Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015281.1 Kokia drynarioides strain JFW-HI SEQ_130326, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 648972
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 207 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:300185 original size:13 final size:12
Alignment explanation
Indices: 300147--300192 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 12
300137 ATTTATTCTA
300147 AAATTTAAATTT
1 AAATTTAAATTT
* *
300159 -ATTTTAAGTTT
1 AAATTTAAATTT
300170 AAATTTAAATTAT
1 AAATTTAAATT-T
300183 AAATTTAAAT
1 AAATTTAAAT
300193 AAGTCCAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
11 9 0.32
12 8 0.29
13 11 0.39
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (12 bp):
AAATTTAAATTT
Found at i:300187 original size:7 final size:6
Alignment explanation
Indices: 300147--300192 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
300137 ATTTATTCTA
* *
300147 AAATTT AAATTT -ATTTT AAGTTT AAATTT AAATTAT AAATTT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATT-T AAATTT AAAT
300193 AAGTCCAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
5 4 0.11
6 25 0.71
7 6 0.17
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:302057 original size:30 final size:30
Alignment explanation
Indices: 302023--302089 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
302013 AACTGTCTAG
302023 AAATTATATTTCGACCCTCAAACTTCTCCA
1 AAATTATATTTCGACCCTCAAACTTCTCCA
* ** *
302053 AAATTACATTTTTACCCTTAAACTTCTCCA
1 AAATTATATTTCGACCCTCAAACTTCTCCA
302083 AAATTAT
1 AAATTAT
302090 TTTTTAACCT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.01, T:0.37
Consensus pattern (30 bp):
AAATTATATTTCGACCCTCAAACTTCTCCA
Found at i:302209 original size:57 final size:56
Alignment explanation
Indices: 302052--302491 Score: 202
Period size: 57 Copynumber: 7.6 Consensus size: 56
302042 AAACTTCTCC
* ** * *
302052 AAAATTA-CATTTTTACCCTTAAACTTCTCCAAAATTATTTTTTAACCTCCGAACTTTCCA
1 AAAATTACCA-TTTTACCC-TAAACTT-TCAAAAATTACATTTTAACCT-CG-ATTTTTCA
* * * * * *
302112 AAATTTACAATTTTACCCTCAAACTTTCCAAATTTCCATTTTAACCTCGATTTTTAA
1 AAAATTACCATTTTACCCT-AAACTTTCAAAAATTACATTTTAACCTCGATTTTTCA
* * **
302169 AAAATTACCATTTTACCACTGAACTTTCAAAAATTACATTTTTA-CTCCTGAACTTTCGA
1 AAAATTACCATTTTACC-CTAAACTTTCAAAAATTACATTTTAACCT-C-GATTTTTC-A
* * * * * *
302228 AAAATT-CAATTTTATCCAC-AAACTTCCAAAAATTATATTTTTACCCTCGCACTCTTC-
1 AAAATTACCATTTTA-CC-CTAAACTTTCAAAAATTACA-TTTTAACCTCG-ATTTTTCA
* * * ** *
302285 AAAATT-CCTTTTTTACCCT-AATTTTCCAAAAATTACAATTTTATCCTCGA-ACTTCC
1 AAAATTACC-ATTTTACCCTAAACTTT-CAAAAATTAC-ATTTTAACCTCGATTTTTCA
* ** **
302341 AAAAGTA-CATTTTTGACCCCGAAC-TTCTAAAAATTTTATTTTTAACCTCGATTTTTCA
1 AAAATTACCA-TTTT-ACCCTAAACTTTC-AAAAATTACA-TTTTAACCTCGATTTTTCA
* * * * *
302399 AAAA-TACCGTTTTACCCTCGAACTTCCAAAAATT-CTATTCTTTACCTCGATTTTTCCC
1 AAAATTACCATTTTACCCT-AAACTTTCAAAAATTAC-ATT-TTAACCTCGATTTTT-CA
* * *
302457 AAAATTATCATTTTACCCCCAAACTTTTAAAAATT
1 AAAATTACCATTTTA-CCCTAAACTTTCAAAAATT
302492 CTATTTTTGA
Statistics
Matches: 293, Mismatches: 57, Indels: 61
0.71 0.14 0.15
Matches are distributed among these distances:
55 4 0.01
56 26 0.09
57 124 0.42
58 55 0.19
59 58 0.20
60 25 0.09
61 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.39
Consensus pattern (56 bp):
AAAATTACCATTTTACCCTAAACTTTCAAAAATTACATTTTAACCTCGATTTTTCA
Found at i:302430 original size:28 final size:28
Alignment explanation
Indices: 302049--302448 Score: 161
Period size: 29 Copynumber: 13.9 Consensus size: 28
302039 CTCAAACTTC
* **
302049 TCCAAAATTACATTTTTACCCTTAAACTT
1 TCCAAAAATACATTTTTACCCTCGAAC-T
* * *
302078 CTCCAAAATTA-TTTTTTAACCTCCGAACTT
1 -TCCAAAAATACATTTTTACCCT-CGAAC-T
* * *
302108 TCCAAAATTTACAATTTTACCCTCAAACTT
1 TCCAAAA-ATACATTTTTACCCTCGAAC-T
** * * **
302138 TCCAAATTTCCA-TTTTAACCTCGATTT
1 TCCAAAAATACATTTTTACCCTCGAACT
**
302165 TTAAAAAATTACCA-TTTTACCACT-GAACT
1 TCCAAAAA-TA-CATTTTTACC-CTCGAACT
*
302194 TTCAAAAATTACATTTTTACTCCT-GAACTT
1 TCCAAAAA-TACATTTTTAC-CCTCGAAC-T
* * * * * *
302224 TCGAAAAATTCAATTTTATCCACAAACT
1 TCCAAAAATACATTTTTACCCTCGAACT
* *
302252 TCCAAAAATTATATTTTTACCCTCGCACT
1 TCCAAAAA-TACATTTTTACCCTCGAACT
* * * * *
302281 CTTCAAAATTCCTTTTTTACCCT--AATTT
1 -TCCAAAAATACATTTTTACCCTCGAA-CT
* *
302309 TCCAAAAATTACAATTTTATCCTCGAACT
1 TCCAAAAA-TACATTTTTACCCTCGAACT
*
302338 TCCAAAAGTACATTTTTGACCC-CGAACT
1 TCCAAAAATACATTTTT-ACCCTCGAACT
* ** * **
302366 TCTAAAAATTTTATTTTTAACCTCGATTT
1 TCCAAAAA-TACATTTTTACCCTCGAACT
* **
302395 TTCAAAAATACCGTTTTACCCTCGAACT
1 TCCAAAAATACATTTTTACCCTCGAACT
*
302423 TCCAAAAATTCTATTCTTTA-CCTCGA
1 TCCAAAAATAC-ATT-TTTACCCTCGA
302449 TTTTTCCCAA
Statistics
Matches: 274, Mismatches: 75, Indels: 43
0.70 0.19 0.11
Matches are distributed among these distances:
27 12 0.04
28 79 0.29
29 123 0.45
30 52 0.19
31 8 0.03
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (28 bp):
TCCAAAAATACATTTTTACCCTCGAACT
Found at i:302489 original size:59 final size:57
Alignment explanation
Indices: 302150--302597 Score: 204
Period size: 57 Copynumber: 7.7 Consensus size: 57
302140 CAAATTTCCA
* * *
302150 TTTTAACCTCGATTTTTAAAAAATTACCATTTTACCACTGAACTT-TCAAAAATTAC-AT
1 TTTTAACCTCGATTTTTCAAAAA-TACCATTTTACCCCCGAACTTCT-AAAAATT-CTAT
* ** * * * * * * *
302208 TTTTACTCCT-GAACTTTCGAAAAATTCAATTTTATCCACAAACTTCCAAAAATTATAT
1 TTTTA-ACCTCGATTTTTC-AAAAATACCATTTTACCCCCGAACTTCTAAAAATTCTAT
* * * * * * * * *
302266 TTTTACCCTCGCACTCTTC-AAAATTCCTTTTTTA--CCCTAATTTTCCAAAAATTAC-AA
1 TTTTAACCTCG-ATTTTTCAAAAATACC-ATTTTACCCCCGAA-CTTCTAAAAATT-CTAT
* ** * * *
302323 TTTTATCCTCGAACTTCCAAAAGTA-CATTTTTGA-CCCCGAACTTCTAAAAATTTTAT
1 TTTTAACCTCGATTTTTCAAAAATACCA-TTTT-ACCCCCGAACTTCTAAAAATTCTAT
* * *
302380 TTTTAACCTCGATTTTTCAAAAATACCGTTTTACCCTCGAACTTCCAAAAATTCTAT
1 TTTTAACCTCGATTTTTCAAAAATACCATTTTACCCCCGAACTTCTAAAAATTCTAT
* * * *
302437 TCTTT-ACCTCGATTTTTCCCAAAATTATCATTTTACCCCCAAACTTTTAAAAATTCTAT
1 T-TTTAACCTCGATTTTT--CAAAAATACCATTTTACCCCCGAACTTCTAAAAATTCTAT
* * * * *
302496 TTTTGA-TTCTGATTTTTTCCAAAAATTTA-CATTTTATCCCTGAA-TGTCT-AAAATTTTAT
1 TTTTAACCTC-GA-TTTTT-CAAAAA--TACCATTTTACCCCCGAACT-TCTAAAAATTCTAT
* * * *
302555 TTTTAACCTCAAACTTTCCTAAAATTACCATTTTACCCCCGAA
1 TTTTAACCTC-GATTTTTC-AAAAATACCATTTTACCCCCGAA
302598 TATCCAAAAT
Statistics
Matches: 293, Mismatches: 69, Indels: 56
0.70 0.17 0.13
Matches are distributed among these distances:
56 13 0.04
57 107 0.37
58 72 0.25
59 77 0.26
60 22 0.08
61 2 0.01
ACGTcount: A:0.33, C:0.23, G:0.04, T:0.41
Consensus pattern (57 bp):
TTTTAACCTCGATTTTTCAAAAATACCATTTTACCCCCGAACTTCTAAAAATTCTAT
Found at i:302952 original size:49 final size:49
Alignment explanation
Indices: 302895--302988 Score: 143
Period size: 49 Copynumber: 1.9 Consensus size: 49
302885 AAAATTTGTG
* **
302895 CCTTAACTTATTAGGTGCAATTTTTCTTCAAATCGAAATAATCGAGTAC
1 CCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAAATAATCGAGTAC
* *
302944 CCTTAACTTACTAGGTGCAACCTTTCTTCAAATTGAGATAATCGA
1 CCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAAATAATCGA
302989 ACATCCTTTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (49 bp):
CCTTAACTTACTAGGTGCAACCTTTCTTCAAATCGAAATAATCGAGTAC
Found at i:313070 original size:100 final size:99
Alignment explanation
Indices: 312892--313109 Score: 246
Period size: 100 Copynumber: 2.2 Consensus size: 99
312882 ACACCATGAA
* ** * *
312892 ACATGAAGGGAAAGATCT-AAGCCGCAACGGCGGATCCAGTACCACATAGACATAAAGGAGAGGG
1 ACATGAAGGGAAAGATCTAAAACCGCAACGGAAGATCCAGTACCACAAAGACATAAAGGAGAAGG
* *
312956 TTTAAGTTGCAACGGCGAACCTTGTACCTTAGA-
66 TTTAAGTCGCAACGGCGAACCTAGTACCTTAGAG
* *
312989 AGCATGAAGGGAAAGATCTAAAACTGCAACGGAAGATCCAGTACCGCAAAGATACA-AAAGG-GA
1 A-CATGAAGGGAAAGATCTAAAACCGCAACGGAAGATCCAGTACCACAAAG--ACATAAAGGAG-
* * *
313052 AAGGTTTAAGTCGTAACGGTGAACCTAGTATCTTAGAG
62 AAGGTTTAAGTCGCAACGGCGAACCTAGTACCTTAGAG
* *
313090 ATATGATGGGAAAGATCTAA
1 ACATGAAGGGAAAGATCTAA
313110 GAAGCAACGG
Statistics
Matches: 101, Mismatches: 14, Indels: 9
0.81 0.11 0.07
Matches are distributed among these distances:
97 1 0.01
98 17 0.17
99 26 0.26
100 53 0.52
101 4 0.04
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.18
Consensus pattern (99 bp):
ACATGAAGGGAAAGATCTAAAACCGCAACGGAAGATCCAGTACCACAAAGACATAAAGGAGAAGG
TTTAAGTCGCAACGGCGAACCTAGTACCTTAGAG
Found at i:313182 original size:52 final size:50
Alignment explanation
Indices: 313098--313531 Score: 262
Period size: 51 Copynumber: 8.7 Consensus size: 50
313088 AGATATGATG
* * * * *
313098 GGAAAGATCTAAGAAGCAACGGCGGATGCAGTACCTCAGAA-AAACACAAC
1 GGAAAGATCTAAGACGCAACGGTGGATCCAGTACCGCA-AAGAAACAAAAC
* * *
313148 GGAAATGATCTAAGACGATAACGGTGGATCCAGTACCGCAAAGATACAAAAT
1 GGAAA-GATCTAAGACG-CAACGGTGGATCCAGTACCGCAAAGAAACAAAAC
* * *
313200 GGAAAGATCTAAG-CTGCAACGGTGGATCCAGTACCACGAAG--ACACAA-
1 GGAAAGATCTAAGAC-GCAACGGTGGATCCAGTACCGCAAAGAAACAAAAC
* * * * * * * **
313247 GGAAAAAGTTTAAGTCGCAATGGT-GAACCTAGCACCTCAAA-AAACACGAC
1 GGAAAGA-TCTAAGACGCAACGGTGGATCC-AGTACCGCAAAGAAACAAAAC
* * *
313297 GGGAAAGATCTAAGACTGCAACGGTGGATTCAGTACCGCAAAGATACAAAAG
1 -GGAAAGATCTAAGAC-GCAACGGTGGATCCAGTACCGCAAAGAAACAAAAC
* * * * * *
313349 GGAAAGATCTAAG-CTGCAACGGCGAATCCAGTACCACGAAG--ACACAAG
1 GGAAAGATCTAAGAC-GCAACGGTGGATCCAGTACCGCAAAGAAACAAAAC
* * * ** * * * **
313397 GGAAAGGTTTAAGTCGCAATAG-CGAACCTAGTACCTCAAA-AAACACTAC
1 GGAAAGATCTAAGACGCAACGGTGGATCC-AGTACCGCAAAGAAACAAAAC
* * * * *
313446 GGGAAAGATCTAAGATCGCAATGGCGGTTCCAGTACCGCAAAGATACAAAAG
1 -GGAAAGATCTAAGA-CGCAACGGTGGATCCAGTACCGCAAAGAAACAAAAC
* *
313498 GGAAAGATCTAAGCCGCAACGGTGGATCAAGTAC
1 GGAAAGATCTAAGACGCAACGGTGGATCCAGTAC
313532 AGCGAAGACA
Statistics
Matches: 296, Mismatches: 66, Indels: 44
0.73 0.16 0.11
Matches are distributed among these distances:
47 13 0.04
48 56 0.19
49 12 0.04
50 84 0.28
51 86 0.29
52 45 0.15
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (50 bp):
GGAAAGATCTAAGACGCAACGGTGGATCCAGTACCGCAAAGAAACAAAAC
Found at i:313228 original size:50 final size:50
Alignment explanation
Indices: 312995--313531 Score: 296
Period size: 50 Copynumber: 10.7 Consensus size: 50
312985 TAGAAGCATG
* **
312995 AAGGGAAAGATCTAAAACTGCAACGGAAGATCCAGTACCGCAAAGATACAA
1 AAGGGAAAGATCT-AAGCTGCAACGGTGGATCCAGTACCGCAAAGATACAA
* * * * * ** * **
313046 AAGGGAAAGGTTTAAG-TCGTAACGGT-GAACCTAGTATCTTAGAGATA-TG
1 AAGGGAAAGATCTAAGCT-GCAACGGTGGATCC-AGTACCGCAAAGATACAA
* ** * * * * *
313095 ATGGGAAAGATCTAAGAAGCAACGGCGGATGCAGTACCTCAGAA-AAACAC
1 AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCGCA-AAGATACAA
* *
313145 AACGGAAATGATCTAAGAC-GATAACGGTGGATCCAGTACCGCAAAGATACAA
1 AAGGGAAA-GATCTAAG-CTG-CAACGGTGGATCCAGTACCGCAAAGATACAA
* * * *
313197 AATGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCACGAAG--ACAC
1 AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCGCAAAGATACAA
* * * * * * * *
313245 AA-GGAAAAAGTTTAAG-TCGCAATGGT-GAACCTAGCACCTCAAA-AAACACG
1 AAGGGAAAGA-TCTAAGCT-GCAACGGTGGATCC-AGTACCGCAAAGATACA-A
* *
313295 ACGGGAAAGATCTAAGACTGCAACGGTGGATTCAGTACCGCAAAGATACAA
1 AAGGGAAAGATCTAAG-CTGCAACGGTGGATCCAGTACCGCAAAGATACAA
* * * * *
313346 AAGGGAAAGATCTAAGCTGCAACGGCGAATCCAGTACCACGAAG--ACAC
1 AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCGCAAAGATACAA
* * ** * * * * *
313394 AAGGGAAAGGTTTAAG-TCGCAATAG-CGAACCTAGTACCTCAAA-AAACACT
1 AAGGGAAAGATCTAAGCT-GCAACGGTGGATCC-AGTACCGCAAAGATACA-A
* * * * *
313444 ACGGGAAAGATCTAAGATCGCAATGGCGGTTCCAGTACCGCAAAGATACAA
1 AAGGGAAAGATCTAAGCT-GCAACGGTGGATCCAGTACCGCAAAGATACAA
* *
313495 AAGGGAAAGATCTAAGCCGCAACGGTGGATCAAGTAC
1 AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTAC
313532 AGCGAAGACA
Statistics
Matches: 364, Mismatches: 92, Indels: 61
0.70 0.18 0.12
Matches are distributed among these distances:
47 15 0.04
48 56 0.15
49 39 0.11
50 109 0.30
51 101 0.28
52 44 0.12
ACGTcount: A:0.40, C:0.20, G:0.24, T:0.15
Consensus pattern (50 bp):
AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCGCAAAGATACAA
Found at i:313600 original size:149 final size:150
Alignment explanation
Indices: 312897--313575 Score: 670
Period size: 149 Copynumber: 4.5 Consensus size: 150
312887 ATGAAACATG
* * * * *
312897 AAGGGAAAGATCTAAGCCGCAACGGCGGATCCAGTACCAC-ATAGACATAAAGGAGAGGGTTTAA
1 AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCACGA-AGACACAAGGGA-AAGGTTTAA
* * * * * * * * **
312961 GTTGCAACGGCGAACCTTGTACCT-TAGAAGCATGAAGGGAAAGATCTAAAACTGCAACGGAAGA
64 GTCGCAATGGCGAACCTAGTACCTCAAAAAACATGACGGGAAAGATCTAAGACTGCAACGGCGGA
313025 -TCCAGTACCGCAAAGATACAA
129 TTCCAGTACCGCAAAGATACAA
* * * * * * * * * *
313046 AAGGGAAAGGTTTAAG-TCGTAACGGT-GAACCTAGTATCTTA-G-AGATATGATGGGAAAGATC
1 AAGGGAAAGATCTAAGCT-GCAACGGTGGATCC-AGTA-C-CACGAAGACA-CAAGGGAAAGGTT
** * ** ** *
313107 TAAGAAGCAACGGCGGATGC-AGTACCTCAGAAAAACACAAC-GGAAATGATCTAAGAC-GATAA
61 TAAGTCGCAATGGC-GAACCTAGTACCTCA-AAAAACATGACGGGAAA-GATCTAAGACTG-CAA
*
313169 CGGTGGA-TCCAGTACCGCAAAGATACAA
122 CGGCGGATTCCAGTACCGCAAAGATACAA
* * *
313197 AATGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCACGAAGACACAAGGAAAAAGTTTAAGT
1 AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCACGAAGACACAAGGGAAAGGTTTAAGT
* * * *
313262 CGCAATGGTGAACCTAGCACCTCAAAAAACACGACGGGAAAGATCTAAGACTGCAACGGTGGATT
66 CGCAATGGCGAACCTAGTACCTCAAAAAACATGACGGGAAAGATCTAAGACTGCAACGGCGGATT
313327 -CAGTACCGCAAAGATACAA
131 CCAGTACCGCAAAGATACAA
* *
313346 AAGGGAAAGATCTAAGCTGCAACGGCGAATCCAGTACCACGAAGACACAAGGGAAAGGTTTAAGT
1 AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCACGAAGACACAAGGGAAAGGTTTAAGT
* *
313411 CGCAATAGCGAACCTAGTACCTCAAAAAACACT-ACGGGAAAGATCTAAGA-TCGCAATGGCGG-
66 CGCAATGGCGAACCTAGTACCTCAAAAAACA-TGACGGGAAAGATCTAAGACT-GCAACGGCGGA
313473 TTCCAGTACCGCAAAGATACAA
129 TTCCAGTACCGCAAAGATACAA
* * *
313495 AAGGGAAAGATCTAAGCCGCAACGGTGGATCAAGTA-CAGCGAAGACACAAGGGGAAGGATTTAA
1 AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCA-CGAAGACACAAGGGAAAGG-TTTAA
*
313559 GTCGCGATGGCGAACCT
64 GTCGCAATGGCGAACCT
313576 TATACCCCAA
Statistics
Matches: 437, Mismatches: 69, Indels: 47
0.79 0.12 0.08
Matches are distributed among these distances:
148 9 0.02
149 283 0.65
150 68 0.16
151 72 0.16
152 5 0.01
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (150 bp):
AAGGGAAAGATCTAAGCTGCAACGGTGGATCCAGTACCACGAAGACACAAGGGAAAGGTTTAAGT
CGCAATGGCGAACCTAGTACCTCAAAAAACATGACGGGAAAGATCTAAGACTGCAACGGCGGATT
CCAGTACCGCAAAGATACAA
Found at i:314829 original size:20 final size:21
Alignment explanation
Indices: 314804--314851 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
314794 ATAATGGCAT
*
314804 TAATAAATATTATTAAA-AAA
1 TAATAAATAATATTAAATAAA
314824 TAAT-AATAATATTAAATAAA
1 TAATAAATAATATTAAATAAA
314844 TAAATAAA
1 T-AATAAA
314852 AGAAATTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 11 0.46
20 8 0.33
21 3 0.12
22 2 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATAAATAATATTAAATAAA
Found at i:315869 original size:30 final size:29
Alignment explanation
Indices: 315832--315948 Score: 110
Period size: 30 Copynumber: 3.9 Consensus size: 29
315822 CCTTGAAGGT
315832 CCCTAAACTGTCTAAAAATTATATTTTGAC
1 CCCTAAACT-TCTAAAAATTATATTTTGAC
* * * *
315862 CCTTAAACTTCTTTAAAATTACATTTTTAC
1 CCCTAAACTTC-TAAAAATTATATTTTGAC
* *
315892 CCCTAATCTT-TACCGAAATTATATTTTGAC
1 CCCTAAACTTCTA--AAAATTATATTTTGAC
* *
315922 CCCCAAACTTCTCCAAAATTATATTTT
1 CCCTAAACTTCT-AAAAATTATATTTT
315949 TACCTTTGAA
Statistics
Matches: 68, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
28 1 0.01
29 2 0.03
30 64 0.94
31 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.40
Consensus pattern (29 bp):
CCCTAAACTTCTAAAAATTATATTTTGAC
Found at i:315978 original size:60 final size:60
Alignment explanation
Indices: 315846--316355 Score: 220
Period size: 60 Copynumber: 8.7 Consensus size: 60
315836 AAACTGTCTA
* **
315846 AAAATTATATTTTGACCCTTAAACTTCTTTAAAATTACATTTTTACCCCTAATCTTTACC
1 AAAATTATATTTTGACCCCTAAACTTCTCCAAAATTACATTTTTACCCCTAATCTTTACC
* * * **
315906 GAAATTATATTTTGACCCCCAAACTTCTCCAAAATTATATTTTTACCTTTGAAT-TTT-CC
1 AAAATTATATTTTGACCCCTAAACTTCTCCAAAATTACATTTTTACCCCT-AATCTTTACC
* * * * *
315965 AAAATTTACATTTTTTACCCCTAAACTT-TCCAAAATTCCATTTTTGACCTCGT--T-TTTTCC
1 AAAA-TTATA-TTTTGACCCCTAAACTTCTCCAAAATTACATTTTT-ACC-CCTAATCTTTACC
* * * * * * *
316025 AAAAGTTACCATTTTAACTCC-GAAGTTCT-AAAAATTACAATTTTACCCTCTAA-C-TT-CC
1 AAAA-TTA-TATTTTGACCCCTAAACTTCTCCAAAATTACATTTTTACCC-CTAATCTTTACC
** * * * * *
316083 AAAAATTCCATTTT-AACCCT-AATTTTTCAAAAATTACATTTTTATCCCTAAAT-TTT-CC
1 -AAAATTATATTTTGACCCCTAAACTTCTCCAAAATTACATTTTTACCCCT-AATCTTTACC
** ** * * *
316141 AAAATTCCATTTTGACCCC-AATTTTTTTCCAAAAATTACCA-TTTTACCTCGAA-C-TT-CC
1 AAAATTATATTTTGACCCCTAA-ACTTCTCC-AAAATTA-CATTTTTACCCCTAATCTTTACC
* * * *
316199 AAAATTATATTTT-ACCCTTAAACTT-TCAAAAATT-CTATTTTGA-CCCTAAT-TTTTCC
1 AAAATTATATTTTGACCCCTAAACTTCTCCAAAATTAC-ATTTTTACCCCTAATCTTTACC
* * * *
316255 AAAAAATATCATTTT-ACCCCTAAACTTC-CAAAAATTCCATTTTGACCCC-AAT-TTT-CTC
1 -AAAATTAT-ATTTTGACCCCTAAACTTCTCCAAAATTACATTTTTACCCCTAATCTTTAC-C
* * * *
316313 AAAATTACCATTTT-ACCCCTATACTT-TCAAAAATTCCATTTTT
1 AAAATTA-TATTTTGACCCCTAAACTTCTCCAAAATTACATTTTT
316356 GATCTCGATT
Statistics
Matches: 359, Mismatches: 53, Indels: 79
0.73 0.11 0.16
Matches are distributed among these distances:
53 1 0.00
54 5 0.01
55 12 0.03
56 14 0.04
57 90 0.25
58 72 0.20
59 43 0.12
60 96 0.27
61 25 0.07
62 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.41
Consensus pattern (60 bp):
AAAATTATATTTTGACCCCTAAACTTCTCCAAAATTACATTTTTACCCCTAATCTTTACC
Found at i:315983 original size:31 final size:30
Alignment explanation
Indices: 315876--316015 Score: 106
Period size: 30 Copynumber: 4.7 Consensus size: 30
315866 AAACTTCTTT
* *
315876 AAAATTACA-TTTTTACCCCTAATCTTTACC
1 AAAATTACATTTTTTACCTCTAAACTTT-CC
* * * * *
315906 GAAATTATA-TTTTGACCCCCAAACTTCTCC
1 AAAATTACATTTTTTACCTCTAAACTT-TCC
* * * *
315936 AAAATTATA-TTTTTACCTTTGAATTTTCC
1 AAAATTACATTTTTTACCTCTAAACTTTCC
*
315965 AAAATTTACATTTTTTACCCCTAAACTTTCC
1 AAAA-TTACATTTTTTACCTCTAAACTTTCC
* *
315996 AAAATTCCATTTTTGACCTC
1 AAAATTACATTTTTTACCTC
316016 GTTTTTTCCA
Statistics
Matches: 87, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
29 7 0.08
30 59 0.68
31 21 0.24
ACGTcount: A:0.31, C:0.24, G:0.03, T:0.41
Consensus pattern (30 bp):
AAAATTACATTTTTTACCTCTAAACTTTCC
Found at i:316007 original size:30 final size:29
Alignment explanation
Indices: 315876--316355 Score: 208
Period size: 29 Copynumber: 16.5 Consensus size: 29
315866 AAACTTCTTT
* *
315876 AAAATTACATTTTTACCCCTAATCTTTACC
1 AAAATTCCATTTTTACCCCTAAACTTT-CC
* ** * *
315906 GAAATTATATTTTGACCCCCAAACTTCTCC
1 AAAATTCCATTTTTACCCCTAAACTT-TCC
** ** * *
315936 AAAATTATATTTTTACCTTTGAATTTTCC
1 AAAATTCCATTTTTACCCCTAAACTTTCC
*
315965 AAAATTTACATTTTTTACCCCTAAACTTTCC
1 AAAA-TTCCA-TTTTTACCCCTAAACTTTCC
* **
315996 AAAATTCCATTTTTGACCTCGT--TTTTTCC
1 AAAATTCCATTTTT-ACC-CCTAAACTTTCC
* * * * *
316025 AAAAGTTACCATTTTAACTCC-GAA-GTTCTA
1 AAAA-TT-CCATTTTTACCCCTAAACTTTC-C
* *
316055 AAAATTACAATTTTACCCTCT-AAC-TTCC
1 AAAATTCCATTTTTACCC-CTAAACTTTCC
* ** *
316083 AAAAATTCCA-TTTTAACCCTAATTTTTCA
1 -AAAATTCCATTTTTACCCCTAAACTTTCC
* * *
316112 AAAATTACATTTTTATCCCTAAATTTTCC
1 AAAATTCCATTTTTACCCCTAAACTTTCC
* **
316141 AAAATTCCATTTTGACCCC-AATTTTTTTCC
1 AAAATTCCATTTTTACCCCTAA--ACTTTCC
* *
316171 AAAAATTACCA-TTTTACCTC-GAAC-TTCC
1 -AAAATT-CCATTTTTACCCCTAAACTTTCC
* *
316199 AAAATT--ATATTTTACCCTTAAACTTTCA
1 AAAATTCCAT-TTTTACCCCTAAACTTTCC
* * **
316227 AAAATTCTATTTTGA-CCCTAATTTTTCC
1 AAAATTCCATTTTTACCCCTAAACTTTCC
316255 AAAAAATAT-CA-TTTTACCCCTAAAC-TTCC
1 --AAAAT-TCCATTTTTACCCCTAAACTTTCC
* *
316284 AAAAATTCCATTTTGACCCC--AATTTTCTC
1 -AAAATTCCATTTTTACCCCTAAACTTTC-C
* *
316313 AAAATTACCA-TTTTACCCCTATACTTTCA
1 AAAATT-CCATTTTTACCCCTAAACTTTCC
316342 AAAATTCCATTTTT
1 AAAATTCCATTTTT
316356 GATCTCGATT
Statistics
Matches: 342, Mismatches: 69, Indels: 79
0.70 0.14 0.16
Matches are distributed among these distances:
24 1 0.00
26 7 0.02
27 14 0.04
28 76 0.22
29 110 0.32
30 86 0.25
31 45 0.13
32 3 0.01
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCTAAACTTTCC
Found at i:316096 original size:28 final size:28
Alignment explanation
Indices: 316054--316354 Score: 199
Period size: 28 Copynumber: 10.5 Consensus size: 28
316044 CCGAAGTTCT
*
316054 AAAAATTACAATTTTACCCTCTAA-CTTCC
1 AAAAATT-CCATTTTACCC-CTAATCTTCC
* * *
316083 AAAAATTCCATTTTAACCCTAATTTTTC
1 AAAAATTCCATTTTACCCCTAATCTTCC
* * *
316111 AAAAATTACATTTTTATCCCTAAATTTTCC
1 AAAAATTCCA-TTTTACCCCT-AATCTTCC
*
316141 -AAAATTCCATTTTGACCCC-AATTTTTTTCC
1 AAAAATTCCATTTT-ACCCCTAA---TCTTCC
* *
316171 AAAAATTACCATTTTACCTCGAA-CTTCC
1 AAAAATT-CCATTTTACCCCTAATCTTCC
** * * *
316199 -AAAATTATATTTTACCCTTAAACTTTC
1 AAAAATTCCATTTTACCCCTAATCTTCC
* *
316226 AAAAATTCTATTTTGA-CCCTAATTTTTCC
1 AAAAATTCCATTTT-ACCCCTAA-TCTTCC
*
316255 AAAAAATAT-CATTTTACCCCTAAACTTCC
1 -AAAAAT-TCCATTTTACCCCTAATCTTCC
*
316284 AAAAATTCCATTTTGACCCC-AATTTTCTC
1 AAAAATTCCATTTT-ACCCCTAATCTTC-C
*
316313 -AAAATTACCATTTTACCCCT-ATACTTTC
1 AAAAATT-CCATTTTACCCCTAAT-CTTCC
316341 AAAAATTCCATTTT
1 AAAAATTCCATTTT
316355 TGATCTCGAT
Statistics
Matches: 219, Mismatches: 29, Indels: 49
0.74 0.10 0.16
Matches are distributed among these distances:
26 10 0.05
27 17 0.08
28 84 0.38
29 58 0.26
30 30 0.14
31 11 0.05
32 9 0.04
ACGTcount: A:0.35, C:0.24, G:0.01, T:0.40
Consensus pattern (28 bp):
AAAAATTCCATTTTACCCCTAATCTTCC
Found at i:316164 original size:57 final size:55
Alignment explanation
Indices: 315876--316355 Score: 210
Period size: 57 Copynumber: 8.3 Consensus size: 55
315866 AAACTTCTTT
* ** * *
315876 AAAATTACATTTTTACCCCT-AATCTTTACCGAAATTATATTTTGACCCCCAAACTTCTCC
1 AAAATTACATTTTTA-CCCTAAAT-TTT-CCAAAATTCCATTTT-A-CCCCAATCTT-TCA
* * * * * *
315936 AAAATTATATTTTTACCTTTGAATTTTCCAAAATTTACATTTTTTACCCCTAAACTTTCC
1 AAAATTACATTTTTACC-CTAAATTTTCCAAAA-TTCCA--TTTTACCCC-AATCTTTCA
* * * *
315996 AAAATTCCATTTTTGACCTCGT--TTTTTCCAAAAGTTACCATTTTAACTCCGAA--GTTCTA
1 AAAATTACATTTTT-ACC-C-TAAATTTTCCAAAA-TT-CCATTTT-AC-CCCAATCTTTC-A
* * * * *
316055 AAAATTACAATTTTACCCTCTAA-CTTCCAAAAATTCCATTTTAACCCTAATTTTTCA
1 AAAATTACATTTTTACCCT-AAATTTTCC-AAAATTCCATTTT-ACCCCAATCTTTCA
*
316112 AAAATTACATTTTTATCCCTAAATTTTCCAAAATTCCATTTTGACCCCAATTTTTTTCCA
1 AAAATTACATTTTTA-CCCTAAATTTTCCAAAATTCCATTTT-ACCCCAA--TCTTT-CA
* * ** * *
316172 AAAATTACCA-TTTTA-CCTCGAA-CTTCCAAAATTATATTTTACCCTTAAACTTTCA
1 AAAATTA-CATTTTTACCCT-AAATTTTCCAAAATTCCATTTTACCC-CAATCTTTCA
* * * *
316227 AAAATT-CTATTTTGACCCTAATTTTTCCAAAAAATAT-CATTTTACCCCTAAACTTCCA
1 AAAATTAC-ATTTTTACCCTAAATTTTCC--AAAAT-TCCATTTTACCCC-AATCTTTCA
* * * *
316285 AAAATTCCATTTTGACCC-CAATTTTCTCAAAATTACCATTTTACCCCTATACTTTCA
1 AAAATTACATTTTTACCCTAAATTTTC-CAAAATT-CCATTTTACCCCAAT-CTTTCA
*
316342 AAAATTCCATTTTT
1 AAAATTACATTTTT
316356 GATCTCGATT
Statistics
Matches: 337, Mismatches: 44, Indels: 81
0.73 0.10 0.18
Matches are distributed among these distances:
53 1 0.00
54 1 0.00
55 14 0.04
56 21 0.06
57 86 0.26
58 82 0.24
59 36 0.11
60 71 0.21
61 20 0.06
62 5 0.01
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (55 bp):
AAAATTACATTTTTACCCTAAATTTTCCAAAATTCCATTTTACCCCAATCTTTCA
Found at i:316231 original size:86 final size:86
Alignment explanation
Indices: 316079--316297 Score: 230
Period size: 86 Copynumber: 2.5 Consensus size: 86
316069 ACCCTCTAAC
* * ** * * *
316079 TTCC-AAAAATTCCATTTTAACCCTAATTTTTCAAAAATTACATTTTTATCCCTAAATTTTCCAA
1 TTCCAAAAAATACCATTTTACCCCTAA-ACTTCCAAAATTACATTTTTATCCCTAAACTTTCAAA
316143 AATTCCATTTTGACCCCAATTTTT
65 AATTCCATTTTGACCCCAA--TTT
* * * *
316167 TTCCAAAAATTACCATTTTACCTC-GAACTTCCAAAATTATA-TTTTA-CCCTTAAACTTTCAAA
1 TTCCAAAAAATACCATTTTACCCCTAAACTTCCAAAATTACATTTTTATCCC-TAAACTTTCAAA
* *
316229 AATTCTATTTTGACCCTAATTT
65 AATTCCATTTTGACCCCAATTT
* *
316251 TTCCAAAAAATATCATTTTACCCCTAAACTTCCAAAAATTCCATTTT
1 TTCCAAAAAATACCATTTTACCCCTAAACTTCC-AAAATTACATTTT
316298 GACCCCAATT
Statistics
Matches: 107, Mismatches: 19, Indels: 11
0.78 0.14 0.08
Matches are distributed among these distances:
84 24 0.22
85 10 0.09
86 39 0.36
87 14 0.13
88 5 0.05
89 15 0.14
ACGTcount: A:0.35, C:0.23, G:0.01, T:0.41
Consensus pattern (86 bp):
TTCCAAAAAATACCATTTTACCCCTAAACTTCCAAAATTACATTTTTATCCCTAAACTTTCAAAA
ATTCCATTTTGACCCCAATTT
Found at i:316356 original size:58 final size:57
Alignment explanation
Indices: 315977--316444 Score: 238
Period size: 58 Copynumber: 8.1 Consensus size: 57
315967 AATTTACATT
* * * *
315977 TTTTACCCCTAAACTTTCCAAAATTCCATTTTTGACCTC-GTTTTTTCCAAAAGTTACCA
1 TTTTACCCCT-AACTTTCAAAAATTCCATTTTTGACCCCAATTTTCT-CAAAA-TTACCA
* * * * * *
316036 TTTTAACTCCGAA-GTTCTAAAAATTACAATTTT-ACCCTCTAA-CTTC-CAAAAATT-CCA
1 TTTT-ACCCCTAACTTTC-AAAAATTCCATTTTTGACCC-C-AATTTTCTC-AAAATTACCA
* * * *
316093 TTTTAACCCTAATTTTTCAAAAATTACATTTTT-ATCCCTAAATTTTC-CAAAATT-CCA
1 TTTTACCCCTAA-CTTTCAAAAATTCCATTTTTGA-CCC-CAATTTTCTCAAAATTACCA
* * * *
316150 TTTTGACCCC-AATTTTTTTCCAAAAATTACCA-TTTT-ACCTCGAA-CTTC-CAAAATTA-TA
1 TTTT-ACCCCTAA---CTTT-CAAAAATT-CCATTTTTGACC-CCAATTTTCTCAAAATTACCA
* * * * *
316208 TTTTACCCTTAAACTTTCAAAAATTCTA-TTTTGACCCTAATTTT-TCCAAAAAATATCA
1 TTTTACCCCT-AACTTTCAAAAATTCCATTTTTGACCCCAATTTTCT-C-AAAATTACCA
*
316266 TTTTACCCCTAAACTTCCAAAAATTCCA-TTTTGACCCCAATTTTCTCAAAATTACCA
1 TTTTACCCCT-AACTTTCAAAAATTCCATTTTTGACCCCAATTTTCTCAAAATTACCA
* * * *
316323 TTTTACCCCTATACTTTCAAAAATTCCATTTTTGATCTCGATTTT-TACAAAATTATCA
1 TTTTACCCCTA-ACTTTCAAAAATTCCATTTTTGACCCCAATTTTCT-CAAAATTACCA
* * * * * * *
316381 TTTTACCCTTAAATGTT-TAAAATTTCATTTTTAACCCCAAACTTTCCCAAAATTACCA
1 TTTTACCCCTAACT-TTCAAAAATTCCATTTTTGACCCC-AATTTTCTCAAAATTACCA
*
316439 ATTTAC
1 TTTTAC
316445 TCTCGAGTGT
Statistics
Matches: 325, Mismatches: 52, Indels: 65
0.74 0.12 0.15
Matches are distributed among these distances:
54 9 0.03
55 13 0.04
56 10 0.03
57 101 0.31
58 135 0.42
59 35 0.11
60 20 0.06
61 2 0.01
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.40
Consensus pattern (57 bp):
TTTTACCCCTAACTTTCAAAAATTCCATTTTTGACCCCAATTTTCTCAAAATTACCA
Found at i:316480 original size:28 final size:28
Alignment explanation
Indices: 316427--316488 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
316417 CCAAACTTTC
* *
316427 CCAAAATTACCAATTTACTCTCGAGTGT
1 CCAAAATTACCAATTTACCCTCGAGTAT
*
316455 CCAAAATTACCATTTTACCC-CTGAGTAT
1 CCAAAATTACCAATTTACCCTC-GAGTAT
316483 CCAAAA
1 CCAAAA
316489 ATCACAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.29
Consensus pattern (28 bp):
CCAAAATTACCAATTTACCCTCGAGTAT
Found at i:318529 original size:18 final size:18
Alignment explanation
Indices: 318494--318528 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
318484 AAAATTGGCT
*
318494 TAAAAAATATTATGAAAA
1 TAAAAAATATTATAAAAA
318512 TAAAAAATATT-TAAAAA
1 TAAAAAATATTATAAAAA
318529 AACTAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
TAAAAAATATTATAAAAA
Found at i:318530 original size:19 final size:19
Alignment explanation
Indices: 318494--318536 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
318484 AAAATTGGCT
**
318494 TAAAAAATATTATGAAAA-
1 TAAAAAATATTAAAAAAAC
318512 TAAAAAATATTTAAAAAAAC
1 TAAAAAATA-TTAAAAAAAC
318532 TAAAA
1 TAAAA
318537 TTAAAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 7 0.33
20 5 0.24
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
TAAAAAATATTAAAAAAAC
Found at i:318552 original size:26 final size:25
Alignment explanation
Indices: 318523--318579 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
318513 AAAAAATATT
* *
318523 TAAAAAAACTAAAATTAAAAAAAAAG
1 TAAAAAAAAT-AAATCAAAAAAAAAG
* *
318549 TAAAAAAAATTAATCAAAGAAAAAG
1 TAAAAAAAATAAATCAAAAAAAAAG
318574 TAAAAA
1 TAAAAA
318580 TTAACGTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
25 18 0.67
26 9 0.33
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (25 bp):
TAAAAAAAATAAATCAAAAAAAAAG
Found at i:319726 original size:8 final size:8
Alignment explanation
Indices: 319713--319758 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
319703 AATTGTTTTT
319713 ATTTAATA
1 ATTTAATA
319721 ATTTAATA
1 ATTTAATA
* *
319729 AATTATTA
1 ATTTAATA
319737 A--T-ATA
1 ATTTAATA
319742 ATTTAATA
1 ATTTAATA
319750 ATTTAATA
1 ATTTAATA
319758 A
1 A
319759 ATTATTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
5 3 0.09
6 1 0.03
7 1 0.03
8 27 0.84
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
ATTTAATA
Found at i:319744 original size:21 final size:20
Alignment explanation
Indices: 319717--319769 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 20
319707 GTTTTTATTT
*
319717 AATAATTTAATAAATTATTA
1 AATAATTTAATAAATTAATA
*
319737 ATATAATTTAATAATTTAATA
1 A-ATAATTTAATAAATTAATA
*
319758 AATTATTTAATA
1 AATAATTTAATA
319770 TTACAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
AATAATTTAATAAATTAATA
Found at i:319745 original size:29 final size:30
Alignment explanation
Indices: 319713--319770 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 30
319703 AATTGTTTTT
319713 ATTTAATAATTTAATAAATTA-TTAATATA
1 ATTTAATAATTTAATAAATTATTTAATATA
319742 ATTTAATAATTTAATAAATTATTTAATAT
1 ATTTAATAATTTAATAAATTATTTAATAT
319771 TACAATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTAATAATTTAATAAATTATTTAATATA
Found at i:319787 original size:19 final size:18
Alignment explanation
Indices: 319763--319798 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
319753 TAATAAATTA
*
319763 TTTAATATTACAATTTTAT
1 TTTAATAATA-AATTTTAT
319782 TTTAATAATAAATTTTA
1 TTTAATAATAAATTTTA
319799 AATAATATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTAATAATAAATTTTAT
Found at i:319903 original size:37 final size:36
Alignment explanation
Indices: 319829--319937 Score: 91
Period size: 37 Copynumber: 3.0 Consensus size: 36
319819 ATTGAAAAAT
*
319829 ATTTATATTAATATTTTAATAATAAATATATATTATA
1 ATTTATA-TAATATTTTAATAATAAATATATAGTATA
*
319866 ATTTATA-AATA-TTTAATAATAAATGTTTAATAGTATA
1 ATTTATATAATATTTTAATAATAAA--TAT-ATAGTATA
* * *
319903 A--AATATGAATATTTTAATTATATATATATGAGTAT
1 ATTTATAT-AATATTTTAATAATAAATATAT-AGTAT
319938 TTGTTTAAAT
Statistics
Matches: 59, Mismatches: 6, Indels: 15
0.74 0.08 0.19
Matches are distributed among these distances:
34 12 0.20
35 9 0.15
36 9 0.15
37 19 0.32
38 10 0.17
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (36 bp):
ATTTATATAATATTTTAATAATAAATATATAGTATA
Found at i:319926 original size:24 final size:23
Alignment explanation
Indices: 319891--319939 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
319881 ATAATAAATG
319891 TTTAATAGTATAAAATATGAATAT
1 TTTAATAGTAT-AAATATGAATAT
* *
319915 TTTAATTA-TATATATATGAGTAT
1 TTTAA-TAGTATAAATATGAATAT
319938 TT
1 TT
319940 GTTTAAATCA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 12 0.55
24 8 0.36
25 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (23 bp):
TTTAATAGTATAAATATGAATAT
Found at i:320117 original size:18 final size:17
Alignment explanation
Indices: 320075--320123 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 17
320065 TATTATATTA
320075 TTTATTATAAAATACTAT
1 TTTATTATAAAATAC-AT
320093 TTTATTATAAAATGA-AT
1 TTTATTATAAAAT-ACAT
320110 TTTGATTATTAAAA
1 TTT-ATTA-TAAAA
320124 GAAAATTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.18
18 17 0.61
19 6 0.21
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (17 bp):
TTTATTATAAAATACAT
Found at i:320925 original size:25 final size:24
Alignment explanation
Indices: 320875--320927 Score: 61
Period size: 25 Copynumber: 2.2 Consensus size: 24
320865 CAATTCGATC
* ** *
320875 AAATAAATTATTAAAAATTTATAA
1 AAATAAAATATTAAAAATAGAGAA
320899 AAATAAAATATTTAAAAATAGAGAA
1 AAATAAAATA-TTAAAAATAGAGAA
320924 AAAT
1 AAAT
320928 CGATCCAATC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (24 bp):
AAATAAAATATTAAAAATAGAGAA
Found at i:324094 original size:66 final size:66
Alignment explanation
Indices: 323988--324118 Score: 253
Period size: 66 Copynumber: 2.0 Consensus size: 66
323978 GCTACCTTTC
323988 ACACTATTATTGTGAAAGCAACTACTAGTTTAACCACTTGCATGAAATGAAATGACAAATCATTG
1 ACACTATTATTGTGAAAGCAACTACTAGTTTAACCACTTGCATGAAATGAAATGACAAATCATTG
324053 A
66 A
*
324054 ACACTATTATTGTGAAAGCAACTACTGGTTTAACCACTTGCATGAAATGAAATGACAAATCATTG
1 ACACTATTATTGTGAAAGCAACTACTAGTTTAACCACTTGCATGAAATGAAATGACAAATCATTG
324119 GAGGAGACAT
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.29
Consensus pattern (66 bp):
ACACTATTATTGTGAAAGCAACTACTAGTTTAACCACTTGCATGAAATGAAATGACAAATCATTG
A
Found at i:328120 original size:18 final size:17
Alignment explanation
Indices: 328076--328124 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
328066 GGATGAGAAT
328076 AAAATTTTAATTAA--A
1 AAAATTTTAATTAATTA
*
328091 TAAATTTT-ATTAATTA
1 AAAATTTTAATTAATTA
328107 AAAATTTTAAATTAATTA
1 AAAATTTT-AATTAATTA
328125 CAATTGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 5 0.18
15 7 0.25
16 8 0.29
18 8 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATTTTAATTAATTA
Found at i:331433 original size:72 final size:72
Alignment explanation
Indices: 331295--331442 Score: 201
Period size: 72 Copynumber: 2.1 Consensus size: 72
331285 GCCCAGCCCA
* * *
331295 TGTGCCTAGCCCGTGTGTCTCTTGTACCTTAAATCACAAAACAGTATGCATACACGGTATGACAC
1 TGTGCCTAGCCCGTGTGTCTCTTATACCTTAAATCACAAAACAGTATGCACACACGATATGACAC
**
331360 ACGTCCG
66 ACACCCG
* *
331367 TGTGCCTAGCCCGTGTGTC-CTCTATACCTTAAATCACAAAACAGTATGTACACACGA-ATTGGC
1 TGTGCCTAGCCCGTGTGTCTCT-TATACCTTAAATCACAAAACAGTATGCACACACGATA-TGAC
331430 ACACACCCG
64 ACACACCCG
331439 TGTG
1 TGTG
331443 TCCAGCCTAT
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
71 3 0.04
72 64 0.96
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.26
Consensus pattern (72 bp):
TGTGCCTAGCCCGTGTGTCTCTTATACCTTAAATCACAAAACAGTATGCACACACGATATGACAC
ACACCCG
Found at i:332554 original size:29 final size:30
Alignment explanation
Indices: 332520--332582 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
332510 AAATTTTGAA
332520 ATTTTTAAAAATTTTAAAATTTCA-AAAATT
1 ATTTTTAAAAA-TTTAAAATTTCATAAAATT
*
332550 ATTTTTTAAAATTTAAAA--TCATTAAAATT
1 ATTTTTAAAAATTTAAAATTTCA-TAAAATT
332579 ATTT
1 ATTT
332583 AAAAAAGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 3 0.10
29 17 0.57
30 10 0.33
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTTTTAAAAATTTAAAATTTCATAAAATT
Found at i:334217 original size:6 final size:6
Alignment explanation
Indices: 334206--334232 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
334196 CCCTCACGTG
334206 CCTGAC CCTGAC CCTGAC CCTGAC CCT
1 CCTGAC CCTGAC CCTGAC CCTGAC CCT
334233 CACTCCGCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.52, G:0.15, T:0.19
Consensus pattern (6 bp):
CCTGAC
Found at i:336069 original size:22 final size:24
Alignment explanation
Indices: 336044--336093 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 24
336034 TATTTTAACC
*
336044 TAAAAATCTTAA-AATAAATTA-A
1 TAAAAATCTTAAGAATAAACTATA
*
336066 TAAAAATTTTAAGAATAAACTATA
1 TAAAAATCTTAAGAATAAACTATA
336090 TAAA
1 TAAA
336094 TAATTACTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 11 0.46
23 8 0.33
24 5 0.21
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (24 bp):
TAAAAATCTTAAGAATAAACTATA
Found at i:336424 original size:24 final size:24
Alignment explanation
Indices: 336377--336425 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
336367 TTTTTGATAC
* *
336377 AAATACATAAAATTTTATAAAAAT
1 AAATAAATAAAATTATATAAAAAT
336401 AAATAAATAAAATTATA-AATAAAT
1 AAATAAATAAAATTATATAA-AAAT
336425 A
1 A
336426 TCATTTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (24 bp):
AAATAAATAAAATTATATAAAAAT
Found at i:337866 original size:5 final size:5
Alignment explanation
Indices: 337856--337927 Score: 51
Period size: 5 Copynumber: 14.2 Consensus size: 5
337846 TATAAACTTA
*
337856 TTATT TTATT TTATTT TTATC TTA-- TTATT TTATT TTGGATTT TTATT
1 TTATT TTATT TTA-TT TTATT TTATT TTATT TTATT TT--A-TT TTATT
* * *
337903 ATACT TT-GT TTATT TTATT TTATT T
1 TTATT TTATT TTATT TTATT TTATT T
337928 GAGTTGTAAG
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
3 3 0.06
4 3 0.06
5 37 0.69
6 6 0.11
7 1 0.02
8 4 0.07
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.74
Consensus pattern (5 bp):
TTATT
Found at i:337884 original size:24 final size:24
Alignment explanation
Indices: 337852--337923 Score: 85
Period size: 24 Copynumber: 2.9 Consensus size: 24
337842 TATTTATAAA
337852 CTTATTATTTTATTTTATTTTTAT
1 CTTATTATTTTATTTTATTTTTAT
337876 CTTATTATTTTATTTTGGATTTTTAT
1 CTTATTATTTTATTTT--ATTTTTAT
337902 -TATACTT-TGTTTATTTTATTTT
1 CT-TA-TTAT-TTTATTTTATTTT
337924 ATTTGAGTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
24 16 0.37
25 6 0.14
26 11 0.26
27 10 0.23
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.72
Consensus pattern (24 bp):
CTTATTATTTTATTTTATTTTTAT
Found at i:338013 original size:2 final size:2
Alignment explanation
Indices: 338006--338034 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
337996 AATTATAGAC
338006 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 T
338035 GAATGAATGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:348697 original size:30 final size:30
Alignment explanation
Indices: 348661--348725 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
348651 ACTTATTTTA
* *
348661 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTACTATTTTAGAGACAT
348691 TTGTTAATTTTGTTACTATTTTAGAGACAT
1 TTGTTAATTTTGTTACTATTTTAGAGACAT
348721 TTGTT
1 TTGTT
348726 TGTTTAGTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTACTATTTTAGAGACAT
Found at i:349693 original size:6 final size:6
Alignment explanation
Indices: 349682--349711 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
349672 AAATAATATA
*
349682 AAAAAG AAAAAG AAAAAG AAAAAG AGAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
349712 GTGTGCAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:353385 original size:18 final size:17
Alignment explanation
Indices: 353341--353391 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 17
353331 TGATATATTC
*
353341 ATTAATAATAGTATTAT
1 ATTAATAATAATATTAT
* *
353358 AATAAATAATAATATTTT
1 -ATTAATAATAATATTAT
353376 ATTAAT--TAATATTAT
1 ATTAATAATAATATTAT
353391 A
1 A
353392 AAATATATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
15 9 0.32
17 5 0.18
18 14 0.50
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTAATAATAATATTAT
Found at i:354421 original size:16 final size:18
Alignment explanation
Indices: 354396--354432 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
354386 AAATGAAACT
*
354396 AAAATGAGAA-TGATATG
1 AAAATGAGAATTGAGATG
354413 AAAAT-AGAATTGAGATG
1 AAAATGAGAATTGAGATG
354430 AAA
1 AAA
354433 CGGATTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.57, C:0.00, G:0.22, T:0.22
Consensus pattern (18 bp):
AAAATGAGAATTGAGATG
Found at i:354430 original size:22 final size:22
Alignment explanation
Indices: 354383--354432 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
354373 TTATTTGATT
*
354383 ATGAAATGAAACTAAAATGAGA
1 ATGAAATGAAAATAAAATGAGA
* *
354405 ATGATATGAAAATAGAATTGAG-
1 ATGAAATGAAAATA-AAATGAGA
354427 ATGAAA
1 ATGAAA
354433 CGGATTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.22
Consensus pattern (22 bp):
ATGAAATGAAAATAAAATGAGA
Found at i:361116 original size:48 final size:47
Alignment explanation
Indices: 360989--361119 Score: 129
Period size: 48 Copynumber: 2.7 Consensus size: 47
360979 TTATTTATAG
* * * * * *
360989 GTTGAAAAAAATATACTAATCAAAGTTAAATAGATGAAGTGTAGTAAA
1 GTTGAAAAACATATTCTAATCAAA-ATAAATAAAAGAAGTGTAATAAA
* * *
361037 GTTGAAAAACCTTATTCAAATTAAAATAAATAAAAGAAGTGTAAT-AA
1 GTTGAAAAA-CATATTCTAATCAAAATAAATAAAAGAAGTGTAATAAA
*
361084 GATTGAAAATCATATTCTAATCAAAATAAAATAAAA
1 G-TTGAAAAACATATTCTAATCAAAAT-AAATAAAA
361120 TAAAATGTAA
Statistics
Matches: 67, Mismatches: 13, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
47 17 0.25
48 40 0.60
49 10 0.15
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.27
Consensus pattern (47 bp):
GTTGAAAAACATATTCTAATCAAAATAAATAAAAGAAGTGTAATAAA
Found at i:364547 original size:28 final size:28
Alignment explanation
Indices: 364485--364547 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 28
364475 TTAGTCTCAG
* *
364485 TTTAGTTTTTTATATAATAAAATATAAA
1 TTTATTTTTTTATATAATAAAAAATAAA
364513 TTCTATTTTTCTTATA-AATAAAAAATAAA
1 TT-TATTTTT-TTATATAATAAAAAATAAA
364542 TTTATT
1 TTTATT
364548 ATTTAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 6 0.19
29 20 0.65
30 5 0.16
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (28 bp):
TTTATTTTTTTATATAATAAAAAATAAA
Found at i:371731 original size:2 final size:2
Alignment explanation
Indices: 371726--371754 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
371716 GCCCCCCATA
371726 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
371755 CCTTTTTAAC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:378676 original size:28 final size:28
Alignment explanation
Indices: 378632--378695 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
378622 AAAATTCCCT
* * * **
378632 AAAAACTTTGACTAATCTTTTTTCATTC
1 AAAAAATTTGACTAATCCTATTTCATAA
378660 AAAAAATTTGA-TGAATCCTATTTCATAA
1 AAAAAATTTGACT-AATCCTATTTCATAA
378688 AAAAAATT
1 AAAAAATT
378696 CAACAACTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 1 0.03
28 29 0.97
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (28 bp):
AAAAAATTTGACTAATCCTATTTCATAA
Found at i:381016 original size:24 final size:26
Alignment explanation
Indices: 380969--381017 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
380959 CATCTTTTGG
380969 AATATCAAAATATTTAATCTTTATAC
1 AATATCAAAATATTTAATCTTTATAC
380995 AATA-CAAAA-ATTT-ATCTATTATA
1 AATATCAAAATATTTAATCT-TTATA
381018 ATTTGGATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 9 0.41
25 5 0.23
26 4 0.18
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (26 bp):
AATATCAAAATATTTAATCTTTATAC
Found at i:382452 original size:18 final size:18
Alignment explanation
Indices: 382425--382463 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
382415 ACATTAAATT
382425 ACATAATTTAGTCATTCA
1 ACATAATTTAGTCATTCA
*
382443 ACATATTTTAGTCATTCA
1 ACATAATTTAGTCATTCA
382461 ACA
1 ACA
382464 CAATGTAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.18, G:0.05, T:0.38
Consensus pattern (18 bp):
ACATAATTTAGTCATTCA
Found at i:382472 original size:18 final size:18
Alignment explanation
Indices: 382433--382472 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
382423 TTACATAATT
* * *
382433 TAGTCATTCAACATATTT
1 TAGTCATTCAACACAATG
382451 TAGTCATTCAACACAATG
1 TAGTCATTCAACACAATG
382469 TAGT
1 TAGT
382473 TCTTTTGGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.17, G:0.10, T:0.38
Consensus pattern (18 bp):
TAGTCATTCAACACAATG
Found at i:383379 original size:3 final size:3
Alignment explanation
Indices: 383371--383410 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
383361 ATTATGTGTG
383371 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
383411 CAATTTTACT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:384803 original size:37 final size:37
Alignment explanation
Indices: 384757--384838 Score: 146
Period size: 37 Copynumber: 2.2 Consensus size: 37
384747 CAGGAATGCA
* *
384757 AATTCTTAATGTAAATGTCGTTAAACCCTTAAAAATT
1 AATTGTTAATGTAAATGTCCTTAAACCCTTAAAAATT
384794 AATTGTTAATGTAAATGTCCTTAAACCCTTAAAAATT
1 AATTGTTAATGTAAATGTCCTTAAACCCTTAAAAATT
384831 AATTGTTA
1 AATTGTTA
384839 CCACTTTGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (37 bp):
AATTGTTAATGTAAATGTCCTTAAACCCTTAAAAATT
Found at i:385556 original size:12 final size:13
Alignment explanation
Indices: 385539--385573 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
385529 TGTAATTCGA
*
385539 CATAAATATAC-T
1 CATAAACATACTT
385551 CATAAACATACTT
1 CATAAACATACTT
385564 CATAAACATA
1 CATAAACATA
385574 TTTTCAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.51, C:0.20, G:0.00, T:0.29
Consensus pattern (13 bp):
CATAAACATACTT
Found at i:386070 original size:17 final size:18
Alignment explanation
Indices: 386043--386077 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
386033 TAACTAAATA
386043 TCATCATCAAACAAAACT
1 TCATCATCAAACAAAACT
386061 TCAT-ATCAAACAAAACT
1 TCATCATCAAACAAAACT
386078 CATTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (18 bp):
TCATCATCAAACAAAACT
Found at i:387598 original size:21 final size:20
Alignment explanation
Indices: 387555--387598 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
387545 TATTTAATAT
* *
387555 TTTTATAAATTTTAATAATA
1 TTTTATAAATTTTAAAAAAA
*
387575 TTTTATAGATTTATAAAAAAA
1 TTTTATAAATTT-TAAAAAAA
387596 TTT
1 TTT
387599 AAAAATTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
TTTTATAAATTTTAAAAAAA
Found at i:392781 original size:25 final size:25
Alignment explanation
Indices: 392752--392802 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
392742 TACACATAGA
*
392752 TATTTTTGAATTCGGAAGTCATGTT
1 TATTTGTGAATTCGGAAGTCATGTT
392777 TATTTGTGAATTCGGAAGTCATGTT
1 TATTTGTGAATTCGGAAGTCATGTT
392802 T
1 T
392803 TATACCTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.08, G:0.22, T:0.47
Consensus pattern (25 bp):
TATTTGTGAATTCGGAAGTCATGTT
Found at i:393490 original size:27 final size:27
Alignment explanation
Indices: 393459--393520 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
393449 AAGAAAAAAG
393459 GAGTAAATCTAGAAACAAAAAAGTGCC
1 GAGTAAATCTAGAAACAAAAAAGTGCC
393486 GAGTAAATCTAGAAACAAAAAAGTGCC
1 GAGTAAATCTAGAAACAAAAAAGTGCC
393513 GAGTAAAT
1 GAGTAAAT
393521 AAAACACTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.52, C:0.13, G:0.19, T:0.16
Consensus pattern (27 bp):
GAGTAAATCTAGAAACAAAAAAGTGCC
Found at i:395704 original size:18 final size:18
Alignment explanation
Indices: 395681--395716 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
395671 ATTATATAAT
395681 ATTTAAACATATAGTTTA
1 ATTTAAACATATAGTTTA
* *
395699 ATTTAAATATATATTTTA
1 ATTTAAACATATAGTTTA
395717 TTTTTGATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTTAAACATATAGTTTA
Found at i:401190 original size:195 final size:191
Alignment explanation
Indices: 400868--401232 Score: 491
Period size: 195 Copynumber: 1.9 Consensus size: 191
400858 CTATACTATA
* * * *
400868 AACTATTCCCTAACGATGTTGCTCACACGAGTTGTCGAGAGTATGCATAAAGCATAGTCCTAGCC
1 AACTATTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCATAAAGCATAATCCTAGCC
* * *
400933 ATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCTCGAGTCACGATACTGCTCACACA
66 ATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCCCAACTCACGATACTGCTCACACA
* * *
400998 AGCTGTCGAATACTCGCAACATATTCTGTACCTCAACCATTGATACGGTATCTGTGCATAT
131 AGCTATCGAAGACTCGCAACATATTCGGTACCTCAACCATTGATACGGTATCTGTGCATAT
* * *
401059 AACTGTTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCACTTATGCATAAAT-CTCA
1 AACTATTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCA-TAAAGCAT-AATCCT-A
* * * *
401123 GCCATCGTAGGGCCTGTAATCCATTCGT-GGATCCTTTTCTCTTTTCCCAACTCACGATGCTGCT
63 GCCATCGTAGGGCCTATAATCCATT--TAGGATCCATATCTC-TTTCCCAACTCACGATACTGCT
* *
401187 CACACGAGCTATCGAGGACTCGCAACATATTCGGTACCTCAACCAT
125 CACACAAGCTATCGAAGACTCGCAACATATTCGGTACCTCAACCAT
401233 CGCTTCAGTT
Statistics
Matches: 149, Mismatches: 19, Indels: 8
0.85 0.11 0.05
Matches are distributed among these distances:
191 43 0.29
192 8 0.05
193 27 0.18
194 11 0.07
195 60 0.40
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (191 bp):
AACTATTCCCTAACGATGCTGCTCACACGAGCTGTCGAGAATATGCATAAAGCATAATCCTAGCC
ATCGTAGGGCCTATAATCCATTTAGGATCCATATCTCTTTCCCAACTCACGATACTGCTCACACA
AGCTATCGAAGACTCGCAACATATTCGGTACCTCAACCATTGATACGGTATCTGTGCATAT
Found at i:407212 original size:18 final size:20
Alignment explanation
Indices: 407186--407222 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
407176 TTATTTTCAT
407186 TTAATAAATAT-AAATTTAC
1 TTAATAAATATGAAATTTAC
407205 TTAA-AAATATGAAATTTA
1 TTAATAAATATGAAATTTA
407223 ATCACTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (20 bp):
TTAATAAATATGAAATTTAC
Found at i:408356 original size:4 final size:4
Alignment explanation
Indices: 408347--408432 Score: 68
Period size: 4 Copynumber: 21.2 Consensus size: 4
408337 AAATAAACGG
* * *
408347 GAAA GAAA GAAA GAAAA GAAG GAAA GAAA GGAA GAAG GAGAA GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * * *
408397 G-AA GAAG GAGAG GAAA GAAA G-AA TAAG GAAA GAAA G
1 GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
408433 GTAATGTTTT
Statistics
Matches: 65, Mismatches: 12, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
3 5 0.08
4 49 0.75
5 11 0.17
ACGTcount: A:0.65, C:0.00, G:0.34, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:408366 original size:13 final size:13
Alignment explanation
Indices: 408348--408399 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
408338 AATAAACGGG
408348 AAAGAAAGAAAGA
1 AAAGAAAGAAAGA
*
408361 AAAGAAGGAAAG-
1 AAAGAAAGAAAGA
* *
408373 AAAGGAAGAAGGA
1 AAAGAAAGAAAGA
*
408386 GAAGAAAGAAAGA
1 AAAGAAAGAAAGA
408399 A
1 A
408400 GAAGGAGAGG
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
12 9 0.30
13 21 0.70
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAGA
Found at i:408402 original size:20 final size:19
Alignment explanation
Indices: 408346--408432 Score: 106
Period size: 20 Copynumber: 4.5 Consensus size: 19
408336 CAAATAAACG
408346 GGAAAGAAAGAAAGAA-AA
1 GGAAAGAAAGAAAGAAGAA
*
408364 -GAAGGAAAGAAAGGAAGAA
1 GGAAAGAAAGAAA-GAAGAA
408383 GGAGAAGAAAGAAAGAAGAA
1 GGA-AAGAAAGAAAGAAGAA
* *
408403 GGAGAGGAAAGAAAGAATAA
1 GGA-AAGAAAGAAAGAAGAA
408423 GGAAAGAAAG
1 GGAAAGAAAG
408433 GTAATGTTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
17 11 0.18
18 3 0.05
19 8 0.13
20 29 0.48
21 9 0.15
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.01
Consensus pattern (19 bp):
GGAAAGAAAGAAAGAAGAA
Found at i:415383 original size:16 final size:17
Alignment explanation
Indices: 415364--415405 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
415354 TTAATTTTTT
415364 TAAAATTATAAAAAT-A
1 TAAAATTATAAAAATAA
*
415380 TAAAA-TATTAAAATAA
1 TAAAATTATAAAAATAA
415396 TAAAATTATA
1 TAAAATTATA
415406 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 8 0.36
16 11 0.50
17 3 0.14
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATTATAAAAATAA
Found at i:431797 original size:24 final size:22
Alignment explanation
Indices: 431760--431805 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 22
431750 CTAATGACAT
431760 TATAAAAATAGAATGATCAAATTA
1 TATAAAAATAGAATG-T-AAATTA
431784 TATAAAAA-AGGAATGTAAATTA
1 TATAAAAATA-GAATGTAAATTA
431806 AATATCGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 6 0.29
23 2 0.10
24 13 0.62
ACGTcount: A:0.59, C:0.02, G:0.11, T:0.28
Consensus pattern (22 bp):
TATAAAAATAGAATGTAAATTA
Found at i:433749 original size:21 final size:21
Alignment explanation
Indices: 433725--433767 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
433715 TAGGGTTCAA
433725 GAAATGCTTGACTGGACAATT
1 GAAATGCTTGACTGGACAATT
433746 GAAATGCTTGACTGGACAATT
1 GAAATGCTTGACTGGACAATT
433767 G
1 G
433768 GCACCTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.28
Consensus pattern (21 bp):
GAAATGCTTGACTGGACAATT
Found at i:451188 original size:29 final size:29
Alignment explanation
Indices: 451132--451188 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
451122 ACGATACATG
* * ** *
451132 AAATATTTAATTAATTTTTTTGGTGAATA
1 AAATATTTAAATAATTTTCTAAGAGAATA
451161 AAATATTTAAATAATTTTCTAAGAGAAT
1 AAATATTTAAATAATTTTCTAAGAGAAT
451189 TACAAACAGC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (29 bp):
AAATATTTAAATAATTTTCTAAGAGAATA
Found at i:456338 original size:3 final size:3
Alignment explanation
Indices: 456330--456359 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
456320 AATTCTCAAA
456330 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
456360 CTCTTCATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:456476 original size:8 final size:8
Alignment explanation
Indices: 456463--456487 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
456453 ATAATAATAA
456463 TAATTATT
1 TAATTATT
456471 TAATTATT
1 TAATTATT
456479 TAATTATT
1 TAATTATT
456487 T
1 T
456488 TTCATAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (8 bp):
TAATTATT
Found at i:456551 original size:14 final size:14
Alignment explanation
Indices: 456532--456583 Score: 61
Period size: 14 Copynumber: 3.8 Consensus size: 14
456522 TTTTTTACTT
456532 TAAACCTTAAATTC
1 TAAACCTTAAATTC
*
456546 TAAACCTCAAATTC
1 TAAACCTTAAATTC
* *
456560 -AAACCCTAAATAC
1 TAAACCTTAAATTC
*
456573 TAAACCATAAA
1 TAAACCTTAAA
456584 CTCAAATCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 10 0.31
14 22 0.69
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (14 bp):
TAAACCTTAAATTC
Found at i:456588 original size:27 final size:27
Alignment explanation
Indices: 456533--456589 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
456523 TTTTTACTTT
* * *
456533 AAACCTTAAATTCTAAACCTCAAATTC
1 AAACCCTAAATACTAAACCTCAAACTC
456560 AAACCCTAAATACTAAACCAT-AAACTC
1 AAACCCTAAATACTAAACC-TCAAACTC
456587 AAA
1 AAA
456590 TCAAAACTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 25 0.96
28 1 0.04
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (27 bp):
AAACCCTAAATACTAAACCTCAAACTC
Found at i:457133 original size:18 final size:17
Alignment explanation
Indices: 457110--457144 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
457100 AATAAATCTT
457110 TAATTAAATAAATTTAAA
1 TAATTAAA-AAATTTAAA
*
457128 TAATTAAAAATTTTAAA
1 TAATTAAAAAATTTAAA
457145 CCCTAAACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATTAAAAAATTTAAA
Found at i:457203 original size:6 final size:6
Alignment explanation
Indices: 457192--457217 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
457182 CACACACCTC
457192 TCATCT TCATCT TCATCT TCATCT TC
1 TCATCT TCATCT TCATCT TCATCT TC
457218 TTCCCTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.35, G:0.00, T:0.50
Consensus pattern (6 bp):
TCATCT
Found at i:465804 original size:15 final size:17
Alignment explanation
Indices: 465776--465807 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
465766 CGCCGCTGCT
465776 GCACACACAGCCGCCGC
1 GCACACACAGCCGCCGC
465793 GCACAC-CA-CCGCCGC
1 GCACACACAGCCGCCGC
465808 CCCTACAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.22, C:0.56, G:0.22, T:0.00
Consensus pattern (17 bp):
GCACACACAGCCGCCGC
Found at i:465806 original size:18 final size:18
Alignment explanation
Indices: 465755--465808 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
465745 CATCCTGTGA
* *
465755 CGCACCACCAGCGCCGCTG
1 CGCA-CACCACCGCCGCCG
*
465774 CTGCACA-CACAGCCGCCG
1 C-GCACACCACCGCCGCCG
465792 CGCACACCACCGCCGCC
1 CGCACACCACCGCCGCC
465809 CCTACAGCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.17
18 18 0.62
19 3 0.10
20 3 0.10
ACGTcount: A:0.19, C:0.56, G:0.22, T:0.04
Consensus pattern (18 bp):
CGCACACCACCGCCGCCG
Found at i:466337 original size:19 final size:20
Alignment explanation
Indices: 466310--466351 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
466300 TAGTTTCATG
* *
466310 TCTCTAAATTCTAAAT-TAT
1 TCTCCAAATTCCAAATATAT
466329 TCTCCAAATTCCAAATATAT
1 TCTCCAAATTCCAAATATAT
466349 TCT
1 TCT
466352 AATTAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (20 bp):
TCTCCAAATTCCAAATATAT
Found at i:466516 original size:2 final size:2
Alignment explanation
Indices: 466509--466544 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
466499 GGTTCATACA
466509 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
466545 TTATGACTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:468581 original size:136 final size:138
Alignment explanation
Indices: 468422--468699 Score: 357
Period size: 140 Copynumber: 2.0 Consensus size: 138
468412 TTTATCCTTG
*
468422 AGGATGTAATCACAATTATCTAACCAACTAACGAAATGAACTAATATATT-AAAAATATTAATTA
1 AGGATGTAATCACAATTATCTAACCAACTAACGAAAT-AACTAATATATTAAAAAACATTAATTA
*** ** * *
468486 AAAA-AACTTG-ATGAAGCAACATGAAATAAAAGTTACAAATGTGAGTAGTAGAA-GAGTCAAAC
65 AAAATAAAAAGCATGAAGCAACATGAAATAAAAAATACAAATATGAGTA-TAGAAGGAATCAAAC
468548 TCGAGACTTA
129 TCGAGACTTA
* * * *
468558 AGGATTTAATTACAATTATCTAACCATCTAACGAAATAACTAATATGTTAAAAAACATTAATTAA
1 AGGATGTAATCACAATTATCTAACCAACTAACGAAATAACTAATATATTAAAAAACATTAATTAA
* * *
468623 AAATTTAAAAAGCTTGAAGCAACATGAAATAAAAAATACAAATATTAGTATCGAAGGAATCAAAC
66 AAA--TAAAAAGCATGAAGCAACATGAAATAAAAAATACAAATATGAGTATAGAAGGAATCAAAC
468688 TCGAGACTTA
129 TCGAGACTTA
468698 AG
1 AG
468700 AATAAAAACA
Statistics
Matches: 121, Mismatches: 15, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
135 11 0.09
136 51 0.42
139 7 0.06
140 52 0.43
ACGTcount: A:0.50, C:0.12, G:0.12, T:0.26
Consensus pattern (138 bp):
AGGATGTAATCACAATTATCTAACCAACTAACGAAATAACTAATATATTAAAAAACATTAATTAA
AAATAAAAAGCATGAAGCAACATGAAATAAAAAATACAAATATGAGTATAGAAGGAATCAAACTC
GAGACTTA
Found at i:468722 original size:140 final size:136
Alignment explanation
Indices: 468432--468733 Score: 322
Period size: 140 Copynumber: 2.2 Consensus size: 136
468422 AGGATGTAAT
* * * ***
468432 CACAATTATCTAACCAACTAACGAAATGAACTAATATATTAAAAATATTAATTAAAAAAACTTGA
1 CACAATCATCTAACCATCTAACGAAATGAACTAATATATTAAAAACATTAATTAAAAAAAAAAGA
** * * *
468497 TGAAGCAACATGAAATAAAAGTTACAAATGTGAGTAGTAGAAGAGTCAAACTCGAGACTTAAGGA
66 TGAAGCAACATGAAATAAAAAATACAAATATGAGTAGTAGAAGAATCAAACTCGAGACTTAAGAA
** *
468562 TTTAAT
131 TAAAAA
* * *
468568 TACAATTATCTAACCATCTAACGAAAT-AACTAATATGTTAAAAAACATTAATTAAAAATTTAAA
1 CACAATCATCTAACCATCTAACGAAATGAACTAATATATT-AAAAACATTAATTAAAAA---AAA
* * *
468632 AAGCTTGAAGCAACATGAAATAAAAAATACAAATATTAGTA-TCGAAGGAATCAAACTCGAGACT
62 AAG-ATGAAGCAACATGAAATAAAAAATACAAATATGAGTAGTAGAA-GAATCAAACTCGAGACT
468696 TAAGAATAAAAA
125 TAAGAATAAAAA
* *
468708 CACTAA-CATTTAACCATCTCACGAAA
1 CAC-AATCATCTAACCATCTAACGAAA
468734 ACTAAAAAAA
Statistics
Matches: 137, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
135 11 0.08
136 42 0.31
139 7 0.05
140 75 0.55
141 2 0.01
ACGTcount: A:0.51, C:0.14, G:0.11, T:0.25
Consensus pattern (136 bp):
CACAATCATCTAACCATCTAACGAAATGAACTAATATATTAAAAACATTAATTAAAAAAAAAAGA
TGAAGCAACATGAAATAAAAAATACAAATATGAGTAGTAGAAGAATCAAACTCGAGACTTAAGAA
TAAAAA
Found at i:477759 original size:5 final size:5
Alignment explanation
Indices: 477751--477781 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
477741 TTAGCCTGGC
*
477751 CTGCT CTGCT CTGCT CTGCT CTGCC CTGCT C
1 CTGCT CTGCT CTGCT CTGCT CTGCT CTGCT C
477782 GACTCTGTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.45, G:0.19, T:0.35
Consensus pattern (5 bp):
CTGCT
Found at i:479172 original size:3 final size:3
Alignment explanation
Indices: 479164--479192 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
479154 GTGAGCTGCC
479164 GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
1 GGA GGA GGA GGA GGA GGA GGA GGA GGA GG
479193 CCAGAAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:483288 original size:19 final size:19
Alignment explanation
Indices: 483264--483308 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
483254 ATTCAAAATA
483264 AAATTATTAATGTAATATT
1 AAATTATTAATGTAATATT
483283 AAATTATTAATGTAATATT
1 AAATTATTAATGTAATATT
483302 AAATTAT
1 AAATTAT
483309 ATCACTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (19 bp):
AAATTATTAATGTAATATT
Found at i:488797 original size:39 final size:39
Alignment explanation
Indices: 488677--488868 Score: 149
Period size: 39 Copynumber: 4.9 Consensus size: 39
488667 TCATAATTTG
* *
488677 GGTAAGAGATCGGATGGTTTTCAATCTGCCACATGATCAA
1 GGTAAGAGATCGGATGG-TTGCAATCTGCCACATGATCGA
* * * * * **
488717 GGTAAGAGATTGG-TTGATG-ATGATTTGTCCTA-TTTCTCGA
1 GGTAAGAGATCGGATGGTTGCA--ATCTG-CC-ACATGATCGA
*
488757 GGTAAAAGATCGGATGGTTGCAATCTGCCACATGATCGA
1 GGTAAGAGATCGGATGGTTGCAATCTGCCACATGATCGA
* * * * * *
488796 GGTCAGAGATTGGATGATTACGATCTGCCTCATGATCG-
1 GGTAAGAGATCGGATGGTTGCAATCTGCCACATGATCGA
*
488834 GGATAAGAGATCGGATGGTTGCAATCTACCACATG
1 GG-TAAGAGATCGGATGGTTGCAATCTGCCACATG
488869 CTTAGGGTAA
Statistics
Matches: 113, Mismatches: 31, Indels: 17
0.70 0.19 0.11
Matches are distributed among these distances:
37 1 0.01
38 4 0.04
39 69 0.61
40 33 0.29
41 5 0.04
42 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (39 bp):
GGTAAGAGATCGGATGGTTGCAATCTGCCACATGATCGA
Found at i:488880 original size:39 final size:38
Alignment explanation
Indices: 488757--488883 Score: 137
Period size: 39 Copynumber: 3.3 Consensus size: 38
488747 TATTTCTCGA
*
488757 GGTAAAAGATCGGATGGTTGCAATCTGCCACATGATCG
1 GGTAAGAGATCGGATGGTTGCAATCTGCCACATGATCG
* * * * * *
488795 AGGTCAGAGATTGGATGATTACGATCTGCCTCATGATCG
1 -GGTAAGAGATCGGATGGTTGCAATCTGCCACATGATCG
* * *
488834 GGATAAGAGATCGGATGGTTGCAATCTACCACATGCTTAG
1 GG-TAAGAGATCGGATGGTTGCAATCTGCCACATG-ATCG
488874 GGTAAGAGAT
1 GGTAAGAGAT
488884 TTGCTGATAA
Statistics
Matches: 70, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
38 2 0.03
39 64 0.91
40 4 0.06
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (38 bp):
GGTAAGAGATCGGATGGTTGCAATCTGCCACATGATCG
Found at i:488952 original size:38 final size:39
Alignment explanation
Indices: 488757--489020 Score: 104
Period size: 39 Copynumber: 6.8 Consensus size: 39
488747 TATTTCTCGA
* * * * *
488757 GGTAAAAGATCGGATGGTTGCAATCTGCCACATGATCGA
1 GGTAAAAGATCAGATGGTTACAATCTGCCTCAAGATCGG
* * ** * * *
488796 GGTCAGAGATTGGATGATTACGATCTGCCTCATGATCGG
1 GGTAAAAGATCAGATGGTTACAATCTGCCTCAAGATCGG
* * * * * * * * **
488835 GATAAGAGATCGGATGGTTGCAATCTACCACATGCTTAG
1 GGTAAAAGATCAGATGGTTACAATCTGCCTCAAGATCGG
* ** * * * * * * *
488874 GGTAAGAGATTTGCTGATAATAATTTGTCCT-AGGTTCGG
1 GGTAAAAGATCAGATGGTTACAATCTG-CCTCAAGATCGG
488913 GGTAAAAGATCAGATGGTTACAATCTGCCT-AAGATCGG
1 GGTAAAAGATCAGATGGTTACAATCTGCCTCAAGATCGG
* * * ** * *
488951 GGTAAGAGAT-TGACT-GATAGTGATCTGCCTCAAGCTTGG
1 GGTAAAAGATCAGA-TGGTTA-CAATCTGCCTCAAGATCGG
* *
488990 GGTAAAAGATCAGATGGTTGCAATTTGCCTC
1 GGTAAAAGATCAGATGGTTACAATCTGCCTC
489021 GAGCTTGGGG
Statistics
Matches: 161, Mismatches: 58, Indels: 12
0.70 0.25 0.05
Matches are distributed among these distances:
37 5 0.03
38 27 0.17
39 123 0.76
40 6 0.04
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (39 bp):
GGTAAAAGATCAGATGGTTACAATCTGCCTCAAGATCGG
Found at i:489006 original size:155 final size:156
Alignment explanation
Indices: 488676--489951 Score: 895
Period size: 155 Copynumber: 8.2 Consensus size: 156
488666 TTCATAATTT
* * * * * * * * *
488676 GGGTAAGAGATCGGATGGTTTTCAATCTGCCACATG-ATCAAGGTAAGAGATTGGTTGATGATGA
1 GGGTAAAAGATCGGATGG-TTGCAATCTGCCTCAAGCTTC-GGGTAAGAGATTTGCTGATGGTGA
* * ** * * * * * * *
488740 TTTGTCCTATTTCTCGAGGTAAAAGATCGGATGGTTGCAATCTGCCACATGATCGAGGTCAGAGA
64 TCTGCCCTA-GGCTCGGGGTAAAAGATCAGATGGTTACAATCTGCCCCAAGATCGGGGTAAGAGA
*** * * *
488805 TTGGA-TGATTACGATCTGCCTCATGATCG
128 TT-GACTGATGGTGATCTACCTCAAGCTCG
* * * * * * ** * *
488834 GGATAAGAGATCGGATGGTTGCAATCTACCACATGCTTAGGGTAAGAGATTTGCTGATAATAATT
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCTCAAGCTTCGGGTAAGAGATTTGCTGATGGTGATC
* * *
488899 TGTCCTAGGTTCGGGGTAAAAGATCAGATGGTTACAATCTG-CCTAAGATCGGGGTAAGAGATTG
66 TGCCCTAGGCTCGGGGTAAAAGATCAGATGGTTACAATCTGCCCCAAGATCGGGGTAAGAGATTG
* * *
488963 ACTGATAGTGATCTGCCTCAAGCTTG
131 ACTGATGGTGATCTACCTCAAGCTCG
* * * * * * *
488989 GGGTAAAAGATCAGATGGTTGCAATTTGCCTCGAGCTTGGGGTAAGA-TTTTGGATGATAGTGA-
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCTCAAGCTTCGGGTAAGAGATTT-GCTGATGGTGAT
* * * * * * * *
489052 CTGCCAC-AAGCTCGAGGTAAAAGATAAGATGGCTACAATCTGTCCCAGGTTTGGGGTAAGAGAT
65 CTGCC-CTAGGCTCGGGGTAAAAGATCAGATGGTTACAATCTGCCCCAAGATCGGGGTAAGAGAT
* * * * *
489116 TGACTGATGATGATCTGCCACAGGCTTG
129 TGACTGATGGTGATCTACCTCAAGCTCG
* * * * * * *
489144 AGGTAAAAGATCAGATGGTTGCAATATGTCTCAAGC-TCGATGTAAGAGATTGGCTAATGGTGAT
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCTCAAGCTTCG-GGTAAGAGATTTGCTGATGGTGAT
* * * * * * * * *
489208 CTGCCCCAAGCTC-GGGTAAAAGATCGGATGGCTACAATTTACCCCATGATTGAGGTAAGAGATT
65 CTGCCCTAGGCTCGGGGTAAAAGATCAGATGGTTACAATCTGCCCCAAGATCGGGGTAAGAGATT
*
489272 GGCTGATGGTGATCTACCTCAAGCTCG
130 GACTGATGGTGATCTACCTCAAGCTCG
* * * * ** *
489299 GGGTAGAAGATCGGATGGCTGTAATCTGCCT-TAGGATCGGAGTATGAGA-TTGACTGATGGTGA
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCTCAAGCTTCGG-GTAAGAGATTTG-CTGATGGTGA
* ** * *
489362 TTTGCCCTAGGCTCGGGGTAAAAGATCAGAATACTGT--AATTTGCCCTAAGATCGGGGTAAGAG
64 TCTGCCCTAGGCTCGGGGTAAAAGATCAG-ATGGT-TACAATCTGCCCCAAGATCGGGGTAAGAG
*
489425 ATTGACTGATGGTGATTTACCTCAAGCTCG
127 ATTGACTGATGGTGATCTACCTCAAGCTCG
* * ** * ***
489455 GGATAAAAGATCGAATGACTGCAATCTACCTCAAGC-TCGGGGTAAGAGATTAATTGATGGTGAT
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCTCAAGCTTC-GGGTAAGAGATTTGCTGATGGTGAT
* * * * * * * ** * *
489519 TTACCCTAAGCTCGGGGTAAAAGTTCGGATGGTTGCAATCTGCCTCAAGATCGAAGTAAAAGACT
65 CTGCCCTAGGCTCGGGGTAAAAGATCAGATGGTTACAATCTGCCCCAAGATCGGGGTAAGAGATT
* * *
489584 -AGTTGATGGTGATCTACCCCAACCTCG
130 GA-CTGATGGTGATCTACCTCAAGCTCG
* ** * ** *
489611 GGGTAAAAGATCAGATTATTGCAATCTGCC-CTAGGATCGAGGTAAGAGA-TTGATTGATGGTGA
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCTCAAGCTTCG-GGTAAGAGATTTG-CTGATGGTGA
* * ** *
489674 TCTG-CCTCAGGTTCAGGGTAAAAGATC-GAATGGTTATTATCTGCCCCAAGCTCGGGGTAAGAG
64 TCTGCCCT-AGGCTCGGGGTAAAAGATCAG-ATGGTTACAATCTGCCCCAAGATCGGGGTAAGAG
* *
489737 ATTGACTGATGGTGATCTACCCCAAGCTCA
127 ATTGACTGATGGTGATCTACCTCAAGCTCG
* *** * * * *
489767 GGGTAAAAAATCGGATAACTGCAATTTACC-CAAGC-TCGGGGTAAGAGA-TTGACTAATGATGA
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCTCAAGCTTC-GGGTAAGAGATTTG-CTGATGGTGA
* * * * * *
489829 TCTACCCTAGGCTCGAGGTAAAAGATCAGATGGTTGCAATCTGCCCCAAGCTTGGGGTAAGAGAC
64 TCTGCCCTAGGCTCGGGGTAAAAGATCAGATGGTTACAATCTGCCCCAAGATCGGGGTAAGAGAT
* *
489894 TGACTGATGGTGATCTGCC-CTTAGCTCG
129 TGACTGATGGTGATCTACCTC-AAGCTCG
* * *
489922 GGGTAAAAGATCGAATGTTTGCAATTTGCC
1 GGGTAAAAGATCGGATGGTTGCAATCTGCC
489952 CCATGATATG
Statistics
Matches: 893, Mismatches: 194, Indels: 65
0.78 0.17 0.06
Matches are distributed among these distances:
154 46 0.05
155 419 0.47
156 358 0.40
157 51 0.06
158 19 0.02
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (156 bp):
GGGTAAAAGATCGGATGGTTGCAATCTGCCTCAAGCTTCGGGTAAGAGATTTGCTGATGGTGATC
TGCCCTAGGCTCGGGGTAAAAGATCAGATGGTTACAATCTGCCCCAAGATCGGGGTAAGAGATTG
ACTGATGGTGATCTACCTCAAGCTCG
Found at i:489019 original size:39 final size:39
Alignment explanation
Indices: 488911--489033 Score: 124
Period size: 39 Copynumber: 3.2 Consensus size: 39
488901 TCCTAGGTTC
* * *
488911 GGGGTAAAAGATCAGATGGTTACAATCTGCCT-AAGATC
1 GGGGTAAAAGATCAGATGGTTGCAATCTGCCTCAAGCTT
* * * * **
488949 GGGGTAAGAGAT-TGACTGATAGTGATCTGCCTCAAGCTT
1 GGGGTAAAAGATCAGA-TGGTTGCAATCTGCCTCAAGCTT
* *
488988 GGGGTAAAAGATCAGATGGTTGCAATTTGCCTCGAGCTT
1 GGGGTAAAAGATCAGATGGTTGCAATCTGCCTCAAGCTT
489027 GGGGTAA
1 GGGGTAA
489034 GATTTTGGAT
Statistics
Matches: 65, Mismatches: 17, Indels: 5
0.75 0.20 0.06
Matches are distributed among these distances:
37 2 0.03
38 22 0.34
39 39 0.60
40 2 0.03
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (39 bp):
GGGGTAAAAGATCAGATGGTTGCAATCTGCCTCAAGCTT
Found at i:489356 original size:78 final size:77
Alignment explanation
Indices: 488676--489954 Score: 866
Period size: 78 Copynumber: 16.4 Consensus size: 77
488666 TTCATAATTT
* * * * ** ** *
488676 GGGTAAGAGATCGGATGGTTTTCAATCTGCCACATGATCAAGGTAAGAGATTGGTTGATGATGAT
1 GGGTAAAAGATCGGATGG-TTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGAT
* * **
488741 TTGTCCTATTTCTCG
65 CTG-CCCA-AGCTCG
* * * * * ***
488756 AGGTAAAAGATCGGATGGTTGCAATCTGCCACATGATCGAGGTCAGAGATTGGA-TGATTACGAT
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATT-GACTGATGGTGAT
* *
488820 CTGCCTCATGATCG
65 CTGCC-CAAGCTCG
* * * * * * ** ** *
488834 GGATAAGAGATCGGATGGTTGCAATCTACCACATGCTTAGGGTAAGAGATTTG-CTGATAATAAT
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGA-TTGACTGATGGTGAT
* * * *
488898 TTGTCCTAGGTTCG
65 CTG-CCCAAGCTCG
* * * *
488912 GGGTAAAAGATCAGATGGTTACAATCTG-CCTAAGATCGGGGTAAGAGATTGACTGATAGTGATC
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGATC
*
488976 TGCCTCAAGCTTG
66 TGCC-CAAGCTCG
* * * * * * ** *
488989 GGGTAAAAGATCAGATGGTTGCAATTTGCCTCGAGCTTGGGGTAAGATTTTGGA-TGATAGTGA-
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATT-GACTGATGGTGAT
489052 CTGCCACAAGCTCG
65 CTGCC-CAAGCTCG
* ** * * * * * * *
489066 AGGTAAAAGATAAGATGGCTACAATCTGTCCCAGGTTTGGGGTAAGAGATTGACTGATGATGATC
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGATC
* *
489131 TGCCACAGGCTTG
66 TGCC-CAAGCTCG
* * * * * * ** * *
489144 AGGTAAAAGATCAGATGGTTGCAATATGTCTCAAGCTCGATGTAAGAGATTGGCTAATGGTGATC
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGATC
489209 TGCCCCAAGCTC-
66 TG-CCCAAGCTCG
* * * * * * * *
489221 GGGTAAAAGATCGGATGGCTACAATTTACCCCATGATTGAGGTAAGAGATTGGCTGATGGTGATC
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGATC
*
489286 TACCTCAAGCTCG
66 TGCC-CAAGCTCG
* * * ** * * * *
489299 GGGTAGAAGATCGGATGGCTGTAATCTGCCTTAGGATCGGAGTATGAGATTGACTGATGGTGATT
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGATC
*
489364 TGCCCTAGGCTCG
66 TGCCC-AAGCTCG
* ** * * *
489377 GGGTAAAAGATCAGAAT-ACTGTAATTTGCCCTAAGATCGGGGTAAGAGATTGACTGATGGTGAT
1 GGGTAAAAGATC-GGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGAT
* *
489441 TTACCTCAAGCTCG
65 CTGCC-CAAGCTCG
* * ** * * * * * *
489455 GGATAAAAGATCGAATGACTGCAATCTACCTCAAGCTCGGGGTAAGAGATTAATTGATGGTGATT
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGATC
*
489520 TACCCTAAGCTCG
66 TGCCC-AAGCTCG
* * ** * * *
489533 GGGTAAAAGTTCGGATGGTTGCAATCTGCCTCAAGATCGAAGTAAAAGACT-AGTTGATGGTGAT
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGA-CTGATGGTGAT
* *
489597 CTACCCCAACCTCG
65 CT-GCCCAAGCTCG
* ** * * * *
489611 GGGTAAAAGATCAGATTATTGCAATCTGCCCTAGGATCGAGGTAAGAGATTGATTGATGGTGATC
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGATC
* * *
489676 TGCCTCAGGTTCA
66 TGCC-CAAGCTCG
* *** *
489689 GGGTAAAAGATCGAATGGTTATTATCTGCCCCAAGCTCGGGGTAAGAGATTGACTGATGGTGATC
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGATC
* *
489754 TACCCCAAGCTCA
66 T-GCCCAAGCTCG
* *** ** * * *
489767 GGGTAAAAAATCGGATAACTGCAAT-TTACCCAAGCTCGGGGTAAGAGATTGACTAATGATGATC
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGATC
* *
489831 TACCCTAGGCTCG
66 TGCCC-AAGCTCG
* * * * *
489844 AGGTAAAAGATCAGATGGTTGCAATCTGCCCCAAGCTTGGGGTAAGAGACTGACTGATGGTGATC
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGATC
*
489909 TGCCCTTAGCTCG
66 TGCCC-AAGCTCG
* * *
489922 GGGTAAAAGATCGAATGTTTGCAATTTGCCCCA
1 GGGTAAAAGATCGGATGGTTGCAATCTGCCCCA
489955 TGATATGGTT
Statistics
Matches: 957, Mismatches: 216, Indels: 54
0.78 0.18 0.04
Matches are distributed among these distances:
76 12 0.01
77 242 0.25
78 627 0.66
79 59 0.06
80 17 0.02
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.27
Consensus pattern (77 bp):
GGGTAAAAGATCGGATGGTTGCAATCTGCCCCAAGATCGGGGTAAGAGATTGACTGATGGTGATC
TGCCCAAGCTCG
Found at i:489456 original size:39 final size:39
Alignment explanation
Indices: 489261--489538 Score: 153
Period size: 39 Copynumber: 7.1 Consensus size: 39
489251 CCATGATTGA
* *
489261 GGTAAGAGATTGGCTGATGGTGATCTACCTCAAGCTCGG
1 GGTAAGAGATTGACTGATGGTGATTTACCTCAAGCTCGG
* * * * * *
489300 GGT-AGA-A--GATCGGATGGCTGTAATCTGCCTTAGGATCGG
1 GGTAAGAGATTGA-CTGATGG-TG--ATTTACCTCAAGCTCGG
* * * *
489339 AGTATGAGATTGACTGATGGTGATTTGCC-CTAGGCTCGG
1 GGTAAGAGATTGACTGATGGTGATTTACCTC-AAGCTCGG
* * * * * *
489378 GGTAAAAGATCAGAAT-ACT-GTAATTTGCC-CTAAGATCGG
1 GGTAAGAGAT-TGACTGA-TGGTGATTTACCTC-AAGCTCGG
489417 GGTAAGAGATTGACTGATGGTGATTTACCTCAAGCTCGG
1 GGTAAGAGATTGACTGATGGTGATTTACCTCAAGCTCGG
* * * * ** *
489456 GATAAAAGATCGAATGACT-GCAATCTACCTCAAGCTCGG
1 GGTAAGAGATTGACTGA-TGGTGATTTACCTCAAGCTCGG
* *
489495 GGTAAGAGATTAATTGATGGTGATTTACC-CTAAGCTCGG
1 GGTAAGAGATTGACTGATGGTGATTTACCTC-AAGCTCGG
489534 GGTAA
1 GGTAA
489539 AAGTTCGGAT
Statistics
Matches: 181, Mismatches: 41, Indels: 34
0.71 0.16 0.13
Matches are distributed among these distances:
35 1 0.01
36 6 0.03
37 3 0.02
38 9 0.05
39 143 0.79
40 8 0.04
41 3 0.02
42 6 0.03
43 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.27
Consensus pattern (39 bp):
GGTAAGAGATTGACTGATGGTGATTTACCTCAAGCTCGG
Found at i:489617 original size:39 final size:39
Alignment explanation
Indices: 489413--489932 Score: 141
Period size: 39 Copynumber: 13.4 Consensus size: 39
489403 TGCCCTAAGA
* * * *
489413 TCGGGGTAAGAGATT-GACTGATGGTGATTTACCTCAAGC
1 TCGGGGTAAAAGATTAG-TTGATGGTGATCTACCCCAAGC
* * * ** *
489452 TCGGGATAAAAGA-TCGAATGACT-GCAATCTACCTCAAGC
1 TCGGGGTAAAAGATTAG-TTGA-TGGTGATCTACCCCAAGC
* * * *
489491 TCGGGGTAAGAGATTAATTGATGGTGATTTACCCTAAGC
1 TCGGGGTAAAAGATTAGTTGATGGTGATCTACCCCAAGC
* * * *
489530 TCGGGGTAAAAG-TTCG--GATGGTTGCAATCTGCCTCAAGA
1 TCGGGGTAAAAGATTAGTTGATGG-TG--ATCTACCCCAAGC
** * *
489569 TCGAAGTAAAAGACTAGTTGATGGTGATCTACCCCAACC
1 TCGGGGTAAAAGATTAGTTGATGGTGATCTACCCCAAGC
* * ** * * * *
489608 TCGGGGTAAAAGATCAGATT-ATTGCAATCTGCCCTAGGA
1 TCGGGGTAAAAGATTAG-TTGATGGTGATCTACCCCAAGC
* * * * * *
489647 TCGAGGTAAGAGATT-GATTGATGGTGATCTGCCTCAGGT
1 TCGGGGTAAAAGATTAG-TTGATGGTGATCTACCCCAAGC
* * * * ** * *
489686 TCAGGGTAAAAGA-TCGAATGGTTATTATCTGCCCCAAGC
1 TCGGGGTAAAAGATTAG-TTGATGGTGATCTACCCCAAGC
* *
489725 TCGGGGTAAGAGATT-GACTGATGGTGATCTACCCCAAGC
1 TCGGGGTAAAAGATTAG-TTGATGGTGATCTACCCCAAGC
* * ** * * ** *
489764 TCAGGGTAAAAAATCGGATAACT-GCAATTTA-CCCAAGC
1 TCGGGGTAAAAGATTAGTTGA-TGGTGATCTACCCCAAGC
* * * * * *
489802 TCGGGGTAAGAGATT-GACTAATGATGATCTACCCTAGGC
1 TCGGGGTAAAAGATTAG-TTGATGGTGATCTACCCCAAGC
* * * * * ** *
489841 TCGAGGTAAAAGATCAGATGGTTGCAATCTGCCCCAAGC
1 TCGGGGTAAAAGATTAGTTGATGGTGATCTACCCCAAGC
* * * * * **
489880 TTGGGGTAAGAGACT-GACTGATGGTGATCTGCCCTTAGC
1 TCGGGGTAAAAGATTAG-TTGATGGTGATCTACCCCAAGC
489919 TCGGGGTAAAAGAT
1 TCGGGGTAAAAGAT
489933 CGAATGTTTG
Statistics
Matches: 340, Mismatches: 120, Indels: 42
0.68 0.24 0.08
Matches are distributed among these distances:
36 5 0.01
37 4 0.01
38 35 0.10
39 279 0.82
40 10 0.03
41 2 0.01
42 5 0.01
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.25
Consensus pattern (39 bp):
TCGGGGTAAAAGATTAGTTGATGGTGATCTACCCCAAGC
Found at i:490015 original size:41 final size:41
Alignment explanation
Indices: 489970--490134 Score: 222
Period size: 41 Copynumber: 4.0 Consensus size: 41
489960 TGGTTAAGAA
489970 ATTGGAATCTTCAATCTGCCCTTCTTGATTAAAGGTAAAAG
1 ATTGGAATCTTCAATCTGCCCTTCTTGATTAAAGGTAAAAG
* * *
490011 ATTGGAATATTCAATATGCCCTTCTTGATTAAGGGTAAAAG
1 ATTGGAATCTTCAATCTGCCCTTCTTGATTAAAGGTAAAAG
* *
490052 ATTGGAATCTTCAATCTGCCTTTCTTGACTAAAGGTAAAAG
1 ATTGGAATCTTCAATCTGCCCTTCTTGATTAAAGGTAAAAG
* ** * * * *
490093 ACTAAAATCTTCAATTTGTCATTCTTGATTAAGGGTAAAAG
1 ATTGGAATCTTCAATCTGCCCTTCTTGATTAAAGGTAAAAG
490134 A
1 A
490135 CTGAATAATG
Statistics
Matches: 108, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 108 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (41 bp):
ATTGGAATCTTCAATCTGCCCTTCTTGATTAAAGGTAAAAG
Found at i:490061 original size:82 final size:82
Alignment explanation
Indices: 489970--490134 Score: 249
Period size: 82 Copynumber: 2.0 Consensus size: 82
489960 TGGTTAAGAA
* * ** *
489970 ATTGGAATCTTCAATCTGCCCTTCTTGATTAAAGGTAAAAGATTGGAATATTCAATATGCCCTTC
1 ATTGGAATCTTCAATCTGCCCTTCTTGACTAAAGGTAAAAGACTAAAATATTCAATATGCCATTC
490035 TTGATTAAGGGTAAAAG
66 TTGATTAAGGGTAAAAG
* * * *
490052 ATTGGAATCTTCAATCTGCCTTTCTTGACTAAAGGTAAAAGACTAAAATCTTCAATTTGTCATTC
1 ATTGGAATCTTCAATCTGCCCTTCTTGACTAAAGGTAAAAGACTAAAATATTCAATATGCCATTC
490117 TTGATTAAGGGTAAAAG
66 TTGATTAAGGGTAAAAG
490134 A
1 A
490135 CTGAATAATG
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 74 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (82 bp):
ATTGGAATCTTCAATCTGCCCTTCTTGACTAAAGGTAAAAGACTAAAATATTCAATATGCCATTC
TTGATTAAGGGTAAAAG
Found at i:501945 original size:44 final size:44
Alignment explanation
Indices: 501892--501979 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
501882 TTGTAATTGG
501892 ACATTTAAATTGAAATTAAAATTTAATTTAAATATTTGTTTATT
1 ACATTTAAATTGAAATTAAAATTTAATTTAAATATTTGTTTATT
501936 ACATTTAAATTGAAATTAAAATTTAATTTAAATATTTGTTTATT
1 ACATTTAAATTGAAATTAAAATTTAATTTAAATATTTGTTTATT
501980 TTTATTATAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (44 bp):
ACATTTAAATTGAAATTAAAATTTAATTTAAATATTTGTTTATT
Found at i:503623 original size:62 final size:62
Alignment explanation
Indices: 503524--503883 Score: 567
Period size: 62 Copynumber: 5.8 Consensus size: 62
503514 ATGAAAGGGC
503524 CTGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGGT
1 CTGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGGT
* * * * **
503586 CGGATGTATTTGTGACATCGTGAGTATTACATGAGAAATGAATCTTATTACGGCCTAAAGGT
1 CTGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGGT
* * *
503648 CTGATTTCTTTTTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACAGATTAAAGGT
1 CTGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGGT
* * * *
503710 CTAATGTCTTTTTGATATCGTGAGTATTACATGAGAAATGAATCTTATTACGGACTAAAGGT
1 CTGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGGT
* *
503772 CTGATGTCTTTTTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACAGATTAAAGGT
1 CTGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGGT
* *
503834 CTAATGTCTTCGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTA
1 CTGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTA
503884 TAGATTTAAG
Statistics
Matches: 271, Mismatches: 27, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 271 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.36
Consensus pattern (62 bp):
CTGATGTCTTTGTGATATCGTGAGTATTACATGAGAAATGAATCCTATTACGGATTAAAGGT
Found at i:509513 original size:13 final size:13
Alignment explanation
Indices: 509497--509522 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
509487 AAATTATCAC
509497 TTTTAATTTGAAT
1 TTTTAATTTGAAT
509510 TTTTAATTTGAAT
1 TTTTAATTTGAAT
509523 AGTGCTCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
TTTTAATTTGAAT
Found at i:510168 original size:20 final size:20
Alignment explanation
Indices: 510143--510181 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
510133 AACCAAAACT
* *
510143 TGAACCCTTAACCTTGAACA
1 TGAACCCTAAACATTGAACA
510163 TGAACCCTAAACATTGAAC
1 TGAACCCTAAACATTGAAC
510182 CCAAACTCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.28, G:0.10, T:0.23
Consensus pattern (20 bp):
TGAACCCTAAACATTGAACA
Found at i:510233 original size:14 final size:15
Alignment explanation
Indices: 510198--510242 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
510188 TCTAGCCCAT
510198 AACCC-AAA-CACTA
1 AACCCTAAATCACTA
*
510211 AACCTTAAATCAC-A
1 AACCCTAAATCACTA
510225 AACCCTAAATC-CTA
1 AACCCTAAATCACTA
510239 AACC
1 AACC
510243 ATGAATCTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
13 5 0.19
14 19 0.70
15 3 0.11
ACGTcount: A:0.49, C:0.36, G:0.00, T:0.16
Consensus pattern (15 bp):
AACCCTAAATCACTA
Found at i:510240 original size:28 final size:28
Alignment explanation
Indices: 510208--510266 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
510198 AACCCAAACA
* *
510208 CTAAACCTTAAATCACAAACCCTAAATC
1 CTAAACCATAAATCACAAACCCAAAATC
* **
510236 CTAAACCATGAATCTTAAACCCAAAATC
1 CTAAACCATAAATCACAAACCCAAAATC
510264 CTA
1 CTA
510267 TATCCGAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.46, C:0.31, G:0.02, T:0.22
Consensus pattern (28 bp):
CTAAACCATAAATCACAAACCCAAAATC
Found at i:512420 original size:16 final size:16
Alignment explanation
Indices: 512401--512435 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
512391 ATAGGGCTGC
*
512401 AATGAAATAGAGTTGT
1 AATGAAATAAAGTTGT
*
512417 AATGGAATAAAGTTGT
1 AATGAAATAAAGTTGT
512433 AAT
1 AAT
512436 TAGTAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (16 bp):
AATGAAATAAAGTTGT
Found at i:512688 original size:34 final size:36
Alignment explanation
Indices: 512650--512718 Score: 99
Period size: 35 Copynumber: 2.0 Consensus size: 36
512640 ATATAATTAT
512650 TTTTATA-TTAAATTATATT-AAAATATT-TTTTTAG
1 TTTTATATTTAAATTAT-TTCAAAATATTATTTTTAG
*
512684 TTTTATATTTAAATTATTTCAAAATTTTATTTTTA
1 TTTTATATTTAAATTATTTCAAAATATTATTTTTA
512719 TATTTTATGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 9 0.29
35 16 0.52
36 6 0.19
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (36 bp):
TTTTATATTTAAATTATTTCAAAATATTATTTTTAG
Found at i:512986 original size:16 final size:15
Alignment explanation
Indices: 512960--512989 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
512950 CTTATATGTG
512960 AATTATTTAATATAC
1 AATTATTTAATATAC
512975 AATTATTATAATATA
1 AATTATT-TAATATA
512990 AAAAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTATTTAATATAC
Found at i:520102 original size:24 final size:23
Alignment explanation
Indices: 520059--520133 Score: 79
Period size: 24 Copynumber: 3.3 Consensus size: 23
520049 TTCTCATGAA
520059 AAAAAAATCATAAAAT---TATT
1 AAAAAAATCATAAAATAAATATT
520079 AAAAAAATCATAAAAATAAATATT
1 AAAAAAATCAT-AAAATAAATATT
*
520103 AAAAAAATTTATCAAAA-AAATA-T
1 AAAAAAA-TCAT-AAAATAAATATT
520126 AAAAAAAT
1 AAAAAAAT
520134 TTATTACATA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
20 11 0.23
21 5 0.10
22 1 0.02
23 8 0.17
24 16 0.33
25 7 0.15
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAAAAATCATAAAATAAATATT
Found at i:520128 original size:23 final size:25
Alignment explanation
Indices: 520075--520137 Score: 87
Period size: 24 Copynumber: 2.6 Consensus size: 25
520065 ATCATAAAAT
*
520075 TATTAAAAAAA-TCATAAAAATAAA
1 TATTAAAAAAATTTATAAAAATAAA
*
520099 TATTAAAAAAATTTATCAAAA-AAA
1 TATTAAAAAAATTTATAAAAATAAA
520123 TA-TAAAAAAATTTAT
1 TATTAAAAAAATTTAT
520138 TACATATTAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 13 0.36
24 16 0.44
25 7 0.19
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (25 bp):
TATTAAAAAAATTTATAAAAATAAA
Found at i:520203 original size:28 final size:28
Alignment explanation
Indices: 520172--520245 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
520162 TGATAAAAAC
* *
520172 TTATAAATATTATAAAAAATTCTAA-ATA
1 TTATAAAAATTATAAAAAA-TCTAATAAA
*
520200 TTATAAAAAATAT-AAAAATCTAATAAA
1 TTATAAAAATTATAAAAAATCTAATAAA
520227 TTATAAAAAATTATAAAAA
1 TTAT-AAAAATTATAAAAA
520246 TAATAAAACA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
26 5 0.13
27 11 0.28
28 19 0.49
29 4 0.10
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.34
Consensus pattern (28 bp):
TTATAAAAATTATAAAAAATCTAATAAA
Found at i:520246 original size:19 final size:19
Alignment explanation
Indices: 520145--520353 Score: 133
Period size: 19 Copynumber: 10.8 Consensus size: 19
520135 TATTACATAT
* *
520145 TAAAAAAATATGAAAATTGA
1 TAAAAAATTATAAAAATT-A
* *
520165 TAAAAACTTATAAATATTA
1 TAAAAAATTATAAAAATTA
* *
520184 TAAAAAATTCTAAATATTA
1 TAAAAAATTATAAAAATTA
*
520203 TAAAAAA-TATAAAAA-TC
1 TAAAAAATTATAAAAATTA
*
520220 TAATAAATTATAAAAAATTA
1 TAAAAAATTAT-AAAAATTA
*
520240 T-AAAAATAATAAAACA-TA
1 TAAAAAATTATAAAA-ATTA
* *
520258 TTAAAAATTTTATAAAAATGCA
1 -TAAAAA-ATTATAAAAAT-TA
* * *
520280 TTAAAATTCTATAAAAATCA
1 TAAAAAAT-TATAAAAATTA
** *
520300 T-AAAGTTTATAAAAAGTA
1 TAAAAAATTATAAAAATTA
*
520318 T-TAAAATTGATATAAAATTA
1 TAAAAAATT-ATA-AAAATTA
520338 TAAAAAATTATAAAAA
1 TAAAAAATTATAAAAA
520354 AAATTCATAA
Statistics
Matches: 151, Mismatches: 25, Indels: 27
0.74 0.12 0.13
Matches are distributed among these distances:
17 7 0.05
18 29 0.19
19 51 0.34
20 36 0.24
21 27 0.18
22 1 0.01
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (19 bp):
TAAAAAATTATAAAAATTA
Found at i:520272 original size:21 final size:20
Alignment explanation
Indices: 520248--520325 Score: 74
Period size: 21 Copynumber: 3.9 Consensus size: 20
520238 TATAAAAATA
*
520248 ATAAAACAT-ATTAAAAATTTT
1 ATAAAA-ATCATT-AAAATTCT
520269 ATAAAAATGCATTAAAATTCT
1 ATAAAAAT-CATTAAAATTCT
*
520290 ATAAAAATCA-TAAAGTT-T
1 ATAAAAATCATTAAAATTCT
520308 ATAAAAAGT-ATTAAAATT
1 ATAAAAA-TCATTAAAATT
520326 GATATAAAAT
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
18 9 0.18
19 13 0.26
20 4 0.08
21 21 0.42
22 3 0.06
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.35
Consensus pattern (20 bp):
ATAAAAATCATTAAAATTCT
Found at i:520354 original size:10 final size:10
Alignment explanation
Indices: 520100--520354 Score: 108
Period size: 10 Copynumber: 26.1 Consensus size: 10
520090 AAAAATAAAT
520100 ATTA-AAAAA
1 ATTATAAAAA
520109 ATTTATCAAAAA
1 A-TTAT-AAAAA
*
520121 AATATAAAAAA
1 ATTAT-AAAAA
* * *
520132 ATTTATTACAT
1 A-TTATAAAAA
520143 ATTA-AAAAA
1 ATTATAAAAA
*
520152 A-TAT-GAAA
1 ATTATAAAAA
520160 ATTGATAAAAA
1 ATT-ATAAAAA
* *
520171 CTTAT-AAAT
1 ATTATAAAAA
520180 ATTATAAAAA
1 ATTATAAAAA
* *
520190 ATTCT-AAAT
1 ATTATAAAAA
520199 ATTATAAAAA
1 ATTATAAAAA
520209 A-TAT-AAAA
1 ATTATAAAAA
* *
520217 A-TCTAATAA
1 ATTATAAAAA
520226 ATTATAAAAA
1 ATTATAAAAA
520236 ATTAT-AAAA
1 ATTATAAAAA
* *
520245 ATAATAAAAC
1 ATTATAAAAA
*
520255 A-TATTAAAA
1 ATTATAAAAA
*
520264 ATTTTATAAAA
1 ATTATA-AAAA
* *
520275 ATGCAT-TAAA
1 AT-TATAAAAA
*
520285 ATTCTATAAAA
1 ATTATA-AAAA
* *
520296 ATCAT-AAAG
1 ATTATAAAAA
*
520305 TTTAT-AAAA
1 ATTATAAAAA
* *
520314 AGTAT-TAAA
1 ATTATAAAAA
*
520323 ATTGATATAAA
1 ATT-ATAAAAA
520334 ATTATAAAAA
1 ATTATAAAAA
520344 ATTATAAAAA
1 ATTATAAAAA
520354 A
1 A
520355 AATTCATAAA
Statistics
Matches: 179, Mismatches: 47, Indels: 39
0.68 0.18 0.15
Matches are distributed among these distances:
8 13 0.07
9 58 0.32
10 62 0.35
11 36 0.20
12 10 0.06
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (10 bp):
ATTATAAAAA
Found at i:520366 original size:10 final size:9
Alignment explanation
Indices: 520143--520353 Score: 131
Period size: 9 Copynumber: 22.1 Consensus size: 9
520133 TTTATTACAT
520143 ATTA-AAAA
1 ATTATAAAA
* *
520151 AATATGAAA
1 ATTATAAAA
520160 ATTGATAAAA
1 ATT-ATAAAA
*
520170 ACTTATAAAT
1 A-TTATAAAA
520180 ATTATAAAAA
1 ATTAT-AAAA
* *
520190 ATTCTAAAT
1 ATTATAAAA
520199 ATTATAAAA
1 ATTATAAAA
*
520208 AATATAAAA
1 ATTATAAAA
*
520217 ATCTA-ATAA
1 AT-TATAAAA
520226 ATTATAAAAA
1 ATTAT-AAAA
520236 ATTATAAAA
1 ATTATAAAA
*
520245 ATAATAAAA
1 ATTATAAAA
520254 CA-TATTAAAA
1 -ATTA-TAAAA
520264 ATTTTATAAAA
1 A--TTATAAAA
*
520275 ATGCATTAAAA
1 AT-TA-TAAAA
*
520286 TTCTATAAAA
1 AT-TATAAAA
* *
520296 ATCATAAAG
1 ATTATAAAA
*
520305 TTTATAAAA
1 ATTATAAAA
* *
520314 AGTATTAAA
1 ATTATAAAA
520323 ATTGATATAAA
1 ATT-ATA-AAA
520334 ATTATAAAAA
1 ATTAT-AAAA
520344 ATTATAAAA
1 ATTATAAAA
520353 A
1 A
520354 AAATTCATAA
Statistics
Matches: 155, Mismatches: 31, Indels: 33
0.71 0.14 0.15
Matches are distributed among these distances:
8 5 0.03
9 72 0.46
10 54 0.35
11 22 0.14
12 2 0.01
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.32
Consensus pattern (9 bp):
ATTATAAAA
Found at i:520498 original size:2 final size:2
Alignment explanation
Indices: 520493--520521 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
520483 TTTATTTTTA
520493 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
520522 ATCTTTTATT
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:520946 original size:17 final size:17
Alignment explanation
Indices: 520924--520961 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
520914 TTAGGATTTT
520924 TTTATA-TTTTTATAATA
1 TTTATACTTTTTATAA-A
520941 TTTATACTTTTTTATAAA
1 TTTATAC-TTTTTATAAA
520959 TTT
1 TTT
520962 GATAAGTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.66
Consensus pattern (17 bp):
TTTATACTTTTTATAAA
Found at i:520951 original size:27 final size:29
Alignment explanation
Indices: 520895--520956 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
520885 GTTTTATTAA
* *
520895 TTTTAT-TTTTTATAATTTATTAGGATTT
1 TTTTATATTTTTATAATATATTAGGACTT
*
520923 TTTTATATTTTTATAATAT-TTA-TACTT
1 TTTTATATTTTTATAATATATTAGGACTT
520950 TTTTATA
1 TTTTATA
520957 AATTTGATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 10 0.33
28 9 0.30
29 11 0.37
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (29 bp):
TTTTATATTTTTATAATATATTAGGACTT
Found at i:521761 original size:23 final size:23
Alignment explanation
Indices: 521718--521761 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
521708 CATTGTTCGT
* *
521718 GAACATGTTCGATTAAGTTAATA
1 GAACATGTTCGATGAAATTAATA
521741 GAACATGTTCG-TGAATATTAA
1 GAACATGTTCGATGAA-ATTAA
521762 ACAAACGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (23 bp):
GAACATGTTCGATGAAATTAATA
Found at i:532413 original size:48 final size:48
Alignment explanation
Indices: 532339--532456 Score: 227
Period size: 48 Copynumber: 2.5 Consensus size: 48
532329 TGGCGTTAAC
*
532339 CACTACTGGGCCATTTCAACCTTAAAGAGAAAAGAAGGCAGACAACAT
1 CACTACTGGGCCATTTCAACCATAAAGAGAAAAGAAGGCAGACAACAT
532387 CACTACTGGGCCATTTCAACCATAAAGAGAAAAGAAGGCAGACAACAT
1 CACTACTGGGCCATTTCAACCATAAAGAGAAAAGAAGGCAGACAACAT
532435 CACTACTGGGCCATTTCAACCA
1 CACTACTGGGCCATTTCAACCA
532457 CACCCTCATC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.17
Consensus pattern (48 bp):
CACTACTGGGCCATTTCAACCATAAAGAGAAAAGAAGGCAGACAACAT
Found at i:533860 original size:19 final size:18
Alignment explanation
Indices: 533836--533883 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
533826 GTAATACTGT
533836 ATAAATATAAAATAAAAAA
1 ATAAATATAAAAT-AAAAA
* *
533855 ATAAATATAAGATAAATA
1 ATAAATATAAAATAAAAA
533873 ATAAATA-AAAA
1 ATAAATATAAAA
533884 GTTACTCCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 3 0.12
18 11 0.42
19 12 0.46
ACGTcount: A:0.75, C:0.00, G:0.02, T:0.23
Consensus pattern (18 bp):
ATAAATATAAAATAAAAA
Found at i:535923 original size:3 final size:3
Alignment explanation
Indices: 535915--535939 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
535905 AGGTCCATTA
535915 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
535940 TTGCAGAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:544196 original size:5 final size:5
Alignment explanation
Indices: 544186--544234 Score: 71
Period size: 5 Copynumber: 9.8 Consensus size: 5
544176 AGGGCACAGC
* * *
544186 AGAGT AGAGT AGAGT AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA AGAG
1 AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA AGAGA AGAG
544235 GGAGAGACAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
5 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.41, T:0.06
Consensus pattern (5 bp):
AGAGA
Done.