Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2556
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: 50805
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:82 original size:1 final size:1
Alignment explanation
Indices: 76--257 Score: 328
Period size: 1 Copynumber: 182.0 Consensus size: 1
66 CTTGTTTGAT
* *
76 AAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
**
141 AAAAAAAAAAAAAAAACCAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
206 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
258 TAACAAAGGA
Statistics
Matches: 175, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
1 175 1.00
ACGTcount: A:0.98, C:0.01, G:0.01, T:0.00
Consensus pattern (1 bp):
A
Found at i:629 original size:13 final size:13
Alignment explanation
Indices: 611--636 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
601 TACACCAAGT
611 ATGTATCGATACA
1 ATGTATCGATACA
624 ATGTATCGATACA
1 ATGTATCGATACA
637 CCAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:634 original size:32 final size:33
Alignment explanation
Indices: 593--656 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
583 TAGCCAAACT
**
593 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
625 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
657 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:2886 original size:21 final size:21
Alignment explanation
Indices: 2853--2897 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
2843 TTGCAAGTTG
*
2853 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
2875 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
2895 AAA
1 AAA
2898 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:4720 original size:15 final size:15
Alignment explanation
Indices: 4700--4730 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4690 TAAAAATGTC
*
4700 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
4715 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
4730 C
1 C
4731 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:6825 original size:13 final size:13
Alignment explanation
Indices: 6807--6832 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6797 ACATTTTTCT
6807 TTGTATCGATACA
1 TTGTATCGATACA
6820 TTGTATCGATACA
1 TTGTATCGATACA
6833 GGGTGATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:6996 original size:20 final size:20
Alignment explanation
Indices: 6953--6998 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
6943 AAATCTTTTG
6953 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
6974 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
6994 CAAAA
1 CAAAA
6999 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:15898 original size:12 final size:12
Alignment explanation
Indices: 15881--15906 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15871 GTTGTGCATA
15881 AATTTGGTTTAT
1 AATTTGGTTTAT
15893 AATTTGGTTTAT
1 AATTTGGTTTAT
15905 AA
1 AA
15907 CACATAGGGG
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:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (12 bp):
AATTTGGTTTAT
Found at i:16574 original size:22 final size:22
Alignment explanation
Indices: 16549--16591 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
16539 GACAAGTCTA
16549 AATGTTTTTC-AAGTAATAAATT
1 AATGTTTTTCAAAGTAA-AAATT
16571 AATGTTTTTCAAAGTAAAAAT
1 AATGTTTTTCAAAGTAAAAAT
16592 ACTTACTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.44, C:0.05, G:0.09, T:0.42
Consensus pattern (22 bp):
AATGTTTTTCAAAGTAAAAATT
Found at i:16730 original size:33 final size:33
Alignment explanation
Indices: 16692--16755 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
16682 CACCCAGATT
*
16692 TATCAATATAAATTGCTAAGTATCGATACACTG
1 TATCAATACAAATTGCTAAGTATCGATACACTG
**
16725 TATCAATACAAATTGCTTTGTATCGATACAC
1 TATCAATACAAATTGCTAAGTATCGATACAC
16756 CATGAATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (33 bp):
TATCAATACAAATTGCTAAGTATCGATACACTG
Found at i:18442 original size:78 final size:78
Alignment explanation
Indices: 18313--18510 Score: 200
Period size: 78 Copynumber: 2.5 Consensus size: 78
18303 AATAACGGGG
* * * * *** * *
18313 TTGGAGTGTTCCCTTGAAAATAACGGGGCTGGAGTATCCCTGGTTGTGAGAAATCGATGA-TTAG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-ATTTAG
*
18377 AAAAAAAATCGAGA
65 AAAAAAAACCGAGA
*
18391 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGG
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATA-TTTAG
* * * * *
18456 GAATAAAGCCGGGG
65 AAAAAAAACCGAGA
* * *
18470 TTGGAGTATCCCCTCGGAAGTAATGGGGTTGGAGTATCCCC
1 TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCC
18511 GATGAAATAA
Statistics
Matches: 99, Mismatches: 19, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
77 1 0.01
78 49 0.49
79 49 0.49
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (78 bp):
TTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTAGA
AAAAAAACCGAGA
Found at i:18527 original size:28 final size:28
Alignment explanation
Indices: 18468--18541 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
18458 ATAAAGCCGG
*** * * *
18468 GGTTGGAGTATCCCCTCGGAAGTAATGG
1 GGTTGGAGTATCCCCGATGAAATAACGA
18496 GGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTATCCCCGATGAAATAACGA
*
18524 GGTTGGAGTATCCTCGAT
1 GGTTGGAGTATCCCCGAT
18542 TGTGAAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGATGAAATAACGA
Found at i:18594 original size:52 final size:52
Alignment explanation
Indices: 18524--19179 Score: 414
Period size: 52 Copynumber: 12.4 Consensus size: 52
18514 GAAATAACGA
*
18524 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGAAAATAAAATCGG
* * * *
18576 AGTTGGAGTATCCCCGATTAAAG-GGAAAATTGGT-GTTTTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT---GTGAAAAATTGGTATTTTTGAAAATAAAATCGG
* * * * * *
18629 GGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAG-CAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTGAAAATAAAATCGG
* *** * *
18681 GGTTGGAGTATCCCCGATTATGAAAAATCAATA-TTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGAAAATAAAATCGG
* *** ** *
18732 GGTTGGAGTATCCCC--TCG-GAAATAATGGGGTTGGAGTATCCCTGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTGTGAAA-AA-----TT-G-GTATTTTTGAAAATAAAATCGG
* *
18787 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGAAAATAAAATCGG
* * * *
18841 AGTTGGAGTATCCCCGATTAAAG-GGAGAATTGGT-GTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATT---GTGAAAAATTGGTATTTTTGAAAATAAAATCGG
* * * * *
18894 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAG-CAATAAAACCGG
1 GGTTGGAGTATCCCCGATTGT-GAAAAATTGGTATTTTTGAAAATAAAATCGG
* *** * *
18946 GGTTGGAGTATCCCCGATTATGAAAAATCAATA-TTTTGGAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGAAAATAAAATCGG
* ** * ** *
18997 GGTTGGAGTATCCCC--TCG-GAAATAACGGGGTTGGAGTATCCTCGATGAT-TAA-CGG
1 GGTTGGAGTATCCCCGATTGTGAAA-AA-----TT-G-GTATTTTTGAAAATAAAATCGG
* *
19052 GGTTGGAGTATCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGAA-AAATTGGT-ATTTTTGAAAATAAAATCGG
* * * *
19106 AGTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTTGAAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTGTGA-AAAATTGGTATTTTTGAAAATAAAATCGG
* *
19158 AGTTGGAATATCCCCGATTGTG
1 GGTTGGAGTATCCCCGATTGTG
19180 GAGAATTGAG
Statistics
Matches: 463, Mismatches: 93, Indels: 95
0.71 0.14 0.15
Matches are distributed among these distances:
48 8 0.02
49 6 0.01
50 10 0.02
51 70 0.15
52 143 0.31
53 93 0.20
54 56 0.12
55 44 0.10
56 8 0.02
57 13 0.03
58 10 0.02
59 2 0.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.30
Consensus pattern (52 bp):
GGTTGGAGTATCCCCGATTGTGAAAAATTGGTATTTTTGAAAATAAAATCGG
Found at i:18930 original size:265 final size:265
Alignment explanation
Indices: 18414--19181 Score: 1303
Period size: 265 Copynumber: 2.9 Consensus size: 265
18404 TCGAAAATAA
* * * *
18414 CGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
* * * * *
18479 CCCCTCGGAAGTAATGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGATTG
66 CCCCTCGGAAATAATGGGGTTGGAGTATCCCTGATG-ATTAACGGGGTTGGAGTATCCCCGATTG
* *
18544 TGAA-AAATTGGT-ATTTTTGAAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATT
130 TGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATT
* *
18607 GGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCCAATTGTGGAAAAATTAGTGTTTTAGCAA
195 GGTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAA
18672 TAAAAC
260 TAAAAC
18678 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
18743 CCCCTCGGAAATAATGGGGTTGGAGTATCCCTGATGATTAACGGGGTTGGAGTATCCCCGATTGT
66 CCCCTCGGAAATAATGGGGTTGGAGTATCCCTGATGATTAACGGGGTTGGAGTATCCCCGATTGT
*
18808 GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAGAATTG
131 GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTG
18873 GTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAAT
196 GTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAAT
18938 AAAAC
261 AAAAC
18943 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
1 CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
*
19008 CCCCTCGGAAATAACGGGGTTGGAGTAT-CCTCGATGATTAACGGGGTTGGAGTATCCCCGATTG
66 CCCCTCGGAAATAATGGGGTTGGAGTATCCCT-GATGATTAACGGGGTTGGAGTATCCCCGATTG
*
19072 TGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTATA--GAAAATT
130 TGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATT
* * *
19135 AGTGTTTTTGAAAATAAAATCGGAGTTGGAATATCCCCGATTGTGGA
195 GGTG-TTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGA
19182 GAATTGAGAA
Statistics
Matches: 480, Mismatches: 20, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
263 38 0.08
264 146 0.30
265 296 0.62
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.29
Consensus pattern (265 bp):
CGGGGTTGGAGTATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTGGAGTAT
CCCCTCGGAAATAATGGGGTTGGAGTATCCCTGATGATTAACGGGGTTGGAGTATCCCCGATTGT
GAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAAGGGAAAATTG
GTGTTTTGAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAAT
AAAAC
Found at i:19029 original size:28 final size:28
Alignment explanation
Indices: 18994--19066 Score: 98
Period size: 27 Copynumber: 2.6 Consensus size: 28
18984 GAAATAAAGT
18994 CGGGGTTGGAGTATCCCCTCG-GAAATAA
1 CGGGGTTGGAGTATCCCCTCGAG-AATAA
*
19022 CGGGGTTGGAGTAT--CCTCGATGATTAA
1 CGGGGTTGGAGTATCCCCTCGA-GAATAA
19049 CGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCC
19067 GATTGTGAAG
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 5 0.12
27 18 0.45
28 15 0.38
29 2 0.05
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.25
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCTCGAGAATAA
Found at i:21565 original size:13 final size:13
Alignment explanation
Indices: 21547--21606 Score: 58
Period size: 13 Copynumber: 5.0 Consensus size: 13
21537 CAAAGAATAG
21547 ATGTATCGATACA
1 ATGTATCGATACA
*
21560 ATGTATTGATACA
1 ATGTATCGATACA
* *
21573 AAG-A---ATA-G
1 ATGTATCGATACA
21581 ATGTATCGATACA
1 ATGTATCGATACA
21594 ATGTATCGATACA
1 ATGTATCGATACA
21607 CAGAAAAATG
Statistics
Matches: 37, Mismatches: 5, Indels: 10
0.71 0.10 0.19
Matches are distributed among these distances:
8 2 0.05
9 4 0.11
12 4 0.11
13 27 0.73
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:21571 original size:34 final size:34
Alignment explanation
Indices: 21526--21626 Score: 168
Period size: 34 Copynumber: 3.0 Consensus size: 34
21516 AACTTCCTAG
21526 ATGTATCGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAATAGATGTATCGATACA
*
21560 ATGTATTGATACAAAGAATAGATGTATCGATACA
1 ATGTATCGATACAAAGAATAGATGTATCGATACA
* *
21594 ATGTATCGATACACAGAA-AAATGTATCGATACA
1 ATGTATCGATACAAAGAATAGATGTATCGATACA
21627 TTCCCTTGGC
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
33 14 0.22
34 49 0.78
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.27
Consensus pattern (34 bp):
ATGTATCGATACAAAGAATAGATGTATCGATACA
Found at i:21670 original size:19 final size:17
Alignment explanation
Indices: 21644--21747 Score: 98
Period size: 19 Copynumber: 6.2 Consensus size: 17
21634 GGCAGTAGCT
21644 AATTATGTATCGATACA
1 AATTATGTATCGATACA
21661 ATACTTATGTATCGATAC-
1 A-A-TTATGTATCGATACA
21679 -A-T-TGTATCGATACA
1 AATTATGTATCGATACA
21693 ATACTTATGTATCGATAC-
1 A-A-TTATGTATCGATACA
21711 -A-T-TGTATCGATACA
1 AATTATGTATCGATACA
21725 ACATTTATGTATCGATACA
1 A-A-TTATGTATCGATACA
21744 AATT
1 AATT
21748 GCTGAAATTC
Statistics
Matches: 73, Mismatches: 0, Indels: 28
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.30
14 2 0.03
16 4 0.05
17 3 0.04
18 4 0.05
19 38 0.52
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.38
Consensus pattern (17 bp):
AATTATGTATCGATACA
Found at i:21686 original size:13 final size:13
Alignment explanation
Indices: 21668--21724 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
21658 ACAATACTTA
21668 TGTATCGATACAT
1 TGTATCGATACAT
21681 TGTATCGATACAATACTT
1 TGTATCGATAC---A--T
21699 ATGTATCGATACAT
1 -TGTATCGATACAT
21713 TGTATCGATACA
1 TGTATCGATACA
21725 ACATTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:21690 original size:32 final size:32
Alignment explanation
Indices: 21649--21743 Score: 172
Period size: 32 Copynumber: 3.0 Consensus size: 32
21639 TAGCTAATTA
21649 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
21681 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAATACTTATGTATCGATACAT
* *
21713 TGTATCGATACAACATTTATGTATCGATACA
1 TGTATCGATACAATACTTATGTATCGATACA
21744 AATTGCTGAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAATACTTATGTATCGATACAT
Found at i:30722 original size:61 final size:61
Alignment explanation
Indices: 30616--31353 Score: 328
Period size: 60 Copynumber: 12.4 Consensus size: 61
30606 AACCACCCTT
*
30616 CTTGACTATATTC-GATCAAGACCTTCCTCATTTGATTGTATTCGATCAAATTTCACCCTCG
1 CTTGACTATATTCAG-TCAAGACCTTCCTCATTTGACTGTATTCGATCAAATTTCACCCTCG
* * * * * * *
30677 CTTGACTATATTCAGTCAAGTCTTTCCTCAATTAAATGTACTCGATCAAATCTT-ACCC-CT
1 CTTGACTATATTCAGTCAAGACCTTCCTCATTTGACTGTATTCGATCAAAT-TTCACCCTCG
* **
30737 CTTGACTGTATTTGGTCAAGACCTTCCTCATTTGACTGTATTC-AGTCAAATTTCACCCTCG
1 CTTGACTATATTCAGTCAAGACCTTCCTCATTTGACTGTATTCGA-TCAAATTTCACCCTCG
* * * * ** * * *
30798 CTTGACTGTATTCAGTCAAGTCTTTCTTTGTTTGACTGTACTC-AGTCAAATTTTACCC-CT
1 CTTGACTATATTCAGTCAAGACCTTCCTCATTTGACTGTATTCGA-TCAAATTTCACCCTCG
* * * * * * *
30858 CTTCATTGTATTCGGTCAAGACCTTCATCATTGGATTGTATTCGATCAAATTTCACCCTCG
1 CTTGACTATATTCAGTCAAGACCTTCCTCATTTGACTGTATTCGATCAAATTTCACCCTCG
* * * * *
30919 CTTGACTATATTTAATCAAGTCTTTCCTTATTTGACTGTACTT-G-----A---C-CCCT--
1 CTTGACTATATTCAGTCAAGACCTTCCTCATTTGACTGTA-TTCGATCAAATTTCACCCTCG
* * * ** * * * * * * *
30969 TTTGACTGTATTCGGTCAATTCCTTTCTCGTTTGACTGTACTAGGTCGAATCTTGC-CCC-CT
1 CTTGACTATATTCAGTCAAGACCTTCCTCATTTGACTGTATTCGATCAAAT-TT-CACCCTCG
* * * * * * *
31030 CTTAACTGTATTCAGTCAAGTCTTTCCTCGTTTGACTGTACTCGGTCAAAATTT-A---TCG
1 CTTGACTATATTCAGTCAAGACCTTCCTCATTTGACTGTATTCGATC-AAATTTCACCCTCG
* * *
31088 CTCTCGACTGTATTCTA-TTAAAACCTTCCTCATTTGACTGTATTC-AGTCAAATTTCACCCTCG
1 CT-T-GACTATATTC-AGTCAAGACCTTCCTCATTTGACTGTATTCGA-TCAAATTTCACCCTCG
* * * * * * *
31151 CTT-AATGTATTTAGTCAAGTCTTTCCTTATTTGATTGT-TCTC-AGTCAAATCTT-ATCCCT--
1 CTTGACTATATTCAGTCAAGACCTTCCTCATTTGACTGTAT-TCGA-TCAAAT-TTCA-CCCTCG
* * * * * * *
31210 TTTGACTGTATTCGGACAAAACCTTCCTCTTTTGACTGTATTCGATCAAATTTTACCCT--
1 CTTGACTATATTCAGTCAAGACCTTCCTCATTTGACTGTATTCGATCAAATTTCACCCTCG
* * * * * * ** *
31269 ATTCGACTGTATTCAGTCAAGTCTTTCTTTATTTGACTACACTT-GATCAAATCTT--GCCTCG
1 CTT-GACTATATTCAGTCAAGACCTTCCTCATTTGACTGTA-TTCGATCAAAT-TTCACCCTCG
* *
31330 CTTGATTGTATTCAGTCAAG-CCTT
1 CTTGACTATATTCAGTCAAGACCTT
31354 TCTTCACCTG
Statistics
Matches: 518, Mismatches: 114, Indels: 92
0.72 0.16 0.13
Matches are distributed among these distances:
49 1 0.00
50 31 0.06
52 4 0.01
53 1 0.00
55 1 0.00
56 1 0.00
58 3 0.01
59 28 0.05
60 249 0.48
61 185 0.36
62 9 0.02
63 5 0.01
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (61 bp):
CTTGACTATATTCAGTCAAGACCTTCCTCATTTGACTGTATTCGATCAAATTTCACCCTCG
Found at i:30785 original size:30 final size:30
Alignment explanation
Indices: 30738--30846 Score: 96
Period size: 30 Copynumber: 3.6 Consensus size: 30
30728 CTTACCCCTC
** * *
30738 TTGACTGTATTTGGTCAAGACCTTCCTCAT
1 TTGACTGTATTCAGTCAAGACTTTCCTCGT
*
30768 TTGACTGTATTCAGTCAA-A-TTTCACCCTCGC
1 TTGACTGTATTCAGTCAAGACTTT---CCTCGT
* * *
30799 TTGACTGTATTCAGTCAAGTCTTTCTTTGT
1 TTGACTGTATTCAGTCAAGACTTTCCTCGT
*
30829 TTGACTGTACTCAGTCAA
1 TTGACTGTATTCAGTCAA
30847 ATTTTACCCC
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.03
29 1 0.02
30 36 0.56
31 22 0.34
33 3 0.05
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.40
Consensus pattern (30 bp):
TTGACTGTATTCAGTCAAGACTTTCCTCGT
Found at i:30838 original size:121 final size:120
Alignment explanation
Indices: 30610--31353 Score: 696
Period size: 121 Copynumber: 6.3 Consensus size: 120
30600 ACCGAAAACC
* * * *
30610 ACCCTTCTTGACTATATTCGATCAAGACCTTCCTCATTTGATTGTATTCGATCAAATTTCACCCT
1 ACCCCTCTTGACTGTATTCGGTCAAGACCTTCCTCATTTGACTGTATTCGATCAAATTTCACCCT
* * * * *
30675 CGCTTGACTATATTCAGTCAAGTCTTTCCTCAATTAAATGTACTCGATCAAATCTT
66 CGCTTGACTGTATTCAGTCAAGTCTTTCCTTATTTGACTGTACTC-ATCAAATCTT
*
30731 ACCCCTCTTGACTGTATTTGGTCAAGACCTTCCTCATTTGACTGTATTC-AGTCAAATTTCACCC
1 ACCCCTCTTGACTGTATTCGGTCAAGACCTTCCTCATTTGACTGTATTCGA-TCAAATTTCACCC
* * *
30795 TCGCTTGACTGTATTCAGTCAAGTCTTTCTTTGTTTGACTGTACTCAGTCAAATTTT
65 TCGCTTGACTGTATTCAGTCAAGTCTTTCCTTATTTGACTGTACTCA-TCAAATCTT
* * * * *
30852 ACCCCTCTTCATTGTATTCGGTCAAGACCTTCATCATTGGATTGTATTCGATCAAATTTCACCCT
1 ACCCCTCTTGACTGTATTCGGTCAAGACCTTCCTCATTTGACTGTATTCGATCAAATTTCACCCT
* * * *
30917 CGCTTGACTATATTTAATCAAGTCTTTCCTTATTTGACTG---T-A-C---T-TG
66 CGCTTGACTGTATTCAGTCAAGTCTTTCCTTATTTGACTGTACTCATCAAATCTT
* ** * * * * * *
30963 ACCCCTTTTGACTGTATTCGGTCAATTCCTTTCTCGTTTGACTGTACTAGGTCGAATCTTGC-CC
1 ACCCCTCTTGACTGTATTCGGTCAAGACCTTCCTCATTTGACTGTATTCGATCAAAT-TT-CACC
* * ** *
31027 C-CTCTTAACTGTATTCAGTCAAGTCTTTCCTCGTTTGACTGTACTCGGTCAAAAT-TT
64 CTCGCTTGACTGTATTCAGTCAAGTCTTTCCTTATTTGACTGTACTC-ATC-AAATCTT
* * * ** * *
31084 ATCGCTCTCGACTGTATTCTATTAAAACCTTCCTCATTTGACTGTATTC-AGTCAAATTTCACCC
1 ACCCCTCTTGACTGTATTCGGTCAAGACCTTCCTCATTTGACTGTATTCGA-TCAAATTTCACCC
* * * *
31148 TCGCTT-AATGTATTTAGTCAAGTCTTTCCTTATTTGATTGTTCTCAGTCAAATCTT
65 TCGCTTGACTGTATTCAGTCAAGTCTTTCCTTATTTGACTGTACTCA-TCAAATCTT
* * * * * *
31204 ATCCCTTTTGACTGTATTCGGACAAAACCTTCCTCTTTTGACTGTATTCGATCAAATTTTACCCT
1 ACCCCTCTTGACTGTATTCGGTCAAGACCTTCCTCATTTGACTGTATTCGATCAAATTTCACCCT
* * ** *
31269 --ATTCGACTGTATTCAGTCAAGTCTTTCTTTATTTGACTACACTTGATCAAATCTT
66 CGCTT-GACTGTATTCAGTCAAGTCTTTCCTTATTTGACTGTAC-TCATCAAATCTT
* * * * *
31324 GCCTCGCTTGATTGTATTCAGTCAAG-CCTT
1 ACCCCTCTTGACTGTATTCGGTCAAGACCTT
31354 TCTTCACCTG
Statistics
Matches: 501, Mismatches: 98, Indels: 50
0.77 0.15 0.08
Matches are distributed among these distances:
111 77 0.15
112 6 0.01
113 1 0.00
114 1 0.00
115 1 0.00
117 2 0.00
118 3 0.01
119 9 0.02
120 154 0.31
121 246 0.49
122 1 0.00
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (120 bp):
ACCCCTCTTGACTGTATTCGGTCAAGACCTTCCTCATTTGACTGTATTCGATCAAATTTCACCCT
CGCTTGACTGTATTCAGTCAAGTCTTTCCTTATTTGACTGTACTCATCAAATCTT
Found at i:31005 original size:30 final size:28
Alignment explanation
Indices: 30969--31078 Score: 85
Period size: 30 Copynumber: 3.7 Consensus size: 28
30959 CTTGACCCCT
*
30969 TTTGACTGTATTCGGTCAATTCCTTTCTCG
1 TTTGACTGTACTCGGTCAA-T-CTTTCTCG
* * * *
30999 TTTGACTGTACTAGGTCGAATCTTGCCCCC
1 TTTGACTGTACTCGGTC-AATCTT-TCTCG
* * *
31029 TCTTAACTGTATTCAGTCAAGTCTTTCCTCG
1 T-TTGACTGTACTCGGTCAA-TCTTT-CTCG
31060 TTTGACTGTACTCGGTCAA
1 TTTGACTGTACTCGGTCAA
31079 AATTTATCGC
Statistics
Matches: 60, Mismatches: 15, Indels: 10
0.71 0.18 0.12
Matches are distributed among these distances:
29 3 0.05
30 36 0.60
31 21 0.35
ACGTcount: A:0.17, C:0.25, G:0.17, T:0.40
Consensus pattern (28 bp):
TTTGACTGTACTCGGTCAATCTTTCTCG
Found at i:32877 original size:20 final size:20
Alignment explanation
Indices: 32852--32918 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
32842 GCCAGTTTCA
32852 TGTATCGATACAATTGAGTG
1 TGTATCGATACAATTGAGTG
32872 TGTATCGATAC-A---A---
1 TGTATCGATACAATTGAGTG
32885 TGTATCGATACAATTGAGTG
1 TGTATCGATACAATTGAGTG
32905 TGTATCGATACAAT
1 TGTATCGATACAAT
32919 GTATCGATAC
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 1 0.03
17 1 0.03
19 1 0.03
20 25 0.62
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (20 bp):
TGTATCGATACAATTGAGTG
Found at i:32890 original size:13 final size:13
Alignment explanation
Indices: 32872--32898 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
32862 CAATTGAGTG
32872 TGTATCGATACAA
1 TGTATCGATACAA
32885 TGTATCGATACAA
1 TGTATCGATACAA
32898 T
1 T
32899 TGAGTGTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:32893 original size:33 final size:33
Alignment explanation
Indices: 32851--32929 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
32841 TGCCAGTTTC
32851 ATGTATCGATACAATTGAGTGTGTATCGATACA
1 ATGTATCGATACAATTGAGTGTGTATCGATACA
32884 ATGTATCGATACAATTGAGTGTGTATCGATACA
1 ATGTATCGATACAATTGAGTGTGTATCGATACA
32917 ATGTATCGATACA
1 ATGTATCGATACA
32930 GAGCATAATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (33 bp):
ATGTATCGATACAATTGAGTGTGTATCGATACA
Found at i:32923 original size:13 final size:13
Alignment explanation
Indices: 32905--32929 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
32895 CAATTGAGTG
32905 TGTATCGATACAA
1 TGTATCGATACAA
32918 TGTATCGATACA
1 TGTATCGATACA
32930 GAGCATAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:33711 original size:13 final size:13
Alignment explanation
Indices: 33693--33749 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
33683 CATAAAGTGT
33693 TGTATCGATACAA
1 TGTATCGATACAA
33706 TGTATCGATACATAA
1 TGTATCGATAC--AA
*
33721 GTGTTGTATTGATACAA
1 ----TGTATCGATACAA
33738 TGTATCGATACA
1 TGTATCGATACA
33750 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 22 0.61
15 2 0.06
17 2 0.06
19 10 0.28
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:33728 original size:32 final size:32
Alignment explanation
Indices: 33673--33773 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
33663 TTCAACGATT
33673 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
*
33706 TGTATCGATACATAAGTGTTGTATTGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
33738 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
33770 TGTA
1 TGTA
33774 AGCTACTGCC
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 52 0.80
33 13 0.20
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:33762 original size:19 final size:18
Alignment explanation
Indices: 33671--33768 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
33661 ATTTCAACGA
33671 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
33690 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
33706 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
33722 TGTTGTATTGATAC--AA-
1 T-TTGTATCGATACATAAG
33738 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
33754 TTTTGTATCGATACA
1 -TTTGTATCGATACA
33769 ATGTAAGCTA
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
15 4 0.06
17 4 0.06
19 23 0.36
20 12 0.19
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:33972 original size:52 final size:52
Alignment explanation
Indices: 33845--33973 Score: 186
Period size: 52 Copynumber: 2.5 Consensus size: 52
33835 CACTAATCTT
* * *
33845 TGTATCGATACATGTAGGTAAATCTGCCCAGAAGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGAAGTATCGATACACTATAAAA
* * * * *
33897 TGTATTGATACATACAGACAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGAAGTATCGATACACTATAAAA
33949 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
33974 TCATATTTCG
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 66 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGAAGTATCGATACACTATAAAA
Found at i:43543 original size:33 final size:33
Alignment explanation
Indices: 43500--43566 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
43490 CTGGGCATAA
* *
43500 TGTATAGATACAATT-CTTCATGTATCAATACAT
1 TGTATAGATAC-ATTGCTCCATGCATCAATACAT
* *
43533 TGTATCGATACATTGCTCCATGCATCGATACAT
1 TGTATAGATACATTGCTCCATGCATCAATACAT
43566 T
1 T
43567 TCACTTAGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.37
Consensus pattern (33 bp):
TGTATAGATACATTGCTCCATGCATCAATACAT
Found at i:43632 original size:13 final size:13
Alignment explanation
Indices: 43614--43673 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
43604 ACAATTGAGT
43614 ATGTATCGATACA
1 ATGTATCGATACA
43627 ATGTATCGATACA
1 ATGTATCGATACA
*
43640 A---AGCG-T--A
1 ATGTATCGATACA
43647 ATGTATCGATACA
1 ATGTATCGATACA
43660 ATGTATCGATACA
1 ATGTATCGATACA
43673 A
1 A
43674 AGCATAATGT
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
7 2 0.05
9 1 0.03
10 6 0.15
11 1 0.03
13 29 0.74
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:43636 original size:33 final size:33
Alignment explanation
Indices: 43594--43692 Score: 148
Period size: 33 Copynumber: 3.0 Consensus size: 33
43584 TGCCACTTTC
*
43594 ATGTATCGATACAATTGAGT-ATGTATCGATACA
1 ATGTATCGATACAA-AGAGTAATGTATCGATACA
*
43627 ATGTATCGATACAAAGCGTAATGTATCGATACA
1 ATGTATCGATACAAAGAGTAATGTATCGATACA
43660 ATGTATCGATACAAAGCA-TAATGTATCGATACA
1 ATGTATCGATACAAAG-AGTAATGTATCGATACA
43693 TCTGGGTGTG
Statistics
Matches: 61, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
32 3 0.05
33 58 0.95
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.29
Consensus pattern (33 bp):
ATGTATCGATACAAAGAGTAATGTATCGATACA
Found at i:43651 original size:20 final size:19
Alignment explanation
Indices: 43626--43692 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
43616 GTATCGATAC
43626 AATGTATCGATACAAAGCGT
1 AATGTATCGATACAAAGC-T
43646 AATGTATCGAT----A-C-
1 AATGTATCGATACAAAGCT
43659 AATGTATCGATACAAAGCAT
1 AATGTATCGATACAAAGC-T
43679 AATGTATCGATACA
1 AATGTATCGATACA
43693 TCTGGGTGTG
Statistics
Matches: 40, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
20 25 0.62
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.27
Consensus pattern (19 bp):
AATGTATCGATACAAAGCT
Found at i:46489 original size:28 final size:28
Alignment explanation
Indices: 46457--46527 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
46447 AAGCAAGATC
*
46457 AAGGAAATGAAATCAA-CAAGAAATATGA
1 AAGGAAA-GAAATCAAGCAAGAAATATCA
*
46485 AAGGAAACGAAAT-AAGCAAGAAATTTCA
1 AAGGAAA-GAAATCAAGCAAGAAATATCA
*
46513 AAGGAAAAAAATCAA
1 AAGGAAAGAAATCAA
46528 TAAAAAAGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.16
28 31 0.84
ACGTcount: A:0.62, C:0.08, G:0.17, T:0.13
Consensus pattern (28 bp):
AAGGAAAGAAATCAAGCAAGAAATATCA
Found at i:48533 original size:50 final size:52
Alignment explanation
Indices: 48442--48585 Score: 152
Period size: 52 Copynumber: 2.8 Consensus size: 52
48432 GGTATTTTTG
* * * *
48442 GAAATAAAATCGGAGTTGGAGTATCCTCGATTAAAGG-AAAATT-G-GTGTTTC
1 GAAATAAAACCGG-GTTGGAGTATCCCCGATT-ATGGAAAAATTAGTGTGTTTA
* * *
48493 GAAATAAAACCGGGGTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTTA
1 GAAATAAAACCGGGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTGTTTA
* *
48545 GCAATAAAACCGGGATTGGAATATCCCCGATTAT-GAAAAAT
1 GAAATAAAACCGGG-TTGGAGTATCCCCGATTATGGAAAAAT
48586 CAATATTTTG
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
49 2 0.03
50 22 0.28
51 13 0.17
52 25 0.32
53 16 0.21
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.27
Consensus pattern (52 bp):
GAAATAAAACCGGGTTGGAGTATCCCCGATTATGGAAAAATTAGTGTGTTTA
Found at i:48644 original size:260 final size:259
Alignment explanation
Indices: 48298--48790 Score: 669
Period size: 260 Copynumber: 1.9 Consensus size: 259
48288 CTCAAAATAA
* * *
48298 CGGGTTGGAGTATCCCAATTATGAGAAATCAATATTTTGGGAATAAAGCCGGGTTGGAGTATCCC
1 CGGGTTGGAATATCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGTTGGAGTATCCC
* *
48363 CTCGAAGTAACGGGGTTGGAGTATCCCCGATGAAAAT-AACAAGGTTGGAGTATCCTCG-CTGTG
66 CTCGAAATAACGGGGTTGGAGTATCCCCGATG---ATCAACAAGGTTGGAGTATCCCCGACTGTG
* *
48426 -A-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCTCGATTAAAGGAAAATTGGT
128 AAGAAATTGGTGATTTTTGGAAATAAAATC-GAGTTGGAGTATCCCCGATTAAA-GAAAATTAGT
*
48488 GT-TTCG-AAATAAAACCGG-GGTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTTAGCAAT
191 GTCTT-GAAAATAAAACCGGAGGTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTTAGCAAT
48550 AAAAC
255 AAAAC
* * *
48555 CGGGATTGGAATATCCCCGATTATGAAAAATCAATATTTTGGAAATAAAGTCGGGGTTTGAGTAT
1 CGGG-TTGGAATAT-CCCAATTATGAAAAATCAATATTTTGGAAATAAAG-CCGGGTTGGAGTAT
** *
48620 CCCCTCGAAATAACGGGGTTGGAGTATCCCCGATGATCAACGGGGTTGGAGTATCCCCGATTGTG
63 CCCCTCGAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTGGAGTATCCCCGACTGTG
* *
48685 AAGAAATTGGTGTTTTTTGGAAATAAAATCGAGTTGGAGTATCCCCGATTATAGAAAATTAGTGT
128 AAGAAATTGGTGATTTTTGGAAATAAAATCGAGTTGGAGTATCCCCGATTAAAGAAAATTAGTGT
* * * *
48750 CTTGAAAATAAAATCGGAGTTGGAATATCCTCGATTTTGGA
193 CTTGAAAATAAAACCGGAGGTGGAATATCCCCGATTGTGGA
48791 GAATTGAGAA
Statistics
Matches: 205, Mismatches: 20, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
257 6 0.03
258 26 0.13
259 36 0.18
260 59 0.29
261 42 0.20
262 36 0.18
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (259 bp):
CGGGTTGGAATATCCCAATTATGAAAAATCAATATTTTGGAAATAAAGCCGGGTTGGAGTATCCC
CTCGAAATAACGGGGTTGGAGTATCCCCGATGATCAACAAGGTTGGAGTATCCCCGACTGTGAAG
AAATTGGTGATTTTTGGAAATAAAATCGAGTTGGAGTATCCCCGATTAAAGAAAATTAGTGTCTT
GAAAATAAAACCGGAGGTGGAATATCCCCGATTGTGGAAAAATTAGTGTTTTTAGCAATAAAAC
Found at i:48678 original size:27 final size:26
Alignment explanation
Indices: 48606--48680 Score: 98
Period size: 27 Copynumber: 2.8 Consensus size: 26
48596 GAAATAAAGT
*
48606 CGGGGTTTGAGTATCCCCTCGA-AATAA
1 CGGGGTTGGAGTAT-CCC-CGATAATAA
*
48633 CGGGGTTGGAGTATCCCCGATGATCAA
1 CGGGGTTGGAGTATCCCCGATAAT-AA
48660 CGGGGTTGGAGTATCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
48681 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.07
26 5 0.11
27 36 0.82
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.24
Consensus pattern (26 bp):
CGGGGTTGGAGTATCCCCGATAATAA
Found at i:48726 original size:53 final size:51
Alignment explanation
Indices: 48664--48785 Score: 140
Period size: 53 Copynumber: 2.4 Consensus size: 51
48654 GATCAACGGG
* * * *
48664 GTTGGAGTATCCCCGATTGT-GAAGAAATTGGTGTTTTTTGGAAATAAAATC-GA
1 GTTGGAGTATCCCCGATTATAG-A-AAATTAGTG--TCTTGAAAATAAAATCGGA
48717 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTCTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTCTTGAAAATAAAATCGGA
* *
48768 GTTGGAATATCCTCGATT
1 GTTGGAGTATCCCCGATT
48786 TTGGAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
50 14 0.23
51 18 0.30
52 8 0.13
53 20 0.33
54 1 0.02
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (51 bp):
GTTGGAGTATCCCCGATTATAGAAAATTAGTGTCTTGAAAATAAAATCGGA
Done.