Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 1 of 25
Found at i:1390 original size:17 final size:17
Alignment explanation
Indices: 1351--1393 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
1341 CATGTTCGTG
* *
1351 GTTCATGAACATTCAAA
1 GTTCATGAATACTCAAA
1368 -TTCATGAATACTCAAA
1 GTTCATGAATACTCAAA
1384 GTTCATGAAT
1 GTTCATGAAT
1394 GTTTATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.40, C:0.16, G:0.12, T:0.33
Consensus pattern (17 bp):
GTTCATGAATACTCAAA
Found at i:7968 original size:21 final size:21
Alignment explanation
Indices: 7940--7979 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
7930 GTTGATTGAA
*
7940 ATTTATCTTCCTT-TTTCTAG
1 ATTTATCTTACTTGTTTCTAG
7960 ATTTCATCTTACTTGTTTCT
1 ATTT-ATCTTACTTGTTTCT
7980 TTGGTCCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 8 0.47
22 5 0.29
ACGTcount: A:0.15, C:0.20, G:0.05, T:0.60
Consensus pattern (21 bp):
ATTTATCTTACTTGTTTCTAG
Found at i:8457 original size:28 final size:28
Alignment explanation
Indices: 8425--8481 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
8415 GCTCAGTATG
8425 TATATGCTCAATTTGAACTTTTTCCCCT
1 TATATGCTCAATTTGAACTTTTTCCCCT
8453 TATATGCTCAATTTGAACTTTTTCCCCT
1 TATATGCTCAATTTGAACTTTTTCCCCT
8481 T
1 T
8482 TTTTTATTCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.25, G:0.07, T:0.47
Consensus pattern (28 bp):
TATATGCTCAATTTGAACTTTTTCCCCT
Found at i:8727 original size:22 final size:22
Alignment explanation
Indices: 8699--8744 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
8689 CATAAATCAT
* *
8699 GAAACTAATCCCACTGAATTAG
1 GAAACTAATCCCACTAAACTAG
8721 GAAACTAATCCCACTAAACTAG
1 GAAACTAATCCCACTAAACTAG
8743 GA
1 GA
8745 GATTGACTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.24, G:0.13, T:0.20
Consensus pattern (22 bp):
GAAACTAATCCCACTAAACTAG
Found at i:10745 original size:18 final size:18
Alignment explanation
Indices: 10722--10758 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
10712 TTTTGGAGAT
*
10722 TCAGGTTCGGACACATGG
1 TCAGGTTCAGACACATGG
*
10740 TCAGGTTCAGACGCATGG
1 TCAGGTTCAGACACATGG
10758 T
1 T
10759 TTGATGTTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.32, T:0.24
Consensus pattern (18 bp):
TCAGGTTCAGACACATGG
Found at i:13546 original size:22 final size:22
Alignment explanation
Indices: 13500--13547 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
13490 AACATAAATC
** *
13500 AGGAAACTAATCCCACTGGATT
1 AGGAAACTAATCCCACTAAACT
*
13522 AGGAAGCTAATCCCACTAAACT
1 AGGAAACTAATCCCACTAAACT
13544 AGGA
1 AGGA
13548 GATTGACTCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.40, C:0.23, G:0.19, T:0.19
Consensus pattern (22 bp):
AGGAAACTAATCCCACTAAACT
Found at i:16198 original size:29 final size:28
Alignment explanation
Indices: 16164--16249 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
16154 TATTCAATTA
16164 ATATTTATTTTCTGTCGATTTATATTGTT
1 ATATTTATTTTCTGTC-ATTTATATTGTT
* *
16193 ATATTTATTGT-TAT-ATTGTCA-A-T-TT
1 ATATTTATTTTCTGTCATT-T-ATATTGTT
16218 ATATTTATTTTCTGTCAATTTATATTGTT
1 ATATTTATTTTCTGTC-ATTTATATTGTT
16247 ATA
1 ATA
16250 CAAAGAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
25 12 0.27
26 7 0.16
27 4 0.09
28 7 0.16
29 15 0.33
ACGTcount: A:0.26, C:0.06, G:0.08, T:0.60
Consensus pattern (28 bp):
ATATTTATTTTCTGTCATTTATATTGTT
Found at i:16208 original size:54 final size:54
Alignment explanation
Indices: 16144--16249 Score: 178
Period size: 54 Copynumber: 2.0 Consensus size: 54
16134 TGTCAATTTG
*
16144 TATTGTTATATAT-TCAATTAATATTTATTTTCTGTCGATTTATATTGTTATATT
1 TATTGTTATAT-TGTCAATTAATATTTATTTTCTGTCAATTTATATTGTTATATT
*
16198 TATTGTTATATTGTCAATTTATATTTATTTTCTGTCAATTTATATTGTTATA
1 TATTGTTATATTGTCAATTAATATTTATTTTCTGTCAATTTATATTGTTATA
16250 CAAAGAAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
53 1 0.02
54 48 0.98
ACGTcount: A:0.27, C:0.06, G:0.08, T:0.59
Consensus pattern (54 bp):
TATTGTTATATTGTCAATTAATATTTATTTTCTGTCAATTTATATTGTTATATT
Found at i:16488 original size:572 final size:572
Alignment explanation
Indices: 15675--16724 Score: 1630
Period size: 571 Copynumber: 1.8 Consensus size: 572
15665 CAACGTAAAA
* * * *
15675 ACAAAGAAAAAGGAAAGAACTTTGGTTGTTGACGTATAACCGAGATAGAGACACGGGAGAGGTGT
1 ACAAAGAAAAAGGAAAAAACTTTGGTTGTTGACGTATAACCAAGATAGAGACACAGGAGAGGAGT
* * *
15740 GAGCTCTGGAACATGTAGAAGTGAAAACAAAGGTTGCGTTGGATGGAGAATGAAAAAAGACTGAA
66 GAGCTCTAGAACATGTAGAAGGGAAAACAAAGGTTGCGTTGGATGGAGAAGGAAAAAAGACTGAA
* * * *
15805 AAGTAATGAATAAAATGATGCTTTTGTTGAGAGATGTGGGGGAAAAAAAAGAAAAATGAAAAATG
131 AACTAATAAATAAAATGACGCTTTTGTTGAGAGATGTGAGGGAAAAAAAAGAAAAATGAAAAATG
*
15870 AAAAAAATATGTAGTAGGAAGTGGGATAAGGTGCAATAATTAGTGAAATAAAATAAAAAGAAAAA
196 AAAAAAATATGTAGTAGGAAGTGGGATAAGGTACAATAATTAGTGAAATAAAATAAAAAG-AAAA
*
15935 TAAGATCTGTGAAAAGAATTAAATTAATTAAAAAGATAATAATAAGTAAATTATAGGTATAACAT
260 TAAGATCTGTGAAAAGAATTAAATTAATTAAAAAGATAATAATAAGTAAATTATAGGTATAAAAT
* *
16000 TAGGGAAAATAAAGTAAAATAATGCTTAAGGGTAAAGGAATACTGGGAAATAGGTACGGTGCAAA
325 TAGGGAAAATAAAGTAAAATAATGCTTAAGGGTAAAGGAATA-TAGGAAATAAGTACGGTGCAAA
* *
16065 GTTGGCATAAAAATAATTTTAAATGTTAAAAATTAGGTATATTGAATTTGGACCTATTGATGAA-
389 GTTGGCATAAAAAT-ATTTTAAATGTTAAAAATTAAGTATATTGAATTTGGACCTATTAATGAAT
* *
16129 TTTTCTGTCAATTTGTATTGTTATATATTCAATTAATATTTATTTTCTGTCGATTTATATTGTTA
453 TTTTCTGGCAATTTATATTGTTATATATTCAATTAATATTTATTTTCTGTCGATTTATATTGTTA
16194 TATTTATTGTTATATTGTCAATTTATATTTATTTTCTGTCAATTTATATTGTTAT
518 TATTTATTGTTATATTGTCAATTTATATTTATTTTCTGTCAATTTATATTGTTAT
* *
16249 ACAAAGAAAAAGGAAAAAACTTTGTTTGTTGAGGGTATAACCAAGATAGAGACA-AGG-GAGGAG
1 ACAAAGAAAAAGGAAAAAACTTTGGTTGTTGA-CGTATAACCAAGATAGAGACACAGGAGAGGAG
* *
16312 TGAGCTCTAGAACATGTAGAAGGGGGAAA-AAA-GTTGCGTTGGATGGAGAAGGAAAATAGACTG
65 TGAGCTCTAGAACATGTAGAA-GGGAAAACAAAGGTTGCGTTGGATGGAGAAGGAAAAAAGACTG
*
16375 AAAACTAATAAAATAAAATGACGTTTTTGTTGAGAGATGTGAGGGAAAAAAGAA-AAGAAA-GAA
129 AAAACTAAT-AAATAAAATGACGCTTTTGTTGAGAGATGTGAGGGAAAAAA-AAGAA-AAATGAA
* * *
16438 AAATG-ACAAAATATGTTGTAGGAAGTGGGATAATGTACAATAATTAGTGAAATAAAATAAAAAG
191 AAATGAAAAAAATATGTAGTAGGAAGTGGGATAAGGTACAATAATTAGTGAAATAAAATAAAAAG
*
16502 AAAATAAGATGTGTGAAAAGAATTAAATTAATTAAAAAGATAATAATAAGTAAATTATAGGTATA
256 AAAATAAGATCTGTGAAAAGAATTAAATTAATTAAAAAGATAATAATAAGTAAATTATAGGTATA
* * * * *
16567 AAATTAGGGAAAATAAGGTAAAATAGTGGTTAAGGGTAAAGGAATATAGGAAATAATTATGGTGC
321 AAATTAGGGAAAATAAAGTAAAATAATGCTTAAGGGTAAAGGAATATAGGAAATAAGTACGGTGC
* * * *
16632 AAAGTTGGCATCAAAATTTTTTGAATTTTAAAAATTAAGTATATTGAATTTGGACCTATTAATGA
386 AAAGTTGGCATAAAAATATTTTAAATGTTAAAAATTAAGTATATTGAATTTGGACCTATTAATGA
*
16697 ATTTTTCTGGCAATTTATTTTGTTATAT
451 ATTTTTCTGGCAATTTATATTGTTATAT
16725 TTATTAAGAA
Statistics
Matches: 432, Mismatches: 38, Indels: 16
0.89 0.08 0.03
Matches are distributed among these distances:
569 44 0.10
570 54 0.12
571 106 0.25
572 92 0.21
573 75 0.17
574 42 0.10
575 19 0.04
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (572 bp):
ACAAAGAAAAAGGAAAAAACTTTGGTTGTTGACGTATAACCAAGATAGAGACACAGGAGAGGAGT
GAGCTCTAGAACATGTAGAAGGGAAAACAAAGGTTGCGTTGGATGGAGAAGGAAAAAAGACTGAA
AACTAATAAATAAAATGACGCTTTTGTTGAGAGATGTGAGGGAAAAAAAAGAAAAATGAAAAATG
AAAAAAATATGTAGTAGGAAGTGGGATAAGGTACAATAATTAGTGAAATAAAATAAAAAGAAAAT
AAGATCTGTGAAAAGAATTAAATTAATTAAAAAGATAATAATAAGTAAATTATAGGTATAAAATT
AGGGAAAATAAAGTAAAATAATGCTTAAGGGTAAAGGAATATAGGAAATAAGTACGGTGCAAAGT
TGGCATAAAAATATTTTAAATGTTAAAAATTAAGTATATTGAATTTGGACCTATTAATGAATTTT
TCTGGCAATTTATATTGTTATATATTCAATTAATATTTATTTTCTGTCGATTTATATTGTTATAT
TTATTGTTATATTGTCAATTTATATTTATTTTCTGTCAATTTATATTGTTAT
Found at i:23536 original size:2 final size:2
Alignment explanation
Indices: 23529--23555 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
23519 GCAGTTTTTC
23529 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 C
23556 AGATTTCTTG
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:23799 original size:2 final size:2
Alignment explanation
Indices: 23794--23821 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
23784 AATCATTCTC
23794 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
23822 TGTGTATCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25406 original size:2 final size:2
Alignment explanation
Indices: 25399--25430 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
25389 TGCTTATGTT
25399 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
25431 CTCTGCCTAT
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):
TA
Found at i:30988 original size:16 final size:16
Alignment explanation
Indices: 30967--31125 Score: 125
Period size: 16 Copynumber: 9.9 Consensus size: 16
30957 TCGAGTTTAA
*
30967 TATTTTAAAATTAAAT
1 TATTTTAAATTTAAAT
30983 TATTTTAAATTTAAAT
1 TATTTTAAATTTAAAT
* *
30999 CA-ATTAAA-TT--AT
1 TATTTTAAATTTAAAT
31011 TA-TTTAAATTTAAAT
1 TATTTTAAATTTAAAT
*
31026 TATTTTAAGTTTAAAT
1 TATTTTAAATTTAAAT
31042 TATTTTAAATTTAAAT
1 TATTTTAAATTTAAAT
* *
31058 TA-ATTAAGTTTAATAAT
1 TATTTTAAATTT-A-AAT
* *
31075 AAATTT-AATTGATACATAT
1 TATTTTAAATT--TA-A-AT
31094 TATTTTAAATTTAAAT
1 TATTTTAAATTTAAAT
31110 TATTTTTTAAATTTAA
1 TA--TTTTAAATTTAA
31126 CTGATTTTTG
Statistics
Matches: 115, Mismatches: 15, Indels: 24
0.75 0.10 0.16
Matches are distributed among these distances:
12 8 0.07
13 2 0.02
14 2 0.02
15 16 0.14
16 50 0.43
17 8 0.07
18 18 0.16
19 7 0.06
20 4 0.03
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (16 bp):
TATTTTAAATTTAAAT
Found at i:31024 original size:27 final size:25
Alignment explanation
Indices: 30975--31025 Score: 84
Period size: 27 Copynumber: 2.0 Consensus size: 25
30965 AATATTTTAA
30975 AATTAAATTATTTTAAATTTAAATC
1 AATTAAATTATTTTAAATTTAAATC
31000 AATTAAATTATTATTTAAATTTAAAT
1 AATTAAATTA-T-TTTAAATTTAAAT
31026 TATTTTAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 10 0.42
26 1 0.04
27 13 0.54
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (25 bp):
AATTAAATTATTTTAAATTTAAATC
Found at i:31077 original size:27 final size:28
Alignment explanation
Indices: 30986--31082 Score: 99
Period size: 27 Copynumber: 3.4 Consensus size: 28
30976 ATTAAATTAT
* * *
30986 TTTAAATTTAAATCAATTAA-ATTATTA
1 TTTAAATTTAAATTAATTAAGTTTAATA
*
31013 TTTAAATTTAAATTATTTTAAGTTTAAATTA
1 TTTAAATTTAAATTA-ATTAAGTTT-AA-TA
31044 TTTTAAATTTAAATTAATTAAGTTTAATA
1 -TTTAAATTTAAATTAATTAAGTTTAATA
*
31073 -ATAAATTTAA
1 TTTAAATTTAA
31083 TTGATACATA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
27 23 0.39
28 4 0.07
29 4 0.07
30 3 0.05
31 10 0.17
32 15 0.25
ACGTcount: A:0.46, C:0.01, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTAAATTTAAATTAATTAAGTTTAATA
Found at i:31078 original size:59 final size:59
Alignment explanation
Indices: 30967--31082 Score: 162
Period size: 59 Copynumber: 2.0 Consensus size: 59
30957 TCGAGTTTAA
* *
30967 TATTTTAAAATTAAATTATTTTAAATTTAAATCAATTAAATTATTATTTAAATTTAAAT
1 TATTTTAAAATTAAATTATTTTAAATTTAAATCAATTAAATTAATATATAAATTTAAAT
** * *
31026 TATTTTAAGTTTAAATTATTTTAAATTTAAATTAATTAAGTTTAATA-ATAAATTTAA
1 TATTTTAAAATTAAATTATTTTAAATTTAAATCAATTAA-ATTAATATATAAATTTAA
31083 TTGATACATA
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
59 45 0.90
60 5 0.10
ACGTcount: A:0.47, C:0.01, G:0.02, T:0.51
Consensus pattern (59 bp):
TATTTTAAAATTAAATTATTTTAAATTTAAATCAATTAAATTAATATATAAATTTAAAT
Found at i:31133 original size:17 final size:18
Alignment explanation
Indices: 31096--31134 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
31086 ATACATATTA
*
31096 TTTTAAATTTAAATTATT
1 TTTTAAATTTAAATGATT
*
31114 TTTTAAATTTAACTGATT
1 TTTTAAATTTAAATGATT
31132 TTT
1 TTT
31135 GAAGGTGTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (18 bp):
TTTTAAATTTAAATGATT
Found at i:31568 original size:32 final size:32
Alignment explanation
Indices: 31526--31593 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 32
31516 ATTATATAAA
* * *
31526 TATTTTAATTATTATAATTATTATTAAAATAT
1 TATTTCAATTAATATAATTACTATTAAAATAT
* *
31558 TATTTCAATTAATATAATTACTCTTAGAATAT
1 TATTTCAATTAATATAATTACTATTAAAATAT
31590 TATT
1 TATT
31594 GTAATATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.53
Consensus pattern (32 bp):
TATTTCAATTAATATAATTACTATTAAAATAT
Found at i:34847 original size:1 final size:1
Alignment explanation
Indices: 34841--34866 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
34831 TATCTTCCCC
34841 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
34867 AGGATTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:44657 original size:37 final size:37
Alignment explanation
Indices: 44577--44689 Score: 111
Period size: 37 Copynumber: 3.1 Consensus size: 37
44567 TCGGTTTCAA
** * *
44577 CCGTGCCACTGGTAAGAATAATAGTTTTTGTTTCGAC
1 CCGTGCCACCAGTAAGAATAGTAGTTTTTGTTCCGAC
* *
44614 CCGTGCCATCAGTAAGAATAGTAGTTTTTGTTCCGAT
1 CCGTGCCACCAGTAAGAATAGTAGTTTTTGTTCCGAC
** * * *
44651 TTGTGCCACCAGTAAAAATAGT-GATTTATGTTCCAAC
1 CCGTGCCACCAGTAAGAATAGTAG-TTTTTGTTCCGAC
44688 CC
1 CC
44690 ACCCATGTCA
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
36 1 0.02
37 59 0.98
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (37 bp):
CCGTGCCACCAGTAAGAATAGTAGTTTTTGTTCCGAC
Found at i:45760 original size:2 final size:2
Alignment explanation
Indices: 45753--45780 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45743 TAAGATTATC
45753 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
45781 TATTTAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45937 original size:16 final size:16
Alignment explanation
Indices: 45913--45944 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
45903 TTTAAAAAAA
*
45913 TTAATATAATTTAAAT
1 TTAAAATAATTTAAAT
45929 TTAAAATAATTTAAAT
1 TTAAAATAATTTAAAT
45945 CTAATTACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATAATTTAAAT
Found at i:46468 original size:19 final size:21
Alignment explanation
Indices: 46446--46493 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
46436 TGAATAACAG
46446 TTTACAT-T-AATAATAAAAA
1 TTTACATATAAATAATAAAAA
*
46465 TTTACAATCATAAATACTAAAAA
1 TTTAC-AT-ATAAATAATAAAAA
46488 TTTACA
1 TTTACA
46494 ACTGCTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.21
20 2 0.08
22 2 0.08
23 15 0.62
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.35
Consensus pattern (21 bp):
TTTACATATAAATAATAAAAA
Found at i:47194 original size:6 final size:6
Alignment explanation
Indices: 47183--47232 Score: 64
Period size: 6 Copynumber: 8.3 Consensus size: 6
47173 TTCTGCCAGA
* * * *
47183 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GAAGGG GGTGGA GGAGGT
1 GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT GGAGGT
47231 GG
1 GG
47233 TGTAGGAGGA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.18, C:0.00, G:0.68, T:0.14
Consensus pattern (6 bp):
GGAGGT
Found at i:48487 original size:3 final size:3
Alignment explanation
Indices: 48481--48511 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
48471 AATAATAATA
*
48481 ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
48512 ATAAATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:48658 original size:266 final size:260
Alignment explanation
Indices: 47883--48843 Score: 1260
Period size: 266 Copynumber: 3.7 Consensus size: 260
47873 TTTTTTTTAT
*
47883 TTTTCATACTATTATTTTTAACATATATTTTTAATCATTTTAATTTTCATAATTAATAAATTAAA
1 TTTTCATACTATCATTTTTAACATATATTTTTAATCATTTTAATTTT-ATAATTAATAAATTAAA
* *
47948 ATAAACATATAATAATAATAATAATTATTATT-ATTATTATTATTAATTAATTAATTAATAAAAT
65 ATAGACATATAATAATAATAATTATTATTATTAATTATTATTA-T-ATTAA-TAA-TAATAAAAT
* **
48012 AATAATAATAATAAATTAAATCCAAACATATCAAAACTCTT-AAAAAAAATAATAATCTAC-TTT
126 AA-AATAATAATAAATTAAATCCGAACCCATCAAAACTCTTAAAAAAAAATAATAATCTACTTTT
* * * * * * *
48075 TCTTATATCACTGTTATTTGAAACCCGTATCTATATAGAGGGTGAAGAATGAGTTCCATTTTCTT
190 TCTTATGTCACTGTTATTT-AAAACCATGTCGATATAGAGGGTGCAGAATGAGTTCCGTTTTCTT
48140 TCATTAC
254 TCATTAC
48147 TTTTCATACTATCATTTTTAACATATATTTTTAATCATTTTAATTTTCATAATTAATAAATTAAA
1 TTTTCATACTATCATTTTTAACATATATTTTTAATCATTTTAATTTT-ATAATTAATAAATTAAA
48212 ATAGAC--AT-ATAATAAT-A--A-TA--ATT-ATTATTATTA-ATTAATAA-AAT--AATAAAA
65 ATAGACATATAATAATAATAATTATTATTATTAATTATTATTATATTAATAATAATAAAATAAAA
* **
48263 TAATAATAAATTAAATCCAAACATATCAAAACTCTTAAAAAAAAAAGGTAATAATCTAC-TTTTC
130 TAATAATAAATTAAATCCGAACCCATCAAAACTCTT-AAAAAAAAA--TAATAATCTACTTTTTC
*
48327 TTATGTCACTGTTATTTGAAACCATGTCGATATAGAGGGTGCAGAATGAGTTCCGTTTTCTTTCA
192 TTATGTCACTGTTATTTAAAACCATGTCGATATAGAGGGTGCAGAATGAGTTCCGTTTTCTTTCA
48392 TTAC
257 TTAC
48396 TTTTCATACTATCATTTTTAACATATATTTTTAATCATTTTAA-TTT-TAATTAATAAATTAAAA
1 TTTTCATACTATCATTTTTAACATATATTTTTAATCATTTTAATTTTATAATTAATAAATTAAAA
48459 TAGACATATAATAATAATAATAATTATTATTATTATTATTATTATTACTATTAATAAATTAATAA
66 TAGAC--AT-ATAATAATAATAATTATTATTATTA--ATTATTATTA-TATTAAT-AA-TAATAA
* *
48524 AATAAAACAATAATAAATTAAATCCGAACCCATCAAAACTCTT-AAAAAAAATAGTAATCTACTT
123 AATAAAATAATAATAAATTAAATCCGAACCCATCAAAACTCTTAAAAAAAAATAATAATCTACTT
* * * * *
48588 TTTTTTATGTTACTGTTATTTAAAATCCGTGTCTATATAGAGGGTGCAGAATGAGTTTCGTTTTC
188 TTTCTTATGTCACTGTTATTTAAAA-CCATGTCGATATAGAGGGTGCAGAATGAGTTCCGTTTTC
48653 TTTCATTAC
252 TTTCATTAC
* *
48662 TTTTTATACTATTATTTTTAACATATATTTTTAATCATTTTAATTTTCATAATTAATAAATTAAA
1 TTTTCATACTATCATTTTTAACATATATTTTTAATCATTTTAATTTT-ATAATTAATAAATTAAA
48727 ATAGACATATAATAATAATAATTATTATTATTAATTA--ATTA-ATTAATAA-AAT---A-AAAA
65 ATAGACATATAATAATAATAATTATTATTATTAATTATTATTATATTAATAATAATAAAATAAAA
* * * *
48784 TAATAATAAATTAAATCCGAACCCATCAAAACCCTTCACAAAAAGTAATAATCTACTTTT
130 TAATAATAAATTAAATCCGAACCCATCAAAACTCTTAAAAAAAAATAATAATCTACTTTT
48844 CTTGAGTATA
Statistics
Matches: 637, Mismatches: 28, Indels: 74
0.86 0.04 0.10
Matches are distributed among these distances:
246 60 0.09
247 5 0.01
248 11 0.02
249 91 0.14
250 32 0.05
251 5 0.01
252 13 0.02
253 39 0.06
254 21 0.03
255 14 0.02
256 2 0.00
257 5 0.01
258 4 0.01
259 2 0.00
260 7 0.01
261 18 0.03
262 6 0.01
263 6 0.01
264 85 0.13
265 23 0.04
266 122 0.19
267 5 0.01
268 39 0.06
269 22 0.03
ACGTcount: A:0.43, C:0.10, G:0.05, T:0.42
Consensus pattern (260 bp):
TTTTCATACTATCATTTTTAACATATATTTTTAATCATTTTAATTTTATAATTAATAAATTAAAA
TAGACATATAATAATAATAATTATTATTATTAATTATTATTATATTAATAATAATAAAATAAAAT
AATAATAAATTAAATCCGAACCCATCAAAACTCTTAAAAAAAAATAATAATCTACTTTTTCTTAT
GTCACTGTTATTTAAAACCATGTCGATATAGAGGGTGCAGAATGAGTTCCGTTTTCTTTCATTAC
Found at i:52374 original size:21 final size:22
Alignment explanation
Indices: 52330--52377 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
52320 AGAAGGAACG
* **
52330 AAAATTAAATTAATTTTACTTT
1 AAAATTAAATTAATTTAAAGTT
52352 AAAATTAAA-TAATTTAAAGTT
1 AAAATTAAATTAATTTAAAGTT
52373 AAAAT
1 AAAAT
52378 GATTTGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 14 0.61
22 9 0.39
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (22 bp):
AAAATTAAATTAATTTAAAGTT
Found at i:52617 original size:21 final size:21
Alignment explanation
Indices: 52573--52617 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
52563 GAGTAATACA
*
52573 ATATGAATATATAATTGATAT
1 ATATGAATATATAATTAATAT
* * *
52594 ATATGTATTTATAATTAATTT
1 ATATGAATATATAATTAATAT
52615 ATA
1 ATA
52618 CGTACATATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (21 bp):
ATATGAATATATAATTAATAT
Found at i:56628 original size:6 final size:6
Alignment explanation
Indices: 56610--56645 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
56600 CTTTACCTCG
* *
56610 TACTAA TAATAA TACTAA TACTAA TACTAA CACTAA
1 TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA
56646 GAATTCAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.53, C:0.17, G:0.00, T:0.31
Consensus pattern (6 bp):
TACTAA
Found at i:58167 original size:2 final size:2
Alignment explanation
Indices: 58152--58185 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
58142 ACCTAATAGA
58152 AT AT -T AT A- 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
58186 GAATGGATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58206 original size:4 final size:4
Alignment explanation
Indices: 58199--58234 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
58189 TGGATGGATG
58199 GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA
58235 AAAATAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:64060 original size:2 final size:2
Alignment explanation
Indices: 64055--64083 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
64045 TCCCTCTCGC
64055 TA 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 TA T
64084 GTGTGCTTCG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64491 original size:2 final size:2
Alignment explanation
Indices: 64484--64509 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
64474 ATAACTTTTA
64484 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
64510 GTGTGTGTGT
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:66177 original size:22 final size:20
Alignment explanation
Indices: 66152--66194 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 20
66142 TTATATTTTT
*
66152 TAAAAATTATTCATAAAATATA
1 TAAAAATTAAT-ATAAAA-ATA
*
66174 TAAATATTAATATAAAAATA
1 TAAAAATTAATATAAAAATA
66194 T
1 T
66195 TTTTTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 6 0.32
22 9 0.47
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAAATTAATATAAAAATA
Found at i:66850 original size:4 final size:4
Alignment explanation
Indices: 66841--66885 Score: 54
Period size: 4 Copynumber: 11.2 Consensus size: 4
66831 AACTCCTATG
* * * *
66841 ATAT ATAT ATAT ATAT ATAT ATGT ATGT ATAT GTAT ATGT ATAT A
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT A
66886 ATTAATAGAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:66852 original size:6 final size:6
Alignment explanation
Indices: 66841--66885 Score: 54
Period size: 6 Copynumber: 7.5 Consensus size: 6
66831 AACTCCTATG
* * * *
66841 ATATAT ATATAT ATATAT ATATGT ATGTAT ATGTAT ATGTAT ATA
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATA
66886 ATTAATAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (6 bp):
ATATAT
Found at i:66856 original size:10 final size:10
Alignment explanation
Indices: 66841--66885 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
66831 AACTCCTATG
66841 ATATATATAT
1 ATATATATAT
66851 ATATATATAT
1 ATATATATAT
* *
66861 ATGTATGTAT
1 ATATATATAT
* *
66871 ATGTATATGT
1 ATATATATAT
66881 ATATA
1 ATATA
66886 ATTAATAGAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (10 bp):
ATATATATAT
Found at i:68022 original size:22 final size:21
Alignment explanation
Indices: 67986--68030 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
67976 TAAATATTAA
*
67986 TTAATATTGATTTGTTTAATTTT
1 TTAATATTAATTTG--TAATTTT
68009 TTAA-ATTAATTTGTAATTTT
1 TTAATATTAATTTGTAATTTT
68029 TT
1 TT
68031 TATTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 9 0.43
22 8 0.38
23 4 0.19
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (21 bp):
TTAATATTAATTTGTAATTTT
Found at i:68115 original size:10 final size:10
Alignment explanation
Indices: 68102--68153 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
68092 ATAATTTATT
*
68102 ATATTTTTAA
1 ATATATTTAA
68112 ATATATTTAA
1 ATATATTTAA
*
68122 ATATATTTAT
1 ATATATTTAA
*
68132 TTAATATTTAA
1 AT-ATATTTAA
*
68143 AAAT-TTTAA
1 ATATATTTAA
68152 AT
1 AT
68154 TTTAAATATT
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
9 6 0.18
10 21 0.62
11 7 0.21
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATATATTTAA
Found at i:68142 original size:31 final size:29
Alignment explanation
Indices: 68091--68182 Score: 74
Period size: 31 Copynumber: 3.3 Consensus size: 29
68081 ATTAATTAAT
* *
68091 AATAATTTATTATATTTTTAAATATATTTA
1 AATAATTTATTATATATTTAAAAAT-TTTA
68121 AATATATTTATT-TAATATTTAAAAATTTTA
1 AATA-ATTTATTAT-ATATTTAAAAATTTTA
*
68151 AAT--TTTA--A-ATATTT-ATAATTTTA
1 AATAATTTATTATATATTTAAAAATTTTA
68174 AA-AATTTAT
1 AATAATTTAT
68183 ATTTACATAC
Statistics
Matches: 53, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
23 10 0.19
24 10 0.19
27 4 0.08
30 12 0.23
31 17 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (29 bp):
AATAATTTATTATATATTTAAAAATTTTA
Found at i:68181 original size:16 final size:16
Alignment explanation
Indices: 68133--68183 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
68123 TATATTTATT
68133 TAATATTTAAAAATTT-
1 TAAT-TTTAAAAATTTA
*
68149 TAAATTTTAAATATTTA
1 T-AATTTTAAAAATTTA
68166 TAATTTTAAAAATTTA
1 TAATTTTAAAAATTTA
68182 TA
1 TA
68184 TTTACATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
16 27 0.87
17 4 0.13
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAATTTTAAAAATTTA
Found at i:70824 original size:2 final size:2
Alignment explanation
Indices: 70817--70850 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
70807 TTGAAACTAA
70817 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
70851 ATATATATAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:72818 original size:6 final size:6
Alignment explanation
Indices: 72807--72844 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
72797 ATTCAAGCAG
72807 GAAAAA GAAAAA GAAAAA GAAGAAA -AAAAA -AAAAA GAA
1 GAAAAA GAAAAA GAAAAA GAA-AAA GAAAAA GAAAAA GAA
72845 CGGAAATAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 8 0.27
6 19 0.63
7 3 0.10
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:73655 original size:3 final size:3
Alignment explanation
Indices: 73647--73682 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
73637 TTTTGGTTGC
73647 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
73683 GTGTGCCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:82861 original size:2 final size:2
Alignment explanation
Indices: 82854--82895 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
82844 AATGGAATTA
* * *
82854 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AC 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
82896 TATGACTCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:83605 original size:2 final size:2
Alignment explanation
Indices: 83565--83590 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
83555 TACTATTACC
83565 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
83591 CTTCATTTCA
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:92969 original size:20 final size:21
Alignment explanation
Indices: 92941--92979 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
92931 ACTAATTAAT
*
92941 ATATATTT-ATATTTATGTGA
1 ATATATTTAATATTAATGTGA
*
92961 ATATTTTTAATATTAATGT
1 ATATATTTAATATTAATGT
92980 TAAAAAGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.56
Consensus pattern (21 bp):
ATATATTTAATATTAATGTGA
Found at i:93721 original size:2 final size:2
Alignment explanation
Indices: 93714--93739 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
93704 GAATCAATCA
93714 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
93740 GTTTATCAAT
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:97255 original size:15 final size:15
Alignment explanation
Indices: 97231--97260 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
97221 CAAACTCAAC
97231 ATTGGCTTGGGTTGG
1 ATTGGCTTGGGTTGG
*
97246 ATTGGGTTGGGTTGG
1 ATTGGCTTGGGTTGG
97261 GTTGATCATA
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:0.07, C:0.03, G:0.50, T:0.40
Consensus pattern (15 bp):
ATTGGCTTGGGTTGG
Found at i:106431 original size:2 final size:2
Alignment explanation
Indices: 106418--106458 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
106408 AGCAAGAGCA
*
106418 AT AT AT AC 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 AT A
106459 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:112232 original size:4 final size:4
Alignment explanation
Indices: 112223--112253 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
112213 ATTACGTTAG
112223 TGGA TGGA TGGA TGGA TGGA TGGA TGGA TGG
1 TGGA TGGA TGGA TGGA TGGA TGGA TGGA TGG
112254 CTGCGAGGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.23, C:0.00, G:0.52, T:0.26
Consensus pattern (4 bp):
TGGA
Found at i:116924 original size:2 final size:2
Alignment explanation
Indices: 116917--116958 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
116907 CTGCTAATTG
116917 AT 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 AT
116959 TCCTATTCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118555 original size:30 final size:30
Alignment explanation
Indices: 118508--118581 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
118498 TAAACCTACA
118508 TATTTATATTATAATAAT-ATATAATACAATAT
1 TATTTAT-TTATAATAATAAT-TAATA-AATAT
118540 TATTTATTT-TAATAATAATTAATAAATAT
1 TATTTATTTATAATAATAATTAATAAATAT
118569 TAATCTTATTTAT
1 T-AT-TTATTTAT
118582 TATTTTAATG
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
29 6 0.16
30 14 0.37
31 10 0.26
32 8 0.21
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTTATTTATAATAATAATTAATAAATAT
Found at i:118719 original size:20 final size:20
Alignment explanation
Indices: 118691--118735 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
118681 ATTGATTGAA
*
118691 ATAACATTTT-AATAATTATT
1 ATAATATTTTAAATAATTA-T
*
118711 ATAATATTTTAAATATTTAT
1 ATAATATTTTAAATAATTAT
118731 ATAAT
1 ATAAT
118736 TATGTTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
ATAATATTTTAAATAATTAT
Found at i:118900 original size:22 final size:22
Alignment explanation
Indices: 118859--118901 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
118849 TAGCTTAATG
*
118859 ATAATTAATTTTAAATATTTTA
1 ATAATTAATTTTAAACATTTTA
118881 ATAATTAATATTT-AACATTTT
1 ATAATTAAT-TTTAAACATTTT
118902 TGTCAGTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATAATTAATTTTAAACATTTTA
Found at i:119003 original size:20 final size:20
Alignment explanation
Indices: 118971--119023 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
118961 TATATTAATA
118971 TTAAT-ATAA-ATAACA-TT
1 TTAATAATAATATAACATTT
*
118988 TTAATAATAATGATAATATTT
1 TTAATAATAAT-ATAACATTT
*
119009 TTAATATTAATATAA
1 TTAATAATAATATAA
119024 TTAACATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
17 5 0.17
18 4 0.13
20 9 0.30
21 12 0.40
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
TTAATAATAATATAACATTT
Found at i:119275 original size:18 final size:19
Alignment explanation
Indices: 119252--119287 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
119242 ATTTGATTAG
119252 TTTAAATTTAAAA-AATAA
1 TTTAAATTTAAAATAATAA
119270 TTTAAATTTAAAATAATA
1 TTTAAATTTAAAATAATA
119288 TGTACAAATT
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:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTTAAATTTAAAATAATAA
Found at i:126767 original size:2 final size:2
Alignment explanation
Indices: 126756--126786 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
126746 TATTTGTATT
126756 TA TA TA -A 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
126787 AGTAATTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:127626 original size:6 final size:6
Alignment explanation
Indices: 127615--127653 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
127605 AATTGAAAGT
127615 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGA
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGA
127654 CATGCTTATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:127753 original size:3 final size:3
Alignment explanation
Indices: 127745--127780 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
127735 TATTCTCAAA
127745 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
127781 ATATGTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:128061 original size:2 final size:2
Alignment explanation
Indices: 128054--128084 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
128044 AACTCAATTA
*
128054 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
128085 AAATGTTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:128773 original size:2 final size:2
Alignment explanation
Indices: 128766--128791 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
128756 TATAATATGC
128766 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
128792 GAGAGAGAGA
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):
TA
Found at i:129207 original size:32 final size:32
Alignment explanation
Indices: 129171--129280 Score: 90
Period size: 32 Copynumber: 3.6 Consensus size: 32
129161 AATAATTAAA
129171 ATATAATATAATATAAATATATATTAAAATTT
1 ATATAATATAATATAAATATATATTAAAATTT
* * * * *
129203 ATATAATATAA-ATTATTAACATATCAAAATTA
1 ATATAATATAATATAAAT-ATATATTAAAATTT
*
129235 ATATAA-AT--TATAAA-ATATGA-TAAAATAT
1 ATATAATATAATATAAATATAT-ATTAAAATTT
*
129263 ATA-AAAATAATATAAATA
1 ATATAATATAATATAAATA
129281 CAAAACTTAT
Statistics
Matches: 60, Mismatches: 11, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
27 2 0.03
28 13 0.22
29 1 0.02
30 9 0.15
31 7 0.12
32 28 0.47
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (32 bp):
ATATAATATAATATAAATATATATTAAAATTT
Found at i:129213 original size:27 final size:27
Alignment explanation
Indices: 129155--129263 Score: 97
Period size: 27 Copynumber: 4.2 Consensus size: 27
129145 AATATTATGT
129155 ATATAAA-ATAATTAAAATATAATATA
1 ATATAAATATAATTAAAATATAATATA
*
129181 ATATAAATATATATTAAAAT-TTATATA
1 ATATAAATATA-ATTAAAATATAATATA
* *
129208 ATATAAAT-T-ATTAACATATCAAAATTA
1 ATATAAATATAATTAAAATAT-AATA-TA
* *
129235 ATATAAAT-T-A-TAAAATATGATAAA
1 ATATAAATATAATTAAAATATAATATA
129259 ATATA
1 ATATA
129264 TAAAAATAAT
Statistics
Matches: 70, Mismatches: 8, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
24 13 0.19
25 3 0.04
26 17 0.24
27 29 0.41
28 8 0.11
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.38
Consensus pattern (27 bp):
ATATAAATATAATTAAAATATAATATA
Found at i:133029 original size:2 final size:2
Alignment explanation
Indices: 133022--133049 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
133012 TAGGCAAGGT
133022 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
133050 GTGTGTACTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:133782 original size:16 final size:15
Alignment explanation
Indices: 133758--133792 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
133748 ATCGTTAAAA
133758 TTTAGTTTATTATTCT
1 TTTAGTTTATTATT-T
*
133774 TTTATTTTATTATTT
1 TTTAGTTTATTATTT
133789 TTTA
1 TTTA
133793 ACTAAAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTAGTTTATTATTT
Found at i:137976 original size:31 final size:28
Alignment explanation
Indices: 137934--137992 Score: 66
Period size: 30 Copynumber: 2.0 Consensus size: 28
137924 ACACAACACG
*
137934 ATTATATTGATATAA-ATTAATAAAAAATA
1 ATTATATTGATA-AATA-TAAAAAAAAATA
137963 ATTATAATATGATAAATATAAAAAAAAATA
1 ATTAT-AT-TGATAAATATAAAAAAAAATA
137993 CATAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
29 5 0.19
30 15 0.58
31 6 0.23
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (28 bp):
ATTATATTGATAAATATAAAAAAAAATA
Found at i:138004 original size:13 final size:13
Alignment explanation
Indices: 137974--138016 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
137964 TTATAATATG
*
137974 ATAAATATA-AAA
1 ATAAATACATAAA
*
137986 AAAAATACATAAA
1 ATAAATACATAAA
137999 ATAAATACATAAA
1 ATAAATACATAAA
138012 ATAAA
1 ATAAA
138017 AATTAAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 7 0.26
13 20 0.74
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (13 bp):
ATAAATACATAAA
Found at i:138428 original size:2 final size:2
Alignment explanation
Indices: 138423--138447 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
138413 ATATATATAT
138423 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
138448 ATCTGTTAAT
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:138806 original size:2 final size:2
Alignment explanation
Indices: 138801--138829 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
138791 TGCATGTATG
138801 TA 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 TA T
138830 CCCTAAAGGC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:139512 original size:2 final size:2
Alignment explanation
Indices: 139505--139544 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
139495 TTTGAGATCA
139505 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
139545 GAAGCAAAGC
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:141870 original size:2 final size:2
Alignment explanation
Indices: 141863--141905 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
141853 ATTTTTACTT
* *
141863 TA TA TA TA TA TA TA CA TA TA TA CA 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 TA TA TA TA
141905 T
1 T
141906 GTATTTCCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:145387 original size:2 final size:2
Alignment explanation
Indices: 145380--145410 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
145370 ATTTCAATCA
145380 AG AG AG 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 AG AG AG A
145411 AAGGAAAGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:149917 original size:2 final size:2
Alignment explanation
Indices: 149910--149945 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
149900 TAAACATTTA
149910 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
149946 CTATCACAGC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:154676 original size:6 final size:6
Alignment explanation
Indices: 154667--154702 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
154657 AGAAGGTCGT
*
154667 GAATTG GAATTG GAATTG GAATTG AAATTAG GAATT
1 GAATTG GAATTG GAATTG GAATTG GAATT-G GAATT
154703 ATATGAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (6 bp):
GAATTG
Found at i:154746 original size:5 final size:5
Alignment explanation
Indices: 154736--154765 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
154726 GGGCACAAGA
154736 CTGAT CTGAT CTGAT CTGAT CTGAT CTGAT
1 CTGAT CTGAT CTGAT CTGAT CTGAT CTGAT
154766 AATTGAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
CTGAT
Found at i:157514 original size:14 final size:15
Alignment explanation
Indices: 157488--157516 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
157478 AATTATAACA
157488 TAATAAATATATTTT
1 TAATAAATATATTTT
157503 TAATAAAT-TATTTT
1 TAATAAATATATTTT
157517 ATAGTCGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATAAATATATTTT
Found at i:158383 original size:31 final size:30
Alignment explanation
Indices: 158348--158517 Score: 151
Period size: 31 Copynumber: 5.5 Consensus size: 30
158338 TCACCAGTTG
***
158348 AGAATAGTGATTTTTGCCAAACCACCGGATA
1 AGAATAGT-ATTTTTGCCGTGCCACCGGATA
* * *
158379 AGAATAGTAGTTTTCGTCGTGCCATCGGATA
1 AGAATAGTA-TTTTTGCCGTGCCACCGGATA
* * *
158410 AGAATAGTAGTTTTCGCAGTGCCATCGGATA
1 AGAATAGTA-TTTTTGCCGTGCCACCGGATA
* * * *
158441 AAAATAGTAGTTTTTGTCGTGCTACCAGATA
1 AGAATAGTA-TTTTTGCCGTGCCACCGGATA
* *
158472 AGAATAGTGATTTTTACCGTGCCACCGGATT
1 AGAATAGT-ATTTTTGCCGTGCCACCGGATA
158503 AGAATAGTGATTTTT
1 AGAATAGT-ATTTTT
158518 ATTCTAACCT
Statistics
Matches: 116, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
30 1 0.01
31 114 0.98
32 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.32
Consensus pattern (30 bp):
AGAATAGTATTTTTGCCGTGCCACCGGATA
Found at i:158517 original size:62 final size:61
Alignment explanation
Indices: 158339--158510 Score: 184
Period size: 62 Copynumber: 2.8 Consensus size: 61
158329 CAAACTGTGT
* * *** *
158339 CACCAGTTGAGAATAGTGATTTTTGCCAAACCACCGGATAAGAATAGTAGTTTTCGTCGTGC
1 CACCAGATAAGAATAGTGATTTTT-CCGTGCCACCGGATAAGAATAGTAGTTTTTGTCGTGC
* * * * *
158401 CATCGGATAAGAATAGT-AGTTTTCGCAGTGCCATCGGATAAAAATAGTAGTTTTTGTCGTGC
1 CACCAGATAAGAATAGTGATTTTTC-C-GTGCCACCGGATAAGAATAGTAGTTTTTGTCGTGC
* *
158463 TACCAGATAAGAATAGTGATTTTTACCGTGCCACCGGATTAGAATAGT
1 CACCAGATAAGAATAGTGATTTTT-CCGTGCCACCGGATAAGAATAGT
158511 GATTTTTATT
Statistics
Matches: 88, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
60 1 0.01
61 6 0.07
62 74 0.84
63 6 0.07
64 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (61 bp):
CACCAGATAAGAATAGTGATTTTTCCGTGCCACCGGATAAGAATAGTAGTTTTTGTCGTGC
Found at i:160021 original size:2 final size:2
Alignment explanation
Indices: 160016--160042 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
160006 TTCTTTTGTT
160016 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
160043 TCTCTAAGAT
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:160172 original size:2 final size:2
Alignment explanation
Indices: 160165--160201 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
160155 AAAATCACAA
160165 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 A
160202 AAAGTGTCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:162098 original size:2 final size:2
Alignment explanation
Indices: 162093--162119 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
162083 TATATATATA
162093 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
162120 AGGAAAAGCA
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:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:162996 original size:2 final size:2
Alignment explanation
Indices: 162989--163013 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
162979 GCACTTGTTT
162989 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
163014 TTCTTAATCA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:167315 original size:5 final size:5
Alignment explanation
Indices: 167305--167340 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
167295 ATTATCCAAC
167305 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
167341 CACTTCCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:168645 original size:27 final size:27
Alignment explanation
Indices: 168615--168674 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
168605 ACTTCTAATA
*
168615 ATTAAGAGTTTTATCCCTTAATTATAT
1 ATTAAGAGTTATATCCCTTAATTATAT
* ** * *
168642 ATTAAAAGTTATATCTTTTGATTATTT
1 ATTAAGAGTTATATCCCTTAATTATAT
168669 ATTAAG
1 ATTAAG
168675 GCTGTAATTG
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.07, G:0.08, T:0.50
Consensus pattern (27 bp):
ATTAAGAGTTATATCCCTTAATTATAT
Found at i:168947 original size:5 final size:5
Alignment explanation
Indices: 168939--168963 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
168929 ATCATTTACG
168939 TAATT TAATT TAATT TAATT TAATT
1 TAATT TAATT TAATT TAATT TAATT
168964 AAAAGAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TAATT
Found at i:170915 original size:1 final size:1
Alignment explanation
Indices: 170909--170938 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
170899 TTCGTGTTTG
*
170909 TTTTTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
170939 GGGGTCCCCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:174114 original size:2 final size:2
Alignment explanation
Indices: 174107--174133 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
174097 GTAATTACCC
174107 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
174134 TCAAATCAAT
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:176420 original size:13 final size:13
Alignment explanation
Indices: 176402--176426 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
176392 TCATGGAACC
176402 AAAAAATAAAAAT
1 AAAAAATAAAAAT
176415 AAAAAATAAAAA
1 AAAAAATAAAAA
176427 ATCGACATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:177350 original size:2 final size:2
Alignment explanation
Indices: 177309--177337 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
177299 AACTTAGACG
177309 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 A
177338 CACAAAATAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:186303 original size:19 final size:19
Alignment explanation
Indices: 186279--186315 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
186269 TTGTGACCAT
186279 AATAAAGTGCATGTGATGA
1 AATAAAGTGCATGTGATGA
186298 AATAAAGTGCATGTGATG
1 AATAAAGTGCATGTGATG
186316 TGAATATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.05, G:0.27, T:0.27
Consensus pattern (19 bp):
AATAAAGTGCATGTGATGA
Found at i:186721 original size:2 final size:2
Alignment explanation
Indices: 186672--186706 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
186662 TAGTGATGTA
186672 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
186707 ACATGCATGG
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:189979 original size:2 final size:2
Alignment explanation
Indices: 189972--189999 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
189962 TGATCCCTCC
189972 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
190000 TTCGGAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:192936 original size:6 final size:6
Alignment explanation
Indices: 192925--192950 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
192915 GAGGACATGA
192925 AAGAGG AAGAGG AAGAGG AAGAGG AA
1 AAGAGG AAGAGG AAGAGG AAGAGG AA
192951 CTGGGGTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.46, T:0.00
Consensus pattern (6 bp):
AAGAGG
Found at i:199129 original size:2 final size:2
Alignment explanation
Indices: 199124--199156 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
199114 TCTCTCTCGC
*
199124 TA TA TA TA TA TA TA TA TA TA TG TA TA T- TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
199157 ATTTCATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:200281 original size:3 final size:3
Alignment explanation
Indices: 200273--200326 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
200263 TTGCCCTTTA
*
200273 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
200321 ATT ATT
1 ATT ATT
200327 TTACTGAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:201566 original size:2 final size:2
Alignment explanation
Indices: 201561--201585 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
201551 ACACACACAC
201561 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
201586 GTGTGTAGAT
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:213821 original size:2 final size:2
Alignment explanation
Indices: 213814--213852 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
213804 AGTTTCATTA
213814 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
213853 GGTCAAAATA
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:215073 original size:2 final size:2
Alignment explanation
Indices: 215066--215093 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
215056 TCTTTAAGAA
215066 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
215094 CCTTCAAACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:218251 original size:2 final size:2
Alignment explanation
Indices: 218244--218275 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
218234 AATTCCTTAA
218244 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
218276 CTTCTAGAGC
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:221340 original size:40 final size:40
Alignment explanation
Indices: 221285--221365 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
221275 ATCTTTCATT
221285 ATTGCTACTAGATTTTCCTTACTTTTTTTGTGGAAAGATG
1 ATTGCTACTAGATTTTCCTTACTTTTTTTGTGGAAAGATG
221325 ATTGCTACTAGATTTTCCTTACTTTTTTTGTGGAAAGATG
1 ATTGCTACTAGATTTTCCTTACTTTTTTTGTGGAAAGATG
221365 A
1 A
221366 AATTAAGAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (40 bp):
ATTGCTACTAGATTTTCCTTACTTTTTTTGTGGAAAGATG
Found at i:221839 original size:6 final size:6
Alignment explanation
Indices: 221824--221853 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
221814 AGGGGAATCA
*
221824 TCTGAT TCTGAA TCTGAT TCTGAT TCTGAT
1 TCTGAT TCTGAT TCTGAT TCTGAT TCTGAT
221854 CAGTGATCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.47
Consensus pattern (6 bp):
TCTGAT
Found at i:223269 original size:133 final size:134
Alignment explanation
Indices: 223031--223300 Score: 461
Period size: 133 Copynumber: 2.0 Consensus size: 134
223021 CTTATTTTGG
* *
223031 CAATATGCTATAATATAATTAAACTTTATTTATTTTGCTGCTGTTATTGGTATTATAGGGCTGTG
1 CAATATGCAATAATATAATTAAACTTTATTTATTTTGCTGCTGTTATTGGTATTATAGGGCTGCG
* *
223096 GCTGGCTGTTGTCACAATTGATACTTGCTTGATGTTTCGTGAACTTTGTATTATT-TTGTTGAAG
66 GCTGGCTGTTGTCACAATTGACACTTGCTTGATGTTTCGTGAACTTTGTATCATTCTTGTTGAAG
223160 CTTT
131 CTTT
* *
223164 CAATATGCAATAATATAATTTATCTTTATTTATTTTGCTGCTGTTATTGGTATTATAGGGCTGCG
1 CAATATGCAATAATATAATTAAACTTTATTTATTTTGCTGCTGTTATTGGTATTATAGGGCTGCG
* *
223229 GCTGGCTGTTGTCACAATTGACCCTTGCTTGATGTTTCGTGTACTTTGTATCATTCTTGTTGAAG
66 GCTGGCTGTTGTCACAATTGACACTTGCTTGATGTTTCGTGAACTTTGTATCATTCTTGTTGAAG
223294 CTTT
131 CTTT
223298 CAA
1 CAA
223301 GAAACCAGGG
Statistics
Matches: 128, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
133 112 0.88
134 16 0.12
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (134 bp):
CAATATGCAATAATATAATTAAACTTTATTTATTTTGCTGCTGTTATTGGTATTATAGGGCTGCG
GCTGGCTGTTGTCACAATTGACACTTGCTTGATGTTTCGTGAACTTTGTATCATTCTTGTTGAAG
CTTT
Found at i:223707 original size:2 final size:2
Alignment explanation
Indices: 223700--223754 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
223690 GAGTTGATGG
*
223700 TC TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
223742 TC TC TC TC TC TC T
1 TC TC TC TC TC TC T
223755 TTGATCCATA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:231397 original size:2 final size:2
Alignment explanation
Indices: 231390--231421 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
231380 ACACATTTCC
231390 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
231422 GCATACAATG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:233756 original size:10 final size:10
Alignment explanation
Indices: 233725--233758 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
233715 AAATTATTTA
233725 ATATATAAAT
1 ATATATAAAT
*
233735 ACATATAAAT
1 ATATATAAAT
*
233745 ATATATATAT
1 ATATATAAAT
233755 ATAT
1 ATAT
233759 TAAGATGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (10 bp):
ATATATAAAT
Found at i:234984 original size:2 final size:2
Alignment explanation
Indices: 234977--235012 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
234967 CAATGGCCAA
234977 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
235013 GGCAGTCAGT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:238459 original size:2 final size:2
Alignment explanation
Indices: 238452--238483 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
238442 ACAGCTGTAA
*
238452 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
238484 TTGCCTTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:238781 original size:26 final size:24
Alignment explanation
Indices: 238742--238792 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
238732 GAGTTTAAGA
**
238742 TTATTATTTAATAATTTTAATATT
1 TTATTATTTAATAATAATAATATT
238766 TTATTATAATTAATAATAATAATATT
1 TTATTAT--TTAATAATAATAATATT
238792 T
1 T
238793 ATAAATATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
26 16 0.70
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTATTTAATAATAATAATATT
Found at i:239918 original size:25 final size:25
Alignment explanation
Indices: 239881--239930 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
239871 GAAAAATTAT
239881 TGTTGAAGATGAAGAAGTGGGGATA
1 TGTTGAAGATGAAGAAGTGGGGATA
* *
239906 TGTTGAAGGTGAAGAAGTGGTGATA
1 TGTTGAAGATGAAGAAGTGGGGATA
239931 AGCAAGCAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.40, T:0.26
Consensus pattern (25 bp):
TGTTGAAGATGAAGAAGTGGGGATA
Found at i:240364 original size:2 final size:2
Alignment explanation
Indices: 240357--240389 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
240347 AAAAGGAACT
240357 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
240390 TTTTTCTGGG
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:241094 original size:16 final size:18
Alignment explanation
Indices: 241075--241118 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
241065 TTAAAATTTT
241075 TTATTATTAA-TAT-TAA
1 TTATTATTAATTATATAA
*
241091 TTATAATTAATTATAATAA
1 TTATTATTAATTAT-ATAA
241110 TTATTATTA
1 TTATTATTA
241119 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 9 0.39
17 3 0.13
19 11 0.48
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATTATTAATTATATAA
Found at i:243368 original size:2 final size:2
Alignment explanation
Indices: 243361--243390 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
243351 ATTCCCTTGT
243361 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
243391 TTCATCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:243944 original size:2 final size:2
Alignment explanation
Indices: 243937--243971 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
243927 CCATTCCCCA
243937 CT CT CT 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 CT CT CT C
243972 CAACTGGACT
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:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:247133 original size:6 final size:6
Alignment explanation
Indices: 247124--247155 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
247114 TGCAGCTGAC
*
247124 TGGTTT TGGTTT TGGTTT TGGTTT TAGTTT TG
1 TGGTTT TGGTTT TGGTTT TGGTTT TGGTTT TG
247156 ATAAGAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.00, G:0.31, T:0.66
Consensus pattern (6 bp):
TGGTTT
Found at i:247421 original size:2 final size:2
Alignment explanation
Indices: 247416--247442 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
247406 ACTATATACA
247416 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 T
247443 TCCTCTCCCC
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:247685 original size:2 final size:2
Alignment explanation
Indices: 247678--247719 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
247668 AAAGACTGAC
247678 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG ATG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A-G AG A
247720 AAGAAAACCC
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (2 bp):
AG
Found at i:247819 original size:2 final size:2
Alignment explanation
Indices: 247812--247838 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
247802 AGGTAATTAA
247812 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
247839 ATATATATAT
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:248113 original size:30 final size:28
Alignment explanation
Indices: 248052--248116 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 28
248042 AATTATATAC
* *
248052 AATTTCATGGTTAATACGTCTAAAAAGT
1 AATTTCATGCTTAATACGTCTAAAAAAT
248080 AATTTCATGCTTAATACATGT-TGAAAAAAT
1 AATTTCATGCTTAATAC--GTCT-AAAAAAT
248110 AATTTCA
1 AATTTCA
248117 GAGAATACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 16 0.50
29 1 0.03
30 15 0.47
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.37
Consensus pattern (28 bp):
AATTTCATGCTTAATACGTCTAAAAAAT
Found at i:251393 original size:14 final size:13
Alignment explanation
Indices: 251376--251418 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
251366 TATTTTTAGT
251376 GTTTAGAGTTTAGA
1 GTTTAGAGTTTA-A
* *
251390 GTTTAAAATTTAA
1 GTTTAGAGTTTAA
*
251403 GATTAGAGTTTAA
1 GTTTAGAGTTTAA
251416 GTT
1 GTT
251419 CAAACAAAAT
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
13 13 0.57
14 10 0.43
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (13 bp):
GTTTAGAGTTTAA
Done.