Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167993.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_25, 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: 17943224
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 94000 characters in sequence are not A, C, G, or T
File 79 of 100
Found at i:14179484 original size:14 final size:15
Alignment explanation
Indices: 14179467--14179509 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
14179457 ACAAAGAAAC
14179467 AAAAGAAAAAAAG-G
1 AAAAGAAAAAAAGTG
**
14179481 AAAAGTGAAAAAGTG
1 AAAAGAAAAAAAGTG
14179496 AAAA-AAAAAAAGTG
1 AAAAGAAAAAAAGTG
14179510 TTATGATATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 19 0.79
15 5 0.21
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (15 bp):
AAAAGAAAAAAAGTG
Found at i:14179492 original size:22 final size:21
Alignment explanation
Indices: 14179467--14179509 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
14179457 ACAAAGAAAC
14179467 AAAA-GAAAAAAAGGAAAAGTGA
1 AAAAGGAAAAAAA--AAAAGTGA
14179489 AAAAGTGAAAAAAAAAAAGTG
1 AAAAG-GAAAAAAAAAAAGTG
14179510 TTATGATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.72, C:0.00, G:0.21, T:0.07
Consensus pattern (21 bp):
AAAAGGAAAAAAAAAAAGTGA
Found at i:14180039 original size:4 final size:4
Alignment explanation
Indices: 14180032--14180070 Score: 60
Period size: 4 Copynumber: 9.2 Consensus size: 4
14180022 GGAAAAAGTG
14180032 AGAA AGAA AGAA AGAA AGAA AGAA AGAA ATGAA ATGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A-GAA A-GAA A
14180071 TGAATAGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 25 0.74
5 9 0.26
ACGTcount: A:0.72, C:0.00, G:0.23, T:0.05
Consensus pattern (4 bp):
AGAA
Found at i:14181096 original size:29 final size:29
Alignment explanation
Indices: 14181036--14181096 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
14181026 TGCACTAATA
** * *
14181036 AAGTTTTAAGCTTAGTTTAACTAGTATCC
1 AAGTTTTAAGCCAAGTTTAACTAGCATAC
* *
14181065 AAGTTTTAAGCCAAGTTTAGCTGGCATAC
1 AAGTTTTAAGCCAAGTTTAACTAGCATAC
14181094 AAG
1 AAG
14181097 CCAATATTAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (29 bp):
AAGTTTTAAGCCAAGTTTAACTAGCATAC
Found at i:14181128 original size:22 final size:23
Alignment explanation
Indices: 14181098--14181140 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
14181088 GCATACAAGC
14181098 CAATATTAGCT-AGCACATAAGTT
1 CAATATTAGCTGA-CACATAAGTT
14181121 CAAT-TTAGCTGACACATAAG
1 CAATATTAGCTGACACATAAG
14181141 CCTAGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.28
Consensus pattern (23 bp):
CAATATTAGCTGACACATAAGTT
Found at i:14181432 original size:32 final size:31
Alignment explanation
Indices: 14181396--14181842 Score: 117
Period size: 32 Copynumber: 13.8 Consensus size: 31
14181386 TTAATACCAT
14181396 ATAAAATTTAAGCCTAGTTTAGCTGACATCTA
1 ATAAAATTTAAGCCTAGTTTAGCTGACA-CTA
* ** * * *
14181428 ATAAAAATTTAAGCCCAGTCAAGTTAACACCCA
1 AT-AAAATTTAAGCCTAGTTTAGCTGACA-CTA
* * * *
14181461 GTAAAATTTAAGCCTGGCTTAG-TTACTACCTA
1 ATAAAATTTAAGCCTAGTTTAGCTGAC-A-CTA
* **
14181493 ATGAAAATATTTAAGCCGAACTTAGCT-AGCACTCA
1 AT--AAA-ATTTAAGCCTAGTTTAGCTGA-CACT-A
* * * * * *
14181528 ATGAAAGTTTAAGCCCAGATTATCTGGCACCA
1 AT-AAAATTTAAGCCTAGTTTAGCTGACACTA
* *
14181560 ATGAAA-TTAAGACTAGTTTAGCT-AGCACTA
1 ATAAAATTTAAGCCTAGTTTAGCTGA-CACTA
* * * * * * *
14181590 AGGAAAATTTAAACCCAATATAGCT-AGCATTC
1 A-TAAAATTTAAGCCTAGTTTAGCTGA-CACTA
* *
14181622 ATGAAAAGATGTAAGCCTAGTTTAGCTAGGACCCCCATGA
1 AT--AAA-ATTTAAGCCTAGTTTAGCT--GA--CAC-T-A
* * *
14181662 A-AAAATTTAAGCCTAGTTTTA-TTGGCACCA
1 ATAAAATTTAAGCCTAG-TTTAGCTGACACTA
* * * *
14181692 ACAAAAATTTAAGCCTAGTTTAGTTGCCATTCA
1 A-TAAAATTTAAGCCTAGTTTAGCTGACACT-A
* * * *
14181725 ATGAAAATTTAAG-CTAGTTCATCTGGCACCA
1 AT-AAAATTTAAGCCTAGTTTAGCTGACACTA
*
14181756 ATGAAAATTTAAG--TAGTTTAGCTTG-CACCA
1 AT-AAAATTTAAGCCTAGTTTAGC-TGACACTA
* *
14181786 ATAGAAATTTAAACCTAGTTTAGCTGGCA-TAA
1 ATA-AAATTTAAGCCTAGTTTAGCTGACACT-A
*
14181818 ATGAAAATTTAAGTCTAGTTTAGCT
1 AT-AAAATTTAAGCCTAGTTTAGCT
14181843 AGTACCTTAT
Statistics
Matches: 306, Mismatches: 75, Indels: 68
0.68 0.17 0.15
Matches are distributed among these distances:
29 1 0.00
30 42 0.14
31 30 0.10
32 109 0.36
33 57 0.19
34 23 0.08
35 19 0.06
36 14 0.05
37 8 0.03
38 1 0.00
39 1 0.00
40 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (31 bp):
ATAAAATTTAAGCCTAGTTTAGCTGACACTA
Found at i:14181776 original size:196 final size:193
Alignment explanation
Indices: 14181525--14181886 Score: 446
Period size: 196 Copynumber: 1.9 Consensus size: 193
14181515 TAGCTAGCAC
* *
14181525 TCAATGAAAGTTTAAGCCCAGATTATCTGGCACCAATGAAATTAAGACTAGTTTAGCTAGCACTA
1 TCAATGAAAATTTAAGCCCAGATTATCTGGCACCAATGAAATTAAGA-TAGTTTAGCTAGCACCA
**
14181590 AG-GAAAATTTAAACCCAATATAGCTAGCATTCATGAAAAGATGTAAGCCTAGTTTAGCTAGGAC
65 AGAG-AAATTTAAACCCAATATAGCTAGCATAAATG-AAA-ATGTAAGCCTAGTTTAGCTAGGA-
*
14181654 CCCCATGAAAAAATTTAAGCCTAGTTT-TATTGGCACCAACAAAAATTTAAGCCTAGTTTAGTTG
126 CCCCATGAAAAAATTTAAGCCAAGTTTAT-TTGGCACCAACAAAAATTTAAGCCTAGTTTAGTTG
14181718 CCAT
190 CCAT
* *
14181722 TCAATGAAAATTTAAG-CTAG-TTCATCTGGCACCAATGAAAATTTAAG-TAGTTTAGCTTGCAC
1 TCAATGAAAATTTAAGCCCAGATT-ATCTGGCACCAATG-AAA-TTAAGATAGTTTAGCTAGCAC
* * * * * * * *
14181784 CAATAGAAATTTAAACCTAGTTTAGCTGGCATAAATGAAAATTTAAGTCTAGTTTAGCTAGTACC
63 CAAGAGAAATTTAAACCCAATATAGCTAGCATAAATGAAAATGTAAGCCTAGTTTAGCTAGGACC
** *
14181849 TTATGAAAAAATTTAAGCCAAGTTTATTTGTCACCAAC
128 CCATGAAAAAATTTAAGCCAAGTTTATTTGGCACCAAC
14181887 CTATATTTTA
Statistics
Matches: 142, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
193 34 0.24
194 21 0.15
195 5 0.04
196 58 0.41
197 19 0.13
198 5 0.04
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (193 bp):
TCAATGAAAATTTAAGCCCAGATTATCTGGCACCAATGAAATTAAGATAGTTTAGCTAGCACCAA
GAGAAATTTAAACCCAATATAGCTAGCATAAATGAAAATGTAAGCCTAGTTTAGCTAGGACCCCA
TGAAAAAATTTAAGCCAAGTTTATTTGGCACCAACAAAAATTTAAGCCTAGTTTAGTTGCCAT
Found at i:14182052 original size:34 final size:35
Alignment explanation
Indices: 14181996--14182062 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
14181986 TTTAAGTCCA
*
14181996 GTTTAGCTGGCACTCATGAAAAG-ATGTAAGCCCG
1 GTTTAGCTGGCACCCATGAAAAGAATGTAAGCCCG
* *
14182030 GTTTAGTTGGCATCCCAT-AAAAGAATTTAAGCC
1 GTTTAGCTGGCA-CCCATGAAAAGAATGTAAGCC
14182063 TAATTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.27
Consensus pattern (35 bp):
GTTTAGCTGGCACCCATGAAAAGAATGTAAGCCCG
Found at i:14183387 original size:20 final size:20
Alignment explanation
Indices: 14183350--14183388 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
14183340 ATGGTGTAAT
***
14183350 AATAAAAAAAATTTAAAAAA
1 AATAAAAAAAAAAGAAAAAA
14183370 AATAAAAAAAAAAGAAAAA
1 AATAAAAAAAAAAGAAAAA
14183389 TGAATATGGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.13
Consensus pattern (20 bp):
AATAAAAAAAAAAGAAAAAA
Found at i:14184642 original size:25 final size:26
Alignment explanation
Indices: 14184608--14184661 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
14184598 TTGTATAGAT
14184608 CATTTGCATC-AGGAAAAGACATTTG
1 CATTTGCATCAAGGAAAAGACATTTG
*
14184633 CATTTGCATCAAGTAAAAGACATTTG
1 CATTTGCATCAAGGAAAAGACATTTG
14184659 CAT
1 CAT
14184662 GTTTTCATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
25 10 0.37
26 17 0.63
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (26 bp):
CATTTGCATCAAGGAAAAGACATTTG
Found at i:14184949 original size:22 final size:23
Alignment explanation
Indices: 14184905--14184948 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
14184895 AAGATAAGAT
14184905 CTTTTGAAACAAAAAGTGAAAAG
1 CTTTTGAAACAAAAAGTGAAAAG
* *
14184928 CTTTTGGAATAAAAAGTGAAA
1 CTTTTGAAACAAAAAGTGAAA
14184949 GTTTTCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (23 bp):
CTTTTGAAACAAAAAGTGAAAAG
Found at i:14185177 original size:41 final size:41
Alignment explanation
Indices: 14185012--14185284 Score: 184
Period size: 40 Copynumber: 6.8 Consensus size: 41
14185002 AAACCTCTGT
* * * * *
14185012 GCAAAATCTTAAATTTTTTATAGAA-TTCCAAAAGCTTC-A
1 GCAAAATCTTAAATTTTTGAAAAAATTTCCAAGACCTTCAA
* * * * *
14185051 GACAAAATCTTAAA-TTGT-AAAATGATTTCCATGACCTCCAG
1 G-CAAAATCTTAAATTTTTGAAAA-AATTTCCAAGACCTTCAA
* * ** * *
14185092 GTAAAACCTTAAATTTTTG-ACTAATTTTCAAGA-CTTGCAT
1 GCAAAATCTTAAATTTTTGAAAAAATTTCCAAGACCTT-CAA
14185132 GCAAAATCTTAAATTTTTGAAAAAATTTCCAAGACCTTCAA
1 GCAAAATCTTAAATTTTTGAAAAAATTTCCAAGACCTTCAA
* * * * ** *
14185173 GCAAAACCTTAAATTTTTTAAAGAATTT-TAAGATTTTCGA
1 GCAAAATCTTAAATTTTTGAAAAAATTTCCAAGACCTTCAA
* * * * *
14185213 GCAAAATTTTAAATTTTTGAAAAATTTTCAAAAACCTCCAA
1 GCAAAATCTTAAATTTTTGAAAAAATTTCCAAGACCTTCAA
* * *
14185254 GTAAAATCTCAAATTTTTG-AAAGATTTCCAA
1 GCAAAATCTTAAATTTTTGAAAAAATTTCCAA
14185285 AGTCTTCGGG
Statistics
Matches: 175, Mismatches: 49, Indels: 19
0.72 0.20 0.08
Matches are distributed among these distances:
38 2 0.01
39 7 0.04
40 98 0.56
41 65 0.37
42 3 0.02
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (41 bp):
GCAAAATCTTAAATTTTTGAAAAAATTTCCAAGACCTTCAA
Found at i:14185187 original size:81 final size:80
Alignment explanation
Indices: 14185053--14185274 Score: 234
Period size: 81 Copynumber: 2.8 Consensus size: 80
14185043 AAGCTTCAGA
* * * * **
14185053 CAAAATCTTAAA-TTGT-AAAATGATTTCCATGACCTCCAGGTAAAACCTTAAATTTTTGACTAA
1 CAAAATCTTAAATTTTTGAAAA-AATTTCCAAGACCTCCAAGTAAAACCTTAAATTTTTGAAGAA
14185116 TTTTCAAGACTTGC-ATG
65 TTTT-AAGACTTGCGA-G
* * *
14185133 CAAAATCTTAAATTTTTGAAAAAATTTCCAAGACCTTCAAGCAAAACCTTAAATTTTTTAAAGAA
1 CAAAATCTTAAATTTTTGAAAAAATTTCCAAGACCTCCAAGTAAAACCTTAAA-TTTTTGAAGAA
* *
14185198 TTTTAAGATTTTCGAG
65 TTTTAAGACTTGCGAG
* * * * * *
14185214 CAAAATTTTAAATTTTTGAAAAATTTTCAAAAACCTCCAAGTAAAATCTCAAATTTTTGAA
1 CAAAATCTTAAATTTTTGAAAAAATTTCCAAGACCTCCAAGTAAAACCTTAAATTTTTGAA
14185275 AGATTTCCAA
Statistics
Matches: 118, Mismatches: 20, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
80 19 0.16
81 82 0.69
82 17 0.14
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.36
Consensus pattern (80 bp):
CAAAATCTTAAATTTTTGAAAAAATTTCCAAGACCTCCAAGTAAAACCTTAAATTTTTGAAGAAT
TTTAAGACTTGCGAG
Found at i:14185352 original size:22 final size:22
Alignment explanation
Indices: 14185293--14185353 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
14185283 AAAGTCTTCG
*
14185293 GGCACAATCTCAAAGTCCTCCA
1 GGCATAATCTCAAAGTCCTCCA
* *
14185315 GGCATTATTTCAAAGTCCTCC-
1 GGCATAATCTCAAAGTCCTCCA
*
14185336 GAGCATAATCTCTAAGTC
1 G-GCATAATCTCAAAGTC
14185354 TTTCAGGTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (22 bp):
GGCATAATCTCAAAGTCCTCCA
Found at i:14186870 original size:19 final size:19
Alignment explanation
Indices: 14186833--14186870 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
14186823 CATGAAAAAC
*
14186833 TAGAGGAAGAAATATGAAA
1 TAGAGGAAGAAATAGGAAA
14186852 TAGAGGAGAGAAA-AGGAAA
1 TAGAGGA-AGAAATAGGAAA
14186871 AAACGTGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.58, C:0.00, G:0.32, T:0.11
Consensus pattern (19 bp):
TAGAGGAAGAAATAGGAAA
Found at i:14187991 original size:20 final size:19
Alignment explanation
Indices: 14187953--14187999 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
14187943 CACATAAAAT
*
14187953 CCTAAATTCTAAACCCTAAA
1 CCTAAATT-AAAACCCTAAA
*
14187973 CCTTAAATTAAAACTCTAAA
1 CC-TAAATTAAAACCCTAAA
14187993 CCTAAAT
1 CCTAAAT
14188000 CCTAATTCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 5 0.21
20 13 0.54
21 6 0.25
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.28
Consensus pattern (19 bp):
CCTAAATTAAAACCCTAAA
Found at i:14187998 original size:33 final size:33
Alignment explanation
Indices: 14187915--14188004 Score: 80
Period size: 33 Copynumber: 2.8 Consensus size: 33
14187905 TTCCCATACC
*
14187915 TTAAAACT-TAAAACCT-AACCCTAAACCCCACA
1 TTAAAACTCT-AAACCTAAACCCTAAACCCCAAA
* **
14187947 -TAAAA-TCCTAAATTCTAAACCCTAAACCTTAAA
1 TTAAAACT-CTAAA-CCTAAACCCTAAACCCCAAA
*
14187980 TTAAAACTCTAAACCTAAATCCTAA
1 TTAAAACTCTAAACCTAAACCCTAA
14188005 TTCCTAAACT
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
30 1 0.02
31 8 0.17
32 3 0.07
33 23 0.50
34 10 0.22
35 1 0.02
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (33 bp):
TTAAAACTCTAAACCTAAACCCTAAACCCCAAA
Found at i:14192306 original size:18 final size:20
Alignment explanation
Indices: 14192275--14192317 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
14192265 TTTAAAATTT
*
14192275 AATATTTTTAAAAAACT-AA
1 AATATTTCTAAAAAACTCAA
*
14192294 AATATTTCT-AAAAATTCAA
1 AATATTTCTAAAAAACTCAA
14192313 AATAT
1 AATAT
14192318 ATTTTGTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (20 bp):
AATATTTCTAAAAAACTCAA
Found at i:14192879 original size:38 final size:38
Alignment explanation
Indices: 14192809--14192885 Score: 93
Period size: 38 Copynumber: 2.0 Consensus size: 38
14192799 TTTTTTAAAA
**
14192809 AATATTTTTAAAATAAAAATTAATATTTAAATATATTT
1 AATATTTTTAAAATAAAAATTAATATAAAAATATATTT
* * *
14192847 AATATATTTTAAAGTTAAAATTAA-ATAAAAATATTTTT
1 AATAT-TTTTAAAATAAAAATTAATATAAAAATATATTT
14192885 A
1 A
14192886 TTTCTTAGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 17 0.52
39 16 0.48
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.45
Consensus pattern (38 bp):
AATATTTTTAAAATAAAAATTAATATAAAAATATATTT
Found at i:14194033 original size:64 final size:63
Alignment explanation
Indices: 14193936--14194083 Score: 156
Period size: 64 Copynumber: 2.3 Consensus size: 63
14193926 ATTTTTGGAT
* * * * * * *
14193936 AAAAATATCTCAAATAATCCCCTTATATTTTTTAAA-GAATATTATTTAAGA-CGTTTTTTATCC
1 AAAAAAATCTTAAATAATCCCCTAATATATTTTAAAGGAA-ATTATTTAAAAGCATTTTTTA--A
14193999 C
63 C
**
14194000 AAAAAAATCTTAAATAATCTTCTAATATATTTTAAAGGAAATTATTTAAAAGCATTTTTTAAC
1 AAAAAAATCTTAAATAATCCCCTAATATATTTTAAAGGAAATTATTTAAAAGCATTTTTTAAC
*
14194063 AAAAAACCTCTTAAATAATCC
1 AAAAAA-ATCTTAAATAATCC
14194084 TTTTTAAAAA
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
63 7 0.10
64 52 0.74
65 11 0.16
ACGTcount: A:0.44, C:0.14, G:0.04, T:0.39
Consensus pattern (63 bp):
AAAAAAATCTTAAATAATCCCCTAATATATTTTAAAGGAAATTATTTAAAAGCATTTTTTAAC
Found at i:14195861 original size:15 final size:16
Alignment explanation
Indices: 14195828--14195862 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
14195818 TGTTTATACT
*
14195828 TTTATTTTGTATTATA
1 TTTATTTTGTATCATA
14195844 TTTATTTT-TATCATA
1 TTTATTTTGTATCATA
14195859 TTTA
1 TTTA
14195863 CCTTATTAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (16 bp):
TTTATTTTGTATCATA
Found at i:14199177 original size:28 final size:29
Alignment explanation
Indices: 14199137--14199195 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 29
14199127 AAGATTGAGA
* *
14199137 TTCAATTCTTAATAC-TTGTAAATTTTCT
1 TTCAATTCTTAATACTTTGCAAAATTTCT
14199165 TTCAATTCTTAATACTTTGCAAAATTTCT
1 TTCAATTCTTAATACTTTGCAAAATTTCT
14199194 TT
1 TT
14199196 TTTTAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 15 0.54
29 13 0.46
ACGTcount: A:0.29, C:0.15, G:0.03, T:0.53
Consensus pattern (29 bp):
TTCAATTCTTAATACTTTGCAAAATTTCT
Found at i:14200053 original size:51 final size:50
Alignment explanation
Indices: 14199875--14200541 Score: 443
Period size: 51 Copynumber: 13.2 Consensus size: 50
14199865 CCCAATAGTA
* * * *
14199875 TTTTCAAAATGTGATTTTTAAAGTTCTTTAACCTATTTTTATAAGCACCTTT
1 TTTTCAAAATGAGATTTTTAAAGTTCCTTAGCCTATTTTTATAAG-AGC-TT
* * **
14199927 TTTTCAAAATGAGATTTTTAAAGTTTCTTAGCCTATTTTTATATGAGCCA
1 TTTTCAAAATGAGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAGCTT
* * *
14199977 TTTTCTAAATGTGAATTTTAAAGTTCCTTAGCCTATTTTTATAAGAGTCTT
1 TTTTCAAAATGAGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAG-CTT
* * * * * * * *
14200028 TTTTCCAAATAAGACTTTTAGAGTTCCCTAGCATATTTTTATAAAAGCCCT
1 TTTTCAAAATGAGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAG-CTT
** * * * *
14200079 TTTTCCCATTAAGATTTTTAAAGTTCCCTAGCCTATTTTTATAGGAGCTCT
1 TTTTCAAAATGAGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAGCT-T
* ** ** *
14200130 TTTTCAAAAT-ATGATTTTTAAAATTTTTTAGCCTATTTTTATAA-ATAATC
1 TTTTCAAAATGA-GATTTTTAAAGTTCCTTAGCCTATTTTTATAAGA-GCTT
* * * * * * * *
14200180 TTTTCCAAATGTGAGTTTTAAGGTTCTTTAACCTATTTGTATAGGCA-CTTT
1 TTTTCAAAATGAGATTTTTAAAGTTCCTTAGCCTATTTTTATAAG-AGC-TT
* ** ** * *
14200231 TTTTAAAAAATTTGAAGTTTAAAGTTCCTTAGCCTATTTTTATAGGAGCCT
1 TTTT-CAAAATGAGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAGCTT
* * * * * * *
14200282 TTTTCCAAATGTGAATTTTAAATTTCCCTAACCTATTTTTATATGAGCATT
1 TTTTCAAAATGAGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAGC-TT
* *** * *
14200333 TTCTCAAAATTTTATATTTAAAGCTCCTTAGCCTATTTTTAT-AGAAGCTCT
1 TTTTCAAAATGAGATTTTTAAAGTTCCTTAGCCTATTTTTATAAG-AGCT-T
* * ** * *
14200384 TTTCCAAAAAGTTATTTTTAAAATT-CTCTAGCCTATTTTTATATA-AGCCAT
1 TTTTCAAAATGAGATTTTTAAAGTTCCT-TAGCCTATTTTTATA-AGAG-CTT
* ** * *
14200435 TTTTCAAAATGAGCA-TTTTAAAGTTCCCTAGCCTACCTTTATAGGAGCCAT
1 TTTTCAAAATGAG-ATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAG-CTT
* * * *
14200486 TTTT-AAAATGAGATTTTTAAAGTTCCTTAGCTTATCTTTATAAAAGC-C
1 TTTTCAAAATGAGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAGCTT
14200534 TTTTCAAA
1 TTTTCAAA
14200542 GTTAATATTT
Statistics
Matches: 485, Mismatches: 108, Indels: 47
0.76 0.17 0.07
Matches are distributed among these distances:
48 4 0.01
49 5 0.01
50 154 0.32
51 244 0.50
52 77 0.16
53 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (50 bp):
TTTTCAAAATGAGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAGCTT
Found at i:14200083 original size:102 final size:102
Alignment explanation
Indices: 14199875--14200537 Score: 501
Period size: 102 Copynumber: 6.5 Consensus size: 102
14199865 CCCAATAGTA
* * *
14199875 TTTTCAAAATGTGATTTTTAAAGTTCTTTAACCTATTTTTATAAGCA-CCTTTTTTTCAAAATGA
1 TTTTCAAAATGTGATTTTTAAAGTTCCTTAGCCTATTTTTATAAG-AGCC-TTTTTTCAAAATAA
* * *
14199939 GATTTTTAAAGTTTCTTAGCCTATTTTTATATG-AG-CCA
64 GACTTTTAAAGTTCCTTAGCCTATTTTTATA-GAAGCCCT
* * * *
14199977 TTTTCTAAATGTGAATTTTAAAGTTCCTTAGCCTATTTTTATAAGAGTCTTTTTTCCAAATAAGA
1 TTTTCAAAATGTGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAGCCTTTTTTCAAAATAAGA
* * * *
14200042 CTTTTAGAGTTCCCTAGCATATTTTTATAAAAGCCCT
66 CTTTTAAAGTTCCTTAGCCTATTTTTATAGAAGCCCT
** * ** * * *
14200079 TTTTCCCATTAAGATTTTTAAAGTTCCCTAGCCTATTTTTATAGGAG-CTCTTTTTCAAAATATG
1 TTTTCAAAATGTGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAGCCT-TTTTTCAAAATAAG
* * ** ***
14200143 ATTTTTAAAATTTTTTAGCCTATTTTTATA-AA-TAAT
65 ACTTTTAAAGTTCCTTAGCCTATTTTTATAGAAGCCCT
* * * * * * *
14200179 CTTTTCCAAATGTGAGTTTTAAGGTTCTTTAACCTATTTGTAT-AG-GCACTTTTTTTAAAA-AA
1 -TTTTCAAAATGTGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAGC-CTTTTTTCAAAATAA
** *
14200241 TTTGAAGTTTAAAGTTCCTTAGCCTATTTTTATAGGAG-CCT
64 ---GACTTTTAAAGTTCCTTAGCCTATTTTTATAGAAGCCCT
* * * * * * * * ***
14200282 TTTTCCAAATGTGAATTTTAAATTTCCCTAACCTATTTTTATATGAGCATTTTCTCAAAATTTTA
1 TTTTCAAAATGTGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAGCCTTTTTTCAAAATAAGA
* *
14200347 -TATTTAAAGCTCCTTAGCCTATTTTTATAGAAGCTCT
66 CT-TTTAAAGTTCCTTAGCCTATTTTTATAGAAGCCCT
* * * * * *
14200384 TTTCCAAAAAGTTATTTTTAAAATT-CTCTAGCCTATTTTTATATA-AGCCATTTTTCAAAATGA
1 TTTTCAAAATGTGATTTTTAAAGTTCCT-TAGCCTATTTTTATA-AGAGCCTTTTTTCAAAATAA
* ** * *
14200447 G-CATTTTAAAGTTCCCTAGCCTACCTTTATAGGAGCCAT
64 GAC-TTTTAAAGTTCCTTAGCCTATTTTTATAGAAGCCCT
* * * *
14200486 TTTT-AAAATGAGATTTTTAAAGTTCCTTAGCTTATCTTTATAAAAGCCTTTT
1 TTTTCAAAATGTGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAGCCTTTT
14200538 CAAAGTTAAT
Statistics
Matches: 436, Mismatches: 102, Indels: 47
0.75 0.17 0.08
Matches are distributed among these distances:
99 2 0.00
100 12 0.03
101 146 0.33
102 261 0.60
103 13 0.03
104 2 0.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.46
Consensus pattern (102 bp):
TTTTCAAAATGTGATTTTTAAAGTTCCTTAGCCTATTTTTATAAGAGCCTTTTTTCAAAATAAGA
CTTTTAAAGTTCCTTAGCCTATTTTTATAGAAGCCCT
Found at i:14200387 original size:203 final size:202
Alignment explanation
Indices: 14199875--14200511 Score: 529
Period size: 203 Copynumber: 3.1 Consensus size: 202
14199865 CCCAATAGTA
* ** *
14199875 TTTTCAAAATGTGATTTTTAAAGTTCTTTAACCTATTTTTATAAGCACCTTTTTTTCAAAATGA-
1 TTTTCCAAATGTGATTTTTAAAGTTCCCTAACCTATTTTTATAAG-AGC-TTTTTTCAAAAT-AT
*
14199939 GATTTTTAAAGTTTCTTAGCCTATTTTTATATG-AGC-CATTTTCTAAATGTGAATTTTAAAGTT
63 GATTTTTAAAGTTTCTTAGCCTATTTTTATA-GAAGCTC-TTTTCCAAATGTGAATTTTAAAGTT
* * * ** ** *
14200002 CCTTAGCCTATTTTTATAAGAGTCTTTTTTCCAAATAAGACTTTTAGAGTTCCCTAGCATATTTT
126 CCTTAACCTATTTGTATAAGACTCTTTTTTAAAAATAAGAAGTTTAAAGTTCCCTAGCATATTTT
14200067 TATAAAAGCCCT
191 TATAAAAGCCCT
* * ** * *
14200079 TTTTCCCATTAAGATTTTTAAAGTTCCCTAGCCTATTTTTATAGGAGCTCTTTTTCAAAATATGA
1 TTTTCCAAATGTGATTTTTAAAGTTCCCTAACCTATTTTTATAAGAGCT-TTTTTCAAAATATGA
* * ** * * *
14200144 TTTTTAAAATTTTTTAGCCTATTTTTATA-AATAATCTTTTCCAAATGTGAGTTTTAAGGTTCTT
65 TTTTTAAAGTTTCTTAGCCTATTTTTATAGAA-GCTCTTTTCCAAATGTGAATTTTAAAGTTCCT
* ** * *
14200208 TAACCTATTTGTATAGGCACT-TTTTTTAAAAAATTTGAAGTTTAAAGTTCCTTAGCCTATTTTT
129 TAACCTATTTGTATAAG-ACTCTTTTTT-AAAAATAAGAAGTTTAAAGTTCCCTAGCATATTTTT
**
14200272 ATAGGAG-CCT
192 ATAAAAGCCCT
* * * * * *
14200282 TTTTCCAAATGTGAATTTTAAATTTCCCTAACCTATTTTTATATGAGCATTTTCTCAAAATTTTA
1 TTTTCCAAATGTGATTTTTAAAGTTCCCTAACCTATTTTTATAAGAGC-TTTTTTCAAAATATGA
* * * * * * *
14200347 TATTTAAAGCTCCTTAGCCTATTTTTATAGAAGCTCTTTTCCAAAAAGTTATTTTTAAAATT-CT
65 TTTTTAAAGTTTCTTAGCCTATTTTTATAGAAGCTCTTTTCC-AAATGTGAATTTTAAAGTTCCT
* * * * * * * * **
14200411 CTAGCCTATTTTTATATA-AGC-CATTTTTCAAAATGAGCATTTTAAAGTTCCCTAGCCTACCTT
129 -TAACCTATTTGTATA-AGA-CTCTTTTTTAAAAATAAGAAGTTTAAAGTTCCCTAGCATATTTT
** *
14200474 TATAGGAGCCAT
191 TATAAAAGCCCT
* *
14200486 TTTT-AAAATGAGATTTTTAAAGTTCC
1 TTTTCCAAATGTGATTTTTAAAGTTCC
14200512 TTAGCTTATC
Statistics
Matches: 344, Mismatches: 74, Indels: 31
0.77 0.16 0.07
Matches are distributed among these distances:
202 3 0.01
203 228 0.66
204 113 0.33
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (202 bp):
TTTTCCAAATGTGATTTTTAAAGTTCCCTAACCTATTTTTATAAGAGCTTTTTTCAAAATATGAT
TTTTAAAGTTTCTTAGCCTATTTTTATAGAAGCTCTTTTCCAAATGTGAATTTTAAAGTTCCTTA
ACCTATTTGTATAAGACTCTTTTTTAAAAATAAGAAGTTTAAAGTTCCCTAGCATATTTTTATAA
AAGCCCT
Found at i:14200456 original size:305 final size:305
Alignment explanation
Indices: 14199875--14200444 Score: 729
Period size: 305 Copynumber: 1.9 Consensus size: 305
14199865 CCCAATAGTA
* * *
14199875 TTTTCAAAATGTGATTTTTAAAGTTCTTTAACCTATTTTTATAAGCACCTTTTTTTCAAAATGAG
1 TTTTCAAAATGTGAGTTTTAAAGTTCTTTAACCTATTTGTATAAGCACCTTTTTTTAAAAATGAG
** * * * *
14199940 ATTTTTAAAGTTTCTTAGCCTATTTTTATATGAGCCATTTTCTAAATGTGAATTTTAAAGTTCCT
66 AAGTTTAAAGTTCCTTAGCCTATTTTTATAGGAGCCATTTTCCAAATGTGAATTTTAAAGTTCCC
* * * * *
14200005 TAGCCTATTTTTATAAGAGTCTTTTTTCCAAATAAGACTTTTAGAGTTCCCTAGCATATTTTTAT
131 TAACCTATTTTTATAAGAGTCTTTTCTCAAAATAAGACTTTTAAAGCTCCCTAGCATATTTTTAT
** * *
14200070 AAAAGCCCTTTTTCCCATTAAGATTTTTAAAGTTCCCTAGCCTATTTTTATAGGAGCTCTTTTTC
196 AAAAGCCCTTTTTCCCAAAAAGATTTTTAAAATTCCCTAGCCTATTTTTATAGAAGCTCTTTTTC
14200135 AAAATATGATTTTTAAAATTTTTTAGCCTATTTTTATAAATAATC
261 AAAATATGATTTTTAAAATTTTTTAGCCTATTTTTATAAATAATC
* * * **
14200180 TTTTCCAAATGTGAGTTTTAAGGTTCTTTAACCTATTTGTATAGGCA-CTTTTTTTAAAAAATTT
1 TTTTCAAAATGTGAGTTTTAAAGTTCTTTAACCTATTTGTATAAGCACCTTTTTTT-AAAAATGA
* *
14200244 GAAGTTTAAAGTTCCTTAGCCTATTTTTATAGGAGCCTTTTTCCAAATGTGAATTTTAAATTTCC
65 GAAGTTTAAAGTTCCTTAGCCTATTTTTATAGGAGCCATTTTCCAAATGTGAATTTTAAAGTTCC
* *** * *
14200309 CTAACCTATTTTTATATGAG-CATTTTCTCAAAATTTTA-TATTTAAAGCTCCTTAGCCTATTTT
130 CTAACCTATTTTTATAAGAGTC-TTTTCTCAAAATAAGACT-TTTAAAGCTCCCTAGCATATTTT
* * * *
14200372 TATAGAAGCTC-TTTT-CCAAAAAGTTATTTTTAAAATTCTCTAGCCTATTTTTATATAAGC-CA
193 TATAAAAGCCCTTTTTCCCAAAAAG--ATTTTTAAAATTCCCTAGCCTATTTTTATAGAAGCTC-
14200434 TTTTTCAAAAT
255 TTTTTCAAAAT
14200445 GAGCATTTTA
Statistics
Matches: 224, Mismatches: 35, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
303 6 0.03
304 15 0.07
305 203 0.91
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (305 bp):
TTTTCAAAATGTGAGTTTTAAAGTTCTTTAACCTATTTGTATAAGCACCTTTTTTTAAAAATGAG
AAGTTTAAAGTTCCTTAGCCTATTTTTATAGGAGCCATTTTCCAAATGTGAATTTTAAAGTTCCC
TAACCTATTTTTATAAGAGTCTTTTCTCAAAATAAGACTTTTAAAGCTCCCTAGCATATTTTTAT
AAAAGCCCTTTTTCCCAAAAAGATTTTTAAAATTCCCTAGCCTATTTTTATAGAAGCTCTTTTTC
AAAATATGATTTTTAAAATTTTTTAGCCTATTTTTATAAATAATC
Found at i:14202380 original size:62 final size:63
Alignment explanation
Indices: 14202242--14202489 Score: 167
Period size: 62 Copynumber: 4.0 Consensus size: 63
14202232 TGTTTTTGTT
* * ** * * * *
14202242 TAGAAAACACCTTAAATAATCTTCTACAAAATTGAAT-GGAATTATTTAAGGTATTTTTT-TGC
1 TAGAAAAAACCTTAAATAATCCTAAAAAAAATTAAATAAG-ATTATTTAAGGCATTTTTTATGC
*
14202304 TAG--AAAACGTTTAAATAATCCCTAAAAAAAATTAAATAAGATTATTTAAGGCATTTTTTAT-C
1 TAGAAAAAAC-CTTAAATAAT-CCTAAAAAAAATTAAATAAGATTATTTAAGGCATTTTTTATGC
* * ** * * *** *
14202366 -AGAAAATACCTTAAATAAT-ATTGATAAATTTTTTTAGAGGATTATTTAA-G-ATTTTTTTTGC
1 TAGAAAAAACCTTAAATAATCCTAAAAAAAATTAAATA-A-GATTATTTAAGGCATTTTTTATGC
* *
14202427 TAGAAAAAACCTTAAATAAT-CTCAAAAAAAATTAAA-CAGAATTATTTAAGGCATTTTTCATGC
1 TAGAAAAAACCTTAAATAATCCT-AAAAAAAATTAAATAAG-ATTATTTAAGGCATTTTTTATGC
14202490 CAAATGCCAT
Statistics
Matches: 140, Mismatches: 32, Indels: 27
0.70 0.16 0.14
Matches are distributed among these distances:
60 22 0.16
61 24 0.17
62 73 0.52
63 21 0.15
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (63 bp):
TAGAAAAAACCTTAAATAATCCTAAAAAAAATTAAATAAGATTATTTAAGGCATTTTTTATGC
Found at i:14204718 original size:19 final size:18
Alignment explanation
Indices: 14204688--14204851 Score: 73
Period size: 18 Copynumber: 9.3 Consensus size: 18
14204678 ATTCTCAAGC
*
14204688 CCTAAACTCTAAACAAAA
1 CCTAAACCCTAAACAAAA
*
14204706 CCTTAAACCCTAAACCAAAT
1 CC-TAAACCCTAAA-CAAAA
14204726 CC-AAACCC-AAAC----
1 CCTAAACCCTAAACAAAA
14204738 CCTAAACCCTAAACTATAAA
1 CCTAAACCCTAAAC-A-AAA
* *
14204758 TCCTAAACCTTAAACCAAA
1 -CCTAAACCCTAAACAAAA
* *
14204777 CATTAAACCCAAAACCAAAA
1 C-CTAAACCCTAAA-CAAAA
*
14204797 TGCTAAACCCT------AA
1 -CCTAAACCCTAAACAAAA
* *
14204810 CCTAAACCCTAAACTAAC
1 CCTAAACCCTAAACAAAA
* *
14204828 CCTAAACCCTAAACCAAC
1 CCTAAACCCTAAACAAAA
14204846 CCTAAA
1 CCTAAA
14204852 ACCCCCTAAA
Statistics
Matches: 112, Mismatches: 14, Indels: 40
0.67 0.08 0.24
Matches are distributed among these distances:
12 11 0.10
13 8 0.07
14 4 0.04
16 1 0.01
17 3 0.03
18 33 0.29
19 22 0.20
20 17 0.15
21 13 0.12
ACGTcount: A:0.49, C:0.35, G:0.01, T:0.16
Consensus pattern (18 bp):
CCTAAACCCTAAACAAAA
Found at i:14204735 original size:6 final size:7
Alignment explanation
Indices: 14204703--14204842 Score: 88
Period size: 7 Copynumber: 21.7 Consensus size: 7
14204693 ACTCTAAACA
*
14204703 AAACCTT
1 AAACCCT
14204710 AAACCCT
1 AAACCCT
14204717 AAA-CC-
1 AAACCCT
*
14204722 AAATCC-
1 AAACCCT
14204728 AAACCC-
1 AAACCCT
14204734 AAACCCT
1 AAACCCT
14204741 AAACCCT
1 AAACCCT
**
14204748 AAACTAT
1 AAACCCT
*
14204755 AAATCCT
1 AAACCCT
*
14204762 AAACCTT
1 AAACCCT
14204769 AAA-CC-
1 AAACCCT
**
14204774 AAACATT
1 AAACCCT
14204781 AAACCC-
1 AAACCCT
* *
14204787 AAAACCA
1 AAACCCT
**
14204794 AAATGCT
1 AAACCCT
14204801 AAACCCT
1 AAACCCT
14204808 -AA-CCT
1 AAACCCT
14204813 AAACCCT
1 AAACCCT
14204820 AAA--CT
1 AAACCCT
14204825 -AACCCT
1 AAACCCT
14204831 AAACCCT
1 AAACCCT
14204838 AAACC
1 AAACC
14204843 AACCCTAAAA
Statistics
Matches: 103, Mismatches: 20, Indels: 20
0.72 0.14 0.14
Matches are distributed among these distances:
4 2 0.02
5 11 0.11
6 27 0.26
7 63 0.61
ACGTcount: A:0.49, C:0.35, G:0.01, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:14204805 original size:20 final size:19
Alignment explanation
Indices: 14204689--14204809 Score: 80
Period size: 19 Copynumber: 6.6 Consensus size: 19
14204679 TTCTCAAGCC
* *
14204689 CTAAACTCTAAA-CAAAAC
1 CTAAACCCTAAACCAAAAT
14204707 CTTAAACCCTAAACC-AAAT
1 C-TAAACCCTAAACCAAAAT
*
14204726 CCAAACCC-AAACC-----
1 CTAAACCCTAAACCAAAAT
*
14204739 CTAAACCCTAAACTATAAAT
1 CTAAACCCTAAACCA-AAAT
*
14204759 CCTAAACCTTAAACCAAACAT
1 -CTAAACCCTAAACCAAA-AT
*
14204780 -TAAACCCAAAACCAAAAT
1 CTAAACCCTAAACCAAAAT
14204798 GCTAAACCCTAA
1 -CTAAACCCTAA
14204810 CCTAAACCCT
Statistics
Matches: 80, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
13 7 0.09
14 4 0.05
17 5 0.06
18 9 0.11
19 28 0.35
20 12 0.15
21 15 0.19
ACGTcount: A:0.50, C:0.32, G:0.01, T:0.17
Consensus pattern (19 bp):
CTAAACCCTAAACCAAAAT
Found at i:14204816 original size:12 final size:12
Alignment explanation
Indices: 14204799--14204842 Score: 54
Period size: 12 Copynumber: 3.6 Consensus size: 12
14204789 AACCAAAATG
14204799 CTAAACCCTAAC
1 CTAAACCCTAAC
*
14204811 CTAAACCCTAAA
1 CTAAACCCTAAC
14204823 CT-AACCCTAAACC
1 CTAAACCCT-AA-C
14204836 CTAAACC
1 CTAAACC
14204843 AACCCTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 6 0.22
12 15 0.56
13 2 0.07
14 4 0.15
ACGTcount: A:0.43, C:0.41, G:0.00, T:0.16
Consensus pattern (12 bp):
CTAAACCCTAAC
Found at i:14204830 original size:11 final size:12
Alignment explanation
Indices: 14204799--14204834 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
14204789 AACCAAAATG
*
14204799 CTAAACCCTAAC
1 CTAAACCCTAAA
14204811 CTAAACCCTAAA
1 CTAAACCCTAAA
14204823 CT-AACCCTAAA
1 CTAAACCCTAAA
14204834 C
1 C
14204835 CCTAAACCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.44, C:0.39, G:0.00, T:0.17
Consensus pattern (12 bp):
CTAAACCCTAAA
Found at i:14204833 original size:18 final size:18
Alignment explanation
Indices: 14204806--14204851 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
14204796 ATGCTAAACC
14204806 CTAA-CCTAAACCCTAAA
1 CTAACCCTAAACCCTAAA
14204823 CTAACCCTAAACCCTAAA
1 CTAACCCTAAACCCTAAA
*
14204841 CCAACCCTAAA
1 CTAACCCTAAA
14204852 ACCCCCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
17 4 0.15
18 23 0.85
ACGTcount: A:0.46, C:0.39, G:0.00, T:0.15
Consensus pattern (18 bp):
CTAACCCTAAACCCTAAA
Found at i:14204846 original size:11 final size:12
Alignment explanation
Indices: 14204832--14204868 Score: 53
Period size: 10 Copynumber: 3.3 Consensus size: 12
14204822 ACTAACCCTA
14204832 AACCCT-AAACC
1 AACCCTAAAACC
14204843 AACCCTAAAACC
1 AACCCTAAAACC
14204855 --CCCTAAAACC
1 AACCCTAAAACC
14204865 AACC
1 AACC
14204869 TTTAACCTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.43
11 6 0.26
12 7 0.30
ACGTcount: A:0.46, C:0.46, G:0.00, T:0.08
Consensus pattern (12 bp):
AACCCTAAAACC
Found at i:14204875 original size:21 final size:21
Alignment explanation
Indices: 14204816--14204868 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 21
14204806 CTAACCTAAA
*
14204816 CCCTAAACTAACCCT-AAA--
1 CCCTAAACCAACCCTAAAACC
14204834 CCCTAAACCAACCCTAAAACC
1 CCCTAAACCAACCCTAAAACC
14204855 CCCTAAAACCAACC
1 CCCT-AAACCAACC
14204869 TTTAACCTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 14 0.47
19 3 0.10
21 4 0.13
22 9 0.30
ACGTcount: A:0.43, C:0.45, G:0.00, T:0.11
Consensus pattern (21 bp):
CCCTAAACCAACCCTAAAACC
Found at i:14208595 original size:17 final size:19
Alignment explanation
Indices: 14208554--14208597 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
14208544 TGTCGTTAAT
*
14208554 TATAAATATATTATTTCGA
1 TATAAATATATTATTGCGA
14208573 TA-AAAT-TATTATTGC-A
1 TATAAATATATTATTGCGA
14208589 TATAAATAT
1 TATAAATAT
14208598 CTGCAGCCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 3 0.14
17 12 0.55
18 5 0.23
19 2 0.09
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (19 bp):
TATAAATATATTATTGCGA
Found at i:14210606 original size:28 final size:27
Alignment explanation
Indices: 14210539--14210606 Score: 64
Period size: 28 Copynumber: 2.4 Consensus size: 27
14210529 AATGAAATTA
*
14210539 AAAATAATAATAAAAGTTATTGTAACTG
1 AAAATAA-AAAAAAAGTTATTGTAACTG
* * **
14210567 TAATTAAAAAAAATAGTTATTGTTGCTG
1 AAAATAAAAAAAA-AGTTATTGTAACTG
*
14210595 AAAATAAGAAAA
1 AAAATAAAAAAA
14210607 TTTAATAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.54, C:0.03, G:0.12, T:0.31
Consensus pattern (27 bp):
AAAATAAAAAAAAAGTTATTGTAACTG
Found at i:14213976 original size:27 final size:27
Alignment explanation
Indices: 14213946--14214001 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
14213936 TAAGTGTATA
14213946 TTGGTCAG-TGGACCATTT-AAGCTTATG
1 TTGG-CAGTTGGACCATTTGAA-CTTATG
*
14213973 TTGGCCGTTGGACCATTTGAACTTATG
1 TTGGCAGTTGGACCATTTGAACTTATG
14214000 TT
1 TT
14214002 AGTCGTTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 2 0.08
27 22 0.85
28 2 0.08
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (27 bp):
TTGGCAGTTGGACCATTTGAACTTATG
Found at i:14214008 original size:27 final size:27
Alignment explanation
Indices: 14213954--14214012 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
14213944 TATTGGTCAG
*
14213954 TGGACCATTTAAGCTTATGTTGGCCGT
1 TGGACCATTTAAGCTTATGTTAGCCGT
*
14213981 TGGACCATTTGAA-CTTATGTTAGTCGT
1 TGGACCATTT-AAGCTTATGTTAGCCGT
14214008 TGGAC
1 TGGAC
14214013 TATATTTGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 27 0.93
28 2 0.07
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (27 bp):
TGGACCATTTAAGCTTATGTTAGCCGT
Found at i:14216245 original size:61 final size:59
Alignment explanation
Indices: 14216182--14216502 Score: 283
Period size: 62 Copynumber: 5.2 Consensus size: 59
14216172 TTGTGCAGGA
*
14216182 AAAATTGATATTTTCAACTTTTTCTCAAAAAAAAACTTTTTTTGAAAATTTATTTTTAAGA
1 AAAATTGATATTTTCAACTTTTTCTC-AAAAAAAA-TTTTTTTGAAAATTTATTTTTAAGG
* * *
14216243 AAAATTGATACTTTCAACTTTCAACTTTTTTTC-AAAAATA-TTTTTTGAAAACTTTGATTTTTG
1 AAAATTGATA---T----TTTCAACTTTTTCTCAAAAAAAATTTTTTTGAAAA-TTT-ATTTTTA
14216306 AGG
57 AGG
* *
14216309 AAAATTGATATTTTCAACTTTTT-TGAAAAAAATATTTTTTGGAAAAATTTATTTTTAAGG
1 AAAATTGATATTTTCAACTTTTTCTCAAAAAAA-ATTTTTTTG-AAAATTTATTTTTAAGG
* * * * ** *** **
14216369 AAAATGGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGGATTCTTTGATTTTCGAGG
1 AAAATTGATATTTTCAACTTTTTCTCAAAAA-AAATTTTTTT-GAAAATTT-ATTTTTAAGG
* *
14216431 AAAATTGATACTTTCAACTTTTTCTC--AAAAACTTTTTTTGAAAATTTATTTTTAAGG
1 AAAATTGATATTTTCAACTTTTTCTCAAAAAAAATTTTTTTGAAAATTTATTTTTAAGG
14216488 AAAATTGATACTTTT
1 AAAATTGATA-TTTT
14216503 TCCCCAAAAA
Statistics
Matches: 210, Mismatches: 32, Indels: 39
0.75 0.11 0.14
Matches are distributed among these distances:
57 18 0.09
58 9 0.04
59 25 0.12
60 33 0.16
61 34 0.16
62 37 0.18
63 1 0.00
64 12 0.06
65 3 0.01
66 24 0.11
68 14 0.07
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.46
Consensus pattern (59 bp):
AAAATTGATATTTTCAACTTTTTCTCAAAAAAAATTTTTTTGAAAATTTATTTTTAAGG
Found at i:14216363 original size:60 final size:58
Alignment explanation
Indices: 14216259--14216501 Score: 240
Period size: 60 Copynumber: 4.1 Consensus size: 58
14216249 GATACTTTCA
** *
14216259 ACTTTCAACTTTTTTTCAAAAATATTTTTTGAAAACTTTGATTTTTGAGGAAAATTGAT
1 ACTTTCAACTTTTTTAAAAAAATATTTTTTGAAAA-TTTGATTTTTAAGGAAAATTGAT
* *
14216318 ATTTTCAACTTTTTTGAAAAAAATATTTTTTGGAAAAATTT-ATTTTTAAGGAAAATGGAT
1 ACTTTCAACTTTTTT-AAAAAAATATTTTTT-G-AAAATTTGATTTTTAAGGAAAATTGAT
** * * *** **
14216378 ACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGGATTCTTTGATTTTCGAGGAAAATTGAT
1 ACTTTCAACTTTT--TTAAAAA-AATATTTTTT-GAAAATTTGATTTTTAAGGAAAATTGAT
* *
14216440 ACTTTCAACTTTTTCTCAAAAACT-TTTTTTGAAAATTT-ATTTTTAAGGAAAATTGAT
1 ACTTTCAACTTTTT-TAAAAAAATATTTTTTGAAAATTTGATTTTTAAGGAAAATTGAT
14216497 ACTTT
1 ACTTT
14216502 TTCCCCAAAA
Statistics
Matches: 151, Mismatches: 25, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
57 22 0.15
58 5 0.03
59 20 0.13
60 44 0.29
61 17 0.11
62 43 0.28
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (58 bp):
ACTTTCAACTTTTTTAAAAAAATATTTTTTGAAAATTTGATTTTTAAGGAAAATTGAT
Found at i:14216486 original size:119 final size:119
Alignment explanation
Indices: 14216182--14216522 Score: 371
Period size: 122 Copynumber: 2.8 Consensus size: 119
14216172 TTGTGCAGGA
*
14216182 AAAATTGATATTTTCAACTTTTTCTCAAAAAAAAACTTTTTTTGAAAATTTATTTTTAAGAAAAA
1 AAAATTGATATTTTCAACTTTTTCTC----AAAAACTTTTTTTGAAAATTTATTTTTAAGGAAAA
* *
14216247 TTGATACTTTCAAC-TTTCAACTTTTTTTCAAAAATA---TTTTTTGAAAACTTTGATTTTTGAG
62 TTGATACTTTCAACTTTTC--C------CCAAAAATATTTTTTTTTGAAAACTTTGATTTTCGAG
14216308 G
119 G
* *
14216309 AAAATTGATATTTTCAACTTTTT-TGAAAAAAATATTTTTTGGAAAAATTTATTTTTAAGGAAAA
1 AAAATTGATATTTTCAACTTTTTCT-CAAAAACT-TTTTTT-G-AAAATTTATTTTTAAGGAAAA
* * **
14216373 TGGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGGATTCTTTGATTTTCGAGG
62 TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAAACTTTGATTTTCGAGG
*
14216431 AAAATTGATACTTTCAACTTTTTCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGGAAAATTGA
1 AAAATTGATATTTTCAACTTTTTCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGGAAAATTGA
14216496 TAC--T----TTTTCCCCAAAAATATTTTTTTT
66 TACTTTCAACTTTTCCCCAAAAATATTTTTTTT
14216523 AGGTTTTATT
Statistics
Matches: 192, Mismatches: 13, Indels: 32
0.81 0.05 0.14
Matches are distributed among these distances:
113 23 0.12
117 1 0.01
119 35 0.18
120 1 0.01
121 6 0.03
122 50 0.26
123 7 0.04
124 6 0.03
125 2 0.01
126 34 0.18
127 27 0.14
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.47
Consensus pattern (119 bp):
AAAATTGATATTTTCAACTTTTTCTCAAAAACTTTTTTTGAAAATTTATTTTTAAGGAAAATTGA
TACTTTCAACTTTTCCCCAAAAATATTTTTTTTTGAAAACTTTGATTTTCGAGG
Found at i:14216548 original size:5 final size:5
Alignment explanation
Indices: 14216538--14216626 Score: 60
Period size: 5 Copynumber: 17.4 Consensus size: 5
14216528 TTATTTAAAG
*
14216538 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAA- AAAAGT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAA-T
* * *
14216583 AAAACA AAAAT AAAAAT TAAAT AAAGAT AAAA- AAAAT TAAAT AA
1 AAAA-T AAAAT -AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AA
14216627 TCCTAATTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
3 3 0.05
4 8 0.12
5 31 0.47
6 20 0.30
7 4 0.06
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:14216586 original size:27 final size:27
Alignment explanation
Indices: 14216568--14216623 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
14216558 AATAAAAGTG
14216568 AAAATAAAAAAAAG-TAAAACAAAAATA
1 AAAATAAAAAAAAGATAAAA-AAAAATA
* * *
14216595 AAAATTAAATAAAGATAAAAAAAATTA
1 AAAATAAAAAAAAGATAAAAAAAAATA
14216622 AA
1 AA
14216624 TAATCCTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.16
Consensus pattern (27 bp):
AAAATAAAAAAAAGATAAAAAAAAATA
Found at i:14216591 original size:32 final size:31
Alignment explanation
Indices: 14216537--14216597 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 31
14216527 TTTATTTAAA
*
14216537 GAAAATAAAATAATAAAAC-AAAATAAAAGT
1 GAAAATAAAAAAATAAAACAAAAATAAAAGT
14216567 GAAAATAAAAAAAAGTAAAACAAAAATAAAA
1 GAAAAT-AAAAAAA-TAAAACAAAAATAAAA
14216598 ATTAAATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 6 0.22
31 6 0.22
32 6 0.22
33 9 0.33
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (31 bp):
GAAAATAAAAAAATAAAACAAAAATAAAAGT
Found at i:14216603 original size:18 final size:18
Alignment explanation
Indices: 14216538--14216603 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 18
14216528 TTATTTAAAG
*
14216538 AAAATAAAATAATAAAAC-
1 AAAATAAAA-AGTAAAACA
*
14216556 AAAAT-AAAAGTGAAA-A
1 AAAATAAAAAGTAAAACA
*
14216572 TAAA-AAAAAGTAAAACA
1 AAAATAAAAAGTAAAACA
*
14216589 AAAATAAAAATTAAA
1 AAAATAAAAAGTAAA
14216604 TAAAGATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
16 17 0.45
17 7 0.18
18 14 0.37
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (18 bp):
AAAATAAAAAGTAAAACA
Found at i:14216604 original size:11 final size:11
Alignment explanation
Indices: 14216590--14216626 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
14216580 AGTAAAACAA
14216590 AAATAAAAATT
1 AAATAAAAATT
*
14216601 AAATAAAGA-T
1 AAATAAAAATT
14216611 AAA-AAAAATT
1 AAATAAAAATT
14216621 AAATAA
1 AAATAA
14216627 TCCTAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 4 0.18
10 8 0.36
11 10 0.45
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (11 bp):
AAATAAAAATT
Found at i:14217532 original size:21 final size:21
Alignment explanation
Indices: 14217489--14217557 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 21
14217479 TAAATAAAAA
*
14217489 AAATTAAATGAAAATAAATCAGAT
1 AAATTAAA--AAAATTAA-CAGAT
14217513 AAATTAAAAAAATTAACAGAT
1 AAATTAAAAAAATTAACAGAT
14217534 AAATTAAAATTAAA-TAACAGAT
1 AAATTAAAA--AAATTAACAGAT
14217556 AA
1 AA
14217558 TACATAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
21 14 0.33
22 17 0.40
23 3 0.07
24 8 0.19
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (21 bp):
AAATTAAAAAAATTAACAGAT
Found at i:14217554 original size:22 final size:21
Alignment explanation
Indices: 14217493--14217557 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 21
14217483 TAAAAAAAAT
*
14217493 TAAATGAAAATAAAT--CAGA
1 TAAATTAAAATAAATAACAGA
14217512 TAAATTAAAA-AAATTAACAGA
1 TAAATTAAAATAAA-TAACAGA
14217533 TAAATTAAAATTAAATAACAGA
1 TAAATTAAAA-TAAATAACAGA
14217555 TAA
1 TAA
14217558 TACATAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
18 3 0.08
19 10 0.25
21 14 0.35
22 10 0.25
23 3 0.08
ACGTcount: A:0.65, C:0.05, G:0.06, T:0.25
Consensus pattern (21 bp):
TAAATTAAAATAAATAACAGA
Found at i:14217674 original size:14 final size:13
Alignment explanation
Indices: 14217655--14217777 Score: 90
Period size: 14 Copynumber: 9.0 Consensus size: 13
14217645 TACCTAAGAT
14217655 AAAAAAAATAAAA
1 AAAAAAAATAAAA
14217668 GAAAAAAAATATAAA
1 -AAAAAAAATA-AAA
14217683 AAAATAATAATAAAA
1 AAAA-AA-AATAAAA
14217698 AAATAAAAATAAAA
1 AAA-AAAAATAAAA
14217712 TAGAAATAAAATAAAA
1 -A-AAA-AAAATAAAA
*** * *
14217728 ATGTAACAT--AC
1 AAAAAAAATAAAA
14217739 AAAAAAAATAAAA
1 AAAAAAAATAAAA
14217752 ATAAAAAAAT-AAA
1 A-AAAAAAATAAAA
*
14217765 AATAAAAATAAAA
1 AAAAAAAATAAAA
14217778 TGAAGAAAAA
Statistics
Matches: 87, Mismatches: 11, Indels: 23
0.72 0.09 0.19
Matches are distributed among these distances:
11 6 0.07
12 7 0.08
13 13 0.15
14 29 0.33
15 16 0.18
16 16 0.18
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (13 bp):
AAAAAAAATAAAA
Found at i:14217705 original size:6 final size:6
Alignment explanation
Indices: 14217658--14217777 Score: 92
Period size: 6 Copynumber: 20.7 Consensus size: 6
14217648 CTAAGATAAA
* * * *
14217658 AAAAAT -AAAAG AAAAA- AAATAT AAAAA- AATAAT AATAA- AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * * *
14217702 AAAAAT -AAAAT AGAAAT -AAAAT AAAAAT GTAACAT ACAAA- AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT -AAAAAT AAAAAT AAAAAT
14217748 AAAAAT AAAAAAAT AAAAAT AAAAAT AAAA
1 AAAAAT --AAAAAT AAAAAT AAAAAT AAAA
14217778 TGAAGAAAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 20
0.73 0.10 0.16
Matches are distributed among these distances:
5 29 0.32
6 52 0.57
7 4 0.04
8 6 0.07
ACGTcount: A:0.80, C:0.02, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:14217724 original size:60 final size:60
Alignment explanation
Indices: 14217659--14217792 Score: 157
Period size: 60 Copynumber: 2.2 Consensus size: 60
14217649 TAAGATAAAA
* *
14217659 AAAATAAAAGAAAAAAAATA-TAAAAAAATAATAATAAAAAAATAAAAATAAAATAGAAAT
1 AAAATAAAA-AAAAAAAATACAAAAAAAATAAAAATAAAAAAATAAAAATAAAATAGAAAT
*** *
14217719 AAAATAAAAATGTAACATACAAAAAAAATAAAAATAAAAAAATAAAAATAAAAATA-AAAT
1 AAAATAAAAAAAAAAAATACAAAAAAAATAAAAATAAAAAAATAAAAAT-AAAATAGAAAT
* *
14217779 -GAAGAAAAAAAAAA
1 AAAATAAAAAAAAAA
14217793 GAACATAGAC
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
59 15 0.25
60 40 0.66
61 6 0.10
ACGTcount: A:0.80, C:0.01, G:0.04, T:0.15
Consensus pattern (60 bp):
AAAATAAAAAAAAAAAATACAAAAAAAATAAAAATAAAAAAATAAAAATAAAATAGAAAT
Found at i:14217778 original size:11 final size:11
Alignment explanation
Indices: 14217658--14217778 Score: 110
Period size: 11 Copynumber: 11.0 Consensus size: 11
14217648 CTAAGATAAA
*
14217658 AAAAATAAAAG
1 AAAAATAAAAT
14217669 AAAAA-AAATAT
1 AAAAATAAA-AT
14217680 AAAAA-AATAAT
1 AAAAATAA-AAT
14217691 AATAAA-AAAAT
1 AA-AAATAAAAT
14217702 AAAAATAAAAT
1 AAAAATAAAAT
*
14217713 AGAAATAAAAT
1 AAAAATAAAAT
*
14217724 AAAAATGTAACAT
1 AAAAA--TAAAAT
14217737 ACAAAA-AAAAT
1 A-AAAATAAAAT
14217748 AAAAATAAAA-
1 AAAAATAAAAT
*
14217758 AAATA-AAAAT
1 AAAAATAAAAT
14217768 AAAAATAAAAT
1 AAAAATAAAAT
14217779 GAAGAAAAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
9 4 0.04
10 18 0.19
11 55 0.59
12 6 0.06
13 6 0.06
14 4 0.04
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:14218083 original size:42 final size:42
Alignment explanation
Indices: 14217983--14218083 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 42
14217973 TTTGATCAAA
* * *
14217983 GCTCCTCCAGGCAGAGGTTCAATGACTTTGAAAAACATAAAT
1 GCTCCTCTAGACAGAGGTTCAATAACTTTGAAAAACATAAAT
*
14218025 GACTCCTCTA-ATCAGAGGTTCAATAACTTTGGAAAA-ATAAATT
1 G-CTCCTCTAGA-CAGAGGTTCAATAACTTTGAAAAACATAAA-T
14218068 GCTCCTCTAGACAGAG
1 GCTCCTCTAGACAGAG
14218084 ACACCACGAC
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
42 19 0.37
43 32 0.63
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (42 bp):
GCTCCTCTAGACAGAGGTTCAATAACTTTGAAAAACATAAAT
Found at i:14218130 original size:41 final size:41
Alignment explanation
Indices: 14218050--14218153 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
14218040 AGGTTCAATA
* *
14218050 ACTTTGGAAAAATAAATTGCTCCTCTAGACAGAGACACCACG
1 ACTTTGG-AAAGTAAATTGCTCCTCTAAACAGAGACACCACG
* *
14218092 ACTTTGGAAAGTAAATTGCTCCTCTAAATAGAGGCACCACG
1 ACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGACACCACG
*
14218133 ACTTTTGAAAGTAAATTGCTC
1 ACTTTGGAAAGTAAATTGCTC
14218154 TTTGACAATC
Statistics
Matches: 57, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 50 0.88
42 7 0.12
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (41 bp):
ACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGACACCACG
Found at i:14219171 original size:8 final size:8
Alignment explanation
Indices: 14219153--14219190 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
14219143 TTTCATTCAC
*
14219153 TTTTTTCT
1 TTTTTTAT
14219161 TTTTCTT-T
1 TTTT-TTAT
14219169 TTTTTTAT
1 TTTTTTAT
14219177 TTTTTTAT
1 TTTTTTAT
14219185 TTTTTT
1 TTTTTT
14219191 TCAAGTATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 2 0.07
8 24 0.86
9 2 0.07
ACGTcount: A:0.05, C:0.05, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTAT
Found at i:14227940 original size:59 final size:57
Alignment explanation
Indices: 14227879--14228243 Score: 457
Period size: 59 Copynumber: 6.2 Consensus size: 57
14227869 TTGTGCAAGA
* * **
14227879 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTCTTTTGAAACTTTAATTTCGAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATT-TTTTGAAAATTTATTTTTAAGG
* * * *
14227937 AAAATTGATACTTTCAAC-TTTTCCTCAAAAAAAAAACATTTTTCAAAATTTATTTTTAAGA
1 AAAATTGATACTTTCAACTTTTTCC-C---AAAAATA-TTTTTTGAAAATTTATTTTTAAGG
*
14227998 AAAATTGATACTTTCAACTTTTTTCCAAAAATATTTTTTGAAAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTG--AAAATTTATTTTTAAGG
*
14228057 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAA-TTT-ATTTTTAAGG
* ** *
14228116 AAAATTGATACTTTTAAC-TTTTCCTCAAAAACCTTTTGTGAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTGAAAATTTATTTTTAAGG
* *
14228173 AAAATTGATACTTTCAACTTTTTCTCAAAAACT-TTTTTTAAAAATTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAAA-TATTTTTTGAAAATTTATTTTTAAGG
14228230 AAAATTGATACTTT
1 AAAATTGATACTTT
14228244 TTCCCCAAAA
Statistics
Matches: 269, Mismatches: 25, Indels: 27
0.84 0.08 0.08
Matches are distributed among these distances:
57 83 0.31
58 42 0.16
59 97 0.36
61 41 0.15
62 6 0.02
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.43
Consensus pattern (57 bp):
AAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGAAAATTTATTTTTAAGG
Found at i:14228291 original size:5 final size:5
Alignment explanation
Indices: 14228281--14228356 Score: 68
Period size: 5 Copynumber: 14.8 Consensus size: 5
14228271 TTATTTAAAG
* *
14228281 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAT AAAA- AAAAT AAAACA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T -AAAAT AAAAT AAAAT AAAA-T
14228331 AAAAT AAAAAT AAAAT AAAGAT AAAA
1 AAAAT -AAAAT AAAAT AAA-AT AAAA
14228357 GAATATTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 16
0.75 0.05 0.20
Matches are distributed among these distances:
3 3 0.05
4 4 0.07
5 32 0.54
6 16 0.27
7 4 0.07
ACGTcount: A:0.79, C:0.03, G:0.04, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:14228314 original size:17 final size:16
Alignment explanation
Indices: 14228293--14228357 Score: 62
Period size: 17 Copynumber: 4.0 Consensus size: 16
14228283 AATAAAATAA
14228293 TAAAACAAAATAAAAG
1 TAAAACAAAATAAAAG
*
14228309 TGAAAATAAAA-AAAA-
1 T-AAAACAAAATAAAAG
*
14228324 TAAAACAAAAATAAAAA
1 TAAAAC-AAAATAAAAG
*
14228341 TAAAATAAAGATAAAAG
1 TAAAACAAA-ATAAAAG
14228358 AATATTAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 4 0.10
15 5 0.12
16 12 0.30
17 19 0.47
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.14
Consensus pattern (16 bp):
TAAAACAAAATAAAAG
Found at i:14228329 original size:31 final size:32
Alignment explanation
Indices: 14228280--14228349 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 32
14228270 TTTATTTAAA
* *
14228280 GAAAAT-AAAATAATAAAAC-AAAATAAAAGT
1 GAAAATAAAAAAAATAAAACAAAAATAAAAAT
14228310 GAAAATAAAAAAAATAAAACAAAAATAAAAAT
1 GAAAATAAAAAAAATAAAACAAAAATAAAAAT
14228342 -AAAATAAA
1 GAAAATAAA
14228350 GATAAAAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 6 0.17
31 20 0.56
32 10 0.28
ACGTcount: A:0.79, C:0.03, G:0.04, T:0.14
Consensus pattern (32 bp):
GAAAATAAAAAAAATAAAACAAAAATAAAAAT
Found at i:14228354 original size:11 final size:10
Alignment explanation
Indices: 14228281--14228356 Score: 68
Period size: 11 Copynumber: 7.4 Consensus size: 10
14228271 TTATTTAAAG
14228281 AAAATAAAAT
1 AAAATAAAAT
*
14228291 --AATAAAAC
1 AAAATAAAAT
14228299 AAAATAAAAGT
1 AAAATAAAA-T
14228310 GAAAATAAAA-
1 -AAAATAAAAT
*
14228320 AAAATAAAACA
1 AAAATAAAA-T
14228331 AAAATAAAAAT
1 AAAAT-AAAAT
14228342 AAAATAAAGAT
1 AAAATAAA-AT
14228353 AAAA
1 AAAA
14228357 GAATATTAAA
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
8 7 0.13
9 9 0.16
10 10 0.18
11 16 0.29
12 13 0.24
ACGTcount: A:0.79, C:0.03, G:0.04, T:0.14
Consensus pattern (10 bp):
AAAATAAAAT
Found at i:14229255 original size:10 final size:10
Alignment explanation
Indices: 14229240--14229278 Score: 51
Period size: 10 Copynumber: 3.6 Consensus size: 10
14229230 TTCCAGCCAG
14229240 ATAAATAAAA
1 ATAAATAAAA
14229250 ATAAATAAAAAA
1 ATAAAT--AAAA
14229262 ATCAAATAAAA
1 AT-AAATAAAA
14229273 ATAAAT
1 ATAAAT
14229279 CAGATAAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
10 10 0.38
11 6 0.23
12 6 0.23
13 4 0.15
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:14229280 original size:15 final size:14
Alignment explanation
Indices: 14229240--14229286 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
14229230 TTCCAGCCAG
14229240 ATAAATAAAAAT-AA
1 ATAAA-AAAAATCAA
14229254 AT-AAAAAAATCAA
1 ATAAAAAAAATCAA
*
14229267 ATAAAAATAAATCAG
1 ATAAAAA-AAATCAA
14229282 ATAAA
1 ATAAA
14229287 TCAAGAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 6 0.21
13 6 0.21
14 6 0.21
15 11 0.38
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.19
Consensus pattern (14 bp):
ATAAAAAAAATCAA
Found at i:14229295 original size:23 final size:24
Alignment explanation
Indices: 14229246--14229308 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 24
14229236 CCAGATAAAT
* * *
14229246 AAAAATAAAT-AAAAAAATCAAAT
1 AAAAATAAATCAGATAAATCAAAG
14229269 AAAAATAAATCAGATAAATC-AAG
1 AAAAATAAATCAGATAAATCAAAG
*
14229292 -AAAATTAA-CAGATAAAT
1 AAAAATAAATCAGATAAAT
14229309 TAAAATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 9 0.26
22 7 0.20
23 12 0.34
24 7 0.20
ACGTcount: A:0.70, C:0.06, G:0.05, T:0.19
Consensus pattern (24 bp):
AAAAATAAATCAGATAAATCAAAG
Found at i:14229446 original size:16 final size:16
Alignment explanation
Indices: 14229427--14229554 Score: 62
Period size: 17 Copynumber: 7.5 Consensus size: 16
14229417 TACCTAAGAT
*
14229427 AAAAAAAATAAAAGAA
1 AAAAAAAATAAAATAA
* * *
14229443 AAAATATAT-ATATAA
1 AAAAAAAATAAAATAA
*
14229458 AAAAACAATAATAATAA
1 AAAAAAAATAA-AATAA
* *
14229475 AAATTAAAATAAAATAG
1 AAA-AAAAATAAAATAA
*
14229492 AAATAAAATAAAAATGTAA
1 AAAAAAAAT-AAAA--TAA
* *
14229511 CATACAAAA-AAAATAA
1 -AAAAAAAATAAAATAA
14229527 ATAAAATAAATAAAATGAA
1 A-AAAA-AAATAAAAT-AA
14229546 GAAAAAAAA
1 -AAAAAAAA
14229555 AAGAACATAG
Statistics
Matches: 84, Mismatches: 16, Indels: 22
0.69 0.13 0.18
Matches are distributed among these distances:
15 11 0.13
16 19 0.23
17 21 0.25
18 18 0.21
19 8 0.10
20 7 0.08
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (16 bp):
AAAAAAAATAAAATAA
Found at i:14229473 original size:6 final size:5
Alignment explanation
Indices: 14229454--14229542 Score: 56
Period size: 5 Copynumber: 16.4 Consensus size: 5
14229444 AAATATATAT
*
14229454 ATAAA AAAACA ATAATA ATAAAA ATTAAA ATAAA ATAGAA ATAAA ATAAAA
1 ATAAA ATAA-A ATAA-A AT-AAA A-TAAA ATAAA ATA-AA ATAAA AT-AAA
* *
14229505 ATGTAAC ATACAA AAAAA AT-AA ATAAA AT-AA ATAAA AT
1 A--TAAA ATA-AA ATAAA ATAAA ATAAA ATAAA ATAAA AT
14229543 GAAGAAAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 20
0.71 0.07 0.21
Matches are distributed among these distances:
4 8 0.12
5 27 0.40
6 25 0.37
7 6 0.09
8 1 0.01
ACGTcount: A:0.74, C:0.03, G:0.02, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:14229486 original size:29 final size:28
Alignment explanation
Indices: 14229427--14229553 Score: 91
Period size: 29 Copynumber: 4.3 Consensus size: 28
14229417 TACCTAAGAT
* *
14229427 AAAAAAAATAA-AAGAAAAAATATATATATA
1 AAAAAAAATAATAA-TAAAAAT-TA-AAATA
14229457 AAAAAACAATAATAATAAAAATTAAAATA
1 AAAAAA-AATAATAATAAAAATTAAAATA
* *
14229486 AAATAGAAATAA-AATAAAAATGTAACATA
1 AAA-AAAAATAATAATAAAAAT-TAAAATA
14229515 CAAAAAAAATAAATAA-AATAAA-TAAAATGA
1 -AAAAAAAAT-AATAATAA-AAATTAAAAT-A
14229545 AGAAAAAAA
1 A-AAAAAAA
14229554 AAAGAACATA
Statistics
Matches: 81, Mismatches: 6, Indels: 20
0.76 0.06 0.19
Matches are distributed among these distances:
28 9 0.11
29 29 0.36
30 25 0.31
31 16 0.20
32 2 0.02
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (28 bp):
AAAAAAAATAATAATAAAAATTAAAATA
Found at i:14229495 original size:11 final size:11
Alignment explanation
Indices: 14229430--14229536 Score: 60
Period size: 11 Copynumber: 9.3 Consensus size: 11
14229420 CTAAGATAAA
*
14229430 AAAAATAAAAGA
1 AAAAATAAAA-T
14229442 AAAAATATATATAT
1 AAAAATA-A-A-AT
14229456 AAAAA-AACAAT
1 AAAAATAA-AAT
*
14229467 AATAATAAAAAT
1 AAAAAT-AAAAT
*
14229479 TAAAATAAAAT
1 AAAAATAAAAT
*
14229490 AGAAATAAAAT
1 AAAAATAAAAT
*
14229501 AAAAATGTAACAT
1 AAAAA--TAAAAT
14229514 ACAAAA-AAAAT
1 A-AAAATAAAAT
14229525 --AAATAAAAT
1 AAAAATAAAAT
14229534 AAA
1 AAA
14229537 TAAAATGAAG
Statistics
Matches: 74, Mismatches: 10, Indels: 23
0.69 0.09 0.21
Matches are distributed among these distances:
8 3 0.04
9 5 0.07
11 29 0.39
12 16 0.22
13 10 0.14
14 10 0.14
15 1 0.01
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.20
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:14230666 original size:15 final size:16
Alignment explanation
Indices: 14230637--14230668 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
14230627 CGTGACACTA
14230637 TATATGTCATCTAGCT
1 TATATGTCATCTAGCT
14230653 TATATGTC-TCTAGCT
1 TATATGTCATCTAGCT
14230668 T
1 T
14230669 TTGGAAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (16 bp):
TATATGTCATCTAGCT
Found at i:14231164 original size:20 final size:21
Alignment explanation
Indices: 14231139--14231185 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
14231129 CCATTAGTAA
*
14231139 TAAATTTTTAG-TAAAAAAAT
1 TAAATTTTTAGAGAAAAAAAT
14231159 TAAA-TTTTAGAGAAAAAAAT
1 TAAATTTTTAGAGAAAAAAAT
14231179 TAGAATT
1 TA-AATT
14231186 AAATTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 6 0.26
20 14 0.61
21 2 0.09
22 1 0.04
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (21 bp):
TAAATTTTTAGAGAAAAAAAT
Found at i:14233610 original size:18 final size:20
Alignment explanation
Indices: 14233583--14233661 Score: 94
Period size: 18 Copynumber: 4.1 Consensus size: 20
14233573 AATGGAAATA
14233583 TTAATTATTATTGATG-ATT
1 TTAATTATTATTGATGAATT
*
14233602 TT-TTTATTATTGA--AATT
1 TTAATTATTATTGATGAATT
*
14233619 TTAACTATTATTGATGAATT
1 TTAATTATTATTGATGAATT
*
14233639 TTAATTATTATCGATAGAATT
1 TTAATTATTATTGAT-GAATT
14233660 TT
1 TT
14233662 TTTATAAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
17 5 0.10
18 19 0.38
19 2 0.04
20 17 0.34
21 7 0.14
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.56
Consensus pattern (20 bp):
TTAATTATTATTGATGAATT
Found at i:14233617 original size:36 final size:38
Alignment explanation
Indices: 14233577--14233649 Score: 105
Period size: 36 Copynumber: 2.0 Consensus size: 38
14233567 ATTACCAATG
* *
14233577 GAAATATTAATTATTATTGATG-ATTTT-TTTATTATT
1 GAAATATTAACTATTATTGATGAATTTTAATTATTATT
*
14233613 GAAATTTTAACTATTATTGATGAATTTTAATTATTAT
1 GAAATATTAACTATTATTGATGAATTTTAATTATTAT
14233650 CGATAGAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
36 20 0.62
37 5 0.16
38 7 0.22
ACGTcount: A:0.36, C:0.01, G:0.08, T:0.55
Consensus pattern (38 bp):
GAAATATTAACTATTATTGATGAATTTTAATTATTATT
Found at i:14239885 original size:17 final size:17
Alignment explanation
Indices: 14239863--14239933 Score: 79
Period size: 17 Copynumber: 3.8 Consensus size: 17
14239853 ATTTTAGTTT
14239863 TTTTATTTTTAAAATTA
1 TTTTATTTTTAAAATTA
14239880 TTTTATTTTTAAAATTTTATA
1 TTTTATTTTTAAAA---T-TA
*
14239901 TTTTTATTTTTAAAATAA
1 -TTTTATTTTTAAAATTA
14239919 TTTTATTTTTTAAAA
1 TTTTA-TTTTTAAAA
14239934 AGTTATGATA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
17 19 0.40
18 10 0.21
19 1 0.02
20 1 0.02
21 2 0.04
22 14 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTATTTTTAAAATTA
Found at i:14239888 original size:22 final size:21
Alignment explanation
Indices: 14239863--14239927 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
14239853 ATTTTAGTTT
14239863 TTTTATTTTT-AAA-A--TTA
1 TTTTATTTTTAAAATATTTTA
14239880 TTTTATTTTTAAAAT-TTTATA
1 TTTTATTTTTAAAATATTT-TA
14239901 TTTTTATTTTTAAAATAATTTTA
1 -TTTTATTTTTAAAAT-ATTTTA
14239924 TTTT
1 TTTT
14239928 TTAAAAAGTT
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
17 10 0.25
18 3 0.08
20 1 0.03
21 2 0.05
22 19 0.47
23 2 0.05
24 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTATTTTTAAAATATTTTA
Found at i:14239911 original size:23 final size:23
Alignment explanation
Indices: 14239880--14239930 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
14239870 TTTAAAATTA
*
14239880 TTTTATTTT-TAA-AATTTTATAT
1 TTTTATTTTAAAATAATTTTAT-T
14239902 TTTTATTTTTAAAATAATTTTATT
1 TTTTA-TTTTAAAATAATTTTATT
14239926 TTTTA
1 TTTTA
14239931 AAAAGTTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
22 5 0.20
23 4 0.16
24 8 0.32
25 8 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (23 bp):
TTTTATTTTAAAATAATTTTATT
Found at i:14239913 original size:39 final size:41
Alignment explanation
Indices: 14239852--14239933 Score: 132
Period size: 39 Copynumber: 2.0 Consensus size: 41
14239842 AATAAAAAAT
* *
14239852 AATTTTAGTTTTTTTATTTTTAAAATTATTTTA-TTTTTAA
1 AATTTTAGTATTTTTATTTTTAAAATAATTTTATTTTTTAA
14239892 AATTTTA-TATTTTTATTTTTAAAATAATTTTATTTTTTAA
1 AATTTTAGTATTTTTATTTTTAAAATAATTTTATTTTTTAA
14239932 AA
1 AA
14239934 AGTTATGATA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
39 23 0.59
40 16 0.41
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (41 bp):
AATTTTAGTATTTTTATTTTTAAAATAATTTTATTTTTTAA
Found at i:14239975 original size:25 final size:25
Alignment explanation
Indices: 14239951--14240009 Score: 57
Period size: 25 Copynumber: 2.4 Consensus size: 25
14239941 ATAAAGTAAT
* *
14239951 TTTTTAAAAAA-CAATAAAATCTAAT
1 TTTTTAAAAAAGAAAAAAAAT-TAAT
** *
14239976 TTTAAAAAAAAGAAAAAAAATTAAA
1 TTTTTAAAAAAGAAAAAAAATTAAT
14240001 TTTTTAAAA
1 TTTTTAAAA
14240010 TTTTTTCAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 2
0.74 0.20 0.06
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (25 bp):
TTTTTAAAAAAGAAAAAAAATTAAT
Found at i:14242057 original size:32 final size:32
Alignment explanation
Indices: 14242007--14242085 Score: 124
Period size: 32 Copynumber: 2.5 Consensus size: 32
14241997 TACAAATGAA
*
14242007 ATCAAATGAAATC-CACATGCATTAATATTTT
1 ATCAAATGAAATCAAACATGCATTAATATTTT
*
14242038 ATCAAATAAAATCAAACATGCATTAATATTTT
1 ATCAAATGAAATCAAACATGCATTAATATTTT
*
14242070 ACCAAATGAAATCAAA
1 ATCAAATGAAATCAAA
14242086 TGAAATCATA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 12 0.28
32 31 0.72
ACGTcount: A:0.49, C:0.15, G:0.05, T:0.30
Consensus pattern (32 bp):
ATCAAATGAAATCAAACATGCATTAATATTTT
Found at i:14243267 original size:23 final size:24
Alignment explanation
Indices: 14243223--14243268 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
14243213 TCTATAATTG
* *
14243223 TAATTGTACTATTTATTAATTTAT
1 TAATTCTACTATTGATTAATTTAT
*
14243247 TAATTCTA-TATTGATTGATTTA
1 TAATTCTACTATTGATTAATTTA
14243269 ATTTGTCAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (24 bp):
TAATTCTACTATTGATTAATTTAT
Found at i:14243357 original size:269 final size:270
Alignment explanation
Indices: 14242858--14243398 Score: 838
Period size: 269 Copynumber: 2.0 Consensus size: 270
14242848 ACGCATGAAA
* *
14242858 TATATCATGAAATACATCAATTACTCAAATGGATACTATATTTAATCAAATATAAATGTGTCAAA
1 TATATCATGAAATACATCAATTACT--AA-GGATACTATATTTAATCAAATATAAATATATCAAA
* * *
14242923 TAATTAATTAGAGAATCACTATTTTATAATTATAATTGTAGTATTTATTAATTTATTAATTATAT
63 TAATTAATTAGAGAATCACAATTCTATAATTATAATTGTACTATTTATTAATTTATTAATTATAT
* *
14242988 ATTGATTGATTTAATTTGTCAAAATAAAATTTTTAAAATTTTAATACTTTTAATATGAATTAAAT
128 ATTGATTGATTTAATTTGTCAAAATAAAAATTTTAAAATTTTAATACTTTTAATATCAATTAAAT
*
14243053 TGAGAGTGATTTAAAATCAATAATAAAAACATAAATATAATCAATTTAGTTTTTTGAATTATATT
193 TGAGAGTGATTTAAAATCAATAATAAAAACATAAATATAATCAATGTAGTTTTTTGAATTATATT
* *
14243118 TGATTTAAAAATT
258 TAAATTAAAAATT
14243131 TATAT-ATGAAATACATCAATTACT-A-GATACTATATTTAATCAAATATAAATATATCAAATAC
1 TATATCATGAAATACATCAATTACTAAGGATACTATATTTAATCAAATATAAATATATCAAATA-
* * *
14243193 CTT-ATTAGAGAATCAACAATTCTATAATTGTAATTGTACTATTTATTAATTTATTAATTCTATA
65 ATTAATTAGAGAATC-ACAATTCTATAATTATAATTGTACTATTTATTAATTTATTAATTATATA
* *
14243257 TTGATTGATTTAATTTGTCAAATTAAGAAATTTTAAAATTTTAATACTTTTAATATCAATTGAAT
129 TTGATTGATTTAATTTGTCAAAATAA-AAATTTTAAAATTTTAATACTTTTAATATCAATTAAAT
* * *
14243322 TGAGAGTGATTTAAGATTAATAATAAAAACATAAATATAATCAATGTAGTTTTTTGAATTATTTT
193 TGAGAGTGATTTAAAATCAATAATAAAAACATAAATATAATCAATGTAGTTTTTTGAATTATATT
14243387 TAAATTAAAAAT
258 TAAATTAAAAAT
14243399 ATATTAAATA
Statistics
Matches: 247, Mismatches: 18, Indels: 10
0.90 0.07 0.04
Matches are distributed among these distances:
267 45 0.18
268 71 0.29
269 107 0.43
272 19 0.08
273 5 0.02
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (270 bp):
TATATCATGAAATACATCAATTACTAAGGATACTATATTTAATCAAATATAAATATATCAAATAA
TTAATTAGAGAATCACAATTCTATAATTATAATTGTACTATTTATTAATTTATTAATTATATATT
GATTGATTTAATTTGTCAAAATAAAAATTTTAAAATTTTAATACTTTTAATATCAATTAAATTGA
GAGTGATTTAAAATCAATAATAAAAACATAAATATAATCAATGTAGTTTTTTGAATTATATTTAA
ATTAAAAATT
Found at i:14244519 original size:63 final size:62
Alignment explanation
Indices: 14244451--14244671 Score: 219
Period size: 63 Copynumber: 3.5 Consensus size: 62
14244441 CTTAAACCCT
* * *
14244451 AAAATATTAAAAAATTATTTAAGACATTTTCTATATATAAACGTCTTAAATAATCCATTTATA
1 AAAATA-TAAAAAATTATTTAAGACATTTTCTATAAAAAAATGTCTTAAATAATCCATTTATA
* * * *
14244514 AAAATATAAAAAGATTATTTAAGACGTTTCTGTATAAAAAAAATTTCTTAAATAATAC-TTATAT
1 AAAATATAAAAA-ATTATTTAAGACATTT-TCTAT-AAAAAAATGTCTTAAATAATCCATT-TAT
14244578 A
62 A
* ** ** * * * *
14244579 GAAATATAGAATGATTATTTAAGGTATTTTCTATACAGAAATGCCTTATATAATCCATTTATA
1 AAAATATA-AAAAATTATTTAAGACATTTTCTATAAAAAAATGTCTTAAATAATCCATTTATA
*
14244642 AAAATATAAAAGAATTATTTAAGATATTTT
1 AAAATATAAAA-AATTATTTAAGACATTTT
14244672 TTGGTTAAAA
Statistics
Matches: 127, Mismatches: 24, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
62 8 0.06
63 64 0.50
64 12 0.09
65 41 0.32
66 2 0.02
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.39
Consensus pattern (62 bp):
AAAATATAAAAAATTATTTAAGACATTTTCTATAAAAAAATGTCTTAAATAATCCATTTATA
Found at i:14244585 original size:65 final size:63
Alignment explanation
Indices: 14244451--14244712 Score: 208
Period size: 63 Copynumber: 4.1 Consensus size: 63
14244441 CTTAAACCCT
* * *
14244451 AAAATATTAAAAA-ATTATTTAAGACATTTTCTATATATAAACGTCTTAAATAATCCATTTATA
1 AAAATA-TAAAAAGATTATTTAAGACATTTTCTATAAAAAAACGTCTTAAATAATACATTTATA
* * **
14244514 AAAATATAAAAAGATTATTTAAGACGTTTCTGTATAAAAAAAATTTCTTAAATAATAC-TTATAT
1 AAAATATAAAAAGATTATTTAAGACATTT-TCTAT-AAAAAAACGTCTTAAATAATACATT-TAT
14244578 A
63 A
* * * ** * * * * * *
14244579 GAAATATAGAATGATTATTTAAGGTATTTTCTATACAGAAATGCCTTATATAATCCATTTATA
1 AAAATATAAAAAGATTATTTAAGACATTTTCTATAAAAAAACGTCTTAAATAATACATTTATA
* * * * * **
14244642 AAAATAT-AAAAGAATTATTTAAGATATTTTTTGGTTAAAAAACATCTTAAATAA-ATTTTTTAT
1 AAAATATAAAAAG-ATTATTTAAGACATTTTCT-ATAAAAAAACGTCTTAAATAATA-CATTTAT
14244705 A
63 A
14244706 AAAATAT
1 AAAATAT
14244713 TAAGCTTAAA
Statistics
Matches: 155, Mismatches: 36, Indels: 15
0.75 0.17 0.07
Matches are distributed among these distances:
62 9 0.06
63 64 0.41
64 38 0.25
65 44 0.28
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.39
Consensus pattern (63 bp):
AAAATATAAAAAGATTATTTAAGACATTTTCTATAAAAAAACGTCTTAAATAATACATTTATA
Found at i:14244682 original size:128 final size:127
Alignment explanation
Indices: 14244464--14244695 Score: 301
Period size: 128 Copynumber: 1.8 Consensus size: 127
14244454 ATATTAAAAA
* * *
14244464 ATTATTTAAGACATTTTCTATATATAAACGTCTTAAATAATCCATTTATAAAAATATAAAAAGAT
1 ATTATTTAAGACATTTTCTATACAGAAACGCCTTAAATAATCCATTTATAAAAATATAAAAAGAT
*
14244529 TATTTAAGACGTTTCTGTATAAAAAAA-ATTTCTTAAATAATACTTATATAGAAATATAGAATG
66 TATTTAAGAAGTTTCTGTATAAAAAAACA--TCTTAAATAATACTTATATAGAAATATAGAATG
** * *
14244592 ATTATTTAAGGTATTTTCTATACAGAAATGCCTTATATAATCCATTTATAAAAATAT-AAAAGAA
1 ATTATTTAAGACATTTTCTATACAGAAACGCCTTAAATAATCCATTTATAAAAATATAAAAAG-A
* *
14244656 TTATTTAAGATATTTTTTGGT-T-AAAAAACATCTTAAATAA
65 TTATTTAAGA-AGTTTCT-GTATAAAAAAACATCTTAAATAA
14244696 ATTTTTTATA
Statistics
Matches: 90, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
127 15 0.17
128 67 0.74
129 6 0.07
130 2 0.02
ACGTcount: A:0.46, C:0.08, G:0.07, T:0.39
Consensus pattern (127 bp):
ATTATTTAAGACATTTTCTATACAGAAACGCCTTAAATAATCCATTTATAAAAATATAAAAAGAT
TATTTAAGAAGTTTCTGTATAAAAAAACATCTTAAATAATACTTATATAGAAATATAGAATG
Found at i:14246075 original size:19 final size:19
Alignment explanation
Indices: 14246031--14246077 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
14246021 ATATTAAAAA
14246031 ATTTTAAAATTTTAGTATC
1 ATTTTAAAATTTTAGTATC
* *
14246050 ATATTAAATATTTTATTAT-
1 ATTTTAAA-ATTTTAGTATC
14246069 ATTTTAAAA
1 ATTTTAAAA
14246078 ATTATTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 1 0.04
19 14 0.58
20 9 0.38
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
ATTTTAAAATTTTAGTATC
Found at i:14250444 original size:239 final size:229
Alignment explanation
Indices: 14250003--14250698 Score: 921
Period size: 239 Copynumber: 3.0 Consensus size: 229
14249993 TAATGAGGGT
* * *
14250003 TTTCTTGAAGTTTTTCTGTATTTATATATTTTTTATATATTTCCTTTATGAAATATATTTAAAAG
1 TTTCTTGAAGTTTTT-TGTATTTATATATTTTTT-CACATTTCCTTTGTGAAATATATTTAAAAG
* *
14250068 CTAAAGATAATATAAAGATTATTTACAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTT
64 CTAAAGATAATGTAAAGATTATTTATAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTT
* * * *
14250133 ATGATAAATTTAAATACTCATATTAACTGTAAATAAATTAAAAATGATAAATTACTTTAAAATTG
129 GTGATAAATTTAAATACTCATATTAACTTTAGATAAATTAAAAAAGATAAATTACTTTAAAATTG
*
14250198 GTTTTAAATTGAGATAAGATTATGTTTGAGGTATAGGAGAAA-C
194 GTTTTAAATTGAGATAAG-----G--TGAGATATAGGA-AAACC
* *
14250241 TTTCTTGAAATTGTTTTGATATTTATATATTGTTTTCACATTTCCTTTGTGAAATATATTTAAAT
1 TTTCTTGAAGTT-TTTTG-TATTTATATATT-TTTTCACATTTCCTTTGTGAAATATATTTAAAA
* *
14250306 GCTAAAGATAATGTAAGGATTATTTATAAAAACTATTAAAGATATTAAATAATATTTTTAAAAGT
63 GCTAAAGATAATGTAAAGATTATTTATAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGT
14250371 TGTGATAAATTTAAATACTCATATTAACTTTAGATAAATTAAAAAAGATAAATTACTTTAAAATT
128 TGTGATAAATTTAAATACTCATATTAACTTTAGATAAATTAAAAAAGATAAATTACTTTAAAATT
** * *
14250436 TATTTTAAATTGAAATAAGGTGATATATAGGAAAACC
193 GGTTTTAAATTGAGATAAGGTGAGATATAGGAAAACC
* * * * * * *
14250473 ATTCCTGAAGTTATTATGGTATTTATATATATTTTCACATTTTCTTTGTGAAGTATATTTAAAAA
1 TTTCTTGAAGTT-TT-TTGTATTTATATATTTTTTCACATTTCCTTTGTGAAATATATTTAAAAG
* * * * * *
14250538 TTGAAGATAATGCAATGAATATTTATAAAAAATATTAAAGATATTAAATAATATTTTTAAAAATT
64 CTAAAGATAATGTAAAGATTATTTATAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTT
*
14250603 GTGATAAATTTAAATACTCATATTAA-TTATAGATAAATTGAAAAAGATAAATTACTTTAAAATT
129 GTGATAAATTTAAATACTCATATTAACTT-TAGATAAATTAAAAAAGATAAATTACTTTAAAATT
*
14250667 GGTTTTAAATTGAGATGAGGTGATG-TATAGGA
193 GGTTTTAAATTGAGATAAGGTGA-GATATAGGA
14250699 GAAAGAAATT
Statistics
Matches: 410, Mismatches: 41, Indels: 21
0.87 0.09 0.04
Matches are distributed among these distances:
230 2 0.00
231 177 0.43
232 33 0.08
233 2 0.00
234 1 0.00
238 13 0.03
239 178 0.43
240 4 0.01
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.42
Consensus pattern (229 bp):
TTTCTTGAAGTTTTTTGTATTTATATATTTTTTCACATTTCCTTTGTGAAATATATTTAAAAGCT
AAAGATAATGTAAAGATTATTTATAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTTGT
GATAAATTTAAATACTCATATTAACTTTAGATAAATTAAAAAAGATAAATTACTTTAAAATTGGT
TTTAAATTGAGATAAGGTGAGATATAGGAAAACC
Found at i:14250610 original size:231 final size:230
Alignment explanation
Indices: 14250020--14250702 Score: 920
Period size: 231 Copynumber: 2.9 Consensus size: 230
14250010 AAGTTTTTCT
* * * *
14250020 GTATTTATATATTTTTTATATATTTCCTTTATGAAATATATTTAAAAGCTAAAGATAATATAAAG
1 GTATTTATATATTTTTCACAT-TTT-CTTTGTGAAATATATTTAAAAGCTAAAGATAATGTAAAG
* *
14250085 ATTATTTACAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTTATGATAAATTTAAATAC
64 ATTATTTATAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTTGTGATAAATTTAAATAC
* * *
14250150 TCATATTAACTGTAAATAAATTAAAAATGATAAATTACTTTAAAATTGGTTTTAAATTGAGATAA
129 TCATATTAACTTTAGATAAATTAAAAAAGATAAATTACTTTAAAATTGGTTTTAAATTGAGATAA
* * * * *
14250215 GATTATGTTTGAGGTATAGGAGAAACTTTCTTGAAATTGTTTTG
194 G-----G--TGATGTATAGGAGAAACATTCCTGAAATTATTATG
* * * *
14250259 ATATTTATATATTGTTTTCACATTTCCTTTGTGAAATATATTTAAATGCTAAAGATAATGTAAGG
1 GTATTTATATA-T-TTTTCACATTTTCTTTGTGAAATATATTTAAAAGCTAAAGATAATGTAAAG
*
14250324 ATTATTTATAAAAACTATTAAAGATATTAAATAATATTTTTAAAAGTTGTGATAAATTTAAATAC
64 ATTATTTATAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTTGTGATAAATTTAAATAC
** *
14250389 TCATATTAACTTTAGATAAATTAAAAAAGATAAATTACTTTAAAATTTATTTTAAATTGAAATAA
129 TCATATTAACTTTAGATAAATTAAAAAAGATAAATTACTTTAAAATTGGTTTTAAATTGAGATAA
* *
14250454 GGTGATATATAGGA-AAACCATTCCTGAAGTTATTATG
194 GGTGATGTATAGGAGAAA-CATTCCTGAAATTATTATG
* ** * * *
14250491 GTATTTATATATATTTTCACATTTTCTTTGTGAAGTATATTTAAAAATTGAAGATAATGCAATGA
1 GTATTTATATAT-TTTTCACATTTTCTTTGTGAAATATATTTAAAAGCTAAAGATAATGTAAAGA
* *
14250556 ATATTTATAAAAAATATTAAAGATATTAAATAATATTTTTAAAAATTGTGATAAATTTAAATACT
65 TTATTTATAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTTGTGATAAATTTAAATACT
* *
14250621 CATATTAA-TTATAGATAAATTGAAAAAGATAAATTACTTTAAAATTGGTTTTAAATTGAGATGA
130 CATATTAACTT-TAGATAAATTAAAAAAGATAAATTACTTTAAAATTGGTTTTAAATTGAGATAA
14250685 GGTGATGTATAGGAGAAA
194 GGTGATGTATAGGAGAAA
14250703 GAAATTTCAT
Statistics
Matches: 396, Mismatches: 43, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
230 2 0.01
231 179 0.45
232 37 0.09
234 1 0.00
239 167 0.42
240 3 0.01
241 7 0.02
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.41
Consensus pattern (230 bp):
GTATTTATATATTTTTCACATTTTCTTTGTGAAATATATTTAAAAGCTAAAGATAATGTAAAGAT
TATTTATAAAAAATATTAAAGATATTAAATAATATTTTTAAAAGTTGTGATAAATTTAAATACTC
ATATTAACTTTAGATAAATTAAAAAAGATAAATTACTTTAAAATTGGTTTTAAATTGAGATAAGG
TGATGTATAGGAGAAACATTCCTGAAATTATTATG
Found at i:14251474 original size:2 final size:2
Alignment explanation
Indices: 14251467--14251505 Score: 51
Period size: 2 Copynumber: 18.5 Consensus size: 2
14251457 TGTTGTAATA
*
14251467 AT AT AT AT AT AT AT AT AT AT AT GAT AT AT GAT AT CT AT A
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT -AT AT AT AT A
14251506 CTATCTAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 29 0.88
3 4 0.12
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:14251657 original size:24 final size:24
Alignment explanation
Indices: 14251622--14251667 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
14251612 AAGAAAAGGA
*
14251622 TAAGCCACATGGTATCTGACATAT
1 TAAGCCACATGGTATCTAACATAT
*
14251646 TAAGCCATATGGTATCTAACAT
1 TAAGCCACATGGTATCTAACAT
14251668 CTAACATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (24 bp):
TAAGCCACATGGTATCTAACATAT
Found at i:14252125 original size:16 final size:16
Alignment explanation
Indices: 14252104--14252137 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
14252094 TTCAAATTGA
14252104 ATAAATTTAACTATTT
1 ATAAATTTAACTATTT
*
14252120 ATAAATTTAATTATTT
1 ATAAATTTAACTATTT
14252136 AT
1 AT
14252138 GAATCTATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAAATTTAACTATTT
Found at i:14258632 original size:135 final size:135
Alignment explanation
Indices: 14258390--14258648 Score: 367
Period size: 135 Copynumber: 1.9 Consensus size: 135
14258380 TTAGCAGTTC
* * * * * * *
14258390 TATTTAGTTAAAACAAATAATATCTTATAAGTTGGTTTCAGTTGCCTACTTACCTAAAATTTTTG
1 TATTTAGTTAAAACAAACAATAGCTCATAAATTGGTTTCAGTTACCTACTCACCTAAAATTTTTC
* *
14258455 TTATCCTCAGAATTAGAAAGATATTTGTTTAGTCCTCTAAACATGTATCAAAACAACTTGTGTTT
66 TTATCCTCAGAATTAGAAAGATATTTGTTTAATCCTCTAAACATGTATAAAAACAACTTGTGTTT
14258520 AAATT
131 AAATT
* * * *
14258525 TATTTAGTTAAAACAAACAATAGCTCATAAATTGGTTTCATTTACTTACTCACTTAGAATTTTTC
1 TATTTAGTTAAAACAAACAATAGCTCATAAATTGGTTTCAGTTACCTACTCACCTAAAATTTTTC
* *
14258590 TTATTCTTAGAATTAG-AAGAATATTTGTTTAATCCTCTAAACATGTATAAAAACAACTT
66 TTATCCTCAGAATTAGAAAG-ATATTTGTTTAATCCTCTAAACATGTATAAAAACAACTT
14258649 ATATTTGGAA
Statistics
Matches: 108, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
134 3 0.03
135 105 0.97
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (135 bp):
TATTTAGTTAAAACAAACAATAGCTCATAAATTGGTTTCAGTTACCTACTCACCTAAAATTTTTC
TTATCCTCAGAATTAGAAAGATATTTGTTTAATCCTCTAAACATGTATAAAAACAACTTGTGTTT
AAATT
Found at i:14263431 original size:18 final size:18
Alignment explanation
Indices: 14263379--14263436 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
14263369 GAGAGTTAAT
* * *
14263379 TAAATTAAATTTAAAATA
1 TAAAATAAATATAATATA
*
14263397 TAAAATAATTATAATATA
1 TAAAATAAATATAATATA
14263415 TAAAATATAATAT-ATAT-
1 TAAAATA-AATATAATATA
14263432 TAAAA
1 TAAAA
14263437 GATTAAAGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 5 0.15
18 25 0.74
19 4 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATAAATATAATATA
Found at i:14263443 original size:25 final size:24
Alignment explanation
Indices: 14263389--14263443 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
14263379 TAAATTAAAT
* *
14263389 TTAAAATATAAAATAATTATAATA
1 TTAAAATATAAAATAATTAAAAGA
*
14263413 TATAAAATATAATATATATTAAAAGA
1 T-TAAAATATAAAATA-ATTAAAAGA
14263439 TTAAA
1 TTAAA
14263444 GAGTACTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
24 1 0.04
25 17 0.65
26 8 0.31
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
TTAAAATATAAAATAATTAAAAGA
Found at i:14270158 original size:17 final size:17
Alignment explanation
Indices: 14270138--14270185 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
14270128 GAAAAAAATT
14270138 TAAAAATTTATTTTTAA
1 TAAAAATTTATTTTTAA
*
14270155 TAAAAACATTA-TTTTAA
1 TAAAAA-TTTATTTTTAA
*
14270172 AATAAAATTTATTT
1 TA-AAAATTTATTT
14270186 ATAAATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TAAAAATTTATTTTTAA
Found at i:14270191 original size:17 final size:17
Alignment explanation
Indices: 14270138--14270191 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
14270128 GAAAAAAATT
*
14270138 TAAAAATTTATTTTTAA
1 TAAAAATTTATTTTAAA
*
14270155 TAAAAACATTATTTTAAA
1 TAAAAA-TTTATTTTAAA
14270173 -ATAAAATTTATTTATAAA
1 TA-AAAATTTATTT-TAAA
14270191 T
1 T
14270192 TTTACTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 13 0.43
18 17 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAAATTTATTTTAAA
Found at i:14271044 original size:2 final size:2
Alignment explanation
Indices: 14271037--14271063 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14271027 AGTAAAGTGC
14271037 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
14271064 TTTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:14272625 original size:77 final size:77
Alignment explanation
Indices: 14272498--14272651 Score: 274
Period size: 77 Copynumber: 2.0 Consensus size: 77
14272488 ATAAATAGGG
*
14272498 CAATTTAGGTATTATCTAGACATCTCATATTCTCTACAACTTTCATACTTTC-TCTTTTCTATTC
1 CAATTTAGGTATTATCTAGACATCTCATATGCTCTACAACTTTCATACTTTCTTC-TTTCTATTC
14272562 CCTCCCATATCGA
65 CCTCCCATATCGA
*
14272575 CAATTTAGGTATTATTTAGACATCTCATATGCTCTACAACTTTCATACTTTCTTCTTTCTATTCC
1 CAATTTAGGTATTATCTAGACATCTCATATGCTCTACAACTTTCATACTTTCTTCTTTCTATTCC
14272640 CTCCCATATCGA
66 CTCCCATATCGA
14272652 TCTCTGACTT
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
77 72 0.97
78 2 0.03
ACGTcount: A:0.25, C:0.27, G:0.06, T:0.43
Consensus pattern (77 bp):
CAATTTAGGTATTATCTAGACATCTCATATGCTCTACAACTTTCATACTTTCTTCTTTCTATTCC
CTCCCATATCGA
Found at i:14275996 original size:8 final size:8
Alignment explanation
Indices: 14275983--14276018 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
14275973 TGTATTTTAT
14275983 TTATATAG
1 TTATATAG
*
14275991 TTATATAT
1 TTATATAG
14275999 TTATATAG
1 TTATATAG
*
14276007 TTATATAT
1 TTATATAG
14276015 TTAT
1 TTAT
14276019 TATTATTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (8 bp):
TTATATAG
Found at i:14276001 original size:16 final size:16
Alignment explanation
Indices: 14275980--14276029 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
14275970 ATATGTATTT
14275980 TATTTATATAGTTATA
1 TATTTATATAGTTATA
14275996 TATTTATATAGTTATA
1 TATTTATATAGTTATA
14276012 TATTTAT-TA-TTAT-
1 TATTTATATAGTTATA
14276025 TATTT
1 TATTT
14276030 TTATCTTGTA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.15
14 4 0.12
15 2 0.06
16 23 0.68
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (16 bp):
TATTTATATAGTTATA
Found at i:14276109 original size:30 final size:33
Alignment explanation
Indices: 14276073--14276133 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
14276063 TTATTTTTAA
*
14276073 TTATCTG-TTA-AATT-TTTTTATTTTTTTCGT
1 TTATCTGATTATAATTATTATTATTTTTTTCGT
*
14276103 TTATCTGATTATTATTATTATTATTTTTTTC
1 TTATCTGATTATAATTATTATTATTTTTTTC
14276134 TTCTTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 7 0.27
31 3 0.12
32 3 0.12
33 13 0.50
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.69
Consensus pattern (33 bp):
TTATCTGATTATAATTATTATTATTTTTTTCGT
Found at i:14276992 original size:5 final size:5
Alignment explanation
Indices: 14276982--14277160 Score: 90
Period size: 5 Copynumber: 34.4 Consensus size: 5
14276972 CGCTCCAGGT
*
14276982 TTTTA TTTTA TTTT- TATT- TTTTA TTTTTA TTTTA TTTTA TTTATTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTTA TTTTA -TT-TTA
* *
14277028 TTTGT- TTTTA TTATT- TATTT- TTTTA -TTTA TTAGATTA GGTTTA TTTAA
1 TTT-TA TTTTA TT-TTA T-TTTA TTTTA TTTTA TT---TTA -TTTTA TTTTA
*
14277076 TATTT- TTTTA TCTTTA TTTTA TTTTTA TTTTTG TTTTA CTTTT- TTTTA
1 T-TTTA TTTTA T-TTTA TTTTA -TTTTA -TTTTA TTTTA -TTTTA TTTTA
*
14277124 TTTTA -TTT- TTTTA TTTTCA TTTTTA TTTTG TTTTA TT
1 TTTTA TTTTA TTTTA TTTT-A -TTTTA TTTTA TTTTA TT
14277161 ATTCAATTTT
Statistics
Matches: 140, Mismatches: 10, Indels: 48
0.71 0.05 0.24
Matches are distributed among these distances:
4 27 0.19
5 63 0.45
6 39 0.28
7 7 0.05
8 3 0.02
9 1 0.01
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:14276996 original size:6 final size:6
Alignment explanation
Indices: 14276981--14277152 Score: 95
Period size: 6 Copynumber: 27.7 Consensus size: 6
14276971 CCGCTCCAGG
* *
14276981 TTTTTA -TTTTA TTTTTA TTTTTTA TTTTTA TTTTATT TTATTTA TTATTTG
1 TTTTTA TTTTTA TTTTTA -TTTTTA TTTTTA TTTT-TA TT-TTTA TT-TTTA
* ** *
14277032 TTTTTA TTATTTA TTTTT- TTATTTA TTAGATTA GGTTTA TTTAATATT
1 TTTTTA TT-TTTA TTTTTA TT-TTTA TT--TTTA TTTTTA TTT--T-TA
* * *
14277080 TTTTTA TCTTTA -TTTTA TTTTTA TTTTT- GTTTTA -CTTT- TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* *
14277124 TTTTATT TTTTTA TTTTCA TTTTTA TTTT
1 TTTT-TA TTTTTA TTTTTA TTTTTA TTTT
14277153 GTTTTATTAT
Statistics
Matches: 128, Mismatches: 22, Indels: 32
0.70 0.12 0.18
Matches are distributed among these distances:
5 21 0.16
6 65 0.51
7 32 0.25
8 6 0.05
9 4 0.03
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:14277004 original size:7 final size:7
Alignment explanation
Indices: 14276987--14277055 Score: 56
Period size: 7 Copynumber: 10.1 Consensus size: 7
14276977 CAGGTTTTTA
14276987 TTTTA-T
1 TTTTATT
14276993 TTTTATT
1 TTTTATT
14277000 TTTTA-T
1 TTTTATT
14277006 TTTTATT
1 TTTTATT
14277013 TTATT-TT
1 TT-TTATT
*
14277020 ATTTATT
1 TTTTATT
* *
14277027 ATTT-GT
1 TTTTATT
14277033 TTTTATT
1 TTTTATT
*
14277040 ATTTATTT
1 TTTTA-TT
14277048 TTTTATT
1 TTTTATT
14277055 T
1 T
14277056 ATTAGATTAG
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
6 17 0.33
7 26 0.51
8 8 0.16
ACGTcount: A:0.17, C:0.00, G:0.01, T:0.81
Consensus pattern (7 bp):
TTTTATT
Found at i:14277037 original size:40 final size:39
Alignment explanation
Indices: 14276983--14277151 Score: 116
Period size: 40 Copynumber: 4.1 Consensus size: 39
14276973 GCTCCAGGTT
*
14276983 TTTATT-TTATTTTTATTTTTTATTTTTATTTTATTTTA
1 TTTATTATTTTTTTTATTTTTTATTTTTATTTTATTTTA
* *
14277021 TTTATTATTTGTTTTTATTATTTATTTTTTTATTTATTAGATTA
1 TTTATTATTT-TTTTTATTTTTTATTTTTAT-TTTATT---TTA
*
14277065 GGTTTATTTAATATTTTTTTA-TCTTTA-TTTTATTTTTATTTT-
1 --TTTA-TT-AT-TTTTTTTATTTTTTATTTTTA-TTTTATTTTA
14277107 TGTT-TTACTTTTTTTTATTTTATT-TTTTTATTTTCATTTTTA
1 T-TTATTA-TTTTTTTTATTTT-TTATTTTTATTTT-A-TTTTA
14277149 TTT
1 TTT
14277152 TGTTTTATTA
Statistics
Matches: 105, Mismatches: 6, Indels: 37
0.71 0.04 0.25
Matches are distributed among these distances:
38 15 0.14
39 11 0.10
40 27 0.26
41 14 0.13
42 1 0.01
43 2 0.02
44 3 0.03
46 14 0.13
47 8 0.08
48 8 0.08
49 2 0.02
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (39 bp):
TTTATTATTTTTTTTATTTTTTATTTTTATTTTATTTTA
Found at i:14277163 original size:13 final size:13
Alignment explanation
Indices: 14276981--14277147 Score: 91
Period size: 13 Copynumber: 12.2 Consensus size: 13
14276971 CCGCTCCAGG
14276981 TTTTTATTTTA--
1 TTTTTATTTTATT
14276992 TTTTTATTTT-TT
1 TTTTTATTTTATT
14277004 ATTTTTATTTTATT
1 -TTTTTATTTTATT
*
14277018 TTATTTATTATT-TG
1 TT-TTTATT-TTATT
14277032 TTTTTATTATTTATT
1 TTTTTA-T-TTTATT
14277047 TTTTTA-TTTATT
1 TTTTTATTTTATT
14277059 AGATTAGGTTTATTTAATATT
1 ---TT---TTTATTT--TATT
14277080 TTTTTATCTTTA--
1 TTTTTAT-TTTATT
*
14277092 -TTTTATTTT-TA
1 TTTTTATTTTATT
*
14277103 TTTTTGTTTTACTTT
1 TTTTTATTTTA--TT
14277118 TTTTTATTTTATT
1 TTTTTATTTTATT
14277131 TTTTTATTTTCATT
1 TTTTTATTTT-ATT
14277145 TTT
1 TTT
14277148 ATTTTGTTTT
Statistics
Matches: 125, Mismatches: 5, Indels: 49
0.70 0.03 0.27
Matches are distributed among these distances:
10 3 0.02
11 16 0.13
12 14 0.11
13 28 0.22
14 22 0.18
15 28 0.22
16 2 0.02
18 6 0.05
19 2 0.02
21 4 0.03
ACGTcount: A:0.18, C:0.02, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTTTATTTTATT
Found at i:14277346 original size:58 final size:57
Alignment explanation
Indices: 14277187--14277585 Score: 516
Period size: 58 Copynumber: 6.8 Consensus size: 57
14277177 ATAAAAATAA
* * * *
14277187 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTC
* *
14277244 AAAAAAGGGTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAA----TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAGTTTC
*
14277306 TAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAGTTTC
* * *
14277364 CAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTC
14277421 AAAAAA-AGGTTTTCTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTTC
1 AAAAAATA---TTT-TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAAG-TTTC
* *
14277483 -AAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAAATAAA-TTTC
1 AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT--GAAAATAAAGTTTC
*
14277540 AAAAAATCAATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTG
1 AAAAAAT--ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
14277586 CACAAGAACA
Statistics
Matches: 305, Mismatches: 20, Indels: 33
0.85 0.06 0.09
Matches are distributed among these distances:
56 1 0.00
57 22 0.07
58 134 0.44
59 9 0.03
60 76 0.25
61 46 0.15
62 17 0.06
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.36
Consensus pattern (57 bp):
AAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAAGTTTC
Found at i:14277473 original size:118 final size:115
Alignment explanation
Indices: 14277186--14277585 Score: 534
Period size: 118 Copynumber: 3.4 Consensus size: 115
14277176 AATAAAAATA
* * * * *
14277186 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAT-AAAATTTCAAAAAA
1 AAAAAAAT-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAA
* * * *
14277250 GGGTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTC
65 ----TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAATTTC
*
14277306 -TAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAA
1 AAAAAAAT-TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAA
14277370 TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
65 TATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
*
14277421 AAAAAAAGGTTTTCTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTTCAAA
1 AAAAAAA--TTTT-TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAA
* *
14277486 AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAAATAAATTTC
63 AATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATA-AAATTTC
* *
14277540 AAAAAATCAATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTG
1 AAAAAA--ATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTG
14277586 CACAAGAACA
Statistics
Matches: 256, Mismatches: 16, Indels: 18
0.88 0.06 0.06
Matches are distributed among these distances:
115 7 0.03
116 45 0.18
117 3 0.01
118 127 0.50
119 61 0.24
120 12 0.05
121 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.36
Consensus pattern (115 bp):
AAAAAAATTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAAT
ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTC
Found at i:14277499 original size:176 final size:176
Alignment explanation
Indices: 14277187--14277584 Score: 649
Period size: 176 Copynumber: 2.2 Consensus size: 176
14277177 ATAAAAATAA
* *
14277187 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAATTTCAAAAAAGG
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAG
* *
14277252 GTTTTTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCTAAAAATATTT
66 GTTTTTCTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCTAAAAATATTT
*
14277317 TTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-GAAAATCAAAGTTTC
131 TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAAT-AAA-TTTC
* *
14277364 CAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAG
1 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAG
14277429 G-TTTTCTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTT-TCAAAAATATT
66 GTTTTTCTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCT-AAAAATATT
*
14277492 TTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAAAAAATAAATTTC
130 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAAAAATAAATTTC
14277540 AAAAAATCAATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAAAT--ATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT
14277585 GCACAAGAAC
Statistics
Matches: 206, Mismatches: 10, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
175 1 0.00
176 100 0.49
177 65 0.32
178 40 0.19
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.36
Consensus pattern (176 bp):
AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAG
GTTTTTCTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCTAAAAATATTT
TTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAATAAATTTC
Found at i:14287189 original size:68 final size:68
Alignment explanation
Indices: 14287080--14287216 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
14287070 TCATGCCACG
14287080 TATCTAAAGCAATTACCAAAGATGACTCTTCGTATTCATGGCTTTGAATTTTGTCATTCAATTTT
1 TATCTAAAGCAATTACCAAAGATGACTCTTCGTATTCATGGCTTTGAATTTTGTCATTCAATTTT
14287145 TTT
66 TTT
*
14287148 TATCTAAAGCAATTACCAAAGATGACTCTTCGTATTTATGGCTTTGAATTTTGTCATTCAATTTT
1 TATCTAAAGCAATTACCAAAGATGACTCTTCGTATTCATGGCTTTGAATTTTGTCATTCAATTTT
14287213 TTT
66 TTT
14287216 T
1 T
14287217 CCTTATTAAA
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (68 bp):
TATCTAAAGCAATTACCAAAGATGACTCTTCGTATTCATGGCTTTGAATTTTGTCATTCAATTTT
TTT
Found at i:14289523 original size:20 final size:20
Alignment explanation
Indices: 14289469--14289526 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
14289459 AAATGCCCCA
* *
14289469 TGGTCAAACTTAGTAAAACT
1 TGGTCAAAATTAGTCAAACT
* *
14289489 TGTTC-AAATAAAGTCAAACT
1 TGGTCAAAAT-TAGTCAAACT
14289509 TGGTCAAAATTAGTCAAA
1 TGGTCAAAATTAGTCAAA
14289527 ATTAGTTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 3 0.10
20 23 0.77
21 4 0.13
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (20 bp):
TGGTCAAAATTAGTCAAACT
Found at i:14290024 original size:143 final size:142
Alignment explanation
Indices: 14289871--14290132 Score: 305
Period size: 143 Copynumber: 1.8 Consensus size: 142
14289861 AACACTCCAA
* * *
14289871 ATCATGGTTTT-ATATTATTTCATGATTTTTAGTGCAATAAAAACCTTGATCGTACC-TAACAAG
1 ATCATGGTTTTCAAATTATTTCATGAATTTTAGTGC-ATAAAAACCTTGATCGCACCTTAA-AAG
* * * *
14289934 GTGTGAAATTACTAGAATACCATTAAAAGGTATTTTTATAATTTGACATTCCTGAGGTTATAGTT
64 GTATGAAATTACGAAAATACCATT-AAAGGTATTTTAATAATTTGA-ATTCCTGAGGTTATAGTT
14289999 TTGCTAAACATTCTAT
127 TTGCTAAACATTCTAT
* * ** * * *
14290015 ATCAT-GTTTTCAAATTATTTTATGAATTTTGGTGCATTGAAACCTTTATTGCACCTTGAAAGGT
1 ATCATGGTTTTCAAATTATTTCATGAATTTTAGTGCATAAAAACCTTGATCGCACCTTAAAAGGT
* ** *
14290079 ATGAAATTACGAAAATACCCTTAGGGGTATTTTAATAATTTGATTTCCTGAGGT
66 ATGAAATTACGAAAATACCATTAAAGGTATTTTAATAATTTGAATTCCTGAGGT
14290133 CGATTTTTCA
Statistics
Matches: 98, Mismatches: 18, Indels: 7
0.80 0.15 0.06
Matches are distributed among these distances:
141 10 0.10
142 18 0.18
143 43 0.44
144 27 0.28
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.40
Consensus pattern (142 bp):
ATCATGGTTTTCAAATTATTTCATGAATTTTAGTGCATAAAAACCTTGATCGCACCTTAAAAGGT
ATGAAATTACGAAAATACCATTAAAGGTATTTTAATAATTTGAATTCCTGAGGTTATAGTTTTGC
TAAACATTCTAT
Found at i:14291716 original size:13 final size:13
Alignment explanation
Indices: 14291698--14291732 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
14291688 CTTAGACCCT
14291698 AATCCTAAACCAA
1 AATCCTAAACCAA
*
14291711 AATCCTAAATCAA
1 AATCCTAAACCAA
*
14291724 AACCCTAAA
1 AATCCTAAA
14291733 ATCAAACCCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (13 bp):
AATCCTAAACCAA
Found at i:14291736 original size:14 final size:14
Alignment explanation
Indices: 14291708--14291759 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 14
14291698 AATCCTAAAC
*
14291708 CAAAATCCT-AAAT
1 CAAAACCCTAAAAT
14291721 CAAAACCCTAAAAT
1 CAAAACCCTAAAAT
* *
14291735 C-AAACCCCAAATT
1 CAAAACCCTAAAAT
*
14291748 CAAAACTCTAAA
1 CAAAACCCTAAA
14291760 CCCAAAACCA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
13 19 0.59
14 13 0.41
ACGTcount: A:0.54, C:0.29, G:0.00, T:0.17
Consensus pattern (14 bp):
CAAAACCCTAAAAT
Found at i:14291765 original size:27 final size:26
Alignment explanation
Indices: 14291701--14291813 Score: 79
Period size: 26 Copynumber: 4.3 Consensus size: 26
14291691 AGACCCTAAT
* * *
14291701 CCTAAACCAAAATCCTAAATCAAAAC
1 CCTAAACCCAAACCCCAAATCAAAAC
**
14291727 CCTAAAATCAAACCCCAAATTCAAAAC
1 CCTAAACCCAAACCCCAAA-TCAAAAC
* * *
14291754 TCTAAACCCAAA-ACCAAACCATAAA-
1 CCTAAACCCAAACCCCAAATCA-AAAC
** *
14291779 CCTAAACCTTAACCCTAAA-CATAAAC
1 CCTAAACCCAAACCCCAAATCA-AAAC
14291805 CCTAAACCC
1 CCTAAACCC
14291814 TAAAATCAAA
Statistics
Matches: 67, Mismatches: 16, Indels: 8
0.74 0.18 0.09
Matches are distributed among these distances:
25 17 0.25
26 34 0.51
27 16 0.24
ACGTcount: A:0.50, C:0.35, G:0.00, T:0.15
Consensus pattern (26 bp):
CCTAAACCCAAACCCCAAATCAAAAC
Found at i:14291779 original size:7 final size:7
Alignment explanation
Indices: 14291750--14291817 Score: 56
Period size: 7 Copynumber: 10.4 Consensus size: 7
14291740 CCCAAATTCA
*
14291750 AAACTCT
1 AAACCCT
14291757 AAACCC-
1 AAACCCT
*
14291763 AAAACC-
1 AAACCCT
*
14291769 AAACCAT
1 AAACCCT
14291776 AAA-CCT
1 AAACCCT
14291782 AAA-CCT
1 AAACCCT
*
14291788 TAACCCT
1 AAACCCT
*
14291795 AAA-CAT
1 AAACCCT
14291801 AAACCCT
1 AAACCCT
14291808 AAACCCT
1 AAACCCT
14291815 AAA
1 AAA
14291818 ATCAAAACCC
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
6 24 0.49
7 25 0.51
ACGTcount: A:0.51, C:0.34, G:0.00, T:0.15
Consensus pattern (7 bp):
AAACCCT
Found at i:14291795 original size:13 final size:13
Alignment explanation
Indices: 14291769--14291812 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
14291759 ACCCAAAACC
* *
14291769 AAACCATAAACCT
1 AAACCTTAACCCT
14291782 AAACCTTAACCCT
1 AAACCTTAACCCT
* *
14291795 AAACATAAACCCT
1 AAACCTTAACCCT
14291808 AAACC
1 AAACC
14291813 CTAAAATCAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (13 bp):
AAACCTTAACCCT
Found at i:14291832 original size:20 final size:19
Alignment explanation
Indices: 14291770--14291832 Score: 65
Period size: 19 Copynumber: 3.2 Consensus size: 19
14291760 CCCAAAACCA
* * *
14291770 AACCATAAACCTAAACCTT
1 AACCCTAAACATAAACCCT
14291789 AACCCTAAACATAAACCCT
1 AACCCTAAACATAAACCCT
14291808 AAACCCTAAA-ATCAAAACCCT
1 -AACCCTAAACAT--AAACCCT
14291829 AACC
1 AACC
14291833 TAGACCTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
19 18 0.47
20 13 0.34
21 7 0.18
ACGTcount: A:0.49, C:0.35, G:0.00, T:0.16
Consensus pattern (19 bp):
AACCCTAAACATAAACCCT
Found at i:14291863 original size:18 final size:19
Alignment explanation
Indices: 14291840--14291880 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
14291830 ACCTAGACCT
*
14291840 TAAACTAAC-ATCAAACTC
1 TAAACTAACTATCAAACCC
*
14291858 TAAACTAACTCTCAAACCC
1 TAAACTAACTATCAAACCC
14291877 TAAA
1 TAAA
14291881 ACCAACTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (19 bp):
TAAACTAACTATCAAACCC
Found at i:14293540 original size:15 final size:13
Alignment explanation
Indices: 14293516--14293550 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
14293506 CTTTGTGTTT
*
14293516 AAAAAAAAAAAGC
1 AAAAAAAAAAAAC
14293529 AAAAAAACAAAAAC
1 AAAAAAA-AAAAAC
14293543 AAAAAAAA
1 AAAAAAAA
14293551 GGAAAAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.89, C:0.09, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:14295425 original size:20 final size:19
Alignment explanation
Indices: 14295372--14295427 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 19
14295362 CTATCAGTAA
14295372 TAAATTTTAGT-AAAAAAT
1 TAAATTTTAGTAAAAAAAT
*
14295390 TAAATTTTAGAGAAAAAAAT
1 TAAATTTTAG-TAAAAAAAT
14295410 TAAATTTTTAGTAAAAAA
1 TAAA-TTTTAGTAAAAAA
14295428 TTCTTCGTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 10 0.30
20 17 0.52
21 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (19 bp):
TAAATTTTAGTAAAAAAAT
Found at i:14296398 original size:19 final size:19
Alignment explanation
Indices: 14296349--14296405 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
14296339 TCATAAATAA
14296349 TAATA-TAAATATTATTTTT
1 TAATATTAAATA-TATTTTT
*
14296368 T-ATCCATAAAATATATTTTT
1 TAAT--ATTAAATATATTTTT
*
14296388 TAATATTAAATATCTTTT
1 TAATATTAAATATATTTT
14296406 ATTTTCCTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 9 0.29
21 7 0.23
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.54
Consensus pattern (19 bp):
TAATATTAAATATATTTTT
Done.