Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 22 of 226
Found at i:9943816 original size:12 final size:11
Alignment explanation
Indices: 9943777--9943818 Score: 59
Period size: 10 Copynumber: 3.8 Consensus size: 11
9943767 TGAGAGAATT
*
9943777 TTGAAAGGAAA
1 TTGAGAGGAAA
9943788 TTGAGAGG-AA
1 TTGAGAGGAAA
9943798 TTGAGAGGAAA
1 TTGAGAGGAAA
9943809 TATGAGAGGA
1 T-TGAGAGGA
9943819 TTTGTTTGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 10 0.36
11 10 0.36
12 8 0.29
ACGTcount: A:0.45, C:0.00, G:0.36, T:0.19
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:9954366 original size:26 final size:25
Alignment explanation
Indices: 9954318--9954392 Score: 78
Period size: 25 Copynumber: 2.8 Consensus size: 25
9954308 TGACTAATGG
*
9954318 AGGTGCCAACTTGAGAAAAAAAATAGTTT
1 AGGTACCAACTTGAG---AAAAA-AGTTT
9954347 AGGTACACAACTTGAGAAAAAAGTTT
1 AGGTAC-CAACTTGAGAAAAAAGTTT
* *
9954373 AGGTACCAATTTGGGAAAAA
1 AGGTACCAACTTGAGAAAAA
9954393 GAGTATAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
25 12 0.29
26 11 0.26
27 5 0.12
29 5 0.12
30 9 0.21
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (25 bp):
AGGTACCAACTTGAGAAAAAAGTTT
Found at i:9958629 original size:236 final size:236
Alignment explanation
Indices: 9958216--9958690 Score: 871
Period size: 236 Copynumber: 2.0 Consensus size: 236
9958206 ACAAAAGCTC
* *
9958216 ATCTATGAGTATTAGCTAGAGTACAGTAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
1 ATCTATGAGAATTAGCTAGAGTACAGCAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
*
9958281 GAAGAGAGAAAAACAAAAAGGAGTAAAACACACCAGTCAAAATTCTACTTTTCACAAAATATTTT
66 GAAGAGAGAAAAACAAAAAGGAGTAAAACACACCAGTCAAAAGTCTACTTTTCACAAAATATTTT
* *
9958346 TTTTTCTTAAAACTGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
131 ATTTTCTTAAAAATGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
9958411 ACTGCC-AACAAGTTCTTACAATATGTAAATACTAAAATTTA
196 ACTGCCGAA-AAGTTCTTACAATATGTAAATACTAAAATTTA
9958452 ATCTATGAGAATTAGCTAGAGTACAGCAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
1 ATCTATGAGAATTAGCTAGAGTACAGCAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
* *
9958517 GAAGAGAGAAAAAGAAAAAGGAGTAAAACACACCAGTCAAAAGTCTACTTTTCACTAAATATTTT
66 GAAGAGAGAAAAACAAAAAGGAGTAAAACACACCAGTCAAAAGTCTACTTTTCACAAAATATTTT
9958582 ATTTTCTTAAAAATGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
131 ATTTTCTTAAAAATGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
9958647 ACTGCCGAAAAGTTCTTACAATATGTAAATACTAAAATTTA
196 ACTGCCGAAAAGTTCTTACAATATGTAAATACTAAAATTTA
9958688 ATC
1 ATC
9958691 GTGAAGTATA
Statistics
Matches: 231, Mismatches: 7, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
236 229 0.99
237 2 0.01
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (236 bp):
ATCTATGAGAATTAGCTAGAGTACAGCAACAGATAAAAACTAATTACATAAAAATCAGTCTAAAA
GAAGAGAGAAAAACAAAAAGGAGTAAAACACACCAGTCAAAAGTCTACTTTTCACAAAATATTTT
ATTTTCTTAAAAATGGGGGAAGGGGAGGACTTCCAGCGATGTGCAGAAAATCTTCAGATGTTGCT
ACTGCCGAAAAGTTCTTACAATATGTAAATACTAAAATTTA
Found at i:9962625 original size:19 final size:19
Alignment explanation
Indices: 9962455--9962630 Score: 83
Period size: 19 Copynumber: 9.2 Consensus size: 19
9962445 AAATATGTAT
* *
9962455 AAAATCATAACAACTTATA
1 AAAATTATAAAAACTTATA
* * *
9962474 AATATTATAAAACCCTATA
1 AAAATTATAAAAACTTATA
* *
9962493 AAAATTCTAATAAA-TTAAA
1 AAAATTATAA-AAACTTATA
* *
9962512 AAAATAATAAGAAA-ATATA
1 AAAATTATAA-AAACTTATA
* *
9962531 AAACA-TATAAATAAATATTTA
1 AAA-ATTATAAA-AACT-TATA
* * *
9962552 AAATTTTATATAAACTTACA
1 AAA-ATTATAAAAACTTATA
9962572 AAAATTATAAAAA--TATA
1 AAAATTATAAAAACTTATA
** * **
9962589 AAAAAAATCAAATTTTATA
1 AAAATTATAAAAACTTATA
*
9962608 AATATTATAAAAACTTATA
1 AAAATTATAAAAACTTATA
9962627 AAAA
1 AAAA
9962631 ATCATACTTT
Statistics
Matches: 111, Mismatches: 38, Indels: 16
0.67 0.23 0.10
Matches are distributed among these distances:
17 12 0.11
18 1 0.01
19 76 0.68
20 8 0.07
21 9 0.08
22 5 0.05
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.31
Consensus pattern (19 bp):
AAAATTATAAAAACTTATA
Found at i:9962627 original size:10 final size:9
Alignment explanation
Indices: 9962455--9962630 Score: 68
Period size: 10 Copynumber: 18.4 Consensus size: 9
9962445 AAATATGTAT
*
9962455 AAAATCATA
1 AAAATTATA
*
9962464 ACAACTTATA
1 A-AAATTATA
*
9962474 AATATTATA
1 AAAATTATA
**
9962483 AAACCCTATA
1 AAA-ATTATA
*
9962493 AAAATTCTA
1 AAAATTATA
*
9962502 ATAAATTAAA
1 A-AAATTATA
*
9962512 AAAATAATA
1 AAAATTATA
*
9962521 AGAAAATATA
1 A-AAATTATA
9962531 AAACA-TATAA
1 AAA-ATTAT-A
*
9962541 ATAAATATTTA
1 A-AAAT-TATA
*
9962552 AAATTTTATA
1 AAA-ATTATA
* *
9962562 TAAACTTACA
1 -AAAATTATA
9962572 AAAATTATA
1 AAAATTATA
9962581 AAAA-TATA
1 AAAATTATA
**
9962589 AAAAAAATCA
1 AAAATTAT-A
**
9962599 AATTTTATA
1 AAAATTATA
*
9962608 AATATTATA
1 AAAATTATA
9962617 AAAACTTATA
1 AAAA-TTATA
9962627 AAAA
1 AAAA
9962631 ATCATACTTT
Statistics
Matches: 123, Mismatches: 30, Indels: 27
0.68 0.17 0.15
Matches are distributed among these distances:
8 8 0.07
9 50 0.41
10 55 0.45
11 8 0.07
12 2 0.02
ACGTcount: A:0.62, C:0.07, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:9964259 original size:29 final size:31
Alignment explanation
Indices: 9964212--9964273 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 31
9964202 TTAATTTAAT
* * *
9964212 GTGCAATTGTATACATG-AACTTTAATT-TG
1 GTGCAATTATACACATGAAACTCTAATTGTG
*
9964241 GTGCAATTATACACGTGAAACTCTAATTGTG
1 GTGCAATTATACACATGAAACTCTAATTGTG
9964272 GT
1 GT
9964274 TTAAATGTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 14 0.52
30 9 0.33
31 4 0.15
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (31 bp):
GTGCAATTATACACATGAAACTCTAATTGTG
Found at i:9969191 original size:13 final size:13
Alignment explanation
Indices: 9969173--9969199 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
9969163 ACAAGCAATC
9969173 TGTAAGTAGAATT
1 TGTAAGTAGAATT
9969186 TGTAAGTAGAATT
1 TGTAAGTAGAATT
9969199 T
1 T
9969200 CCTGTTCTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.22, T:0.41
Consensus pattern (13 bp):
TGTAAGTAGAATT
Found at i:9977195 original size:21 final size:21
Alignment explanation
Indices: 9977154--9977195 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
9977144 CTTCCTCCAT
*
9977154 CTCCTCTTCATCAATTTCTTC
1 CTCCTCTTCATCAATTACTTC
9977175 CTCCTCTTCATC-ATATACTTC
1 CTCCTCTTCATCAAT-TACTTC
9977196 TTCTTCTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.17, C:0.38, G:0.00, T:0.45
Consensus pattern (21 bp):
CTCCTCTTCATCAATTACTTC
Found at i:9978719 original size:6 final size:6
Alignment explanation
Indices: 9978708--9978732 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9978698 GCTATAAATT
9978708 ATACAC ATACAC ATACAC ATACAC A
1 ATACAC ATACAC ATACAC ATACAC A
9978733 CGCACACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (6 bp):
ATACAC
Found at i:9980799 original size:3 final size:3
Alignment explanation
Indices: 9980791--9980824 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
9980781 TGCATTTTCG
9980791 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
1 AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT AGT A
9980825 AAGTTTCTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
AGT
Found at i:10012518 original size:27 final size:26
Alignment explanation
Indices: 10012473--10012523 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 26
10012463 AAAATTAAAT
*
10012473 ATAAAATATTTTAGTAATATGAAAAAA
1 ATAAAATATTTTAGAAATAT-AAAAAA
10012500 ATAAAATCATTTTA-AAATATAAAA
1 ATAAAAT-ATTTTAGAAATATAAAA
10012524 GTAACTTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 4 0.18
27 12 0.55
28 6 0.27
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (26 bp):
ATAAAATATTTTAGAAATATAAAAAA
Found at i:10013108 original size:29 final size:27
Alignment explanation
Indices: 10013031--10013113 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 27
10013021 ATATACCGAA
* *
10013031 AAAAAACTAAGAAAAAAAATT-AAATTT
1 AAAAAACT-ATAAAAATAATTAAAATTT
10013058 AAAAATACT-TAAATCAATAATTAAAATTT
1 AAAAA-ACTATAAA--AATAATTAAAATTT
10013087 AAAAAACTGATAAAAATGAATTGAAAA
1 AAAAAACT-ATAAAAAT-AATT-AAAA
10013114 AGAAAAACTA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
26 3 0.07
27 5 0.11
28 15 0.33
29 15 0.33
30 8 0.17
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.25
Consensus pattern (27 bp):
AAAAAACTATAAAAATAATTAAAATTT
Found at i:10013243 original size:20 final size:20
Alignment explanation
Indices: 10013207--10013246 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
10013197 CTGGAATTTG
10013207 ATTAAAAATTAAGAAATAGA
1 ATTAAAAATTAAGAAATAGA
10013227 ATTAGAAAATTAA-AAATAGA
1 ATTA-AAAATTAAGAAATAGA
10013247 GAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (20 bp):
ATTAAAAATTAAGAAATAGA
Found at i:10013256 original size:21 final size:21
Alignment explanation
Indices: 10013210--10013256 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
10013200 GAATTTGATT
**
10013210 AAAAATTAAGAAATAGAATTA
1 AAAAATTAAGAAATAGAAAAA
*
10013231 GAAAATTAA-AAATAGAGAAAA
1 AAAAATTAAGAAATAGA-AAAA
10013252 AAAAA
1 AAAAA
10013257 AGAAAAAAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (21 bp):
AAAAATTAAGAAATAGAAAAA
Found at i:10016891 original size:40 final size:39
Alignment explanation
Indices: 10016835--10016969 Score: 139
Period size: 40 Copynumber: 3.4 Consensus size: 39
10016825 ACCAGTTTGG
*
10016835 CACCCAGTGCCTCATCGGATAATTTGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGATAATCTGAAGT-ATAAATTGA
* * * * * *
10016875 TACCCAATGTCTCATCGGCTAAACTGAAG--TAAATTGG
1 CACCCAGTGCCTCATCGGATAATCTGAAGTATAAATTGA
* *
10016912 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATCTGAAGTA-TAAATTGA
*
10016953 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
10016970 ACTCGAAGTC
Statistics
Matches: 75, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
37 21 0.28
38 8 0.11
40 23 0.31
41 23 0.31
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (39 bp):
CACCCAGTGCCTCATCGGATAATCTGAAGTATAAATTGA
Found at i:10016957 original size:41 final size:40
Alignment explanation
Indices: 10016835--10016970 Score: 134
Period size: 41 Copynumber: 3.5 Consensus size: 40
10016825 ACCAGTTTGG
* * *
10016835 CACCCAGTGCCTCATCGGATAATTTGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGAATAATCTGAAGTAGTAAATTGA
* * * ** * *
10016875 TACCCAATGTCTCATCGGCTAAACTG-A--AGTAAATTGG
1 CACCCAGTGCCTCATCGAATAATCTGAAGTAGTAAATTGA
*
10016912 CACCCAGTGCCTCATCGAATTAATCCGAAGTAGTAAATTGA
1 CACCCAGTGCCTCATCGAA-TAATCTGAAGTAGTAAATTGA
*
10016953 CACCCAGTGTCTCATCGA
1 CACCCAGTGCCTCATCGA
10016971 CTCGAAGTCG
Statistics
Matches: 75, Mismatches: 17, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
37 22 0.29
38 5 0.07
39 2 0.03
40 20 0.27
41 26 0.35
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.26
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGAATAATCTGAAGTAGTAAATTGA
Found at i:10017502 original size:18 final size:19
Alignment explanation
Indices: 10017476--10017511 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
10017466 TAAAATAAAT
*
10017476 TTAACTCCCT-AATTTCAC
1 TTAAATCCCTAAATTTCAC
10017494 TTAAATCCCTAAATTTCA
1 TTAAATCCCTAAATTTCA
10017512 AAATTTTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATCCCTAAATTTCAC
Found at i:10017809 original size:11 final size:10
Alignment explanation
Indices: 10017793--10017854 Score: 54
Period size: 11 Copynumber: 5.8 Consensus size: 10
10017783 GTCTTTCTCC
10017793 TTTTCTTTCCT
1 TTTTCTTT-CT
10017804 TTTTCTTTCT
1 TTTTCTTTCT
10017814 TTTTCCTTT-T
1 TTTT-CTTTCT
10017824 TGTTTCGTTTCT
1 T-TTTC-TTTCT
* *
10017836 ATCTTGTTTCT
1 -TTTTCTTTCT
10017847 TTTTCTTT
1 TTTTCTTT
10017855 TATTTAATCG
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 15 0.36
11 23 0.55
12 3 0.07
13 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.05, T:0.74
Consensus pattern (10 bp):
TTTTCTTTCT
Found at i:10017890 original size:18 final size:17
Alignment explanation
Indices: 10017868--10017901 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
10017858 TTAATCGTTT
10017868 TATTATTAT-ATA-ATA
1 TATTATTATAATATATA
10017883 TATTATTATAATATATA
1 TATTATTATAATATATA
10017900 TA
1 TA
10017902 CTAAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 3 0.18
17 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATTATTATAATATATA
Found at i:10017894 original size:13 final size:13
Alignment explanation
Indices: 10017871--10017925 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
10017861 ATCGTTTTAT
10017871 TATTA-TATAATA
1 TATTATTATAATA
10017883 TATTATTATAATA
1 TATTATTATAATA
*
10017896 TATATACTA-AATA
1 TAT-TATTATAATA
10017909 TATTTTATTATAATA
1 TA--TTATTATAATA
10017924 TA
1 TA
10017926 CATTAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
12 5 0.14
13 16 0.44
14 8 0.22
15 7 0.19
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (13 bp):
TATTATTATAATA
Found at i:10017932 original size:26 final size:27
Alignment explanation
Indices: 10017880--10017933 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
10017870 TTATTATATA
*
10017880 ATATATTATTATAATATATATACTAAAT
1 ATATATTATTATAATATACATA-TAAAT
*
10017908 ATATTTTATTATAATATACAT-TAAAT
1 ATATATTATTATAATATACATATAAAT
10017934 TTTACATAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
28 19 0.79
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATATTATTATAATATACATATAAAT
Found at i:10018145 original size:13 final size:13
Alignment explanation
Indices: 10018127--10018162 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
10018117 ACTAACTTCG
10018127 TAAATATTTATAA
1 TAAATATTTATAA
*
10018140 TAAATATTTATTA
1 TAAATATTTATAA
10018153 TAAATATTTA
1 TAAATATTTA
10018163 CGAGTCTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAAATATTTATAA
Found at i:10019614 original size:135 final size:135
Alignment explanation
Indices: 10019449--10019723 Score: 523
Period size: 135 Copynumber: 2.0 Consensus size: 135
10019439 CCCCGACTCA
10019449 GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATGACATGTGTCTGGGTTGAGTCAATTTTTGA
1 GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATGACATGTGTCTGGGTTGAGTCAATTTTTGA
*
10019514 CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATATGTTTGA
66 CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATATGTTTAA
10019579 ATTAT
131 ATTAT
*
10019584 GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATGACATGTGTCTGGGTTTAGTCAATTTTTGA
1 GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATGACATGTGTCTGGGTTGAGTCAATTTTTGA
10019649 CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATATGTTTAA
66 CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATATGTTTAA
*
10019714 ATTGT
131 ATTAT
10019719 GCAAA
1 GCAAA
10019724 CTAGGTTGTC
Statistics
Matches: 137, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
135 137 1.00
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (135 bp):
GCAAAATTTGTGTAATTCTGTTTTGTTTTAAGTATGACATGTGTCTGGGTTGAGTCAATTTTTGA
CATAATATGTGACTTATGAACTTTTGGAGTTGGAATTGGTATTTTGAAAGTGACTATATGTTTAA
ATTAT
Found at i:10022774 original size:25 final size:24
Alignment explanation
Indices: 10022745--10022791 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
10022735 TATAGCCCTG
10022745 ATAAGCTTCCTATTACATGGCTCAC
1 ATAAGCTTCCT-TTACATGGCTCAC
*
10022770 ATAAGCTTCCTTTATATGGCTC
1 ATAAGCTTCCTTTACATGGCTC
10022792 GAGAGAGTGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.36
Consensus pattern (24 bp):
ATAAGCTTCCTTTACATGGCTCAC
Found at i:10027353 original size:21 final size:20
Alignment explanation
Indices: 10027324--10027362 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
10027314 TTAGAAATGT
10027324 TTTCATTTT-GTCTTTTTTAA
1 TTTCATTTTAGT-TTTTTTAA
10027344 TTTCAATTTTAGTTTTTTT
1 TTTC-ATTTTAGTTTTTTT
10027363 CAACTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 4 0.24
21 11 0.65
22 2 0.12
ACGTcount: A:0.15, C:0.08, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTCATTTTAGTTTTTTTAA
Found at i:10043629 original size:14 final size:15
Alignment explanation
Indices: 10043604--10043632 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
10043594 ATGGTTACTC
10043604 TTTTTAATAATTTTA
1 TTTTTAATAATTTTA
10043619 TTTTTAA-AATTTTA
1 TTTTTAATAATTTTA
10043633 ACTTCATTCT
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:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTTTAATAATTTTA
Found at i:10045046 original size:85 final size:87
Alignment explanation
Indices: 10044840--10045054 Score: 208
Period size: 85 Copynumber: 2.5 Consensus size: 87
10044830 GCCTAAAGTG
* * * *
10044840 TAAAAAA-ACCCT-AAACTTTTTCAAAAAAAGTAATTAAGTCTTTGTTTTTTTTTTCACTTAATT
1 TAAAAAATACCCTCAAACTTTTTCAAAAAAAGCAATTAAG-C-CTGTTTTTTTTGTCACTCAATT
** *
10044903 AGATACTTAAGCTTTCAAAATGTA
64 AGATACTTAAAATTTCAAAATGCA
** ****
10044927 TAAAAAATGTCCTC-AACTTAAAAAAAGAAGAAGCAATTAAGCCT-TTTTTTTTGT-ACTCAATT
1 TAAAAAATACCCTCAAACTTTTTCAAA-AA-AAGCAATTAAGCCTGTTTTTTTTGTCACTCAATT
*
10044989 -GGTACTTAAAATTTCAAAATGCA
64 AGATACTTAAAATTTCAAAATGCA
*
10045012 TAAAAAAATACCCTCAAACTTTTTCAAAAAAAGCAAGTAAGCC
1 T-AAAAAATACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCC
10045055 ACTACTTTTT
Statistics
Matches: 101, Mismatches: 21, Indels: 14
0.74 0.15 0.10
Matches are distributed among these distances:
85 32 0.32
86 20 0.20
87 24 0.24
88 12 0.12
89 3 0.03
90 10 0.10
ACGTcount: A:0.43, C:0.15, G:0.08, T:0.34
Consensus pattern (87 bp):
TAAAAAATACCCTCAAACTTTTTCAAAAAAAGCAATTAAGCCTGTTTTTTTTGTCACTCAATTAG
ATACTTAAAATTTCAAAATGCA
Found at i:10045249 original size:19 final size:20
Alignment explanation
Indices: 10045227--10045271 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
10045217 AAAATTATAA
10045227 AAAAAACAATAAATGTT-AT
1 AAAAAACAATAAATGTTAAT
** *
10045246 AAAAATTAATAAATTTTAAT
1 AAAAAACAATAAATGTTAAT
10045266 AAAAAA
1 AAAAAA
10045272 GTAAAAAATA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
AAAAAACAATAAATGTTAAT
Found at i:10045314 original size:20 final size:19
Alignment explanation
Indices: 10045264--10045355 Score: 73
Period size: 18 Copynumber: 4.7 Consensus size: 19
10045254 ATAAATTTTA
10045264 ATAAAAA-AGTAAAAAATAT
1 ATAAAAATA-TAAAAAATAT
*
10045283 TTAAAAAT-TAAAAAATAT
1 ATAAAAATATAAAAAATAT
*
10045301 ATAAAAATCATAAAATAT-T
1 ATAAAAAT-ATAAAAAATAT
* *
10045320 GTAAAAATTTATAAAAATCAT
1 ATAAAAATATA-AAAAAT-AT
*
10045341 AAAAAAATTATAAAA
1 ATAAAAA-TATAAAA
10045356 TGCATCAAAA
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
18 19 0.33
19 19 0.33
20 7 0.12
21 9 0.16
22 3 0.05
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (19 bp):
ATAAAAATATAAAAAATAT
Found at i:10045355 original size:10 final size:10
Alignment explanation
Indices: 10045264--10045355 Score: 54
Period size: 10 Copynumber: 9.6 Consensus size: 10
10045254 ATAAATTTTA
*
10045264 ATAAAAAAGT
1 ATAAAAAATT
10045274 A-AAAAATATT
1 ATAAAAA-ATT
10045284 -T-AAAAA-T
1 ATAAAAAATT
10045291 -TAAAAAA-T
1 ATAAAAAATT
*
10045299 ATATAAAAATC
1 ATA-AAAAATT
*
10045310 ATAAAATATT
1 ATAAAAAATT
* *
10045320 GTAAAAATTT
1 ATAAAAAATT
*
10045330 AT-AAAAATC
1 ATAAAAAATT
10045339 ATAAAAAAATT
1 AT-AAAAAATT
10045350 ATAAAA
1 ATAAAA
10045356 TGCATCAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 16
0.70 0.12 0.18
Matches are distributed among these distances:
7 2 0.03
8 7 0.11
9 18 0.29
10 25 0.40
11 11 0.17
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:10045355 original size:29 final size:28
Alignment explanation
Indices: 10045285--10045356 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 28
10045275 AAAAATATTT
*
10045285 AAAAATTAAAAAATATATAAAAATCATA
1 AAAAATTATAAAATATATAAAAATCATA
* * *
10045313 AAATATTGTAAAAATTTATAAAAATCATAA
1 AAAAATTAT-AAAATATATAAAAATCAT-A
10045343 AAAAATTATAAAAT
1 AAAAATTATAAAAT
10045357 GCATCAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 6 0.17
29 22 0.61
30 8 0.22
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (28 bp):
AAAAATTATAAAATATATAAAAATCATA
Found at i:10045366 original size:20 final size:20
Alignment explanation
Indices: 10045285--10045355 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
10045275 AAAAATATTT
*
10045285 AAAAATTA-AAAAAT-ATAT
1 AAAAATTATAAAAATCATAA
* **
10045303 AAAAATCATAAAATATTGT-A
1 AAAAATTATAAAA-ATCATAA
*
10045323 AAAATTTATAAAAATCATAA
1 AAAAATTATAAAAATCATAA
10045343 AAAAATTATAAAA
1 AAAAATTATAAAA
10045356 TGCATCAAAA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
18 7 0.17
19 7 0.17
20 26 0.63
21 1 0.02
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (20 bp):
AAAAATTATAAAAATCATAA
Found at i:10045565 original size:19 final size:20
Alignment explanation
Indices: 10045543--10045590 Score: 80
Period size: 19 Copynumber: 2.5 Consensus size: 20
10045533 TACAATAATT
10045543 TTTTTTTACAAATTTTAT-A
1 TTTTTTTACAAATTTTATAA
10045562 TTTTTTTACAAATTTTATAA
1 TTTTTTTACAAATTTTATAA
*
10045582 TTTTCTTAC
1 TTTTTTTAC
10045591 GACTTTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTTTACAAATTTTATAA
Found at i:10045754 original size:28 final size:28
Alignment explanation
Indices: 10045690--10045758 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
10045680 ACGATATTTG
*
10045690 TAATTTTTTCTAATTTTTAATAAAAATT
1 TAATTTTTTATAATTTTTAATAAAAATT
* * *
10045718 AAACATTTTTAT-ATTTTTATTAAAAATAT
1 TAA-TTTTTTATAATTTTTAATAAAAAT-T
10045747 TAA-TTTTTATAA
1 TAATTTTTTATAA
10045759 ATTTAATTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
27 7 0.21
28 17 0.52
29 9 0.27
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (28 bp):
TAATTTTTTATAATTTTTAATAAAAATT
Found at i:10048754 original size:49 final size:49
Alignment explanation
Indices: 10048622--10048756 Score: 216
Period size: 49 Copynumber: 2.8 Consensus size: 49
10048612 GATAATAACA
* * * * *
10048622 TGCCAAAGCCATGTCCCAAACATGGCCTTACATGAGATGTTTCCTGTAC
1 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGATGTTTCCTGTAC
10048671 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGATGTTTCCTGTAC
1 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGATGTTTCCTGTAC
*
10048720 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGA
1 TGCCAATGCCATATCCCAGATATGGCCTTACATGGGA
10048757 GTTCTCATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 80 1.00
ACGTcount: A:0.25, C:0.27, G:0.20, T:0.28
Consensus pattern (49 bp):
TGCCAATGCCATATCCCAGATATGGCCTTACATGGGATGTTTCCTGTAC
Found at i:10048860 original size:50 final size:53
Alignment explanation
Indices: 10048779--10048907 Score: 140
Period size: 50 Copynumber: 2.4 Consensus size: 53
10048769 GTGCCCATGC
* * *
10048779 CATGTCCCATACATGGTCTTACGGGGAACCTCTC-ATCTCAGTG-T-CAACGT
1 CATGTCCCAGACATGGTCTTACGGAGAACCTCTCAATCTCAATGATACAACGT
* * *
10048829 CATGTCCTAGACATGGTCTTACATGAG-ACCTCTCATAATCTCAATGATACCAATGT
1 CATGTCCCAGACATGGTCTTAC-GGAGAACCTCTC--AATCTCAATGATA-CAACGT
10048885 CATGTCCCAGACATGGTCTTACG
1 CATGTCCCAGACATGGTCTTACG
10048908 TGGGATCTCT
Statistics
Matches: 64, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
50 27 0.42
51 2 0.03
53 8 0.12
54 1 0.02
56 26 0.41
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.29
Consensus pattern (53 bp):
CATGTCCCAGACATGGTCTTACGGAGAACCTCTCAATCTCAATGATACAACGT
Found at i:10051059 original size:23 final size:20
Alignment explanation
Indices: 10051025--10051078 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
10051015 TAGCAATTTT
*
10051025 TAAATATTTTTATCATTTTAA
1 TAAATATTTTTAT-AGTTTAA
10051046 TAAATATATATTTATAGTTTAA
1 TAAATAT-T-TTTATAGTTTAA
*
10051068 T-GATATTTTTA
1 TAAATATTTTTA
10051079 AAATTTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 4 0.14
20 1 0.03
21 11 0.38
22 8 0.28
23 5 0.17
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TAAATATTTTTATAGTTTAA
Found at i:10063948 original size:51 final size:51
Alignment explanation
Indices: 10063904--10064003 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
10063894 AATTATTTAA
*
10063904 AAATAGGGATTTAAGAGAAATTTA-AGAGGAACTTGAGAGCAAATTGAGATT
1 AAATAGGAATTTAAGAGAAATTTAGA-AGGAACTTGAGAGCAAATTGAGATT
* * * *
10063955 AAATATGAATTTGAGAGAAATTTGGAAGGAATTTGAGAGCAAATTGAGA
1 AAATAGGAATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGA
10064004 GGAAATTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.45, C:0.03, G:0.26, T:0.26
Consensus pattern (51 bp):
AAATAGGAATTTAAGAGAAATTTAGAAGGAACTTGAGAGCAAATTGAGATT
Found at i:10063976 original size:11 final size:11
Alignment explanation
Indices: 10063962--10064039 Score: 65
Period size: 11 Copynumber: 7.0 Consensus size: 11
10063952 ATTAAATATG
10063962 AATTTGAGAGA
1 AATTTGAGAGA
*
10063973 AATTTG-GAAGG
1 AATTTGAG-AGA
10063984 AATTTGAGAGCA
1 AATTTGAGAG-A
10063996 AA-TTGAGAGGA
1 AATTTGAGA-GA
*
10064007 AATTT-AAAGGA
1 AATTTGAGA-GA
10064018 AA-TTGAGAGGA
1 AATTTGAGA-GA
10064029 AATTTGAGAGA
1 AATTTGAGAGA
10064040 GGATTAGTTT
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
10 3 0.05
11 41 0.73
12 12 0.21
ACGTcount: A:0.45, C:0.01, G:0.29, T:0.24
Consensus pattern (11 bp):
AATTTGAGAGA
Found at i:10064006 original size:22 final size:22
Alignment explanation
Indices: 10063962--10064039 Score: 90
Period size: 22 Copynumber: 3.5 Consensus size: 22
10063952 ATTAAATATG
10063962 AATTTGAGAGAAATTTG-GAAGG-
1 AATTTGAGAGAAA-TTGAG-AGGA
10063984 AATTTGAGAGCAAATTGAGAGGA
1 AATTTGAGAG-AAATTGAGAGGA
*
10064007 AATTT-AAAGGAAATTGAGAGGA
1 AATTTGAGA-GAAATTGAGAGGA
10064029 AATTTGAGAGA
1 AATTTGAGAGA
10064040 GGATTAGTTT
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
22 37 0.76
23 12 0.24
ACGTcount: A:0.45, C:0.01, G:0.29, T:0.24
Consensus pattern (22 bp):
AATTTGAGAGAAATTGAGAGGA
Found at i:10064017 original size:33 final size:35
Alignment explanation
Indices: 10063962--10064038 Score: 106
Period size: 33 Copynumber: 2.3 Consensus size: 35
10063952 ATTAAATATG
* *
10063962 AATTTGAGA-GAAATTTGGAAGGAATTTGAGAGCA
1 AATTTGAGAGGAAATTTGAAAGGAAATTGAGAGCA
*
10063996 AA-TTGAGAGGAAATTT-AAAGGAAATTGAGAGGA
1 AATTTGAGAGGAAATTTGAAAGGAAATTGAGAGCA
10064029 AATTTGAGAG
1 AATTTGAGAG
10064039 AGGATTAGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 22 0.58
34 16 0.42
ACGTcount: A:0.44, C:0.01, G:0.30, T:0.25
Consensus pattern (35 bp):
AATTTGAGAGGAAATTTGAAAGGAAATTGAGAGCA
Found at i:10069957 original size:22 final size:22
Alignment explanation
Indices: 10069932--10069987 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 22
10069922 AGTTTTCAAT
* *
10069932 ATTTATATATTTTGTCAATTTA
1 ATTTATATATTTTGTAAATTAA
*
10069954 ATTT-T-TATTTTTTAAATTAA
1 ATTTATATATTTTGTAAATTAA
10069974 ATTTAGTTATATTT
1 ATTTA--TATATTT
10069988 AAAAGTCTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 16 0.59
21 1 0.04
22 4 0.15
23 1 0.04
24 5 0.19
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.62
Consensus pattern (22 bp):
ATTTATATATTTTGTAAATTAA
Found at i:10076301 original size:27 final size:27
Alignment explanation
Indices: 10076271--10076329 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
10076261 CCTATCAGGT
10076271 AGGCGCCAATGAAGGTGCCTCATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
*
10076298 AGGCGCCAATGAAGGTGCCTTATAGAG
1 AGGCGCCAATGAAGGTGCCTCATAGAG
10076325 AGGCG
1 AGGCG
10076330 TCATTACTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.29, C:0.20, G:0.36, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAAGGTGCCTCATAGAG
Found at i:10076519 original size:20 final size:21
Alignment explanation
Indices: 10076494--10076536 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
10076484 AATAAACACC
10076494 AAAAAAT-TTTTAAAAATAAA
1 AAAAAATATTTTAAAAATAAA
10076514 AAAAAATATTTTAAAAATAAA
1 AAAAAATATTTTAAAAATAAA
10076535 AA
1 AA
10076537 TTAAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAAATATTTTAAAAATAAA
Found at i:10076815 original size:19 final size:19
Alignment explanation
Indices: 10076793--10076830 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10076783 AATTTAATTT
*
10076793 ATTAGTAATAAATTACTAA
1 ATTACTAATAAATTACTAA
*
10076812 ATTACTAATAAGTTACTAA
1 ATTACTAATAAATTACTAA
10076831 TAAATTTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (19 bp):
ATTACTAATAAATTACTAA
Found at i:10076960 original size:27 final size:27
Alignment explanation
Indices: 10076929--10077000 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
10076919 TACCGACATT
* *
10076929 CAATATTCATACAAAATTATAATATTA
1 CAATATTCATACAAAATTACAAAATTA
*
10076956 CAATAGTCATACAAAATTACAAAATTA
1 CAATATTCATACAAAATTACAAAATTA
*
10076983 CAATATTCATATAAAATT
1 CAATATTCATACAAAATT
10077001 GCAATATTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.33
Consensus pattern (27 bp):
CAATATTCATACAAAATTACAAAATTA
Found at i:10077231 original size:19 final size:19
Alignment explanation
Indices: 10077209--10077246 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
10077199 TATAAATTTA
*
10077209 TTAGTAACTTATTAGTAAT
1 TTAGTAACTTATTACTAAT
*
10077228 TTAGTAATTTATTACTAAT
1 TTAGTAACTTATTACTAAT
10077247 AAATTAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (19 bp):
TTAGTAACTTATTACTAAT
Found at i:10077497 original size:27 final size:27
Alignment explanation
Indices: 10077459--10077530 Score: 135
Period size: 27 Copynumber: 2.7 Consensus size: 27
10077449 CCGGCCCGGC
10077459 CCATTGGCGCCTCTCAGAATGGCACCA
1 CCATTGGCGCCTCTCAGAATGGCACCA
10077486 CCATTGGCGCCTCTCAGAATGGCACCA
1 CCATTGGCGCCTCTCAGAATGGCACCA
*
10077513 CCATTGGCGCCTCCCAGA
1 CCATTGGCGCCTCTCAGA
10077531 TAGGCGCCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.21, C:0.39, G:0.22, T:0.18
Consensus pattern (27 bp):
CCATTGGCGCCTCTCAGAATGGCACCA
Found at i:10077607 original size:29 final size:29
Alignment explanation
Indices: 10077574--10077629 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
10077564 TACTAACCCG
*
10077574 AAAAAGTATAAAATTA-TATTTTATTCAA
1 AAAAAATATAAAATTATTATTTTATTCAA
* **
10077602 AAAAAATTTATTATTATTATTTTATTCA
1 AAAAAATATAAAATTATTATTTTATTCA
10077630 TTGGCGCCTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 12 0.52
29 11 0.48
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (29 bp):
AAAAAATATAAAATTATTATTTTATTCAA
Found at i:10077738 original size:28 final size:29
Alignment explanation
Indices: 10077665--10077738 Score: 66
Period size: 28 Copynumber: 2.6 Consensus size: 29
10077655 TGAAAAAAGT
*
10077665 AACCTATTT-TGGTAAATATTTTTTCTGAC
1 AACCTATTTAT-GTAAAAATTTTTTCTGAC
* **
10077694 ACCCTATTTCA-GT-AAAATTTTTT-TTTC
1 AACCTATTT-ATGTAAAAATTTTTTCTGAC
10077721 AACCTATTTATGTAAAAA
1 AACCTATTTATGTAAAAA
10077739 ATCCAGAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
26 1 0.03
27 12 0.33
28 13 0.36
29 10 0.28
ACGTcount: A:0.32, C:0.15, G:0.07, T:0.46
Consensus pattern (29 bp):
AACCTATTTATGTAAAAATTTTTTCTGAC
Found at i:10086335 original size:18 final size:17
Alignment explanation
Indices: 10086312--10086348 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
10086302 AATACCATTA
*
10086312 TATTAATATTAATTATTT
1 TATTAAAATTAATT-TTT
10086330 TATTAAAATTAATTTTT
1 TATTAAAATTAATTTTT
10086347 TA
1 TA
10086349 AATAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTAAAATTAATTTTT
Found at i:10086349 original size:14 final size:14
Alignment explanation
Indices: 10086322--10086361 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 14
10086312 TATTAATATT
10086322 AATT-ATTTTATTAA
1 AATTAATTTT-TTAA
10086336 AATTAATTTTTT-A
1 AATTAATTTTTTAA
10086349 AA-TAATTTTTTAA
1 AATTAATTTTTTAA
10086362 GTGAATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 9 0.38
13 4 0.17
14 6 0.25
15 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
AATTAATTTTTTAA
Found at i:10086754 original size:27 final size:28
Alignment explanation
Indices: 10086676--10086771 Score: 167
Period size: 28 Copynumber: 3.5 Consensus size: 28
10086666 AAAATAAAAT
*
10086676 TTTATCAAAATATTATAACTTTTTTTTA
1 TTTACCAAAATATTATAACTTTTTTTTA
10086704 TTTACCAAAATATTATAACTTTTTTTTA
1 TTTACCAAAATATTATAACTTTTTTTTA
*
10086732 TTTACTAAAATATTATAAC-TTTTTTTA
1 TTTACCAAAATATTATAACTTTTTTTTA
10086759 TTTACCAAAATAT
1 TTTACCAAAATAT
10086772 ACAAAAAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
27 20 0.31
28 45 0.69
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (28 bp):
TTTACCAAAATATTATAACTTTTTTTTA
Found at i:10092633 original size:44 final size:44
Alignment explanation
Indices: 10092570--10092656 Score: 165
Period size: 44 Copynumber: 2.0 Consensus size: 44
10092560 TGAATGCATT
*
10092570 CATCTATGTTAATTACAATATAATCTGCAAATAAACAATCTATA
1 CATCTATATTAATTACAATATAATCTGCAAATAAACAATCTATA
10092614 CATCTATATTAATTACAATATAATCTGCAAATAAACAATCTAT
1 CATCTATATTAATTACAATATAATCTGCAAATAAACAATCTAT
10092657 CTTAATTAGA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 42 1.00
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.34
Consensus pattern (44 bp):
CATCTATATTAATTACAATATAATCTGCAAATAAACAATCTATA
Found at i:10099083 original size:19 final size:18
Alignment explanation
Indices: 10099046--10099084 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
10099036 AGTGAATATT
*
10099046 AAAATTAAATTAAACATA
1 AAAATTAAATCAAACATA
*
10099064 AAAATTAAACTCACACATA
1 AAAATTAAA-TCAAACATA
10099083 AA
1 AA
10099085 TTTTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.64, C:0.13, G:0.00, T:0.23
Consensus pattern (18 bp):
AAAATTAAATCAAACATA
Found at i:10101301 original size:17 final size:17
Alignment explanation
Indices: 10101291--10101335 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
10101281 TTTGTTTTAA
10101291 TGTAATATTTGTATATT
1 TGTAATATTTGTATATT
10101308 TGTAATATTTGTATATT
1 TGTAATATTTGTATATT
10101325 TGTAAATATTT
1 TGT-AATATTT
10101336 ATGAATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (17 bp):
TGTAATATTTGTATATT
Found at i:10101303 original size:9 final size:9
Alignment explanation
Indices: 10101291--10101335 Score: 67
Period size: 8 Copynumber: 5.1 Consensus size: 9
10101281 TTTGTTTTAA
10101291 TGTAATATT
1 TGTAATATT
10101300 TGT-ATATT
1 TGTAATATT
10101308 TGTAATATT
1 TGTAATATT
10101317 TGT-ATATT
1 TGTAATATT
10101325 TGTAAATATT
1 TGT-AATATT
10101335 T
1 T
10101336 ATGAATATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
8 16 0.48
9 11 0.33
10 6 0.18
ACGTcount: A:0.31, C:0.00, G:0.11, T:0.58
Consensus pattern (9 bp):
TGTAATATT
Found at i:10105093 original size:2 final size:2
Alignment explanation
Indices: 10105086--10105113 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
10105076 AGAATGCAGT
10105086 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA
10105114 AAACAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:10109750 original size:61 final size:60
Alignment explanation
Indices: 10109652--10109774 Score: 144
Period size: 61 Copynumber: 2.0 Consensus size: 60
10109642 GTCATTACAT
*
10109652 TGAATGCTTTAGCTGTTTTTAGTTTATGATTATGGAGTTGCATT-AAATTTTGAGCAAGGA
1 TGAATGCTTTAGCTGTTTTTAGTTTATGATTATGGAGTTGC-TTCAAATTTTGAACAAGGA
* ** *
10109712 TGAATGCTTTAG-TTTTTCTCTAGTTTATTTTTGA-GGAGTTGCTTCAAATTTTGAACGAGGA
1 TGAATGCTTTAGCTGTTT-T-TAGTTTATGATT-ATGGAGTTGCTTCAAATTTTGAACAAGGA
10109773 TG
1 TG
10109775 GACAAGGCTA
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
59 4 0.07
60 15 0.28
61 34 0.63
62 1 0.02
ACGTcount: A:0.24, C:0.08, G:0.23, T:0.45
Consensus pattern (60 bp):
TGAATGCTTTAGCTGTTTTTAGTTTATGATTATGGAGTTGCTTCAAATTTTGAACAAGGA
Found at i:10110195 original size:17 final size:17
Alignment explanation
Indices: 10110173--10110206 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
10110163 GAGGCTCATA
*
10110173 TCCGTCATTGCTCTGTT
1 TCCGTCATTGCTATGTT
*
10110190 TCCGTCCTTGCTATGTT
1 TCCGTCATTGCTATGTT
10110207 CCTCTAGCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.29, G:0.18, T:0.47
Consensus pattern (17 bp):
TCCGTCATTGCTATGTT
Found at i:10114992 original size:31 final size:30
Alignment explanation
Indices: 10114935--10115001 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
10114925 ATATATATAT
*
10114935 TAATTTGGTACAATTATACACGTGAAACTC
1 TAATTTGGTACAAATATACACGTGAAACTC
* * * *
10114965 TAATTGTGGTTCAAATATATACTTGAAACTT
1 TAATT-TGGTACAAATATACACGTGAAACTC
10114996 TAATTT
1 TAATTT
10115002 TGACTTAATC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
30 6 0.19
31 25 0.81
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (30 bp):
TAATTTGGTACAAATATACACGTGAAACTC
Found at i:10116271 original size:29 final size:30
Alignment explanation
Indices: 10116208--10116276 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
10116198 AAAACAATAC
* *
10116208 ATGAACTTTGATTTAATGTGCAATTATATAT
1 ATGAATTTTGATTTAATGT-CAATTATATAA
* *
10116239 ATGAATTTTGATTTTATGT-AATTTTATAA
1 ATGAATTTTGATTTAATGTCAATTATATAA
10116268 ATGAATTTT
1 ATGAATTTT
10116277 TTATTGATCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 17 0.50
31 17 0.50
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.51
Consensus pattern (30 bp):
ATGAATTTTGATTTAATGTCAATTATATAA
Found at i:10116781 original size:25 final size:25
Alignment explanation
Indices: 10116753--10116805 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
10116743 TCTTTTCTTC
*
10116753 TTTTACAAAATTTAATCA-TTTTATT
1 TTTTACAAAAGTTAAT-ATTTTTATT
* *
10116778 TTTTCCATAAGTTAATATTTTTATT
1 TTTTACAAAAGTTAATATTTTTATT
10116803 TTT
1 TTT
10116806 GTGCAACCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 1 0.04
25 23 0.96
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTACAAAAGTTAATATTTTTATT
Found at i:10116984 original size:21 final size:21
Alignment explanation
Indices: 10116958--10117001 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
10116948 TTCAGGATTT
*
10116958 GGGTTCGAGATTTAAGGTTTA
1 GGGTTCGAGATTCAAGGTTTA
10116979 GGGTTCGAGATTCAAGGTTTA
1 GGGTTCGAGATTCAAGGTTTA
10117000 GG
1 GG
10117002 TCTAGGGTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.23, C:0.07, G:0.36, T:0.34
Consensus pattern (21 bp):
GGGTTCGAGATTCAAGGTTTA
Found at i:10118159 original size:16 final size:16
Alignment explanation
Indices: 10118135--10118165 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
10118125 CCCGAAATAA
10118135 ACAGAGGCCCAAAATT
1 ACAGAGGCCCAAAATT
*
10118151 ACAGTGGCCCAAAAT
1 ACAGAGGCCCAAAAT
10118166 AGTTTCAGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.13
Consensus pattern (16 bp):
ACAGAGGCCCAAAATT
Found at i:10120376 original size:12 final size:12
Alignment explanation
Indices: 10120359--10120386 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
10120349 ATATATCATT
10120359 GATTTCCCTTTA
1 GATTTCCCTTTA
10120371 GATTTCCCTTTA
1 GATTTCCCTTTA
10120383 GATT
1 GATT
10120387 CATTTATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.21, G:0.11, T:0.50
Consensus pattern (12 bp):
GATTTCCCTTTA
Found at i:10120399 original size:24 final size:24
Alignment explanation
Indices: 10120372--10120421 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
10120362 TTCCCTTTAG
10120372 ATTTCCCTTTAG-ATTCATTTATAT
1 ATTT-CCTTTAGAATTCATTTATAT
* *
10120396 ATTTTCTTTCGAATTCATTTATAT
1 ATTTCCTTTAGAATTCATTTATAT
10120420 AT
1 AT
10120422 ACACATACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.26, C:0.14, G:0.04, T:0.56
Consensus pattern (24 bp):
ATTTCCTTTAGAATTCATTTATAT
Found at i:10121719 original size:8 final size:8
Alignment explanation
Indices: 10121706--10121730 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
10121696 TTTTAATTTA
10121706 TATATATT
1 TATATATT
10121714 TATATATT
1 TATATATT
10121722 TATATATT
1 TATATATT
10121730 T
1 T
10121731 TCTTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TATATATT
Found at i:10142939 original size:6 final size:6
Alignment explanation
Indices: 10142928--10142956 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
10142918 AGGAAGATAA
10142928 TGATGG TGATGG TGATGG TGATGG TGATG
1 TGATGG TGATGG TGATGG TGATGG TGATG
10142957 ATAAAGATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.48, T:0.34
Consensus pattern (6 bp):
TGATGG
Found at i:10147781 original size:6 final size:6
Alignment explanation
Indices: 10147770--10147794 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
10147760 TTAATATTGA
10147770 AATTTT AATTTT AATTTT AATTTT A
1 AATTTT AATTTT AATTTT AATTTT A
10147795 TAGAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (6 bp):
AATTTT
Found at i:10155415 original size:17 final size:16
Alignment explanation
Indices: 10155390--10155426 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
10155380 ATTAATAAGT
*
10155390 TTATTATTATTTAATTA
1 TTATGATTATTT-ATTA
10155407 TTATGATTATTTATTA
1 TTATGATTATTTATTA
10155423 TTAT
1 TTAT
10155427 ATTTCTCTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTATGATTATTTATTA
Found at i:10164417 original size:47 final size:47
Alignment explanation
Indices: 10164363--10164458 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 47
10164353 AGCACAATAA
10164363 AAAATATCATAAAACTTATTATACGATGAAACTTGCAACAAAACAAG
1 AAAATATCATAAAACTTATTATACGATGAAACTTGCAACAAAACAAG
** * * *
10164410 AAAATATCATTGAATTTATTATATGATGAAACTTGTAACAAAACAAG
1 AAAATATCATAAAACTTATTATACGATGAAACTTGCAACAAAACAAG
10164457 AA
1 AA
10164459 GAACGAGTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.52, C:0.11, G:0.09, T:0.27
Consensus pattern (47 bp):
AAAATATCATAAAACTTATTATACGATGAAACTTGCAACAAAACAAG
Found at i:10165661 original size:7 final size:7
Alignment explanation
Indices: 10165649--10165688 Score: 80
Period size: 7 Copynumber: 5.7 Consensus size: 7
10165639 AAAAATGTGC
10165649 AAAAAAT
1 AAAAAAT
10165656 AAAAAAT
1 AAAAAAT
10165663 AAAAAAT
1 AAAAAAT
10165670 AAAAAAT
1 AAAAAAT
10165677 AAAAAAT
1 AAAAAAT
10165684 AAAAA
1 AAAAA
10165689 GCAAGATAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:10169914 original size:2 final size:2
Alignment explanation
Indices: 10169907--10169935 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10169897 AGTTAAAGCA
10169907 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
10169936 ACACACACAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:10185342 original size:16 final size:16
Alignment explanation
Indices: 10185321--10185351 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10185311 AAGGAACTGT
10185321 TTGTAACATCATTTGG
1 TTGTAACATCATTTGG
10185337 TTGTAACATCATTTG
1 TTGTAACATCATTTG
10185352 AGTAGAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (16 bp):
TTGTAACATCATTTGG
Found at i:10187256 original size:30 final size:30
Alignment explanation
Indices: 10187211--10187274 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
10187201 TGATAGTTAC
* * *
10187211 ATAATAAATAAACTTACTTTTATTACTCAT
1 ATAACAAACAAACTTACTTTTATGACTCAT
*
10187241 ATAACAAACAAACTTACTTTTATGACTTAT
1 ATAACAAACAAACTTACTTTTATGACTCAT
10187271 ATAA
1 ATAA
10187275 AATAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (30 bp):
ATAACAAACAAACTTACTTTTATGACTCAT
Found at i:10188333 original size:71 final size:70
Alignment explanation
Indices: 10188217--10188352 Score: 218
Period size: 71 Copynumber: 1.9 Consensus size: 70
10188207 CTTCCTCCAA
* *
10188217 CTTTTCGTCAAGCGAAGTGTTCGATAAAATGCTTCACTGATGAAAAAGTAAGGCCTTTCAAATTC
1 CTTTTCGTCAAGCGAAGTGTTCGATAAAATCCTTCACTGATGAAAAAG-AAAGCCTTTCAAATTC
10188282 TTTCAT
65 TTTCAT
* * *
10188288 CTTTTCGTCGAGCGAGGTGTTCGATAAAATCCTTCACTGTTGAAAAAGAAAGCCTTTCAAATTCT
1 CTTTTCGTCAAGCGAAGTGTTCGATAAAATCCTTCACTGATGAAAAAGAAAGCCTTTCAAATTCT
10188353 AACGTTTGTG
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
70 16 0.27
71 44 0.73
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (70 bp):
CTTTTCGTCAAGCGAAGTGTTCGATAAAATCCTTCACTGATGAAAAAGAAAGCCTTTCAAATTCT
TTCAT
Found at i:10205263 original size:16 final size:16
Alignment explanation
Indices: 10205207--10205275 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
10205197 ATTTTTAAAT
*
10205207 TAAAA-ATATTTAAT-
1 TAAAATATAATTAATA
* *
10205221 TAAAATGTATTTAATA
1 TAAAATATAATTAATA
*
10205237 TTAAATATAATTACATA
1 TAAAATATAATTA-ATA
*
10205254 TAAAAT-TAATTGATTA
1 TAAAATATAATT-AATA
10205270 TAAAAT
1 TAAAAT
10205276 GATTTTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
14 5 0.11
15 8 0.18
16 23 0.51
17 9 0.20
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (16 bp):
TAAAATATAATTAATA
Found at i:10205874 original size:17 final size:18
Alignment explanation
Indices: 10205854--10205894 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
10205844 ATCATTTAAA
10205854 AAAATT-ATT-TATTTTCT
1 AAAATTGATTCTATTTT-T
*
10205871 AAAATTGTTTCTATTTTT
1 AAAATTGATTCTATTTTT
10205889 AAAATT
1 AAAATT
10205895 CTTGCATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 9 0.43
19 6 0.29
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (18 bp):
AAAATTGATTCTATTTTT
Found at i:10207014 original size:58 final size:60
Alignment explanation
Indices: 10206874--10207019 Score: 174
Period size: 58 Copynumber: 2.5 Consensus size: 60
10206864 ATGTGCTACG
* * * *
10206874 TAACAATCGATTTAAACATATAAACAATTGATTCAAAAGAAGAAAAAGCAGTATTCTACTA
1 TAACAATTGATTTAAACATATAAACAATTGATTC-AAAGAACAAAAAGCAATATTCCACTA
* * *
10206935 TAAC-ATTCGATTTAAATATATAAACAATTTATTC-AA-AACAATAAGCAATATTCCA-TCA
1 TAACAATT-GATTTAAACATATAAACAATTGATTCAAAGAACAAAAAGCAATATTCCACT-A
10206993 TAACAATTGATTTAAACATATAAACAA
1 TAACAATTGATTTAAACATATAAACAA
10207020 CAAATTCGAA
Statistics
Matches: 74, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
57 1 0.01
58 38 0.51
59 5 0.07
60 2 0.03
61 28 0.38
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (60 bp):
TAACAATTGATTTAAACATATAAACAATTGATTCAAAGAACAAAAAGCAATATTCCACTA
Found at i:10209024 original size:14 final size:14
Alignment explanation
Indices: 10209005--10209037 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
10208995 ATTGTTATAT
10209005 AAATTCATTT-AATA
1 AAATTC-TTTCAATA
10209019 AAATTCTTTCAATA
1 AAATTCTTTCAATA
10209033 AAATT
1 AAATT
10209038 AAATTTATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (14 bp):
AAATTCTTTCAATA
Found at i:10223450 original size:20 final size:17
Alignment explanation
Indices: 10223415--10223459 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 17
10223405 ATTTGTATGG
10223415 TTTTATGATTTTTAATAAT
1 TTTTAT-ATTTTTAAT-AT
10223434 TATTTATATTTTGTAATAT
1 T-TTTATATTTT-TAATAT
10223453 TTTTATA
1 TTTTATA
10223460 ATATTTTGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.25
19 9 0.38
20 9 0.38
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (17 bp):
TTTTATATTTTTAATAT
Found at i:10227202 original size:20 final size:22
Alignment explanation
Indices: 10227173--10227213 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
10227163 AACATTATTT
10227173 TAAAAATA-T-TTTTTAAAATA
1 TAAAAATATTGTTTTTAAAATA
*
10227193 TAAAATTATTGTTTTTAAAAT
1 TAAAAATATTGTTTTTAAAAT
10227214 TTATTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 1 0.06
22 10 0.56
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAAAAATATTGTTTTTAAAATA
Found at i:10237444 original size:39 final size:38
Alignment explanation
Indices: 10237387--10237461 Score: 89
Period size: 40 Copynumber: 1.9 Consensus size: 38
10237377 AAATTTTTAA
*
10237387 TTTTTAATAATTAAAA-TTTAAAAATTATTTTTATATGC
1 TTTTTAATAATTAAAATTTTAAAAA-TAGTTTTATATGC
* *
10237425 TTTTTAGATAATTTTAATTTTTAAAAATAGTTTTATA
1 TTTTTA-ATAA-TTAAAATTTTAAAAATAGTTTTATA
10237462 ATTTTTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
38 6 0.19
39 4 0.13
40 13 0.42
41 8 0.26
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.55
Consensus pattern (38 bp):
TTTTTAATAATTAAAATTTTAAAAATAGTTTTATATGC
Found at i:10237486 original size:38 final size:37
Alignment explanation
Indices: 10237380--10237486 Score: 94
Period size: 38 Copynumber: 2.8 Consensus size: 37
10237370 ATATAAGAAA
*
10237380 TTTT-TAATTTTTAATAA-TTAAAATTTAAAAATTAT
1 TTTTATAATTTTTAATAATTTAAAATTTAAAAATTAG
* **
10237415 TTTTATATGCTTTTTAGATAATTTTAATTTTTAAAAA-TAG
1 TTTTATA--ATTTTTA-ATAA-TTTAAAATTTAAAAATTAG
*
10237455 TTTTATAATTTTTATAAAATTTAAAAATTTAA
1 TTTTATAATTTTTA-ATAATTT-AAAATTTAA
10237487 TTAAATGCTG
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
35 4 0.07
36 2 0.04
37 3 0.05
38 22 0.39
39 4 0.07
40 9 0.16
41 12 0.21
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (37 bp):
TTTTATAATTTTTAATAATTTAAAATTTAAAAATTAG
Found at i:10242562 original size:16 final size:16
Alignment explanation
Indices: 10242522--10242565 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
10242512 AAAACACGCA
10242522 TATTTAAAATAACAAT
1 TATTTAAAATAACAAT
* *
10242538 T-TTAAAAAATAACCAT
1 TATT-TAAAATAACAAT
10242554 TATTTAAAATAA
1 TATTTAAAATAA
10242566 GCGTTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (16 bp):
TATTTAAAATAACAAT
Found at i:10255191 original size:19 final size:18
Alignment explanation
Indices: 10255167--10255205 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
10255157 CTATTATAGC
10255167 TTTCTA-GGTACTTTGTCTT
1 TTTCTATGGTA-TTTGT-TT
10255186 TTTCTATGGTATTTGTTT
1 TTTCTATGGTATTTGTTT
10255204 TT
1 TT
10255206 CAGTTACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 11 0.58
20 4 0.21
ACGTcount: A:0.10, C:0.10, G:0.15, T:0.64
Consensus pattern (18 bp):
TTTCTATGGTATTTGTTT
Found at i:10288548 original size:39 final size:37
Alignment explanation
Indices: 10288505--10288588 Score: 87
Period size: 39 Copynumber: 2.2 Consensus size: 37
10288495 GCCCATTTTT
10288505 AAAATAAACATTAAAAATATTTTAAAAATAAAAAAATAA
1 AAAATAAACATTAAAAATATTTT-AAAATAAAAAAAT-A
** ** * * *
10288544 AAAATTTATTTTAAAAGTATTTTCAAATTAAAAAATA
1 AAAATAAACATTAAAAATATTTTAAAATAAAAAAATA
10288581 AAAATAAA
1 AAAATAAA
10288589 AATATATATT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
37 7 0.19
38 11 0.31
39 18 0.50
ACGTcount: A:0.65, C:0.02, G:0.01, T:0.31
Consensus pattern (37 bp):
AAAATAAACATTAAAAATATTTTAAAATAAAAAAATA
Found at i:10291360 original size:21 final size:21
Alignment explanation
Indices: 10291334--10291397 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
10291324 CTGACCTTTA
10291334 TACTATTTGCTCCTTTTTGCC
1 TACTATTTGCTCCTTTTTGCC
10291355 TACTATTT--T-C--TTT--C
1 TACTATTTGCTCCTTTTTGCC
*
10291369 TGCTATTTGCTCCTTTTTGCC
1 TACTATTTGCTCCTTTTTGCC
10291390 TACTATTT
1 TACTATTT
10291398 TCTGTCTGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
14 8 0.24
16 4 0.12
17 1 0.03
18 1 0.03
19 4 0.12
21 16 0.47
ACGTcount: A:0.11, C:0.25, G:0.08, T:0.56
Consensus pattern (21 bp):
TACTATTTGCTCCTTTTTGCC
Found at i:10291375 original size:35 final size:35
Alignment explanation
Indices: 10291336--10291406 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
10291326 GACCTTTATA
*
10291336 CTATTTGCTCCTTTTTGCCTACTATTTTCTTTCTG
1 CTATTTGCTCCTTTTTGCCTACTATTTTCTGTCTG
10291371 CTATTTGCTCCTTTTTGCCTACTATTTTCTGTCTG
1 CTATTTGCTCCTTTTTGCCTACTATTTTCTGTCTG
10291406 C
1 C
10291407 CTTTTCTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.08, C:0.27, G:0.10, T:0.55
Consensus pattern (35 bp):
CTATTTGCTCCTTTTTGCCTACTATTTTCTGTCTG
Found at i:10312689 original size:2 final size:2
Alignment explanation
Indices: 10312639--10312673 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
10312629 ATGAATGTAA
10312639 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10312674 AGAAACAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10312749 original size:22 final size:22
Alignment explanation
Indices: 10312690--10312751 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
10312680 AACCATATAT
**
10312690 TACTAAGCTCTCATGGCTAACG
1 TACTAAGCTCTCATGTTTAACG
*
10312712 TACTAAGCTCTCATGTTTCACG
1 TACTAAGCTCTCATGTTTAACG
10312734 TACTAAGCTCTCATGTTT
1 TACTAAGCTCTCATGTTT
10312752 GAACAATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (22 bp):
TACTAAGCTCTCATGTTTAACG
Found at i:10314598 original size:24 final size:25
Alignment explanation
Indices: 10314552--10314603 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
10314542 TAGTCAAATA
*
10314552 AAAATCTATAAAAAAATGTTAT-AT
1 AAAATCTATAAAAAAATGATATAAT
*
10314576 AAAATCATATAAACAAAT-ATATAAT
1 AAAATC-TATAAAAAAATGATATAAT
10314601 AAA
1 AAA
10314604 GCTAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.63, C:0.06, G:0.02, T:0.29
Consensus pattern (25 bp):
AAAATCTATAAAAAAATGATATAAT
Found at i:10320520 original size:79 final size:81
Alignment explanation
Indices: 10320387--10320540 Score: 276
Period size: 79 Copynumber: 1.9 Consensus size: 81
10320377 AGGAAAAATC
*
10320387 TGATTTGTCATTTTCCTATTAAAAAGGGATAGGGATGATGTGGAATCACAATTTCATACAATTCC
1 TGATTTGTCATTTTCCTATTAAAAAGGGATAGGGATGATGTGGAATCACAATTTCATACAATCCC
10320452 TTCTCTTTTGGCATAA
66 TTCTCTTTTGGCATAA
*
10320468 TGATTTGTCATTTT-CTATTGAAAA-GGATAGGGATGATGTGGAATCACAATTTCATACAATCCC
1 TGATTTGTCATTTTCCTATTAAAAAGGGATAGGGATGATGTGGAATCACAATTTCATACAATCCC
10320531 TTCTCTTTTG
66 TTCTCTTTTG
10320541 ATATAATGCC
Statistics
Matches: 71, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
79 48 0.68
80 9 0.13
81 14 0.20
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.39
Consensus pattern (81 bp):
TGATTTGTCATTTTCCTATTAAAAAGGGATAGGGATGATGTGGAATCACAATTTCATACAATCCC
TTCTCTTTTGGCATAA
Found at i:10326048 original size:16 final size:16
Alignment explanation
Indices: 10326027--10326057 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
10326017 CTTTCAGTCG
10326027 GAGAAGAAAGAGACAA
1 GAGAAGAAAGAGACAA
10326043 GAGAAGAAAGAGACA
1 GAGAAGAAAGAGACA
10326058 GAAGTGTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.06, G:0.32, T:0.00
Consensus pattern (16 bp):
GAGAAGAAAGAGACAA
Found at i:10344639 original size:2 final size:2
Alignment explanation
Indices: 10344627--10344665 Score: 69
Period size: 2 Copynumber: 19.0 Consensus size: 2
10344617 AAAGCAAAAG
10344627 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10344666 TGTTAGAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 34 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:10351696 original size:46 final size:46
Alignment explanation
Indices: 10351618--10351802 Score: 316
Period size: 46 Copynumber: 4.0 Consensus size: 46
10351608 ACATTGCTAT
* * *
10351618 AACTCAGTATGGTTTTCTTCACGGAAATACCATGCCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
* * *
10351664 AACTCAGTATGGTTTTCCTCACTGAAACACCATACCTACTTTTCAT
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
10351710 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
10351756 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
10351802 A
1 A
10351803 CTTTGTCATG
Statistics
Matches: 131, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 131 1.00
ACGTcount: A:0.28, C:0.29, G:0.10, T:0.34
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACCGAAACACCATACCTACTTTTCAC
Found at i:10353077 original size:16 final size:17
Alignment explanation
Indices: 10353031--10353078 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
10353021 AAATTCTTTT
*
10353031 TAAACCACAAAATTCAA
1 TAAATCACAAAATTCAA
*
10353048 TAAATCACAAAATTCAC
1 TAAATCACAAAATTCAA
*
10353065 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
10353079 TTCTAAATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 7 0.25
17 21 0.75
ACGTcount: A:0.54, C:0.21, G:0.00, T:0.25
Consensus pattern (17 bp):
TAAATCACAAAATTCAA
Found at i:10363191 original size:6 final size:6
Alignment explanation
Indices: 10363180--10363205 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
10363170 GTGCCTCTCT
10363180 TGCACA TGCACA TGCACA TGCACA TG
1 TGCACA TGCACA TGCACA TGCACA TG
10363206 GTTAATGCAA
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:0.31, C:0.31, G:0.19, T:0.19
Consensus pattern (6 bp):
TGCACA
Found at i:10382394 original size:19 final size:19
Alignment explanation
Indices: 10382365--10382407 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
10382355 AAAATATGGG
10382365 AAATG-TATGTGTATTTTA
1 AAATGTTATGTGTATTTTA
10382383 AAATGTTATGTGTATTTTA
1 AAATGTTATGTGTATTTTA
10382402 AAATGT
1 AAATGT
10382408 GCATGCATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.49
Consensus pattern (19 bp):
AAATGTTATGTGTATTTTA
Found at i:10384306 original size:2 final size:2
Alignment explanation
Indices: 10384295--10384327 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
10384285 TTAGATTTTA
10384295 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10384328 TCTTTTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:10384550 original size:21 final size:21
Alignment explanation
Indices: 10384526--10384591 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 21
10384516 AAATATTTTT
10384526 AAAATTTAAAATTAAAAATAA
1 AAAATTTAAAATTAAAAATAA
***
10384547 AAAATTTATTTTTAAAAATTAA
1 AAAATTTAAAATTAAAAA-TAA
10384569 AAATTATTTAAAGTATTAAAAAT
1 AAA--ATTTAAA--ATTAAAAAT
10384592 TATAAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 15 0.44
22 6 0.18
24 5 0.15
25 1 0.03
26 7 0.21
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
AAAATTTAAAATTAAAAATAA
Found at i:10384563 original size:20 final size:20
Alignment explanation
Indices: 10384537--10384577 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
10384527 AAATTTAAAA
10384537 TTAAAAATAAAAAATTTATTT
1 TTAAAAATAAAAAA-TTATTT
*
10384558 TTAAAAATTAAAAATTATTT
1 TTAAAAATAAAAAATTATTT
10384578 AAAGTATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
TTAAAAATAAAAAATTATTT
Found at i:10384604 original size:19 final size:19
Alignment explanation
Indices: 10384560--10384604 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
10384550 ATTTATTTTT
**
10384560 AAAA-ATTAAAAATTATTT
1 AAAATATTAAAAATTATAA
*
10384578 AAAGTATTAAAAATTATAA
1 AAAATATTAAAAATTATAA
10384597 AAAATATT
1 AAAATATT
10384605 TTATACTTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAATATTAAAAATTATAA
Found at i:10385847 original size:12 final size:12
Alignment explanation
Indices: 10385830--10385854 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
10385820 TAACCTCTCT
10385830 AAATTTTATTAA
1 AAATTTTATTAA
10385842 AAATTTTATTAA
1 AAATTTTATTAA
10385854 A
1 A
10385855 CAACTTCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
AAATTTTATTAA
Found at i:10387442 original size:24 final size:25
Alignment explanation
Indices: 10387382--10387443 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 25
10387372 CTGTTAGCTT
10387382 ATTATTTTTAATTCATAAATTTAAAA
1 ATTATTTTTAA-TCATAAATTTAAAA
** *
10387408 AACATTATTAAT-AT-AATTTAAACA
1 ATTATTTTTAATCATAAATTTAAA-A
10387432 ATTATTTTTAAT
1 ATTATTTTTAAT
10387444 TTCTTGTATA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
23 8 0.28
24 12 0.41
25 1 0.03
26 8 0.28
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (25 bp):
ATTATTTTTAATCATAAATTTAAAA
Found at i:10392644 original size:3 final size:3
Alignment explanation
Indices: 10392636--10392661 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10392626 TCAATGGGCA
10392636 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
10392662 CAACGTGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10405640 original size:2 final size:2
Alignment explanation
Indices: 10405633--10405658 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10405623 CTTTGGCTTT
10405633 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
10405659 CCCTTTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:10412516 original size:24 final size:24
Alignment explanation
Indices: 10412484--10412532 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
10412474 AAGTATATAG
*
10412484 AAAAGAATAGATAAATTT-TTTTAA
1 AAAAAAATA-ATAAATTTATTTTAA
*
10412508 AAAAAAATAATACATTTATTTTAA
1 AAAAAAATAATAAATTTATTTTAA
10412532 A
1 A
10412533 CTGGAGTAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
AAAAAAATAATAAATTTATTTTAA
Found at i:10414961 original size:3 final size:3
Alignment explanation
Indices: 10414953--10414978 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
10414943 GAGACTCTGT
10414953 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
10414979 ATATCAGCGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:10415949 original size:21 final size:21
Alignment explanation
Indices: 10415925--10415968 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
10415915 AATTGCTGTG
*
10415925 GCTGCTGCCACCGCAGCTGCA
1 GCTGATGCCACCGCAGCTGCA
* **
10415946 GCTGATGCCGCCGTGGCTGCA
1 GCTGATGCCACCGCAGCTGCA
10415967 GC
1 GC
10415969 AAAGGCGGCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.11, C:0.39, G:0.34, T:0.16
Consensus pattern (21 bp):
GCTGATGCCACCGCAGCTGCA
Found at i:10431547 original size:50 final size:50
Alignment explanation
Indices: 10431420--10431605 Score: 162
Period size: 50 Copynumber: 3.7 Consensus size: 50
10431410 GAATATAACA
* * * ** ** * * *
10431420 TGCCAAAGCTATGTCCCAGACATATTCTTACATGGGATGTTTCCTAT-AC
1 TGCCAACGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCAG
* ** *
10431469 TGCCAATC-CCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAA-CGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCAG
* * * *
10431519 TGCTC-ATGCCATGTCCTAGATATGGTCTTACAGGGGACCTCTCATCTCAG
1 TGC-CAACGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCAG
*
10431569 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
1 TGCCAACGCCATGTCCCAGATATGGTCTTACATGGGA
10431606 TCTCATCACC
Statistics
Matches: 108, Mismatches: 24, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
49 37 0.34
50 70 0.65
51 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGATATGGTCTTACATGGGACCTCTCATATCAG
Found at i:10434224 original size:56 final size:56
Alignment explanation
Indices: 10434147--10434253 Score: 153
Period size: 56 Copynumber: 1.9 Consensus size: 56
10434137 ATTAGCAGTC
* * *
10434147 ACCTAATTATTAATAATTTTTTTAGTT-ATTCAATTATGAAAAGTTATAAAATAGTT
1 ACCTAATTATTAATAAATTTTTT-GTTCACTCAATTATAAAAAGTTATAAAATAGTT
* *
10434203 ACCTAATTATTAGTAAATTTTTTTTTCACTCAATTATAAAAAGTTATAAAA
1 ACCTAATTATTAATAAATTTTTTGTTCACTCAATTATAAAAAGTTATAAAA
10434254 CGGTGACCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
55 2 0.04
56 43 0.96
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (56 bp):
ACCTAATTATTAATAAATTTTTTGTTCACTCAATTATAAAAAGTTATAAAATAGTT
Found at i:10437059 original size:19 final size:18
Alignment explanation
Indices: 10437019--10437059 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
10437009 ATAACTCTAA
10437019 AATAGTAACAAAATTAAC
1 AATAGTAACAAAATTAAC
10437037 AATAG-AACAAAAGTTATAC
1 AATAGTAACAAAA-TTA-AC
10437056 AATA
1 AATA
10437060 TTTAAATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 8 0.38
19 6 0.29
ACGTcount: A:0.61, C:0.10, G:0.07, T:0.22
Consensus pattern (18 bp):
AATAGTAACAAAATTAAC
Found at i:10449690 original size:15 final size:17
Alignment explanation
Indices: 10449670--10449706 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
10449660 ACAAGTAAGA
10449670 TTTAAATATT-TC-TTT
1 TTTAAATATTATCATTT
10449685 TTTAAATATTATCATTT
1 TTTAAATATTATCATTT
10449702 TTTAA
1 TTTAA
10449707 TTTTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.50
16 2 0.10
17 8 0.40
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAAATATTATCATTT
Found at i:10454757 original size:61 final size:61
Alignment explanation
Indices: 10454662--10454785 Score: 230
Period size: 61 Copynumber: 2.0 Consensus size: 61
10454652 AGCCAATCTT
*
10454662 GTGTTTATCATTAGAGAAAAGACTAAATTAAGCAAGATTATTTTTCAAGGATTTTTATGTG
1 GTGTTTAGCATTAGAGAAAAGACTAAATTAAGCAAGATTATTTTTCAAGGATTTTTATGTG
*
10454723 GTGTTTAGCATTAGAGAAAAGACTGAATTAAGCAAGATTATTTTTCAAGGATTTTTATGTG
1 GTGTTTAGCATTAGAGAAAAGACTAAATTAAGCAAGATTATTTTTCAAGGATTTTTATGTG
10454784 GT
1 GT
10454786 CTACTTACCT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (61 bp):
GTGTTTAGCATTAGAGAAAAGACTAAATTAAGCAAGATTATTTTTCAAGGATTTTTATGTG
Found at i:10477091 original size:78 final size:78
Alignment explanation
Indices: 10476962--10477118 Score: 287
Period size: 78 Copynumber: 2.0 Consensus size: 78
10476952 ATCTAAAGTA
* *
10476962 AGCAAAGTTCGAGGAAAAACAAAGGCAAACACTATCAAAGCTAAAAAGTAAAACCCCAAACGGAT
1 AGCAAAGTTCGAGGAAAAACAAAGGCAAACACTACCAAACCTAAAAAGTAAAACCCCAAACGGAT
10477027 ACTCAACATTTCC
66 ACTCAACATTTCC
*
10477040 AGCAAAGTTCGAGGAAAAACTAAGGCAAACACTACCAAACCTAAAAAGTAAAACCCCAAACGGAT
1 AGCAAAGTTCGAGGAAAAACAAAGGCAAACACTACCAAACCTAAAAAGTAAAACCCCAAACGGAT
10477105 ACTCAACATTTCC
66 ACTCAACATTTCC
10477118 A
1 A
10477119 TCCAAACCAA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 76 1.00
ACGTcount: A:0.48, C:0.24, G:0.13, T:0.14
Consensus pattern (78 bp):
AGCAAAGTTCGAGGAAAAACAAAGGCAAACACTACCAAACCTAAAAAGTAAAACCCCAAACGGAT
ACTCAACATTTCC
Found at i:10488156 original size:43 final size:42
Alignment explanation
Indices: 10488048--10488232 Score: 255
Period size: 42 Copynumber: 4.3 Consensus size: 42
10488038 ACGTCGCTAA
* *
10488048 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAGATCATGTT
*
10488092 CTTTAGCGGCGCTTAGGAAAAAACGCTGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
*
10488134 CTTTAGCGGCGCTTAGGAAAAAACGCCACTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
* * *
10488176 CTTTAGCGGCGCTTTGGAAGAAAACGCCTCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAGA-TCATGTT
*
10488219 CTATAGCGGCGCTT
1 CTTTAGCGGCGCTT
10488233 GTTTCACAAA
Statistics
Matches: 130, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
42 85 0.65
43 32 0.25
44 13 0.10
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:10488713 original size:21 final size:21
Alignment explanation
Indices: 10488669--10488713 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
10488659 GCTTCTATCG
* *
10488669 CTGCTTCTCTCGCTGCGGCAT
1 CTGCTTCCCTCGCTGCCGCAT
*
10488690 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCCCTCGCTGCCGCAT
10488711 CTG
1 CTG
10488714 ATTTAAGTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.02, C:0.44, G:0.22, T:0.31
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCCGCAT
Found at i:10493732 original size:261 final size:261
Alignment explanation
Indices: 10493268--10493823 Score: 927
Period size: 261 Copynumber: 2.1 Consensus size: 261
10493258 AGAGTAAAAA
*
10493268 CGCCACTAATAACACAGACAAAACGGCATCGTCATAAGATAACATTAAACATTTTTGCGGCGCTT
1 CGCCACTAATAACACAGACAAAACGGCACCGTCATAAGATAACATTAAACATTTTTGCGGCGCTT
* * * *
10493333 CAGCTAAAGCGCCACTAATAAAAATAGGAAATGGCTCCGTTTCCTCAGCTCGTAATAAATATTTG
66 CAGCTAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAATAAATATTTC
10493398 TGGCATTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCGTTACGATTAAA
131 TGGCATTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCGTTACGATTAAA
* *
10493463 GGAAATTTGTGGCGTTTCTTCGTAAAATGCCGGTAATATATCACCTTTAGCGGTGTTTTTCAAAT
196 GGAAATTTGTGGCGTTTCTTCGTAAAACGCCGGTAATATATCACCTTTAGCGGCGTTTTTCAAAT
10493528 G
261 G
* * *
10493529 CGCCACTAATAACACGGACAAAACGGCACCGTTATAAGATAGCATTAAACATTTTTGCGGCGCTT
1 CGCCACTAATAACACAGACAAAACGGCACCGTCATAAGATAACATTAAACATTTTTGCGGCGCTT
*
10493594 TAGCTAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAATAAATATTTC
66 CAGCTAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAATAAATATTTC
* *
10493659 TGGCGTTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTTGTTAC-AGTTAA
131 TGGCATTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCGTTACGA-TTAA
*
10493723 AGGAAATTTGTGGCGTTTCTTCGTAAAACGCCGGTAATATATCACTTTTAGCGGCGTTTTTCAAA
195 AGGAAATTTGTGGCGTTTCTTCGTAAAACGCCGGTAATATATCACCTTTAGCGGCGTTTTTCAAA
10493788 TG
260 TG
* *
10493790 CGCCACTAAAAGAAAACA-ACAAAACGGCACCGTC
1 CGCCACT--AATAACACAGACAAAACGGCACCGTC
10493824 TTTGTTACAG
Statistics
Matches: 274, Mismatches: 18, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
260 1 0.00
261 252 0.92
262 15 0.05
263 6 0.02
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.26
Consensus pattern (261 bp):
CGCCACTAATAACACAGACAAAACGGCACCGTCATAAGATAACATTAAACATTTTTGCGGCGCTT
CAGCTAAAGCGCCACTAATAAAAATAGGAAACGACGCCGTTTCCTCAGCTCGTAATAAATATTTC
TGGCATTTTTAAAATGCGCCACTAAAAGAAAACAACAAAACGGCACCGTCTTCGTTACGATTAAA
GGAAATTTGTGGCGTTTCTTCGTAAAACGCCGGTAATATATCACCTTTAGCGGCGTTTTTCAAAT
G
Done.