757370 original size:10 final size:10
Alignment explanation
Indices: 3757317--3757379 Score: 67
Period size: 10 Copynumber: 6.4 Consensus size: 10
3757307 TTTCATATAT
*
3757317 TTTTTTATAA
1 TTTTTTAAAA
3757327 TTTTTTAAAA
1 TTTTTTAAAA
* *
3757337 GTTTTTAGAA
1 TTTTTTAAAA
*
3757347 TTTTTTAGAA
1 TTTTTTAAAA
3757357 --TTTTAAAA
1 TTTTTTAAAA
3757365 TTTTTTAGAAA
1 TTTTTTA-AAA
3757376 TTTT
1 TTTT
3757380 CTTTTTATGA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
8 7 0.16
10 31 0.69
11 7 0.16
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (10 bp):
TTTTTTAAAA
Found at i:3760159 original size:18 final size:18
Alignment explanation
Indices: 3760136--3760182 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 18
3760126 AGAAAGTTTC
**
3760136 CATTTTGGAATCCATTTT
1 CATTTTGGAAAACATTTT
*
3760154 CATTTTAGAAAACATTTT
1 CATTTTGGAAAACATTTT
3760172 CATTTT-GAAAA
1 CATTTTGGAAAA
3760183 TGCAACTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 5 0.19
18 21 0.81
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.45
Consensus pattern (18 bp):
CATTTTGGAAAACATTTT
Found at i:3763817 original size:17 final size:16
Alignment explanation
Indices: 3763784--3763817 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3763774 ATTTTTAATT
*
3763784 AAAAATAAAATATGTA
1 AAAAATAAAATAAGTA
3763800 AAAAATAAAGATAAGTA
1 AAAAATAAA-ATAAGTA
3763817 A
1 A
3763818 GTGAATCAAA
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:0.71, C:0.00, G:0.09, T:0.21
Consensus pattern (16 bp):
AAAAATAAAATAAGTA
Found at i:3769304 original size:17 final size:17
Alignment explanation
Indices: 3769282--3769330 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
3769272 GGCAACCCAA
3769282 GTTTTTCTTTTCATGTT
1 GTTTTTCTTTTCATGTT
3769299 GTTTTTCTTTTC-T-TT
1 GTTTTTCTTTTCATGTT
*
3769314 -TTTTTTTTGTTCATGTT
1 GTTTTTCTT-TTCATGTT
3769331 TGTGTATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
14 7 0.25
15 5 0.18
16 2 0.07
17 14 0.50
ACGTcount: A:0.04, C:0.10, G:0.10, T:0.76
Consensus pattern (17 bp):
GTTTTTCTTTTCATGTT
Found at i:3770275 original size:17 final size:17
Alignment explanation
Indices: 3770234--3770278 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
3770224 GAAAAAGAAT
3770234 GAAAAAAAT-AATAAAA
1 GAAAAAAATAAATAAAA
* *
3770250 TAAAGAAAATAAATGAAA
1 GAAA-AAAATAAATAAAA
3770268 GAAAAAAATAA
1 GAAAAAAATAA
3770279 GCAAGCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 3 0.12
17 12 0.50
18 9 0.38
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.13
Consensus pattern (17 bp):
GAAAAAAATAAATAAAA
Found at i:3770372 original size:14 final size:16
Alignment explanation
Indices: 3770353--3770390 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
3770343 CATAGCAAAG
3770353 AAAGAAAAG-AAG-AA
1 AAAGAAAAGTAAGCAA
*
3770367 AAAGAAAAGTATGCAA
1 AAAGAAAAGTAAGCAA
3770383 AAAGAAAA
1 AAAGAAAA
3770391 TTTAGGGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 9 0.43
15 2 0.10
16 10 0.48
ACGTcount: A:0.74, C:0.03, G:0.18, T:0.05
Consensus pattern (16 bp):
AAAGAAAAGTAAGCAA
Found at i:3778830 original size:12 final size:12
Alignment explanation
Indices: 3778810--3778840 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3778800 TGTAGTATGG
*
3778810 TATTCTTGTAAA
1 TATTTTTGTAAA
3778822 TATTTTTGTAAA
1 TATTTTTGTAAA
3778834 TATTTTT
1 TATTTTT
3778841 TTCGTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.03, G:0.06, T:0.61
Consensus pattern (12 bp):
TATTTTTGTAAA
Found at i:3780278 original size:62 final size:62
Alignment explanation
Indices: 3780176--3780292 Score: 216
Period size: 62 Copynumber: 1.9 Consensus size: 62
3780166 GATGCAGATG
*
3780176 GGGTAGATTGCTAATGCCCTTAACACTTGCCTTCAAGGTATCCTTCCCAGTAACACTAAAAT
1 GGGTAGATTGCTAATGCCCTTAACACTTGCCTTCAAGGTATCCTTCCCAGCAACACTAAAAT
*
3780238 GGGTAGATTGCTAATGCCCTTAACACTTGCCTTCATGGTATCCTTCCCAGCAACA
1 GGGTAGATTGCTAATGCCCTTAACACTTGCCTTCAAGGTATCCTTCCCAGCAACA
3780293 TTGAAACCAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.26, C:0.27, G:0.17, T:0.29
Consensus pattern (62 bp):
GGGTAGATTGCTAATGCCCTTAACACTTGCCTTCAAGGTATCCTTCCCAGCAACACTAAAAT
Found at i:3785265 original size:16 final size:16
Alignment explanation
Indices: 3785240--3785279 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
3785230 AAAATAATTA
*
3785240 AAAAGGAAAGAAAAAG
1 AAAAGAAAAGAAAAAG
*
3785256 AAAAGAAAAGAAAACG
1 AAAAGAAAAGAAAAAG
3785272 AATAAGAA
1 AA-AAGAA
3785280 TAAAGTGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.75, C:0.03, G:0.20, T:0.03
Consensus pattern (16 bp):
AAAAGAAAAGAAAAAG
Found at i:3789112 original size:8 final size:8
Alignment explanation
Indices: 3789099--3789142 Score: 88
Period size: 8 Copynumber: 5.5 Consensus size: 8
3789089 ATTTCTCTTT
3789099 CTTTGATG
1 CTTTGATG
3789107 CTTTGATG
1 CTTTGATG
3789115 CTTTGATG
1 CTTTGATG
3789123 CTTTGATG
1 CTTTGATG
3789131 CTTTGATG
1 CTTTGATG
3789139 CTTT
1 CTTT
3789143 ATTTGTACAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 36 1.00
ACGTcount: A:0.11, C:0.14, G:0.23, T:0.52
Consensus pattern (8 bp):
CTTTGATG
Found at i:3793804 original size:22 final size:23
Alignment explanation
Indices: 3793779--3793822 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3793769 TGCAAATTGT
*
3793779 AAACT-AAATCATATAGGCCAAG
1 AAACTAAAATCATATAAGCCAAG
3793801 AAACTAAAATCATATAAGCCAA
1 AAACTAAAATCATATAAGCCAA
3793823 ATATAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.55, C:0.18, G:0.09, T:0.18
Consensus pattern (23 bp):
AAACTAAAATCATATAAGCCAAG
Found at i:3794989 original size:18 final size:18
Alignment explanation
Indices: 3794966--3795001 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3794956 AAGCTGCCAC
3794966 AAGTTTTGTCACCACCTG
1 AAGTTTTGTCACCACCTG
*
3794984 AAGTTTTGTTACCACCTG
1 AAGTTTTGTCACCACCTG
3795002 TTGCCTCCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (18 bp):
AAGTTTTGTCACCACCTG
Found at i:3795455 original size:15 final size:15
Alignment explanation
Indices: 3795435--3795465 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3795425 ATAGAGCTTG
3795435 CTCTCTAAATTTCAT
1 CTCTCTAAATTTCAT
3795450 CTCTCTAAATTTCAT
1 CTCTCTAAATTTCAT
3795465 C
1 C
3795466 CAAAGGTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.29, G:0.00, T:0.45
Consensus pattern (15 bp):
CTCTCTAAATTTCAT
Found at i:3798116 original size:41 final size:41
Alignment explanation
Indices: 3798052--3798130 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
3798042 ATATTTTTAG
* * *
3798052 CTTATTTAAAATCTTCTAGAAGCTTTAATATGTAACTCTAA
1 CTTATTTAAAATCTTCCAAAAGCTTTAATATGAAACTCTAA
*
3798093 CTTATTTAAAATCTTCCAAAAGCTTTTATATGAAACTC
1 CTTATTTAAAATCTTCCAAAAGCTTTAATATGAAACTC
3798131 CTTCCTTCCT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.37, C:0.16, G:0.06, T:0.41
Consensus pattern (41 bp):
CTTATTTAAAATCTTCCAAAAGCTTTAATATGAAACTCTAA
Found at i:3809740 original size:130 final size:131
Alignment explanation
Indices: 3809466--3810241 Score: 771
Period size: 129 Copynumber: 6.0 Consensus size: 131
3809456 AGTTGTTGTC
* * * **
3809466 AAAACTTGTTTTTATTTGCTAGGATTTTTCAATGTTGTTGCTTAA---GCTTTTTTAATATTTTA
1 AAAACTT-ATTTTATTTGCAACGATTTTTCAATGTTGTTGCTTAATTTATTTTTTTAATATTTTA
* * ** * * * *
3809528 TACAATGAC-AAAAAGTTGTTACACAAGTACTTATCA-AATTGTAACGATAAAATATTATCGTTG
65 TACAATGACAAAAAAGTTGTTACAAAAATTTTTATCATATTTGTAACGATAAAAAATTATTGTTA
*
3809591 TG
130 CG
* * *
3809593 AAAACTTATTTTATTTACAATGA-TTTTCAATGTTATTGCTTAATTTATTTTTTTAATATTTTAT
1 AAAACTTATTTTATTTGCAACGATTTTTCAATGTTGTTGCTTAATTTATTTTTTTAATATTTTAT
* * * * *
3809657 ATAATGACAAAAAAGTTGCTACAAAAATTTTTATAATATTTGGAACAATAAAAAATTATTGTTAC
66 ACAATGACAAAAAAGTTGTTACAAAAATTTTTATCATATTTGTAACGATAAAAAATTATTGTTAC
*
3809722 A
131 G
* * * * *
3809723 AAAACTTCTTTTATTTACAATGATTTTTAAATGTTGTTGCTTAATTTATTCTTTTAATATTTTAT
1 AAAACTTATTTTATTTGCAACGATTTTTCAATGTTGTTGCTTAATTTATTTTTTTAATATTTTAT
* * *
3809788 A-AATGACAAAAAA-TTGTTACAAAAATTTTTATCATGTTTGCAATGATAAAAAATTATTGTTAC
66 ACAATGACAAAAAAGTTGTTACAAAAATTTTTATCATATTTGTAACGATAAAAAATTATTGTTAC
3809851 G
131 G
*
3809852 AAAACTTATTTTATTTGTAACGATTTTTCAATGTTGTTGCTTAATTTATTTTTTTAATATTTTAT
1 AAAACTTATTTTATTTGCAACGATTTTTCAATGTTGTTGCTTAATTTATTTTTTTAATATTTTAT
** * * * * * *
3809917 ACAAACAAAAAAAAAAGTTGTT-CTAAAACTTTTTGTCATATTTGTAATGATAAAAACTTATTAT
66 AC-AA-TGACAAAAAAGTTGTTAC-AAAAATTTTTATCATATTTGTAACGATAAAAAATTATTGT
*
3809981 TACA
128 TACG
* * * * *
3809985 AAAATTTATTTTATTTGCAACAATTTTTCAATGTCGTTGCTTTACTTA-TTTTTTAATATTTTAT
1 AAAACTTATTTTATTTGCAACGATTTTTCAATGTTGTTGCTTAATTTATTTTTTTAATATTTTAT
* ** ** * * * * *
3810049 ATAACAATTAAAATGTTGTTAAAAAAATTTTTATCATATTTATAACAATAAAAAAATTATTGTTG
66 ACAATGACAAAAAAGTTGTTACAAAAATTTTTATCATATTTGTAACGAT-AAAAAATTATTGTTA
*
3810114 TG
130 CG
* * * * * * * *
3810116 AAATCCTAATTTCTTTGCAACAAATTTTAAATGTCGTTGCTTAATTTATTTTTTTAATATTTTTA
1 AAAACTTATTTTATTTGCAACGATTTTTCAATGTTGTTGCTTAATTTATTTTTTTAATA-TTTTA
** * * * * * *
3810181 TACAATGACAAAAAAAATATTACAAACATTTCTATCATATTTGTAATGATTAAAAACTATT
65 TACAATGACAAAAAAGTTGTTACAAAAATTTTTATCATATTTGTAACGATAAAAAATTATT
3810242 ATTGCAAAAT
Statistics
Matches: 537, Mismatches: 97, Indels: 25
0.81 0.15 0.04
Matches are distributed among these distances:
125 19 0.04
126 12 0.02
127 7 0.01
128 23 0.04
129 125 0.23
130 89 0.17
131 94 0.18
132 44 0.08
133 124 0.23
ACGTcount: A:0.38, C:0.09, G:0.08, T:0.46
Consensus pattern (131 bp):
AAAACTTATTTTATTTGCAACGATTTTTCAATGTTGTTGCTTAATTTATTTTTTTAATATTTTAT
ACAATGACAAAAAAGTTGTTACAAAAATTTTTATCATATTTGTAACGATAAAAAATTATTGTTAC
G
Found at i:3810287 original size:263 final size:259
Alignment explanation
Indices: 3809758--3810291 Score: 582
Period size: 263 Copynumber: 2.0 Consensus size: 259
3809748 TTTAAATGTT
* * *
3809758 GTTGCTTAATTTATTCTTTTAATATTTTATAAATGACAAAAAATTGTTACAAAAATTTTTATCAT
1 GTTGCTTAACTTATTCTTTTAATATTTTAT-AATAACAAAAAATTGTTAAAAAAATTTTTATCAT
* * ** * * * * * * *
3809823 GTTTGCAATGATAAAAAATTATTGTTACGAAAACTTATTTTATTTGTAACGATTTTTCAATGTTG
65 ATTTACAACAATAAAAAATTATTGTTACGAAAACCTAATTTATTTGCAACAAATTTTAAATGTCG
* * *
3809888 TTGCTTAATTTATTTTTTTAATATTTTATACAAACAAAAAAAAAAGTTGTTCTAAAACTTTTTGT
130 TTGCTTAATTTATTTTTTTAATATTTTATACAAACAAAAAAAAAAG-TGTACTAAAACTTTCTAT
*** **
3809953 CATATTTGTAATGATAAAAACTTATTATTACAAAAATTTATTTTATTTGCAACAATTTTTCAATG
194 CATATTTGTAATGATAAAAACTTATTATTACAAAAATTTATAACATTTGCAACAATTTCACAA-G
3810018 TC
258 TC
*
3810020 GTTGCTTTACTTATT-TTTTAATATTTTAT-ATAACAATTAAAATGTTGTTAAAAAAATTTTTAT
1 GTTGCTTAACTTATTCTTTTAATATTTTATAATAACAA--AAAA--TTGTTAAAAAAATTTTTAT
* ** * *
3810083 CATATTTATAACAATAAAAAAATTATTGTTGTGAAATCCTAATTTCTTTGCAACAAATTTTAAAT
62 CATATTTACAACAAT-AAAAAATTATTGTTACGAAAACCTAATTTATTTGCAACAAATTTTAAAT
*
3810148 GTCGTTGCTTAATTTATTTTTTTAATATTTTTATACAATGACAAAAAAAATA-T-TAC--AAACA
126 GTCGTTGCTTAATTTATTTTTTTAATA-TTTTATACAA--ACAAAAAAAAAAGTGTACTAAAAC-
* *
3810209 TTTCTATCATATTTGTAATGATTAAAAAC-TATTATTGC-AAAATATTATAACATTTGCAATGAC
187 TTTCTATCATATTTGTAATGA-TAAAAACTTATTATTACAAAAAT-TTATAACATTTGCAA-CA-
3810272 ATTTCACAA-TC
248 ATTTCACAAGTC
3810283 GTTGCTTAA
1 GTTGCTTAA
3810292 TTTCTTTTTT
Statistics
Matches: 227, Mismatches: 32, Indels: 25
0.80 0.11 0.09
Matches are distributed among these distances:
259 6 0.03
261 18 0.08
262 22 0.10
263 77 0.34
264 75 0.33
265 18 0.08
267 11 0.05
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.45
Consensus pattern (259 bp):
GTTGCTTAACTTATTCTTTTAATATTTTATAATAACAAAAAATTGTTAAAAAAATTTTTATCATA
TTTACAACAATAAAAAATTATTGTTACGAAAACCTAATTTATTTGCAACAAATTTTAAATGTCGT
TGCTTAATTTATTTTTTTAATATTTTATACAAACAAAAAAAAAAGTGTACTAAAACTTTCTATCA
TATTTGTAATGATAAAAACTTATTATTACAAAAATTTATAACATTTGCAACAATTTCACAAGTC
Found at i:3810905 original size:23 final size:23
Alignment explanation
Indices: 3810861--3810906 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
3810851 ATTTACAATT
** *
3810861 TTTTAAAATATATTTATTCAAAA
1 TTTTAAAATATAAATATCCAAAA
*
3810884 TTTTAAAATTTAAATATCCAAAA
1 TTTTAAAATATAAATATCCAAAA
3810907 ATAAACAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (23 bp):
TTTTAAAATATAAATATCCAAAA
Found at i:3813466 original size:23 final size:23
Alignment explanation
Indices: 3813440--3813495 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
3813430 GGTTTTGTCC
*
3813440 TATTTATCTTCCATTTTATAGGT
1 TATTGATCTTCCATTTTATAGGT
** * *
3813463 TATTGATCTTTTATTTTGTATGT
1 TATTGATCTTCCATTTTATAGGT
3813486 TATTGATCTT
1 TATTGATCTT
3813496 TTATTCTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.61
Consensus pattern (23 bp):
TATTGATCTTCCATTTTATAGGT
Found at i:3813496 original size:23 final size:23
Alignment explanation
Indices: 3813452--3813500 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
3813442 TTTATCTTCC
3813452 ATTTTATAGGTTATTGATCTTTT
1 ATTTTATAGGTTATTGATCTTTT
* *
3813475 ATTTTGTATGTTATTGATCTTTT
1 ATTTTATAGGTTATTGATCTTTT
3813498 ATT
1 ATT
3813501 CTATGTCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.63
Consensus pattern (23 bp):
ATTTTATAGGTTATTGATCTTTT
Found at i:3815821 original size:89 final size:89
Alignment explanation
Indices: 3815629--3815975 Score: 407
Period size: 89 Copynumber: 3.9 Consensus size: 89
3815619 ACTAGGACAG
* * *
3815629 AACCACAAGCCAAAATAAGGTGACCAAGACTGAGTCAAGGTAAAAAATAAATGATC-AGATGGAA
1 AACCACGAGTCAAAATAAGGTGACCAAGACTGAGTCAAGGTCAAAAATAAATGATCGAGATGGAA
* * *
3815693 CTACAAATCATGTGATTGGGATGA
66 CCACAAATCATGTGATCGAGATGA
*
3815717 AACCACGAGTCAAAATAAGGTGACCAAGA-TCGAGTCAAGGTCAAAAATAAATGATCGAGATGGG
1 AACCACGAGTCAAAATAAGGTGACCAAGACT-GAGTCAAGGTCAAAAATAAATGATCGAGATGGA
* * * *
3815781 ACCACAAATCATTTGACCAAGATAA
65 ACCACAAATCATGTGATCGAGATGA
* * * * *
3815806 AACCATGAGTCAAAATAAGGTGACCAGGACTGAGTCGAGGTCAAAAATAAATGA-CTGGGATGAA
1 AACCACGAGTCAAAATAAGGTGACCAAGACTGAGTCAAGGTCAAAAATAAATGATC-GAGATGGA
** *
3815870 ACCATGAATCATGCGATCGAGATGA
65 ACCACAAATCATGTGATCGAGATGA
* * * *
3815895 AACCACGAGTTAAAATAAAGTGACCAAGA-TCGAGTCAAGATCAAAAATAAATGATC-AGGATGA
1 AACCACGAGTCAAAATAAGGTGACCAAGACT-GAGTCAAGGTCAAAAATAAATGATCGA-GATGG
*
3815958 AACCACGAATCATGTGAT
64 AACCACAAATCATGTGAT
3815976 TCGTGGTTTA
Statistics
Matches: 219, Mismatches: 33, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
87 1 0.00
88 53 0.24
89 163 0.74
90 2 0.01
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.18
Consensus pattern (89 bp):
AACCACGAGTCAAAATAAGGTGACCAAGACTGAGTCAAGGTCAAAAATAAATGATCGAGATGGAA
CCACAAATCATGTGATCGAGATGA
Found at i:3816078 original size:34 final size:33
Alignment explanation
Indices: 3815988--3816081 Score: 88
Period size: 34 Copynumber: 2.8 Consensus size: 33
3815978 GTGGTTTAAA
3815988 AAATAAGTTTTCAAAATAAT--AAAAATCCTTT
1 AAATAAGTTTTCAAAATAATAAAAAAATCCTTT
* * * *
3816019 ATAA-AA-TTTATAAAAAACAAAAAAAAAATCTTTT
1 A-AATAAGTTT-T-CAAAATAATAAAAAAATCCTTT
3816053 CAAATAAGTTTTCAAAATAATAAAAAAAT
1 -AAATAAGTTTTCAAAATAATAAAAAAAT
3816082 ATTTATAAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
30 3 0.06
31 4 0.08
32 8 0.17
34 26 0.54
35 4 0.08
36 3 0.06
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (33 bp):
AAATAAGTTTTCAAAATAATAAAAAAATCCTTT
Found at i:3816115 original size:18 final size:20
Alignment explanation
Indices: 3816094--3816136 Score: 63
Period size: 18 Copynumber: 2.2 Consensus size: 20
3816084 TTATAAAAAC
3816094 AAAAAAAATC-CTTTC-AAT
1 AAAAAAAATCTCTTTCAAAT
*
3816112 AAAAAAAATCTTTTTCAAAT
1 AAAAAAAATCTCTTTCAAAT
3816132 AAAAA
1 AAAAA
3816137 TCTTTGCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 10 0.45
19 4 0.18
20 8 0.36
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAAAAATCTCTTTCAAAT
Found at i:3816146 original size:16 final size:18
Alignment explanation
Indices: 3816097--3816151 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
3816087 TAAAAACAAA
* *
3816097 AAAAATCCTTT-CAATAAA
1 AAAAATCTTTTGCAA-AAT
*
3816115 AAAAATCTTTTTC-AAAT
1 AAAAATCTTTTGCAAAAT
3816132 AAAAATC-TTTGCAAAAT
1 AAAAATCTTTTGCAAAAT
3816149 AAA
1 AAA
3816152 TTAATGAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
16 4 0.12
17 16 0.50
18 11 0.34
19 1 0.03
ACGTcount: A:0.55, C:0.13, G:0.02, T:0.31
Consensus pattern (18 bp):
AAAAATCTTTTGCAAAAT
Found at i:3816252 original size:3 final size:3
Alignment explanation
Indices: 3816244--3816276 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3816234 TCAGTTTTCA
3816244 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3816277 GAAAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3817608 original size:17 final size:17
Alignment explanation
Indices: 3817586--3817618 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3817576 GTGAAAAGAT
3817586 GAAAAAAATGGAAAAAG
1 GAAAAAAATGGAAAAAG
3817603 GAAAAAAATGGAAAAA
1 GAAAAAAATGGAAAAA
3817619 AAAAAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.21, T:0.06
Consensus pattern (17 bp):
GAAAAAAATGGAAAAAG
Found at i:3817609 original size:19 final size:19
Alignment explanation
Indices: 3817587--3817668 Score: 71
Period size: 19 Copynumber: 4.3 Consensus size: 19
3817577 TGAAAAGATG
*
3817587 AAAAAAATGGAAAAAG--G
1 AAAAAAATGGAAAAAGAAA
*
3817604 AAAAAAATGGAAAAAAAAAA
1 AAAAAAATGG-AAAAAGAAA
*
3817624 AGAAAAAATAGAAAAA-AAA
1 A-AAAAAATGGAAAAAGAAA
*
3817643 AGAAAAAATGGAAAATGGAAA
1 A-AAAAAATGGAAAA-AGAAA
3817664 AAAAA
1 AAAAA
3817669 TACAAAGAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
17 10 0.19
18 5 0.09
19 17 0.31
20 10 0.19
21 12 0.22
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (19 bp):
AAAAAAATGGAAAAAGAAA
Found at i:3817667 original size:10 final size:10
Alignment explanation
Indices: 3817586--3817657 Score: 53
Period size: 10 Copynumber: 7.5 Consensus size: 10
3817576 GTGAAAAGAT
3817586 GAAAAAAATG
1 GAAAAAAATG
3817596 G--AAAAA-G
1 GAAAAAAATG
3817603 GAAAAAAATG
1 GAAAAAAATG
**
3817613 GAAAAAAAAA
1 GAAAAAAATG
* *
3817623 AAGAAAAAATA
1 GA-AAAAAATG
**
3817634 GAAAAAAAAA
1 GAAAAAAATG
3817644 G-AAAAAATG
1 GAAAAAAATG
3817653 GAAAA
1 GAAAA
3817658 TGGAAAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
7 2 0.04
8 5 0.10
9 12 0.24
10 22 0.45
11 8 0.16
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.06
Consensus pattern (10 bp):
GAAAAAAATG
Found at i:3817684 original size:26 final size:23
Alignment explanation
Indices: 3817597--3817685 Score: 76
Period size: 26 Copynumber: 3.7 Consensus size: 23
3817587 AAAAAAATGG
*
3817597 AAAAAGGAAAAAAATGG-AAAAA
1 AAAAAAGAAAAAAATGGAAAAAA
*
3817619 AAAAAAG-AAAAAATAGAAAAAA
1 AAAAAAGAAAAAAATGGAAAAAA
3817641 AAAGAAA-AAATGGAAAATGGAAAAAA
1 AAA-AAAGAAA---AAAATGGAAAAAA
3817667 AATACAAAGAAAGAAAATG
1 AA-A-AAAGAAA-AAAATG
3817686 AATACTCAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
21 8 0.15
22 14 0.25
23 5 0.09
26 21 0.38
27 4 0.07
28 3 0.05
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.07
Consensus pattern (23 bp):
AAAAAAGAAAAAAATGGAAAAAA
Found at i:3818738 original size:24 final size:24
Alignment explanation
Indices: 3818711--3818762 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
3818701 AAAAATAATG
3818711 AGAATCTTTAAATAAGAATCTTTA
1 AGAATCTTTAAATAAGAATCTTTA
* * *
3818735 AGAATTTTTGAATGAGAATCTTTA
1 AGAATCTTTAAATAAGAATCTTTA
3818759 AGAA
1 AGAA
3818763 ATTTTGAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (24 bp):
AGAATCTTTAAATAAGAATCTTTA
Found at i:3818767 original size:24 final size:24
Alignment explanation
Indices: 3818725--3818773 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
3818715 TCTTTAAATA
*
3818725 AGAATCTTTAAGAATTTTTGAATG
1 AGAATCTTTAAGAAATTTTGAATG
3818749 AGAATCTTTAAGAAATTTTGAATG
1 AGAATCTTTAAGAAATTTTGAATG
3818773 A
1 A
3818774 AAATATATCG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (24 bp):
AGAATCTTTAAGAAATTTTGAATG
Found at i:3819009 original size:108 final size:108
Alignment explanation
Indices: 3818773--3819141 Score: 526
Period size: 108 Copynumber: 3.4 Consensus size: 108
3818763 ATTTTGAATG
* * *
3818773 AAAATATATCGAATGTGAATCTTTGAACTCGAATGAGAAGCTTTTG-ACTTTTGGATGTGAACCC
1 AAAATCTATCAAATGTGAATCTTTGAACTCGAATGAGAATC-TTTGAACTTTTGGATGTGAACCC
**
3818837 TAAATTTTTTTGAATGAGGCCCTTTGAATTTAGATGTGAAACTCT
65 TAAA-TTTTTTGAATGAGAACCTTTGAATTTAGATGTGAAACTCT
** *
3818882 AAAATCTATGGAATATGAATCTTTGAACTCGAATGAGAATCTTTGAACTTTTGGATGTGAA-CCT
1 AAAATCTATCAAATGTGAATCTTTGAACTCGAATGAGAATCTTTGAACTTTTGGATGTGAACCCT
* *
3818946 CAAATTTTTTGAATGAGAACCTTTGGATTTGGATGTGAAACTCT
66 -AAATTTTTTGAATGAGAACCTTTGAATTTAGATGTGAAACTCT
* *
3818990 AAAATCTACCAAATGTGAATCTTTGAACTCGAATGAGAATCTTTGAACTTATGGATGTGAACCCT
1 AAAATCTATCAAATGTGAATCTTTGAACTCGAATGAGAATCTTTGAACTTTTGGATGTGAACCCT
* * *
3819055 AAATTTTTTGAATGAGAAGCTTTAAATTTATATGTGAAACTCT
66 AAATTTTTTGAATGAGAACCTTTGAATTTAGATGTGAAACTCT
* * * *
3819098 AGAATCTATCAAATGTGAATCTTTGATCTTGAATGAAAATCTTT
1 AAAATCTATCAAATGTGAATCTTTGAACTCGAATGAGAATCTTT
3819142 AAGAAATTTT
Statistics
Matches: 234, Mismatches: 23, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
108 176 0.75
109 58 0.25
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (108 bp):
AAAATCTATCAAATGTGAATCTTTGAACTCGAATGAGAATCTTTGAACTTTTGGATGTGAACCCT
AAATTTTTTGAATGAGAACCTTTGAATTTAGATGTGAAACTCT
Found at i:3819029 original size:20 final size:20
Alignment explanation
Indices: 3819001--3819038 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
3818991 AAATCTACCA
*
3819001 AATGTGAATCTTTGAACTCG
1 AATGAGAATCTTTGAACTCG
3819021 AATGAGAATCTTTGAACT
1 AATGAGAATCTTTGAACT
3819039 TATGGATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (20 bp):
AATGAGAATCTTTGAACTCG
Found at i:3819413 original size:32 final size:32
Alignment explanation
Indices: 3819318--3819415 Score: 90
Period size: 33 Copynumber: 3.0 Consensus size: 32
3819308 TCTCAAATGT
**
3819318 GAATCTTAAAATCTTGAG-AATCAAATTCTTAT
1 GAATCTTAAAATCTTGAGAAAT-AAATTCTTGC
* * * * *
3819350 GAACCTAAAAAATCTTGTGAATCTAAGTTCTTGC
1 GAATCT-TAAAATCTTGAGAA-ATAAATTCTTGC
*
3819384 GAATCTTAAAACCTTGAGAAATAAATTCTTGC
1 GAATCTTAAAATCTTGAGAAATAAATTCTTGC
3819416 AAGCCTAAAA
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
32 15 0.30
33 21 0.42
34 13 0.26
35 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.34
Consensus pattern (32 bp):
GAATCTTAAAATCTTGAGAAATAAATTCTTGC
Found at i:3819546 original size:18 final size:18
Alignment explanation
Indices: 3819523--3819577 Score: 74
Period size: 18 Copynumber: 3.1 Consensus size: 18
3819513 AATCTTTGTG
*
3819523 TCTTGCGAACCTGTAAAT
1 TCTTGCGAACCTGAAAAT
*
3819541 TCTTGCGAATCTGAAAAT
1 TCTTGCGAACCTGAAAAT
* *
3819559 TCTTGCGAAACTAAAAAT
1 TCTTGCGAACCTGAAAAT
3819577 T
1 T
3819578 TTTGTGAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (18 bp):
TCTTGCGAACCTGAAAAT
Found at i:3824861 original size:5 final size:5
Alignment explanation
Indices: 3824840--3824926 Score: 93
Period size: 5 Copynumber: 17.0 Consensus size: 5
3824830 CAATCGAGTT
* *
3824840 TATATA TATATA TATAA TATAA TATAA TATAA TATAC TATAA TACAA TATAA
1 TATA-A TATA-A TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
* * * * *
3824892 TATAC TATAA TACAA TATAA GATAA GATAA GATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA
3824927 ACACTATCCA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
5 62 0.86
6 10 0.14
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (5 bp):
TATAA
Found at i:3827442 original size:22 final size:24
Alignment explanation
Indices: 3827416--3827462 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3827406 ATTTTTCATA
3827416 TTTTTCC-AAA-AAAAAAATCTTT
1 TTTTTCCTAAACAAAAAAATCTTT
*
3827438 TTTTTCCTAAACCTAAAAAATCTTT
1 TTTTTCCTAAA-CAAAAAAATCTTT
3827463 GAAAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 7 0.33
23 3 0.14
25 11 0.52
ACGTcount: A:0.40, C:0.17, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTTTCCTAAACAAAAAAATCTTT
Found at i:3827717 original size:6 final size:6
Alignment explanation
Indices: 3827706--3827750 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
3827696 TCCTATTAAC
**
3827706 TAAAAA TAAAAA TAAAAA TAGGAA TAAAAA T-AAAA T-AAAA TAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAA
3827751 TAATAAAGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 10 0.29
6 24 0.71
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (6 bp):
TAAAAA
Found at i:3827755 original size:24 final size:24
Alignment explanation
Indices: 3827706--3827757 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
3827696 TCCTATTAAC
* *
3827706 TAAAAATAAAAATAAAAATAGGAA
1 TAAAAATAAAAATAAAAAAAAGAA
*
3827730 TAAAAAT-AAAATAAAATAAAATAA
1 TAAAAATAAAAATAAAA-AAAAGAA
3827754 TAAA
1 TAAA
3827758 GCCCATAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (24 bp):
TAAAAATAAAAATAAAAAAAAGAA
Found at i:3828862 original size:12 final size:12
Alignment explanation
Indices: 3828845--3828871 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3828835 TGGATCACAT
3828845 AAAAAATTATAA
1 AAAAAATTATAA
3828857 AAAAAATTATAA
1 AAAAAATTATAA
3828869 AAA
1 AAA
3828872 TGCAAACATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (12 bp):
AAAAAATTATAA
Found at i:3841225 original size:33 final size:33
Alignment explanation
Indices: 3841183--3841248 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
3841173 GAACTATTAT
3841183 ATATTTGAAACTAAAGTTATGAAACCTAATTGA
1 ATATTTGAAACTAAAGTTATGAAACCTAATTGA
3841216 ATATTTGAAACTAAAGTTATGAAACCTAATTGA
1 ATATTTGAAACTAAAGTTATGAAACCTAATTGA
3841249 CTAGTCTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.12, T:0.33
Consensus pattern (33 bp):
ATATTTGAAACTAAAGTTATGAAACCTAATTGA
Found at i:3845990 original size:32 final size:32
Alignment explanation
Indices: 3845950--3846021 Score: 108
Period size: 32 Copynumber: 2.2 Consensus size: 32
3845940 TGATATATAC
* * * *
3845950 TTATTTAATATTGAAGGCAATTGTTGTTCTTT
1 TTATTTAATATTAAAGGAAAATGTTATTCTTT
3845982 TTATTTAATATTAAAGGAAAATGTTATTCTTT
1 TTATTTAATATTAAAGGAAAATGTTATTCTTT
3846014 TTATTTAA
1 TTATTTAA
3846022 ATGATATGTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.32, C:0.04, G:0.11, T:0.53
Consensus pattern (32 bp):
TTATTTAATATTAAAGGAAAATGTTATTCTTT
Found at i:3846492 original size:74 final size:74
Alignment explanation
Indices: 3846366--3846519 Score: 254
Period size: 74 Copynumber: 2.1 Consensus size: 74
3846356 TACTAGAGGA
* * *
3846366 GAATGCTCCTATTTTATTACATTCACTGATGTTTATATAAGATATGGTTATGTGCATTTAATGAA
1 GAAT-CTCCTATTTCATTACATTCACTGATGTTCATACAAGATATGGTTATGTGCATTTAATGAA
3846431 ACACAAGTTT
65 ACACAAGTTT
*
3846441 GAATCTCCTATTTCATTACATTCACTGATGTTCATACAAGATATGGTTATGTGTATTTAATGAAA
1 GAATCTCCTATTTCATTACATTCACTGATGTTCATACAAGATATGGTTATGTGCATTTAATGAAA
3846506 CACAAGTTT
66 CACAAGTTT
*
3846515 AAATC
1 GAATC
3846520 CTTTGAAAAG
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
74 70 0.95
75 4 0.05
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (74 bp):
GAATCTCCTATTTCATTACATTCACTGATGTTCATACAAGATATGGTTATGTGCATTTAATGAAA
CACAAGTTT
Found at i:3852537 original size:22 final size:22
Alignment explanation
Indices: 3852506--3852547 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3852496 TTAATATTCG
3852506 TTTAATTTTCAAGTTCATTTACT
1 TTTAATTTTCAAGTT-ATTTACT
*
3852529 TTTAA-TTTCATGTTATTTA
1 TTTAATTTTCAAGTTATTTA
3852548 GCTCTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.60
Consensus pattern (22 bp):
TTTAATTTTCAAGTTATTTACT
Found at i:3852655 original size:15 final size:15
Alignment explanation
Indices: 3852627--3852668 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
3852617 TTTCATGCTT
3852627 TCTTTAATTTTCAA-C
1 TCTTTAA-TTTCAAGC
*
3852642 TACTTTAGTTTCAAGC
1 T-CTTTAATTTCAAGC
3852658 TCTTTAATTTC
1 TCTTTAATTTC
3852669 TTGGCACTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.24, C:0.19, G:0.05, T:0.52
Consensus pattern (15 bp):
TCTTTAATTTCAAGC
Found at i:3856905 original size:16 final size:16
Alignment explanation
Indices: 3856884--3857013 Score: 53
Period size: 16 Copynumber: 8.3 Consensus size: 16
3856874 TCATACTCCC
3856884 TTTAATTTTTATGCTA
1 TTTAATTTTTATGCTA
*
3856900 TTTAATTTTCATG-TA
1 TTTAATTTTTATGCTA
* * * *
3856915 CTTT-AGTTTCAAGCTC
1 -TTTAATTTTTATGCTA
*
3856931 TTTAATTTCCT-TGC-A
1 TTTAATTT-TTATGCTA
*
3856946 -TTATATGTTTTATGCAA
1 TTTA-AT-TTTTATGCTA
*
3856963 TTTAATTTTGCATGCTA
1 TTTAATTTT-TATGCTA
3856980 TTT-ATTTTT-TCGC-A
1 TTTAATTTTTAT-GCTA
* *
3856994 TTT-ACTTTTATGTTA
1 TTTAATTTTTATGCTA
3857009 TTTAA
1 TTTAA
3857014 AATTTCATAT
Statistics
Matches: 85, Mismatches: 15, Indels: 28
0.66 0.12 0.22
Matches are distributed among these distances:
14 14 0.16
15 22 0.26
16 35 0.41
17 11 0.13
18 3 0.04
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.57
Consensus pattern (16 bp):
TTTAATTTTTATGCTA
Found at i:3859662 original size:7 final size:7
Alignment explanation
Indices: 3859618--3859655 Score: 58
Period size: 7 Copynumber: 5.3 Consensus size: 7
3859608 TAATTTTGTT
3859618 AATAAAA
1 AATAAAA
3859625 AATAAAA
1 AATAAAA
3859632 AATAAAA
1 AATAAAA
*
3859639 AACAAAA
1 AATAAAA
3859646 AATGAAAA
1 AAT-AAAA
3859654 AA
1 AA
3859656 AAGAAAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
7 22 0.79
8 6 0.21
ACGTcount: A:0.84, C:0.03, G:0.03, T:0.11
Consensus pattern (7 bp):
AATAAAA
Found at i:3861175 original size:45 final size:46
Alignment explanation
Indices: 3861089--3861192 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 46
3861079 CCAAAAATTT
3861089 TAAAAAGAAAATTTCTAAATAAACCCAAATAGTGAAAAATTTAGAAA
1 TAAAAA-AAAATTTCTAAATAAACCCAAATAGTGAAAAATTTAGAAA
** * * *
3861136 TAAAAAAAAATTT-TAAATTGACCGAAATGGTGGAAAATTTAGAAA
1 TAAAAAAAAATTTCTAAATAAACCCAAATAGTGAAAAATTTAGAAA
3861181 TAAAATAAAAAT
1 TAAAA-AAAAAT
3861193 AAAAATAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
45 32 0.63
46 13 0.25
47 6 0.12
ACGTcount: A:0.59, C:0.06, G:0.11, T:0.25
Consensus pattern (46 bp):
TAAAAAAAAATTTCTAAATAAACCCAAATAGTGAAAAATTTAGAAA
Found at i:3861193 original size:6 final size:6
Alignment explanation
Indices: 3861178--3861207 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
3861168 GAAAATTTAG
3861178 AAAT-A AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA AAATAA A
3861208 TCCAGATGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:3862818 original size:19 final size:18
Alignment explanation
Indices: 3862794--3862833 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
3862784 AGATGCACTA
*
3862794 CTATAGTAGTTCACATACC
1 CTATAG-AGTACACATACC
*
3862813 CTATAGGGTACACATACC
1 CTATAGAGTACACATACC
3862831 CTA
1 CTA
3862834 AAATGCCATC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (18 bp):
CTATAGAGTACACATACC
Found at i:3865360 original size:9 final size:9
Alignment explanation
Indices: 3865341--3865373 Score: 50
Period size: 8 Copynumber: 3.7 Consensus size: 9
3865331 ATAATGAGTG
3865341 AAAAATGGAA
1 AAAAAT-GAA
3865351 AAAAATG-A
1 AAAAATGAA
3865359 AAAAATGAA
1 AAAAATGAA
3865368 AAAAAT
1 AAAAAT
3865374 CAATAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
9 8 0.36
10 6 0.27
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (9 bp):
AAAAATGAA
Found at i:3865361 original size:8 final size:8
Alignment explanation
Indices: 3865350--3865459 Score: 61
Period size: 8 Copynumber: 13.6 Consensus size: 8
3865340 GAAAAATGGA
3865350 AAAAAATG
1 AAAAAATG
3865358 AAAAAATG
1 AAAAAATG
*
3865366 AAAAAAATC
1 -AAAAAATG
*
3865375 AATAATTAATAT
1 AA-AA--AAT-G
*
3865387 AAAAAAAG
1 AAAAAATG
*
3865395 -AGAAATG
1 AAAAAATG
3865402 -AAAAA-G
1 AAAAAATG
*
3865408 AAAAACA-A
1 AAAAA-ATG
3865416 AAAAAATG
1 AAAAAATG
*
3865424 GAAAAAT-
1 AAAAAATG
3865431 AAAAAATG
1 AAAAAATG
3865439 -AAAAATG
1 AAAAAATG
3865446 AAAAAATG
1 AAAAAATG
3865454 TAAAAA
1 -AAAAA
3865460 GAGAGAAGAA
Statistics
Matches: 80, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
6 1 0.01
7 27 0.34
8 29 0.36
9 16 0.20
11 5 0.06
12 2 0.03
ACGTcount: A:0.75, C:0.02, G:0.10, T:0.14
Consensus pattern (8 bp):
AAAAAATG
Found at i:3865361 original size:17 final size:17
Alignment explanation
Indices: 3865341--3865451 Score: 62
Period size: 15 Copynumber: 6.8 Consensus size: 17
3865331 ATAATGAGTG
3865341 AAAAATGGAAAAAAATGA
1 AAAAAT-GAAAAAAATGA
*
3865359 AAAAATGAAAAAAATCA
1 AAAAATGAAAAAAATGA
*
3865376 ATAATTAAT-ATAAAAAAAG-
1 A-AA--AATGA-AAAAAATGA
*
3865395 AGAAATG--AAAAA-GA
1 AAAAATGAAAAAAATGA
*
3865409 AAAACA--AAAAAAATGG
1 AAAA-ATGAAAAAAATGA
3865425 AAAAAT--AAAAAATG-
1 AAAAATGAAAAAAATGA
3865439 AAAAATGAAAAAA
1 AAAAATGAAAAAA
3865452 TGTAAAAAGA
Statistics
Matches: 74, Mismatches: 6, Indels: 28
0.69 0.06 0.26
Matches are distributed among these distances:
13 1 0.01
14 14 0.19
15 15 0.20
16 13 0.18
17 11 0.15
18 9 0.12
19 2 0.03
20 9 0.12
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.13
Consensus pattern (17 bp):
AAAAATGAAAAAAATGA
Found at i:3865412 original size:22 final size:21
Alignment explanation
Indices: 3865387--3865451 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
3865377 TAATTAATAT
*
3865387 AAAAAAAGAGAAATGAAAAAGA
1 AAAAAAAGAAAAATGAAAAA-A
*
3865409 AAAACAAA-AAAAATGGAAAAAT
1 AAAA-AAAGAAAAAT-GAAAAAA
*
3865431 AAAAAATGAAAAATGAAAAAA
1 AAAAAAAGAAAAATGAAAAAA
3865452 TGTAAAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
21 8 0.22
22 19 0.53
23 9 0.25
ACGTcount: A:0.78, C:0.02, G:0.12, T:0.08
Consensus pattern (21 bp):
AAAAAAAGAAAAATGAAAAAA
Found at i:3865437 original size:15 final size:16
Alignment explanation
Indices: 3865416--3865459 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 16
3865406 AGAAAAACAA
3865416 AAAAAATGGAAAAAT-
1 AAAAAATGGAAAAATG
3865431 AAAAAAT-GAAAAATG
1 AAAAAATGGAAAAATG
*
3865446 AAAAAATGTAAAAA
1 AAAAAATGGAAAAA
3865460 GAGAGAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 7 0.27
15 14 0.54
16 5 0.19
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (16 bp):
AAAAAATGGAAAAATG
Found at i:3865452 original size:22 final size:22
Alignment explanation
Indices: 3865397--3865459 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 22
3865387 AAAAAAAGAG
3865397 AAATGAAAAA-GAAAAACAAAAA
1 AAATGAAAAATGAAAAA-AAAAA
**
3865419 AAATGGAAAAAT-AAAAAATGAA
1 AAAT-GAAAAATGAAAAAAAAAA
*
3865441 AAATGAAAAAATGTAAAAA
1 AAATG-AAAAATGAAAAAA
3865460 GAGAGAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
21 1 0.03
22 17 0.50
23 16 0.47
ACGTcount: A:0.76, C:0.02, G:0.11, T:0.11
Consensus pattern (22 bp):
AAATGAAAAATGAAAAAAAAAA
Found at i:3866689 original size:20 final size:20
Alignment explanation
Indices: 3866636--3866681 Score: 83
Period size: 20 Copynumber: 2.3 Consensus size: 20
3866626 TAGATTATTA
*
3866636 CATTTGTATAATTAAGAATG
1 CATTTGTATAATTAAGAAAG
3866656 CATTTGTATAATTAAGAAAG
1 CATTTGTATAATTAAGAAAG
3866676 CATTTG
1 CATTTG
3866682 CATCATTATC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.39, C:0.07, G:0.15, T:0.39
Consensus pattern (20 bp):
CATTTGTATAATTAAGAAAG
Found at i:3866830 original size:33 final size:33
Alignment explanation
Indices: 3866764--3866833 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
3866754 TTAGAGGAAA
* * *
3866764 GCATAGCATGCATTGCATTTCTAAATATTTAGT
1 GCATAGCATACATTGCATTTCAAAATATCTAGT
*
3866797 GCATAGCATACATTGCATTT-AAGAATGTCTAGT
1 GCATAGCATACATTGCATTTCAA-AATATCTAGT
3866830 GCAT
1 GCAT
3866834 GAAAGAGGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 1 0.03
33 31 0.97
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (33 bp):
GCATAGCATACATTGCATTTCAAAATATCTAGT
Found at i:3867185 original size:44 final size:44
Alignment explanation
Indices: 3867110--3867434 Score: 246
Period size: 44 Copynumber: 7.3 Consensus size: 44
3867100 GATTGTCAAA
* * * * *
3867110 GAGCTTTATTTA-TTTTTCAAAATTGTTGAGCCTCTGCTTAAAT
1 GAGCTTTATTTATTTTTTGAAAGTCGTTGAGCCTTTGCTTAAAG
* ** *
3867153 GAGCTTTATTTATTTTTTGAAAGTTGTTGAGCCTTTATTTGAAG
1 GAGCTTTATTTATTTTTTGAAAGTCGTTGAGCCTTTGCTTAAAG
* * * *
3867197 GAGCTTTATTTAATTTTTG-ACGTCATTGAGCCTCTGCTTAAAG
1 GAGCTTTATTTATTTTTTGAAAGTCGTTGAGCCTTTGCTTAAAG
* *
3867240 GAGTTTTATTTATTTTTT-AAAGTCGTTAAGCTTCTGAGCCTTTGCTTAGAG
1 GAGCTTTATTTATTTTTTGAAAGTC-----G--T-TGAGCCTTTGCTTAAAG
* * * ** * * *
3867291 TATCCTTATTTATTTTTAAAAAGTCGTTGAGCCTCTGTTTAGAG
1 GAGCTTTATTTATTTTTTGAAAGTCGTTGAGCCTTTGCTTAAAG
* * * * *
3867335 GAGCTTTATTTATTTTTCG-AAGTAGTTGAGCCTTTGTTTAGAT
1 GAGCTTTATTTATTTTTTGAAAGTCGTTGAGCCTTTGCTTAAAG
** * *
3867378 GAGCTTTATTTATTTTTCAAAAGTCCTTGAGCCTTTACTTAAAG
1 GAGCTTTATTTATTTTTTGAAAGTCGTTGAGCCTTTGCTTAAAG
3867422 GAG-TCTTATTTAT
1 GAGCT-TTATTTAT
3867435 GAGCCTCTGT
Statistics
Matches: 226, Mismatches: 43, Indels: 25
0.77 0.15 0.09
Matches are distributed among these distances:
43 89 0.39
44 100 0.44
45 1 0.00
47 1 0.00
50 1 0.00
51 28 0.12
52 6 0.03
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.46
Consensus pattern (44 bp):
GAGCTTTATTTATTTTTTGAAAGTCGTTGAGCCTTTGCTTAAAG
Done.