Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold813
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: 28457
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Found at i:2917 original size:52 final size:52
Alignment explanation
Indices: 2839--2969 Score: 217
Period size: 52 Copynumber: 2.5 Consensus size: 52
2829 TCCCGAATAT
** *
2839 GAAAATTTATCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGG
*
2891 GAAAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGG
*
2943 GCAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
2970 AAGATCGGTG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGG
Found at i:3062 original size:13 final size:13
Alignment explanation
Indices: 3044--3070 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3034 AGTAGCTTAA
3044 ATTGTATCGATAC
1 ATTGTATCGATAC
3057 ATTGTATCGATAC
1 ATTGTATCGATAC
3070 A
1 A
3071 ACATTTTATG
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:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (13 bp):
ATTGTATCGATAC
Found at i:4002 original size:67 final size:68
Alignment explanation
Indices: 3880--4006 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
3870 ATCGGGTTTT
* * *
3880 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAAATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAAATG
3945 AGA
66 AGA
* * * *
3948 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
4007 GAAAAAGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAAATG
AGA
Found at i:4178 original size:49 final size:49
Alignment explanation
Indices: 4019--4638 Score: 739
Period size: 49 Copynumber: 12.7 Consensus size: 49
4009 AAAAGGATGT
* *
4019 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AG-AAGGTGC
* *
4070 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT-----A-AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
4113 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
* * * **
4162 CAATATGCTAATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
*
4211 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGC
* * * **
4260 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTTAATGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGAC-TTAAAGAAGAAGGTGC
*
4309 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA-AATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAA-GAAGGTGC
* * * **
4358 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTTAATGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGAC-TTAAAGAAGAAGGTGC
* * *
4407 CAATGTGTTGAGTCAAGGCCAACTACATTGGACTTAAAGATA-AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGC
* * * **
4456 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTTAATGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGAC-TTAAAGAAGAAGGTGC
4505 CAATGTGCTGAGTT-AAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGC
1 CAATGTGCTGA-TTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGC
*
4554 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGC
* * *
4603 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
4639 GAAGGGTTGC
Statistics
Matches: 487, Mismatches: 61, Indels: 44
0.82 0.10 0.07
Matches are distributed among these distances:
43 40 0.08
48 16 0.03
49 383 0.79
50 16 0.03
51 32 0.07
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
Found at i:4257 original size:98 final size:98
Alignment explanation
Indices: 4019--4638 Score: 954
Period size: 98 Copynumber: 6.4 Consensus size: 98
4009 AAAAGGATGT
*
4019 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATATGCTGATTC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT--AAAGGTGCCAATATGCTGATTC
4084 AAGGCCAGCTATATTGGAC-TT-AA----AGGTGC
64 AAGGCCAGCTATATTGGACTTTAAAGGTGAGGTGC
*
4113 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATGCTAATTCA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCA
4177 AGGCCAGCTATATTGGAC-TTAAAGGTGAAGGTGC
65 AGGCCAGCTATATTGGACTTTAAAGGTG-AGGTGC
*
4211 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
*
4276 GGCCAGCTATATTGGACTTTAATGGTGAGGTGC
66 GGCCAGCTATATTGGACTTTAAAGGTGAGGTGC
*
4309 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
*
4374 GGCCAGCTATATTGGACTTTAATGGTGAGGTGC
66 GGCCAGCTATATTGGACTTTAAAGGTGAGGTGC
* * *
4407 CAATGTGTTGAGTCAAGGCCAACTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
*
4472 GGCCAGCTATATTGGACTTTAATGGTGAGGTGC
66 GGCCAGCTATATTGGACTTTAAAGGTGAGGTGC
* *
4505 CAATGTGCTGAGTT-AAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCA
1 CAATGTGCTGA-TTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCA
* * *
4569 AGGCCAGCTACATTGGAC-TTAAAGATAAAGGTGC
65 AGGCCAGCTATATTGGACTTTAAAGGT-GAGGTGC
* * *
4603 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
4639 GAAGGGTTGC
Statistics
Matches: 491, Mismatches: 23, Indels: 20
0.92 0.04 0.04
Matches are distributed among these distances:
91 1 0.00
92 41 0.08
93 2 0.00
94 39 0.08
97 8 0.02
98 390 0.79
99 10 0.02
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (98 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTTAAAGGTGAGGTGC
Found at i:4307 original size:147 final size:147
Alignment explanation
Indices: 4010--4643 Score: 838
Period size: 147 Copynumber: 4.3 Consensus size: 147
4000 AAGATGAGAA
* * * * *
4010 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAGGTGCCAATA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT-G-AAGGTGCCAATA
* * *
4075 TGCTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAAGGCCA
63 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCA
4134 GCTACATTGGACTTAAAGA-
128 GCTACATTGGACTTAAAGAT
* *
4153 AGAAGGTGCCAATATGCTAATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATGTG
1 A-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATG
* *
4218 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGC
65 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGC
* * *
4283 TATATTGGACTTTAATGGT
130 TACATTGGAC-TTAAAGAT
* * * ** *
4302 -GAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAAATAAAGGTGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATGC
* * * * * * *
4366 TGATTCAAGGCCAGCTATATTGGACTTTAATGGT-GAGGTGCCAATGTGTTGAGTCAAGGCCAAC
66 TGAGTCAAGGCCAGCTACATTGGAC-TTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGC
4430 TACATTGGACTTAAAGAT
130 TACATTGGACTTAAAGAT
* *
4448 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTTAATGGTG-AGGTGCCAATGTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-TTAAAGGTGAAGGTGCCAATATG
*
4512 CTGAGTTAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGC
65 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGC
4577 TACATTGGACTTAAAGAT
130 TACATTGGACTTAAAGAT
*
4595 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAGAAGG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-AAGG
4644 GTTGCTACCG
Statistics
Matches: 426, Mismatches: 51, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
141 37 0.09
142 2 0.00
143 39 0.09
144 4 0.01
146 15 0.04
147 313 0.73
148 16 0.04
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (147 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGAAGGTGCCAATATGC
TGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATGTGCTGAGTCAAGGCCAGCT
ACATTGGACTTAAAGAT
Found at i:4687 original size:33 final size:31
Alignment explanation
Indices: 4631--4762 Score: 176
Period size: 33 Copynumber: 4.1 Consensus size: 31
4621 CCAGCTATAT
*
4631 TGGGC-TTAGAAGGGTTGCTACCGACTTGTG
1 TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
*
4661 TGGGCTTTAGAGAGTGGTTGCCACCGACTTATG
1 TGGGCTTTAGA-AG-GGTTGCCACCGACTTGTG
*
4694 TGGGCTTTGGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAG--GGTTGCCACCGACTTGTG
*
4727 TGGGCTTTAGGAAGAGTTGCCACCGACTTGTG
1 TGGGCTTTA-GAAGGGTTGCCACCGACTTGTG
4759 TGGG
1 TGGG
4763 TTTTGGGAAG
Statistics
Matches: 90, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
30 5 0.06
31 5 0.06
32 25 0.28
33 51 0.57
34 4 0.04
ACGTcount: A:0.17, C:0.17, G:0.36, T:0.29
Consensus pattern (31 bp):
TGGGCTTTAGAAGGGTTGCCACCGACTTGTG
Found at i:4772 original size:66 final size:67
Alignment explanation
Indices: 4638--4768 Score: 196
Period size: 66 Copynumber: 2.0 Consensus size: 67
4628 TATTGGGCTT
* *
4638 AGAAGGGTTGCTACCGACTTGTGTGGGCTTTAGAGAGTGGTTGCCACCGACTTATGTGGGCTTTG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAGTAGTTGCCACCGACTTATGTGGGCTTTG
4703 GA
66 GA
* *
4705 AGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG-GAAG-AGTTGCCACCGACTTGTGTGGGTTTT
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAG-AGTAGTTGCCACCGACTTATGTGGGCTTT
4767 GG
65 GG
4769 GAAGGGGGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
65 26 0.44
66 29 0.49
67 4 0.07
ACGTcount: A:0.18, C:0.17, G:0.36, T:0.30
Consensus pattern (67 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAGAGAGTAGTTGCCACCGACTTATGTGGGCTTTG
GA
Found at i:4828 original size:35 final size:33
Alignment explanation
Indices: 4777--6026 Score: 821
Period size: 34 Copynumber: 38.8 Consensus size: 33
4767 GGGAAGGGGG
* *
4777 AAAGATGCCACGGAGTTGTGGACTTAAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAA-GAA
*
4811 AAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* * *
4846 AAAGGTGCCACGGAGTTGTGGGCTTAGAAGGAG
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
*
4879 AAATGTGCCACGGAGTTGTGGGCTT-AAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* * *
4909 ---GGTGCCACAGAGTTGTGGACTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAA-AGAA
*
4940 AAAGGGTGCCACGGAGTTGTGGGCTT-CAAAG--
1 AAA-GGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
4971 ---GGTGCCACGGAGTTGTGGACTTAAAGATG-A
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-AAGAA
* *
5001 AAAGAGTGCCACGGAGTTGTGGGCTTTGATAAG--
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* * *
5034 -AAGGTGCCACGGAGTCGTGGACTTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAA-AGAA
* **** *
5068 AAAGAGTGGCTTAAAGTTGTGGGCTTTGAAAAGGGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TT-AAAA-AGAA
* *
5105 AAATAGTTCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAA-GGTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* * *
5140 AAA-GTGCCACGGAGTGGTGGGCTTTGAGAAG-A
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* *
5172 AAAGGTTGCCACGGAATTGTGGGCTTTAAAAG--
1 AAAGG-TGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
5204 ---GGTGCCACGGAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* **
5234 CAAGGGTGCCACGGAGTTGTGGGCTTAAATGGATA
1 -AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGA-A
*
5269 AAAGAGTGCCACGAAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* * * *
5304 AAACGTGCCACGGAGTTGTGGGCTTAGAAGGAG
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
5337 AAAGGTGCCACGGAGTTGTGGGCTT-AAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
*
5367 ---GGTGCCACGGAGTTGTGGGCTT-ACAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* * *
5394 ---GGTTCCACGGAGTTGTGGACTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAA-AGAA
5425 AAAGAGTGCCACGGAGTTGTGGGCTT-AAAAG--
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
5456 ---GGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-AAGAA
* * * *
5487 AAAAGTGCCACAGAGTTGTGGGCTTTGATAAG--
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* ** *
5519 -AAGGTGCCACGGAGTCGTGGAATTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGG-GCTTAAAA-AGAA
* *
5553 AAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TT-AAAA-AGAA
* *
5590 AAATAGTTCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAA-GGTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* * *
5625 AAA-GTGCCACGGAGTGGTGGGCTTTGAGAAGAA
1 AAAGGTGCCACGGAGTTGTGGGC-TTAAAAAGAA
* * *
5658 AAAGGTTGCCATGGAATTGTGGGCTTTAAAAG--
1 AAAGG-TGCCACGGAGTTGTGGGCTTAAAAAGAA
* * *
5690 ---GGTGCCACGTAGTTGTGGACTTAAAAGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* * * **
5720 CAAGGGTGCCATGGAGTTATGGGCTTAAATGGATA
1 -AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGA-A
5755 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAG-GTGCCACGGAGTTGTGGGC-TTAAAAAGAA
5790 AAAGGTGCCACGGAGTTGTGGGCTT-AAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
*
5820 ---GGTGCCACGGAGTTGTGGACTT-AAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
* * *
5847 ---GGTGCCACGGAGTTATGGACTTAAAAGGGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAA-AGAA
* * *
5878 AAGGAGTGCCACAGAGTTGTGGGCTTAAAAGGGAA
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAA-AGAA
*
5913 AAAGAGTGCCACAGAGTTGTGGGCTT-AAAAG--
1 AAAG-GTGCCACGGAGTTGTGGGCTTAAAAAGAA
* *
5944 ---GGTGCCACGGAGTTGTGGACTTAAAGATGAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAAA-AAGAA
*
5975 AAAAGTGCCACGGAGTTGTGGGCTT-AAAAG--
1 AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
6005 ---GGTGCCACGGAGTTGTGGGCTT
1 AAAGGTGCCACGGAGTTGTGGGCTT
6027 TGTTAAGAAG
Statistics
Matches: 986, Mismatches: 143, Indels: 181
0.75 0.11 0.14
Matches are distributed among these distances:
27 193 0.20
28 57 0.06
29 13 0.01
31 43 0.04
32 22 0.02
33 130 0.13
34 208 0.21
35 199 0.20
36 61 0.06
37 60 0.06
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (33 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAAAAAGAA
Found at i:4921 original size:27 final size:27
Alignment explanation
Indices: 4883--5065 Score: 123
Period size: 27 Copynumber: 6.0 Consensus size: 27
4873 AAGGAGAAAT
*
4883 GTGCCACGGAGTTGTGGGCTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
*
4910 GTGCCACAGAGTTGTGGACTTAAAAGGGAAAAAGG
1 GTGCCACGGAGTTGTGGACTT--------AAAAGG
* *
4945 GTGCCACGGAGTTGTGGGCTTCAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
4972 GTGCCACGGAGTTGTGGACTTAAAGATGAAAAG
1 GTGCCACGGAGTTGTGGACTTAAA-A-G----G
* *
5005 AGTGCCACGGAGTTGTGGGCTTTGATAAGAAG
1 -GTGCCACGGAGTTGTGGAC-TT-A-AA-AGG
*
5037 GTGCCACGGAGTCGTGGACTTTAAAAGG
1 GTGCCACGGAGTTGTGGAC-TTAAAAGG
5065 G
1 G
5066 AAAAAGAGTG
Statistics
Matches: 126, Mismatches: 12, Indels: 35
0.73 0.07 0.20
Matches are distributed among these distances:
27 46 0.37
28 4 0.03
29 3 0.02
30 1 0.01
31 20 0.16
32 1 0.01
33 1 0.01
34 18 0.14
35 27 0.21
36 1 0.01
37 4 0.03
ACGTcount: A:0.27, C:0.14, G:0.37, T:0.21
Consensus pattern (27 bp):
GTGCCACGGAGTTGTGGACTTAAAAGG
Found at i:4961 original size:62 final size:61
Alignment explanation
Indices: 4844--6026 Score: 606
Period size: 62 Copynumber: 18.4 Consensus size: 61
4834 CTTTAAAAAG
* * * *
4844 AAAAAGGTGCCACGGAGTTGTGGGCTTAGAAGGAGAAA-TGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTT
* *
4904 AAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGAAAAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAA-GGAAAAAGGGTGCCACGGAGTTGTGGGCTT
* * * *
4966 CAAAGGGTGCCACGGAGTTGTGGACTTAAAGATG-AAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAA-AGGAAAAAGGGTGCCACGGAGTTGTGGGC-TT
* * * * * ****
5028 GATAAGAAGGTGCCACGGAGTCGTGGACTTTAAAAGGGAAAAAGAGTGGCTTAAAGTTGTGGGCT
1 -A-AA-AGGGTGCCACGGAGTTGTGGGC-TTAAAA-GGAAAAAGGGTGCCACGGAGTTGTGGGC-
5093 TT
60 TT
* *
5095 GAAAAGGGAAAAATAGTTCCACGGAGTTGTGGGCTTTAAAAAGAAAAA--GTGCCACGGAGTGGT
1 -AAAAGGG-----T-G--CCACGGAGTTGTGGGC-TTAAAAGGAAAAAGGGTGCCACGGAGTTGT
5158 GGGCTTT
56 GGGC-TT
* * * *
5165 GAGAAGAAAAGGTTGCCACGGAATTGTGGGCTT------TAAAAGGGTGCCACGGAGTTGTGGAC
1 ------AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGC
5224 TT
60 TT
* * *
5226 AAAAGGAACAAGGGTGCCACGGAGTTGTGGGCTTAAATGGATAAAAGAGTGCCACGAAGTTGTGG
1 ------AA-AAGGGTGCCACGGAGTTGTGGGCTTAAAAGGA-AAAAGGGTGCCACGGAGTTGTGG
5291 GCTTT
58 GC-TT
* * *
5296 AAAAAGAAAAACGTGCCACGGAGTTGTGGGCTTAGAAGGAGAAA-GGTGCCACGGAGTTGTGGGC
1 -AAAAG-----GGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGC
5360 TT
60 TT
* * *
5362 AAAAGGGTGCCACGGAGTTGTGGGCTT-------ACAAGGGTTCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTT
5416 AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTT-------AAAAGGGTGCCACGGAGTTGTGG
1 AAAA--G-----G-GTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGG
*
5474 ACTT
58 GCTT
* * ** * * *
5478 AAAGATGAAAAAAGTGCCACAGAGTTGTGGGCTT-TGA-TAAGAA-GGTGCCACGGAGTCGTGGA
1 AAA-A-G-----GGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGG-
**
5540 ATTT
58 GCTT
* ** *
5544 AAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAATAGTTCCACGGAGTTG
1 AAAA--G-----G-GTGCCACGGAGTTGTGGGC-TT-AAAA-GGAAAAAGGGTGCCACGGAGTTG
5609 TGGGCTTT
55 TGGGC-TT
* * * * * *
5617 AAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTGAGAA-GAAAAAGGTTGCCATGGAATTGTGGG
1 -AAAAG----GGTGCCACGGAGTTGTGGGC-TT-AAAAGGAAAAAGGGTGCCACGGAGTTGTGGG
5681 CTTT
59 C-TT
* * * * *
5685 AAAAGGGTGCCACGTAGTTGTGGACTTAAAAGGAACAAGGGTGCCATGGAGTTATGGGCTTAAAT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGC-----T
5750 GGAT
61 ---T
* *
5754 AAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAA-GGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGGC-TTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTT
* * *
5815 AAAAGGGTGCCACGGAGTTGTGGACTT-------AAAAGGGTGCCACGGAGTTATGGACTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTT
* * *
5869 AAAAGGGAAAAGGAGTGCCACAGAGTTGTGGGCTTAAAAGGGAAAAAGAGTGCCACAGAGTTGTG
1 -------AAAAGG-GTGCCACGGAGTTGTGGGCTTAAAA-GGAAAAAGGGTGCCACGGAGTTGTG
5934 GGCTT
57 GGCTT
* * *
5939 AAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAA-AGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTTAAA-AGGAAAAAGGGTGCCACGGAGTTGTGGGCTT
6000 AAAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGGCTT
6027 TGTTAAGAAG
Statistics
Matches: 915, Mismatches: 116, Indels: 183
0.75 0.10 0.15
Matches are distributed among these distances:
53 6 0.01
54 44 0.05
56 1 0.00
60 54 0.06
61 138 0.15
62 219 0.24
63 25 0.03
64 6 0.01
65 49 0.05
66 28 0.03
67 82 0.09
68 29 0.03
69 90 0.10
70 79 0.09
71 5 0.01
72 11 0.01
73 38 0.04
74 4 0.00
75 7 0.01
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTT
Found at i:5253 original size:294 final size:294
Alignment explanation
Indices: 4790--5848 Score: 819
Period size: 294 Copynumber: 3.5 Consensus size: 294
4780 GATGCCACGG
4790 AGTTGTGGACTTAAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCC
1 AGTTGTGGACTTAAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCC
* * *
4855 ACGGAGTTGTGGGCTTAGAAGGAGAAATGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACAGA
66 ACGGAGTGGTGGGCTTAGAAGGAGAAAGGTGCCACGGAATTGTGGGCTTAAAAGGGTGCCACAGA
*
4920 GTTGTGGACTTAAAAGGGAAAAAGGGTGCCACGGAGTTGTGGGCTTCAAA-G-G-GTGCCACGGA
131 GTTGTGGACTTAAAAGGGAAAAAGGGTGCCACGGAGTTGTGGGCTT-AAAGGAGAGTGCCACGAA
* *
4982 GTTGTGGAC-TTAAAGATGAAAAGA-GTGCCACGGAGTTGTGGGCTTTGATA-AG-AAGGTGCCA
195 GTTGTGGACTTTAAA-AAGAAAA-ACGTGCCACGGAGTTGTGGGCTTAGA-AGAGAAAGGTGCCA
5043 CGGAGTCGTGGACTTTAAAAGGGAAAAAGAGTGGCTTAA
257 CGGAGTCGTGGAC-TTAAAAGGGAAAAAGAGTGGCTTAA
* * * * *
5082 AGTTGTGGGCTTTGAAAAGGGAAAAATAGTTCCACGGAGTTGTGGGCTTTAAAAAGAAAAA-GTG
1 AGTTGTGGAC-TT-AAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTG
5146 CCACGGAGTGGTGGGCTTTGAGAA-GA-AAAGGTTGCCACGGAATTGTGGGCTTTAAAAGGGTGC
64 CCACGGAGTGGTGGGC-TT-AGAAGGAGAAAGG-TGCCACGGAATTGTGGGC-TTAAAAGGGTGC
* *
5209 CACGGAGTTGTGGACTTAAAA-GGAACAAGGGTGCCACGGAGTTGTGGGCTTAAATGGATAAAAG
125 CACAGAGTTGTGGACTTAAAAGGGAAAAAGGGTGCCACGGAGTTGTGGGCTTAAA-GG-----AG
*
5273 AGTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAACGTGCCACGGAGTTGTGGGCTTAGAAGGAGA
184 AGTGCCACGAAGTTGTGGACTTTAAAAAGAAAAACGTGCCACGGAGTTGTGGGCTTAGAA-GAGA
* * *** *
5338 AAGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGGCTTACAAGGGTTCCA
248 AAGGTGCCACGGAGTCGTGGACTTAAAA-GG-G--AAAAAG-AGT-GGCTT---A-------A
* *
5401 CGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AAAAG-----GGT
1 ---AGTTGTGGACTTAAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGT
* * * * * * *
5459 GCCACGGAGTTGTGGACTTA-AAGATGAAAAAAGTGCCACAGAGTTGTGGGCTTTGATAAGAAGG
63 GCCACGGAGTGGTGGGCTTAGAAG--GAGAAAGGTGCCACGGAATTGTGGGC-TT-A-AA-AGGG
* * * * *
5523 TGCCACGGAGTCGTGGAATTTAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGGG
122 TGCCACAGAGTTGTGG-ACTTAAAAGGGAAAAAGGGTGCCACGGAGTTGTGGGC-TT--AAA-GG
* * * * *
5588 AAAAATAGTTCCACGGAGTTGTGGGCTTTAAAAAGAAAAA-GTGCCACGGAGTGGTGGGCTTTGA
182 ----AGAGTGCCACGAAGTTGTGGACTTTAAAAAGAAAAACGTGCCACGGAGTTGTGGGC-TT-A
* * * * * * ****
5652 GAAGAAAAAGGTTGCCATGGAATTGTGGGCTTTAAAA--G-----G-GTGCCACGT
241 GAAGAGAAAGG-TGCCACGGAGTCGTGGAC-TTAAAAGGGAAAAAGAGTGGCTTAA
* * ** * **
5700 AGTTGTGGACTT-AAAAGGAACAAGGGTGCCATGGAGTTATGGGC-TTAAATGGATAAAAGAGTG
1 AGTTGTGGACTTAAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGA-AAAAG-GTG
* * * * *
5763 CCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCAC
64 CCACGGAGTGGTGGGC-TTAGAAGGAGAAAGGTGCCACGGAATTGTGGGCTTAAAAGGGTGCCAC
*
5828 GGAGTTGTGGACTTAAAAGGG
128 AGAGTTGTGGACTTAAAAGGG
5849 TGCCACGGAG
Statistics
Matches: 639, Mismatches: 62, Indels: 126
0.77 0.07 0.15
Matches are distributed among these distances:
292 9 0.01
293 27 0.04
294 93 0.15
295 66 0.10
296 15 0.02
298 10 0.02
299 18 0.03
300 2 0.00
301 4 0.01
302 49 0.08
303 55 0.09
304 25 0.04
305 3 0.00
307 3 0.00
308 2 0.00
309 7 0.01
310 2 0.00
311 2 0.00
312 3 0.00
313 2 0.00
314 38 0.06
315 5 0.01
316 2 0.00
317 18 0.03
318 12 0.02
319 29 0.05
320 51 0.08
321 47 0.07
322 34 0.05
323 6 0.01
ACGTcount: A:0.31, C:0.12, G:0.35, T:0.22
Consensus pattern (294 bp):
AGTTGTGGACTTAAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCC
ACGGAGTGGTGGGCTTAGAAGGAGAAAGGTGCCACGGAATTGTGGGCTTAAAAGGGTGCCACAGA
GTTGTGGACTTAAAAGGGAAAAAGGGTGCCACGGAGTTGTGGGCTTAAAGGAGAGTGCCACGAAG
TTGTGGACTTTAAAAAGAAAAACGTGCCACGGAGTTGTGGGCTTAGAAGAGAAAGGTGCCACGGA
GTCGTGGACTTAAAAGGGAAAAAGAGTGGCTTAA
Found at i:5374 original size:27 final size:27
Alignment explanation
Indices: 5308--5875 Score: 191
Period size: 27 Copynumber: 18.0 Consensus size: 27
5298 AAAGAAAAAC
5308 GTGCCACGGAGTTGTGGGCTTAGAAGGAGAAAG
1 GTGCCACGGAGTTGTGGGCTTA-AA--AG---G
5341 GTGCCACGGAGTTGTGGGCTTAAAAGG
1 GTGCCACGGAGTTGTGGGCTTAAAAGG
*
5368 GTGCCACGGAGTTGTGGGCTTACAAGG
1 GTGCCACGGAGTTGTGGGCTTAAAAGG
* *
5395 GTTCCACGGAGTTGTGGACTTAAAAGGGAAAAAG
1 GTGCCACGGAGTTGTGGGCTTAAAA--G-----G
5429 AGTGCCACGGAGTTGTGGGCTTAAAAGG
1 -GTGCCACGGAGTTGTGGGCTTAAAAGG
* *
5457 GTGCCACGGAGTTGTGGACTTAAAGATGAAAAAA
1 GTGCCACGGAGTTGTGGGCTTAAA-A-G-----G
* *
5491 GTGCCACAGAGTTGTGGGCTTTGATAAGAAG
1 GTGCCACGGAGTTGTGGGC-TT-A-AA-AGG
* **
5522 GTGCCACGGAGTCGTGGAATTTAAAAGGGAAAAAG
1 GTGCCACGGAGTTGTGG-GCTTAAAA--G-----G
*
5557 AGTGCCACAGAGTTGTGGGCTTTGAAAAGG
1 -GTGCCACGGAGTTGTGGGC-TT-AAAAGG
*
5587 GAAAAATAGTTCCACGGAGTTGTGGGCTTTAAAAAGAAAAA
1 G-----T-G--CCACGGAGTTGTGGGC-TT-AAAAG----G
*
5628 GTGCCACGGAGTGGTGGGCTTTGAGAAGAAAAAGG
1 GTGCCACGGAGTTGTGGGC-TT-------AAAAGG
* * *
5663 TTGCCATGGAATTGTGGGCTTTAAAAGG
1 GTGCCACGGAGTTGTGGGC-TTAAAAGG
* *
5691 GTGCCACGTAGTTGTGGACTTAAAAGGAACAAGG
1 GTGCCACGGAGTTGTGGGCTT------AA-AAGG
* * *
5725 GTGCCATGGAGTTATGGGCTTAAATGGATAAAAGA
1 GTGCCACGGAGTTGTGGGC-----T---TAAAAGG
5760 GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG
1 GTGCCACGGAGTTGTGGGC-TT-AAAAG-----G
5794 GTGCCACGGAGTTGTGGGCTTAAAAGG
1 GTGCCACGGAGTTGTGGGCTTAAAAGG
*
5821 GTGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGGCTTAAAAGG
* *
5848 GTGCCACGGAGTTATGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGGCTTAAAAGG
5875 G
1 G
5876 AAAAGGAGTG
Statistics
Matches: 421, Mismatches: 46, Indels: 142
0.69 0.08 0.23
Matches are distributed among these distances:
27 128 0.30
28 24 0.06
29 10 0.02
30 4 0.01
31 18 0.04
32 7 0.02
33 45 0.11
34 57 0.14
35 67 0.16
36 21 0.05
37 31 0.07
39 7 0.02
41 1 0.00
42 1 0.00
ACGTcount: A:0.30, C:0.13, G:0.35, T:0.22
Consensus pattern (27 bp):
GTGCCACGGAGTTGTGGGCTTAAAAGG
Found at i:5413 original size:485 final size:484
Alignment explanation
Indices: 4777--6027 Score: 1957
Period size: 485 Copynumber: 2.6 Consensus size: 484
4767 GGGAAGGGGG
* *
4777 AAAGA-TGCCACGGAGTTGTGGAC-TTAAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA-GAAAAA-AGTGCCACGGAGTTGTGGGC-TT--
* *
4840 AAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAGAAGGAGAAATGTGCCACGGAGTTGTGGGCTTA
61 AAAGAGAAAGGTGCCACGGAGTTGTGGGCTTA-AA--AG---GGTGCCACGGAGTTGTGGGCTTA
* *
4905 AAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGAAAAAGGGTGCCACGGAGTTGTGGGCTTCAAA
120 AAAGGGTGCCACAGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAA
*
4970 GGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAGAGTGCCACGGAGTTGTGGGCTTTGATAAGA
185 GGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGATAAGA
* **
5035 AGGTGCCACGGAGTCGTGGACTTTAAAAGGGAAAAAGAGTGGCTTAAAGTTGTGGGCTTTGAAAA
250 AGGTGCCACGGAGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTGAAAA
5100 GGGAAAAATAGTTCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTT
315 GGGAAAAATAGTTCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTT
5165 GAGAAG-AAAAGGTTGCCACGGAATTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAA
380 GAGAAGAAAAAGGTTGCCACGGAATTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAA
*
5229 AGGAACAAGGGTGCCACGGAGTTGTGGGCTTAAATGGATA
445 AGGAACAAGGGTGCCACGGAGTTATGGGCTTAAATGGATA
* *
5269 AAAGAGTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAACGTGCCACGGAGTTGTGGGCTTAGAAG
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTA-AA-
* *
5334 GAGAAAGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGGCTTACAAGGGTTC
64 GAGAAAGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGC
*
5399 CACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCAC
129 CACAGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCAC
*
5464 GGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACAGAGTTGTGGGCTTTGATAAGAAGGTGCCAC
194 GGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGATAAGAAGGTGCCAC
* *
5529 GGAGTCGTGGAATTTAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAT
259 GGAGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTGAAAAGGGAAAAAT
5594 AGTTCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTGAGAAGAAA
324 AGTTCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTGAGAAGAAA
* *
5659 AAGGTTGCCATGGAATTGTGGGCTTTAAAAGGGTGCCACGTAGTTGTGGACTTAAAAGGAACAAG
389 AAGGTTGCCACGGAATTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAG
*
5724 GGTGCCATGGAGTTATGGGCTTAAATGGATA
454 GGTGCCACGGAGTTATGGGCTTAAATGGATA
*
5755 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTAAA-A
1 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAGA
* * *
5819 G---GGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTATGGACTTAAAAGGGAAAAG
66 GAAAGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGGCTT-------AAAAG
* *
5881 GAGTGCCACAGAGTTGTGGGCTTAAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAAAGGG
124 G-GTGCCACAGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGG
*
5946 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGC-TT-A-AA-AGGG
188 TGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGATAAGAAGG
* *
6007 TGCCACGGAGTTGTGGGCTTT
253 TGCCACGGAGTCGTGGACTTT
6028 GTTAAGAAGG
Statistics
Matches: 709, Mismatches: 37, Indels: 34
0.91 0.05 0.04
Matches are distributed among these distances:
480 46 0.06
483 2 0.00
484 21 0.03
485 280 0.39
486 154 0.22
487 7 0.01
488 112 0.16
489 1 0.00
490 4 0.01
491 30 0.04
492 23 0.03
493 22 0.03
494 7 0.01
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (484 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTAAAGA
GAAAGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCA
CAGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACGG
AGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGATAAGAAGGTGCCACGG
AGTCGTGGACTTTAAAAGGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTGAAAAGGGAAAAATAG
TTCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGTGCCACGGAGTGGTGGGCTTTGAGAAGAAAAA
GGTTGCCACGGAATTGTGGGCTTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGAACAAGGG
TGCCACGGAGTTATGGGCTTAAATGGATA
Found at i:5455 original size:89 final size:87
Alignment explanation
Indices: 5311--5478 Score: 282
Period size: 89 Copynumber: 1.9 Consensus size: 87
5301 GAAAAACGTG
* * *
5311 CCACGGAGTTGTGGGCTTAGAAGGAGAAAGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACG
1 CCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACG
*
5376 GAGTTGTGGGCTTACAAGGGTT
66 GAGTTGTGGACTTACAAGGGTT
5398 CCACGGAGTTGTGGACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCA
1 CCACGGAGTTGTGGACTTAAAA-GGAAAAAG-GTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCA
5463 CGGAGTTGTGGACTTA
64 CGGAGTTGTGGACTTA
5479 AAGATGAAAA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
87 20 0.27
88 7 0.09
89 48 0.64
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (87 bp):
CCACGGAGTTGTGGACTTAAAAGGAAAAAGGTGCCACGGAGTTGTGGGCTTAAAAGGGTGCCACG
GAGTTGTGGACTTACAAGGGTT
Found at i:5943 original size:27 final size:27
Alignment explanation
Indices: 5912--6026 Score: 131
Period size: 27 Copynumber: 4.0 Consensus size: 27
5902 TTAAAAGGGA
*
5912 AAAAGAGTGCCACAGAGTTGTGGGCTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTT
* *
5939 AAAAGGGTGCCACGGAGTTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTT
5966 AAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTT
1 AAA-A-G-----AGTGCCACGGAGTTGTGGGCTT
*
6000 AAAAGGGTGCCACGGAGTTGTGGGCTT
1 AAAAGAGTGCCACGGAGTTGTGGGCTT
6027 TGTTAAGAAG
Statistics
Matches: 75, Mismatches: 6, Indels: 14
0.79 0.06 0.15
Matches are distributed among these distances:
27 48 0.64
28 1 0.01
29 1 0.01
32 1 0.01
33 1 0.01
34 23 0.31
ACGTcount: A:0.29, C:0.14, G:0.36, T:0.22
Consensus pattern (27 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTT
Found at i:5991 original size:61 final size:59
Alignment explanation
Indices: 5753--6022 Score: 289
Period size: 61 Copynumber: 4.4 Consensus size: 59
5743 CTTAAATGGA
* * *
5753 TAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCT
1 TAAAAGGGTGCCACGGAGTTGTGGAC-TT-AAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
* * *
5814 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAG-----GGTGCCACGGAGTTATGGACT
1 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
* * *
5868 TAAAAGGGAAAAGGAGTGCCACAGAGTTGTGGGCTTAAAAGGGAAAAAGAGTGCCACAGAGTTGT
1 T-------AAAAGG-GTGCCACGGAGTTGTGGACTTAAAA--GAAAAA-AGTGCCACGGAGTTGT
5933 GGGCT
55 GGGCT
5938 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCT
1 TAAAAGGGTGCCACGGAGTTGTGGACTTAAA-A-GAAAAAAGTGCCACGGAGTTGTGGGCT
5999 TAAAAGGGTGCCACGGAGTTGTGG
1 TAAAAGGGTGCCACGGAGTTGTGG
6023 GCTTTGTTAA
Statistics
Matches: 178, Mismatches: 14, Indels: 34
0.79 0.06 0.15
Matches are distributed among these distances:
54 20 0.11
59 5 0.03
60 2 0.01
61 74 0.42
62 51 0.29
63 7 0.04
64 1 0.01
70 18 0.10
ACGTcount: A:0.31, C:0.13, G:0.36, T:0.20
Consensus pattern (59 bp):
TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCT
Found at i:9275 original size:19 final size:19
Alignment explanation
Indices: 9231--9286 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
9221 CTGCCAGTTT
**
9231 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
9251 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
9270 CATGTATCGATACAATG
1 CATGTATCGATACAATG
9287 TATCAATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.16, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:9313 original size:33 final size:32
Alignment explanation
Indices: 9252--9316 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
9242 ACAATTGTGC
* * *
9252 ATGTATCGATACAATGAACATGTATCGATACA
1 ATGTATCAATACAAAGAAAATGTATCGATACA
9284 ATGTATCAATACAAAGCAAAATGTATCGATACA
1 ATGTATCAATACAAAG-AAAATGTATCGATACA
9317 TCTAGATATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.45, C:0.15, G:0.14, T:0.26
Consensus pattern (32 bp):
ATGTATCAATACAAAGAAAATGTATCGATACA
Found at i:10347 original size:20 final size:20
Alignment explanation
Indices: 10322--10359 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
10312 GTAAAAAGAC
*
10322 AGAATGTATCGACACATTGG
1 AGAATGTAACGACACATTGG
*
10342 AGAATGTAACGATACATT
1 AGAATGTAACGACACATT
10360 CATACATGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (20 bp):
AGAATGTAACGACACATTGG
Found at i:20041 original size:2 final size:2
Alignment explanation
Indices: 20027--20067 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
20017 TAGCCTATTT
* *
20027 TG TG TG GG T- TG TG TG TG TG TG TG TG TG TG TG TG TG CG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
20068 GACATAACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.00, C:0.02, G:0.51, T:0.46
Consensus pattern (2 bp):
TG
Found at i:21276 original size:12 final size:11
Alignment explanation
Indices: 21229--21276 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
21219 GTAAAATTAA
21229 ATTAATTTTAT
1 ATTAATTTTAT
21240 A-TAA--TTAT
1 ATTAATTTTAT
21248 -TTAATTTTAT
1 ATTAATTTTAT
21258 ATATAATTTATAT
1 AT-TAATTT-TAT
21271 ATTAAT
1 ATTAAT
21277 AAATTAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
8 7 0.23
10 7 0.23
11 2 0.06
12 10 0.32
13 5 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTAATTTTAT
Found at i:21467 original size:15 final size:15
Alignment explanation
Indices: 21435--21492 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
21425 TTTATTTATT
21435 TAAAAAATTAATAAAA
1 TAAAAAATTAAT-AAA
21451 TAAAAAA-T-AT-AA
1 TAAAAAATTAATAAA
*
21463 TAATAAATTAAATAAA
1 TAAAAAATT-AATAAA
*
21479 T-ATAAATTAATAAA
1 TAAAAAATTAATAAA
21493 AATTATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
12 8 0.22
13 1 0.03
14 8 0.22
15 10 0.27
16 10 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TAAAAAATTAATAAA
Found at i:21505 original size:15 final size:15
Alignment explanation
Indices: 21437--21515 Score: 52
Period size: 16 Copynumber: 4.7 Consensus size: 15
21427 TATTTATTTA
21437 AAAAATTA-ATAAAAT
1 AAAAATTATA-AAAAT
21452 AAAAAATATAATAATAAATT
1 -AAAAAT-T-ATAA-AAA-T
*
21472 AAATAAATATAAATTAAT
1 AAA-AATTATAAA--AAT
21490 AAAAATTATAAAAAT
1 AAAAATTATAAAAAT
21505 ATAAAATTATA
1 A-AAAATTATA
21516 TAATTTTATA
Statistics
Matches: 52, Mismatches: 2, Indels: 18
0.72 0.03 0.25
Matches are distributed among these distances:
15 4 0.08
16 15 0.29
17 10 0.19
18 10 0.19
19 10 0.19
20 3 0.06
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAAATTATAAAAAT
Found at i:21540 original size:20 final size:20
Alignment explanation
Indices: 21502--21550 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
21492 AAATTATAAA
* *
21502 AATATAAAATTATATAATTT
1 AATATAAAATAATATAATTG
*
21522 TATATAAAATAAGTA-AATTG
1 AATATAAAATAA-TATAATTG
21542 AATATAAAA
1 AATATAAAA
21551 CTGTATTAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 22 0.92
21 2 0.08
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (20 bp):
AATATAAAATAATATAATTG
Found at i:23571 original size:29 final size:29
Alignment explanation
Indices: 23531--23595 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
23521 TAAAGTAACT
*
23531 CTAAAATGCATGAAATTATATAATAATAA
1 CTAAAATACATGAAATTATATAATAATAA
* *
23560 CTAAAATACATGAAATTATATAGTAATCA
1 CTAAAATACATGAAATTATATAATAATAA
23589 CTAAAAT
1 CTAAAAT
23596 GCACAGAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.54, C:0.09, G:0.06, T:0.31
Consensus pattern (29 bp):
CTAAAATACATGAAATTATATAATAATAA
Found at i:23642 original size:29 final size:29
Alignment explanation
Indices: 23589--23651 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
23579 ATAGTAATCA
* * *
23589 CTAAAATGCACAGAATGATATAAAAGTTC
1 CTAAAATGCACAGAATGACAAAAAAATTC
*
23618 CTAAAATGCA-AGAAATGACAAAAAAATTT
1 CTAAAATGCACAG-AATGACAAAAAAATTC
23647 CTAAA
1 CTAAA
23652 TCATAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.54, C:0.13, G:0.11, T:0.22
Consensus pattern (29 bp):
CTAAAATGCACAGAATGACAAAAAAATTC
Found at i:23664 original size:58 final size:57
Alignment explanation
Indices: 23602--23752 Score: 151
Period size: 58 Copynumber: 2.6 Consensus size: 57
23592 AAATGCACAG
* *
23602 AATGATATAAAAGTTCCTAAAATGCAAGAAATGACAAAAAAATTTCTAAATCATAAAA
1 AATGATTTAAAAGTTCC-AAAATGCATGAAATGACAAAAAAATTTCTAAATCATAAAA
* * * * * * *
23660 AATGACTTTAATA-TCTCCAAAATACATGAAATGATATAATAATTTGTAAATCATAGAA
1 AATGA-TTTAAAAGT-TCCAAAATGCATGAAATGACAAAAAAATTTCTAAATCATAAAA
* * * *
23718 ACTGATTTAAATGTACCCAAATGCATGAAATGACA
1 AATGATTTAAAAGTTCCAAAATGCATGAAATGACA
23753 TAATAATCTT
Statistics
Matches: 74, Mismatches: 16, Indels: 7
0.76 0.16 0.07
Matches are distributed among these distances:
57 22 0.30
58 44 0.59
59 8 0.11
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (57 bp):
AATGATTTAAAAGTTCCAAAATGCATGAAATGACAAAAAAATTTCTAAATCATAAAA
Found at i:23756 original size:57 final size:58
Alignment explanation
Indices: 23620--23759 Score: 167
Period size: 58 Copynumber: 2.4 Consensus size: 58
23610 AAAAGTTCCT
* * *
23620 AAAATGCAAGAAATGACAAAAAAATTTCTAAATCATAAAAAATGACTTTAATATCTCC
1 AAAATGCATGAAATGACATAATAATTTCTAAATCATAAAAAATGACTTTAATATCTCC
* * * * * *
23678 AAAATACATGAAATGATATAATAATTTGTAAATCATAGAAACTGA-TTTAA-ATGTACC
1 AAAATGCATGAAATGACATAATAATTTCTAAATCATAAAAAATGACTTTAATATCT-CC
*
23735 CAAATGCATGAAATGACATAATAAT
1 AAAATGCATGAAATGACATAATAAT
23760 CTTTAGTATA
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
56 3 0.04
57 29 0.42
58 37 0.54
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.28
Consensus pattern (58 bp):
AAAATGCATGAAATGACATAATAATTTCTAAATCATAAAAAATGACTTTAATATCTCC
Found at i:28018 original size:13 final size:13
Alignment explanation
Indices: 28000--28024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27990 CAAAGATCAG
28000 TGTATCGATACAA
1 TGTATCGATACAA
28013 TGTATCGATACA
1 TGTATCGATACA
28025 TTTGAGTAAT
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:28087 original size:13 final size:13
Alignment explanation
Indices: 28069--28120 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
28059 AGCTTCGTAG
28069 CGATACATTGTAT
1 CGATACATTGTAT
28082 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
28101 CGATACATTGTAT
1 CGATACATTGTAT
28114 CGATACA
1 CGATACA
28121 ACACTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:28101 original size:19 final size:19
Alignment explanation
Indices: 28077--28141 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
28067 AGCGATACAT
28077 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
28096 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
*
28109 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
28128 TGTATCGATACAAA
1 TGTATCGATACAAA
28142 TTGTTGAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.28
14 1 0.03
16 2 0.05
18 1 0.03
19 24 0.62
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:28110 original size:32 final size:32
Alignment explanation
Indices: 28069--28139 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
28059 AGCTTCGTAG
28069 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
28101 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
28133 CGATACA
1 CGATACA
28140 AATTGTTGAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Done.