Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2031
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: 365977
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 2 of 3
Found at i:164174 original size:27 final size:27
Alignment explanation
Indices: 164048--164765 Score: 438
Period size: 27 Copynumber: 24.7 Consensus size: 27
164038 CTTTTCTTCA
*
164048 AAGTCCACAACTCCGTGGCATCCTTTTT
1 AAGTCCACAACTCCGTGGCA-CCCTTTT
* * ** *
164076 AAGCCCACAAGTTAGTGGCACCCTTTCA
1 AAGTCCACAACTCCGTGGCACCCTTT-T
* * * *
164104 AAGCCCATAAGTCAGTGGCACCCCTTTTT
1 AAGTCCACAACTCCGTGGCA-CCC-TTTT
* * * *
164133 AAGCCCACAACTCTGTGGCACTCTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * *
164160 AAGTCCATAACTCTGTGGCACCCTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
164187 AAGTCTACAACTCC-CGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * *
164213 AAGTTCGCAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* * * *
164240 AGGTCCACAACTCCATGGCTCTCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
**
164267 AAAGTCCACAACTCCGTGGCATTCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* *
164295 AAAGTCCACCACTTCGTGGCACCCTTTT
1 -AAGTCCACAACTCCGTGGCACCCTTTT
* *
164323 AGGTCTACAACTCCGTGGCA-CCTATTT
1 AAGTCCACAACTCCGTGGCACCCT-TTT
* *
164350 AAGCCCATAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
* *
164377 AAGTCCACAACTCCGTGGAACCTTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
164404 AAGTCCACAACTCCATGGCA-CCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
164430 AAATCCACAAC-CCTGTGGCACCTTTTCTTTTT
1 AAGTCCACAACTCC-GTGGCACC----C-TTTT
* *
164462 AAGTCCACGACTCCATGGCACCCTTTTCCCATTT
1 AAGTCCACAACTCCGTGGCACCC---T----TTT
* **
164496 AAG-CACACAATTTTGTGGCACTCTGTTTCCTTTT
1 AAGTC-CACAACTCCGTGGCA--C-----CCTTTT
* *
164530 AAGTTCACAACTCCGTGGTACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
164557 AAGTCCACAACTCCGTGGCACCTTTTTCTTTT
1 AAGTCCACAACTCCGTGGCACC-----CTTTT
* **
164589 AAAGCCCACAACTCTATGGCACCCTTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCA--C-----CCTTTT
*
164624 AAGTCCACAACTTCGTGGCACCTTTTTCTTTTT
1 AAGTCCACAACTCCGTGGCACC-----C-TTTT
* *
164657 AAAGCCCACAACTCTGTGGCACTCTTTTTCCTTTT
1 -AAGTCCACAACTCCGTGGCA--C-----CCTTTT
164692 AAGTCCACAACTCCGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
*
164719 AAGTCCACAACTCTGTGGCACCCTTTT
1 AAGTCCACAACTCCGTGGCACCCTTTT
164746 AAGTCCACAACTCCGTGGCA
1 AAGTCCACAACTCCGTGGCA
164766 TCTTTCTCCT
Statistics
Matches: 545, Mismatches: 88, Indels: 115
0.73 0.12 0.15
Matches are distributed among these distances:
25 2 0.00
26 43 0.08
27 232 0.43
28 87 0.16
29 20 0.04
30 5 0.01
31 1 0.00
32 29 0.05
33 24 0.04
34 84 0.15
35 10 0.02
36 3 0.01
38 1 0.00
40 1 0.00
41 3 0.01
ACGTcount: A:0.23, C:0.32, G:0.14, T:0.31
Consensus pattern (27 bp):
AAGTCCACAACTCCGTGGCACCCTTTT
Found at i:164632 original size:34 final size:34
Alignment explanation
Indices: 164551--164745 Score: 223
Period size: 34 Copynumber: 6.0 Consensus size: 34
164541 TCCGTGGTAC
*
164551 CCTTTTAAGTCCACAACTCCGTGGCA-CCTTTTT
1 CCTTTTAAGTCCACAACTCTGTGGCACCCTTTTT
* *
164584 -CTTTTAAAGCCCACAACTCTATGGCACCCTTTTT
1 CCTTTT-AAGTCCACAACTCTGTGGCACCCTTTTT
164618 CCTTTTAAGTCCACAACT-TCGTGGCA-CCTTTTT
1 CCTTTTAAGTCCACAACTCT-GTGGCACCCTTTTT
* * *
164651 CTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 CCTTTT-AAGTCCACAACTCTGTGGCACCCTTTTT
*
164686 CCTTTTAAGTCCACAACTCCGTGGCA--C-----
1 CCTTTTAAGTCCACAACTCTGTGGCACCCTTTTT
164713 CCTTTTAAGTCCACAACTCTGTGGCACCCTTTT
1 CCTTTTAAGTCCACAACTCTGTGGCACCCTTTT
164746 AAGTCCACAA
Statistics
Matches: 137, Mismatches: 12, Indels: 26
0.78 0.07 0.15
Matches are distributed among these distances:
27 25 0.18
29 1 0.01
32 6 0.04
33 30 0.22
34 58 0.42
35 17 0.12
ACGTcount: A:0.20, C:0.32, G:0.12, T:0.36
Consensus pattern (34 bp):
CCTTTTAAGTCCACAACTCTGTGGCACCCTTTTT
Found at i:164683 original size:29 final size:28
Alignment explanation
Indices: 164651--164862 Score: 122
Period size: 27 Copynumber: 7.1 Consensus size: 28
164641 GCACCTTTTT
*
164651 CTTTTTAAAGCCCACAACTCTGTGGCAC
1 CTTTTTAAAGCCCACAACTCAGTGGCAC
* * *
164679 TCTTTTTCCTTTTAAGTCCACAACTCCGTGGCAC
1 -C---TT--TTTAAAGCCCACAACTCAGTGGCAC
* * *
164713 CCTTTT-AAGTCCACAACTCTGTGGCAC
1 CTTTTTAAAGCCCACAACTCAGTGGCAC
* * * *
164740 CCTTTT-AAGTCCACAACTCCGTGGCAT
1 CTTTTTAAAGCCCACAACTCAGTGGCAC
*
164767 CTTTCTCCTATTAAGCCCACAAGTCAGTGGCAC
1 CTTT-T--TA--AAGCCCACAACTCAGTGGCAC
* *
164800 CTTTTTCAAAAGCCCACAAGTCGGTGGCACC
1 CTTTTT--AAAGCCCACAACTCAGTGGCA-C
* * *
164831 CCTTTCAAAGCCCACAAGTCAGTGGCAAC
1 CTTTTTAAAGCCCACAACTCAGTGGC-AC
164860 CTT
1 CTT
164863 CAAAAGCACA
Statistics
Matches: 151, Mismatches: 17, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
27 48 0.32
28 4 0.03
29 23 0.15
30 23 0.15
31 5 0.03
32 4 0.03
33 22 0.15
34 22 0.15
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.28
Consensus pattern (28 bp):
CTTTTTAAAGCCCACAACTCAGTGGCAC
Found at i:164691 original size:68 final size:65
Alignment explanation
Indices: 164424--164806 Score: 311
Period size: 68 Copynumber: 6.0 Consensus size: 65
164414 CTCCATGGCA
* * * **
164424 CCTTTTAAATCCACAAC-CCTGTGGCACC-TTTTCTTTTTAAGTCCACGACTCCATGGCACCCTT
1 CCTTTTAAGTCCACAACTCC-GTGGCACCTTTTTC-TTTTAAGCCCACAACTCTGTGGCA-CCTT
*
164487 TTC
63 TTT
* * ** * ** * *
164490 CCATTTAAG-CACACAATTTTGTGGCACTCTGTTTCCTTTTAAGTTCACAACTCCGTGGTA-C--
1 CCTTTTAAGTC-CACAACTCCGTGGCAC-CT-TTTTCTTTTAAGCCCACAACTCTGTGGCACCTT
164551 ---
63 TTT
*
164551 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTATGGCACCCTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTT-AAGCCCACAACTCTGTGGCA-CCTTT
164616 TT
64 TT
*
164618 CCTTTTAAGTCCACAACTTCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTC-TTTT-AAGCCCACAACTCTGTGGCAC-CTT
164683 TTT
63 TTT
*
164686 CCTTTTAAGTCCACAACTCCGTGGCACC-----CTTTTAAGTCCACAACTCTGTGGCA-C-----
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGCCCACAACTCTGTGGCACCTTTTT
* * * * *
164740 CCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCTATTAAGCCCACAAGTCAGTGGCACCTTTT
1 CCTTTTAAGTCCACAACTCCGTGGCACCTTT-TTCTTTTAAGCCCACAACTCTGTGGCACCTTTT
164805 T
65 T
164806 C
1 C
164807 AAAAGCCCAC
Statistics
Matches: 260, Mismatches: 29, Indels: 56
0.75 0.08 0.16
Matches are distributed among these distances:
54 27 0.10
59 9 0.03
60 38 0.15
61 41 0.16
62 6 0.02
63 1 0.00
65 1 0.00
66 21 0.08
67 35 0.13
68 77 0.30
69 4 0.02
ACGTcount: A:0.21, C:0.32, G:0.13, T:0.35
Consensus pattern (65 bp):
CCTTTTAAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAGCCCACAACTCTGTGGCACCTTTTT
Found at i:164815 original size:30 final size:28
Alignment explanation
Indices: 164779--164908 Score: 122
Period size: 29 Copynumber: 4.4 Consensus size: 28
164769 TTCTCCTATT
164779 AAGCCCACAAGTCAGTGGCACCTTTTTCAA
1 AAGCCCACAAGTCAGTGGCACC--TTTCAA
*
164809 AAGCCCACAAGTCGGTGGCACCCCTTTC-A
1 AAGCCCACAAGTCAGTGGCA--CCTTTCAA
164838 AAGCCCACAAGTCAGTGGCAACC-TTCAA
1 AAGCCCACAAGTCAGTGGC-ACCTTTCAA
* **
164866 AAGCACACAAGTTGGT-GCAACCCTTTCAA
1 AAGCCCACAAGTCAGTGGC-A-CCTTTCAA
164895 AAGCCGACACAAGT
1 AAGCC--CACAAGT
164909 TGGTGCCGTC
Statistics
Matches: 86, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
27 7 0.08
28 18 0.21
29 28 0.33
30 24 0.28
31 7 0.08
32 2 0.02
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.18
Consensus pattern (28 bp):
AAGCCCACAAGTCAGTGGCACCTTTCAA
Found at i:164899 original size:57 final size:57
Alignment explanation
Indices: 164779--164895 Score: 166
Period size: 57 Copynumber: 2.0 Consensus size: 57
164769 TTCTCCTATT
* *
164779 AAGCCCACAAGTCAGTGGCACCTTTTTCAAAAGCCCACAAGTCGGTGGCACCCCTTTCA
1 AAGCCCACAAGTCAGTGGCACC--TTTCAAAAGCACACAAGTCGGTGGCAACCCTTTCA
*
164838 AAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCACACAAGTTGGT-GCAACCCTTTCA
1 AAGCCCACAAGTCAGTGGC-ACCTTTCAAAAGCACACAAGTCGGTGGCAACCCTTTCA
164894 AA
1 AA
164896 AGCCGACACA
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
56 13 0.24
57 19 0.35
59 19 0.35
60 3 0.06
ACGTcount: A:0.32, C:0.32, G:0.18, T:0.19
Consensus pattern (57 bp):
AAGCCCACAAGTCAGTGGCACCTTTCAAAAGCACACAAGTCGGTGGCAACCCTTTCA
Found at i:165032 original size:87 final size:87
Alignment explanation
Indices: 164920--165567 Score: 1052
Period size: 87 Copynumber: 7.5 Consensus size: 87
164910 GGTGCCGTCT
* *
164920 TCTTCTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCT
1 TCTT-TAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCT
* *
164985 TGAATCATCATATTGGAACCTTG
65 TGAATCAGCATATTGGCACCTTG
* * *
165008 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTAGCACAAGCCCAATATCACTGGCCTT
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTT
165073 GAATCAGCATATTGGCACCTTG
66 GAATCAGCATATTGGCACCTTG
* * *
165095 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGAACATTAGCACTAGCCCAATATCGCTGGCCTT
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTT
165160 GAATCAGCATATTGGCACCTTG
66 GAATCAGCATATTGGCACCTTG
* *
165182 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTAGCACAAG-CC---ATCACTGGCCTT
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTT
165243 GAATCAGCATATTGGCACCTTG
66 GAATCAGCATATTGGCACCTTG
* *
165265 TTTTTAAAACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTT
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTT
165330 GAATCAGCATATTGGCACCTTG
66 GAATCAGCATATTGGCACCTTG
*
165352 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCATAAGCCCAATATCGCTGGCCTT
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTT
*
165417 GAATCAGCATATTAGCACCTTG
66 GAATCAGCATATTGGCACCTTG
* * *
165439 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAACACATTGGCATAAGCCCAATATCGCTGGCCCT
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTT
*
165504 AAATCAGCATATTGGCACCTTG
66 GAATCAGCATATTGGCACCTTG
* * *
165526 TCTTTAAGACCAATATCACTGGCCTTGAATCAGTACATTGGC
1 TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGC
165568 GCCTTAATCT
Statistics
Matches: 526, Mismatches: 30, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
83 77 0.15
84 2 0.00
86 2 0.00
87 441 0.84
88 4 0.01
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (87 bp):
TCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACATTGGCACAAGCCCAATATCGCTGGCCTT
GAATCAGCATATTGGCACCTTG
Found at i:165127 original size:48 final size:48
Alignment explanation
Indices: 165056--165225 Score: 196
Period size: 48 Copynumber: 3.7 Consensus size: 48
165046 TAGCACAAGC
* * *
165056 CCAATATCACTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTGTCTTTAAGA
* * *
165104 CCAATGTCGCTGGCCTTGAATCAGAACATTAGCA------C--T-AGC
1 CCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTGTCTTTAAGA
* *
165143 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGA
1 CCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTGTCTTTAAGA
*
165191 CCAATGTCGCTGGCCTTGAATCAGCACATTAGCAC
1 CCAATATCGCTGGCCTTGAATCAGCACATTAGCAC
165226 AAGCCATCAC
Statistics
Matches: 99, Mismatches: 14, Indels: 18
0.76 0.11 0.14
Matches are distributed among these distances:
39 32 0.32
40 1 0.01
42 1 0.01
45 1 0.01
47 1 0.01
48 63 0.64
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (48 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTAGCACCTTGTCTTTAAGA
Found at i:165306 original size:48 final size:47
Alignment explanation
Indices: 165235--165658 Score: 338
Period size: 48 Copynumber: 9.4 Consensus size: 47
165225 CAAGCCATCA
* * *
165235 CTGGCCTTGAATCAGCATATTGGCACCTTGTTTTTAAAACCAATGTCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTG-TTTTAAGACCAATATCG
*
165283 CTGGCCTTGAATCAGCACATTGGCA-C-------AAGCCCAATATCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTGTTTTAAGACCAATATCG
* *
165322 CTGGCCTTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTGT-TTTAAGACCAATATCG
*
165370 CTGGCCTTGAATCAGCACATTGGCA--------TAAGCCCAATATCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTGTTTTAAGACCAATATCG
* * *
165409 CTGGCCTTGAATCAGCATATTAGCACCTTGTCTTTAAGACCAATGTCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTGT-TTTAAGACCAATATCG
* *
165457 CTGGCCTTGAATCAACACATTGGCA--------TAAGCCCAATATCG
1 CTGGCCTTGAATCAGCACATTGGCACCTTGTTTTAAGACCAATATCG
* * * *
165496 CTGGCCCTAAATCAGCATATTGGCACCTTGTCTTTAAGACCAATATCA
1 CTGGCCTTGAATCAGCACATTGGCACCTTGT-TTTAAGACCAATATCG
* * * ** *
165544 CTGGCCTTGAATCAGTACATTGGCGCCTTAATCTTTAAGTTCGATATCG
1 CTGGCCTTGAATCAGCACATTGGCACCTT-GT-TTTAAGACCAATATCG
* * * * * *
165593 CTGGCCTTAAATCAGTACATTGCCATCTTCATCTTTAAGTCCAATATCG
1 CTGGCCTTGAATCAGCACATTGGCACCTT-GT-TTTAAGACCAATATCG
* *
165642 TTGGTCTTGAATCAGCA
1 CTGGCCTTGAATCAGCA
165659 TATTAGCATC
Statistics
Matches: 302, Mismatches: 46, Indels: 55
0.75 0.11 0.14
Matches are distributed among these distances:
39 102 0.34
40 1 0.00
47 1 0.00
48 129 0.43
49 69 0.23
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.30
Consensus pattern (47 bp):
CTGGCCTTGAATCAGCACATTGGCACCTTGTTTTAAGACCAATATCG
Found at i:165597 original size:49 final size:48
Alignment explanation
Indices: 165482--165656 Score: 188
Period size: 49 Copynumber: 3.6 Consensus size: 48
165472 CACATTGGCA
* * * * *
165482 TAAGCCCAATATCGCTGGCCCTAAATCAGCATATTGGCACCTTGTCTT
1 TAAGTCCAATATCGCTGGCCTTAAATCAGTACATTGGCACCTTATCTT
* * * *
165530 TAAGACCAATATCACTGGCCTTGAATCAGTACATTGGCGCCTTAATCTT
1 TAAGTCCAATATCGCTGGCCTTAAATCAGTACATTGGCACCTT-ATCTT
* * * *
165579 TAAGTTCGATATCGCTGGCCTTAAATCAGTACATTGCCATCTTCATCTT
1 TAAGTCCAATATCGCTGGCCTTAAATCAGTACATTGGCACCTT-ATCTT
* * *
165628 TAAGTCCAATATCGTTGGTCTTGAATCAG
1 TAAGTCCAATATCGCTGGCCTTAAATCAG
165657 CATATTAGCA
Statistics
Matches: 104, Mismatches: 22, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
48 36 0.35
49 68 0.65
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.33
Consensus pattern (48 bp):
TAAGTCCAATATCGCTGGCCTTAAATCAGTACATTGGCACCTTATCTT
Found at i:166000 original size:10 final size:10
Alignment explanation
Indices: 165981--166014 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
165971 CCTTCCAAAC
165981 TCTACACCAA
1 TCTACACCAA
*
165991 TCTACCCCAA
1 TCTACACCAA
*
166001 TCTACACCTA
1 TCTACACCAA
166011 TCTA
1 TCTA
166015 AGGAGGTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.26
Consensus pattern (10 bp):
TCTACACCAA
Found at i:169733 original size:2 final size:2
Alignment explanation
Indices: 169720--169756 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
169710 TTGTTTTATT
*
169720 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
169757 TTTTTGAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:183990 original size:28 final size:28
Alignment explanation
Indices: 183954--184566 Score: 731
Period size: 28 Copynumber: 21.5 Consensus size: 28
183944 CGTTTATCTC
*
183954 TTCAAAGCCCACAAGTTAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
*
183982 TTTAAAGCCCACAAGTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
* * *
184010 TTCGAAGCCCACAAGTTAATGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CT
* *
184038 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
184066 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTC-T
* * * *
184095 TTTAAAGCCCATAAGTTAGTGTCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CT
* *
184123 TTCAAAGGCCACAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
*
184151 TTCAAAGCCCACGCAAGTCAG-GGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACTCT
184180 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTC-T
* * *
184209 TTCAAAGGCCACAAGTCAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
*
184237 TTCAAAGCCCACGAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTC-T
* *
184266 TTCAAAGCCCACAAGTCAGCGACA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CT
184294 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CT
*
184322 TTCAAAGCCCACGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCA--CAAGTCAGTGGCACTCT
*
184352 TTCAAAGCCCACAAGTCAGTAGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACT-CT
*
184380 TTCAAAGCCCACGCAAGTCAATGGCAC-CAT
1 TTCAAAGCCCA--CAAGTCAGTGGCACTC-T
184410 TTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
*
184438 TGTCAAAGCCCACAAGTTAGTGGCA-TCCT
1 T-TCAAAGCCCACAAGTCAGTGGCACT-CT
* *
184467 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCT
184495 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTC-T
*
184524 TTCAAAGCCCACAAG-CTAGTGGTAACTCTT
1 TTCAAAGCCCACAAGTC-AGTGG-CACTC-T
184554 TTCAAAGCCCACA
1 TTCAAAGCCCACA
184567 CGAGTCGGGG
Statistics
Matches: 513, Mismatches: 46, Indels: 50
0.84 0.08 0.08
Matches are distributed among these distances:
27 9 0.02
28 291 0.57
29 137 0.27
30 76 0.15
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCT
Found at i:184124 original size:57 final size:57
Alignment explanation
Indices: 183954--184566 Score: 794
Period size: 57 Copynumber: 10.7 Consensus size: 57
183944 CGTTTATCTC
* * *
183954 TTCAAAGCCCACAAGTTAGTGGCACT-CTTTTAAAGCCCACAAGTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * *
184010 TTCGAAGCCCACAAGTTAATGGCA-TCCTTTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * * *
184066 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAGCCCATAAGTTAGTGTCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
*
184123 TTCAAAGGCCACAAGTCAGTGGCAC-CCTTTCAAAGCCCACGCAAGTCAG-GGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCT
* * *
184180 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGGCCACAAGTCAGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
* * * * *
184237 TTCAAAGCCCACGAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAGCGACATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
184294 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACGCAAGTCAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCT
* * *
184352 TTCAAAGCCCACAAGTCAGTAGCA-TCCTTTCAAAGCCCACGCAAGTCAATGGCACCAT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCA--CAAGTCAGTGGCACCCT
* *
184410 TTCAAAGCCCACAAGTCAGTGGCACT-CTTGTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTT-TCAAAGCCCACAAGTCAGTGGCACCCT
* *
184467 TTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCAC-CCT
* *
184524 TTCAAAGCCCACAAG-CTAGTGGTAACTCTTTTCAAAGCCCACA
1 TTCAAAGCCCACAAGTC-AGTGG-CACTCCTTTCAAAGCCCACA
184567 CGAGTCGGGG
Statistics
Matches: 492, Mismatches: 50, Indels: 27
0.86 0.09 0.05
Matches are distributed among these distances:
55 1 0.00
56 126 0.26
57 224 0.46
58 115 0.23
59 26 0.05
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTCAGTGGCACCCT
Found at i:184146 original size:85 final size:85
Alignment explanation
Indices: 183954--184566 Score: 847
Period size: 85 Copynumber: 7.2 Consensus size: 85
183944 CGTTTATCTC
* * * *
183954 TTCAAAGCCCACAAGTTAGTGGCACTCTTTTAAAGCCCACAAGTCAGTGGCACTC-TTTCGAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
*
184018 CCACAAGTTAATGGCATCCT
66 CCACAAGTTAGTGGCATCCT
* *
184038 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTTAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
* *
184103 CCATAAGTTAGTGTCATCCT
66 CCACAAGTTAGTGGCATCCT
* *
184123 TTCAAAGGCCACAAGTCAGTGGCACCCTTTCAAAGCCCACGCAAGTCAG-GGCAC-CCTTTCAAA
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTTCAAA
* *
184186 GCCCACAAGTCAGTGGCACTCTT
64 GCCCACAAGTTAGTGGCA-TCCT
* * *
184209 TTCAAAGGCCACAAGTCAGTGGTACCCTTTCAAAGCCCACGAGTCAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
184274 CCACAAGTCAGCGACATCCT
66 CCACAAGTTAGTGGCATCCT
* *
184294 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACGCAAGTCAGTGGCAC-CCTTTCAAA
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCA--CAAGTCAGTGGCACTCTTTTCAAA
* *
184358 GCCCACAAGTCAGTAGCATCCT
64 GCCCACAAGTTAGTGGCATCCT
* * *
184380 TTCAAAGCCCACGCAAGTCAATGGCACCATTTCAAAGCCCACAAGTCAGTGGCACTCTTGTCAAA
1 TTCAAAGCCCA--CAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAA
184445 GCCCACAAGTTAGTGGCATCCT
64 GCCCACAAGTTAGTGGCATCCT
*
184467 TTCAAAGCCCACAAGTTAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
* * *
184532 CCACAAGCTAGTGGTAACTCTT
66 CCACAAGTTAGTGG-CA-TCCT
184554 TTCAAAGCCCACA
1 TTCAAAGCCCACA
184567 CGAGTCGGGG
Statistics
Matches: 473, Mismatches: 43, Indels: 23
0.88 0.08 0.04
Matches are distributed among these distances:
84 60 0.13
85 190 0.40
86 123 0.26
87 75 0.16
88 25 0.05
ACGTcount: A:0.29, C:0.31, G:0.18, T:0.22
Consensus pattern (85 bp):
TTCAAAGCCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGC
CCACAAGTTAGTGGCATCCT
Found at i:185512 original size:20 final size:20
Alignment explanation
Indices: 185489--185653 Score: 177
Period size: 20 Copynumber: 7.7 Consensus size: 20
185479 AAGTACCCAG
185489 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
185509 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
185529 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
185549 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
185569 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
185589 ATGTATCGATACATTCTATCCTTTTGCCCA
1 ATGTATCGAT--A--C-AT--TTTT---CA
185619 GATGTATCGATACATTTTTCA
1 -ATGTATCGATACATTTTTCA
185640 ATGTATCGATACAT
1 ATGTATCGATACAT
185654 CTAGTTAAAA
Statistics
Matches: 122, Mismatches: 12, Indels: 22
0.78 0.08 0.14
Matches are distributed among these distances:
20 95 0.78
21 2 0.02
22 1 0.01
24 5 0.04
25 2 0.02
26 2 0.02
27 3 0.02
29 1 0.01
30 1 0.01
31 10 0.08
ACGTcount: A:0.30, C:0.16, G:0.13, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:185552 original size:40 final size:40
Alignment explanation
Indices: 185489--185603 Score: 203
Period size: 40 Copynumber: 2.9 Consensus size: 40
185479 AAGTACCCAG
* * *
185489 ATGTATCGATACATTTTTCAATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATGAATGTATCGATACATTTTTCA
185529 ATGTATCGATACATGTATGAATGTATCGATACATTTTTCA
1 ATGTATCGATACATGTATGAATGTATCGATACATTTTTCA
185569 ATGTATCGATACATGTATGAATGTATCGATACATT
1 ATGTATCGATACATGTATGAATGTATCGATACATT
185604 CTATCCTTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (40 bp):
ATGTATCGATACATGTATGAATGTATCGATACATTTTTCA
Found at i:185582 original size:60 final size:60
Alignment explanation
Indices: 185489--185602 Score: 201
Period size: 60 Copynumber: 1.9 Consensus size: 60
185479 AAGTACCCAG
* *
185489 ATGTATCGATACATTTTTCAATGTATCGATACATTTTTCAATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCAATGTATCGATACATGTATCAATGTATCGATACATGTATGA
*
185549 ATGTATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1 ATGTATCGATACATTTTTCAATGTATCGATACATGTATCAATGTATCGATACAT
185603 TCTATCCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.40
Consensus pattern (60 bp):
ATGTATCGATACATTTTTCAATGTATCGATACATGTATCAATGTATCGATACATGTATGA
Found at i:186540 original size:20 final size:21
Alignment explanation
Indices: 186504--186546 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
186494 CCTAGTAGCC
*
186504 TTTCATGCATTTTTTTATTATG
1 TTTCATGCA-TTTTTTAATATG
186526 TTTCATGCA-TTTTTAATATG
1 TTTCATGCATTTTTTAATATG
186546 T
1 T
186547 CCAGCATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
22 9 0.45
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.60
Consensus pattern (21 bp):
TTTCATGCATTTTTTAATATG
Found at i:187445 original size:10 final size:10
Alignment explanation
Indices: 187430--187463 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
187420 CCATTAGGAA
187430 AAAGATTTTT
1 AAAGATTTTT
187440 AAAGATTTTT
1 AAAGATTTTT
*
187450 GAAATATTTTT
1 -AAAGATTTTT
187461 AAA
1 AAA
187464 TCGATCCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (10 bp):
AAAGATTTTT
Found at i:189082 original size:105 final size:105
Alignment explanation
Indices: 188944--189257 Score: 497
Period size: 105 Copynumber: 3.0 Consensus size: 105
188934 TGACAACTCG
* **
188944 TCTAATAACTTATCAATTAAGGGAATTAAGAACTTATCTTTTACAATAAAATGATTGAGCTTTC-
1 TCTAATAACTTATCAATTAAGGGAATTAGGAACTTATCTTTTACAATAAGGTGATTGAGCTTTCG
*
189008 AGTAATCCACATAAAGTCTCCAGGTACTATCTTTCTTTTTA
66 A-TAATCCACATAAAGTCTCCAAGTACTATCTTTCTTTTTA
* *
189049 TCTAATAACTTATCAATTAAGAGAATTAGGAACTTATCTTTTACAATAAGGTGATTGAGCTATCG
1 TCTAATAACTTATCAATTAAGGGAATTAGGAACTTATCTTTTACAATAAGGTGATTGAGCTTTCG
189114 ATAATCCACATAAAGTCTCCAAGTACTATCTTTCTTTTTA
66 ATAATCCACATAAAGTCTCCAAGTACTATCTTTCTTTTTA
* *
189154 TCTAATAACTTATCAATTAAGGGAATTAGGAACTTATCTTTTATAGTAAGGTGATTGAG-TTATC
1 TCTAATAACTTATCAATTAAGGGAATTAGGAACTTATCTTTTACAATAAGGTGATTGAGCTT-TC
* * *
189218 GATAATCCATATAAAGTCTCCAAGTATTGTCTTTCTTTTT
65 GATAATCCACATAAAGTCTCCAAGTACTATCTTTCTTTTT
189258 TACCATAACT
Statistics
Matches: 194, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
104 1 0.01
105 192 0.99
106 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (105 bp):
TCTAATAACTTATCAATTAAGGGAATTAGGAACTTATCTTTTACAATAAGGTGATTGAGCTTTCG
ATAATCCACATAAAGTCTCCAAGTACTATCTTTCTTTTTA
Found at i:192758 original size:20 final size:20
Alignment explanation
Indices: 192708--192768 Score: 77
Period size: 20 Copynumber: 3.0 Consensus size: 20
192698 TCAAAAACCT
*
192708 ATAATATATCGATACAATTGTA
1 ATAATGTATCGATAC-ATT-TA
**
192730 AGCATGTATCGATACATTTA
1 ATAATGTATCGATACATTTA
192750 ATAATGTATCGATACATTT
1 ATAATGTATCGATACATTT
192769 CTTTGGCAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 19 0.56
21 3 0.09
22 12 0.35
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.38
Consensus pattern (20 bp):
ATAATGTATCGATACATTTA
Found at i:195703 original size:24 final size:24
Alignment explanation
Indices: 195671--195722 Score: 104
Period size: 24 Copynumber: 2.2 Consensus size: 24
195661 ATTTTAGAAA
195671 TTATTAGATTGATTTCCTACTTGT
1 TTATTAGATTGATTTCCTACTTGT
195695 TTATTAGATTGATTTCCTACTTGT
1 TTATTAGATTGATTTCCTACTTGT
195719 TTAT
1 TTAT
195723 CGATCTCTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.56
Consensus pattern (24 bp):
TTATTAGATTGATTTCCTACTTGT
Found at i:195835 original size:14 final size:15
Alignment explanation
Indices: 195809--195839 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
195799 GATAACTATG
195809 AATAAAGTAAAATAA
1 AATAAAGTAAAATAA
195824 AATAAA-TAAAATAA
1 AATAAAGTAAAATAA
195838 AA
1 AA
195840 AAGTGGGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.19
Consensus pattern (15 bp):
AATAAAGTAAAATAA
Found at i:196747 original size:22 final size:22
Alignment explanation
Indices: 196719--196785 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 22
196709 TTAAGTTATA
196719 ATTTAAAATTATTATTTATTTT
1 ATTTAAAATTATTATTTATTTT
*
196741 ATTTAAATTTATTTTTAATTTATTTT
1 ATTTAAA---ATTATT-ATTTATTTT
* *
196767 ATTTATATTTATTATTTAT
1 ATTTAAAATTATTATTTAT
196786 AAATAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 13 0.35
23 4 0.11
25 5 0.14
26 15 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTAAAATTATTATTTATTTT
Found at i:196752 original size:15 final size:15
Alignment explanation
Indices: 196732--196779 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 15
196722 TAAAATTATT
196732 ATTTATTTTATTTAA
1 ATTTATTTTATTTAA
196747 ATTTA--TT-TTT-A
1 ATTTATTTTATTTAA
*
196758 ATTTATTTTATTTAT
1 ATTTATTTTATTTAA
196773 ATTTATT
1 ATTTATT
196780 ATTTATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
11 6 0.21
12 3 0.11
13 4 0.14
14 3 0.11
15 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTATTTTATTTAA
Found at i:196763 original size:26 final size:27
Alignment explanation
Indices: 196732--196784 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 27
196722 TAAAATTATT
196732 ATTTATTTTATTTAAATTTATT-TTTA
1 ATTTATTTTATTTAAATTTATTATTTA
*
196758 ATTTATTTTATTTATATTTATTATTTA
1 ATTTATTTTATTTAAATTTATTATTTA
196785 TAAATAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 21 0.84
27 4 0.16
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (27 bp):
ATTTATTTTATTTAAATTTATTATTTA
Found at i:197724 original size:26 final size:27
Alignment explanation
Indices: 197692--197759 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
197682 TATAATTTTG
*
197692 ATAAAAAATAAATAAATAA-ATTTAAA
1 ATAAAATATAAATAAATAATATTTAAA
*
197718 ATTAAAATTATAAA-AAATAATTTTTAAA
1 A-TAAAA-TATAAATAAATAATATTTAAA
197746 ATAAAATATAAATA
1 ATAAAATATAAATA
197760 TAAAAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
26 7 0.19
27 17 0.47
28 12 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
ATAAAATATAAATAAATAATATTTAAA
Found at i:200150 original size:33 final size:33
Alignment explanation
Indices: 200069--200150 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
200059 TAGCCTTCAA
*
200069 AGAGAAAGAAGAGAGAGGAGGGATGATAGGAGG
1 AGAGAAAGAAGAGATAGGAGGGATGATAGGAGG
*
200102 AGAGATAGTAA-AGATAGGAGGGATGATAGGAGG
1 AGAGAAAG-AAGAGATAGGAGGGATGATAGGAGG
* *
200135 AGAGACAGGAGAGATA
1 AGAGAAAGAAGAGATA
200151 ATAGAGAGAG
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
32 1 0.02
33 40 0.93
34 2 0.05
ACGTcount: A:0.45, C:0.01, G:0.44, T:0.10
Consensus pattern (33 bp):
AGAGAAAGAAGAGATAGGAGGGATGATAGGAGG
Found at i:200163 original size:42 final size:43
Alignment explanation
Indices: 200099--200182 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
200089 GGATGATAGG
* * *
200099 AGGAGAGATAGTAAAGATAGGAGGGATGATAGGAGG-AGAGAC
1 AGGAGAGATAATAAAGAGAGGAGGGATGACAGGAGGAAGAGAC
*
200141 AGGAGAGATAATAGAGAGAGGAGGGATGACAGGAGGAAGAGA
1 AGGAGAGATAATAAAGAGAGGAGGGATGACAGGAGGAAGAGA
200183 GAAGAAGATG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 32 0.86
43 5 0.14
ACGTcount: A:0.44, C:0.02, G:0.44, T:0.10
Consensus pattern (43 bp):
AGGAGAGATAATAAAGAGAGGAGGGATGACAGGAGGAAGAGAC
Found at i:205542 original size:8 final size:8
Alignment explanation
Indices: 205531--205572 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
205521 TAATAAATAG
205531 AAAAATTA
1 AAAAATTA
*
205539 AAAAA--C
1 AAAAATTA
205545 AAAAATTA
1 AAAAATTA
205553 AAAAATTA
1 AAAAATTA
205561 AAAAATTA
1 AAAAATTA
205569 AAAA
1 AAAA
205573 TATATAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 5 0.17
8 25 0.83
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (8 bp):
AAAAATTA
Found at i:205550 original size:14 final size:15
Alignment explanation
Indices: 205525--205572 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
205515 ATTTCATAAT
205525 AAATAGAAAAATTAAA
1 AAATA-AAAAATTAAA
*
205541 AAA-CAAAAATTAAA
1 AAATAAAAAATTAAA
205555 AAATTAAAAAATTAAA
1 AAA-TAAAAAATTAAA
205571 AA
1 AA
205573 TATATAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 13 0.46
16 15 0.54
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (15 bp):
AAATAAAAAATTAAA
Found at i:205555 original size:7 final size:7
Alignment explanation
Indices: 205531--205573 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
205521 TAATAAATAG
205531 AAAAATT
1 AAAAATT
**
205538 AAAAAAC
1 AAAAATT
205545 AAAAATT
1 AAAAATT
205552 AAAAAATT
1 -AAAAATT
205560 AAAAAATT
1 -AAAAATT
205568 AAAAAT
1 AAAAAT
205574 ATATAAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
7 16 0.52
8 15 0.48
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAAATT
Found at i:205593 original size:18 final size:18
Alignment explanation
Indices: 205566--205606 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
205556 AATTAAAAAA
*
205566 TTAAAAATATATAAAT-T
1 TTAAAAATATAAAAATCT
205583 TTAAAATATATAAAAATCT
1 TTAAAA-ATATAAAAATCT
205602 TTAAA
1 TTAAA
205607 TCTTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.29
18 9 0.43
19 6 0.29
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (18 bp):
TTAAAAATATAAAAATCT
Found at i:205649 original size:27 final size:24
Alignment explanation
Indices: 205609--205674 Score: 80
Period size: 24 Copynumber: 2.7 Consensus size: 24
205599 TCTTTAAATC
205609 TTTTAAAAATAAAAATTCAAAAATAA
1 TTTTAAAAATAAAAATT-AAAAA-AA
*
205635 TTTATAAAAAT-AAAATTTAAAAAA
1 TTT-TAAAAATAAAAATTAAAAAAA
*
205659 TTTTCAAAATAAAAAT
1 TTTTAAAAATAAAAAT
205675 AATTTTTTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
23 6 0.17
24 10 0.28
25 4 0.11
26 9 0.25
27 7 0.19
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (24 bp):
TTTTAAAAATAAAAATTAAAAAAA
Found at i:205655 original size:13 final size:13
Alignment explanation
Indices: 205610--205657 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
205600 CTTTAAATCT
205610 TTTAAAAATAAAAA
1 TTTAAAAAT-AAAA
* *
205624 TTCAAAAAT-AAT
1 TTTAAAAATAAAA
205636 TTATAAAAATAAAA
1 TT-TAAAAATAAAA
205650 TTTAAAAA
1 TTTAAAAA
205658 ATTTTCAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 4 0.14
13 12 0.43
14 12 0.43
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (13 bp):
TTTAAAAATAAAA
Found at i:205659 original size:14 final size:14
Alignment explanation
Indices: 205613--205659 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
205603 TAAATCTTTT
* *
205613 AAAAATAAAAATTC
1 AAAAATAAAATTTA
205627 AAAAAT--AATTTA
1 AAAAATAAAATTTA
205639 TAAAAATAAAATTTA
1 -AAAAATAAAATTTA
205654 AAAAAT
1 AAAAAT
205660 TTTCAAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 4 0.14
13 6 0.21
14 12 0.43
15 6 0.21
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAATAAAATTTA
Found at i:205730 original size:19 final size:18
Alignment explanation
Indices: 205697--205749 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
205687 TTAATTTATC
*
205697 AAAA-TTTATAAAAATTA
1 AAAATTTTAAAAAAATTA
*
205714 AAAATTATTAAAAAAATGA
1 AAAATT-TTAAAAAAATTA
*
205733 AAAGTTTTAAAAAAATT
1 AAAATTTTAAAAAAATT
205750 TAACATAACA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 4 0.13
18 11 0.37
19 15 0.50
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (18 bp):
AAAATTTTAAAAAAATTA
Found at i:205813 original size:15 final size:15
Alignment explanation
Indices: 205783--205820 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
205773 TTTGTTTTTT
*
205783 AAAAATTT-AAATTA
1 AAAAATTTAAAAATA
205797 AAAAATTTAAAAATA
1 AAAAATTTAAAAATA
*
205812 AAATATTTA
1 AAAAATTTA
205821 TTTTATGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAAATTTAAAAATA
Found at i:205900 original size:2 final size:2
Alignment explanation
Indices: 205895--205938 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
205885 TTATAAAATT
205895 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
205937 GA
1 GA
205939 AGGGCAAAGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:209949 original size:21 final size:19
Alignment explanation
Indices: 209925--209973 Score: 55
Period size: 18 Copynumber: 2.5 Consensus size: 19
209915 TATGATGAGT
*
209925 ATAATTATATTATTAAATTTA
1 ATAATTATATT-TTAAA-ATA
209946 ATAATTAT-TTTTAAAATA
1 ATAATTATATTTTAAAATA
*
209964 TTAATTATAT
1 ATAATTATAT
209974 AAAAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 9 0.36
19 6 0.24
20 2 0.08
21 8 0.32
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAATTATATTTTAAAATA
Found at i:211430 original size:20 final size:22
Alignment explanation
Indices: 211391--211439 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
211381 TAGTTTTTAC
211391 CATATAAAAAATAAATATATAT
1 CATATAAAAAATAAATATATAT
211413 CATATAAAAAATAAATATATAT
1 CATATAAAAAATAAATATATAT
*
211435 AATAT
1 CATAT
211440 TATAGTGCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (22 bp):
CATATAAAAAATAAATATATAT
Found at i:215488 original size:19 final size:19
Alignment explanation
Indices: 215464--215501 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
215454 CCAATTTAAC
215464 TCAAAATTCATGGTTATTT
1 TCAAAATTCATGGTTATTT
*
215483 TCAAAATTCGTGGTTATTT
1 TCAAAATTCATGGTTATTT
215502 ATTTTACTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (19 bp):
TCAAAATTCATGGTTATTT
Found at i:218401 original size:20 final size:20
Alignment explanation
Indices: 218363--218414 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
218353 TTACAATTTT
*
218363 TATCGATACAATTAGTGAATA
1 TATCGATAC-ATAAGTGAATA
*
218384 TATCGATACATAAGTGAATG
1 TATCGATACATAAGTGAATA
*
218404 TATCGACACAT
1 TATCGATACAT
218415 GTCACAAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.68
21 9 0.32
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
TATCGATACATAAGTGAATA
Found at i:218492 original size:20 final size:20
Alignment explanation
Indices: 218463--218514 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
218453 GTAAAAAAAT
218463 TGTATC-ATACATAAGTAAA
1 TGTATCGATACATAAGTAAA
* *
218482 TGTATCGATACATAATTGAA
1 TGTATCGATACATAAGTAAA
*
218502 TGTATCGACACAT
1 TGTATCGATACAT
218515 GTCTCAAATG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 6 0.21
20 23 0.79
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
TGTATCGATACATAAGTAAA
Found at i:220801 original size:2 final size:2
Alignment explanation
Indices: 220796--220824 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
220786 TTTTTTTAGA
220796 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
220825 ATGCTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:223738 original size:46 final size:46
Alignment explanation
Indices: 223634--223754 Score: 142
Period size: 46 Copynumber: 2.6 Consensus size: 46
223624 CACATAGCTA
* *
223634 GTAGCTTTTGCACAT-A-GAAAGCTATAAACCTTCCAATAAACAACCT
1 GTAGCTTTTG--CATGAGGAAAGCTACAAACCTTCCAACAAACAACCT
*
223680 -TAAGCTTTTGCATGAGGAAAGCTACAAATCTTCCAACAAACAACCT
1 GT-AGCTTTTGCATGAGGAAAGCTACAAACCTTCCAACAAACAACCT
*
223726 GTAGCTTTTGCATG-GAGAAATCTACAAAC
1 GTAGCTTTTGCATGAG-GAAAGCTACAAAC
223755 TATCCTTTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
44 3 0.05
45 3 0.05
46 58 0.89
47 1 0.02
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (46 bp):
GTAGCTTTTGCATGAGGAAAGCTACAAACCTTCCAACAAACAACCT
Found at i:230425 original size:19 final size:19
Alignment explanation
Indices: 230401--230467 Score: 83
Period size: 19 Copynumber: 3.8 Consensus size: 19
230391 CAGTAGCTAA
230401 TTATGTATCGATACAACAC
1 TTATGTATCGATACAACAC
230420 TTATGTATCGAT---ACA-
1 TTATGTATCGATACAACAC
230435 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAACAC
*
230452 TTATGTATCAATACAA
1 TTATGTATCGATACAA
230468 ATCGTTGAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 9 0.22
14 1 0.02
16 6 0.15
18 1 0.02
19 24 0.59
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.34
Consensus pattern (19 bp):
TTATGTATCGATACAACAC
Found at i:230441 original size:13 final size:13
Alignment explanation
Indices: 230423--230447 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
230413 ACAACACTTA
230423 TGTATCGATACAT
1 TGTATCGATACAT
230436 TGTATCGATACA
1 TGTATCGATACA
230448 ACACTTATGT
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:230445 original size:32 final size:32
Alignment explanation
Indices: 230404--230466 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
230394 TAGCTAATTA
*
230404 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCAATACAT
230436 TGTATCGATACAACACTTATGTATCAATACA
1 TGTATCGATACAACACTTATGTATCAATACA
230467 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCAATACAT
Found at i:231336 original size:66 final size:66
Alignment explanation
Indices: 231189--231448 Score: 385
Period size: 66 Copynumber: 3.9 Consensus size: 66
231179 ATTGGGTTTC
* * ** * * * * * *
231189 AAAGATGACAAAGACGCCAATATGCAGATTCAAGGCCAGCAATATTGGACTGAAAGATGGAGGTG
1 AAAG-TGATAAAGATGCCAATATGTTGATTCACGACCAACGATATTGGGCTTAAA-ATGGAGGTG
231254 AGA
64 AGA
231257 AAAGTGATAAAGATGCCAATATGTTGATTCACGACCAACGATATTGGGCTTAAAATGGAGGTGAG
1 AAAGTGATAAAGATGCCAATATGTTGATTCACGACCAACGATATTGGGCTTAAAATGGAGGTGAG
231322 A
66 A
231323 AAAGTGATAAAGATGCCAATATGTTGATTCACGACCAACGATATTGGGCTTAAAATGGAGGTGAG
1 AAAGTGATAAAGATGCCAATATGTTGATTCACGACCAACGATATTGGGCTTAAAATGGAGGTGAG
231388 A
66 A
* *
231389 AAAGTGATAAAGATGCCAATATGTTGATTCACGGCCAATGATATTGGGCTTAAAAATGGA
1 AAAGTGATAAAGATGCCAATATGTTGATTCACGACCAACGATATTGGGCTT-AAAATGGA
231449 AAAAGGATGT
Statistics
Matches: 179, Mismatches: 12, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
66 127 0.71
67 48 0.27
68 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.26, T:0.23
Consensus pattern (66 bp):
AAAGTGATAAAGATGCCAATATGTTGATTCACGACCAACGATATTGGGCTTAAAATGGAGGTGAG
A
Found at i:231869 original size:13 final size:13
Alignment explanation
Indices: 231851--231876 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
231841 TACACCAAGT
231851 ATGTATCGATACA
1 ATGTATCGATACA
231864 ATGTATCGATACA
1 ATGTATCGATACA
231877 CAAATAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:231874 original size:32 final size:33
Alignment explanation
Indices: 231833--231896 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
231823 TAGCCAAACT
*
231833 TGTATCGATACACCAAGT-A-TGTATCGATACAA
1 TGTATCGATACA-CAAATAATTGTATCGATACAA
231865 TGTATCGATACACAAATAATTGTATCGATACA
1 TGTATCGATACACAAATAATTGTATCGATACA
231897 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 4 0.14
32 13 0.45
33 12 0.41
ACGTcount: A:0.39, C:0.17, G:0.14, T:0.30
Consensus pattern (33 bp):
TGTATCGATACACAAATAATTGTATCGATACAA
Found at i:234117 original size:21 final size:21
Alignment explanation
Indices: 234084--234128 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
234074 TTGCAAGATG
*
234084 AAATAAAGAAGTTGGCTAAAGA
1 AAATAAAGAAGTTAGCT-AAGA
*
234106 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
234126 AAA
1 AAA
234129 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 7 0.33
22 7 0.33
ACGTcount: A:0.56, C:0.04, G:0.20, T:0.20
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:235951 original size:15 final size:15
Alignment explanation
Indices: 235931--235961 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
235921 TAAACATGTC
*
235931 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
235946 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
235961 C
1 C
235962 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:238048 original size:13 final size:13
Alignment explanation
Indices: 238030--238068 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
238020 ACATTTTTCC
238030 TTGTATCGATACA
1 TTGTATCGATACA
238043 TTGTATCGATACA
1 TTGTATCGATACA
*
238056 TTATATCGATACA
1 TTGTATCGATACA
238069 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:240638 original size:13 final size:13
Alignment explanation
Indices: 240620--240645 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
240610 TACATCAAGT
240620 ATGTATCGATACA
1 ATGTATCGATACA
240633 ATGTATCGATACA
1 ATGTATCGATACA
240646 CAAATAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:240643 original size:32 final size:33
Alignment explanation
Indices: 240602--240665 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
240592 TAGCCAAACT
*
240602 TGTATCGATACATCAAGT-A-TGTATCGATACAA
1 TGTATCGATACA-CAAATAATTGTATCGATACAA
240634 TGTATCGATACACAAATAATTGTATCGATACA
1 TGTATCGATACACAAATAATTGTATCGATACA
240666 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 4 0.14
32 13 0.45
33 12 0.41
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (33 bp):
TGTATCGATACACAAATAATTGTATCGATACAA
Found at i:241502 original size:43 final size:43
Alignment explanation
Indices: 241402--242067 Score: 801
Period size: 43 Copynumber: 14.7 Consensus size: 43
241392 GCTTTCATGT
* * *
241402 TGATTCATGGCCAGGTACATTGGACTTAAAGAAGAAGATGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTT--A-AAG--G-TGCCAATGTGC
* * *
241451 TGATTCAAGGCCAGCTATATCGGACTCAAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
* * *
241494 TGAGTCAAGGCTAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGAC-T-----TAAAGGTGCCAATGTGC
* * *
241543 TGACTCAAGGCCAGCTATATTGGACTTAAAGGTGCTAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
241586 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
* * *
241629 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTT----A-AAGGTGCCAATGTGC
*
241677 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
*
241720 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGAC-T-----TAAAGGTGCCAATGTGC
*
241769 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
*
241812 TGATTCAAGGCCAGCTACATTGGACTTAAAGATGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
* * *
241855 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTT----A-AAGGTGCCAATGTGC
*
241903 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
*
241946 TGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 TGATTCAAGGCCAGCTACATTGGACTT-AA-A-G--G-TGCCAATGTGC
*
241995 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
242038 TGATTCAAGGCCAGCTACATTGGACTTAAA
1 TGATTCAAGGCCAGCTACATTGGACTTAAA
242068 AGAAGATGCC
Statistics
Matches: 543, Mismatches: 46, Indels: 62
0.83 0.07 0.10
Matches are distributed among these distances:
43 310 0.57
44 8 0.01
45 1 0.00
46 5 0.01
47 4 0.01
48 80 0.15
49 135 0.25
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (43 bp):
TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGC
Found at i:241574 original size:22 final size:21
Alignment explanation
Indices: 241549--241617 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 21
241539 ATGCTGACTC
241549 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
* *
241571 AAGG--TGCTAATGTGCTGA-TTC
1 AAGGCCAGCTAAT-TG--GACTTA
241592 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
241614 AAGG
1 AAGG
241618 TGCCAATGTG
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 8 0.22
22 12 0.33
23 6 0.17
24 2 0.06
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (21 bp):
AAGGCCAGCTAATTGGACTTA
Found at i:241574 original size:92 final size:92
Alignment explanation
Indices: 241402--242067 Score: 841
Period size: 92 Copynumber: 7.3 Consensus size: 92
241392 GCTTTCATGT
* * *
241402 TGATTCATGGCCAGGTACATTGGACTTAAAGA-AGAAGATGCCAATATGCTGATTCAAGGCCAGC
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATGCTGATTCAAGGCCAGC
* *
241466 TATATCGGACTCAAAGGTGCCAATGTGC
65 TATATTGGACTTAAAGGTGCCAATGTGC
* * *
241494 TGAGTCAAGGCTAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGACTCAAGGCCAGCT
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
*
241559 ATATTGGACTTAAAGGTGCTAATGTGC
66 ATATTGGACTTAAAGGTGCCAATGTGC
* *
241586 TGATTCAAGGCCAGCTACATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCG
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* * *
241645 ACATTGGTCTTAAAGACAAGGTGCCAATATGC
66 ATATTGGACTT----A-AAGGTGCCAATGTGC
* *
241677 TGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCT
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* *
241736 ACATTGGACTTAAAGATAAAGGTGCCAATATGC
66 ATATTGGAC-T-----TAAAGGTGCCAATGTGC
* *
241769 TGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCT
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* *
241828 ACATTGGACTTAAAGATGCCAATGTGC
66 ATATTGGACTTAAAGGTGCCAATGTGC
* * *
241855 TGATTCAAGGCCAGCGACATTGGTCTTAAAGA-CAAGGTGCCAATATGCTGATTCAAGGCCAGCT
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
241919 ATATTGGACTTAAAGGTGCCAATGTGC
66 ATATTGGACTTAAAGGTGCCAATGTGC
* *
241946 TGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCT
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
242011 ATATTGGACTTAAAGGTGCCAATGTGC
66 ATATTGGACTTAAAGGTGCCAATGTGC
242038 TGATTCAAGGCCAGCTACATTGGACTTAAA
1 TGATTCAAGGCCAGCTACATTGGACTTAAA
242068 AGAAGATGCC
Statistics
Matches: 521, Mismatches: 34, Indels: 38
0.88 0.06 0.06
Matches are distributed among these distances:
86 76 0.15
87 1 0.00
90 1 0.00
91 165 0.32
92 275 0.53
93 2 0.00
97 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (92 bp):
TGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
ATATTGGACTTAAAGGTGCCAATGTGC
Found at i:241602 original size:23 final size:23
Alignment explanation
Indices: 241576--241643 Score: 56
Period size: 21 Copynumber: 3.1 Consensus size: 23
241566 ACTTAAAGGT
241576 GCTAATGTGCTGATTCAAGGCCA
1 GCTAATGTGCTGATTCAAGGCCA
* *
241599 GCTACAT-TG--GACTTAAAGG--T
1 GCTA-ATGTGCTGA-TTCAAGGCCA
*
241619 GCCAATGTGCTGATTCAAGGCCA
1 GCTAATGTGCTGATTCAAGGCCA
241642 GC
1 GC
241644 GACATTGGTC
Statistics
Matches: 33, Mismatches: 5, Indels: 14
0.63 0.10 0.27
Matches are distributed among these distances:
19 2 0.06
20 5 0.15
21 8 0.24
22 8 0.24
23 8 0.24
24 2 0.06
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.25
Consensus pattern (23 bp):
GCTAATGTGCTGATTCAAGGCCA
Found at i:241759 original size:183 final size:176
Alignment explanation
Indices: 241402--242067 Score: 780
Period size: 183 Copynumber: 3.7 Consensus size: 176
241392 GCTTTCATGT
* * *
241402 TGATTCATGGCCAGGTACATTGGACTTAAAGAAGAAGATGCCAATATGCTGATTCAAGGCCAGCT
1 TGATTCAAGGCCAGCTACATTGGACTT--A-AAG--G-TGCCAATGTGCTGATTCAAGGCCAGCT
* * * * *
241467 ATATCGGAC-T---CAAAGGTGCCAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGATA
60 ACATTGGACTTAAAGAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC-T-----TA
* *
241528 AAGGTGCCAATATGCTGACTCAAGGCCAGCTATATTGGACTTAAAGGTGCTAATGTGC
119 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGC
*
241586 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTG
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
* * *
241651 GTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAAT
66 GACTTAAAGA-AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAAT
* * *
241716 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGCCAATATGC
130 ATGCTGATTCAAGGCCAGCTATATTGGAC-T-----TAAAGGTGCCAATGTGC
*
241769 TGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
1 TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
* *
241834 GACTTAAAG--A--TGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGC
66 GACTTAAAGAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT----A-AAGGTGC
241895 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGC
126 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGC
*
241946 TGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCT
1 TGATTCAAGGCCAGCTACATTGGACTT-AA-A-G--G-TGCCAATGTGCTGATTCAAGGCCAGCT
*
242011 ATATTGGACTT----AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
60 ACATTGGACTTAAAGAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAA
242068 AGAAGATGCC
Statistics
Matches: 424, Mismatches: 32, Indels: 58
0.82 0.06 0.11
Matches are distributed among these distances:
177 81 0.19
178 70 0.17
179 4 0.01
180 2 0.00
181 4 0.01
182 6 0.01
183 232 0.55
184 25 0.06
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (176 bp):
TGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTG
GACTTAAAGAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATA
TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGC
Found at i:241834 original size:226 final size:226
Alignment explanation
Indices: 241402--242067 Score: 1190
Period size: 226 Copynumber: 2.9 Consensus size: 226
241392 GCTTTCATGT
* * * *
241402 TGATTCATGGCCAG-GTACATTGGACTTAAAGAAGAAGATGCCAATATGCTGATTCAAGGCCAGC
1 TGATTCAAGGCCAGCG-ACATTGGTCTTAAAG-ACAAGGTGCCAATATGCTGATTCAAGGCCAGC
* * * *
241466 TATATCGGACTCAAAGGTGCCAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGATAAAG
64 TATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAG
* *
241531 GTGCCAATATGCTGACTCAAGGCCAGCTATATTGGACTTAAAGGTGCTAATGTGCTGATTCAAGG
129 GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
*
241596 CCAGCTACATTGGACTTAAAGGTGCCAATGTGC
194 CCAGCTACATTGGACTTAAAGATGCCAATGTGC
241629 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
241694 TATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGT
66 TATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGT
241759 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
131 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
241824 AGCTACATTGGACTTAAAGATGCCAATGTGC
196 AGCTACATTGGACTTAAAGATGCCAATGTGC
241855 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
1 TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
* *
241920 TATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGAT
66 TATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGT
241985 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
131 GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
242050 AGCTACATTGGACTTAAA
196 AGCTACATTGGACTTAAA
242068 AGAAGATGCC
Statistics
Matches: 425, Mismatches: 13, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
226 397 0.93
227 27 0.06
228 1 0.00
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.26
Consensus pattern (226 bp):
TGATTCAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGATTCAAGGCCAGCTA
TATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGT
GCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCC
AGCTACATTGGACTTAAAGATGCCAATGTGC
Found at i:242226 original size:32 final size:33
Alignment explanation
Indices: 242101--242249 Score: 135
Period size: 34 Copynumber: 4.5 Consensus size: 33
242091 GGCTTTTGAA
* * *
242101 AAGGAGAAAGATGCCAC-AGAGTTGTGGACTTAAA
1 AAGGAAAAAGGTGCCACGA-AGTTGTGGACTT-AG
* * *
242135 AAGAAAAAAAGTGCCACGGAGTTGTGGACTTAG
1 AAGGAAAAAGGTGCCACGAAGTTGTGGACTTAG
* *
242168 AAGGAAAAAGAGTGCCATGAAGTTGTGGGCTTA-
1 AAGGAAAAAG-GTGCCACGAAGTTGTGGACTTAG
* * *
242201 AATGAAAAAGGTGCCACGAAATTGTGGACTTTG
1 AAGGAAAAAGGTGCCACGAAGTTGTGGACTTAG
242234 AA-G-AAAAGGATGCCAC
1 AAGGAAAAAGG-TGCCAC
242250 TGAGTCGTAG
Statistics
Matches: 95, Mismatches: 16, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
31 6 0.06
32 25 0.26
33 20 0.21
34 44 0.46
ACGTcount: A:0.40, C:0.12, G:0.30, T:0.19
Consensus pattern (33 bp):
AAGGAAAAAGGTGCCACGAAGTTGTGGACTTAG
Found at i:242227 original size:66 final size:66
Alignment explanation
Indices: 242107--242248 Score: 164
Period size: 66 Copynumber: 2.2 Consensus size: 66
242097 TGAAAAGGAG
* * *
242107 AAAGATGCCA-CAGAGTTGTGGACTTAAAAAGAAAAAAAGTGCCACGGAGTTGTGGACTTAGAAG
1 AAAGATGCCATGA-AGTTGTGGACTTAAAAAGAAAAAAAGTGCCACGAAATTGTGGACTTAGAA-
242171 GAA
64 GAA
* * * *
242174 AAAGAGTGCCATGAAGTTGTGGGCTT-AAATG-AAAAAGGTGCCACGAAATTGTGGACTTTGAAG
1 AAAGA-TGCCATGAAGTTGTGGACTTAAAAAGAAAAAAAGTGCCACGAAATTGTGGACTTAGAAG
242237 AA
65 AA
*
242239 AAGGATGCCA
1 AAAGATGCCA
242249 CTGAGTCGTA
Statistics
Matches: 65, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
64 5 0.08
65 7 0.11
66 27 0.42
67 9 0.14
68 16 0.25
69 1 0.02
ACGTcount: A:0.39, C:0.12, G:0.29, T:0.20
Consensus pattern (66 bp):
AAAGATGCCATGAAGTTGTGGACTTAAAAAGAAAAAAAGTGCCACGAAATTGTGGACTTAGAAGA
A
Found at i:242315 original size:31 final size:31
Alignment explanation
Indices: 242224--242361 Score: 165
Period size: 31 Copynumber: 4.5 Consensus size: 31
242214 CCACGAAATT
*
242224 GTGGACTTTGAAGAAAAGGA-TGCCACTGAGTC
1 GTGGACTTTG-AGAAGA-GATTGCCACTGAGTC
* *
242256 GTAGACTTTGAGACA-A-AATGCCACTGAGTC
1 GTGGACTTTGAGA-AGAGATTGCCACTGAGTC
* *
242286 GTGGGCTTTGAGAAGAGATTGTCACTGAGTC
1 GTGGACTTTGAGAAGAGATTGCCACTGAGTC
*
242317 GTGGACTTTGAGAAGAGATTGCCACTAAGTC
1 GTGGACTTTGAGAAGAGATTGCCACTGAGTC
*
242348 GTGGACTTTAAGAA
1 GTGGACTTTGAGAA
242362 AGTATTTGAA
Statistics
Matches: 93, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
29 2 0.02
30 24 0.26
31 57 0.61
32 10 0.11
ACGTcount: A:0.30, C:0.15, G:0.30, T:0.25
Consensus pattern (31 bp):
GTGGACTTTGAGAAGAGATTGCCACTGAGTC
Found at i:247476 original size:13 final size:13
Alignment explanation
Indices: 247458--247495 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
247448 CAGCATTCTC
*
247458 TGTATCGATACAT
1 TGTATCGATACAG
247471 TGTATCGATACAG
1 TGTATCGATACAG
247484 TGTATCGATACA
1 TGTATCGATACA
247496 AAGGGTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:249391 original size:21 final size:22
Alignment explanation
Indices: 249351--249394 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
249341 CGAAATTGTC
249351 AAATTATTTTATTAAGGGGGAG
1 AAATTATTTTATTAAGGGGGAG
249373 AAATT-TTTTGATTAAGGGGGAG
1 AAATTATTTT-ATTAAGGGGGAG
249395 GGAAAAGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.34, C:0.00, G:0.30, T:0.36
Consensus pattern (22 bp):
AAATTATTTTATTAAGGGGGAG
Found at i:249973 original size:20 final size:21
Alignment explanation
Indices: 249950--250000 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
249940 GATTGCATAT
**
249950 TATCGATACATGACCA-AATG
1 TATCGATACATGAAAAGAATG
*
249970 TATCGATACTTGAAAAGAATG
1 TATCGATACATGAAAAGAATG
249991 TATCGATACA
1 TATCGATACA
250001 GGTCATTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (21 bp):
TATCGATACATGAAAAGAATG
Found at i:253030 original size:21 final size:21
Alignment explanation
Indices: 252991--253030 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
252981 TAATGTACCT
*
252991 AGACATTTTCAATTTAATTCA
1 AGACATTTTCAATTCAATTCA
**
253012 AGACATTTTGGATTCAATT
1 AGACATTTTCAATTCAATT
253031 TTTGTCATGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (21 bp):
AGACATTTTCAATTCAATTCA
Found at i:255622 original size:12 final size:12
Alignment explanation
Indices: 255605--255629 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
255595 CAATTTTTGG
255605 TGTATCGATACA
1 TGTATCGATACA
255617 TGTATCGATACA
1 TGTATCGATACA
255629 T
1 T
255630 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TGTATCGATACA
Found at i:255639 original size:31 final size:32
Alignment explanation
Indices: 255584--255647 Score: 103
Period size: 31 Copynumber: 2.0 Consensus size: 32
255574 TTACAAGCCA
**
255584 ATGTATCGATACAATTTTTGGTGTATCGATAC
1 ATGTATCGATACAATACTTGGTGTATCGATAC
255616 ATGTATCGATAC-ATACTTGGTGTATCGATAC
1 ATGTATCGATACAATACTTGGTGTATCGATAC
255647 A
1 A
255648 AGTTTGGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 18 0.60
32 12 0.40
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (32 bp):
ATGTATCGATACAATACTTGGTGTATCGATAC
Found at i:260285 original size:15 final size:15
Alignment explanation
Indices: 260262--260300 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
260252 GTTCATCAAT
*
260262 TTCAGTTTGAGCTTC
1 TTCATTTTGAGCTTC
260277 TTCATTTTGAGCTTC
1 TTCATTTTGAGCTTC
*
260292 CTCATTTTG
1 TTCATTTTG
260301 GACATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.13, C:0.21, G:0.15, T:0.51
Consensus pattern (15 bp):
TTCATTTTGAGCTTC
Found at i:265508 original size:23 final size:23
Alignment explanation
Indices: 265478--265522 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
265468 AGAGCCACTC
*
265478 TTTTTTTTATTGATGTTCATTCT
1 TTTTTTTTATTGATATTCATTCT
* *
265501 TTTTTTTTCTTGCTATTCATTC
1 TTTTTTTTATTGATATTCATTC
265523 CCATTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.13, G:0.07, T:0.69
Consensus pattern (23 bp):
TTTTTTTTATTGATATTCATTCT
Found at i:275173 original size:11 final size:11
Alignment explanation
Indices: 275150--275208 Score: 66
Period size: 11 Copynumber: 5.3 Consensus size: 11
275140 CCTTCATACC
*
275150 AAAAAA-AATA
1 AAAAAACAAAA
275160 AAAAAACAAAA
1 AAAAAACAAAA
275171 AAAAAACAAAA
1 AAAAAACAAAA
*
275182 AAAATAAGGAAAA
1 AAAA-AA-CAAAA
*
275195 AAATAACAAAA
1 AAAAAACAAAA
275206 AAA
1 AAA
275209 CAGAATGGGG
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
10 6 0.14
11 25 0.60
12 4 0.10
13 7 0.17
ACGTcount: A:0.86, C:0.05, G:0.03, T:0.05
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:275174 original size:12 final size:12
Alignment explanation
Indices: 275150--275208 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
275140 CCTTCATACC
*
275150 AAAAA-AAATAA
1 AAAAACAAAAAA
275161 AAAAAC-AAAAA
1 AAAAACAAAAAA
275172 AAAAACAAAAAA
1 AAAAACAAAAAA
* **
275184 AATAAGGAAAAA
1 AAAAACAAAAAA
*
275196 AATAACAAAAAA
1 AAAAACAAAAAA
275208 A
1 A
275209 CAGAATGGGG
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
11 15 0.38
12 25 0.62
ACGTcount: A:0.86, C:0.05, G:0.03, T:0.05
Consensus pattern (12 bp):
AAAAACAAAAAA
Found at i:276461 original size:28 final size:28
Alignment explanation
Indices: 276423--277015 Score: 585
Period size: 28 Copynumber: 20.4 Consensus size: 28
276413 CTTTCATCTC
*
276423 TTCAAAGCCCATAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
276451 TTCAAAACCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
** * * **
276479 TTCAAAGCTAACGAGTCAGTGGTAACTTTT
1 TTCAAAGCCCACAAGTCAGTGG-CA-TCCT
* *
276509 TTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* **
276538 TTCAAAGCTCACACGAGTCAGTGGCAACTGAT
1 TTCAAAGC-C-CACAAGTCAGTGGC-A-TCCT
* *
276570 TTCAAAGCCCACAAGACAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * *
276598 TTCAAAGCTCAGACAATGTCGGTGGCAACTCTT
1 TTCAAAGC-C-CACAA-GTCAGTGGC-A-TCCT
* *
276631 TTCATAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
276659 TTCAAAGCCCACGAGTCCGTGACAACTCAT
1 TTCAAAGCCCACAAGTCAGTGGC-A-TCCT
*
276689 TTCAAGGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
276717 TTCAAAGCCCACGAGTCGGTGACAACACTT
1 TTCAAAGCCCACAAGTCAGTGGCATC-C-T
* *
276747 TTCAAAGCCCATAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
276775 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
276803 TTCAAAGCCCACAAGTCAGTGGCA-CTCT
1 TTCAAAGCCCACAAGTCAGTGGCATC-CT
276831 TTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
276859 TTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* *
276888 TTCAAAGCCCATAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
276916 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
276944 TTCAAAGCCCACAAGTCAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCA-TCCT
* *
276973 TTCAAAGCCCACACAAGTCGGTGGCAACTCTT
1 TTCAAAG-CC-CACAAGTCAGTGGC-A-TCCT
277005 TTCAAAGCCCA
1 TTCAAAGCCCA
277016 TACAAGTTAA
Statistics
Matches: 473, Mismatches: 71, Indels: 40
0.81 0.12 0.07
Matches are distributed among these distances:
27 1 0.00
28 249 0.53
29 57 0.12
30 91 0.19
31 39 0.08
32 27 0.06
33 9 0.02
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:276833 original size:56 final size:57
Alignment explanation
Indices: 276423--277015 Score: 608
Period size: 58 Copynumber: 10.2 Consensus size: 57
276413 CTTTCATCTC
* *
276423 TTCAAAGCCCATAAGTCAGTGGCA-TCCTTTCAAAACCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACT-CT
** * * **
276479 TTCAAAGCTAACGAGTCAGTGGTAACTTTTTTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGG-CACTCCTTTCAAAGCCCACAAGTTAGTGGCACTC-T
* ** ** *
276538 TTCAAAGCTCACACGAGTCAGTGGCAACTGATTTCAAAGCCCACAAGACAGTGGCACCCT
1 TTCAAAGC-C-CACAAGTCAGTGGC-ACTCCTTTCAAAGCCCACAAGTTAGTGGCACTCT
* * * *
276598 TTCAAAGCTCAGACAATGTCGGTGGCAACTCTTTTCATAGCCCACAAGTTAGTGGCA-TCCT
1 TTCAAAGC-C-CACAA-GTCAGTGGC-ACTCCTTTCAAAGCCCACAAGTTAGTGGCACT-CT
* * * * * *
276659 TTCAAAGCCCACGAGTCCGTGACAACTCATTTCAAGGCCCACAAGTCAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGC-ACTCCTTTCAAAGCCCACAAGTTAGTGGCACT-CT
* * * * * *
276717 TTCAAAGCCCACGAGTCGGTGACAACACTTTTCAAAGCCCATAAGTTAGTGGCA-TCCT
1 TTCAAAGCCCACAAGTCAGTGGC-ACTCCTTTCAAAGCCCACAAGTTAGTGGCACT-CT
* *
276775 TTCAAAGCCCACAAGTTAGTGGCAC-CCTTTCAAAGCCCACAAGTCAGTGGCACTCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACTCT
276831 TTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTTAGTGGCACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACTC-T
* * *
276888 TTCAAAGCCCATAAGTTAGTGGCA-TCCTTTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACTCT
* **
276944 TTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACACAAGTCGGTGGCAACTCTT
1 TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAG-CC-CACAAGTTAGTGGC-ACTC-T
277005 TTCAAAGCCCA
1 TTCAAAGCCCA
277016 TACAAGTTAA
Statistics
Matches: 463, Mismatches: 57, Indels: 29
0.84 0.10 0.05
Matches are distributed among these distances:
56 119 0.26
57 67 0.14
58 137 0.30
59 25 0.05
60 19 0.04
61 96 0.21
ACGTcount: A:0.29, C:0.29, G:0.18, T:0.24
Consensus pattern (57 bp):
TTCAAAGCCCACAAGTCAGTGGCACTCCTTTCAAAGCCCACAAGTTAGTGGCACTCT
Found at i:277164 original size:44 final size:45
Alignment explanation
Indices: 277095--277220 Score: 119
Period size: 49 Copynumber: 2.7 Consensus size: 45
277085 CTGTCTCACA
* ***
277095 TCGCTAGCATTGAATCAGTGTATTGGCACTT-TATTAGCCCAATG
1 TCGCTAGCCTTGAATCAGCACATTGGCACTTCTATTAGCCCAATG
* *
277139 TCGCTAGCCTTGAATCAGCACATTGGTCCACTTTTCTCTTAGCCTAATG
1 TCGCTAGCCTTGAATCAGCACATTGG--CAC--TTCTATTAGCCCAATG
* * **
277188 TCGCTGGCCTTAAATTGGCACATTGGCACTTCT
1 TCGCTAGCCTTGAATCAGCACATTGGCACTTCT
277221 CTCATCTCTA
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
44 22 0.33
45 4 0.06
46 3 0.04
47 3 0.04
48 2 0.03
49 33 0.49
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.34
Consensus pattern (45 bp):
TCGCTAGCCTTGAATCAGCACATTGGCACTTCTATTAGCCCAATG
Found at i:277944 original size:14 final size:14
Alignment explanation
Indices: 277925--277953 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
277915 TGTATGAATG
277925 TATCGATACATTCT
1 TATCGATACATTCT
277939 TATCGATACATTCT
1 TATCGATACATTCT
277953 T
1 T
277954 CAATGTATCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (14 bp):
TATCGATACATTCT
Found at i:277972 original size:20 final size:19
Alignment explanation
Indices: 277885--277970 Score: 74
Period size: 20 Copynumber: 4.6 Consensus size: 19
277875 TACCTAGATT
*
277885 TATCGATACATTTTTCATTG
1 TATCGATACA-TTTTCAATG
* * *
277905 TATCAATACATGTATGAATG
1 TATCGATACAT-TTTCAATG
277925 TATCGATACA--TTC--T-
1 TATCGATACATTTTCAATG
277939 TATCGATACATTCTTCAATG
1 TATCGATACATT-TTCAATG
277959 TATCGATACATT
1 TATCGATACATT
277971 CTGTCTTTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 14
0.71 0.10 0.19
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
17 4 0.08
19 2 0.04
20 35 0.67
ACGTcount: A:0.31, C:0.16, G:0.10, T:0.42
Consensus pattern (19 bp):
TATCGATACATTTTCAATG
Found at i:282704 original size:28 final size:28
Alignment explanation
Indices: 282635--282958 Score: 287
Period size: 28 Copynumber: 11.5 Consensus size: 28
282625 TCACCCTTTC
* * *
282635 AAAGCCCACAAGTCAGTGGCATCTTTTCC
1 AAAGCCCACAAGTCAGTGGCAAC-CTTCA
*
282664 AAAGCCCATAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * *
282692 AAAGCCTACAAGTCAGTGGTATCCTTTC-
1 AAAGCCCACAAGTCAGTGGCAACC-TTCA
* * *
282720 AAAGTCCACAAGTCAATGGCAACCTCCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * *
282748 AAAGCCCACAAGTTAGTGGTATCCTTTC-
1 AAAGCCCACAAGTCAGTGGCAACC-TTCA
* ** *
282776 AAAGCCCACAAGTCATTGGCAATTTTTCC
1 AAAGCCCACAAGTCAGTGGCAA-CCTTCA
* *
282805 AAAGCCCACAAGTCAGTAGTAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
282833 AAAGCCCACAAGTTAGTGGCATCTTTTA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
* *
282861 CAAAGCCCACAAGTTAGTGGCAATCTTCA
1 -AAAGCCCACAAGTCAGTGGCAACCTTCA
* ** *
282890 AAAGCGCACAAGTCAGTGATATCCTTTC-
1 AAAGCCCACAAGTCAGTGGCAACC-TTCA
*
282918 AAAGCCCATAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGCAACCTTCA
282946 AAAGCACC-CAAGT
1 AAAGC-CCACAAGT
282959 TGATGTAACC
Statistics
Matches: 232, Mismatches: 54, Indels: 19
0.76 0.18 0.06
Matches are distributed among these distances:
27 5 0.02
28 153 0.66
29 74 0.32
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.22
Consensus pattern (28 bp):
AAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:282734 original size:56 final size:56
Alignment explanation
Indices: 282635--282936 Score: 288
Period size: 57 Copynumber: 5.3 Consensus size: 56
282625 TCACCCTTTC
* * *
282635 AAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCATAAGTCAGTGGCAACCTTCA
1 AAAGCCCACAAGTCAGTGGTATCCTTT-CAAAGCCCACAAGTCAGTGGCAACCTTCA
* * * *
282692 AAAGCCTACAAGTCAGTGGTATCCTTTCAAAGTCCACAAGTCAATGGCAACCTCCA
1 AAAGCCCACAAGTCAGTGGTATCCTTTCAAAGCCCACAAGTCAGTGGCAACCTTCA
* * ** *
282748 AAAGCCCACAAGTTAGTGGTATCCTTTCAAAGCCCACAAGTCATTGGCAATTTTTCC
1 AAAGCCCACAAGTCAGTGGTATCCTTTCAAAGCCCACAAGTCAGTGGCAA-CCTTCA
* * * * * *
282805 AAAGCCCACAAGTCAGTAGTAACC-TTCAAAAGCCCACAAGTTAGTGGCATCTTTTA
1 AAAGCCCACAAGTCAGTGGTATCCTTTC-AAAGCCCACAAGTCAGTGGCAACCTTCA
* * * ** *
282861 CAAAGCCCACAAGTTAGTGGCAAT-C-TTCAAAAGCGCACAAGTCAGTGATATCCTTTC-
1 -AAAGCCCACAAGTCAGTGG-TATCCTTTC-AAAGCCCACAAGTCAGTGGCAACC-TTCA
*
282918 AAAGCCCATAAGTCAGTGG
1 AAAGCCCACAAGTCAGTGG
282937 CAACCTTCAA
Statistics
Matches: 204, Mismatches: 36, Indels: 11
0.81 0.14 0.04
Matches are distributed among these distances:
56 94 0.46
57 107 0.52
58 3 0.01
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (56 bp):
AAAGCCCACAAGTCAGTGGTATCCTTTCAAAGCCCACAAGTCAGTGGCAACCTTCA
Found at i:282894 original size:85 final size:84
Alignment explanation
Indices: 282632--282943 Score: 299
Period size: 85 Copynumber: 3.7 Consensus size: 84
282622 TCCTCACCCT
* * * * * *
282632 TTCAAAGCCCACAAGTCAGTGGCATCTTTTCCAAAGCCCATAAGTCAGTGGCAACCTTCA-AAAG
1 TTCAAAGCCCACAAGTCAGTGGCAAC-CTTCAAAAGCCCACAAGTCAGTGGCATCCTTTACAAAG
* *
282696 CCTACAAGTCAGTGG-TATCC
65 CCCACAAGTCAGTGGCAAT-C
* * * * *
282716 TTTCAAAGTCCACAAGTCAATGGCAACCTCCAAAAGCCCACAAGTTAGTGGTATCCTTT-CAAAG
1 -TTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCATCCTTTACAAAG
* *
282780 CCCACAAGTCATTGGCAATTT
65 CCCACAAGTCAGTGGCAA-TC
* * * *
282801 TTCCAAAGCCCACAAGTCAGTAGTAACCTTCAAAAGCCCACAAGTTAGTGGCATCTTTTACAAAG
1 TT-CAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCATCCTTTACAAAG
*
282866 CCCACAAGTTAGTGGCAATC
65 CCCACAAGTCAGTGGCAATC
* ** * * *
282886 TTCAAAAGCGCACAAGTCAGTGATATCCTTTC-AAAGCCCATAAGTCAGTGGCAACCTT
1 TTC-AAAGCCCACAAGTCAGTGGCAACC-TTCAAAAGCCCACAAGTCAGTGGCATCCTT
282944 CAAAAGCACC
Statistics
Matches: 187, Mismatches: 33, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
84 44 0.24
85 118 0.63
86 25 0.13
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (84 bp):
TTCAAAGCCCACAAGTCAGTGGCAACCTTCAAAAGCCCACAAGTCAGTGGCATCCTTTACAAAGC
CCACAAGTCAGTGGCAATC
Found at i:283132 original size:22 final size:22
Alignment explanation
Indices: 283064--283132 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
283054 TTAAAACCCA
*
283064 ATATCGTTGGCCTTGAATCAGC
1 ATATCATTGGCCTTGAATCAGC
* * * *
283086 ATATTGA-T-ACCTTTAAGTCCG-
1 ATA-TCATTGGCCTTGAA-TCAGC
283107 ATATCATTGGCCTTGAATCAGC
1 ATATCATTGGCCTTGAATCAGC
283129 ATAT
1 ATAT
283133 TGGTACCGAC
Statistics
Matches: 33, Mismatches: 9, Indels: 10
0.63 0.17 0.19
Matches are distributed among these distances:
20 2 0.06
21 13 0.39
22 17 0.52
23 1 0.03
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (22 bp):
ATATCATTGGCCTTGAATCAGC
Found at i:283147 original size:93 final size:92
Alignment explanation
Indices: 283006--283183 Score: 214
Period size: 93 Copynumber: 1.9 Consensus size: 92
282996 CGTCTTCTTC
* * *** *
283006 TAAGTCCTATATCGCTGGCCTTGAACTAGCATATTGGCACCTTTATCTTTAAAACCCAATATCGT
1 TAAGTCCGATATCACTGGCCTTGAACTAGCATATTGGCACCGACATCTTTAAAA-CCAATATCGC
*
283071 TGGCCTTGAATCAGCATATTGATACCTT
65 TGGCCTTGAATCAGCACATTGATACCTT
* * * * * *
283099 TAAGTCCGATATCATTGGCCTTGAA-TCAGCATATTGGTACCGACATCTTTAAGACTAATGTTGC
1 TAAGTCCGATATCACTGGCCTTGAACT-AGCATATTGGCACCGACATCTTTAAAACCAATATCGC
283163 TGGCCTTGAATCAGCACATTG
65 TGGCCTTGAATCAGCACATTG
283184 GCATAAGCCC
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
92 27 0.38
93 44 0.62
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.33
Consensus pattern (92 bp):
TAAGTCCGATATCACTGGCCTTGAACTAGCATATTGGCACCGACATCTTTAAAACCAATATCGCT
GGCCTTGAATCAGCACATTGATACCTT
Found at i:283251 original size:87 final size:87
Alignment explanation
Indices: 283115--283312 Score: 252
Period size: 87 Copynumber: 2.3 Consensus size: 87
283105 CGATATCATT
* * *** *
283115 GGCCTTGAATCAGCATATTGGTACCGACATCTTTAAGACTAATGTTGCTGGCCTTGAATCAGCAC
1 GGCCGTGAATCAGCATATTGGCACC-TTGTCTTTAAGACCAATGTTGCTGGCCTTGAATCAGCAC
* *
283180 ATTGGCATAAGCCCAATATCGTC
65 ATCGGCACAAGCCCAATATCGTC
** * * *
283203 GGCTTTGAATCGGCGTATTGGCACCTTGTCTTTAAGTCCAATGTTGCTGGCCTTGAATCAGCACA
1 GGCCGTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTTGCTGGCCTTGAATCAGCACA
* *
283268 TCGGCACAAGTCCAATATCGTT
66 TCGGCACAAGCCCAATATCGTC
283290 GGCCGTGAATCAGCATATTGGCA
1 GGCCGTGAATCAGCATATTGGCA
283313 TCTTTATCAC
Statistics
Matches: 93, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
87 72 0.77
88 21 0.23
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.29
Consensus pattern (87 bp):
GGCCGTGAATCAGCATATTGGCACCTTGTCTTTAAGACCAATGTTGCTGGCCTTGAATCAGCACA
TCGGCACAAGCCCAATATCGTC
Found at i:284193 original size:32 final size:32
Alignment explanation
Indices: 284157--284224 Score: 118
Period size: 32 Copynumber: 2.1 Consensus size: 32
284147 TTCAACGATT
284157 TGTATCCATACATAAGTGTTGTATCGATACAA
1 TGTATCCATACATAAGTGTTGTATCGATACAA
* *
284189 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCCATACATAAGTGTTGTATCGATACAA
284221 TGTA
1 TGTA
284225 CAGTTACGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCCATACATAAGTGTTGTATCGATACAA
Found at i:284194 original size:13 final size:13
Alignment explanation
Indices: 284176--284200 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
284166 ACATAAGTGT
284176 TGTATCGATACAA
1 TGTATCGATACAA
284189 TGTATCGATACA
1 TGTATCGATACA
284201 TAAGTTTTGT
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:284213 original size:19 final size:19
Alignment explanation
Indices: 284155--284219 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
284145 ATTTCAACGA
*
284155 TTTGTATCCATACATAAGT
1 TTTGTATCGATACATAAGT
*
284174 GTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
284189 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
284206 TTTGTATCGATACA
1 TTTGTATCGATACA
284220 ATGTACAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:290649 original size:50 final size:50
Alignment explanation
Indices: 290580--290675 Score: 156
Period size: 50 Copynumber: 1.9 Consensus size: 50
290570 TTTTACAATT
* **
290580 TGTATCGATACATTCTTCATTGTTTCGATACATTCTGGGTTTTACCTAGA
1 TGTATCGATACATTCTTCATTGTATCGATACATTAAGGGTTTTACCTAGA
*
290630 TGTATCGATACATTTTTCATTGTATCGATACATTAAGGGTTTTACC
1 TGTATCGATACATTCTTCATTGTATCGATACATTAAGGGTTTTACC
290676 CTTAATAGAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.24, C:0.17, G:0.16, T:0.44
Consensus pattern (50 bp):
TGTATCGATACATTCTTCATTGTATCGATACATTAAGGGTTTTACCTAGA
Found at i:290839 original size:226 final size:226
Alignment explanation
Indices: 290445--290902 Score: 862
Period size: 226 Copynumber: 2.0 Consensus size: 226
290435 TCATTTCCCA
*
290445 TTACCCTTAATAGAGGTACGTGTTCGGGATGCAAACAGTTTGGAAAAATCACATTTTTGCCAAAA
1 TTACCCTTAATAGAGGTACGTGTTCGGGATGCAAAAAGTTTGGAAAAATCACATTTTTGCCAAAA
290510 TGTATCGATACATGCCCTTGATGTATCGATACAAGGTCTCAAAAGTAAAAAATTCAAAATTTTTA
66 TGTATCGATACATGCCCTTGATGTATCGATACAAGGTCTCAAAAGTAAAAAATTCAAAATTTTTA
*
290575 CAATTTGTATCGATACATTCTTCATTGTTTCGATACATTCTGGGTTTTACCTAGATGTATCGATA
131 CAATTTGTATCGATACATTCTTCATTGTTTCGATACATTCTGAGTTTTACCTAGATGTATCGATA
290640 CATTTTTCATTGTATCGATACATTAAGGGTT
196 CATTTTTCATTGTATCGATACATTAAGGGTT
290671 TTACCCTTAATAGAGGTACGTGTTCGGGATGCAAAAAGTTTGGAAAAATCACATTTTTGCCAAAA
1 TTACCCTTAATAGAGGTACGTGTTCGGGATGCAAAAAGTTTGGAAAAATCACATTTTTGCCAAAA
* *
290736 TGTATCGATACATGCCCTTGATGTATCGATACAAGGTCTCAACAGTCAAAAATTCAAAATTTTTA
66 TGTATCGATACATGCCCTTGATGTATCGATACAAGGTCTCAAAAGTAAAAAATTCAAAATTTTTA
290801 CAATTTGTATCGATACATTCTTCATTGTTTCGATACATTCTGAGTTTTACCTAGATGTATCGATA
131 CAATTTGTATCGATACATTCTTCATTGTTTCGATACATTCTGAGTTTTACCTAGATGTATCGATA
**
290866 CATTTTTCATTGTATCGATACATTCTGGGTT
196 CATTTTTCATTGTATCGATACATTAAGGGTT
290897 TTACCC
1 TTACCC
290903 AGATGTATCG
Statistics
Matches: 226, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
226 226 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (226 bp):
TTACCCTTAATAGAGGTACGTGTTCGGGATGCAAAAAGTTTGGAAAAATCACATTTTTGCCAAAA
TGTATCGATACATGCCCTTGATGTATCGATACAAGGTCTCAAAAGTAAAAAATTCAAAATTTTTA
CAATTTGTATCGATACATTCTTCATTGTTTCGATACATTCTGAGTTTTACCTAGATGTATCGATA
CATTTTTCATTGTATCGATACATTAAGGGTT
Found at i:290866 original size:30 final size:28
Alignment explanation
Indices: 290830--290919 Score: 79
Period size: 30 Copynumber: 3.4 Consensus size: 28
290820 CTTCATTGTT
290830 TCGATACATTCTGAGTTTTACCTAGATGTA
1 TCGATACATTCTG-GTTTTACC-AGATGTA
*
290860 TCGATACA---T--TTTT--CA-TTGTA
1 TCGATACATTCTGGTTTTACCAGATGTA
290880 TCGATACATTCTGGGTTTTACCCAGATGTA
1 TCGATACATTCT-GGTTTTA-CCAGATGTA
290910 TCGATACATT
1 TCGATACATT
290920 TCTCTATGTA
Statistics
Matches: 48, Mismatches: 2, Indels: 20
0.69 0.03 0.29
Matches are distributed among these distances:
20 12 0.25
21 1 0.02
22 1 0.02
23 1 0.02
24 4 0.08
26 4 0.08
27 1 0.02
29 2 0.04
30 22 0.46
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.41
Consensus pattern (28 bp):
TCGATACATTCTGGTTTTACCAGATGTA
Found at i:290875 original size:50 final size:50
Alignment explanation
Indices: 290806--290939 Score: 207
Period size: 50 Copynumber: 2.7 Consensus size: 50
290796 TTTTACAATT
* * *
290806 TGTATCGATACATTCTTCATTGTTTCGATACATTCTGAGTTTTACCTAGA
1 TGTATCGATACATTTTTCATTGTATCGATACATTCTGAGTTTTACCCAGA
*
290856 TGTATCGATACATTTTTCATTGTATCGATACATTCTGGGTTTTACCCAGA
1 TGTATCGATACATTTTTCATTGTATCGATACATTCTGAGTTTTACCCAGA
*
290906 TGTATCGATACATTTCTC-TATGTATCGATACATT
1 TGTATCGATACATTTTTCAT-TGTATCGATACATT
290940 GAGGCATTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
49 1 0.01
50 77 0.99
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (50 bp):
TGTATCGATACATTTTTCATTGTATCGATACATTCTGAGTTTTACCCAGA
Found at i:293416 original size:79 final size:77
Alignment explanation
Indices: 293261--293530 Score: 278
Period size: 78 Copynumber: 3.5 Consensus size: 77
293251 TTATTTTCAT
* * * * *
293261 AACACCGATTTTTCATAATCGGGGGTACTCCAACCCCTTATTTCTGAGGGGATACTCCAACCCCT
1 AACATCGATTTTCCATAATCGAGGATACTCCAACCCATTATTTCTGAGGGGATACTCCAA-CCC-
**
293326 AGCCTTT-TTTCTAA
64 -GGTTTTATTTCTAA
* * * * *
293340 AACATCAATTTTTCATAATCGAGGATACTCCAACCCTGTTATTTTTAAGGGGATACTCCAATCCC
1 AACATCGATTTTCCATAATCGAGGATACTCCAACCC-ATTATTTCTGAGGGGATACTCCAA-CCC
293405 GGTTTTATTTCTAA
64 GGTTTTATTTCTAA
* * *
293419 AATATTGATTTTCCATAAT-G-GGAATACTCCAACCCCATTATTTCGGAGGGGATACTCCAACCT
1 AACATCGATTTTCCATAATCGAGG-ATACTCCAA-CCCATTATTTCTGAGGGGATACTCCAACC-
*
293482 CGGTTTTATTTCCAA
63 CGGTTTTATTTCTAA
**
293497 AACATCGATTTTCCACCATCGAGGATA-TCCAACC
1 AACATCGATTTTCCATAATCGAGGATACTCCAACC
293531 TCGATTTTAT
Statistics
Matches: 161, Mismatches: 23, Indels: 16
0.81 0.12 0.08
Matches are distributed among these distances:
77 6 0.04
78 68 0.42
79 61 0.38
80 26 0.16
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (77 bp):
AACATCGATTTTCCATAATCGAGGATACTCCAACCCATTATTTCTGAGGGGATACTCCAACCCGG
TTTTATTTCTAA
Found at i:293573 original size:50 final size:51
Alignment explanation
Indices: 293466--293579 Score: 140
Period size: 50 Copynumber: 2.3 Consensus size: 51
293456 TTATTTCGGA
* * * *
293466 GGGGATACTCCAACCTCGGTTTTATTTCCAAAACATCGATTTTCCACCATC
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAACAACGATTTTCCACAACC
* * * *
293517 GAGGATA-TCCAACCTCGATTTTATTTCTAGAACAACGATTTTTCACAACC
1 GGGGATACTCCAACCTCGATTTTATTTCCAAAACAACGATTTTCCACAACC
*
293567 GGGGATATTCCAA
1 GGGGATACTCCAA
293580 TCTCATTATT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
50 42 0.79
51 11 0.21
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCTCGATTTTATTTCCAAAACAACGATTTTCCACAACC
Found at i:293606 original size:78 final size:77
Alignment explanation
Indices: 293515--293704 Score: 190
Period size: 78 Copynumber: 2.5 Consensus size: 77
293505 TTTTCCACCA
* *** *
293515 TCGA-GGATATCCAACCTCGATTTTATTTCTAGAACAACGATTTTTCACAACCGGGGATATTCCA
1 TCGAGGGATATCCAACCTCGATTTTATTTCTAAAACAACGATTTTTCACAACCAAAGATACTCCA
293579 A-TCTCATTATTT
66 ACTCT-ATTATTT
* ** * *
293591 TCGAGGGATACTCCAA-CTCCGATTTTAGTTT-GAAAACATTGATTTTTCACAATCAAATATACT
1 TCGAGGGATA-TCCAACCT-CGATTTTA-TTTCTAAAACAACGATTTTTCACAACCAAAGATACT
*
293654 CCAACTCTGTTATTT
63 CCAACTCTATTATTT
* *
293669 TCGAGGGGATATCCAACCCCGATTTTATCTCTAAAA
1 TCGA-GGGATATCCAACCTCGATTTTATTTCTAAAA
293705 TATTAAACTT
Statistics
Matches: 92, Mismatches: 14, Indels: 14
0.77 0.12 0.12
Matches are distributed among these distances:
76 4 0.04
77 9 0.10
78 66 0.72
79 13 0.14
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (77 bp):
TCGAGGGATATCCAACCTCGATTTTATTTCTAAAACAACGATTTTTCACAACCAAAGATACTCCA
ACTCTATTATTT
Found at i:295150 original size:20 final size:20
Alignment explanation
Indices: 295125--295178 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
295115 GTTGGGCACA
** *
295125 ATGTATCGATACTTTTTACT
1 ATGTATCGATACAATGTACT
* *
295145 ATGTATCAATACAATGTCCT
1 ATGTATCGATACAATGTACT
295165 ATGTATCGATACAA
1 ATGTATCGATACAA
295179 ATAGTGGAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACAATGTACT
Found at i:299558 original size:44 final size:44
Alignment explanation
Indices: 299475--299573 Score: 114
Period size: 44 Copynumber: 2.2 Consensus size: 44
299465 ATTGAAGATG
299475 TTTTTCCAAATGAGTCAATTTCAAGATTGCTATCAAAGTA-TTTC
1 TTTTT-CAAATGAGTCAATTTCAAGATTGCTATCAAAGTATTTTC
**
299519 TTTTTCAAAT-AGATCAATCTTCAAGATTGC-AGTTGAAGTATTTTC
1 TTTTTCAAATGAG-TCAAT-TTCAAGATTGCTA-TCAAAGTATTTTC
*
299564 TTTTTAAAAT
1 TTTTTCAAAT
299574 TGAACTTATT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
42 2 0.04
43 11 0.23
44 22 0.46
45 13 0.27
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.43
Consensus pattern (44 bp):
TTTTTCAAATGAGTCAATTTCAAGATTGCTATCAAAGTATTTTC
Found at i:299834 original size:65 final size:63
Alignment explanation
Indices: 299723--299908 Score: 202
Period size: 65 Copynumber: 2.9 Consensus size: 63
299713 TAGGATAACG
* * * * *
299723 AAGTATTGTC-TTTTATAAATTGAACTCA-TTTCTTCAAATGGGTTAAGCTTCAGGATTACCCTC
1 AAGTATT-TCTTTTTA-AAATCGAA-TCATTTTTTTCAAATAGGTTAAGCTTCAAGATTACCATC
299786 A
63 A
*
299787 AAGTATTATCTTTTTAAAATCGAATTCATTTTTTTCAAATAGGTTAAGCTTCAAGATTATCATCA
1 AAGTATT-TCTTTTTAAAATCGAA-TCATTTTTTTCAAATAGGTTAAGCTTCAAGATTACCATCA
299852 AAGTATTTCTTTTTTAAAAATCGAA-C-TTATTTTT-AAACTAGGTTAAGCTTCAAGATT
1 AAGTATTTC-TTTTT-AAAATCGAATCATT-TTTTTCAAA-TAGGTTAAGCTTCAAGATT
299909 GTTGTTGAAG
Statistics
Matches: 108, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
63 5 0.05
64 46 0.43
65 48 0.44
66 9 0.08
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (63 bp):
AAGTATTTCTTTTTAAAATCGAATCATTTTTTTCAAATAGGTTAAGCTTCAAGATTACCATCA
Found at i:299923 original size:64 final size:64
Alignment explanation
Indices: 299723--299908 Score: 211
Period size: 64 Copynumber: 2.9 Consensus size: 64
299713 TAGGATAACG
* * * * * * * *
299723 AAGTATTGTCTTTTAT-AAATTGAACTCATTTCTTCAAATGGGTTAAGCTTCAGGATTACCCTCA
1 AAGTATT-TCTTTTTTAAAATCGAATTCATTTTTTCAAATAGGTTAAGCTTCAAGATTATCATCA
299787 AAGTATTATC-TTTTTAAAATCGAATTCATTTTTTTCAAATAGGTTAAGCTTCAAGATTATCATC
1 AAGTATT-TCTTTTTTAAAATCGAATTCA-TTTTTTCAAATAGGTTAAGCTTCAAGATTATCATC
299851 A
64 A
299852 AAGTATTTCTTTTTTAAAAATCGAACTT-A-TTTTT-AAACTAGGTTAAGCTTCAAGATT
1 AAGTATTTCTTTTTT-AAAATCGAA-TTCATTTTTTCAAA-TAGGTTAAGCTTCAAGATT
299909 GTTGTTGAAG
Statistics
Matches: 107, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
63 7 0.07
64 45 0.42
65 43 0.40
66 10 0.09
67 2 0.02
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (64 bp):
AAGTATTTCTTTTTTAAAATCGAATTCATTTTTTCAAATAGGTTAAGCTTCAAGATTATCATCA
Found at i:304621 original size:20 final size:19
Alignment explanation
Indices: 304595--304667 Score: 83
Period size: 20 Copynumber: 3.7 Consensus size: 19
304585 CTGCCAGTTT
304595 CATGTATCGATACAATTGAG
1 CATGTATCGATACAA-TGAG
* *
304615 TATGTATCGATATAATGAG
1 CATGTATCGATACAATGAG
* *
304634 CATGTATCGATACAAAGCAT
1 CATGTATCGATACAATG-AG
*
304654 AATGTATCGATACA
1 CATGTATCGATACA
304668 CCTAGATGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 18 0.40
20 27 0.60
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAG
Found at i:304638 original size:19 final size:20
Alignment explanation
Indices: 304595--304648 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
304585 CTGCCAGTTT
304595 CATGTATCGATACAATTGAG
1 CATGTATCGATACAATTGAG
* *
304615 TATGTATCGATATAA-TGAG
1 CATGTATCGATACAATTGAG
304634 CATGTATCGATACAA
1 CATGTATCGATACAA
304649 AGCATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 17 0.57
20 13 0.43
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAG
Found at i:304860 original size:30 final size:30
Alignment explanation
Indices: 304826--304885 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
304816 CTCTAAAACA
304826 TTATTGATATTGAAAATCACTTAGAACACG
1 TTATTGATATTGAAAATCACTTAGAACACG
304856 TTATTGATATTGAAAATCACTTAGAACACG
1 TTATTGATATTGAAAATCACTTAGAACACG
304886 ATTTTAGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (30 bp):
TTATTGATATTGAAAATCACTTAGAACACG
Found at i:305307 original size:21 final size:20
Alignment explanation
Indices: 305283--305329 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
305273 AGAGATTTCA
305283 AAAATACAATTCCCCCTTAAT
1 AAAATA-AATTCCCCCTTAAT
*
305304 AAAAT-AATTCCCCCTTGAT
1 AAAATAAATTCCCCCTTAAT
305323 AAAATAA
1 AAAATAA
305330 CTAAAGCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 18 0.75
20 1 0.04
21 5 0.21
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.28
Consensus pattern (20 bp):
AAAATAAATTCCCCCTTAAT
Found at i:305314 original size:19 final size:19
Alignment explanation
Indices: 305290--305329 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
305280 TCAAAAATAC
305290 AATTCCCCCTTAATAAAAT
1 AATTCCCCCTTAATAAAAT
*
305309 AATTCCCCCTTGATAAAAT
1 AATTCCCCCTTAATAAAAT
305328 AA
1 AA
305330 CTAAAGCTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.42, C:0.25, G:0.03, T:0.30
Consensus pattern (19 bp):
AATTCCCCCTTAATAAAAT
Found at i:308689 original size:15 final size:16
Alignment explanation
Indices: 308659--308689 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
308649 CAACATTTCC
308659 TCTATTAAAAACTTTT
1 TCTATTAAAAACTTTT
308675 TCTATTAAAAA-TTTT
1 TCTATTAAAAACTTTT
308690 GAAAGCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (16 bp):
TCTATTAAAAACTTTT
Found at i:313249 original size:31 final size:31
Alignment explanation
Indices: 313214--313272 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
313204 ATTGGAAACT
*
313214 TAAATTTATAGGCTAGAATGTTGACATAACC
1 TAAATTTATAGGCTAAAATGTTGACATAACC
*
313245 TAAATTTATAGGCTAAAATGTTGGCATA
1 TAAATTTATAGGCTAAAATGTTGACATA
313273 CTCGTTAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.10, G:0.17, T:0.34
Consensus pattern (31 bp):
TAAATTTATAGGCTAAAATGTTGACATAACC
Found at i:313438 original size:20 final size:19
Alignment explanation
Indices: 313413--313468 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
313403 ATTTGGCACA
*
313413 ATGTATCGATACATTTCATC
1 ATGTATCGATACATTTC-CC
*
313433 ATGTATCGATACAATGTCCC
1 ATGTATCGATAC-ATTTCCC
*
313453 ATGTATCAATACATTT
1 ATGTATCGATACATTT
313469 AACTTAGGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
19 3 0.10
20 24 0.77
21 4 0.13
ACGTcount: A:0.32, C:0.20, G:0.11, T:0.38
Consensus pattern (19 bp):
ATGTATCGATACATTTCCC
Found at i:314521 original size:33 final size:33
Alignment explanation
Indices: 314459--314523 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
314449 CGTTACAAGC
* **
314459 AATGTATCGATACAATTCATCATTTATCGATAT
1 AATGTATCGATACAATTCACCATCCATCGATAT
314492 AATGTATCGATACAATGT-ACCATCCATCGATA
1 AATGTATCGATACAAT-TCACCATCCATCGATA
314524 CAAACAGTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (33 bp):
AATGTATCGATACAATTCACCATCCATCGATAT
Found at i:315182 original size:120 final size:120
Alignment explanation
Indices: 314969--315208 Score: 417
Period size: 120 Copynumber: 2.0 Consensus size: 120
314959 TTGCATTTTT
*
314969 GGGTAGCATTTATAAACTTACCGATTTGTTCAGGCTTGTATACAATTATTTTCTTTGTATCAACA
1 GGGTAGCATTTATAAACTTACCGATTTGTTCAGGCTTGTATACAATCATTTTCTTTGTATCAACA
* * ***
315034 TAATTCATAACCTGTAATCTGATACACAACTTCAAGAAATGTATTAGAAAAGTTC
66 TAATTCATAACCTATAATCTGATACACAACATCAAGAAACACATTAGAAAAGTTC
*
315089 GGGTAGCATTTATAAACTTACCGATTTGTTCAGGCTTGTATATAATCATTTTCTTTGTATCAACA
1 GGGTAGCATTTATAAACTTACCGATTTGTTCAGGCTTGTATACAATCATTTTCTTTGTATCAACA
315154 TAATTCATAACCTATAATCTGATACACAACATCAAGAAACACATTAGAAAAGTTC
66 TAATTCATAACCTATAATCTGATACACAACATCAAGAAACACATTAGAAAAGTTC
315209 AGGGATCAAA
Statistics
Matches: 113, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 113 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (120 bp):
GGGTAGCATTTATAAACTTACCGATTTGTTCAGGCTTGTATACAATCATTTTCTTTGTATCAACA
TAATTCATAACCTATAATCTGATACACAACATCAAGAAACACATTAGAAAAGTTC
Found at i:317256 original size:13 final size:13
Alignment explanation
Indices: 317238--317262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
317228 TAGTAACCCA
317238 TGTATCGATACAG
1 TGTATCGATACAG
317251 TGTATCGATACA
1 TGTATCGATACA
317263 AAGAATATTG
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:0.20, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:320632 original size:19 final size:18
Alignment explanation
Indices: 320608--320668 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 18
320598 CGATACATTA
320608 TATCGATACAAAACTTATG
1 TATCGATAC-AAACTTATG
320627 TATCGATAC--A--T-TG
1 TATCGATACAAACTTATG
*
320640 TATCAATACAACACTTATG
1 TATCGATACAA-ACTTATG
320659 TATCGATACA
1 TATCGATACA
320669 TTGTATCGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
13 10 0.29
14 1 0.03
16 2 0.06
18 1 0.03
19 20 0.59
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.33
Consensus pattern (18 bp):
TATCGATACAAACTTATG
Found at i:320643 original size:13 final size:13
Alignment explanation
Indices: 320625--320681 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
320615 ACAAAACTTA
320625 TGTATCGATACAT
1 TGTATCGATACAT
*
320638 TGTATCAATACAACACTT
1 TGTATCGAT---ACA--T
320656 ATGTATCGATACAT
1 -TGTATCGATACAT
320670 TGTATCGATACA
1 TGTATCGATACA
320682 AATTGTTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
14 1 0.03
16 6 0.17
18 1 0.03
19 8 0.22
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:320649 original size:32 final size:32
Alignment explanation
Indices: 320593--320683 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
320583 GCAGTAGCTT
* *
320593 TGTAGCGATACATTATATCGATACAAAACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
* *
320625 TGTATCGATACATTGTATCAATACAACACTTA
1 TGTATCGATACATTGTATCGATACAAAACTTA
320657 TGTATCGATACATTGTATCGATACAAA
1 TGTATCGATACATTGTATCGATACAAA
320684 TTGTTGAAAT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAAAACTTA
Found at i:321386 original size:39 final size:39
Alignment explanation
Indices: 321332--321409 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
321322 AGTGATTAAG
321332 GTGCCAATATGCTGATTC-AGGACCAACGATATTAGACTT
1 GTGCCAATATGCTGATTCAAGG-CCAACGATATTAGACTT
* * *
321371 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTT
1 GTGCCAATATGCTGATTCAAGGCCAACGATATTAGACTT
321410 AAAGACAAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
39 32 0.91
40 3 0.09
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (39 bp):
GTGCCAATATGCTGATTCAAGGCCAACGATATTAGACTT
Found at i:321479 original size:43 final size:43
Alignment explanation
Indices: 321329--321586 Score: 211
Period size: 43 Copynumber: 5.8 Consensus size: 43
321319 AAGAGTGATT
* **
321329 AAGGTGCCAATATGCTGATTC-AGGACCAACGATATTAGACTT-
1 AAGGTGCCAATATGCTGATTCAAGG-CCAGCGATATCGGACTTA
* *
321371 ---GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTT----A
* * *
321415 CAAGGTGCCAATATGCCGATTCAAAGCCAACGATATCGGACTTA
1 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTA
* * * **
321459 AAGGTGTCAATATGTTGATTCAAGGCCAGCGATATTGGGTTTTAAAGA
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATA-TCGGACTT----A
* *
321507 TACAGGTGCCAATATGCTGGTTCAAGGCCAGCGATATCGAACTTA
1 -A-AGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTA
* *
321552 AAGGTGTCAATATGCTGATTCAAGGCCAGTGATAT
1 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATAT
321587 TGGGTTTTAA
Statistics
Matches: 173, Mismatches: 26, Indels: 33
0.75 0.11 0.14
Matches are distributed among these distances:
39 32 0.18
40 3 0.02
43 60 0.35
44 7 0.04
45 1 0.01
48 35 0.20
49 5 0.03
50 30 0.17
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (43 bp):
AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATCGGACTTA
Found at i:321535 original size:50 final size:50
Alignment explanation
Indices: 321457--321639 Score: 211
Period size: 50 Copynumber: 3.8 Consensus size: 50
321447 ATATCGGACT
* *
321457 TAAAGGTGTCAATATGTTGATTCAAGGCCAGCGATATTGGGTTTTAAAGA
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGA
* * * **
321507 TACAGGTGCCAATATGCTGGTTCAAGGCCAGCGATA-T-CG-----AACT
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGA
* *
321550 TAAAGGTGTCAATATGCTGATTCAAGGCCAGTGATATTGGGTTTTAAAGA
1 TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGA
*
321600 TAAAGGTGCCAATATGCT-AGTTCAAAGCCAGCGATATTGG
1 TAAAGGTGCCAATATGCTGA-TTCAAGGCCAGCGATATTGG
321640 ACTTAGATGA
Statistics
Matches: 108, Mismatches: 17, Indels: 16
0.77 0.12 0.11
Matches are distributed among these distances:
43 34 0.31
44 1 0.01
45 1 0.01
48 1 0.01
49 2 0.02
50 69 0.64
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (50 bp):
TAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGA
Found at i:321542 original size:93 final size:92
Alignment explanation
Indices: 321375--321644 Score: 398
Period size: 93 Copynumber: 2.9 Consensus size: 92
321365 AGACTTGTGC
* ** * * *
321375 CAATGTGCTGATTCAAGGCCAGCGATATT-GGACTTAAAGACAAGGTGCCAATATGCCGATTCAA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGATAAGGTGCCAATATGCTGGTTCAA
*
321439 AGCCAACGATATCGGACTTAAAGGTGT
66 AGCCAGCGATATCGGACTTAAAGGTGT
*
321466 CAATATGTTGATTCAAGGCCAGCGATATTGGGTTTTAAAGATACAGGTGCCAATATGCTGGTTCA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGATA-AGGTGCCAATATGCTGGTTCA
* *
321531 AGGCCAGCGATATCGAACTTAAAGGTGT
65 AAGCCAGCGATATCGGACTTAAAGGTGT
* *
321559 CAATATGCTGATTCAAGGCCAGTGATATTGGGTTTTAAAGATAAAGGTGCCAATATGCTAGTTCA
1 CAATATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGAT-AAGGTGCCAATATGCTGGTTCA
*
321624 AAGCCAGCGATATTGGACTTA
65 AAGCCAGCGATATCGGACTTA
321645 GATGAAGACG
Statistics
Matches: 160, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
91 27 0.17
92 10 0.06
93 122 0.76
94 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (92 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGGTTTTAAAGATAAGGTGCCAATATGCTGGTTCAA
AGCCAGCGATATCGGACTTAAAGGTGT
Done.