Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006164.1 Corchorus capsularis cultivar CVL-1 contig06182, 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: 145571
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:3185 original size:16 final size:16
Alignment explanation
Indices: 3164--3194 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3154 CTTTTCATGA
3164 AAAAAAAAAACAAAAC
1 AAAAAAAAAACAAAAC
3180 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
3195 TATGCACCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAACAAAAC
Found at i:12414 original size:11 final size:11
Alignment explanation
Indices: 12400--12459 Score: 52
Period size: 11 Copynumber: 5.6 Consensus size: 11
12390 AAATAATTTA
*
12400 TTATATATTTT
1 TTATATATATT
*
12411 TTATATATATC
1 TTATATATATT
* * *
12422 ATAAATATA-A
1 TTATATATATT
12432 TT-TATATATT
1 TTATATATATT
*
12442 TTACATATATT
1 TTATATATATT
12453 TTATATA
1 TTATATA
12460 GACTAAATAG
Statistics
Matches: 37, Mismatches: 10, Indels: 4
0.73 0.20 0.08
Matches are distributed among these distances:
9 5 0.14
10 3 0.08
11 29 0.78
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (11 bp):
TTATATATATT
Found at i:12439 original size:20 final size:20
Alignment explanation
Indices: 12414--12459 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
12404 ATATTTTTTA
12414 TATATATCATAAATATAATT
1 TATATATCATAAATATAATT
** * *
12434 TATATATTTTACATATATTT
1 TATATATCATAAATATAATT
12454 TATATA
1 TATATA
12460 GACTAAATAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.52
Consensus pattern (20 bp):
TATATATCATAAATATAATT
Found at i:13172 original size:13 final size:13
Alignment explanation
Indices: 13154--13178 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13144 GAAGACATAA
13154 CATTTCAAGAATG
1 CATTTCAAGAATG
13167 CATTTCAAGAAT
1 CATTTCAAGAAT
13179 TATTCAAAAT
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:0.40, C:0.16, G:0.12, T:0.32
Consensus pattern (13 bp):
CATTTCAAGAATG
Found at i:14649 original size:9 final size:9
Alignment explanation
Indices: 14637--14666 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
14627 TTTAAACTGC
14637 CTAAACCGA
1 CTAAACCGA
14646 CTAAACCGA
1 CTAAACCGA
14655 CTAAACCG-
1 CTAAACCGA
14663 CTAA
1 CTAA
14667 GTCACCGAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 4 0.19
9 17 0.81
ACGTcount: A:0.43, C:0.33, G:0.10, T:0.13
Consensus pattern (9 bp):
CTAAACCGA
Found at i:16792 original size:19 final size:20
Alignment explanation
Indices: 16764--16809 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
16754 AAAAATTACT
*
16764 TTTTTCTATTTCTTCTTTTC
1 TTTTTCTATTTCCTCTTTTC
16784 TTTTT-TATTTCCTCTTTTC
1 TTTTTCTATTTCCTCTTTTC
16803 TTTTTCT
1 TTTTTCT
16810 TCTTCCTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTCTATTTCCTCTTTTC
Found at i:18592 original size:66 final size:66
Alignment explanation
Indices: 18533--18721 Score: 251
Period size: 66 Copynumber: 2.9 Consensus size: 66
18523 AAGATGAAAA
* * * *
18533 TGACCTTTCGACCGGAAGGGTGTTTTTGGAAACGAAGATACTAAACTTGAATGCTAAAGACAATA
1 TGACCTTTCGACCGAAAGGGTATTTTTGGAAATGAAGATACTAAACTTGAATGCAAAAGACAATA
18598 C
66 C
18599 TGACCCTTT-GACCGAAAGGGTATTCTTT-GAAATG-AGAATACTAAACTTGAATGCAAAAGACA
1 TGA-CCTTTCGACCGAAAGGGTATT-TTTGGAAATGAAG-ATACTAAACTTGAATGCAAAAGACA
18661 ATAC
63 ATAC
* * *
18665 TGACCCTTCGACCGAAAGGGTATTTCTGGAAATGAAAATACCT-AACTTGAATGCAAA
1 TGACCTTTCGACCGAAAGGGTATTTTTGGAAATGAAGATA-CTAAACTTGAATGCAAA
18722 GGTACTCTTT
Statistics
Matches: 109, Mismatches: 7, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
65 8 0.07
66 90 0.83
67 11 0.10
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.25
Consensus pattern (66 bp):
TGACCTTTCGACCGAAAGGGTATTTTTGGAAATGAAGATACTAAACTTGAATGCAAAAGACAATA
C
Found at i:18856 original size:65 final size:67
Alignment explanation
Indices: 18769--19015 Score: 284
Period size: 67 Copynumber: 3.7 Consensus size: 67
18759 CAACCTGATA
** *
18769 AAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAA-GTTAA-ACTAAACCTGAATGCAAAAAGA
1 AAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTGAATGCAAAAAGA
18832 TG
66 TG
* * *
18834 AAACTGACCCTTCGACCAAAAGGGTATTTCTGGAAACAAAAATACTAAACTTGAATGCAAAAAGA
1 AAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTGAATGCAAAAAGA
**
18899 CA
66 TG
* * *
18901 AAACTGACCCTGT-GACCGAAAGGGTATTTTTGGAAATGAAAATACTAGACTTAAATGCAACAAC
1 AAACTGACCCT-TCGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTGAATGCAA-AA-
*
18965 CTGATG
63 -AGATG
* * * *
18971 AAACCGACCCTTTGACCGGAAGGGTATTTTTGGAAAGAGAAAATA
1 AAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAA-CGAAAATA
19016 AAACTTTACT
Statistics
Matches: 154, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
65 34 0.22
66 2 0.01
67 73 0.47
68 3 0.02
69 1 0.01
70 34 0.22
71 7 0.05
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.22
Consensus pattern (67 bp):
AAACTGACCCTTCGACCGAAAGGGTATTTTTGGAAACGAAAATACTAAACTTGAATGCAAAAAGA
TG
Found at i:19673 original size:16 final size:16
Alignment explanation
Indices: 19652--19682 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19642 CCAAGCTAAT
19652 TAAATTACTAAATCCC
1 TAAATTACTAAATCCC
*
19668 TAAATTACTATATCC
1 TAAATTACTAAATCC
19683 TGAATCTCTA
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:0.42, C:0.23, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAATTACTAAATCCC
Found at i:20009 original size:14 final size:15
Alignment explanation
Indices: 19974--20012 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
19964 CCTAGCCTTC
* *
19974 CTTTTCTTTTCTTTT
1 CTTTTCCTTTATTTT
19989 CTTTTCCTTTATTTT
1 CTTTTCCTTTATTTT
20004 -TTTTCCTTT
1 CTTTTCCTTT
20013 TTCTTCCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (15 bp):
CTTTTCCTTTATTTT
Found at i:23129 original size:36 final size:36
Alignment explanation
Indices: 23086--23250 Score: 186
Period size: 32 Copynumber: 4.8 Consensus size: 36
23076 CGGAGTTCAG
* *
23086 ATTAAGTTCTTTATTGACTCCACTTAATTACCCAGG
1 ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
23122 ATTAAGTTCTTTA-T---TCCACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
* * *
23154 ATTAAG-CCTTTTATTGACCCCACTTAATTACCCCGA
1 ATTAAGTTC-TTTATTGACTCCACTTAATTACCCTGA
23190 ATTAAGTTCTTTATT--CT--ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
** *
23222 ATTAAGCCCTTTATTGACTCTACTTAATT
1 ATTAAGTTCTTTATTGACTCCACTTAATT
23251 TCCTTCCCTG
Statistics
Matches: 109, Mismatches: 10, Indels: 20
0.78 0.07 0.14
Matches are distributed among these distances:
31 1 0.01
32 53 0.49
33 1 0.01
34 3 0.03
35 1 0.01
36 49 0.45
37 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (36 bp):
ATTAAGTTCTTTATTGACTCCACTTAATTACCCTGA
Found at i:23167 original size:68 final size:68
Alignment explanation
Indices: 23094--23250 Score: 260
Period size: 68 Copynumber: 2.3 Consensus size: 68
23084 AGATTAAGTT
*
23094 CTTTATTGACTCCACTTAATTACCCAGGATTAAGTTCTTTATTCCACTTAATTACCCTGAATTAA
1 CTTTATTGACTCCACTTAATTACCCAGAATTAAGTTCTTTATTCCACTTAATTACCCTGAATTAA
23159 GCC
66 GCC
* * * *
23162 TTTTATTGACCCCACTTAATTACCCCGAATTAAGTTCTTTATTCTACTTAATTACCCTGAATTAA
1 CTTTATTGACTCCACTTAATTACCCAGAATTAAGTTCTTTATTCCACTTAATTACCCTGAATTAA
23227 GCC
66 GCC
*
23230 CTTTATTGACTCTACTTAATT
1 CTTTATTGACTCCACTTAATT
23251 TCCTTCCCTG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 81 1.00
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (68 bp):
CTTTATTGACTCCACTTAATTACCCAGAATTAAGTTCTTTATTCCACTTAATTACCCTGAATTAA
GCC
Found at i:23291 original size:41 final size:41
Alignment explanation
Indices: 23246--23476 Score: 293
Period size: 41 Copynumber: 5.5 Consensus size: 41
23236 TGACTCTACT
*
23246 TAATTTCCTTCCCTGAAATTAAGTATGCGCTTTTCTTTACC
1 TAATTTCCTTCCTTGAAATTAAGTATGCGCTTTTCTTTACC
* *
23287 TAATTTCTTTCCTTGAAATTAAGTATGCGCTTGTCTTTACC
1 TAATTTCCTTCCTTGAAATTAAGTATGCGCTTTTCTTTACC
* * *
23328 TAATTTCCTTCCTTGAAATTAAGTATGTGCTTTACTATACC
1 TAATTTCCTTCCTTGAAATTAAGTATGCGCTTTTCTTTACC
* * *
23369 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTATCTTTACC
1 TAATTTCCTTCCTTGAAATTAAGTATGCGCTTTTCTTTACC
* * * *
23410 TAATTTCCTTCATTGAAATTAAGTCTTTTGACTGCTGTT-TTTACT
1 TAATTTCCTTCCTTGAAATTAAG---TATG-C-GCTTTTCTTTACC
23455 TAATTTCCTTCCTTGAAATTAA
1 TAATTTCCTTCCTTGAAATTAA
23477 TTCTTTTAAC
Statistics
Matches: 166, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
41 133 0.80
44 3 0.02
45 26 0.16
46 4 0.02
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (41 bp):
TAATTTCCTTCCTTGAAATTAAGTATGCGCTTTTCTTTACC
Found at i:23416 original size:123 final size:125
Alignment explanation
Indices: 23246--23476 Score: 333
Period size: 123 Copynumber: 1.8 Consensus size: 125
23236 TGACTCTACT
* * *
23246 TAATTTCCTTCCCTGAAATTAAGTATGCGCTTTTCTTTACCTAATTTCTTTCCTTGAAATTAAG-
1 TAATTTCCTTCCCTGAAATTAAGTATGCGCTTATCTTTACCTAATTTCCTTCATTGAAATTAAGT
23310 TATG-C-GCTTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTATGTGCTTTACTATACC
66 TATGACTGC-TGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTATGTGCTTTACTATACC
* * *
23369 TAATTTCCTTCCTTGAAATTAAGTCTGTGCTTATCTTTACCTAATTTCCTTCATTGAAATTAAGT
1 TAATTTCCTTCCCTGAAATTAAGTATGCGCTTATCTTTACCTAATTTCCTTCATTGAAATTAAG-
* * *
23434 CTTTTGACTGCTGTTTTTACTTAATTTCCTTCCTTGAAATTAA
65 -TTATGACTGCTGTCTTTACCTAATTTCCTTCCTTGAAATTAA
23477 TTCTTTTAAC
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
123 58 0.62
126 3 0.03
127 31 0.33
128 2 0.02
ACGTcount: A:0.24, C:0.20, G:0.10, T:0.46
Consensus pattern (125 bp):
TAATTTCCTTCCCTGAAATTAAGTATGCGCTTATCTTTACCTAATTTCCTTCATTGAAATTAAGT
TATGACTGCTGTCTTTACCTAATTTCCTTCCTTGAAATTAAGTATGTGCTTTACTATACC
Found at i:23463 original size:45 final size:44
Alignment explanation
Indices: 23242--23504 Score: 174
Period size: 41 Copynumber: 6.3 Consensus size: 44
23232 TTATTGACTC
* *
23242 TACTTAATTTCCTTCCCTGAAATTAAG---TATG-C-GCTTTTCTT
1 TACTTAATTTCCTTCCTTGAAATTAAGTCTTTTGACTGC-TTT-TT
* * *
23283 TACCTAATTTCTTTCCTTGAAATTAAG---TATG-C-GCTTGTCTT
1 TACTTAATTTCCTTCCTTGAAATTAAGTCTTTTGACTGCTT-T-TT
* * *
23324 TACCTAATTTCCTTCCTTGAAATTAAG---TATG--TGCTTTACTA
1 TACTTAATTTCCTTCCTTGAAATTAAGTCTTTTGACTGCTTT--TT
*
23365 TACCTAATTTCCTTCCTTGAAATTAAGTC---TG--TGCTTATCTT
1 TACTTAATTTCCTTCCTTGAAATTAAGTCTTTTGACTGCTT-T-TT
* *
23406 TACCTAATTTCCTTCATTGAAATTAAGTCTTTTGACTGCTGTTTT
1 TACTTAATTTCCTTCCTTGAAATTAAGTCTTTTGACTGCT-TTTT
* *
23451 TACTTAATTTCCTTCCTTGAAATTAATTCTTTTAACTGC--TTT
1 TACTTAATTTCCTTCCTTGAAATTAAGTCTTTTGACTGCTTTTT
23493 TACTTAATTTCC
1 TACTTAATTTCC
23505 ATGAATTAAG
Statistics
Matches: 199, Mismatches: 11, Indels: 23
0.85 0.05 0.10
Matches are distributed among these distances:
40 3 0.02
41 135 0.68
42 16 0.08
44 2 0.01
45 37 0.19
46 5 0.03
47 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.09, T:0.48
Consensus pattern (44 bp):
TACTTAATTTCCTTCCTTGAAATTAAGTCTTTTGACTGCTTTTT
Found at i:23723 original size:36 final size:37
Alignment explanation
Indices: 23471--24076 Score: 690
Period size: 36 Copynumber: 16.5 Consensus size: 37
23461 CCTTCCTTGA
* * * *
23471 AATTAATTCTTTTAACTGCTTTTACTTAATTTCCATG
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
* * *
23508 AATTAAGTCATTTTACTGCTTTTACTTAATTACCATG
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
* *
23545 AATTAAGTCCTTTTACTGCTTTTACTTAATTACCCGG
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
*
23582 AATTAAGTCCTTTAACTGTTTTTACTTAATTACCCTG
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
**
23619 AATTAAGTCCTTTAACTATTTTTACTTAATTACCCTG
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
* *
23656 AATTAAGTCCTTCAACTGCTTTTTACTTAATTACCCGG
1 AATTAAGTCCTTTAACTGC-TTTTACTTAATTACCCTG
* *
23694 AATTAAGT-CTTTGACTGCTTTTACTTAATTACCCTT
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
* *
23730 AATTAAAGTCCTCTAACTGCTTTTTACTTAATTACCCTT
1 AATT-AAGTCCTTTAACTGC-TTTTACTTAATTACCCTG
*
23769 AATTAAAGTCCTCTAACTGCTTTTTACTTAATTACCCTG
1 AATT-AAGTCCTTTAACTGC-TTTTACTTAATTACCCTG
* *
23808 AATTTAGTCCTTT-ACTGCTTTTACTTAATTACCCTT
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
* *
23844 AATTAAGTCCTCT-ACTGCTCTTACTTAATTACCCTG
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
* ** *
23880 AATTAAGTCC-TTGACTAATTTTACTTAATTACCCTT
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
* *
23916 AATTAAGTCCTCT-ACTGCTCTTACTTAATTACCCTG
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
* ** * *
23952 AATTAAGTCC-TTGACTAATTTTACTTAACTACCCTT
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
* * * * *
23988 AATTAAGTCCTCT-ATTGCTCTTATTTAATTACCATG
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
* * * * * *
24024 AACTAAGTTCTCT-ACTGATTTTACTTAATTACCTTC
1 AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
*
24060 AATTAAGTTC-TTAACTG
1 AATTAAGTCCTTTAACTG
24077 TGTTCTTTTG
Statistics
Matches: 496, Mismatches: 64, Indels: 19
0.86 0.11 0.03
Matches are distributed among these distances:
35 3 0.01
36 221 0.45
37 172 0.35
38 40 0.08
39 60 0.12
ACGTcount: A:0.27, C:0.21, G:0.07, T:0.44
Consensus pattern (37 bp):
AATTAAGTCCTTTAACTGCTTTTACTTAATTACCCTG
Found at i:24620 original size:25 final size:25
Alignment explanation
Indices: 24592--24659 Score: 82
Period size: 25 Copynumber: 2.7 Consensus size: 25
24582 AACCACACTA
**
24592 AAAGTTTAAAAGCCCAAATGCATTC
1 AAAGTTTAAAAGCCCAAATGCACGC
* *
24617 AAAGTTTAGAGGCCCAAATGCACGC
1 AAAGTTTAAAAGCCCAAATGCACGC
*
24642 AAAATTTAAAAAGCCCAA
1 AAAGTTT-AAAAGCCCAA
24660 GTCTAGAAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
25 27 0.77
26 8 0.23
ACGTcount: A:0.46, C:0.21, G:0.15, T:0.19
Consensus pattern (25 bp):
AAAGTTTAAAAGCCCAAATGCACGC
Found at i:27103 original size:96 final size:96
Alignment explanation
Indices: 26981--27179 Score: 389
Period size: 96 Copynumber: 2.1 Consensus size: 96
26971 CATTGTTGTA
26981 TGCTTGCTGCCATGAATCCTTTGAGACTAGTATCTTGTTCTGTTTGCTCTTTCTTGTTGCTTCTT
1 TGCTTGCTGCCATGAATCCTTTGAGACTAGTATCTTGTTCTGTTTGCTCTTTCTTGTTGCTTCTT
27046 TGTTGTTTGGTTTCTTACTCTTTCATGCTTC
66 TGTTGTTTGGTTTCTTACTCTTTCATGCTTC
27077 TGCTTGCTGCCATGAATCCTTTGAGACTAGTATCTTGTTCTGTTTGCTCTTTCTTGTTGCTTCTT
1 TGCTTGCTGCCATGAATCCTTTGAGACTAGTATCTTGTTCTGTTTGCTCTTTCTTGTTGCTTCTT
27142 TGTTGTTTGGTTTCTTACTCTTTCATGCTTC
66 TGTTGTTTGGTTTCTTACTCTTTCATGCTTC
27173 TGTCTTG
1 TG-CTTG
27180 TATGTTATCT
Statistics
Matches: 102, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 98 0.96
97 4 0.04
ACGTcount: A:0.09, C:0.21, G:0.18, T:0.52
Consensus pattern (96 bp):
TGCTTGCTGCCATGAATCCTTTGAGACTAGTATCTTGTTCTGTTTGCTCTTTCTTGTTGCTTCTT
TGTTGTTTGGTTTCTTACTCTTTCATGCTTC
Found at i:27520 original size:3 final size:3
Alignment explanation
Indices: 27512--27552 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
27502 CTAAATAATT
27512 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27553 TCTTAATTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:31868 original size:67 final size:66
Alignment explanation
Indices: 31805--31932 Score: 175
Period size: 66 Copynumber: 1.9 Consensus size: 66
31795 ACACCCAAAT
* * *
31805 ACCCGATCAAAAACCCAAACTGGAACAAGGATTTCCAGCAAAATCAAATGAACAAAAAAACCCAT
1 ACCCAATC-AAAACCC-AACTGGAACAAGGAATTACAGCAAAATCAAATGAACAAAAAAACCCAT
31870 ACA
64 ACA
* * * *
31873 ACCCAATCAAAATCCAAGTGGAGCAAGGAATTACAGCAAAATCAAATGAGCAAAAAAACC
1 ACCCAATCAAAACCCAACTGGAACAAGGAATTACAGCAAAATCAAATGAACAAAAAAACC
31933 AAAACATCTC
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
66 40 0.75
67 6 0.11
68 7 0.13
ACGTcount: A:0.52, C:0.24, G:0.12, T:0.12
Consensus pattern (66 bp):
ACCCAATCAAAACCCAACTGGAACAAGGAATTACAGCAAAATCAAATGAACAAAAAAACCCATAC
A
Found at i:32182 original size:14 final size:14
Alignment explanation
Indices: 32163--32192 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
32153 TTTTCTTTGA
32163 TAAAAATTCAAACT
1 TAAAAATTCAAACT
32177 TAAAAATTCAAACT
1 TAAAAATTCAAACT
32191 TA
1 TA
32193 GATTAAACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAAAATTCAAACT
Found at i:32724 original size:13 final size:12
Alignment explanation
Indices: 32708--32783 Score: 53
Period size: 13 Copynumber: 5.7 Consensus size: 12
32698 AGAGTAAAAA
32708 AAAAGAAAGAAGG
1 AAAAGAAA-AAGG
*
32721 AAAAGAAAAAGA
1 AAAAGAAAAAGG
32733 AAAAGAAGAAAAGAG
1 AAAAG-A-AAAAG-G
*
32748 AAAAATAAAAAAGG
1 -AAAA-GAAAAAGG
*
32762 AAAACGAAAAAAG
1 AAAA-GAAAAAGG
32775 AAAGAGAAA
1 AAA-AGAAA
32784 GCCACGTCAT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
12 8 0.16
13 26 0.51
14 7 0.14
15 5 0.10
16 5 0.10
ACGTcount: A:0.76, C:0.01, G:0.21, T:0.01
Consensus pattern (12 bp):
AAAAGAAAAAGG
Found at i:32726 original size:26 final size:25
Alignment explanation
Indices: 32688--32739 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
32678 CAGGTTGAGG
*
32688 AAGAAGGAGAAGAGTAAAA-AAAAAGA
1 AAGAAGGA-AA-AGAAAAAGAAAAAGA
32714 AAGAAGGAAAAGAAAAAGAAAAAGA
1 AAGAAGGAAAAGAAAAAGAAAAAGA
32739 A
1 A
32740 GAAAAGAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 6 0.25
25 10 0.42
26 8 0.33
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (25 bp):
AAGAAGGAAAAGAAAAAGAAAAAGA
Found at i:32729 original size:20 final size:20
Alignment explanation
Indices: 32706--32779 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 20
32696 GAAGAGTAAA
32706 AAAAAAGAAAGAAGGAAAAG
1 AAAAAAGAAAGAAGGAAAAG
*
32726 AAAAAGAAAAAGAA-GAAAAG
1 AAAAA-AGAAAGAAGGAAAAG
* *
32746 AGAAAAATAAAAAAGGAAAACG
1 A-AAAAAGAAAGAAGGAAAA-G
32768 AAAAAAGAAAGA
1 AAAAAAGAAAGA
32780 GAAAGCCACG
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
20 18 0.40
21 25 0.56
22 2 0.04
ACGTcount: A:0.77, C:0.01, G:0.20, T:0.01
Consensus pattern (20 bp):
AAAAAAGAAAGAAGGAAAAG
Found at i:32732 original size:6 final size:6
Alignment explanation
Indices: 32703--32783 Score: 53
Period size: 6 Copynumber: 13.3 Consensus size: 6
32693 GGAGAAGAGT
*
32703 AAAA-A AAAAGA AAGAAGG AAAAGA AAAAGA AAAAG- --AAGA AAAGAGA
1 AAAAGA AAAAGA AA-AAGA AAAAGA AAAAGA AAAAGA AAAAGA AAA-AGA
* * *
32749 AAAATAA AAAAGGA AAACGAA AAAAGA AAGAGA AA
1 AAAA-GA AAAA-GA AAAAG-A AAAAGA AAAAGA AA
32784 GCCACGTCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 15
0.72 0.10 0.18
Matches are distributed among these distances:
3 3 0.05
5 4 0.07
6 28 0.47
7 25 0.42
ACGTcount: A:0.78, C:0.01, G:0.20, T:0.01
Consensus pattern (6 bp):
AAAAGA
Found at i:32745 original size:29 final size:31
Alignment explanation
Indices: 32704--32776 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 31
32694 GAGAAGAGTA
* * *
32704 AAAAAAAAG-AAAGAAGGAAAA-GAAAAA-G
1 AAAAAGAAGAAAAGAAGAAAAATAAAAAAGG
32732 AAAAAGAAGAAAAG-AGAAAAATAAAAAAGG
1 AAAAAGAAGAAAAGAAGAAAAATAAAAAAGG
*
32762 AAAACGAA-AAAAGAA
1 AAAAAGAAGAAAAGAA
32777 AGAGAAAGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
28 14 0.38
29 14 0.38
30 9 0.24
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (31 bp):
AAAAAGAAGAAAAGAAGAAAAATAAAAAAGG
Found at i:32772 original size:7 final size:7
Alignment explanation
Indices: 32706--32777 Score: 60
Period size: 7 Copynumber: 10.4 Consensus size: 7
32696 GAAGAGTAAA
32706 AAAAAAG
1 AAAAAAG
*
32713 AAAGAAG
1 AAAAAAG
*
32720 -GAAAAG
1 AAAAAAG
32726 -AAAAAG
1 AAAAAAG
32732 -AAAAAG
1 AAAAAAG
32738 AAGAAAAG
1 AA-AAAAG
*
32746 AGAAAAAT
1 A-AAAAAG
32754 AAAAAAG
1 AAAAAAG
* *
32761 GAAAACG
1 AAAAAAG
32768 AAAAAAG
1 AAAAAAG
32775 AAA
1 AAA
32778 GAGAAAGCCA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
6 15 0.29
7 25 0.48
8 11 0.21
9 1 0.02
ACGTcount: A:0.78, C:0.01, G:0.19, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:38839 original size:54 final size:54
Alignment explanation
Indices: 38751--38857 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
38741 TCCTTAGATA
** *
38751 TCCTGCGGTGTGGCGTAAAACCTTCGGAAAGGGGAGGTTAGTTCCTACGGGGTGT
1 TCCTGCGGTGTGGCGTAAAACCTTCAAAAAGGGGAGGATAGTTCCTA-GGGGTGT
38806 TCCTGCAGG-GTGGCGT-AAACCTTCAAAAAGGGGAGGATAGTTCCTAGGGGTG
1 TCCTGC-GGTGTGGCGTAAAACCTTCAAAAAGGGGAGGATAGTTCCTAGGGGTG
38858 GCGTAAAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
53 6 0.12
54 27 0.56
55 13 0.27
56 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.37, T:0.23
Consensus pattern (54 bp):
TCCTGCGGTGTGGCGTAAAACCTTCAAAAAGGGGAGGATAGTTCCTAGGGGTGT
Found at i:38876 original size:27 final size:28
Alignment explanation
Indices: 38838--38892 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
38828 TCAAAAAGGG
38838 GAGGATAGTTCCT-AGGGGTGGCGTAAA
1 GAGGATAGTTCCTGAGGGGTGGCGTAAA
* *
38865 GAGGTTAGTTCCTGCGGGGTGGCGTAAA
1 GAGGATAGTTCCTGAGGGGTGGCGTAAA
38893 ACCTTCGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.22, C:0.13, G:0.42, T:0.24
Consensus pattern (28 bp):
GAGGATAGTTCCTGAGGGGTGGCGTAAA
Found at i:38933 original size:42 final size:42
Alignment explanation
Indices: 38865--39046 Score: 274
Period size: 42 Copynumber: 4.3 Consensus size: 42
38855 GTGGCGTAAA
38865 GAGGTTAGTTCCTGCGGGGTGGCGTAAAACCTTCGAAAAGGG
1 GAGGTTAGTTCCTGCGGGGTGGCGTAAAACCTTCGAAAAGGG
* * * *
38907 GAGGTTAGTTCCTGCGGAGTGTCGTAAAAACCTTCAAAAAAGG
1 GAGGTTAGTTCCTGCGGGGTGGCGT-AAAACCTTCGAAAAGGG
* * * *
38950 GAGGTTAGTTCCTTCGTGGTGGCGTCAAACCTTCGAAAATGG
1 GAGGTTAGTTCCTGCGGGGTGGCGTAAAACCTTCGAAAAGGG
*
38992 GAGGTTAGTTCCTGCGGGGTGGCTTAAAACCTTCGAAAAGGG
1 GAGGTTAGTTCCTGCGGGGTGGCGTAAAACCTTCGAAAAGGG
39034 GAGGTTAGTTCCT
1 GAGGTTAGTTCCT
39047 AGCAGTCAAT
Statistics
Matches: 123, Mismatches: 16, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
42 87 0.71
43 36 0.29
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (42 bp):
GAGGTTAGTTCCTGCGGGGTGGCGTAAAACCTTCGAAAAGGG
Found at i:39008 original size:85 final size:84
Alignment explanation
Indices: 38865--39046 Score: 274
Period size: 85 Copynumber: 2.2 Consensus size: 84
38855 GTGGCGTAAA
*
38865 GAGGTTAGTTCCTGCGGGGTGGCGTAAAACCTTCGAAAAGGGGAGGTTAGTTCCTGCGGAGTGTC
1 GAGGTTAGTTCCTGCGGGGTGGCGTAAAACCTTCGAAAAGGGGAGGTTAGTTCCTGCGGAGTGGC
38930 GTAAAAACCTTCAAAAAAGG
66 -TAAAAACCTTCAAAAAAGG
* * * * *
38950 GAGGTTAGTTCCTTCGTGGTGGCGTCAAACCTTCGAAAATGGGAGGTTAGTTCCTGCGGGGTGGC
1 GAGGTTAGTTCCTGCGGGGTGGCGTAAAACCTTCGAAAAGGGGAGGTTAGTTCCTGCGGAGTGGC
* * *
39015 TTAAAACCTTCGAAAAGGG
66 TAAAAACCTTCAAAAAAGG
39034 GAGGTTAGTTCCT
1 GAGGTTAGTTCCT
39047 AGCAGTCAAT
Statistics
Matches: 88, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
84 29 0.33
85 59 0.67
ACGTcount: A:0.25, C:0.17, G:0.33, T:0.25
Consensus pattern (84 bp):
GAGGTTAGTTCCTGCGGGGTGGCGTAAAACCTTCGAAAAGGGGAGGTTAGTTCCTGCGGAGTGGC
TAAAAACCTTCAAAAAAGG
Found at i:39443 original size:79 final size:79
Alignment explanation
Indices: 39310--39466 Score: 260
Period size: 79 Copynumber: 2.0 Consensus size: 79
39300 CTTGGATAAG
* *
39310 GATCGGTTTGAATCATTAGTGTTCAAGTTGGGTGTTACGAGTCTTCACGCGCCAACTTGAGGAGG
1 GATCGGTTTGAATCATTAGTGTTCAAGTTGGGCGTTACGAATCTTCACGCGCCAACTTGAGGAGG
*
39375 GAGTGGTGAAATCA
66 GAGTGATGAAATCA
* *
39389 GATCGGTTTGAATCATTAGTGTTCAAGTTGGGCGTTGCGAATCTTCACGTGCCAACTTGAGGAGG
1 GATCGGTTTGAATCATTAGTGTTCAAGTTGGGCGTTACGAATCTTCACGCGCCAACTTGAGGAGG
*
39454 GATTGATGAAATC
66 GAGTGATGAAATC
39467 GGTCAATAGT
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 72 1.00
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.30
Consensus pattern (79 bp):
GATCGGTTTGAATCATTAGTGTTCAAGTTGGGCGTTACGAATCTTCACGCGCCAACTTGAGGAGG
GAGTGATGAAATCA
Found at i:39561 original size:30 final size:30
Alignment explanation
Indices: 39525--39581 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
39515 TGATGGAATC
39525 AAGTCAACAGTGCATTTACAGCAGGATTCA
1 AAGTCAACAGTGCATTTACAGCAGGATTCA
* ** *
39555 AAGTCAATAGTGTGTTTACAGCGGGAT
1 AAGTCAACAGTGCATTTACAGCAGGAT
39582 CCTAGATTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.16, G:0.25, T:0.26
Consensus pattern (30 bp):
AAGTCAACAGTGCATTTACAGCAGGATTCA
Found at i:42602 original size:26 final size:26
Alignment explanation
Indices: 42513--42603 Score: 103
Period size: 26 Copynumber: 3.5 Consensus size: 26
42503 ACGCGCGAAG
* *
42513 TCACGTGTGGGGTCGTACGTTGGAGG
1 TCACGTGTGGAGTCGTACGTTGGAGA
* * * *
42539 TCACATGTTGAGAT-ATCCGTTGGAGA
1 TCACGTGTGGAG-TCGTACGTTGGAGA
*
42565 TCACGTGAGGAGTCGTACGTTGGAGA
1 TCACGTGTGGAGTCGTACGTTGGAGA
42591 TCACGTGTGGAGT
1 TCACGTGTGGAGT
42604 GCCAGCTGGC
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
25 1 0.02
26 49 0.96
27 1 0.02
ACGTcount: A:0.20, C:0.15, G:0.37, T:0.27
Consensus pattern (26 bp):
TCACGTGTGGAGTCGTACGTTGGAGA
Found at i:42671 original size:23 final size:24
Alignment explanation
Indices: 42643--42797 Score: 171
Period size: 23 Copynumber: 6.8 Consensus size: 24
42633 CTTGTGGTCA
* *
42643 TAAGTGGTCAGG-CGCCGGGCCTG
1 TAAGTGGTCAGGTCGCCAGGCTTG
*
42666 TAAGTGGTC-GGTTGCCAGGCTTG
1 TAAGTGGTCAGGTCGCCAGGCTTG
* *
42689 TAAGTGGTC-GGTCGTCGGGCTTG
1 TAAGTGGTCAGGTCGCCAGGCTTG
* *
42712 TAAGTGGT-AGGTTGCTAGGCTTG
1 TAAGTGGTCAGGTCGCCAGGCTTG
*
42735 TAAGTGGTC-GGTCGCCGGGCTTG
1 TAAGTGGTCAGGTCGCCAGGCTTG
* *
42758 TAAGTGGT-AGGTTGCTAGGCTTG
1 TAAGTGGTCAGGTCGCCAGGCTTG
42781 TAAGTGGTCA-GTCGCCA
1 TAAGTGGTCAGGTCGCCA
42798 AGCAATTGTG
Statistics
Matches: 109, Mismatches: 18, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
22 2 0.02
23 106 0.97
24 1 0.01
ACGTcount: A:0.14, C:0.17, G:0.40, T:0.28
Consensus pattern (24 bp):
TAAGTGGTCAGGTCGCCAGGCTTG
Found at i:42714 original size:46 final size:46
Alignment explanation
Indices: 42643--42796 Score: 247
Period size: 46 Copynumber: 3.3 Consensus size: 46
42633 CTTGTGGTCA
* * *
42643 TAAGTGGTCAGG-CGCCGGGCCTGTAAGTGGTCGGTTGCCAGGCTTG
1 TAAGTGGTC-GGTCGCCGGGCTTGTAAGTGGTAGGTTGCTAGGCTTG
*
42689 TAAGTGGTCGGTCGTCGGGCTTGTAAGTGGTAGGTTGCTAGGCTTG
1 TAAGTGGTCGGTCGCCGGGCTTGTAAGTGGTAGGTTGCTAGGCTTG
42735 TAAGTGGTCGGTCGCCGGGCTTGTAAGTGGTAGGTTGCTAGGCTTG
1 TAAGTGGTCGGTCGCCGGGCTTGTAAGTGGTAGGTTGCTAGGCTTG
*
42781 TAAGTGGTCAGTCGCC
1 TAAGTGGTCGGTCGCC
42797 AAGCAATTGT
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
45 2 0.02
46 99 0.98
ACGTcount: A:0.14, C:0.18, G:0.40, T:0.29
Consensus pattern (46 bp):
TAAGTGGTCGGTCGCCGGGCTTGTAAGTGGTAGGTTGCTAGGCTTG
Found at i:43414 original size:37 final size:37
Alignment explanation
Indices: 43357--43793 Score: 613
Period size: 37 Copynumber: 11.8 Consensus size: 37
43347 GAGGTGGTCT
* * *
43357 GTGGCGATCGACACATTTTGTCAGCTTGTCGAACGAT
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
* * *
43394 GTGCCGGTCGACACTTTTTGTCAGCTTGTCGAGCGAT
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
* *
43431 GTGGCGGTCGACACGTTTTGTCAACTTGTCGAGCGAC
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
* * *
43468 GTGGCGGTCGACACTTTTTGTCATCTTCGTCGAGCGAT
1 GTGGCGGTCGACACATTTTGTCAGCTT-GTCGAGCGAC
*
43506 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGTGAC
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
* *
43543 TTGGCGGTCGACATATTTTGTCAGCTTGTCGAGCGAC
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
* *
43580 GTGGCGGTCGACATATTTTTTCAGCTTGTCGAGCGAC
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
* *
43617 GTGGCGGTCGGCACATTTTGTCAGCTTGTCGAGCAAC
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
*
43654 GTGGCGGTCGACATATTTTGTCAGCTTTGTCGAGCGAC
1 GTGGCGGTCGACACATTTTGTCAGC-TTGTCGAGCGAC
* * *
43692 GTGGCGGTCGACACATTTTGACAACTTGTCGAACGAC
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
* * *
43729 GTGGCGGTCGACACATTTTGTCAGCTTGTCGGGCAAT
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
**
43766 GTGGCGGTCGACACATTTCATCAGCTTG
1 GTGGCGGTCGACACATTTTGTCAGCTTG
43794 GCTTTGTTGC
Statistics
Matches: 359, Mismatches: 39, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
37 292 0.81
38 67 0.19
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (37 bp):
GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGAC
Found at i:43626 original size:149 final size:148
Alignment explanation
Indices: 43356--43793 Score: 601
Period size: 149 Copynumber: 2.9 Consensus size: 148
43346 TGAGGTGGTC
* * *
43356 TGTGGCGATCGACACATTTTGTCAGCTTGTCGAACGA-TGTGCCGGTCGACACT-TTTTGTCAGC
1 TGTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGACT-TGGCGGTCGACA-TATTTTGTCAGC
* * * *
43419 TTGTCGAGCGATGTGGCGGTCGACACGTTTTGTCAACTTGTCGAGCGACGTGGCGGTCGACACTT
64 TTGTCGAGCGACGTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGACGTGGCGGTCGACACAT
* *
43484 TTTGTCATCTTCGTCGAGCGA
129 TTTGTCAGCTT-GTCGAGCAA
*
43505 TGTGGCGGTCGACACATTTTGTCAGCTTGTCGAGTGACTTGGCGGTCGACATATTTTGTCAGCTT
1 TGTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGACTTGGCGGTCGACATATTTTGTCAGCTT
* * *
43570 GTCGAGCGACGTGGCGGTCGACATATTTTTTCAGCTTGTCGAGCGACGTGGCGGTCGGCACATTT
66 GTCGAGCGACGTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGACGTGGCGGTCGACACATTT
43635 TGTCAGCTTGTCGAGCAA
131 TGTCAGCTTGTCGAGCAA
* * * * * *
43653 CGTGGCGGTCGACATATTTTGTCAGCTTTGTCGAGCGACGTGGCGGTCGACACATTTTGACAACT
1 TGTGGCGGTCGACACATTTTGTCAGC-TTGTCGAGCGACTTGGCGGTCGACATATTTTGTCAGCT
* * * *
43718 TGTCGAACGACGTGGCGGTCGACACATTTTGTCAGCTTGTCGGGCAATGTGGCGGTCGACACATT
65 TGTCGAGCGACGTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGACGTGGCGGTCGACACATT
**
43783 TCATCAGCTTG
130 TTGTCAGCTTG
43794 GCTTTGTTGC
Statistics
Matches: 257, Mismatches: 29, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
148 33 0.13
149 223 0.87
150 1 0.00
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (148 bp):
TGTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGACTTGGCGGTCGACATATTTTGTCAGCTT
GTCGAGCGACGTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGACGTGGCGGTCGACACATTT
TGTCAGCTTGTCGAGCAA
Found at i:43688 original size:186 final size:186
Alignment explanation
Indices: 43357--43793 Score: 626
Period size: 186 Copynumber: 2.3 Consensus size: 186
43347 GAGGTGGTCT
* * * *
43357 GTGGCGATCGACACATTTTGTCAGCTTGTCGAACGATGTGCCGGTCGACACT-TTTTGTCAGCTT
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGATGTGGCGGTCGACA-TATTTTATCAGCTT
* * *
43421 GTCGAGCGATGTGGCGGTCGACACGTTTTGTCAACTTGTCGAGCGACGTGGCGGTCGACACTTTT
65 GTCGAGCGACGTGGCGGTCGACACATTTTGTCAACTTGTCGAGCAACGTGGCGGTCGACACTTTT
* * * * **
43486 TGTCATCTTCGTCGAGCGATGTGGCGGTCGACACATTTTGTCAGCTTGTCGAGTGAC
130 TGTCAGCTTCGTCGAGCGACGTGGCGGTCGACACATTTTGACAACTTGTCGAACGAC
* * * *
43543 TTGGCGGTCGACATATTTTGTCAGCTTGTCGAGCGACGTGGCGGTCGACATATTTTTTCAGCTTG
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGATGTGGCGGTCGACATATTTTATCAGCTTG
* *
43608 TCGAGCGACGTGGCGGTCGGCACATTTTGTCAGCTTGTCGAGCAACGTGGCGGTCGACA-TATTT
66 TCGAGCGACGTGGCGGTCGACACATTTTGTCAACTTGTCGAGCAACGTGGCGGTCGACACT-TTT
*
43672 TGTCAGCTTTGTCGAGCGACGTGGCGGTCGACACATTTTGACAACTTGTCGAACGAC
130 TGTCAGCTTCGTCGAGCGACGTGGCGGTCGACACATTTTGACAACTTGTCGAACGAC
* * * *
43729 GTGGCGGTCGACACATTTTGTCAGCTTGTCGGGCAATGTGGCGGTCGACACATTTCATCAGCTTG
1 GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGATGTGGCGGTCGACATATTTTATCAGCTTG
43794 GCTTTGTTGC
Statistics
Matches: 222, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
185 2 0.01
186 220 0.99
ACGTcount: A:0.17, C:0.23, G:0.30, T:0.30
Consensus pattern (186 bp):
GTGGCGGTCGACACATTTTGTCAGCTTGTCGAGCGATGTGGCGGTCGACATATTTTATCAGCTTG
TCGAGCGACGTGGCGGTCGACACATTTTGTCAACTTGTCGAGCAACGTGGCGGTCGACACTTTTT
GTCAGCTTCGTCGAGCGACGTGGCGGTCGACACATTTTGACAACTTGTCGAACGAC
Found at i:45416 original size:44 final size:44
Alignment explanation
Indices: 45348--45579 Score: 401
Period size: 44 Copynumber: 5.3 Consensus size: 44
45338 TTCTTGCTTT
* * **
45348 TGGTCGGTCGACTAGTTACATTTCTTCTTACTTTGAATGTGATG
1 TGGTCGATCGACTAGTTACTTTTCTTCTTGGTTTGAATGTGATG
45392 TGGTCGATCGACTAGTTACTTTTCTTCTTGGTTTGAATGTGATG
1 TGGTCGATCGACTAGTTACTTTTCTTCTTGGTTTGAATGTGATG
45436 TGGTCGATCGACTAGTTACTTTTCTTCTTGGTTTGAATGTGATG
1 TGGTCGATCGACTAGTTACTTTTCTTCTTGGTTTGAATGTGATG
*
45480 TGGTCGATCGACTAGTTACTTTTCTTCGTGGTTTGAATGTGATG
1 TGGTCGATCGACTAGTTACTTTTCTTCTTGGTTTGAATGTGATG
*
45524 TGGTCGATCGACTAGTTACCTTTCTTCTTGGTTTGAATGTGATG
1 TGGTCGATCGACTAGTTACTTTTCTTCTTGGTTTGAATGTGATG
*
45568 TGGTTGATCGAC
1 TGGTCGATCGAC
45580 GCATTTCTCC
Statistics
Matches: 180, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 180 1.00
ACGTcount: A:0.16, C:0.15, G:0.25, T:0.44
Consensus pattern (44 bp):
TGGTCGATCGACTAGTTACTTTTCTTCTTGGTTTGAATGTGATG
Found at i:45616 original size:132 final size:131
Alignment explanation
Indices: 45346--45621 Score: 367
Period size: 132 Copynumber: 2.1 Consensus size: 131
45336 AGTTCTTGCT
* *
45346 TTTGGTCGGTCGACTAGTTACATTTCTTCTTACTTTGAATGTGATGTGGTCGATCGACTAGTTAC
1 TTTGGTCGATCGACTAGTTACATTTCTTCGTACTTTGAATGTGATGTGGTCGATCGACTAGTTAC
* * * *
45411 TTTTCTTCTTGGTTTGAATGTGATGTGGTCGATCGACTAGTTACTTTTCTTCTTGGTTTGAATGT
66 CTTTCTTCTTGGTTTGAATGTGATGTGGTCGATCGACCAGTTACTTTTCTTC-TGGCTTGAATGC
*
45476 GA
130 AA
* * **
45478 TGTGGTCGATCGACTAGTTACTTTTCTTCGTGGTTTGAATGTGATGTGGTCGATCGACTAGTTAC
1 TTTGGTCGATCGACTAGTTACATTTCTTCGTACTTTGAATGTGATGTGGTCGATCGACTAGTTAC
* * **
45543 CTTTCTTCTTGGTTTGAATGTGATGTGGTTGATCGACGCA-TTTCTCCTTTCTTC-GGCTTGGGT
66 CTTTCTTCTTGGTTTGAATGTGATGTGGTCGATCGAC-CAGTTACT--TTTCTTCTGGCTTGAAT
45606 GCAA
128 GCAA
45610 TTTGGTCGATCG
1 TTTGGTCGATCG
45622 CCACCTTTTC
Statistics
Matches: 125, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
132 117 0.94
133 1 0.01
134 7 0.06
ACGTcount: A:0.15, C:0.16, G:0.25, T:0.43
Consensus pattern (131 bp):
TTTGGTCGATCGACTAGTTACATTTCTTCGTACTTTGAATGTGATGTGGTCGATCGACTAGTTAC
CTTTCTTCTTGGTTTGAATGTGATGTGGTCGATCGACCAGTTACTTTTCTTCTGGCTTGAATGCA
A
Found at i:45891 original size:25 final size:25
Alignment explanation
Indices: 45863--45924 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
45853 CATTCGGCGC
45863 TTGGCGAGCGTCCTACGCTTCGCGT
1 TTGGCGAGCGTCCTACGCTTCGCGT
45888 TTGGCGAGCGTCCTACGCTTCGCGT
1 TTGGCGAGCGTCCTACGCTTCGCGT
* *
45913 TAGGCGAACGTC
1 TTGGCGAGCGTC
45925 ATCTTTTTCG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.11, C:0.31, G:0.32, T:0.26
Consensus pattern (25 bp):
TTGGCGAGCGTCCTACGCTTCGCGT
Found at i:46613 original size:89 final size:87
Alignment explanation
Indices: 46500--46719 Score: 296
Period size: 89 Copynumber: 2.5 Consensus size: 87
46490 ATCGTCTACC
* *
46500 CTGCTGGCGTTGAGCCTCTTGGGGCGTTCATCGTTCCCATAAGTTGGGAGCCATGCTAGGTCAGG
1 CTGCTGGCGTTGAGCC-CTTGGGGCATTCATCATTCCCATAAGTTGGGAGCCATGCTAGGTCAGG
* * *
46565 GTCAAATCTTGTCGATCGCCCGG
65 GTCAAATCTTGTCAATCACCCCG
* * *
46588 CTGCTGGGGTTGAGTCCCTTGGGGGCATTCGTCATTCCCATAAGTTGGGGGCCATGCTAGGTCAG
1 CTGCTGGCGTTGAG-CCCTT-GGGGCATTCATCATTCCCATAAGTTGGGAGCCATGCTAGGTCAG
*
46653 GGTCAACTCTTGTCAATCACCCCG
64 GGTCAAATCTTGTCAATCACCCCG
*
46677 CGTGCTGGCGTTGAGCCCCTTAGGGGCATTCATAATTCCCATA
1 C-TGCTGGCGTTGAG-CCCTT-GGGGCATTCATCATTCCCATA
46720 CTTGTCCAGG
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
88 16 0.14
89 63 0.55
90 36 0.31
ACGTcount: A:0.16, C:0.27, G:0.30, T:0.27
Consensus pattern (87 bp):
CTGCTGGCGTTGAGCCCTTGGGGCATTCATCATTCCCATAAGTTGGGAGCCATGCTAGGTCAGGG
TCAAATCTTGTCAATCACCCCG
Found at i:46909 original size:90 final size:90
Alignment explanation
Indices: 46755--46926 Score: 272
Period size: 90 Copynumber: 1.9 Consensus size: 90
46745 ATCTCCTACT
* *** *
46755 AGTTGGGGGCCATGTTAGGTCAAGGTCGGTTCTTGTCGATCGCCCAGCCTGCTGGCGTTAAGCCC
1 AGTTGGGGGCCATGCTAGGTCAAGGTCAAATCTTGTCGATCGCCCAGCCTGCTAGCGTTAAGCCC
46820 CTTGGGGGCGTTCGTCATTCCCATA
66 CTTGGGGGCGTTCGTCATTCCCATA
* * *
46845 AGTTGGGGGCCATGCTAGGTCAGGGTCAAATCTTGTCGATCGCCCCGCCTGCTAGCGTTGAGCCC
1 AGTTGGGGGCCATGCTAGGTCAAGGTCAAATCTTGTCGATCGCCCAGCCTGCTAGCGTTAAGCCC
46910 CTTGGGGGCGTTCGTCA
66 CTTGGGGGCGTTCGTCA
46927 AGTATAATTT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
90 74 1.00
ACGTcount: A:0.13, C:0.27, G:0.33, T:0.26
Consensus pattern (90 bp):
AGTTGGGGGCCATGCTAGGTCAAGGTCAAATCTTGTCGATCGCCCAGCCTGCTAGCGTTAAGCCC
CTTGGGGGCGTTCGTCATTCCCATA
Found at i:49619 original size:23 final size:23
Alignment explanation
Indices: 49580--49640 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
49570 CCTTGTGGTC
* *
49580 GTAAGTGGTCAAG-CGCCGGGCCT
1 GTAAGTGGTC-GGTCGCCAGGCCT
*
49603 GTAAGTGGTCGGTCGCCAGGCTT
1 GTAAGTGGTCGGTCGCCAGGCCT
*
49626 ATAAGTGGTCGGTCG
1 GTAAGTGGTCGGTCG
49641 ACAGTGGTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.16, C:0.21, G:0.39, T:0.23
Consensus pattern (23 bp):
GTAAGTGGTCGGTCGCCAGGCCT
Found at i:49651 original size:23 final size:23
Alignment explanation
Indices: 49604--49652 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
49594 GCCGGGCCTG
* *
49604 TAAGTGGTCGGTCGCCAGGCTTA
1 TAAGTGGTCGGTCGACAGGCGTA
49627 TAAGTGGTCGGTCGACAGTG-GTA
1 TAAGTGGTCGGTCGACAG-GCGTA
49650 TAA
1 TAA
49653 TTGTCACTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.22, C:0.16, G:0.35, T:0.27
Consensus pattern (23 bp):
TAAGTGGTCGGTCGACAGGCGTA
Found at i:53098 original size:1 final size:1
Alignment explanation
Indices: 53092--53125 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
53082 CGGGTGTAAG
53092 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
53126 GAGTGAGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:54251 original size:81 final size:81
Alignment explanation
Indices: 54116--54382 Score: 525
Period size: 81 Copynumber: 3.3 Consensus size: 81
54106 CTACCGTTGG
54116 TTTAAACTCCAAACTAATTTCTATAGTAAATGAATTTAGAGTTTAAAGTTTAAATTTTAAGTTTA
1 TTTAAACTCCAAACTAATTTCTATAGTAAATGAATTTAGAGTTTAAAGTTTAAATTTTAAGTTTA
54181 GACTATGGAGGCTTCT
66 GACTATGGAGGCTTCT
54197 TTTAAACTCCAAACTAATTTCTATAGTAAATGAATTTAGAGTTTAAAGTTTAAATTTTAAGTTTA
1 TTTAAACTCCAAACTAATTTCTATAGTAAATGAATTTAGAGTTTAAAGTTTAAATTTTAAGTTTA
54262 GACTATGGAGGCTTCT
66 GACTATGGAGGCTTCT
54278 TTTAAACTCCAAACTAATTTCTATAGTAAATGAATTTAGAGTTTAAAGTTTAAATTTTAAGTTTA
1 TTTAAACTCCAAACTAATTTCTATAGTAAATGAATTTAGAGTTTAAAGTTTAAATTTTAAGTTTA
54343 GACTATGGAGGCTTCT
66 GACTATGGAGGCTTCT
*
54359 TTTAAACTCCAAACTAATCTCTAT
1 TTTAAACTCCAAACTAATTTCTAT
54383 CGGATAACTT
Statistics
Matches: 185, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 185 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.40
Consensus pattern (81 bp):
TTTAAACTCCAAACTAATTTCTATAGTAAATGAATTTAGAGTTTAAAGTTTAAATTTTAAGTTTA
GACTATGGAGGCTTCT
Found at i:54721 original size:45 final size:45
Alignment explanation
Indices: 54655--54744 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
54645 GATTACTTCT
*
54655 CCAGCTCATCATTAATCCGGGGT-AGGAATCTTTCAGTAATTCCAC
1 CCAGCTCATCAATAATCCGGGGTAAGG-ATCTTTCAGTAATTCCAC
* * *
54700 CCAGCTCATCAATAATTCGGGGTAAGGGTCTTTTAGTAATTCCAC
1 CCAGCTCATCAATAATCCGGGGTAAGGATCTTTCAGTAATTCCAC
54745 TACTCTATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 37 0.93
46 3 0.08
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (45 bp):
CCAGCTCATCAATAATCCGGGGTAAGGATCTTTCAGTAATTCCAC
Found at i:54946 original size:3 final size:3
Alignment explanation
Indices: 54940--55003 Score: 119
Period size: 3 Copynumber: 21.0 Consensus size: 3
54930 ATGTAGTATA
54940 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
54988 TAT TAT TAT ATAT TAT
1 TAT TAT TAT -TAT TAT
55004 ACTAGGTACA
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:59151 original size:26 final size:28
Alignment explanation
Indices: 59104--59158 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
59094 CCATGGGCTA
59104 AAAAGATGACCAAAATAACCCT-GGTGT
1 AAAAGATGACCAAAATAACCCTCGGTGT
**
59131 AAAA-ATGACCAAAATGCCCCTCGGTGT
1 AAAAGATGACCAAAATAACCCTCGGTGT
59158 A
1 A
59159 GGAATGATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (28 bp):
AAAAGATGACCAAAATAACCCTCGGTGT
Found at i:63813 original size:2 final size:2
Alignment explanation
Indices: 63808--63848 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
63798 ATTTCCCTGT
* * *
63808 TA TA TA TA TA TA TA TA TG TA TG TA TG 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 TA T
63849 GATTTTTCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:67026 original size:31 final size:31
Alignment explanation
Indices: 66991--67059 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
66981 TTTTTAGGTA
*
66991 CAAATTGAACAAATTTTGAAAGGTTTAAGCT
1 CAAATTGAACAAATTTTGAAAGATTTAAGCT
* * *
67022 CAAATTGAGCAAATTTTGAAAGATTTAGGTT
1 CAAATTGAACAAATTTTGAAAGATTTAAGCT
67053 CAAATTG
1 CAAATTG
67060 GTCAACTTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (31 bp):
CAAATTGAACAAATTTTGAAAGATTTAAGCT
Found at i:67571 original size:12 final size:12
Alignment explanation
Indices: 67554--67585 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
67544 CACCAACCAT
67554 AGTAAATAACCC
1 AGTAAATAACCC
67566 AGTAAATAACCC
1 AGTAAATAACCC
*
67578 AATAAATA
1 AGTAAATA
67586 CTATCTAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19
Consensus pattern (12 bp):
AGTAAATAACCC
Found at i:69999 original size:2 final size:2
Alignment explanation
Indices: 69992--70025 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
69982 TAATAAATTT
69992 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
70026 TATATATATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:76065 original size:6 final size:6
Alignment explanation
Indices: 76054--76083 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
76044 GCAAAAGAAT
76054 TTGGAA TTGGAA TTGGAA TTGGAA TTGGAA
1 TTGGAA TTGGAA TTGGAA TTGGAA TTGGAA
76084 ATACAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
TTGGAA
Found at i:79999 original size:31 final size:31
Alignment explanation
Indices: 79938--80045 Score: 119
Period size: 31 Copynumber: 3.5 Consensus size: 31
79928 AATAAATTAA
* * * *
79938 AGTTTAGGGTGTAAGTTGTCCAA-AATTTAT
1 AGTTTAGGGTGCAAATTGTCCAATTACTTAT
* * ** *
79968 AGTGTAGGATGCAAATTGTTGAATTGCTTAT
1 AGTTTAGGGTGCAAATTGTCCAATTACTTAT
*
79999 AGTTTAGGGTGCAAATTGTCCATTTACTTAT
1 AGTTTAGGGTGCAAATTGTCCAATTACTTAT
80030 AGTTTAGGGTGCAAAT
1 AGTTTAGGGTGCAAAT
80046 ATATACTATA
Statistics
Matches: 62, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
30 17 0.27
31 45 0.73
ACGTcount: A:0.29, C:0.08, G:0.24, T:0.39
Consensus pattern (31 bp):
AGTTTAGGGTGCAAATTGTCCAATTACTTAT
Found at i:81084 original size:112 final size:109
Alignment explanation
Indices: 80869--81090 Score: 291
Period size: 112 Copynumber: 2.0 Consensus size: 109
80859 TTGAATTTGC
* * * *
80869 TAACCAGCTACTCACATATATGATAAGAACTGAGAGAAAAAAAAACTTTATAACTAAAATGATTT
1 TAACCACCTACTCACATATATGATAAGAACCGAGAGAAAAAAAAACTCTAAAACTAAAATGATTT
* * * * ** * * *
80934 GCTAGCCACACATCAAGAATGCTTTACGCGCTAACGTGAGCCGA
66 ACTAGCCACAAATCAAAAATACTCGACACGCCAACGTGAACCGA
80978 TAACCACCTACTCACATATATGATAAGAACCGAGAGAAAAAAAAAAAACTCTAAAACTAAAATGA
1 TAACCACCTACTCACATATATGATAAGAACCGAGAG---AAAAAAAAACTCTAAAACTAAAATGA
*
81043 TTTACTAGCCACAAATCAAAAATACTCGACACGCCAGCGTGAACCGA
63 TTTACTAGCCACAAATCAAAAATACTCGACACGCCAACGTGAACCGA
81090 T
1 T
81091 CAACTTGTAG
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
109 34 0.35
112 62 0.65
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.20
Consensus pattern (109 bp):
TAACCACCTACTCACATATATGATAAGAACCGAGAGAAAAAAAAACTCTAAAACTAAAATGATTT
ACTAGCCACAAATCAAAAATACTCGACACGCCAACGTGAACCGA
Found at i:85029 original size:27 final size:27
Alignment explanation
Indices: 84976--85095 Score: 127
Period size: 27 Copynumber: 4.5 Consensus size: 27
84966 TTAGGAGGCT
* * *
84976 TTTG-CATGAATCCCAACTGCAGAAGC
1 TTTGACATGAGTCCCAACTGCGGGAGC
*
85002 TTTGACATGAGTCCCAACCGCGGGAGC
1 TTTGACATGAGTCCCAACTGCGGGAGC
* *
85029 -TTCAGTATGAGTCCCAACTGCGGGAGC
1 TTTGA-CATGAGTCCCAACTGCGGGAGC
** *
85056 TTCAACATGAGTCCCAACTACGGGAGC
1 TTTGACATGAGTCCCAACTGCGGGAGC
*
85083 TTTGGCATGAGTC
1 TTTGACATGAGTC
85096 ATTCAGCATA
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
26 7 0.09
27 68 0.88
28 2 0.03
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.23
Consensus pattern (27 bp):
TTTGACATGAGTCCCAACTGCGGGAGC
Found at i:85093 original size:54 final size:54
Alignment explanation
Indices: 84933--85095 Score: 159
Period size: 54 Copynumber: 3.0 Consensus size: 54
84923 CAACACAAAA
* * * * * *
84933 CCCAACTGCGGGAGCTTCAACCTAAGTCCTAATTTA--GGAGGCTTTTGCATGAAT
1 CCCAACTGCGGGAGCTTCAACATGAGTCCCAA-CTACGGGA-GCTTTAGCATGAGT
* * ** ** * *
84987 CCCAACTGCAGAAGCTTTGACATGAGTCCCAACCGCGGGAGCTTCAGTATGAGT
1 CCCAACTGCGGGAGCTTCAACATGAGTCCCAACTACGGGAGCTTTAGCATGAGT
*
85041 CCCAACTGCGGGAGCTTCAACATGAGTCCCAACTACGGGAGCTTTGGCATGAGT
1 CCCAACTGCGGGAGCTTCAACATGAGTCCCAACTACGGGAGCTTTAGCATGAGT
85095 C
1 C
85096 ATTCAGCATA
Statistics
Matches: 84, Mismatches: 23, Indels: 4
0.76 0.21 0.04
Matches are distributed among these distances:
54 81 0.96
55 3 0.04
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (54 bp):
CCCAACTGCGGGAGCTTCAACATGAGTCCCAACTACGGGAGCTTTAGCATGAGT
Found at i:86136 original size:24 final size:24
Alignment explanation
Indices: 86109--86182 Score: 67
Period size: 24 Copynumber: 3.1 Consensus size: 24
86099 GTTAATCATA
*
86109 ATTCTACCGCAGAAGTCAAACACC
1 ATTCTACCGCAGAAGCCAAACACC
** * * * *
86133 ATTCCGCTGTAGAAGCCAACCACA
1 ATTCTACCGCAGAAGCCAAACACC
* *
86157 ATTTTACCGCAGAAGCCAAGCACC
1 ATTCTACCGCAGAAGCCAAACACC
86181 AT
1 AT
86183 GCTGCCACAT
Statistics
Matches: 36, Mismatches: 14, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.35, C:0.32, G:0.15, T:0.18
Consensus pattern (24 bp):
ATTCTACCGCAGAAGCCAAACACC
Found at i:94672 original size:32 final size:32
Alignment explanation
Indices: 94636--94700 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
94626 TCTATTAGAG
94636 TTAAAACAGTTGATTCATTTGGTTCTTTTGGA
1 TTAAAACAGTTGATTCATTTGGTTCTTTTGGA
**
94668 TTAAAACAGTTGATTCATTTTTTTCTTTTGGA
1 TTAAAACAGTTGATTCATTTGGTTCTTTTGGA
94700 T
1 T
94701 GCCTATACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (32 bp):
TTAAAACAGTTGATTCATTTGGTTCTTTTGGA
Found at i:101472 original size:32 final size:32
Alignment explanation
Indices: 101391--101473 Score: 139
Period size: 32 Copynumber: 2.6 Consensus size: 32
101381 TGACCATCAT
* * *
101391 ATAACACATAAATACTAAAAAACAACACTGTT
1 ATAACACATAAATACCATAAAACAACACTGTC
101423 ATAACACATAAATACCATAAAACAACACTGTC
1 ATAACACATAAATACCATAAAACAACACTGTC
101455 ATAACACATAAATACCATA
1 ATAACACATAAATACCATA
101474 TACAACAGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.55, C:0.22, G:0.02, T:0.20
Consensus pattern (32 bp):
ATAACACATAAATACCATAAAACAACACTGTC
Found at i:101473 original size:16 final size:16
Alignment explanation
Indices: 101423--101473 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
101413 CAACACTGTT
101423 ATAACACATAAATACC
1 ATAACACATAAATACC
* * **
101439 ATAAAACA-ACACTGTC
1 ATAACACATA-AATACC
101455 ATAACACATAAATACC
1 ATAACACATAAATACC
101471 ATA
1 ATA
101474 TACAACAGAA
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
15 1 0.04
16 23 0.92
17 1 0.04
ACGTcount: A:0.55, C:0.24, G:0.02, T:0.20
Consensus pattern (16 bp):
ATAACACATAAATACC
Found at i:101545 original size:34 final size:34
Alignment explanation
Indices: 101482--101593 Score: 165
Period size: 34 Copynumber: 3.3 Consensus size: 34
101472 TATACAACAG
*
101482 AATTCATGTTTTCCAAGTAC-AACAACAATATGA
1 AATTCATGTTTTCCAAGTACAAACAACAATATCA
101515 AATTCATGTTTTCCAAGTACAAACAACAATATCA
1 AATTCATGTTTTCCAAGTACAAACAACAATATCA
* * *
101549 AATACATGTTTTCCAAGTACAAAGAA-AAGCATCA
1 AATTCATGTTTTCCAAGTACAAACAACAA-TATCA
101583 AATTCATGTTT
1 AATTCATGTTT
101594 AACAATCTCA
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
33 22 0.31
34 50 0.69
ACGTcount: A:0.43, C:0.18, G:0.09, T:0.30
Consensus pattern (34 bp):
AATTCATGTTTTCCAAGTACAAACAACAATATCA
Found at i:101825 original size:16 final size:15
Alignment explanation
Indices: 101792--101821 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
101782 CAAGGAAATT
*
101792 AAAAAAAATGAAAAG
1 AAAAAAAAAGAAAAG
101807 AAAAAAAAAGAAAAG
1 AAAAAAAAAGAAAAG
101822 GAAAGGAAAC
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:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAAAAGAAAAG
Found at i:113400 original size:219 final size:219
Alignment explanation
Indices: 113021--113456 Score: 773
Period size: 219 Copynumber: 2.0 Consensus size: 219
113011 TAGGGCTATG
113021 AAGCTTGTTGGAATGTGAAAACCAATGATGCTCTGTTTTATTTGAGAAAACAGTTGTTTACTTCT
1 AAGCTTGTTGGAATGTGAAAACCAATGATGCTCTGTTTTATTTGAGAAAACAGTTGTTTACTTCT
* * *
113086 TAGCACTTTTCATGTCCTTAAATTTCATAATGCGAAAGTTATGCATGCGTCTGTTTCACCACGAC
66 TAGCACTTGTCATGTCCTTAAATTTCATAATGCGAAAGTTATGCATACGTCTGTTTCAACACGAC
* *
113151 TTTTCATACAATGGCCATACAACAAACATGTCACCAAAATCTTGCCAAAGTGTTAAAACCAGTTG
131 TTTTCATACAATGGCCATACAACAAACATGTCACCAAAACCTTGCCAAAATGTTAAAACCAGTTG
113216 AAGCTTGCCCCCTTTCCCAAACGA
196 AAGCTTGCCCCCTTTCCCAAACGA
113240 AAGCTTGTTGGAATGTGAAAACCAATGATGCTCTGTTTTATTTGAGAAAACAGTTGTTTACTTCT
1 AAGCTTGTTGGAATGTGAAAACCAATGATGCTCTGTTTTATTTGAGAAAACAGTTGTTTACTTCT
* *
113305 TAGCACTTGTCATGTCTTTAAATTTCATAATGTGAAAGTTATGCATACGTCTGTTTCAACACGAC
66 TAGCACTTGTCATGTCCTTAAATTTCATAATGCGAAAGTTATGCATACGTCTGTTTCAACACGAC
* * *
113370 TTTTCATACTATGGCCATACAATAAACATGTCACCAAAACCTTGCCAAAATGTTAAATCCAGTTG
131 TTTTCATACAATGGCCATACAACAAACATGTCACCAAAACCTTGCCAAAATGTTAAAACCAGTTG
*
113435 AAGCTTGTCCCCTTTCCCAAAC
196 AAGCTTGCCCCCTTTCCCAAAC
113457 AGGCCAACAC
Statistics
Matches: 206, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
219 206 1.00
ACGTcount: A:0.31, C:0.21, G:0.15, T:0.33
Consensus pattern (219 bp):
AAGCTTGTTGGAATGTGAAAACCAATGATGCTCTGTTTTATTTGAGAAAACAGTTGTTTACTTCT
TAGCACTTGTCATGTCCTTAAATTTCATAATGCGAAAGTTATGCATACGTCTGTTTCAACACGAC
TTTTCATACAATGGCCATACAACAAACATGTCACCAAAACCTTGCCAAAATGTTAAAACCAGTTG
AAGCTTGCCCCCTTTCCCAAACGA
Found at i:119532 original size:34 final size:33
Alignment explanation
Indices: 119478--119543 Score: 96
Period size: 34 Copynumber: 2.0 Consensus size: 33
119468 TCAAGGAAAA
* * *
119478 TGAGAATTTTTTTTGTAGATAAGATGTTCTTTTT
1 TGAGAATTATTATTGGAGATAAGATGTT-TTTTT
119512 TGAGAATTATTATTGGAGATAAGATGTTTTTT
1 TGAGAATTATTATTGGAGATAAGATGTTTTTT
119544 AATGTATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 4 0.14
34 25 0.86
ACGTcount: A:0.27, C:0.02, G:0.20, T:0.52
Consensus pattern (33 bp):
TGAGAATTATTATTGGAGATAAGATGTTTTTTT
Found at i:119684 original size:22 final size:23
Alignment explanation
Indices: 119644--119689 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
119634 AAAATAAAAT
* * *
119644 AAAAACTACCCATTTTAG-ATAA
1 AAAAAATACCCACTATAGAATAA
119666 AAAAAATACCCACTATAGAATAA
1 AAAAAATACCCACTATAGAATAA
119689 A
1 A
119690 TACAATATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.57, C:0.17, G:0.04, T:0.22
Consensus pattern (23 bp):
AAAAAATACCCACTATAGAATAA
Found at i:124590 original size:2 final size:2
Alignment explanation
Indices: 124585--124619 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
124575 TGTGTGTATG
*
124585 TA TA TA TA TG TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
124620 AGAAATTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:124594 original size:10 final size:10
Alignment explanation
Indices: 124581--124613 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
124571 TGTGTGTGTG
124581 TATGTATATA
1 TATGTATATA
124591 TATGTATATA
1 TATGTATATA
*
124601 TATATATATA
1 TATGTATATA
124611 TAT
1 TAT
124614 ATTATAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (10 bp):
TATGTATATA
Found at i:131301 original size:2 final size:2
Alignment explanation
Indices: 131294--131323 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
131284 GTGTTGCTTT
131294 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
131324 GTATTATCAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:142528 original size:6 final size:6
Alignment explanation
Indices: 142517--142541 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
142507 GCTATCCTCC
142517 AAGAGA AAGAGA AAGAGA AAGAGA A
1 AAGAGA AAGAGA AAGAGA AAGAGA A
142542 GCAGAAACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAGAGA
Found at i:142754 original size:10 final size:10
Alignment explanation
Indices: 142739--142768 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
142729 GAACGTAGCA
142739 AAAGAGAGAG
1 AAAGAGAGAG
142749 AAAGAGAGAG
1 AAAGAGAGAG
*
142759 AGAGAGAGAG
1 AAAGAGAGAG
142769 GGGGTTGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.43, T:0.00
Consensus pattern (10 bp):
AAAGAGAGAG
Done.