Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032255.1 Gossypioides kirkii chromosome KI_13
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: 42971368
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2600 characters in sequence are not A, C, G, or T
File 89 of 143
Found at i:27906188 original size:29 final size:29
Alignment explanation
Indices: 27906126--27906189 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
27906116 ATATAAAAAT
* * *
27906126 ATAATATTAATATAAATATTATTAATTAC
1 ATAATATTAATACAAATAATATAAATTAC
*
27906155 TTAATATTAATAACAAATAATATAAATTA-
1 ATAATATTAAT-ACAAATAATATAAATTAC
27906184 ATAATA
1 ATAATA
27906190 ATTGATAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 15 0.52
30 14 0.48
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (29 bp):
ATAATATTAATACAAATAATATAAATTAC
Found at i:27906319 original size:21 final size:21
Alignment explanation
Indices: 27906269--27906341 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
27906259 AAATCCCCAA
*
27906269 TCTCTTCTTCACG-AAGCCCT
1 TCTCTTCTTCACGCACGCCCT
* * *
27906289 TTTGTTCTTCACGCACGCTCT
1 TCTCTTCTTCACGCACGCCCT
27906310 TCTCTTCTTCACGCACGCCCT
1 TCTCTTCTTCACGCACGCCCT
27906331 TCTCTTCTTCA
1 TCTCTTCTTCA
27906342 GTCTTATCTT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 11 0.24
21 34 0.76
ACGTcount: A:0.11, C:0.40, G:0.10, T:0.40
Consensus pattern (21 bp):
TCTCTTCTTCACGCACGCCCT
Found at i:27908519 original size:28 final size:28
Alignment explanation
Indices: 27908464--27908519 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
27908454 ATATAGTTTC
*
27908464 TATTATAAATTAATAATATACACTAATT
1 TATTATAAATTAATAATATACACAAATT
*
27908492 TATTATAAATTAATAATATATACAAATT
1 TATTATAAATTAATAATATACACAAATT
27908520 CCTCTGATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (28 bp):
TATTATAAATTAATAATATACACAAATT
Found at i:27908627 original size:14 final size:14
Alignment explanation
Indices: 27908608--27908663 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
27908598 TTAGTTAATT
27908608 AAATATTTAATTTA
1 AAATATTTAATTTA
27908622 AAATATTTAATTATTTA
1 AAATATTT-A--ATTTA
*
27908639 ATTATATTTAA-TT-
1 A-AATATTTAATTTA
27908652 AAATATTTAATT
1 AAATATTTAATT
27908664 ATTTACTTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
12 8 0.23
13 2 0.06
14 10 0.29
15 2 0.06
17 7 0.20
18 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
AAATATTTAATTTA
Found at i:27908631 original size:22 final size:23
Alignment explanation
Indices: 27908603--27908663 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
27908593 CAGTATTAGT
27908603 TAATTAAATATTTAATTTA-AAA
1 TAATTAAATATTTAATTTATAAA
* * **
27908625 TATTTAATTATTTAA-TTATATT
1 TAATTAAATATTTAATTTATAAA
27908647 TAATTAAATATTTAATT
1 TAATTAAATATTTAATT
27908664 ATTTACTTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
21 3 0.10
22 27 0.87
23 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TAATTAAATATTTAATTTATAAA
Found at i:27908647 original size:18 final size:18
Alignment explanation
Indices: 27908624--27908690 Score: 83
Period size: 18 Copynumber: 4.1 Consensus size: 18
27908614 TTAATTTAAA
27908624 ATATTTAATTATTTAATT
1 ATATTTAATTATTTAATT
27908642 ATATTT-A--A-TTAA--
1 ATATTTAATTATTTAATT
*
27908654 ATATTTAATTATTTACTT
1 ATATTTAATTATTTAATT
27908672 ATATTTAATTATTTAATT
1 ATATTTAATTATTTAATT
27908690 A
1 A
27908691 ATAAAAATAG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
12 6 0.15
13 1 0.02
14 4 0.10
15 2 0.05
16 3 0.07
17 1 0.02
18 24 0.59
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (18 bp):
ATATTTAATTATTTAATT
Found at i:27908658 original size:30 final size:30
Alignment explanation
Indices: 27908610--27908682 Score: 119
Period size: 30 Copynumber: 2.4 Consensus size: 30
27908600 AGTTAATTAA
27908610 ATATTTAATTTAAAATATTTAATTATTTAATT
1 ATATTTAA-TT-AAATATTTAATTATTTAATT
*
27908642 ATATTTAATTAAATATTTAATTATTTACTT
1 ATATTTAATTAAATATTTAATTATTTAATT
27908672 ATATTTAATTA
1 ATATTTAATTA
27908683 TTTAATTAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 30 0.75
31 2 0.05
32 8 0.20
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (30 bp):
ATATTTAATTAAATATTTAATTATTTAATT
Found at i:27908688 original size:8 final size:8
Alignment explanation
Indices: 27908625--27908690 Score: 64
Period size: 8 Copynumber: 8.2 Consensus size: 8
27908615 TAATTTAAAA
27908625 TATTTAAT
1 TATTTAAT
27908633 TATTTAAT
1 TATTTAAT
*
27908641 TA--TATT
1 TATTTAAT
* *
27908647 TAATTAAA
1 TATTTAAT
27908655 TATTTAAT
1 TATTTAAT
*
27908663 TATTTACTT
1 TATTTA-AT
27908672 ATATTTAAT
1 -TATTTAAT
27908681 TATTTAAT
1 TATTTAAT
27908689 TA
1 TA
27908691 ATAAAAATAG
Statistics
Matches: 47, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
6 5 0.11
8 34 0.72
9 2 0.04
10 6 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (8 bp):
TATTTAAT
Found at i:27908692 original size:30 final size:30
Alignment explanation
Indices: 27908610--27908692 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
27908600 AGTTAATTAA
*
27908610 ATATTTAATTTAAAATATTTAATTATTTAATT
1 ATATTTAA-TT-AAATAATTAATTATTTAATT
* *
27908642 ATATTTAATTAAATATTTAATTATTTACTT
1 ATATTTAATTAAATAATTAATTATTTAATT
**
27908672 ATATTTAATTATTTAATTAAT
1 ATATTTAATTAAATAATTAAT
27908693 AAAAATAGCT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
30 37 0.79
31 2 0.04
32 8 0.17
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (30 bp):
ATATTTAATTAAATAATTAATTATTTAATT
Found at i:27910544 original size:42 final size:42
Alignment explanation
Indices: 27910447--27910654 Score: 202
Period size: 42 Copynumber: 4.9 Consensus size: 42
27910437 GGAAAAAAAT
* * * *
27910447 CATGTTCTTTAGTGGCGTTTGTGAGAAAAGCGTCGTTAAA-AA
1 CATGTTCTTTAGCGGCGTTTATG-GAAAAGCGCCGCTAAAGAA
* *
27910489 CCATGTTCTTTAGCGGGGTTTTTGGAAAAGCGCCGCTAAAGAA
1 -CATGTTCTTTAGCGGCGTTTATGGAAAAGCGCCGCTAAAGAA
* * * ** *
27910532 CATATTCATTAGCGGCGTTTGTGGCAAAAGCTTCACTAAAGAA
1 CATGTTCTTTAGCGGCGTTTATGG-AAAAGCGCCGCTAAAGAA
* * * *
27910575 CATGTTCTTTAGAGGCATTTATGGGAAAGCGCCGCTAAAGAT
1 CATGTTCTTTAGCGGCGTTTATGGAAAAGCGCCGCTAAAGAA
* * * *
27910617 CATGTTCTATAGTGGCGTTTACGGGAAAGCGCCGCTAA
1 CATGTTCTTTAGCGGCGTTTATGGAAAAGCGCCGCTAA
27910655 TGATAATATT
Statistics
Matches: 137, Mismatches: 26, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
42 81 0.59
43 56 0.41
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (42 bp):
CATGTTCTTTAGCGGCGTTTATGGAAAAGCGCCGCTAAAGAA
Found at i:27910634 original size:85 final size:85
Alignment explanation
Indices: 27910445--27910636 Score: 228
Period size: 85 Copynumber: 2.3 Consensus size: 85
27910435 GTGGAAAAAA
* ** * **
27910445 ATCATGTTCTTTAGTGGCGTTTGTGAGAAAAGCGTCGTTAAAAACCATGTTCTTTAGCGGGGTTT
1 ATCATGTTCTATAGTGGCGTTTGTGAGAAAAGCGTCACTAAAAACCATGTTCTTTAGAGGCATTT
*
27910510 TTGGAAAAGCGCCGCTAAAG
66 ATGGAAAAGCGCCGCTAAAG
* * * *
27910530 AACATATTC-ATTAGCGGCGTTTGTG-GCAAAAGCTTCACTAAAGAA-CATGTTCTTTAGAGGCA
1 ATCATGTTCTA-TAGTGGCGTTTGTGAG-AAAAGCGTCACTAAA-AACCATGTTCTTTAGAGGCA
*
27910592 TTTATGGGAAAGCGCCGCTAAAG
63 TTTATGGAAAAGCGCCGCTAAAG
27910615 ATCATGTTCTATAGTGGCGTTT
1 ATCATGTTCTATAGTGGCGTTT
27910637 ACGGGAAAGC
Statistics
Matches: 88, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
84 1 0.01
85 84 0.95
86 3 0.03
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (85 bp):
ATCATGTTCTATAGTGGCGTTTGTGAGAAAAGCGTCACTAAAAACCATGTTCTTTAGAGGCATTT
ATGGAAAAGCGCCGCTAAAG
Found at i:27910667 original size:42 final size:42
Alignment explanation
Indices: 27910592--27910678 Score: 129
Period size: 42 Copynumber: 2.1 Consensus size: 42
27910582 TTTAGAGGCA
* * * *
27910592 TTTATGGGAAAGCGCCGCTAAAGATCATGTTCTATAGTGGCG
1 TTTACGGGAAAGCGCCGCTAAAGATAATATTCTATAGTAGCG
*
27910634 TTTACGGGAAAGCGCCGCTAATGATAATATTCTATAGTAGCG
1 TTTACGGGAAAGCGCCGCTAAAGATAATATTCTATAGTAGCG
27910676 TTT
1 TTT
27910679 TTCCTCATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.31
Consensus pattern (42 bp):
TTTACGGGAAAGCGCCGCTAAAGATAATATTCTATAGTAGCG
Found at i:27917979 original size:19 final size:19
Alignment explanation
Indices: 27917957--27918001 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
27917947 TTATATTAGG
27917957 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
27917976 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
27917995 ATTTAAT
1 ATTTAAT
27918002 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:27920427 original size:21 final size:21
Alignment explanation
Indices: 27920402--27920451 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
27920392 GAATTTCAGC
*
27920402 AGCAATCTATAGATTTCCAAA
1 AGCAAACTATAGATTTCCAAA
* * *
27920423 AGCAAACTGTGGATTTTCAAA
1 AGCAAACTATAGATTTCCAAA
*
27920444 AGAAAACT
1 AGCAAACT
27920452 GAGGCATCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (21 bp):
AGCAAACTATAGATTTCCAAA
Found at i:27920452 original size:21 final size:21
Alignment explanation
Indices: 27920413--27920452 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
27920403 GCAATCTATA
*
27920413 GATTTCCAAAAGCAAACTGTG
1 GATTTCCAAAAGAAAACTGTG
*
27920434 GATTTTCAAAAGAAAACTG
1 GATTTCCAAAAGAAAACTG
27920453 AGGCATCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
GATTTCCAAAAGAAAACTGTG
Found at i:27924515 original size:16 final size:17
Alignment explanation
Indices: 27924491--27924549 Score: 77
Period size: 16 Copynumber: 3.5 Consensus size: 17
27924481 GGCAACCTAA
27924491 TTATTTTTATTTTTTAT
1 TTATTTTTATTTTTTAT
27924508 TT-TTTTTATTTTTCTAT
1 TTATTTTTATTTTT-TAT
*
27924525 CTTATTTTT-TTATTTAT
1 -TTATTTTTATTTTTTAT
27924542 TTATTTTT
1 TTATTTTT
27924550 GTCCAGGAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
16 19 0.50
17 8 0.21
18 6 0.16
19 5 0.13
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.81
Consensus pattern (17 bp):
TTATTTTTATTTTTTAT
Found at i:27926699 original size:29 final size:29
Alignment explanation
Indices: 27926667--27926759 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
27926657 AAATCAAGGT
27926667 TAAAAATGGGATTTTGGAAAGTTCGGGGG
1 TAAAAATGGGATTTTGGAAAGTTCGGGGG
** ** *
27926696 TAAAACA-GTAACTTTTGGTGAAA--TCAAGGT
1 TAAAA-ATGGGA-TTTT-G-GAAAGTTCGGGGG
27926726 TAAAAATGGGATTTTGGAAAGTTCGGGGG
1 TAAAAATGGGATTTTGGAAAGTTCGGGGG
27926755 TAAAA
1 TAAAA
27926760 CGGTAATTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 14
0.66 0.14 0.20
Matches are distributed among these distances:
27 4 0.09
28 1 0.02
29 21 0.45
30 16 0.34
31 1 0.02
32 4 0.09
ACGTcount: A:0.37, C:0.05, G:0.30, T:0.28
Consensus pattern (29 bp):
TAAAAATGGGATTTTGGAAAGTTCGGGGG
Found at i:27926889 original size:59 final size:59
Alignment explanation
Indices: 27926452--27926887 Score: 527
Period size: 59 Copynumber: 7.4 Consensus size: 59
27926442 ATTTCTGACT
* ** ** *
27926452 TTCGGGGGTAAAAATGTAATTTTTGGTGAAA-TTAGGGTCAAAAATGGAATTTTGGAAAG
1 TTCGAGGGTAAAACGGTAATTTTTGGTGAAACCGA-GGTTAAAAATGGAATTTTGGAAAG
* * * *
27926511 TTCGAGGGTAAAACGATAATTTTTGGTAAAATCGAGGTTAAAAAT-GAGGTTTTGGAAAG
1 TTCGAGGGTAAAACGGTAATTTTTGGTGAAACCGAGGTTAAAAATGGA-ATTTTGGAAAG
** * * * *
27926570 TTAAAGGGTAAAATGGTAATTTTTGATGAAACTGGGGTTAAAAATGGAATTTTGGAAAG
1 TTCGAGGGTAAAACGGTAATTTTTGGTGAAACCGAGGTTAAAAATGGAATTTTGGAAAG
* * * * *
27926629 TTTGAGGGTAAAAGGGTAATTTTTGGTGAAATCAAGGTTAAAAATGGGATTTTGGAAAG
1 TTCGAGGGTAAAACGGTAATTTTTGGTGAAACCGAGGTTAAAAATGGAATTTTGGAAAG
* * * * * *
27926688 TTCGGGGGTAAAACAGTAACTTTTGGTGAAATCAAGGTTAAAAATGGGATTTTGGAAAG
1 TTCGAGGGTAAAACGGTAATTTTTGGTGAAACCGAGGTTAAAAATGGAATTTTGGAAAG
* * *
27926747 TTCGGGGGTAAAACGGTAATTTTTGGTGAAACCGAGGTCAAAAATGGAATTTTGGAATG
1 TTCGAGGGTAAAACGGTAATTTTTGGTGAAACCGAGGTTAAAAATGGAATTTTGGAAAG
* *
27926806 TTCGGGGGTAAAATGGTAATTTTTGGTGAAACCGAGGTT-AAAATGGAATTTTGGAAAG
1 TTCGAGGGTAAAACGGTAATTTTTGGTGAAACCGAGGTTAAAAATGGAATTTTGGAAAG
* *
27926864 TTTGAGGGTAAAATGGTAATTTTT
1 TTCGAGGGTAAAACGGTAATTTTT
27926888 TGAAAGTTTT
Statistics
Matches: 329, Mismatches: 45, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
58 42 0.13
59 284 0.86
60 3 0.01
ACGTcount: A:0.35, C:0.04, G:0.29, T:0.32
Consensus pattern (59 bp):
TTCGAGGGTAAAACGGTAATTTTTGGTGAAACCGAGGTTAAAAATGGAATTTTGGAAAG
Found at i:27926896 original size:30 final size:30
Alignment explanation
Indices: 27926811--27926896 Score: 90
Period size: 30 Copynumber: 2.9 Consensus size: 30
27926801 GAATGTTCGG
**
27926811 GGGTAAAATGGTAATTTTTGGTGAAA--CCGA
1 GGGTAAAATGGTAATTTTT--TGAAAGTTTGA
* *
27926841 GGTTAAAATGG-AA-TTTTGGAAAGTTTGA
1 GGGTAAAATGGTAATTTTTTGAAAGTTTGA
27926869 GGGTAAAATGGTAATTTTTTGAAAGTTT
1 GGGTAAAATGGTAATTTTTTGAAAGTTT
27926897 TAAGGTCAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
26 4 0.09
28 16 0.35
29 4 0.09
30 22 0.48
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (30 bp):
GGGTAAAATGGTAATTTTTTGAAAGTTTGA
Found at i:27928052 original size:20 final size:21
Alignment explanation
Indices: 27928016--27928063 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
27928006 ATTTTCTTTG
* *
27928016 TATTA-TTATTTTATATTTAA
1 TATTATTTATTATATATTAAA
27928036 TATTATTTATTAT-TATTAAA
1 TATTATTTATTATATATTAAA
27928056 TA-TATTTA
1 TATTATTTA
27928064 ATGTGTACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 6 0.24
20 13 0.52
21 6 0.24
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TATTATTTATTATATATTAAA
Found at i:27928842 original size:6 final size:6
Alignment explanation
Indices: 27928825--27928910 Score: 56
Period size: 6 Copynumber: 15.0 Consensus size: 6
27928815 TTGGATATCT
* * *
27928825 AATTTA ATTTTA AATTTA AATTTA TAA--TA AATTTA AATTT- TATGTA
1 AATTTA AATTTA AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA
* * * **
27928871 AATTTA AATTCA AA-ATA AATCT- AATTTA AAACTA AATTTA
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
27928911 TATCCCATCG
Statistics
Matches: 59, Mismatches: 15, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
4 2 0.03
5 12 0.20
6 43 0.73
7 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:27928857 original size:17 final size:17
Alignment explanation
Indices: 27928835--27928910 Score: 82
Period size: 17 Copynumber: 4.5 Consensus size: 17
27928825 AATTTAATTT
*
27928835 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* **
27928852 TAAATTTAAATTTTATG
1 TAAATTTAAATTTAAAA
*
27928869 TAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
*
27928886 TAAATCT-AATTTAAAA
1 TAAATTTAAATTTAAAA
27928902 CTAAATTTA
1 -TAAATTTA
27928911 TATCCCATCG
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
16 8 0.17
17 38 0.83
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:27929209 original size:18 final size:20
Alignment explanation
Indices: 27929168--27929203 Score: 58
Period size: 18 Copynumber: 1.9 Consensus size: 20
27929158 TTAAAAATAT
27929168 TATTATTAATATATTTTTAA
1 TATTATTAATATATTTTTAA
27929188 TATT-TTAAT-TATTTTT
1 TATTATTAATATATTTTT
27929204 GCTATTGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.44
19 5 0.31
20 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTATTAATATATTTTTAA
Found at i:27938939 original size:21 final size:21
Alignment explanation
Indices: 27938895--27938939 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
27938885 TTTTGAGTAA
*
27938895 TTTAATTTTTTTTTATGTTCT
1 TTTAATTTTTTTTTATGTTAT
*
27938916 TTTAACTTTTTTTTTCT-TTAT
1 TTTAA-TTTTTTTTTATGTTAT
27938937 TTT
1 TTT
27938940 CCATTCTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.13, C:0.07, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTAATTTTTTTTTATGTTAT
Found at i:27947536 original size:11 final size:11
Alignment explanation
Indices: 27947520--27947546 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
27947510 ATTTTTTATG
27947520 ATAATAAAAAT
1 ATAATAAAAAT
27947531 ATAATAAAAAT
1 ATAATAAAAAT
27947542 ATAAT
1 ATAAT
27947547 TTTATTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
ATAATAAAAAT
Found at i:27952871 original size:18 final size:17
Alignment explanation
Indices: 27952848--27952881 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27952838 ATCCATTTAT
27952848 TTTTATATAAAAAATTTG
1 TTTTATA-AAAAAATTTG
*
27952866 TTTTATAAAATAATTT
1 TTTTATAAAAAAATTT
27952882 ATTTCCAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTTATAAAAAAATTTG
Found at i:27953134 original size:28 final size:28
Alignment explanation
Indices: 27953089--27953154 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 28
27953079 TGATTTAAGG
* * ** *
27953089 TTTAAGAGTTGGAATTTTTTATTCGAGA
1 TTTAAGATTTAGAATTTTAAATTCAAGA
*
27953117 TTTAAGATTTAGAGTTTTAAATTCAAGA
1 TTTAAGATTTAGAATTTTAAATTCAAGA
*
27953145 TTTAGGATTT
1 TTTAAGATTT
27953155 GAAATTCTGG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (28 bp):
TTTAAGATTTAGAATTTTAAATTCAAGA
Found at i:27953159 original size:21 final size:21
Alignment explanation
Indices: 27953120--27953161 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
27953110 TTCGAGATTT
*
27953120 AAGATTTAGAGTTTTAAATTC
1 AAGATTTAGAGTTTGAAATTC
27953141 AAGATTTAG-GATTTGAAATTC
1 AAGATTTAGAG-TTTGAAATTC
27953162 TGGGTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (21 bp):
AAGATTTAGAGTTTGAAATTC
Found at i:27956043 original size:17 final size:17
Alignment explanation
Indices: 27956021--27956059 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
27956011 ATTAATAATT
*
27956021 TAAAATTTATATTTGCA
1 TAAAATTTACATTTGCA
*
27956038 TAAAATTTACATTTTCA
1 TAAAATTTACATTTGCA
27956055 TAAAA
1 TAAAA
27956060 ACTATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAAATTTACATTTGCA
Found at i:27958765 original size:5 final size:5
Alignment explanation
Indices: 27958755--27958787 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
27958745 ATAGACCTGA
27958755 CATGC CATGC CATGC CATGC CATGC CATGC CAT
1 CATGC CATGC CATGC CATGC CATGC CATGC CAT
27958788 TACATGATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.21, C:0.39, G:0.18, T:0.21
Consensus pattern (5 bp):
CATGC
Found at i:27962882 original size:17 final size:18
Alignment explanation
Indices: 27962847--27962883 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
27962837 ATATATTGAA
*
27962847 TTTTATCGATAACATCTT
1 TTTTATCGATAACAACTT
27962865 TTTTATCGAT-ACAACTT
1 TTTTATCGATAACAACTT
27962882 TT
1 TT
27962884 GCATTCTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.27, C:0.16, G:0.05, T:0.51
Consensus pattern (18 bp):
TTTTATCGATAACAACTT
Found at i:27964130 original size:32 final size:33
Alignment explanation
Indices: 27964094--27964166 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 33
27964084 AAAATAAATA
27964094 AATTTATTTC-TCAACCTTTAAAAAAATAGTCG
1 AATTTATTTCATCAACCTTTAAAAAAATAGTCG
* *
27964126 AATTTGA--TCATCAACTTTTTAAAAAATAGTCG
1 AATTT-ATTTCATCAACCTTTAAAAAAATAGTCG
*
27964158 AATTGATTT
1 AATTTATTT
27964167 TTTAATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
31 3 0.09
32 29 0.85
33 2 0.06
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (33 bp):
AATTTATTTCATCAACCTTTAAAAAAATAGTCG
Found at i:27964286 original size:17 final size:18
Alignment explanation
Indices: 27964255--27964302 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
27964245 ATTTTTTAAA
*
27964255 ATTTTATGAATTTTTATAT
1 ATTTT-TGAATTTTAATAT
* *
27964274 ATTTTTTAATTTTAATTT
1 ATTTTTGAATTTTAATAT
27964292 ATTTTTGAATT
1 ATTTTTGAATT
27964303 ATTTGTTGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
18 20 0.80
19 5 0.20
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (18 bp):
ATTTTTGAATTTTAATAT
Found at i:27966386 original size:18 final size:18
Alignment explanation
Indices: 27966337--27966398 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
27966327 TGACGTGATA
27966337 GATATAAATTTAA-AAAAT
1 GATATAAA-TTAATAAAAT
*
27966355 -A-ATAAATCT-TTAAAAT
1 GATATAAAT-TAATAAAAT
*
27966371 GATATAAATTAATAAAAA
1 GATATAAATTAATAAAAT
*
27966389 AATATAAATT
1 GATATAAATT
27966399 TTTCATTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
15 1 0.03
16 11 0.31
17 3 0.09
18 20 0.57
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (18 bp):
GATATAAATTAATAAAAT
Found at i:27966891 original size:32 final size:31
Alignment explanation
Indices: 27966850--27966915 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
27966840 GTAAACATGC
*
27966850 TTTTTAGTTCTTTTATATATATATATTATAAA
1 TTTTAAGTTCTTTTATA-ATATATATTATAAA
* * *
27966882 TTTTAAGTTCTTTTATAATTTTTTTTATAAA
1 TTTTAAGTTCTTTTATAATATATATTATAAA
27966913 TTT
1 TTT
27966916 ATATTTTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 14 0.47
32 16 0.53
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (31 bp):
TTTTAAGTTCTTTTATAATATATATTATAAA
Found at i:27967017 original size:25 final size:24
Alignment explanation
Indices: 27966968--27967018 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
27966958 GGGCTTTTTA
* *
27966968 TATAATTTTAATTGTATATAAATT
1 TATAAGTTTAATTATATATAAATT
*
27966992 TATAAGTTTATATTATATATATATT
1 TATAAGTTTA-ATTATATATAAATT
27967017 TA
1 TA
27967019 AAATAATAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 9 0.39
25 14 0.61
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (24 bp):
TATAAGTTTAATTATATATAAATT
Found at i:27969183 original size:37 final size:39
Alignment explanation
Indices: 27969123--27969209 Score: 124
Period size: 37 Copynumber: 2.3 Consensus size: 39
27969113 TAAAATATAT
*
27969123 TTATATTAAAAAACACTATAAAAATATAATAAATGTTTTA
1 TTATATT-AAAAACACTATAAAAATATAATAAATATTTTA
*
27969163 TTATATTAAAAATAC-A-AAAAATATAATAAATATTTTA
1 TTATATTAAAAACACTATAAAAATATAATAAATATTTTA
*
27969200 TTGTATTAAA
1 TTATATTAAA
27969210 TATAATTTTT
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 29 0.66
38 1 0.02
39 7 0.16
40 7 0.16
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.39
Consensus pattern (39 bp):
TTATATTAAAAACACTATAAAAATATAATAAATATTTTA
Found at i:27969275 original size:45 final size:45
Alignment explanation
Indices: 27969215--27969314 Score: 182
Period size: 45 Copynumber: 2.2 Consensus size: 45
27969205 TTAAATATAA
27969215 TTTTTTATATTTTATATTTTGGGTAGAGGTATTTAGTTGGATAAGTG
1 TTTTTT-T-TTTTATATTTTGGGTAGAGGTATTTAGTTGGATAAGTG
27969262 TTTTTTTTTTTATATTTTGGGTAGAGGTATTTAGTTGGATAAGTG
1 TTTTTTTTTTTATATTTTGGGTAGAGGTATTTAGTTGGATAAGTG
27969307 TTTTTTTT
1 TTTTTTTT
27969315 AGGTTTGGAT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
45 46 0.87
46 1 0.02
47 6 0.11
ACGTcount: A:0.20, C:0.00, G:0.22, T:0.58
Consensus pattern (45 bp):
TTTTTTTTTTTATATTTTGGGTAGAGGTATTTAGTTGGATAAGTG
Found at i:27974958 original size:17 final size:17
Alignment explanation
Indices: 27974936--27975005 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
27974926 ATAATTTAAT
27974936 TTTTAAAATTAAATTTA
1 TTTTAAAATTAAATTTA
*
27974953 TTTTAAATTTAAATTTA
1 TTTTAAAATTAAATTTA
* * *
27974970 CTTAAAAATTTAAGTTTA
1 TTTTAAAA-TTAAATTTA
* *
27974988 TTATAAATTTAAATTTA
1 TTTTAAAATTAAATTTA
27975005 T
1 T
27975006 AAATTAAATT
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
17 30 0.71
18 12 0.29
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (17 bp):
TTTTAAAATTAAATTTA
Found at i:27975804 original size:3 final size:3
Alignment explanation
Indices: 27975784--27975823 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
27975774 TGAAATATTA
*
27975784 AAT AAT ATT AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
27975824 ACATTAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27976145 original size:15 final size:16
Alignment explanation
Indices: 27976122--27976159 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
27976112 TAAATATTTT
27976122 CAAAGAAAATAAAGAA
1 CAAAGAAAATAAAGAA
*
27976138 CAAA-AAAATGAAGAA
1 CAAAGAAAATAAAGAA
*
27976153 TAAAGAA
1 CAAAGAA
27976160 CAAAAAAATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (16 bp):
CAAAGAAAATAAAGAA
Found at i:27976155 original size:22 final size:22
Alignment explanation
Indices: 27976129--27976186 Score: 116
Period size: 22 Copynumber: 2.6 Consensus size: 22
27976119 TTTCAAAGAA
27976129 AATAAAGAACAAAAAAATGAAG
1 AATAAAGAACAAAAAAATGAAG
27976151 AATAAAGAACAAAAAAATGAAG
1 AATAAAGAACAAAAAAATGAAG
27976173 AATAAAGAACAAAA
1 AATAAAGAACAAAA
27976187 GAAGAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.74, C:0.05, G:0.12, T:0.09
Consensus pattern (22 bp):
AATAAAGAACAAAAAAATGAAG
Found at i:27977146 original size:59 final size:58
Alignment explanation
Indices: 27976975--27977228 Score: 329
Period size: 58 Copynumber: 4.4 Consensus size: 58
27976965 CCCAAACAGT
* * * *
27976975 CCAAAAATTA-CATTTTGACCCCGAAA-CTTCCAAAATTCTATTTTTAACCTCGACTTCA
1 CCAAAAATTACCATTTT-ACCCC-AAATCTTCTAAAATTCCATTTTTAACCCCGATTTCA
* *
27977033 CCAAAAATTACCATCTTACCCCCAATCTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCAAATCTTCTAAAATTCCATTTTTAACCCCGATTTCA
* * *
27977091 CCAAAAATTACCATTTTATCCCCAAACCTTCTAAAATTCCATTTTTGACCTCGATTTCA
1 CCAAAAATTACCATTTTA-CCCCAAATCTTCTAAAATTCCATTTTTAACCCCGATTTCA
*
27977150 CCAAAAATTACCATTTTACCTCC-AATCTTCTAAAATTCCA-TTTTAACCCCGATTTTA
1 CCAAAAATTACCATTTTACC-CCAAATCTTCTAAAATTCCATTTTTAACCCCGATTTCA
*
27977207 CCAAAAA-TGCCATTTTAACCCC
1 CCAAAAATTACCATTTT-ACCCC
27977229 GATTTTACCT
Statistics
Matches: 175, Mismatches: 16, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
56 10 0.06
57 26 0.15
58 78 0.45
59 61 0.35
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCAAATCTTCTAAAATTCCATTTTTAACCCCGATTTCA
Found at i:27977219 original size:29 final size:29
Alignment explanation
Indices: 27977016--27977309 Score: 149
Period size: 30 Copynumber: 10.1 Consensus size: 29
27977006 AAAATTCTAT
* * *
27977016 TTTTAACCTCGACTTCACCAAAAATTACCA
1 TTTTAACCCCGATTTTACCAAAAA-TACCA
* * * * * *
27977046 TCTTACCCCCAATCTT--CTAAAATTCCA
1 TTTTAACCCCGATTTTACCAAAAATACCA
*
27977073 TTTTTAACCCCGATTTCACCAAAAATTACCA
1 -TTTTAACCCCGATTTTACCAAAAA-TACCA
* * ** * *
27977104 TTTTATCCCCAAACCTT--CTAAAATTCCA
1 TTTTAACCCC-GATTTTACCAAAAATACCA
* * *
27977132 TTTTTGACCTCGATTTCACCAAAAATTACCA
1 -TTTTAACCCCGATTTTACCAAAAA-TACCA
* * * *
27977163 TTTT-ACCTCCAATCTT--CTAAAATTCCA
1 TTTTAACC-CCGATTTTACCAAAAATACCA
*
27977190 TTTTAACCCCGATTTTACCAAAAATGCCA
1 TTTTAACCCCGATTTTACCAAAAATACCA
*
27977219 TTTTAACCCCGATTTTACCTAAAATTACCA
1 TTTTAACCCCGATTTTACC-AAAAATACCA
** * *
27977249 TTTT-ACCCCTGA-ACT-CCCAAAATTCCA
1 TTTTAACCCC-GATTTTACCAAAAATACCA
* *
27977276 TTTTAAACCCCGATTTCACCAAAATTACCA
1 TTTT-AACCCCGATTTTACCAAAAATACCA
27977306 TTTT
1 TTTT
27977310 GCCCTCGGGT
Statistics
Matches: 190, Mismatches: 55, Indels: 38
0.67 0.19 0.13
Matches are distributed among these distances:
27 29 0.15
28 34 0.18
29 54 0.28
30 63 0.33
31 10 0.05
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTTAACCCCGATTTTACCAAAAATACCA
Found at i:27977241 original size:58 final size:57
Alignment explanation
Indices: 27976975--27977286 Score: 314
Period size: 58 Copynumber: 5.4 Consensus size: 57
27976965 CCCAAACAGT
* * * * * *
27976975 CCAAAAATTA-CATTTTGACCCCGAAACTTCCAAAATTCTATTTTTAACCTCGACTTCA
1 CCAAAAATTACCATTTTAACCCC-AATCTTCTAAAATTCCA-TTTTAACCCCGATTTCA
* *
27977033 CCAAAAATTACCATCTTACCCCCAATCTTCTAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTAACCCCAATCTTCTAAAATTCCA-TTTTAACCCCGATTTCA
* * * *
27977091 CCAAAAATTACCATTTTATCCCCAAACCTTCTAAAATTCCATTTTTGACCTCGATTTCA
1 CCAAAAATTACCATTTTAACCCC-AATCTTCTAAAATTCCA-TTTTAACCCCGATTTCA
*
27977150 CCAAAAATTACCATTTT-ACCTCCAATCTTCTAAAATTCCATTTTAACCCCGATTTTA
1 CCAAAAATTACCATTTTAACC-CCAATCTTCTAAAATTCCATTTTAACCCCGATTTCA
* * * **
27977207 CCAAAAA-TGCCATTTTAACCCCGATTTTACCTAAAATTACCATTTT-ACCCCTGAACTC-
1 CCAAAAATTACCATTTTAACCCCAATCTT--CTAAAATT-CCATTTTAACCCC-GATTTCA
27977265 CC-AAAATT-CCATTTTAAACCCC
1 CCAAAAATTACCATTTT-AACCCC
27977287 GATTTCACCA
Statistics
Matches: 220, Mismatches: 24, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
56 14 0.06
57 35 0.16
58 101 0.46
59 70 0.32
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (57 bp):
CCAAAAATTACCATTTTAACCCCAATCTTCTAAAATTCCATTTTAACCCCGATTTCA
Found at i:27977243 original size:86 final size:86
Alignment explanation
Indices: 27976975--27977309 Score: 238
Period size: 86 Copynumber: 3.8 Consensus size: 86
27976965 CCCAAACAGT
* * * * *
27976975 CCAAAAATTA-CATTTTGACCCCGAAACTTCCAAAATTCTATTTTTAACCTCGACTTCACCAAAA
1 CCAAAAATTACCATTTT-ACCCCG-AACTCCCAAAATTCCATTTTAAACCCCGATTTCACCAAAA
* * *
27977039 ATTACCATCTTACCCCCAATCTT--
64 A-TACCATTTTAACCCCGAT-TTCA
* ** * *** ** *
27977062 -CTAAAATT-CCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT-ATCCCC-AAACCTTCT
1 CCAAAAATTACCA-TTTT-ACCCCGAACTC-CC-AAAATT-CCATTTTAAACCCCGATTTCACCA
* * *
27977123 AAAATTCCATTTTTGACCTCGATTTCA
61 AAAATACCA-TTTTAACCCCGATTTCA
* * *
27977150 CCAAAAATTACCATTTTACCTCC-AATCTTCTAAAATTCCATTTT-AACCCCGATTTTACCAAAA
1 CCAAAAATTACCATTTTACC-CCGAA-CTCCCAAAATTCCATTTTAAACCCCGATTTCACCAAAA
* *
27977213 ATGCCATTTTAACCCCGATTTTA
64 ATACCATTTTAACCCCGATTTCA
* *
27977236 CCTAAAATTACCATTTTACCCCTGAACTCCCAAAATTCCATTTTAAACCCCGATTTCACCAAAAT
1 CCAAAAATTACCATTTTACCCC-GAACTCCCAAAATTCCATTTTAAACCCCGATTTCACCAAAAA
27977301 TACCATTTT
65 TACCATTTT
27977310 GCCCTCGGGT
Statistics
Matches: 189, Mismatches: 43, Indels: 32
0.72 0.16 0.12
Matches are distributed among these distances:
85 2 0.01
86 78 0.41
87 71 0.38
88 15 0.08
89 20 0.11
90 3 0.02
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (86 bp):
CCAAAAATTACCATTTTACCCCGAACTCCCAAAATTCCATTTTAAACCCCGATTTCACCAAAAAT
ACCATTTTAACCCCGATTTCA
Found at i:27977252 original size:117 final size:117
Alignment explanation
Indices: 27976975--27977228 Score: 381
Period size: 117 Copynumber: 2.2 Consensus size: 117
27976965 CCCAAACAGT
* * *
27976975 CCAAAAATTA-CATTTTGACCCCGAAA-CTTCCAAAATTCTATTTTTAACCTCGACTTCACCAAA
1 CCAAAAATTACCATTTTAACCCC-AAACCTTCTAAAATTCCATTTTTAACCTCGACTTCACCAAA
27977038 AATTACCATCTTACCCCCAATCTTCTAAAATTCCATTTTTAACCCCGATTTCA
65 AATTACCATCTTACCCCCAATCTTCTAAAATTCCATTTTTAACCCCGATTTCA
* * *
27977091 CCAAAAATTACCATTTTATCCCCAAACCTTCTAAAATTCCATTTTTGACCTCGATTTCACCAAAA
1 CCAAAAATTACCATTTTAACCCCAAACCTTCTAAAATTCCATTTTTAACCTCGACTTCACCAAAA
* * *
27977156 ATTACCATTTTACCTCCAATCTTCTAAAATTCCA-TTTTAACCCCGATTTTA
66 ATTACCATCTTACCCCCAATCTTCTAAAATTCCATTTTTAACCCCGATTTCA
*
27977207 CCAAAAA-TGCCATTTTAACCCC
1 CCAAAAATTACCATTTTAACCCC
27977229 GATTTTACCT
Statistics
Matches: 125, Mismatches: 11, Indels: 5
0.89 0.08 0.04
Matches are distributed among these distances:
115 13 0.10
116 36 0.29
117 76 0.61
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (117 bp):
CCAAAAATTACCATTTTAACCCCAAACCTTCTAAAATTCCATTTTTAACCTCGACTTCACCAAAA
ATTACCATCTTACCCCCAATCTTCTAAAATTCCATTTTTAACCCCGATTTCA
Found at i:27981860 original size:23 final size:23
Alignment explanation
Indices: 27981809--27981861 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 23
27981799 TACATTTATT
27981809 TATTAAAATAGAGAAAAGATAAA
1 TATTAAAATAGAGAAAAGATAAA
*
27981832 TA-TAAAATTATA-AAAA-ATAGAA
1 TATTAAAA-TAGAGAAAAGATA-AA
27981854 TATTAAAA
1 TATTAAAA
27981862 ATTTTAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 3 0.12
22 13 0.50
23 10 0.38
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (23 bp):
TATTAAAATAGAGAAAAGATAAA
Found at i:27982238 original size:31 final size:30
Alignment explanation
Indices: 27982203--27982260 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
27982193 CAAAATGATG
27982203 ACTGAACTATT-AGAAAGTTTTCATTTAAGTC
1 ACTGAACTATTCA-AAA-TTTTCATTTAAGTC
*
27982234 ACTGAACTATTCAAAATTTTTATTTAA
1 ACTGAACTATTCAAAATTTTCATTTAA
27982261 TTCATTAGGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 10 0.40
31 14 0.56
32 1 0.04
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (30 bp):
ACTGAACTATTCAAAATTTTCATTTAAGTC
Found at i:27988307 original size:16 final size:16
Alignment explanation
Indices: 27988269--27988308 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
27988259 CTAAATATAT
27988269 TTAATAATTTTATAGA
1 TTAATAATTTTATAGA
*
27988285 TTTATAATTTTATTA-A
1 TTAATAATTTTA-TAGA
27988301 TTAATAAT
1 TTAATAAT
27988309 ATATTATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
16 19 0.90
17 2 0.10
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TTAATAATTTTATAGA
Found at i:27994776 original size:12 final size:12
Alignment explanation
Indices: 27994759--27994844 Score: 72
Period size: 12 Copynumber: 7.5 Consensus size: 12
27994749 ACATCCAAAT
*
27994759 AACAAAAACAGC
1 AACAAAAACAAC
27994771 AAC-AAAACAAC
1 AACAAAAACAAC
27994782 AAC--AAA-AAC
1 AACAAAAACAAC
* *
27994791 AACAAAAATAGC
1 AACAAAAACAAC
*
27994803 AGCAAAAACAAC
1 AACAAAAACAAC
*
27994815 AACAAAAATAAC
1 AACAAAAACAAC
* *
27994827 AGCAAAAGCAAC
1 AACAAAAACAAC
*
27994839 ACCAAA
1 AACAAA
27994845 TAGTAAAAAT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
9 6 0.10
10 3 0.05
11 13 0.22
12 38 0.63
ACGTcount: A:0.69, C:0.23, G:0.06, T:0.02
Consensus pattern (12 bp):
AACAAAAACAAC
Found at i:27994782 original size:20 final size:20
Alignment explanation
Indices: 27994770--27994816 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
27994760 ACAAAAACAG
27994770 CAACAAAACAACAACAAAAA
1 CAACAAAACAACAACAAAAA
*
27994790 CAACAAAA-ATAGCAGCAAAAA
1 CAACAAAACA-A-CAACAAAAA
27994811 CAACAA
1 CAACAA
27994817 CAAAAATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 9 0.38
21 14 0.58
ACGTcount: A:0.70, C:0.23, G:0.04, T:0.02
Consensus pattern (20 bp):
CAACAAAACAACAACAAAAA
Found at i:27994816 original size:33 final size:32
Alignment explanation
Indices: 27994759--27994827 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
27994749 ACATCCAAAT
27994759 AACAAAAACAGCAACAAAACAACAACAAAAAC
1 AACAAAAACAGCAACAAAACAACAACAAAAAC
* * *
27994791 AACAAAAATAGCAGCAAAAACAACAACAAAAAT
1 AACAAAAACAGCAAC-AAAACAACAACAAAAAC
27994824 AACA
1 AACA
27994828 GCAAAAGCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.71, C:0.22, G:0.04, T:0.03
Consensus pattern (32 bp):
AACAAAAACAGCAACAAAACAACAACAAAAAC
Found at i:27994820 original size:24 final size:24
Alignment explanation
Indices: 27994788--27994844 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
27994778 CAACAACAAA
*
27994788 AACAACAAAAATAGCAGCAAAAAC
1 AACAACAAAAATAACAGCAAAAAC
*
27994812 AACAACAAAAATAACAGCAAAAGC
1 AACAACAAAAATAACAGCAAAAAC
*
27994836 AACACCAAA
1 AACAACAAA
27994845 TAGTAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.67, C:0.23, G:0.07, T:0.04
Consensus pattern (24 bp):
AACAACAAAAATAACAGCAAAAAC
Found at i:27997598 original size:25 final size:25
Alignment explanation
Indices: 27997549--27997621 Score: 92
Period size: 25 Copynumber: 2.8 Consensus size: 25
27997539 GCTTACTGTT
* *
27997549 CAGCACTGTGTGTGCCTACTGTTTCCC
1 CAGCACT-TATGTG-CTTCTGTTTCCC
27997576 CAGCACTTATGTGCTTCTGTTTCCC
1 CAGCACTTATGTGCTTCTGTTTCCC
* *
27997601 CAACACTTATGCGCTTCTGTT
1 CAGCACTTATGTGCTTCTGTT
27997622 AAGTACTTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
25 30 0.71
26 5 0.12
27 7 0.17
ACGTcount: A:0.14, C:0.32, G:0.18, T:0.37
Consensus pattern (25 bp):
CAGCACTTATGTGCTTCTGTTTCCC
Found at i:28010260 original size:27 final size:27
Alignment explanation
Indices: 28010226--28010279 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
28010216 AATCCATCCA
28010226 TAATAATTTGACACATGGCATCTTGAG
1 TAATAATTTGACACATGGCATCTTGAG
*
28010253 TAATAATTTGACACCTGGCATCTTGAG
1 TAATAATTTGACACATGGCATCTTGAG
28010280 ACAGAGAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (27 bp):
TAATAATTTGACACATGGCATCTTGAG
Found at i:28011447 original size:16 final size:17
Alignment explanation
Indices: 28011426--28011458 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28011416 AGGCCAAACA
28011426 AATCAAACA-AAGATTC
1 AATCAAACACAAGATTC
*
28011442 AATCAAAGACAAGATTC
1 AATCAAACACAAGATTC
28011459 GAGAACGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.55, C:0.18, G:0.09, T:0.18
Consensus pattern (17 bp):
AATCAAACACAAGATTC
Found at i:28022754 original size:379 final size:379
Alignment explanation
Indices: 28022055--28022813 Score: 1500
Period size: 379 Copynumber: 2.0 Consensus size: 379
28022045 AAAATGGGGG
28022055 GGAGAGGTTCAACGTAAAAAAATCCATATGTTAAAATAAAATATGATATGAAATTGAAAAAAGAT
1 GGAGAGGTTCAACGTAAAAAAATCCATATGTTAAAATAAAATATGATATGAAATTGAAAAAAGAT
28022120 TAATGAGACAGAAATAAGGAATCATAAATAGAGTTTGGGTTCGAATTGTAAGGCCTTTAAAATCA
66 TAATGAGACAGAAATAAGGAATCATAAATAGAGTTTGGGTTCGAATTGTAAGGCCTTTAAAATCA
28022185 TCCTCCTAAATTTTGTAAAATGTTATATTTAGAAAGTGTATAATTGAATTATCGAGTAAATGAAA
131 TCCTCCTAAATTTTGTAAAATGTTATATTTAGAAAGTGTATAATTGAATTATCGAGTAAATGAAA
*
28022250 TAAAGTACATCAATGTTAGTAAAGAAAGGTATTGGATAATGAAGAAAGTCCAAAAAAAAATAAAT
196 TAAAGTACATCAATGTTAGTAAAGAAAGGTATTGGATAATGAAGAAAGTCCAAAAAAAAAAAAAT
28022315 TATAAAATATATATAGTATTATATTGTGATAAATAAATTTGAGGTATTGATTAAATTGAGAAAAA
261 TATAAAATATATATAGTATTATATTGTGATAAATAAATTTGAGGTATTGATTAAATTGAGAAAAA
*
28022380 GTAAAAAGTGATAGGGTCAAAAGCGTGAATATTCAAAAATCGAGAGGTTAAAAT
326 GTAAAAAATGATAGGGTCAAAAGCGTGAATATTCAAAAATCGAGAGGTTAAAAT
28022434 GGAGAGGTTCAACGTAAAAAAATCCATATGTTAAAATAAAATATGATATGAAATTGAAAAAAGAT
1 GGAGAGGTTCAACGTAAAAAAATCCATATGTTAAAATAAAATATGATATGAAATTGAAAAAAGAT
28022499 TAATGAGACAGAAATAAGGAATCATAAATAGAGTTTGGGTTCGAATTGTAAGGCCTTTAAAATCA
66 TAATGAGACAGAAATAAGGAATCATAAATAGAGTTTGGGTTCGAATTGTAAGGCCTTTAAAATCA
28022564 TCCTCCTAAATTTTGTAAAATGTTATATTTAGAAAGTGTATAATTGAATTATCGAGTAAATGAAA
131 TCCTCCTAAATTTTGTAAAATGTTATATTTAGAAAGTGTATAATTGAATTATCGAGTAAATGAAA
28022629 TAAAGTACATCAATGTTAGTAAAGAAAGGTATTGGATAATGAAGAAAGTCCAAAAAAAAAAAAAT
196 TAAAGTACATCAATGTTAGTAAAGAAAGGTATTGGATAATGAAGAAAGTCCAAAAAAAAAAAAAT
28022694 TATAAAATATATATAGTATTATATTGTGATAAATAAATTTGAGGTATTGATTAAATTGAGAAAAA
261 TATAAAATATATATAGTATTATATTGTGATAAATAAATTTGAGGTATTGATTAAATTGAGAAAAA
28022759 GTAAAAAATGATAGGGTCAAAAGCGTGAATATTCAAAAATCGAGAGGTTAAAAT
326 GTAAAAAATGATAGGGTCAAAAGCGTGAATATTCAAAAATCGAGAGGTTAAAAT
28022813 G
1 G
28022814 TAATTTAAAA
Statistics
Matches: 378, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
379 378 1.00
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (379 bp):
GGAGAGGTTCAACGTAAAAAAATCCATATGTTAAAATAAAATATGATATGAAATTGAAAAAAGAT
TAATGAGACAGAAATAAGGAATCATAAATAGAGTTTGGGTTCGAATTGTAAGGCCTTTAAAATCA
TCCTCCTAAATTTTGTAAAATGTTATATTTAGAAAGTGTATAATTGAATTATCGAGTAAATGAAA
TAAAGTACATCAATGTTAGTAAAGAAAGGTATTGGATAATGAAGAAAGTCCAAAAAAAAAAAAAT
TATAAAATATATATAGTATTATATTGTGATAAATAAATTTGAGGTATTGATTAAATTGAGAAAAA
GTAAAAAATGATAGGGTCAAAAGCGTGAATATTCAAAAATCGAGAGGTTAAAAT
Found at i:28025437 original size:32 final size:33
Alignment explanation
Indices: 28025396--28025458 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
28025386 CTTCGTTTGG
* *
28025396 TTTCTAAAAATA-TTTTCTATTTTT-ATTTTTAT
1 TTTCAAAAAATAGATTT-TATTTTTCATTTTTAT
28025428 TTTCAAAAAATAGATTTTATTTTTCATTTTT
1 TTTCAAAAAATAGATTTTATTTTTCATTTTT
28025459 TTAAAATTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 18 0.67
33 9 0.33
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (33 bp):
TTTCAAAAAATAGATTTTATTTTTCATTTTTAT
Found at i:28026120 original size:2 final size:2
Alignment explanation
Indices: 28026109--28026152 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
28026099 AGAATTTTTA
*
28026109 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28026150 AT A
1 AT A
28026153 ATTTTGCACT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:28032205 original size:49 final size:49
Alignment explanation
Indices: 28032116--28032211 Score: 120
Period size: 49 Copynumber: 2.0 Consensus size: 49
28032106 TGTGTTAGCT
* * * *
28032116 TTTGGTAATTTCCACCAACCACATTAGCTACGGCTGACGATCAAACCAA
1 TTTGGTAACTTCCACCAACCACATCAGCTACCGCTAACGATCAAACCAA
* * * *
28032165 TTTGGTAACTTCCATCAACTATATCAGTTACCGCTAACGATCAAACC
1 TTTGGTAACTTCCACCAACCACATCAGCTACCGCTAACGATCAAACC
28032212 GATCAACGAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.27
Consensus pattern (49 bp):
TTTGGTAACTTCCACCAACCACATCAGCTACCGCTAACGATCAAACCAA
Found at i:28037511 original size:16 final size:17
Alignment explanation
Indices: 28037469--28037509 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
28037459 GCTTTCAAAG
28037469 TTTTATAAATTTTTTAT
1 TTTTATAAATTTTTTAT
*
28037486 TTTT-TGAATTATTTT-T
1 TTTTATAAATT-TTTTAT
28037502 TTTTATAA
1 TTTTATAA
28037510 TTTCTCTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTATAAATTTTTTAT
Found at i:28037663 original size:18 final size:18
Alignment explanation
Indices: 28037637--28037725 Score: 57
Period size: 18 Copynumber: 5.2 Consensus size: 18
28037627 GTAAGAGTTA
*
28037637 ATTTTATTTTTTAATATT
1 ATTTAATTTTTTAATATT
28037655 ATTTAA-TTTTT--TA-T
1 ATTTAATTTTTTAATATT
* *
28037669 -TTT-ATTTTTATAATCTG
1 ATTTAATTTTT-TAATATT
*
28037686 A-TAAATATTTTTAATATT
1 ATTTAAT-TTTTTAATATT
* *
28037704 ATTTAATTTTTTTATTTT
1 ATTTAATTTTTTAATATT
28037722 ATTT
1 ATTT
28037726 TTATAATTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 18
0.66 0.11 0.22
Matches are distributed among these distances:
12 1 0.02
13 7 0.13
14 2 0.04
15 2 0.04
16 1 0.02
17 6 0.11
18 26 0.49
19 8 0.15
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.69
Consensus pattern (18 bp):
ATTTAATTTTTTAATATT
Found at i:28037720 original size:13 final size:14
Alignment explanation
Indices: 28037700--28037738 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
28037690 ATATTTTTAA
28037700 TATTATTTAATTTT
1 TATTATTTAATTTT
*
28037714 T-TTATTTTATTTT
1 TATTATTTAATTTT
*
28037727 TATAATTTAATT
1 TATTATTTAATT
28037739 AATATATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TATTATTTAATTTT
Found at i:28037743 original size:50 final size:49
Alignment explanation
Indices: 28037644--28037749 Score: 167
Period size: 50 Copynumber: 2.1 Consensus size: 49
28037634 TTAATTTTAT
*
28037644 TTTTTAATATTATTTAATTTTTTATTTTATTTTTATAATCTGATAAATA
1 TTTTTAATATTATTTAATTTTTTATTTTATTTTTATAATCTAATAAATA
*
28037693 TTTTTAATATTATTTAATTTTTTTATTTTATTTTTATAATTTAATTAATATA
1 TTTTTAATATTATTTAA-TTTTTTATTTTATTTTTATAATCTAA-TAA-ATA
28037745 TTTTT
1 TTTTT
28037750 TATAATTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
49 17 0.33
50 24 0.46
51 3 0.06
52 8 0.15
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (49 bp):
TTTTTAATATTATTTAATTTTTTATTTTATTTTTATAATCTAATAAATA
Found at i:28038686 original size:7 final size:7
Alignment explanation
Indices: 28038674--28038713 Score: 53
Period size: 7 Copynumber: 5.7 Consensus size: 7
28038664 ATAACATAGT
*
28038674 GTATTTC
1 GTATTTA
28038681 GTATTTA
1 GTATTTA
* *
28038688 ATATTTG
1 GTATTTA
28038695 GTATTTA
1 GTATTTA
28038702 GTATTTA
1 GTATTTA
28038709 GTATT
1 GTATT
28038714 ATGTATATCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (7 bp):
GTATTTA
Found at i:28038700 original size:21 final size:21
Alignment explanation
Indices: 28038674--28038713 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28038664 ATAACATAGT
*
28038674 GTATTTCGTATTTAATATTTG
1 GTATTTAGTATTTAATATTTG
*
28038695 GTATTTAGTATTTAGTATT
1 GTATTTAGTATTTAATATT
28038714 ATGTATATCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.03, G:0.15, T:0.57
Consensus pattern (21 bp):
GTATTTAGTATTTAATATTTG
Found at i:28038719 original size:21 final size:20
Alignment explanation
Indices: 28038673--28038719 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
28038663 CATAACATAG
*
28038673 TGTATTTCGTATTTAATATT
1 TGTATTTAGTATTTAATATT
*
28038693 TGGTATTTAGTATTTAGTATT
1 T-GTATTTAGTATTTAATATT
28038714 ATGTAT
1 -TGTAT
28038720 ATCACTAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 21 0.91
22 1 0.04
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (20 bp):
TGTATTTAGTATTTAATATT
Found at i:28039329 original size:18 final size:18
Alignment explanation
Indices: 28039303--28039337 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28039293 GCCAGGGGCT
28039303 TATCATAACCCTTATATG
1 TATCATAACCCTTATATG
* *
28039321 TATCCTAACTCTTATAT
1 TATCATAACCCTTATAT
28039338 ATACCCATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.23, G:0.03, T:0.43
Consensus pattern (18 bp):
TATCATAACCCTTATATG
Found at i:28039871 original size:62 final size:59
Alignment explanation
Indices: 28039746--28039875 Score: 163
Period size: 62 Copynumber: 2.2 Consensus size: 59
28039736 ATTTATTTCG
* * * *
28039746 AATATTTTTGTAAACATTATTTTTATATTGTATCATTTAATGAAATTGAAATTCTTTTG
1 AATATTTTTGTAAACATTATTTTCATATTGTATCATTTAATGAAATTGAAACTATTTTA
* *
28039805 AATATTTTTGTACACATTAATTTTGACATATTGTATCATTTAATGAAATAT-AAGCTATTTTA
1 AATATTTTTGTAAACATT-ATTTT--CATATTGTATCATTTAATGAAAT-TGAAACTATTTTA
28039867 AATATTTTT
1 AATATTTTT
28039876 CAACACGTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
59 17 0.28
60 5 0.08
62 38 0.62
63 1 0.02
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (59 bp):
AATATTTTTGTAAACATTATTTTCATATTGTATCATTTAATGAAATTGAAACTATTTTA
Found at i:28043300 original size:23 final size:24
Alignment explanation
Indices: 28043274--28043348 Score: 75
Period size: 26 Copynumber: 3.1 Consensus size: 24
28043264 CTAAATAATT
* *
28043274 AAAAACCTAAACTCTAATT--TAA
1 AAAAACCTAAACCCTAATTAACAA
28043296 AAAAACCATAAACCCTAATTAAACAA
1 AAAAACC-TAAACCCTAATT-AACAA
28043322 AAAAATCCTAAACCCTAA-TAATCAA
1 AAAAA-CCTAAACCCTAATTAA-CAA
28043347 AA
1 AA
28043349 TAGCAAATTT
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
22 7 0.16
23 11 0.24
24 2 0.04
25 6 0.13
26 17 0.38
27 2 0.04
ACGTcount: A:0.59, C:0.21, G:0.00, T:0.20
Consensus pattern (24 bp):
AAAAACCTAAACCCTAATTAACAA
Found at i:28043302 original size:22 final size:24
Alignment explanation
Indices: 28043274--28043324 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
28043264 CTAAATAATT
* *
28043274 AAAAACC-TAAACTCTAATTTAA-
1 AAAAACCATAAACCCTAATTAAAC
28043296 AAAAACCATAAACCCTAATTAAAC
1 AAAAACCATAAACCCTAATTAAAC
28043320 AAAAA
1 AAAAA
28043325 AATCCTAAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 7 0.28
23 13 0.52
24 5 0.20
ACGTcount: A:0.61, C:0.20, G:0.00, T:0.20
Consensus pattern (24 bp):
AAAAACCATAAACCCTAATTAAAC
Found at i:28043333 original size:26 final size:25
Alignment explanation
Indices: 28043294--28043348 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
28043284 ACTCTAATTT
28043294 AAAAAAACCATAAACCCTAATTAAAC
1 AAAAAAACCATAAACCCTAA-TAAAC
*
28043320 AAAAAAATCC-TAAACCCTAATAATC
1 AAAAAAA-CCATAAACCCTAATAAAC
28043345 AAAA
1 AAAA
28043349 TAGCAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 8 0.30
26 17 0.63
27 2 0.07
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (25 bp):
AAAAAAACCATAAACCCTAATAAAC
Found at i:28045460 original size:14 final size:14
Alignment explanation
Indices: 28045443--28045487 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
28045433 AATATTTGAA
*
28045443 AAAATATAAATTTT
1 AAAATATAAAATTT
28045457 AAAATATTAAAATTT
1 AAAATA-TAAAATTT
* *
28045472 AAAAAATAAAAATT
1 AAAATATAAAATTT
28045486 AA
1 AA
28045488 TAAAAATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AAAATATAAAATTT
Found at i:28046688 original size:17 final size:17
Alignment explanation
Indices: 28046633--28046695 Score: 65
Period size: 18 Copynumber: 3.5 Consensus size: 17
28046623 ATATTTTATC
28046633 TTTAAAATATTTTTT-A
1 TTTAAAATATTTTTTAA
*
28046649 TTAAAAATTATATTTTTACA
1 TTTAAAA-TAT-TTTTTA-A
*
28046669 TTTAATATATTTTTTAA
1 TTTAAAATATTTTTTAA
28046686 TTTCAAAATA
1 TTT-AAAATA
28046696 CATACTGACA
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
16 6 0.16
17 7 0.18
18 16 0.42
19 3 0.08
20 6 0.16
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAAAATATTTTTTAA
Found at i:28047989 original size:25 final size:26
Alignment explanation
Indices: 28047934--28047987 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 26
28047924 AATTAAAATT
*
28047934 TATTTTTATTTATTTATTTTCTAAAA
1 TATTTTTATTTATTTATTATCTAAAA
28047960 TATTTTTA-TTATTTATATATCATAAAA
1 TATTTTTATTTATTTAT-TATC-TAAAA
28047987 T
1 T
28047988 TTGTCAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 8 0.32
26 11 0.44
27 6 0.24
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (26 bp):
TATTTTTATTTATTTATTATCTAAAA
Found at i:28048259 original size:18 final size:17
Alignment explanation
Indices: 28048235--28048280 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
28048225 TGCTTTACAA
28048235 ATTTTTAAAAAATTAAT
1 ATTTTTAAAAAATTAAT
* **
28048252 ATTTTTTAAAATATTTTT
1 A-TTTTTAAAAAATTAAT
28048270 ATTTTTAAAAA
1 ATTTTTAAAAA
28048281 CTAAGCTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTTAAAAAATTAAT
Found at i:28049070 original size:38 final size:38
Alignment explanation
Indices: 28048990--28049071 Score: 92
Period size: 38 Copynumber: 2.2 Consensus size: 38
28048980 GGCATCGTGG
* * * * * *
28048990 AACGAATATCAACTGGTCCTTTGCGGCGACATCGTGAC
1 AACGATTATCAACTGGTCCTTCGAGGCCACACCATGAC
* *
28049028 AACGATTATCTACTGGTCCTTCGAGGCCACACCATGAT
1 AACGATTATCAACTGGTCCTTCGAGGCCACACCATGAC
28049066 AACGAT
1 AACGAT
28049072 ATATAGGTCA
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (38 bp):
AACGATTATCAACTGGTCCTTCGAGGCCACACCATGAC
Found at i:28056018 original size:16 final size:16
Alignment explanation
Indices: 28055997--28056048 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
28055987 AGGTTTTATC
28055997 TGAAATGGATATTAAT
1 TGAAATGGATATTAAT
*
28056013 TGAAATGGTTA-T-AT
1 TGAAATGGATATTAAT
*
28056027 CTGAAATGGATATCAAT
1 -TGAAATGGATATTAAT
28056044 TGAAA
1 TGAAA
28056049 AGGTCATATC
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
14 2 0.07
15 11 0.37
16 15 0.50
17 2 0.07
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.35
Consensus pattern (16 bp):
TGAAATGGATATTAAT
Found at i:28056028 original size:31 final size:31
Alignment explanation
Indices: 28055981--28056073 Score: 132
Period size: 31 Copynumber: 3.0 Consensus size: 31
28055971 TTTGAAAAGG
* *
28055981 TTGAAAAGGTTTTATCTGAAATGGATATTAA
1 TTGAAAAGGTTATATCTGAAATGGATATCAA
*
28056012 TTGAAATGGTTATATCTGAAATGGATATCAA
1 TTGAAAAGGTTATATCTGAAATGGATATCAA
* **
28056043 TTGAAAAGGTCATATCCAAAATGGATATCAA
1 TTGAAAAGGTTATATCTGAAATGGATATCAA
28056074 ACGGAAAGGC
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (31 bp):
TTGAAAAGGTTATATCTGAAATGGATATCAA
Found at i:28056033 original size:15 final size:15
Alignment explanation
Indices: 28055982--28056035 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
28055972 TTGAAAAGGT
* *
28055982 TGAAAAGGTTTTATC
1 TGAAATGGTTATATC
*
28055997 TGAAATGGATATTAAT-
1 TGAAATGGTTA-T-ATC
28056013 TGAAATGGTTATATC
1 TGAAATGGTTATATC
28056028 TGAAATGG
1 TGAAATGG
28056036 ATATCAATTG
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
14 2 0.06
15 17 0.53
16 11 0.34
17 2 0.06
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (15 bp):
TGAAATGGTTATATC
Found at i:28058505 original size:51 final size:51
Alignment explanation
Indices: 28058428--28058565 Score: 170
Period size: 51 Copynumber: 2.7 Consensus size: 51
28058418 TAAACGAAAA
* * * *
28058428 GGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAA
1 GGTCTAATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATTAAG
* *
28058479 GGT-TCAATGACTAAGTGTCATTGTGAGTAAATGAATCCATGATGGATTAAG
1 GGTCT-AATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATTAAG
* ** *
28058530 GGTCTGATGACTTTGTGTCATCGTGAGTATATGAAT
1 GGTCTAATGACTAAGTGTCATCGTGAGTAAATGAAT
28058566 TCCTATATGG
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
50 1 0.01
51 72 0.97
52 1 0.01
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (51 bp):
GGTCTAATGACTAAGTGTCATCGTGAGTAAATGAATCCATGACGGATTAAG
Found at i:28061931 original size:23 final size:24
Alignment explanation
Indices: 28061892--28061943 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
28061882 TAATAGGGAT
28061892 TTTCAATTTACAATTCA-TATCAC
1 TTTCAATTTACAATTCACTATCAC
* *
28061915 TTTCAA-TTCCAACTTCACTTTCAC
1 TTTCAATTTACAA-TTCACTATCAC
28061939 TTTCA
1 TTTCA
28061944 CTTTCACTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 5 0.20
23 10 0.40
24 10 0.40
ACGTcount: A:0.29, C:0.27, G:0.00, T:0.44
Consensus pattern (24 bp):
TTTCAATTTACAATTCACTATCAC
Found at i:28061934 original size:18 final size:18
Alignment explanation
Indices: 28061911--28061958 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
28061901 ACAATTCATA
28061911 TCACTTTCAATTCCAAC-T
1 TCACTTTCAATTCC-ACTT
* *
28061929 TCACTTTCACTTTCACTT
1 TCACTTTCAATTCCACTT
28061947 TCACTTTCAATT
1 TCACTTTCAATT
28061959 TTGATCACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (18 bp):
TCACTTTCAATTCCACTT
Found at i:28061939 original size:6 final size:6
Alignment explanation
Indices: 28061928--28061955 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
28061918 CAATTCCAAC
28061928 TTCACT TTCACT TTCACT TTCACT TTCA
1 TTCACT TTCACT TTCACT TTCACT TTCA
28061956 ATTTTGATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.00, T:0.50
Consensus pattern (6 bp):
TTCACT
Found at i:28064509 original size:9 final size:10
Alignment explanation
Indices: 28064479--28064509 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
28064469 TTGTGTTTAT
28064479 ATGTGATTAA
1 ATGTGATTAA
28064489 ATGTGATTAA
1 ATGTGATTAA
28064499 ATGTG-TTAA
1 ATGTGATTAA
28064508 AT
1 AT
28064510 ATTAATGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (10 bp):
ATGTGATTAA
Found at i:28064534 original size:23 final size:23
Alignment explanation
Indices: 28064500--28064612 Score: 156
Period size: 23 Copynumber: 4.9 Consensus size: 23
28064490 TGTGATTAAA
28064500 TGTG-TTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
** *
28064522 TAAGCTTAAATATTAATATGATT
1 TGTGCTTAAATATTAATGTGATT
28064545 TGTGCTTAAATATTAATGTGATT
1 TGTGCTTAAATATTAATGTGATT
* * *
28064568 TGTGCTTAAATATTATTTTAATT
1 TGTGCTTAAATATTAATGTGATT
28064591 TGTGCTTAAATATTAAATGTGA
1 TGTGCTTAAATATT-AATGTGA
28064613 CTATATGTGA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
22 2 0.03
23 71 0.92
24 4 0.05
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.48
Consensus pattern (23 bp):
TGTGCTTAAATATTAATGTGATT
Found at i:28064638 original size:16 final size:16
Alignment explanation
Indices: 28064617--28064688 Score: 58
Period size: 16 Copynumber: 4.4 Consensus size: 16
28064607 ATGTGACTAT
28064617 ATGTGATTAATATGTG
1 ATGTGATTAATATGTG
*
28064633 ATGTGATAAATAT-TG
1 ATGTGATTAATATGTG
** * *
28064648 AAAT-ATTCATATGATTAA
1 ATGTGATTAATATG--T-G
28064666 ATGTGATTAATATGTG
1 ATGTGATTAATATGTG
28064682 ATGTGAT
1 ATGTGAT
28064689 AAACGTTGAA
Statistics
Matches: 41, Mismatches: 10, Indels: 10
0.67 0.16 0.16
Matches are distributed among these distances:
14 6 0.15
15 4 0.10
16 19 0.46
17 2 0.05
18 2 0.05
19 8 0.20
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (16 bp):
ATGTGATTAATATGTG
Found at i:28064670 original size:49 final size:48
Alignment explanation
Indices: 28064610--28064723 Score: 165
Period size: 49 Copynumber: 2.3 Consensus size: 48
28064600 ATATTAAATG
*
28064610 TGACTATATGTGATTAATATGTGATGTGATAAATATTGAAATATTCATA
1 TGACTA-ATGTGATTAATATGTGATGTGATAAACATTGAAATATTCATA
* * * *
28064659 TGATTAAATGTGATTAATATGTGATGTGATAAACGTTGAAATATTTATG
1 TGACT-AATGTGATTAATATGTGATGTGATAAACATTGAAATATTCATA
28064708 TGACTAATGTGATTAA
1 TGACTAATGTGATTAA
28064724 ATGAGACTAA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
48 11 0.19
49 46 0.79
50 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (48 bp):
TGACTAATGTGATTAATATGTGATGTGATAAACATTGAAATATTCATA
Found at i:28064709 original size:23 final size:23
Alignment explanation
Indices: 28064633--28064710 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
28064623 TTAATATGTG
*
28064633 ATGTGATAAATATTGAAATATTC
1 ATGTGATAAATGTTGAAATATTC
* *
28064656 ATATGATTAAATG-TGATTAATATGTG
1 ATGTGA-TAAATGTTGA--AATAT-TC
* *
28064682 ATGTGATAAACGTTGAAATATTT
1 ATGTGATAAATGTTGAAATATTC
28064705 ATGTGA
1 ATGTGA
28064711 CTAATGTGAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
23 15 0.34
24 10 0.23
25 10 0.23
26 9 0.20
ACGTcount: A:0.40, C:0.03, G:0.18, T:0.40
Consensus pattern (23 bp):
ATGTGATAAATGTTGAAATATTC
Found at i:28064737 original size:68 final size:68
Alignment explanation
Indices: 28064663--28064794 Score: 228
Period size: 68 Copynumber: 1.9 Consensus size: 68
28064653 TTCATATGAT
* *
28064663 TAAATGTGATTAATATGTGATGTGATAAACGTTGAAATATTTATGTGACTAATGTGATTAAATGA
1 TAAATGTGATTAATATGTGATGTGATAAACGTTAAAATATTCATGTGACTAATGTGATTAAATGA
28064728 GAC
66 GAC
**
28064731 TAAATGTGATTAATATGTGATGTGATAAATTTTAAAATATTCATGTGACTAATGTGATTAAATG
1 TAAATGTGATTAATATGTGATGTGATAAACGTTAAAATATTCATGTGACTAATGTGATTAAATG
28064795 TGATTAATAT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 60 1.00
ACGTcount: A:0.39, C:0.04, G:0.19, T:0.39
Consensus pattern (68 bp):
TAAATGTGATTAATATGTGATGTGATAAACGTTAAAATATTCATGTGACTAATGTGATTAAATGA
GAC
Found at i:28064799 original size:58 final size:58
Alignment explanation
Indices: 28064606--28064853 Score: 203
Period size: 68 Copynumber: 4.3 Consensus size: 58
28064596 TTAAATATTA
* * *
28064606 AATGTGACTATATGTGATTAATATGTGATGTGATAAATATTGAAATATTC-----A-T
1 AATGTGATTAAATGTGATTAATATGTGATGTGATAAATTTTGAAATATTCATGTGACT
** *
28064658 -A--TGATTAAATGTGATTAATATGTGATGTGATAAACGTTGAAATATTTATGTGACT
1 AATGTGATTAAATGTGATTAATATGTGATGTGATAAATTTTGAAATATTCATGTGACT
*
28064713 AATGTGATTAAATGAGACTAAATGTGATTAATATGTGATGTGATAAATTTTAAAATATTCATGTG
1 AATGTG-----AT-----TAAATGTGATTAATATGTGATGTGATAAATTTTGAAATATTCATGTG
28064778 ACT
56 ACT
* * * * *
28064781 AATGTGATTAAATGTGATTAATATGTGTTGTGTTAAATATTT-AAGTACTCATGTGATT
1 AATGTGATTAAATGTGATTAATATGTGATGTGATAAAT-TTTGAAATATTCATGTGACT
*
28064839 AATGCGATT-AATGTG
1 AATGTGATTAAATGTG
28064854 TAAAAGAATT
Statistics
Matches: 161, Mismatches: 15, Indels: 35
0.76 0.07 0.17
Matches are distributed among these distances:
49 41 0.25
51 1 0.01
54 1 0.01
55 1 0.01
56 1 0.01
57 6 0.04
58 51 0.32
59 3 0.02
63 4 0.02
68 52 0.32
ACGTcount: A:0.37, C:0.04, G:0.19, T:0.40
Consensus pattern (58 bp):
AATGTGATTAAATGTGATTAATATGTGATGTGATAAATTTTGAAATATTCATGTGACT
Found at i:28069189 original size:15 final size:14
Alignment explanation
Indices: 28069136--28069205 Score: 51
Period size: 14 Copynumber: 5.1 Consensus size: 14
28069126 TTTGAAATAG
*
28069136 TTAAATTATTATAAA
1 TTAAAATATTAT-AA
28069151 TTAAAATA--ATAA
1 TTAAAATATTATAA
28069163 TTTTAAAA-ATTATCAA
1 --TTAAAATATTAT-AA
*
28069179 TTAAAATATTATTA
1 TTAAAATATTATAA
28069193 TT-AAATATT-TAA
1 TTAAAATATTATAA
28069205 T
1 T
28069206 GCAAAGATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
12 5 0.11
13 10 0.22
14 15 0.33
15 14 0.30
16 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAAATATTATAA
Found at i:28076344 original size:51 final size:52
Alignment explanation
Indices: 28076187--28076376 Score: 285
Period size: 52 Copynumber: 3.7 Consensus size: 52
28076177 AAACGAAAAG
*
28076187 GGTCCGATGACTATGTGTCATTGTGAGTATATAAATCCTTTACGAATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATAAATCCTTTACGAATTATGA
*
28076239 GGTCCGATGACTATGTGTCATCATGAGTATATAAATCCTTTACGAATTATGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATAAATCCTTTACGAATTATGA
* * * ** *
28076291 GGTCCGATGACTAT-TATCATCGTGAGTATATGAATCCTTTGCGGGTTAAGA
1 GGTCCGATGACTATGTGTCATCGTGAGTATATAAATCCTTTACGAATTATGA
*
28076342 GGTTCGATGACTATGTGTCATCGTGAGTAT-TAAAT
1 GGTCCGATGACTATGTGTCATCGTGAGTATATAAAT
28076377 GAAAATTAAT
Statistics
Matches: 125, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
51 47 0.38
52 78 0.62
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (52 bp):
GGTCCGATGACTATGTGTCATCGTGAGTATATAAATCCTTTACGAATTATGA
Found at i:28076369 original size:103 final size:103
Alignment explanation
Indices: 28076187--28076376 Score: 283
Period size: 103 Copynumber: 1.8 Consensus size: 103
28076177 AAACGAAAAG
* * *
28076187 GGTCCGATGACTATGTGTCATTGTGAGTATATAAATCCTTTACGAATTATGAGGTCCGATGACTA
1 GGTCCGATGACTATGTATCATCGTGAGTATATAAATCCTTTACGAATTAAGAGGTCCGATGACTA
28076252 TGTGTCATCATGAGTATATAAATCCTTTACGAATTATGA
66 TGTGTCATCATGAGTAT-TAAATCCTTTACGAATTATGA
* * ** *
28076291 GGTCCGATGACTAT-TATCATCGTGAGTATATGAATCCTTTGCGGGTTAAGAGGTTCGATGACTA
1 GGTCCGATGACTATGTATCATCGTGAGTATATAAATCCTTTACGAATTAAGAGGTCCGATGACTA
*
28076355 TGTGTCATCGTGAGTATTAAAT
66 TGTGTCATCATGAGTATTAAAT
28076377 GAAAATTAAT
Statistics
Matches: 77, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
102 5 0.06
103 58 0.75
104 14 0.18
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (103 bp):
GGTCCGATGACTATGTATCATCGTGAGTATATAAATCCTTTACGAATTAAGAGGTCCGATGACTA
TGTGTCATCATGAGTATTAAATCCTTTACGAATTATGA
Found at i:28088905 original size:38 final size:35
Alignment explanation
Indices: 28088806--28088909 Score: 109
Period size: 38 Copynumber: 2.8 Consensus size: 35
28088796 TCGTTATTCG
* *
28088806 TTTTACTCCCTGTTGACCCCAAAAGTCATGATGCTCA
1 TTTTACTCCCTGTTGA--CCAAAGGTCATGATACTCA
* *
28088843 TTTTACTCCCTGTTGACACGAAGGTCATTATACTCA
1 TTTTACTCCCTGTTGAC-CAAAGGTCATGATACTCA
*
28088879 TTTTTTTCTCCCTGTTGATCCAAAGGTCATG
1 --TTTTACTCCCTGTTGA-CCAAAGGTCATG
28088910 CCTGTTACCA
Statistics
Matches: 56, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
35 1 0.02
36 14 0.25
37 16 0.29
38 24 0.43
39 1 0.02
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (35 bp):
TTTTACTCCCTGTTGACCAAAGGTCATGATACTCA
Found at i:28108166 original size:51 final size:51
Alignment explanation
Indices: 28108107--28108210 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
28108097 CACAAGCCAT
28108107 ATTTTGATTAGATTTATTGAATTCTAGCAAGTCGGACACAGAAATTAATTG
1 ATTTTGATTAGATTTATTGAATTCTAGCAAGTCGGACACAGAAATTAATTG
28108158 ATTTTGATTAGATTTATTGAATTCTAGCAAGTCGGACACAGAAATTAATTG
1 ATTTTGATTAGATTTATTGAATTCTAGCAAGTCGGACACAGAAATTAATTG
28108209 AT
1 AT
28108211 GTTATTGTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.36, C:0.10, G:0.17, T:0.38
Consensus pattern (51 bp):
ATTTTGATTAGATTTATTGAATTCTAGCAAGTCGGACACAGAAATTAATTG
Found at i:28108775 original size:30 final size:30
Alignment explanation
Indices: 28108719--28108776 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
28108709 GGCTCAACCA
*
28108719 AAATTTTATTTTAATATTTTTTTTACATTT
1 AAATTTTATTTTAATATTTTTATTACATTT
*
28108749 AAATTTTATTTTGCATA-TTTTATTACAT
1 AAATTTTATTTT-AATATTTTTATTACAT
28108777 CCATTAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.88
31 3 0.12
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.62
Consensus pattern (30 bp):
AAATTTTATTTTAATATTTTTATTACATTT
Found at i:28118627 original size:28 final size:29
Alignment explanation
Indices: 28118596--28118685 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 29
28118586 TTTTTTCTAG
*
28118596 TTTTTAATAAATTTTAT-CTTTTTATATT
1 TTTTTATTAAATTTTATACTTTTTATATT
* * *
28118624 TTTTTATTAAAATTTAATAATTTTTATA-C
1 TTTTTATT-AAATTTTATACTTTTTATATT
* * *
28118653 TTTTTATTGATTTTTATACTTATTATATT
1 TTTTTATTAAATTTTATACTTTTTATATT
28118682 TTTT
1 TTTT
28118686 GCCACATGTC
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
28 21 0.43
29 20 0.41
30 8 0.16
ACGTcount: A:0.29, C:0.03, G:0.01, T:0.67
Consensus pattern (29 bp):
TTTTTATTAAATTTTATACTTTTTATATT
Found at i:28118658 original size:19 final size:19
Alignment explanation
Indices: 28118596--28118673 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 19
28118586 TTTTTTCTAG
*
28118596 TTTTTAATAAATTTTAT-C
1 TTTTTAATAATTTTTATAC
* *
28118614 TTTTT-ATATTTTTTTATTAA
1 TTTTTAATA-ATTTTTA-TAC
**
28118634 AATTTAATAATTTTTATAC
1 TTTTTAATAATTTTTATAC
* *
28118653 TTTTTATTGATTTTTATAC
1 TTTTTAATAATTTTTATAC
28118672 TT
1 TT
28118674 ATTATATTTT
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
17 3 0.07
18 10 0.22
19 20 0.44
20 9 0.20
21 3 0.07
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (19 bp):
TTTTTAATAATTTTTATAC
Found at i:28118685 original size:19 final size:18
Alignment explanation
Indices: 28118643--28118684 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
28118633 AAATTTAATA
28118643 ATTTTTATACTTTTTATT
1 ATTTTTATACTTTTTATT
*
28118661 GATTTTTATACTTATTA-T
1 -ATTTTTATACTTTTTATT
28118679 ATTTTT
1 ATTTTT
28118685 TGCCACATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 1 0.05
19 15 0.68
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (18 bp):
ATTTTTATACTTTTTATT
Found at i:28132585 original size:45 final size:45
Alignment explanation
Indices: 28132512--28132631 Score: 168
Period size: 45 Copynumber: 2.7 Consensus size: 45
28132502 TACTATTCTA
* * *
28132512 GGAGCGATATACTGAATTGGTTCATAAGAGCGGTATACCATATTG
1 GGAGCGATATACTGTATTGGCTCATAAGAGCGGTATACCATACTG
* * *
28132557 GGAGCGATATACTGTACTGGCTCGTAAGAGCGGTATACTATACTG
1 GGAGCGATATACTGTATTGGCTCATAAGAGCGGTATACCATACTG
* *
28132602 GGAGCGATATGCTGTATTGACTCATAAGAG
1 GGAGCGATATACTGTATTGGCTCATAAGAG
28132632 TGATATATTG
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 65 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (45 bp):
GGAGCGATATACTGTATTGGCTCATAAGAGCGGTATACCATACTG
Found at i:28132594 original size:26 final size:26
Alignment explanation
Indices: 28132558--28132770 Score: 153
Period size: 26 Copynumber: 9.0 Consensus size: 26
28132548 ACCATATTGG
28132558 GAGCGATATACTGTACTGGCTCGTAA
1 GAGCGATATACTGTACTGGCTCGTAA
* *
28132584 GAGCGGTATACTATACT-G---G---
1 GAGCGATATACTGTACTGGCTCGTAA
* * * *
28132603 GAGCGATATGCTGTATTGACTCATAA
1 GAGCGATATACTGTACTGGCTCGTAA
* * *
28132629 GAGTGATATATTGTATTGGCTCGTAA
1 GAGCGATATACTGTACTGGCTCGTAA
28132655 GAGCGATATACTGTACT-G---G---
1 GAGCGATATACTGTACTGGCTCGTAA
28132674 GAGCGATATACTGTACTGGCTCGTAA
1 GAGCGATATACTGTACTGGCTCGTAA
*
28132700 GAGCGATATATTGTA----CT--T-A
1 GAGCGATATACTGTACTGGCTCGTAA
* *
28132719 GAGCGAAATACTGAACTGGCTCGTAA
1 GAGCGATATACTGTACTGGCTCGTAA
* *
28132745 GAGGGATATACTGTACTGGCTTGTAA
1 GAGCGATATACTGTACTGGCTCGTAA
28132771 AAATGAATCT
Statistics
Matches: 142, Mismatches: 24, Indels: 42
0.68 0.12 0.20
Matches are distributed among these distances:
19 43 0.30
20 2 0.01
22 4 0.03
23 3 0.02
25 3 0.02
26 87 0.61
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (26 bp):
GAGCGATATACTGTACTGGCTCGTAA
Found at i:28132638 original size:71 final size:71
Alignment explanation
Indices: 28132558--28132716 Score: 237
Period size: 71 Copynumber: 2.2 Consensus size: 71
28132548 ACCATATTGG
* * * *
28132558 GAGCGATATACTGTACTGGCTCGTAAGAGCGGTATACTATACTGGGAGCGATATGCTGTATTGAC
1 GAGCGATATATTGTACTGGCTCGTAAGAGCGATATACTATACTGGGAGCGATATACTGTACTGAC
28132623 TCATAA
66 TCATAA
* * * *
28132629 GAGTGATATATTGTATTGGCTCGTAAGAGCGATATACTGTACTGGGAGCGATATACTGTACTGGC
1 GAGCGATATATTGTACTGGCTCGTAAGAGCGATATACTATACTGGGAGCGATATACTGTACTGAC
*
28132694 TCGTAA
66 TCATAA
28132700 GAGCGATATATTGTACT
1 GAGCGATATATTGTACT
28132717 TAGAGCGAAA
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
71 77 1.00
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (71 bp):
GAGCGATATATTGTACTGGCTCGTAAGAGCGATATACTATACTGGGAGCGATATACTGTACTGAC
TCATAA
Found at i:28132679 original size:19 final size:19
Alignment explanation
Indices: 28132655--28132692 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
28132645 TGGCTCGTAA
28132655 GAGCGATATACTGTACTGG
1 GAGCGATATACTGTACTGG
28132674 GAGCGATATACTGTACTGG
1 GAGCGATATACTGTACTGG
28132693 CTCGTAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (19 bp):
GAGCGATATACTGTACTGG
Found at i:28132697 original size:45 final size:45
Alignment explanation
Indices: 28132633--28132763 Score: 190
Period size: 45 Copynumber: 2.9 Consensus size: 45
28132623 TCATAAGAGT
* *
28132633 GATATATTGTATTGGCTCGTAAGAGCGATATACTGTACTGGGAGC
1 GATATACTGTACTGGCTCGTAAGAGCGATATACTGTACTGGGAGC
* **
28132678 GATATACTGTACTGGCTCGTAAGAGCGATATATTGTACTTAGAGC
1 GATATACTGTACTGGCTCGTAAGAGCGATATACTGTACTGGGAGC
* * *
28132723 GAAATACTGAACTGGCTCGTAAGAGGGATATACTGTACTGG
1 GATATACTGTACTGGCTCGTAAGAGCGATATACTGTACTGG
28132764 CTTGTAAAAA
Statistics
Matches: 75, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (45 bp):
GATATACTGTACTGGCTCGTAAGAGCGATATACTGTACTGGGAGC
Found at i:28132723 original size:116 final size:116
Alignment explanation
Indices: 28132517--28132770 Score: 310
Period size: 116 Copynumber: 2.2 Consensus size: 116
28132507 TTCTAGGAGC
* * * * *
28132517 GATATACTGAATTGGTTCATAAGAGCGGTATACCATATTGGGAGCGATATACTGTACTGGCTCGT
1 GATATACTGTATTGGCTCGTAAGAGCGATATACCATACTGGGAGCGATATACTGTACTGGCTCGT
* * * * * * *
28132582 AAGAGCGGTATACTATACTGGGAGCGATATGCTGTATTGACTCATAAGAGT
66 AAGAGCGATATACTATACTGAGAGCGAAATACTGAACTGACTCATAAGAGG
* **
28132633 GATATATTGTATTGGCTCGTAAGAGCGATATACTGTACTGGGAGCGATATACTGTACTGGCTCGT
1 GATATACTGTATTGGCTCGTAAGAGCGATATACCATACTGGGAGCGATATACTGTACTGGCTCGT
* * * * *
28132698 AAGAGCGATATATTGTACTTAGAGCGAAATACTGAACTGGCTCGTAAGAGG
66 AAGAGCGATATACTATACTGAGAGCGAAATACTGAACTGACTCATAAGAGG
* *
28132749 GATATACTGTACTGGCTTGTAA
1 GATATACTGTATTGGCTCGTAA
28132771 AAATGAATCT
Statistics
Matches: 115, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
116 115 1.00
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (116 bp):
GATATACTGTATTGGCTCGTAAGAGCGATATACCATACTGGGAGCGATATACTGTACTGGCTCGT
AAGAGCGATATACTATACTGAGAGCGAAATACTGAACTGACTCATAAGAGG
Found at i:28134875 original size:29 final size:29
Alignment explanation
Indices: 28134820--28134875 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
28134810 TTTCCACTTC
* *
28134820 TCCCAAATTGGTACCTATAGTTCTTTTTG
1 TCCCAAATTGGTACCGATACTTCTTTTTG
28134849 TCCCAAATTGGTACTCGA-ACTT-TTTTT
1 TCCCAAATTGGTAC-CGATACTTCTTTTT
28134876 CCGTCCACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.21
29 17 0.71
30 2 0.08
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (29 bp):
TCCCAAATTGGTACCGATACTTCTTTTTG
Found at i:28135912 original size:12 final size:12
Alignment explanation
Indices: 28135878--28135958 Score: 65
Period size: 12 Copynumber: 6.8 Consensus size: 12
28135868 ATAACATCCA
*
28135878 AACAACCAAAAC
1 AACAACAAAAAC
*
28135890 AACAACCAAAAC
1 AACAACAAAAAC
*
28135902 AACAACAAAAAT
1 AACAACAAAAAC
* * *
28135914 AA-TAGAAAAAT
1 AACAACAAAAAC
* *
28135925 AGCAACAAAAAT
1 AACAACAAAAAC
*
28135937 AACAATAAAAAC
1 AACAACAAAAAC
*
28135949 AACACCAAAA
1 AACAACAAAA
28135959 TAGTAAAAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
11 8 0.14
12 48 0.86
ACGTcount: A:0.70, C:0.21, G:0.02, T:0.06
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:28135923 original size:23 final size:24
Alignment explanation
Indices: 28135878--28135958 Score: 74
Period size: 24 Copynumber: 3.4 Consensus size: 24
28135868 ATAACATCCA
* * **
28135878 AACAACCAAAACAACAACCAAAAC
1 AACAACAAAAATAACAAGAAAAAC
* *
28135902 AACAACAAAAATAA-TAGAAAAAT
1 AACAACAAAAATAACAAGAAAAAC
* *
28135925 AGCAACAAAAATAACAATAAAAAC
1 AACAACAAAAATAACAAGAAAAAC
*
28135949 AACACCAAAA
1 AACAACAAAA
28135959 TAGTAAAAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
23 18 0.41
24 26 0.59
ACGTcount: A:0.70, C:0.21, G:0.02, T:0.06
Consensus pattern (24 bp):
AACAACAAAAATAACAAGAAAAAC
Found at i:28135969 original size:23 final size:23
Alignment explanation
Indices: 28135943--28136084 Score: 74
Period size: 22 Copynumber: 5.8 Consensus size: 23
28135933 AAATAACAAT
*
28135943 AAAAACAACACCAAAATAGTAAA
1 AAAAACAACACCAAAACAGTAAA
* *
28135966 AAAAATAGCACCAAAACAGCAATTAAAA
1 AAAAACAACACCAAAACAG----T-AAA
*
28135994 CAGTAAAAAAAGCACCAAAACAGT-AA
1 -A--AAAACAA-CACCAAAACAGTAAA
*
28136020 AAACACAACACCAAAACAGT--A
1 AAAAACAACACCAAAACAGTAAA
* * *
28136041 AAAAACAGCAACCAAAATAGCAAAAA
1 AAAAACAAC-ACCAAAACAG--TAAA
*
28136067 AAAAACAGCACCAAAACA
1 AAAAACAACACCAAAACA
28136085 ACAATATAAT
Statistics
Matches: 93, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
21 8 0.09
22 21 0.23
23 21 0.23
25 9 0.10
26 12 0.13
27 1 0.01
28 4 0.04
29 1 0.01
31 5 0.05
32 11 0.12
ACGTcount: A:0.65, C:0.21, G:0.07, T:0.06
Consensus pattern (23 bp):
AAAAACAACACCAAAACAGTAAA
Found at i:28136034 original size:22 final size:21
Alignment explanation
Indices: 28135990--28136067 Score: 104
Period size: 22 Copynumber: 3.7 Consensus size: 21
28135980 AACAGCAATT
28135990 AAAACAGTAAAAAA-AGCACC
1 AAAACAGTAAAAAACAGCACC
*
28136010 AAAACAGTAAAAACACAACACC
1 AAAACAGTAAAAA-ACAGCACC
28136032 AAAACAGTAAAAAACAGCAACC
1 AAAACAGTAAAAAACAGC-ACC
* *
28136054 AAAATAGCAAAAAA
1 AAAACAGTAAAAAA
28136068 AAAACAGCAC
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.25
21 5 0.10
22 33 0.65
ACGTcount: A:0.67, C:0.21, G:0.08, T:0.05
Consensus pattern (21 bp):
AAAACAGTAAAAAACAGCACC
Found at i:28136807 original size:12 final size:12
Alignment explanation
Indices: 28136790--28136837 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
28136780 ACCCAATTCC
*
28136790 ATTTTTCTTATT
1 ATTTTTATTATT
28136802 ATTTTTATTTATTT
1 ATTTTTA-TTA-TT
28136816 ATTTATTTATTATT
1 A-TT-TTTATTATT
28136830 ATTTTTAT
1 ATTTTTAT
28136838 GAACATAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 11 0.35
13 5 0.16
14 6 0.19
15 5 0.16
16 4 0.13
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (12 bp):
ATTTTTATTATT
Found at i:28136899 original size:63 final size:64
Alignment explanation
Indices: 28136798--28136961 Score: 235
Period size: 63 Copynumber: 2.5 Consensus size: 64
28136788 CCATTTTTCT
*
28136798 TATTATTTTTA-TTTATTTATTTATTTATTATTATTTTTATGAACATAAATAAAT-A-TAAAATA
1 TATTAATTTTATTTTA-TTATTTATTTATTATTA-TTTTATGAACATAAATAAATAAGTAAAATA
28136860 A
64 A
*
28136861 TATTAATTTTATTTTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAAT
1 TATTAATTTTATTTTATTATTTATTTA-TTATTATTTTATGAACATAAATAAAT-AA-GTAAAAT
28136926 AA
63 AA
*
28136928 TATTAATTTTGTTTTATTATTTATTTATTATTAT
1 TATTAATTTTATTTTATTATTTATTTATTATTAT
28136962 AAATAAATAA
Statistics
Matches: 92, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
63 40 0.43
64 10 0.11
65 1 0.01
66 7 0.08
67 34 0.37
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (64 bp):
TATTAATTTTATTTTATTATTTATTTATTATTATTTTATGAACATAAATAAATAAGTAAAATAA
Found at i:28136918 original size:67 final size:65
Alignment explanation
Indices: 28136798--28136982 Score: 238
Period size: 67 Copynumber: 2.9 Consensus size: 65
28136788 CCATTTTTCT
* *
28136798 TATTATTTTTA-TTTATTTATTTATTTATTATTATTTT-T-ATGA-ACATAAATAAATATAAAAT
1 TATTAATTTTATTTTA-TTATTTATTTATTATTATTTTATAAT-ATAAATAAATAAATATAAAAT
28136859 AA
64 AA
*
28136861 TATTAATTTTATTTTATTATTTATTTATTTATTATTTTATGAATATAAATAAATAAATGTAAAAT
1 TATTAATTTTATTTTATTATTTATTTA-TTATTATTTTAT-AATATAAATAAATAAATATAAAAT
28136926 AA
64 AA
* **
28136928 TATTAATTTTGTTTTATTATTTATTTATTATTA-TAAATAA-ATAAATAAATAAATA
1 TATTAATTTTATTTTATTATTTATTTATTATTATTTTATAATATAAATAAATAAATA
28136983 ACAAACCAAA
Statistics
Matches: 109, Mismatches: 7, Indels: 12
0.85 0.05 0.09
Matches are distributed among these distances:
63 35 0.32
64 16 0.15
65 4 0.04
66 7 0.06
67 47 0.43
ACGTcount: A:0.43, C:0.01, G:0.02, T:0.54
Consensus pattern (65 bp):
TATTAATTTTATTTTATTATTTATTTATTATTATTTTATAATATAAATAAATAAATATAAAATAA
Found at i:28141908 original size:15 final size:15
Alignment explanation
Indices: 28141897--28141956 Score: 67
Period size: 14 Copynumber: 4.3 Consensus size: 15
28141887 ATAAAAAATT
28141897 AAAAAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
*
28141912 AAAAAAAG-ACAAAG
1 AAAAAAAGAAAAAAG
28141926 ---AAAAGAAAAAAG
1 AAAAAAAGAAAAAAG
*
28141938 AAGAAAAG-AAAAAG
1 AAAAAAAGAAAAAAG
28141952 AAAAA
1 AAAAA
28141957 GGGGAGGTCG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
11 5 0.13
12 5 0.13
14 15 0.39
15 13 0.34
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAAAAAG
Found at i:28141915 original size:21 final size:20
Alignment explanation
Indices: 28141879--28141955 Score: 56
Period size: 19 Copynumber: 4.0 Consensus size: 20
28141869 AGAAATTTAA
* *
28141879 AAAAAAAG-ATAAA-AAATT
1 AAAAAAAGAAAAAAGAAAAT
28141897 AAAAAAAGAAAAAAGAAAA-
1 AAAAAAAGAAAAAAGAAAAT
*
28141916 AAAGACAAAGAAAAGAA-AAAAG
1 AAA-A-AAAGAAAA-AAGAAAAT
*
28141938 AAGAAAAG-AAAAAGAAAA
1 AAAAAAAGAAAAAAGAAAA
28141956 AGGGGAGGTC
Statistics
Matches: 49, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
18 10 0.20
19 14 0.29
20 8 0.16
21 13 0.27
22 4 0.08
ACGTcount: A:0.82, C:0.01, G:0.13, T:0.04
Consensus pattern (20 bp):
AAAAAAAGAAAAAAGAAAAT
Found at i:28141956 original size:21 final size:20
Alignment explanation
Indices: 28141900--28141956 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
28141890 AAAAATTAAA
28141900 AAAAGAAAAA-AGAAAAAAAG
1 AAAAGAAAAAGA-AAAAAAAG
28141920 ACAAAG-AAAAGAAAAAAGAAG
1 A-AAAGAAAAAGAAAAAA-AAG
28141941 AAAAGAAAAAGAAAAA
1 AAAAGAAAAAGAAAAA
28141957 GGGGAGGTCG
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAGAAAAAAAAG
Found at i:28142946 original size:50 final size:50
Alignment explanation
Indices: 28142894--28143058 Score: 190
Period size: 50 Copynumber: 3.3 Consensus size: 50
28142884 TAAAGCGGTG
*
28142894 GAGGTGCAGATTGAAACTGTAATGGTAAATCTCATACACCTAAAGCTATG
1 GAGGTGCAGATTGAAACTGTAATGGTAAATCTCATACACCTAAAGCTATA
* * *
28142944 GAGGTGCAGATTGAAACCGCAAT-GTCAAATCTCATACACCTAAAGCTGTA
1 GAGGTGCAGATTGAAACTGTAATGGT-AAATCTCATACACCTAAAGCTATA
* * * * **
28142994 GAGGGGCAGAATGAAGCTGTAATGGCAAATCTCAGT-CATTTAAAGCTATA
1 GAGGTGCAGATTGAAACTGTAATGGTAAATCTCA-TACACCTAAAGCTATA
* *
28143044 GAGGAGAAGATTGAA
1 GAGGTGCAGATTGAA
28143059 GTTATAAGGA
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
49 2 0.02
50 92 0.96
51 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (50 bp):
GAGGTGCAGATTGAAACTGTAATGGTAAATCTCATACACCTAAAGCTATA
Found at i:28144409 original size:80 final size:80
Alignment explanation
Indices: 28143113--28144405 Score: 2180
Period size: 80 Copynumber: 16.2 Consensus size: 80
28143103 AATTACAGCC
* * *
28143113 TCCAATCTTTTACCCTCACCAGAGGGCAAGATTGAAAACCATCAGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
* *
28143178 GGTAAATTGAAGAAA
66 GGCAGATTGAAGAAA
* *
28143193 ACCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
28143258 GGAAGATTGAAGAAA
66 GGCAGATTGAAGAAA
28143273 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
28143338 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* *
28143353 TCCAATCTTTTACCCTAATCAGAGGGTAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
* *
28143418 GGCAAATTAAAGAAA
66 GGCAGATTGAAGAAA
*
28143433 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATAG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
28143498 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* *
28143513 TCCAATCTTTTACCCTAACTAGAGAGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
28143578 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* *
28143593 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAAACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
28143658 GGCAGATTAAAGAAA
66 GGCAGATTGAAGAAA
*
28143673 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCTGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
28143738 GGCAGATTAAAGAAA
66 GGCAGATTGAAGAAA
*
28143753 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTCTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
28143818 GGCAAATTGAAGAAA
66 GGCAGATTGAAGAAA
* *
28143833 TCTAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTCTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
28143898 GGCAAATTGAAGAAA
66 GGCAGATTGAAGAAA
*
28143913 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
*
28143978 GGCAGATTAAAGAAA
66 GGCAGATTGAAGAAA
28143993 TCCAATCTTTTACCCTAACCAGAGGG-AAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
28144057 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* *
28144072 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTCTACCCCGATCATGA
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
28144137 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * *
28144152 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAAACCATCTGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
28144217 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* *
28144232 TCCAATCTTTTACCCTAACTAGAGGGCAAGATTGAAGACCATCTGATCTTTTACCCCGATCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
28144297 GGCAGATTGAAGAAA
66 GGCAGATTGAAGAAA
* * * * *
28144312 TCCAATCTTTTACCCTAACCAAAGGGC-AGATTGAAGACCATCAGATCTCTTACCTCGACCATGG
1 TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
28144376 GGCA-AGTTGAA-ACAA
66 GGCAGA-TTGAAGA-AA
*
28144391 TCTAATCTTTTACCC
1 TCCAATCTTTTACCC
28144406 CTAAAGTTAT
Statistics
Matches: 1155, Mismatches: 55, Indels: 7
0.95 0.05 0.01
Matches are distributed among these distances:
78 2 0.00
79 136 0.12
80 1017 0.88
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (80 bp):
TCCAATCTTTTACCCTAACCAGAGGGCAAGATTGAAGACCATCCGATCTTTTACCCCGATCATGG
GGCAGATTGAAGAAA
Done.