Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 97 of 208
Found at i:29022859 original size:20 final size:20
Alignment explanation
Indices: 29022836--29022909 Score: 112
Period size: 20 Copynumber: 3.7 Consensus size: 20
29022826 ATGAGCCGAA
* *
29022836 TTGAGCTCGAATGTGCTGAC
1 TTGAGCTCGAATGAGCTAAC
*
29022856 TTGAGCTCGGATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
*
29022876 TTGAGCTCGAATGAACTAAC
1 TTGAGCTCGAATGAGCTAAC
29022896 TTGAGCTCGAATGA
1 TTGAGCTCGAATGA
29022910 ACAAAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:29025498 original size:11 final size:11
Alignment explanation
Indices: 29025482--29025534 Score: 79
Period size: 11 Copynumber: 4.6 Consensus size: 11
29025472 ATACAAACTC
*
29025482 TTTTTTTTGAA
1 TTTTTTTTCAA
29025493 TTTTTTTTTCAAA
1 -TTTTTTTTC-AA
29025506 TTTTTTTTCAA
1 TTTTTTTTCAA
29025517 TTTTTTTTCAA
1 TTTTTTTTCAA
29025528 TTTTTTT
1 TTTTTTT
29025535 AAAATAGCGT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
11 20 0.51
12 17 0.44
13 2 0.05
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:29025499 original size:12 final size:12
Alignment explanation
Indices: 29025482--29025534 Score: 81
Period size: 12 Copynumber: 4.5 Consensus size: 12
29025472 ATACAAACTC
*
29025482 TTTTTTTTGAAT
1 TTTTTTTTCAAT
*
29025494 TTTTTTTTCAAA
1 TTTTTTTTCAAT
29025506 TTTTTTTTCAA-
1 TTTTTTTTCAAT
29025517 TTTTTTTTCAAT
1 TTTTTTTTCAAT
29025529 TTTTTT
1 TTTTTT
29025535 AAAATAGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 11 0.29
12 27 0.71
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTTTTTCAAT
Found at i:29027412 original size:10 final size:10
Alignment explanation
Indices: 29027387--29027451 Score: 57
Period size: 10 Copynumber: 6.5 Consensus size: 10
29027377 GTTCAAGCTT
29027387 AATGAGC-CG
1 AATGAGCTCG
29027396 AATTGAGCTCG
1 AA-TGAGCTCG
29027407 AATGAGCT-G
1 AATGAGCTCG
*
29027416 ACTTGAGCTCG
1 A-ATGAGCTCG
29027427 AATGAGCT--
1 AATGAGCTCG
29027435 AACTTGAGCTCG
1 AA--TGAGCTCG
29027447 AATGA
1 AATGA
29027452 ACTAACTTGA
Statistics
Matches: 46, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
8 2 0.04
9 4 0.09
10 32 0.70
11 6 0.13
12 2 0.04
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.23
Consensus pattern (10 bp):
AATGAGCTCG
Found at i:29027412 original size:20 final size:21
Alignment explanation
Indices: 29027387--29027471 Score: 106
Period size: 20 Copynumber: 4.2 Consensus size: 21
29027377 GTTCAAGCTT
29027387 AATGAGCCGAA-TTGAGCTCG
1 AATGAGCCGAACTTGAGCTCG
*
29027407 AATGAGCTG-ACTTGAGCTCG
1 AATGAGCCGAACTTGAGCTCG
*
29027427 AATGAG-CTAACTTGAGCTCG
1 AATGAGCCGAACTTGAGCTCG
* *
29027447 AATGA-ACTAACTTGAGCTCG
1 AATGAGCCGAACTTGAGCTCG
29027467 AATGA
1 AATGA
29027472 ACTAAAAAAT
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
19 1 0.02
20 58 0.98
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.24
Consensus pattern (21 bp):
AATGAGCCGAACTTGAGCTCG
Found at i:29027472 original size:20 final size:20
Alignment explanation
Indices: 29027398--29027476 Score: 131
Period size: 20 Copynumber: 4.0 Consensus size: 20
29027388 ATGAGCCGAA
* *
29027398 TTGAGCTCGAATGAGCTGAC
1 TTGAGCTCGAATGAACTAAC
*
29027418 TTGAGCTCGAATGAGCTAAC
1 TTGAGCTCGAATGAACTAAC
29027438 TTGAGCTCGAATGAACTAAC
1 TTGAGCTCGAATGAACTAAC
29027458 TTGAGCTCGAATGAACTAA
1 TTGAGCTCGAATGAACTAA
29027477 AAAATGAGCT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 57 1.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (20 bp):
TTGAGCTCGAATGAACTAAC
Found at i:29034758 original size:22 final size:23
Alignment explanation
Indices: 29034715--29034760 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
29034705 AAAAATGCTA
*
29034715 AAAATCATTTAAAATTATAAAAT
1 AAAATAATTTAAAATTATAAAAT
*
29034738 AAAATAATTTAAATTTA-AAAAT
1 AAAATAATTTAAAATTATAAAAT
29034760 A
1 A
29034761 TATATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (23 bp):
AAAATAATTTAAAATTATAAAAT
Found at i:29038976 original size:21 final size:21
Alignment explanation
Indices: 29038947--29038995 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
29038937 GTTTCTAATA
* *
29038947 TCACCGCTATAGTATCCAATC
1 TCACCGCTACAGTAACCAATC
* *
29038968 TCACTGCTACAGTAACTAATC
1 TCACCGCTACAGTAACCAATC
29038989 TCACCGC
1 TCACCGC
29038996 CACCGCTGTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.29, C:0.35, G:0.10, T:0.27
Consensus pattern (21 bp):
TCACCGCTACAGTAACCAATC
Found at i:29044504 original size:25 final size:25
Alignment explanation
Indices: 29044476--29044523 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
29044466 TATGTGTGTC
*
29044476 TATGTTCCAATTGCTCTACCACATA
1 TATGTTCCAATTGCTCCACCACATA
29044501 TATGTTCCAATTGCTCCACCACA
1 TATGTTCCAATTGCTCCACCACA
29044524 ATAAAAGATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.33
Consensus pattern (25 bp):
TATGTTCCAATTGCTCCACCACATA
Found at i:29046646 original size:32 final size:31
Alignment explanation
Indices: 29046605--29046670 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 31
29046595 AATATAATTT
*
29046605 AAAATAAAATATTTTAATATAATTCAATATA
1 AAAATAAAATATTTTAATATAATTCAAAATA
*
29046636 AAAATAAAAATATTTTAATATAATTTAAAATA
1 AAAAT-AAAATATTTTAATATAATTCAAAATA
29046668 AAA
1 AAA
29046671 TATTTTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 5 0.16
32 27 0.84
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (31 bp):
AAAATAAAATATTTTAATATAATTCAAAATA
Found at i:29046675 original size:25 final size:25
Alignment explanation
Indices: 29046595--29046685 Score: 119
Period size: 25 Copynumber: 3.4 Consensus size: 25
29046585 TTTATTTCAA
29046595 AATATAATTTAAAATAAAATATTTT
1 AATATAATTTAAAATAAAATATTTT
29046620 AATATAATTCAATATAAAAATAAAAATATTTT
1 AATATAA-T---T-T-AAAAT-AAAATATTTT
29046652 AATATAATTTAAAATAAAATATTTT
1 AATATAATTTAAAATAAAATATTTT
29046677 AATATAATT
1 AATATAATT
29046686 AATTACATTG
Statistics
Matches: 59, Mismatches: 0, Indels: 14
0.81 0.00 0.19
Matches are distributed among these distances:
25 26 0.44
26 6 0.10
27 1 0.02
28 1 0.02
29 1 0.02
30 1 0.02
31 6 0.10
32 17 0.29
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
AATATAATTTAAAATAAAATATTTT
Found at i:29052954 original size:18 final size:18
Alignment explanation
Indices: 29052931--29052993 Score: 72
Period size: 18 Copynumber: 3.3 Consensus size: 18
29052921 TGATCATTGG
29052931 AATGTGATGTTATGGTGA
1 AATGTGATGTTATGGTGA
* *
29052949 AATGTGATGTTATGCTTA
1 AATGTGATGTTATGGTGA
29052967 ATTTCATGTGATGTTATGGTGA
1 A----ATGTGATGTTATGGTGA
29052989 AATGT
1 AATGT
29052994 TAACATGTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
18 21 0.57
22 16 0.43
ACGTcount: A:0.27, C:0.03, G:0.27, T:0.43
Consensus pattern (18 bp):
AATGTGATGTTATGGTGA
Found at i:29054644 original size:6 final size:6
Alignment explanation
Indices: 29054633--29054685 Score: 61
Period size: 6 Copynumber: 8.8 Consensus size: 6
29054623 TAACTTAACC
* * * * *
29054633 ATTTTT ATTTTT ATTTTT ATTATA ATTTTT GTTTTT AGTTTA ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
29054681 ATTTT
1 ATTTT
29054686 CTAATATTTC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (6 bp):
ATTTTT
Found at i:29054660 original size:18 final size:18
Alignment explanation
Indices: 29054639--29054685 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
29054629 AACCATTTTT
29054639 ATTTTTATTTTTA-TTATA
1 ATTTTTATTTTTAGTT-TA
*
29054657 ATTTTTGTTTTTAGTTTA
1 ATTTTTATTTTTAGTTTA
29054675 ATTTTTATTTT
1 ATTTTTATTTT
29054686 CTAATATTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 24 0.92
19 2 0.08
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.74
Consensus pattern (18 bp):
ATTTTTATTTTTAGTTTA
Found at i:29058661 original size:16 final size:17
Alignment explanation
Indices: 29058628--29058671 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
29058618 GCTTAGATTT
29058628 TATTTTTATTTTAAGTTA
1 TATTTTTATTTT-AGTTA
*
29058646 TATTATTATTTT-GTTA
1 TATTTTTATTTTAGTTA
29058662 TATTTTTATT
1 TATTTTTATT
29058672 ATATTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 13 0.54
18 11 0.46
ACGTcount: A:0.25, C:0.00, G:0.05, T:0.70
Consensus pattern (17 bp):
TATTTTTATTTTAGTTA
Found at i:29060287 original size:24 final size:24
Alignment explanation
Indices: 29060260--29060311 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
29060250 AGTTTATTTG
*
29060260 TTTTCCTTTTA-GTTTAATTTTAAT
1 TTTTCATTTTATGTTT-ATTTTAAT
* *
29060284 TTTTTATTTTATGTTTATTTTTAT
1 TTTTCATTTTATGTTTATTTTAAT
29060308 TTTT
1 TTTT
29060312 AGTTATTTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 20 0.83
25 4 0.17
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.75
Consensus pattern (24 bp):
TTTTCATTTTATGTTTATTTTAAT
Found at i:29060288 original size:25 final size:24
Alignment explanation
Indices: 29060266--29060311 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
29060256 TTTGTTTTCC
29060266 TTTTA-GTTTAATTTTAATTTTTTA
1 TTTTATGTTT-ATTTTAATTTTTTA
*
29060290 TTTTATGTTTATTTTTATTTTT
1 TTTTATGTTTATTTTAATTTTT
29060312 AGTTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.20, C:0.00, G:0.04, T:0.76
Consensus pattern (24 bp):
TTTTATGTTTATTTTAATTTTTTA
Found at i:29065010 original size:19 final size:19
Alignment explanation
Indices: 29064963--29065012 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
29064953 TTATATAGCC
29064963 ATTAACTTAAGTAAAGTAAT
1 ATTAA-TTAAGTAAAGTAAT
**
29064983 ATTTTTTAAGTAAAGT-AT
1 ATTAATTAAGTAAAGTAAT
29065001 AGTTAATTAAGT
1 A-TTAATTAAGT
29065013 TAATTAGCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 3 0.12
19 19 0.76
20 3 0.12
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (19 bp):
ATTAATTAAGTAAAGTAAT
Found at i:29065034 original size:22 final size:21
Alignment explanation
Indices: 29065003--29065047 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
29064993 TAAAGTATAG
*
29065003 TTAATTAAGT-TAATTAGCAAA
1 TTAATTAAGTATAAATAG-AAA
29065024 TTAATCTAAGTATAAATAGAAA
1 TTAAT-TAAGTATAAATAGAAA
29065046 TT
1 TT
29065048 CAAGTGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 5 0.24
22 10 0.48
23 6 0.29
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (21 bp):
TTAATTAAGTATAAATAGAAA
Found at i:29068297 original size:22 final size:23
Alignment explanation
Indices: 29068248--29068297 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
29068238 ATCAATTCAA
*
29068248 ACCATTTCAAACTACCAAACATT
1 ACCATTTCAAACTACCAAACAAT
*
29068271 ACCATTT-AAAC-ACCAATCAAT
1 ACCATTTCAAACTACCAAACAAT
29068292 AGCCAT
1 A-CCAT
29068298 ATGCATATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.38
22 8 0.33
23 7 0.29
ACGTcount: A:0.44, C:0.30, G:0.02, T:0.24
Consensus pattern (23 bp):
ACCATTTCAAACTACCAAACAAT
Found at i:29068943 original size:13 final size:13
Alignment explanation
Indices: 29068927--29068959 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
29068917 ATCCATTTCA
*
29068927 CATTTCATATTTT
1 CATTTCACATTTT
29068940 CATTTCACATTTT
1 CATTTCACATTTT
29068953 CATTTCA
1 CATTTCA
29068960 AGTATCCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (13 bp):
CATTTCACATTTT
Found at i:29068969 original size:13 final size:13
Alignment explanation
Indices: 29068953--29069009 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
29068943 TTCACATTTT
*
29068953 CATTTCAAGTATC
1 CATTTCAAATATC
*
29068966 CATTTCAAATATG
1 CATTTCAAATATC
* *
29068979 CATTTCATATAAC
1 CATTTCAAATATC
* *
29068992 CATTTTACAT-TC
1 CATTTCAAATATC
29069004 CATTTC
1 CATTTC
29069010 CACCAGATGA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
12 6 0.17
13 29 0.83
ACGTcount: A:0.32, C:0.23, G:0.04, T:0.42
Consensus pattern (13 bp):
CATTTCAAATATC
Found at i:29069092 original size:25 final size:25
Alignment explanation
Indices: 29069052--29069112 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
29069042 ACCTGGGAAC
29069052 AATGCTCACACAAGCTATGACGGTA
1 AATGCTCACACAAGCTATGACGGTA
* ** *
29069077 TATGCTCACATGAGCTATGACTGTA
1 AATGCTCACACAAGCTATGACGGTA
29069102 AATGCTCACAC
1 AATGCTCACAC
29069113 GAACTGTGAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (25 bp):
AATGCTCACACAAGCTATGACGGTA
Found at i:29073048 original size:17 final size:17
Alignment explanation
Indices: 29073026--29073059 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
29073016 AAGAGAGTTG
29073026 TGAGAGAGGATGA-GAGA
1 TGAGAG-GGATGATGAGA
29073043 TGAGAGGGATGATGAGA
1 TGAGAGGGATGATGAGA
29073060 AATGAGCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.38, C:0.00, G:0.47, T:0.15
Consensus pattern (17 bp):
TGAGAGGGATGATGAGA
Found at i:29086502 original size:51 final size:51
Alignment explanation
Indices: 29086433--29086628 Score: 243
Period size: 51 Copynumber: 3.9 Consensus size: 51
29086423 CAATGATGTT
* * *
29086433 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATC
* * ** *
29086484 CGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATC
* * * ** *
29086535 CGGTACGCATAGTAGCCTGCACATAGTACTACACATGCAACC--TATCATTC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTACCA-TC
29086585 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
29086629 AACTTTCACT
Statistics
Matches: 119, Mismatches: 23, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
49 2 0.02
50 39 0.33
51 78 0.66
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (51 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTACCATC
Found at i:29086622 original size:101 final size:101
Alignment explanation
Indices: 29086440--29086624 Score: 309
Period size: 101 Copynumber: 1.8 Consensus size: 101
29086430 GTTCGGTTCA
**
29086440 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCAACCA-TACCATCCGATACACGTAGTAGCCTGCA
29086505 CATAGTACTACACACGTGATCAAAACTATCCGGTACG
65 CATAGTACTACACACGTGATCAAAACTATCCGGTACG
* *
29086542 CATAGTAGCCTGCACATAGTACTACACATGCAACC-TATCATTCCGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCAACCATACCA-TCCGATACACGTAGTAGCCTGCA
29086606 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
29086625 CCATAACTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 4 0.05
101 41 0.53
102 33 0.42
ACGTcount: A:0.32, C:0.29, G:0.17, T:0.23
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCAACCATACCATCCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATCAAAACTATCCGGTACG
Found at i:29087668 original size:17 final size:18
Alignment explanation
Indices: 29087648--29087683 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
29087638 CATAAAAATA
29087648 TAATGAAAAT-AATTTTT
1 TAATGAAAATAAATTTTT
*
29087665 TAATTAAAATAAATTTTT
1 TAATGAAAATAAATTTTT
29087683 T
1 T
29087684 CTCGTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
TAATGAAAATAAATTTTT
Found at i:29089653 original size:11 final size:11
Alignment explanation
Indices: 29089637--29089684 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
29089627 ATTACATCTT
29089637 TTAAATGTGTC
1 TTAAATGTGTC
*
29089648 TTAAATATGT-
1 TTAAATGTGTC
29089658 TT-AATGTGTC
1 TTAAATGTGTC
* *
29089668 TTAAAAGTGTT
1 TTAAATGTGTC
29089679 TTAAAT
1 TTAAAT
29089685 TTTGTTCAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
9 6 0.20
10 4 0.13
11 20 0.67
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (11 bp):
TTAAATGTGTC
Found at i:29100425 original size:27 final size:27
Alignment explanation
Indices: 29100353--29100537 Score: 141
Period size: 27 Copynumber: 6.9 Consensus size: 27
29100343 ATCTGGACTT
* * *
29100353 AAATACCCCCGAAGGGTAAAATGATCA
1 AAATACCCTCGATGGGTAAAATGATCG
** * *
29100380 AAATACCCTTAAAGAGTAAAATGATCG
1 AAATACCCTCGATGGGTAAAATGATCG
29100407 AAATACCCTCGATGGGTAAAATGA-CTG
1 AAATACCCTCGATGGGTAAAATGATC-G
* *
29100434 GAATACCTTCGATGGGTAAAATGA-CTG
1 AAATACCCTCGATGGGTAAAATGATC-G
* * *
29100461 AAATGCCC-CCATAGGGTGAAATGATCG
1 AAATACCCTCGAT-GGGTAAAATGATCG
* *
29100488 AAATACCCTC-TTAGGGTAGAAT-ACTC-
1 AAATACCCTCGAT-GGGTAAAATGA-TCG
29100514 AAATACCCTC-ATAGGGTAAAATGA
1 AAATACCCTCGAT-GGGTAAAATGA
29100538 CCATAATACC
Statistics
Matches: 130, Mismatches: 22, Indels: 12
0.79 0.13 0.07
Matches are distributed among these distances:
26 25 0.19
27 103 0.79
28 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (27 bp):
AAATACCCTCGATGGGTAAAATGATCG
Found at i:29100464 original size:54 final size:55
Alignment explanation
Indices: 29100348--29100538 Score: 164
Period size: 54 Copynumber: 3.5 Consensus size: 55
29100338 TCGATATCTG
* * * * * *
29100348 GACTTAAATACCCCCGA-AGGGTAAAATGA-TCAAAATACCCTTAAAGAGTAAAAT
1 GACTGAAATACCCTC-ATAGGGTAAAATGACTCGAAATACCCTCATAGGGTAAAAT
* *
29100402 GA-TCGAAATACCCTCGAT-GGGTAAAATGACT-GGAATACCTTCGAT-GGGTAAAAT
1 GACT-GAAATACCCTC-ATAGGGTAAAATGACTCGAAATACCCTC-ATAGGGTAAAAT
* * * * *
29100456 GACTGAAATGCCCCCATAGGGTGAAATGA-TCGAAATACCCTCTTAGGGTAGAAT
1 GACTGAAATACCCTCATAGGGTAAAATGACTCGAAATACCCTCATAGGGTAAAAT
*
29100510 -ACTCAAATACCCTCATAGGGTAAAATGAC
1 GACTGAAATACCCTCATAGGGTAAAATGAC
29100539 CATAATACCC
Statistics
Matches: 109, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
53 29 0.27
54 77 0.71
55 3 0.03
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (55 bp):
GACTGAAATACCCTCATAGGGTAAAATGACTCGAAATACCCTCATAGGGTAAAAT
Found at i:29100549 original size:27 final size:27
Alignment explanation
Indices: 29100365--29100657 Score: 120
Period size: 27 Copynumber: 10.9 Consensus size: 27
29100355 ATACCCCCGA
* * * *
29100365 AGGGTAAAATGATCAAAATACCCTTAA
1 AGGGTAAAATGACCATAATACCCTCAT
* *
29100392 AGAGTAAAATGATCGA-AATACCCTCGAT
1 AGGGTAAAATGA-CCATAATACCCTC-AT
*** *
29100420 -GGGTAAAATGACTGGAATACCTTCGAT
1 AGGGTAAAATGACCATAATACCCTC-AT
* * *
29100447 -GGGTAAAATGACTGA-AATGCCCCCAT
1 AGGGTAAAATGAC-CATAATACCCTCAT
* * *
29100473 AGGGTGAAATGATCGA-AATACCCTCTT
1 AGGGTAAAATGA-CCATAATACCCTCAT
*
29100500 AGGGTAGAAT-ACTCA-AATACCCTCAT
1 AGGGTAAAATGAC-CATAATACCCTCAT
**
29100526 AGGGTAAAATGACCATAATACCCTTGT
1 AGGGTAAAATGACCATAATACCCTCAT
* * *** *
29100553 AGAGTAAAATAATTGTAATAACCCT-GT
1 AGGGTAAAATGACCATAAT-ACCCTCAT
* * * *
29100580 AGAGTAAAATGACCGTAATGCCC-CTGT
1 AGGGTAAAATGACCATAATACCCTC-AT
* * *
29100607 AGGGTAAAATGATCGTAATGCCC-CTAT
1 AGGGTAAAATGACCATAATACCCTC-AT
* * *
29100634 AAGGTAAAATGACCGTAATGCCCT
1 AGGGTAAAATGACCATAATACCCT
29100658 GGTGGGTAAA
Statistics
Matches: 214, Mismatches: 39, Indels: 25
0.77 0.14 0.09
Matches are distributed among these distances:
25 1 0.00
26 29 0.14
27 176 0.82
28 8 0.04
ACGTcount: A:0.38, C:0.18, G:0.20, T:0.24
Consensus pattern (27 bp):
AGGGTAAAATGACCATAATACCCTCAT
Found at i:29100590 original size:54 final size:54
Alignment explanation
Indices: 29100518--29100657 Score: 165
Period size: 54 Copynumber: 2.6 Consensus size: 54
29100508 ATACTCAAAT
* * * *
29100518 ACCCTCATAGGGTAAAATGACCATAATACCCTTGTAGAGTAAAATAATTGTAATA
1 ACCCT-ATAAGGTAAAATGACCGTAATGCCCTTGTAGAGTAAAATAATCGTAATA
* * * * *
29100573 ACCCTGT-AGAGTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGATCGTAATG
1 ACCCTATAAG-GTAAAATGACCGTAATGCCCTTGTAGAGTAAAATAATCGTAATA
*
29100627 CCCCTATAAGGTAAAATGACCGTAATGCCCT
1 ACCCTATAAGGTAAAATGACCGTAATGCCCT
29100658 GGTGGGTAAA
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
53 1 0.01
54 63 0.89
55 7 0.10
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (54 bp):
ACCCTATAAGGTAAAATGACCGTAATGCCCTTGTAGAGTAAAATAATCGTAATA
Found at i:29100988 original size:32 final size:32
Alignment explanation
Indices: 29100944--29101190 Score: 202
Period size: 32 Copynumber: 7.7 Consensus size: 32
29100934 GTTGCAATGC
* *
29100944 TACTGATTGCTTTGTGCCAATCATAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
*
29100976 TACTGATGGCTTTGTACCGATCATAGTACCGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
* * **
29101008 TACTGATGGCTTTATGCCGATCATATTAATGT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
* *
29101040 TACTGATGG-TTGTGTGCCGATCAT-TTCACTGT
1 TACTGATGGCTT-TGTGCCGATCATAGT-ACCGT
* **
29101072 TACTGATGGCTGTGTGCCGATCATA--ACATT
1 TACTGATGGCTTTGTGCCGATCATAGTACCGT
* * *
29101102 ACTACTAATGGTTTTGTACCGATCAT-GTTA-CGAT
1 --TACTGATGGCTTTGTGCCGATCATAG-TACCG-T
* ***
29101136 TACTGATGGCTGTGTGCCGATCATA-TCACTAC
1 TACTGATGGCTTTGTGCCGATCATAGT-ACCGT
*
29101168 TACTGATGGCTTTGTGCCAATCA
1 TACTGATGGCTTTGTGCCGATCA
29101191 CATTACTGTA
Statistics
Matches: 174, Mismatches: 28, Indels: 26
0.76 0.12 0.11
Matches are distributed among these distances:
30 3 0.02
31 5 0.03
32 163 0.94
33 1 0.01
34 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.36
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATAGTACCGT
Found at i:29101031 original size:64 final size:62
Alignment explanation
Indices: 29100944--29101182 Score: 225
Period size: 64 Copynumber: 3.7 Consensus size: 62
29100934 GTTGCAATGC
* * * *
29100944 TACTGATTGCTTTGTGCCAATCATAGTACCGTTACTGATGGCTTTGTACCGATCATAGTACCGT
1 TACTGATGGCTGTGTGCCGATCATA-TACTGTTACTGATGGCTTTGTACCGATCAT-GTACCGT
* * * * * *
29101008 TACTGATGGCTTTATGCCGATCATATTAATGTTACTGATGG-TTGTGTGCCGATCATTTCACTGT
1 TACTGATGGCTGTGTGCCGATCATA-TACTGTTACTGATGGCTT-TGTACCGATCATGT-ACCGT
* *
29101072 TACTGATGGCTGTGTGCCGATCATA-ACAT-TACTACTAATGGTTTTGTACCGATCATGTTA-CG
1 TACTGATGGCTGTGTGCCGATCATATAC-TGT--TACTGATGGCTTTGTACCGATCATG-TACCG
29101134 AT
62 -T
**
29101136 TACTGATGGCTGTGTGCCGATCATATCACTACTACTGATGGCTTTGT
1 TACTGATGGCTGTGTGCCGATCATAT-ACTGTTACTGATGGCTTTGT
29101183 GCCAATCACA
Statistics
Matches: 145, Mismatches: 19, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
62 2 0.01
63 5 0.03
64 132 0.91
65 4 0.03
66 2 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (62 bp):
TACTGATGGCTGTGTGCCGATCATATACTGTTACTGATGGCTTTGTACCGATCATGTACCGT
Found at i:29101237 original size:22 final size:22
Alignment explanation
Indices: 29101212--29101266 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
29101202 TTATGGATTG
*
29101212 TAGCCATTCTGTTTATAGCT-T
1 TAGCCATTCTGTTTACAGCTCT
* * *
29101233 ATAGCTATCCTATTTACAGCTCT
1 -TAGCCATTCTGTTTACAGCTCT
29101256 TAGCCATTCTG
1 TAGCCATTCTG
29101267 ACTACTGGCA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.42
Consensus pattern (22 bp):
TAGCCATTCTGTTTACAGCTCT
Found at i:29105320 original size:42 final size:42
Alignment explanation
Indices: 29105236--29105378 Score: 180
Period size: 42 Copynumber: 3.4 Consensus size: 42
29105226 GGCTCAGTAC
** * **
29105236 CTAGCAGGCTTGTTGCCAATGAAAT-CTTTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGATGAAATAAATTCAGACTTTACGT
*
29105277 CTAGCAGGCTTAATGCCGATGAAGTAAATTCAGACTTTACGT
1 CTAGCAGGCTTAATGCCGATGAAATAAATTCAGACTTTACGT
* * * *
29105319 CTAGCAGGCTTAATGCTGGTGAAATAAATTCGGACTATACGT
1 CTAGCAGGCTTAATGCCGATGAAATAAATTCAGACTTTACGT
*
29105361 CTAGCAGGCTTAAAGCCG
1 CTAGCAGGCTTAATGCCG
29105379 GTGTACTGAA
Statistics
Matches: 88, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
41 21 0.24
42 67 0.76
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (42 bp):
CTAGCAGGCTTAATGCCGATGAAATAAATTCAGACTTTACGT
Found at i:29107526 original size:21 final size:19
Alignment explanation
Indices: 29107480--29107554 Score: 132
Period size: 19 Copynumber: 3.8 Consensus size: 19
29107470 AATCTTCAAG
29107480 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29107499 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29107518 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
29107539 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
29107555 AGATATGATT
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
19 35 0.65
21 19 0.35
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29107576 original size:23 final size:22
Alignment explanation
Indices: 29107480--29107577 Score: 95
Period size: 19 Copynumber: 4.7 Consensus size: 22
29107470 AATCTTCAAG
29107480 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
*
29107499 GATATGCAATCTTAG-ATATGAT
1 GATATGCAATCTTAGAAGAT-AT
29107521 -ATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
29107539 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
29107561 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
29107578 GATTTAATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
18 2 0.03
19 28 0.42
21 15 0.22
22 10 0.15
23 12 0.18
ACGTcount: A:0.37, C:0.09, G:0.16, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:29108503 original size:3 final size:3
Alignment explanation
Indices: 29108497--29108541 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
29108487 TTATCTTTTC
29108497 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
29108542 GTTGTTGTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29108546 original size:3 final size:3
Alignment explanation
Indices: 29108540--29108580 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
29108530 ATTATTATTA
* * *
29108540 TTG TTG TTG TTG TTG TTG TTG TTA TTA TTA TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
29108581 CTTGATCATG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.07, C:0.00, G:0.24, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:29116358 original size:48 final size:48
Alignment explanation
Indices: 29116298--29116393 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
29116288 AACACACCAT
*
29116298 TTGTGGACAAGCCACCATATAAATATCGATAAACAACCAAATAA-CACA
1 TTGTGGACAAGCCACCACATAAATATCGAT-AACAACCAAATAATCACA
* * * *
29116346 TTGTGGATAAGCCACCACATAATTGTCGATAACAACCACATAATCACA
1 TTGTGGACAAGCCACCACATAAATATCGATAACAACCAAATAATCACA
29116394 AATAAACTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
47 12 0.29
48 30 0.71
ACGTcount: A:0.44, C:0.24, G:0.11, T:0.21
Consensus pattern (48 bp):
TTGTGGACAAGCCACCACATAAATATCGATAACAACCAAATAATCACA
Found at i:29116385 original size:21 final size:22
Alignment explanation
Indices: 29116345--29116389 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
29116335 CAAATAACAC
* *
29116345 ATTGTGGATAAGCCACCACATA
1 ATTGTCGATAAGCAACCACATA
29116367 ATTGTCGATAA-CAACCACATA
1 ATTGTCGATAAGCAACCACATA
29116388 AT
1 AT
29116390 CACAAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.24
Consensus pattern (22 bp):
ATTGTCGATAAGCAACCACATA
Found at i:29128723 original size:18 final size:18
Alignment explanation
Indices: 29128701--29128744 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
29128691 TTTTCTCTCA
*
29128701 CTTTTTCGATCTCTTTTT
1 CTTTTTCAATCTCTTTTT
* * *
29128719 GTTTTGCAATTTCTTTTT
1 CTTTTTCAATCTCTTTTT
29128737 CTTTTTCA
1 CTTTTTCA
29128745 TTTTCGTTTT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.09, C:0.18, G:0.07, T:0.66
Consensus pattern (18 bp):
CTTTTTCAATCTCTTTTT
Found at i:29128749 original size:18 final size:18
Alignment explanation
Indices: 29128712--29128769 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
29128702 TTTTTCGATC
* * *
29128712 TCTTTTTGTTTTGCAATT
1 TCTTTTTCTTTTTCATTT
29128730 TCTTTTTCTTTTTCATTT
1 TCTTTTTCTTTTTCATTT
*
29128748 TCGTTTTCTTGTTT--TTT
1 TCTTTTTCTT-TTTCATTT
29128765 TCTTT
1 TCTTT
29128770 CAATTTCTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 7 0.21
18 24 0.71
19 3 0.09
ACGTcount: A:0.05, C:0.14, G:0.07, T:0.74
Consensus pattern (18 bp):
TCTTTTTCTTTTTCATTT
Found at i:29128782 original size:6 final size:6
Alignment explanation
Indices: 29128728--29128769 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
29128718 TGTTTTGCAA
* * *
29128728 TTTCTT TTTCTT TTTCAT TTTCGT TTTCTT GTT-TT TTTCTT T
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT T
29128770 CAATTTCTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTCTT
Found at i:29128820 original size:21 final size:21
Alignment explanation
Indices: 29128765--29128812 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
29128755 CTTGTTTTTT
29128765 TCTTTCAATTTCTTTTTCCAC
1 TCTTTCAATTTCTTTTTCCAC
29128786 TCTTTCAATTTCTTTTTCCAC
1 TCTTTCAATTTCTTTTTCCAC
29128807 TCTTTC
1 TCTTTC
29128813 TTTTTCTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.12, C:0.29, G:0.00, T:0.58
Consensus pattern (21 bp):
TCTTTCAATTTCTTTTTCCAC
Found at i:29128850 original size:22 final size:21
Alignment explanation
Indices: 29128809--29128850 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
29128799 TTTTCCACTC
*
29128809 TTTCTTTTTCTTCTCTTTCAA
1 TTTCTTTTCCTTCTCTTTCAA
*
29128830 TTTCTTGTTCCTTTTCTTTCA
1 TTTCTT-TTCCTTCTCTTTCA
29128851 TCTTTCTTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.07, C:0.24, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTCTTTTCCTTCTCTTTCAA
Found at i:29131613 original size:24 final size:22
Alignment explanation
Indices: 29131561--29131615 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 22
29131551 TTCGGCTACT
*
29131561 GATGTGTTCACACAACAATTAAA
1 GATG-GTTCACACAAAAATTAAA
*
29131584 -AGGGTTCACACTAAAACATTAAA
1 GATGGTTCACAC-AAAA-ATTAAA
29131607 GATGGTTCA
1 GATGGTTCA
29131616 TGAATTCGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 8 0.31
22 5 0.19
23 6 0.23
24 7 0.27
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (22 bp):
GATGGTTCACACAAAAATTAAA
Found at i:29132215 original size:34 final size:34
Alignment explanation
Indices: 29132172--29132240 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
29132162 TTAATTCATG
29132172 TATGAGCAAAATTGACCAGCCACAATCTTCCCCT
1 TATGAGCAAAATTGACCAGCCACAATCTTCCCCT
29132206 TATGAGCAAAATTGACCAGCCACAATCTTCCCCT
1 TATGAGCAAAATTGACCAGCCACAATCTTCCCCT
29132240 T
1 T
29132241 TAAGGAATGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.32, C:0.32, G:0.12, T:0.25
Consensus pattern (34 bp):
TATGAGCAAAATTGACCAGCCACAATCTTCCCCT
Found at i:29132337 original size:27 final size:27
Alignment explanation
Indices: 29132307--29132358 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
29132297 TCATTGAAGC
*
29132307 ATCTTCATTGCTGTCCATGCATGTATT
1 ATCTTCAATGCTGTCCATGCATGTATT
29132334 ATCTTCAATGCTGTCCATGCATGTA
1 ATCTTCAATGCTGTCCATGCATGTA
29132359 CCTACAAACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.40
Consensus pattern (27 bp):
ATCTTCAATGCTGTCCATGCATGTATT
Found at i:29134465 original size:18 final size:18
Alignment explanation
Indices: 29134444--29134478 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
29134434 TTTTTATTTT
29134444 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
29134462 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
29134479 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:29134529 original size:18 final size:18
Alignment explanation
Indices: 29134508--29134592 Score: 55
Period size: 18 Copynumber: 4.4 Consensus size: 18
29134498 TTTTCTCTCA
29134508 CTTTTTCGATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
** *
29134526 CTTTAGCAATTTCTTTTT
1 CTTTTTCGATTTCTTTTT
* *
29134544 CATTTTCTCGCTCGCGCTCTTTTT
1 C-TTTT-TCGAT----TTCTTTTT
29134568 CTTTTTC-ACTTTCTTTTT
1 CTTTTTCGA-TTTCTTTTT
29134586 CTTTTTC
1 CTTTTTC
29134593 TTCTTTTTCA
Statistics
Matches: 50, Mismatches: 10, Indels: 14
0.68 0.14 0.19
Matches are distributed among these distances:
18 30 0.60
19 3 0.06
20 2 0.04
22 3 0.06
23 4 0.08
24 8 0.16
ACGTcount: A:0.07, C:0.24, G:0.06, T:0.64
Consensus pattern (18 bp):
CTTTTTCGATTTCTTTTT
Found at i:29134606 original size:6 final size:6
Alignment explanation
Indices: 29134561--29134594 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
29134551 TCGCTCGCGC
**
29134561 TCTTTT TCTTTT TCACTT TCTTTT TCTTTT TCTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTT
29134595 CTTTTTCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (6 bp):
TCTTTT
Found at i:29138948 original size:22 final size:18
Alignment explanation
Indices: 29138910--29138964 Score: 58
Period size: 22 Copynumber: 2.8 Consensus size: 18
29138900 ATAACAATGT
29138910 TAACAA-TATACTAAAATA
1 TAACAATTA-ACTAAAATA
29138928 TTAATCATATTAATCTAAAATA
1 -TAA-CA-ATTAA-CTAAAATA
29138950 TAACAATTAACTAAA
1 TAACAATTAACTAAA
29138965 GGAAAAAGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
18 5 0.16
19 8 0.25
20 4 0.12
21 5 0.16
22 10 0.31
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (18 bp):
TAACAATTAACTAAAATA
Found at i:29142215 original size:22 final size:23
Alignment explanation
Indices: 29142190--29142241 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
29142180 TCGACAAGCC
29142190 ACCACATAATTGTC-GATAAA-TG
1 ACCACATAATT-TCAGATAAACTG
*
29142212 ACCACCTAATTTCAGATAAACTG
1 ACCACATAATTTCAGATAAACTG
29142235 -CCACATA
1 ACCACATA
29142242 TCTTCCTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 2 0.08
22 22 0.85
23 2 0.08
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (23 bp):
ACCACATAATTTCAGATAAACTG
Found at i:29144764 original size:54 final size:54
Alignment explanation
Indices: 29144654--29144793 Score: 244
Period size: 54 Copynumber: 2.6 Consensus size: 54
29144644 GCATGCCTTA
29144654 GGTCTAGCACATCTGCTATTCTGGATTTGCAACTCAACTAGCATGCCCTACCAGT
1 GGTCTAGCACATCTGCTATTCTGG-TTTGCAACTCAACTAGCATGCCCTACCAGT
* * *
29144709 GGTCTAGCACATATGCTATTCTGGTTTGCAACTCAACTAGCATGCCTTACTAGT
1 GGTCTAGCACATCTGCTATTCTGGTTTGCAACTCAACTAGCATGCCCTACCAGT
29144763 GGTCTAGCACATCTGCTATTCTGGTTTGCAA
1 GGTCTAGCACATCTGCTATTCTGGTTTGCAA
29144794 ATAACAAGCC
Statistics
Matches: 81, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
54 58 0.72
55 23 0.28
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (54 bp):
GGTCTAGCACATCTGCTATTCTGGTTTGCAACTCAACTAGCATGCCCTACCAGT
Found at i:29146472 original size:71 final size:71
Alignment explanation
Indices: 29146397--29146609 Score: 162
Period size: 71 Copynumber: 3.1 Consensus size: 71
29146387 ACCGAAATTA
* *
29146397 ATTAATATAATTGTTTATATTAATAAATTCGGTAATATATAATTAATATTTTGTATGAATCAAAT
1 ATTAATATAATTCTTTATATTAATAAATTCGATAATATATAATTAATATTTTGTATGAATCAAAT
29146462 TCATAT
66 TCATAT
** * * ** ** *
29146468 ATTAAT-TATATTCTTTCCA-AAATAATATT-AATTTTTATATCTTTTATATTTTG-ACT--A--
1 ATTAATATA-ATTCTTTATATTAATAA-ATTCGA-TAATATATAATTAATATTTTGTA-TGAATC
29146525 AAA-T--TA-
62 AAATTCATAT
*
29146531 ATTAATATAATTTTTTATATTAATAAATTCGATAAAATATATACCATTAATATTTTGTATGAATC
1 ATTAATATAATTCTTTATATTAATAAATTCGAT--AATATATA--ATTAATATTTTGTATGAATC
29146596 AAATTCATAT
62 AAATTCATAT
29146606 ATTA
1 ATTA
29146610 GTTATATTCT
Statistics
Matches: 101, Mismatches: 21, Indels: 36
0.64 0.13 0.23
Matches are distributed among these distances:
63 17 0.17
64 10 0.10
65 5 0.05
66 1 0.01
67 14 0.14
68 1 0.01
69 2 0.02
70 8 0.08
71 36 0.36
72 1 0.01
74 2 0.02
75 4 0.04
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (71 bp):
ATTAATATAATTCTTTATATTAATAAATTCGATAATATATAATTAATATTTTGTATGAATCAAAT
TCATAT
Found at i:29146587 original size:67 final size:67
Alignment explanation
Indices: 29146513--29146725 Score: 157
Period size: 67 Copynumber: 3.1 Consensus size: 67
29146503 TATATCTTTT
*
29146513 ATATTTTGACTAAAATTAATTAATATAATTTTTTATATTAATAAATTCGATAAAATATATACCAT
1 ATATTTTGACTAAAATTAATTAATATAATTATTTATATTAATAAATTCGATAAAATATATACCAT
29146578 TA
66 TA
* * * * ** * * *
29146580 ATATTTTG--TATGAATCAAATTCATAT-ATTAGTTATATTCTTTCCAAA--AGAATATTAATTT
1 ATATTTTGACTA-AAAT-TAATTAATATAATTATTTATATT-AAT--AAATTCG-ATA--AAATA
** * *
29146640 TCATGTCTTTT
58 T-ATACCATTA
* * *
29146651 ATATTTTGACCAAAATTAATTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACCAT
1 ATATTTTGACTAAAATTAATTAATATAATTATTTATATTAATAAATTCGATAAAATATATACCAT
29146716 TA
66 TA
29146718 ATATTTTG
1 ATATTTTG
29146726 TATGAATCAA
Statistics
Matches: 102, Mismatches: 30, Indels: 28
0.64 0.19 0.17
Matches are distributed among these distances:
65 2 0.02
66 13 0.13
67 31 0.30
68 7 0.07
69 6 0.06
70 6 0.06
71 23 0.23
72 13 0.13
73 1 0.01
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (67 bp):
ATATTTTGACTAAAATTAATTAATATAATTATTTATATTAATAAATTCGATAAAATATATACCAT
TA
Found at i:29146635 original size:138 final size:138
Alignment explanation
Indices: 29146254--29146892 Score: 1045
Period size: 138 Copynumber: 4.7 Consensus size: 138
29146244 TGTTAACCTT
* * *
29146254 AATTAATCAATATAACTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTGTAT
1 AATTAATTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTAT
* *
29146319 GAATCAAATTCATATATTAATTATATTCTTTCCAAAATAATATTAATTTCCA-AGTCTTTTATAT
66 GAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCATA-TCTTTTATAT
* *
29146383 TTTTACCGA
130 TTTGACCAA
29146392 AATTAATTAATATAATTGTTTATATTAATAAATTCGGT--AATATAT--AATTAATATTTTGTAT
1 AATTAATTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTAT
* *
29146453 GAATCAAATTCATATATTAATTATATTCTTTCCAAAATAATATTAATTTTTATATCTTTTATATT
66 GAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCATATCTTTTATATT
*
29146518 TTGACTAA
131 TTGACCAA
* * *
29146526 AATTAATTAATATAATTTTTTATATTAATAAATTCGATAAAATATATACCATTAATATTTTGTAT
1 AATTAATTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTAT
* *
29146591 GAATCAAATTCATATATTAGTTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATT
66 GAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCATATCTTTTATATT
29146656 TTGACCAA
131 TTGACCAA
*
29146664 AATTAATTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACCATTAATATTTTGTAT
1 AATTAATTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTAT
* *
29146729 GAATCAAATTCATATATTAGTTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATT
66 GAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCATATCTTTTATATT
29146794 TTGACCAA
131 TTGACCAA
* *
29146802 AATTAATTAATATAATTGTTTATATTAATAAATTTGGTAAAATATATACAATTAATATTTTTTAT
1 AATTAATTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTAT
*
29146867 GAATCGAATTCATATATTAATTATAT
66 GAATCAAATTCATATATTAATTATAT
29146893 ATATATTCTC
Statistics
Matches: 473, Mismatches: 23, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
134 118 0.25
135 1 0.00
136 14 0.03
138 340 0.72
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.47
Consensus pattern (138 bp):
AATTAATTAATATAATTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTAT
GAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTTCATATCTTTTATATT
TTGACCAA
Found at i:29146657 original size:71 final size:71
Alignment explanation
Indices: 29146580--29146796 Score: 186
Period size: 71 Copynumber: 3.1 Consensus size: 71
29146570 TATACCATTA
29146580 ATATTTTGTATGAATCAAATTCATATATTAGTTATATTCTTTCCAAAAGAATATTAATTTTCATG
1 ATATTTTGTATGAATCAAATTCATATATTAGTTATATTCTTTCCAAAAGAATATTAATTTTCATG
29146645 TCTTTT
66 TCTTTT
** * * * * *
29146651 ATATTTTG-ACCAAAAT-TAATTAATATAATT-GTT-TA-T-ATT--AATA-AAT-TCGGTAAAA
1 ATATTTTGTA--TGAATCAAATTCATAT-ATTAGTTATATTCTTTCCAAAAGAATAT---T-AAT
* ** * *
29146706 TAT-ATACCATTA
59 TTTCATGTCTTTT
29146718 ATATTTTGTATGAATCAAATTCATATATTAGTTATATTCTTTCCAAAAGAATATTAATTTTCATG
1 ATATTTTGTATGAATCAAATTCATATATTAGTTATATTCTTTCCAAAAGAATATTAATTTTCATG
29146783 TCTTTT
66 TCTTTT
29146789 ATATTTTG
1 ATATTTTG
29146797 ACCAAAATTA
Statistics
Matches: 104, Mismatches: 24, Indels: 36
0.63 0.15 0.22
Matches are distributed among these distances:
64 1 0.01
65 3 0.03
66 9 0.09
67 25 0.24
68 9 0.09
69 2 0.02
70 9 0.09
71 33 0.32
72 9 0.09
73 3 0.03
74 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.07, T:0.47
Consensus pattern (71 bp):
ATATTTTGTATGAATCAAATTCATATATTAGTTATATTCTTTCCAAAAGAATATTAATTTTCATG
TCTTTT
Found at i:29147052 original size:12 final size:12
Alignment explanation
Indices: 29147035--29147060 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29147025 CTTCGTTTCA
29147035 ACTAAATACAAT
1 ACTAAATACAAT
29147047 ACTAAATACAAT
1 ACTAAATACAAT
29147059 AC
1 AC
29147061 AAGACCCTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.19, G:0.00, T:0.23
Consensus pattern (12 bp):
ACTAAATACAAT
Found at i:29149017 original size:12 final size:12
Alignment explanation
Indices: 29148993--29149034 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
29148983 CATTTACTTA
29148993 ATTTTAGGTTTTT
1 ATTTTA-GTTTTT
29149006 ATTTTAGTTTTT
1 ATTTTAGTTTTT
*
29149018 ATTTTAGTTTTC
1 ATTTTAGTTTTT
29149030 ATTTT
1 ATTTT
29149035 CTTTCCAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
12 22 0.79
13 6 0.21
ACGTcount: A:0.17, C:0.02, G:0.10, T:0.71
Consensus pattern (12 bp):
ATTTTAGTTTTT
Found at i:29151680 original size:20 final size:20
Alignment explanation
Indices: 29151657--29151699 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
29151647 ACTTGATGAA
* *
29151657 AGGTATCGATACTTTTTTAT
1 AGGTATCAAAACTTTTTTAT
*
29151677 AGGTATCAAAACTTTTTTTT
1 AGGTATCAAAACTTTTTTAT
29151697 AGG
1 AGG
29151700 GGGTTGCGCG
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:0.28, C:0.09, G:0.16, T:0.47
Consensus pattern (20 bp):
AGGTATCAAAACTTTTTTAT
Found at i:29154823 original size:12 final size:12
Alignment explanation
Indices: 29154792--29154824 Score: 52
Period size: 10 Copynumber: 2.9 Consensus size: 12
29154782 CATTCATATG
29154792 TCCAAAACACAT
1 TCCAAAACACAT
29154804 T-C-AAACACAT
1 TCCAAAACACAT
29154814 TCCAAAACACA
1 TCCAAAACACA
29154825 CCAAATAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.47
11 2 0.11
12 8 0.42
ACGTcount: A:0.52, C:0.33, G:0.00, T:0.15
Consensus pattern (12 bp):
TCCAAAACACAT
Found at i:29155518 original size:15 final size:15
Alignment explanation
Indices: 29155484--29155528 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
29155474 TATTATTTTT
29155484 ATAACCTTTTCCATCA
1 ATAACCTTTT-CATCA
*
29155500 ATAACCTTTTCATCG
1 ATAACCTTTTCATCA
*
29155515 ATAACTTTTTCATC
1 ATAACCTTTTCATC
29155529 CTTTTCATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 17 0.63
16 10 0.37
ACGTcount: A:0.29, C:0.27, G:0.02, T:0.42
Consensus pattern (15 bp):
ATAACCTTTTCATCA
Found at i:29167123 original size:13 final size:12
Alignment explanation
Indices: 29167074--29167116 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
29167064 CTTTCTCTTC
29167074 TTTTTTTCAATT
1 TTTTTTTCAATT
*
29167086 TTTTTTTCAAAT
1 TTTTTTTCAATT
*
29167098 TTTTTTTGAATT
1 TTTTTTTCAATT
29167110 TTTTTTT
1 TTTTTTT
29167117 TGAATTTACA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:29170403 original size:25 final size:28
Alignment explanation
Indices: 29170372--29170457 Score: 90
Period size: 29 Copynumber: 3.1 Consensus size: 28
29170362 AGTCAAACAA
29170372 TAATTAG-ATA-T-TATTAAATATGTCC
1 TAATTAGTATAGTGTATTAAATATGTCC
* *
29170397 TAATTAGTTTAGGTGTTTTAAATATGTCC
1 TAATTAGTATA-GTGTATTAAATATGTCC
*
29170426 TAATTAGT-TCAAGTGTTTTAAATATGTCC
1 TAATTAGTAT--AGTGTATTAAATATGTCC
29170455 TAA
1 TAA
29170458 ACTAATACAT
Statistics
Matches: 53, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
25 7 0.13
26 2 0.04
28 2 0.04
29 41 0.77
30 1 0.02
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (28 bp):
TAATTAGTATAGTGTATTAAATATGTCC
Found at i:29170427 original size:29 final size:29
Alignment explanation
Indices: 29170385--29170457 Score: 128
Period size: 29 Copynumber: 2.5 Consensus size: 29
29170375 TTAGATATTA
* *
29170385 TTAAATATGTCCTAATTAGTTTAGGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
29170414 TTAAATATGTCCTAATTAGTTCAAGTGTT
1 TTAAATATGTCCTAATTAGTTCAAGTGTT
29170443 TTAAATATGTCCTAA
1 TTAAATATGTCCTAA
29170458 ACTAATACAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.45
Consensus pattern (29 bp):
TTAAATATGTCCTAATTAGTTCAAGTGTT
Found at i:29172615 original size:15 final size:15
Alignment explanation
Indices: 29172575--29172646 Score: 81
Period size: 15 Copynumber: 4.7 Consensus size: 15
29172565 TATTATTTGT
*
29172575 ATAACCTTTTCAATCA
1 ATAACCTTTTC-ATCG
29172591 ATAACCTTTTCATCG
1 ATAACCTTTTCATCG
*
29172606 ATAGCCTTTTCATCG
1 ATAACCTTTTCATCG
* *
29172621 GTAACCTTTTTCATCA
1 ATAACC-TTTTCATCG
*
29172637 ATAACATTTT
1 ATAACCTTTT
29172647 AATCCTTTTC
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
15 25 0.52
16 23 0.48
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.42
Consensus pattern (15 bp):
ATAACCTTTTCATCG
Found at i:29173761 original size:10 final size:9
Alignment explanation
Indices: 29173730--29173791 Score: 58
Period size: 10 Copynumber: 6.9 Consensus size: 9
29173720 TTTTTATGTT
*
29173730 TTAAATATA
1 TTAATTATA
29173739 TTAA-TATA
1 TTAATTATA
*
29173747 TTATTTA-A
1 TTAATTATA
29173755 TTATATTATA
1 TTA-ATTATA
29173765 TTATATTATA
1 TTA-ATTATA
29173775 TTATATTATA
1 TTA-ATTATA
29173785 TT-ATTAT
1 TTAATTAT
29173792 GTAAAATAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
8 16 0.33
9 9 0.19
10 23 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
TTAATTATA
Found at i:29173764 original size:5 final size:5
Alignment explanation
Indices: 29173735--29173788 Score: 80
Period size: 5 Copynumber: 11.6 Consensus size: 5
29173725 ATGTTTTAAA
29173735 TATAT TA-A- TATAT TAT-T TA-AT TATAT TATAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
29173781 TATAT TAT
1 TATAT TAT
29173789 TATGTAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
3 2 0.04
4 8 0.18
5 35 0.78
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
TATAT
Found at i:29175182 original size:39 final size:41
Alignment explanation
Indices: 29175137--29175231 Score: 104
Period size: 45 Copynumber: 2.3 Consensus size: 41
29175127 TGCCGACTAT
* *
29175137 TGTTACTGTTAT-C-GATTCGGCACTTTGTGTGTCGAATAC
1 TGTTACTGTTATACAAATTCAGCACTTTGTGTGTCGAATAC
* *
29175176 TGTTACTGCTATTGTTACAAATTCAGCACTTTGTGTGTTGAATAC
1 TGTTACTG---TT-ATACAAATTCAGCACTTTGTGTGTCGAATAC
29175221 TGTTACTGTTA
1 TGTTACTGTTA
29175232 CTGTTACTGT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
39 8 0.18
42 4 0.09
43 1 0.02
44 1 0.02
45 31 0.69
ACGTcount: A:0.21, C:0.16, G:0.20, T:0.43
Consensus pattern (41 bp):
TGTTACTGTTATACAAATTCAGCACTTTGTGTGTCGAATAC
Found at i:29175207 original size:45 final size:45
Alignment explanation
Indices: 29175151--29175238 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
29175141 ACTGTTATCG
* *
29175151 ATTCGGCACTTTGTGTGTCGAATACTGTTACTGCTATTGTTACAA
1 ATTCAGCACTTTGTGTGTCGAATACTGTTACTGCTACTGTTACAA
* *
29175196 ATTCAGCACTTTGTGTGTTGAATACTGTTACTGTTACTGTTAC
1 ATTCAGCACTTTGTGTGTCGAATACTGTTACTGCTACTGTTAC
29175239 TGTTACTGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (45 bp):
ATTCAGCACTTTGTGTGTCGAATACTGTTACTGCTACTGTTACAA
Found at i:29175229 original size:6 final size:6
Alignment explanation
Indices: 29175218--29175267 Score: 73
Period size: 6 Copynumber: 8.2 Consensus size: 6
29175208 GTGTGTTGAA
* *
29175218 TACTGT TACTGT TACTGT TACTGT TACTGC TACCGT TACTGAT TACTGT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT TACTG-T TACTGT
29175267 T
1 T
29175268 TACTAGTGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
6 33 0.85
7 6 0.15
ACGTcount: A:0.18, C:0.20, G:0.16, T:0.46
Consensus pattern (6 bp):
TACTGT
Found at i:29182491 original size:29 final size:29
Alignment explanation
Indices: 29182449--29182520 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
29182439 TGTGTTAGAA
*
29182449 AGAAAATGAGAGAAGAAAAATATGTTGAG
1 AGAAAATGAGAGAAGAAAAAGATGTTGAG
* *
29182478 AGAAAATGGGAGAAGAAAAAGATGTTGGG
1 AGAAAATGAGAGAAGAAAAAGATGTTGAG
*
29182507 AGAAATTGAGAGAA
1 AGAAAATGAGAGAA
29182521 TTTTGATAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.53, C:0.00, G:0.32, T:0.15
Consensus pattern (29 bp):
AGAAAATGAGAGAAGAAAAAGATGTTGAG
Found at i:29185547 original size:24 final size:25
Alignment explanation
Indices: 29185515--29185574 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
29185505 TGATTTAGAA
* *
29185515 TTCGGTTTTA-TTTAAAAT-ATTTAT
1 TTCGATTTTATTTTAAAATGATTT-C
*
29185539 TTCGATTTTAATTTTAAATTGATTTC
1 TTCGATTTT-ATTTTAAAATGATTTC
29185565 TTCGATTTTA
1 TTCGATTTTA
29185575 CCTTAGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
24 8 0.27
25 2 0.07
26 16 0.53
27 4 0.13
ACGTcount: A:0.27, C:0.07, G:0.08, T:0.58
Consensus pattern (25 bp):
TTCGATTTTATTTTAAAATGATTTC
Found at i:29185554 original size:26 final size:26
Alignment explanation
Indices: 29185525--29185574 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
29185515 TTCGGTTTTA
*
29185525 TTTAAAAT-ATTTATTTCGATTTTAAT
1 TTTAAAATGATTT-CTTCGATTTTAAT
*
29185551 TTTAAATTGATTTCTTCGATTTTA
1 TTTAAAATGATTTCTTCGATTTTA
29185575 CCTTAGTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 17 0.81
27 4 0.19
ACGTcount: A:0.30, C:0.06, G:0.06, T:0.58
Consensus pattern (26 bp):
TTTAAAATGATTTCTTCGATTTTAAT
Found at i:29188170 original size:12 final size:12
Alignment explanation
Indices: 29188150--29188185 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
29188140 ATTACTCAAC
*
29188150 TATTTTTATTAT
1 TATTGTTATTAT
29188162 TATTGTTATTAT
1 TATTGTTATTAT
*
29188174 TAATGTTATTAT
1 TATTGTTATTAT
29188186 AACTATTAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.67
Consensus pattern (12 bp):
TATTGTTATTAT
Found at i:29191456 original size:49 final size:49
Alignment explanation
Indices: 29191399--29191502 Score: 172
Period size: 49 Copynumber: 2.1 Consensus size: 49
29191389 TCATGTGTTA
* * * *
29191399 TAATTTTATAAAGTGTTGAGCTTTTGATTCATGATATTGAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTATTGATTCATGATATTAAACTTAATTT
29191448 TAATTTTATAAAGTGTTCACCTATTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTATTGATTCATGATATTAAACTTAATTT
29191497 TAATTT
1 TAATTT
29191503 GTTTTTTTCT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.49
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTATTGATTCATGATATTAAACTTAATTT
Found at i:29194497 original size:41 final size:41
Alignment explanation
Indices: 29194440--29194692 Score: 425
Period size: 41 Copynumber: 6.1 Consensus size: 41
29194430 TATCTTATGC
*
29194440 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGT
*
29194481 GATCTGAATCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGT
* *
29194522 GATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGTCGGT
1 GATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGT
*
29194563 GATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGT
*
29194604 GATCTGAATCAGGTTATAAACCTAGCAGGCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGT
* *
29194645 GATCTGAATCAGGCTATAAGCCTAGCAGCCTAAGTGCCGGT
1 GATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGT
29194686 GAATCTG
1 G-ATCTG
29194693 TTAAATTAAG
Statistics
Matches: 204, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
41 199 0.98
42 5 0.02
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (41 bp):
GATCTGAATCAGGCTATAAACCTAGCAGGCTAAGTGCCGGT
Found at i:29196061 original size:21 final size:21
Alignment explanation
Indices: 29196020--29196062 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
29196010 AATAAAGTAG
*
29196020 ATTATACATTATTTTTATAGT
1 ATTATACATTATATTTATAGT
*
29196041 ATTATATATTATGATTT-TAGT
1 ATTATACATTAT-ATTTATAGT
29196062 A
1 A
29196063 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
ATTATACATTATATTTATAGT
Found at i:29196317 original size:121 final size:121
Alignment explanation
Indices: 29196027--29196386 Score: 622
Period size: 121 Copynumber: 3.0 Consensus size: 121
29196017 TAGATTATAC
*
29196027 ATTAT-TTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATAATT-ATATT--G
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* *
29196088 AATTTTATTAAATTATATATTTTTATTAAATAATATTTAATAATAATTAT-TTTAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
*
29196143 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATACGAATATTTAATATTAAG
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
29196208 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
*
29196264 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAT
1 ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
* *
29196329 AATTTTTTTAAATTATATATTTTTATTAAATTATATTTAATAATAATTAAGTTAAA
66 AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
29196385 AT
1 AT
29196387 ATGATTAAAT
Statistics
Matches: 231, Mismatches: 8, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
116 5 0.02
117 48 0.21
118 5 0.02
120 50 0.22
121 123 0.53
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.52
Consensus pattern (121 bp):
ATTATATTTTATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAG
AATTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAA
Found at i:29196352 original size:18 final size:18
Alignment explanation
Indices: 29196317--29196364 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
29196307 TATAAGAATA
29196317 TTTAATATTA-ATAATTTT
1 TTTAA-ATTATATAATTTT
29196335 TTTAAATTATAT-ATTTT
1 TTTAAATTATATAATTTT
29196352 TATTAAATTATAT
1 T-TTAAATTATAT
29196365 TTAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.36
18 18 0.64
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAAATTATATAATTTT
Found at i:29200957 original size:69 final size:69
Alignment explanation
Indices: 29200843--29200978 Score: 209
Period size: 69 Copynumber: 2.0 Consensus size: 69
29200833 GCAAAATCGA
* *
29200843 TATAAATATATTATTTATATTATAAATTCACTTAATAATAATGTTAATTTCAGTTATAAAATAAA
1 TATAAATATATTAGTTATATTATAAATTCACTTAATAATAATGTTAATATCAGTTATAAAATAAA
29200908 TGTG
66 TGTG
* * * * *
29200912 TATAAGTATATTAGTTGTATTATAAATTCACTTAATGATACTGTTAATATCAGTTATGAAATAAA
1 TATAAATATATTAGTTATATTATAAATTCACTTAATAATAATGTTAATATCAGTTATAAAATAAA
29200977 TG
66 TG
29200979 CTTATATATA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.43
Consensus pattern (69 bp):
TATAAATATATTAGTTATATTATAAATTCACTTAATAATAATGTTAATATCAGTTATAAAATAAA
TGTG
Found at i:29206530 original size:54 final size:54
Alignment explanation
Indices: 29206436--29206547 Score: 145
Period size: 54 Copynumber: 2.1 Consensus size: 54
29206426 TCCAAATGCC
* *
29206436 CAATAATTTTCTTTTGAACAGTAGTCTCCCACTGATCAGTAGCTTCCCCTTGAA
1 CAATAATTTTCTTTTGAACAGTAGTCTCCCACTGAACAGTAGCTTCCCCTTAAA
* * ** *
29206490 CAATAGTTTT-TTTTGGAACAGTAGTTTCCCTTTTAACAGTAGCTTCCCCTTAAA
1 CAATAATTTTCTTTT-GAACAGTAGTCTCCCACTGAACAGTAGCTTCCCCTTAAA
29206544 CAAT
1 CAAT
29206548 GGTGTTATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
53 4 0.08
54 46 0.92
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (54 bp):
CAATAATTTTCTTTTGAACAGTAGTCTCCCACTGAACAGTAGCTTCCCCTTAAA
Found at i:29206545 original size:18 final size:18
Alignment explanation
Indices: 29206506--29206545 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
29206496 TTTTTTTTGG
* * *
29206506 AACAGTAGTTTCCCTTTT
1 AACAGTAGCTTCCCCTTA
29206524 AACAGTAGCTTCCCCTTA
1 AACAGTAGCTTCCCCTTA
29206542 AACA
1 AACA
29206546 ATGGTGTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.33
Consensus pattern (18 bp):
AACAGTAGCTTCCCCTTA
Found at i:29213751 original size:24 final size:24
Alignment explanation
Indices: 29213723--29213774 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
29213713 TTTCTAGAAA
* **
29213723 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAACATAATAT
29213747 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATTAACATAATAT
29213771 ATTT
1 ATTT
29213775 GAATTATGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAACATAATAT
Found at i:29215448 original size:19 final size:19
Alignment explanation
Indices: 29215420--29215468 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
29215410 TGCAGGTCTT
29215420 GAGTGGAGGCAACTCGTTG
1 GAGTGGAGGCAACTCGTTG
*
29215439 GAGTGAAGGCAACTCGTTG
1 GAGTGGAGGCAACTCGTTG
29215458 GAGTGGAGGCA
1 GAGTGGAGGCA
29215469 CTATTGTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.24, C:0.14, G:0.43, T:0.18
Consensus pattern (19 bp):
GAGTGGAGGCAACTCGTTG
Found at i:29215908 original size:13 final size:12
Alignment explanation
Indices: 29215886--29215914 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
29215876 TGCAAAATTA
29215886 AGAAAGAAAAAG
1 AGAAAGAAAAAG
29215898 AGAAAGAAAAA-
1 AGAAAGAAAAAG
29215909 AGAAAG
1 AGAAAG
29215915 GAGACGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAG
Found at i:29219146 original size:17 final size:17
Alignment explanation
Indices: 29219124--29219162 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
29219114 GCTAAGAACG
29219124 TCCTAGCCCTCAATTCT
1 TCCTAGCCCTCAATTCT
29219141 TCCTAGCCCTCAATTCT
1 TCCTAGCCCTCAATTCT
29219158 TCCTA
1 TCCTA
29219163 TCTTAGTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.41, G:0.05, T:0.36
Consensus pattern (17 bp):
TCCTAGCCCTCAATTCT
Found at i:29222358 original size:50 final size:50
Alignment explanation
Indices: 29222235--29222472 Score: 217
Period size: 50 Copynumber: 4.7 Consensus size: 50
29222225 GATAATAAAC
* * ** * * * *
29222235 GCCAAAGCCATGTCCCAGAAATGGTCTTACATGGGATGTTTCTTGT-ACT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGT
* * * * **
29222284 GCCAATGCCATATCCCAAATATGGTCTTACATGAGAGTTCTCATATCAGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGT
* ** * *
29222334 GCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGT
* * *
29222384 GCCAACGCGATGTCCCAGGCATGGTCTTACATGGGACCTCTCATAACCTCAATGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC-A-G-T
29222440 GCCAATGCCATGTCCCAGACATGGTCTTACATG
1 GCCAATGCCATGTCCCAGACATGGTCTTACATG
29222473 AGATCTCTTT
Statistics
Matches: 149, Mismatches: 33, Indels: 7
0.79 0.17 0.04
Matches are distributed among these distances:
49 36 0.24
50 79 0.53
53 2 0.01
55 1 0.01
56 31 0.21
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.26
Consensus pattern (50 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAGT
Found at i:29230554 original size:56 final size:50
Alignment explanation
Indices: 29230336--29230581 Score: 242
Period size: 50 Copynumber: 4.8 Consensus size: 50
29230326 GATAATAAAC
* ** * * *
29230336 GCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGT-ACT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGT
* * * ** * *
29230385 GCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCGGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGT
* * **
29230435 GCCCATGCCATGTCTCAGACATGGTCTTATGTGGGACCTCTCATCTCAGT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGT
* * *
29230485 GCCAACGCGATGTCCCAGGCATGGTCTTACATGGGACCTCTCATAACCTCAATGAT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT---CTC-A-G-T
*
29230541 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
29230582 TAACCCAAAT
Statistics
Matches: 158, Mismatches: 32, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
49 38 0.24
50 77 0.49
53 3 0.02
54 1 0.01
55 1 0.01
56 38 0.24
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.28
Consensus pattern (50 bp):
GCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGT
Found at i:29231506 original size:169 final size:169
Alignment explanation
Indices: 29231226--29231565 Score: 572
Period size: 169 Copynumber: 2.0 Consensus size: 169
29231216 GTATTTTTAC
* * *
29231226 AAATATGAACCCTTGGTGAAATTATTGCTAGAATAAGCTAAATCAAATTACCGGGGCTTCAAAAA
1 AAATATGAACCCTAGGTGAAATTATTGCTAGAATAAGCTAAATCAAATTACCGAGACTTCAAAAA
29231291 CGTAAAGAACATTAAAAACGGGGCTTGGAATCACTTACTATGGAGCTTAGAAGCTTGAAAACCCT
66 CGTAAAGAACATTAAAAACGGGGCTTGGAATCACTTACTATGGAGCTTAGAAGCTTGAAAACCCT
*
29231356 AACTATGACTTCCCCCTTGCTAATTTCGGCCAAATGAAG
131 AACTATGACTTCCCCCTTGCTAAATTCGGCCAAATGAAG
* * *
29231395 AAATATGAACCCTAGGTTAAATTATTGCTAGAATAAGCTAAATCAAGTTATCGAGACTTCAAAAA
1 AAATATGAACCCTAGGTGAAATTATTGCTAGAATAAGCTAAATCAAATTACCGAGACTTCAAAAA
* * *
29231460 CGTAAAGAACATTAAAAACGGGGCTTGGGATCACTTACTGTGGAGCTTGGAAGCTTGAAAACCCT
66 CGTAAAGAACATTAAAAACGGGGCTTGGAATCACTTACTATGGAGCTTAGAAGCTTGAAAACCCT
* *
29231525 AACTATGGCTTCTCCCTTGCTAAATTCGGCCAAATGAAG
131 AACTATGACTTCCCCCTTGCTAAATTCGGCCAAATGAAG
29231564 AA
1 AA
29231566 GATGACCACA
Statistics
Matches: 159, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
169 159 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (169 bp):
AAATATGAACCCTAGGTGAAATTATTGCTAGAATAAGCTAAATCAAATTACCGAGACTTCAAAAA
CGTAAAGAACATTAAAAACGGGGCTTGGAATCACTTACTATGGAGCTTAGAAGCTTGAAAACCCT
AACTATGACTTCCCCCTTGCTAAATTCGGCCAAATGAAG
Found at i:29238856 original size:93 final size:93
Alignment explanation
Indices: 29238697--29238882 Score: 363
Period size: 93 Copynumber: 2.0 Consensus size: 93
29238687 TGAACATTAC
29238697 ATGTTATAAGTACAAGTATTATGATTAACAAGTATATGTTTAGCTTTTGGAGTTTAATGAAATTT
1 ATGTTATAAGTACAAGTATTATGATTAACAAGTATATGTTTAGCTTTTGGAGTTTAATGAAATTT
29238762 ATTCGATATTTGATTATCCCCCTACATG
66 ATTCGATATTTGATTATCCCCCTACATG
*
29238790 ATGTTATAAGTACAAGTATTATGATTAATAAGTATATGTTTAGCTTTTGGAGTTTAATGAAATTT
1 ATGTTATAAGTACAAGTATTATGATTAACAAGTATATGTTTAGCTTTTGGAGTTTAATGAAATTT
29238855 ATTCGATATTTGATTATCCCCCTACATG
66 ATTCGATATTTGATTATCCCCCTACATG
29238883 CAGGTTAGGT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 92 1.00
ACGTcount: A:0.32, C:0.10, G:0.15, T:0.42
Consensus pattern (93 bp):
ATGTTATAAGTACAAGTATTATGATTAACAAGTATATGTTTAGCTTTTGGAGTTTAATGAAATTT
ATTCGATATTTGATTATCCCCCTACATG
Found at i:29258722 original size:9 final size:9
Alignment explanation
Indices: 29258710--29258743 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
29258700 AGATTTGAAA
29258710 TCTTGATTT
1 TCTTGATTT
29258719 TCTTGA--T
1 TCTTGATTT
29258726 TCTTGATTT
1 TCTTGATTT
29258735 TCTTGATTT
1 TCTTGATTT
29258744 CCAAGATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 7 0.30
9 16 0.70
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (9 bp):
TCTTGATTT
Found at i:29258731 original size:16 final size:16
Alignment explanation
Indices: 29258710--29258742 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
29258700 AGATTTGAAA
29258710 TCTTGATTTTCTTGAT
1 TCTTGATTTTCTTGAT
29258726 TCTTGATTTTCTTGAT
1 TCTTGATTTTCTTGAT
29258742 T
1 T
29258743 TCCAAGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (16 bp):
TCTTGATTTTCTTGAT
Found at i:29262563 original size:42 final size:43
Alignment explanation
Indices: 29262464--29262626 Score: 152
Period size: 43 Copynumber: 3.8 Consensus size: 43
29262454 AGCTCGTACA
* ** * *
29262464 ATGCCAACGTCCCAGATGTGGTCTTACTTGTAATCAAATAACG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCAAATAACG
* * *
29262507 ATGCCACTGTCCCAGACAAGGTCTTACATGAAATCATAT-ACG
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAATCAAATAACG
* *
29262549 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATCTCAAGT--CG
1 ATGCCAATGTCCCAGACATGGTCTTACATG-AAA--TCAAATAACG
* ** *
29262593 ATGCCAACGTCCCAGATGTGGTCTTACACGAAAT
1 ATGCCAATGTCCCAGACATGGTCTTACATGAAAT
29262627 AATATATCGG
Statistics
Matches: 101, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
41 1 0.01
42 30 0.30
43 37 0.37
44 29 0.29
45 4 0.04
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACATGGTCTTACATGAAATCAAATAACG
Found at i:29267860 original size:20 final size:19
Alignment explanation
Indices: 29267805--29267849 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
29267795 CATTTCATTG
*
29267805 AGCTCCAATTAGCTCATTTCC
1 AGCTCC-ATGAGCTCATTT-C
*
29267826 AGCTCCATGAACTCATTTC
1 AGCTCCATGAGCTCATTTC
29267845 AGCTC
1 AGCTC
29267850 ATTTGAGCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.31
Consensus pattern (19 bp):
AGCTCCATGAGCTCATTTC
Found at i:29272198 original size:21 final size:21
Alignment explanation
Indices: 29272156--29272198 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
29272146 CTGATTCTAG
*
29272156 TGTGGATGCATCTGGCTTTGT
1 TGTGGATGCATCTGGCTGTGT
29272177 TGTGGATGCATCTGAG-TGTGT
1 TGTGGATGCATCTG-GCTGTGT
29272198 T
1 T
29272199 AATTGTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.12, C:0.12, G:0.35, T:0.42
Consensus pattern (21 bp):
TGTGGATGCATCTGGCTGTGT
Found at i:29276502 original size:14 final size:14
Alignment explanation
Indices: 29276483--29276510 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29276473 GTATGGAGTG
29276483 AGCCTATTATCTCA
1 AGCCTATTATCTCA
29276497 AGCCTATTATCTCA
1 AGCCTATTATCTCA
29276511 TCCAACTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (14 bp):
AGCCTATTATCTCA
Found at i:29280370 original size:25 final size:24
Alignment explanation
Indices: 29280236--29280366 Score: 149
Period size: 25 Copynumber: 5.3 Consensus size: 24
29280226 ACCACGACTT
* *
29280236 GTATGAGCTTACCAATTTTAGCTC
1 GTATGAGCTTACCGATTCTAGCTC
*
29280260 GTGA-GAGCTTACCGATTTTAGCTC
1 GT-ATGAGCTTACCGATTCTAGCTC
29280284 GTGA-GAGCTTACCGATTCTCAGCTC
1 GT-ATGAGCTTACCGATTCT-AGCTC
*
29280309 GTATGAGCTTACCGATTTCCAGCTC
1 GTATGAGCTTACCGA-TTCTAGCTC
* *
29280334 GTAAGAGCATACCGATTCATAGCTC
1 GTATGAGCTTACCGATTC-TAGCTC
29280359 GTATGAGC
1 GTATGAGC
29280367 ATACATGTAT
Statistics
Matches: 95, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
24 43 0.45
25 49 0.52
26 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.31
Consensus pattern (24 bp):
GTATGAGCTTACCGATTCTAGCTC
Found at i:29288185 original size:22 final size:20
Alignment explanation
Indices: 29288146--29288192 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 20
29288136 AATAAAGTTG
29288146 ATAATAATTAATATATATT-
1 ATAATAATTAATATATATTA
29288165 ATAATAGATATAATTATATATTA
1 ATAATA-AT-TAA-TATATATTA
29288188 ATAAT
1 ATAAT
29288193 TATCATCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 2 0.08
21 3 0.12
22 8 0.33
23 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (20 bp):
ATAATAATTAATATATATTA
Found at i:29288330 original size:30 final size:30
Alignment explanation
Indices: 29288273--29288334 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
29288263 GCTTTTTGAA
* *
29288273 AATATTTACAAAAAAAAGCATCTAATTTTT
1 AATATTTACAAAAAAAAGCACCAAATTTTT
*
29288303 AATATTTAC-AAAAAGAGCAACCAAATTTTT
1 AATATTTACAAAAAAAAGC-ACCAAATTTTT
29288333 AA
1 AA
29288335 AAATAATTCA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 8 0.29
30 20 0.71
ACGTcount: A:0.52, C:0.11, G:0.05, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAAAAGCACCAAATTTTT
Found at i:29288331 original size:29 final size:30
Alignment explanation
Indices: 29288273--29288331 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
29288263 GCTTTTTGAA
* * *
29288273 AATATTTACAAAAAAAAGCATCTAATTTTT
1 AATATTTACAAAAAAAAGCAACCAAATTTT
*
29288303 AATATTTAC-AAAAAGAGCAACCAAATTTT
1 AATATTTACAAAAAAAAGCAACCAAATTTT
29288332 TAAAAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.51, C:0.12, G:0.05, T:0.32
Consensus pattern (30 bp):
AATATTTACAAAAAAAAGCAACCAAATTTT
Found at i:29300636 original size:41 final size:42
Alignment explanation
Indices: 29300585--29300666 Score: 123
Period size: 41 Copynumber: 2.0 Consensus size: 42
29300575 TTTAATATAA
29300585 AATATTAAATATAAAATA-TATTCCAAATTACTAG-AATCTTT
1 AATATTAAATATAAAATACT-TTCCAAATTACTAGAAATCTTT
**
29300626 AATATTAAATATAAAATACTTTGTAAATTACTAGAAATCTT
1 AATATTAAATATAAAATACTTTCCAAATTACTAGAAATCTT
29300667 ATCGCACGCG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 30 0.81
42 7 0.19
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.39
Consensus pattern (42 bp):
AATATTAAATATAAAATACTTTCCAAATTACTAGAAATCTTT
Found at i:29301449 original size:6 final size:6
Alignment explanation
Indices: 29301426--29301459 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
29301416 CTCCTTGCAT
* *
29301426 AAAATA AAATTT AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAA
29301460 AGCTTAAACC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
AAAATA
Found at i:29338239 original size:32 final size:32
Alignment explanation
Indices: 29338195--29338256 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
29338185 GTACCTTTTT
*
29338195 GCTATCTCTAAAAGGATGCCTTTATGGCTAAG
1 GCTATCTCTAAAAGGAAGCCTTTATGGCTAAG
*
29338227 GCTATC-CTTAAAAGGAAGCCTTTGTGGCTA
1 GCTATCTC-TAAAAGGAAGCCTTTATGGCTA
29338257 TCTCTATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (32 bp):
GCTATCTCTAAAAGGAAGCCTTTATGGCTAAG
Found at i:29338296 original size:29 final size:29
Alignment explanation
Indices: 29338234--29338296 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
29338224 AAGGCTATCC
* ** *
29338234 TTAAAAGGAAGCCTTTGTGGCTATCTCTA
1 TTAAAAGAAAGCCTTTGTGGAAAACTCTA
29338263 TTAAAAGAAAGCCTTTGTGGAAAACT-TA
1 TTAAAAGAAAGCCTTTGTGGAAAACTCTA
29338291 TCTAAA
1 T-TAAA
29338297 GAGGAACGCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 3 0.10
29 26 0.90
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (29 bp):
TTAAAAGAAAGCCTTTGTGGAAAACTCTA
Found at i:29349090 original size:10 final size:10
Alignment explanation
Indices: 29349075--29349099 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
29349065 GCTCGCTTAG
29349075 TTTCCTACAT
1 TTTCCTACAT
29349085 TTTCCTACAT
1 TTTCCTACAT
29349095 TTTCC
1 TTTCC
29349100 CGAATTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (10 bp):
TTTCCTACAT
Found at i:29351899 original size:23 final size:23
Alignment explanation
Indices: 29351873--29351916 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
29351863 TAAATATTGT
29351873 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
*
29351896 TTTATTATTATTTTACTTAGA
1 TTTATTAATATTTTACTTAGA
29351917 AAATGGTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:29356292 original size:27 final size:27
Alignment explanation
Indices: 29355828--29356281 Score: 547
Period size: 27 Copynumber: 16.9 Consensus size: 27
29355818 CAAGACCCCA
*
29355828 AAATACCCCCATAGGGTAAAATGACTG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
29355855 AAATA-ACTCGTAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
29355881 AAATACCCCCGTAAGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
29355908 AAATACCCCCATAGGGTAAAATAATCG
1 AAATACCCCCATAGGGTAAAATGACCG
**
29355935 AAATACCCCCATAGGGTAAAATGATTG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
29355962 AAATAACCCCATAGGGTAAAATGACTG
1 AAATACCCCCATAGGGTAAAATGACCG
*
29355989 AAATACCCCCGTAGGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* *
29356016 AAATACCCCTATAGGGTAAAATGACCT
1 AAATACCCCCATAGGGTAAAATGACCG
*
29356043 AAATACCCCCATATGGTAAAATG-CTCG
1 AAATACCCCCATAGGGTAAAATGAC-CG
* * *
29356070 AAATACCTCTATAGGGTAAAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
*
29356097 AAATACCCCCATAGGGT-AAATGATCG
1 AAATACCCCCATAGGGTAAAATGACCG
**
29356123 AAATACCCCCATAGGGT-AAATGACAA
1 AAATACCCCCATAGGGTAAAATGACCG
** * *
29356149 AAATACCTTCGTAAGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
**
29356176 AAATACCCCCATAGGGTAAAATGACAA
1 AAATACCCCCATAGGGTAAAATGACCG
** * *
29356203 AAATACCTTCGTAAGGTAAAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
* * *
29356230 AAATACCCCCGTAAGGTAGAATGACCG
1 AAATACCCCCATAGGGTAAAATGACCG
29356257 AAATACCCCCATAGGGTAAAATGAC
1 AAATACCCCCATAGGGTAAAATGAC
29356282 TATTATACCC
Statistics
Matches: 366, Mismatches: 57, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
26 68 0.19
27 298 0.81
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.19
Consensus pattern (27 bp):
AAATACCCCCATAGGGTAAAATGACCG
Found at i:29356670 original size:28 final size:28
Alignment explanation
Indices: 29356632--29356771 Score: 181
Period size: 28 Copynumber: 5.0 Consensus size: 28
29356622 CACTGTACTG
29356632 GTTACTGTATTGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* * *
29356660 GTTACTATATTGGGCTAAGTCCGACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* * *
29356688 GATACTGTATTGGGCTAAAGCCAACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* * *
29356716 ATTACAGTATTAGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
* *
29356744 GTTACTGCATCGGGCTAAGGCCCACACT
1 GTTACTGTATTGGGCTAAGGCCCACACT
29356772 ATACTGTTAC
Statistics
Matches: 93, Mismatches: 19, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 93 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (28 bp):
GTTACTGTATTGGGCTAAGGCCCACACT
Found at i:29357365 original size:12 final size:12
Alignment explanation
Indices: 29357348--29357372 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29357338 GGCGTTCATT
29357348 CGGTTAACCGAC
1 CGGTTAACCGAC
29357360 CGGTTAACCGAC
1 CGGTTAACCGAC
29357372 C
1 C
29357373 CGAAATAACA
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:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:29357544 original size:9 final size:9
Alignment explanation
Indices: 29357530--29357623 Score: 143
Period size: 9 Copynumber: 10.4 Consensus size: 9
29357520 TTTGGTTAAA
29357530 AATTAACCG
1 AATTAACCG
29357539 AATTAACCG
1 AATTAACCG
*
29357548 AATTACCCG
1 AATTAACCG
29357557 AATTAACCG
1 AATTAACCG
29357566 AATTAACCG
1 AATTAACCG
* *
29357575 GATTACCCG
1 AATTAACCG
29357584 AATTAACCG
1 AATTAACCG
*
29357593 AATTACCCG
1 AATTAACCG
*
29357602 AATTAATCG
1 AATTAACCG
29357611 AATTAACCG
1 AATTAACCG
29357620 AATT
1 AATT
29357624 GAATCACTAC
Statistics
Matches: 75, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 75 1.00
ACGTcount: A:0.40, C:0.23, G:0.12, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:29357769 original size:18 final size:18
Alignment explanation
Indices: 29357726--29357769 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
29357716 AATTTTTATG
**
29357726 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGAATA
*
29357744 ATTAGGTTGGGTTGAATA
1 ATTGGGTTGGGTTGAATA
*
29357762 CTTGGGTT
1 ATTGGGTT
29357770 TGGATTGGGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.16, C:0.02, G:0.41, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGAATA
Found at i:29358365 original size:75 final size:75
Alignment explanation
Indices: 29358227--29358376 Score: 230
Period size: 75 Copynumber: 2.0 Consensus size: 75
29358217 AAGGAAAACC
* * *
29358227 AAGATTATTCCCTTATTAATAGAGAAGGCAAATGGAAAGTTAGAAAAAGCTATTACATTCTTTCC
1 AAGATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGCAATTACATGCTTTCC
*
29358292 AAAAGAATAT
66 AAAAAAATAT
* *
29358302 AAGATTATTCCCTTATTAATAGAGAAGACAAATGGAAATTTAGAAAAATG-AATTATATGCTTTC
1 AAGATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAA-GCAATTACATGCTTTC
29358366 CAAAAAAATAT
65 CAAAAAAATAT
29358377 TAATTTCCAT
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 67 0.99
76 1 0.01
ACGTcount: A:0.46, C:0.11, G:0.13, T:0.30
Consensus pattern (75 bp):
AAGATTATTCCCTTATTAATAGAGAAGACAAATGGAAAGTTAGAAAAAGCAATTACATGCTTTCC
AAAAAAATAT
Found at i:29366090 original size:27 final size:28
Alignment explanation
Indices: 29365998--29366078 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 28
29365988 AATATATTAA
*
29365998 ATATATATTT-TTTTTAT-TTTTAAAAT
1 ATATATATTTATTTTTATGTTTAAAAAT
29366024 ATA-ATAGTTTAAGTTTTTTATGTTTAAAAAT
1 ATATATA-TTT-A--TTTTTATGTTTAAAAAT
29366055 ATATATATTTATTTTTATGTTTAA
1 ATATATATTTATTTTTATGTTTAA
29366079 GTTATTAGTA
Statistics
Matches: 47, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
25 3 0.06
26 6 0.13
28 13 0.28
30 8 0.17
31 14 0.30
32 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (28 bp):
ATATATATTTATTTTTATGTTTAAAAAT
Found at i:29366680 original size:13 final size:13
Alignment explanation
Indices: 29366662--29366689 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29366652 ATTGAAATGA
29366662 TGAAGAAGGGGTC
1 TGAAGAAGGGGTC
29366675 TGAAGAAGGGGTC
1 TGAAGAAGGGGTC
29366688 TG
1 TG
29366690 TAAGGAAATT
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:0.29, C:0.07, G:0.46, T:0.18
Consensus pattern (13 bp):
TGAAGAAGGGGTC
Found at i:29367474 original size:18 final size:18
Alignment explanation
Indices: 29367447--29367510 Score: 85
Period size: 18 Copynumber: 3.4 Consensus size: 18
29367437 TTCGGTCCTC
*
29367447 ATAGACTTTTTTACTGTA
1 ATAGATTTTTTTACTGTA
29367465 ATAGA-TTTTTTACTGCTA
1 ATAGATTTTTTTACTG-TA
29367483 ATAGATTTTTATTCACTGTA
1 ATAGATTTTT-TT-ACTGTA
29367503 ATAGATTT
1 ATAGATTT
29367511 CATTAATTTC
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.24
18 12 0.29
19 4 0.10
20 12 0.29
21 4 0.10
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.50
Consensus pattern (18 bp):
ATAGATTTTTTTACTGTA
Found at i:29368387 original size:28 final size:28
Alignment explanation
Indices: 29368346--29368414 Score: 129
Period size: 28 Copynumber: 2.5 Consensus size: 28
29368336 ATTTTGTTTG
*
29368346 AACCTATTTTTATATTTAATAAAATATA
1 AACCTATTTGTATATTTAATAAAATATA
29368374 AACCTATTTGTATATTTAATAAAATATA
1 AACCTATTTGTATATTTAATAAAATATA
29368402 AACCTATTTGTAT
1 AACCTATTTGTAT
29368415 CAAAGTATGC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.43, C:0.09, G:0.03, T:0.45
Consensus pattern (28 bp):
AACCTATTTGTATATTTAATAAAATATA
Done.