Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2558
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: 23333
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.30
Found at i:4656 original size:20 final size:20
Alignment explanation
Indices: 4631--4715 Score: 94
Period size: 20 Copynumber: 4.6 Consensus size: 20
4621 CGATACAATT
4631 TATCGATACATTGAATAATG
1 TATCGATACATTGAATAATG
*
4651 TATCGATATATTGAATAATG
1 TATCGATACATTGAATAATG
4671 TATCGATAC-------AATG
1 TATCGATACATTGAATAATG
* *
4684 CATCGATACATTGAATAATT
1 TATCGATACATTGAATAATG
4704 TATCGATACATT
1 TATCGATACATT
4716 TCCTTGGCAG
Statistics
Matches: 53, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
13 12 0.23
20 41 0.77
ACGTcount: A:0.39, C:0.12, G:0.13, T:0.36
Consensus pattern (20 bp):
TATCGATACATTGAATAATG
Found at i:4689 original size:33 final size:33
Alignment explanation
Indices: 4647--4713 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
4637 TACATTGAAT
* *
4647 AATGTATCGATATATTGAATAATGTATCGATAC
1 AATGCATCGATACATTGAATAATGTATCGATAC
*
4680 AATGCATCGATACATTGAATAATTTATCGATAC
1 AATGCATCGATACATTGAATAATGTATCGATAC
4713 A
1 A
4714 TTTCCTTGGC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.34
Consensus pattern (33 bp):
AATGCATCGATACATTGAATAATGTATCGATAC
Found at i:5711 original size:49 final size:50
Alignment explanation
Indices: 5642--6264 Score: 210
Period size: 49 Copynumber: 13.6 Consensus size: 50
5632 ATGTTAAAGA
* * * *
5642 TGCCAATATGATAATTCAAGGCCAACGATATCGGACTT-AAGGATGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
* * ** * * * *
5691 TGTCAATGTGCTGATTCAAGGCCAGCGACATTAGATTTGAA-AATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
* * * *
5740 TGCCAATATGCTGATTCAAAGCCAGCGACATTGGACTT-AAAGATGGTTGAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGAT-G--AAGG
* * * * *
5792 TGTCGATGTGCTGATTCAAGGCCAACGACATCGGTCTTCAAGG-TGAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
* * *
5841 TGCCAATATGCTGATTCAAGGCCAGCG--AT---A-TT--GGGCT-CA--
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
* * * * *
5880 TGCTAATGTGTTGATTCAAGGCCAGCGACATTGGGC-T------T----G
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
* * * * * * *
5919 TGCCAATGTGCTAATTCAAGTCCAGCGACATTGGTCTT-AAAGA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
* * * ***
5967 TACCAACATGCTGATTCAAGGCCAG-TA-AT---A-TT---GG--GCTTG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
* * * * * * *
6006 TGCTAATGTGCTGATTCAAAGCCAGCGACATTGGGCTTGAA-GA-CAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
* *
6054 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA--AT----G
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
* ** * * *
6097 TGCCAATATGCTGATTCAAGGCCAGCAACATTTGTCTT-AAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
* *
6146 TGCCAATATGCTGATTCAAGGCCAGCGATATAGGACTT--A--A--AA-G
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
* * * * * * *
6189 TGCCAATGTGCTGATTCAAGG-TAGCAACATTGGTCTT-AAAGATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
*
6237 TGCCAATATGCTGATTTAAGGCCAGCGA
1 TGCCAATATGCTGATTCAAGGCCAGCGA
6265 TAGTAGACTT
Statistics
Matches: 435, Mismatches: 91, Indels: 96
0.70 0.15 0.15
Matches are distributed among these distances:
39 76 0.17
40 4 0.01
41 7 0.02
42 14 0.03
43 61 0.14
44 3 0.01
45 5 0.01
46 4 0.01
47 8 0.02
48 78 0.18
49 134 0.31
50 2 0.00
51 1 0.00
52 35 0.08
53 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.26
Consensus pattern (50 bp):
TGCCAATATGCTGATTCAAGGCCAGCGACATCGGACTTCAAGGATGAAGG
Found at i:5719 original size:101 final size:100
Alignment explanation
Indices: 5636--5822 Score: 243
Period size: 98 Copynumber: 1.9 Consensus size: 100
5626 TTAGGAATGT
* * *
5636 TAAAGATGCCAATATGATAATTCAAGGCCAACGATATCGGACTTAAGGAT-G-AAGGTGTCAATG
1 TAAAGATGCCAATATGATAATTCAAAGCCAACGACATCGGACTTAAAGATGGTAAGGTGTCAATG
*
5699 TGCTGATTCAAGGCCAGCGACATTAGATTTGAAAA
66 TGCTGATTCAAGGCCAGCGACATTAGATTGGAAAA
* * * * * * *
5734 TAAAGGTGCCAATATGCTGATTCAAAGCCAGCGACATTGGACTTAAAGATGGTTGAGGTGTCGAT
1 TAAAGATGCCAATATGATAATTCAAAGCCAACGACATCGGACTTAAAGATGG-TAAGGTGTCAAT
*
5799 GTGCTGATTCAAGGCCAACGACAT
65 GTGCTGATTCAAGGCCAGCGACAT
5823 CGGTCTTCAA
Statistics
Matches: 75, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
98 42 0.56
99 1 0.01
101 32 0.43
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (100 bp):
TAAAGATGCCAATATGATAATTCAAAGCCAACGACATCGGACTTAAAGATGGTAAGGTGTCAATG
TGCTGATTCAAGGCCAGCGACATTAGATTGGAAAA
Found at i:5807 original size:52 final size:49
Alignment explanation
Indices: 5546--5868 Score: 170
Period size: 49 Copynumber: 6.5 Consensus size: 49
5536 CGAAGAATGA
* * * *
5546 CAATGTGTTGATTCATGGCCAGCGACATTAGACTTGAAGAA-GAA--TGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAA-AATAAAGGTGT
** * * * ** * *
5593 CAATGTGCTGAGACAAGGCTAGCGACATTGGGCTTAGGAATGTTAAAGATGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTT--GAA-AATAAAGGTGT
* * * * * ** * *
5645 CAATATGATAATTCAAGGCCAACGATATCGGACTT-AAGGATGAAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAA-AATAAAGGTGT
* *
5694 CAATGTGCTGATTCAAGGCCAGCGACATTAGATTTGAAAATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAAAATAAAGGTGT
* * * **
5743 CAATATGCTGATTCAAAGCCAGCGACATTGGACTT-AAAGATGGTTGAGGTGT
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAAA-A---TAAAGGTGT
* * ** * * ** * *
5795 CGATGTGCTGATTCAAGGCCAACGACATCGGTCTTCAAGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAAAATAAAGGTGT
*
5844 CAATATGCTGATTCAAGGCCAGCGA
1 CAATGTGCTGATTCAAGGCCAGCGA
5869 TATTGGGCTC
Statistics
Matches: 207, Mismatches: 58, Indels: 20
0.73 0.20 0.07
Matches are distributed among these distances:
47 28 0.14
48 3 0.01
49 107 0.52
50 4 0.02
52 63 0.30
53 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTAGACTTGAAAATAAAGGTGT
Found at i:5841 original size:101 final size:101
Alignment explanation
Indices: 5636--5874 Score: 270
Period size: 101 Copynumber: 2.4 Consensus size: 101
5626 TTAGGAATGT
* * * * * * * * *
5636 TAAAGATGCCAATATGATAATTCAAGGCCAACGATATCGGACTTAAGGAT-G--AAGGTGTCAAT
1 TAAAGGTGCCAATATGCTGATTCAAAGCCAGCGACATTGGACTTAAAGATGGTTGAGGTGTCAAT
* *
5698 GTGCTGATTCAAGGCCAGCGACATTAGATTTGAAAA
66 GTGCTGATTCAAGGCCAACGACATTAGATTTCAAAA
*
5734 TAAAGGTGCCAATATGCTGATTCAAAGCCAGCGACATTGGACTTAAAGATGGTTGAGGTGTCGAT
1 TAAAGGTGCCAATATGCTGATTCAAAGCCAGCGACATTGGACTTAAAGATGGTTGAGGTGTCAAT
* * **
5799 GTGCTGATTCAAGGCCAACGACA-TCGGTCTTCAAGG
66 GTGCTGATTCAAGGCCAACGACATTAGAT-TTCAAAA
* * *
5835 TGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGG
1 TAAAGGTGCCAATATGCTGATTCAAAGCCAGCGACATTGG
5875 GCTCATGCTA
Statistics
Matches: 118, Mismatches: 19, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
98 42 0.36
99 1 0.01
100 3 0.03
101 72 0.61
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.25
Consensus pattern (101 bp):
TAAAGGTGCCAATATGCTGATTCAAAGCCAGCGACATTGGACTTAAAGATGGTTGAGGTGTCAAT
GTGCTGATTCAAGGCCAACGACATTAGATTTCAAAA
Found at i:5906 original size:39 final size:39
Alignment explanation
Indices: 5841--6128 Score: 153
Period size: 39 Copynumber: 6.8 Consensus size: 39
5831 AAGGTGAAGG
* *
5841 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGGCTCA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTCA
* * **
5880 TGCTAATGTGTTGATTCAAGGCCAGCGACATTGGGCTTG
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTCA
* * *
5919 TGCCAATGTGCTAATTCAAGTCCAGCGACATTGGTCTTAAAGACAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGC-T-----C-A
* ** ** * **
5965 GGTACCAACATGCTGATTCAAGGCCAGTAATATTGGGCTTG
1 --TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTCA
* *
6006 TGCTAATGTGCTGATTCAAAGCCAGCGACATTGGGCTTGAAGACAA
1 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGC-T-----C-A
* * * *
6052 GGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAA
1 --TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGC-T-CA
* *
6095 TGTGCCAATATGCTGATTCAAGGCCAGCAACATT
1 --TGCCAATGTGCTGATTCAAGGCCAGCGACATT
6129 TGTCTTAAAG
Statistics
Matches: 188, Mismatches: 43, Indels: 32
0.71 0.16 0.12
Matches are distributed among these distances:
39 92 0.49
40 2 0.01
43 32 0.17
44 1 0.01
47 1 0.01
48 60 0.32
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.26
Consensus pattern (39 bp):
TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGGCTCA
Found at i:5998 original size:126 final size:127
Alignment explanation
Indices: 5797--6044 Score: 354
Period size: 126 Copynumber: 2.0 Consensus size: 127
5787 TGAGGTGTCG
* * ** * *
5797 ATGTGCTGATTCAAGGCCAACGACATCGGTCTTCAAGGTGAAGGTGCCAATATGCTGATTCAAGG
1 ATGTGCTAATTCAAGGCCAACGACATCGGTCTTCAAAGACAAGGTACCAACATGCTGATTCAAGG
* * *
5862 CCAGCGATATTGGGCTCATGCTAATGTGTTGATTCAAGGCCAGCGACATTGGGCTTGTGCCA
66 CCAGCAATATTGGGCTCATGCTAATGTGCTGATTCAAAGCCAGCGACATTGGGCTTGTGCCA
* * *
5924 ATGTGCTAATTCAAGTCCAGCGACATTGGTCTT-AAAGACAAGGTACCAACATGCTGATTCAAGG
1 ATGTGCTAATTCAAGGCCAACGACATCGGTCTTCAAAGACAAGGTACCAACATGCTGATTCAAGG
* **
5988 CCAGTAATATTGGGCTTGTGCTAATGTGCTGATTCAAAGCCAGCGACATTGGGCTTG
66 CCAGCAATATTGGGCTCATGCTAATGTGCTGATTCAAAGCCAGCGACATTGGGCTTG
6045 AAGACAAGGT
Statistics
Matches: 106, Mismatches: 15, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
126 77 0.73
127 29 0.27
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.27
Consensus pattern (127 bp):
ATGTGCTAATTCAAGGCCAACGACATCGGTCTTCAAAGACAAGGTACCAACATGCTGATTCAAGG
CCAGCAATATTGGGCTCATGCTAATGTGCTGATTCAAAGCCAGCGACATTGGGCTTGTGCCA
Found at i:6037 original size:87 final size:87
Alignment explanation
Indices: 5891--6266 Score: 450
Period size: 87 Copynumber: 4.2 Consensus size: 87
5881 GCTAATGTGT
* * * *
5891 TGATTCAAGGCCAGCGACATTGGGCTTGTGCCAATGTGCTAATTCAAGTCCAGCGACATTGGTCT
1 TGATTCAAGGCCAGCGATATTGGACTTGTGCCAATGTGCTGATTCAAG-CCAGCAACATTGGTCT
* * *
5956 TAAAGA-CAAGGTACCAACATGC
65 TAAAGATAAAGGTGCCAATATGC
** * * * *
5978 TGATTCAAGGCCAGTAATATTGGGCTTGTGCTAATGTGCTGATTCAAAGCCAGCGACATTGGGCT
1 TGATTCAAGGCCAGCGATATTGGACTTGTGCCAATGTGCTGATTC-AAGCCAGCAACATTGGTCT
* *
6043 TGAAGA-CAAGGTGCCAATATGC
65 TAAAGATAAAGGTGCCAATATGC
* *
6065 TGATTCAAGGCCAGCGATATTGGACTTAAATGTGCCAATATGCTGATTCAAGGCCAGCAACATTT
1 TGATTCAAGGCCAGCGATATTGGAC-T---TGTGCCAATGTGCTGATTCAA-GCCAGCAACATTG
6130 GTCTTAAAGATAAAGGTGCCAATATGC
61 GTCTTAAAGATAAAGGTGCCAATATGC
* **
6157 TGATTCAAGGCCAGCGATATAGGACTTAAAAGTGCCAATGTGCTGATTCAAGGTAGCAACATTGG
1 TGATTCAAGGCCAGCGATATTGGACTT----GTGCCAATGTGCTGATTCAAGCCAGCAACATTGG
6222 TCTTAAAGATAAAGGTGCCAATATGC
62 TCTTAAAGATAAAGGTGCCAATATGC
*
6248 TGATTTAAGGCCAGCGATA
1 TGATTCAAGGCCAGCGATA
6267 GTAGACTTAA
Statistics
Matches: 253, Mismatches: 25, Indels: 18
0.85 0.08 0.06
Matches are distributed among these distances:
87 96 0.38
88 5 0.02
90 2 0.01
91 92 0.36
92 58 0.23
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (87 bp):
TGATTCAAGGCCAGCGATATTGGACTTGTGCCAATGTGCTGATTCAAGCCAGCAACATTGGTCTT
AAAGATAAAGGTGCCAATATGC
Found at i:6168 original size:92 final size:91
Alignment explanation
Indices: 5891--6284 Score: 473
Period size: 91 Copynumber: 4.4 Consensus size: 91
5881 GCTAATGTGT
* * * * *
5891 TGATTCAAGGCCAGCGACATTGGGC-T---TGTGCCAATGTGCTAATTCAAGTCCAGCGACATTG
1 TGATTCAAGGCCAGCGATATTGGACTTAAATGTGCCAATGTGCTGATTCAAGGCCAGCAACATTG
* * *
5952 GTCTTAAAGACAAGGTACCAACATGC
66 GTCTTAAAGAAAAGGTGCCAATATGC
** * * * *
5978 TGATTCAAGGCCAGTAATATTGGGC-T---TGTGCTAATGTGCTGATTCAAAGCCAGCGACATTG
1 TGATTCAAGGCCAGCGATATTGGACTTAAATGTGCCAATGTGCTGATTCAAGGCCAGCAACATTG
* * *
6039 GGCTTGAAGACAAGGTGCCAATATGC
66 GTCTTAAAGAAAAGGTGCCAATATGC
* *
6065 TGATTCAAGGCCAGCGATATTGGACTTAAATGTGCCAATATGCTGATTCAAGGCCAGCAACATTT
1 TGATTCAAGGCCAGCGATATTGGACTTAAATGTGCCAATGTGCTGATTCAAGGCCAGCAACATTG
6130 GTCTTAAAGATAAAGGTGCCAATATGC
66 GTCTTAAAGA-AAAGGTGCCAATATGC
* * *
6157 TGATTCAAGGCCAGCGATATAGGACTTAAAAGTGCCAATGTGCTGATTCAAGG-TAGCAACATTG
1 TGATTCAAGGCCAGCGATATTGGACTTAAATGTGCCAATGTGCTGATTCAAGGCCAGCAACATTG
6221 GTCTTAAAGATAAAGGTGCCAATATGC
66 GTCTTAAAGA-AAAGGTGCCAATATGC
* * * *
6248 TGATTTAAGGCCAGCGATAGTAGACTTAAAGGTGCCA
1 TGATTCAAGGCCAGCGATATTGGACTTAAATGTGCCA
6285 CGGAGTTGTG
Statistics
Matches: 270, Mismatches: 32, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
87 98 0.36
88 1 0.00
91 106 0.39
92 65 0.24
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.26
Consensus pattern (91 bp):
TGATTCAAGGCCAGCGATATTGGACTTAAATGTGCCAATGTGCTGATTCAAGGCCAGCAACATTG
GTCTTAAAGAAAAGGTGCCAATATGC
Found at i:6350 original size:34 final size:33
Alignment explanation
Indices: 6278--6632 Score: 311
Period size: 34 Copynumber: 10.8 Consensus size: 33
6268 TAGACTTAAA
*
6278 GGTGCCACGGAGTTGTGGACTT-AAAGGAAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAG
**
6310 TATGCCACGGAGTTGTGGACTTAAAAGGGAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAA-GGAAAAG
* *
6344 GGTGCCACAGAGTTGTGGACTTAAAAAGAAAA-
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAG
* * *
6376 TGTGCCATGGAGTTGTGGACTTTGAAAGGAACAA-
1 GGTGCCACGGAGTTGTGGAC-TTAAAAGGAA-AAG
* * * *
6410 GGTGCCACAGAGTAGTTGACTTAAAAGGAAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAG
* * *
6443 GATGCCATGGAGTTGTGGACTTCAAAGGAAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAGG-AAAAG
* * *
6477 AGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAG
** *
6510 GGTGCCATAGAGTTGTAGACTTACAGAA--AAAAG
1 GGTGCCACGGAGTTGTGGACTTA-A-AAGGAAAAG
* * *
6543 GGATGCCACAGAGGTATAGG-CTT------AAAAG
1 GG-TGCCACGGAGTTGT-GGACTTAAAAGGAAAAG
*
6571 GGTGCCACGGAGTTGTGAACTTAAAAGGAAAAAG
1 GGTGCCACGGAGTTGTGGACTTAAAAGG-AAAAG
*
6605 AGTGCCACGGAGTTGTGGACTTAAAAGG
1 GGTGCCACGGAGTTGTGGACTTAAAAGG
6633 GTGCTACAAA
Statistics
Matches: 259, Mismatches: 46, Indels: 34
0.76 0.14 0.10
Matches are distributed among these distances:
26 1 0.00
27 14 0.05
28 7 0.03
32 39 0.15
33 77 0.30
34 118 0.46
35 3 0.01
ACGTcount: A:0.36, C:0.12, G:0.32, T:0.20
Consensus pattern (33 bp):
GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAG
Found at i:6462 original size:67 final size:65
Alignment explanation
Indices: 6275--6720 Score: 396
Period size: 67 Copynumber: 6.9 Consensus size: 65
6265 TAGTAGACTT
* *
6275 AAAGGTGCCACGGAGTTGTGGACTT-AAAGGAAAAATATGCCACGGAGTTGTGGACTTAAAAGGG
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAA-GTGCCACGGAGTTGTGGACTTAAAA-GG
6339 AA
64 AA
* * * * *
6341 AAGGGTGCCACAGAGTTGTGGACTTAAAAAGAAAATGTGCCATGGAGTTGTGGACTTTGAAAGGA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGTGCCACGGAGTTGTGGAC-TTAAAAGGA
6406 A
65 A
* * * * *
6407 CAAGGTGCCACAGAGTAGTTGACTTAAAAGGAAAAAGATGCCATGGAGTTGTGGACTTCAAAGGA
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAG-TGCCACGGAGTTGTGGACTTAAAAGGA
6472 A
65 A
* * * * ** * * *
6473 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAGGGTGCCATAGAGTTGTAGACTT-ACAGA
1 AAAG-GTGCCACAGAGTTGTGGACTTAAAAGGAAAA-AGTGCCACGGAGTTGTGGACTTAAAAGG
6537 AA
64 AA
* * *
6539 AAAGGGATGCCACAGAGGTATAGG-CTTAAAAGG-----GTGCCACGGAGTTGTGAACTTAAAAG
1 AAA-GG-TGCCACAGAGTTGT-GGACTTAAAAGGAAAAAGTGCCACGGAGTTGTGGACTTAAAAG
6598 GAA
63 GAA
* * **
6601 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGG-----GTGCTACAAAGTTGTGGACTTTAAAAGG
1 AAAG-GTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGTGCCACGGAGTTGTGGAC-TTAAAAGG
6661 AA
64 AA
* * * * *
6663 CAAGGTGCCACAGAGTTGTGGACCTAAAAGGAAAAATTTGCCACGAAGTGGTGGACTT
1 AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAA-GTGCCACGGAGTTGTGGACTT
6721 TGAGAAGAGA
Statistics
Matches: 313, Mismatches: 49, Indels: 36
0.79 0.12 0.09
Matches are distributed among these distances:
60 2 0.01
61 78 0.25
62 22 0.07
66 98 0.31
67 110 0.35
68 3 0.01
ACGTcount: A:0.36, C:0.13, G:0.31, T:0.20
Consensus pattern (65 bp):
AAAGGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGTGCCACGGAGTTGTGGACTTAAAAGGAA
Found at i:6593 original size:27 final size:27
Alignment explanation
Indices: 6563--6660 Score: 88
Period size: 34 Copynumber: 3.3 Consensus size: 27
6553 GAGGTATAGG
*
6563 CTTAAAAGGGTGCCACGGAGTTGTGAA
1 CTTAAAAGGGTGCCACGGAGTTGTGGA
6590 CTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGA
1 CTTAAAA-G-----G-GTGCCACGGAGTTGTGGA
* **
6624 CTTAAAAGGGTGCTACAAAGTTGTGGA
1 CTTAAAAGGGTGCCACGGAGTTGTGGA
6651 CTTTAAAAGG
1 C-TTAAAAGG
6661 AACAAGGTGC
Statistics
Matches: 59, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
27 23 0.39
28 10 0.17
33 2 0.03
34 24 0.41
ACGTcount: A:0.35, C:0.12, G:0.31, T:0.22
Consensus pattern (27 bp):
CTTAAAAGGGTGCCACGGAGTTGTGGA
Found at i:6593 original size:61 final size:61
Alignment explanation
Indices: 6505--6693 Score: 170
Period size: 61 Copynumber: 3.1 Consensus size: 61
6495 GCTTAAAAAG
* * *
6505 AAAAGGGTGCCATAGAGTTGTAGACTT-ACAGAAAAAAGGGATGCCACAGAGGTATAGG-CTT
1 AAAAGGGTGCCACAGAGTTGTAGACTTAAAAGAAAAAAGAG-TGCCACAGAGGTAT-GGACTT
* * * * *
6566 AAAAGGGTGCCACGGAGTTGT-GAACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT
1 AAAAGGGTGCCACAGAGTTGTAG-ACTTAAAAGAAAAAAGAGTGCCACAGAGGTATGGACTT
* * * * * * * *
6627 AAAAGGGTGCTACAAAGTTGTGGACTTTAAAAGGAACAAG-GTGCCACAGAGTTGTGGACCT
1 AAAAGGGTGCCACAGAGTTGTAGAC-TTAAAAGAAAAAAGAGTGCCACAGAGGTATGGACTT
6688 AAAAGG
1 AAAAGG
6694 AAAAATTTGC
Statistics
Matches: 109, Mismatches: 14, Indels: 10
0.82 0.11 0.08
Matches are distributed among these distances:
60 3 0.03
61 82 0.75
62 24 0.22
ACGTcount: A:0.37, C:0.13, G:0.31, T:0.20
Consensus pattern (61 bp):
AAAAGGGTGCCACAGAGTTGTAGACTTAAAAGAAAAAAGAGTGCCACAGAGGTATGGACTT
Found at i:6680 original size:34 final size:34
Alignment explanation
Indices: 6627--6721 Score: 95
Period size: 33 Copynumber: 2.8 Consensus size: 34
6617 TTGTGGACTT
* * *
6627 AAAAGGGTGCTACAAAGTTGTGGACTTTAAAAGG
1 AAAAAGGTGCCACAGAGTTGTGGACTTTAAAAGG
* *
6661 AACAAGGTGCCACAGAGTTGTGGAC-CTAAAAGG
1 AAAAAGGTGCCACAGAGTTGTGGACTTTAAAAGG
** *
6694 AAAAATTTGCCAC-GAAGTGGTGGACTTT
1 AAAAAGGTGCCACAG-AGTTGTGGACTTT
6722 GAGAAGAGAT
Statistics
Matches: 49, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
32 1 0.02
33 26 0.53
34 22 0.45
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (34 bp):
AAAAAGGTGCCACAGAGTTGTGGACTTTAAAAGG
Found at i:6706 original size:33 final size:34
Alignment explanation
Indices: 6627--6698 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
6617 TTGTGGACTT
* * * *
6627 AAAAGGGTGCTACAAAGTTGTGGACTTTAAAAGG
1 AAAAAGGTGCCACAGAGTTGTGGACTCTAAAAGG
*
6661 AACAAGGTGCCACAGAGTTGTGGAC-CTAAAAGG
1 AAAAAGGTGCCACAGAGTTGTGGACTCTAAAAGG
6694 AAAAA
1 AAAAA
6699 TTTGCCACGA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
33 11 0.34
34 21 0.66
ACGTcount: A:0.42, C:0.12, G:0.28, T:0.18
Consensus pattern (34 bp):
AAAAAGGTGCCACAGAGTTGTGGACTCTAAAAGG
Found at i:6814 original size:95 final size:93
Alignment explanation
Indices: 6714--7069 Score: 350
Period size: 95 Copynumber: 3.8 Consensus size: 93
6704 CACGAAGTGG
*
6714 TGGACTTTG-AGAAGAGATTGCCACTAAGT-GTGGACTTTGAAGAAAAGATGCCACTGAGTCATG
1 TGGACTTTGAAGAAGAGA-TGCCACTAAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTG
*
6777 GACTTTGAAAATAAAAAGGTGCCACAGAGTCA
65 GACTTTG--AA-AAAAAGGTGCCACTGAGTCA
* * *
6809 TGGACTTTG-GGAAGAGATTGCCACTGAGTCGTGGACTTTGAAGAAAAGAGACGCCACTGAGTCG
1 TGGACTTTGAAGAAGAGA-TGCCACTAAGTCGTGGACTTTGAAG-AAA-AGATGCCACTGAGTCG
* * *
6873 TGGAC-TTG-AGAAGAGATGCCACTGAGTCA
63 TGGACTTTGAAAAAAAGGTGCCACTGAGTCA
* * * * *
6902 TGGACTTTGAAGAAAAGAGACGCCACTGAGTCGTGGAC-TT-AGGAAGAGATGCCACTGAGTTGT
1 TGGACTTTGAAG--AAGAGATGCCACTAAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGT
*
6965 GGACTTTGAAGAAAAAGGATGCCACTGAGTCG
64 GGACTTTGAA-AAAAAGG-TGCCACTGAGTCA
* * * * * * *
6997 TGGACTTAGGAAGAAAAGGATGCCACTAAGTCGTGGACTTAGAA-AAGAGATGTCACTAAGTTGT
1 TGGACTT-TGAAGAAGA-GATGCCACTAAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGT
7061 GGACTTTGA
64 GGACTTTGA
7070 GAAGAGAGAT
Statistics
Matches: 221, Mismatches: 26, Indels: 27
0.81 0.09 0.10
Matches are distributed among these distances:
91 19 0.09
92 5 0.02
93 28 0.13
94 11 0.05
95 81 0.37
96 51 0.23
97 7 0.03
98 19 0.09
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (93 bp):
TGGACTTTGAAGAAGAGATGCCACTAAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGG
ACTTTGAAAAAAAGGTGCCACTGAGTCA
Found at i:6869 original size:33 final size:32
Alignment explanation
Indices: 6713--7079 Score: 345
Period size: 33 Copynumber: 11.7 Consensus size: 32
6703 CCACGAAGTG
*
6713 GTGGACTTTGAG--AAGAGATTGCCACTAAGT-
1 GTGGACTTTGAGAAAAGAGA-TGCCACTGAGTC
6743 GTGGACTTTGA-AGAAA-AGATGCCACTGAGTC
1 GTGGACTTTGAGA-AAAGAGATGCCACTGAGTC
* * * * *
6774 ATGGACTTTGAAAATAAAAAGGTGCCACAGAGTC
1 GTGGACTTTG-AGA-AAAGAGATGCCACTGAGTC
* *
6808 ATGGACTTTG-G-GAAGAGATTGCCACTGAGTC
1 GTGGACTTTGAGAAAAGAGA-TGCCACTGAGTC
*
6839 GTGGACTTTGAAGAAAAGAGACGCCACTGAGTC
1 GTGGACTTTG-AGAAAAGAGATGCCACTGAGTC
6872 GTGGAC-TTGAG--AAGAGATGCCACTGAGTC
1 GTGGACTTTGAGAAAAGAGATGCCACTGAGTC
* *
6901 ATGGACTTTGAAGAAAAGAGACGCCACTGAGTC
1 GTGGACTTTG-AGAAAAGAGATGCCACTGAGTC
* *
6934 GTGGAC-TT-AG-GAAGAGATGCCACTGAGTT
1 GTGGACTTTGAGAAAAGAGATGCCACTGAGTC
6963 GTGGACTTTGAAGAAAA-AGGATGCCACTGAGTC
1 GTGGACTTTG-AGAAAAGA-GATGCCACTGAGTC
* *
6996 GTGGACTTAGGAAGAAAAG-GATGCCACTAAGTC
1 GTGGACTT-TG-AGAAAAGAGATGCCACTGAGTC
* * *
7029 GTGGAC-TT-AGAAAAGAGATGTCACTAAGTT
1 GTGGACTTTGAGAAAAGAGATGCCACTGAGTC
*
7059 GTGGACTTTGAGAAGAGAGAT
1 GTGGACTTTGAGAAAAGAGAT
7080 TTGAAGAATT
Statistics
Matches: 284, Mismatches: 28, Indels: 48
0.79 0.08 0.13
Matches are distributed among these distances:
29 51 0.18
30 50 0.18
31 38 0.13
32 22 0.08
33 86 0.30
34 37 0.13
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (32 bp):
GTGGACTTTGAGAAAAGAGATGCCACTGAGTC
Found at i:6906 original size:62 final size:63
Alignment explanation
Indices: 6713--7076 Score: 406
Period size: 62 Copynumber: 5.8 Consensus size: 63
6703 CCACGAAGTG
* *
6713 GTGGACTTTG-AG--AAGAGATTGCCACTAAGT-GTGGACTTTGAAGAAAAGATGCCACTGAGTC
1 GTGGACTTTGAAGAAAAGAGA-TGCCACTGAGTCGTGGACTTTG-AGAAGAGATGCCACTGAGTC
* * * * * * *
6774 ATGGACTTTGAAAATAAAAAGGTGCCACAGAGTCATGGACTTTGGGAAGAGATTGCCACTGAGTC
1 GTGGACTTTGAAGA-AAAGAGATGCCACTGAGTCGTGGACTTTGAGAAGAGA-TGCCACTGAGTC
*
6839 GTGGACTTTGAAGAAAAGAGACGCCACTGAGTCGTGGAC-TTGAGAAGAGATGCCACTGAGTC
1 GTGGACTTTGAAGAAAAGAGATGCCACTGAGTCGTGGACTTTGAGAAGAGATGCCACTGAGTC
* * * *
6901 ATGGACTTTGAAGAAAAGAGACGCCACTGAGTCGTGGACTTAG-GAAGAGATGCCACTGAGTT
1 GTGGACTTTGAAGAAAAGAGATGCCACTGAGTCGTGGACTTTGAGAAGAGATGCCACTGAGTC
* * *
6963 GTGGACTTTGAAGAAAA-AGGATGCCACTGAGTCGTGGACTTAGGAAGAAAAGGATGCCACTAAG
1 GTGGACTTTGAAGAAAAGA-GATGCCACTGAGTCGTGGACTT-TG-AGAAGA-GATGCCACTGAG
7027 TC
62 TC
* * *
7029 GTGGAC-TT--AGAAAAGAGATGTCACTAAGTTGTGGACTTTGAGAAGAGA
1 GTGGACTTTGAAGAAAAGAGATGCCACTGAGTCGTGGACTTTGAGAAGAGA
7077 GATTTGAAGA
Statistics
Matches: 259, Mismatches: 31, Indels: 27
0.82 0.10 0.09
Matches are distributed among these distances:
60 2 0.01
61 15 0.06
62 107 0.41
63 38 0.15
64 36 0.14
65 43 0.17
66 18 0.07
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (63 bp):
GTGGACTTTGAAGAAAAGAGATGCCACTGAGTCGTGGACTTTGAGAAGAGATGCCACTGAGTC
Found at i:8346 original size:9 final size:9
Alignment explanation
Indices: 8334--8365 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
8324 TTTTTGTATG
8334 TTTTTTTGT
1 TTTTTTTGT
8343 TTTTTTTGT
1 TTTTTTTGT
*
8352 TTTTTTTAT
1 TTTTTTTGT
8361 TTTTT
1 TTTTT
8366 CATCATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.03, C:0.00, G:0.06, T:0.91
Consensus pattern (9 bp):
TTTTTTTGT
Found at i:13837 original size:52 final size:51
Alignment explanation
Indices: 13759--13907 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
13749 CGAAATATGA
13759 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
13811 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
13863 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
13908 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:13914 original size:13 final size:13
Alignment explanation
Indices: 13896--13920 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13886 CAAAGATCAG
13896 TGTATCGATACAA
1 TGTATCGATACAA
13909 TGTATCGATACA
1 TGTATCGATACA
13921 TTTAAGTGAT
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:14001 original size:13 final size:13
Alignment explanation
Indices: 13983--14007 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13973 CAAAAAAATA
13983 TGTATCGATACAT
1 TGTATCGATACAT
13996 TGTATCGATACA
1 TGTATCGATACA
14008 CACTTATGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:19036 original size:20 final size:20
Alignment explanation
Indices: 18983--19037 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
18973 AAATTTCCAG
**
18983 ATGTATCGATACAAAGATCA
1 ATGTATCGATACATTGATCA
19003 ATGTATCGATACATTGAAT-A
1 ATGTATCGATACATTG-ATCA
19023 ATGTATCGATACATT
1 ATGTATCGATACATT
19038 TCCTTAGTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (20 bp):
ATGTATCGATACATTGATCA
Found at i:20209 original size:13 final size:13
Alignment explanation
Indices: 20191--20216 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20181 ACATTATGCT
20191 TTGTATCGATACA
1 TTGTATCGATACA
20204 TTGTATCGATACA
1 TTGTATCGATACA
20217 GATTCATTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:22472 original size:30 final size:30
Alignment explanation
Indices: 22416--22472 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
22406 AAGCGGAGGG
* **
22416 GAAAGGAAAAAAATAATAATGCTAAAATTA
1 GAAAAGAAAAAAATAATAATAATAAAATTA
22446 GAAAAGAAAAGAAATAATAA-AATAAAA
1 GAAAAGAAAA-AAATAATAATAATAAAA
22473 AAACGTAAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
30 14 0.61
31 9 0.39
ACGTcount: A:0.70, C:0.02, G:0.12, T:0.16
Consensus pattern (30 bp):
GAAAAGAAAAAAATAATAATAATAAAATTA
Done.