Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold52
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: 1774672
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 127110 characters in sequence are not A, C, G, or T
File 3 of 9
Found at i:511003 original size:2 final size:2
Alignment explanation
Indices: 510996--511029 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
510986 CTTTTTCTCA
510996 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
511030 TCGGAGTTTG
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
Found at i:513156 original size:32 final size:33
Alignment explanation
Indices: 513119--513180 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
513109 AATTTATATT
*
513119 AATTTTAATATATTAATC-ATTTATATTATGTA
1 AATTTTAAGATATTAATCTATTTATATTATGTA
* *
513151 AATTTTAAGATTTTTATCTATTTATATTAT
1 AATTTTAAGATATTAATCTATTTATATTAT
513181 ATTTATATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.56
Consensus pattern (33 bp):
AATTTTAAGATATTAATCTATTTATATTATGTA
Found at i:513203 original size:11 final size:11
Alignment explanation
Indices: 513171--513209 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
513161 TTTTTATCTA
*
513171 TTTATATTATA
1 TTTATATTATT
513182 TTTATATTATT
1 TTTATATTATT
*
513193 TTTTTATTATT
1 TTTATATTATT
*
513204 TATATA
1 TTTATA
513210 ATCATGACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTATATTATT
Found at i:513902 original size:6 final size:7
Alignment explanation
Indices: 513887--513911 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
513877 AACAATGTAC
513887 TTTTATT
1 TTTTATT
513894 TTTTATT
1 TTTTATT
513901 TTTTATT
1 TTTTATT
513908 TTTT
1 TTTT
513912 GAATGGGCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:514172 original size:2 final size:2
Alignment explanation
Indices: 514165--514204 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
514155 GACAAAGCAA
514165 AT AT AT 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 AT AT AT
514205 GAAATTAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:515378 original size:2 final size:2
Alignment explanation
Indices: 515373--515399 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
515363 GTTTTTTCAT
515373 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
515400 GTGGTATGTG
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:515811 original size:23 final size:22
Alignment explanation
Indices: 515767--515811 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
515757 GTGGGTTTTT
* *
515767 TTTTTAATATAAAAAAAGTTAC
1 TTTTTAAGATAAAAAAAATTAC
515789 TTTTTAAGATAAAAAATAATTAC
1 TTTTTAAGATAAAAAA-AATTAC
515812 AAAAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (22 bp):
TTTTTAAGATAAAAAAAATTAC
Found at i:517884 original size:135 final size:135
Alignment explanation
Indices: 517642--517910 Score: 430
Period size: 135 Copynumber: 2.0 Consensus size: 135
517632 AGCAGCTTGC
* *
517642 CTCTTTCTTAACACAAGCAGTTAAATTCATTCGTTTTTCAGGGGGAACCAAACTAACAGAATGAC
1 CTCTTTATTAACACAAGCAGTTAAATTCATTCGTTTTTCAGGGGGAACCAAACCAACAGAATGAC
* * *
517707 TAGATTTAGTTCTTCGACAGAAATGGTGCTTTATTATCCTCTTTGGCCTGGCATCTTCTGATATA
66 TAGATTTAGCTCTTCGACAGAAATGGTGCTTTATTATCCTCTTTGACCTGGCATCTTCCGATATA
517772 TTGGA
131 TTGGA
* * *
517777 CTCTTTATTAACACAAGCAGTTAATTTCTTTCGTTTTTCTGGGGGAACCAAACCAACAGAATGAC
1 CTCTTTATTAACACAAGCAGTTAAATTCATTCGTTTTTCAGGGGGAACCAAACCAACAGAATGAC
* * * *
517842 TAGATTTAGCTCTTCTACTGAAATGGTGCTTTATTATCCTCTTTGACCTGGCGTCTTCCGATGTA
66 TAGATTTAGCTCTTCGACAGAAATGGTGCTTTATTATCCTCTTTGACCTGGCATCTTCCGATATA
517907 TTGG
131 TTGG
517911 CCTTCTCATC
Statistics
Matches: 122, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
135 122 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (135 bp):
CTCTTTATTAACACAAGCAGTTAAATTCATTCGTTTTTCAGGGGGAACCAAACCAACAGAATGAC
TAGATTTAGCTCTTCGACAGAAATGGTGCTTTATTATCCTCTTTGACCTGGCATCTTCCGATATA
TTGGA
Found at i:523409 original size:25 final size:24
Alignment explanation
Indices: 523371--523419 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
523361 TCTAATTTTT
* *
523371 TTTAAATATTAATATTCAAAATATA
1 TTTAAATATAAATA-TAAAAATATA
*
523396 TTTATATATAAATATAAAAATATA
1 TTTAAATATAAATATAAAAATATA
523420 ATTTTTTAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTAAATATAAATATAAAAATATA
Found at i:526118 original size:15 final size:16
Alignment explanation
Indices: 526093--526122 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
526083 ATTCGAATTT
526093 TTTATTTTTTAATATA
1 TTTATTTTTTAATATA
526109 TTTA-TTTTTAATAT
1 TTTATTTTTTAATAT
526123 TTAATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTATTTTTTAATATA
Found at i:534381 original size:9 final size:9
Alignment explanation
Indices: 534327--534421 Score: 50
Period size: 9 Copynumber: 9.6 Consensus size: 9
534317 TTTATTTTTA
534327 TTAA-AAAT
1 TTAATAAAT
534335 ATTAATATAAT
1 -TTAATA-AAT
*
534346 TATAACAAAT
1 T-TAATAAAT
534356 TTAATTTAAAT
1 TTAA--TAAAT
534367 AATTAATAAAT
1 --TTAATAAAT
534378 TTAATAAAAAT
1 TTAAT--AAAT
*
534389 TTAATTTAAT
1 TTAA-TAAAT
*
534399 TAAATAAAT
1 TTAATAAAT
534408 TTAA-ATAAT
1 TTAATA-AAT
534417 TTAAT
1 TTAAT
534422 TTTTATCTCC
Statistics
Matches: 68, Mismatches: 6, Indels: 23
0.70 0.06 0.24
Matches are distributed among these distances:
8 1 0.01
9 26 0.38
10 12 0.18
11 24 0.35
12 1 0.01
13 4 0.06
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (9 bp):
TTAATAAAT
Found at i:534389 original size:33 final size:32
Alignment explanation
Indices: 534331--534397 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 32
534321 TTTTTATTAA
534331 AAATATTAATATAATTATAACAAATTTAATTT
1 AAATATTAATATAATTATAACAAATTTAATTT
534363 AAATAATTAATA-AATTTAATAA-AAATTTAATTT
1 AAAT-ATTAATATAA-TT-ATAACAAATTTAATTT
534396 AA
1 AA
534398 TTAAATAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 6 0.19
33 22 0.69
34 4 0.12
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (32 bp):
AAATATTAATATAATTATAACAAATTTAATTT
Found at i:534423 original size:33 final size:30
Alignment explanation
Indices: 534331--534423 Score: 84
Period size: 33 Copynumber: 3.0 Consensus size: 30
534321 TTTTTATTAA
*
534331 AAAT-ATTAATATAATTATAACAAATTTAATTT
1 AAATAATTAATA-AATT-TAA-TAATTTAATTT
*
534363 AAATAATTAATAAATTTAATAA--AAATTT
1 AAATAATTAATAAATTTAATAATTTAATTT
*
534391 AATTTAATTAAATAAATTTAAATAATTTAATTT
1 AA-ATAATT-AATAAATTT-AATAATTTAATTT
534424 TTATCTCCAC
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
28 7 0.14
29 5 0.10
30 11 0.22
31 8 0.16
32 8 0.16
33 12 0.24
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (30 bp):
AAATAATTAATAAATTTAATAATTTAATTT
Found at i:543850 original size:21 final size:21
Alignment explanation
Indices: 543808--543851 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
543798 GATACATTGG
* * *
543808 TTGGATGAAAGAATGCATTTT
1 TTGGATGAAAAAATACAATTT
*
543829 TTGGATGAAAAAATATAATTT
1 TTGGATGAAAAAATACAATTT
543850 TT
1 TT
543852 AAAAACTAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.39, C:0.02, G:0.18, T:0.41
Consensus pattern (21 bp):
TTGGATGAAAAAATACAATTT
Found at i:544395 original size:7 final size:7
Alignment explanation
Indices: 544383--544419 Score: 53
Period size: 6 Copynumber: 5.7 Consensus size: 7
544373 GTTTGTAGCC
544383 CACAAAT
1 CACAAAT
544390 CACAAAT
1 CACAAAT
544397 CAC-AAT
1 CACAAAT
544403 CAC-AAT
1 CACAAAT
544409 CA-AAAT
1 CACAAAT
544415 CACAA
1 CACAA
544420 TCAATCAACA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 16 0.57
7 12 0.43
ACGTcount: A:0.57, C:0.30, G:0.00, T:0.14
Consensus pattern (7 bp):
CACAAAT
Found at i:544405 original size:6 final size:6
Alignment explanation
Indices: 544387--544422 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
544377 GTAGCCCACA
*
544387 AATCAC AAATCAC AATCAC AATCAA AATCAC AATCA
1 AATCAC -AATCAC AATCAC AATCAC AATCAC AATCA
544423 ATCAACAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 21 0.78
7 6 0.22
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.17
Consensus pattern (6 bp):
AATCAC
Found at i:544416 original size:18 final size:19
Alignment explanation
Indices: 544387--544422 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
544377 GTAGCCCACA
544387 AATCACAAATCACAATCAC
1 AATCACAAATCACAATCAC
544406 AATCA-AAATCACAATCA
1 AATCACAAATCACAATCA
544423 ATCAACAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.17
Consensus pattern (19 bp):
AATCACAAATCACAATCAC
Found at i:551641 original size:2 final size:2
Alignment explanation
Indices: 551634--551665 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
551624 TTTAAATTTG
551634 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
551666 TCAAGCTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:552148 original size:19 final size:19
Alignment explanation
Indices: 552100--552155 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
552090 TGTTTTTTCA
552100 TAATTAAATTTAATAA-TT
1 TAATTAAATTTAATAATTT
** *
552118 TAATTTTTATTTATTAATTT
1 TAA-TTAAATTTAATAATTT
552138 TAATTAAATTTAATAATT
1 TAATTAAATTTAATAATT
552156 AATGTATTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 3 0.10
19 22 0.73
20 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TAATTAAATTTAATAATTT
Found at i:558420 original size:15 final size:13
Alignment explanation
Indices: 558392--558418 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
558382 CTACACAGTC
558392 TTTCTCTAATATA
1 TTTCTCTAATATA
558405 TTTCTCTAATATA
1 TTTCTCTAATATA
558418 T
1 T
558419 ATATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTCTCTAATATA
Found at i:558628 original size:19 final size:18
Alignment explanation
Indices: 558604--558655 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
558594 AATTATATTG
*
558604 AATATTTATTATTTATTTA
1 AATATTTATTA-TAATTTA
*
558623 AATATTTTTTATAATTTA
1 AATATTTATTATAATTTA
558641 AA-ATTTTATT-TAATT
1 AATA-TTTATTATAATT
558656 GAATTTGAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 6 0.21
18 13 0.45
19 10 0.34
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATATTTATTATAATTTA
Found at i:558639 original size:18 final size:19
Alignment explanation
Indices: 558604--558647 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
558594 AATTATATTG
* *
558604 AATATTTATTATTTATTTA
1 AATATTTTTTATTAATTTA
558623 AATATTTTTTA-TAATTTA
1 AATATTTTTTATTAATTTA
558641 AA-ATTTT
1 AATATTTT
558648 ATTTAATTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 8 0.35
19 10 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
AATATTTTTTATTAATTTA
Found at i:558654 original size:17 final size:18
Alignment explanation
Indices: 558612--558655 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
558602 TGAATATTTA
558612 TTATTT-ATTTAAATATT
1 TTATTTAATTTAAATATT
558629 TT-TTATAATTTAAA-ATT
1 TTATT-TAATTTAAATATT
558646 TTATTTAATT
1 TTATTTAATT
558656 GAATTTGAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 9 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTATTTAATTTAAATATT
Found at i:558737 original size:11 final size:11
Alignment explanation
Indices: 558717--558783 Score: 68
Period size: 11 Copynumber: 6.3 Consensus size: 11
558707 GAATTGAGAC
558717 ATAATATAAAT
1 ATAATATAAAT
*
558728 ATAATTTAAA-
1 ATAATATAAAT
*
558738 A-AAT-TAAGAC
1 ATAATATAA-AT
* *
558748 ATAACATAAAA
1 ATAATATAAAT
558759 ATAATATAAAT
1 ATAATATAAAT
558770 ATAATATAAAT
1 ATAATATAAAT
558781 ATA
1 ATA
558784 TAAATGTATC
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
8 3 0.06
9 4 0.09
10 2 0.04
11 35 0.74
12 3 0.06
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.31
Consensus pattern (11 bp):
ATAATATAAAT
Found at i:558751 original size:31 final size:31
Alignment explanation
Indices: 558708--558768 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
558698 ATGTAAAATG
* * * *
558708 AATTGAGACATAATATAAATATAATTTAAAA
1 AATTAAGACATAACATAAAAATAATATAAAA
558739 AATTAAGACATAACATAAAAATAATATAAA
1 AATTAAGACATAACATAAAAATAATATAAA
558769 TATAATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.28
Consensus pattern (31 bp):
AATTAAGACATAACATAAAAATAATATAAAA
Found at i:564252 original size:24 final size:21
Alignment explanation
Indices: 564225--564279 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
564215 ATAAATTATT
*
564225 TATAAATATTAAAATTTATATA
1 TATAAATATTAAAATTT-TAAA
* *
564247 TATATATATATAATATTTTAAA
1 TATAAATAT-TAAAATTTTAAA
564269 TATAAATATTA
1 TATAAATATTA
564280 TACGTATGTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.07
22 19 0.68
23 7 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATAAATATTAAAATTTTAAA
Found at i:564529 original size:15 final size:15
Alignment explanation
Indices: 564511--564540 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
564501 ATTTTATTTT
*
564511 TAAAAAATTTAAAAA
1 TAAAAAACTTAAAAA
564526 TAAAAAACTTAAAAA
1 TAAAAAACTTAAAAA
564541 ATATATATGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAAAAACTTAAAAA
Found at i:565794 original size:18 final size:18
Alignment explanation
Indices: 565771--565840 Score: 56
Period size: 18 Copynumber: 3.9 Consensus size: 18
565761 AATATTATAA
565771 TAATATATTTATAAATTT
1 TAATATATTTATAAATTT
** *
565789 TAATATAAATATTAA---
1 TAATATATTTATAAATTT
565804 TAACTCATATTATATAAATTT
1 TAA-T-ATATT-TATAAATTT
*
565825 TAATATATTCATAAAT
1 TAATATATTTATAAAT
565841 ATATATCATA
Statistics
Matches: 39, Mismatches: 7, Indels: 12
0.67 0.12 0.21
Matches are distributed among these distances:
15 3 0.08
16 1 0.03
17 3 0.08
18 23 0.59
19 5 0.13
20 1 0.03
21 3 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (18 bp):
TAATATATTTATAAATTT
Found at i:565842 original size:24 final size:24
Alignment explanation
Indices: 565789--565843 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
565779 TTATAAATTT
565789 TAATATAAATATTAATAACTCATA
1 TAATATAAATATTAATAACTCATA
* * *
565813 TTATATAAATTTTAATATATTCATA
1 TAATATAAATATTAATA-ACTCATA
565838 -AATATA
1 TAATATA
565844 TATCATATCT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (24 bp):
TAATATAAATATTAATAACTCATA
Found at i:566724 original size:16 final size:16
Alignment explanation
Indices: 566705--566808 Score: 70
Period size: 16 Copynumber: 6.9 Consensus size: 16
566695 AAAATAATTA
566705 AAATATTATATAATAT
1 AAATATTATATAATAT
566721 AAATATT-T-TAA-AT
1 AAATATTATATAATAT
566734 ---T-TTATATAATAT
1 AAATATTATATAATAT
566746 AAATTATTA-AT-ATAT
1 AAA-TATTATATAATAT
566761 CAAA-ATTTATATAATAT
1 -AAATA-TTATATAATAT
566778 AAAATAATT-TA-AATAT
1 -AAAT-ATTATATAATAT
*
566794 AATTATTATATAATA
1 AAATATTATATAATA
566809 AATATACCAA
Statistics
Matches: 70, Mismatches: 2, Indels: 32
0.67 0.02 0.31
Matches are distributed among these distances:
9 2 0.03
10 2 0.03
11 3 0.04
12 2 0.03
13 2 0.03
14 7 0.10
15 13 0.19
16 24 0.34
17 12 0.17
18 2 0.03
19 1 0.01
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (16 bp):
AAATATTATATAATAT
Found at i:566725 original size:25 final size:25
Alignment explanation
Indices: 566696--566760 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
566686 TTTTATTAAA
566696 AAATAATTAAAATATTATATAATAT
1 AAATAATTAAAATATTATATAATAT
* * *
566721 AAATATTTTAAATTTTATATAATAT
1 AAATAATTAAAATATTATATAATAT
* *
566746 AAATTATTAATATAT
1 AAATAATTAAAATAT
566761 CAAAATTTAT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
AAATAATTAAAATATTATATAATAT
Found at i:566803 original size:32 final size:30
Alignment explanation
Indices: 566708--566808 Score: 90
Period size: 32 Copynumber: 3.4 Consensus size: 30
566698 ATAATTAAAA
566708 TATTATATAATATAAATATTT---TA-AAT
1 TATTATATAATATAAATATTTAAATATAAT
566734 T-TTATATAATATAAAT-TATTAATATATCAA-
1 TATTATATAATATAAATAT-TTAA-ATAT-AAT
*
566764 AATTTATATAATATAAAATAATTTAAATATAAT
1 TA-TTATATAATAT-AAAT-ATTTAAATATAAT
566797 TATTATATAATA
1 TATTATATAATA
566809 AATATACCAA
Statistics
Matches: 60, Mismatches: 2, Indels: 20
0.73 0.02 0.24
Matches are distributed among these distances:
24 1 0.02
25 17 0.28
26 1 0.02
29 2 0.03
31 2 0.03
32 23 0.38
33 9 0.15
34 4 0.07
35 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (30 bp):
TATTATATAATATAAATATTTAAATATAAT
Found at i:567103 original size:19 final size:21
Alignment explanation
Indices: 567052--567148 Score: 66
Period size: 20 Copynumber: 4.6 Consensus size: 21
567042 TTTATTTAAA
567052 TTTAAAA-ATATTTAATATACTT
1 TTTAAAATATATTTAATATA--T
567074 TTGATATAAATATATTTAAT-T-T
1 TT--TA-AAATATATTTAATATAT
567096 TTTAAAAT-T-TTTAATATAT
1 TTTAAAATATATTTAATATAT
567115 TTTAAAATTATATATT--TATA-
1 TTTAAAA-TATAT-TTAATATAT
567135 TTTAAATATATATT
1 TTTAAA-ATATATT
567149 ATTTTAAATA
Statistics
Matches: 64, Mismatches: 0, Indels: 25
0.72 0.00 0.28
Matches are distributed among these distances:
17 6 0.09
18 2 0.03
19 13 0.20
20 14 0.22
21 6 0.09
22 6 0.09
23 2 0.03
24 2 0.03
25 4 0.06
26 9 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (21 bp):
TTTAAAATATATTTAATATAT
Found at i:567145 original size:16 final size:16
Alignment explanation
Indices: 567112--567160 Score: 62
Period size: 16 Copynumber: 2.8 Consensus size: 16
567102 ATTTTTAATA
567112 TATTTTAAAATTATATATT
1 TATTTT-AAA-TATATA-T
567131 TATATTTAAATATATAT
1 TAT-TTTAAATATATAT
567148 TATTTTAAATATA
1 TATTTTAAATATA
567161 AATATTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 10 0.34
17 4 0.14
18 6 0.21
19 6 0.21
20 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTTAAATATATAT
Found at i:567152 original size:21 final size:21
Alignment explanation
Indices: 567083--567148 Score: 61
Period size: 19 Copynumber: 3.3 Consensus size: 21
567073 TTTGATATAA
*
567083 ATATATTTAATTTTTTAAAATT
1 ATATATTT-ATATTTTAAAATT
* *
567105 -TTTA-ATATATTTTAAAATT
1 ATATATTTATATTTTAAAATT
567124 ATATATTTATA-TTT-AAA-T
1 ATATATTTATATTTTAAAATT
567142 ATATATT
1 ATATATT
567149 ATTTTAAATA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 8 0.22
19 15 0.41
20 7 0.19
21 7 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATATTTATATTTTAAAATT
Found at i:567165 original size:20 final size:19
Alignment explanation
Indices: 567112--567181 Score: 65
Period size: 19 Copynumber: 3.8 Consensus size: 19
567102 ATTTTTAATA
* *
567112 TATTTTAAAATTATATATT
1 TATTTTAAAAATAAATATT
*
567131 TATATTT--AAATATATA-T
1 TAT-TTTAAAAATAAATATT
*
567148 TATTTTAAATATAAATATT
1 TATTTTAAAAATAAATATT
*
567167 TTTTTTAAAAATAAA
1 TATTTTAAAAATAAA
567182 AAATTTTAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
16 3 0.07
17 4 0.10
18 15 0.36
19 17 0.40
20 3 0.07
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATTTTAAAAATAAATATT
Found at i:567166 original size:15 final size:16
Alignment explanation
Indices: 567111--567168 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
567101 AATTTTTAAT
567111 ATATTTTAAAATTATATA
1 ATATTTT-AAA-TATATA
*
567129 TTTATATTTAAATATATA
1 -ATAT-TTTAAATATATA
*
567147 TTATTTTAAATATA-A
1 ATATTTTAAATATATA
567162 ATATTTT
1 ATATTTT
567169 TTTTAAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
15 7 0.19
16 10 0.28
17 4 0.11
18 6 0.17
19 6 0.17
20 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATTTTAAATATATA
Found at i:567188 original size:19 final size:19
Alignment explanation
Indices: 567150--567188 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
567140 ATATATATTA
* * *
567150 TTTTAAATATAAATATTTT
1 TTTTAAAAATAAAAAATTT
567169 TTTTAAAAATAAAAAATTT
1 TTTTAAAAATAAAAAATTT
567188 T
1 T
567189 AATAATATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTAAAAATAAAAAATTT
Found at i:569723 original size:3 final size:3
Alignment explanation
Indices: 569713--569752 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
569703 TATTAAAAGT
569713 TAA T-A TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
569753 ACTTTGTAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
2 4 0.11
3 31 0.89
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:570181 original size:2 final size:2
Alignment explanation
Indices: 570169--570210 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
570159 CTATGTTAAA
*
570169 AT AT TT AT 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 AT AT AT AT
570211 GACTGGGTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:574231 original size:2 final size:2
Alignment explanation
Indices: 574224--574256 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
574214 GCCTTTTTAG
574224 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
574257 TTCATTCCCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:574559 original size:13 final size:11
Alignment explanation
Indices: 574510--574566 Score: 51
Period size: 13 Copynumber: 4.8 Consensus size: 11
574500 TAAAGTATTA
*
574510 ATTTTAAATTT
1 ATTTTTAATTT
*
574521 TTTATTTAAATTT
1 ATT-TTT-AATTT
574534 ATTTTTAATTT
1 ATTTTTAATTT
574545 ATTTTTATTATTT
1 ATTTTTA--ATTT
*
574558 ATATTTAAT
1 ATTTTTAAT
574567 AATTAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 16 0.42
12 5 0.13
13 17 0.45
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
ATTTTTAATTT
Found at i:574571 original size:17 final size:17
Alignment explanation
Indices: 574551--574602 Score: 50
Period size: 17 Copynumber: 3.0 Consensus size: 17
574541 ATTTATTTTT
574551 ATTATTTATATTTAATA
1 ATTATTTATATTTAATA
* * * *
574568 ATTAATAAAATTTAAAA
1 ATTATTTATATTTAATA
*
574585 ATTATTTTTATATTAATA
1 ATTATTTATAT-TTAATA
574603 TTTAAATGAA
Statistics
Matches: 25, Mismatches: 9, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTATTTATATTTAATA
Found at i:574647 original size:20 final size:19
Alignment explanation
Indices: 574611--574674 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 19
574601 TATTTAAATG
*
574611 AAAATATTATTTTAATTAT
1 AAAATATTATTTAAATTAT
574630 AAAATATTAATTTAAATTAAAT
1 AAAATATT-ATTTAAATT--AT
*
574652 TAAAT-TTATTTAAATTAAT
1 AAAATATTATTTAAATT-AT
574671 AAAA
1 AAAA
574675 AATTTATTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
19 14 0.36
20 17 0.44
21 2 0.05
22 6 0.15
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AAAATATTATTTAAATTAT
Found at i:574648 original size:10 final size:10
Alignment explanation
Indices: 574635--574670 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
574625 ATTATAAAAT
574635 ATTAATTTAA
1 ATTAATTTAA
*
574645 ATTAAATTAA
1 ATTAATTTAA
*
574655 ATTTATTTAA
1 ATTAATTTAA
574665 ATTAAT
1 ATTAAT
574671 AAAAAATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATTAATTTAA
Found at i:574784 original size:17 final size:19
Alignment explanation
Indices: 574762--574805 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
574752 TTAATTAAAT
574762 AAATATAAAAGTAAT-T-A
1 AAATATAAAAGTAATATAA
* *
574779 AAATATAATATTAATATAA
1 AAATATAAAAGTAATATAA
574798 AAATATAA
1 AAATATAA
574806 TATTTATGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 13 0.57
18 1 0.04
19 9 0.39
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
AAATATAAAAGTAATATAA
Found at i:577164 original size:27 final size:27
Alignment explanation
Indices: 577126--577181 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
577116 AGACTTAAAC
577126 TTCTTTGTCATAACCTGCACTATGTGT
1 TTCTTTGTCATAACCTGCACTATGTGT
577153 TTCTTTGTCATAACCTGCACTATGTGT
1 TTCTTTGTCATAACCTGCACTATGTGT
577180 TT
1 TT
577182 ATCTCCTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.18, C:0.21, G:0.14, T:0.46
Consensus pattern (27 bp):
TTCTTTGTCATAACCTGCACTATGTGT
Found at i:581044 original size:20 final size:20
Alignment explanation
Indices: 581019--581065 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
581009 TTTAAAAGTC
* *
581019 TTAATAATTTAATTTTTGAT
1 TTAATAATTTAAATATTGAT
*
581039 TTAATATTTTAAATATTGAT
1 TTAATAATTTAAATATTGAT
581059 TTCAATA
1 TT-AATA
581066 TTGGTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.55
Consensus pattern (20 bp):
TTAATAATTTAAATATTGAT
Found at i:585257 original size:16 final size:15
Alignment explanation
Indices: 585223--585258 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
585213 TATTTATTTG
*
585223 ATAAATAAAATTTAT
1 ATAAATAAAATTTAA
585238 ATAAATAAAATTTTAA
1 ATAAATAAAA-TTTAA
585254 ATAAA
1 ATAAA
585259 AATTTTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
ATAAATAAAATTTAA
Found at i:586665 original size:2 final size:2
Alignment explanation
Indices: 586660--586689 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
586650 ACACACACAC
586660 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
586690 GCGTATAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:590861 original size:14 final size:14
Alignment explanation
Indices: 590842--590871 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
590832 TATGATAGAC
*
590842 AATATATAATTAAA
1 AATATATAAGTAAA
590856 AATATATAAGTAAA
1 AATATATAAGTAAA
590870 AA
1 AA
590872 GTTAGGTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.30
Consensus pattern (14 bp):
AATATATAAGTAAA
Found at i:596203 original size:14 final size:14
Alignment explanation
Indices: 596180--596217 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
596170 ATAATTTTAA
*
596180 AATATGATATAAAT
1 AATATAATATAAAT
596194 AATATAATATAAAT
1 AATATAATATAAAT
596208 AATA-AATATA
1 AATATAATATA
596218 TTAAATATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 6 0.26
14 17 0.74
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
AATATAATATAAAT
Found at i:596768 original size:8 final size:7
Alignment explanation
Indices: 596752--596804 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
596742 GTTTCAACGT
596752 TATTTTA
1 TATTTTA
596759 TATTTATA
1 TATTT-TA
596767 TATTTTA
1 TATTTTA
*
596774 TTATATTA
1 -TATTTTA
*
596782 TA-ATTA
1 TATTTTA
596788 TAATTTTA
1 T-ATTTTA
596796 TATTTTA
1 TATTTTA
596803 TA
1 TA
596805 AATAAAATTC
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
6 5 0.12
7 18 0.45
8 17 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TATTTTA
Found at i:596782 original size:23 final size:22
Alignment explanation
Indices: 596751--596805 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
596741 CGTTTCAACG
*
596751 TTATTTTATATTTATATATTTTA
1 TTATTTTATAATTATA-ATTTTA
*
596774 TTATATTATAATTATAATTTTA
1 TTATTTTATAATTATAATTTTA
596796 -TATTTTATAA
1 TTATTTTATAA
596806 ATAAAATTCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 9 0.31
22 6 0.21
23 14 0.48
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTATTTTATAATTATAATTTTA
Found at i:596805 original size:15 final size:15
Alignment explanation
Indices: 596752--596805 Score: 58
Period size: 15 Copynumber: 3.7 Consensus size: 15
596742 GTTTCAACGT
596752 TATTTTAT-ATTTATA
1 TATTTTATAATTT-TA
* *
596767 TATTTTATTATATTA
1 TATTTTATAATTTTA
*
596782 TA-ATTATAATTTTA
1 TATTTTATAATTTTA
596796 TATTTTATAA
1 TATTTTATAA
596806 ATAAAATTCT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
14 11 0.34
15 18 0.56
16 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TATTTTATAATTTTA
Found at i:596813 original size:21 final size:22
Alignment explanation
Indices: 596768--596813 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
596758 ATATTTATAT
* *
596768 ATTTTATTATATTATAATTATA
1 ATTTTATTATATTATAAATAAA
*
596790 ATTTTA-TATTTTATAAATAAA
1 ATTTTATTATATTATAAATAAA
596811 ATT
1 ATT
596814 CTTCATTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTTATTATATTATAAATAAA
Found at i:598404 original size:18 final size:17
Alignment explanation
Indices: 598367--598417 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
598357 ATATTTTAAA
598367 ATTAATATAATACAAA-TT
1 ATTAATAT-ATA-AAATTT
598385 ATTAATATATTAAAATTT
1 ATTAATATA-TAAAATTT
598403 ATATAA-ATATAAAAT
1 AT-TAATATATAAAAT
598418 ATTTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
17 10 0.33
18 17 0.57
19 3 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTAATATATAAAATTT
Found at i:601276 original size:26 final size:26
Alignment explanation
Indices: 601217--601277 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 26
601207 GATCATTAAA
601217 TTTGATA-A-TTTATATTATAAATTT
1 TTTGATATATTTTATATTATAAATTT
* * *
601241 TTTAAAATATTTTATATT-TATATATT
1 TTTGATATATTTTATATTATAAAT-TT
601267 TTTGATATATT
1 TTTGATATATT
601278 AATAATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
24 5 0.17
25 5 0.17
26 19 0.66
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (26 bp):
TTTGATATATTTTATATTATAAATTT
Found at i:601341 original size:19 final size:19
Alignment explanation
Indices: 601317--601376 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
601307 CAATCATATA
*
601317 TTAATATTGTATTTATTTT
1 TTAATATTATATTTATTTT
*
601336 TTAATATTAT-TTTATATT
1 TTAATATTATATTTATTTT
* *
601354 TTATATTTTATTTTTATTTT
1 TTA-ATATTATATTTATTTT
601374 TTA
1 TTA
601377 TTTTTATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 10 0.29
19 15 0.43
20 10 0.29
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.72
Consensus pattern (19 bp):
TTAATATTATATTTATTTT
Found at i:601347 original size:13 final size:13
Alignment explanation
Indices: 601328--601386 Score: 66
Period size: 13 Copynumber: 4.6 Consensus size: 13
601318 TAATATTGTA
601328 TTTATTTTTTAAT
1 TTTATTTTTTAAT
* *
601341 ATTATTTTAT-AT
1 TTTATTTTTTAAT
* *
601353 TTTATATTTTATT
1 TTTATTTTTTAAT
*
601366 TTTATTTTTTATT
1 TTTATTTTTTAAT
601379 TTTATTTT
1 TTTATTTT
601387 AAATTCATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
12 9 0.24
13 29 0.76
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTATTTTTTAAT
Found at i:601353 original size:7 final size:7
Alignment explanation
Indices: 601343--601387 Score: 62
Period size: 6 Copynumber: 7.0 Consensus size: 7
601333 TTTTTAATAT
601343 TATTTTA
1 TATTTTA
601350 TATTTTA
1 TATTTTA
601357 TATTTTA
1 TATTTTA
601364 T-TTTTA
1 TATTTTA
601370 T-TTTT-
1 TATTTTA
601375 TATTTT-
1 TATTTTA
601381 TATTTTA
1 TATTTTA
601388 AATTCATATC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
5 1 0.03
6 20 0.56
7 15 0.42
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (7 bp):
TATTTTA
Found at i:601370 original size:6 final size:6
Alignment explanation
Indices: 601345--601386 Score: 57
Period size: 7 Copynumber: 6.5 Consensus size: 6
601335 TTTAATATTA
601345 TTTTAT ATTTTAT ATTTTAT TTTTATT TTTTAT TTTTAT TTT
1 TTTTAT -TTTTAT -TTTTAT TTTTA-T TTTTAT TTTTAT TTT
601387 AAATTCATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 15 0.44
7 19 0.56
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:601378 original size:18 final size:18
Alignment explanation
Indices: 601328--601386 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 18
601318 TAATATTGTA
*
601328 TTTATTTTTTAATATTATT
1 TTTATTTTTT-ATTTTATT
*
601347 TTATATTTTATATTTTATT
1 TT-TATTTTTTATTTTATT
601366 TTTATTTTTTATTTTTATT
1 TTTATTTTTTA-TTTTATT
601385 TT
1 TT
601387 AAATTCATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
18 8 0.23
19 20 0.57
20 7 0.20
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTATTTTTTATTTTATT
Found at i:601387 original size:18 final size:18
Alignment explanation
Indices: 601328--601387 Score: 75
Period size: 18 Copynumber: 3.2 Consensus size: 18
601318 TAATATTGTA
* *
601328 TTTATTTTTTAATATTAT
1 TTTATTTTTTATTTTTAT
*
601346 TTTATATTTTATATTTTATT
1 TTTATTTTTTAT-TTTTA-T
601366 TTTATTTTTTATTTTTAT
1 TTTATTTTTTATTTTTAT
601384 TTTA
1 TTTA
601388 AATTCATATC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
18 15 0.42
19 9 0.25
20 12 0.33
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTATTTTTTATTTTTAT
Found at i:601725 original size:2 final size:2
Alignment explanation
Indices: 601718--601746 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
601708 AGCATTTCAG
601718 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
601747 AAAAACCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:604019 original size:19 final size:20
Alignment explanation
Indices: 603976--604032 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
603966 AAATTATTTA
*
603976 TTTAAGATTTAATAAAATCTG
1 TTTAATATTTAA-AAAATCTG
*
603997 TTT-A-ATTTAAAAAATCTAT
1 TTTAATATTTAAAAAATCT-G
604016 TTTAATATTTAAAAAAT
1 TTTAATATTTAAAAAAT
604033 AAAAATAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
18 7 0.22
19 9 0.28
20 2 0.06
21 14 0.44
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (20 bp):
TTTAATATTTAAAAAATCTG
Found at i:604266 original size:3 final size:3
Alignment explanation
Indices: 604260--604292 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
604250 TTTTTTTTTC
604260 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
604293 TGTGGTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:604627 original size:18 final size:18
Alignment explanation
Indices: 604604--604654 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
604594 AATATAATGA
604604 AAATGTAAAAAAATAATT
1 AAATGTAAAAAAATAATT
* * *
604622 AAATGTTAATAAATTATTT
1 AAATG-TAAAAAAATAATT
*
604641 AAAT-TAAAATAATA
1 AAATGTAAAAAAATA
604655 TTGTATTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
17 7 0.27
18 5 0.19
19 14 0.54
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
AAATGTAAAAAAATAATT
Found at i:605275 original size:25 final size:27
Alignment explanation
Indices: 605238--605298 Score: 65
Period size: 25 Copynumber: 2.3 Consensus size: 27
605228 TTTATATTTG
*
605238 ATATATATATTTA-AATATAAATATAAA
1 ATATATATATTTATAA-ATAAATAAAAA
*
605265 ATATA-AT-TTTATAAATATATAAAAA
1 ATATATATATTTATAAATAAATAAAAA
*
605290 ATAAATATA
1 ATATATATA
605299 CTTTTATCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
25 17 0.61
26 6 0.21
27 5 0.18
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (27 bp):
ATATATATATTTATAAATAAATAAAAA
Found at i:605488 original size:19 final size:19
Alignment explanation
Indices: 605452--605490 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
605442 CTAAGGATCT
**
605452 TAAATATATTTATATAATA
1 TAAATATAAATATATAATA
*
605471 TAAATATAAATATTTAATA
1 TAAATATAAATATATAATA
605490 T
1 T
605491 TTATGTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TAAATATAAATATATAATA
Found at i:607623 original size:2 final size:2
Alignment explanation
Indices: 607616--607647 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
607606 TAGTGCTTTA
607616 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
607648 TATGAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:609713 original size:5 final size:5
Alignment explanation
Indices: 609703--609728 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
609693 GGTAATCTTA
609703 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
609729 TAACTACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:610445 original size:26 final size:26
Alignment explanation
Indices: 610416--610468 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
610406 CTGGTCTCTA
610416 TTTTCCTATTCCAAAACTGATCAATC
1 TTTTCCTATTCCAAAACTGATCAATC
*
610442 TTTTCCTATTCCAAGACTGATCAATC
1 TTTTCCTATTCCAAAACTGATCAATC
610468 T
1 T
610469 CGAACGTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (26 bp):
TTTTCCTATTCCAAAACTGATCAATC
Found at i:628212 original size:17 final size:17
Alignment explanation
Indices: 628186--628225 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
628176 AAAAAAATTG
*
628186 AAATTAATAT-AATATTA
1 AAATTTATATAAATA-TA
628203 AAATTTATATAAATATA
1 AAATTTATATAAATATA
628220 AAATTT
1 AAATTT
628226 TTTAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:628445 original size:26 final size:23
Alignment explanation
Indices: 628404--628453 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 23
628394 TCCAAAGTTT
628404 ATTTTTTTTAATTTAAATATATTAA
1 ATTTTTTTTAATTT-AAT-TATTAA
628429 ATTTTTATTT-ATATTAATTATTAA
1 ATTTTT-TTTAAT-TTAATTATTAA
628453 A
1 A
628454 AATTTTTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 7 0.30
25 11 0.48
26 5 0.22
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTTTTTTAATTTAATTATTAA
Found at i:628511 original size:21 final size:22
Alignment explanation
Indices: 628470--628511 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
628460 TACAAATTAA
*
628470 ATTTTAATTAAATTTAAAATAT
1 ATTTTAATTAAATTAAAAATAT
628492 ATTTT-ATTAAA-TAAATAATA
1 ATTTTAATTAAATTAAA-AATA
628512 ATTAAACGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
20 3 0.17
21 10 0.56
22 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATTTTAATTAAATTAAAAATAT
Found at i:629852 original size:30 final size:31
Alignment explanation
Indices: 629794--629875 Score: 96
Period size: 30 Copynumber: 2.7 Consensus size: 31
629784 TTTTATATTT
**
629794 TTTATATTTAAAT-ATTTTTTAATATTTTAA
1 TTTATATTTAAATAAAATTTTAATATTTTAA
* *
629824 TTTATATTTAAATAAAATTTTAA-CTTTTAT
1 TTTATATTTAAATAAAATTTTAATATTTTAA
* *
629854 TTTATATCTAAATAAACTTTTA
1 TTTATATTTAAATAAAATTTTA
629876 GAATAAATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 38 0.84
31 7 0.16
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (31 bp):
TTTATATTTAAATAAAATTTTAATATTTTAA
Found at i:630473 original size:21 final size:22
Alignment explanation
Indices: 630449--630497 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
630439 AATAAAAAAT
630449 TATTTTTA-AATT-AATAT-AA
1 TATTTTTAGAATTAAATATAAA
*
630468 TATATTTTAGAATTAAATTTAAA
1 TAT-TTTTAGAATTAAATATAAA
630491 TATTTTT
1 TATTTTT
630498 TTAATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 3 0.12
20 5 0.20
21 4 0.16
22 8 0.32
23 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTTTTAGAATTAAATATAAA
Found at i:630987 original size:21 final size:18
Alignment explanation
Indices: 630946--630989 Score: 52
Period size: 21 Copynumber: 2.3 Consensus size: 18
630936 TTTTGAATAA
*
630946 ATTTAAATAATATGATAT
1 ATTTAAATAACATGATAT
630964 ATTTAATATAACATGTATTAT
1 ATTTAA-ATAACATG-A-TAT
630985 ATTTA
1 ATTTA
630990 TATTAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 6 0.27
19 7 0.32
20 1 0.05
21 8 0.36
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (18 bp):
ATTTAAATAACATGATAT
Found at i:637959 original size:30 final size:29
Alignment explanation
Indices: 637925--637994 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 29
637915 TTTATTATCG
*
637925 TTAAATTTTAAGTTATTTAA-TAAATTAAAT
1 TTAAATTTTAA--TATTTAATTAAAATAAAT
637955 TTAAATATTTTAATATTTAATTAAAATAAAT
1 TT-AA-ATTTTAATATTTAATTAAAATAAAT
637986 TATAAATTT
1 T-TAAATTT
637995 AATTAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
30 13 0.37
31 14 0.40
32 8 0.23
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
TTAAATTTTAATATTTAATTAAAATAAAT
Found at i:637981 original size:21 final size:21
Alignment explanation
Indices: 637944--638000 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
637934 AAGTTATTTA
* *
637944 ATAAATTAAATTTAAAT-ATT
1 ATAAATTTAATTAAAATAATT
*
637964 TTAATATTTAATTAAAATAAATT
1 ATAA-ATTTAATTAAAAT-AATT
637987 ATAAATTTAATTAA
1 ATAAATTTAATTAA
638001 TTTTTATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 3 0.10
21 11 0.37
22 10 0.33
23 6 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATAAATTTAATTAAAATAATT
Found at i:637992 original size:32 final size:31
Alignment explanation
Indices: 637929--637992 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 31
637919 TTATCGTTAA
*
637929 ATTTTAAGTTATTTAATAAATTAAATTTAAAT
1 ATTTTAAG-TATTTAATAAAATAAATTTAAAT
637961 ATTTTAA-TATTTAATTAAAATAAATTATAAAT
1 ATTTTAAGTATTTAA-TAAAATAAATT-TAAAT
637993 TTAATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 7 0.24
31 10 0.34
32 12 0.41
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (31 bp):
ATTTTAAGTATTTAATAAAATAAATTTAAAT
Found at i:638067 original size:21 final size:22
Alignment explanation
Indices: 638023--638067 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
638013 TTTTTATTAT
**
638023 TTTTAATTTATATTATAAAAAA
1 TTTTAATTTATAACATAAAAAA
*
638045 TTTTAATTTA-AACATAAATAA
1 TTTTAATTTATAACATAAAAAA
638066 TT
1 TT
638068 AAAAATATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTTAATTTATAACATAAAAAA
Found at i:638479 original size:19 final size:20
Alignment explanation
Indices: 638454--638509 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
638444 CATTGGCTAC
*
638454 TAATATAATTATTAAATATA
1 TAATATAATTATTAAAAATA
* *
638474 -AATATATTTAATAAAAATA
1 TAATATAATTATTAAAAATA
*
638493 TAAT-TAATTTTTAAAAA
1 TAATATAATTATTAAAAA
638510 AAAAATTATG
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 26 0.90
20 3 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
TAATATAATTATTAAAAATA
Found at i:638486 original size:15 final size:15
Alignment explanation
Indices: 638454--638500 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
638444 CATTGGCTAC
638454 TAATAT-AAT-TATT
1 TAATATAAATATATT
*
638467 AAATATAAATATATT
1 TAATATAAATATATT
* *
638482 TAATAAAAATATAAT
1 TAATATAAATATATT
638497 TAAT
1 TAAT
638501 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 5 0.18
14 3 0.11
15 20 0.71
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATATAAATATATT
Found at i:645108 original size:2 final size:2
Alignment explanation
Indices: 645101--645133 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
645091 AGTTTTAACA
645101 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
645134 GTGGAAAATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:656829 original size:13 final size:14
Alignment explanation
Indices: 656794--656837 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
656784 TCTAACAAGC
*
656794 TTAAAATTAATATTT
1 TTAAATTTAATA-TT
656809 TATAAATTTAA-ATT
1 T-TAAATTTAATATT
656823 TTAAATTTAATATT
1 TTAAATTTAATATT
656837 T
1 T
656838 ATAATAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 9 0.35
14 7 0.27
15 2 0.08
16 8 0.31
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAAATTTAATATT
Found at i:664702 original size:9 final size:9
Alignment explanation
Indices: 664657--664703 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
664647 AATATATTAT
664657 AAAAATATA
1 AAAAATATA
* *
664666 AAAATTTTA
1 AAAAATATA
664675 ATAAAA-ATA
1 A-AAAATATA
664684 AAATAATATA
1 AAA-AATATA
664694 AAAAATATA
1 AAAAATATA
664703 A
1 A
664704 TTTAATTTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
8 2 0.06
9 20 0.65
10 9 0.29
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAAATATA
Found at i:664787 original size:17 final size:17
Alignment explanation
Indices: 664755--664801 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
664745 ATATTATATT
*
664755 TATATTTAA-ATTTTAA
1 TATATTTAATTTTTTAA
664771 TATATTTAATTTTTTAA
1 TATATTTAATTTTTTAA
664788 -A-ATTTATATTTTTT
1 TATATTTA-ATTTTTT
664802 TCGATCGATA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 5 0.18
16 17 0.61
17 6 0.21
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATATTTAATTTTTTAA
Found at i:665164 original size:21 final size:19
Alignment explanation
Indices: 665127--665165 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
665117 AATCTAAAAA
*
665127 TTTAAATAATTATTTAATT
1 TTTAAATAATTAATTAATT
665146 TTTAAATAAAATTAATTAAT
1 TTTAAAT--AATTAATTAAT
665166 AATACTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
21 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTAAATAATTAATTAATT
Found at i:665680 original size:61 final size:62
Alignment explanation
Indices: 665585--665710 Score: 236
Period size: 61 Copynumber: 2.0 Consensus size: 62
665575 TCGTTTGTCC
*
665585 ATTTTCAGTGATTACCCAAAGCAAAACTCTAATCTTCA-ATATATATATATATATATATAAT
1 ATTTTCAGTGATTACCCAAAGCAAAAATCTAATCTTCATATATATATATATATATATATAAT
665646 ATTTTCAGTGATTACCCAAAGCAAAAATCTAATCTTCATATATATATATATATATATATAAT
1 ATTTTCAGTGATTACCCAAAGCAAAAATCTAATCTTCATATATATATATATATATATATAAT
665708 ATT
1 ATT
665711 GAAAAGGCCA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
61 37 0.59
62 26 0.41
ACGTcount: A:0.43, C:0.13, G:0.05, T:0.39
Consensus pattern (62 bp):
ATTTTCAGTGATTACCCAAAGCAAAAATCTAATCTTCATATATATATATATATATATATAAT
Found at i:666147 original size:2 final size:2
Alignment explanation
Indices: 666140--666173 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
666130 ACTCAATAAG
666140 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
666174 TGGAATAACC
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
Found at i:669346 original size:2 final size:2
Alignment explanation
Indices: 669339--669371 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
669329 CAAGAGGTAT
669339 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
669372 GTGGGTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:670607 original size:16 final size:16
Alignment explanation
Indices: 670579--670655 Score: 100
Period size: 16 Copynumber: 4.8 Consensus size: 16
670569 GATTGACTCG
*
670579 AAATAATTCGAATTTA
1 AAATGATTCGAATTTA
* *
670595 AAATGATTTGAATTTG
1 AAATGATTCGAATTTA
* * *
670611 AAATAATTTGAATTCA
1 AAATGATTCGAATTTA
670627 AAATGATTCGAATTTA
1 AAATGATTCGAATTTA
670643 AAATGATTCGAAT
1 AAATGATTCGAAT
670656 AATTAATTCG
Statistics
Matches: 52, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (16 bp):
AAATGATTCGAATTTA
Found at i:670614 original size:32 final size:32
Alignment explanation
Indices: 670578--670655 Score: 111
Period size: 32 Copynumber: 2.4 Consensus size: 32
670568 TGATTGACTC
* *
670578 GAAATAATTCGAATTTAAAATGATTTGAATTT
1 GAAATAATTCGAATTCAAAATGATTCGAATTT
*
670610 GAAATAATTTGAATTCAAAATGATTCGAATTT
1 GAAATAATTCGAATTCAAAATGATTCGAATTT
* *
670642 AAAATGATTCGAAT
1 GAAATAATTCGAAT
670656 AATTAATTCG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.45, C:0.05, G:0.13, T:0.37
Consensus pattern (32 bp):
GAAATAATTCGAATTCAAAATGATTCGAATTT
Found at i:671029 original size:6 final size:7
Alignment explanation
Indices: 671016--671043 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
671006 TAAATAATTA
671016 TTATTTT
1 TTATTTT
671023 TTATTTT
1 TTATTTT
671030 TTATTTT
1 TTATTTT
671037 TTATTTT
1 TTATTTT
671044 GAATAAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (7 bp):
TTATTTT
Found at i:671340 original size:61 final size:61
Alignment explanation
Indices: 671269--671394 Score: 236
Period size: 61 Copynumber: 2.1 Consensus size: 61
671259 TTCAAACATA
671269 ATGATATACCTTGCTATTTTTTTATTTATAAATATAAAAAATATAAAATGACTCAAA-CTCG
1 ATGATATACCTTGCTATTTTTTTATTTATAAATATAAAAAATATAAAATGACTCAAATC-CG
671330 ATGATATACCTTGCTATTTTTTTATTTATAAATATAAAAAATATAAAATGACTCAAATCCG
1 ATGATATACCTTGCTATTTTTTTATTTATAAATATAAAAAATATAAAATGACTCAAATCCG
671391 ATGA
1 ATGA
671395 ATCTAACTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
61 63 0.98
62 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (61 bp):
ATGATATACCTTGCTATTTTTTTATTTATAAATATAAAAAATATAAAATGACTCAAATCCG
Found at i:679738 original size:24 final size:24
Alignment explanation
Indices: 679711--679791 Score: 69
Period size: 26 Copynumber: 3.3 Consensus size: 24
679701 TATTTATTAA
679711 TTAAAATAATATTTTATTTAAATT
1 TTAAAATAATATTTTATTTAAATT
* *
679735 TTAAAAATATATAATATTAATT-AATT
1 TT-AAAATA-AT-ATTTTATTTAAATT
**
679761 TTAATAATAAT-TTAAATTTAAA-T
1 TTAA-AATAATATTTTATTTAAATT
679784 TTAAAATA
1 TTAAAATA
679792 TTAAAAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
22 4 0.09
23 9 0.20
24 4 0.09
25 10 0.22
26 12 0.26
27 7 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAAAATAATATTTTATTTAAATT
Found at i:679767 original size:48 final size:50
Alignment explanation
Indices: 679696--679789 Score: 122
Period size: 48 Copynumber: 1.9 Consensus size: 50
679686 AACTATTTAG
* *
679696 ATAATTATTTATTAATTAAAATAAT-ATTT-TATTTAAATTTTAAAAATAT
1 ATAATTATTAATTAATTAAAATAATAATTTAAATTTAAA-TTTAAAAATAT
**
679745 ATAA-TATTAATTAATTTTAATAATAATTTAAATTTAAATTTAAAA
1 ATAATTATTAATTAATTAAAATAATAATTTAAATTTAAATTTAAAA
679790 TATTAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 17 0.44
49 15 0.38
50 7 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (50 bp):
ATAATTATTAATTAATTAAAATAATAATTTAAATTTAAATTTAAAAATAT
Found at i:679830 original size:39 final size:42
Alignment explanation
Indices: 679726--679830 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 42
679716 ATAATATTTT
** *
679726 ATTTAAATTTTAAAAATATATAATATTAATTAATTTTAATAATA
1 ATTTAAA-TTTAAATTTATA-AATATTAATAAATTTTAATAATA
*
679770 ATTTAAATTTAAATTTA-AAATATTAA-AAATTTTAA-ATTA
1 ATTTAAATTTAAATTTATAAATATTAATAAATTTTAATAATA
* *
679809 TTTTTAATTT-AATTTATAAATA
1 ATTTAAATTTAAATTTATAAATA
679831 AATTTATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
38 6 0.11
39 16 0.30
40 8 0.15
41 8 0.15
42 1 0.02
43 8 0.15
44 7 0.13
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (42 bp):
ATTTAAATTTAAATTTATAAATATTAATAAATTTTAATAATA
Found at i:689644 original size:60 final size:60
Alignment explanation
Indices: 689508--689693 Score: 327
Period size: 60 Copynumber: 3.1 Consensus size: 60
689498 ATCAAACGCA
689508 GTAAATCTCTTTACTTTCAGGTTCCCATTTTCCTATACATGATTTTACTGGTCATTGTTATT
1 GTAAATCTC-TTACTTTCAGGTTCCCATTTTCCTATACATGA-TTTACTGGTCATTGTTATT
* *
689570 GTAAATCTCTTACTTTCAGGTTCCCATTTTCCTATACAGGATTTACTGTTCATTGTTATT
1 GTAAATCTCTTACTTTCAGGTTCCCATTTTCCTATACATGATTTACTGGTCATTGTTATT
*
689630 GTAAATCTCTTACTTTCAGGTTCCCATTTTCCTATACATGATATACTGGTCATTGTTATT
1 GTAAATCTCTTACTTTCAGGTTCCCATTTTCCTATACATGATTTACTGGTCATTGTTATT
689690 GTAA
1 GTAA
689694 TTTCTAAATC
Statistics
Matches: 119, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
60 79 0.66
61 31 0.26
62 9 0.08
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (60 bp):
GTAAATCTCTTACTTTCAGGTTCCCATTTTCCTATACATGATTTACTGGTCATTGTTATT
Found at i:694649 original size:2 final size:2
Alignment explanation
Indices: 694642--694677 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
694632 GTGATCATGG
694642 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
694678 AAGAATCCAA
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:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:695178 original size:18 final size:18
Alignment explanation
Indices: 695150--695243 Score: 70
Period size: 18 Copynumber: 5.2 Consensus size: 18
695140 AATTTTTTAA
695150 AAATT-TTAATATAATAT
1 AAATTATTAATATAATAT
*
695167 AAATTATTAATAT-ATAA
1 AAATTATTAATATAATAT
*
695184 AAATTATATAAATATAAAAT
1 AAATTAT-T-AATATAATAT
** *
695204 ATTTTA-AATATATAATA-
1 AAATTATTA-ATATAATAT
*
695221 AAATTTATAAATATAATAT
1 AAA-TTATTAATATAATAT
695240 AAAT
1 AAAT
695244 ATATAAATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
17 17 0.28
18 27 0.45
19 10 0.17
20 6 0.10
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAATTATTAATATAATAT
Found at i:695183 original size:20 final size:18
Alignment explanation
Indices: 695149--695251 Score: 83
Period size: 19 Copynumber: 5.7 Consensus size: 18
695139 AAATTTTTTA
695149 AAAATTT-T-AATATAAT
1 AAAATTTATAAATATAAT
*
695165 ATAAA-TTATTAATAT-AT
1 A-AAATTTATAAATATAAT
695182 AAAAATTATATAAATATAA-
1 -AAAATT-TATAAATATAAT
*
695201 AATATTT-TAAATATATAAT
1 AAAATTTAT-AA-ATATAAT
695220 AAAATTTATAAATATAAT
1 AAAATTTATAAATATAAT
*
695238 ATAAATATATAAAT
1 A-AAATTTATAAAT
695252 TATTATATAT
Statistics
Matches: 71, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
16 4 0.06
17 12 0.17
18 26 0.37
19 27 0.38
20 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAATTTATAAATATAAT
Found at i:695222 original size:11 final size:11
Alignment explanation
Indices: 695175--695249 Score: 50
Period size: 11 Copynumber: 6.8 Consensus size: 11
695165 ATAAATTATT
695175 AATATATAA-A
1 AATATATAATA
695185 AATTATATAAATA
1 AA-TATAT-AATA
* **
695198 TAAAATATTTTA
1 -AATATATAATA
695210 AATATATAATA
1 AATATATAATA
*
695221 AA-AT-TTATA
1 AATATATAATA
695230 AATATA-ATATA
1 AATATATA-ATA
695241 AATATATAA
1 AATATATAA
695250 ATTATTATAT
Statistics
Matches: 49, Mismatches: 8, Indels: 15
0.68 0.11 0.21
Matches are distributed among these distances:
9 6 0.12
10 6 0.12
11 25 0.51
12 5 0.10
13 5 0.10
14 2 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATATATAATA
Found at i:695263 original size:18 final size:17
Alignment explanation
Indices: 695150--695263 Score: 77
Period size: 17 Copynumber: 7.0 Consensus size: 17
695140 AATTTTTTAA
695150 AAATT-TTAATATAATAT
1 AAATTATTAATAT-ATAT
*
695167 AAATTATTAATATATAA
1 AAATTATTAATATATAT
695184 AAATTATATAA-ATATA-
1 AAATTAT-TAATATATAT
*
695200 AAATATTTTAAATATATAAT
1 AAAT-TATT-AATATAT-AT
* *
695220 AAA--ATTTATAAATAT
1 AAATTATTAATATATAT
695235 -AA-TA-TAA-ATATAT
1 AAATTATTAATATATAT
695248 AAATTATT-ATATATAT
1 AAATTATTAATATATAT
695264 TTTTTAAGTA
Statistics
Matches: 78, Mismatches: 7, Indels: 25
0.71 0.06 0.23
Matches are distributed among these distances:
13 5 0.06
14 6 0.08
15 6 0.08
16 17 0.22
17 26 0.33
18 14 0.18
19 1 0.01
20 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTATTAATATATAT
Found at i:696817 original size:2 final size:2
Alignment explanation
Indices: 696810--696845 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
696800 TTACGTGGAT
*
696810 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
696846 AATAAAATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:696850 original size:10 final size:10
Alignment explanation
Indices: 696811--696851 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
696801 TACGTGGATT
*
696811 ATATATATAT
1 ATATATATAA
*
696821 ATATATATAT
1 ATATATATAA
696831 ATATATATAA
1 ATATATATAA
*
696841 ATATAAATAA
1 ATATATATAA
696851 A
1 A
696852 ATAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATATAA
Found at i:697219 original size:2 final size:2
Alignment explanation
Indices: 697212--697256 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
697202 GAACTCGTAT
697212 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
697254 AG A
1 AG A
697257 AAACATATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:704037 original size:2 final size:2
Alignment explanation
Indices: 704030--704054 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
704020 GAAAACGAAA
704030 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
704055 ATGACTTATT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:704568 original size:27 final size:27
Alignment explanation
Indices: 704538--704610 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
704528 TACAACTCAA
704538 TTAATTAAAAATAATTTTTATTTAA-AT
1 TTAATTAAAAATAATTTTT-TTTAATAT
* *
704565 TTAATTATAAA-AATTATTTTTTAATTT
1 TTAATTAAAAATAATT-TTTTTTAATAT
*
704592 TTAATAATAAAATAATTTT
1 TTAATTA-AAAATAATTTT
704611 ATAAATTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 9 0.24
27 20 0.53
28 5 0.13
29 4 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
TTAATTAAAAATAATTTTTTTTAATAT
Found at i:704617 original size:27 final size:27
Alignment explanation
Indices: 704564--704617 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
704554 TTTATTTAAA
* * *
704564 TTTAATTATAAAAATTATTTTTTAATT
1 TTTAATAATAAAAATAATTTTTAAATT
704591 TTTAATAAT-AAAATAATTTTATAAATT
1 TTTAATAATAAAAATAATTTT-TAAATT
704618 AATCTGATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 10 0.43
27 13 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TTTAATAATAAAAATAATTTTTAAATT
Found at i:704940 original size:13 final size:13
Alignment explanation
Indices: 704921--704952 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
704911 TTTATTTTTT
704921 AAATATTTATATC
1 AAATATTTATATC
*
704934 TAATATTTATATC
1 AAATATTTATATC
704947 AAATAT
1 AAATAT
704953 ATATTTTGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (13 bp):
AAATATTTATATC
Found at i:707982 original size:28 final size:28
Alignment explanation
Indices: 707927--707986 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
707917 TTGAATATAA
* *** *
707927 ATATATAAATTTTAAAAAGCTTTTAAAT
1 ATATAAAAATTTTAAAAAAAATTAAAAT
707955 ATATAAAAATTTTAAAAAAAATTAAAAT
1 ATATAAAAATTTTAAAAAAAATTAAAAT
707983 ATAT
1 ATAT
707987 TTATATTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (28 bp):
ATATAAAAATTTTAAAAAAAATTAAAAT
Found at i:709787 original size:22 final size:22
Alignment explanation
Indices: 709762--709804 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
709752 TATTTATAAA
709762 ATATTTTTAT-ATTAAAATTTAT
1 ATATTTTTATAATT-AAATTTAT
709784 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
709805 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:713266 original size:2 final size:2
Alignment explanation
Indices: 713259--713303 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
713249 AAGTTATCTT
*
713259 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
713301 TA T
1 TA T
713304 GAAAGATCTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:713836 original size:19 final size:18
Alignment explanation
Indices: 713812--713869 Score: 63
Period size: 17 Copynumber: 3.4 Consensus size: 18
713802 AATTTAAGAT
*
713812 TTTTAAATTTTTATATGA
1 TTTTAAATTTTTATATCA
713830 GTTTTAAA--TTTATATCA
1 -TTTTAAATTTTTATATCA
713847 TTTTAAATTTTT-TAT--
1 TTTTAAATTTTTATATCA
713862 TTTTAAAT
1 TTTTAAAT
713870 CATTTTAAGT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 8 0.22
16 7 0.19
17 11 0.31
18 3 0.08
19 7 0.19
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTAAATTTTTATATCA
Found at i:713852 original size:16 final size:17
Alignment explanation
Indices: 713821--713856 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
713811 TTTTTAAATT
*
713821 TTTATATGAGTTTTAAA
1 TTTATATCAGTTTTAAA
713838 TTTATATCA-TTTTAAA
1 TTTATATCAGTTTTAAA
713854 TTT
1 TTT
713857 TTTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.58
Consensus pattern (17 bp):
TTTATATCAGTTTTAAA
Found at i:713965 original size:29 final size:28
Alignment explanation
Indices: 713916--713973 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
713906 CTTAAAATTA
*
713916 AATTAAATCAAATTTAAATAAATTATTT
1 AATTAAATCAAAATTAAATAAATTATTT
* * *
713944 AATTAAATTAAACATTAGATAAATTTTTT
1 AATTAAATCAAA-ATTAAATAAATTATTT
713973 A
1 A
713974 CAAATTTGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (28 bp):
AATTAAATCAAAATTAAATAAATTATTT
Found at i:723445 original size:2 final size:2
Alignment explanation
Indices: 723440--723464 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
723430 AAAAAAAAAA
723440 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
723465 AGGATTGAAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Done.