Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 145 of 193
Found at i:45260086 original size:11 final size:12
Alignment explanation
Indices: 45260064--45260088 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45260054 TTTAGAACCC
45260064 AAAATACAAAAA
1 AAAATACAAAAA
45260076 AAAATACAAAAA
1 AAAATACAAAAA
45260088 A
1 A
45260089 GGAAGAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAATACAAAAA
Found at i:45261941 original size:49 final size:49
Alignment explanation
Indices: 45261869--45262316 Score: 309
Period size: 49 Copynumber: 9.1 Consensus size: 49
45261859 ACAGGTTTCA
* *
45261869 GTACCATGAAGATATGAAGGGAAAGGTTTAAGTCGTAACGACGAACCTT
1 GTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTT
* * * * * * *
45261918 GTACCTCAGAAG-CACGAAGGGAAAGATTTAAGCCGCAACGATGAATCC-A
1 GTACCAC-GAAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAA-CCTT
* * * *
45261967 GTACCACGGAGATATGAAGGGAAAGGTTTAAGTCGTAACAACAAACCTT
1 GTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTT
** * * ** * * *
45262016 GTACCTTGGAAGATGA-GATGGGAAAGATTTAACCCGCAACGGCGAATCTA
1 GTACC-ACGAAGAT-ATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTT
* *
45262066 GTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACAAACCTT
1 GTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTT
* * * * * * ** * *
45262115 GTACCTCAGAAG-CACGAAGGGAAAGATTTAAGCCGTAACGGTGAAAAC-A
1 GTACCAC-GAAGATATGAAGGGAAAGGTTTAAGTCGCAACGACG-AACCTT
*
45262164 GTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTT
1 GTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTT
* * * * * ** * *
45262213 GTTCCTTAC-AAGATGA-GATGGGAAAGATTTAAGCCTCAACGGTGAATCTA
1 GTACC--ACGAAGAT-ATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTT
* * * * *
45262263 GTACCACGAAGATATGGAGAGAAAGATTTAAGTTGTAAC-AGCGAACCTT
1 GTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGA-CGAACCTT
45262312 GTACC
1 GTACC
45262317 TCAGAAACAT
Statistics
Matches: 297, Mismatches: 85, Indels: 34
0.71 0.20 0.08
Matches are distributed among these distances:
48 16 0.05
49 194 0.65
50 83 0.28
51 4 0.01
ACGTcount: A:0.37, C:0.18, G:0.26, T:0.20
Consensus pattern (49 bp):
GTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTT
Found at i:45262081 original size:99 final size:98
Alignment explanation
Indices: 45261868--45262388 Score: 591
Period size: 98 Copynumber: 5.3 Consensus size: 98
45261858 TACAGGTTTC
*
45261868 AGTACCATGAAGATATGAAGGGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAGAAGCAC
1 AGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAGAAGCAC
* *
45261933 GAAGGGAAAGATTTAAGCCGCAACGATGAATCC
66 GAAGGGAAAGATTTAAGCCGCAACGGTGAATCT
* * * ** *
45261966 AGTACCACGGAGATATGAAGGGAAAGGTTTAAGTCGTAACAACAAACCTTGTACCTTGGAAG-AT
1 AGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAGAAGCAC
* *
45262030 GAGATGGGAAAGATTTAACCCGCAACGGCGAATCT
66 GA-A-GGGAAAGATTTAAGCCGCAACGGTGAATCT
* * *
45262065 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACAAACCTTGTACCTCAGAAGCAC
1 AGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAGAAGCAC
* *
45262130 GAAGGGAAAGATTTAAGCCGTAACGGTGAAAAC-
66 GAAGGGAAAGATTTAAGCCGCAACGGTG-AATCT
* * * * * *
45262163 AGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTGTTCCTTACAAG-AT
1 AGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAGAAGCAC
*
45262227 GAGATGGGAAAGATTTAAGCCTCAACGGTGAATCT
66 GA-A-GGGAAAGATTTAAGCCGCAACGGTGAATCT
* * * * *
45262262 AGTACCACGAAGATATGGAGAGAAAGATTTAAGTTGTAAC-AGCGAACCTTGTACCTCAGAAACA
1 AGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGTAACGA-CGAACCTTGTACCTCAGAAGCA
* * * * * * * * *
45262326 TGAAAGGAAATATTGAAGCCACAACAGCGAGTCC
65 CGAAGGGAAAGATTTAAGCCGCAACGGTGAATCT
* * * *
45262360 GGTACCATGAAGATTTGACGGGAAAGGTT
1 AGTACCACGAAGATATGAAGGGAAAGGTT
45262389 ATGACCGCGA
Statistics
Matches: 357, Mismatches: 57, Indels: 18
0.83 0.13 0.04
Matches are distributed among these distances:
97 6 0.02
98 183 0.51
99 161 0.45
100 7 0.02
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.19
Consensus pattern (98 bp):
AGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAGAAGCAC
GAAGGGAAAGATTTAAGCCGCAACGGTGAATCT
Found at i:45262407 original size:197 final size:196
Alignment explanation
Indices: 45261868--45262388 Score: 702
Period size: 197 Copynumber: 2.6 Consensus size: 196
45261858 TACAGGTTTC
* *
45261868 AGTACCATGAAGATATGAAGGGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAGAAGCAC
1 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAGAAGCAC
*
45261933 GAAGGGAAAGATTTAAGCCGCAACGATGAATCCAGTACCACGGAGATATGAAGGGAAAGGTTTAA
66 GAAGGGAAAGATTTAAGCCGCAACG-TGAATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAA
* * * **
45261998 GTCGTAACAACAAACCTTGTACCTTGGAAGATGAGATGGGAAAGATTTAACCCGCAACGGCGAAT
130 GTCGCAACAGCGAACCTTGTACCTTACAAGATGAGATGGGAAAGATTTAACCCGCAACGGCGAAT
45262063 CT
195 CT
* *
45262065 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACGACAAACCTTGTACCTCAGAAGCAC
1 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAGAAGCAC
* **
45262130 GAAGGGAAAGATTTAAGCCGTAACGGTGAAAACAGTACCACGAAGATATGAAGGGAAAGGTTTAA
66 GAAGGGAAAGATTTAAGCCGCAAC-GTGAATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAA
* * * * *
45262195 GTCGCAACGGCGAACCTTGTTCCTTACAAGATGAGATGGGAAAGATTTAAGCCTCAACGGTGAAT
130 GTCGCAACAGCGAACCTTGTACCTTACAAGATGAGATGGGAAAGATTTAACCCGCAACGGCGAAT
45262260 CT
195 CT
* * * *
45262262 AGTACCACGAAGATATGGAGAGAAAGATTTAAGTTGTAAC-AGCGAACCTTGTACCTCAGAAACA
1 AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGTAACGA-CGAACCTTGTACCTCAGAAGCA
* * * * * * * * * * *
45262326 TGAAAGGAAATATTGAAGCCACAACAGCGAGTCCGGTACCATGAAGATTTGACGGGAAAGGTT
65 CGAAGGGAAAGATTTAAGCCGCAAC-GTGAATCCAGTACCACGAAGATATGAAGGGAAAGGTT
45262389 ATGACCGCGA
Statistics
Matches: 283, Mismatches: 39, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
196 1 0.00
197 281 0.99
198 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.26, T:0.19
Consensus pattern (196 bp):
AGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGTAACGACGAACCTTGTACCTCAGAAGCAC
GAAGGGAAAGATTTAAGCCGCAACGTGAATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAG
TCGCAACAGCGAACCTTGTACCTTACAAGATGAGATGGGAAAGATTTAACCCGCAACGGCGAATC
T
Found at i:45263525 original size:19 final size:19
Alignment explanation
Indices: 45263476--45263525 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
45263466 CTCCTCGGCT
*
45263476 CCCAAGATCG-TTCTTCTG
1 CCCAAGATCGTTTCCTCTG
*
45263494 CCCGAGA-CGTTTCCTCTG
1 CCCAAGATCGTTTCCTCTG
45263512 CCCAAGATCGTTTC
1 CCCAAGATCGTTTC
45263526 TCGATCCCCG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
17 2 0.07
18 19 0.70
19 6 0.22
ACGTcount: A:0.16, C:0.36, G:0.18, T:0.30
Consensus pattern (19 bp):
CCCAAGATCGTTTCCTCTG
Found at i:45283099 original size:41 final size:42
Alignment explanation
Indices: 45283018--45283097 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 42
45283008 AATATTTTTA
*
45283018 TTTAATTTAGAGTTTTTTTAAGGAGAGAAAATTAATTTTGGG
1 TTTAATTTAGAGTTTTTTTAAGGAGACAAAATTAATTTTGGG
*
45283060 TTTAGTTTATGAGTTTTTTTAA-GA-ACAAAATTATATTT
1 TTTAATTTA-GAGTTTTTTTAAGGAGACAAAATTA-ATTT
45283098 GGATAAGGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 8 0.24
42 14 0.41
43 12 0.35
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (42 bp):
TTTAATTTAGAGTTTTTTTAAGGAGACAAAATTAATTTTGGG
Found at i:45284366 original size:12 final size:12
Alignment explanation
Indices: 45284349--45284374 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
45284339 TTATAAACTC
45284349 AAAATAAAATAA
1 AAAATAAAATAA
45284361 AAAATAAAATAA
1 AAAATAAAATAA
45284373 AA
1 AA
45284375 TAATTCTAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:45284914 original size:13 final size:12
Alignment explanation
Indices: 45284887--45284932 Score: 51
Period size: 11 Copynumber: 3.9 Consensus size: 12
45284877 ATGATAATAA
45284887 ATTTAATTTTAT
1 ATTTAATTTTAT
*
45284899 ATTTATATTTTTT
1 ATTTA-ATTTTAT
*
45284912 A-TTAATTTAAT
1 ATTTAATTTTAT
45284923 -TTTAATTTTA
1 ATTTAATTTTA
45284933 AAAAATAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
11 13 0.46
12 8 0.29
13 7 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATTTAATTTTAT
Found at i:45295336 original size:17 final size:16
Alignment explanation
Indices: 45295305--45295338 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
45295295 TCAATAAAAA
*
45295305 TAAAATTATTAAATAT
1 TAAAATAATTAAATAT
45295321 TAAAATAATATAAATAT
1 TAAAATAAT-TAAATAT
45295338 T
1 T
45295339 TTTAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATAATTAAATAT
Found at i:45305361 original size:22 final size:22
Alignment explanation
Indices: 45305319--45305361 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
45305309 TGAACGGAAT
**
45305319 AAAAAAAAAGGTTTTTTTTGAC
1 AAAAAAAAAGGTTTTAATTGAC
45305341 AAAAAAAAA-GTATTTAATTGA
1 AAAAAAAAAGGT-TTTAATTGA
45305362 TTAAAATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (22 bp):
AAAAAAAAAGGTTTTAATTGAC
Found at i:45307617 original size:59 final size:59
Alignment explanation
Indices: 45307513--45308098 Score: 738
Period size: 58 Copynumber: 10.0 Consensus size: 59
45307503 AAGAAACGAC
* * * *** * *
45307513 GAAATCGGGGTTGAAAATGAGACTTTTGGATA-TCCGGGGGAAAAATAGTAATTTTTGGT
1 GAAATCGGGGTTAAAAATG-GAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
* * * *
45307572 TAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTAAAATAGTAA--TTTGGT
1 GAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
**
45307629 GAAATCAAGGTTAAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
1 GAAATCGGGGTT-AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
* * * *
45307689 AAAAAT-GGGGTTAAAAATGGAATTTTGGGAAGTTCAGGGGTAAAATGGCAATTTTTGGT
1 -GAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
*
45307748 GAAATTGGGGTTAAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
1 GAAATCGGGGTT-AAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
* * ** *
45307808 GAAATTGGGGTTAAAAATGGAATTTTGGGAAGTTCGGGGGT-AAATGGCAATTTTTGGT
1 GAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
* * *
45307866 GAAATTGGGTTTAAAAATGAAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
1 GAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
* *
45307925 GAAACCGAGGTT-AAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
1 GAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
* * *
45307983 GAAACCGAGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT-AAATGGAAATTTTTGG-
1 GAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
* * * **
45308040 CAAGATCGGGGTTAAAAACGGAATTTTAGAAAGTTCGGGGGTAAAATGGTAATTTTTGG
1 GAA-ATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGG
45308099 ACCATCCAGG
Statistics
Matches: 468, Mismatches: 48, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
57 18 0.04
58 206 0.44
59 174 0.37
60 66 0.14
61 4 0.01
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.32
Consensus pattern (59 bp):
GAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGTAAAATGGTAATTTTTGGT
Found at i:45308096 original size:117 final size:119
Alignment explanation
Indices: 45307549--45308098 Score: 758
Period size: 117 Copynumber: 4.7 Consensus size: 119
45307539 TGGATATCCG
* * * * * *
45307549 GGGGAAAAATAGTAATTTTTGGTTAAATCAGGGTTAAAAATGGAATTTTAGAAAGTTTAGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTA
* *
45307614 AAATAGTAA--TTTGGTGAAATCAAGGTTAAAAAATGGAATTTTGGAAAGTTTA
66 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAATGGAATTTTGGAAAGTTTA
* *
45307666 GGGGTAAAATGGTAATTTTTGGTAAAAAT-GGGGTTAAAAATGGAATTTTGGGAAGTTCAGGGGT
1 GGGGTAAAATGGTAATTTTTGGT-GAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGT
* * *
45307730 AAAATGGCAATTTTTGGTGAAATTGGGGTTAAAAAATGGAATTTTGGAAAGTTTA
65 AAAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAATGGAATTTTGGAAAGTTTA
* * *
45307785 GGGGTAAAATGGTAATTTTTGGTGAAATTGGGGTTAAAAATGGAATTTTGGGAAGTTCGGGGGT-
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTA
* * * *
45307849 AAATGGCAATTTTTGGTGAAATTG-GGTTTAAAAATGAAATTTTGGAAAGTTTA
66 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAATGGAATTTTGGAAAGTTTA
* * *
45307902 GGGGTAAAATGGTAATTTTTGGTGAAACCGAGGTT-AAAATGGAATTTTGGAAAGTTTAGGGGTA
1 GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTA
*
45307966 AAATGGTAATTTTTGGTGAAACCGAGGTT-AAAAATGGAATTTTGGAAAGTTTA
66 AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAATGGAATTTTGGAAAGTTTA
* * * * *
45308019 GGGGT-AAATGGAAATTTTTGG-CAAGATCGGGGTTAAAAACGGAATTTTAGAAAGTTCGGGGGT
1 GGGGTAAAATGGTAATTTTTGGTGAA-ATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGT
45308082 AAAATGGTAATTTTTGG
65 AAAATGGTAATTTTTGG
45308099 ACCATCCAGG
Statistics
Matches: 391, Mismatches: 34, Indels: 16
0.89 0.08 0.04
Matches are distributed among these distances:
115 2 0.01
116 47 0.12
117 209 0.53
118 36 0.09
119 97 0.25
ACGTcount: A:0.35, C:0.03, G:0.29, T:0.33
Consensus pattern (119 bp):
GGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTCAGGGGTA
AAATGGTAATTTTTGGTGAAATCGAGGTTAAAAAATGGAATTTTGGAAAGTTTA
Found at i:45309789 original size:24 final size:26
Alignment explanation
Indices: 45309761--45309818 Score: 75
Period size: 28 Copynumber: 2.2 Consensus size: 26
45309751 GGTTTGGGCC
45309761 AATTGGG-CCAA-TGAATTTGTTTGT
1 AATTGGGCCCAATTGAATTTGTTTGT
*
45309785 AATTGGGCCCCAATTTGAGTTTGTTTGT
1 AATTGGG-CCCAA-TTGAATTTGTTTGT
45309813 AATTGG
1 AATTGG
45309819 ACATTTGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 7 0.24
26 4 0.14
28 18 0.62
ACGTcount: A:0.22, C:0.10, G:0.26, T:0.41
Consensus pattern (26 bp):
AATTGGGCCCAATTGAATTTGTTTGT
Found at i:45309887 original size:6 final size:6
Alignment explanation
Indices: 45309872--45309930 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
45309862 TTAAATTTGA
* * *
45309872 TTAAAC TTAAAT TTAAA- GTAAAT TTAAAT GAGTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT --TTAAAT TTAAAT TTAAAT
*
45309920 ATAAAT TTAAA
1 TTAAAT TTAAA
45309931 ACCCTTTTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 8
0.74 0.12 0.14
Matches are distributed among these distances:
5 8 0.19
6 29 0.69
8 5 0.12
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (6 bp):
TTAAAT
Found at i:45309907 original size:14 final size:14
Alignment explanation
Indices: 45309888--45309914 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
45309878 TTAAATTTAA
45309888 AGTAAATTTAAATG
1 AGTAAATTTAAATG
45309902 AGTAAATTTAAAT
1 AGTAAATTTAAAT
45309915 TTAAAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (14 bp):
AGTAAATTTAAATG
Found at i:45310275 original size:24 final size:24
Alignment explanation
Indices: 45310240--45310288 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
45310230 ATCTTCTCCC
*
45310240 CTATTCTCGTACCACGAACTGCTT
1 CTATTCTCGTACCACGAACTACTT
* *
45310264 CTATTCTTGTACCGCGAACTACTT
1 CTATTCTCGTACCACGAACTACTT
45310288 C
1 C
45310289 GAGTGTGGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (24 bp):
CTATTCTCGTACCACGAACTACTT
Found at i:45313035 original size:27 final size:28
Alignment explanation
Indices: 45312965--45313035 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 28
45312955 CCCGCCCATA
*
45312965 TTATTT-TTAATTTTTTAAAAATATTTT
1 TTATTTATTAAATTTTTAAAAATATTTT
* *
45312992 TAATATTTAAT-AA-TTTT-AATATATTTT
1 T--TATTTATTAAATTTTTAAAAATATTTT
45313019 TTATTTATTAAATTTTT
1 TTATTTATTAAATTTTT
45313036 TTATATAGTC
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
25 7 0.20
26 2 0.06
27 15 0.43
28 4 0.11
29 6 0.17
30 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
TTATTTATTAAATTTTTAAAAATATTTT
Found at i:45313036 original size:28 final size:27
Alignment explanation
Indices: 45312965--45313042 Score: 72
Period size: 28 Copynumber: 2.9 Consensus size: 27
45312955 CCCGCCCATA
*
45312965 TTATTT-TTAATTTTTTAAAAATATTTT
1 TTATTTATTAATTTTTT-AATATATTTT
*
45312992 TAATATTTAATAA--TTTTAATATATTTT
1 T--TATTTATTAATTTTTTAATATATTTT
*
45313019 TTATTTATTAAATTTTTTTATATA
1 TTATTTATT-AATTTTTTAATATA
45313043 GTCATCTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
25 7 0.17
26 2 0.05
27 11 0.27
28 13 0.32
29 5 0.12
30 3 0.07
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (27 bp):
TTATTTATTAATTTTTTAATATATTTT
Found at i:45321515 original size:2 final size:2
Alignment explanation
Indices: 45321510--45321538 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
45321500 AAAAAAAACT
45321510 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
45321539 TTTTTGTTTA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:45327640 original size:18 final size:18
Alignment explanation
Indices: 45327617--45327653 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
45327607 AAAATTTTAC
45327617 TATAATATCTCTATATAA
1 TATAATATCTCTATATAA
*
45327635 TATAATATCTTTATATAA
1 TATAATATCTCTATATAA
45327653 T
1 T
45327654 TTTGTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (18 bp):
TATAATATCTCTATATAA
Found at i:45332179 original size:12 final size:12
Alignment explanation
Indices: 45332164--45332250 Score: 113
Period size: 12 Copynumber: 7.3 Consensus size: 12
45332154 AAACAGTAGT
*
45332164 AAAAATAACAGC
1 AAAAATAACAAC
*
45332176 -AAAACAACAAC
1 AAAAATAACAAC
*
45332187 AAAAACAACAAC
1 AAAAATAACAAC
45332199 AAAAATAACAAC
1 AAAAATAACAAC
*
45332211 AAAAATAGCAAC
1 AAAAATAACAAC
45332223 AAAAATAACAAC
1 AAAAATAACAAC
* *
45332235 AAAAACAACATC
1 AAAAATAACAAC
45332247 AAAA
1 AAAA
45332251 CAGTAAAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
11 9 0.13
12 58 0.87
ACGTcount: A:0.72, C:0.20, G:0.02, T:0.06
Consensus pattern (12 bp):
AAAAATAACAAC
Found at i:45332186 original size:3 final size:3
Alignment explanation
Indices: 45332178--45332244 Score: 53
Period size: 3 Copynumber: 22.3 Consensus size: 3
45332168 ATAACAGCAA
* * * * * * *
45332178 AAC AAC AAC AAA AAC AAC AAC AAA AAT AAC AAC AAA AAT AGC AAC AAA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC
* *
45332226 AAT AAC AAC AAA AAC AAC A
1 AAC AAC AAC AAC AAC AAC A
45332245 TCAAAACAGT
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.73, C:0.21, G:0.01, T:0.04
Consensus pattern (3 bp):
AAC
Found at i:45332258 original size:20 final size:20
Alignment explanation
Indices: 45332243--45332316 Score: 58
Period size: 20 Copynumber: 3.5 Consensus size: 20
45332233 ACAAAAACAA
45332243 CATCAAAACAGTAAAAAAAG
1 CATCAAAACAGTAAAAAAAG
* ** *
45332263 TATCAAAACAACAACCAAAACAA
1 CATCAAAACAGTAA--AAAA-AG
*
45332286 CAACCAAAACAGTAAAAAAAG
1 C-ATCAAAACAGTAAAAAAAG
*
45332307 CACCAAAACA
1 CATCAAAACA
45332317 ATGATATAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
20 20 0.49
21 2 0.05
22 8 0.20
23 1 0.02
24 10 0.24
ACGTcount: A:0.65, C:0.23, G:0.05, T:0.07
Consensus pattern (20 bp):
CATCAAAACAGTAAAAAAAG
Found at i:45332281 original size:12 final size:12
Alignment explanation
Indices: 45332266--45332296 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
45332256 AAAAAAGTAT
45332266 CAAAACAACAAC
1 CAAAACAACAAC
45332278 CAAAACAACAAC
1 CAAAACAACAAC
45332290 CAAAACA
1 CAAAACA
45332297 GTAAAAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (12 bp):
CAAAACAACAAC
Found at i:45332282 original size:44 final size:43
Alignment explanation
Indices: 45332140--45332317 Score: 142
Period size: 44 Copynumber: 3.9 Consensus size: 43
45332130 TCTAAATAAC
* * * *
45332140 CAAAATAACAATCAAAACAGTAGTAAAAATAACAGCAAAACAACAA
1 CAAAACAACAACCAAAACAGTA--AAAAA-AGCACCAAAACAACAA
* ** * * *
45332186 CAAAAACAACAACAAAAATAACAACAAAAATAGCAACAAAAATAACAA
1 C-AAAACAACAAC--CAA-AACAGTAAAAAAAGC-ACCAAAACAACAA
* * *
45332234 CAAAAACAAC-ATCAAAACAGTAAAAAAAGTATCAAAACAACAA
1 C-AAAACAACAACCAAAACAGTAAAAAAAGCACCAAAACAACAA
45332277 CCAAAACAACAACCAAAACAGTAAAAAAAGCACCAAAACAA
1 -CAAAACAACAACCAAAACAGTAAAAAAAGCACCAAAACAA
45332318 TGATATAATT
Statistics
Matches: 103, Mismatches: 22, Indels: 16
0.73 0.16 0.11
Matches are distributed among these distances:
43 18 0.17
44 39 0.38
45 2 0.02
46 1 0.01
47 12 0.12
48 24 0.23
49 2 0.02
50 5 0.05
ACGTcount: A:0.68, C:0.20, G:0.04, T:0.07
Consensus pattern (43 bp):
CAAAACAACAACCAAAACAGTAAAAAAAGCACCAAAACAACAA
Found at i:45332293 original size:24 final size:24
Alignment explanation
Indices: 45332175--45332296 Score: 92
Period size: 24 Copynumber: 5.3 Consensus size: 24
45332165 AAAATAACAG
45332175 CAAAACAACAACAAAAACAACAAC
1 CAAAACAACAACAAAAACAACAAC
* * * *
45332199 AAAAATAACAACAAAAATAGCAAC
1 CAAAACAACAACAAAAACAACAAC
* * *
45332223 AAAAATAACAACAAAAACAAC-AT
1 CAAAACAACAACAAAAACAACAAC
** ** *
45332246 C--AA-AACAGTAAAAA-AAGTAT
1 CAAAACAACAACAAAAACAACAAC
*
45332266 CAAAACAACAACCAAAACAACAAC
1 CAAAACAACAACAAAAACAACAAC
45332290 CAAAACA
1 CAAAACA
45332297 GTAAAAAAAG
Statistics
Matches: 76, Mismatches: 17, Indels: 10
0.74 0.17 0.10
Matches are distributed among these distances:
19 2 0.03
20 12 0.16
21 2 0.03
22 2 0.03
23 9 0.12
24 49 0.64
ACGTcount: A:0.70, C:0.22, G:0.02, T:0.06
Consensus pattern (24 bp):
CAAAACAACAACAAAAACAACAAC
Found at i:45335334 original size:3 final size:3
Alignment explanation
Indices: 45335326--45335363 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
45335316 TTGAGGTCAC
45335326 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
45335364 GAAAAAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:45335829 original size:6 final size:6
Alignment explanation
Indices: 45335818--45335887 Score: 56
Period size: 6 Copynumber: 12.0 Consensus size: 6
45335808 TGGGATTTAT
** *
45335818 TTTAAA TTTAAA TTTATT TTTAAA TTTGAA TTT--- TTTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
* **
45335864 TTTAAA TATATG TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
45335888 ATTATTCTAA
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
3 3 0.06
6 43 0.88
7 3 0.06
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:45335840 original size:18 final size:18
Alignment explanation
Indices: 45335812--45335893 Score: 76
Period size: 18 Copynumber: 4.4 Consensus size: 18
45335802 TTATTTTGGG
45335812 ATTTA-TTTTAAATTTAA
1 ATTTATTTTTAAATTTAA
*
45335829 ATTTATTTTTAAATTTGA
1 ATTTATTTTTAAATTTAA
*
45335847 ATTTTTTAAAATTTAAATTTAA
1 ATTTATT----TTTAAATTTAA
* *
45335869 ATATATGTTTAAATTTAA
1 ATTTATTTTTAAATTTAA
*
45335887 AATTATT
1 ATTTATT
45335894 CTAAATAATG
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
17 5 0.10
18 32 0.63
22 14 0.27
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
ATTTATTTTTAAATTTAA
Found at i:45335854 original size:15 final size:16
Alignment explanation
Indices: 45335817--45335866 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
45335807 TTGGGATTTA
45335817 TTTT-AAATTTAAATTT
1 TTTTAAAATTTAAA-TT
* *
45335833 ATTTTTAAATTTGAATT
1 -TTTTAAAATTTAAATT
45335850 TTTTAAAATTTAAATT
1 TTTTAAAATTTAAATT
45335866 T
1 T
45335867 AAATATATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 15 0.52
17 6 0.21
18 8 0.28
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
TTTTAAAATTTAAATT
Found at i:45343826 original size:23 final size:22
Alignment explanation
Indices: 45343796--45344012 Score: 195
Period size: 23 Copynumber: 9.4 Consensus size: 22
45343786 ACACTAGCGC
* * *
45343796 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCAC-TTTTGT
*
45343819 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACT-TTTGT
45343844 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
45343867 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
45343890 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
*
45343913 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
* * *
45343936 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACT-TTTGT
*
45343959 GCTCTCTG-TTGCCCAGCACTTATGT
1 GCTCTCTGATT----AGCACTTTTGT
* *
45343984 GCTCTCTG-TTAGTACTTTGGT
1 GCTCTCTGATTAGCACTTTTGT
*
45344005 ACTCTCTG
1 GCTCTCTG
45344013 CTTGTTCCGT
Statistics
Matches: 169, Mismatches: 16, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
21 15 0.09
22 3 0.02
23 112 0.66
24 2 0.01
25 31 0.18
26 6 0.04
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.43
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTTTGT
Found at i:45343896 original size:46 final size:46
Alignment explanation
Indices: 45343817--45344012 Score: 238
Period size: 46 Copynumber: 4.2 Consensus size: 46
45343807 AGCACGTCTC
*
45343817 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTG--ATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
45343865 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
* * * *
45343911 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
* *
45343957 GTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATT----AGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
*
45344003 GTACTCTCTG
1 GTGCTCTCTG
45344013 CTTGTTCCGT
Statistics
Matches: 133, Mismatches: 11, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
45 2 0.02
46 96 0.72
47 9 0.07
48 22 0.17
49 4 0.03
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (46 bp):
GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
Found at i:45343931 original size:69 final size:69
Alignment explanation
Indices: 45343797--45344012 Score: 262
Period size: 69 Copynumber: 3.1 Consensus size: 69
45343787 CACTAGCGCG
* * * *
45343797 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
1 CTCTCTGATTAGCACTGTGT-GTGCTCTCTG--ATTAGCACTTTGTGTGCTCTCTGATTAGTACT
*
45343861 TTGTGTG
63 TTGTGTA
*
45343868 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTG
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTG
45343933 TGTA
66 TGTA
* *
45343937 CTCTCTGTTTAGCACTGTGTGTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTAC
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGATT----AGCACTTTGTGTGCTCTCTGATTAGTAC
45343999 TTTG-GTA
62 TTTGTGTA
45344006 CTCTCTG
1 CTCTCTG
45344013 CTTGTTCCGT
Statistics
Matches: 131, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
68 2 0.02
69 74 0.56
70 11 0.08
71 37 0.28
72 7 0.05
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (69 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTG
TGTA
Found at i:45351244 original size:23 final size:22
Alignment explanation
Indices: 45351214--45351430 Score: 195
Period size: 23 Copynumber: 9.4 Consensus size: 22
45351204 ACACTAGCGC
* * *
45351214 GCTCTCTGTTTAGCACGTCTCGT
1 GCTCTCTGATTAGCAC-TTTTGT
*
45351237 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACT-TTTGT
45351262 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
45351285 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
45351308 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
*
45351331 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGATTAGCACTTT-TGT
* * *
45351354 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGATTAGCACT-TTTGT
*
45351377 GCTCTCTG-TTGCCCAGCACTTATGT
1 GCTCTCTGATT----AGCACTTTTGT
* *
45351402 GCTCTCTG-TTAGTACTTTGGT
1 GCTCTCTGATTAGCACTTTTGT
*
45351423 ACTCTCTG
1 GCTCTCTG
45351431 CTTGTTCCGT
Statistics
Matches: 169, Mismatches: 16, Indels: 20
0.82 0.08 0.10
Matches are distributed among these distances:
21 15 0.09
22 3 0.02
23 112 0.66
24 2 0.01
25 31 0.18
26 6 0.04
ACGTcount: A:0.12, C:0.24, G:0.22, T:0.43
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTTTGT
Found at i:45351314 original size:46 final size:46
Alignment explanation
Indices: 45351235--45351430 Score: 238
Period size: 46 Copynumber: 4.2 Consensus size: 46
45351225 AGCACGTCTC
*
45351235 GTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTG--ATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
45351283 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
1 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
* * * *
45351329 GTGCTCTCTGATTAGTACTTTGTGTACTCTCTGTTTAGCACTGTGT
1 GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
* *
45351375 GTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTACTTTG-
1 GTGCTCTCTGATT----AGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
*
45351421 GTACTCTCTG
1 GTGCTCTCTG
45351431 CTTGTTCCGT
Statistics
Matches: 133, Mismatches: 11, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
45 2 0.02
46 96 0.72
47 9 0.07
48 22 0.17
49 4 0.03
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (46 bp):
GTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGT
Found at i:45351349 original size:69 final size:69
Alignment explanation
Indices: 45351215--45351430 Score: 262
Period size: 69 Copynumber: 3.1 Consensus size: 69
45351205 CACTAGCGCG
* * * *
45351215 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTGTGTGTGCTCTCTGATTAGCACT
1 CTCTCTGATTAGCACTGTGT-GTGCTCTCTG--ATTAGCACTTTGTGTGCTCTCTGATTAGTACT
*
45351279 TTGTGTG
63 TTGTGTA
*
45351286 CTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTG
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTG
45351351 TGTA
66 TGTA
* *
45351355 CTCTCTGTTTAGCACTGTGTGTGCTCTCTG-TTGCCCAGCAC-TTATGTGCTCTCTG-TTAGTAC
1 CTCTCTGATTAGCACTGTGTGTGCTCTCTGATT----AGCACTTTGTGTGCTCTCTGATTAGTAC
45351417 TTTG-GTA
62 TTTGTGTA
45351424 CTCTCTG
1 CTCTCTG
45351431 CTTGTTCCGT
Statistics
Matches: 131, Mismatches: 9, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
68 2 0.02
69 74 0.56
70 11 0.08
71 37 0.28
72 7 0.05
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.43
Consensus pattern (69 bp):
CTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCTCTGATTAGTACTTTG
TGTA
Found at i:45360874 original size:206 final size:204
Alignment explanation
Indices: 45360509--45360903 Score: 470
Period size: 206 Copynumber: 1.9 Consensus size: 204
45360499 TCAACACTCA
*
45360509 AATGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCAAAGCAATAA
1 AATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCAAAGCAATAA
* * * * *
45360574 ATGGTTAGCTTCCTGATGAGACACTGAGAAGTGACCAAATTCGTCTTCCTAAGGAAATCCAGAGA
66 ATGGTTAGCTTCCTGATGAGACACAGAGAAGTAACCAAATCCGTCTTCCTAAGAAAACCCAGAGA
* *** * * * *
45360639 AGTGAATTAAAACAAGTGATGCGGTCATCTTCTTGATGAAACACTGAGAAGAAGACCAAATCAAA
131 AGTGAATCAAAACAAACAACGCAGTCATCTTCCTGATAAAACACTGAGAAGAAGACCAAATCAAA
45360704 CCCAAGCTC
196 CCCAAGCTC
* * * * * * *
45360713 AATGCGAGTAAATCTTCGAACCTCAGCTTTCTGATGAGATACTGAGAAGCATATTGAAATG--AT
1 AATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGA-TCAAA-GCAAT
* * * **
45360776 AAAATGGTTAGCTTTCTGATGCGATACAGAGAAGTAAACCAAATCCGTCTTCCTGTGAAAACCCA
64 -AAATGGTTAGCTTCCTGATGAGACACAGAGAAGT-AACCAAATCCGTCTTCCTAAGAAAACCCA
* ** *
45360841 GAGAAGTGGATCAAAACAAACAACGCAGTCATCTTCCTGATAAAATGCTGAGAAGAAGGCCAA
127 GAGAAGTGAATCAAAACAAACAACGCAGTCATCTTCCTGATAAAACACTGAGAAGAAGACCAA
45360904 GTTAATGAAA
Statistics
Matches: 157, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
204 48 0.31
205 34 0.22
206 75 0.48
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (204 bp):
AATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGACACTAAGAAGCAGATCAAAGCAATAA
ATGGTTAGCTTCCTGATGAGACACAGAGAAGTAACCAAATCCGTCTTCCTAAGAAAACCCAGAGA
AGTGAATCAAAACAAACAACGCAGTCATCTTCCTGATAAAACACTGAGAAGAAGACCAAATCAAA
CCCAAGCTC
Found at i:45361099 original size:18 final size:18
Alignment explanation
Indices: 45361072--45361113 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
45361062 CAATAAAGCG
*
45361072 AAGGGTGGACCCATTGAA
1 AAGGGCGGACCCATTGAA
45361090 AAGGGCGGACCCATTGAA
1 AAGGGCGGACCCATTGAA
45361108 AAGGGC
1 AAGGGC
45361114 AACAAAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.36, T:0.12
Consensus pattern (18 bp):
AAGGGCGGACCCATTGAA
Found at i:45361264 original size:6 final size:6
Alignment explanation
Indices: 45361253--45361321 Score: 52
Period size: 6 Copynumber: 11.8 Consensus size: 6
45361243 TGGGATTTAT
** * * *
45361253 TTTAAA TTTAAA TTTATT TTTAAA TTTGAA TTT--G TTAAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* **
45361299 TTTAAA TATATG TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAA
45361322 GATTATTCTA
Statistics
Matches: 46, Mismatches: 15, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
4 2 0.04
6 44 0.96
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:45361275 original size:18 final size:18
Alignment explanation
Indices: 45361247--45361321 Score: 71
Period size: 18 Copynumber: 4.0 Consensus size: 18
45361237 CCATTTTGGG
45361247 ATTTA-TTTTAAATTTAA
1 ATTTATTTTTAAATTTAA
*
45361264 ATTTATTTTTAAATTTGA
1 ATTTATTTTTAAATTTAA
*
45361282 ATTTGTTAAAATTTAAATTTAA
1 ATTTATT----TTTAAATTTAA
* *
45361304 ATATATGTTTAAATTTAA
1 ATTTATTTTTAAATTTAA
45361322 GATTATTCTA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
17 5 0.11
18 28 0.60
22 14 0.30
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (18 bp):
ATTTATTTTTAAATTTAA
Found at i:45361312 original size:24 final size:22
Alignment explanation
Indices: 45361271--45361321 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
45361261 TAAATTTATT
*
45361271 TTTAAATTTGAATTTGTTAAAA
1 TTTAAATTTAAATTTGTTAAAA
*
45361293 TTTAAATTTAAATATATGTTTAAA
1 TTTAAATTTAAAT-T-TGTTAAAA
45361317 TTTAA
1 TTTAA
45361322 GATTATTCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 12 0.48
23 1 0.04
24 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (22 bp):
TTTAAATTTAAATTTGTTAAAA
Found at i:45364999 original size:1 final size:1
Alignment explanation
Indices: 45364993--45365017 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
45364983 ATTGAACTAT
45364993 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
45365018 AAAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:45374817 original size:15 final size:15
Alignment explanation
Indices: 45374795--45374833 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
45374785 CACGACAAAT
45374795 TCCCTCTCCTTATCC
1 TCCCTCTCCTTATCC
* * *
45374810 TTCCTCTCTTTCTCC
1 TCCCTCTCCTTATCC
45374825 TCCCTCTCC
1 TCCCTCTCC
45374834 CTCCTCTCCT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.54, G:0.00, T:0.44
Consensus pattern (15 bp):
TCCCTCTCCTTATCC
Found at i:45377821 original size:15 final size:15
Alignment explanation
Indices: 45377799--45377837 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
45377789 CACGACAAAT
45377799 TCCCTCTCCTTATCC
1 TCCCTCTCCTTATCC
* * *
45377814 TTCCTCTCTTTCTCC
1 TCCCTCTCCTTATCC
45377829 TCCCTCTCC
1 TCCCTCTCC
45377838 CTCCTCTCCT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.03, C:0.54, G:0.00, T:0.44
Consensus pattern (15 bp):
TCCCTCTCCTTATCC
Found at i:45379383 original size:35 final size:35
Alignment explanation
Indices: 45379343--45379414 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
45379333 CGCCCATCCT
* *
45379343 TAGGAGGGACTAGATAAAATTTAAGACACCCTTAG
1 TAGGAGGGACTAGATAAAATTCAAGAAACCCTTAG
*
45379378 TAGGAGGGACTAGATAAAATTCAAGAAATCCTTAG
1 TAGGAGGGACTAGATAAAATTCAAGAAACCCTTAG
45379413 TA
1 TA
45379415 TGATTAATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.24
Consensus pattern (35 bp):
TAGGAGGGACTAGATAAAATTCAAGAAACCCTTAG
Found at i:45381367 original size:16 final size:16
Alignment explanation
Indices: 45381348--45381378 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45381338 CGAGTTATTA
*
45381348 AATTAATTTAAATTTG
1 AATTAAGTTAAATTTG
45381364 AATTAAGTTAAATTT
1 AATTAAGTTAAATTT
45381379 AAATAATTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (16 bp):
AATTAAGTTAAATTTG
Found at i:45381520 original size:20 final size:20
Alignment explanation
Indices: 45381492--45381541 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
45381482 TCAACAAAAA
45381492 TTATAAAAAAATT-AAAATAAT
1 TTAT-AAAAAATTCAAAAT-AT
*
45381513 TT-TTAAAAATTCAAAATAT
1 TTATAAAAAATTCAAAATAT
45381532 TTATAAAAAA
1 TTATAAAAAA
45381542 ATTTTAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 11 0.44
20 12 0.48
21 2 0.08
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (20 bp):
TTATAAAAAATTCAAAATAT
Found at i:45381522 original size:19 final size:19
Alignment explanation
Indices: 45381498--45381540 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
45381488 AAAATTATAA
*
45381498 AAAAATT-AAAATAATTTTT
1 AAAAATTCAAAAT-ATTTAT
45381517 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
45381536 AAAAA
1 AAAAA
45381541 AATTTTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.77
20 5 0.23
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:45381541 original size:41 final size:41
Alignment explanation
Indices: 45381486--45381585 Score: 102
Period size: 41 Copynumber: 2.5 Consensus size: 41
45381476 TTTTTCTCAA
45381486 CAAAAA-TTAT-AAAAAA-ATTAA-A-ATAATTTTTAAAAATT
1 CAAAAATTTATAAAAAAATATTAATATATAA--TTTAAAAATT
* *
45381524 CAAAATATTTATAAAAAAATTTTAATATATAATTTAAAATTT
1 CAAAA-ATTTATAAAAAAATATTAATATATAATTTAAAAATT
* *
45381566 TAAAAATTTATAAAATAATA
1 CAAAAATTTATAAAAAAATA
45381586 ATTTTTGAGA
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
38 5 0.10
39 1 0.02
40 4 0.08
41 19 0.37
42 17 0.33
43 1 0.02
44 4 0.08
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (41 bp):
CAAAAATTTATAAAAAAATATTAATATATAATTTAAAAATT
Found at i:45382456 original size:45 final size:45
Alignment explanation
Indices: 45382407--45382493 Score: 104
Period size: 45 Copynumber: 1.9 Consensus size: 45
45382397 ATGATTAAAT
* *
45382407 TTTTTAGAATTTGA-ATTAAAATGAAAAAATTTGTAAATATTAATA
1 TTTTTA-AATTTAAGATTAAAATGAAAAAATATGTAAATATTAATA
* * * *
45382452 TTTTTATATTTAAGATTAAATTGATAGAATATGTAAATATTA
1 TTTTTAAATTTAAGATTAAAATGAAAAAATATGTAAATATTA
45382494 GACGATTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 5 0.14
45 30 0.86
ACGTcount: A:0.46, C:0.00, G:0.09, T:0.45
Consensus pattern (45 bp):
TTTTTAAATTTAAGATTAAAATGAAAAAATATGTAAATATTAATA
Found at i:45390801 original size:46 final size:46
Alignment explanation
Indices: 45390736--45390828 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
45390726 TTCAAATCCA
*
45390736 ATTATTAGATTACTTTTTAAACACTATCTGAGATTTAAAAAAAGTT
1 ATTACTAGATTACTTTTTAAACACTATCTGAGATTTAAAAAAAGTT
45390782 ATTACTAGATTACTTTTTAAACACTATCTGAGATTTAAAAAAAGTT
1 ATTACTAGATTACTTTTTAAACACTATCTGAGATTTAAAAAAAGTT
45390828 A
1 A
45390829 ATAACATATA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.40
Consensus pattern (46 bp):
ATTACTAGATTACTTTTTAAACACTATCTGAGATTTAAAAAAAGTT
Found at i:45404751 original size:22 final size:23
Alignment explanation
Indices: 45404696--45404752 Score: 80
Period size: 24 Copynumber: 2.5 Consensus size: 23
45404686 TTTGACCCTC
*
45404696 AGATTTTAATGAGTCTTCAGCGT
1 AGATTTTAATGAGTCTTCAACGT
45404719 CAGATTTTAATGAGTCTTCAACGT
1 -AGATTTTAATGAGTCTTCAACGT
*
45404743 -GTTTTTAATG
1 AGATTTTAATG
45404753 GGAAATTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 9 0.29
24 22 0.71
ACGTcount: A:0.26, C:0.12, G:0.19, T:0.42
Consensus pattern (23 bp):
AGATTTTAATGAGTCTTCAACGT
Found at i:45404835 original size:20 final size:22
Alignment explanation
Indices: 45404807--45404847 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
45404797 TTAATTAAAT
45404807 TTAGAGTTTTT-AAATTAGGGC
1 TTAGAGTTTTTAAAATTAGGGC
45404828 TTAG-GTTTTTAAAATTAGGG
1 TTAGAGTTTTTAAAATTAGGG
45404848 TTTTGATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.29, C:0.02, G:0.24, T:0.44
Consensus pattern (22 bp):
TTAGAGTTTTTAAAATTAGGGC
Found at i:45405647 original size:18 final size:18
Alignment explanation
Indices: 45405623--45405666 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
45405613 AAAACGATGA
*
45405623 AAATTGAGGTGGCTATTG
1 AAATTGAGGTGGCGATTG
*
45405641 GAATTGAGGTGGCGATTG
1 AAATTGAGGTGGCGATTG
45405659 AAATTGAG
1 AAATTGAG
45405667 TTGAGCTCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.30, C:0.05, G:0.36, T:0.30
Consensus pattern (18 bp):
AAATTGAGGTGGCGATTG
Found at i:45407407 original size:31 final size:31
Alignment explanation
Indices: 45407370--45407438 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
45407360 TCACATGAAA
*
45407370 AATATAAAA-AATTTAAT-TAAATTATAAAAAT
1 AATATAAAATAATTAAATAT-AATTA-AAAAAT
*
45407401 AATATAAAATAATTAAATATTATTAAAAAAT
1 AATATAAAATAATTAAATATAATTAAAAAAT
45407432 AAT-TAAA
1 AATATAAA
45407439 TTATAAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
30 4 0.12
31 18 0.53
32 11 0.32
33 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (31 bp):
AATATAAAATAATTAAATATAATTAAAAAAT
Found at i:45407408 original size:18 final size:17
Alignment explanation
Indices: 45407383--45407448 Score: 63
Period size: 17 Copynumber: 4.1 Consensus size: 17
45407373 ATAAAAAATT
45407383 TAATTAAATTATAAAAA
1 TAATTAAATTATAAAAA
45407400 TAATATAAA--ATAATTAAA
1 TAAT-TAAATTATAA--AAA
45407418 T-ATT--ATTA-AAAAA
1 TAATTAAATTATAAAAA
45407431 TAATTAAATTATAAAAA
1 TAATTAAATTATAAAAA
45407448 T
1 T
45407449 TAAATAATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 18
0.69 0.00 0.31
Matches are distributed among these distances:
13 4 0.10
14 4 0.10
15 2 0.05
16 10 0.25
17 12 0.30
18 8 0.20
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
TAATTAAATTATAAAAA
Found at i:45407449 original size:14 final size:15
Alignment explanation
Indices: 45407384--45407468 Score: 54
Period size: 16 Copynumber: 5.5 Consensus size: 15
45407374 TAAAAAATTT
45407384 AATTAAAT-TATAAA
1 AATTAAATATATAAA
45407398 AA-T-AATATA-AAA
1 AATTAAATATATAAA
45407410 TAATTAAATATTATTAAAAAA
1 -AATTAAATA-TA-T---AAA
45407431 TAATTAAAT-TATAAA
1 -AATTAAATATATAAA
45407446 AATTAAATAATATAAA
1 AATTAAAT-ATATAAA
*
45407462 AAATAAA
1 AATTAAA
45407469 ATTAACTTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 22
0.72 0.01 0.27
Matches are distributed among these distances:
12 6 0.10
13 5 0.09
14 11 0.19
15 7 0.12
16 14 0.24
18 1 0.02
19 2 0.03
21 12 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTAAATATATAAA
Found at i:45407464 original size:18 final size:18
Alignment explanation
Indices: 45407397--45407464 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
45407387 TAAATTATAA
*
45407397 AAATAATATAAAATAATT
1 AAATAATATAAAAAAATT
* *
45407415 AAATATTATTAAAAAA-T
1 AAATAATATAAAAAAATT
* *
45407432 AATTAA-ATTATAAAAATT
1 AAATAATA-TAAAAAAATT
45407450 AAATAATATAAAAAA
1 AAATAATATAAAAAA
45407465 TAAAATTAAC
Statistics
Matches: 38, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
16 1 0.03
17 11 0.29
18 25 0.66
19 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
AAATAATATAAAAAAATT
Found at i:45407598 original size:18 final size:19
Alignment explanation
Indices: 45407575--45407612 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
45407565 TTGTGTAAAA
45407575 AAATTTGAGA-ATTTAGAG
1 AAATTTGAGAGATTTAGAG
*
45407593 AAATTTGAGAGCTTTAGAG
1 AAATTTGAGAGATTTAGAG
45407612 A
1 A
45407613 GAAATTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.42, C:0.03, G:0.24, T:0.32
Consensus pattern (19 bp):
AAATTTGAGAGATTTAGAG
Found at i:45407646 original size:12 final size:12
Alignment explanation
Indices: 45407625--45407658 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
45407615 AATTTGTTTG
*
45407625 AAATTTAGAGAA
1 AAATTGAGAGAA
45407637 AAATTGAGAG-A
1 AAATTGAGAGAA
45407648 AAATTGAGAGA
1 AAATTGAGAGA
45407659 GAATGAGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.21
Consensus pattern (12 bp):
AAATTGAGAGAA
Found at i:45407652 original size:11 final size:11
Alignment explanation
Indices: 45407625--45407671 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
45407615 AATTTGTTTG
*
45407625 AAATTTAGAGAA
1 AAATTGAGAG-A
45407637 AAATTGAGAGA
1 AAATTGAGAGA
45407648 AAATTGAGAGA
1 AAATTGAGAGA
* *
45407659 GAA-TGAGTGA
1 AAATTGAGAGA
45407669 AAA
1 AAA
45407672 AATAAAAGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
10 8 0.26
11 14 0.45
12 9 0.29
ACGTcount: A:0.55, C:0.00, G:0.26, T:0.19
Consensus pattern (11 bp):
AAATTGAGAGA
Found at i:45407695 original size:2 final size:2
Alignment explanation
Indices: 45407690--45407720 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
45407680 GTGGGGGGTT
45407690 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45407721 TTTTTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45407852 original size:32 final size:31
Alignment explanation
Indices: 45407815--45407893 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 31
45407805 AACACGGCCT
*
45407815 AAAACG-TGTCCACGTGTGCGCTC-CTTTGAGCA
1 AAAACGCT-TCCACGTGAGCG-TCACTTTG-GCA
*
45407847 AAAACGCTTCCACGTGAGCGTCATTTTGGCA
1 AAAACGCTTCCACGTGAGCGTCACTTTGGCA
45407878 AAAACGC-TCCTACGTG
1 AAAACGCTTCC-ACGTG
45407894 GATGCGCTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
30 3 0.07
31 17 0.40
32 21 0.50
33 1 0.02
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (31 bp):
AAAACGCTTCCACGTGAGCGTCACTTTGGCA
Found at i:45408411 original size:29 final size:30
Alignment explanation
Indices: 45408379--45408450 Score: 78
Period size: 29 Copynumber: 2.4 Consensus size: 30
45408369 TAAATATTTG
*
45408379 TTTTATAATTTTTACACTTTTTAAA-AT-AA
1 TTTTATAATTTTTA-AATTTTTAAATATGAA
* *
45408408 TTTTA-ATTATTTTAAATTTTTAAATATGAT
1 TTTTATAAT-TTTTAAATTTTTAAATATGAA
45408438 TTTTATAATTTTT
1 TTTTATAATTTTT
45408451 TTTGAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
28 11 0.31
29 12 0.34
30 10 0.29
31 2 0.06
ACGTcount: A:0.35, C:0.03, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTTATAATTTTTAAATTTTTAAATATGAA
Found at i:45427694 original size:20 final size:21
Alignment explanation
Indices: 45427671--45427716 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
45427661 AATAGTCAAA
45427671 GTCAACGATCAAAT-TCAACG
1 GTCAACGATCAAATATCAACG
*
45427691 GTCAACGATCAACTATCAACG
1 GTCAACGATCAAATATCAACG
45427712 GTCAA
1 GTCAA
45427717 TGCATTCGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.20
Consensus pattern (21 bp):
GTCAACGATCAAATATCAACG
Found at i:45438813 original size:19 final size:19
Alignment explanation
Indices: 45438791--45438840 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
45438781 TTATATTAGG
45438791 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
45438810 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
*
45438829 ATTTAATTTTTA
1 ATTTAATATTTA
45438841 TTTATCTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 3 0.12
19 23 0.88
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:45441263 original size:21 final size:21
Alignment explanation
Indices: 45441238--45441287 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
45441228 GAATTTCAGC
*
45441238 AGCAATCTATAGATTTCCAAA
1 AGCAAACTATAGATTTCCAAA
* * *
45441259 AGCAAACTGTGGATTTTCAAA
1 AGCAAACTATAGATTTCCAAA
*
45441280 AGAAAACT
1 AGCAAACT
45441288 GAGGCATCTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.26
Consensus pattern (21 bp):
AGCAAACTATAGATTTCCAAA
Found at i:45441288 original size:21 final size:21
Alignment explanation
Indices: 45441249--45441288 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
45441239 GCAATCTATA
*
45441249 GATTTCCAAAAGCAAACTGTG
1 GATTTCCAAAAGAAAACTGTG
*
45441270 GATTTTCAAAAGAAAACTG
1 GATTTCCAAAAGAAAACTG
45441289 AGGCATCTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (21 bp):
GATTTCCAAAAGAAAACTGTG
Found at i:45444670 original size:26 final size:25
Alignment explanation
Indices: 45444637--45444691 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 25
45444627 TATTTTTATT
*
45444637 TTTTATTTTTTTATTT-TTCTATCTTA
1 TTTTATTTATTTATTTATT-TAT-TTA
45444663 TTTTATTTATTTATTTATTTATTTA
1 TTTTATTTATTTATTTATTTATTTA
45444688 TTTT
1 TTTT
45444692 TGTCCAGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
25 7 0.26
26 18 0.67
27 2 0.07
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTATTTATTTATTTATTTATTTA
Found at i:45444673 original size:4 final size:4
Alignment explanation
Indices: 45444631--45444690 Score: 70
Period size: 4 Copynumber: 14.8 Consensus size: 4
45444621 CCCAATTATT
*
45444631 TTTA TTT- TTTA TTTT TTTA TTT- TTCTA TCTTA TTTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TT-TA T-TTA -TTTA TTTA TTTA TTTA
45444680 TTTA TTTA TTT
1 TTTA TTTA TTT
45444691 TTGTCCAGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
3 5 0.10
4 36 0.73
5 6 0.12
6 2 0.04
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:45446112 original size:5 final size:5
Alignment explanation
Indices: 45446102--45446130 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
45446092 AAAGACTTGG
45446102 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
45446131 TAAAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:45446174 original size:19 final size:19
Alignment explanation
Indices: 45446152--45446196 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
45446142 TTATATTAGG
45446152 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
45446171 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
45446190 ATTTAAT
1 ATTTAAT
45446197 TTATATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:45452071 original size:16 final size:16
Alignment explanation
Indices: 45452031--45452071 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
45452021 AATTCAATCA
*
45452031 AACTCAAAACTCGAAT
1 AACTCAAAATTCGAAT
*
45452047 AACTC--AATTCGATT
1 AACTCAAAATTCGAAT
45452061 AACTCAAAATT
1 AACTCAAAATT
45452072 TAATTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
14 12 0.57
16 9 0.43
ACGTcount: A:0.46, C:0.22, G:0.05, T:0.27
Consensus pattern (16 bp):
AACTCAAAATTCGAAT
Found at i:45461247 original size:61 final size:59
Alignment explanation
Indices: 45461166--45461561 Score: 395
Period size: 61 Copynumber: 6.6 Consensus size: 59
45461156 TAAAAAAAAT
* * *
45461166 TGGTGTCGGCCATGCAATGGCCAATAACAAAAAAATTGATTTATTTTATCAGATAAAAAGG
1 TGGTGTCGGCCATGCAATGGCCAACACCAAAAAAATTGA-TT-TTTTATCAAATAAAAAGG
* * *
45461227 TGGTGTCGGCCAATGC-ATGGCCAACACAAAAAAAATTAATTTTTTTGTCAAATAAAAAAGG
1 TGGTGTCGGCC-ATGCAATGGCCAACACCAAAAAAATTGA-TTTTTTATCAAAT-AAAAAGG
* *** * * *
45461288 TGGCGTCCATCATTCAATGGCCAACACCAAAAAATTTGAACTTTTTATCAAATAAAAAGG
1 TGGTGTCGGCCATGCAATGGCCAACACCAAAAAAATTG-ATTTTTTATCAAATAAAAAGG
* **
45461348 TGGTGTCGGTCATGCAATGGCCAACACCAAAAAAA-T-ATTTTTTATCTGATAAAAAGG
1 TGGTGTCGGCCATGCAATGGCCAACACCAAAAAAATTGATTTTTTATCAAATAAAAAGG
* * * * * ** *
45461405 TGATGTCGGTCAATGC-ATGACCAATACCAAAAATATTTTGATTTTTTATCTGATAAAAAAGA
1 TGGTGTCGG-CCATGCAATGGCCAACACCAAAAA-A-ATTGATTTTTTATCAAAT-AAAAAGG
*
45461467 TGGTGTCGGCCATGCAATGGTCAACACCAAAAAAATTTGATTTTTTATCAAATAAAAAGG
1 TGGTGTCGGCCATGCAATGGCCAACACCAAAAAAA-TTGATTTTTTATCAAATAAAAAGG
* * * * *
45461527 TGATGTCGACTATACAATGACCAACACCAAAAAAA
1 TGGTGTCGGCCATGCAATGGCCAACACCAAAAAAA
45461562 AAATTTGTTA
Statistics
Matches: 277, Mismatches: 46, Indels: 25
0.80 0.13 0.07
Matches are distributed among these distances:
57 41 0.15
58 5 0.02
59 1 0.00
60 85 0.31
61 112 0.40
62 33 0.12
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.28
Consensus pattern (59 bp):
TGGTGTCGGCCATGCAATGGCCAACACCAAAAAAATTGATTTTTTATCAAATAAAAAGG
Found at i:45461517 original size:179 final size:182
Alignment explanation
Indices: 45461166--45461561 Score: 473
Period size: 179 Copynumber: 2.2 Consensus size: 182
45461156 TAAAAAAAAT
* * * *
45461166 TGGTGTCGGCCATGCAATGGCCAATAACAAAAAAATTGATTTATTTTATCAGATAAAAAGGTGGT
1 TGGTGTCGGACATGCAATGGCCAACACCAAAAAAATTGATTTATTTTATCAGATAAAAAGGTGAT
* * *
45461231 GTCGGCCAATGCATGGCCAACACAAAAAAAATTAATTTTTTTGTCAAATAAAAAAGGTGGCGTCC
66 GTCGGCCAATGCATGACCAACACAAAAAAAATTAATTTTTTTATCAAATAAAAAAGATGGCGTCC
* *
45461296 ATCATTCAATGGCCAACACCAAAAAATTTGAACTTTTTATCAAATAAAAAGG
131 ACCATGCAATGGCCAACACCAAAAAATTTGAACTTTTTATCAAATAAAAAGG
* *
45461348 TGGTGTCGGTCATGCAATGGCCAACACCAAAAAAA-T-A-TT-TTTTATCTGATAAAAAGGTGAT
1 TGGTGTCGGACATGCAATGGCCAACACCAAAAAAATTGATTTATTTTATCAGATAAAAAGGTGAT
* * * * * ** *
45461409 GTCGGTCAATGCATGACCAATACCAAAAATATT-TTGATTTTTTATCTGATAAAAAAGATGGTGT
66 GTCGGCCAATGCATGACCAACACAAAAAAAATTAAT--TTTTTTATCAAATAAAAAAGATGGCGT
** * *
45461473 CGGCCATGCAATGGTCAACACCAAAAAAATTTG-ATTTTTTATCAAATAAAAAGG
129 CCACCATGCAATGGCCAACACC-AAAAAATTTGAACTTTTTATCAAATAAAAAGG
* * *
45461527 TGATGTC-GACTATACAATGACCAACACCAAAAAAA
1 TGGTGTCGGAC-ATGCAATGGCCAACACCAAAAAAA
45461562 AAATTTGTTA
Statistics
Matches: 184, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
177 1 0.01
178 50 0.27
179 89 0.48
180 11 0.06
181 1 0.01
182 32 0.17
ACGTcount: A:0.40, C:0.16, G:0.17, T:0.28
Consensus pattern (182 bp):
TGGTGTCGGACATGCAATGGCCAACACCAAAAAAATTGATTTATTTTATCAGATAAAAAGGTGAT
GTCGGCCAATGCATGACCAACACAAAAAAAATTAATTTTTTTATCAAATAAAAAAGATGGCGTCC
ACCATGCAATGGCCAACACCAAAAAATTTGAACTTTTTATCAAATAAAAAGG
Found at i:45461654 original size:59 final size:59
Alignment explanation
Indices: 45461586--45461699 Score: 151
Period size: 59 Copynumber: 1.9 Consensus size: 59
45461576 AAATTGGTTG
* * *
45461586 ACAC-AAAAAAAATTGATTTTTTATCAGA-TAAAAAGGTGGTGTCGGCCATGCAATGATTA
1 ACACAAAAAAAAAAT-A-TTTTTATCAAATTAAAAAGGTGGTGTCAGCCATGCAATGATTA
* *
45461645 ACACCAAAAAAAAATATTTTTGTCAAATTAAAAAGGTGGTGTCAGCCATGCAATG
1 ACACAAAAAAAAAATATTTTTATCAAATTAAAAAGGTGGTGTCAGCCATGCAATG
45461700 GCCAACACCA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 9 0.18
59 31 0.63
60 9 0.18
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (59 bp):
ACACAAAAAAAAAATATTTTTATCAAATTAAAAAGGTGGTGTCAGCCATGCAATGATTA
Found at i:45462836 original size:157 final size:153
Alignment explanation
Indices: 45462556--45462865 Score: 548
Period size: 157 Copynumber: 2.0 Consensus size: 153
45462546 AAAATAAAAT
45462556 AAAAACCCAACAAAGGGGAGGTTAATTCTAGAAAATCATAAAAAAATTATTTATCTAAAATTATT
1 AAAAACCCAACAAAGGGGAGGTTAATTCTAGAAAATCATAAAAAAATTATTTATCTAAAATTATT
* *
45462621 ATCTGATAAAATATTTTTGGGACATATTTGACTTTGAAATAAATGATGTGACTTTCCAACCCATC
66 ATCTGATAAAAAATTTTGGGGACATATTTGACTTTGAAATAAATGATGTGACTTTCCAACCCATC
*
45462686 TTGAAATAAAAAATTGGGATAAA
131 TTGAAATAAAAAATAGGGATAAA
45462709 AAAAACCCAACAAAGGGGAGGTTAATTCTAGAAAATCATAAAAAAAAAATTATTTATCTAAAATT
1 AAAAACCCAACAAAGGGGAGGTTAATTCTAGAAAATCAT---AAAAAAATTATTTATCTAAAATT
*
45462774 ATTATCTGATAAAAAAATTTTGGGGACATATTTGACTTTGTAATAAATGATGTGACTTTCCAACC
63 ATTATCTGAT-AAAAAATTTTGGGGACATATTTGACTTTGAAATAAATGATGTGACTTTCCAACC
45462839 CATCTTGAAATAAAAAATAGGGATAAA
127 CATCTTGAAATAAAAAATAGGGATAAA
45462866 TCCCGAATCT
Statistics
Matches: 149, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
153 39 0.26
156 33 0.22
157 77 0.52
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (153 bp):
AAAAACCCAACAAAGGGGAGGTTAATTCTAGAAAATCATAAAAAAATTATTTATCTAAAATTATT
ATCTGATAAAAAATTTTGGGGACATATTTGACTTTGAAATAAATGATGTGACTTTCCAACCCATC
TTGAAATAAAAAATAGGGATAAA
Found at i:45463039 original size:41 final size:40
Alignment explanation
Indices: 45462984--45463066 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 40
45462974 TCAAAACTTA
*
45462984 CATAATAATTATTAACATTATCAAATTACTACTTTTTTTAT
1 CATAATAATTATTAACATTATCAAATTACTA-TTATTTTAT
*
45463025 CATAATAATTATTAACATTATCAAATTATTATTATTTTAT
1 CATAATAATTATTAACATTATCAAATTACTATTATTTTAT
45463065 CA
1 CA
45463067 CTCGTCTGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 10 0.25
41 30 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (40 bp):
CATAATAATTATTAACATTATCAAATTACTATTATTTTAT
Found at i:45463057 original size:20 final size:20
Alignment explanation
Indices: 45462991--45463058 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
45462981 TTACATAATA
45462991 ATTATTAACATTATCAAATT
1 ATTATTAACATTATCAAATT
* *** *
45463011 ACTACTT-TTTTTATCATAATA
1 ATTA-TTAACATTATCA-AATT
45463032 ATTATTAACATTATCAAATT
1 ATTATTAACATTATCAAATT
45463052 ATTATTA
1 ATTATTA
45463059 TTTTATCACT
Statistics
Matches: 35, Mismatches: 10, Indels: 6
0.69 0.20 0.12
Matches are distributed among these distances:
20 21 0.60
21 14 0.40
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTATTAACATTATCAAATT
Found at i:45464067 original size:20 final size:20
Alignment explanation
Indices: 45464042--45464083 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
45464032 AAAATCTAAC
45464042 TAATATATCACATTA-ATAAA
1 TAATAT-TCACATTATATAAA
*
45464062 TAATATTCATATTATATAAA
1 TAATATTCACATTATATAAA
45464082 TA
1 TA
45464084 TTCAATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
TAATATTCACATTATATAAA
Found at i:45464929 original size:15 final size:16
Alignment explanation
Indices: 45464903--45464936 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
45464893 TGTTATTAAA
*
45464903 TATTTTTATAAAATTT
1 TATTTTTATAAAATAT
45464919 TATTTTT-TAAAATAT
1 TATTTTTATAAAATAT
45464934 TAT
1 TAT
45464937 AATATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
TATTTTTATAAAATAT
Found at i:45470438 original size:30 final size:28
Alignment explanation
Indices: 45470384--45470439 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
45470374 GGTTGAAATC
45470384 ACCCATTTTCGTATATAATTTTTTACCT
1 ACCCATTTTCGTATATAATTTTTTACCT
* *
45470412 ACCCATTTTGGTAATTATATTTTTTTAC
1 ACCCATTTTCGT-A-TATAATTTTTTAC
45470440 ATTATTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.46
29 1 0.04
30 12 0.50
ACGTcount: A:0.25, C:0.18, G:0.05, T:0.52
Consensus pattern (28 bp):
ACCCATTTTCGTATATAATTTTTTACCT
Found at i:45471163 original size:28 final size:28
Alignment explanation
Indices: 45471115--45471168 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
45471105 CTCGTATCTA
*
45471115 AAATAAACAAAAATTTATATCAAAAAAT
1 AAATAAACAAAAATTCATATCAAAAAAT
* * *
45471143 AAATAAATAAAAATTCGTATCCAAAA
1 AAATAAACAAAAATTCATATCAAAAA
45471169 TTATTATCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.65, C:0.09, G:0.02, T:0.24
Consensus pattern (28 bp):
AAATAAACAAAAATTCATATCAAAAAAT
Found at i:45471579 original size:19 final size:20
Alignment explanation
Indices: 45471547--45471595 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
45471537 ATAATAATTG
45471547 TAAAAAAAATTTAAAAATCT
1 TAAAAAAAATTTAAAAATCT
* *
45471567 TAAAAATAA-TTAAAAATCA
1 TAAAAAAAATTTAAAAATCT
*
45471586 TATAAAAAAT
1 TAAAAAAAAT
45471596 AAATTGTAGC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAAAAATTTAAAAATCT
Found at i:45492340 original size:31 final size:29
Alignment explanation
Indices: 45492280--45492335 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
45492270 TACAAAATGA
45492280 TCACTGAACTATTGAATTTTTTATTTAAG
1 TCACTGAACTATTGAATTTTTTATTTAAG
* *
45492309 TCACTGTACTATT-AAGTTTTTTTTTTA
1 TCACTGAACTATTGAA-TTTTTTATTTA
45492336 TAAGTTCAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.54
Consensus pattern (29 bp):
TCACTGAACTATTGAATTTTTTATTTAAG
Found at i:45494781 original size:24 final size:24
Alignment explanation
Indices: 45494740--45494786 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
45494730 ATAATCTTTA
45494740 AATTAAACTCTATATATTTGTTTC
1 AATTAAACTCTATATATTTGTTTC
* * *
45494764 AATTAAATTTTATTTATTTGTTT
1 AATTAAACTCTATATATTTGTTT
45494787 GAGTCAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.06, G:0.04, T:0.57
Consensus pattern (24 bp):
AATTAAACTCTATATATTTGTTTC
Found at i:45497225 original size:25 final size:24
Alignment explanation
Indices: 45497188--45497239 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
45497178 AGGGGTTTTA
45497188 TTATTTAATATTAATATAAATATTT
1 TTATTTAATATTAATAT-AATATTT
* *
45497213 TTATTTAGA-ATTATTATTATATTT
1 TTATTTA-ATATTAATATAATATTT
45497237 TTA
1 TTA
45497240 AAAATATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 9 0.38
25 14 0.58
26 1 0.04
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TTATTTAATATTAATATAATATTT
Found at i:45497706 original size:19 final size:19
Alignment explanation
Indices: 45497663--45497707 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
45497653 ATAAATTTCT
* *
45497663 TAATTTTTATAATTTTATA
1 TAATTTTAATAATTTTAAA
* *
45497682 TTATTTTAATATTTTTAAA
1 TAATTTTAATAATTTTAAA
45497701 TAATTTT
1 TAATTTT
45497708 TTTATAATTA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TAATTTTAATAATTTTAAA
Found at i:45498279 original size:28 final size:29
Alignment explanation
Indices: 45498246--45498301 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
45498236 TCCTTTTCCA
*
45498246 TTTTTA-ATAAACGGCCCAATATTTTTAC
1 TTTTTACATAAACGGCCCAATATGTTTAC
* *
45498274 TTTTTACGTAAATGGCCCAATATGTTTA
1 TTTTTACATAAACGGCCCAATATGTTTA
45498302 TGCTTATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (29 bp):
TTTTTACATAAACGGCCCAATATGTTTAC
Found at i:45506278 original size:18 final size:18
Alignment explanation
Indices: 45506255--45506290 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
45506245 TGGACATATT
45506255 GTTGTCCTGGTTCATTTG
1 GTTGTCCTGGTTCATTTG
45506273 GTTGTCCTGGTTCATTTG
1 GTTGTCCTGGTTCATTTG
45506291 ATCAGGACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.06, C:0.17, G:0.28, T:0.50
Consensus pattern (18 bp):
GTTGTCCTGGTTCATTTG
Found at i:45507234 original size:28 final size:28
Alignment explanation
Indices: 45507193--45507254 Score: 72
Period size: 29 Copynumber: 2.2 Consensus size: 28
45507183 GATATATATA
* * *
45507193 TATTTTTAGGTCATTATT-ATTTAATTT
1 TATTTTTAGCTCATTATTAATGTAATTC
*
45507220 TATTTTTACGCTCATTTTTAATGTAATTC
1 TATTTTTA-GCTCATTATTAATGTAATTC
45507249 TATTTT
1 TATTTT
45507255 AAAATATCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 8 0.28
28 8 0.28
29 13 0.45
ACGTcount: A:0.24, C:0.08, G:0.06, T:0.61
Consensus pattern (28 bp):
TATTTTTAGCTCATTATTAATGTAATTC
Found at i:45514682 original size:61 final size:61
Alignment explanation
Indices: 45514610--45514812 Score: 159
Period size: 61 Copynumber: 3.3 Consensus size: 61
45514600 TATCTCATGT
* *
45514610 CTTTTAAATCTTTTAAATTTCCTTTTTTATACCCTTAATAATATATATTTTACCAATTTAC
1 CTTTAAAATCTTTTAAATTTACTTTTTTATACCCTTAATAATATATATTTTACCAATTTAC
** ** * * ** *** *
45514671 CTTTAAAATCTTTTAAATTTAAATTTGCATAGTCACGTGGT--T-TCCCTTCTTAGCTC-ATATA
1 CTTTAAAATCTTTTAAATTTACTTTTTTATA--CCCTTAATAATATATATT-TTA-C-CAATTTA
45514732 -
61 C
* *
45514732 ATTT-AAATCATTTT-AATTTTCTTTTTTATACCCTTAATAATATATATTTTACCAATTTAC
1 CTTTAAAATC-TTTTAAATTTACTTTTTTATACCCTTAATAATATATATTTTACCAATTTAC
45514792 CTTTAAAATCTTTTAAATTTA
1 CTTTAAAATCTTTTAAATTTA
45514813 AATTTGCATA
Statistics
Matches: 99, Mismatches: 30, Indels: 26
0.64 0.19 0.17
Matches are distributed among these distances:
58 5 0.05
59 5 0.05
60 30 0.30
61 49 0.49
62 5 0.05
63 5 0.05
ACGTcount: A:0.32, C:0.15, G:0.03, T:0.50
Consensus pattern (61 bp):
CTTTAAAATCTTTTAAATTTACTTTTTTATACCCTTAATAATATATATTTTACCAATTTAC
Found at i:45514720 original size:121 final size:121
Alignment explanation
Indices: 45514589--45514860 Score: 465
Period size: 121 Copynumber: 2.2 Consensus size: 121
45514579 CACACATGTT
* * **
45514589 GTTTCCCTTCTTATCTCATGTCTTTTAAATC-TTTTAAATTTCCTTTTTTATACCCTTAATAATA
1 GTTTCCCTTCTTAGCTCATATAATTTAAATCATTTT-AATTTCCTTTTTTATACCCTTAATAATA
45514653 TATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGTCACGTG
65 TATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGTCACGTG
*
45514710 GTTTCCCTTCTTAGCTCATATAATTTAAATCATTTTAATTTTCTTTTTTATACCCTTAATAATAT
1 GTTTCCCTTCTTAGCTCATATAATTTAAATCATTTTAATTTCCTTTTTTATACCCTTAATAATAT
45514775 ATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGTCACGTG
66 ATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGTCACGTG
**
45514831 GTTTCCCTTCTTAGCTCATACCATTTAAAT
1 GTTTCCCTTCTTAGCTCATATAATTTAAAT
45514861 ATATGCTGTA
Statistics
Matches: 143, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
121 139 0.97
122 4 0.03
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.49
Consensus pattern (121 bp):
GTTTCCCTTCTTAGCTCATATAATTTAAATCATTTTAATTTCCTTTTTTATACCCTTAATAATAT
ATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGTCACGTG
Found at i:45517703 original size:50 final size:50
Alignment explanation
Indices: 45517527--45517963 Score: 306
Period size: 49 Copynumber: 8.8 Consensus size: 50
45517517 CCATGAAGGC
* * *
45517527 ATGAAGGGAAAGATTTAAGCCGCAATGGCAAATCTAATACCGCGAAGATA
1 ATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACCACGAAGATA
* * * * * * *
45517577 ATGGAGGGAAAGGTTTAAGTCGCAACGGCGAA-CTTTGTACCTCAGAAG--C
1 ATGAAGGGAAAGATTTAAGCCGCAATGGCGAATC-TAGTACCAC-GAAGATA
* * * *
45517626 ATGAAAGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACGAGGATA
1 ATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACCACGAAGATA
* * * * *
45517676 ATGAAGGGAAAGATTTAAGCCGTAACGGTGAATCCAGTACCTCGAAGATA
1 ATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACCACGAAGATA
* * * * * * *
45517726 AT-AGAGGGAAA-AGTTGAGTCACAACGGCGAACCTTGTACCTTA-GAAG-TA
1 ATGA-AGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACC--ACGAAGATA
* *
45517775 CA--AAGGGAAAGATTTAAGCCGCAATGACGAATCCAGTACCACGAAGATA
1 -ATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACCACGAAGATA
* * * * * * * * **
45517824 CA--AAGGGAAGGGTTTAAGTCACAATGGCGAACCTTGTACCTC-AAAAGC
1 -ATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACCACGAAGATA
* * * * *
45517872 ACGAAGGGAAAGATTCAAGCTGCAATGACGAATCCAGTACCACGAAGATA
1 ATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACCACGAAGATA
* *
45517922 ATGGAA-GGAAAGATTTAAGCCGCGATGGCGAATCCAGTACCA
1 AT-GAAGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACCA
45517964 AGCAGACATT
Statistics
Matches: 298, Mismatches: 73, Indels: 32
0.74 0.18 0.08
Matches are distributed among these distances:
47 2 0.01
48 17 0.06
49 145 0.49
50 127 0.43
51 7 0.02
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.18
Consensus pattern (50 bp):
ATGAAGGGAAAGATTTAAGCCGCAATGGCGAATCTAGTACCACGAAGATA
Found at i:45517703 original size:99 final size:99
Alignment explanation
Indices: 45517525--45517703 Score: 259
Period size: 99 Copynumber: 1.8 Consensus size: 99
45517515 TACCATGAAG
* * * * *
45517525 GCATGAAGGGAAAGATTTAAGCCGCAATGGCAAATCTAATACCGCGAAGATAATGGAGGGAAAGG
1 GCATGAAAGGAAAGATTTAAGCCGCAACGGCAAATCTAATACCACGAAGATAATGAAGGGAAAGA
*
45517590 TTTAAGTCGCAACGGCGAACTTTGTACCTCAGAA
66 TTTAAGCCGCAACGGCGAACTTTGTACCTCAGAA
* * * *
45517624 GCATGAAAGGAAAGATTTAAGTCGCAACGGCGAATCTAGTACCACGAGGATAATGAAGGGAAAGA
1 GCATGAAAGGAAAGATTTAAGCCGCAACGGCAAATCTAATACCACGAAGATAATGAAGGGAAAGA
*
45517689 TTTAAGCCGTAACGG
66 TTTAAGCCGCAACGG
45517704 TGAATCCAGT
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
99 69 1.00
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.18
Consensus pattern (99 bp):
GCATGAAAGGAAAGATTTAAGCCGCAACGGCAAATCTAATACCACGAAGATAATGAAGGGAAAGA
TTTAAGCCGCAACGGCGAACTTTGTACCTCAGAA
Found at i:45517790 original size:148 final size:149
Alignment explanation
Indices: 45517527--45517823 Score: 391
Period size: 148 Copynumber: 2.0 Consensus size: 149
45517517 CCATGAAGGC
* * * *
45517527 ATGAAGGGAAAGATTTAAGCCGCAATGGCAAATCTAATACCGCGAAGATAATGGAGGGAAAGGTT
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAATACCGCGAAGATAATAGAGGGAAAAGTT
* * * * *
45517592 TAAGTCGCAACGGCGAACTTTGTACCTCAGAAGCATGAAAGGAAAGATTTAAGTCGCAACGGCGA
66 TAAGTCACAACGGCGAACCTTGTACCTCAGAAGCATCAAAGGAAAGATTTAAGCCGCAACGACGA
* *
45517657 ATCTAGTACCACGAGGATA
131 ATCCAGTACCACGAAGATA
* ** * *
45517676 ATGAAGGGAAAGATTTAAGCCGTAACGGTGAATCCAGTACCTCGAAGATAATAGAGGGAAAAG-T
1 ATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAATACCGCGAAGATAATAGAGGGAAAAGTT
* * * *
45517740 TGAGTCACAACGGCGAACCTTGTACCTTAGAAGTA-CAAAGGGAAAGATTTAAGCCGCAATGACG
66 TAAGTCACAACGGCGAACCTTGTACCTCAGAAGCATCAAA-GGAAAGATTTAAGCCGCAACGACG
45517804 AATCCAGTACCACGAAGATA
130 AATCCAGTACCACGAAGATA
45517824 CAAAGGGAAG
Statistics
Matches: 127, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
147 3 0.02
148 70 0.55
149 54 0.43
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (149 bp):
ATGAAGGGAAAGATTTAAGCCGCAACGGCAAATCCAATACCGCGAAGATAATAGAGGGAAAAGTT
TAAGTCACAACGGCGAACCTTGTACCTCAGAAGCATCAAAGGAAAGATTTAAGCCGCAACGACGA
ATCCAGTACCACGAAGATA
Found at i:45520226 original size:61 final size:61
Alignment explanation
Indices: 45520159--45520352 Score: 152
Period size: 61 Copynumber: 3.2 Consensus size: 61
45520149 ATCTTTTATC
45520159 TCTTTTAAATTTCCTTTTTTATACCCTGAATAATATATATTTTACCAATTTACCTTTAAAA
1 TCTTTTAAATTTCCTTTTTTATACCCTGAATAATATATATTTTACCAATTTACCTTTAAAA
*** ** * * *** * *
45520220 TCTTTTAAATTTAAATTTGCATAGTCACGTG-GT--T-TCCCTTCTTAGCTC-ATATA-ATTT-A
1 TCTTTTAAATTTCCTTTTTTATA--C-CCTGAATAATATATATT-TTA-C-CAATTTACCTTTAA
45520278 AA
60 AA
*
45520280 TCATTTT-AATTTCCTTTTTTATACCCTTAATAATATATATTTTACCAATTTACCTTTAAAA
1 TC-TTTTAAATTTCCTTTTTTATACCCTGAATAATATATATTTTACCAATTTACCTTTAAAA
45520341 TCTTTTAAATTT
1 TCTTTTAAATTT
45520353 AAATTTGCAT
Statistics
Matches: 93, Mismatches: 25, Indels: 30
0.63 0.17 0.20
Matches are distributed among these distances:
57 2 0.02
58 3 0.03
59 5 0.05
60 30 0.32
61 42 0.45
62 5 0.05
63 3 0.03
64 3 0.03
ACGTcount: A:0.31, C:0.16, G:0.04, T:0.49
Consensus pattern (61 bp):
TCTTTTAAATTTCCTTTTTTATACCCTGAATAATATATATTTTACCAATTTACCTTTAAAA
Found at i:45520262 original size:121 final size:121
Alignment explanation
Indices: 45520130--45520401 Score: 456
Period size: 121 Copynumber: 2.2 Consensus size: 121
45520120 CACACATGTT
* ** **
45520130 GTTTCCCTTCTTATCTCATATCTTTTATCTC-TTTTAAATTTCCTTTTTTATACCCTGAATAATA
1 GTTTCCCTTCTTAGCTCATATAATTTAAATCATTTT-AATTTCCTTTTTTATACCCTGAATAATA
45520194 TATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGTCACGTG
65 TATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGTCACGTG
*
45520251 GTTTCCCTTCTTAGCTCATATAATTTAAATCATTTTAATTTCCTTTTTTATACCCTTAATAATAT
1 GTTTCCCTTCTTAGCTCATATAATTTAAATCATTTTAATTTCCTTTTTTATACCCTGAATAATAT
45520316 ATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGTCACGTG
66 ATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGTCACGTG
**
45520372 GTTTCCCTTCTTAGCTCATACCATTTAAAT
1 GTTTCCCTTCTTAGCTCATATAATTTAAAT
45520402 ATATGCTGTA
Statistics
Matches: 142, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
121 138 0.97
122 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.48
Consensus pattern (121 bp):
GTTTCCCTTCTTAGCTCATATAATTTAAATCATTTTAATTTCCTTTTTTATACCCTGAATAATAT
ATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTGCATAGTCACGTG
Found at i:45523209 original size:50 final size:50
Alignment explanation
Indices: 45523130--45523565 Score: 333
Period size: 49 Copynumber: 8.8 Consensus size: 50
45523120 CCATGAAGGC
* *
45523130 ATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCCAATACCGCGAAGATA
1 ATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCCAGTACCTCGAAGATA
* * ** *
45523180 ATGGAGGGAAAGGTTTAAGTCGCAATGGCGAA-CTTTGTACCTCAGAAG--C
1 ATGAAGGGAAAGATTTAAGTCGCAATGGCGAATC-CAGTACCTC-GAAGATA
* * * * * *
45523229 ATGAAAGGAAAGATTTAAGTCGCAACGACGAATCTAGTACCACGAGGATA
1 ATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCCAGTACCTCGAAGATA
* *
45523279 ATGAAGGGAAAGATTTAAG-CTGCAACGGTGAATCCAGTACCTCGAAGATA
1 ATGAAGGGAAAGATTTAAGTC-GCAATGGCGAATCCAGTACCTCGAAGATA
* * * ** *
45523329 ATGGAGGGAAA-AGTTGAGTCATAATGGCGAA-CCTTGTACCTCAGAAG-TA
1 ATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCC-AGTACCTC-GAAGATA
* * *
45523378 CA--AAGGGAAAGATTTAAGCCGCAATGACGAATCCAGTACCACGAAGATA
1 -ATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCCAGTACCTCGAAGATA
* * * * * * **
45523427 CA--AAGTGAAGGGTTTAAGTCACAATGGCGAA-CCTTGTACCTC-AAAAGC
1 -ATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCC-AGTACCTCGAAGATA
* * * * *
45523475 ACGAAGGGAAAGATTCAAGCCGCAATGACGAATCCAGTACCACGAAGATA
1 ATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCCAGTACCTCGAAGATA
* **
45523525 ATGGAA-GGAAAGATTTAAGCCGTGATGGCGAATCCAGTACC
1 AT-GAAGGGAAAGATTTAAGTCGCAATGGCGAATCCAGTACC
45523566 AAGCAGACAT
Statistics
Matches: 300, Mismatches: 67, Indels: 38
0.74 0.17 0.09
Matches are distributed among these distances:
47 1 0.00
48 21 0.07
49 138 0.46
50 133 0.44
51 7 0.02
ACGTcount: A:0.38, C:0.18, G:0.26, T:0.19
Consensus pattern (50 bp):
ATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCCAGTACCTCGAAGATA
Found at i:45523319 original size:99 final size:98
Alignment explanation
Indices: 45523128--45523325 Score: 238
Period size: 99 Copynumber: 2.0 Consensus size: 98
45523118 TACCATGAAG
* * * * * *
45523128 GCATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCCAATACCGCGAAGATAATGGAGGGAAAGG
1 GCATGAAAGGAAAGATTTAAGTCGCAACGACGAATCCAATACCACGAAGATAATGAAGGGAAAGA
* **
45523193 TTTAAGTCGCAATGGCGAACTTTGTACCTCAGAA
66 TTTAAGTCGCAACGGCGAACTCAGTACCTC-GAA
* * *
45523227 GCATGAAAGGAAAGATTTAAGTCGCAACGACGAATCTAGTACCACGAGGATAATGAAGGGAAAGA
1 GCATGAAAGGAAAGATTTAAGTCGCAACGACGAATCCAATACCACGAAGATAATGAAGGGAAAGA
*
45523292 TTTAAG-CTGCAACGGTGAA-TCCAGTACCTCGAA
66 TTTAAGTC-GCAACGGCGAACT-CAGTACCTCGAA
45523325 G
1 G
45523326 ATAATGGAGG
Statistics
Matches: 84, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
98 6 0.07
99 78 0.93
ACGTcount: A:0.37, C:0.17, G:0.27, T:0.19
Consensus pattern (98 bp):
GCATGAAAGGAAAGATTTAAGTCGCAACGACGAATCCAATACCACGAAGATAATGAAGGGAAAGA
TTTAAGTCGCAACGGCGAACTCAGTACCTCGAA
Found at i:45523401 original size:148 final size:149
Alignment explanation
Indices: 45523130--45523426 Score: 420
Period size: 148 Copynumber: 2.0 Consensus size: 149
45523120 CCATGAAGGC
* *
45523130 ATGAAGGGAAAGATTTAAGTCGCAATGGCGAATCCAATACCGCGAAGATAATGGAGGGAAAGGTT
1 ATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAATACCGCGAAGATAATGGAGGGAAAAGTT
* * * *
45523195 TAAGTCGCAATGGCGAACTTTGTACCTCAGAAGCATGAAAGGAAAGATTTAAGTCGCAACGACGA
66 TAAGTCACAATGGCGAACCTTGTACCTCAGAAGCATCAAAGGAAAGATTTAAGCCGCAACGACGA
* *
45523260 ATCTAGTACCACGAGGATA
131 ATCCAGTACCACGAAGATA
* * *
45523279 ATGAAGGGAAAGATTTAAG-CTGCAACGGTGAATCCAGTACCTCGAAGATAATGGAGGGAAAAG-
1 ATGAAGGGAAAGATTTAAGTC-GCAACGGCGAATCCAATACCGCGAAGATAATGGAGGGAAAAGT
* * * *
45523342 TTGAGTCATAATGGCGAACCTTGTACCTCAGAAGTA-CAAAGGGAAAGATTTAAGCCGCAATGAC
65 TTAAGTCACAATGGCGAACCTTGTACCTCAGAAGCATCAAA-GGAAAGATTTAAGCCGCAACGAC
45523406 GAATCCAGTACCACGAAGATA
129 GAATCCAGTACCACGAAGATA
45523427 CAAAGTGAAG
Statistics
Matches: 131, Mismatches: 15, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
147 3 0.02
148 72 0.55
149 56 0.43
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.19
Consensus pattern (149 bp):
ATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCCAATACCGCGAAGATAATGGAGGGAAAAGTT
TAAGTCACAATGGCGAACCTTGTACCTCAGAAGCATCAAAGGAAAGATTTAAGCCGCAACGACGA
ATCCAGTACCACGAAGATA
Found at i:45525258 original size:15 final size:15
Alignment explanation
Indices: 45525238--45525271 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
45525228 AAAATTGAAA
45525238 TTTTTTTCTCTAAAT-
1 TTTTTTTCT-TAAATG
45525253 TTTTTTTCTTAAATG
1 TTTTTTTCTTAAATG
45525268 TTTT
1 TTTT
45525272 AGCTGTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.18, C:0.09, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTTTTTCTTAAATG
Found at i:45525698 original size:112 final size:113
Alignment explanation
Indices: 45525487--45525712 Score: 391
Period size: 112 Copynumber: 2.0 Consensus size: 113
45525477 CACACACACA
* ** *
45525487 CGGGGTTTCCCTTCTTATCTCATATCTTTTAAATCTTTTTAATTTCCTTTTTTATACCTTTAATA
1 CGGGGTTTCCCTTCTTAGCTCATATAATTTAAATCTTTTTAATTTCCTTTTTTATACCCTTAATA
*
45525552 ATATATATTTTACCAATTTACCTTTAAAATCTTTTAAATTTAAATTTG
66 ATATATATTTTAACAATTTACCTTTAAAATCTTTTAAATTTAAATTTG
45525600 CGGGGTTTCCCTTCTTAGCTCATATAATTTAAATCTTTTTAATTTCC-TTTTTATACCCTTAATA
1 CGGGGTTTCCCTTCTTAGCTCATATAATTTAAATCTTTTTAATTTCCTTTTTTATACCCTTAATA
*
45525664 ATATATATTTTAACAATTTACTTTTAAAATCTTTTAAATTTAAATTTG
66 ATATATATTTTAACAATTTACCTTTAAAATCTTTTAAATTTAAATTTG
45525712 C
1 C
45525713 ATAGTCTACC
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
112 63 0.59
113 44 0.41
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.51
Consensus pattern (113 bp):
CGGGGTTTCCCTTCTTAGCTCATATAATTTAAATCTTTTTAATTTCCTTTTTTATACCCTTAATA
ATATATATTTTAACAATTTACCTTTAAAATCTTTTAAATTTAAATTTG
Found at i:45528463 original size:3 final size:3
Alignment explanation
Indices: 45528455--45528515 Score: 122
Period size: 3 Copynumber: 20.3 Consensus size: 3
45528445 ACAACGATAG
45528455 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
45528503 AGA AGA AGA AGA A
1 AGA AGA AGA AGA A
45528516 AATTGGGTTT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 58 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:45534015 original size:22 final size:22
Alignment explanation
Indices: 45533967--45534015 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
45533957 TCTTTGATGC
*
45533967 TTTTTTTATTGTTTTGGTTACT
1 TTTTTTTATCGTTTTGGTTACT
* *
45533989 ATTTTTTGTCGTTTTGTGTTA-T
1 TTTTTTTATCGTTTTG-GTTACT
45534011 TTTTT
1 TTTTT
45534016 ACTATTTTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.08, C:0.04, G:0.14, T:0.73
Consensus pattern (22 bp):
TTTTTTTATCGTTTTGGTTACT
Found at i:45534064 original size:23 final size:23
Alignment explanation
Indices: 45534038--45534099 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
45534028 TTTTTTACTA
*
45534038 TTTTGGTTGCTGTTTTCG-TGTTG
1 TTTTGGTTGCTATTTT-GTTGTTG
* *
45534061 TTTTTGTTGTTATTTTGTTGTTG
1 TTTTGGTTGCTATTTTGTTGTTG
**
45534084 TTTTTATTGCTATTTT
1 TTTTGGTTGCTATTTT
45534100 TATTATTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
22 1 0.03
23 32 0.97
ACGTcount: A:0.05, C:0.05, G:0.21, T:0.69
Consensus pattern (23 bp):
TTTTGGTTGCTATTTTGTTGTTG
Found at i:45534071 original size:12 final size:12
Alignment explanation
Indices: 45534038--45534162 Score: 73
Period size: 12 Copynumber: 10.9 Consensus size: 12
45534028 TTTTTTACTA
* *
45534038 TTTTGGTTGCTG
1 TTTTTGTTGTTG
*
45534050 TTTTCG-TGTTG
1 TTTTTGTTGTTG
45534061 TTTTTGTTGTT-
1 TTTTTGTTGTTG
*
45534072 ATTTTGTTGTTG
1 TTTTTGTTGTTG
* *
45534084 TTTTTATTG--C
1 TTTTTGTTGTTG
* * *
45534094 TATTT-TTATTA
1 TTTTTGTTGTTG
**
45534105 TTTTTAATGTTG
1 TTTTTGTTGTTG
*
45534117 -TTTTGTTGTTA
1 TTTTTGTTGTTG
*
45534128 TTTTTGCTGTTG
1 TTTTTGTTGTTG
* *
45534140 TTTTGGTTGTTA
1 TTTTTGTTGTTG
45534152 TTTTTGTTGTT
1 TTTTTGTTGTT
45534163 TAGATGTTAT
Statistics
Matches: 84, Mismatches: 23, Indels: 12
0.71 0.19 0.10
Matches are distributed among these distances:
9 2 0.02
10 4 0.05
11 31 0.37
12 47 0.56
ACGTcount: A:0.07, C:0.03, G:0.20, T:0.70
Consensus pattern (12 bp):
TTTTTGTTGTTG
Found at i:45534078 original size:17 final size:17
Alignment explanation
Indices: 45534058--45534091 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
45534048 TGTTTTCGTG
*
45534058 TTGTTTTTGTTGTTATT
1 TTGTTGTTGTTGTTATT
*
45534075 TTGTTGTTGTTTTTATT
1 TTGTTGTTGTTGTTATT
45534092 GCTATTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.00, G:0.18, T:0.76
Consensus pattern (17 bp):
TTGTTGTTGTTGTTATT
Found at i:45534148 original size:24 final size:23
Alignment explanation
Indices: 45534048--45534162 Score: 87
Period size: 23 Copynumber: 5.0 Consensus size: 23
45534038 TTTTGGTTGC
* *
45534048 TGTTTTCG-TGTTGTTTTTGTTGT
1 TGTTTT-GTTGTTATTTTTGATGT
* *
45534071 TATTTTGTTGTTGTTTTT-A--T
1 TGTTTTGTTGTTATTTTTGATGT
* *
45534091 TGCTATTT-TTATTATTTTTAATGT
1 TG-T-TTTGTTGTTATTTTTGATGT
*
45534115 TGTTTTGTTGTTATTTTTGCTGT
1 TGTTTTGTTGTTATTTTTGATGT
*
45534138 TGTTTTGGTTGTTATTTTTGTTGT
1 TGTTTT-GTTGTTATTTTTGATGT
45534162 T
1 T
45534163 TAGATGTTAT
Statistics
Matches: 75, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
20 2 0.03
21 10 0.13
22 8 0.11
23 35 0.47
24 20 0.27
ACGTcount: A:0.08, C:0.03, G:0.19, T:0.70
Consensus pattern (23 bp):
TGTTTTGTTGTTATTTTTGATGT
Found at i:45534370 original size:27 final size:26
Alignment explanation
Indices: 45534280--45534368 Score: 87
Period size: 27 Copynumber: 3.5 Consensus size: 26
45534270 ACTATCTTAA
* * *
45534280 TATAAATTTTTTAATGTATTTTAAATT
1 TATATATTTTTTAATGTATTTGATA-T
* *
45534307 TATTTATTTTTTAATG--TTTG-TTT
1 TATATATTTTTTAATGTATTTGATAT
*
45534330 TA-ATATTTTTAAATGTATTTGATAT
1 TATATATTTTTTAATGTATTTGATAT
45534355 TATATATTTTTTAA
1 TATATATTTTTTAA
45534369 ATTTGTTGTA
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
22 11 0.22
23 3 0.06
24 4 0.08
25 7 0.14
26 10 0.20
27 14 0.29
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (26 bp):
TATATATTTTTTAATGTATTTGATAT
Found at i:45539485 original size:30 final size:29
Alignment explanation
Indices: 45539423--45539506 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 29
45539413 AATTATCTAG
* ***
45539423 AAATTACATTTTGACCCCAAAAATTTTTGA
1 AAATTACATTTT-ACCCCAAAACTTCAAGA
*
45539453 AAATTACATTTTAACCCCGAAACTTCAAGA
1 AAATTACATTTT-ACCCCAAAACTTCAAGA
*
45539483 AAA-TACCATTTTACCCCTAAACTT
1 AAATTA-CATTTTACCCCAAAACTT
45539507 TCCTAAATTC
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
29 13 0.28
30 33 0.72
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (29 bp):
AAATTACATTTTACCCCAAAACTTCAAGA
Found at i:45539521 original size:58 final size:57
Alignment explanation
Indices: 45539453--45539644 Score: 210
Period size: 58 Copynumber: 3.3 Consensus size: 57
45539443 AAATTTTTGA
* *
45539453 AAATTACATTTTAACCCCGAAACTTCA-AGAAAA-TACCATTTTACCCCTAAACTTTCCT
1 AAATTCCATTTTAACCCCG--ATTTCACA-AAAATTACCATTTTACCCCTAAACTTTCCT
* * *
45539511 AAATTCCATTTTAACCCCGATTTCACCCAAAATTACCATTTTAACCTTAAACTTT-CT
1 AAATTCCATTTTAACCCCGATTTCA-CAAAAATTACCATTTTACCCCTAAACTTTCCT
* * *
45539568 AAAATTCCATTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCCTCGAACCTTCCA
1 -AAATTCCATTTTAACCCCGATTTCA-CAAAAATTACCATTTTACCCCT-AAACTTTCCT
* *
45539628 AAATCCCCTTTTAACCC
1 AAATTCCATTTTAACCC
45539645 TAAATTTTCC
Statistics
Matches: 115, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
56 5 0.04
57 6 0.05
58 83 0.72
59 20 0.17
60 1 0.01
ACGTcount: A:0.34, C:0.31, G:0.03, T:0.32
Consensus pattern (57 bp):
AAATTCCATTTTAACCCCGATTTCACAAAAATTACCATTTTACCCCTAAACTTTCCT
Found at i:45539527 original size:29 final size:29
Alignment explanation
Indices: 45539483--45539586 Score: 85
Period size: 28 Copynumber: 3.6 Consensus size: 29
45539473 AACTTCAAGA
*
45539483 AAATACCATTTT-ACCCCTAAACTTTCCT
1 AAATTCCATTTTAACCCCTAAACTTTCCT
* *
45539511 AAATTCCATTTTAACCCC--GA-TTTCACCCA
1 AAATTCCATTTTAACCCCTAAACTTT---CCT
*
45539540 AAATTACCATTTTAA-CCTTAAACTTT-CT
1 AAATT-CCATTTTAACCCCTAAACTTTCCT
45539568 AAAATTCCATTTTAACCCC
1 -AAATTCCATTTTAACCCC
45539587 GATTTCACCA
Statistics
Matches: 59, Mismatches: 7, Indels: 19
0.69 0.08 0.22
Matches are distributed among these distances:
26 3 0.05
27 1 0.02
28 21 0.36
29 21 0.36
30 9 0.15
31 1 0.02
32 3 0.05
ACGTcount: A:0.34, C:0.30, G:0.01, T:0.36
Consensus pattern (29 bp):
AAATTCCATTTTAACCCCTAAACTTTCCT
Found at i:45539600 original size:29 final size:30
Alignment explanation
Indices: 45539511--45539615 Score: 105
Period size: 29 Copynumber: 3.6 Consensus size: 30
45539501 AAACTTTCCT
*
45539511 AAATT-CCATTTTAACCCCGATTTCACCCA
1 AAATTACCATTTTAACCCCGATTTCACCAA
*** *
45539540 AAATTACCATTTTAACCTTAAACTTT---CTA
1 AAATTACCATTTTAACC-CCGA-TTTCACCAA
45539569 AAATT-CCATTTTAACCCCGATTTCACCAA
1 AAATTACCATTTTAACCCCGATTTCACCAA
45539598 AAATTACCATTTT-ACCCC
1 AAATTACCATTTTAACCCC
45539616 TCGAACCTTC
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
26 3 0.05
27 1 0.02
28 11 0.18
29 24 0.39
30 18 0.30
31 1 0.02
32 3 0.05
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (30 bp):
AAATTACCATTTTAACCCCGATTTCACCAA
Found at i:45539631 original size:30 final size:29
Alignment explanation
Indices: 45539452--45539644 Score: 103
Period size: 29 Copynumber: 6.7 Consensus size: 29
45539442 AAAATTTTTG
* *
45539452 AAAATTA-CATTTTAACCCCGAAACTTCA
1 AAAATTACCATTTTAACCCCGAACCTTCC
* * *
45539480 AGAAAATACCATTTT-ACCCCTAAACTTTCC
1 A-AAATTACCATTTTAACCCC-GAACCTTCC
* ** **
45539510 TAAATT-CCATTTTAACCCCGATTTCACCC
1 AAAATTACCATTTTAACCCCGA-ACCTTCC
*** * *
45539539 AAAATTACCATTTTAACCTTAAACTTTCT
1 AAAATTACCATTTTAACCCCGAACCTTCC
*
45539568 AAAATT-CCATTTTAACCCCG-A-TTTCACC
1 AAAATTACCATTTTAACCCCGAACCTT--CC
*
45539596 AAAAATTACCATTTTACCCCTCGAACCTTCC
1 -AAAATTACCATTTTAACCC-CGAACCTTCC
* *
45539627 AAAA-TCCCCTTTTAACCC
1 AAAATTACCATTTTAACCC
45539645 TAAATTTTCC
Statistics
Matches: 120, Mismatches: 32, Indels: 25
0.68 0.18 0.14
Matches are distributed among these distances:
26 3 0.03
27 1 0.01
28 21 0.17
29 50 0.42
30 38 0.32
31 4 0.03
32 1 0.01
33 2 0.02
ACGTcount: A:0.35, C:0.31, G:0.03, T:0.32
Consensus pattern (29 bp):
AAAATTACCATTTTAACCCCGAACCTTCC
Found at i:45539660 original size:59 final size:57
Alignment explanation
Indices: 45539482--45539668 Score: 209
Period size: 58 Copynumber: 3.2 Consensus size: 57
45539472 AAACTTCAAG
* *
45539482 AAAA-TACCATTTTACCCCTAAACTTTCCTAAATTCCATTTTAACCCCGATTTCACCC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGATTT-TCCC
* * *
45539539 AAAATTACCATTTTAACCTTAAACTTTCTAAAATTCCATTTTAACCCCGA-TTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGATTTTC-CC
* * * * **
45539596 AAAAATTACCATTTTACCCCTCGAACCTTCCAAAATCCCCTTTTAACCCTAAATTTTCCC
1 -AAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTAACCC-CGATTTTCCC
45539656 AAAATTA-CATTTT
1 AAAATTACCATTTT
45539669 TGCCCTCGTA
Statistics
Matches: 110, Mismatches: 14, Indels: 11
0.81 0.10 0.08
Matches are distributed among these distances:
56 1 0.01
57 8 0.07
58 65 0.59
59 29 0.26
60 3 0.03
61 4 0.04
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.35
Consensus pattern (57 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTAACCCCGATTTTCCC
Found at i:45539667 original size:116 final size:115
Alignment explanation
Indices: 45539452--45539668 Score: 262
Period size: 116 Copynumber: 1.9 Consensus size: 115
45539442 AAAATTTTTG
* * *
45539452 AAAATTACATTTTAACCCCGAAACTTCAAGAAAATACCATTTTACCCCTAAACTTTCCTAAATTC
1 AAAATTACATTTTAACCCCG-AACTTCAAGAAAATACCATTTTACCCCTAAACCTTCCAAAATCC
**
45539517 CATTTTAACCCCGATTTCACCCAAAATTACCATTTTAACCTTAAACTTTCT
65 CATTTTAACCCAAATTTCACCCAAAATTACCATTTTAACCTTAAACTTTCT
* * *
45539568 AAAATTCCATTTTAACCCCG-ATTTCACCA-AAAATTACCATTTTACCCCTCGAACCTTCCAAAA
1 AAAATTACATTTTAACCCCGAACTTCA--AGAAAA-TACCATTTTACCCCT-AAACCTTCCAAAA
* *
45539631 TCCCCTTTTAACCCTAAATTT-TCCCAAAATTA-CATTTT
62 TCCCATTTTAACCC-AAATTTCACCCAAAATTACCATTTT
45539669 TGCCCTCGTA
Statistics
Matches: 86, Mismatches: 10, Indels: 10
0.81 0.09 0.09
Matches are distributed among these distances:
114 5 0.06
115 4 0.05
116 41 0.48
117 32 0.37
118 4 0.05
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (115 bp):
AAAATTACATTTTAACCCCGAACTTCAAGAAAATACCATTTTACCCCTAAACCTTCCAAAATCCC
ATTTTAACCCAAATTTCACCCAAAATTACCATTTTAACCTTAAACTTTCT
Found at i:45539668 original size:29 final size:28
Alignment explanation
Indices: 45539452--45539668 Score: 102
Period size: 29 Copynumber: 7.5 Consensus size: 28
45539442 AAAATTTTTG
* *
45539452 AAAATTACATTTTAACCCCGAAAC-TTCA
1 AAAATTACATTTTAA-CCCTAAACTTTCC
* *
45539480 AGAAAATACCATTTTACCCCTAAACTTTCC
1 A-AAATTA-CATTTTAACCCTAAACTTTCC
* * **
45539510 TAAATTCCATTTTAACCC-CGA-TTTCACCC
1 AAAATTACATTTTAACCCTAAACTTT---CC
* *
45539539 AAAATTACCATTTTAACCTTAAACTTTCT
1 AAAATTA-CATTTTAACCCTAAACTTTCC
* **
45539568 AAAATTCCATTTTAACCC-CGA-TTTCACC
1 AAAATTACATTTTAACCCTAAACTTT--CC
* * *
45539596 AAAAATTACCATTTTACCCCTCGAACCTTCC
1 -AAAATTA-CATTTTAACCCT-AAACTTTCC
** * *
45539627 AAAATCCCCTTTTAACCCTAAATTTTCCC
1 AAAATTACATTTTAACCCTAAACTTT-CC
45539656 AAAATTACATTTT
1 AAAATTACATTTT
45539669 TGCCCTCGTA
Statistics
Matches: 136, Mismatches: 36, Indels: 33
0.66 0.18 0.16
Matches are distributed among these distances:
26 6 0.04
27 2 0.01
28 26 0.19
29 58 0.43
30 35 0.26
31 3 0.02
32 4 0.03
33 2 0.01
ACGTcount: A:0.35, C:0.29, G:0.02, T:0.34
Consensus pattern (28 bp):
AAAATTACATTTTAACCCTAAACTTTCC
Found at i:45545369 original size:24 final size:24
Alignment explanation
Indices: 45545342--45545416 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
45545332 AGAAATAATA
* *
45545342 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
45545366 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
*
45545390 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
45545414 TTT
1 TTT
45545417 GAGTCAAATT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 48 1.00
ACGTcount: A:0.25, C:0.12, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:45546311 original size:13 final size:13
Alignment explanation
Indices: 45546295--45546349 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
45546285 TACTTTTGAG
45546295 AAGTATTTTTAAA
1 AAGTATTTTTAAA
* *
45546308 AAGTGTTTTAAAA
1 AAGTATTTTTAAA
*
45546321 AAGTGA-TTTTGAA
1 AAGT-ATTTTTAAA
45546334 AAGTATTTTTGAAA
1 AAGTATTTTT-AAA
45546348 AA
1 AA
45546350 TTTGGTGTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
12 1 0.03
13 28 0.85
14 4 0.12
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (13 bp):
AAGTATTTTTAAA
Done.