Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007328.1 Corchorus capsularis cultivar CVL-1 contig07349, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 72670
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:2393 original size:33 final size:33
Alignment explanation
Indices: 2323--2430 Score: 139
Period size: 33 Copynumber: 3.3 Consensus size: 33
2313 CGGAGACAAG
2323 ACCGGCCACGCGACATGGACATGGCCGGCCATC-
1 ACCGGCCACGCGACATGGACATGGCCGGCCA-CA
*
2356 ACCGGCCACGCGACATGGACATGGCCGGCTACA
1 ACCGGCCACGCGACATGGACATGGCCGGCCACA
** * *
2389 ACCGGCCAAACGAC-TCGGCCATGCCCGGCCACA
1 ACCGGCCACGCGACAT-GGACATGGCCGGCCACA
2422 ACCGGCCAC
1 ACCGGCCAC
2431 ACGATCCTTT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
32 2 0.03
33 64 0.97
ACGTcount: A:0.23, C:0.42, G:0.28, T:0.07
Consensus pattern (33 bp):
ACCGGCCACGCGACATGGACATGGCCGGCCACA
Found at i:5305 original size:49 final size:49
Alignment explanation
Indices: 5142--5515 Score: 459
Period size: 48 Copynumber: 7.6 Consensus size: 49
5132 TTTACTTACA
* *
5142 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTATTTTACTTGCTG
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTA-T-TTTTACTTGCTT
* * *
5193 TTTCCCGAAATGCCCTTCCCGGACGGAAGGCACTTA-TTTTACTT-ATT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTT
* * * ** * * *
5240 GTTTCCCAAAATGCCCTTTCCGGATGGAAAACACCTATTTTTACATGCTA
1 -TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTT
5290 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTA-TTTTACTTGCTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTT
* *
5338 TTTCCCAGAACGCCCTTCCCAGACGGAAGGCACTTATTTTTACTTGCTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTT
* * * *
5387 TTTCCCTAAACGCCCTTCCCGGACGAAAGGCACTCAATTTTAACTTGCTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACT-TATTTTTACTTGCTT
* * *
5437 TTTCCCTAAACGCCCTTCCCGGACGGAAGGCACTT-CTTTTATTTGCTT
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTT
* **
5485 TTTCCTAAAACGCCCTTCTTGGACGGAAGGC
1 TTTCCCAAAACGCCCTTCCCGGACGGAAGGC
5516 GTTGATTTTA
Statistics
Matches: 281, Mismatches: 37, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
47 1 0.00
48 119 0.42
49 79 0.28
50 47 0.17
51 35 0.12
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.32
Consensus pattern (49 bp):
TTTCCCAAAACGCCCTTCCCGGACGGAAGGCACTTATTTTTACTTGCTT
Found at i:5310 original size:97 final size:98
Alignment explanation
Indices: 5142--5549 Score: 459
Period size: 97 Copynumber: 4.2 Consensus size: 98
5132 TTTACTTACA
* * * *
5142 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACTTATTATTTTACTTGCTGTTTCCCGAAATGCC
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACCTA-TATTTTACTTGCTTTTTCCCAAAACGCC
5207 CTTCCCGGACGGAAGGCACTTATTTTACTT-ATT
65 CTTCCCGGACGGAAGGCACTTATTTTACTTGATT
* * ** * *
5240 GTTTCCCAAAATGCCCTTTCCGGATGGAAAACACCTAT-TTTTACATGCTATTTCCCAAAACGCC
1 -TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACCTATATTTTACTTGCTTTTTCCCAAAACGCC
*
5304 CTTCCCGGACGGAAGGCACTTATTTTACTTGCTT
65 CTTCCCGGACGGAAGGCACTTATTTTACTTGATT
* * * * *
5338 TTTCCCAGAACGCCCTTCCCAGACGGAAGGCACTTAT-TTTTACTTGCTTTTTCCCTAAACGCCC
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACCTATATTTTACTTGCTTTTTCCCAAAACGCCC
* * *
5402 TTCCCGGACGAAAGGCACTCAATTTTAACTTGCTT
66 TTCCCGGACGGAAGGCACT-TATTTT-ACTTGATT
* * * * *
5437 TTTCCCTAAACGCCCTTCCCGGACGGAAGGCA-CT-TCTTTTATTTGCTTTTTCCTAAAACGCCC
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACCTATATTTTACTTGCTTTTTCCCAAAACGCCC
** * *
5500 TTCTTGGACGGAAGGC-GTTGATTTTACTCGATT
66 TTCCCGGACGGAAGGCACTT-ATTTTACTTGATT
* *
5533 TTTCTCAGAATGCCCTT
1 TTTCCCAAAATGCCCTT
5550 TCAAACAAAG
Statistics
Matches: 263, Mismatches: 41, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
96 19 0.07
97 130 0.49
98 46 0.17
99 68 0.26
ACGTcount: A:0.22, C:0.29, G:0.16, T:0.33
Consensus pattern (98 bp):
TTTCCCAAAATGCCCTTCCCGGACGGAAGGCACCTATATTTTACTTGCTTTTTCCCAAAACGCCC
TTCCCGGACGGAAGGCACTTATTTTACTTGATT
Found at i:5754 original size:62 final size:61
Alignment explanation
Indices: 5604--5765 Score: 175
Period size: 63 Copynumber: 2.6 Consensus size: 61
5594 AGCACTTTCG
* * * * * *
5604 ATTTCCCAAAATACCCTTTCGGACAAAGGGAT-GGCTTCGTCACCTTCTTGCATTTAAGTTT
1 ATTTCCCAAAATACCCTTTCGGACAAAGGG-TCAGTTTCGTCACATTCCTGCACTTAAGTCT
* ** *
5665 AGCATTCCCAAAATACCCTTTTAGACAAAGGGTCAGTTTCTTCACATTCCTGCACTT-AGATCCT
1 A--TTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCGTCACATTCCTGCACTTAAG-T-CT
5729 ATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTT
1 ATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTT
5766 AGCCATGTTT
Statistics
Matches: 83, Mismatches: 13, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
61 1 0.01
62 36 0.43
63 44 0.53
64 2 0.02
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (61 bp):
ATTTCCCAAAATACCCTTTCGGACAAAGGGTCAGTTTCGTCACATTCCTGCACTTAAGTCT
Found at i:7168 original size:90 final size:90
Alignment explanation
Indices: 7047--7224 Score: 356
Period size: 90 Copynumber: 2.0 Consensus size: 90
7037 TTCAATGGAA
7047 TTTAATTACATAAACATGCCTGACCAAAAACATAAGCACATAAATGCCATAATCAATATCATATA
1 TTTAATTACATAAACATGCCTGACCAAAAACATAAGCACATAAATGCCATAATCAATATCATATA
7112 CATGCCACATAAAATTCAATCATTC
66 CATGCCACATAAAATTCAATCATTC
7137 TTTAATTACATAAACATGCCTGACCAAAAACATAAGCACATAAATGCCATAATCAATATCATATA
1 TTTAATTACATAAACATGCCTGACCAAAAACATAAGCACATAAATGCCATAATCAATATCATATA
7202 CATGCCACATAAAATTCAATCAT
66 CATGCCACATAAAATTCAATCAT
7225 GCTTCATAAA
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 88 1.00
ACGTcount: A:0.46, C:0.22, G:0.06, T:0.26
Consensus pattern (90 bp):
TTTAATTACATAAACATGCCTGACCAAAAACATAAGCACATAAATGCCATAATCAATATCATATA
CATGCCACATAAAATTCAATCATTC
Found at i:8353 original size:12 final size:12
Alignment explanation
Indices: 8336--8409 Score: 68
Period size: 12 Copynumber: 6.5 Consensus size: 12
8326 CATTAGCAAC
8336 AAAACAACCATG
1 AAAACAACCATG
8348 AAAACAACCATG
1 AAAACAACCATG
* *
8360 AAAACAGCCA-C
1 AAAACAACCATG
*
8371 AATAGCAA-C---
1 AA-AACAACCATG
*
8380 AAAACAGCCATG
1 AAAACAACCATG
8392 AAAACAACCATG
1 AAAACAACCATG
8404 AAAACA
1 AAAACA
8410 GCCACAATAG
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
8 3 0.06
9 3 0.06
11 3 0.06
12 41 0.82
ACGTcount: A:0.58, C:0.26, G:0.09, T:0.07
Consensus pattern (12 bp):
AAAACAACCATG
Found at i:8370 original size:44 final size:44
Alignment explanation
Indices: 8303--8442 Score: 235
Period size: 44 Copynumber: 3.2 Consensus size: 44
8293 AATTAGCAAC
* * * *
8303 AAAACAGCCATGAAAAATAGCCACATTAGCAACAAAACAACCATG
1 AAAACAACCATG-AAAACAGCCACAATAGCAACAAAACAGCCATG
8348 AAAACAACCATGAAAACAGCCACAATAGCAACAAAACAGCCATG
1 AAAACAACCATGAAAACAGCCACAATAGCAACAAAACAGCCATG
8392 AAAACAACCATGAAAACAGCCACAATAGCAACAAAACAGCCATG
1 AAAACAACCATGAAAACAGCCACAATAGCAACAAAACAGCCATG
8436 AAAACAA
1 AAAACAA
8443 ACACTAAAAA
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
44 80 0.88
45 11 0.12
ACGTcount: A:0.56, C:0.26, G:0.11, T:0.08
Consensus pattern (44 bp):
AAAACAACCATGAAAACAGCCACAATAGCAACAAAACAGCCATG
Found at i:8379 original size:24 final size:24
Alignment explanation
Indices: 8352--8423 Score: 82
Period size: 24 Copynumber: 3.2 Consensus size: 24
8342 ACCATGAAAA
8352 CAACCATGAAAACAGCCACAATAG
1 CAACCATGAAAACAGCCACAATAG
* *
8376 CAA-C---AAAACAGCCATGAA-AA
1 CAACCATGAAAACAGCCA-CAATAG
8396 CAACCATGAAAACAGCCACAATAG
1 CAACCATGAAAACAGCCACAATAG
8420 CAAC
1 CAAC
8424 AAAACAGCCA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 14 0.37
21 3 0.08
23 3 0.08
24 18 0.47
ACGTcount: A:0.53, C:0.29, G:0.11, T:0.07
Consensus pattern (24 bp):
CAACCATGAAAACAGCCACAATAG
Found at i:8385 original size:20 final size:20
Alignment explanation
Indices: 8360--8433 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 20
8350 AACAACCATG
8360 AAAACAGCCACAATAGCAAC
1 AAAACAGCCACAATAGCAAC
* *
8380 AAAACAGCCATGAA-AACAACC
1 AAAACAGCCA-CAATAGCAA-C
8401 ATGAAAACAGCCACAATAGCAAC
1 ---AAAACAGCCACAATAGCAAC
8424 AAAACAGCCA
1 AAAACAGCCA
8434 TGAAAACAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
20 24 0.55
21 3 0.07
23 3 0.07
24 14 0.32
ACGTcount: A:0.55, C:0.28, G:0.11, T:0.05
Consensus pattern (20 bp):
AAAACAGCCACAATAGCAAC
Found at i:8428 original size:32 final size:32
Alignment explanation
Indices: 8392--8506 Score: 113
Period size: 32 Copynumber: 3.5 Consensus size: 32
8382 AACAGCCATG
*
8392 AAAACAACCATGAAAACAGCCACAATAGCAAC
1 AAAACAGCCATGAAAACAGCCACAATAGCAAC
** * **
8424 AAAACAGCCATGAAAACAAACACTAAAAAGCCATG
1 AAAACAGCCATGAAAACAGCCAC--AATAG-CAAC
* * * *
8459 AAAACAGCCCTAAAAACAGCGACATTAGCAAC
1 AAAACAGCCATGAAAACAGCCACAATAGCAAC
8491 AAAACAGCCATGAAAA
1 AAAACAGCCATGAAAA
8507 TAAGTACTAT
Statistics
Matches: 63, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
32 36 0.57
33 3 0.05
34 4 0.06
35 20 0.32
ACGTcount: A:0.56, C:0.25, G:0.11, T:0.08
Consensus pattern (32 bp):
AAAACAGCCATGAAAACAGCCACAATAGCAAC
Found at i:8441 original size:12 final size:12
Alignment explanation
Indices: 8424--8478 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
8414 CAATAGCAAC
8424 AAAACAGCCATG
1 AAAACAGCCATG
**
8436 AAAACAAACACT-
1 AAAACAGCCA-TG
8448 AAAA-AGCCATG
1 AAAACAGCCATG
* *
8459 AAAACAGCCCTA
1 AAAACAGCCATG
8471 AAAACAGC
1 AAAACAGC
8479 GACATTAGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
10 1 0.03
11 7 0.21
12 25 0.74
13 1 0.03
ACGTcount: A:0.56, C:0.25, G:0.11, T:0.07
Consensus pattern (12 bp):
AAAACAGCCATG
Found at i:8461 original size:67 final size:68
Alignment explanation
Indices: 8380--8506 Score: 202
Period size: 67 Copynumber: 1.9 Consensus size: 68
8370 CAATAGCAAC
*
8380 AAAACAGCCATGAAAACAACCATGAAAACAGCCACAATAGCAACAAAACAGCCATGAAAACAAAC
1 AAAACAGCCATGAAAACAACCATAAAAACAGCCACAATAGCAACAAAACAGCCATGAAAACAAAC
8445 ACT
66 ACT
* * * *
8448 AAAA-AGCCATGAAAACAGCCCTAAAAACAGCGACATTAGCAACAAAACAGCCATGAAAA
1 AAAACAGCCATGAAAACAACCATAAAAACAGCCACAATAGCAACAAAACAGCCATGAAAA
8507 TAAGTACTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
67 50 0.93
68 4 0.07
ACGTcount: A:0.55, C:0.25, G:0.12, T:0.08
Consensus pattern (68 bp):
AAAACAGCCATGAAAACAACCATAAAAACAGCCACAATAGCAACAAAACAGCCATGAAAACAAAC
ACT
Found at i:12087 original size:29 final size:29
Alignment explanation
Indices: 12042--12100 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
12032 TAGTTTAAAG
*
12042 TAATAAGTTATGCACGTATCTCATGGTTA
1 TAATAAGTTATGCACGTATCTCATGCTTA
* * *
12071 TAATTAGTTATGTACGTATTTCATGCTTA
1 TAATAAGTTATGCACGTATCTCATGCTTA
12100 T
1 T
12101 CGTAGTGTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.12, G:0.15, T:0.44
Consensus pattern (29 bp):
TAATAAGTTATGCACGTATCTCATGCTTA
Found at i:16572 original size:18 final size:18
Alignment explanation
Indices: 16549--16584 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
16539 TAGCATTCAA
16549 TTTAGCAATTAGTTAGAC
1 TTTAGCAATTAGTTAGAC
16567 TTTAGCAATTAGTTAGAC
1 TTTAGCAATTAGTTAGAC
16585 ATGCACAAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (18 bp):
TTTAGCAATTAGTTAGAC
Found at i:19760 original size:26 final size:26
Alignment explanation
Indices: 19730--19816 Score: 90
Period size: 26 Copynumber: 3.2 Consensus size: 26
19720 GTAATCAGTA
19730 AATCAGTAATTAAGTGAAAAGAGATT
1 AATCAGTAATTAAGTGAAAAGAGATT
*
19756 AATCAG-AGTTAAAGT-AATAAGA-ATCAGT
1 AATCAGTAATT-AAGTGAA-AAGAGAT---T
19784 AAATCAGTAATTAAGTGAAAAGAGATT
1 -AATCAGTAATTAAGTGAAAAGAGATT
19811 AATCAG
1 AATCAG
19817 AGTCAAAGTA
Statistics
Matches: 50, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
25 7 0.14
26 20 0.40
27 1 0.02
28 1 0.02
29 14 0.28
30 7 0.14
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.25
Consensus pattern (26 bp):
AATCAGTAATTAAGTGAAAAGAGATT
Found at i:19783 original size:55 final size:55
Alignment explanation
Indices: 19719--19871 Score: 254
Period size: 55 Copynumber: 2.8 Consensus size: 55
19709 CAGTCCGAAC
*
19719 AGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTTAAAGTAAT
1 AGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAAT
19774 AAG-AATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAAT
1 -AGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAAT
* * *
19829 AGTAATCAGTAAATTAGTAGTTAAGTAAAAAGAGATTAATCAG
1 AGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAG
19872 TAAATTGATA
Statistics
Matches: 92, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
54 2 0.02
55 88 0.96
56 2 0.02
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (55 bp):
AGTAATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAGTCAAAGTAAT
Found at i:19825 original size:26 final size:25
Alignment explanation
Indices: 19741--19825 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 25
19731 ATCAGTAATT
19741 AAGTGAAAAGAGATTAATCAGAGTTA
1 AAGTGAAAAGAGATTAATCAGAG-TA
* *
19767 AAGT-AATAAGA-ATCAGTAAATCAGTAATT
1 AAGTGAA-AAGAGAT---T-AATCAG-AGTA
19796 AAGTGAAAAGAGATTAATCAGAGTCA
1 AAGTGAAAAGAGATTAATCAGAGT-A
19822 AAGT
1 AAGT
19826 AATAGTAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 18
0.68 0.06 0.26
Matches are distributed among these distances:
25 6 0.13
26 18 0.39
27 1 0.02
28 1 0.02
29 15 0.33
30 5 0.11
ACGTcount: A:0.51, C:0.06, G:0.20, T:0.24
Consensus pattern (25 bp):
AAGTGAAAAGAGATTAATCAGAGTA
Found at i:19887 original size:34 final size:35
Alignment explanation
Indices: 19831--19958 Score: 106
Period size: 34 Copynumber: 3.7 Consensus size: 35
19821 AAAGTAATAG
*
19831 TAATCAGTAAATT-AGTAGTTAAGTAAAAAGAGAT
1 TAATCAGTAAATTGAGTAATTAAGTAAAAAGAGAT
**
19865 TAATCAGTAAATTGA-TAATTAAG-AGTCAAG-GTAAT
1 TAATCAGTAAATTGAGTAATTAAGTA-AAAAGAG--AT
* * * *
19900 AGTAATCAGTAAA-TCAGTAATCAAGTAAAAAGATAA
1 --TAATCAGTAAATTGAGTAATTAAGTAAAAAGAGAT
19936 TAATCAGTAAATTGA-TAATTAAG
1 TAATCAGTAAATTGAGTAATTAAG
19959 AGTCAAGGTA
Statistics
Matches: 73, Mismatches: 11, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
33 2 0.03
34 41 0.56
35 5 0.07
36 3 0.04
37 21 0.29
38 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.16, T:0.29
Consensus pattern (35 bp):
TAATCAGTAAATTGAGTAATTAAGTAAAAAGAGAT
Found at i:19890 original size:71 final size:71
Alignment explanation
Indices: 19815--19969 Score: 256
Period size: 71 Copynumber: 2.2 Consensus size: 71
19805 GAGATTAATC
* * * * *
19815 AGAGTCAAAGTAATAGTAATCAGTAAATTAGTAGTTAAGTAAAAAGAGATTAATCAGTAAATTGA
1 AGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGAGAATAATCAGTAAATTGA
19880 TAATTA
66 TAATTA
*
19886 AGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGATAATAATCAGTAAATTGA
1 AGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGAGAATAATCAGTAAATTGA
19951 TAATTA
66 TAATTA
19957 AGAGTCAAGGTAA
1 AGAGTCAAGGTAA
19970 GAGATTTATC
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 78 1.00
ACGTcount: A:0.50, C:0.06, G:0.17, T:0.27
Consensus pattern (71 bp):
AGAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAAAAGAGAATAATCAGTAAATTGA
TAATTA
Found at i:19911 original size:37 final size:37
Alignment explanation
Indices: 19865--19969 Score: 112
Period size: 34 Copynumber: 2.9 Consensus size: 37
19855 AAAAAGAGAT
*
19865 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAG
1 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAA
* * **
19902 TAATCAGTAAA-TCAGTAA-TCA-AGT-AA-AAAGATAA
1 TAATCAGTAAATTGA-TAATTAAGAGTCAAGGTA-ATAA
19936 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAA
1 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAA
19970 GAGATTTATC
Statistics
Matches: 52, Mismatches: 9, Indels: 14
0.69 0.12 0.19
Matches are distributed among these distances:
33 1 0.02
34 19 0.37
35 7 0.13
36 7 0.13
37 17 0.33
38 1 0.02
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.28
Consensus pattern (37 bp):
TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAA
Found at i:20191 original size:24 final size:24
Alignment explanation
Indices: 20163--20209 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
20153 GAGATTGGTA
*
20163 ATTAAAGTAGTAATTAAGATTCAT
1 ATTAAAATAGTAATTAAGATTCAT
* *
20187 ATTAAAATGGTAATTGAGATTCA
1 ATTAAAATAGTAATTAAGATTCA
20210 AAGTAAGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36
Consensus pattern (24 bp):
ATTAAAATAGTAATTAAGATTCAT
Found at i:20518 original size:27 final size:27
Alignment explanation
Indices: 20488--20602 Score: 103
Period size: 25 Copynumber: 4.3 Consensus size: 27
20478 TAAAAATGGT
*
20488 AGTAAAAAATGGTAATTAAGTAAAAAG
1 AGTAAAAAATGGTAATTCAGTAAAAAG
* * *
20515 AGTAAAAAGTGGT-ATTCAGTCAAAAC
1 AGTAAAAAATGGTAATTCAGTAAAAAG
* *
20541 AGAAAGAAAATGGGTAA-TCACTAAAAAG
1 AGTAA-AAAAT-GGTAATTCAGTAAAAAG
* * *
20569 AGTAAAATAT-ATAA-TCAGTACAAAG
1 AGTAAAAAATGGTAATTCAGTAAAAAG
20594 AGTAAAAAA
1 AGTAAAAAA
20603 AAATGGTAAT
Statistics
Matches: 70, Mismatches: 15, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
25 20 0.29
26 14 0.20
27 20 0.29
28 15 0.21
29 1 0.01
ACGTcount: A:0.57, C:0.06, G:0.17, T:0.20
Consensus pattern (27 bp):
AGTAAAAAATGGTAATTCAGTAAAAAG
Found at i:25598 original size:3 final size:3
Alignment explanation
Indices: 25584--25622 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
25574 AGGTGGGCTG
*
25584 CTT CTC CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
25623 TTTTGGCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (3 bp):
CTT
Found at i:26672 original size:26 final size:25
Alignment explanation
Indices: 26643--26704 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
26633 TTAACAACAG
* *
26643 TTCACAACAATGTGCTGACCCTGCCA
1 TTCACAACAATATGATG-CCCTGCCA
* * *
26669 TTCACTAGAATATTATGCCCTGCCA
1 TTCACAACAATATGATGCCCTGCCA
*
26694 TTGACAACAAT
1 TTCACAACAAT
26705 CATTTTCTGT
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
25 16 0.57
26 12 0.43
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (25 bp):
TTCACAACAATATGATGCCCTGCCA
Found at i:27403 original size:12 final size:12
Alignment explanation
Indices: 27386--27428 Score: 59
Period size: 12 Copynumber: 3.3 Consensus size: 12
27376 TGTGAGTTAC
27386 TGTTCATGACTG
1 TGTTCATGACTG
27398 TGTTCATGACTCTG
1 TGTTCATGA--CTG
27412 TTGTTCATGACTG
1 -TGTTCATGACTG
27425 TGTT
1 TGTT
27429 TCTGTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 13 0.46
13 3 0.11
14 3 0.11
15 9 0.32
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.47
Consensus pattern (12 bp):
TGTTCATGACTG
Found at i:27418 original size:15 final size:15
Alignment explanation
Indices: 27386--27428 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
27376 TGTGAGTTAC
27386 TGTTCATGA--CTG-
1 TGTTCATGACTCTGT
27398 TGTTCATGACTCTGT
1 TGTTCATGACTCTGT
*
27413 TGTTCATGACTGTGT
1 TGTTCATGACTCTGT
27428 T
1 T
27429 TCTGTGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 9 0.33
14 3 0.11
15 15 0.56
ACGTcount: A:0.14, C:0.16, G:0.23, T:0.47
Consensus pattern (15 bp):
TGTTCATGACTCTGT
Found at i:29754 original size:41 final size:41
Alignment explanation
Indices: 29707--29792 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
29697 CAACCCTCTT
29707 GCAACTGAAAAAGCCAGACAGAACCACCAATATACCATTAA
1 GCAACTGAAAAAGCCAGACAGAACCACCAATATACCATTAA
*
29748 GCAACTGAAAAAGCCAGACAGAACTACCAATATACCATTAA
1 GCAACTGAAAAAGCCAGACAGAACCACCAATATACCATTAA
29789 GCAA
1 GCAA
29793 AGCAACACAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.49, C:0.26, G:0.13, T:0.13
Consensus pattern (41 bp):
GCAACTGAAAAAGCCAGACAGAACCACCAATATACCATTAA
Found at i:36427 original size:34 final size:30
Alignment explanation
Indices: 36381--36461 Score: 92
Period size: 30 Copynumber: 2.6 Consensus size: 30
36371 ACTTGTAGCG
36381 TTTGGA-AGTTTTGCCCCATGAACTGAACTTCAAT
1 TTTGGACA-TTTTGCCCCATGAACT---C-TCAAT
*
36415 TTTGGACATTTTGCCCCCTGAACTCTCAAT
1 TTTGGACATTTTGCCCCATGAACTCTCAAT
*
36445 TTTGGACGTTTTGCCCC
1 TTTGGACATTTTGCCCC
36462 CTCTCAAACG
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
30 21 0.48
31 1 0.02
34 21 0.48
35 1 0.02
ACGTcount: A:0.20, C:0.26, G:0.17, T:0.37
Consensus pattern (30 bp):
TTTGGACATTTTGCCCCATGAACTCTCAAT
Found at i:36461 original size:29 final size:29
Alignment explanation
Indices: 36403--36463 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
36393 GCCCCATGAA
36403 CTGAACTTCAATTTTGGACATTTTGCCCC
1 CTGAACTTCAATTTTGGACATTTTGCCCC
*
36432 CTGAACTCTCAATTTTGGACGTTTTGCCCC
1 CTGAACT-TCAATTTTGGACATTTTGCCCC
36462 CT
1 CT
36464 CTCAAACGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.18, C:0.30, G:0.15, T:0.38
Consensus pattern (29 bp):
CTGAACTTCAATTTTGGACATTTTGCCCC
Found at i:38449 original size:166 final size:166
Alignment explanation
Indices: 38146--38627 Score: 567
Period size: 166 Copynumber: 2.9 Consensus size: 166
38136 AACATAGGGA
* * ** * * * *
38146 AATTACTAAAAGATCCCTACCCCGGATTAATGAGGAGCGAGAGAA-TTAATTTTTTTCGTCTTTT
1 AATTAATAAAAGATCCCCACCAAGGATTGATGATGAACTAGAGAACTT-ATTTTTTTCGTCTTTT
* * * * * * * *
38210 CCCATTTGACCGATTACTTAAATGCCCTAACTTTTGATTCTTGAGGTCATTAAATAACTAAACTT
65 CCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGG-GATTAAATAACTAATCTT
*
38275 TTTGGTCATTTCTCAATTGACTTT-AATGGAGTAGTGG
129 TTTGGTCATTTCTCAATTGACTTTGAATAGAGTAGTGG
* * * * * ** *
38312 AATTACTAAAAGATCCCTACCAATGCTTGCTTTTGGAATTAGAGAACTTATTTTTTTCGTCTTTT
1 AATTAATAAAAGATCCCCACCAAGGATTGATGAT-GAACTAGAGAACTTATTTTTTTCGTCTTTT
* *
38377 CCTACTTGGCAGATTACTCAAATGTCCTAACTTTTGATTCTTAAGGGATTAAATAAGTAATCTTT
65 CCTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGATTAAATAACTAATCTTT
*
38442 TTGGTCATTTCTCAATGGA-TTTGAATAGAGTAGTGG
130 TTGGTCATTTCTCAATTGACTTTGAATAGAGTAGTGG
* * * * * *
38478 AATTAATAAAAGATCCCCATCAAGGATTGATGATGAGCTAGAAAACTAATCTTTTTCGTCTTTAC
1 AATTAATAAAAGATCCCCACCAAGGATTGATGATGAACTAGAGAACTTATTTTTTTCGTCTTTTC
* *
38543 CTACTTGGCAGATTACTTAAATGTCCTAACGTTTGATTCTTGAGGGGATTAAATAACTAAAT-TT
66 CTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTT-AAGGGATTAAATAACT-AATCTT
38607 TTTGGTCATTTCTCAATTGAC
129 TTTGGTCATTTCTCAATTGAC
38628 AAATGACTCA
Statistics
Matches: 267, Mismatches: 43, Indels: 11
0.83 0.13 0.03
Matches are distributed among these distances:
165 67 0.25
166 132 0.49
167 66 0.25
168 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (166 bp):
AATTAATAAAAGATCCCCACCAAGGATTGATGATGAACTAGAGAACTTATTTTTTTCGTCTTTTC
CTACTTGGCAGATTACTTAAATGTCCTAACTTTTGATTCTTAAGGGATTAAATAACTAATCTTTT
TGGTCATTTCTCAATTGACTTTGAATAGAGTAGTGG
Found at i:38827 original size:17 final size:17
Alignment explanation
Indices: 38805--38862 Score: 68
Period size: 17 Copynumber: 3.5 Consensus size: 17
38795 GCAAGCAATT
38805 AATTAACTTAAACGGCA
1 AATTAACTTAAACGGCA
38822 AATTAAC-TAAA--GCA
1 AATTAACTTAAACGGCA
*
38836 ATTAATAACTTAAACGGCA
1 A--ATTAACTTAAACGGCA
38855 AATTAACT
1 AATTAACT
38863 AAAAGGGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 4 0.12
16 9 0.26
17 17 0.50
19 4 0.12
ACGTcount: A:0.50, C:0.16, G:0.09, T:0.26
Consensus pattern (17 bp):
AATTAACTTAAACGGCA
Found at i:38874 original size:34 final size:34
Alignment explanation
Indices: 38797--38865 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 34
38787 AAAGGTGAGC
38797 AAGCAATTAATTAACTTAAACGGCAAATTAACTA
1 AAGCAATTAATTAACTTAAACGGCAAATTAACTA
38831 AAGCAATTAA-TAACTTAAACGGCAAATTAACTA
1 AAGCAATTAATTAACTTAAACGGCAAATTAACTA
38864 AA
1 AA
38866 AGGGATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 25 0.71
34 10 0.29
ACGTcount: A:0.52, C:0.14, G:0.09, T:0.25
Consensus pattern (34 bp):
AAGCAATTAATTAACTTAAACGGCAAATTAACTA
Found at i:39823 original size:8 final size:7
Alignment explanation
Indices: 39790--39822 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
39780 GTGGCTATTA
39790 AAAAATT
1 AAAAATT
39797 AAAAATT
1 AAAAATT
39804 AAAAATT
1 AAAAATT
39811 AAAAATT
1 AAAAATT
39818 AAAAA
1 AAAAA
39823 AAAACGTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAAATT
Found at i:40154 original size:23 final size:23
Alignment explanation
Indices: 40128--40189 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
40118 TTTCGAATCG
*
40128 AGGCTTTCTAGGGTTAAAAGCAA
1 AGGCTTTCGAGGGTTAAAAGCAA
* *
40151 AGGCTTTCGAGGGTTAAAATCGA
1 AGGCTTTCGAGGGTTAAAAGCAA
40174 AGGCTTTGCGAGGGTT
1 AGGCTTT-CGAGGGTT
40190 TGAAGAAAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 27 0.77
24 8 0.23
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.27
Consensus pattern (23 bp):
AGGCTTTCGAGGGTTAAAAGCAA
Found at i:40460 original size:26 final size:27
Alignment explanation
Indices: 40404--40467 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
40394 TGTTAAAGTT
* *
40404 TTGATTGATTTTGGGTTAGTTAATTTG
1 TTGACTGATTTTGGGTTAGTTAATTTC
40431 TTGACTGATTTTGGGTT-GTTAATTTC
1 TTGACTGATTTTGGGTTAGTTAATTTC
*
40457 TTGACTAATTT
1 TTGACTGATTT
40468 ATTGAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
26 18 0.53
27 16 0.47
ACGTcount: A:0.19, C:0.05, G:0.22, T:0.55
Consensus pattern (27 bp):
TTGACTGATTTTGGGTTAGTTAATTTC
Found at i:40568 original size:27 final size:29
Alignment explanation
Indices: 40538--40591 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
40528 AATTATTGAT
40538 TGATTTT-GG-GTTAGTTAATTTCTTGGC
1 TGATTTTAGGTGTTAGTTAATTTCTTGGC
* *
40565 TGATTTTAGGTTTTTGTTAATTTCTTG
1 TGATTTTAGGTGTTAGTTAATTTCTTG
40592 ACTAAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 7 0.30
28 2 0.09
29 14 0.61
ACGTcount: A:0.15, C:0.06, G:0.22, T:0.57
Consensus pattern (29 bp):
TGATTTTAGGTGTTAGTTAATTTCTTGGC
Found at i:41254 original size:15 final size:15
Alignment explanation
Indices: 41234--41263 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41224 GTAATGGTGA
41234 ATTAGAAAACAATGT
1 ATTAGAAAACAATGT
*
41249 ATTAGATAACAATGT
1 ATTAGAAAACAATGT
41264 TGGAGAGGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (15 bp):
ATTAGAAAACAATGT
Found at i:43521 original size:49 final size:50
Alignment explanation
Indices: 43460--43602 Score: 150
Period size: 50 Copynumber: 2.9 Consensus size: 50
43450 TAGTGAAATC
* * * *
43460 TTTGAGTAATTTGTAAATAGAAATG-GGATCTTTGGACT-AAA-ATTGAACT
1 TTTGATTAATTTGTAAATAAAAATGAGG-CCTTTGGACTAAAAGATTGAA-A
*
43509 TTTGATTAATTTGGAAATAAAAATGAGGCCTTTGGACTAAAAGATTGAAA
1 TTTGATTAATTTGTAAATAAAAATGAGGCCTTTGGACTAAAAGATTGAAA
* * * *
43559 TTTGATTCATTTATAAATAAAAGTGAGACCTTT-GAGCTAAAAGA
1 TTTGATTAATTTGTAAATAAAAATGAGGCCTTTGGA-CTAAAAGA
43603 CCGACTTCTG
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
49 33 0.41
50 41 0.51
51 6 0.08
ACGTcount: A:0.40, C:0.07, G:0.19, T:0.34
Consensus pattern (50 bp):
TTTGATTAATTTGTAAATAAAAATGAGGCCTTTGGACTAAAAGATTGAAA
Found at i:44453 original size:40 final size:38
Alignment explanation
Indices: 44370--44749 Score: 280
Period size: 40 Copynumber: 9.4 Consensus size: 38
44360 TGTCTTATTC
*
44370 CCAGTTTGCCCTTCCCAGTCGGGGGAAGGTGTTGTTTATATT
1 CCAGTTTGCCCTTCCC-GTC---GGAAGGTGTTGTTTACATT
44412 CCCAGTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTACATT
1 -CCAGTTTGCCCTTCCC-GTCGGAAGGTGTTGTTTACATT
* * * * *
44452 CCTGTTTTGGCGTTCCTC-ACAGGAAGGTGTTGTTTATATT
1 CCAG-TTTGCCCTTCC-CGTC-GGAAGGTGTTGTTTACATT
* *
44492 CCCAATTTGCCCTTCACGGTCGGAAGGTGTTGTTTACATT
1 -CCAGTTTGCCCTTC-CCGTCGGAAGGTGTTGTTTACATT
* * *
44532 CCTGTTTTACCCTTCCACATCGGAAGGTGTTGTTTACTCATT
1 CCAG-TTTGCCCTTCC-CGTCGGAAGGTGTTGTTTA--CATT
** *
44574 CCTAGTTTGCCCTTCGCAATCGGAAGGTGTTGTTTACACT
1 CC-AGTTTGCCCTTC-CCGTCGGAAGGTGTTGTTTACATT
** ** * *
44614 CTTGTTTTGCCCTTCCTCACCAGAAGGTATTGTTTACTCATT
1 CCAG-TTTGCCCTTCC-CGTCGGAAGGTGTTGTTTA--CATT
* * *
44656 CCCAATTTGCCTTTCCAAGTCGGAAGGTGTTGTTTACATT
1 -CCAGTTTGCCCTTCC-CGTCGGAAGGTGTTGTTTACATT
** *
44696 CTTGTTTCCCCTTCCC--CGGAAGGTGTTGTTTACTCATT
1 CCAGTTTGCCCTTCCCGTCGGAAGGTGTTGTTTA--CATT
44734 CCAGTTTGCCCTTCCC
1 CCAGTTTGCCCTTCCC
44750 AAATTGCCCT
Statistics
Matches: 269, Mismatches: 49, Indels: 43
0.75 0.14 0.12
Matches are distributed among these distances:
36 16 0.06
38 17 0.06
39 19 0.07
40 130 0.48
41 5 0.02
42 60 0.22
43 22 0.08
ACGTcount: A:0.15, C:0.26, G:0.21, T:0.38
Consensus pattern (38 bp):
CCAGTTTGCCCTTCCCGTCGGAAGGTGTTGTTTACATT
Found at i:44526 original size:80 final size:81
Alignment explanation
Indices: 44393--44748 Score: 442
Period size: 82 Copynumber: 4.5 Consensus size: 81
44383 CCCAGTCGGG
*
44393 GGAAGGTGTTGTTTA-T-ATTCCCAGTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTACATTCCTG
1 GGAAGGTGTTGTTTACTCATTCCCAGTTTGCCCTT-CCAGTCGGAAGGTGTTGTTTACATTCCTG
* * *
44456 TTTTGGCGTTCCTCACA
65 TTTTGCCCTTCCTCACC
* *
44473 GGAAGGTGTTGTTTA-T-ATTCCCAATTTGCCCTTCACGGTCGGAAGGTGTTGTTTACATTCCTG
1 GGAAGGTGTTGTTTACTCATTCCCAGTTTGCCCTTC-CAGTCGGAAGGTGTTGTTTACATTCCTG
* * *
44536 TTTTACCCTTCCACATC
65 TTTTGCCCTTCCTCACC
* * * *
44553 GGAAGGTGTTGTTTACTCATTCCTAGTTTGCCCTTCGCAATCGGAAGGTGTTGTTTACACTCTTG
1 GGAAGGTGTTGTTTACTCATTCCCAGTTTGCCCTTC-CAGTCGGAAGGTGTTGTTTACATTCCTG
44618 TTTTGCCCTTCCTCACC
65 TTTTGCCCTTCCTCACC
* * * * *
44635 AGAAGGTATTGTTTACTCATTCCCAATTTGCCTTTCCAAGTCGGAAGGTGTTGTTTACATTCTTG
1 GGAAGGTGTTGTTTACTCATTCCCAGTTTGCCCTTCC-AGTCGGAAGGTGTTGTTTACATTCCTG
*
44700 -TTTCCCCTT-C-C-CC
65 TTTTGCCCTTCCTCACC
44713 GGAAGGTGTTGTTTACTCATT-CCAGTTTGCCCTTCC
1 GGAAGGTGTTGTTTACTCATTCCCAGTTTGCCCTTCC
44749 CAAATTGCCC
Statistics
Matches: 243, Mismatches: 29, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
77 13 0.05
78 21 0.09
79 2 0.01
80 87 0.36
81 10 0.04
82 110 0.45
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (81 bp):
GGAAGGTGTTGTTTACTCATTCCCAGTTTGCCCTTCCAGTCGGAAGGTGTTGTTTACATTCCTGT
TTTGCCCTTCCTCACC
Found at i:44900 original size:50 final size:49
Alignment explanation
Indices: 44786--44965 Score: 220
Period size: 50 Copynumber: 3.7 Consensus size: 49
44776 TTGTTTATTA
* * * *
44786 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCACAGCTTTC-TTCTCT-A
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG-TTTCTTTATCTGT
* *
44834 TTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCCTGTTTCCTTTATTTGT
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTT-CTTTATCTGT
* * *
44884 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTCTGT
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTG-TTTCTTTATCTGT
* *
44934 TTCCCAAAATGCCCCTTCTCGGTCGGAAGGTC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTC
44966 TAGTTTTCTC
Statistics
Matches: 116, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
47 3 0.03
48 34 0.29
49 4 0.03
50 72 0.62
51 3 0.03
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.33
Consensus pattern (49 bp):
TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCTGTTTCTTTATCTGT
Found at i:44901 original size:98 final size:100
Alignment explanation
Indices: 44786--44965 Score: 260
Period size: 98 Copynumber: 1.8 Consensus size: 100
44776 TTGTTTATTA
44786 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCAC-AGCTTTC-TTCTCT-ATTCCAAAAATGCCC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTC-CTAGCTTTCTTTCTCTGATTCCAAAAATGCCC
44848 CTTC-CTGGTCGGAAGGTCCCTGTTTCCTTTATTTGT
65 CTTCTC-GGTCGGAAGGTCCCTGTTTCCTTTATTTGT
* * * * * *
44884 TTCCCAAAATGCCCCTTCCCGGTCGGAAGGTCCTTGTTTTCTTTGTCTGTTTCCCAAAATGCCCC
1 TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCTAGCTTTCTTTCTCTGATTCCAAAAATGCCCC
44949 TTCTCGGTCGGAAGGTC
66 TTCTCGGTCGGAAGGTC
44966 TAGTTTTCTC
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
97 1 0.01
98 36 0.50
99 5 0.07
100 29 0.40
101 1 0.01
ACGTcount: A:0.17, C:0.31, G:0.19, T:0.33
Consensus pattern (100 bp):
TTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCTAGCTTTCTTTCTCTGATTCCAAAAATGCCCC
TTCTCGGTCGGAAGGTCCCTGTTTCCTTTATTTGT
Found at i:47277 original size:67 final size:66
Alignment explanation
Indices: 47131--47571 Score: 437
Period size: 67 Copynumber: 6.6 Consensus size: 66
47121 ATGACAAATT
** * * * * ** *
47131 TGACCCTTTGACCGTAAGGGCATTTTTGG-AAGATGAA-ACTAAACTTTAGATGTAAAAAGACAA
1 TGACCCTTCCACCGAAAGGGTATTTTTGGAAAGA-AAATACTAAAC-TTAAATGGGAAAAGACGA
47194 AAA
64 AAA
* * * *
47197 TAACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAATGCTAAACTTAAATGGGAAAAGAAGAA
1 TGACCCTTCCACCGAAAGGGTATTTTTGGAAA-GAAAATACTAAACTTAAATGGGAAAAGACGAA
47262 AA
65 AA
** **
47264 TGACCCTTTGACCGAAAGGG-ATATTTTGGAAAAGAAAATACTAAACTTAAATGCAAAAAGACGA
1 TGACCCTTCCACCGAAAGGGTAT-TTTTGG-AAAGAAAATACTAAACTTAAATGGGAAAAGACGA
47328 AAA
64 AAA
* *
47331 TGACCCTTCCACTGAAAGGGTATTTTTGGAAAAGCAAAATGCTAAACTTAAATGCGG-AAAGACG
1 TGACCCTTCCACCGAAAGGGTATTTTTGG-AAAG-AAAATACTAAACTTAAATG-GGAAAAGACG
*
47395 GAAA
63 AAAA
* *
47399 TGACCCTTCCACCGAAAGGGTATTTTTGGAACA-AACAAAACTAAACTAAAATGCGG-AAAGACG
1 TGACCCTTCCACCGAAAGGGTATTTTTGGAA-AGAA-AATACTAAACTTAAATG-GGAAAAGACG
47462 AAAA
63 AAAA
** * * **
47466 TGACCCTTCCACAAAAAGGGTATTTTTGGAACA-AACAAAACTAAACTAAAATACGAAAAGACGA
1 TGACCCTTCCACCGAAAGGGTATTTTTGGAA-AGAA-AATACTAAACTTAAATGGGAAAAGACGA
47530 AAA
64 AAA
* * *
47533 TGACCCTTCAACCGAAAGGGTAATTTTGGAAAAAAAATA
1 TGACCCTTCCACCGAAAGGGTATTTTTGGAAAGAAAATA
47572 AAATTAAACT
Statistics
Matches: 325, Mismatches: 38, Indels: 24
0.84 0.10 0.06
Matches are distributed among these distances:
66 34 0.10
67 221 0.68
68 70 0.22
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (66 bp):
TGACCCTTCCACCGAAAGGGTATTTTTGGAAAGAAAATACTAAACTTAAATGGGAAAAGACGAAA
A
Found at i:47406 original size:135 final size:133
Alignment explanation
Indices: 47131--47566 Score: 497
Period size: 135 Copynumber: 3.2 Consensus size: 133
47121 ATGACAAATT
* * * * ** * * *
47131 TGACCCTTTGACCGTAAGGGCATTTTTGG-AAGATGAAACTAAACTTTAGATGTAAAAAGACAAA
1 TGACCCTTCGACCGAAAGGGTA-TTTTGGAAAAACAAAACTAAAC-TTAAATGCAAAAAGACGAA
* * * *
47195 AATAACCCTTCGACCGAAAGGGTATTTTTGGAAATG-AAAATGCTAAACTTAAATG-GGAAAAGA
64 AATGACCCTTCCACAGAAAGGGTATTTTTGGAAAAGCAAAATGCTAAACTTAAATGCGG-AAAGA
*
47258 AGAAAA
128 CGAAAA
*
47264 TGACCCTTTGACCGAAAGGGATATTTTGGAAAAGA-AAATACTAAACTTAAATGCAAAAAGACGA
1 TGACCCTTCGACCGAAAGGG-TATTTTGGAAAA-ACAAA-ACTAAACTTAAATGCAAAAAGACGA
*
47328 AAATGACCCTTCCACTGAAAGGGTATTTTTGGAAAAGCAAAATGCTAAACTTAAATGCGGAAAGA
63 AAATGACCCTTCCACAGAAAGGGTATTTTTGGAAAAGCAAAATGCTAAACTTAAATGCGGAAAGA
*
47393 CGGAAA
128 CGAAAA
* * **
47399 TGACCCTTCCACCGAAAGGGTATTTTTGGAACAAACAAAACTAAACTAAAATGCGGAAAGACGAA
1 TGACCCTTCGACCGAAAGGGTA-TTTTGGAA-AAACAAAACTAAACTTAAATGCAAAAAGACGAA
* * * * *
47464 AATGACCCTTCCACAAAAAGGGTATTTTTGGAACAAACAAAA--CTAAACTAAAATACGAAAAGA
64 AATGACCCTTCCACAGAAAGGGTATTTTTGGAA-AAGCAAAATGCTAAACTTAAATGCGGAAAGA
47527 CGAAAA
128 CGAAAA
*
47533 TGACCCTTCAACCGAAAGGGTAATTTTGGAAAAA
1 TGACCCTTCGACCGAAAGGGT-ATTTTGGAAAAA
47567 AAATAAAATT
Statistics
Matches: 266, Mismatches: 26, Indels: 22
0.85 0.08 0.07
Matches are distributed among these distances:
133 28 0.11
134 106 0.40
135 118 0.44
136 14 0.05
ACGTcount: A:0.44, C:0.16, G:0.19, T:0.21
Consensus pattern (133 bp):
TGACCCTTCGACCGAAAGGGTATTTTGGAAAAACAAAACTAAACTTAAATGCAAAAAGACGAAAA
TGACCCTTCCACAGAAAGGGTATTTTTGGAAAAGCAAAATGCTAAACTTAAATGCGGAAAGACGA
AAA
Found at i:47552 original size:202 final size:201
Alignment explanation
Indices: 47194--47565 Score: 502
Period size: 202 Copynumber: 1.8 Consensus size: 201
47184 AAAAAGACAA
* ** *
47194 AAATAACCCTTCGACCGAAAGGGTATTTTTGGAAATGAAAATGCTAAACTTAAATGGGAAAAGAA
1 AAATAACCCTTCCACCGAAAGGGTATTTTTGGAAA-GAAAAAACTAAACTAAAATGGGAAAAGAA
** ** * *
47259 GAAAATGACCCTTTGACCGAAAGGGATATTTTGGAAAAGAAAATACTAAACTTAAATGCAAAAAG
65 GAAAATGACCCTTCCACAAAAAGGGATATTTTGGAAAAGAAAATACTAAACTAAAATACAAAAAG
* * *
47324 ACGAAAATGACCCTTCCACTGAAAGGGTATTTTTGGAAAAGCAAAATGCTAAACTTAAATGCGGA
130 ACGAAAATGACCCTTCAACCGAAAGGGTAATTTTGGAAAAGCAAAATGCTAAACTTAAATGCGGA
47389 AAGACGG
195 AAGACGG
*
47396 AAATGACCCTTCCACCGAAAGGGTATTTTTGGAACA-AACAAAACTAAACTAAAATGCGG-AAAG
1 AAATAACCCTTCCACCGAAAGGGTATTTTTGGAA-AGAA-AAAACTAAACTAAAATG-GGAAAAG
* *
47459 ACGAAAATGACCCTTCCACAAAAAGGG-TATTTTTGGAACAA-ACAAA-ACTAAACTAAAATACG
63 AAGAAAATGACCCTTCCACAAAAAGGGATA-TTTTGGAA-AAGA-AAATACTAAACTAAAATACA
47521 AAAAGACGAAAATGACCCTTCAACCGAAAGGGTAATTTTGGAAAA
125 AAAAGACGAAAATGACCCTTCAACCGAAAGGGTAATTTTGGAAAA
47566 AAAATAAAAT
Statistics
Matches: 148, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
201 4 0.03
202 136 0.92
203 8 0.05
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.20
Consensus pattern (201 bp):
AAATAACCCTTCCACCGAAAGGGTATTTTTGGAAAGAAAAAACTAAACTAAAATGGGAAAAGAAG
AAAATGACCCTTCCACAAAAAGGGATATTTTGGAAAAGAAAATACTAAACTAAAATACAAAAAGA
CGAAAATGACCCTTCAACCGAAAGGGTAATTTTGGAAAAGCAAAATGCTAAACTTAAATGCGGAA
AGACGG
Found at i:50918 original size:18 final size:18
Alignment explanation
Indices: 50895--50930 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
50885 ACCTTGTAAT
50895 TTGAACATGAGAAAGAAA
1 TTGAACATGAGAAAGAAA
50913 TTGAACATGAGAAAGAAA
1 TTGAACATGAGAAAGAAA
50931 GGACTCGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.06, G:0.22, T:0.17
Consensus pattern (18 bp):
TTGAACATGAGAAAGAAA
Found at i:53945 original size:12 final size:12
Alignment explanation
Indices: 53928--53958 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
53918 GTTGTGGCCG
53928 GATGGCCCGTGC
1 GATGGCCCGTGC
53940 GATGGCCCGTGC
1 GATGGCCCGTGC
53952 GATGGCC
1 GATGGCC
53959 GGTTGTGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.32, G:0.42, T:0.16
Consensus pattern (12 bp):
GATGGCCCGTGC
Found at i:53981 original size:42 final size:42
Alignment explanation
Indices: 53912--54005 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
53902 AAGGGTCAAG
* * * *
53912 TGGCAGGTTGTGGCCGGATGGCCCGTGCGATGGCCCGTGCGA
1 TGGCCGGTTGTGGCCGGATCGCCCGTGCAATGGCCCATGCGA
* *
53954 TGGCCGGTTGTGGCCGGATCGCTCGTGCAATGGCCCATGCGT
1 TGGCCGGTTGTGGCCGGATCGCCCGTGCAATGGCCCATGCGA
53996 TGGCCGGTTG
1 TGGCCGGTTG
54006 CTCCATGCGA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.09, C:0.27, G:0.43, T:0.22
Consensus pattern (42 bp):
TGGCCGGTTGTGGCCGGATCGCCCGTGCAATGGCCCATGCGA
Found at i:59673 original size:30 final size:30
Alignment explanation
Indices: 59629--59685 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
59619 CAAGTTTATA
59629 ATAAGTCCTTGGCGCATCATTCCCTCCATG
1 ATAAGTCCTTGGCGCATCATTCCCTCCATG
59659 ATAAG-CCTTGGGCGCATCATTCCCTCC
1 ATAAGTCCTT-GGCGCATCATTCCCTCC
59686 CCCTTGAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 4 0.15
30 22 0.85
ACGTcount: A:0.19, C:0.35, G:0.18, T:0.28
Consensus pattern (30 bp):
ATAAGTCCTTGGCGCATCATTCCCTCCATG
Found at i:60065 original size:33 final size:33
Alignment explanation
Indices: 60026--60132 Score: 196
Period size: 33 Copynumber: 3.2 Consensus size: 33
60016 CTTTTCACCA
**
60026 AAAACAGAATTATTTTTAATGCTATGATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
60059 AAAACAGAATTATTTGCAATGCTATGATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
60092 AAAACAGAATTATTTGCAATGCTATGATCAACC
1 AAAACAGAATTATTTGCAATGCTATGATCAACC
60125 AAAACAGA
1 AAAACAGA
60133 TTTGTTTTCA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.45, C:0.17, G:0.11, T:0.27
Consensus pattern (33 bp):
AAAACAGAATTATTTGCAATGCTATGATCAACC
Found at i:60227 original size:33 final size:33
Alignment explanation
Indices: 60125--60227 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
60115 ATGATCAACC
* * *
60125 AAAACAGATTT-GTTTTCATCAC-AACTAGCATCC
1 AAAACAGATTTAG-TATCATCACAAAC-AACATCT
60158 AAAACAGATTTAGTATCATCACAAACAACA-CTT
1 AAAACAGATTTAGTATCATCACAAACAACATC-T
* * **
60191 AAAACAGATTTTGTATTATTGCAAACAACATCT
1 AAAACAGATTTAGTATCATCACAAACAACATCT
60224 AAAA
1 AAAA
60228 TACTCTTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
32 1 0.02
33 53 0.90
34 5 0.08
ACGTcount: A:0.45, C:0.19, G:0.08, T:0.28
Consensus pattern (33 bp):
AAAACAGATTTAGTATCATCACAAACAACATCT
Found at i:62152 original size:30 final size:30
Alignment explanation
Indices: 62106--62166 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
62096 AAAACACACT
* *
62106 TACCCGAGCCTACTTCTCATCACCTTCCCA
1 TACCAGAGCCTACTTCTCACCACCTTCCCA
*
62136 TACCAGAGCCTTCTTCTCACCACCTTCCCA
1 TACCAGAGCCTACTTCTCACCACCTTCCCA
62166 T
1 T
62167 CTCACCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.20, C:0.46, G:0.07, T:0.28
Consensus pattern (30 bp):
TACCAGAGCCTACTTCTCACCACCTTCCCA
Found at i:68503 original size:34 final size:36
Alignment explanation
Indices: 68460--68530 Score: 128
Period size: 34 Copynumber: 2.0 Consensus size: 36
68450 TTGGAATATT
68460 AGAGAGTCATGGTTTTCAAAAATG-TTT-TTCAAAA
1 AGAGAGTCATGGTTTTCAAAAATGTTTTCTTCAAAA
68494 AGAGAGTCATGGTTTTCAAAAATGTTTTCTTCAAAA
1 AGAGAGTCATGGTTTTCAAAAATGTTTTCTTCAAAA
68530 A
1 A
68531 ATGTTTTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
34 24 0.69
35 3 0.09
36 8 0.23
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (36 bp):
AGAGAGTCATGGTTTTCAAAAATGTTTTCTTCAAAA
Found at i:68901 original size:6 final size:6
Alignment explanation
Indices: 68890--68917 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
68880 TCAATAAAAA
68890 AAAATC AAAATC AAAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAA
68918 GCGAAAGTGT
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:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATC
Found at i:69272 original size:8 final size:8
Alignment explanation
Indices: 69250--69301 Score: 81
Period size: 8 Copynumber: 6.8 Consensus size: 8
69240 AAAAAAAATG
69250 AATG-AAA
1 AATGAAAA
69257 AATG-AAA
1 AATGAAAA
*
69264 AATAAAAA
1 AATGAAAA
69272 AATGAAAA
1 AATGAAAA
69280 AATGAAAA
1 AATGAAAA
69288 AATGAAAA
1 AATGAAAA
69296 AATGAA
1 AATGAA
69302 TGGAAAAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
7 10 0.24
8 32 0.76
ACGTcount: A:0.75, C:0.00, G:0.12, T:0.13
Consensus pattern (8 bp):
AATGAAAA
Found at i:69281 original size:24 final size:26
Alignment explanation
Indices: 69241--69301 Score: 83
Period size: 24 Copynumber: 2.4 Consensus size: 26
69231 AGTGCAATGA
69241 AAAAAAATGAATGAAAAATG-AAAAAT
1 AAAAAAATGAA-GAAAAATGAAAAAAT
69267 AAAAAAATG-A-AAAAATGAAAAAAT
1 AAAAAAATGAAGAAAAATGAAAAAAT
*
69291 GAAAAAATGAA
1 AAAAAAATGAA
69302 TGGAAAAGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
23 7 0.22
24 14 0.44
25 2 0.06
26 9 0.28
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.13
Consensus pattern (26 bp):
AAAAAAATGAAGAAAAATGAAAAAAT
Found at i:70346 original size:8 final size:8
Alignment explanation
Indices: 70330--70386 Score: 69
Period size: 8 Copynumber: 7.1 Consensus size: 8
70320 AATGATCTCT
70330 TTCTTCAA
1 TTCTTCAA
*
70338 TTATTCAA
1 TTCTTCAA
*
70346 TGCTTCAA
1 TTCTTCAA
* *
70354 CTCTTCCA
1 TTCTTCAA
*
70362 TTATTCAA
1 TTCTTCAA
70370 TTCTTCAA
1 TTCTTCAA
70378 TTCTTCAA
1 TTCTTCAA
70386 T
1 T
70387 GATTCAATTT
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
8 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.02, T:0.47
Consensus pattern (8 bp):
TTCTTCAA
Found at i:70353 original size:16 final size:16
Alignment explanation
Indices: 70330--70395 Score: 69
Period size: 16 Copynumber: 4.1 Consensus size: 16
70320 AATGATCTCT
70330 TTCTTCAATTATTCAA
1 TTCTTCAATTATTCAA
* * * *
70346 TGCTTCAACTCTTCCA
1 TTCTTCAATTATTCAA
* *
70362 TTATTCAATTCTTCAA
1 TTCTTCAATTATTCAA
*
70378 TTCTTCAATGATTCAA
1 TTCTTCAATTATTCAA
70394 TT
1 TT
70396 TATCTCTTCG
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (16 bp):
TTCTTCAATTATTCAA
Found at i:70395 original size:24 final size:24
Alignment explanation
Indices: 70271--70395 Score: 101
Period size: 24 Copynumber: 5.0 Consensus size: 24
70261 GCTAATCTTG
*
70271 TTCAATTCGCTTCAATTATTCAATCC
1 TTCAATT--CTTCAATTATTCAATTC
*
70297 TTCAATGCTTCAATTTATTTCAAAATGATC
1 TTCAATTCTTCAA-TTA-TTC--AAT--TC
* *
70327 -TC-TTTCTTCAATTATTCAATGC
1 TTCAATTCTTCAATTATTCAATTC
* *
70349 TTCAACTCTTCCATTATTCAATTC
1 TTCAATTCTTCAATTATTCAATTC
*
70373 TTCAATTCTTCAATGATTCAATT
1 TTCAATTCTTCAATTATTCAATT
70396 TATCTCTTCG
Statistics
Matches: 79, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
22 1 0.01
23 2 0.03
24 45 0.57
25 3 0.04
26 12 0.15
27 3 0.04
28 10 0.13
29 2 0.03
30 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.04, T:0.46
Consensus pattern (24 bp):
TTCAATTCTTCAATTATTCAATTC
Found at i:70430 original size:37 final size:37
Alignment explanation
Indices: 70331--70441 Score: 100
Period size: 37 Copynumber: 2.9 Consensus size: 37
70321 ATGATCTCTT
* * * *
70331 TCTTCAATTATTCAATGCTTCAACTCTTCCAT-TATTCAAT
1 TCTTCAATTATTCAATGATTCAA-T-TT--ATCTCTTCGAC
*
70371 TCTTCAATTCTTCAATGATTCAATTTATCTCTTCGAC
1 TCTTCAATTATTCAATGATTCAATTTATCTCTTCGAC
* *
70408 TCTTTAATTATTCAAT-ACTTCAATTTATTTCTTC
1 TCTTCAATTATTCAATGA-TTCAATTTATCTCTTC
70442 AATTCTTGGA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
36 3 0.05
37 34 0.56
38 2 0.03
39 1 0.02
40 21 0.34
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.49
Consensus pattern (37 bp):
TCTTCAATTATTCAATGATTCAATTTATCTCTTCGAC
Found at i:70597 original size:14 final size:14
Alignment explanation
Indices: 70570--70910 Score: 161
Period size: 14 Copynumber: 23.7 Consensus size: 14
70560 ACTTCTGGTC
*
70570 ATTCTTCGATTTCA
1 ATTCTTCAATTTCA
*
70584 ATTTTTCAATTTCA
1 ATTCTTCAATTTCA
* *
70598 ATTCTACAACGCTTCA
1 ATTCTTCAA--TTTCA
70614 A-T-TTCAATTCTACA
1 ATTCTTCAATT-T-CA
*
70628 GTGT-TTCAATTTCA
1 AT-TCTTCAATTTCA
**
70642 ATTCTTCAAGCCTCA
1 ATTCTTCAA-TTTCA
*
70657 A-T-TTCAATTCCA
1 ATTCTTCAATTTCA
*
70669 ATGCTTCAATTTCA
1 ATTCTTCAATTTCA
70683 ATTCTTCAATTTCA
1 ATTCTTCAATTTCA
* * *
70697 ATCCTTTAGTGTTTCA
1 ATTCTTCA--ATTTCA
70713 ATTCTTCAATTCTTCA
1 ATTCTTCAA-T-TTCA
70729 A-T-TTCAATTCTTCA
1 ATTCTTCAA-T-TTCA
*
70743 ATGCTTCAATTTCA
1 ATTCTTCAATTTCA
* *
70757 ATTCCTCAAATTCA
1 ATTCTTCAATTTCA
*
70771 ATCCTTCAATGTTTCA
1 ATTCTTCAA--TTTCA
*
70787 A-T-TTCAATTCTCC
1 ATTCTTCAATT-TCA
*
70800 A-TATTCAATCCTTCA
1 ATTCTTCAAT--TTCA
*
70815 ATGT-TTTAATTTCA
1 AT-TCTTCAATTTCA
*
70829 ATTCTTCAAATTCA
1 ATTCTTCAATTTCA
*
70843 ATCCTTCAATGTTTCA
1 ATTCTTCAA--TTTCA
70859 A-T-TTCAACGTTTCA
1 ATTCTTCAA--TTTCA
*
70873 ATGCTTCAATTTCA
1 ATTCTTCAATTTCA
*
70887 ATTCTCCAGA-TTCA
1 ATTCTTCA-ATTTCA
*
70901 ATCCTTCAAT
1 ATTCTTCAAT
70911 GTTTCAATTT
Statistics
Matches: 251, Mismatches: 45, Indels: 62
0.70 0.13 0.17
Matches are distributed among these distances:
12 6 0.02
13 13 0.05
14 163 0.65
15 13 0.05
16 55 0.22
17 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.44
Consensus pattern (14 bp):
ATTCTTCAATTTCA
Found at i:70616 original size:22 final size:22
Alignment explanation
Indices: 70588--70692 Score: 135
Period size: 22 Copynumber: 4.9 Consensus size: 22
70578 ATTTCAATTT
*
70588 TTCAATTTCAATTCTACAACGC
1 TTCAATTTCAATTCTACAATGC
* *
70610 TTCAATTTCAATTCTACAGTGT
1 TTCAATTTCAATTCTACAATGC
*
70632 TTCAATTTCAATTCTTCAA-GC
1 TTCAATTTCAATTCTACAATGC
*
70653 CTCAATTTCAATTC--CAATGC
1 TTCAATTTCAATTCTACAATGC
*
70673 TTCAATTTCAATTCTTCAAT
1 TTCAATTTCAATTCTACAAT
70693 TTCAATCCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
19 3 0.04
20 15 0.21
21 14 0.19
22 40 0.56
ACGTcount: A:0.30, C:0.24, G:0.05, T:0.42
Consensus pattern (22 bp):
TTCAATTTCAATTCTACAATGC
Found at i:70649 original size:36 final size:36
Alignment explanation
Indices: 70570--70865 Score: 292
Period size: 36 Copynumber: 8.0 Consensus size: 36
70560 ACTTCTGGTC
* **
70570 ATTCTTCGATTTCAATTTTTCAA--TTTCAATTCTACA
1 ATTCTTCAATTTCAATCCTTCAATGTTTCAATT-T-CA
** * * *
70606 ACGCTTCAATTTCAATTCTACAGTGTTTCAATTTCA
1 ATTCTTCAATTTCAATCCTTCAATGTTTCAATTTCA
** * *
70642 ATTCTTCAAGCCTCAATTTCAATTCCAATGCTTCAATTTCA
1 ATTCTTCAA-TTTCAA--TC-CTT-CAATGTTTCAATTTCA
* *
70683 ATTCTTCAATTTCAATCCTTTAGTGTTTCAATTCTTCA
1 ATTCTTCAATTTCAATCCTTCAATGTTTCAA-T-TTCA
* *
70721 ATTCTTCAATTTCAATTCTTCAATGCTTCAATTTCA
1 ATTCTTCAATTTCAATCCTTCAATGTTTCAATTTCA
* *
70757 ATTCCTCAAATTCAATCCTTCAATGTTTCAATTTCA
1 ATTCTTCAATTTCAATCCTTCAATGTTTCAATTTCA
* *
70793 ATTC-TCCATATTCAATCCTTCAATGTTTTAATTTCA
1 ATTCTTCAAT-TTCAATCCTTCAATGTTTCAATTTCA
*
70829 ATTCTTCAAATTCAATCCTTCAATGTTTCAATTTCA
1 ATTCTTCAATTTCAATCCTTCAATGTTTCAATTTCA
70865 A
1 A
70866 CGTTTCAATG
Statistics
Matches: 214, Mismatches: 35, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
35 3 0.01
36 129 0.60
37 12 0.06
38 41 0.19
39 1 0.00
40 5 0.02
41 23 0.11
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (36 bp):
ATTCTTCAATTTCAATCCTTCAATGTTTCAATTTCA
Found at i:70690 original size:8 final size:8
Alignment explanation
Indices: 70580--70797 Score: 83
Period size: 8 Copynumber: 30.1 Consensus size: 8
70570 ATTCTTCGAT
*
70580 TTCAATTT
1 TTCAATTC
70588 TTCAA-T-
1 TTCAATTC
70594 TTCAATTC
1 TTCAATTC
* **
70602 TACAACGC
1 TTCAATTC
70610 TTCAA-T-
1 TTCAATTC
70616 TTCAATTC
1 TTCAATTC
* *
70624 TACAGTGT-
1 TTCAAT-TC
70632 TTCAA-T-
1 TTCAATTC
70638 TTCAATTC
1 TTCAATTC
*
70646 TTCAA-GC
1 TTCAATTC
*
70653 CTCAA-T-
1 TTCAATTC
70659 TTCAATTC
1 TTCAATTC
*
70667 --CAATGC
1 TTCAATTC
70673 TTCAA-T-
1 TTCAATTC
70679 TTCAATTC
1 TTCAATTC
70687 TTCAA-T-
1 TTCAATTC
*
70693 TTCAATCC
1 TTCAATTC
* *
70701 TTTAGTGT-
1 TTCAAT-TC
70709 TTCAATTC
1 TTCAATTC
70717 TTCAATTC
1 TTCAATTC
70725 TTCAA-T-
1 TTCAATTC
70731 TTCAATTC
1 TTCAATTC
*
70739 TTCAATGC
1 TTCAATTC
70747 TTCAA-T-
1 TTCAATTC
70753 TTCAATTC
1 TTCAATTC
* *
70761 CTCAA--A
1 TTCAATTC
*
70767 TTCAATCC
1 TTCAATTC
70775 TTCAATGT-
1 TTCAAT-TC
70783 TTCAA-T-
1 TTCAATTC
70789 TTCAATTC
1 TTCAATTC
70797 T
1 T
70798 CCATATTCAA
Statistics
Matches: 156, Mismatches: 28, Indels: 52
0.66 0.12 0.22
Matches are distributed among these distances:
6 55 0.35
7 17 0.11
8 83 0.53
9 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (8 bp):
TTCAATTC
Found at i:70733 original size:22 final size:22
Alignment explanation
Indices: 70708--70891 Score: 127
Period size: 22 Copynumber: 8.5 Consensus size: 22
70698 TCCTTTAGTG
70708 TTTCAATTCTTCAATTCTTCAA
1 TTTCAATTCTTCAATTCTTCAA
*
70730 TTTCAATTCTTCAATGCTTCAA
1 TTTCAATTCTTCAATTCTTCAA
* *
70752 TTTCAATTCCTCAA--ATTCAA
1 TTTCAATTCTTCAATTCTTCAA
70772 TCCTTCAATGT-TTCAA-T-TTCAA
1 T--TTCAAT-TCTTCAATTCTTCAA
* * *
70794 TTCTCCA-TATTCAATCCTTCAA
1 TT-TCAATTCTTCAATTCTTCAA
*
70816 TGTTTTAA-T-TTCAATTCTTCAA
1 --TTTCAATTCTTCAATTCTTCAA
* *
70838 ATTCAATCCTTCAATGT-TTCAA
1 TTTCAATTCTTCAAT-TCTTCAA
* *
70860 TTTCAACGT-TTCAATGCTTCAA
1 TTTCAA-TTCTTCAATTCTTCAA
70882 TTTCAATTCT
1 TTTCAATTCT
70892 CCAGATTCAA
Statistics
Matches: 129, Mismatches: 17, Indels: 32
0.72 0.10 0.18
Matches are distributed among these distances:
19 1 0.01
20 16 0.12
21 4 0.03
22 101 0.78
23 5 0.04
24 2 0.02
ACGTcount: A:0.28, C:0.23, G:0.03, T:0.46
Consensus pattern (22 bp):
TTTCAATTCTTCAATTCTTCAA
Found at i:70814 original size:94 final size:91
Alignment explanation
Indices: 70629--70924 Score: 307
Period size: 94 Copynumber: 3.2 Consensus size: 91
70619 AATTCTACAG
* *
70629 TGTTTCAATTTCAATTCTTCAAGCCTCAATTTCAATTC-CAATGCTTCAAT-TTCAAT-TCTTCA
1 TGTTTCAATTTCAATTCTTCAAGCTTCAATTTCAATTCTCAA--ATTCAATCTTCAATGT-TTCA
* ** * *
70691 ATTTCAATCCTTTAGTGTTTCAATTCTTCAA
63 ATTTCAATTCTCCA-T-ATTCAATCCTTCAA
70722 T-TCTTCAATTTCAATTCTTCAATGCTTCAATTTCAATTCCTCAAATTCAATCCTTCAATGTTTC
1 TGT-TTCAATTTCAATTCTTCAA-GCTTCAATTTCAATT-CTCAAATTCAAT-CTTCAATGTTTC
70786 AATTTCAATTCTCCATATTCAATCCTTCAA
62 AATTTCAATTCTCCATATTCAATCCTTCAA
* * * * *
70816 TGTTTTAATTTCAATTCTTCAA-ATTCAATCCTTCAATGTTTCAATTTCAA-CGTTTCAATGCTT
1 TGTTTCAATTTCAATTCTTCAAGCTTCAAT--TTCAAT-TCTCAAATTCAATC--TTCAATGTTT
*
70879 CAATTTCAATTCTCCAGATTCAATCCTTCAA
61 CAATTTCAATTCTCCATATTCAATCCTTCAA
70910 TGTTTCAATTTCAAT
1 TGTTTCAATTTCAAT
70925 ATGTCAACGC
Statistics
Matches: 176, Mismatches: 14, Indels: 25
0.82 0.07 0.12
Matches are distributed among these distances:
92 8 0.05
93 20 0.11
94 119 0.68
95 4 0.02
96 24 0.14
97 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (91 bp):
TGTTTCAATTTCAATTCTTCAAGCTTCAATTTCAATTCTCAAATTCAATCTTCAATGTTTCAATT
TCAATTCTCCATATTCAATCCTTCAA
Found at i:70911 original size:58 final size:58
Alignment explanation
Indices: 70811--70923 Score: 190
Period size: 58 Copynumber: 1.9 Consensus size: 58
70801 TATTCAATCC
* * *
70811 TTCAATGTTTTAATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAATTTCAACGT
1 TTCAATGCTTCAATTTCAATTCTCCAAATTCAATCCTTCAATGTTTCAATTTCAACGT
*
70869 TTCAATGCTTCAATTTCAATTCTCCAGATTCAATCCTTCAATGTTTCAATTTCAA
1 TTCAATGCTTCAATTTCAATTCTCCAAATTCAATCCTTCAATGTTTCAATTTCAA
70924 TATGTCAACG
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 51 1.00
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.44
Consensus pattern (58 bp):
TTCAATGCTTCAATTTCAATTCTCCAAATTCAATCCTTCAATGTTTCAATTTCAACGT
Found at i:70924 original size:14 final size:14
Alignment explanation
Indices: 70847--70924 Score: 63
Period size: 14 Copynumber: 5.4 Consensus size: 14
70837 AATTCAATCC
70847 TTCAATGTTTCAAT
1 TTCAATGTTTCAAT
*
70861 TTCAACGTTTCAAT
1 TTCAATGTTTCAAT
70875 GCTTCAA--TTTCAAT
1 --TTCAATGTTTCAAT
* *
70889 TCTCCA-GATTCAAT
1 T-TCAATGTTTCAAT
70903 CCTTCAATGTTTCAAT
1 --TTCAATGTTTCAAT
70919 TTCAAT
1 TTCAAT
70925 ATGTCAACGC
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
12 1 0.02
13 3 0.06
14 32 0.62
15 3 0.06
16 13 0.25
ACGTcount: A:0.28, C:0.22, G:0.06, T:0.44
Consensus pattern (14 bp):
TTCAATGTTTCAAT
Found at i:70937 original size:58 final size:58
Alignment explanation
Indices: 70822--70940 Score: 184
Period size: 58 Copynumber: 2.1 Consensus size: 58
70812 TCAATGTTTT
* * * *
70822 AATTTCAATTCTTCAAATTCAATCCTTCAATGTTTCAATTTCAACGTTTCAATGCTTC
1 AATTTCAATTCTCCAAATTCAATCCTTCAATGTTTCAATTTCAACATGTCAACGCTTC
* *
70880 AATTTCAATTCTCCAGATTCAATCCTTCAATGTTTCAATTTCAATATGTCAACGCTTC
1 AATTTCAATTCTCCAAATTCAATCCTTCAATGTTTCAATTTCAACATGTCAACGCTTC
70938 AAT
1 AAT
70941 GATCAAGGGT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (58 bp):
AATTTCAATTCTCCAAATTCAATCCTTCAATGTTTCAATTTCAACATGTCAACGCTTC
Found at i:70987 original size:8 final size:7
Alignment explanation
Indices: 70975--71031 Score: 55
Period size: 8 Copynumber: 7.9 Consensus size: 7
70965 TTCTCCATTA
70975 TTCAATG
1 TTCAATG
70982 TCTCAAT-
1 T-TCAATG
*
70989 TTCAATT
1 TTCAATG
70996 TTCAATG
1 TTCAATG
71003 CTTCAA-G
1 -TTCAATG
71010 TTCAATG
1 TTCAATG
71017 TGTCAATG
1 T-TCAATG
71025 CTTCAAT
1 -TTCAAT
71032 TTTAATTCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
6 10 0.23
7 11 0.26
8 21 0.49
9 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.42
Consensus pattern (7 bp):
TTCAATG
Found at i:71047 original size:22 final size:22
Alignment explanation
Indices: 70975--71202 Score: 157
Period size: 22 Copynumber: 10.2 Consensus size: 22
70965 TTCTCCATTA
70975 TTCAATG-TCTCAATTTCAATT-
1 TTCAATGCT-TCAATTTCAATTC
*
70996 TTCAATGCTTCAAGTTCAATGT-
1 TTCAATGCTTCAATTTCAAT-TC
* *
71018 GTCAATGCTTCAATTTTAATTC
1 TTCAATGCTTCAATTTCAATTC
* *
71040 TTCGATGCTTCAATTTCCATTC
1 TTCAATGCTTCAATTTCAATTC
* * *
71062 TTCAACGCTTCAATGCTTAAATGC
1 TTCAATGCTTCAAT--TTCAATTC
71086 TTCAAT-C-TCATATTTCAATGT-
1 TTCAATGCTTCA-ATTTCAAT-TC
* *
71107 TTCAATGTTTCAAATTCAATTC
1 TTCAATGCTTCAATTTCAATTC
* *
71129 TTCAA--ATTCAATACTTCAATTA
1 TTCAATGCTTCAAT--TTCAATTC
*
71151 TTCAATGCTTCAATTTTTCAATTA
1 TTCAATGCTTCAA--TTTCAATTC
* *
71175 TTCAATTCTTCAATCCTTCAATTA
1 TTCAATGCTTCAAT--TTCAATTC
71199 TTCA
1 TTCA
71203 GTTTATTTCA
Statistics
Matches: 166, Mismatches: 23, Indels: 33
0.75 0.10 0.15
Matches are distributed among these distances:
20 5 0.03
21 30 0.18
22 77 0.46
23 6 0.04
24 47 0.28
26 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (22 bp):
TTCAATGCTTCAATTTCAATTC
Found at i:71074 original size:8 final size:8
Alignment explanation
Indices: 70996--71196 Score: 90
Period size: 8 Copynumber: 26.8 Consensus size: 8
70986 AATTTCAATT
70996 TTCAATGC
1 TTCAATGC
71004 TTCAA-G-
1 TTCAATGC
71010 TTCAATG-
1 TTCAATGC
71017 TGTCAATGC
1 T-TCAATGC
71026 TTCAAT--
1 TTCAATGC
* *
71032 TTTAATTC
1 TTCAATGC
*
71040 TTCGATGC
1 TTCAATGC
71048 TTCAAT--
1 TTCAATGC
* *
71054 TTCCATTC
1 TTCAATGC
*
71062 TTCAACGC
1 TTCAATGC
71070 TTCAATGC
1 TTCAATGC
*
71078 TTAAATGC
1 TTCAATGC
71086 TTCAAT-C
1 TTCAATGC
71093 -TCATAT--
1 TTCA-ATGC
*
71099 TTCAATGT
1 TTCAATGC
*
71107 TTCAATGT
1 TTCAATGC
*
71115 TTCAA--A
1 TTCAATGC
*
71121 TTCAATTC
1 TTCAATGC
*
71129 TTCAA--A
1 TTCAATGC
*
71135 TTCAATAC
1 TTCAATGC
**
71143 TTCAATTA
1 TTCAATGC
71151 TTCAATGC
1 TTCAATGC
**
71159 TTCAATTT
1 TTCAATGC
**
71167 TTCAATTA
1 TTCAATGC
*
71175 TTCAATTC
1 TTCAATGC
*
71183 TTCAATCC
1 TTCAATGC
71191 TTCAAT
1 TTCAAT
71197 TATTCAGTTT
Statistics
Matches: 153, Mismatches: 25, Indels: 30
0.74 0.12 0.14
Matches are distributed among these distances:
6 30 0.20
7 9 0.06
8 113 0.74
9 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.44
Consensus pattern (8 bp):
TTCAATGC
Found at i:71126 original size:14 final size:14
Alignment explanation
Indices: 71107--71163 Score: 69
Period size: 14 Copynumber: 3.9 Consensus size: 14
71097 ATTTCAATGT
*
71107 TTCAATGTTTCAAA
1 TTCAATGCTTCAAA
*
71121 TTCAATTCTTCAAA
1 TTCAATGCTTCAAA
*
71135 TTCAATACTTCAATTA
1 TTCAATGCTTCAA--A
71151 TTCAATGCTTCAA
1 TTCAATGCTTCAA
71164 TTTTTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
14 24 0.65
16 13 0.35
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (14 bp):
TTCAATGCTTCAAA
Done.