Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1875
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: 42537
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Found at i:4426 original size:20 final size:21
Alignment explanation
Indices: 4399--4455 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
4389 TCAAAAACCT
4399 AGAATGTATCAATACAATG-A
1 AGAATGTATCAATACAATGCA
* * *
4419 ATAATGTATCGATACATTGCA
1 AGAATGTATCAATACAATGCA
*
4440 AGCATGTATCAATACA
1 AGAATGTATCAATACA
4456 TTAACTTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (21 bp):
AGAATGTATCAATACAATGCA
Found at i:4565 original size:20 final size:21
Alignment explanation
Indices: 4537--4587 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
4527 TGCTAGCATA
*
4537 TATCAATACATTCA-TT-TATG
1 TATCGATACATTCACTTGT-TG
*
4557 TATCGATACATTGACTTGTTG
1 TATCGATACATTCACTTGTTG
4578 TATCGATACA
1 TATCGATACA
4588 AATTGTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 12 0.44
21 14 0.52
22 1 0.04
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (21 bp):
TATCGATACATTCACTTGTTG
Found at i:5603 original size:3 final size:3
Alignment explanation
Indices: 5595--5654 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
5585 ACATGAAAAT
5595 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5643 TAA TAA TAA TAA
1 TAA TAA TAA TAA
5655 ATATCAATCT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:12504 original size:14 final size:15
Alignment explanation
Indices: 12478--12508 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12468 GTTATTTCTT
12478 TTTCTATTTTTTTTC
1 TTTCTATTTTTTTTC
12493 TTTCTATTTTTTTTC
1 TTTCTATTTTTTTTC
12508 T
1 T
12509 AGTTTTCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (15 bp):
TTTCTATTTTTTTTC
Found at i:15668 original size:52 final size:52
Alignment explanation
Indices: 15590--15718 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
15580 CGAAATATGA
* * *
15590 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGT
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
*
15642 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
15694 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
15719 AAGATCAGGG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGC
Found at i:16455 original size:67 final size:68
Alignment explanation
Indices: 16333--16459 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
16323 ATTGGGTTTT
* * *
16333 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
16398 AGA
66 AGA
* * * *
16401 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
16460 GAAACAGGAT
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:0.25, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:16509 original size:55 final size:52
Alignment explanation
Indices: 16409--17003 Score: 405
Period size: 43 Copynumber: 12.6 Consensus size: 52
16399 GAAAAGTGAT
* * * * * * **
16409 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-GA
** *
16462 AACAGGATGTTAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AA-AGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
16516 AAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
*
16559 AAAGGTGCCAATATGTTGATTCAAGGCCAGCTACATTG-ACTTAAAGA---A
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * * *
16607 GAAGGTGCCAATATGCTG-TTCAAGGCTAGCAATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
16649 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
16699 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
16741 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
16791 -AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
16833 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
16883 -AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
16925 AAAGGTGCCAATGTGATGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
16975 -AAGGTGCCAATATGCTGATTCAAGGCCAG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAG
17004 TGATATTGGG
Statistics
Matches: 452, Mismatches: 47, Indels: 90
0.77 0.08 0.15
Matches are distributed among these distances:
42 18 0.04
43 170 0.38
44 4 0.01
46 1 0.00
47 17 0.04
48 21 0.05
49 144 0.32
51 1 0.00
52 31 0.07
53 4 0.01
54 6 0.01
55 35 0.08
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:16581 original size:43 final size:44
Alignment explanation
Indices: 16520--17022 Score: 581
Period size: 43 Copynumber: 11.0 Consensus size: 44
16510 GATGGAAAAT
16520 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-AAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAG
* *
16563 GTGCCAATATGTTGATTCAAGGCCAGCTACATT-GACTTAAAGAAGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-----AGAAG
* *
16611 GTGCCAATATGCTG-TTCAAGGCTAGCAATATTGGACTTA-AAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAG
* *
16653 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A-GAAG
*
16702 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAG
* *
16745 GTGCCAATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A-GAAG
16794 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-AAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAG
* *
16837 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A-GAAG
16886 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA-AAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAG
* * *
16929 GTGCCAATGTGATGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A-GAAG
*
16978 GTGCCAATATGCTGATTCAAGGCCAG-TGATATTGGGCTTAGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCT-ATATTGGACTTAGAAG
17022 G
1 G
17023 GTTGCCACCG
Statistics
Matches: 398, Mismatches: 29, Indels: 65
0.81 0.06 0.13
Matches are distributed among these distances:
42 21 0.05
43 171 0.43
44 5 0.01
45 4 0.01
47 20 0.05
48 22 0.06
49 155 0.39
ACGTcount: A:0.31, C:0.17, G:0.25, T:0.26
Consensus pattern (44 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAGAAG
Found at i:16584 original size:21 final size:21
Alignment explanation
Indices: 16520--16584 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
16510 GATGGAAAAT
*
16520 GTGCCAATATGCTGATTCAA-
1 GTGCCAATATGTTGATTCAAG
* * *
16540 G-GCCAGCTATATTGGACTTAAAG
1 GTGCCA-ATATGTT-GA-TTCAAG
16563 GTGCCAATATGTTGATTCAAG
1 GTGCCAATATGTTGATTCAAG
16584 G
1 G
16585 CCAGCTACAT
Statistics
Matches: 33, Mismatches: 7, Indels: 9
0.67 0.14 0.18
Matches are distributed among these distances:
19 4 0.12
20 5 0.15
21 8 0.24
22 6 0.18
23 6 0.18
24 4 0.12
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (21 bp):
GTGCCAATATGTTGATTCAAG
Found at i:16750 original size:92 final size:92
Alignment explanation
Indices: 16473--17022 Score: 926
Period size: 92 Copynumber: 6.0 Consensus size: 92
16463 ACAGGATGTT
* *
16473 AATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTC
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGATTC
16538 AAGGCCAGCTATATTGGACTTAAAGGTGCC
63 AAGGCCAGCTATATTGGACTTAAAGGTGCC
* * *
16568 AATATGTTGATTCAAGGCCAGCTACATT-GACTTAAAGAAGAAGGTGCCAATATGCTG-TTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAG
* *
16631 GCTAGCAATATTGGACTTAAAGGTGCC
66 GCCAGCTATATTGGACTTAAAGGTGCC
16658 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAG
*
16723 GCCAGCGATATTGGACTTAAAGGTGCC
66 GCCAGCTATATTGGACTTAAAGGTGCC
* *
16750 AATGTGCTGATTCAAGGCCAGCTATATTGAACTTAAAGATGAAGGTGCCAATATGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAG
16815 GCCAGCTATATTGGACTTAAAGGTGCC
66 GCCAGCTATATTGGACTTAAAGGTGCC
16842 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAG
16907 GCCAGCTATATTGGACTTAAAGGTGCC
66 GCCAGCTATATTGGACTTAAAGGTGCC
*
16934 AATGTGATGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAG
1 AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAG
*
16999 GCCAG-TGATATTGGGCTTAGAAGG
66 GCCAGCT-ATATTGGACTTA-AAGG
17023 GTTGCCACCG
Statistics
Matches: 432, Mismatches: 19, Indels: 10
0.94 0.04 0.02
Matches are distributed among these distances:
90 57 0.13
91 45 0.10
92 290 0.67
93 5 0.01
94 9 0.02
95 26 0.06
ACGTcount: A:0.32, C:0.17, G:0.25, T:0.26
Consensus pattern (92 bp):
AATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAG
GCCAGCTATATTGGACTTAAAGGTGCC
Found at i:17061 original size:33 final size:33
Alignment explanation
Indices: 17017--17317 Score: 472
Period size: 33 Copynumber: 9.2 Consensus size: 33
17007 TATTGGGCTT
17017 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
17050 AGAATGGTTGCCACCAACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
17083 AG-AGGGTTGCCACCGACTTGTGTGGGCTTT-G
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
17114 A-AAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
17146 AAGAA-GGTTGCCACCGACTTGTGTGGGCTTTAG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
17179 AGAAGGGTTGCCACCGACTTGTGTGGGTTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
*
17212 AAGAA-GGTTGCCACCAACTTGTGTGGGCTTTAG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
17245 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
* *
17278 AAGAA-GGTTGCCACCAACTTGTGTGGGCTTTGG
1 -AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
17311 A-AAGGGT
1 AGAAGGGT
17318 GAAAGATGCC
Statistics
Matches: 249, Mismatches: 10, Indels: 19
0.90 0.04 0.07
Matches are distributed among these distances:
31 32 0.13
32 39 0.16
33 168 0.67
34 10 0.04
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.28
Consensus pattern (33 bp):
AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:17426 original size:34 final size:34
Alignment explanation
Indices: 17319--17663 Score: 306
Period size: 34 Copynumber: 10.8 Consensus size: 34
17309 GGAAAGGGTG
* * *
17319 AAAGA-TGCCACGAAGTTGTGGACTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
17352 GAAG-GTGCCACGGAGTTGTGGGCTTTAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGAC-TTAGAA-GGAA
17387 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
17421 AAAGAGTGCCACGGAGTTGT-GAGCTT-------A
1 AAAGAGTGCCACGGAGTTGTGGA-CTTAGAAGGAA
*
17448 AAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
17482 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
*
17516 AAAGAGTGCCACGGAGTTGTGGGCTT-------A
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
17543 AAAGGGTGCCACGGAGTTGTGGACTTTG-ATG-A
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
17575 GAAG-GTGCCACAGAGTTGTGGACTTAAAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* * *
17608 AAAGAGTGTCACAGAGTCGTGGACTT-GAA-G-A
1 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
* **
17639 AAAGA-TGCCACTGAGCCGTGGACTT
1 AAAGAGTGCCACGGAGTTGTGGACTT
17664 TGGAAAGAGA
Statistics
Matches: 267, Mismatches: 24, Indels: 45
0.79 0.07 0.13
Matches are distributed among these distances:
27 48 0.18
28 2 0.01
30 17 0.06
31 26 0.10
32 7 0.03
33 27 0.10
34 111 0.42
35 11 0.04
36 18 0.07
ACGTcount: A:0.32, C:0.13, G:0.34, T:0.20
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAA
Found at i:17457 original size:61 final size:60
Alignment explanation
Indices: 17385--17716 Score: 238
Period size: 61 Copynumber: 5.4 Consensus size: 60
17375 TTTAAAAGGG
*
17385 AAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGAGCTT
1 AAAAAGGGTGCCACGGAGTTGTGGACTTA-AAGGAAAAAGAGTGCCACGGAGTTGTG-GCTT
17447 -AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAAGGGTGCCACGGAGTTGTGGACTTA-AAGGAAAAAGAGTGCCACGGAGTTGT-GGCTT
* * *
17508 AGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT------AAAAGGGTGCCACGGAGTTGTGGAC
1 ------AAAAAGGGTGCCACGGAGTTGTGGACTTAAAGGAAAAAGAGTGCCACGGAGTTGTGG-C
17567 TTT
59 -TT
* * * * *
17570 GATGAGAA-GGTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGTCACAGAGTCGTGGACTT
1 -A--AAAAGGGTGCCACGGAGTTGTGGACTT-AAAGGAAAAAGAGTGCCACGGAGTTGTGG-CTT
* * * ** * * *
17634 GAAGAAAAGATGCCACTGAGCCGTGGACTT--TGGAAAGAGA-TGCCACTGAGTTGTGGGCTT
1 -AA-AAAGGGTGCCACGGAGTTGTGGACTTAAAGGAAAAAGAGTGCCACGGAGTTGT-GGCTT
*
17694 -AAAAGGGTGCCACAGAGTTGTGG
1 AAAAAGGGTGCCACGGAGTTGTGG
17717 GCTTTGAGAC
Statistics
Matches: 221, Mismatches: 27, Indels: 49
0.74 0.09 0.16
Matches are distributed among these distances:
57 19 0.09
58 20 0.09
59 3 0.01
60 16 0.07
61 89 0.40
62 4 0.02
63 2 0.01
64 22 0.10
65 21 0.10
68 25 0.11
ACGTcount: A:0.31, C:0.14, G:0.35, T:0.20
Consensus pattern (60 bp):
AAAAAGGGTGCCACGGAGTTGTGGACTTAAAGGAAAAAGAGTGCCACGGAGTTGTGGCTT
Found at i:17495 original size:95 final size:95
Alignment explanation
Indices: 17355--17624 Score: 402
Period size: 95 Copynumber: 2.9 Consensus size: 95
17345 AAAAGAAGAA
* *
17355 GGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGA
1 GGTGCCACGGAGTTGTGGAC-TTAGAA-GGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGA
17420 AAAAGAGTGCCACGGAGTTGTGAGCTTAAAAG
64 AAAAGAGTGCCACGGAGTTGTGAGCTTAAAAG
*
17452 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAA
1 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAA
*
17517 AAGAGTGCCACGGAGTTGTGGGCTTAAAAG
66 AAGAGTGCCACGGAGTTGTGAGCTTAAAAG
* * * * *
17547 GGTGCCACGGAGTTGTGGACTTTG-ATG-AGAAG-GTGCCACAGAGTTGTGGACTTAAAAGGAAA
1 GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAA
* *
17609 AAGAGTGTCACAGAGT
66 AAGAGTGCCACGGAGT
17625 CGTGGACTTG
Statistics
Matches: 161, Mismatches: 12, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
92 41 0.25
93 4 0.02
94 2 0.01
95 90 0.56
96 5 0.03
97 19 0.12
ACGTcount: A:0.31, C:0.13, G:0.36, T:0.20
Consensus pattern (95 bp):
GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAA
AAGAGTGCCACGGAGTTGTGAGCTTAAAAG
Found at i:17564 original size:27 final size:27
Alignment explanation
Indices: 17515--17605 Score: 103
Period size: 27 Copynumber: 3.2 Consensus size: 27
17505 CTTAGAAGGA
* *
17515 AAAAGAGTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTT
17542 AAAAGGGTGCCACGGAGTTGTGGACTTT
1 AAAAGGGTGCCACGGAGTTGTGGAC-TT
*
17570 GATGAGAA-GGTGCCACAGAGTTGTGGACTT
1 -A--A-AAGGGTGCCACGGAGTTGTGGACTT
17600 AAAAGG
1 AAAAGG
17606 AAAAAGAGTG
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
26 2 0.04
27 25 0.45
28 2 0.04
29 2 0.04
30 2 0.04
31 20 0.36
32 2 0.04
ACGTcount: A:0.29, C:0.13, G:0.36, T:0.22
Consensus pattern (27 bp):
AAAAGGGTGCCACGGAGTTGTGGACTT
Found at i:17648 original size:95 final size:91
Alignment explanation
Indices: 17387--17699 Score: 362
Period size: 95 Copynumber: 3.4 Consensus size: 91
17377 TAAAAGGGAA
*
17387 AAAGAGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGT-GAGCTTAAAA
1 AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGA-CTTAAAA
*
17451 GGGTGCCACGGAGTTGTGGACTTAGAAGG
65 GGGTGCCACGGAGTTGTGGACTTTG-A-G
* * *
17480 AAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAA
1 --AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAA
17545 AGGGTGCCACGGAGTTGTGGACTTTGATG
64 AGGGTGCCACGGAGTTGTGGACTTTGA-G
* * * *
17574 AGAAG-GTGCCACAGAGTTGTGGACTTAAAAGGAAAAAGAGTGTCACAGAGTCGTGGACTTGAAG
1 A-AAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTT--A-
* * * **
17638 AAAAGATGCCACTGAGCCGTGGACTTTG-G
62 AAAGGGTGCCACGGAGTTGTGGACTTTGAG
* *
17667 AAAGAGATGCCACTGAGTTGTGGGCTTAAAAGG
1 AAAGAG-TGCCACGGAGTTGTGGACTTAAAAGG
17700 GTGCCACAGA
Statistics
Matches: 193, Mismatches: 18, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
92 52 0.27
93 6 0.03
94 27 0.14
95 107 0.55
96 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.20
Consensus pattern (91 bp):
AAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGACTTAAAAG
GGTGCCACGGAGTTGTGGACTTTGAG
Found at i:17662 original size:64 final size:65
Alignment explanation
Indices: 17542--17663 Score: 147
Period size: 64 Copynumber: 1.9 Consensus size: 65
17532 TTGTGGGCTT
* * * * * * **
17542 AAAAGGGTGCCACGGAGTTGTGGACTTTGATGAGAAGGTGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACAGAGTCGTGGACTTTGAAGAAAAGATGCCACAGAGCCGTGGACTTAAAAGGA
* *
17607 AAAAGAGTGTCACAGAGTCGTGGAC-TTGAAGAAAAGATGCCACTGAGCCGTGGACTT
1 AAAAGAGTGCCACAGAGTCGTGGACTTTGAAGAAAAGATGCCACAGAGCCGTGGACTT
17664 TGGAAAGAGA
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
64 26 0.55
65 21 0.45
ACGTcount: A:0.32, C:0.15, G:0.33, T:0.20
Consensus pattern (65 bp):
AAAAGAGTGCCACAGAGTCGTGGACTTTGAAGAAAAGATGCCACAGAGCCGTGGACTTAAAAGGA
Found at i:17747 original size:30 final size:29
Alignment explanation
Indices: 17621--17777 Score: 117
Period size: 30 Copynumber: 5.3 Consensus size: 29
17611 GAGTGTCACA
*
17621 GAGTCGTGGACTTGAAGAAA-AGATGCCACT
1 GAGTCGTGGGCTTG-AGAAAGA-ATGCCACT
* *
17651 GAGCCGTGGACTTTG-GAAAGAGATGCCACT
1 GAGTCGTGGGC-TTGAGAAAGA-ATGCCACT
* ** *
17681 GAGTTGTGGGCTT-A-AAAGGGTGCCACA
1 GAGTCGTGGGCTTGAGAAAGAATGCCACT
*
17708 GAGTTGTGGGCTTTGAGACAA-AATGCCACT
1 GAGTCGTGGGC-TTGAGA-AAGAATGCCACT
*
17738 GAGTCGTGGGCATTGAGAAGAGATTGCCACT
1 GAGTCGTGGGC-TTGAGAA-AGAATGCCACT
*
17769 TAGTCGTGG
1 GAGTCGTGG
17778 AATTTAAGAA
Statistics
Matches: 104, Mismatches: 14, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
27 17 0.16
28 6 0.06
29 8 0.08
30 52 0.50
31 21 0.20
ACGTcount: A:0.27, C:0.17, G:0.34, T:0.23
Consensus pattern (29 bp):
GAGTCGTGGGCTTGAGAAAGAATGCCACT
Found at i:17759 original size:87 final size:88
Alignment explanation
Indices: 17607--17777 Score: 206
Period size: 87 Copynumber: 2.0 Consensus size: 88
17597 CTTAAAAGGA
* *
17607 AAAAGAGTGTCACAGAGTCGTGGACTTGAAGAAAAGATGCCACTGAGCCGTGGACTTTGGAAAGA
1 AAAAGAGTGCCACAGAGTCGTGGACTTGAAGAAAAGATGCCACTGAGCCGTGGACATTGGAAAGA
*
17672 GA-TGCCACTGAGTTGTGGGCTT
66 GATTGCCACTGAGTCGTGGGCTT
* * * * *
17694 AAAAGGGTGCCACAGAGTTGTGGGCTTTG-AGACAAA-ATGCCACTGAGTCGTGGGCATT-GAGA
1 AAAAGAGTGCCACAGAGTCGTGGAC-TTGAAGA-AAAGATGCCACTGAGCCGTGGACATTGGA-A
*
17756 AGAGATTGCCACTTAGTCGTGG
63 AGAGATTGCCACTGAGTCGTGG
17778 AATTTAAGAA
Statistics
Matches: 71, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
86 2 0.03
87 49 0.69
88 20 0.28
ACGTcount: A:0.29, C:0.16, G:0.33, T:0.22
Consensus pattern (88 bp):
AAAAGAGTGCCACAGAGTCGTGGACTTGAAGAAAAGATGCCACTGAGCCGTGGACATTGGAAAGA
GATTGCCACTGAGTCGTGGGCTT
Found at i:18772 original size:22 final size:23
Alignment explanation
Indices: 18744--18788 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
18734 CTTTTCTTCT
18744 TTTTTTTTGTTTTTTTG-GTTTG
1 TTTTTTTTGTTTTTTTGCGTTTG
*
18766 TTTTTTTTTTTTTTTTGCGTTTG
1 TTTTTTTTGTTTTTTTGCGTTTG
18789 GAAAAGAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.00, C:0.02, G:0.16, T:0.82
Consensus pattern (23 bp):
TTTTTTTTGTTTTTTTGCGTTTG
Found at i:18773 original size:23 final size:23
Alignment explanation
Indices: 18743--18788 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
18733 CCTTTTCTTC
18743 TTTTTTTTTGTTTTTTTG-GTTTG
1 TTTTTTTTT-TTTTTTTGCGTTTG
18766 TTTTTTTTTTTTTTTTGCGTTTG
1 TTTTTTTTTTTTTTTTGCGTTTG
18789 GAAAAGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (23 bp):
TTTTTTTTTTTTTTTTGCGTTTG
Found at i:29003 original size:52 final size:52
Alignment explanation
Indices: 28918--29042 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
28908 ATATGAAAAG
* *
28918 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
28970 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
29022 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
29043 AAGATCGGTG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:29055 original size:52 final size:52
Alignment explanation
Indices: 28918--29062 Score: 195
Period size: 52 Copynumber: 2.8 Consensus size: 52
28908 ATATGAAAAG
* *
28918 TTGCTTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAAT
*** *
28970 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAAT
*
29022 TTGCCTGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATAAGAT-AGTGTATCGATACA
29063 ATGTATCGAT
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
51 4 0.05
52 79 0.95
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAAT
Found at i:29069 original size:13 final size:13
Alignment explanation
Indices: 29051--29075 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29041 CAAAGATCGG
29051 TGTATCGATACAA
1 TGTATCGATACAA
29064 TGTATCGATACA
1 TGTATCGATACA
29076 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:29156 original size:13 final size:13
Alignment explanation
Indices: 29138--29162 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29128 ACAAAAAATA
29138 TGTATCGATACAT
1 TGTATCGATACAT
29151 TGTATCGATACA
1 TGTATCGATACA
29163 ACACTTTATG
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:29158 original size:32 final size:33
Alignment explanation
Indices: 29117--29182 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
29107 AGTAGCTTAA
29117 ATTGTATCGATACAA-AAAATATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
***
29149 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAAAATATGTATCGATAC
29182 A
1 A
29183 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.50
33 15 0.50
ACGTcount: A:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAACAAAATATGTATCGATAC
Found at i:30126 original size:52 final size:52
Alignment explanation
Indices: 29992--30191 Score: 237
Period size: 49 Copynumber: 3.8 Consensus size: 52
29982 GAAAAGTGAT
* * * * *
29992 AAAGATGCCAATATG-TCGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCT-GATTCAAGGCCAGCTATATTGGACTTAAAGATG-G-A
* * * *
30046 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
30099 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
*
30149 -AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
30192 GAAGGGTTGC
Statistics
Matches: 129, Mismatches: 15, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
49 42 0.33
51 1 0.01
52 39 0.30
53 6 0.05
54 5 0.04
55 35 0.27
56 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGGA
Found at i:30322 original size:30 final size:30
Alignment explanation
Indices: 30212--30665 Score: 375
Period size: 30 Copynumber: 15.5 Consensus size: 30
30202 CACCGACTTG
* * *
30212 TGTGGGCTTTGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
30242 TGTGGGC-TTTG--AAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
30269 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
30297 TGTGGGCTTTTGAAAAATATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* * *
30327 TGTGGGCTTTTGAACAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
30357 TGTGGGCTTTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
** *
30385 TGTGGGCTTTTGAAAAATATGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* *
30415 TGTGGGCTTTTGAAAAGGGTGCCACTAACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* *
30445 TGTGGGC---TGAAAA-GAGTGCTA-TAGAGT
1 TGTGGGCTTTTGAAAAGGA-TGCCACT-GACT
* ** * * *
30472 TGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTT----TTGAAAAGGA-TGCCACTGACT
* * *
30507 TGTGGACTTTGGAAAA-GATGCCACCGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
** * *
30536 TGTGGGCTTCGGAAAAGGGTGCCACTGATT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
30566 TGTGGGC-TTT--AAAGGTTGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
* ** *
30593 TGTGGGCTTTCGAAAAAAATGCCACCGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
**
30623 TGTGGGC-TTTGAAAAAAATGCCACTGACT
1 TGTGGGCTTTTGAAAAGGATGCCACTGACT
*
30652 TGTGGACTTTTGAA
1 TGTGGGCTTTTGAA
30666 GGGTGATGAA
Statistics
Matches: 350, Mismatches: 52, Indels: 44
0.78 0.12 0.10
Matches are distributed among these distances:
26 2 0.01
27 61 0.17
28 57 0.16
29 53 0.15
30 149 0.43
31 5 0.01
34 5 0.01
35 18 0.05
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.30
Consensus pattern (30 bp):
TGTGGGCTTTTGAAAAGGATGCCACTGACT
Found at i:30378 original size:58 final size:59
Alignment explanation
Indices: 30196--30665 Score: 322
Period size: 57 Copynumber: 8.0 Consensus size: 59
30186 GGCTTAGAAG
* * * *
30196 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AA
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
* *
30255 GGTTGCCACTGACTTGTGGGCTTTT--AAAGGTTGCCACTGACTTGTGGGCTTTTGAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
** *
30312 AATATGCCACTGACTTGTGGGCTTTTGAACAGGGTGCCACTAACTTGTGGGCTTTT-AAA
1 GGT-TGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
***
30371 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTAACTTGTGGGCTTTTGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAA
* * * * * * **
30431 GGGTGCCACTAACTTGTGGGC---TGAAAAGAGTGCTA-TAGAGTTGTGAGCTTACAAAAGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTA-ACTTGTGGGCTT----TTG--AA
30492 A
59 A
* * * * * ** **
30493 GAG-TGCCACGGAGTTGTGGACTTTGGAAAA-GATGCCACCGACTTGTGGGCTTCGGAAAA
1 G-GTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAA
* * * * *
30552 GGGTGCCACTGATTTGTGGGC-TTT--AAAGGTTGCCACTGACTTGTGGGCTTTCGAAAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAA
*** * *** * *
30609 AAATGCCACCGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGACTTTTGAA
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAA
30666 GGGTGATGAA
Statistics
Matches: 332, Mismatches: 57, Indels: 45
0.76 0.13 0.10
Matches are distributed among these distances:
55 22 0.07
56 9 0.03
57 77 0.23
58 76 0.23
59 60 0.18
60 48 0.14
61 1 0.00
62 19 0.06
63 1 0.00
64 14 0.04
65 5 0.02
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.29
Consensus pattern (59 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTTTGAAA
Found at i:30381 original size:88 final size:87
Alignment explanation
Indices: 30196--30452 Score: 383
Period size: 88 Copynumber: 2.9 Consensus size: 87
30186 GGCTTAGAAG
* * *** * *
30196 GGTTGCCACCGACTTGTGTGGGCTTTGGAAAAGGGTGCCACTGATTTGTGGGC-TTTG-AAGGTT
1 GGTTGCCACTGAC-T-TGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGT
*
30259 GCCACTGACTTGTGGGCTTTTAAA
64 GCCACTAACTTGTGGGCTTTTAAA
30283 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAACAGGGTG
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAA-AGGGTG
30348 CCACTAACTTGTGGGCTTTTAAA
65 CCACTAACTTGTGGGCTTTTAAA
*
30371 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTAACTTGTGGGCTTTTGAAAAGGGTG
1 GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTG-AAAGGGTG
30436 CCACTAACTTGTGGGCT
65 CCACTAACTTGTGGGCT
30453 GAAAAGAGTG
Statistics
Matches: 157, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
85 32 0.20
86 5 0.03
87 13 0.08
88 105 0.67
89 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.32
Consensus pattern (87 bp):
GGTTGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTGACTTGTGGGCTTTTGAAAGGGTGC
CACTAACTTGTGGGCTTTTAAA
Found at i:30596 original size:121 final size:116
Alignment explanation
Indices: 30374--30656 Score: 300
Period size: 121 Copynumber: 2.4 Consensus size: 116
30364 TTTTAAAGGT
* * * **
30374 TGCCACTGACTTGTGGGCTTTTGAAAAATATGCCACTAACTTGTGGGCTTTTGAAAAGGGTGCCA
1 TGCCACCGACTTGTGGGC-TTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCA
* * *
30439 CTAACTTGTGGGCTGAAAAGAGTGCTATAGAGTTGTGAGCTTACAAAAGAAAAAGAG
65 CTAACTTGTGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTAC----GAAAAA-AA
* * * * * *
30496 TGCCACGGAGTTGTGGACTTTGGAAAAGATGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCAC
1 TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCAC
* * ** * *
30561 TGATTTGTGGGCTTTAAAG-GTTGCCACT-GACTTGTGGGCTTTCGAAAAAAA
66 TAACTTGTGGGCTGAAAAGAG-TGCCA-TAGACTTGTGAGCTTACGAAAAAAA
30612 TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
1 TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGG
30657 ACTTTTGAAG
Statistics
Matches: 135, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
116 40 0.30
117 6 0.04
120 1 0.01
121 72 0.53
122 16 0.12
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (116 bp):
TGCCACCGACTTGTGGGCTTTGAAAAAAATGCCACTGACTTGTGGGCTTCGGAAAAGGGTGCCAC
TAACTTGTGGGCTGAAAAGAGTGCCATAGACTTGTGAGCTTACGAAAAAAA
Found at i:32092 original size:1 final size:1
Alignment explanation
Indices: 32088--32200 Score: 73
Period size: 1 Copynumber: 113.0 Consensus size: 1
32078 CCGGACCCCC
* * * * * * * * *
32088 TTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTGTTTTTTTTTTCTTTTGTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** ** * ** *
32153 TCATTCATTTTTTTTTGTTTTTTCATTTTTTTTGTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
32201 GGAGGACGCC
Statistics
Matches: 81, Mismatches: 31, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 81 1.00
ACGTcount: A:0.04, C:0.04, G:0.08, T:0.85
Consensus pattern (1 bp):
T
Found at i:32125 original size:33 final size:31
Alignment explanation
Indices: 32088--32201 Score: 122
Period size: 33 Copynumber: 3.5 Consensus size: 31
32078 CCGGACCCCC
*
32088 TTTTTGTTTTTGTTTGTTTTTTTATTGTTTTTG
1 TTTTT-TTTTTTTTTGTTTTTTTATT-TTTTTG
*
32121 TTTTTTTTTTCTTTTGTTTTTTTGTTTTTTT-
1 TTTTTTTTTT-TTTTGTTTTTTTATTTTTTTG
* *
32152 TTCATTCATTTTTTTTTGTTTTTTCATTTTTTTTG
1 TT--TT-TTTTTTTTTTGTTTTTTTA-TTTTTTTG
32187 TTTTTTTTTTTTTTG
1 TTTTTTTTTTTTTTG
32202 GAGGACGCCG
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
31 2 0.03
32 20 0.29
33 33 0.48
34 12 0.17
35 2 0.03
ACGTcount: A:0.04, C:0.04, G:0.09, T:0.84
Consensus pattern (31 bp):
TTTTTTTTTTTTTTGTTTTTTTATTTTTTTG
Found at i:41905 original size:10 final size:10
Alignment explanation
Indices: 41890--41916 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
41880 ATGTATCAAG
41890 CAAAAACAAA
1 CAAAAACAAA
41900 CAAAAACAAA
1 CAAAAACAAA
41910 CAAAAAC
1 CAAAAAC
41917 TTAGTTAGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (10 bp):
CAAAAACAAA
Done.