Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold441
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: 262355
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.31
Warning! 24019 characters in sequence are not A, C, G, or T
Found at i:7606 original size:3 final size:3
Alignment explanation
Indices: 7585--7655 Score: 54
Period size: 3 Copynumber: 23.0 Consensus size: 3
7575 TTATTTATCA
* * * * *
7585 TAT TAT TAC TAC TAC TAT TAT TAT TGT TAG TAT TA- TATT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
*
7630 TAT TACT TGAT TAT TAT TAT AAT TAT
1 TAT TA-T T-AT TAT TAT TAT TAT TAT
7656 CTACTCATTC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.04
3 47 0.84
4 6 0.11
5 1 0.02
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:8070 original size:20 final size:20
Alignment explanation
Indices: 8025--8062 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
8015 TATATATATA
*
8025 TATATATGCGTACATATTCT
1 TATATATGCATACATATTCT
*
8045 TATATATGCATACTTATT
1 TATATATGCATACATATT
8063 TTTTTATACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (20 bp):
TATATATGCATACATATTCT
Found at i:8097 original size:18 final size:18
Alignment explanation
Indices: 8074--8128 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 18
8064 TTTTATACTT
*
8074 TATATATATACATGTATA
1 TATATATATACACGTATA
8092 TATATATATACACGTATA
1 TATATATATACACGTATA
*
8110 CATATATATAC-C-TATA
1 TATATATATACACGTATA
8126 TAT
1 TAT
8129 GCATATTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
16 6 0.18
17 1 0.03
18 27 0.79
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (18 bp):
TATATATATACACGTATA
Found at i:8109 original size:16 final size:16
Alignment explanation
Indices: 8074--8128 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
8064 TTTTATACTT
*
8074 TATATATATACATGTATA
1 TATATATATACACG--TA
8092 TATATATATACACGTA
1 TATATATATACACGTA
* * *
8108 TACATATATATACCTA
1 TATATATATACACGTA
8124 TATAT
1 TATAT
8129 GCATATTGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
16 19 0.59
18 13 0.41
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.42
Consensus pattern (16 bp):
TATATATATACACGTA
Found at i:12934 original size:35 final size:32
Alignment explanation
Indices: 12879--12955 Score: 93
Period size: 35 Copynumber: 2.3 Consensus size: 32
12869 GACCCAATCC
*
12879 CAAAA-AAAAAAAGAAAAATCAAAGTCAAAAG
1 CAAAAGAAAAAAAGAAAAATCAAAATCAAAAG
*
12910 CAAAAGAAAAAAAGAAAAATAATCAAAATCAAAAT
1 CAAAAGAAAAAAAG--AAA-AATCAAAATCAAAAG
12945 CAAAATGAAAA
1 CAAAA-GAAAA
12956 TAAAAAATGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
31 5 0.13
32 8 0.21
34 3 0.08
35 18 0.46
36 5 0.13
ACGTcount: A:0.74, C:0.09, G:0.08, T:0.09
Consensus pattern (32 bp):
CAAAAGAAAAAAAGAAAAATCAAAATCAAAAG
Found at i:13236 original size:7 final size:7
Alignment explanation
Indices: 13224--13257 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
13214 GATTTCAACA
13224 AAAAATG
1 AAAAATG
13231 AAAAAT-
1 AAAAATG
*
13237 AAGAATG
1 AAAAATG
13244 AAAAATG
1 AAAAATG
13251 AAAAATG
1 AAAAATG
13258 GAGAAGCTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
AAAAATG
Found at i:14624 original size:87 final size:87
Alignment explanation
Indices: 14475--14938 Score: 694
Period size: 87 Copynumber: 5.3 Consensus size: 87
14465 GGATCAGTGA
* * * *
14475 AGATCAAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCAGGTTAAAGATAGTAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
* * * * *
14540 ATTCCTGCATTGACAGCAAAAC
66 CTTCCTGCGTTAACAGCGAAGC
* ** * *
14562 AGATCGAAAACAAAGCCTTGCCTCCACCGGTTCCAGTGGAGCTGGTTGAAGATAGCAAATCTTAC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
* *
14627 CTTCCTGCGTTAACAGTGAAGT
66 CTTCCTGCGTTAACAGCGAAGC
*
14649 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
14714 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* *
14736 AGATCGAAAACAAAGCCTTGCCTCCGTCGGTTGCAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
14801 CTTCCTGCGTTAACAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
14823 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
1 AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
* * *
14888 CTTCTTGCATTAGCAGCGAAGC
66 CTTCCTGCGTTAACAGCGAAGC
* * **
14910 AGATCAAAAATAAAATCTTGCCTCCATCG
1 AGATCGAAAACAAAGCCTTGCCTCCATCG
14939 ATTACAACTG
Statistics
Matches: 341, Mismatches: 36, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 341 1.00
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (87 bp):
AGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGC
CTTCCTGCGTTAACAGCGAAGC
Found at i:14758 original size:43 final size:43
Alignment explanation
Indices: 14709--14845 Score: 129
Period size: 42 Copynumber: 3.2 Consensus size: 43
14699 GATAGCAGAT
14709 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
* * * * * * * *
14752 CTTGCC-TCC-GTCGGTT-GCAGTGGAGCTGGTTGAAGATAGCAGA-T
1 CTTGCCTTCCTG-C-GTTAACAGCGAAGCAGATCGAA-A-A-CAAAGC
14796 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
1 CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
14839 CTTGCCT
1 CTTGCCT
14846 CCATCGGTTG
Statistics
Matches: 69, Mismatches: 16, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
41 1 0.01
42 19 0.28
43 18 0.26
44 11 0.16
45 19 0.28
46 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.25, T:0.23
Consensus pattern (43 bp):
CTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGC
Found at i:23293 original size:14 final size:15
Alignment explanation
Indices: 23257--23300 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
23247 GTTTTGTTTA
*
23257 TATTTTTACATTAATT
1 TATTTTTA-ATTATTT
*
23273 TATTTTTATTTATTT
1 TATTTTTAATTATTT
23288 TA-TTTTAATTATT
1 TATTTTTAATTATT
23301 GTTTTATACG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 10 0.40
15 7 0.28
16 8 0.32
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTTAATTATTT
Found at i:24873 original size:11 final size:11
Alignment explanation
Indices: 24857--24883 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
24847 GATAAATGTT
24857 ATTTTATTAAG
1 ATTTTATTAAG
24868 ATTTTATTAAG
1 ATTTTATTAAG
24879 ATTTT
1 ATTTT
24884 TAGTATTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (11 bp):
ATTTTATTAAG
Found at i:35473 original size:21 final size:21
Alignment explanation
Indices: 35449--35488 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
35439 CAAAACAATG
35449 TAATTTT-ACCTTTTAACTTGA
1 TAATTTTGA-CTTTTAACTTGA
35470 TAATTTTGACTTTTAACTT
1 TAATTTTGACTTTTAACTT
35489 TAGATAAGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (21 bp):
TAATTTTGACTTTTAACTTGA
Found at i:43270 original size:112 final size:112
Alignment explanation
Indices: 43137--43453 Score: 390
Period size: 112 Copynumber: 2.8 Consensus size: 112
43127 AAAAAAAAAA
*
43137 TTTGGGTGCTGGCCTGTCAATGGCCGACACCCAGTACAAATTTAAAAAAAAATTCTTTTTTTTTT
1 TTTGGGTGCT-GCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAAATTCTTTTTTTTTT
*
43202 CATGTCAGAATCAGATATCAGTATACGAAAAAAA-TAAAAAAACAATT
65 CGTGTCAGAATCAGATATCAGTATACGAAAAAAATTAAAAAAACAATT
* * *
43249 TTTGGGTGCTAGCCTGTCAATGGCAGGCACCCAGTACAAATTTTAAAAAAAA-TC-ATTTTTTTT
1 TTTGGGTGCT-GCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAAATTCTTTTTTTTTT
* * * ****
43312 CGTGTCAAAATCAAATATCAGTTTACGAAAAAAATTTAAAAAATTTTTT
65 CGTGTCAGAATCAGATATCAGTATACGAAAAAAA-TTAAAAAAACAATT
* * *
43361 TTTGGGTGGTGACCTGTCAATGGCCGGCACCCAGTAC-AATTTAAAAAAGATTATTTTTTTCTTT
1 TTTGGGTGCTG-CCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAA-A--A-ATTCTT-TTT
43425 TTTTTCGTGTCAGAATCAGATATCAGTAT
60 TTTTTCGTGTCAGAATCAGATATCAGTAT
43454 GCCATTCACA
Statistics
Matches: 173, Mismatches: 22, Indels: 14
0.83 0.11 0.07
Matches are distributed among these distances:
110 38 0.22
111 13 0.08
112 91 0.53
114 1 0.01
116 1 0.01
118 29 0.17
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (112 bp):
TTTGGGTGCTGCCTGTCAATGGCCGGCACCCAGTACAAATTTAAAAAAAAATTCTTTTTTTTTTC
GTGTCAGAATCAGATATCAGTATACGAAAAAAATTAAAAAAACAATT
Found at i:43686 original size:115 final size:112
Alignment explanation
Indices: 43454--44237 Score: 677
Period size: 111 Copynumber: 7.4 Consensus size: 112
43444 ATATCAGTAT
* * *
43454 GCCATTCACAGGCCACCA-CC-AAATTTTTTTTAATTTTTTTCGTATATTGATATCTGATTCTGA
1 GCCATTGACAGGCCAGCACCCAAAATTTTTTTTAATTTTTTTCGTATACTGATATCTGATTCTGA
* *
43517 TACG--AAAAAA-AAAGATT-T-TTTTT-AAATTGTACTGGGTGCCG
66 CACGAAAAAAAAGAAAAATTATATTTTTAAAATTGTACTGGGTGCCG
* *
43558 GCCATTGAAAGGCCAGCACCCAAAAATTTTTTTTTGATTTTTTTCGTATACTGATATCTGATTCT
1 GCCATTGACAGGCCAGCACCC-AAAA-TTTTTTTTAATTTTTTTCGTATACTGATATCTGATTCT
43623 GACACGAAAAAAAAGAAAAATATATATTTTTAAAATTGTACTGGGTGCCG
64 GACACGAAAAAAAAGAAAAAT-TATATTTTTAAAATTGTACTGGGTGCCG
*
43673 GCCATTGACAGGCCAGCACCCAAAATTTTTTTTAATTTTTTTCGTATACTGATATCTGATTTTGA
1 GCCATTGACAGGCCAGCACCCAAAATTTTTTTTAATTTTTTTCGTATACTGATATCTGATTCTGA
* * *
43738 CAC-AAAAAAAAG---AATT-TTTTTTTAAAAAATTGTACTGGGAGCAG
66 CACGAAAAAAAAGAAAAATTATATTTTT--AAAATTGTACTGGGTGCCG
* * * * *
43782 GCCATTGACAGGCCAGCACCCAAAAAAATGTTTTTAAATTTTTTCGTATACTGATATCTAATTTT
1 GCCATTGACAGGCCAGCACCC--AAAATTTTTTTTAATTTTTTTCGTATACTGATATCTGATTCT
* **
43847 GACACG------AA-AAAAA--A-A-TTTTAAAATTGTACTGGATGCTA
64 GACACGAAAAAAAAGAAAAATTATATTTTTAAAATTGTACTGGGTGCCG
* * * * * *
43885 GCCATTGATAGACTAGCACCCAAAAAAATTTTTTTT-ACTCTTTTCGCATACTGATATCTGATTC
1 GCCATTGACAGGCCAGCACCC---AAAATTTTTTTTAATTTTTTTCGTATACTGATATCTGATTC
* *
43949 TAACACG-------A-AAAAA--A-A-TTTT--AATTGTATTGGGTGCCG
63 TGACACGAAAAAAAAGAAAAATTATATTTTTAAAATTGTACTGGGTGCCG
* * *
43985 GCCATTGACAGGCCAGCACCC---A--------AATTTTTTTCGTATATTGATATTTGATTTTGA
1 GCCATTGACAGGCCAGCACCCAAAATTTTTTTTAATTTTTTTCGTATACTGATATCTGATTCTGA
* * * *
44039 CACGAAAAAAAAG---AATTTTTTTTTTAAATTTGTACTGGGTGCTG
66 CACGAAAAAAAAGAAAAATTATATTTTTAAAATTGTACTGGGTGCCG
*
44083 GCCATTGACAGGCCAGCACCTAAAAATTTTTTTTTAATTTTTTTCGTATACTGATATCTGATTCT
1 GCCATTGACAGGCCAGCACC-CAAAA-TTTTTTTTAATTTTTTTCGTATACTGATATCTGATTCT
** * *
44148 GACAC-AAAAAAAAGAAAAAAAAATTTTCTTTAAATTTGTACTGGGTGCCG
64 GACACGAAAAAAAAG-AAAAATTATATT-TTTAAAATTGTACTGGGTGCCG
* * **
44198 ACCATTGACAGGCTAGCACCCAATTTTTTTTTTAATTTTT
1 GCCATTGACAGGCCAGCACCCAAAATTTTTTTTAATTTTT
44238 AATTTTTTTC
Statistics
Matches: 561, Mismatches: 65, Indels: 99
0.77 0.09 0.14
Matches are distributed among these distances:
87 28 0.05
92 2 0.00
94 2 0.00
96 4 0.01
98 34 0.06
100 31 0.06
102 13 0.02
103 62 0.11
104 27 0.05
105 6 0.01
106 2 0.00
107 9 0.02
108 44 0.08
109 41 0.07
110 15 0.03
111 80 0.14
112 10 0.02
113 57 0.10
114 17 0.03
115 77 0.14
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (112 bp):
GCCATTGACAGGCCAGCACCCAAAATTTTTTTTAATTTTTTTCGTATACTGATATCTGATTCTGA
CACGAAAAAAAAGAAAAATTATATTTTTAAAATTGTACTGGGTGCCG
Found at i:44225 original size:111 final size:109
Alignment explanation
Indices: 44007--44237 Score: 293
Period size: 115 Copynumber: 2.1 Consensus size: 109
43997 CCAGCACCCA
* * * ** *
44007 AATTTTTTTCGTATATTGATATTTGATTTTGACACGAAAAAAAAGAATTTTTTTTTTAAATTTGT
1 AATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAGAAAATTTTCTTTAAATTTGT
* *
44072 ACTGGGTGCTGGCCATTGACAGGCCAGCACCTAAAAATTTTTTTTT
66 ACTGGGTGCCGACCATTGACAGGCCAGCACC--AAAATTTTTTTTT
44118 AATTTTTTTCGTATACTGATATCTGATTCTGACAC-AAAAAAAAGAAAAAAAAATTTTCTTTAAA
1 AATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAG-----AAAATTTTCTTTAAA
* * *
44182 TTTGTACTGGGTGCCGACCATTGACAGGCTAGCACCCAATTTTTTTTTT
61 TTTGTACTGGGTGCCGACCATTGACAGGCCAGCACCAAAATTTTTTTTT
44231 AATTTTT
1 AATTTTT
44238 AATTTTTTTC
Statistics
Matches: 104, Mismatches: 11, Indels: 8
0.85 0.09 0.07
Matches are distributed among these distances:
110 9 0.09
111 32 0.31
113 18 0.17
115 45 0.43
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.41
Consensus pattern (109 bp):
AATTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAAAAAGAAAATTTTCTTTAAATTTGT
ACTGGGTGCCGACCATTGACAGGCCAGCACCAAAATTTTTTTTT
Found at i:44798 original size:14 final size:14
Alignment explanation
Indices: 44779--44812 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
44769 CGGATCACAT
44779 TTATCACTTGTCAC
1 TTATCACTTGTCAC
44793 TTATCACTTGTCAC
1 TTATCACTTGTCAC
*
44807 TGATCA
1 TTATCA
44813 GATAAGTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.09, T:0.41
Consensus pattern (14 bp):
TTATCACTTGTCAC
Found at i:44900 original size:7 final size:7
Alignment explanation
Indices: 44884--44914 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
44874 GCTAAGCTAC
*
44884 CACTTAT
1 CACTTGT
44891 CACTTGT
1 CACTTGT
44898 CACTTGT
1 CACTTGT
44905 CACTTGT
1 CACTTGT
44912 CAC
1 CAC
44915 CGATCAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.19, C:0.32, G:0.10, T:0.39
Consensus pattern (7 bp):
CACTTGT
Found at i:44907 original size:57 final size:57
Alignment explanation
Indices: 44779--44958 Score: 275
Period size: 57 Copynumber: 3.3 Consensus size: 57
44769 CGGATCACAT
* *
44779 TTATCACTTGTCACTTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTTGTCACCGATCAGATAAGTGTAGCT-AAGCTACCAC
*
44837 -T-T-A----TCACTTGTCACTTGTCACCGATTAGATAAGTGTAGCTAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTTGTCACCGATCAGATAAGTGTAGCTAAGCTACCAC
44887 TTATCACTTGTCACTTGTCACTTGTCACCGATCAGATAAGTGTAGCTAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTTGTCACCGATCAGATAAGTGTAGCTAAGCTACCAC
44944 TTATCACTTGTCACT
1 TTATCACTTGTCACT
44959 GATCAGAAGT
Statistics
Matches: 111, Mismatches: 4, Indels: 15
0.85 0.03 0.12
Matches are distributed among these distances:
50 10 0.09
51 35 0.32
52 1 0.01
53 1 0.01
55 1 0.01
56 1 0.01
57 62 0.56
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.33
Consensus pattern (57 bp):
TTATCACTTGTCACTTGTCACTTGTCACCGATCAGATAAGTGTAGCTAAGCTACCAC
Found at i:56570 original size:21 final size:21
Alignment explanation
Indices: 56514--56571 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
56504 ACAAGTGCTA
* *
56514 AACGGAAACTCATAAGGGTTG
1 AACGGAAACTCATAAGAGCTG
* * *
56535 AACAGAAGCTTATAAGAGCTG
1 AACGGAAACTCATAAGAGCTG
*
56556 AACGGAAACCCATAAG
1 AACGGAAACTCATAAG
56572 GGTTAAACTG
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.16
Consensus pattern (21 bp):
AACGGAAACTCATAAGAGCTG
Found at i:56607 original size:42 final size:42
Alignment explanation
Indices: 56514--56620 Score: 124
Period size: 42 Copynumber: 2.5 Consensus size: 42
56504 ACAAGTGCTA
* * * * * *
56514 AACGGAAACTCATAAGGGTTGAACAGAAGCTTATAAGAGCTG
1 AACGAAAACCCATAAGGGTTAAACAGAAGCTTAAAAAAGCAG
* *
56556 AACGGAAACCCATAAGGGTTAAACTGAAGCTTAAAAAAGCAG
1 AACGAAAACCCATAAGGGTTAAACAGAAGCTTAAAAAAGCAG
* *
56598 AACTAAAACCCATTAGGGTTAAA
1 AACGAAAACCCATAAGGGTTAAA
56621 TGGAAACTCA
Statistics
Matches: 56, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 56 1.00
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.18
Consensus pattern (42 bp):
AACGAAAACCCATAAGGGTTAAACAGAAGCTTAAAAAAGCAG
Found at i:82719 original size:45 final size:44
Alignment explanation
Indices: 82626--82720 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 44
82616 TTACACCTCT
* * *
82626 ATTACATTCAACCAAACACAAGAATACTATTACGCCTCTATTCT
1 ATTACATTCAACCAAACACAAGAATACTATTACACCTCTAATCC
* * *
82670 ATTACATTCAACCAAACA-ATTGATTTGCTATTACACCTCTAATCC
1 ATTACATTCAACCAAACACA-AGA-ATACTATTACACCTCTAATCC
82715 ATTACA
1 ATTACA
82721 CCTCTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
43 1 0.02
44 20 0.47
45 22 0.51
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (44 bp):
ATTACATTCAACCAAACACAAGAATACTATTACACCTCTAATCC
Found at i:82720 original size:16 final size:16
Alignment explanation
Indices: 82699--82768 Score: 86
Period size: 16 Copynumber: 4.4 Consensus size: 16
82689 TTGATTTGCT
*
82699 ATTACACCTCTAATCC
1 ATTACACCTCTATTCC
82715 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
***
82731 ATTATGTCTCTATTCC
1 ATTACACCTCTATTCC
*
82747 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
*
82763 AATACA
1 ATTACA
82769 GCGAACCAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.27, C:0.33, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:87476 original size:16 final size:16
Alignment explanation
Indices: 87455--87485 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
87445 CTGTGGATTG
87455 TGAAAACTATAGACTT
1 TGAAAACTATAGACTT
*
87471 TGAAAACTCTAGACT
1 TGAAAACTATAGACT
87486 CTGTAGTCTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (16 bp):
TGAAAACTATAGACTT
Found at i:88259 original size:9 final size:9
Alignment explanation
Indices: 88230--88259 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
88220 TGAATTTTAC
88230 AATTCAAAT
1 AATTCAAAT
*
88239 AACTCAAAT
1 AATTCAAAT
88248 AATTCAAAT
1 AATTCAAAT
88257 AAT
1 AAT
88260 AGATTGATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (9 bp):
AATTCAAAT
Found at i:88420 original size:21 final size:20
Alignment explanation
Indices: 88394--88432 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
88384 AAAATTAATA
88394 TTTTAAAAAAGTTTATAAATT
1 TTTTAAAAAAG-TTATAAATT
88415 TTTTAAAAAAGTTATAAA
1 TTTTAAAAAAGTTATAAA
88433 AAATATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTTAAAAAAGTTATAAATT
Found at i:88422 original size:20 final size:20
Alignment explanation
Indices: 88394--88432 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
88384 AAAATTAATA
88394 TTTT-AAAAAAGTTTATAAAT
1 TTTTAAAAAAAG-TTATAAAT
*
88414 TTTTTAAAAAAGTTATAAA
1 TTTTAAAAAAAGTTATAAA
88433 AAATATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (20 bp):
TTTTAAAAAAAGTTATAAAT
Found at i:88667 original size:14 final size:14
Alignment explanation
Indices: 88650--88676 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
88640 TTAATTTTTT
88650 TAATTTAACTCGAA
1 TAATTTAACTCGAA
88664 TAATTTAACTCGA
1 TAATTTAACTCGA
88677 CTCAAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (14 bp):
TAATTTAACTCGAA
Found at i:93843 original size:178 final size:178
Alignment explanation
Indices: 93544--94077 Score: 1032
Period size: 178 Copynumber: 3.0 Consensus size: 178
93534 CTAACCTCCA
* *
93544 ACACACCACTTACTAACGACAGATAATGTGTTTAAGTATAACATTGCAGCGGAGTTATTTCATAT
1 ACACACCACTTACTAACGACAGATAATGTGTTTAAGTATAACATTGCAGCAGAGTTATTTCATAC
93609 ACAAAATATAAACATATGAGCTTATAAAATATCAAAGGAAAGGTTTGCATGTCAACAGTAAAAAC
66 ACAAAATATAAACATATGAGCTTATAAAATATCAAAGGAAAGGTTTGCATGTCAACAGTAAAAAC
*
93674 ACTCAAAGGTTCGCAAACAATAAATAACATAAGTTTGCATAGCAGCAT
131 ACTCAAGGGTTCGCAAACAATAAATAACATAAGTTTGCATAGCAGCAT
93722 ACACACCACTTACTAACGACAGATAATGTGTTTAAGTATAACATTGCAGCAGAGTTATTTCATAC
1 ACACACCACTTACTAACGACAGATAATGTGTTTAAGTATAACATTGCAGCAGAGTTATTTCATAC
93787 ACAAAATATAAACATATGAGCTTATAAAATATCAAAGGAAAGGTTTGCATGTCAACAGTAAAAAC
66 ACAAAATATAAACATATGAGCTTATAAAATATCAAAGGAAAGGTTTGCATGTCAACAGTAAAAAC
*
93852 ACTCAAGGGTTCGCAAACAATAAATAACATAAGTTTGCATAGTAGCAT
131 ACTCAAGGGTTCGCAAACAATAAATAACATAAGTTTGCATAGCAGCAT
93900 ACACACCACTTACTAACGACAGATAATGTGTTTAAGTATAACATTGCAGCAGAGTTATTTCATAC
1 ACACACCACTTACTAACGACAGATAATGTGTTTAAGTATAACATTGCAGCAGAGTTATTTCATAC
93965 ACAAAATATAAACATATGAGCTTATAAAATATCAAAGGAAAGGTTTGCATGTCAACAGTAAAAAC
66 ACAAAATATAAACATATGAGCTTATAAAATATCAAAGGAAAGGTTTGCATGTCAACAGTAAAAAC
94030 ACTCAAGGGTTCGCAAACAATAAATAACATAAGTTTGCATAGCAGCAT
131 ACTCAAGGGTTCGCAAACAATAAATAACATAAGTTTGCATAGCAGCAT
94078 CATGAGTTCG
Statistics
Matches: 351, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
178 351 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.26
Consensus pattern (178 bp):
ACACACCACTTACTAACGACAGATAATGTGTTTAAGTATAACATTGCAGCAGAGTTATTTCATAC
ACAAAATATAAACATATGAGCTTATAAAATATCAAAGGAAAGGTTTGCATGTCAACAGTAAAAAC
ACTCAAGGGTTCGCAAACAATAAATAACATAAGTTTGCATAGCAGCAT
Found at i:96845 original size:21 final size:21
Alignment explanation
Indices: 96799--96866 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
96789 TGAATACACC
96799 AACAGAAGCTCG-AA-AGCTG
1 AACAGAAGCTCGTAAGAGCTG
96818 AACAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
* *
96839 GATAGAAGCTCGTAAGAGCTG
1 AACAGAAGCTCGTAAGAGCTG
96860 AACAGAA
1 AACAGAA
96867 AGTAAAACAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.28
20 2 0.05
21 29 0.67
ACGTcount: A:0.41, C:0.18, G:0.28, T:0.13
Consensus pattern (21 bp):
AACAGAAGCTCGTAAGAGCTG
Found at i:99501 original size:44 final size:42
Alignment explanation
Indices: 99452--99558 Score: 115
Period size: 44 Copynumber: 2.5 Consensus size: 42
99442 TGCGATATCG
* *
99452 TGTAAGACCAAGTCTGGGACGTTGGCATCGATTTAAGATTTACA
1 TGTAAGACCAAGTCTGGGACATTGGCATCG-TATAAGA-TTACA
* * * * *
99496 TGTAAGACCATGTCTGTGACATTGGCGTCGTATATGATTACG
1 TGTAAGACCAAGTCTGGGACATTGGCATCGTATAAGATTACA
* *
99538 TGTAAGACCCAGTCTAGGACA
1 TGTAAGACCAAGTCTGGGACA
99559 GTGAAATCAT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
42 21 0.40
43 5 0.10
44 26 0.50
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (42 bp):
TGTAAGACCAAGTCTGGGACATTGGCATCGTATAAGATTACA
Found at i:104414 original size:17 final size:17
Alignment explanation
Indices: 104379--104415 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
104369 TTGTCGCTTG
*
104379 AATTAATTTAATTATAT
1 AATTAATTTAATTAGAT
*
104396 AATTAATTTAATTGGAT
1 AATTAATTTAATTAGAT
104413 AAT
1 AAT
104416 CAAATATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (17 bp):
AATTAATTTAATTAGAT
Found at i:107397 original size:39 final size:39
Alignment explanation
Indices: 107229--107394 Score: 242
Period size: 39 Copynumber: 4.3 Consensus size: 39
107219 GTATTGCGAT
107229 ATATATGCTTGAATGTTATGTGATTATATGAGTATTGTG
1 ATATATGCTTGAATGTTATGTGATTATATGAGTATTGTG
* * * *
107268 ACATATGCTTGAATGTTATGTGATTACATAAGTATTGCG
1 ATATATGCTTGAATGTTATGTGATTATATGAGTATTGTG
* *
107307 ATATATGCTTGAACGTTATGTAATTATATGAGTATTGTG
1 ATATATGCTTGAATGTTATGTGATTATATGAGTATTGTG
* * * *
107346 ATATATGCTTAAATGTTATGTGGTTATATGTGTAATGTG
1 ATATATGCTTGAATGTTATGTGATTATATGAGTATTGTG
107385 ATATATGCTT
1 ATATATGCTT
107395 AAAAGTGAAC
Statistics
Matches: 111, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 111 1.00
ACGTcount: A:0.30, C:0.05, G:0.21, T:0.44
Consensus pattern (39 bp):
ATATATGCTTGAATGTTATGTGATTATATGAGTATTGTG
Found at i:108803 original size:22 final size:22
Alignment explanation
Indices: 108777--108821 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
108767 AGATCAACAC
108777 AAATAT-AATTACATACATATCA
1 AAATATCAATTACAT-CATATCA
*
108799 AAATATCAATTTCATCATATCA
1 AAATATCAATTACATCATATCA
108821 A
1 A
108822 TCATCATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (22 bp):
AAATATCAATTACATCATATCA
Found at i:109014 original size:22 final size:22
Alignment explanation
Indices: 108989--109037 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
108979 GGACAAGCCA
*
108989 CCACTGATTTGTAGATAAACTG
1 CCACTGATTTGCAGATAAACTG
109011 CCACTGATTTGCAGATAAACTG
1 CCACTGATTTGCAGATAAACTG
109033 CCACT
1 CCACT
109038 AATAACACTG
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:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (22 bp):
CCACTGATTTGCAGATAAACTG
Found at i:113138 original size:5 final size:5
Alignment explanation
Indices: 113128--113156 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
113118 TATCTTGTAA
113128 AGATT AGATT AGATT AGATT AGATT AGAT
1 AGATT AGATT AGATT AGATT AGATT AGAT
113157 ATGGCATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (5 bp):
AGATT
Found at i:114003 original size:19 final size:19
Alignment explanation
Indices: 113979--114015 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
113969 TTTGCAAACT
113979 TCATTTTCTAGATCAAGAC
1 TCATTTTCTAGATCAAGAC
113998 TCATTTTCTAGATCAAGA
1 TCATTTTCTAGATCAAGA
114016 TGTTCCTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (19 bp):
TCATTTTCTAGATCAAGAC
Found at i:121147 original size:28 final size:28
Alignment explanation
Indices: 121076--121244 Score: 160
Period size: 28 Copynumber: 6.0 Consensus size: 28
121066 CATGACAATT
* * * *
121076 AAGAATAGCCTTTGTAGCGAATTATGAA
1 AAGAATAGCCTGTGTGGCGAACTCTGAA
*** *
121104 AAGAATATATTTTGTGGCGAACTCTGAA
1 AAGAATAGCCTGTGTGGCGAACTCTGAA
*
121132 AAGAATAGCCTGTGTGGCAAAC-CATGAA
1 AAGAATAGCCTGTGTGGCGAACTC-TGAA
* * * * *
121160 AAAAATAACCTATGTGTCGAACTATGAA
1 AAGAATAGCCTGTGTGGCGAACTCTGAA
* **
121188 AAGAATAGCTTGTGTGGTAAACTCTGAA
1 AAGAATAGCCTGTGTGGCGAACTCTGAA
*
121216 AAGAATAGCCCGTGTGGCGAACTCTGAA
1 AAGAATAGCCTGTGTGGCGAACTCTGAA
121244 A
1 A
121245 GGGATGCCTT
Statistics
Matches: 110, Mismatches: 29, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
27 1 0.01
28 109 0.99
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.25
Consensus pattern (28 bp):
AAGAATAGCCTGTGTGGCGAACTCTGAA
Found at i:123007 original size:34 final size:34
Alignment explanation
Indices: 122964--123087 Score: 149
Period size: 34 Copynumber: 3.6 Consensus size: 34
122954 ACATATACGA
* * * *
122964 ATATCATATCAGAATGTCACATTACCAGAAACAT
1 ATATCAGATCAGAATGTCATATTTCCAAAAACAT
* *
122998 ATATCATATCAAAATGTCATATTTCCAAAAACAT
1 ATATCAGATCAGAATGTCATATTTCCAAAAACAT
* * *
123032 ATATCAGATTAGAATGTCATATTTTCATAAACAT
1 ATATCAGATCAGAATGTCATATTTCCAAAAACAT
* *
123066 ATATTAGATCAGAATGTTATAT
1 ATATCAGATCAGAATGTCATAT
123088 CAAATCAGAA
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 78 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.34
Consensus pattern (34 bp):
ATATCAGATCAGAATGTCATATTTCCAAAAACAT
Found at i:138354 original size:2 final size:2
Alignment explanation
Indices: 138347--138377 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
138337 ATTTCAACCA
*
138347 AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
138378 AACCAAGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:148015 original size:17 final size:17
Alignment explanation
Indices: 147993--148043 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
147983 ATAAAATTAC
147993 ATTTTATAAAATATTTT
1 ATTTTATAAAATATTTT
* *
148010 ATTTTATGAAATATTATC
1 ATTTTATAAAATATT-TT
*
148028 A-TTTAAAAAATATTTT
1 ATTTTATAAAATATTTT
148044 TGAATTAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
16 1 0.04
17 25 0.89
18 2 0.07
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTTATAAAATATTTT
Found at i:148040 original size:34 final size:33
Alignment explanation
Indices: 147962--148043 Score: 98
Period size: 34 Copynumber: 2.5 Consensus size: 33
147952 TTCAATTTCT
*
147962 TTTTAAAAAGT-TTTTATTCTTATAAAATTACA
1 TTTTAAAAAATATTTTATTCTTATAAAATTACA
*
147994 TTTTATAAAATATTTTATT-TTATGAAATATTATCA
1 TTTTAAAAAATATTTTATTCTTAT-AAA-ATTA-CA
148029 -TTTAAAAAATATTTT
1 TTTTAAAAAATATTTT
148044 TGAATTAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
32 13 0.30
33 10 0.23
34 18 0.42
35 2 0.05
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (33 bp):
TTTTAAAAAATATTTTATTCTTATAAAATTACA
Found at i:149985 original size:1 final size:1
Alignment explanation
Indices: 149979--150011 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
149969 TGGTATGTGC
149979 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
150012 AAAAAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:152184 original size:31 final size:32
Alignment explanation
Indices: 152129--152201 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
152119 TATAAAATAT
152129 TTTAAA-AA-TTAAATATAATAATAAA-TGAGA
1 TTTAAATAATTTAAATATAATAATAAACT-AGA
* *
152159 TTTAAATAATTTAAA-ATAATGATAAACTATA
1 TTTAAATAATTTAAATATAATAATAAACTAGA
152190 TTTAAATAATTT
1 TTTAAATAATTT
152202 CATTTAATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
30 6 0.16
31 26 0.68
32 6 0.16
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.40
Consensus pattern (32 bp):
TTTAAATAATTTAAATATAATAATAAACTAGA
Found at i:152818 original size:16 final size:17
Alignment explanation
Indices: 152797--152830 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
152787 TGTTTAGGAC
152797 TGCTATTTTT-AGTGTT
1 TGCTATTTTTAAGTGTT
152813 TGCTATTTTTAAGTGTT
1 TGCTATTTTTAAGTGTT
152830 T
1 T
152831 TGTTATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.15, C:0.06, G:0.18, T:0.62
Consensus pattern (17 bp):
TGCTATTTTTAAGTGTT
Found at i:157206 original size:17 final size:16
Alignment explanation
Indices: 157160--157207 Score: 69
Period size: 16 Copynumber: 2.9 Consensus size: 16
157150 TTTAGGACTC
*
157160 CTATTTTGAGTGTTTG
1 CTATTTTTAGTGTTTG
*
157176 CTATTTTTAATGTTTG
1 CTATTTTTAGTGTTTG
157192 CTATTTTTAGGTGTTT
1 CTATTTTTA-GTGTTT
157208 TGTTATTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 23 0.82
17 5 0.18
ACGTcount: A:0.15, C:0.06, G:0.19, T:0.60
Consensus pattern (16 bp):
CTATTTTTAGTGTTTG
Found at i:159230 original size:15 final size:15
Alignment explanation
Indices: 159212--159242 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
159202 TGGTTTAAAT
159212 TTATATATTATCATC
1 TTATATATTATCATC
*
159227 TTATATATTATTATC
1 TTATATATTATCATC
159242 T
1 T
159243 ATGTTAAAAT
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:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATATTATCATC
Found at i:159559 original size:20 final size:21
Alignment explanation
Indices: 159511--159562 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
159501 ATACATACTT
* *
159511 ATATATATTCTTTATATTCTC
1 ATATATATTTTTTATATTCAC
* *
159532 AAAAATATTTTTTA-ATTCAC
1 ATATATATTTTTTATATTCAC
159552 ATATATATTTT
1 ATATATATTTT
159563 CTTACATTAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.37, C:0.10, G:0.00, T:0.54
Consensus pattern (21 bp):
ATATATATTTTTTATATTCAC
Found at i:163890 original size:22 final size:22
Alignment explanation
Indices: 163865--163913 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
163855 AAATTCAATA
*
163865 TCAATTTCCTTCAAAAATTCTC
1 TCAAATTCCTTCAAAAATTCTC
*
163887 TCAAATTCCTTCCAAAATTCTC
1 TCAAATTCCTTCAAAAATTCTC
163909 TCAAA
1 TCAAA
163914 CTCTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.29, G:0.00, T:0.37
Consensus pattern (22 bp):
TCAAATTCCTTCAAAAATTCTC
Found at i:163920 original size:30 final size:30
Alignment explanation
Indices: 163884--163942 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
163874 TTCAAAAATT
*
163884 CTCTCAAATTCCTTCCAAAATTCTCTCAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAA
163914 CTCTCAAATTCCTTCCAAAATCCTCTCAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAA
163943 TTTCCTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (30 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAA
Found at i:163948 original size:52 final size:51
Alignment explanation
Indices: 163865--163964 Score: 137
Period size: 52 Copynumber: 1.9 Consensus size: 51
163855 AAATTCAATA
* * * *
163865 TCAATTTCCTTCAAAAATTCTCTCAAATTCCTTCCAAAATTCTCTCAAACTC
1 TCAAATTCCTTCAAAAATCCTCTCAAATTCCTTCAAAAAATCTC-CAAACTC
* *
163917 TCAAATTCCTTCCAAAATCCTCTCAATTTCCTTCAAAAAATCTCCAAA
1 TCAAATTCCTTCAAAAATCCTCTCAAATTCCTTCAAAAAATCTCCAAA
163965 TCCATATTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 4 0.10
52 38 0.90
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.34
Consensus pattern (51 bp):
TCAAATTCCTTCAAAAATCCTCTCAAATTCCTTCAAAAAATCTCCAAACTC
Found at i:163953 original size:21 final size:22
Alignment explanation
Indices: 163914--163955 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
163904 TTCTCTCAAA
163914 CTCTCAAATTCCTTCCAAAATC
1 CTCTCAAATTCCTTCCAAAATC
* *
163936 CTCTCAATTTCCTTCAAAAA
1 CTCTCAAATTCCTTCCAAAA
163956 ATCTCCAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (22 bp):
CTCTCAAATTCCTTCCAAAATC
Found at i:167549 original size:17 final size:18
Alignment explanation
Indices: 167512--167552 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
167502 GGTAAGAAAC
167512 TTTTATATTTCGACCATA
1 TTTTATATTTCGACCATA
* *
167530 TTTTATATTT-TACTATA
1 TTTTATATTTCGACCATA
167547 TTTTAT
1 TTTTAT
167553 TTATTATATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.27, C:0.10, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTATATTTCGACCATA
Found at i:171373 original size:13 final size:13
Alignment explanation
Indices: 171357--171383 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
171347 TAATTAAAGG
171357 GTTAAAATTTAAA
1 GTTAAAATTTAAA
171370 GTTAAAATTTAAA
1 GTTAAAATTTAAA
171383 G
1 G
171384 ATGATAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (13 bp):
GTTAAAATTTAAA
Found at i:171452 original size:9 final size:9
Alignment explanation
Indices: 171438--171503 Score: 66
Period size: 9 Copynumber: 7.6 Consensus size: 9
171428 AACTTTGGAT
171438 CATAACTTA
1 CATAACTTA
171447 CATAACTTA
1 CATAACTTA
171456 CATAA--TA
1 CATAACTTA
*
171463 CATAA-ATA
1 CATAACTTA
* * *
171471 TATATCATA
1 CATAACTTA
171480 TCATAACTTA
1 -CATAACTTA
171490 CATAACTTA
1 CATAACTTA
171499 CATAA
1 CATAA
171504 AACTTTGGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
7 7 0.14
8 5 0.10
9 31 0.63
10 6 0.12
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.33
Consensus pattern (9 bp):
CATAACTTA
Found at i:171631 original size:7 final size:7
Alignment explanation
Indices: 171619--171643 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
171609 ACACCCATTA
171619 GATACTT
1 GATACTT
171626 GATACTT
1 GATACTT
171633 GATACTT
1 GATACTT
171640 GATA
1 GATA
171644 TGTATTATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (7 bp):
GATACTT
Found at i:180982 original size:43 final size:43
Alignment explanation
Indices: 180934--181053 Score: 168
Period size: 43 Copynumber: 2.8 Consensus size: 43
180924 GGGGGAAAGC
** * * * *
180934 GCCGCTAAAGAACATGACCTATAGCGGCATTTTTGTGAGCAAT
1 GCCGCTAAAGGTCATGATCTATAGCGGCGTTTTTGTGAGAAAA
*
180977 GCCGCTAAAGGTCATGTTCTATAGCGGCGTTTTTGTGAGAAAA
1 GCCGCTAAAGGTCATGATCTATAGCGGCGTTTTTGTGAGAAAA
*
181020 GCCGCTAAAGGTTATGATCTATAGCGGCGTTTTT
1 GCCGCTAAAGGTCATGATCTATAGCGGCGTTTTT
181054 CCATATAAAC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 68 1.00
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
GCCGCTAAAGGTCATGATCTATAGCGGCGTTTTTGTGAGAAAA
Found at i:181887 original size:88 final size:87
Alignment explanation
Indices: 181738--181902 Score: 294
Period size: 88 Copynumber: 1.9 Consensus size: 87
181728 TTGAAAATAA
* * *
181738 AAATATAGAGGTTAAATTCTAAATTTATAAAGAGTATATAGACTTATAATATATTTTAATCTTTT
1 AAATATAAAGGCTAAATTCCAAATTTATAAAGAGTATATAGACTTATAATATATTTTAATCTTTT
181803 ATTTTTTTTGTTGATTTGGATTT
66 A-TTTTTTTGTTGATTTGGATTT
181826 AAATATAAAGGCTAAATTCCAAATTTATAAAGAGTATATAGACTTATAATATATTTTAATCTTTT
1 AAATATAAAGGCTAAATTCCAAATTTATAAAGAGTATATAGACTTATAATATATTTTAATCTTTT
181891 ATTTTTTTGTTG
66 ATTTTTTTGTTG
181903 GCTTGAATTT
Statistics
Matches: 74, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
87 11 0.15
88 63 0.85
ACGTcount: A:0.37, C:0.05, G:0.10, T:0.48
Consensus pattern (87 bp):
AAATATAAAGGCTAAATTCCAAATTTATAAAGAGTATATAGACTTATAATATATTTTAATCTTTT
ATTTTTTTGTTGATTTGGATTT
Found at i:183792 original size:20 final size:19
Alignment explanation
Indices: 183759--183796 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
183749 TTTTAATTTA
183759 ATAATAATTAAAATATTTTT
1 ATAATAATTAAAAT-TTTTT
183779 ATAATTAATT-AAATTTTT
1 ATAA-TAATTAAAATTTTT
183797 ATTATTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
ATAATAATTAAAATTTTTT
Found at i:204145 original size:21 final size:19
Alignment explanation
Indices: 204107--204145 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
204097 TTGTTTATAT
204107 TATTTTTATATTATTATTG
1 TATTTTTATATTATTATTG
*
204126 TATTTGTTATCATTGTTATT
1 TATTT-TTAT-ATTATTATT
204146 ATGACATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 4 0.24
21 8 0.47
ACGTcount: A:0.23, C:0.03, G:0.08, T:0.67
Consensus pattern (19 bp):
TATTTTTATATTATTATTG
Found at i:215937 original size:31 final size:32
Alignment explanation
Indices: 215901--215963 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
215891 AGATAATTTT
215901 AAAGAG-TTTTATTAGGATTCAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
*
215932 AAAGAGTTTTTATTAGGATTTAATTACTCTTG
1 AAAGAGTTTTTATTAGGATTCAATTACTCTTG
215964 TAATTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 6 0.20
32 24 0.80
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (32 bp):
AAAGAGTTTTTATTAGGATTCAATTACTCTTG
Found at i:224300 original size:44 final size:43
Alignment explanation
Indices: 224199--224787 Score: 306
Period size: 44 Copynumber: 13.6 Consensus size: 43
224189 GGATCTCAGA
* * * * *
224199 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGATC--GCATCTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAGAAACAAG
224239 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CAAAGTAAACAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATC-AAG-AAACAAG
* * * * *
224283 TCTTATC-CTCCTAAAGTTGCAGT-AAGGCAGATTGAAGATGACAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TCAAGA-AACAAG
* *
224328 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-TA-AAGCTGATAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAGAAAC--A-AG
*
224372 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTA-AAACATTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAGAAACA--AG
* * * * * * *
224415 ATCTTATCTCTCTAAAGTTGTAG-AGAGCAGATC--GCATCTAG
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAGAAACAAG
* *
224456 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGA-CTAAGTAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATC-AAG-AAACAAG
* * * ** *
224500 TCTTATC-CTCCTGAAGTTGCAGTGGGGCTGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGAGCAGA-TCAAGA-AACAAG
* *
224545 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGAT-TA-AATCTGATAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAGAAAC--A-AG
* * * * *
224589 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAA-AACCTTAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAGAAAC-AAG
* * ** * *
224632 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATC--CCATCTAG
1 -TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAGAAACAAG
* * * *
224673 TCTTATCTCCCTGAAGTTGCAGTGGAGCAAACTAAATAAGCAAG
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TCAAGAAACAAG
* * * ** *
224717 TTTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGCAAA
1 TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TCAAGA-AACAAG
*
224762 TCTTATCTCCCTGAAGTTGTAGTGGA
1 TCTTATCTCCCTGAAGTTGCAGTGGA
224788 ATAGATTGAA
Statistics
Matches: 433, Mismatches: 71, Indels: 84
0.74 0.12 0.14
Matches are distributed among these distances:
40 64 0.15
41 27 0.06
42 6 0.01
43 33 0.08
44 203 0.47
45 94 0.22
46 6 0.01
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (43 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATCAAGAAACAAG
Found at i:224571 original size:217 final size:217
Alignment explanation
Indices: 224196--224787 Score: 986
Period size: 217 Copynumber: 2.7 Consensus size: 217
224186 AGTGGATCTC
224196 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAG
1 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAG
* * * * * *
224261 TGGAGCAGACAAAGTAAACAAGTCTTATCCTCCTAAAGTTGCAGTAAGGCAGATTGAAGATGACA
66 TGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
*
224326 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATAGTCTTATCTCCCTGAAGTTG
131 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATAGTCCTATCTCCCTGAAGTTG
224391 CAGTGGAGCAGACTAAAACATT
196 CAGTGGAGCAGACTAAAACATT
* * *
224413 AGATCTTATCTCTCTAAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGTAG
1 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAG
* *
224478 TGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGGGGCTGACTGAAGATGGCA
66 TGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
*
224543 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATCTGATAGTCCTATCTCCCTGAAGTTG
131 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATAGTCCTATCTCCCTGAAGTTG
* * *
224608 CAGTGGAGCGGATTAAAACCTT
196 CAGTGGAGCAGACTAAAACATT
*
224630 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCCCATCTAGTCTTATCTCCCTGAAGTTGCAG
1 AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAG
* * * *
224695 TGGAGCAAACTAAATAAGCAAGTTTTATCCTCCTGAAGTTGTAGTGAGGCAGACTGAAGATGGCA
66 TGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
*
224760 AATCTTATCTCCCTGAAGTTGTAGTGGA
131 AATCTTATCTCCCTGAAGTTGCAGTGGA
224788 ATAGATTGAA
Statistics
Matches: 348, Mismatches: 27, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
217 348 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (217 bp):
AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAG
TGGAGCAGACTAAGTAAGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCA
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGATAGTCCTATCTCCCTGAAGTTG
CAGTGGAGCAGACTAAAACATT
Found at i:224723 original size:84 final size:85
Alignment explanation
Indices: 224199--224735 Score: 334
Period size: 89 Copynumber: 6.2 Consensus size: 85
224189 GGATCTCAGA
*
224199 TCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTG
*
224263 GAGCAGAC-AAAGTAAACAAG
66 GAGCAGACTAAA-TAAGCAAG
* * * * *
224283 TCTTATC-CTCCTAAAGTTGCAGTA-AGGCAGATTGAAGATGACAAATCTTATCTCCCTGAAGTT
1 TCTTATCTCT-CTGAAGTTGCAGTAGA-GCAGA-T-CACAT--CTAGTCTTATCTCCCTGAAGTT
* ***
224346 GCAGTGGAGCAGATTAAAGCTG-ATAG
60 GCAGTGGAGCAGACTAAATAAGCA-AG
* * * * * *
224372 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAACAT-TAGATCTTATCTCTCTAAAGTTGT
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-T--CACATCTAG-TCTTATCTCCCTGAAGTTGC
* ** *
224436 AG-AGAGCAGA-TCGCAT---CTAG
62 AGTGGAGCAGACT-AAATAAGCAAG
* * * * * * *
224456 TCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTAAGTAAGCAAGTCTTATC-CTCCTGAAGTTGC
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCA--CATCTAGTCTTATCTC-CCTGAAGTTGC
* * * *
224520 AGTGGGGCTGACTGAAGAT-GGCAAA
62 AGTGGAGCAGACT-AA-ATAAGCAAG
* * * * *
224545 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAATCTGATAGTCCTATCTCCCTGAAGTTGCA
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATC---TAGTCTTATCTCCCTGAAGTTGCA
* * * *
224610 GTGGAGCGGA-TTAA-AACCTTAG
63 GTGGAGCAGACTAAATAAGC-AAG
*
224632 ATCTTATCTCTCTGAAGTTGCAG-AGAGCAGATCCCATCTAGTCTTATCTCCCTGAAGTTGCAGT
1 -TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGT
*
224696 GGAGCAAACTAAATAAGCAAG
65 GGAGCAGACTAAATAAGCAAG
*
224717 TTTTATC-CTCCTGAAGTTG
1 TCTTATCTCT-CTGAAGTTG
224736 TAGTGAGGCA
Statistics
Matches: 353, Mismatches: 66, Indels: 68
0.72 0.14 0.14
Matches are distributed among these distances:
82 2 0.01
83 5 0.01
84 117 0.33
85 18 0.05
86 11 0.03
87 26 0.07
88 44 0.12
89 120 0.34
90 10 0.03
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (85 bp):
TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTG
GAGCAGACTAAATAAGCAAG
Found at i:225072 original size:14 final size:15
Alignment explanation
Indices: 225044--225072 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
225034 CTAAAATCCG
225044 GTGGCCCAAATACAA
1 GTGGCCCAAATACAA
225059 GTGGCCCAAA-ACAA
1 GTGGCCCAAATACAA
225073 ATGAAGAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 4 0.29
15 10 0.71
ACGTcount: A:0.41, C:0.28, G:0.21, T:0.10
Consensus pattern (15 bp):
GTGGCCCAAATACAA
Found at i:233577 original size:25 final size:26
Alignment explanation
Indices: 233534--233594 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
233524 TACATCTTAG
** *
233534 CATTCATTTTTGAGCTAA-TATTTTTT
1 CATTC-TTTTTGAAATAATTATTCTTT
233560 CATTCTTTTTGAAATAATTATTCTTT
1 CATTCTTTTTGAAATAATTATTCTTT
233586 CATTCTTTT
1 CATTCTTTT
233595 GGATTTTCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 10 0.32
26 21 0.68
ACGTcount: A:0.23, C:0.13, G:0.05, T:0.59
Consensus pattern (26 bp):
CATTCTTTTTGAAATAATTATTCTTT
Found at i:236166 original size:43 final size:42
Alignment explanation
Indices: 236039--236261 Score: 101
Period size: 44 Copynumber: 5.1 Consensus size: 42
236029 GCCTTACCTC
*
236039 CCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
1 CCTGGGTTACAGCGGAGCAGGTT-AAAATAGCAGATCTTGCC-T
**** * * * * * * * *
236083 CCTGTACCGACAGCGAAGTAGATCGAAGACACCAG-CCTTGCCT
1 CCTG-GGTTACAGCGGAGCAGGT-TAAAATAGCAGATCTTGCCT
236126 CTCTGGGTTACAGCGGAGCAGGTTAAAATAGCAGATCTTGCCGT
1 C-CTGGGTTACAGCGGAGCAGGTTAAAATAGCAGATCTTGCC-T
**** * * * * *
236170 CCTGCACCGACAGCGAAGCAGATCGAAGATATC--ATCCTTGCCT
1 CCTG-GGTTACAGCGGAGCAGGT-TAAAATAGCAGAT-CTTGCCT
* *
236213 CCCTAGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTT
1 -CCTGGGTTACAGCGGAGCAGGTT-AAAATAGCAGATCTTGCC-T
236258 CCTG
1 CCTG
236262 CACCGATAGC
Statistics
Matches: 120, Mismatches: 46, Indels: 26
0.62 0.24 0.14
Matches are distributed among these distances:
42 7 0.06
43 42 0.35
44 45 0.38
45 26 0.22
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.22
Consensus pattern (42 bp):
CCTGGGTTACAGCGGAGCAGGTTAAAATAGCAGATCTTGCCT
Found at i:236497 original size:43 final size:42
Alignment explanation
Indices: 236444--236584 Score: 102
Period size: 43 Copynumber: 3.2 Consensus size: 42
236434 CCTGTACCGA
236444 CAGCGAAGCAGATCGAAGACACTAGCCTTACCTCCCTGGGTTG
1 CAGCGAAGCAGATCGAAGACAC-AGCCTTACCTCCCTGGGTTG
* * ** * * * * ****
236487 CAGCGGAGCAGGTTAAAAATAGCAGATCTTACCTTCCTGCACCG
1 CAGCGAAGCAGATCGAAGACA-CAG-CCTTACCTCCCTGGGTTG
* *
236531 ACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCTCTGGGTTG
1 -CAGCGAAGCAGATCGAAGACA-CAGCCTTACCTCCCTGGGTTG
*
236575 CAGCGGAGCA
1 CAGCGAAGCA
236585 AGTTAAAAAT
Statistics
Matches: 67, Mismatches: 28, Indels: 6
0.66 0.28 0.06
Matches are distributed among these distances:
43 26 0.39
44 23 0.34
45 18 0.27
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (42 bp):
CAGCGAAGCAGATCGAAGACACAGCCTTACCTCCCTGGGTTG
Found at i:236852 original size:88 final size:88
Alignment explanation
Indices: 235897--236822 Score: 1264
Period size: 88 Copynumber: 10.5 Consensus size: 88
235887 AAGATAACAA
* * * * * *
235897 ATCTTACCTTCCTGCACCGATAGCGAAACAGATCAAAGATACCAGCCTTGCCTCCCTGGGTTGTA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
*
235962 GCTGAGCAGGTTAAAAATAGCAG
66 GCGGAGCAGGTTAAAAATAGCAG
* * * * * *
235985 ACCTTGCCTTCCTGCACCAACGGCGAAGTAGATCGAAGACACTAGCCTTACCTCCCTGGGTTGCA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
236050 GCGGAGCAGGTTAAAAATAGCAG
66 GCGGAGCAGGTTAAAAATAGCAG
* * * *
236073 ATCTTGCCTTCCTGTACCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCTCTGGGTTACA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
236138 GCGGAGCAGGTT-AAAATAGCAG
66 GCGGAGCAGGTTAAAAATAGCAG
* * * * *
236160 ATCTTGCCGTCCTGCACCGACAGCGAAGCAGATCGAAGATATCATCCTTGCCTCCCTAGGTTGCA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
236225 GCGGAGCAGGTTAAAAATAGCAG
66 GCGGAGCAGGTTAAAAATAGCAG
* * * * * *
236248 ATCTTGCCTTCCTGCACCGATAGCGAAGTAGATCAAAGACACCAGCCTTGCTTTCCTGGGTTACA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
* *
236313 GCAGAGCAAGTTAAAAATTA-CAG
66 GCGGAGCAGGTTAAAAA-TAGCAG
* * * * * *
236336 ATCTTGCCTTCCT-CAATCGACAGCGAAGAAGATCGAAGAAACCAGTCTTGCTTCCCTGGGTTGT
1 ATCTTGCCTTCCTGC-ACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGC
*
236400 AGTGGAGCAGGTTAAAAATAGCAG
65 AGCGGAGCAGGTTAAAAATAGCAG
* * * *
236424 ATCTTGCCATCCTGTACCGACAGCGAAGCAGATCGAAGACACTAGCCTTACCTCCCTGGGTTGCA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
236489 GCGGAGCAGGTTAAAAATAGCAG
66 GCGGAGCAGGTTAAAAATAGCAG
* *
236512 ATCTTACCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCTCTGGGTTGCA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
*
236577 GCGGAGCAAGTTAAAAATAGCAG
66 GCGGAGCAGGTTAAAAATAGCAG
* * * * **
236600 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGATACCAGCCTTGTCTCCTTAGACTGCA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
*
236665 GCAGAGCAGGTTAAAAATAGCAG
66 GCGGAGCAGGTTAAAAATAGCAG
* * *
236688 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAACCTTGCCTCCCTAGGTTGCA
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
*
236753 GCGAAGCAGGTTAAAAATAGCAG
66 GCGGAGCAGGTTAAAAATAGCAG
* ** * * *
236776 ATCTTGTCTTCCAACACCGACAGCGAAGTAGATCGATGACCCCAGCC
1 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
236823 CTATCTCCCT
Statistics
Matches: 733, Mismatches: 100, Indels: 10
0.87 0.12 0.01
Matches are distributed among these distances:
87 81 0.11
88 650 0.89
89 2 0.00
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (88 bp):
ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCA
GCGGAGCAGGTTAAAAATAGCAG
Found at i:236871 original size:44 final size:43
Alignment explanation
Indices: 236822--236943 Score: 156
Period size: 44 Copynumber: 2.8 Consensus size: 43
236812 TGACCCCAGC
*
236822 CCTATCTCCCTAGACAGCAGTGGAATAGGTTGAAGATTGT-AAGT
1 CCTATCTCCCT-GACAGCAGTGGAATAGGTTGAAGATTATGAA-T
*
236866 CCTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATTATGAAT
1 CCTATCTCCCT-GACAGCAGTGGAATAGGTTGAAGATTATGAAT
* * *
236910 CTTATCTCCCTGAGCAACAGTGGAGTAGGTTGAA
1 CCTATCTCCCTGA-CAGCAGTGGAATAGGTTGAA
236944 AATAGTAGAT
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 1 0.01
44 66 0.96
45 2 0.03
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (43 bp):
CCTATCTCCCTGACAGCAGTGGAATAGGTTGAAGATTATGAAT
Found at i:236948 original size:264 final size:264
Alignment explanation
Indices: 235897--236992 Score: 771
Period size: 264 Copynumber: 4.2 Consensus size: 264
235887 AAGATAACAA
* * * * * * * * * * *
235897 ATCTTACCTTCCTGCACCGATAGCGAAACAGATCAAAGATACCAGCCTTGCCTCCCTGGGTTGTA
1 ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGACACTAACCTTACCTCCCTAGGTTGCA
* * ** * * *
235962 GCTG-AGCAGGTTAAAAATAGCAGACCTTGCCTTCCTGCACCAACGGCGAAGTAGATCGAAGACA
66 GC-GAAGCAGGTTAAAAATAGCAGATCTTACCTTCCAACACCGACAGCGAAGCAGATCGAAGACA
* * * *** * * * * * * * *
236026 CTAGCCTTACCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGTACC
130 CCAGCCCTACCTCCCTAGACAGCAGCGGAACAAGTTAAAAATAGAAGATCCTACCTCCCTGCACA
* * * ** *** *
236091 GACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCTCTG-GGTTACAGCGGAGCAGGTT-AAAA
195 GACAGCGAAGCAGATCGAAGATACCAACCTTATCTC-CTGAGACAACAGTGGAGCAGGTTAAAAA
236154 TAGCAG
259 TAGCAG
* * * * *
236160 ATCTTGCCGTCCTGCACCGACAGCGAAGCAGATCGAAGATA-TCATCCTTGCCTCCCTAGGTTGC
1 ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGACACT-AACCTTACCTCCCTAGGTTGC
* * ** * * *
236224 AGCGGAGCAGGTTAAAAATAGCAGATCTTGCCTTCCTGCACCGATAGCGAAGTAGATCAAAGACA
65 AGCGAAGCAGGTTAAAAATAGCAGATCTTACCTTCCAACACCGACAGCGAAGCAGATCGAAGACA
* * * * * ** * * * * * *
236289 CCAGCCTTGCTTTCCTGGGTTA-CAGCAGAGCAAGTTAAAAATTA-CAGATCTTGCCTTCCT-CA
130 CCAGCCCTACCTCCCT-AGACAGCAGCGGAACAAGTTAAAAA-TAGAAGATCCTACCTCCCTGCA
* * ** * *****
236351 -ATCGACAGCGAAGAAGATCGAAGAAACCAGTCTT-GCTTCCCTG-GGTTGTAGTGGAGCAGGTT
193 CA--GACAGCGAAGCAGATCGAAGATACCAACCTTATC-T-CCTGAGACAACAGTGGAGCAGGTT
236413 AAAAATAGCAG
254 AAAAATAGCAG
* * *
236424 ATCTTGCCATCCTGTACCGACAGCGAAGCAGATCGAAGACACTAGCCTTACCTCCCTGGGTTGCA
1 ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGACACTAACCTTACCTCCCTAGGTTGCA
* **
236489 GCGGAGCAGGTTAAAAATAGCAGATCTTACCTTCCTGCACCGACAGCGAAGCAGATCGAAGACAC
66 GCGAAGCAGGTTAAAAATAGCAGATCTTACCTTCCAACACCGACAGCGAAGCAGATCGAAGACAC
* * * * *** * * * * * *
236554 CAGCCTTGCCTCTCTGGGTTGCAGCGGAGCAAGTTAAAAATAGCAGATCTTGCCTTCCTGCACCG
131 CAGCCCTACCTCCCTAGACAGCAGCGGAACAAGTTAAAAATAGAAGATCCTACCTCCCTGCACAG
* * * ** **
236619 ACAGCGAAGCAGATCGAAGATACCAGCCTTGTCTCCTTAGACTGCAGCAGAGCAGGTTAAAAATA
196 ACAGCGAAGCAGATCGAAGATACCAACCTTATCTCCTGAGACAACAGTGGAGCAGGTTAAAAATA
236684 GCAG
261 GCAG
* *
236688 ATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAACCTTGCCTCCCTAGGTTGCA
1 ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGACACTAACCTTACCTCCCTAGGTTGCA
** * * *
236753 GCGAAGCAGGTTAAAAATAGCAGATCTTGTCTTCCAACACCGACAGCGAAGTAGATCGATGACCC
66 GCGAAGCAGGTTAAAAATAGCAGATCTTACCTTCCAACACCGACAGCGAAGCAGATCGAAGACAC
* * * * * * * * **
236818 CAGCCCTATCTCCCTAGACAGCAGTGGAATAGGTTGAAGATTGTAAG-TCCTATCTCCCTGGTCA
131 CAGCCCTACCTCCCTAGACAGCAGCGGAACAAGTTAAAAATAG-AAGATCCTACCTCCCTGCACA
* * * * ** * * *
236882 G-CAGTGGAA-TAGGTTGAAGATTATGAATCTTATCTCCCTGAG-CAACAGTGGAGTAGGTTGAA
195 GACAG-CGAAGCAGATCGAAGA-TACCAACCTTATCT-CCTGAGACAACAGTGGAGCAGGTTAAA
*
236944 AATAGTAG
257 AATAGCAG
* * * * *
236952 ATCTTGCCTTCTTGTACTGGCAGTGAAGCAGATCAAAGACA
1 ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGACA
236993 TCAGTCTTAT
Statistics
Matches: 696, Mismatches: 117, Indels: 39
0.82 0.14 0.05
Matches are distributed among these distances:
262 3 0.00
263 224 0.32
264 458 0.66
265 11 0.02
ACGTcount: A:0.29, C:0.26, G:0.24, T:0.22
Consensus pattern (264 bp):
ATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCGAAGACACTAACCTTACCTCCCTAGGTTGCA
GCGAAGCAGGTTAAAAATAGCAGATCTTACCTTCCAACACCGACAGCGAAGCAGATCGAAGACAC
CAGCCCTACCTCCCTAGACAGCAGCGGAACAAGTTAAAAATAGAAGATCCTACCTCCCTGCACAG
ACAGCGAAGCAGATCGAAGATACCAACCTTATCTCCTGAGACAACAGTGGAGCAGGTTAAAAATA
GCAG
Found at i:237312 original size:44 final size:44
Alignment explanation
Indices: 237257--237415 Score: 148
Period size: 44 Copynumber: 3.7 Consensus size: 44
237247 GAAGATGACG
* *
237257 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGCCAAT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTCAAACCAAT
* * * *
237301 AATCCTATCTCCCTGAAGTTATAGTGGAG-TGAATTCAAACCACT
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAG-ATTCAAACCAAT
* * * * *
237345 AATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCACATC--T
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTCAAACCAAT
* * *
237385 AGTGTTATCTCCCTGAAGTTGCAGTGGAGCA
1 AATCTTATCTCCCTGAAGTTACAGTGGAGCA
237416 TACCAAGAAA
Statistics
Matches: 94, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
40 22 0.23
41 5 0.05
42 5 0.05
43 5 0.05
44 57 0.61
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTCAAACCAAT
Found at i:250039 original size:11 final size:11
Alignment explanation
Indices: 250023--250051 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
250013 ATAAATAAGT
250023 TCATTTAAAGC
1 TCATTTAAAGC
250034 TCATTTAAAGC
1 TCATTTAAAGC
250045 TCATTTA
1 TCATTTA
250052 TTATTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.34, C:0.17, G:0.07, T:0.41
Consensus pattern (11 bp):
TCATTTAAAGC
Found at i:252036 original size:1 final size:1
Alignment explanation
Indices: 252032--252057 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
252022 GGGGGCACCC
252032 GGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGG
252058 TCGGTCTNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Done.