Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 4 of 27
Found at i:430513 original size:28 final size:27
Alignment explanation
Indices: 430456--430513 Score: 62
Period size: 28 Copynumber: 2.1 Consensus size: 27
430446 TCATATAAAA
* * **
430456 TTTTCAAATACATTTTGCAAAAGTTTT
1 TTTTCAAATAAATTTTGAAAAAGTCAT
*
430483 TTTTCAAGTAAATATTTGAAAAAGTCAT
1 TTTTCAAATAAAT-TTTGAAAAAGTCAT
430511 TTT
1 TTT
430514 AAGAATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.47
Consensus pattern (27 bp):
TTTTCAAATAAATTTTGAAAAAGTCAT
Found at i:430976 original size:32 final size:33
Alignment explanation
Indices: 430940--431011 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
430930 TAAATTCGAT
*
430940 TAATTTAAACTCAAAATAACTTAAA-ATTTTAA
1 TAATTTAAACTAAAAATAACTTAAATATTTTAA
** * *
430972 TAATTCGAATTAAAAATAATTTAAATATTTTAA
1 TAATTTAAACTAAAAATAACTTAAATATTTTAA
431005 -AATTTAA
1 TAATTTAA
431012 TAATTTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
32 25 0.78
33 7 0.22
ACGTcount: A:0.53, C:0.06, G:0.01, T:0.40
Consensus pattern (33 bp):
TAATTTAAACTAAAAATAACTTAAATATTTTAA
Found at i:433734 original size:2 final size:2
Alignment explanation
Indices: 433727--433752 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
433717 TGTCCTCTCC
433727 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
433753 CCAATATGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:436728 original size:19 final size:19
Alignment explanation
Indices: 436695--436744 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
436685 ATGTAACTAG
*
436695 TAATATTTATATATAATTTC
1 TAATATTT-TATATAATTTA
*
436715 TAATATTTTATATAGTTTA
1 TAATATTTTATATAATTTA
*
436734 TAATGTTTTAT
1 TAATATTTTAT
436745 GCAATTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 19 0.70
20 8 0.30
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
TAATATTTTATATAATTTA
Found at i:436770 original size:20 final size:19
Alignment explanation
Indices: 436682--436770 Score: 61
Period size: 19 Copynumber: 4.6 Consensus size: 19
436672 AAGGTAATGG
* *
436682 TTTATGTAACTAGTAATAT
1 TTTATGTAATTAATAATAT
* **
436701 TTATATATAATTTCTAATAT
1 TT-TATGTAATTAATAATAT
* * * *
436721 TTTATATAGTTTATAATGT
1 TTTATGTAATTAATAATAT
* *
436740 TTTATGCAATTAATAATGT
1 TTTATGTAATTAATAATAT
436759 TTATATGTAATT
1 TT-TATGTAATT
436771 GTAATAAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
19 33 0.59
20 23 0.41
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (19 bp):
TTTATGTAATTAATAATAT
Found at i:436879 original size:19 final size:19
Alignment explanation
Indices: 436855--436910 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
436845 CTTTATATGT
436855 AATTACATAAAATATTAAA
1 AATTACATAAAATATTAAA
* **
436874 AATTACGTATAAATATTATC
1 AATTACATA-AAATATTAAA
* *
436894 AATTATATGAAATATTA
1 AATTACATAAAATATTA
436911 TAAGTTACGT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (19 bp):
AATTACATAAAATATTAAA
Found at i:439059 original size:20 final size:19
Alignment explanation
Indices: 439034--439071 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
439024 TCTATCTTTC
*
439034 ATTTTTATATTTAATATTTT
1 ATTTTTAAATTTAA-ATTTT
439054 ATTTTTAAATTTAAATTT
1 ATTTTTAAATTTAAATTT
439072 AAATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTTAAATTTAAATTTT
Found at i:440256 original size:19 final size:19
Alignment explanation
Indices: 440216--440261 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
440206 TAATAATTTT
440216 TATTATATAAATTTTAAAA
1 TATTATATAAATTTTAAAA
**
440235 TATT-TATAAATTTATATTA
1 TATTATATAAATTT-TAAAA
440254 TATTATAT
1 TATTATAT
440262 TTGTTTAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 9 0.39
19 11 0.48
20 3 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TATTATATAAATTTTAAAA
Found at i:440746 original size:26 final size:27
Alignment explanation
Indices: 440688--440750 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
440678 TTTATTCCCC
*
440688 AAATAAA-A-AAATATTTTTAATTTTA
1 AAATAAATATAAATAATTTTAATTTTA
*
440713 AAATAAATATAAATAATTTTATTTTTA
1 AAATAAATATAAATAATTTTAATTTTA
*
440740 ATA-AAATATAA
1 AAATAAATATAA
440751 TTTCATCATC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 7 0.21
26 9 0.27
27 17 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
AAATAAATATAAATAATTTTAATTTTA
Found at i:442388 original size:20 final size:18
Alignment explanation
Indices: 442363--442401 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
442353 ATTTAATAAG
442363 TAAATAGTAAACGTGATATT
1 TAAATAGTAAA-GT-ATATT
*
442383 TAAATATTAAAGTATATT
1 TAAATAGTAAAGTATATT
442401 T
1 T
442402 TATATTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 2 0.11
20 10 0.56
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (18 bp):
TAAATAGTAAAGTATATT
Found at i:445019 original size:22 final size:24
Alignment explanation
Indices: 444994--445046 Score: 65
Period size: 22 Copynumber: 2.2 Consensus size: 24
444984 ATTTATACGG
*
444994 TTATTTTTATTTTAAA-A-AATAA
1 TTATTTTTATATTAAATATAATAA
*
445016 TTATTATTATATTAAATATAATAA
1 TTATTTTTATATTAAATATAATAA
445040 TTCATTT
1 TT-ATTT
445047 ACATATCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 14 0.56
23 1 0.04
24 7 0.28
25 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATTTTTATATTAAATATAATAA
Found at i:447154 original size:28 final size:30
Alignment explanation
Indices: 447105--447168 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 30
447095 TACTAAAAAT
*
447105 ATAAAAAATATATAAAACATATTA-AT-AA
1 ATAAAAAATATATAAAACATATAAGATAAA
* *
447133 ATAAAAAATAATTTTAAA-ATATAAGATAAA
1 ATAAAAAAT-ATATAAAACATATAAGATAAA
447163 ATAAAA
1 ATAAAA
447169 TAAAATAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 14 0.47
29 8 0.27
30 8 0.27
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (30 bp):
ATAAAAAATATATAAAACATATAAGATAAA
Found at i:447234 original size:11 final size:13
Alignment explanation
Indices: 447205--447253 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
447195 ATTATATACG
447205 ATATAAAAATATA
1 ATATAAAAATATA
447218 ATATAAAAATA-A
1 ATATAAAAATATA
447230 A-AT--AAATATA
1 ATATAAAAATATA
* *
447240 TTATAAATATATA
1 ATATAAAAATATA
447253 A
1 A
447254 ATATTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
9 5 0.17
10 1 0.03
11 4 0.14
12 2 0.07
13 17 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (13 bp):
ATATAAAAATATA
Found at i:447236 original size:22 final size:23
Alignment explanation
Indices: 447211--447256 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
447201 TACGATATAA
447211 AAATATAATATAAAAATA-AAAT
1 AAATATAATATAAAAATATAAAT
* *
447233 AAATATATTATAAATATATAAAT
1 AAATATAATATAAAAATATAAAT
447256 A
1 A
447257 TTTTTAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATAATATAAAAATATAAAT
Found at i:447288 original size:31 final size:32
Alignment explanation
Indices: 447235--447325 Score: 78
Period size: 31 Copynumber: 2.8 Consensus size: 32
447225 AATAAAATAA
* * *
447235 ATATATTATAAATATATAAATATTTTTAA-ATTT
1 ATATAATAT-AATATATAAATA-TATCAATATTT
*
447268 ATATAATATAAT-TATTAATATATCAATATTT
1 ATATAATATAATATATAAATATATCAATATTT
*
447299 ATATAATTATAAAATAATATAATATAT
1 ATATAA-TATAATAT-ATA-AATATAT
447326 AATTTCTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
30 4 0.09
31 17 0.36
32 8 0.17
33 9 0.19
34 2 0.04
35 7 0.15
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (32 bp):
ATATAATATAATATATAAATATATCAATATTT
Found at i:447289 original size:39 final size:38
Alignment explanation
Indices: 447231--447327 Score: 114
Period size: 39 Copynumber: 2.6 Consensus size: 38
447221 TAAAAATAAA
* *
447231 ATAAATAT-ATTATAAATATATAAATATTTTTA-AATTT
1 ATAAATATAATTATTAATATATAAATATTTATATAA-TT
*
447268 ATATAATATAATTATTAATATATCAATATTTATATAATT
1 ATA-AATATAATTATTAATATATAAATATTTATATAATT
447307 ATAAA-ATAA-TA-TAATATATAA
1 ATAAATATAATTATTAATATATAA
447328 TTTCTTTTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
35 9 0.17
36 2 0.04
37 7 0.13
38 7 0.13
39 26 0.49
40 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (38 bp):
ATAAATATAATTATTAATATATAAATATTTATATAATT
Found at i:447872 original size:21 final size:20
Alignment explanation
Indices: 447840--447890 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
447830 TTCAATTTCG
447840 TATTAATAATAAATTTAAAAA
1 TATTAAT-ATAAATTTAAAAA
*
447861 TATTAA-ATATAATTATATAAA
1 TATTAATATA-AATT-TAAAAA
447882 TA-TAATATA
1 TATTAATATA
447891 TATAAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.12
20 7 0.27
21 16 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TATTAATATAAATTTAAAAA
Found at i:447878 original size:15 final size:15
Alignment explanation
Indices: 447860--447905 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
447850 AAATTTAAAA
447860 ATATTAAATATAATT
1 ATATTAAATATAATT
447875 ATA-TAAATATAATAT
1 ATATTAAATATAAT-T
* *
447890 ATATAAAAAATAATT
1 ATATTAAATATAATT
447905 A
1 A
447906 AAATATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 10 0.37
15 9 0.33
16 8 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATATTAAATATAATT
Found at i:447888 original size:38 final size:38
Alignment explanation
Indices: 447845--447974 Score: 106
Period size: 38 Copynumber: 3.3 Consensus size: 38
447835 TTTCGTATTA
447845 ATAATAAATTTAAAAATATTAAATATAATTATATAAAT
1 ATAATAAATTTAAAAATATTAAATATAATTATATAAAT
* *
447883 ATAATATATATAAAAAATAATTAAAATATAATATGATATAAAT
1 ATAATAAAT-TTAAAAAT-ATT-AAATATAAT-T-ATATAAAT
* * *
447926 AT-AT-ATTTTAAAATTTTTATAATATAAATTAT-T-AAT
1 ATAATAAATTTAAAAATATTA-AATAT-AATTATATAAAT
* *
447962 ATATTAAAATTAA
1 ATAATAAATTTAA
447975 TATAATTATA
Statistics
Matches: 73, Mismatches: 10, Indels: 18
0.72 0.10 0.18
Matches are distributed among these distances:
36 5 0.07
37 2 0.03
38 16 0.22
39 15 0.21
40 12 0.16
41 10 0.14
42 3 0.04
43 10 0.14
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.42
Consensus pattern (38 bp):
ATAATAAATTTAAAAATATTAAATATAATTATATAAAT
Found at i:447937 original size:30 final size:29
Alignment explanation
Indices: 447860--447978 Score: 88
Period size: 29 Copynumber: 4.1 Consensus size: 29
447850 AAATTTAAAA
*
447860 ATAT-TAAATATA-ATTATATAAATATAAT
1 ATATATAAATATATATTTTA-AAATATAAT
* *
447888 ATATATAAA-AAATA-ATTAAAATATAAT
1 ATATATAAATATATATTTTAAAATATAAT
**
447915 ATGATATAAATATATATTTTAAAAT-TTTT
1 AT-ATATAAATATATATTTTAAAATATAAT
*
447944 ATAATATAAATTATTAATATATTAAAAT-TAAT
1 AT-ATATAAA-TA-T-ATATTTTAAAATATAAT
447976 ATA
1 ATA
447979 ATTATAAAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
27 11 0.15
28 15 0.21
29 20 0.28
30 9 0.12
31 2 0.03
32 15 0.21
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
ATATATAAATATATATTTTAAAATATAAT
Found at i:451788 original size:20 final size:20
Alignment explanation
Indices: 451765--451838 Score: 82
Period size: 20 Copynumber: 3.8 Consensus size: 20
451755 TGAGTAATTT
*
451765 TTTTTTGAAGAAAATAGATA
1 TTTTTTGAAGAAAGTAGATA
* *
451785 TTTTTTTAA-AAAGTA-ATT
1 TTTTTTGAAGAAAGTAGATA
451803 TTTTTTCGAAGAAAGTAGATA
1 TTTTTT-GAAGAAAGTAGATA
*
451824 TTTTTTTAA-AAAGTA
1 TTTTTTGAAGAAAGTA
451839 ATTTTTATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
18 8 0.18
19 13 0.29
20 16 0.36
21 8 0.18
ACGTcount: A:0.41, C:0.01, G:0.12, T:0.46
Consensus pattern (20 bp):
TTTTTTGAAGAAAGTAGATA
Found at i:451800 original size:39 final size:39
Alignment explanation
Indices: 451744--451844 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
451734 AGTTAGATAA
* *
451744 ATTTTTTTAAATGAGTAATTTTTTTTTGAAGAAAATAGAT
1 ATTTTTTTAAA-AAGTAATTTTTTTTCGAAGAAAATAGAT
*
451784 ATTTTTTTAAAAAGTAATTTTTTTTCGAAGAAAGTAGAT
1 ATTTTTTTAAAAAGTAATTTTTTTTCGAAGAAAATAGAT
451823 ATTTTTTTAAAAAGTAATTTTT
1 ATTTTTTTAAAAAGTAATTTTT
451845 ATTAAAAATA
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
39 47 0.81
40 11 0.19
ACGTcount: A:0.38, C:0.01, G:0.11, T:0.50
Consensus pattern (39 bp):
ATTTTTTTAAAAAGTAATTTTTTTTCGAAGAAAATAGAT
Found at i:451805 original size:16 final size:16
Alignment explanation
Indices: 451784--451880 Score: 70
Period size: 17 Copynumber: 5.6 Consensus size: 16
451774 GAAAATAGAT
451784 ATTTTTTTAAAAAGTA
1 ATTTTTTTAAAAAGTA
451800 ATTTTTTTTCGAAGAAAGTAGA
1 A-TTTTTTT--AA-AAAGT--A
451822 TATTTTTTTAAAAAGTA
1 -ATTTTTTTAAAAAGTA
451839 ATTTTTATTAAAAA-TA
1 ATTTTT-TTAAAAAGTA
** * *
451855 AAATATTTAAAAAATA
1 ATTTTTTTAAAAAGTA
451871 ATTATTTTTA
1 ATT-TTTTTA
451881 TTTTATCTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 19
0.72 0.07 0.21
Matches are distributed among these distances:
15 7 0.11
16 15 0.23
17 20 0.31
19 7 0.11
20 7 0.11
22 8 0.12
23 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.06, T:0.47
Consensus pattern (16 bp):
ATTTTTTTAAAAAGTA
Found at i:451880 original size:17 final size:17
Alignment explanation
Indices: 451826--451880 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 17
451816 AGTAGATATT
*
451826 TTTTTAAAAAGTAATT-
1 TTTTTAAAAAATAATTA
*
451842 TTTATT-AAAAATAA-AA
1 TTT-TTAAAAAATAATTA
*
451858 TATTTAAAAAATAATTA
1 TTTTTAAAAAATAATTA
451875 TTTTTA
1 TTTTTA
451881 TTTTATCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
15 2 0.07
16 20 0.67
17 8 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TTTTTAAAAAATAATTA
Found at i:452071 original size:12 final size:12
Alignment explanation
Indices: 452054--452094 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
452044 TAATTTAATA
452054 TTATATTATATT
1 TTATATTATATT
*
452066 TTATATTACATT
1 TTATATTATATT
*
452078 TTA-ATTATTTT
1 TTATATTATATT
452089 TTATAT
1 TTATAT
452095 CTTAAGATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.36
12 16 0.64
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (12 bp):
TTATATTATATT
Found at i:452490 original size:39 final size:41
Alignment explanation
Indices: 452447--452523 Score: 106
Period size: 39 Copynumber: 1.9 Consensus size: 41
452437 ACAAGTAAAC
452447 TAATAAAATAAAATAATA-ATTATTTT-T-ATAAAATATATT
1 TAATAAAATAAAATAATATA-TATTTTATAATAAAATATATT
* *
452486 TAATAATATAATATAATATATATTTTATAATAAAATAT
1 TAATAAAATAAAATAATATATATTTTATAATAAAATAT
452524 CTTATTCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 22 0.67
40 2 0.06
41 9 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (41 bp):
TAATAAAATAAAATAATATATATTTTATAATAAAATATATT
Found at i:452506 original size:24 final size:24
Alignment explanation
Indices: 452473--452523 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
452463 TAATTATTTT
*
452473 TATAAAATATATTTAATAATATAA
1 TATAAAATATATTTAATAATAAAA
* *
452497 TATAATATATATTTTATAATAAAA
1 TATAAAATATATTTAATAATAAAA
452521 TAT
1 TAT
452524 CTTATTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TATAAAATATATTTAATAATAAAA
Found at i:452514 original size:14 final size:14
Alignment explanation
Indices: 452462--452517 Score: 52
Period size: 14 Copynumber: 4.4 Consensus size: 14
452452 AAATAAAATA
452462 ATAAT-TAT-TTTT
1 ATAATATATATTTT
* *
452474 ATAAAATATATTTA
1 ATAATATATATTTT
452488 ATAATATA-A---T
1 ATAATATATATTTT
452498 ATAATATATATTTT
1 ATAATATATATTTT
452512 ATAATA
1 ATAATA
452518 AAATATCTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
12 4 0.12
13 4 0.12
14 17 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATAATATATATTTT
Found at i:452566 original size:16 final size:16
Alignment explanation
Indices: 452545--452611 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 16
452535 TAAACTCAAA
452545 TTAAAAATTTATTTAT
1 TTAAAAATTTATTTAT
*
452561 TT-AAAATTTGATATTTT
1 TTAAAAATTT-AT-TTAT
452578 TTAAATAAATTT-TTTA-
1 TT-AA-AAATTTATTTAT
452594 TT-AAAATTTATTT-T
1 TTAAAAATTTATTTAT
452608 TTAA
1 TTAA
452612 TACAATAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 17
0.68 0.03 0.28
Matches are distributed among these distances:
13 6 0.15
14 6 0.15
15 8 0.20
16 6 0.15
17 7 0.17
18 1 0.02
19 1 0.02
20 6 0.15
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (16 bp):
TTAAAAATTTATTTAT
Found at i:452582 original size:33 final size:32
Alignment explanation
Indices: 452545--452635 Score: 93
Period size: 33 Copynumber: 2.8 Consensus size: 32
452535 TAAACTCAAA
452545 TTAA-AAATTTATTTATTTAAAATTTGATATTTT
1 TTAATAAATTTATTTATTTAAAATTT--TATTTT
452578 TTAAATAAATTT-TTTA-TTAAAA-TTTATTTT
1 TT-AATAAATTTATTTATTTAAAATTTTATTTT
*
452608 TTAATACAA-TAATTTTATTTAAAATTTT
1 TTAATA-AATTTA-TTTATTTAAAATTTT
452636 TAAATTATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
29 5 0.10
30 10 0.20
31 4 0.08
32 8 0.16
33 11 0.22
34 6 0.12
35 6 0.12
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (32 bp):
TTAATAAATTTATTTATTTAAAATTTTATTTT
Found at i:454305 original size:21 final size:20
Alignment explanation
Indices: 454280--454323 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
454270 CCCTTATCTT
*
454280 TTTCT-GTTTGTCTTCTTTTTA
1 TTTCTGGTTT-TCTT-TTTTGA
454301 TTTCTGGTTTTCTTTTTTGA
1 TTTCTGGTTTTCTTTTTTGA
454321 TTT
1 TTT
454324 ATTGTAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 8 0.38
21 9 0.43
22 4 0.19
ACGTcount: A:0.05, C:0.11, G:0.11, T:0.73
Consensus pattern (20 bp):
TTTCTGGTTTTCTTTTTTGA
Found at i:456041 original size:23 final size:25
Alignment explanation
Indices: 455987--456043 Score: 64
Period size: 27 Copynumber: 2.3 Consensus size: 25
455977 AAAAAAAAAT
455987 TAAAATTTTATTTAAATTATTTAAA
1 TAAAATTTTATTTAAATTATTTAAA
* *
456012 TTTAAAATTTTATTT-TATTTTTTAAA
1 --TAAAATTTTATTTAAATTATTTAAA
456038 -AAAATT
1 TAAAATT
456044 AAAATATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 6 0.21
26 9 0.32
27 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TAAAATTTTATTTAAATTATTTAAA
Found at i:456447 original size:22 final size:22
Alignment explanation
Indices: 456412--456453 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
456402 ATATGATTAT
* *
456412 ATAATTTAAGTATAATATAAAA
1 ATAATTAAAATATAATATAAAA
456434 ATAATTAAAATATAATATAA
1 ATAATTAAAATATAATATAA
456454 TATAAAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (22 bp):
ATAATTAAAATATAATATAAAA
Found at i:460015 original size:21 final size:22
Alignment explanation
Indices: 459977--460017 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
459967 ATATAATTAT
*
459977 ATAATTTAAATATAATATAAAA
1 ATAATTTAAAAATAATATAAAA
*
459999 ATAA-TTAAAAATGATATAA
1 ATAATTTAAAAATAATATAA
460018 CATAAAGCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (22 bp):
ATAATTTAAAAATAATATAAAA
Found at i:460302 original size:15 final size:14
Alignment explanation
Indices: 460278--460307 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
460268 TTTTAAATTA
460278 ATTTTTATTTTTAT
1 ATTTTTATTTTTAT
460292 ATTTTTAATTTTTAT
1 ATTTTT-ATTTTTAT
460307 A
1 A
460308 ATTACATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
ATTTTTATTTTTAT
Found at i:460316 original size:21 final size:21
Alignment explanation
Indices: 460275--460316 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
460265 ATTTTTTAAA
** *
460275 TTAATTTTTATTTTTATATTT
1 TTAATTTTTATAATTACATTT
460296 TTAATTTTTATAATTACATTT
1 TTAATTTTTATAATTACATTT
460317 AAAAATGAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTAATTTTTATAATTACATTT
Found at i:460437 original size:14 final size:14
Alignment explanation
Indices: 460418--460468 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
460408 TGTTTATATT
*
460418 AATTTTATGTTTTA
1 AATTTTATATTTTA
* *
460432 AATTTTGTATATTA
1 AATTTTATATTTTA
460446 AATATTTATAATTTT-
1 AAT-TTTAT-ATTTTA
460461 AATTTTAT
1 AATTTTAT
460469 TTACATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
14 19 0.63
15 7 0.23
16 4 0.13
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (14 bp):
AATTTTATATTTTA
Found at i:460464 original size:29 final size:27
Alignment explanation
Indices: 460412--460466 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
460402 AAAATATGTT
*
460412 TATATTAATTTTATGTTTTAAATTTTG
1 TATATTAATTTTATATTTTAAATTTTG
460439 TATATTAAATATTTATAATTTT-AATTTT
1 TATATT-AAT-TTTAT-ATTTTAAATTTT
460467 ATTTACATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 3 0.12
29 11 0.46
30 4 0.17
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.62
Consensus pattern (27 bp):
TATATTAATTTTATATTTTAAATTTTG
Found at i:461659 original size:255 final size:255
Alignment explanation
Indices: 461208--461718 Score: 1022
Period size: 255 Copynumber: 2.0 Consensus size: 255
461198 TCCTTGCACA
461208 GTTGCAGAAAATTTCCATGGATACCCAAACCTTCCTGTTGGCTAACGGCTGCCCTCTTTCACCAA
1 GTTGCAGAAAATTTCCATGGATACCCAAACCTTCCTGTTGGCTAACGGCTGCCCTCTTTCACCAA
461273 GTCCCAAGTATATTCTTCCTCTAGACAAAAGACCAAACCTGTCCCGGACATCCCTTTTGGCTTCA
66 GTCCCAAGTATATTCTTCCTCTAGACAAAAGACCAAACCTGTCCCGGACATCCCTTTTGGCTTCA
461338 ATTCCTATCATCGACTTGATGGAACCATCTGCATTAGTTGTAGATCAAATCTCCAAAGCTTGCGA
131 ATTCCTATCATCGACTTGATGGAACCATCTGCATTAGTTGTAGATCAAATCTCCAAAGCTTGCGA
461403 GGAATATGGCTTCTTTCAGATCATCAATCATGGCGTTCCATTAGAATTATGTGACAGAAT
196 GGAATATGGCTTCTTTCAGATCATCAATCATGGCGTTCCATTAGAATTATGTGACAGAAT
461463 GTTGCAGAAAATTTCCATGGATACCCAAACCTTCCTGTTGGCTAACGGCTGCCCTCTTTCACCAA
1 GTTGCAGAAAATTTCCATGGATACCCAAACCTTCCTGTTGGCTAACGGCTGCCCTCTTTCACCAA
461528 GTCCCAAGTATATTCTTCCTCTAGACAAAAGACCAAACCTGTCCCGGACATCCCTTTTGGCTTCA
66 GTCCCAAGTATATTCTTCCTCTAGACAAAAGACCAAACCTGTCCCGGACATCCCTTTTGGCTTCA
461593 ATTCCTATCATCGACTTGATGGAACCATCTGCATTAGTTGTAGATCAAATCTCCAAAGCTTGCGA
131 ATTCCTATCATCGACTTGATGGAACCATCTGCATTAGTTGTAGATCAAATCTCCAAAGCTTGCGA
461658 GGAATATGGCTTCTTTCAGATCATCAATCATGGCGTTCCATTAGAATTATGTGACAGAAT
196 GGAATATGGCTTCTTTCAGATCATCAATCATGGCGTTCCATTAGAATTATGTGACAGAAT
461718 G
1 G
461719 ATGGCTGTTA
Statistics
Matches: 256, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
255 256 1.00
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (255 bp):
GTTGCAGAAAATTTCCATGGATACCCAAACCTTCCTGTTGGCTAACGGCTGCCCTCTTTCACCAA
GTCCCAAGTATATTCTTCCTCTAGACAAAAGACCAAACCTGTCCCGGACATCCCTTTTGGCTTCA
ATTCCTATCATCGACTTGATGGAACCATCTGCATTAGTTGTAGATCAAATCTCCAAAGCTTGCGA
GGAATATGGCTTCTTTCAGATCATCAATCATGGCGTTCCATTAGAATTATGTGACAGAAT
Found at i:462135 original size:4 final size:4
Alignment explanation
Indices: 462126--462152 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
462116 CAAATACAAA
462126 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
462153 AAGGATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:462575 original size:118 final size:117
Alignment explanation
Indices: 462367--462602 Score: 463
Period size: 118 Copynumber: 2.0 Consensus size: 117
462357 TTGGTGAGAA
462367 GCCTGTTCTTCGACAACAGGGGAACTACCATCCACCATGTCCAGACCCTGAGCTTACATTGGGAC
1 GCCTGTTCTTCGACAACAGGGGAACTACCATCCACCATGTCCAGACCCTGAGCTTACATTGGGAC
462432 TAAATGTTCATACCGATTTCAATGCACTCACAATTGTTAGGCAATCAGAAGGT
66 TAAATGTTCATACCGATTTCAATGCACTCACAATTGTTAGGC-ATCAGAAGGT
462485 GCCTGTTCTTCGACAACAGGGGAACTACCATCCACCATGTCCAGACCCTGAGCTTACATTGGGAC
1 GCCTGTTCTTCGACAACAGGGGAACTACCATCCACCATGTCCAGACCCTGAGCTTACATTGGGAC
462550 TAAATGTTCATACCGATTTCAATGCACTCACAATTGTTAGGCATCAGAAGGT
66 TAAATGTTCATACCGATTTCAATGCACTCACAATTGTTAGGCATCAGAAGGT
462602 G
1 G
462603 TAACTGGACT
Statistics
Matches: 118, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
117 11 0.09
118 107 0.91
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (117 bp):
GCCTGTTCTTCGACAACAGGGGAACTACCATCCACCATGTCCAGACCCTGAGCTTACATTGGGAC
TAAATGTTCATACCGATTTCAATGCACTCACAATTGTTAGGCATCAGAAGGT
Found at i:464267 original size:17 final size:17
Alignment explanation
Indices: 464245--464303 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 17
464235 TTGTCAATTT
464245 ATATAAATAAAATTTTA
1 ATATAAATAAAATTTTA
*
464262 ATATAAAT-AAATATTA
1 ATATAAATAAAATTTTA
* *
464278 A-ATATATTAAATTATTA
1 ATATAAATAAAATT-TTA
*
464295 ATAAAAATA
1 ATATAAATA
464304 TGTATTTAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
15 5 0.15
16 12 0.36
17 12 0.36
18 4 0.12
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATAAATAAAATTTTA
Found at i:468828 original size:3 final size:3
Alignment explanation
Indices: 468820--468861 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
468810 CTTGGGACAC
468820 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
468862 AGGTGTTAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:469175 original size:30 final size:29
Alignment explanation
Indices: 469141--469215 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
469131 TTACCGGAAC
*
469141 TAAATTATGATATCAAA-TTTCAAG-AATCTT
1 TAAATT-TGAGATCAAACTTT-AAGAAAT-TT
*
469171 TAAATTTGAGATTAAACTTTAAGAAATTT
1 TAAATTTGAGATCAAACTTTAAGAAATTT
*
469200 TAAATTTGAGACCAAA
1 TAAATTTGAGATCAAA
469216 ATCCAAGTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
29 27 0.69
30 12 0.31
ACGTcount: A:0.45, C:0.08, G:0.09, T:0.37
Consensus pattern (29 bp):
TAAATTTGAGATCAAACTTTAAGAAATTT
Found at i:470632 original size:3 final size:3
Alignment explanation
Indices: 470624--470650 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
470614 AGATTTACTT
470624 TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA
470651 AATAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:470974 original size:28 final size:28
Alignment explanation
Indices: 470916--470971 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
470906 ATTTTATATT
*
470916 AATTTATTAGATTATTATATGATAATAA
1 AATTTATTAGATTATTATATAATAATAA
*
470944 AATTTATTATA-TATT-TATAATAATAA
1 AATTTATTAGATTATTATATAATAATAA
470970 AA
1 AA
470972 AATAATCACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 12 0.46
27 4 0.15
28 10 0.38
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (28 bp):
AATTTATTAGATTATTATATAATAATAA
Found at i:471546 original size:18 final size:18
Alignment explanation
Indices: 471507--471546 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
471497 ATATTTATAT
*
471507 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
471525 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTGTT-AA
471543 ATAA
1 ATAA
471547 TTTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:472975 original size:2 final size:2
Alignment explanation
Indices: 472968--473002 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
472958 GAAGTACTCC
472968 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
473003 ACATCTGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:477946 original size:21 final size:21
Alignment explanation
Indices: 477904--477947 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
477894 GAAATTAAAA
*
477904 AAAAACAATATTCAAATATAT
1 AAAAACAAAATTCAAATATAT
*
477925 AAAAACATAAATTCATAT-TAT
1 AAAAACA-AAATTCAAATATAT
477946 AA
1 AA
477948 TATATCTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAACAAAATTCAAATATAT
Found at i:481842 original size:41 final size:41
Alignment explanation
Indices: 481734--481842 Score: 128
Period size: 41 Copynumber: 2.7 Consensus size: 41
481724 AATTTTAACA
* * *
481734 GTGTTTTATCAAAAAATGCAATTATATGAGTTAATTTAGTG
1 GTGTTTTATCAAAAAACGCCATTATATGAGTTAATTTAATG
** * * * *
481775 GCATTTTATTAAGAAACACCACTATATGAGTTAATTTAATG
1 GTGTTTTATCAAAAAACGCCATTATATGAGTTAATTTAATG
*
481816 GTGTTTTATCAAAAAACGCCGTTATAT
1 GTGTTTTATCAAAAAACGCCATTATAT
481843 TGTTTAACTC
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (41 bp):
GTGTTTTATCAAAAAACGCCATTATATGAGTTAATTTAATG
Found at i:481989 original size:21 final size:21
Alignment explanation
Indices: 481964--482004 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
481954 CGCCATTATA
481964 TGATTGAATTTAACGACGTTC
1 TGATTGAATTTAACGACGTTC
*
481985 TGATTTAATTTAACGACGTT
1 TGATTGAATTTAACGACGTT
482005 TTATCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.41
Consensus pattern (21 bp):
TGATTGAATTTAACGACGTTC
Found at i:486214 original size:2 final size:2
Alignment explanation
Indices: 486207--486240 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
486197 GTCTTATTGT
486207 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
486241 ACATGCAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:486887 original size:44 final size:42
Alignment explanation
Indices: 486760--486887 Score: 112
Period size: 37 Copynumber: 3.1 Consensus size: 42
486750 AAAGATATAA
*
486760 AATA-ATTAATATATGATTT-GAATATATATTTTAAAATTTAAT
1 AATATATTAA-ATATGATTTAAAATATATATTTTAAAATTT-AT
* * *
486802 AATATA--AATTATTATATTAAAAT-T-TA-TTT--AATTTAA
1 AATATATTAAATATGAT-TTAAAATATATATTTTAAAATTTAT
486838 AATATATTAAATATGATTTAAAATATATATTTTAAAAATTTAGT
1 AATATATTAAATATGATTTAAAATATATATTTT-AAAATTTA-T
486882 AATATA
1 AATATA
486888 AATTATTATT
Statistics
Matches: 67, Mismatches: 7, Indels: 22
0.70 0.07 0.23
Matches are distributed among these distances:
36 7 0.10
37 12 0.18
38 8 0.12
39 5 0.07
40 10 0.15
41 5 0.07
42 7 0.10
43 7 0.10
44 6 0.09
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (42 bp):
AATATATTAAATATGATTTAAAATATATATTTTAAAATTTAT
Found at i:486888 original size:80 final size:80
Alignment explanation
Indices: 486754--486934 Score: 262
Period size: 83 Copynumber: 2.2 Consensus size: 80
486744 GAGTATAAAG
*
486754 ATATAAAATA-ATTAATATATGATTTGAATATATATTTTAAAATTTAATAATAT-AA-ATTATTA
1 ATATAAAATATATTAA-ATATGATTTAAATATATATTTTAAAATTTAATAATATAAATATTATTA
486816 TATTAAAATTTATTT-A
65 TATTAAAATTT-TTTAA
* *
486832 ATTTAAAATATATTAAATATGATTTAAAATATATATTTTAAAAATTTAGTAATATAAATTATTAT
1 ATATAAAATATATTAAATATGATTT-AAATATATATTTT-AAAATTTAATAATATAAA-TATTAT
486897 TATATTAAAATTTTTTAA
63 TATATTAAAATTTTTTAA
486915 ATATAAAATATATTAAATAT
1 ATATAAAATATATTAAATAT
486935 AATTATGATA
Statistics
Matches: 92, Mismatches: 4, Indels: 9
0.88 0.04 0.09
Matches are distributed among these distances:
78 18 0.20
79 17 0.18
80 14 0.15
81 2 0.02
82 3 0.03
83 38 0.41
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (80 bp):
ATATAAAATATATTAAATATGATTTAAATATATATTTTAAAATTTAATAATATAAATATTATTAT
ATTAAAATTTTTTAA
Found at i:486921 original size:16 final size:16
Alignment explanation
Indices: 486882--486936 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
486872 AAAATTTAGT
*
486882 AATATAAATTATTATTA
1 AATATAAAATA-TATTA
* * *
486899 TAT-TAAAATTTTTTA
1 AATATAAAATATATTA
486914 AATATAAAATATATTA
1 AATATAAAATATATTA
486930 AATATAA
1 AATATAA
486937 TTATGATACA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
15 6 0.20
16 22 0.73
17 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATATAAAATATATTA
Found at i:486972 original size:18 final size:18
Alignment explanation
Indices: 486949--486984 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
486939 ATGATACATC
486949 AAAATATATAAATATAAT
1 AAAATATATAAATATAAT
*
486967 AAAATATATAAATTTAAT
1 AAAATATATAAATATAAT
486985 TATAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATATATAAATATAAT
Found at i:487454 original size:25 final size:27
Alignment explanation
Indices: 487422--487481 Score: 74
Period size: 25 Copynumber: 2.4 Consensus size: 27
487412 TTTAAATAAC
*
487422 ATATATATTAAAAAT-ATTATA-TTAT
1 ATATATATTAAAAATCATTATATTTAA
*
487447 ATATATA-T-AAATTCATTATATTTAA
1 ATATATATTAAAAATCATTATATTTAA
487472 ATATATATTA
1 ATATATATTA
487482 TTTTTATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 4 0.14
24 7 0.24
25 17 0.59
26 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATATATTAAAAATCATTATATTTAA
Found at i:487483 original size:15 final size:14
Alignment explanation
Indices: 487465--487513 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
487455 AAATTCATTA
487465 TATTTAAATATATAT
1 TATTTAAATATAT-T
*
487480 TATTT--TTATATT
1 TATTTAAATATATT
487492 TA-TTAAATATATT
1 TATTTAAATATATT
487505 TAATTTAAA
1 T-ATTTAAA
487514 ATTATCAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
11 2 0.07
12 3 0.11
13 12 0.43
14 1 0.04
15 10 0.36
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TATTTAAATATATT
Found at i:487518 original size:24 final size:26
Alignment explanation
Indices: 487468--487532 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 26
487458 TTCATTATAT
* * *
487468 TTAAATATATATTATTTTTATATTTA
1 TTAAATATATATTATATTTAAAATTA
487494 TTAAATATAT-TTA-ATTTAAAATTA
1 TTAAATATATATTATATTTAAAATTA
* *
487518 TCAAATTTAATATTA
1 TTAAATAT-ATATTA
487533 AGTACGGAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 14 0.44
25 5 0.16
26 13 0.41
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (26 bp):
TTAAATATATATTATATTTAAAATTA
Found at i:487865 original size:4 final size:4
Alignment explanation
Indices: 487856--487882 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
487846 ATATGACTTG
487856 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
487883 TTCATTACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:490295 original size:38 final size:39
Alignment explanation
Indices: 490251--490328 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
490241 TATAAATTTT
* * *
490251 AATTTTAATTT-AATTTATTTATAT-AATTATTTTTTAAA
1 AATTTTAATTTAAAATT-TTAATATAAATAATTTTTTAAA
490289 AATTTTAATTTAAAATTTTAATATAAATAATTTTTTAAA
1 AATTTTAATTTAAAATTTTAATATAAATAATTTTTTAAA
490328 A
1 A
490329 TTGAGTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
38 17 0.49
39 18 0.51
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (39 bp):
AATTTTAATTTAAAATTTTAATATAAATAATTTTTTAAA
Found at i:490300 original size:14 final size:14
Alignment explanation
Indices: 490283--490322 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
490273 ATAATTATTT
490283 TTTAAAAATTTTAA
1 TTTAAAAATTTTAA
490297 TTT-AAAATTTTAA
1 TTTAAAAATTTTAA
*
490310 TATAAATAATTTT
1 TTTAAA-AATTTT
490323 TTAAAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 12 0.52
14 5 0.22
15 6 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTTAAAAATTTTAA
Found at i:492052 original size:34 final size:35
Alignment explanation
Indices: 492013--492098 Score: 106
Period size: 34 Copynumber: 2.5 Consensus size: 35
492003 ATTAAATGAC
492013 TAAATAATTTTAAAATA-TTT-AAATAAAAATAAGT
1 TAAATAATTTTAAAATATTTTCAAATAAAAATAA-T
* *
492047 TAAATAA-CTTAAAAAATTTTCAAATAAAAATAAT
1 TAAATAATTTTAAAATATTTTCAAATAAAAATAAT
*
492081 TAAAAAATATTTAAAATA
1 TAAATAAT-TTTAAAATA
492099 AGATGGTAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
33 7 0.16
34 17 0.40
35 12 0.28
36 7 0.16
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (35 bp):
TAAATAATTTTAAAATATTTTCAAATAAAAATAAT
Found at i:492097 original size:26 final size:26
Alignment explanation
Indices: 492048--492099 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
492038 AAAATAAGTT
*
492048 AAATAACTTAAAAAATTTTCAAATAA
1 AAATAACTTAAAAAATTTTAAAATAA
492074 AAATAA-TTAAAAAATATTTAAAATAA
1 AAATAACTTAAAAAAT-TTTAAAATAA
492100 GATGGTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (26 bp):
AAATAACTTAAAAAATTTTAAAATAA
Found at i:493011 original size:2 final size:2
Alignment explanation
Indices: 493004--493039 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
492994 ATTAAGTCTC
493004 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
493040 TATATATAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:493409 original size:6 final size:7
Alignment explanation
Indices: 493393--493421 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
493383 TCTCATTTGC
493393 AAAAATA
1 AAAAATA
493400 AAAAATA
1 AAAAATA
493407 AAAAATA
1 AAAAATA
493414 AAAAATA
1 AAAAATA
493421 A
1 A
493422 TTTCTCTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (7 bp):
AAAAATA
Found at i:493766 original size:4 final size:4
Alignment explanation
Indices: 493757--493784 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
493747 TTATCAGTTT
493757 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA
493785 ACAAAACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:494040 original size:2 final size:2
Alignment explanation
Indices: 494024--494068 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
494014 TATATTTCAA
*
494024 AT AT -T AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
494065 AT AT
1 AT AT
494069 TTACTTACCC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:499661 original size:22 final size:22
Alignment explanation
Indices: 499636--499678 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
499626 ACAATGCACG
499636 TTAGTGTATATATATATATATA
1 TTAGTGTATATATATATATATA
499658 TTAGTGTATATATATATATAT
1 TTAGTGTATATATATATATAT
499679 TAGTATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TTAGTGTATATATATATATATA
Found at i:499669 original size:20 final size:20
Alignment explanation
Indices: 499644--499682 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
499634 CGTTAGTGTA
499644 TATATATATATATATTAGTG
1 TATATATATATATATTAGTG
499664 TATATATATATATATTAGT
1 TATATATATATATATTAGT
499683 ATAAAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
TATATATATATATATTAGTG
Found at i:509060 original size:16 final size:16
Alignment explanation
Indices: 509041--509073 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
509031 GATATGTAAA
509041 TTTAAATTTTAATATT
1 TTTAAATTTTAATATT
*
509057 TTTAATTTTTAATATT
1 TTTAAATTTTAATATT
509073 T
1 T
509074 AAATTATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTAAATTTTAATATT
Found at i:509078 original size:15 final size:15
Alignment explanation
Indices: 509040--509078 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
509030 TGATATGTAA
509040 ATTTAAA-TTTTAAT
1 ATTTAAATTTTTAAT
*
509054 ATTTTTAATTTTTAAT
1 A-TTTAAATTTTTAAT
509070 ATTTAAATT
1 ATTTAAATT
509079 ATAATTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
14 1 0.05
15 12 0.57
16 8 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
ATTTAAATTTTTAAT
Found at i:510594 original size:17 final size:17
Alignment explanation
Indices: 510533--510607 Score: 66
Period size: 17 Copynumber: 4.4 Consensus size: 17
510523 AATAAAATAT
510533 AAATATAATAAATATATTA
1 AAATAT-AT-AATATATTA
* *
510552 AAATTTAT-ATA-ATTT
1 AAATATATAATATATTA
510567 AAAT-TATTAATATATTA
1 AAATATA-TAATATATTA
*
510584 AAATATATAATATTTTA
1 AAATATATAATATATTA
*
510601 AATTATA
1 AAATATA
510608 GTATTATATA
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.04
15 8 0.17
16 6 0.13
17 22 0.47
18 4 0.09
19 5 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AAATATATAATATATTA
Found at i:510607 original size:15 final size:15
Alignment explanation
Indices: 510564--510612 Score: 53
Period size: 17 Copynumber: 3.1 Consensus size: 15
510554 ATTTATATAA
510564 TTTAAATTATTAATAT
1 TTTAAATTA-TAATAT
*
510580 ATTAAAATATATAATAT
1 -TTTAAAT-TATAATAT
*
510597 TTTAAATTATAGTAT
1 TTTAAATTATAATAT
510612 T
1 T
510613 ATATATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 8 0.29
16 6 0.21
17 12 0.43
18 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TTTAAATTATAATAT
Found at i:510627 original size:33 final size:33
Alignment explanation
Indices: 510543--510606 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
510533 AAATATAATA
* *
510543 AATATATTAAAATTTAT-ATAATTTAAATTATT
1 AATATATTAAAATATATAATATTTTAAATTATT
510575 AATATATTAAAATATATAATATTTTAAATTAT
1 AATATATTAAAATATATAATATTTTAAATTAT
510607 AGTATTATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 16 0.55
33 13 0.45
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
AATATATTAAAATATATAATATTTTAAATTATT
Found at i:511098 original size:24 final size:25
Alignment explanation
Indices: 511067--511114 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
511057 TTTTTTTTGG
511067 TAAAAAAATT-TATAAT-TTAAAATA
1 TAAAAAAATTATA-AATATTAAAATA
511091 TAAAAAAATTATAAATATTAAAAT
1 TAAAAAAATTATAAATATTAAAAT
511115 TATTAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
TAAAAAAATTATAAATATTAAAATA
Found at i:511115 original size:15 final size:16
Alignment explanation
Indices: 511095--511124 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
511085 AAAATATAAA
511095 AAAATTA-TAAATATT
1 AAAATTATTAAATATT
511110 AAAATTATTAAATAT
1 AAAATTATTAAATAT
511125 ATTTTTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAATTATTAAATATT
Found at i:511449 original size:20 final size:21
Alignment explanation
Indices: 511424--511464 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
511414 GCTGTGAACT
511424 ATTTTTAAATT-TAAGTTTTA
1 ATTTTTAAATTATAAGTTTTA
* *
511444 ATTTTTATATTATAATTTTTA
1 ATTTTTAAATTATAAGTTTTA
511465 TAAAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTTTAAATTATAAGTTTTA
Found at i:511450 original size:14 final size:14
Alignment explanation
Indices: 511442--511486 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
511432 ATTTAAGTTT
511442 TAATTTTTATATTA
1 TAATTTTTATATTA
**
511456 TAATTTTTATAAAA
1 TAATTTTTATATTA
*
511470 TTAATTTTTTTATTA
1 -TAATTTTTATATTA
511485 TA
1 TA
511487 TTAATTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TAATTTTTATATTA
Found at i:511479 original size:17 final size:17
Alignment explanation
Indices: 511459--511493 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
511449 TATATTATAA
511459 TTTTTATAAAATTAATT
1 TTTTTATAAAATTAATT
* *
511476 TTTTTATTATATTAATT
1 TTTTTATAAAATTAATT
511493 T
1 T
511494 AAAATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTTTATAAAATTAATT
Found at i:511748 original size:16 final size:17
Alignment explanation
Indices: 511727--511761 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
511717 TTAATATAAA
*
511727 TATAAT-TAAATCTTTT
1 TATAATGTAAATATTTT
511743 TATAATGTAAATATTTT
1 TATAATGTAAATATTTT
511760 TA
1 TA
511762 ATTATTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (17 bp):
TATAATGTAAATATTTT
Found at i:511762 original size:27 final size:27
Alignment explanation
Indices: 511718--511771 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
511708 TTTTAAATAT
*
511718 TAATATAAATATAATTAAATCTTTTTA
1 TAATATAAATATAATTAAATATTTTTA
* ** *
511745 TAATGTAAATATTTTTAATTATTTTTA
1 TAATATAAATATAATTAAATATTTTTA
511772 ATATTTTAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TAATATAAATATAATTAAATATTTTTA
Found at i:512071 original size:29 final size:29
Alignment explanation
Indices: 512009--512072 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
511999 AATTAAATTA
*
512009 AAAATTTTAAAATAATGTAATAAAAAGAT
1 AAAATTTTAAAATAATATAATAAAAAGAT
* *
512038 TAAATTTATAAAA-ATTATAATAAAAA-ACT
1 AAAATTT-TAAAATAATATAATAAAAAGA-T
512067 AAAATT
1 AAAATT
512073 CAAATCTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.03
29 23 0.79
30 5 0.17
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (29 bp):
AAAATTTTAAAATAATATAATAAAAAGAT
Found at i:512303 original size:6 final size:6
Alignment explanation
Indices: 512294--512409 Score: 68
Period size: 6 Copynumber: 19.8 Consensus size: 6
512284 AATAAAAAAT
* * **
512294 ATATAA ATATTAA A-ATTA ATATAA A-ATAA ATTATAA ATATATTA AAATTT
1 ATATAA ATA-TAA ATATAA ATATAA ATATAA A-TATAA ATATA--A ATATAA
* * *
512344 ATATAA ATATAA A-AT-A TTTTAA ATATAA TTAT-A ATA-AA ATA-ATA
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATA-A
512388 ATATAA ATAT-A ATATAA ATATA
1 ATATAA ATATAA ATATAA ATATA
512410 TACGCCCAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
4 1 0.01
5 24 0.29
6 45 0.54
7 10 0.12
8 4 0.05
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (6 bp):
ATATAA
Found at i:512307 original size:18 final size:18
Alignment explanation
Indices: 512266--512410 Score: 61
Period size: 17 Copynumber: 7.7 Consensus size: 18
512256 AAAAAATAAT
*
512266 TAATATAAACTATTAAAA
1 TAATATAAAATATTAAAA
*
512284 -AATAAAAAATA-TATAAA
1 TAATATAAAATATTA-AAA
512301 T-AT-TAAAATTAATATAAAA
1 TAATATAAAA-T-AT-TAAAA
512320 TAAATTATAAATATATTAAAA
1 T-AA-TATAAA-ATATTAAAA
*
512341 T-TTATATAAATA-TAAAA
1 TAATATA-AAATATTAAAA
* * *
512358 TATTTTAAATATAATTATAA
1 TAATATAAA-AT-ATTAAAA
*
512378 TAAAATAATAATA-TAAATA
1 TAATATAA-AATATTAAA-A
512397 TAATATAAATATAT
1 TAATATAAA-ATAT
512411 ACGCCCAATT
Statistics
Matches: 96, Mismatches: 11, Indels: 38
0.66 0.08 0.26
Matches are distributed among these distances:
16 6 0.06
17 23 0.24
18 18 0.19
19 19 0.20
20 13 0.14
21 8 0.08
22 3 0.03
23 5 0.05
24 1 0.01
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (18 bp):
TAATATAAAATATTAAAA
Found at i:512332 original size:38 final size:38
Alignment explanation
Indices: 512290--512411 Score: 103
Period size: 38 Copynumber: 3.2 Consensus size: 38
512280 AAAAAATAAA
512290 AAATATATAAATATTAAAATTAATATAAAATAAATTAT
1 AAATATATAAATATTAAAATTAATATAAAATAAATTAT
* * * *
512328 AAATATATTAAA-ATTTATATAAATATAAAAT--ATTTT
1 AAATATA-TAAATATTAAAATTAATATAAAATAAATTAT
* *
512364 AAATATA-ATTATAATAAAA-TAATAATATAAATATAA-TAT
1 AAATATATA-AATATTAAAATTAAT-ATA-AAATA-AATTAT
512403 AAATATATA
1 AAATATATA
512412 CGCCCAATTG
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
34 1 0.02
35 4 0.06
36 18 0.28
37 4 0.06
38 23 0.35
39 13 0.20
40 2 0.03
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (38 bp):
AAATATATAAATATTAAAATTAATATAAAATAAATTAT
Found at i:512408 original size:11 final size:11
Alignment explanation
Indices: 512294--512409 Score: 79
Period size: 11 Copynumber: 11.0 Consensus size: 11
512284 AATAAAAAAT
512294 ATATAAATAT-
1 ATATAAATATA
512304 -TA-AAAT-TA
1 ATATAAATATA
512312 ATATAAA-ATAA
1 ATATAAATAT-A
512323 ATTATAAATATA
1 A-TATAAATATA
* *
512335 TTA-AAAT-TT
1 ATATAAATATA
512344 ATATAAATATA
1 ATATAAATATA
* * *
512355 AAAT-ATTTTAA
1 ATATAAATAT-A
*
512366 ATATAATTATA
1 ATATAAATATA
512377 ATA-AAATAATA
1 ATATAAAT-ATA
512388 ATATAAATATA
1 ATATAAATATA
512399 ATATAAATATA
1 ATATAAATATA
512410 TACGCCCAAT
Statistics
Matches: 83, Mismatches: 10, Indels: 25
0.70 0.08 0.21
Matches are distributed among these distances:
7 1 0.01
8 4 0.05
9 7 0.08
10 18 0.22
11 36 0.43
12 15 0.18
13 2 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
ATATAAATATA
Found at i:516605 original size:15 final size:14
Alignment explanation
Indices: 516580--516613 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
516570 TAAAAATTAT
516580 TAAATAATAATAAA
1 TAAATAATAATAAA
516594 TAAATAAATAATAAA
1 TAAAT-AATAATAAA
*
516609 AAAAT
1 TAAAT
516614 CTACCAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAATAATAATAAA
Found at i:516835 original size:2 final size:2
Alignment explanation
Indices: 516830--516868 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
516820 AATTAAAATC
516830 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
516869 GATTACTTTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:519175 original size:16 final size:17
Alignment explanation
Indices: 519145--519176 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
519135 AAATAATATA
519145 TTATAAAATTATTTTTT
1 TTATAAAATTATTTTTT
519162 TTATAAAA-TATTTTT
1 TTATAAAATTATTTTT
519177 ATAATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTATAAAATTATTTTTT
Found at i:519183 original size:16 final size:16
Alignment explanation
Indices: 519147--519189 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
519137 ATAATATATT
* *
519147 ATAAAATTATTTTTTTT
1 ATAAAA-TATTTTTATA
519164 ATAAAATATTTTTATA
1 ATAAAATATTTTTATA
*
519180 ATAATATATT
1 ATAAAATATT
519190 ATAAAAGTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATAAAATATTTTTATA
Found at i:519428 original size:15 final size:15
Alignment explanation
Indices: 519408--519439 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
519398 AACATAATTA
519408 TTTATTTAAATAAAT
1 TTTATTTAAATAAAT
519423 TTTATTTAAATAAAT
1 TTTATTTAAATAAAT
519438 TT
1 TT
519440 GTCTTTTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TTTATTTAAATAAAT
Found at i:519563 original size:5 final size:5
Alignment explanation
Indices: 519553--519582 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
519543 ATTAAGTACT
519553 ATATA ATATA ATATA ATATA ATAATA ATAT
1 ATATA ATATA ATATA ATATA AT-ATA ATAT
519583 TATTATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATATA
Found at i:519671 original size:15 final size:16
Alignment explanation
Indices: 519641--519677 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
519631 TTAATCTAAT
519641 TAAAATAAAAATATAA
1 TAAAATAAAAATATAA
519657 TAAAATAAAAA-ATAA
1 TAAAATAAAAATATAA
*
519672 TTAAAT
1 TAAAAT
519678 CAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
TAAAATAAAAATATAA
Found at i:520662 original size:20 final size:20
Alignment explanation
Indices: 520626--520664 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
520616 TATTTTTGTT
*
520626 AAATTAATATTTTTAAAATA
1 AAATTAATATTTATAAAATA
520646 AAATT-ATATTTAATAAAAT
1 AAATTAATATTT-ATAAAAT
520665 TAAGATAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAATTAATATTTATAAAATA
Found at i:521219 original size:2 final size:2
Alignment explanation
Indices: 521212--521236 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
521202 AAATATACTC
521212 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
521237 ACTCAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:521728 original size:22 final size:22
Alignment explanation
Indices: 521672--521730 Score: 57
Period size: 21 Copynumber: 2.6 Consensus size: 22
521662 ATTTTTATAA
521672 AAAATTATAATTATATAAATTAATT
1 AAAA-TATAA-TAT-TAAATTAATT
* **
521697 AAATTA-AATATTAAATTTTTT
1 AAAATATAATATTAAATTAATT
521718 AAAATATAATATT
1 AAAATATAATATT
521731 TTGAATAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 13 0.45
22 9 0.31
23 2 0.07
24 2 0.07
25 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAATATAATATTAAATTAATT
Found at i:526296 original size:13 final size:13
Alignment explanation
Indices: 526278--526316 Score: 64
Period size: 13 Copynumber: 3.2 Consensus size: 13
526268 TATTTTTTAA
526278 AATATTTATATTT
1 AATATTTATATTT
526291 AATATTTATATTT
1 AATATTTATATTT
526304 AATA--TATATTT
1 AATATTTATATTT
526315 AA
1 AA
526317 ATATAAACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 9 0.35
13 17 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATATTTATATTT
Found at i:526313 original size:11 final size:11
Alignment explanation
Indices: 526284--526321 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 11
526274 TTAAAATATT
526284 TATATTTAATA
1 TATATTTAATA
526295 TTTATATTTAATA
1 --TATATTTAATA
526308 TATATTTAA-A
1 TATATTTAATA
526318 TATA
1 TATA
526322 AACATAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.20
11 9 0.36
13 11 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
TATATTTAATA
Found at i:527410 original size:18 final size:18
Alignment explanation
Indices: 527376--527411 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
527366 TATATTTTAA
**
527376 AATATTAAATATGTATTT
1 AATATTAAATACATATTT
527394 AATATTAAATACATATTT
1 AATATTAAATACATATTT
527412 GATACGAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (18 bp):
AATATTAAATACATATTT
Found at i:531094 original size:7 final size:8
Alignment explanation
Indices: 531077--531106 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
531067 TCCATTGCTA
531077 TTTTTATT
1 TTTTTATT
531085 TTTTTATT
1 TTTTTATT
531093 TTTTTATT
1 TTTTTATT
531101 TCTTTT
1 T-TTTT
531107 TGTTTTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTATT
Found at i:531746 original size:25 final size:26
Alignment explanation
Indices: 531692--531746 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
531682 TTTAAATTAT
531692 TATTTAATAATAAAAATTTTATATAA
1 TATTTAATAATAAAAATTTTATATAA
* * *
531718 -ATTTAATTAT-AAAATTTTTTTTAA
1 TATTTAATAATAAAAATTTTATATAA
531742 TATTT
1 TATTT
531747 TTAATATTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (26 bp):
TATTTAATAATAAAAATTTTATATAA
Found at i:531795 original size:11 final size:11
Alignment explanation
Indices: 531755--531800 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
531745 TTTTAATATT
*
531755 ATTTAAATAATA
1 ATTTAAAT-TTA
531767 ATTT-AATTT-
1 ATTTAAATTTA
531776 ATTTAAATTTA
1 ATTTAAATTTA
*
531787 ATTTAAATTAA
1 ATTTAAATTTA
531798 ATT
1 ATT
531801 AAAAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
9 4 0.13
10 6 0.20
11 16 0.53
12 4 0.13
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:533163 original size:2 final size:2
Alignment explanation
Indices: 533156--533231 Score: 75
Period size: 2 Copynumber: 38.0 Consensus size: 2
533146 TGAAGCCAAA
* *
533156 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T GACC AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -A-T AT AT AT
** *
533199 -T AT GC AT AT AT AT AT AT AT AT AT AT AG AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
533232 TTGTCCTTGA
Statistics
Matches: 61, Mismatches: 9, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
1 2 0.03
2 58 0.95
3 1 0.02
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:533692 original size:3 final size:3
Alignment explanation
Indices: 533679--533711 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
533669 TGTAACTCAC
533679 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
533712 TGGTTTCAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:534150 original size:33 final size:34
Alignment explanation
Indices: 534074--534150 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 34
534064 TGGAAAATAT
* * *
534074 ATAATATTATGATTATATAATTGTAACATCCAAAA
1 ATAAT-TTAAGATTATAAAATTATAACATCCAAAA
* * *
534109 ACATTTTAAGATTA-AAAATTATAACCTCCAAAA
1 ATAATTTAAGATTATAAAATTATAACATCCAAAA
534142 ATAATTTAA
1 ATAATTTAA
534151 AATACCAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
33 23 0.68
34 8 0.24
35 3 0.09
ACGTcount: A:0.51, C:0.10, G:0.04, T:0.35
Consensus pattern (34 bp):
ATAATTTAAGATTATAAAATTATAACATCCAAAA
Found at i:534448 original size:27 final size:26
Alignment explanation
Indices: 534418--534492 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
534408 TAGTAATTTT
* *
534418 TATTTGATTTAATTTATTATTAAAATA
1 TATTTAATTTAATTTATAATT-AAATA
* *
534445 TATTTTTATTT-ATGTAATAATTAAATA
1 TA-TTTAATTTAAT-TTATAATTAAATA
*
534472 TATTTAATTTAATTTTTAATT
1 TATTTAATTTAATTTATAATT
534493 TTTAATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
26 13 0.33
27 13 0.33
28 13 0.33
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (26 bp):
TATTTAATTTAATTTATAATTAAATA
Found at i:534491 original size:7 final size:7
Alignment explanation
Indices: 534479--534504 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
534469 ATATATTTAA
534479 TTTAATT
1 TTTAATT
534486 TTTAATT
1 TTTAATT
534493 TTTAATT
1 TTTAATT
534500 TTTAA
1 TTTAA
534505 CTTTAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTAATT
Found at i:534593 original size:28 final size:27
Alignment explanation
Indices: 534562--534630 Score: 79
Period size: 26 Copynumber: 2.6 Consensus size: 27
534552 TTTATTTATT
*
534562 TTTTAATTTTATAATATAAAAATAAATA
1 TTTTAATTTTATAAAATAAAAA-AAATA
*
534590 TTTT-ATTTT-TAAAATAATAAAAATA
1 TTTTAATTTTATAAAATAAAAAAAATA
*
534615 TTATAAATTTTATAAA
1 TT-TTAATTTTATAAA
534631 TTTTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
25 7 0.20
26 10 0.29
27 10 0.29
28 8 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (27 bp):
TTTTAATTTTATAAAATAAAAAAAATA
Found at i:538936 original size:33 final size:34
Alignment explanation
Indices: 538893--538957 Score: 105
Period size: 33 Copynumber: 1.9 Consensus size: 34
538883 AAAAGATATT
*
538893 ATTTGAAATGATTTTTTTT-TTTATAAAATTGTA
1 ATTTAAAATGATTTTTTTTATTTATAAAATTGTA
538926 ATTTAAAATGATTTTTTTTAATTTATAAAATT
1 ATTTAAAATGATTTTTTTT-ATTTATAAAATT
538958 ATCATATGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 18 0.62
35 11 0.38
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.57
Consensus pattern (34 bp):
ATTTAAAATGATTTTTTTTATTTATAAAATTGTA
Found at i:540200 original size:24 final size:24
Alignment explanation
Indices: 540171--540217 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
540161 ATTATATGTC
* *
540171 ATAATTTATGAATCAGATTATAAT
1 ATAATTTAAGAATCAAATTATAAT
*
540195 ATAATTTAAGTATCAAATTATAA
1 ATAATTTAAGAATCAAATTATAA
540218 ATTTTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.40
Consensus pattern (24 bp):
ATAATTTAAGAATCAAATTATAAT
Found at i:540246 original size:19 final size:19
Alignment explanation
Indices: 540194--540247 Score: 54
Period size: 23 Copynumber: 2.6 Consensus size: 19
540184 CAGATTATAA
*
540194 TATAATTTAAGTATCAAAT
1 TATAATTTAAATATCAAAT
*
540213 TATAAATTTTTTAAATATTAAAT
1 TAT-AA---TTTAAATATCAAAT
540236 TATAATTTAAAT
1 TATAATTTAAAT
540248 TATAATATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
19 10 0.34
20 2 0.07
22 2 0.07
23 15 0.52
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
TATAATTTAAATATCAAAT
Found at i:540791 original size:18 final size:18
Alignment explanation
Indices: 540780--540816 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
540770 ATATAATATC
540780 TTTTATAAATATCACATTAA
1 TTTTATAAATAT-A-ATTAA
540800 TTTTATAAATATAATTA
1 TTTTATAAATATAATTA
540817 TATTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 1 0.06
20 12 0.71
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
TTTTATAAATATAATTAA
Found at i:540968 original size:2 final size:2
Alignment explanation
Indices: 540961--540987 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
540951 ATTATTTAAA
540961 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
540988 AAGAGTTTGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:543189 original size:1 final size:1
Alignment explanation
Indices: 543183--543209 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
543173 CTCTCGGCTG
543183 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
543210 GCAATGGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:544520 original size:26 final size:27
Alignment explanation
Indices: 544482--544544 Score: 126
Period size: 27 Copynumber: 2.3 Consensus size: 27
544472 TTTTTTTTTT
544482 AAATTTTGTTTTTGAACGAAATTTTAA
1 AAATTTTGTTTTTGAACGAAATTTTAA
544509 AAATTTTGTTTTTGAACGAAATTTTAA
1 AAATTTTGTTTTTGAACGAAATTTTAA
544536 AAATTTTGT
1 AAATTTTGT
544545 ATCAATTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (27 bp):
AAATTTTGTTTTTGAACGAAATTTTAA
Found at i:544645 original size:13 final size:12
Alignment explanation
Indices: 544627--544671 Score: 63
Period size: 12 Copynumber: 3.7 Consensus size: 12
544617 ATTTGATGAA
544627 ATAAAAAATAATT
1 ATAAAAAATAA-T
544640 ATAAAAAATAAT
1 ATAAAAAATAAT
* *
544652 ATTAAAAATAAA
1 ATAAAAAATAAT
544664 ATAAAAAA
1 ATAAAAAA
544672 ACAAACCATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 18 0.62
13 11 0.38
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:546219 original size:18 final size:19
Alignment explanation
Indices: 546193--546228 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
546183 TTTTAAAAAG
546193 TGAATAAATTAATTGAATT
1 TGAATAAATTAATTGAATT
546212 TGAA-AAATTAATTGAAT
1 TGAATAAATTAATTGAAT
546229 CAATAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (19 bp):
TGAATAAATTAATTGAATT
Found at i:546309 original size:25 final size:25
Alignment explanation
Indices: 546281--546328 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
546271 TAGTTGGTTT
*
546281 GATATGATCGATTATGTTTATTTAA
1 GATATGATCGATTATGTTGATTTAA
* *
546306 GATATGGTTGATTATGTTGATTT
1 GATATGATCGATTATGTTGATTT
546329 GAGTTTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.27, C:0.02, G:0.21, T:0.50
Consensus pattern (25 bp):
GATATGATCGATTATGTTGATTTAA
Found at i:547297 original size:2 final size:2
Alignment explanation
Indices: 547290--547323 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
547280 GTTTACATAC
547290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
547324 GCTCATAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.