Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000058.1 Hibiscus syriacus cultivar Beakdansim tig00000088_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 181416
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:865 original size:14 final size:13
Alignment explanation
Indices: 786--852 Score: 55
Period size: 14 Copynumber: 4.9 Consensus size: 13
776 TTATGCAAAG
*
786 TGCAAATGCAAAAA
1 TGCAAATG-TAAAA
*
800 TGAAAATGT-AAA
1 TGCAAATGTAAAA
* *
812 TACAAACGTAAAAA
1 TGCAAATGT-AAAA
826 TGCAAAAATGTAAAA
1 TGC--AAATGTAAAA
841 TGCAAATGTAAA
1 TGCAAATGTAAA
853 TATGTGAATG
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
12 9 0.21
13 9 0.21
14 12 0.29
15 7 0.17
16 5 0.12
ACGTcount: A:0.58, C:0.09, G:0.13, T:0.19
Consensus pattern (13 bp):
TGCAAATGTAAAA
Found at i:2960 original size:2 final size:2
Alignment explanation
Indices: 2953--2977 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2943 TCTAAGGAAG
2953 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
2978 GAGTTTTGTA
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:3259 original size:16 final size:15
Alignment explanation
Indices: 3233--3277 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
3223 AAATATATTT
*
3233 ATATAATTAAAAATA
1 ATATAAATAAAAATA
3248 ATGATAAATAAAAATA
1 AT-ATAAATAAAAATA
3264 ATA-AAATAATAAAT
1 ATATAAATAA-AAAT
3278 TAGATATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 6 0.22
15 7 0.26
16 14 0.52
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (15 bp):
ATATAAATAAAAATA
Found at i:9561 original size:24 final size:24
Alignment explanation
Indices: 9534--9579 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
9524 GGAGAAGACA
*
9534 CGCCACCAAAGAAACAAGAAGATG
1 CGCCACCAAAGAAACAAAAAGATG
9558 CGCCACCAAAGAAACAAAAAGA
1 CGCCACCAAAGAAACAAAAAGA
9580 CGAATCTTCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.54, C:0.26, G:0.17, T:0.02
Consensus pattern (24 bp):
CGCCACCAAAGAAACAAAAAGATG
Found at i:13286 original size:24 final size:24
Alignment explanation
Indices: 13217--13286 Score: 56
Period size: 24 Copynumber: 3.0 Consensus size: 24
13207 TGGTCCTTAT
* **
13217 GGACAAATTTTATATGGCACTTCG
1 GGACAAATTCTACGTGGCACTTCG
* *
13241 GTG-C-ATTTCTACGCGGTC-CTTCG
1 G-GACAAATTCTACGTGG-CACTTCG
13264 GGACAAATTCTACGTGGCACTTC
1 GGACAAATTCTACGTGGCACTTC
13287 AGATCAATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 10
0.67 0.14 0.20
Matches are distributed among these distances:
22 1 0.03
23 15 0.44
24 17 0.50
25 1 0.03
ACGTcount: A:0.21, C:0.24, G:0.23, T:0.31
Consensus pattern (24 bp):
GGACAAATTCTACGTGGCACTTCG
Found at i:14480 original size:43 final size:43
Alignment explanation
Indices: 14407--14489 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
14397 TATAAATTGT
* * * *
14407 TATTTTGATTAAATAAATTTGTCACAATTTTTTATTTTGACAA
1 TATTATGATGAAATAAATTTGACACAATTTTTTACTTTGACAA
**
14450 TATTATGATGAAATAAATTTGACATGATTTTTTACTTTGA
1 TATTATGATGAAATAAATTTGACACAATTTTTTACTTTGA
14490 TTAAATTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (43 bp):
TATTATGATGAAATAAATTTGACACAATTTTTTACTTTGACAA
Found at i:17005 original size:3 final size:3
Alignment explanation
Indices: 16997--17072 Score: 77
Period size: 3 Copynumber: 25.3 Consensus size: 3
16987 GGTCTACAAA
* *
16997 AAT AAT AAT AAT AA- AA- AAT AAT AAT AAT AAA AAT AAT AA- AAT ATT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
17042 AAT AAT AGT AAT AAT AAAT AAAT AAAT AAT A
1 AAT AAT AAT AAT AAT -AAT -AAT -AAT AAT A
17073 TTTTTTAAAC
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
2 6 0.09
3 47 0.73
4 11 0.17
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:17044 original size:23 final size:24
Alignment explanation
Indices: 16998--17072 Score: 82
Period size: 23 Copynumber: 3.1 Consensus size: 24
16988 GTCTACAAAA
16998 ATAATAATAATAAAAAATAATAATA
1 ATAATAATAAT-AAAAATAATAATA
* *
17023 ATAAAAATAAT-AAAATATTAATA
1 ATAATAATAATAAAAATAATAATA
* *
17046 ATAGTAATAATAAATA-AATAAATA
1 ATAATAATAATAAAAATAAT-AATA
17070 ATA
1 ATA
17073 TTTTTTAAAC
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
23 22 0.52
24 10 0.24
25 10 0.24
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.29
Consensus pattern (24 bp):
ATAATAATAATAAAAATAATAATA
Found at i:17441 original size:31 final size:34
Alignment explanation
Indices: 17397--17480 Score: 104
Period size: 31 Copynumber: 2.6 Consensus size: 34
17387 CTCGAAGGTA
*
17397 TTTGTGTTTCAAGAGAAAC-ATTTTCAAAGG-TTT
1 TTTGTGTTCCAAGAGAAACGA-TTTCAAAGGATTT
*
17430 TTT-T-TTCCAAGAAAAACGATTTCAAAGGATTT
1 TTTGTGTTCCAAGAGAAACGATTTCAAAGGATTT
*
17462 TTTGTGTTTCAAGAGAAAC
1 TTTGTGTTCCAAGAGAAAC
17481 TGTGTCAAGG
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
31 20 0.47
32 8 0.19
33 4 0.09
34 11 0.26
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (34 bp):
TTTGTGTTCCAAGAGAAACGATTTCAAAGGATTT
Found at i:17594 original size:103 final size:100
Alignment explanation
Indices: 17466--17729 Score: 325
Period size: 103 Copynumber: 2.6 Consensus size: 100
17456 GGATTTTTTG
* **
17466 TGTTTCAAGAGAAACTGTGTCAAGGGAGGTAAAATTTATTTCAAGAGAAACATGTTCAAAGATTG
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGAGAAAC-TGTTCAAAGATT-
17531 GTGTTTCAAGAGAAGA-AGTCTCAAGAGAGACAAAACTT
64 GTGTTTCAAGAGAA-ACAGTCTCAAGAGAGACAAAA-TT
* * *
17569 TGTTTCAAGGGAAACTGTCTTAAGGGAGACAAAATTTTGTTTCAAGAGAAACT-TATACAAAGAT
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTTATTTCAAGAGAAACTGT-T-CAAAGAT
* * *
17633 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
63 TGTGTTTCAAGAGAAACAGTCTCAAGAGAGACAAAATT
* * * *
17671 TGTTTCAAGTGAAACTTTCTCAAGAGAGACAAAATTTATTTAAAGAGAAACTGTCTCAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGAGAAACTGT-TCAA
17730 GAGAGACAAA
Statistics
Matches: 140, Mismatches: 16, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
101 19 0.14
102 36 0.26
103 61 0.44
104 24 0.17
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.28
Consensus pattern (100 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTATTTCAAGAGAAACTGTTCAAAGATTGT
GTTTCAAGAGAAACAGTCTCAAGAGAGACAAAATT
Found at i:17674 original size:36 final size:36
Alignment explanation
Indices: 17633--18036 Score: 315
Period size: 36 Copynumber: 11.0 Consensus size: 36
17623 ATACAAAGAT
*
17633 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
17669 TTTGTTTCAAGTGAAACTTTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
17705 TTTATTTAAAGAGAAACTGTCTCAAGAGAGACAAAGATAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC------AAAA
* * * *
17747 TTTGTCTGAAGAGAAACTGTCTCGAGAGAGATAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * * * *
17783 CTTAGTTCCAAAAGATATTGTCTCAAGGGAGACGAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
17820 TTTGTTT-AATGTA-AAACATAT-TC-A-A-AG----AT
1 TTTGTTTCAA-G-AGAAAC-TGTCTCAAGAGAGACAAAA
*
17849 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
17885 TTTGTTTTAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* *
17921 TTTGTTTTAAGAGAAATTGTCTCAAGAGAGACAAAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTC-A-AGAG----AGACAAAA
17963 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* ** * * * *
17999 CCTAATTCCAAAAGACACTGTCTCAAGGGAGACAAAA
1 -TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
18036 T
1 T
18037 CTGGCTTGAA
Statistics
Matches: 295, Mismatches: 46, Indels: 54
0.75 0.12 0.14
Matches are distributed among these distances:
28 2 0.01
29 15 0.05
30 3 0.01
31 1 0.00
32 2 0.01
33 2 0.01
35 3 0.01
36 140 0.47
37 58 0.20
38 4 0.01
40 4 0.01
41 1 0.00
42 60 0.20
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:17864 original size:216 final size:216
Alignment explanation
Indices: 17548--18036 Score: 721
Period size: 216 Copynumber: 2.3 Consensus size: 216
17538 AAGAGAAGAA
* * ** *
17548 GTCTCAAGAGAGACAAAACTTTGTTTCAAGGGAAACTGTCTTAAGGGAGACAAAATTTTGTTTCA
1 GTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAA-TTTGTTTCA
*
17613 AGAGAAACTTATACAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCA
65 AGAGAAACATATACAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCA
* * *
17678 AGTGAAACTTTCTCAAGAGAGACAAAATTTATTTAAAGAGAAACTGTCTCAAGAGAGACAAAGAT
130 AGGGAAACTGTCTCAAGAGAGACAAAATTTATTTAAAGAGAAACTGTCTCAAGAGAGACAAAGAC
*
17743 AAAATTTGTCTGAAGAGAAACT
195 AAAATTTGTCTCAAGAGAAACT
* * * * *
17765 GTCTCGAGAGAGATAAAACTTAGTTCCAAAAGATATTGTCTCAAGGGAGACGAAATTTGTTT-AA
1 GTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA
* *
17829 TGTA-AAACATATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTT
66 -G-AGAAACATATACAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTC
* * *
17893 AAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAATTGTCTCAAGAGAGACAAAGA
129 AAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTAAAGAGAAACTGTCTCAAGAGAGACAAAGA
*
17958 CAAAATTTGTTTCAAGAGAAACT
194 CAAAATTTGTCTCAAGAGAAACT
* * *
17981 GTCTCAAGAGAGACAAAACCTAATTCCAAAAGACACTGTCTCAAGGGAGACAAAAT
1 GTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAAT
18037 CTGGCTTGAA
Statistics
Matches: 242, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
215 2 0.01
216 194 0.80
217 46 0.19
ACGTcount: A:0.41, C:0.13, G:0.19, T:0.26
Consensus pattern (216 bp):
GTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAA
GAGAAACATATACAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAA
GGGAAACTGTCTCAAGAGAGACAAAATTTATTTAAAGAGAAACTGTCTCAAGAGAGACAAAGACA
AAATTTGTCTCAAGAGAAACT
Found at i:17934 original size:21 final size:21
Alignment explanation
Indices: 17872--17934 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
17862 AAACTGTCTC
17872 AAGAGAGACAAAATTTGTTTT
1 AAGAGAGACAAAATTTGTTTT
* * *
17893 AAG-G-G---AAA-CTGTCTC
1 AAGAGAGACAAAATTTGTTTT
17908 AAGAGAGACAAAATTTGTTTT
1 AAGAGAGACAAAATTTGTTTT
17929 AAGAGA
1 AAGAGA
17935 AATTGTCTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
15 7 0.23
16 4 0.13
17 1 0.03
19 1 0.03
20 4 0.13
21 13 0.43
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (21 bp):
AAGAGAGACAAAATTTGTTTT
Found at i:17975 original size:42 final size:42
Alignment explanation
Indices: 17877--17997 Score: 173
Period size: 42 Copynumber: 3.0 Consensus size: 42
17867 GTCTCAAGAG
*
17877 AGACAAAATTTGTTTTAAGGGAAACTGTCTC-A-AGAG----
1 AGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAA
*
17913 AGACAAAATTTGTTTTAAGAGAAATTGTCTCAAGAGAGACAA
1 AGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAA
*
17955 AGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
1 AGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAA
17997 A
1 A
17998 ACCTAATTCC
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
36 29 0.39
37 1 0.01
38 4 0.05
42 41 0.55
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.25
Consensus pattern (42 bp):
AGACAAAATTTGTTTTAAGAGAAACTGTCTCAAGAGAGACAA
Found at i:18459 original size:32 final size:32
Alignment explanation
Indices: 18404--18482 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
18394 CGTATCAGGG
* * * *
18404 TGTTGAATCCCCGAAGATGCCCCAACATTCGA
1 TGTTGAATCTCCAAAAATACCCCAACATTCGA
*
18436 TGTTGAATCTCCAAAAATACCCCAACATTTGA
1 TGTTGAATCTCCAAAAATACCCCAACATTCGA
*
18468 TGTTGAATCTTCAAA
1 TGTTGAATCTCCAAA
18483 GGTGCCCCCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTTGAATCTCCAAAAATACCCCAACATTCGA
Found at i:19592 original size:15 final size:16
Alignment explanation
Indices: 19564--19609 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
19554 TTTCTTCACT
19564 TTTTC-CTTTGTTTT-
1 TTTTCTCTTTGTTTTA
19578 TGTTTCTCTTT-TTTTA
1 T-TTTCTCTTTGTTTTA
19594 TTTTCTCTTTGCTTTT
1 TTTTCTCTTTG-TTTT
19610 TCTTTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 17 0.63
16 5 0.19
17 4 0.15
ACGTcount: A:0.02, C:0.15, G:0.07, T:0.76
Consensus pattern (16 bp):
TTTTCTCTTTGTTTTA
Found at i:19621 original size:31 final size:30
Alignment explanation
Indices: 19564--19629 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 30
19554 TTTCTTCACT
*
19564 TTTTCCTTTGTTTTTGTTTCTCTTTTTTTA
1 TTTTCCTTTGTTTTTCTTTCTCTTTTTTTA
* * *
19594 TTTTCTCTTTGCTTTTTCTTTGTTTTTTTTTC
1 TTTTC-CTTTG-TTTTTCTTTCTCTTTTTTTA
19626 TTTT
1 TTTT
19630 TTGTTCTAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 5 0.17
31 5 0.17
32 20 0.67
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.79
Consensus pattern (30 bp):
TTTTCCTTTGTTTTTCTTTCTCTTTTTTTA
Found at i:19628 original size:25 final size:25
Alignment explanation
Indices: 19576--19626 Score: 66
Period size: 27 Copynumber: 2.0 Consensus size: 25
19566 TTCCTTTGTT
19576 TTTGTTTCTCTTTTTTTATTTTCTC
1 TTTGTTTCTCTTTTTTTATTTTCTC
* *
19601 TTTGCTTTTTCTTTGTTTTTTTTTCT
1 TTTG-TTTCTCTTT-TTTTATTTTCT
19627 TTTTTGTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.18
26 8 0.36
27 10 0.45
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.78
Consensus pattern (25 bp):
TTTGTTTCTCTTTTTTTATTTTCTC
Found at i:21598 original size:19 final size:20
Alignment explanation
Indices: 21561--21597 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
21551 GCAAATAATA
21561 AAAATAAAATGAAAGAAAAC
1 AAAATAAAATGAAAGAAAAC
21581 AAAA-AAAATG-AAGAAAA
1 AAAATAAAATGAAAGAAAA
21598 AAGTTAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 6 0.35
20 4 0.24
ACGTcount: A:0.78, C:0.03, G:0.11, T:0.08
Consensus pattern (20 bp):
AAAATAAAATGAAAGAAAAC
Found at i:21632 original size:12 final size:12
Alignment explanation
Indices: 21615--21682 Score: 64
Period size: 12 Copynumber: 5.3 Consensus size: 12
21605 TGAGATAATG
21615 ATAATAATCAAA
1 ATAATAATCAAA
*
21627 ATAATAATGAAA
1 ATAATAATCAAA
* *
21639 ATAAAAAATCCTAATG
1 AT-AATAAT-C-AA-A
21655 ATAATAATCAAA
1 ATAATAATCAAA
*
21667 ATAATAATGAAA
1 ATAATAATCAAA
21679 ATAA
1 ATAA
21683 AAAATCCTAC
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
12 28 0.62
13 7 0.16
14 1 0.02
15 7 0.16
16 2 0.04
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.25
Consensus pattern (12 bp):
ATAATAATCAAA
Found at i:21653 original size:19 final size:19
Alignment explanation
Indices: 21631--21691 Score: 77
Period size: 19 Copynumber: 3.1 Consensus size: 19
21621 ATCAAAATAA
21631 TAATGAAAATAAAAAATCC
1 TAATGAAAATAAAAAATCC
* **
21650 TAATGATAATAATCAAAATAA
1 TAATGAAAATAA--AAAATCC
21671 TAATGAAAATAAAAAATCC
1 TAATGAAAATAAAAAATCC
21690 TA
1 TA
21692 CCCCACATGA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 18 0.53
21 16 0.47
ACGTcount: A:0.62, C:0.08, G:0.05, T:0.25
Consensus pattern (19 bp):
TAATGAAAATAAAAAATCC
Found at i:21658 original size:40 final size:40
Alignment explanation
Indices: 21610--21691 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
21600 GTTAGTGAGA
21610 TAATGATAATAATCAAAATAATAATGAAAATAAAAAATCC
1 TAATGATAATAATCAAAATAATAATGAAAATAAAAAATCC
21650 TAATGATAATAATCAAAATAATAATGAAAATAAAAAATCC
1 TAATGATAATAATCAAAATAATAATGAAAATAAAAAATCC
21690 TA
1 TA
21692 CCCCACATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (40 bp):
TAATGATAATAATCAAAATAATAATGAAAATAAAAAATCC
Found at i:22754 original size:14 final size:14
Alignment explanation
Indices: 22718--22746 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
22708 CAAATAAAAT
22718 AAAA-TAAAATTAA
1 AAAATTAAAATTAA
22731 AAAATTAAAATTAA
1 AAAATTAAAATTAA
22745 AA
1 AA
22747 TTTTAAAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAATTAAAATTAA
Found at i:22754 original size:20 final size:18
Alignment explanation
Indices: 22711--22754 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
22701 AAAGGAACAA
22711 ATAAAATAAAATAAAATT
1 ATAAAATAAAATAAAATT
*
22729 AAAAAATTAAAATTAAAATT
1 ATAAAA-TAAAA-TAAAATT
*
22749 TTAAAA
1 ATAAAA
22755 GTAATAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 5 0.24
19 5 0.24
20 11 0.52
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
ATAAAATAAAATAAAATT
Found at i:23337 original size:13 final size:13
Alignment explanation
Indices: 23319--23346 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
23309 AAAATGAAAC
23319 TTGAAATATAATA
1 TTGAAATATAATA
23332 TTGAAATATAATA
1 TTGAAATATAATA
23345 TT
1 TT
23347 TCAAACTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (13 bp):
TTGAAATATAATA
Found at i:24194 original size:3 final size:3
Alignment explanation
Indices: 24171--24227 Score: 69
Period size: 3 Copynumber: 18.0 Consensus size: 3
24161 TATGGGGCCT
* *
24171 ATA AAA ATA AAA ATAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATAA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA AT-A
24218 ATAA ATA ATA
1 AT-A ATA ATA
24228 TTTTTTAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
3 38 0.79
4 10 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:25613 original size:21 final size:21
Alignment explanation
Indices: 25588--25641 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
25578 GATTCTGACT
25588 ATCGCATTGTGATTTTCC-AA
1 ATCGCATTGTGATTTTCCGAA
* *
25608 ATTCGCGTTGCGATTTTCCGAA
1 A-TCGCATTGTGATTTTCCGAA
*
25630 ATCGCAATGTGA
1 ATCGCATTGTGA
25642 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.04
21 23 0.85
22 3 0.11
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (21 bp):
ATCGCATTGTGATTTTCCGAA
Found at i:25653 original size:20 final size:20
Alignment explanation
Indices: 25628--25726 Score: 144
Period size: 20 Copynumber: 5.0 Consensus size: 20
25618 CGATTTTCCG
*
25628 AAATCGCAATGTGAATATGT
1 AAATCGCAATGCGAATATGT
25648 AAATCGCAATGCGAATATGT
1 AAATCGCAATGCGAATATGT
**
25668 AAATCAAAATGCGAATATGT
1 AAATCGCAATGCGAATATGT
*
25688 AAATCGCAATACGAATATGT
1 AAATCGCAATGCGAATATGT
* *
25708 AAATCACAATGCGATTATG
1 AAATCGCAATGCGAATATG
25727 ACTATCACAA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (20 bp):
AAATCGCAATGCGAATATGT
Found at i:25733 original size:20 final size:20
Alignment explanation
Indices: 25718--25817 Score: 137
Period size: 20 Copynumber: 5.0 Consensus size: 20
25708 AAATCACAAT
* * *
25718 GCGATTATGACTATCACAAT
1 GCGATTCTGACTATCGCAAC
*
25738 TCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
* *
25758 GCGATTCTAATTATCGCAAC
1 GCGATTCTGACTATCGCAAC
*
25778 GAGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
25798 GCGATTCTGACTATCGCAAC
1 GCGATTCTGACTATCGCAAC
25818 ACTGAATTTC
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.29, C:0.26, G:0.17, T:0.28
Consensus pattern (20 bp):
GCGATTCTGACTATCGCAAC
Found at i:26670 original size:24 final size:24
Alignment explanation
Indices: 26643--26692 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
26633 TCAAAATTTA
26643 ATCTTGGTCAATACCCGGACTTTG
1 ATCTTGGTCAATACCCGGACTTTG
* *
26667 ATCTTGGTCAATACTCGGATTTTG
1 ATCTTGGTCAATACCCGGACTTTG
26691 AT
1 AT
26693 GACGTTTCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.22, C:0.20, G:0.20, T:0.38
Consensus pattern (24 bp):
ATCTTGGTCAATACCCGGACTTTG
Found at i:28665 original size:20 final size:20
Alignment explanation
Indices: 28640--28742 Score: 134
Period size: 20 Copynumber: 5.2 Consensus size: 20
28630 GAAGTATATT
*
28640 GATAGTCAGGATCGCGTTAC
1 GATAGTCAGAATCGCGTTAC
* *
28660 GATAGTCAGGATCGTGTTAC
1 GATAGTCAGAATCGCGTTAC
* *
28680 GATAGTCAGAATCTCGTTGC
1 GATAGTCAGAATCGCGTTAC
*
28700 GATAGTCAGAATCGCGTTGC
1 GATAGTCAGAATCGCGTTAC
* *
28720 GATAGTCATAATCGCATTAC
1 GATAGTCAGAATCGCGTTAC
28740 GAT
1 GAT
28743 TTACATATTC
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 74 1.00
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.28
Consensus pattern (20 bp):
GATAGTCAGAATCGCGTTAC
Found at i:28778 original size:20 final size:20
Alignment explanation
Indices: 28726--28781 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
28716 TTGCGATAGT
* *
28726 CATAATCGCATTACGATTTA
1 CATATTCGCATTGCGATTTA
28746 CATATTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
28766 CATATTCGCATTGCGA
1 CATATTCGCATTGCGA
28782 ATTCGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (20 bp):
CATATTCGCATTGCGATTTA
Found at i:28802 original size:21 final size:21
Alignment explanation
Indices: 28778--28823 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
28768 TATTCGCATT
28778 GCGAATTCGA-AAAATCGCAAC
1 GCGAATT-GAGAAAATCGCAAC
* *
28799 GCGAATTTAGAAAATCGCAAT
1 GCGAATTGAGAAAATCGCAAC
28820 GCGA
1 GCGA
28824 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.41, C:0.20, G:0.22, T:0.17
Consensus pattern (21 bp):
GCGAATTGAGAAAATCGCAAC
Found at i:28832 original size:22 final size:21
Alignment explanation
Indices: 28788--28832 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
28778 GCGAATTCGA
* *
28788 AAAATCGCAACGCGAATTTAG
1 AAAATCGCAACGCGAAGTCAG
*
28809 AAAATCGCAATGCGATAGTCAG
1 AAAATCGCAACGCGA-AGTCAG
28831 AA
1 AA
28833 TCGCGTTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.18
Consensus pattern (21 bp):
AAAATCGCAACGCGAAGTCAG
Found at i:29150 original size:21 final size:21
Alignment explanation
Indices: 29126--29178 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
29116 ATTCTGACTA
29126 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* **
29147 TCGCGTTGCGATTTTCTGAAT
1 TCGCATTGCGATTTTCCAAAT
*
29168 TCGCAATGCGA
1 TCGCATTGCGA
29179 ATATGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:29193 original size:20 final size:20
Alignment explanation
Indices: 29168--29218 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
29158 TTTTCTGAAT
29168 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
29188 TCGCAATGCGAATATGTAAA
1 TCGCAATGCGAATATGTAAA
*
29208 TCTCAATGCGA
1 TCGCAATGCGA
29219 TTATAACTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (20 bp):
TCGCAATGCGAATATGTAAA
Found at i:29234 original size:20 final size:20
Alignment explanation
Indices: 29211--29253 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29201 ATGTAAATCT
29211 CAATGCGATTATAACTATCG
1 CAATGCGATTATAACTATCG
* * *
29231 CAATGTGATTCTGACTATCG
1 CAATGCGATTATAACTATCG
29251 CAA
1 CAA
29254 CGTGATTCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (20 bp):
CAATGCGATTATAACTATCG
Found at i:29258 original size:20 final size:20
Alignment explanation
Indices: 29224--29314 Score: 128
Period size: 20 Copynumber: 4.5 Consensus size: 20
29214 TGCGATTATA
*
29224 ACTATCGCAATGTGATTCTG
1 ACTATCGCAACGTGATTCTG
29244 ACTATCGCAACGTGATTCTG
1 ACTATCGCAACGTGATTCTG
* *
29264 ATTATCGCAACGAGATTCTG
1 ACTATCGCAACGTGATTCTG
* *
29284 ACTATCACAACGCGATTCTG
1 ACTATCGCAACGTGATTCTG
*
29304 ACTGTCGCAAC
1 ACTATCGCAAC
29315 ACTGAATTTC
Statistics
Matches: 63, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (20 bp):
ACTATCGCAACGTGATTCTG
Found at i:33794 original size:20 final size:20
Alignment explanation
Indices: 33771--33877 Score: 103
Period size: 20 Copynumber: 5.5 Consensus size: 20
33761 TCTGAAACTT
33771 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
33791 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** **
33811 ACTATCGCAACGA-GAATTTG
1 AAAATCGCAAC-ACGAAAATG
** *
33831 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACACGAAAATG
* *
33850 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
33869 AAAATCGCA
1 AAAATCGCA
33878 TTGCGATTCT
Statistics
Matches: 74, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
19 24 0.32
20 49 0.66
21 1 0.01
ACGTcount: A:0.47, C:0.22, G:0.17, T:0.14
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:34290 original size:22 final size:22
Alignment explanation
Indices: 34259--34315 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
34249 GATGGAGATA
* *
34259 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCAGAGATCGG
* *
34281 GACTGATTTCGTCAGAGATCGG
1 GACGGATTTCGCCAGAGATCGG
34303 GACGGATTTCGCC
1 GACGGATTTCGCC
34316 TTAGAGAGTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.19, C:0.21, G:0.37, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGCCAGAGATCGG
Found at i:34493 original size:20 final size:20
Alignment explanation
Indices: 34463--34616 Score: 123
Period size: 20 Copynumber: 7.7 Consensus size: 20
34453 GCGCTTTGAA
* *
34463 AATCGCATTGCGATAGTAAG
1 AATCGCGTTGCGATAGTCAG
*
34483 CATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
34503 AATCACGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
34523 AATCTCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
** * *
34543 AATCGTATTGCGAT-TTACAT
1 AATCGCGTTGCGATAGT-CAG
* * * *
34563 ATTCGCATTGCGA-ATTCGAAA
1 AATCGCGTTGCGATAGTC--AG
**
34584 AATCGCAATGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
34604 AATCGCGTTGCGA
1 AATCGCGTTGCGA
34617 ATCTGGAAAC
Statistics
Matches: 109, Mismatches: 20, Indels: 10
0.78 0.14 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.84
21 12 0.11
22 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:35791 original size:19 final size:19
Alignment explanation
Indices: 35758--35794 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35748 ATTTTATTGT
* *
35758 TTTATATTCTGGTTATTTA
1 TTTATATTATAGTTATTTA
35777 TTTATATTATAGTTATTT
1 TTTATATTATAGTTATTT
35795 TAATTTTGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.24, C:0.03, G:0.08, T:0.65
Consensus pattern (19 bp):
TTTATATTATAGTTATTTA
Found at i:40489 original size:36 final size:36
Alignment explanation
Indices: 40416--40489 Score: 94
Period size: 36 Copynumber: 2.1 Consensus size: 36
40406 CACAGTTATA
* * * * *
40416 CATTTTCATTTGTGGCATCCTTTTATGTCAATTATG
1 CATTTTCATTTATGGCATCATTTCATGCCAATAATG
*
40452 CATTTTCATTTATGGCATCATTTCATGCCGATAATG
1 CATTTTCATTTATGGCATCATTTCATGCCAATAATG
40488 CA
1 CA
40490 CCATTATGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.45
Consensus pattern (36 bp):
CATTTTCATTTATGGCATCATTTCATGCCAATAATG
Found at i:40498 original size:46 final size:46
Alignment explanation
Indices: 40447--40870 Score: 668
Period size: 46 Copynumber: 9.2 Consensus size: 46
40437 TTTATGTCAA
* *
40447 TTATGCATTTTCATTTATGGCATCATTTCATGCCGATAATGCACCA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
40493 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* *
40539 TTATGCATTTTCATTTATAGCATCCTTTCATGCCGATAATGCACCA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * * **
40585 TTATACATTTTCATTTATGGCATCATTTCATACCGATAATGCATAG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* *
40631 TTATGCATTTTCATTTATGACATCCTTTCATTCCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* **
40677 TTATACATTTTCATTTATGATATCCTTTCATGCCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* *
40723 TTATGCATTTTCATTTGTGGTATCCTTTCATGCCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
*
40769 TTATGTATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* *
40815 TTATGCATTTTCATTTATGGCATTCTTTCATGTCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
*
40861 TTAGGCATTT
1 TTATGCATTT
40871 AACTTTTCAT
Statistics
Matches: 348, Mismatches: 30, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 348 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.41
Consensus pattern (46 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
Found at i:45992 original size:30 final size:30
Alignment explanation
Indices: 45948--46011 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
45938 AGTTCTTTTA
*
45948 TTTA-TTAAATGAACAAAGATAAACAAGAT
1 TTTATTTAAATGAACAAACATAAACAAGAT
* *
45977 TTTATTTATATGAACAAACATAAACAATAT
1 TTTATTTAAATGAACAAACATAAACAAGAT
46007 TTTAT
1 TTTAT
46012 GTTCATTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 4 0.13
30 27 0.87
ACGTcount: A:0.50, C:0.08, G:0.06, T:0.36
Consensus pattern (30 bp):
TTTATTTAAATGAACAAACATAAACAAGAT
Found at i:46103 original size:14 final size:14
Alignment explanation
Indices: 46084--46122 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
46074 TAATCTATTC
*
46084 GTTTATGTTCATTT
1 GTTTATGTTCACTT
46098 GTTTATGTTCACTT
1 GTTTATGTTCACTT
*
46112 GTTTATATTCA
1 GTTTATGTTCA
46123 ACCTAATCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.18, C:0.10, G:0.13, T:0.59
Consensus pattern (14 bp):
GTTTATGTTCACTT
Found at i:50602 original size:21 final size:21
Alignment explanation
Indices: 50578--50618 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
50568 TGAAAAAGTC
50578 TTTTAAATCCAAATAAAAATA
1 TTTTAAATCCAAATAAAAATA
50599 TTTTAAATCCAAATAAAAAT
1 TTTTAAATCCAAATAAAAAT
50619 CAATTCCTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.56, C:0.10, G:0.00, T:0.34
Consensus pattern (21 bp):
TTTTAAATCCAAATAAAAATA
Found at i:58667 original size:30 final size:30
Alignment explanation
Indices: 58633--58693 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
58623 AAATCGTTTG
58633 GAAAATCTTAAAATTAC-TTTAACTTAATTT
1 GAAAATCTTAAAA-TACATTTAACTTAATTT
*
58663 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCTTAAAATACATTTAACTTAATTT
58693 G
1 G
58694 TTATATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (30 bp):
GAAAATCTTAAAATACATTTAACTTAATTT
Found at i:61183 original size:21 final size:21
Alignment explanation
Indices: 61101--61184 Score: 80
Period size: 21 Copynumber: 3.9 Consensus size: 21
61091 CAGAACCCCA
* *
61101 GGGGGGTATCGATTCCC-CTG
1 GGGGGGAATCGATTCCCTCAG
* *
61121 TGGGGGGAATCGGTTCCCCTTCAA
1 -GGGGGGAATCGATT-CCC-TCAG
* *
61145 AGGGGGAATCGGTTCCCTCAG
1 GGGGGGAATCGATTCCCTCAG
61166 GGGGGGAATCGATTCCCTC
1 GGGGGGAATCGATTCCCTC
61185 TGCACCAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
21 32 0.62
22 6 0.12
23 13 0.25
24 1 0.02
ACGTcount: A:0.15, C:0.25, G:0.37, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCTCAG
Found at i:65022 original size:22 final size:21
Alignment explanation
Indices: 64980--65019 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
64970 GAGTTTGTTT
*
64980 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
65001 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
65020 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:67267 original size:30 final size:30
Alignment explanation
Indices: 67233--67293 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
67223 AAATCGTTTG
67233 GAAAATCTTAAAATTAC-TTTAACTTAATTT
1 GAAAATCTTAAAA-TACATTTAACTTAATTT
*
67263 GAAAATCTTAAAATCCATTTAACTTAATTT
1 GAAAATCTTAAAATACATTTAACTTAATTT
67293 G
1 G
67294 TTATATCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.41
Consensus pattern (30 bp):
GAAAATCTTAAAATACATTTAACTTAATTT
Found at i:69779 original size:2 final size:2
Alignment explanation
Indices: 69772--69814 Score: 77
Period size: 2 Copynumber: 21.0 Consensus size: 2
69762 TAATTAAAAC
69772 AT AT AT AT AT CAT 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
69815 TAATTATACA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 38 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:77639 original size:16 final size:16
Alignment explanation
Indices: 77618--77648 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
77608 AATAATAATA
77618 ATATTTTAATTATATG
1 ATATTTTAATTATATG
*
77634 ATATTTTTATTATAT
1 ATATTTTAATTATAT
77649 TATTGTTGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (16 bp):
ATATTTTAATTATATG
Found at i:80530 original size:13 final size:13
Alignment explanation
Indices: 80514--80539 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
80504 TATATTAATT
80514 GTGTATATATAAC
1 GTGTATATATAAC
80527 GTGTATATATAAC
1 GTGTATATATAAC
80540 CACAATTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
GTGTATATATAAC
Found at i:80565 original size:9 final size:9
Alignment explanation
Indices: 80551--80576 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
80541 ACAATTTATT
80551 ATATGTATA
1 ATATGTATA
80560 ATATGTATA
1 ATATGTATA
80569 ATATGTAT
1 ATATGTAT
80577 TTTGATTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (9 bp):
ATATGTATA
Found at i:80786 original size:21 final size:22
Alignment explanation
Indices: 80745--80787 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
80735 TGTAGCAGTT
*
80745 CTGTAGCAGGGGAATCGATTCC
1 CTGTAGCAGGGGAACCGATTCC
*
80767 CTGTAGCA-GGGTACCGATTCC
1 CTGTAGCAGGGGAACCGATTCC
80788 GTATTTGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (22 bp):
CTGTAGCAGGGGAACCGATTCC
Found at i:86942 original size:30 final size:30
Alignment explanation
Indices: 86908--86970 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
86898 GTTATATGAG
* *
86908 CTATGTGATAAAGGTATGTAAATGATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
86938 CTATGTGATAAAGGTATGGAAATAATATGT
1 CTATGTGATAAAGGTATGGAAATAATATGT
86968 CTA
1 CTA
86971 CGCGATATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.38, C:0.05, G:0.22, T:0.35
Consensus pattern (30 bp):
CTATGTGATAAAGGTATGGAAATAATATGT
Found at i:87300 original size:24 final size:23
Alignment explanation
Indices: 87212--87297 Score: 104
Period size: 23 Copynumber: 3.7 Consensus size: 23
87202 ACGTATTATA
*
87212 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
87235 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
87258 CGGTC-CTTTGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-C-AATTCTACG
87282 TGGCACTTCGGTGCAA
1 TGGCACTTCGGTGCAA
87298 ATTTATATGA
Statistics
Matches: 53, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
22 1 0.02
23 33 0.62
24 18 0.34
25 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.27, T:0.28
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:87897 original size:21 final size:22
Alignment explanation
Indices: 87856--87898 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
87846 TGTAGCAGTA
*
87856 CTGTAGCAGGGGAATCGATTCC
1 CTGTAGCAGGGGAACCGATTCC
*
87878 CTGTAGCA-GGGTACCGATTCC
1 CTGTAGCAGGGGAACCGATTCC
87899 GTATTTGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.21, C:0.26, G:0.30, T:0.23
Consensus pattern (22 bp):
CTGTAGCAGGGGAACCGATTCC
Found at i:93825 original size:78 final size:79
Alignment explanation
Indices: 93682--93835 Score: 190
Period size: 78 Copynumber: 2.0 Consensus size: 79
93672 ATATAGAAAG
* * *
93682 TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTTAATTCATATTTAATTCAGAATGATTA
1 TAAACATTAAAAGAATGTAATTCAAATTACAACTCTTTTAATTCATATTTAATTCAGAATAATTA
93747 AATAAGTTTTTTTAA
66 AATAA-TTTTTTTAA
* * * *
93762 TAAACATT-AAAGATTGTAATTCAAATTATAAGTC-TTTAATGT-ATATTTAATT-TGAATTAAT
1 TAAACATTAAAAGAATGTAATTCAAATTACAACTCTTTTAAT-TCATATTTAATTCAGAA-TAAT
93823 TAAATAATTTTTT
64 TAAATAATTTTTT
93836 ATTTATTAAT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
77 9 0.14
78 26 0.40
79 22 0.34
80 8 0.12
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTCAAATTACAACTCTTTTAATTCATATTTAATTCAGAATAATTA
AATAATTTTTTTAA
Found at i:100247 original size:29 final size:29
Alignment explanation
Indices: 100205--100293 Score: 162
Period size: 29 Copynumber: 3.1 Consensus size: 29
100195 CTACAGTGAG
100205 CTTGGAGGTCGCCATGGCATCCGAGCGAC
1 CTTGGAGGTCGCCATGGCATCCGAGCGAC
100234 CTTGGAGGTCGCCATGGCATCC-AGGCGAC
1 CTTGGAGGTCGCCATGGCATCCGA-GCGAC
100263 CTTGGAGGTCGCCATGGCATCCGAGCGAC
1 CTTGGAGGTCGCCATGGCATCCGAGCGAC
100292 CT
1 CT
100294 ATGGGGTGTT
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
28 1 0.02
29 56 0.97
30 1 0.02
ACGTcount: A:0.17, C:0.31, G:0.34, T:0.18
Consensus pattern (29 bp):
CTTGGAGGTCGCCATGGCATCCGAGCGAC
Found at i:100616 original size:14 final size:14
Alignment explanation
Indices: 100599--100633 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
100589 CATCCGAGAT
100599 CATCCGACCGAGGC
1 CATCCGACCGAGGC
100613 CATCCGACCGAGGC
1 CATCCGACCGAGGC
100627 CATCCGA
1 CATCCGA
100634 AAGCATCCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.23, C:0.43, G:0.26, T:0.09
Consensus pattern (14 bp):
CATCCGACCGAGGC
Found at i:100648 original size:20 final size:20
Alignment explanation
Indices: 100620--100674 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
100610 GGCCATCCGA
100620 CCGAGGCCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
* *
100640 CCGATGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
100660 CCGAGGCCATCCGAA
1 CCGAGGCCATCCGAA
100675 CGAGCTATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.27, C:0.36, G:0.25, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:100700 original size:10 final size:10
Alignment explanation
Indices: 100620--100734 Score: 68
Period size: 10 Copynumber: 10.9 Consensus size: 10
100610 GGCCATCCGA
*
100620 CCGAGGCCAT
1 CCGAGGGCAT
**
100630 CCGAAAGCAT
1 CCGAGGGCAT
* *
100640 CCGATGCCAT
1 CCGAGGGCAT
*
100650 CCGAGAGCAT
1 CCGAGGGCAT
*
100660 CCGAGGCCAT
1 CCGAGGGCAT
*
100670 CCGAACGAGCTAT
1 CCG-A-GGGC-AT
**
100683 GTGAGGGCAT
1 CCGAGGGCAT
100693 CCGAGGGCAT
1 CCGAGGGCAT
100703 CCGAGCGAGCTAT
1 CCGAG-G-GC-AT
* *
100716 GCGAGGGAAT
1 CCGAGGGCAT
100726 CCGAGGGCA
1 CCGAGGGCA
100735 ACCGGGCGAC
Statistics
Matches: 77, Mismatches: 22, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
10 56 0.73
11 6 0.08
12 6 0.08
13 9 0.12
ACGTcount: A:0.25, C:0.30, G:0.33, T:0.12
Consensus pattern (10 bp):
CCGAGGGCAT
Found at i:100732 original size:33 final size:33
Alignment explanation
Indices: 100658--100743 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
100648 ATCCGAGAGC
* * * *
100658 ATCCGAGGCCATCCGAACGAGCTATGTGAGGGC
1 ATCCGAGGGCATCCGAGCGAGCTATGCGAGGGA
100691 ATCCGAGGGCATCCGAGCGAGCTATGCGAGGGA
1 ATCCGAGGGCATCCGAGCGAGCTATGCGAGGGA
* *
100724 ATCCGAGGGCAACCGGGCGA
1 ATCCGAGGGCATCCGAGCGA
100744 CCTACCCTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.24, C:0.27, G:0.37, T:0.12
Consensus pattern (33 bp):
ATCCGAGGGCATCCGAGCGAGCTATGCGAGGGA
Found at i:100793 original size:33 final size:33
Alignment explanation
Indices: 100750--100840 Score: 128
Period size: 33 Copynumber: 2.8 Consensus size: 33
100740 GCGACCTACC
* *
100750 CTCGCACGGTTGCCCTCGGATTCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
100783 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
1 CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
* * * *
100816 CTCGTTCGGATGGCCTTGGATGCCC
1 CTCGCTCGGTTGCCCTCGGATGCCC
100841 AGCGTGTTGG
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.10, C:0.37, G:0.27, T:0.25
Consensus pattern (33 bp):
CTCGCTCGGTTGCCCTCGGATGCCCTCGCATAG
Found at i:104220 original size:17 final size:18
Alignment explanation
Indices: 104200--104248 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
104190 AATTTATTTC
*
104200 ATATAATTAATTATT-AA
1 ATATTATTAATTATTAAA
*
104217 ATATTATTAAATATTAAA
1 ATATTATTAATTATTAAA
104235 ATATTATATAATTA
1 ATATTAT-TAATTA
104249 GATAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 13 0.48
18 9 0.33
19 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATTATTAATTATTAAA
Found at i:104224 original size:10 final size:10
Alignment explanation
Indices: 104209--104241 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
104199 CATATAATTA
104209 ATTATTAAAT
1 ATTATTAAAT
104219 ATTATTAAAT
1 ATTATTAAAT
104229 ATTA--AAAT
1 ATTATTAAAT
104237 ATTAT
1 ATTAT
104242 ATAATTAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.36
10 14 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
ATTATTAAAT
Found at i:104950 original size:14 final size:16
Alignment explanation
Indices: 104930--104966 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
104920 TCCTTGTGAT
104930 GTATAAAAACA-TTCA
1 GTATAAAAACACTTCA
*
104945 -TATAAAAATACTTCA
1 GTATAAAAACACTTCA
104960 GTATAAA
1 GTATAAA
104967 TCAGTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 9 0.47
15 4 0.21
16 6 0.32
ACGTcount: A:0.54, C:0.11, G:0.05, T:0.30
Consensus pattern (16 bp):
GTATAAAAACACTTCA
Found at i:109009 original size:22 final size:22
Alignment explanation
Indices: 108981--109030 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
108971 AAAATCCAAT
*
108981 AAAGAAATCG-AAGCACTCAAA
1 AAAGAAATCGAAAACACTCAAA
*
109002 AGAAGAAATTGAAAACACTCAAA
1 A-AAGAAATCGAAAACACTCAAA
109025 AAAGAA
1 AAAGAA
109031 GAAAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 13 0.52
23 11 0.44
ACGTcount: A:0.62, C:0.14, G:0.14, T:0.10
Consensus pattern (22 bp):
AAAGAAATCGAAAACACTCAAA
Found at i:109043 original size:14 final size:14
Alignment explanation
Indices: 109024--109056 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
109014 AAACACTCAA
109024 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
109038 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
109052 AAAAG
1 AAAAG
109057 TTGAAGTACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:111583 original size:2 final size:2
Alignment explanation
Indices: 111576--111613 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
111566 TGTATAAAAC
111576 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
111614 CAAAATATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:118136 original size:15 final size:15
Alignment explanation
Indices: 118116--118150 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
118106 GAACCTGAGT
118116 TGGATCTAGAAATTG
1 TGGATCTAGAAATTG
118131 TGGATCTAGAAATTG
1 TGGATCTAGAAATTG
118146 TGGAT
1 TGGAT
118151 ATGAACTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.31, C:0.06, G:0.29, T:0.34
Consensus pattern (15 bp):
TGGATCTAGAAATTG
Found at i:118364 original size:16 final size:16
Alignment explanation
Indices: 118345--118376 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
118335 GAATTGGTAC
118345 GATATTTACCTAACTT
1 GATATTTACCTAACTT
*
118361 GATATTTACCTGACTT
1 GATATTTACCTAACTT
118377 ATAAGTTACC
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:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (16 bp):
GATATTTACCTAACTT
Found at i:118578 original size:17 final size:17
Alignment explanation
Indices: 118544--118578 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
118534 TTAATTATAA
*
118544 TCATTAAATTATTAATT
1 TCATTAAATAATTAATT
*
118561 TCATTAAATAATTTATT
1 TCATTAAATAATTAATT
118578 T
1 T
118579 ATTGAACATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (17 bp):
TCATTAAATAATTAATT
Found at i:119112 original size:18 final size:20
Alignment explanation
Indices: 119067--119114 Score: 55
Period size: 23 Copynumber: 2.4 Consensus size: 20
119057 AACAAAAGAC
119067 ATTGCATCAATTCAACAAGTATT
1 ATTGCATCAATTCAAC-A--ATT
119090 ATTGCATCAATTCAAC-ATT
1 ATTGCATCAATTCAACAATT
119109 -TTGCAT
1 ATTGCAT
119115 TCAACAAACA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 6 0.24
19 3 0.12
23 16 0.64
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (20 bp):
ATTGCATCAATTCAACAATT
Found at i:122908 original size:2 final size:2
Alignment explanation
Indices: 122901--122939 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
122891 ATTTATACTT
122901 TA TA TA TA TA 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 TA TA TA TA TA T
122940 TGTCATGGAT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:134021 original size:11 final size:11
Alignment explanation
Indices: 134005--134029 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
133995 CTGAAGTGTT
134005 AGGAAAACTTA
1 AGGAAAACTTA
134016 AGGAAAACTTA
1 AGGAAAACTTA
134027 AGG
1 AGG
134030 TTGCTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.08, G:0.24, T:0.16
Consensus pattern (11 bp):
AGGAAAACTTA
Found at i:137246 original size:12 final size:11
Alignment explanation
Indices: 137202--137271 Score: 56
Period size: 10 Copynumber: 6.3 Consensus size: 11
137192 CCCCATGACA
*
137202 ATATATA-TAT
1 ATATATACTTT
*
137212 ATATATA-TAT
1 ATATATACTTT
*
137222 ATATATA-TAT
1 ATATATACTTT
137232 ATATATACTTGT
1 ATATATACTT-T
137244 ATATATACTTT
1 ATATATACTTT
137255 ATACTTTATACTTT
1 ATA---TATACTTT
137269 ATA
1 ATA
137272 CTTTATTAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
10 27 0.50
11 5 0.09
12 11 0.20
14 11 0.20
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.51
Consensus pattern (11 bp):
ATATATACTTT
Found at i:137250 original size:2 final size:2
Alignment explanation
Indices: 137202--137238 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
137192 CCCCATGACA
137202 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
137239 CTTGTATATA
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:137259 original size:7 final size:7
Alignment explanation
Indices: 137247--137277 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
137237 TACTTGTATA
137247 TATACTT
1 TATACTT
137254 TATACTT
1 TATACTT
137261 TATACTT
1 TATACTT
137268 TATACTT
1 TATACTT
137275 TAT
1 TAT
137278 TAATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (7 bp):
TATACTT
Found at i:137264 original size:16 final size:16
Alignment explanation
Indices: 137245--137358 Score: 55
Period size: 16 Copynumber: 7.4 Consensus size: 16
137235 TATACTTGTA
137245 TATATACTTTATAC-T
1 TATATACTTTATACTT
137260 T-TATACTTTATACTT
1 TATATACTTTATACTT
*
137275 TAT-TA-ATT-TA-TT
1 TATATACTTTATACTT
*
137287 TAT-TAATTTATACTT
1 TATATACTTTATACTT
* *
137302 ATATATATATATATATAC-A
1 -TATATA-CT-T-TATACTT
* * * *
137321 CACACACTTTATAGTT
1 TATATACTTTATACTT
*
137337 TATATACTTTATAGTT
1 TATATACTTTATACTT
137353 TATATA
1 TATATA
137359 GTACATAGAA
Statistics
Matches: 76, Mismatches: 12, Indels: 21
0.70 0.11 0.19
Matches are distributed among these distances:
12 7 0.09
13 4 0.05
14 16 0.21
15 11 0.14
16 24 0.32
17 3 0.04
18 5 0.07
19 1 0.01
20 5 0.07
ACGTcount: A:0.36, C:0.10, G:0.02, T:0.53
Consensus pattern (16 bp):
TATATACTTTATACTT
Found at i:137290 original size:12 final size:12
Alignment explanation
Indices: 137273--137297 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
137263 TACTTTATAC
137273 TTTATTAATTTA
1 TTTATTAATTTA
137285 TTTATTAATTTA
1 TTTATTAATTTA
137297 T
1 T
137298 ACTTATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTATTAATTTA
Found at i:138895 original size:21 final size:19
Alignment explanation
Indices: 138867--138912 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
138857 TCATTGAATC
138867 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
138887 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
138906 ACTTAGT
1 A-TTAGT
138913 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:145134 original size:13 final size:13
Alignment explanation
Indices: 145116--145149 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
145106 GATGATGGTC
145116 TTGATGAAGGATG
1 TTGATGAAGGATG
*
145129 TTGATGATGGATG
1 TTGATGAAGGATG
*
145142 ATGATGAA
1 TTGATGAA
145150 ATGGCTATGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (13 bp):
TTGATGAAGGATG
Found at i:149280 original size:5 final size:5
Alignment explanation
Indices: 149270--149327 Score: 68
Period size: 5 Copynumber: 11.6 Consensus size: 5
149260 CTCTTTTGAA
149270 TTTCT TTTCT TTTCT TTTC- -TTCT TTTCT TTTCT TCTT-T TTGTCTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T-TTCT TT-TC-T
149315 TTTCT TTTCT TTT
1 TTTCT TTTCT TTT
149328 GGCACTCCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
3 3 0.06
4 1 0.02
5 36 0.77
6 4 0.09
7 3 0.06
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:149292 original size:13 final size:13
Alignment explanation
Indices: 149276--149327 Score: 70
Period size: 13 Copynumber: 3.9 Consensus size: 13
149266 TGAATTTCTT
149276 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
149289 TTCTTTTCTTTTC
1 TTCTTTTCTTTTC
*
149302 TTCTTTT-TGTCTTT
1 TTCTTTTCT-T-TTC
149316 TTCTTTTCTTTT
1 TTCTTTTCTTTT
149328 GGCACTCCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
12 1 0.03
13 23 0.66
14 10 0.29
15 1 0.03
ACGTcount: A:0.00, C:0.19, G:0.02, T:0.79
Consensus pattern (13 bp):
TTCTTTTCTTTTC
Found at i:154798 original size:16 final size:16
Alignment explanation
Indices: 154777--154812 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
154767 ATTTGGTATT
154777 ACCTGACATGTTATCA
1 ACCTGACATGTTATCA
*
154793 ACCTGACATGTTATGA
1 ACCTGACATGTTATCA
154809 ACCT
1 ACCT
154813 AACTTGTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.31
Consensus pattern (16 bp):
ACCTGACATGTTATCA
Found at i:155358 original size:2 final size:2
Alignment explanation
Indices: 155351--155387 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
155341 TACCCCTTTA
155351 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
155388 CTTTTTTGAA
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:155792 original size:14 final size:16
Alignment explanation
Indices: 155763--155794 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
155753 CGTTCGTGAA
155763 CGTTCGATTATATGTT
1 CGTTCGATTATATGTT
155779 CGTTC-ATT-TATGTT
1 CGTTCGATTATATGTT
155793 CG
1 CG
155795 AATAGATGGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 8 0.50
15 3 0.19
16 5 0.31
ACGTcount: A:0.16, C:0.16, G:0.19, T:0.50
Consensus pattern (16 bp):
CGTTCGATTATATGTT
Found at i:156082 original size:23 final size:24
Alignment explanation
Indices: 156056--156113 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 24
156046 GTGTTTGTGT
156056 TGTTCGTTTATGTTCATTT-ATTA
1 TGTTCGTTTATGTTCATTTGATTA
* * * *
156079 TGTTTGTTTATGTTCGTTTGTTTG
1 TGTTCGTTTATGTTCATTTGATTA
156103 TGTTCGTTTAT
1 TGTTCGTTTAT
156114 CATTTAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 17 0.59
24 12 0.41
ACGTcount: A:0.10, C:0.07, G:0.19, T:0.64
Consensus pattern (24 bp):
TGTTCGTTTATGTTCATTTGATTA
Found at i:156099 original size:14 final size:14
Alignment explanation
Indices: 156080--156111 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
156070 CATTTATTAT
156080 GTTTGTTTATGTTC
1 GTTTGTTTATGTTC
*
156094 GTTTGTTTGTGTTC
1 GTTTGTTTATGTTC
156108 GTTT
1 GTTT
156112 ATCATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.03, C:0.06, G:0.25, T:0.66
Consensus pattern (14 bp):
GTTTGTTTATGTTC
Found at i:156191 original size:16 final size:16
Alignment explanation
Indices: 156167--156215 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
156157 CAAAAAAAAT
*
156167 TGTTTGTTTATGTTCG
1 TGTTCGTTTATGTTCG
156183 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
156199 TATTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
156215 T
1 T
156216 TTATTTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.08, C:0.10, G:0.22, T:0.59
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:156377 original size:2 final size:2
Alignment explanation
Indices: 156370--156405 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
156360 AAATACATAC
*
156370 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
156406 GCGTAAGTAT
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:157837 original size:27 final size:24
Alignment explanation
Indices: 157802--157870 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 24
157792 CATTTAAATG
*
157802 ATAAATGAACTCAAACAAACGAACATA
1 ATAAATGAAC-C--ACAAACGAACACA
*
157829 ATAAATGAA-CATAAACGAACACA
1 ATAAATGAACCACAAACGAACACA
157852 ATAAATGAACAACACAAAC
1 ATAAATGAAC--CACAAAC
157871 ACAAAAAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
23 20 0.56
25 1 0.03
26 6 0.17
27 9 0.25
ACGTcount: A:0.61, C:0.19, G:0.07, T:0.13
Consensus pattern (24 bp):
ATAAATGAACCACAAACGAACACA
Found at i:157844 original size:23 final size:23
Alignment explanation
Indices: 157818--157862 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
157808 GAACTCAAAC
*
157818 AAACGAACATAATAAATGAACAT
1 AAACGAACACAATAAATGAACAT
157841 AAACGAACACAATAAATGAACA
1 AAACGAACACAATAAATGAACA
157863 ACACAAACAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.62, C:0.16, G:0.09, T:0.13
Consensus pattern (23 bp):
AAACGAACACAATAAATGAACAT
Found at i:158144 original size:14 final size:14
Alignment explanation
Indices: 158125--158170 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 14
158115 GCAATCTGTT
158125 CGAACATAAATGAA
1 CGAACATAAATGAA
158139 CGAACATAAATGAA
1 CGAACATAAATGAA
*
158153 CAAACATATAATCGAA
1 CGAACATA-AAT-GAA
158169 CG
1 CG
158171 TTCACGAACT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 21 0.75
15 3 0.11
16 4 0.14
ACGTcount: A:0.54, C:0.17, G:0.13, T:0.15
Consensus pattern (14 bp):
CGAACATAAATGAA
Found at i:158392 original size:21 final size:21
Alignment explanation
Indices: 158341--158392 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
158331 TTTACAGGCT
158341 TACCCAAAACTGAAGCCTAAA
1 TACCCAAAACTGAAGCCTAAA
*
158362 TACTCAAAACTGAAGCCTAAA
1 TACCCAAAACTGAAGCCTAAA
*
158383 TACCCGAAAC
1 TACCCAAAAC
158393 ACACCCCAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.46, C:0.29, G:0.10, T:0.15
Consensus pattern (21 bp):
TACCCAAAACTGAAGCCTAAA
Found at i:159059 original size:13 final size:13
Alignment explanation
Indices: 159041--159085 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
159031 TGCTGGACCT
159041 AAAAATAAAATAA
1 AAAAATAAAATAA
159054 AAAAATAAAA-AA
1 AAAAATAAAATAA
159066 ACAAAAT-AAATAA
1 A-AAAATAAAATAA
*
159079 ATAAATA
1 AAAAATA
159086 CATAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 10 0.36
13 18 0.64
ACGTcount: A:0.82, C:0.02, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAATAA
Found at i:159060 original size:8 final size:8
Alignment explanation
Indices: 159047--159095 Score: 53
Period size: 8 Copynumber: 5.9 Consensus size: 8
159037 ACCTAAAAAT
159047 AAAATAAA
1 AAAATAAA
159055 AAAATAAA
1 AAAATAAA
*
159063 AAAACAAA
1 AAAATAAA
159071 ATAAATAAA
1 A-AAATAAA
* *
159080 TAAATACAT
1 AAAATA-AA
159089 AAAATAA
1 AAAATAA
159096 CCGATAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
8 22 0.65
9 12 0.35
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (8 bp):
AAAATAAA
Found at i:159092 original size:21 final size:21
Alignment explanation
Indices: 159041--159095 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
159031 TGCTGGACCT
159041 AAAAATAAAATAAAAAAATAA
1 AAAAATAAAATAAAAAAATAA
* *
159062 AAAAACAAAATAAATAAATAA
1 AAAAATAAAATAAAAAAATAA
* *
159083 ATACATAAAATAA
1 AAAAATAAAATAA
159096 CCGATAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.80, C:0.04, G:0.00, T:0.16
Consensus pattern (21 bp):
AAAAATAAAATAAAAAAATAA
Found at i:159183 original size:39 final size:38
Alignment explanation
Indices: 159128--159592 Score: 357
Period size: 36 Copynumber: 12.2 Consensus size: 38
159118 AAAAAATCAT
*
159128 TTTTCTAAAAAA--ATATATTATACATTTTCAAAAATATG
1 TTTT-TAAAAAATTATATATTATACGTTTTCAAAAAT-TG
* *
159166 TTTTTAAAAAATTATATATTATACGTTTT-AAAAAGTA
1 TTTTTAAAAAATTATATATTATACGTTTTCAAAAATTG
* * * * *
159203 TTTTTTAAAAACTATATATTATATGGTTTTTAAAAAATG
1 TTTTTAAAAAATTATATATTATA-CGTTTTCAAAAATTG
* * * * *
159242 TTTTTTTAAAAACTATATATTATACATTTTTAAAAATATATA
1 -TTTTTAAAAAATTATATATTATAC-GTTTTCAAAA-AT-TG
* * * *
159284 TTTTTTAAAAATTATATATTATACATTTTTAAAAATATT
1 TTTTTAAAAAATTATATATTATACGTTTTCAAAAAT-TG
159323 TTTTTAAAAAATTATATATTATACGTTTTCAAAAATTG
1 TTTTTAAAAAATTATATATTATACGTTTTCAAAAATTG
* ** *
159361 TTTTTCAAAGCTATATAATATATATATGTTTTCAAAAATTG
1 TTTTTAAAAAAT-TAT-ATAT-TATACGTTTTCAAAAATTG
* * *
159402 TTTTT--GAAATTATATAATATATGTTTTCAAAAATTG
1 TTTTTAAAAAATTATATATTATACGTTTTCAAAAATTG
* * *
159438 TTTTT--AAAACTATATATTATAGGTTTTCAAATATTG
1 TTTTTAAAAAATTATATATTATACGTTTTCAAAAATTG
* * **
159474 TTTTTCAAAATTATATAATATATATATATTTTC---AATT-
1 TTTTTAAAAAAT-TAT-ATAT-TATACGTTTTCAAAAATTG
** * ** *
159511 TTTTT-TGAAATTATATAATATATATTTTCAAAAATTA
1 TTTTTAAAAAATTATATATTATACGTTTTCAAAAATTG
159548 TTTTTAAAATAA-TAT-T-TTATACGTTTTCAAAAATTG
1 TTTTTAAAA-AATTATATATTATACGTTTTCAAAAATTG
159584 TTTTTAAAA
1 TTTTTAAAA
159593 CTATATAATA
Statistics
Matches: 356, Mismatches: 49, Indels: 46
0.79 0.11 0.10
Matches are distributed among these distances:
33 11 0.03
34 3 0.01
35 3 0.01
36 87 0.24
37 43 0.12
38 37 0.10
39 68 0.19
40 47 0.13
41 56 0.16
42 1 0.00
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (38 bp):
TTTTTAAAAAATTATATATTATACGTTTTCAAAAATTG
Found at i:159277 original size:25 final size:23
Alignment explanation
Indices: 159244--159321 Score: 96
Period size: 24 Copynumber: 3.6 Consensus size: 23
159234 AAAAAATGTT
159244 TTTTTAAAAACTATATATTATACA
1 TTTTTAAAAA-TATATATTATACA
159268 TTTTT-AAAA-ATATA-TAT---
1 TTTTTAAAAATATATATTATACA
159285 TTTTTAAAAATTATATATTATACA
1 TTTTTAAAAA-TATATATTATACA
159309 TTTTTAAAAATAT
1 TTTTTAAAAATAT
159322 TTTTTTAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 15
0.76 0.00 0.24
Matches are distributed among these distances:
17 5 0.11
18 4 0.09
20 8 0.17
21 8 0.17
23 7 0.15
24 15 0.32
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTTAAAAATATATATTATACA
Found at i:159286 original size:16 final size:17
Alignment explanation
Indices: 159260--159303 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
159250 AAAACTATAT
*
159260 ATTATACATTTTTAAAA
1 ATTATATATTTTTAAAA
159277 A-TATATATTTTTTAAAA
1 ATTATATA-TTTTTAAAA
159294 ATTATATATT
1 ATTATATATT
159304 ATACATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 5 0.21
17 13 0.54
18 6 0.25
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
ATTATATATTTTTAAAA
Found at i:159416 original size:157 final size:157
Alignment explanation
Indices: 159126--159495 Score: 399
Period size: 157 Copynumber: 2.4 Consensus size: 157
159116 TAAAAAAATC
159126 ATTTTTCTAAAAAAATATATTATACATTTTCAAAAATATGTTTTTAAAAAATTATATATTATACG
1 ATTTTTCTAAAAAAATATATTATACATTTTCAAAAATATGTTTTTAAAAAATTATATATTATACG
*
159191 TTTTAAAAAGTATTTTTTAAAAACTATATATTATATGGTTTTTAAAAAATGTTTTTTTAAAAACT
66 TTTTAAAAAGTATTTTTTAAAAACTATATATTATATGGTTTTTAAAAAATGTGTTTTTAAAAACT
*
159256 ATATATTATACATTTTTAAAAATATAT
131 ATATAATATACATTTTTAAAAATATAT
* * *
159283 ATTTTT-TAAAAATTATATATTATACATTTTTAAAAATATTTTTTTAAAAAATTATATATTATAC
1 ATTTTTCTAAAAA-AATATATTATACATTTTCAAAAATATGTTTTTAAAAAATTATATATTATAC
* * * *
159347 GTTTTCAAAAA-T-TGTTTTTCAAAGCTATATAATATATAT-ATGTTTTCAAAAAT-TGTTTTT-
65 GTTTT-AAAAAGTAT-TTTTTAAAAACTATAT-AT-TATATGGT-TTTTAAAAAATGTGTTTTTA
* * *
159407 GAAATTATATAATAT--ATGTTTTCAAAA-AT-T
125 AAAACTATATAATATACAT-TTTTAAAAATATAT
* ** ** * * *
159437 -GTTTT-TAAAACTATATATTATAGGTTTTCAAATAT-TGTTTTT-CAAAATTATATAATATA
1 ATTTTTCTAAAAAAATATATTATACATTTTCAAAAATATGTTTTTAAAAAATTATATATTATA
159496 TATATATTTT
Statistics
Matches: 185, Mismatches: 21, Indels: 21
0.81 0.09 0.09
Matches are distributed among these distances:
150 15 0.08
151 6 0.03
152 20 0.11
153 9 0.05
154 1 0.01
155 4 0.02
156 15 0.08
157 86 0.46
158 14 0.08
159 15 0.08
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (157 bp):
ATTTTTCTAAAAAAATATATTATACATTTTCAAAAATATGTTTTTAAAAAATTATATATTATACG
TTTTAAAAAGTATTTTTTAAAAACTATATATTATATGGTTTTTAAAAAATGTGTTTTTAAAAACT
ATATAATATACATTTTTAAAAATATAT
Found at i:159429 original size:36 final size:36
Alignment explanation
Indices: 159152--159670 Score: 332
Period size: 36 Copynumber: 13.8 Consensus size: 36
159142 ATATTATACA
* *
159152 TTTTCAAAAATATGTTTTTAAAAAATTATATATTATACG
1 TTTTCAAAAAT-TGTTTTT--AAAATTATATAATATATG
* *
159191 TTTT-AAAAAGTAT-TTTTTAAAAACTATATATTATATGG
1 TTTTCAAAAA-T-TGTTTTT-AAAATTATATAATATAT-G
* * * *
159229 TTTTTAAAAAATGTTTTTTTAAAAACTATATATTATACAT-
1 -TTTTCAAAAAT-TGTTTTT-AAAA-T-TATATAATATATG
* * * **
159269 TTTTAAAAATATATATTTTTTAAAAATTATATATTATACA
1 TTTTCAAAA-AT-T-GTTTTT-AAAATTATATAATATATG
* * * *
159309 TTTTTAAAAATATTTTTTTAAAAAATTATATATTATACG
1 TTTTCAAAAAT-TGTTTTT--AAAATTATATAATATATG
*
159348 TTTTCAAAAATTGTTTTTCAAAGCTATATAATATATATATG
1 TTTTCAAAAATTGTTTTT-AAA-AT-TAT-ATA-ATATATG
*
159389 TTTTCAAAAATTGTTTTTGAAATTATATAATATATG
1 TTTTCAAAAATTGTTTTTAAAATTATATAATATATG
* * *
159425 TTTTCAAAAATTGTTTTTAAAACTATATATTATAGG
1 TTTTCAAAAATTGTTTTTAAAATTATATAATATATG
* *
159461 TTTTCAAATATTGTTTTTCAAAATTATATAATATATA
1 TTTTCAAAAATTGTTTTT-AAAATTATATAATATATG
*** * * *
159498 TATATT-TTCAATTTTTTTTGAAATTATATAATATATA
1 T-T-TTCAAAAATTGTTTTTAAAATTATATAATATATG
* * ** *
159535 TTTTCAAAAATTATTTTTAAAATAATATTTTATACG
1 TTTTCAAAAATTGTTTTTAAAATTATATAATATATG
*
159571 TTTTCAAAAATTGTTTTTAAAACTATATAATATATG
1 TTTTCAAAAATTGTTTTTAAAATTATATAATATATG
* * * ** *
159607 TTTTTAAAACA-TATTTTCAAAACCATATTATATAT-
1 TTTTCAAAA-ATTGTTTTTAAAATTATATAATATATG
**
159642 TTTT-AAAAACAGATTTTTAAAATTATATA
1 TTTTCAAAAATTG-TTTTTAAAATTATATA
159671 TTATTGATTT
Statistics
Matches: 394, Mismatches: 64, Indels: 48
0.78 0.13 0.09
Matches are distributed among these distances:
33 1 0.00
34 4 0.01
35 18 0.05
36 136 0.35
37 56 0.14
38 36 0.09
39 68 0.17
40 32 0.08
41 34 0.09
42 9 0.02
ACGTcount: A:0.42, C:0.05, G:0.04, T:0.49
Consensus pattern (36 bp):
TTTTCAAAAATTGTTTTTAAAATTATATAATATATG
Found at i:159658 original size:146 final size:145
Alignment explanation
Indices: 159378--159659 Score: 334
Period size: 146 Copynumber: 1.9 Consensus size: 145
159368 AAGCTATATA
* * * * *
159378 ATATATATATGTTTTCAAAAATTGTTTTTGAAATTATATAATATATGTTTTCAAAAATTGTTTTT
1 ATATATATATATTTTCAAAAATTATTTTTAAAATAATATAATATACGTTTTCAAAAATTGTTTTT
* * * ** ****
159443 AAAACTATATATTATAGGTTTTCAAATATTGTTTTTCAAAATTATATAATATATATATATTTTCA
66 AAAACTATATAATATAGGTTTTCAAATAATGATTTTCAAAACCATATAATATATATATAAAAACA
159508 ATTTTTTTTGAAATT
131 ATTTTTTTTGAAATT
**
159523 ATATAATATATATTTTCAAAAATTATTTTTAAAATAATATTTTATACGTTTTCAAAAATTGTTTT
1 ATAT-ATATATATTTTCAAAAATTATTTTTAAAATAATATAATATACGTTTTCAAAAATTGTTTT
* * * * *
159588 TAAAACTATATAATATATGTTTTTAAA-ACAT-ATTTTCAAAACCATATTATATATTTTTAAAAA
65 TAAAACTATATAATATAGGTTTTCAAATA-ATGATTTTCAAAACCATATAATATATATATAAAAA
159651 CAGATTTTT
129 CA-ATTTTT
159660 AAAATTATAT
Statistics
Matches: 113, Mismatches: 21, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
145 29 0.26
146 84 0.74
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (145 bp):
ATATATATATATTTTCAAAAATTATTTTTAAAATAATATAATATACGTTTTCAAAAATTGTTTTT
AAAACTATATAATATAGGTTTTCAAATAATGATTTTCAAAACCATATAATATATATATAAAAACA
ATTTTTTTTGAAATT
Found at i:159682 original size:35 final size:34
Alignment explanation
Indices: 159584--159684 Score: 96
Period size: 35 Copynumber: 2.9 Consensus size: 34
159574 TCAAAAATTG
* * *
159584 TTTTTAAAACTATATAATATATGTTTTTAAAACATA
1 TTTTTAAAACTATATATTAT-TG-TTTAAAAACAGA
* *
159620 TTTTCAAAACCATATTATATATT-TTTAAAAACAGA
1 TTTTTAAAACTATA-TAT-TATTGTTTAAAAACAGA
*
159655 TTTTTAAAATTATATATTATTGATTTAAAA
1 TTTTTAAAACTATATATTATTG-TTTAAAA
159685 TGTTTAAATT
Statistics
Matches: 53, Mismatches: 8, Indels: 9
0.76 0.11 0.13
Matches are distributed among these distances:
33 4 0.08
34 3 0.06
35 28 0.53
36 12 0.23
37 3 0.06
38 3 0.06
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.47
Consensus pattern (34 bp):
TTTTTAAAACTATATATTATTGTTTAAAAACAGA
Found at i:169719 original size:21 final size:21
Alignment explanation
Indices: 169690--169752 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
169680 ATTGCTAGTA
* * *
169690 GCAATATCATTGCTGTGGCAT
1 GCAACATCATTGTTGTGGCAC
*
169711 GCAACATCATTTTTGTGGCAC
1 GCAACATCATTGTTGTGGCAC
*
169732 ACAACATCATTGTTGTGGCAC
1 GCAACATCATTGTTGTGGCAC
169753 TCATCCCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.32
Consensus pattern (21 bp):
GCAACATCATTGTTGTGGCAC
Found at i:175875 original size:3 final size:3
Alignment explanation
Indices: 175869--175925 Score: 62
Period size: 3 Copynumber: 19.0 Consensus size: 3
175859 AAATTATTAT
* *
175869 TAA TAA TAA TAC TAA TAT TAA TAA TAA TAA TAA -ATA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
* *
175914 TTA TTA TAA TAA
1 TAA TAA TAA TAA
175926 GTATAATATT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
2 1 0.02
3 44 0.96
4 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:175889 original size:18 final size:18
Alignment explanation
Indices: 175866--175914 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
175856 CCAAAATTAT
*
175866 TATTAATAATAATACTAA
1 TATTAATAATAATAATAA
175884 TATTAATAATAATAATAA
1 TATTAATAATAATAATAA
175902 -ATATAATAATAAT
1 TAT-TAATAATAAT
175915 TATTATAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 2 0.07
18 27 0.93
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TATTAATAATAATAATAA
Found at i:176590 original size:132 final size:131
Alignment explanation
Indices: 176162--177205 Score: 1754
Period size: 132 Copynumber: 7.9 Consensus size: 131
176152 TCTGCCCAAT
* * * *
176162 GTCTTAGGGATGGCCCAGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGAAGGAC
1 GTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
* *
176227 TTACAAATCAAGAAACCCCCGAAGTCTTAGTTTCTAAAATCTCATTTGAAAACATCATGCACTGA
66 TTACAAATCAAGAAA-CCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGA
176292 AG
130 AG
* *
176294 GTCTTATGGATGGCCCGGAGGACTTACACATCATGCTTGGAAGACTTACTGATGGCCCGGACGAC
1 GTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
*
176359 TTACAAATCAAGAAA-CCCGAAGGCTTAGTTTCTAAAATATCATTTGAAAACATCCTGCACTGAA
66 TTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAA
176423 G
131 G
*
176424 GTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGTCCGGAGGAC
1 GTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
*
176489 TTACAAATCAAGAAACCCTCGAAGGCTTAGTTTCTTAAAATCTCATTTGAAAACAT-CTTCACTG
66 TTACAAATCAAGAAACCC-CGAAGGCTTAGTTTC-TAAAATCTCATTTGAAAACATCCTGCACTG
176553 AAG
129 AAG
* *
176556 GTCTTATGGATGTCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCAGAGGAC
1 GTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
*
176621 TTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAATATCCTGCACTGA
66 TTACAAATCAAGAAA-CCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGA
176686 AG
130 AG
* *
176688 GTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCTCGGAGGAC
1 GTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
* *
176753 TTACAAATCAAGAAACGCCCGAAGGGTTAGTTT-TAAAATATCATTTGAAAACATCCTGCACTGA
66 TTACAAATCAAGAAAC-CCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGA
176817 AG
130 AG
176819 GTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
1 GTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
176884 TTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAAATCTCATTTGAAAACATCCTGCACTG
66 TTACAAATCAAGAAA-CCCCGAAGGCTTAGTTTC-TAAAATCTCATTTGAAAACATCCTGCACTG
176949 AAG
129 AAG
* * *
176952 GTCTTATGGATGGCCCAGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCTGGAGGAC
1 GTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
* *
177017 TTACAAATCAAGAAACCCCAAAGGATTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAA
66 TTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAA
177082 G
131 G
*
177083 GTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCC-GAGGAC
1 GTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
* *
177147 TTACAAATCAAGAAACGCCCGAAGGGTTAGTTTCTAAAATATCATTTGAAAACATCCTG
66 TTACAAATCAAGAAAC-CCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTG
177206 TTATTTGGGT
Statistics
Matches: 862, Mismatches: 40, Indels: 21
0.93 0.04 0.02
Matches are distributed among these distances:
130 146 0.17
131 275 0.32
132 309 0.36
133 132 0.15
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.25
Consensus pattern (131 bp):
GTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
TTACAAATCAAGAAACCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAA
G
Found at i:176884 original size:20 final size:21
Alignment explanation
Indices: 176827--176888 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
176817 AGGTCTTATG
176827 GATGGCCCGGAGGACTTACACAT
1 GATGGCCCGGAGGACTT--ACAT
* * *
176850 CAT-GCTCGGAAGACTTAC-T
1 GATGGCCCGGAGGACTTACAT
176869 GATGGCCCGGAGGACTTACA
1 GATGGCCCGGAGGACTTACA
176889 AATCAAGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
19 3 0.10
20 15 0.48
22 11 0.35
23 2 0.06
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (21 bp):
GATGGCCCGGAGGACTTACAT
Found at i:177048 original size:395 final size:395
Alignment explanation
Indices: 176162--177205 Score: 1853
Period size: 395 Copynumber: 2.6 Consensus size: 395
176152 TCTGCCCAAT
* *
176162 GTCTTAGGGATGGCCCAGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGAAGGAC
1 GTCTTATGGATGGCCCAGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
* *
176227 TTACAAATCAAGAAACCCCCGAAGTCTTAGTTTCTAAAATCTCATTTGAAAACATCATGCACTGA
66 TTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGA
* * *
176292 AGGTCTTATGGATGGCCCGGAGGACTTACACATCATGCTTGGAAGACTTACTGATGGCCCGGACG
131 AGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGG-CCGGAGG
*
176357 ACTTACAAATCAAGAAA--CCCGAAGGCTTAGTTTCTAAAATATCATTTGAAAACATCCTGCACT
195 ACTTACAAATCAAGAAACGCCCGAAGGGTTAGTTTCTAAAATATCATTTGAAAACATCCTGCACT
*
176420 GAAGGTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGTCCGGA
260 GAAGGTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGA
* *
176485 GGACTTACAAATCAAGAAACCCTCGAAGGCTTAGTTTCTTAAAATCTCATTTGAAAACATCTTCA
325 GGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAAATCTCATTTGAAAACATCTGCA
176550 CTGAAG
390 CTGAAG
* * * *
176556 GTCTTATGGATGTCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCAGAGGAC
1 GTCTTATGGATGGCCCAGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
*
176621 TTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAATATCCTGCACTGA
66 TTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGA
176686 AGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCTCGGAGG
131 AGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGC-CGGAGG
176751 ACTTACAAATCAAGAAACGCCCGAAGGGTTAGTTT-TAAAATATCATTTGAAAACATCCTGCACT
195 ACTTACAAATCAAGAAACGCCCGAAGGGTTAGTTTCTAAAATATCATTTGAAAACATCCTGCACT
176815 GAAGGTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGA
260 GAAGGTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGA
176880 GGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAAATCTCATTTGAAAACATCCTGC
325 GGACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAAATCTCATTTGAAAACAT-CTGC
176945 ACTGAAG
389 ACTGAAG
*
176952 GTCTTATGGATGGCCCAGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCTGGAGGAC
1 GTCTTATGGATGGCCCAGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
* *
177017 TTACAAATCAAGAAA-CCCCAAAGGATTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGA
66 TTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGA
*
177081 AGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGAGGA
131 AGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCGGAGGA
177146 CTTACAAATCAAGAAACGCCCGAAGGGTTAGTTTCTAAAATATCATTTGAAAACATCCTG
196 CTTACAAATCAAGAAACGCCCGAAGGGTTAGTTTCTAAAATATCATTTGAAAACATCCTG
177206 TTATTTGGGT
Statistics
Matches: 620, Mismatches: 25, Indels: 9
0.95 0.04 0.01
Matches are distributed among these distances:
393 1 0.00
394 238 0.38
395 281 0.45
396 100 0.16
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.25
Consensus pattern (395 bp):
GTCTTATGGATGGCCCAGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCCGGAGGAC
TTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGA
AGGTCTTATGGATGGCCCGGAGGACTTACGCATCATGCTCGGAAGACTTACTGATGGCCGGAGGA
CTTACAAATCAAGAAACGCCCGAAGGGTTAGTTTCTAAAATATCATTTGAAAACATCCTGCACTG
AAGGTCTTATGGATGGCCCGGAGGACTTACACATCATGCTCGGAAGACTTACTGATGGCCCGGAG
GACTTACAAATCAAGAAACCCCCGAAGGCTTAGTTTCTTAAAATCTCATTTGAAAACATCTGCAC
TGAAG
Found at i:178531 original size:27 final size:28
Alignment explanation
Indices: 178451--178528 Score: 122
Period size: 28 Copynumber: 2.8 Consensus size: 28
178441 GGTTGACTTA
*
178451 GGAAGGT-ACGTGTTTCAGGTTAATTTG
1 GGAAGGTAATGTGTTTCAGGTTAATTTG
* *
178478 GGGAGGTAATGCGTTTCAGGTTAATTTG
1 GGAAGGTAATGTGTTTCAGGTTAATTTG
178506 GGAAGGTAATGTGTTTCAGGTTA
1 GGAAGGTAATGTGTTTCAGGTTA
178529 TTTTTGGTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 6 0.13
28 39 0.87
ACGTcount: A:0.23, C:0.06, G:0.35, T:0.36
Consensus pattern (28 bp):
GGAAGGTAATGTGTTTCAGGTTAATTTG
Found at i:179220 original size:12 final size:12
Alignment explanation
Indices: 179203--179292 Score: 53
Period size: 12 Copynumber: 7.3 Consensus size: 12
179193 ATCTCGTTCC
*
179203 TTTTTCTTTACT
1 TTTTTCTTTAAT
*
179215 TTTTTCTTCT-TT
1 TTTTTCTT-TAAT
*
179227 TTTTTCTTT-GT
1 TTTTTCTTTAAT
179238 TTTTTGCTTTATAT
1 TTTTT-CTTTA-AT
179252 TTTTTCTTT-AT
1 TTTTTCTTTAAT
*
179263 TATCCTTGCTTTAAT
1 T-T--TTTCTTTAAT
*
179278 TTTTT-TTTCAT
1 TTTTTCTTTAAT
179289 TTTT
1 TTTT
179293 CCTCTTTCTG
Statistics
Matches: 64, Mismatches: 6, Indels: 17
0.74 0.07 0.20
Matches are distributed among these distances:
11 19 0.30
12 24 0.38
13 5 0.08
14 13 0.20
15 3 0.05
ACGTcount: A:0.09, C:0.12, G:0.03, T:0.76
Consensus pattern (12 bp):
TTTTTCTTTAAT
Found at i:179232 original size:24 final size:26
Alignment explanation
Indices: 179203--179282 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 26
179193 ATCTCGTTCC
179203 TTTTTCTTTACTTTTTT-CTTCT-T-T
1 TTTTTCTTTACTTTTTTGCTT-TATAT
*
179227 TTTTTCTTT-GTTTTTTGCTTTATAT
1 TTTTTCTTTACTTTTTTGCTTTATAT
*
179252 TTTTTCTTTA-TTATCCTTGCTTTA-AT
1 TTTTTCTTTACTT-T-TTTGCTTTATAT
179278 TTTTT
1 TTTTT
179283 TTTCATTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
23 7 0.15
24 13 0.27
25 12 0.25
26 8 0.17
27 8 0.17
ACGTcount: A:0.09, C:0.12, G:0.04, T:0.75
Consensus pattern (26 bp):
TTTTTCTTTACTTTTTTGCTTTATAT
Found at i:179254 original size:14 final size:13
Alignment explanation
Indices: 179203--179262 Score: 56
Period size: 12 Copynumber: 4.8 Consensus size: 13
179193 ATCTCGTTCC
*
179203 TTTTTCTTTA-CT
1 TTTTTCTTTATAT
179215 TTTTTCTTCT-T-T
1 TTTTTCTT-TATAT
*
179227 TTTTTCTTTGT-T
1 TTTTTCTTTATAT
*
179239 TTTTGCTTTATAT
1 TTTTTCTTTATAT
179252 TTTTTCTTTAT
1 TTTTTCTTTAT
179263 TATCCTTGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
11 1 0.02
12 28 0.68
13 12 0.29
ACGTcount: A:0.07, C:0.12, G:0.03, T:0.78
Consensus pattern (13 bp):
TTTTTCTTTATAT
Found at i:179295 original size:27 final size:28
Alignment explanation
Indices: 179224--179295 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 28
179214 TTTTTTCTTC
**
179224 TTTTTTTTC-TTTGTTTTTTGCTTTATAT
1 TTTTTTTTCATTT-TTCCTTGCTTTATAT
*
179252 TTTTTCTTT-A-TTATCCTTGCTTTA-AT
1 TTTTT-TTTCATTTTTCCTTGCTTTATAT
179278 TTTTTTTTCATTTTTCCT
1 TTTTTTTTCATTTTTCCT
179296 CTTTCTGCTC
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
25 3 0.08
26 8 0.22
27 15 0.42
28 7 0.19
29 3 0.08
ACGTcount: A:0.10, C:0.12, G:0.04, T:0.74
Consensus pattern (28 bp):
TTTTTTTTCATTTTTCCTTGCTTTATAT
Found at i:180453 original size:6 final size:6
Alignment explanation
Indices: 180437--180568 Score: 59
Period size: 6 Copynumber: 20.5 Consensus size: 6
180427 AAAATGTTTA
* * *
180437 AAATG- AAATGC AAATGC AAAATGC AAAGATGT AAATGC AGATGC AAATGTA
1 AAATGC AAATGC AAATGC -AAATGC -AA-ATGC AAATGC AAATGC AAATG-C
* * * * * *
180488 AAGATGT AAATGC AGATGT AAATGC AAATATGT AAATAC AGATGC AAAATGC
1 AA-ATGC AAATGC AAATGC AAATGC -AA-ATGC AAATGC AAATGC -AAATGC
* * *
180540 AAAGATGT AAATGC ATATGC AAATAC AAA
1 -AA-ATGC AAATGC AAATGC AAATGC AAA
180569 GATGTAAATG
Statistics
Matches: 96, Mismatches: 22, Indels: 17
0.71 0.16 0.13
Matches are distributed among these distances:
5 5 0.05
6 50 0.52
7 29 0.30
8 12 0.12
ACGTcount: A:0.51, C:0.10, G:0.18, T:0.21
Consensus pattern (6 bp):
AAATGC
Done.