Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold376
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: 900718
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 6
Found at i:538880 original size:50 final size:50
Alignment explanation
Indices: 538819--538980 Score: 155
Period size: 51 Copynumber: 3.2 Consensus size: 50
538809 TTTCGAGGAA
* * *
538819 ATACTCTAACTCCAATTTTTTTCTAAAATACCAATTTTCCATAATCGGGG
1 ATACTCCAACTCCAATTTATTTCTAAAACACCAATTTTCCATAATCGGGG
* * * *
538869 ATACTCCAACTCTAATTTCATTTCCAAAACACCAA-TTTCTCACAATCGAGG
1 ATACTCCAACTCCAATTT-ATTTCTAAAACACCAATTTTC-CATAATCGGGG
* * *** * * *
538920 ATACTCTAACCCCGGCCTTATTTCTAAAGCATCGATTTTCCATAATCGGGG
1 ATACTCCAACTCC-AATTTATTTCTAAAACACCAATTTTCCATAATCGGGG
538971 ATACTCCAAC
1 ATACTCCAAC
538981 CTTGTTATTT
Statistics
Matches: 88, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
50 20 0.23
51 62 0.70
52 6 0.07
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.32
Consensus pattern (50 bp):
ATACTCCAACTCCAATTTATTTCTAAAACACCAATTTTCCATAATCGGGG
Found at i:540170 original size:30 final size:30
Alignment explanation
Indices: 540103--540322 Score: 163
Period size: 33 Copynumber: 7.0 Consensus size: 30
540093 ACCCTTCCCA
* * * *
540103 AAGTCTACGACTTAGTGGCATCTCTTCTCTA
1 AAGTCCACGACTCAGTGGCATCTCTT-TTTC
* *
540134 AAGTCCACAACTCAGTGGCATATCTTTTTC
1 AAGTCCACGACTCAGTGGCATCTCTTTTTC
* * *
540164 AAGTCCATGACTTAGTGGCATCCCTTTTTCTTCC
1 AAGTCCACGACTCAGTGGCAT--CTCTTT-TT-C
* * *
540198 AAATCCACGACCCAGTGGCATCTCTTTTCC
1 AAGTCCACGACTCAGTGGCATCTCTTTTTC
* *
540228 AAGTCCACGACTCAATGGCATCCTTTTTTTTCC
1 AAGTCCACGACTCAGTGGCAT-C-TCTTTTT-C
* * *
540261 AAGTCCATGACTTAGTGGCATCCCTTTTCTTCC
1 AAGTCCACGACTCAGTGGCATCTC-TTT-TT-C
* *
540294 AAGTCCATGACTCACTGGCATC-CTTTTTC
1 AAGTCCACGACTCAGTGGCATCTCTTTTTC
540323 TTTTCAAAAA
Statistics
Matches: 151, Mismatches: 29, Indels: 20
0.75 0.14 0.10
Matches are distributed among these distances:
29 1 0.01
30 41 0.27
31 27 0.18
32 19 0.13
33 45 0.30
34 18 0.12
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (30 bp):
AAGTCCACGACTCAGTGGCATCTCTTTTTC
Found at i:540224 original size:64 final size:63
Alignment explanation
Indices: 540137--540324 Score: 223
Period size: 64 Copynumber: 2.9 Consensus size: 63
540127 TTCTCTAAAG
* * * *
540137 TCCACAACTCAGTGGCATATCTTTTTCAAGTCCATGACTTAGTGGCATCCCTTTTTCTTCCAAA
1 TCCACGACTCAGTGGCATCTCTTTTTCAAGTCCATGACTCAATGGCAT-CCTTTTTCTTCCAAA
* * * * *
540201 TCCACGACCCAGTGGCATCTCTTTTCCAAGTCCACGACTCAATGGCATCCTTTTTTTTCCAAG
1 TCCACGACTCAGTGGCATCTCTTTTTCAAGTCCATGACTCAATGGCATCCTTTTTCTTCCAAA
* * * *
540264 TCCATGACTTAGTGGCATCCCTTTTCTTCCAAGTCCATGACTCACTGGCATCCTTTTTCTT
1 TCCACGACTCAGTGGCATCTC-TTT-TT-CAAGTCCATGACTCAATGGCATCCTTTTTCTT
540325 TTCAAAAACC
Statistics
Matches: 104, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
63 30 0.29
64 44 0.42
65 1 0.01
66 29 0.28
ACGTcount: A:0.20, C:0.31, G:0.13, T:0.36
Consensus pattern (63 bp):
TCCACGACTCAGTGGCATCTCTTTTTCAAGTCCATGACTCAATGGCATCCTTTTTCTTCCAAA
Found at i:540322 original size:33 final size:33
Alignment explanation
Indices: 540134--540324 Score: 196
Period size: 33 Copynumber: 5.9 Consensus size: 33
540124 CTCTTCTCTA
** * *
540134 AAGTCCACAACTCAGTGGCAT-ATCTTT-TT-C
1 AAGTCCATGACTCAGTGGCATCCTTTTTCTTCC
*
540164 AAGTCCATGACTTAGTGGCATCCCTTTTTCTTCC
1 AAGTCCATGACTCAGTGGCAT-CCTTTTTCTTCC
* * * *
540198 AAATCCACGACCCAGTGGCAT-C-TCTT-TTCC
1 AAGTCCATGACTCAGTGGCATCCTTTTTCTTCC
* * *
540228 AAGTCCACGACTCAATGGCATCCTTTTTTTTCC
1 AAGTCCATGACTCAGTGGCATCCTTTTTCTTCC
* *
540261 AAGTCCATGACTTAGTGGCATCCCTTTTCTTCC
1 AAGTCCATGACTCAGTGGCATCCTTTTTCTTCC
*
540294 AAGTCCATGACTCACTGGCATCCTTTTTCTT
1 AAGTCCATGACTCAGTGGCATCCTTTTTCTT
540325 TTCAAAAACC
Statistics
Matches: 132, Mismatches: 22, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
30 40 0.30
31 4 0.03
32 8 0.06
33 62 0.47
34 18 0.14
ACGTcount: A:0.21, C:0.30, G:0.14, T:0.35
Consensus pattern (33 bp):
AAGTCCATGACTCAGTGGCATCCTTTTTCTTCC
Found at i:540518 original size:60 final size:60
Alignment explanation
Indices: 540309--540558 Score: 253
Period size: 60 Copynumber: 4.2 Consensus size: 60
540299 CATGACTCAC
* * ** * *
540309 TGGCATCCTTTTTCTTTTCAAAAACCCATGACTCTGTGGCATCTTTTAAGTTCACAACTCCG
1 TGGCA-CCTTTTTCTTTTC-AAAGCCCATAACTCCATGGCACCTTTTAAGTCCACAACTCCG
* * * * **
540371 TGGCACCTTTTTTCTCTTCAAAGCCTACAGCTCCATGGCACCCCTTTTAAGTCCACAACTTTG
1 TGGCACC-TTTTTCTTTTCAAAGCCCATAACTCCATGGCA--CCTTTTAAGTCCACAACTCCG
* * *
540434 TGGCACC-----CTTTT--AAGTCTATAACTCCGTGGCACCTTTTAAGTCCACAACTCCG
1 TGGCACCTTTTTCTTTTCAAAGCCCATAACTCCATGGCACCTTTTAAGTCCACAACTCCG
* *
540487 TGGCACCTTTTTCTTTTCAAAGCCCATAACTCCATGGCATCTTTTAAGTCCACAACTCTG
1 TGGCACCTTTTTCTTTTCAAAGCCCATAACTCCATGGCACCTTTTAAGTCCACAACTCCG
540547 TGGCACCTTTTT
1 TGGCACCTTTTT
540559 AAGTCCACAA
Statistics
Matches: 154, Mismatches: 24, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
53 26 0.17
55 16 0.10
57 4 0.03
58 5 0.03
60 48 0.31
61 16 0.10
62 15 0.10
63 24 0.16
ACGTcount: A:0.22, C:0.30, G:0.13, T:0.35
Consensus pattern (60 bp):
TGGCACCTTTTTCTTTTCAAAGCCCATAACTCCATGGCACCTTTTAAGTCCACAACTCCG
Found at i:540571 original size:113 final size:115
Alignment explanation
Indices: 540339--540571 Score: 335
Period size: 113 Copynumber: 2.0 Consensus size: 115
540329 AAAACCCATG
* * * * *
540339 ACTCTGTGGCATCTTTTAAGTTCACAACTCCGTGGCACCTTTTTTCTCTTCAAAGCCTACAGCTC
1 ACTCCGTGGCACCTTTTAAGTCCACAACTCCGTGGCACCTTTTTTCTCTTCAAAGCCCACAACTC
* * *
540404 CATGGCACCCCTTTTAAGTCCACAACTTTGTGGCACCCTTTTAAGTCTATA
66 CATGGCA-CCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACA
* *
540455 ACTCCGTGGCACCTTTTAAGTCCACAACTCCGTGGCACC-TTTTTCTTTTCAAAGCCCATAACTC
1 ACTCCGTGGCACCTTTTAAGTCCACAACTCCGTGGCACCTTTTTTCTCTTCAAAGCCCACAACTC
* *
540519 CATGGCA-TCTTTTAAGTCCACAACTCTGTGGCACCTTTTTAAGTCCACA
66 CATGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACA
540568 ACTC
1 ACTC
540572 TGTGTCACTT
Statistics
Matches: 105, Mismatches: 12, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
113 41 0.39
115 28 0.27
116 36 0.34
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.33
Consensus pattern (115 bp):
ACTCCGTGGCACCTTTTAAGTCCACAACTCCGTGGCACCTTTTTTCTCTTCAAAGCCCACAACTC
CATGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACA
Found at i:540582 original size:26 final size:27
Alignment explanation
Indices: 540406--540646 Score: 164
Period size: 26 Copynumber: 8.4 Consensus size: 27
540396 TACAGCTCCA
* *
540406 TGGCACCCCTTTTAAGTCCACAACTTTG
1 TGGCA-CCTTTTTAAGTCCACAACTCTG
* * * *
540434 TGGCACCCTTTTAAGTCTATAACTCCG
1 TGGCACCTTTTTAAGTCCACAACTCTG
*
540461 TGGCACC-TTTTAAGTCCACAACTCCG
1 TGGCACCTTTTTAAGTCCACAACTCTG
* * **
540487 TGGCACCTTTTTCTTTTCAAAGCCCATAACTCCA
1 TGGCACC----T-TTTT--AAGTCCACAACTCTG
*
540521 TGGCATC-TTTTAAGTCCACAACTCTG
1 TGGCACCTTTTTAAGTCCACAACTCTG
540547 TGGCACCTTTTTAAGTCCACAACTCTG
1 TGGCACCTTTTTAAGTCCACAACTCTG
* * *
540574 TGTCACTTTTTTCTTTTCAAAGCCCACAACTCTG
1 TGGCAC------CTTTT-TAAGTCCACAACTCTG
* *
540608 TGGCACC-TTTTAAGTCCATAACTCCG
1 TGGCACCTTTTTAAGTCCACAACTCTG
540634 TGGCACCCTTTTT
1 TGGCA-CCTTTTT
540647 CCTTTTACGT
Statistics
Matches: 172, Mismatches: 23, Indels: 36
0.74 0.10 0.16
Matches are distributed among these distances:
26 58 0.34
27 54 0.31
28 14 0.08
32 4 0.02
33 5 0.03
34 37 0.22
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.34
Consensus pattern (27 bp):
TGGCACCTTTTTAAGTCCACAACTCTG
Found at i:540590 original size:87 final size:87
Alignment explanation
Indices: 540434--540646 Score: 311
Period size: 87 Copynumber: 2.4 Consensus size: 87
540424 CACAACTTTG
*
540434 TGGCACCCTTTTAAGTCTATAACTCCGTGGCACC-TTTTAAGTCCACAACTCCGTGGCACCTTTT
1 TGGCA-CCTTTTAAGTCCATAACTCCGTGGCACCTTTTTAAGTCCACAACTCCGTGGCACCTTTT
*
540498 TCTTTTCAAAGCCCATAACTCCA
65 TCTTTTCAAAGCCCACAACTCCA
* * * * * *
540521 TGGCATCTTTTAAGTCCACAACTCTGTGGCACCTTTTTAAGTCCACAACTCTGTGTCACTTTTTT
1 TGGCACCTTTTAAGTCCATAACTCCGTGGCACCTTTTTAAGTCCACAACTCCGTGGCACCTTTTT
**
540586 CTTTTCAAAGCCCACAACTCTG
66 CTTTTCAAAGCCCACAACTCCA
540608 TGGCACCTTTTAAGTCCATAACTCCGTGGCACCCTTTTT
1 TGGCACCTTTTAAGTCCATAACTCCGTGGCA-CCTTTTT
540647 CCTTTTACGT
Statistics
Matches: 111, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
86 24 0.22
87 80 0.72
88 7 0.06
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.35
Consensus pattern (87 bp):
TGGCACCTTTTAAGTCCATAACTCCGTGGCACCTTTTTAAGTCCACAACTCCGTGGCACCTTTTT
CTTTTCAAAGCCCACAACTCCA
Found at i:540609 original size:61 final size:60
Alignment explanation
Indices: 540536--540728 Score: 215
Period size: 63 Copynumber: 3.1 Consensus size: 60
540526 TCTTTTAAGT
* *
540536 CCACAACTCTGTGGCACCTTTTTAAGTCCACAACTCTGTGTCACTTTTTTCTTTTCAAAGC
1 CCACAACTCTGTGGCACC-TTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTCAAAGC
* * ** *
540597 CCACAACTCTGTGGCACCTTTTAAGTCCATAACTCCGTGGCACCCTTTTTCCTTTTACGTAGT
1 CCACAACTCTGTGGCACCTTTTAAGTCCACAACTCCGTGGCA--CTTTTTTCTTTT-CAAAGC
* * * * *
540660 CCATAATTCTGTGGCACCCTTTTAAGTACACAACGCCGTGGCACTTTTTTTCTTCTCTAAAGC
1 CCACAACTCTGTGGCA-CCTTTTAAGTCCACAACTCCGTGGCAC-TTTTTTCTTTTC-AAAGC
540723 CCACAA
1 CCACAA
540729 AAGTTGGTGG
Statistics
Matches: 108, Mismatches: 18, Indels: 10
0.79 0.13 0.07
Matches are distributed among these distances:
60 21 0.19
61 18 0.17
62 13 0.12
63 33 0.31
64 23 0.21
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.35
Consensus pattern (60 bp):
CCACAACTCTGTGGCACCTTTTAAGTCCACAACTCCGTGGCACTTTTTTCTTTTCAAAGC
Found at i:540651 original size:34 final size:35
Alignment explanation
Indices: 540613--540682 Score: 97
Period size: 37 Copynumber: 2.0 Consensus size: 35
540603 CTCTGTGGCA
540613 CCTTTTA-AGTCCATAACTCCGTGGCACCCTTTTT
1 CCTTTTACAGTCCATAACTCCGTGGCACCCTTTTT
* *
540647 CCTTTTACGTAGTCCATAATTCTGTGGCACCCTTTT
1 CCTTTTAC--AGTCCATAACTCCGTGGCACCCTTTT
540683 AAGTACACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 7 0.23
37 24 0.77
ACGTcount: A:0.17, C:0.30, G:0.13, T:0.40
Consensus pattern (35 bp):
CCTTTTACAGTCCATAACTCCGTGGCACCCTTTTT
Found at i:541001 original size:52 final size:52
Alignment explanation
Indices: 540873--541052 Score: 137
Period size: 52 Copynumber: 3.5 Consensus size: 52
540863 TGGCACTAGC
*
540873 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTACCATCTTTAAGT
* * * * * * ** *
540925 CTAGTGTCACTGGCCTTGAGTCAGCACATTGGCACTTTTTTC-TTTCTTAAGT
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTACCATCT-TTAAGT
* * * * * * ** **
540977 CCAATATCGCAGGCTTTGAATCAGCATATTAGTACCCTTGTCATCTTTAAAC
1 CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTACCATCTTTAAGT
* **
541029 CCAATATCACTCACCTTGAATCAG
1 CCAATATCGCTGGCCTTGAATCAG
541053 TATATCGGCA
Statistics
Matches: 95, Mismatches: 31, Indels: 4
0.73 0.24 0.03
Matches are distributed among these distances:
51 2 0.02
52 91 0.96
53 2 0.02
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (52 bp):
CCAATATCGCTGGCCTTGAATCAGCACATTGGCACCTTTACCATCTTTAAGT
Found at i:541063 original size:104 final size:104
Alignment explanation
Indices: 540873--541063 Score: 220
Period size: 104 Copynumber: 1.8 Consensus size: 104
540863 TGGCACTAGC
* * * ** * * * **
540873 CCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTACCATCTTTAAGTCTAGTGTCACTGG
1 CCAATATCGCAGGCCTTGAATCAGCATATTAGCACCCTTACCATCTTTAAACCCAATATCACTCA
* *
540938 CCTTGAGTCAGCACATTGGCACTTTTTTCTTTCTTAAGT
66 CCTTGAATCAGCACATCGGCACTTTTTTCTTTCTTAAGT
* * **
540977 CCAATATCGCAGGCTTTGAATCAGCATATTAGTACCCTTGTCATCTTTAAACCCAATATCACTCA
1 CCAATATCGCAGGCCTTGAATCAGCATATTAGCACCCTTACCATCTTTAAACCCAATATCACTCA
* *
541042 CCTTGAATCAGTATATCGGCAC
66 CCTTGAATCAGCACATCGGCAC
541064 ATTTCTCAGT
Statistics
Matches: 69, Mismatches: 18, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
104 69 1.00
ACGTcount: A:0.25, C:0.26, G:0.15, T:0.34
Consensus pattern (104 bp):
CCAATATCGCAGGCCTTGAATCAGCATATTAGCACCCTTACCATCTTTAAACCCAATATCACTCA
CCTTGAATCAGCACATCGGCACTTTTTTCTTTCTTAAGT
Found at i:541889 original size:20 final size:20
Alignment explanation
Indices: 541864--541938 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
541854 ATTGCCAAGG
541864 AAATGTATCGATACATTATT
1 AAATGTATCGATACATTATT
**
541884 AAATGTATCGATACATGCTT
1 AAATGTATCGATACATTATT
* *
541904 ACAATTTTATTGATACATTATT
1 A-AA-TGTATCGATACATTATT
* *
541926 CAATATATCGATA
1 AAATGTATCGATA
541939 GCAGGCAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 27 0.61
21 4 0.09
22 13 0.30
ACGTcount: A:0.39, C:0.12, G:0.09, T:0.40
Consensus pattern (20 bp):
AAATGTATCGATACATTATT
Found at i:542592 original size:28 final size:29
Alignment explanation
Indices: 542552--542611 Score: 104
Period size: 28 Copynumber: 2.1 Consensus size: 29
542542 GTTTTAGTTG
542552 TCTCATCATTTTAGTGAACTTATCAT-TT
1 TCTCATCATTTTAGTGAACTTATCATGTT
*
542580 TCTCATCGTTTTAGTGAACTTATCATGTT
1 TCTCATCATTTTAGTGAACTTATCATGTT
542609 TCT
1 TCT
542612 AGGGCCCTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 25 0.83
29 5 0.17
ACGTcount: A:0.22, C:0.18, G:0.10, T:0.50
Consensus pattern (29 bp):
TCTCATCATTTTAGTGAACTTATCATGTT
Found at i:547498 original size:23 final size:24
Alignment explanation
Indices: 547465--547516 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
547455 GATGCTAGGT
*
547465 AGGGGGCTGCT-GGCAAAGATGGGC
1 AGGGGGCTGCTCGAC-AAGATGGGC
*
547489 AGGGGG-TGCTCGACAAGGTGGGC
1 AGGGGGCTGCTCGACAAGATGGGC
547512 AGGGG
1 AGGGG
547517 TGGTACAAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.19, C:0.15, G:0.54, T:0.12
Consensus pattern (24 bp):
AGGGGGCTGCTCGACAAGATGGGC
Found at i:550885 original size:20 final size:19
Alignment explanation
Indices: 550843--550936 Score: 55
Period size: 20 Copynumber: 4.7 Consensus size: 19
550833 TTTTAACTAG
* **
550843 ATGTATCGATACACTGTTTA
1 ATGTATCGATACATTG-AAA
550863 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAA-A
* * * * *
550883 ATGT-GCCAGTACCTTCATAC
1 ATGTATCGA-TACATTGA-AA
*
550903 ATGTATCGATATATTGAAAA
1 ATGTATCGATACATTG-AAA
550923 ATGTATCGATACAT
1 ATGTATCGATACAT
550937 CTGGGTAAAA
Statistics
Matches: 54, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
19 2 0.04
20 48 0.89
21 4 0.07
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (19 bp):
ATGTATCGATACATTGAAA
Found at i:551601 original size:28 final size:28
Alignment explanation
Indices: 551546--551675 Score: 134
Period size: 28 Copynumber: 4.5 Consensus size: 28
551536 TATCGACTCG
* *
551546 TGTGAGCTTTGAAAAGAGTGCTACTGACT
1 TGTGGGCTTTG-AAAGAGTGCCACTGACT
* *
551575 TGTGGGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
* *
551603 TGTGGGCTTTGAAAAGAGTGCCACTAAAT
1 TGTGGGCTTTG-AAAGAGTGCCACTGACT
* * *
551632 TATGGCCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGAGTGCCACTGACT
*
551660 TGCGTGGGCGTTGAAA
1 T--GTGGGCTTTGAAA
551676 ATTCAATGCT
Statistics
Matches: 82, Mismatches: 16, Indels: 5
0.80 0.16 0.05
Matches are distributed among these distances:
28 40 0.49
29 32 0.39
30 10 0.12
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGAGTGCCACTGACT
Found at i:551882 original size:256 final size:256
Alignment explanation
Indices: 551423--551931 Score: 754
Period size: 256 Copynumber: 2.0 Consensus size: 256
551413 ATGCTGATTT
* * *
551423 AATGCTAGCGATGCCAAACAGTGGTGATTTGCAAAGGGTTGCCACCGACTTGTGTAGGATTTTTT
1 AATGCTAGCGAAGCCAAACAGTGGTGATTTGAAAAGGGTTGCCACCAACTTGTGTAGGATTTTTT
* *
551488 TTATAAAAAATGGTGCCACTAACTAGTGTAGGCTTTGAAAAGAGTTGCTATCGACTCGTGTGAGC
66 TTATAAAAAATGGTGCCACTAACTAGTGTAGGCTTTGAAAAGAGTTGCTACCGACTCGTGCGAGC
* * * * *
551553 TTTGAAAAGAGTGCTACTGACTTGTGGGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTTGAAAA
131 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTAAATTGTGGGCTTTGAAAA
551618 GAGTGCCACTAAATT-ATGGCCTTTGAAAGGGTGCCACTGACTTGCGTGGGCGTTGAAAATTC
196 GAGTGCCACTAAATTCATGGCCTTTGAAAGGGTGCCACTGACTT--GTGGGCGTTGAAAATTC
* * *
551680 AATGCTAGCGAAGCCAGACAGTGGTGATTTGAAAAGGGTTGCCACCAACTTGTGTGGGCTTTTTT
1 AATGCTAGCGAAGCCAAACAGTGGTGATTTGAAAAGGGTTGCCACCAACTTGTGTAGGATTTTTT
* * *
551745 TTA-AAAAAATGGTGCCACTAACTCGTGTGGGCTTTGAAAAGAGTTGCTGCCGACTCGTGCGAGC
66 TTATAAAAAATGGTGCCACTAACTAGTGTAGGCTTTGAAAAGAGTTGCTACCGACTCGTGCGAGC
551809 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTAAATTGTGGGCTTTG-AA
131 TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTAAATTGTGGGCTTTGAAA
* * * * * * *
551873 AGGGTGCCACTGACTTGCGTGGGCTTTGAAATGGTGCCACTGACTTGTGGGCTTTGAAA
195 AGAGTGCCACTAAATT-CATGGCCTTTGAAAGGGTGCCACTGACTTGTGGGCGTTGAAA
551932 GGATGCCACT
Statistics
Matches: 226, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
256 115 0.51
257 86 0.38
258 25 0.11
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (256 bp):
AATGCTAGCGAAGCCAAACAGTGGTGATTTGAAAAGGGTTGCCACCAACTTGTGTAGGATTTTTT
TTATAAAAAATGGTGCCACTAACTAGTGTAGGCTTTGAAAAGAGTTGCTACCGACTCGTGCGAGC
TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTAAATTGTGGGCTTTGAAAA
GAGTGCCACTAAATTCATGGCCTTTGAAAGGGTGCCACTGACTTGTGGGCGTTGAAAATTC
Found at i:551883 original size:28 final size:28
Alignment explanation
Indices: 551807--552582 Score: 960
Period size: 28 Copynumber: 27.3 Consensus size: 28
551797 ACTCGTGCGA
*
551807 GCTTTGAAAAGAGTGCCACTGACTTGTGG
1 GCTTTG-AAAGGGTGCCACTGACTTGTGG
* * *
551836 GCTTTGAAAAGAGTGCCACTAAATTGTGG
1 GCTTTG-AAAGGGTGCCACTGACTTGTGG
551865 GCTTTGAAAGGGTGCCACTGACTTGCGTGG
1 GCTTTGAAAGGGTGCCACTGACTT--GTGG
*
551895 GCTTTGAAATGGTGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* * *
551923 GCTTTGAAAGGATGCCACTAACTTATGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
*
551951 GCTTTGAAAGGGTACCACTGACTTGCATGG
1 GCTTTGAAAGGGTGCCACTGACTTG--TGG
*
551981 GCATTGAAAGGGTGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* * *
552009 GCTTTGAAAGGATGCTACTAACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* * *
552037 GCTTTGAAAAGAGTGCAACCGACTTGTGG
1 GCTTTG-AAAGGGTGCCACTGACTTGTGG
* *
552066 GCTTTGAAAGGGTGACACTAACTTGCGTGG
1 GCTTTGAAAGGGTGCCACTGACTT--GTGG
*
552096 GCTTTGAAAGGGTGCCACTGACTTGAGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* *
552124 GCTTTGAAAGGATGCCACTAACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* *
552152 GCTTTGAAAGCGTGCCACTGACTCGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
*
552180 GCTTTGAAAGAGTGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* *
552208 GCTTTGAAAGGGTGCCACTAACTAGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* ** *
552236 GCTTTGAAAGGGTGCCACAGACTCATGA
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* * *
552264 GCTTTAAAAGGGTGCCACTAACTAGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* *
552292 GCTTTGAAAGGGTGCCACTGACTCGCGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* *
552320 GCTTTGAAAGGGTGCCACTGACTCGCGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* * *
552348 GCTTTGAAAGTGAGCCACTAAC-TGATGG
1 GCTTTGAAAGGGTGCCACTGACTTG-TGG
* *
552376 GCTTTGAAAGGGTGCCACTAACTTATGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
* * * * *
552404 GCTTTGAAAGAGTGCTAATAACTTATGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
*
552432 GCTTTGAAAGGGTGCCACTGACTCGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
552460 GCTTTGAAAGGGTGCCACTGACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
*
552488 GCTTTGAAAGGGTGCCACTAACTTGTGG
1 GCTTTGAAAGGGTGCCACTGACTTGTGG
*
552516 GCTTTGAAAAGAGTGCCACTGACTTGTGG
1 GCTTTG-AAAGGGTGCCACTGACTTGTGG
* * *
552545 GCTTTAAAAAGTGTGCCACTAACTTGTGG
1 GCTTT-GAAAGGGTGCCACTGACTTGTGG
552574 GCTTTGAAA
1 GCTTTGAAA
552583 AGGATGAACG
Statistics
Matches: 651, Mismatches: 85, Indels: 23
0.86 0.11 0.03
Matches are distributed among these distances:
27 1 0.00
28 464 0.71
29 107 0.16
30 79 0.12
ACGTcount: A:0.24, C:0.18, G:0.31, T:0.27
Consensus pattern (28 bp):
GCTTTGAAAGGGTGCCACTGACTTGTGG
Found at i:553797 original size:1 final size:1
Alignment explanation
Indices: 553793--553855 Score: 63
Period size: 1 Copynumber: 63.0 Consensus size: 1
553783 TTTTTCTTGG
* * * * * * *
553793 TTTTTTTCTGTTTTTTTGTTTTTTTGTTTTTTTTGTTTTTTTGTTTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
553856 GGGTATGAAG
Statistics
Matches: 48, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.02, G:0.10, T:0.89
Consensus pattern (1 bp):
T
Found at i:553812 original size:8 final size:8
Alignment explanation
Indices: 553771--553855 Score: 86
Period size: 8 Copynumber: 10.5 Consensus size: 8
553761 CCCTTTTCTG
553771 TTTTTTGT
1 TTTTTTGT
*
553779 TATTTT-T
1 TTTTTTGT
* *
553786 TTCTTGGTT
1 TTTTTTG-T
553795 TTTTTCTGT
1 TTTTT-TGT
553804 TTTTTTGT
1 TTTTTTGT
553812 TTTTTTGTT
1 TTTTTTG-T
553821 TTTTTTGT
1 TTTTTTGT
553829 TTTTTTGT
1 TTTTTTGT
553837 TTTTTT-T
1 TTTTTTGT
553844 TTTGTTT-T
1 TTT-TTTGT
553852 TTTT
1 TTTT
553856 GGGTATGAAG
Statistics
Matches: 66, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
7 9 0.14
8 37 0.56
9 19 0.29
10 1 0.02
ACGTcount: A:0.01, C:0.02, G:0.11, T:0.86
Consensus pattern (8 bp):
TTTTTTGT
Found at i:553835 original size:25 final size:25
Alignment explanation
Indices: 553771--553855 Score: 104
Period size: 25 Copynumber: 3.5 Consensus size: 25
553761 CCCTTTTCTG
* * *
553771 TTTTTTGTTATTTT-TTTCTTGGTT
1 TTTTTTGTTTTTTTGTTTTTTTGTT
553795 TTTTTCTGTTTTTTTGTTTTTTTGTT
1 TTTTT-TGTTTTTTTGTTTTTTTGTT
553821 TTTTTTGTTTTTTTGTTTTTTT-TT
1 TTTTTTGTTTTTTTGTTTTTTTGTT
*
553845 TTGTTT-TTTTT
1 TTTTTTGTTTTT
553856 GGGTATGAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
23 5 0.09
24 12 0.22
25 25 0.45
26 13 0.24
ACGTcount: A:0.01, C:0.02, G:0.11, T:0.86
Consensus pattern (25 bp):
TTTTTTGTTTTTTTGTTTTTTTGTT
Found at i:553856 original size:9 final size:9
Alignment explanation
Indices: 553782--553856 Score: 82
Period size: 9 Copynumber: 8.0 Consensus size: 9
553772 TTTTTGTTAT
553782 TTTTTTCTTGG
1 TTTTTT-TT-G
553793 TTTTTTTCTG
1 TTTTTTT-TG
553803 -TTTTTTTG
1 TTTTTTTTG
553811 -TTTTTTTG
1 TTTTTTTTG
553819 TTTTTTTTG
1 TTTTTTTTG
*
553828 TTTTTTTGTTT
1 -TTTTTT-TTG
553839 TTTTTTTTG
1 TTTTTTTTG
553848 TTTTTTTTG
1 TTTTTTTTG
553857 GGTATGAAGG
Statistics
Matches: 58, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
8 10 0.17
9 25 0.43
10 14 0.24
11 9 0.16
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:557797 original size:33 final size:33
Alignment explanation
Indices: 557755--557819 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
557745 TAGCCAAACT
* *
557755 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
*
557788 TGTATCGATATACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
557820 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 24 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:564138 original size:20 final size:20
Alignment explanation
Indices: 564095--564140 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
564085 AAATCTTTTG
564095 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
564116 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
564136 CAAAA
1 CAAAA
564141 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:566568 original size:20 final size:20
Alignment explanation
Indices: 566543--566607 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
566533 TAGCCAAACT
566543 TGTATCGATACACCAAAGTA
1 TGTATCGATACACCAAAGTA
566563 TGTATCGAT--A-C--A--A
1 TGTATCGATACACCAAAGTA
566576 TGTATCGATACACCAAAGTA
1 TGTATCGATACACCAAAGTA
566596 TGTATCGATACA
1 TGTATCGATACA
566608 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 22 0.58
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.28
Consensus pattern (20 bp):
TGTATCGATACACCAAAGTA
Found at i:566580 original size:13 final size:13
Alignment explanation
Indices: 566562--566620 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 13
566552 ACACCAAAGT
566562 ATGTATCGATACA
1 ATGTATCGATACA
566575 ATGTATCGATACACCAAA
1 ATGTATCGAT--A-C--A
566593 GTATGTATCGATACA
1 --ATGTATCGATACA
566608 ATGTATCGATACA
1 ATGTATCGATACA
566621 CAAAAAATTG
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 23 0.59
15 2 0.05
16 1 0.03
17 1 0.03
18 2 0.05
20 10 0.26
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:566585 original size:33 final size:33
Alignment explanation
Indices: 566543--566640 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
566533 TAGCCAAACT
566543 TGTATCGATACACCAAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAGTATGTATCGATACAA
566576 TGTATCGATACACCAAAGTATGTATCGATACAA
1 TGTATCGATACACCAAAGTATGTATCGATACAA
**
566609 TGTATCGATACA-CAAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAGTA-TGTATCGATACA
566641 TTGGCTTGTA
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
32 5 0.08
33 57 0.92
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAGTATGTATCGATACAA
Found at i:577790 original size:20 final size:19
Alignment explanation
Indices: 577759--577835 Score: 91
Period size: 20 Copynumber: 3.9 Consensus size: 19
577749 GTAAAAAGAT
577759 AAAATGTATCGATACATTG
1 AAAATGTATCGATACATTG
* *
577778 AAGAATTTATCGATACATTC
1 AA-AATGTATCGATACATTG
* *
577798 ATACATGTATCGATATATTG
1 A-AAATGTATCGATACATTG
577818 AAAAATGTATCGATACAT
1 -AAAATGTATCGATACAT
577836 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
19 2 0.04
20 43 0.91
21 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.13, T:0.34
Consensus pattern (19 bp):
AAAATGTATCGATACATTG
Found at i:578352 original size:17 final size:19
Alignment explanation
Indices: 578311--578359 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 19
578301 ATATAGGGAA
578311 TGTATCGATACATTAGTAAT
1 TGTATCGATACATTAGT-AT
578331 TGTATCGATACATTA-T-T
1 TGTATCGATACATTAGTAT
578348 TGTATCGATACA
1 TGTATCGATACA
578360 ATCTAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
17 13 0.45
19 1 0.03
20 15 0.52
ACGTcount: A:0.33, C:0.12, G:0.14, T:0.41
Consensus pattern (19 bp):
TGTATCGATACATTAGTAT
Found at i:579140 original size:20 final size:21
Alignment explanation
Indices: 579115--579165 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
579105 GTTACAAGCA
*
579115 ATGTATCGAT-ACAAT-TCATC
1 ATGTATCGATAACAATGT-ACC
579135 ATGTATCGATAACAATGTACC
1 ATGTATCGATAACAATGTACC
579156 ATGTATCGAT
1 ATGTATCGAT
579166 GCAAACGGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 10 0.36
21 17 0.61
22 1 0.04
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Consensus pattern (21 bp):
ATGTATCGATAACAATGTACC
Found at i:579223 original size:20 final size:20
Alignment explanation
Indices: 579198--579272 Score: 116
Period size: 20 Copynumber: 3.8 Consensus size: 20
579188 CTGCCAGTTT
579198 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
579218 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
* **
579238 AATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTC
579257 CATGTATCGATACAAT
1 CATGTATCGATACAAT
579273 GTATCAATAC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 16 0.32
20 34 0.68
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGTC
Found at i:587726 original size:52 final size:51
Alignment explanation
Indices: 587667--587785 Score: 175
Period size: 52 Copynumber: 2.3 Consensus size: 51
587657 AACACCTAGA
***
587667 AGGGATACTCCAACCCCATTTTTATTTTTGAAATATTTAAATTTTTCATCTC
1 AGGGATACTCCAACCCCATTTTTATTTCCAAAATA-TTAAATTTTTCATCTC
*
587719 AGGGATACTCCAACCCCGTTTTTATTTCCAAAATATTAAATTTTTCATCTC
1 AGGGATACTCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTC
* *
587770 AAGGATACTCTAACCC
1 AGGGATACTCCAACCC
587786 TATTATTTTC
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
51 30 0.49
52 31 0.51
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (51 bp):
AGGGATACTCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTC
Found at i:587779 original size:51 final size:52
Alignment explanation
Indices: 587669--587785 Score: 173
Period size: 51 Copynumber: 2.3 Consensus size: 52
587659 CACCTAGAAG
*** *
587669 GGATACTCCAACCCCATTTTTATTTTTGAAATATTTAAATTTTTCATCTCAG
1 GGATACTCCAACCCCATTTTTATTTCCAAAATATTTAAATTTTTCATCTCAA
*
587721 GGATACTCCAACCCCGTTTTTATTTCCAAAATA-TTAAATTTTTCATCTCAA
1 GGATACTCCAACCCCATTTTTATTTCCAAAATATTTAAATTTTTCATCTCAA
*
587772 GGATACTCTAACCC
1 GGATACTCCAACCC
587786 TATTATTTTC
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
51 30 0.51
52 29 0.49
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.39
Consensus pattern (52 bp):
GGATACTCCAACCCCATTTTTATTTCCAAAATATTTAAATTTTTCATCTCAA
Found at i:587951 original size:80 final size:78
Alignment explanation
Indices: 587723--588096 Score: 337
Period size: 79 Copynumber: 4.7 Consensus size: 78
587713 CATCTCAGGG
* * *
587723 ATACTCCAACCCCGTTTTTATTTCCAAAATATTAAATTTTTCATCTCAAGGATACTCTAACCCTA
1 ATACTCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCAAGGATACTCCAACCCCA
* *
587788 TTATTT-TCATGGGG
66 TTATTTCT-A-AGGA
* * *
587802 ATACTCCAACCGCATTTTTATTTTCAAAATATTATAA-TTTTCATCTC--GGAAATACTCCAACT
1 ATACTCCAACCCCATTTTTATTTCCAAAATATTA-AATTTTTCATCTCAAGG--ATACTCCAACC
* *
587864 CCGTTATTTCTAAGGCT
63 CCATTATTTCTAAGG-A
*
587881 ATA-TGCCAATCCCATTTTTATTTCCAAAATATTAAATTTTTTCATCTCAAGGATACTCCAACCC
1 ATACT-CCAACCCCATTTTTATTTCCAAAATATTAAA-TTTTTCATCTCAAGGATACTCCAACCC
* *
587945 CATTATTTTCGAATGA
64 CATTA-TTTCTAAGGA
* * ** * *
587961 ATACTCCAACCCCATTTTTATTTCCAAAATA-TCAATTTTTCACCATCGGGGATACTCGAAACCC
1 ATACTCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATC-TCAAGGATACTCCAACCCC
*
588025 ATAATTTCTGAAGGA
65 ATTATTTCT-AAGGA
* * ** * * * * * *
588040 ATATTCCAACCCTATTTAAACTCCCAAAATTTTAAAATTTTCATCACGAGGATACTC
1 ATACTCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCAAGGATACTC
588097 TAAACCCACC
Statistics
Matches: 241, Mismatches: 39, Indels: 30
0.78 0.13 0.10
Matches are distributed among these distances:
77 2 0.01
78 17 0.07
79 146 0.61
80 66 0.27
81 8 0.03
82 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (78 bp):
ATACTCCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCAAGGATACTCCAACCCCA
TTATTTCTAAGGA
Found at i:588032 original size:159 final size:158
Alignment explanation
Indices: 587728--588096 Score: 415
Period size: 159 Copynumber: 2.3 Consensus size: 158
587718 CAGGGATACT
* * *
587728 CCAACCCCGTTTTTATTTCCAAAATATTAAATTTTTCATCTCAAGGATACTCTAACCCTATTATT
1 CCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCAAGGATACTCCAACCCCATTATT
* * * * *
587793 TTCATGGGGATACTCCAACCGCATTTTTATTTTCAAAATATTATAATTTTCATCTCGGAAATACT
66 TTCAT-GGAATACTCCAACCCCATTTTTATTTCCAAAATATCATAATTTTCACCTCGGAAATACT
* * *
587858 CCAACTCCGTTATTTCT-AAGGCTATATG
130 CAAACTCCATAATTTCTGAAGGCTATATG
*
587886 CCAATCCCATTTTTATTTCCAAAATATTAAATTTTTTCATCTCAAGGATACTCCAACCCCATTAT
1 CCAACCCCATTTTTATTTCCAAAATATTAAA-TTTTTCATCTCAAGGATACTCCAACCCCATTAT
* **
587951 TTTCGAAT-GAATACTCCAACCCCATTTTTATTTCCAAAATATCA-ATTTTTCACCATCGGGGAT
65 TTTC--ATGGAATACTCCAACCCCATTTTTATTTCCAAAATATCATAATTTTCACC-TCGGAAAT
* *
588014 ACTCGAAAC-CCATAATTTCTGAAGG-AATATT
127 ACTC-AAACTCCATAATTTCTGAAGGCTATATG
* ** * * * * * *
588045 CCAACCCTATTTAAACTCCCAAAATTTTAAAATTTTCATCACGAGGATACTC
1 CCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCAAGGATACTC
588097 TAAACCCACC
Statistics
Matches: 178, Mismatches: 27, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
158 55 0.31
159 114 0.64
160 7 0.04
161 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.37
Consensus pattern (158 bp):
CCAACCCCATTTTTATTTCCAAAATATTAAATTTTTCATCTCAAGGATACTCCAACCCCATTATT
TTCATGGAATACTCCAACCCCATTTTTATTTCCAAAATATCATAATTTTCACCTCGGAAATACTC
AAACTCCATAATTTCTGAAGGCTATATG
Found at i:595655 original size:13 final size:13
Alignment explanation
Indices: 595637--595661 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
595627 CAAAGATTAG
595637 TGTATCGATACAA
1 TGTATCGATACAA
595650 TGTATCGATACA
1 TGTATCGATACA
595662 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:595738 original size:19 final size:19
Alignment explanation
Indices: 595714--595778 Score: 70
Period size: 19 Copynumber: 3.7 Consensus size: 19
595704 ACCAATACAG
595714 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
595733 TGTATCGATAC---A--T-
1 TGTATCGATACAAAACTTA
* *
595746 TGTATCGTTACAACACTTA
1 TGTATCGATACAAAACTTA
595765 TGTATCGATACAAA
1 TGTATCGATACAAA
595779 TCGTTGAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
13 10 0.27
14 1 0.03
16 2 0.05
18 1 0.03
19 23 0.62
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:595750 original size:32 final size:32
Alignment explanation
Indices: 595708--595776 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
595698 CTTCGTACCA
595708 ATACAGTGTATCGATACAAAACTTATGTATCG
1 ATACAGTGTATCGATACAAAACTTATGTATCG
* * *
595740 ATACATTGTATCGTTACAACACTTATGTATCG
1 ATACAGTGTATCGATACAAAACTTATGTATCG
595772 ATACA
1 ATACA
595777 AATCGTTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
ATACAGTGTATCGATACAAAACTTATGTATCG
Found at i:596611 original size:43 final size:43
Alignment explanation
Indices: 596552--597104 Score: 422
Period size: 43 Copynumber: 11.9 Consensus size: 43
596542 ATGTCAATAG
*
596552 GCTGATTCAATGCCAGCGATATTAGACTTAAAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAATGT
* ** * * * * *
596595 GTTGAGACAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGGCGCCAATAT
1 GCTGATTCAAGGCCAGCGATATTAGAC-T-----T---AAAGGTGCCAATGT
*
596647 ACTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAATGT
* * * * *
596690 GCTAATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATAT
1 GCTGATTCAAGGCCAGCGATATTAGACTT----A--AAGGTGCCAATGT
*
596739 GCTGATTCAAGGCCAGCGTTATTAGACTTAAAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAATGT
* *
596782 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGCACCAATGT
1 GCTGATTCAAGGCCAGCGATATTAGACTTAAAG--G--TG--CCAATGT
*
596831 GCTAATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAATGT
* *
596874 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGCACCAATGT
1 GCTGATTCAAGGCCAGCGATATTAGACTTAAAG--G--TG--CCAATGT
* * * *
596923 GCTAATTCAAGGCCAGCGACATTGGACTTAAAGATGACAAAGGTGCCAATAT
1 GCTGATTCAAGGCCAGCGATATTAGAC-T-----T---AAAGGTGCCAATGT
* * *
596975 ACTGATTCAAGGCTAGCGATATTGGACTTAAAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAATGT
* * * *
597018 GCTGATTCAAGGCCGGCGACATTAGTCTTAAAGACAAGGTGCCAATAT
1 GCTGATTCAAGGCCAGCGATATTAGACTT----A-AAGGTGCCAATGT
* **
597066 GCTGATTCAAGGCCAGCGATATTGGTTTTAAAGGTGCCA
1 GCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCA
597105 TGAAGTTGTG
Statistics
Matches: 410, Mismatches: 59, Indels: 82
0.74 0.11 0.15
Matches are distributed among these distances:
43 182 0.44
44 2 0.00
45 4 0.01
46 2 0.00
47 5 0.01
48 37 0.09
49 107 0.26
50 1 0.00
51 2 0.00
52 61 0.15
54 1 0.00
55 1 0.00
56 1 0.00
58 4 0.01
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (43 bp):
GCTGATTCAAGGCCAGCGATATTAGACTTAAAGGTGCCAATGT
Found at i:596790 original size:92 final size:92
Alignment explanation
Indices: 596490--597098 Score: 627
Period size: 92 Copynumber: 6.4 Consensus size: 92
596480 AGAAGAATGT
* * * * * *
596490 CAATATGCTGATTCAAGGCCAGCGACATTGGGTTTTAAAGATGAAAAAAAGGATGTCAATAGGCT
1 CAATGTGCTGATTCAAGGCCAGCGATATT-GGTCTTAAAGATG-----AAGG-CGCCAATATGCT
*
596555 GATTCAATGCCAGCGATATTAGACTTAAAGGTGC
59 GATTCAAGGCCAGCGATATTAGACTTAAAGGTGC
* ** * *
596589 CAATGTGTTGAGACAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGGCGCCAATATACTGATT
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATG---AAGGCGCCAATATGCTGATT
596654 CAAGGCCAGCGATATTAGACTTAAAGGTGC
63 CAAGGCCAGCGATATTAGACTTAAAGGTGC
* * *
596684 CAATGTGCTAATTCAAGGCCAGCGACATTGGTCTTAAAGATGAAGGTGCCAATATGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAGGCGCCAATATGCTGATTCAA
*
596749 GGCCAGCGTTATTAGACTTAAAGGTGC
66 GGCCAGCGATATTAGACTTAAAGGTGC
* * * *
596776 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGCACCAATGTGCTAATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAGGCGCCAATATGCTGATTCAA
596841 GGCCAGCGATATTAGACTTAAAGGTGC
66 GGCCAGCGATATTAGACTTAAAGGTGC
* * * *
596868 CAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGCACCAATGTGCTAATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAGGCGCCAATATGCTGATTCAA
* *
596933 GGCCAGCGACATTGGACTTAAAGATGACAAAGGTGC
66 GGCCAGCGATATTAGAC-T-----T---AAAGGTGC
* * * * * *
596969 CAATATACTGATTCAAGGCTAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAA
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAGGCGCCAATATGCTGATTCAA
* * *
597028 GGCCGGCGACATTAGTCTTAAAGACAAGGTGC
66 GGCCAGCGATATTAGACTT----A-AAGGTGC
* *
597060 CAATATGCTGATTCAAGGCCAGCGATATTGGTTTTAAAG
1 CAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTAAAG
597099 GTGCCATGAA
Statistics
Matches: 452, Mismatches: 43, Indels: 34
0.85 0.08 0.06
Matches are distributed among these distances:
89 1 0.00
90 2 0.00
91 38 0.08
92 211 0.47
93 1 0.00
94 1 0.00
95 113 0.25
96 6 0.01
97 1 0.00
98 13 0.03
99 25 0.06
101 40 0.09
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (92 bp):
CAATGTGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGAAGGCGCCAATATGCTGATTCAA
GGCCAGCGATATTAGACTTAAAGGTGC
Found at i:597090 original size:91 final size:95
Alignment explanation
Indices: 596860--597104 Score: 318
Period size: 91 Copynumber: 2.6 Consensus size: 95
596850 TATTAGACTT
* *
596860 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGCACCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG--G--TG--CCAATGTGC
*
596925 TAATTCAAGGCCAGCGACATTGGACTTAAAGATGAC
60 TAATTCAAGGCCAGCGACATTAGACTTAAAGATGAC
* * *
596961 AAAGGTGCCAATATACTGATTCAAGGCTAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTAATTC
* *
597026 AAGGCCGGCGACATTAGTCTT-AA-A-GAC
66 AAGGCCAGCGACATTAGACTTAAAGATGAC
**
597053 -AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGTTTTAAAGGTGCCA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCA
597105 TGAAGTTGTG
Statistics
Matches: 132, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
91 48 0.36
92 3 0.02
93 1 0.01
94 2 0.02
95 32 0.24
97 1 0.01
99 1 0.01
101 44 0.33
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (95 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTAATTC
AAGGCCAGCGACATTAGACTTAAAGATGAC
Found at i:597219 original size:58 final size:57
Alignment explanation
Indices: 597157--597481 Score: 438
Period size: 58 Copynumber: 5.6 Consensus size: 57
597147 AGCTTAAAAG
* * *
597157 GAAAAAGATGGCCACGGACTTGTGGGCTTTTGAAGGTTGCCACTAATTTGTGGGCTTT
1 GAAAAAGAT-GCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT
*
597215 GAAAAATGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT
1 GAAAAA-GATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT
* * * *
597273 GGGAAAAGGGTGCTACTGATTTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTT
1 --GAAAAAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT
* *
597331 GAAAAAGATGCCACTGACTTTTTGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT
1 GAAAAAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT
* * * *
597388 GGGAAAAAGGTGCCACTGATTTATGGGC-TTTGAAGGTTGCCACTGACTTGTGGCCTTT
1 --GAAAAAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT
* *
597446 GAAAAAGATGCCACTGCCTTGTGAGCTTTTGAAGGT
1 GAAAAAGATGCCACTGACTTGTGGGCTTTTGAAGGT
597482 GAGGAATGTC
Statistics
Matches: 237, Mismatches: 23, Indels: 15
0.86 0.08 0.05
Matches are distributed among these distances:
56 41 0.17
57 39 0.16
58 110 0.46
59 42 0.18
60 5 0.02
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (57 bp):
GAAAAAGATGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTT
Found at i:597374 original size:115 final size:115
Alignment explanation
Indices: 597156--597481 Score: 483
Period size: 115 Copynumber: 2.8 Consensus size: 115
597146 GAGCTTAAAA
* * * * *
597156 GGAAAAAGATGGCCACGGACTTGTGGGCTTTTGAAGGTTGCCACTAATTTGTGGGCTTTGAAAAA
1 GGAAAAAGGT-GCCACTGATTTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAAA
* * *
597221 TGGTGCCACTGACTTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTG
64 -GATGCCACTGACTTTTTGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTG
* *
597274 GGAAAAGGGTGCTACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAAAGA
1 GGAAAAAGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAAAGA
597339 TGCCACTGACTTTTTGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTG
66 TGCCACTGACTTTTTGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTG
* *
597389 GGAAAAAGGTGCCACTGATTTATGGGCTTTGAAGGTTGCCACTGACTTGTGGCCTTTGAAAAAGA
1 GGAAAAAGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAAAGA
* *
597454 TGCCACTG-CCTTGTGAGCTTTTGAAGGT
66 TGCCACTGACTTTTTG-GCTTTTGAAGGT
597482 GAGGAATGTC
Statistics
Matches: 191, Mismatches: 16, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
114 5 0.03
115 130 0.68
116 34 0.18
117 14 0.07
118 8 0.04
ACGTcount: A:0.21, C:0.16, G:0.31, T:0.32
Consensus pattern (115 bp):
GGAAAAAGGTGCCACTGATTTGTGGGCTTTGAAGGTTGCCACTGACTTGTGGGCTTTGAAAAAGA
TGCCACTGACTTTTTGGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTG
Found at i:612938 original size:52 final size:52
Alignment explanation
Indices: 612790--612918 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
612780 CGAAATATGA
612790 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
612842 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
612894 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
612919 AAGATCAGTG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:612945 original size:13 final size:13
Alignment explanation
Indices: 612927--612951 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
612917 CAAAGATCAG
612927 TGTATCGATACAA
1 TGTATCGATACAA
612940 TGTATCGATACA
1 TGTATCGATACA
612952 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:613012 original size:13 final size:13
Alignment explanation
Indices: 612990--613047 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 13
612980 GGTAGTAGCT
*
612990 TTGTAGCGATACA
1 TTGTATCGATACA
613003 TTGTATCGATACAATA
1 TTGTATCGATAC---A
613019 CTTATGTATCGATACA
1 --T-TGTATCGATACA
613035 TTGTATCGATACA
1 TTGTATCGATACA
613048 ACAATTATGT
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
13 23 0.61
14 1 0.03
16 2 0.05
18 1 0.03
19 11 0.29
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:613028 original size:19 final size:17
Alignment explanation
Indices: 613004--613069 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 17
612994 AGCGATACAT
613004 TGTATCGATACAATACTTA
1 TGTATCGATACAA-A-TTA
613023 TGTATCGATAC--A-T-
1 TGTATCGATACAAATTA
613036 TGTATCGATACAACAATTA
1 TGTATCGATAC-A-AATTA
613055 TGTATCGATACAAAT
1 TGTATCGATACAAAT
613070 CATTGAATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.27
14 1 0.02
16 1 0.02
17 4 0.10
18 2 0.05
19 22 0.54
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (17 bp):
TGTATCGATACAAATTA
Found at i:613037 original size:32 final size:32
Alignment explanation
Indices: 612991--613066 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
612981 GTAGTAGCTT
* * *
612991 TGTAGCGATACATTGTATCGATACAATACTTA
1 TGTATCGATACATTGTATCGATACAACAATTA
613023 TGTATCGATACATTGTATCGATACAACAATTA
1 TGTATCGATACATTGTATCGATACAACAATTA
613055 TGTATCGATACA
1 TGTATCGATACA
613067 AATCATTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (32 bp):
TGTATCGATACATTGTATCGATACAACAATTA
Found at i:616839 original size:35 final size:35
Alignment explanation
Indices: 616704--616958 Score: 223
Period size: 35 Copynumber: 7.4 Consensus size: 35
616694 AATCCCCGAA
* * * *
616704 TTTCATCATCGTATGGCTATATCTAGTCAAACACT
1 TTTCATCATCATTTGGCTGTATCTAGTCAAACTCT
* * ** * *
616739 CTTCATTATTGTTTGACTGCAAT-T-GATCAAACTCT
1 TTTCATCATCATTTGGCTG-TATCTAG-TCAAACTCT
* *
616774 CTTCATCATCGTTTGGCT-TATCTAGTCAAACTCT
1 TTTCATCATCATTTGGCTGTATCTAGTCAAACTCT
* * *
616808 TTTCATCATCATTTAGCTGCATCTAGTCAAAC-CC
1 TTTCATCATCATTTGGCTGTATCTAGTCAAACTCT
616842 TTTCATCATCATTTGGCT-TATCTAGTCAAACTCT
1 TTTCATCATCATTTGGCTGTATCTAGTCAAACTCT
* * * * * *
616876 CTTCATTATCATTTGGTTGCATCTAATCAAACCCT
1 TTTCATCATCATTTGGCTGTATCTAGTCAAACTCT
* * * * *
616911 TTTCATCATTATTTAGTTGTATCTGGTCAAGCTCT
1 TTTCATCATCATTTGGCTGTATCTAGTCAAACTCT
616946 TTTCATCATCATT
1 TTTCATCATCATT
616959 ATCGACACCT
Statistics
Matches: 177, Mismatches: 36, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
33 14 0.08
34 60 0.34
35 101 0.57
36 2 0.01
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (35 bp):
TTTCATCATCATTTGGCTGTATCTAGTCAAACTCT
Found at i:616872 original size:68 final size:68
Alignment explanation
Indices: 616704--616958 Score: 248
Period size: 68 Copynumber: 3.7 Consensus size: 68
616694 AATCCCCGAA
* * * * **
616704 TTTCATCATCGTATGGCTATATCTAGTCAAACACTCTTCATTATTGTTTGACTGCAAT-T-GATC
1 TTTCATCATCATTTGGCTATATCTAGTCAAACTCTCTTCATCATCATTTG-CTGC-ATCTAG-TC
*
616767 AAACTC
63 AAACCC
* *
616773 TCTTCATCATCGTTTGGCT-TATCTAGTCAAACTCTTTTCATCATCATTTAGCTGCATCTAGTCA
1 T-TTCATCATCATTTGGCTATATCTAGTCAAACTCTCTTCATCATCATTT-GCTGCATCTAGTCA
616837 AACCC
64 AACCC
* * *
616842 TTTCATCATCATTTGGCT-TATCTAGTCAAACTCTCTTCATTATCATTTGGTTGCATCTAATCAA
1 TTTCATCATCATTTGGCTATATCTAGTCAAACTCTCTTCATCATCATTT-GCTGCATCTAGTCAA
616906 ACCC
65 ACCC
* * * * * * *
616910 TTTTCATCATTATTTAGTTGTATCTGGTCAAGCTCTTTTCATCATCATT
1 -TTTCATCATCATTTGGCTATATCTAGTCAAACTCTCTTCATCATCATT
616959 ATCGACACCT
Statistics
Matches: 160, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
68 63 0.39
69 54 0.34
70 43 0.27
ACGTcount: A:0.24, C:0.24, G:0.10, T:0.42
Consensus pattern (68 bp):
TTTCATCATCATTTGGCTATATCTAGTCAAACTCTCTTCATCATCATTTGCTGCATCTAGTCAAA
CCC
Found at i:620404 original size:35 final size:35
Alignment explanation
Indices: 620379--620811 Score: 383
Period size: 35 Copynumber: 12.6 Consensus size: 35
620369 GCTACATTTC
* * *
620379 GTCAAACTCTTTTCATCATCGTTTGGTTGCATGTG
1 GTCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
* * *
620414 GTCAGACACTC-TTT-ATCATCATTTGGCTATATCTA
1 GTCA-A-ACTCTTTTCATCATCGTTTGGTTGTATCTA
* *
620449 GTCAAACCCTTTTCATCATCATTTGGTTGTATCTA
1 GTCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
* * * * * *
620484 GTCAAACTCTCTTCATCATCATGTGGCTGTATTTG
1 GTCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
* ** *
620519 GTCAAACTCTTTTCATGATCGTTTGGTTCCATCTC
1 GTCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
* * *
620554 GTCAAACACTTTTCATCATTGTTT-GTCTGTATCTC
1 GTCAAACTCTTTTCATCATCGTTTGGT-TGTATCTA
* *
620589 GTCAAACTCTCTTT-ATCATCATTTGGTTGCATCT-
1 GTCAAACTCT-TTTCATCATCGTTTGGTTGTATCTA
*
620623 GCTC---CTC-TTT-ATCATCATTTGGTTGTATCT-
1 G-TCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
*
620653 GTTCAAACTCTTTTCATCATCGTTTGGTTGTATCTG
1 G-TCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
* *
620689 GTTAAACTCTTTTCATCATCGTTTGGTTGCATCT-
1 GTCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
* * * ** * *
620723 G---GATTCTTTTCATCTTTATTTGGCTGCATCTA
1 GTCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
*
620755 ATCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
1 GTCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
*
620790 GTCAAACTCTTTTTATCATCGT
1 GTCAAACTCTTTTCATCATCGT
620812 CCTTTTGTCA
Statistics
Matches: 326, Mismatches: 54, Indels: 36
0.78 0.13 0.09
Matches are distributed among these distances:
30 25 0.08
31 24 0.07
32 3 0.01
33 6 0.02
34 11 0.03
35 243 0.75
36 10 0.03
37 4 0.01
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (35 bp):
GTCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
Found at i:620544 original size:105 final size:101
Alignment explanation
Indices: 620379--620809 Score: 435
Period size: 105 Copynumber: 4.2 Consensus size: 101
620369 GCTACATTTC
* * **
620379 GTCAAACTCTTTTCATCATCGTTTGGTTGCATGTGGTCAGACACTCTTTATCATCATTTGGCTAT
1 GTCAAACTCTTTTCATCATCATTTGGTTGCATCTGGT----CACTCTTTATCATCATTTGGCTGC
* *
620444 ATCTAGTCAAACCCTTTTCATCATCATTTGGTTGTATCTA
62 ATCTAGTCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
* * * * * * * * *
620484 GTCAAACTCTCTTCATCATCATGTGGCTGTATTTGGTCAAACTCTTTTCATGATCGTTTGGTTCC
1 GTCAAACTCTTTTCATCATCATTTGGTTGCATCTGGTC--ACTC-TTT-ATCATCATTTGGCTGC
* * * *
620549 ATCTCGTCAAACACTTTTCATCATTGTTT-GTCTGTATCTC
62 ATCTAGTCAAACTCTTTTCATCATCGTTTGGT-TGTATCTA
* * *
620589 GTCAAACTCTCTTT-ATCATCATTTGGTTGCATCTGCTC-CTCTTTATCATCATTTGGTTGTATC
1 GTCAAACTCT-TTTCATCATCATTTGGTTGCATCTGGTCACTCTTTATCATCATTTGGCTGCATC
*
620652 T-GTTCAAACTCTTTTCATCATCGTTTGGTTGTATCTG
65 TAG-TCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
* * *
620689 GTTAAACTCTTTTCATCATCGTTTGGTTGCATCTGG--ATTCTTT-TCATCTTTATTTGGCTGCA
1 GTCAAACTCTTTTCATCATCATTTGGTTGCATCTGGTCACTCTTTATCATC---ATTTGGCTGCA
*
620751 TCTAATCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
63 TCTAGTCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
*
620790 GTCAAACTCTTTTTATCATC
1 GTCAAACTCTTTTCATCATC
620810 GTCCTTTTGT
Statistics
Matches: 273, Mismatches: 39, Indels: 32
0.79 0.11 0.09
Matches are distributed among these distances:
98 5 0.02
99 9 0.03
100 73 0.27
101 69 0.25
102 3 0.01
103 4 0.01
104 5 0.02
105 103 0.38
106 2 0.01
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (101 bp):
GTCAAACTCTTTTCATCATCATTTGGTTGCATCTGGTCACTCTTTATCATCATTTGGCTGCATCT
AGTCAAACTCTTTTCATCATCGTTTGGTTGTATCTA
Found at i:620633 original size:30 final size:30
Alignment explanation
Indices: 620597--620653 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
620587 TCGTCAAACT
620597 CTCTTTATCATCATTTGGTTGCATCTGCTC
1 CTCTTTATCATCATTTGGTTGCATCTGCTC
*
620627 CTCTTTATCATCATTTGGTTGTATCTG
1 CTCTTTATCATCATTTGGTTGCATCTG
620654 TTCAAACTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.14, C:0.23, G:0.14, T:0.49
Consensus pattern (30 bp):
CTCTTTATCATCATTTGGTTGCATCTGCTC
Found at i:620907 original size:35 final size:35
Alignment explanation
Indices: 620819--620919 Score: 132
Period size: 35 Copynumber: 2.9 Consensus size: 35
620809 CGTCCTTTTG
* *
620819 TCATCGTTTAGCTATATCTAGTCAAACACTTTTCA
1 TCATCGTTTGGCTATATCTAGTCAAACTCTTTTCA
* *
620854 TTATTGTTTGG-TCATATCTAGTCAAACTCTTTTCA
1 TCATCGTTTGGCT-ATATCTAGTCAAACTCTTTTCA
* *
620889 TCATCGTTTGGCTGTATCTGGTCAAACTCTT
1 TCATCGTTTGGCTATATCTAGTCAAACTCTT
620920 CCTATCATCA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
34 1 0.02
35 54 0.96
36 1 0.02
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.44
Consensus pattern (35 bp):
TCATCGTTTGGCTATATCTAGTCAAACTCTTTTCA
Found at i:620927 original size:35 final size:35
Alignment explanation
Indices: 620819--620943 Score: 92
Period size: 35 Copynumber: 3.6 Consensus size: 35
620809 CGTCCTTTTG
* * * * *
620819 TCATCGTTTAGCTATATCTAGTCAAACACTTTTCA
1 TCATCATTTGGCTGTATCTAGTCAAACTCTTCTCA
* ** * *
620854 TTATTGTTTGG-TCATATCTAGTCAAACTCTTTTCA
1 TCATCATTTGGCT-GTATCTAGTCAAACTCTTCTCA
* *
620889 TCATCGTTTGGCTGTATCTGGTCAAACTCTTC-CTA
1 TCATCATTTGGCTGTATCTAGTCAAACTCTTCTC-A
* *
620924 TCATCATTTGGTTGCATCTA
1 TCATCATTTGGCTGTATCTA
620944 TGCAAACCCT
Statistics
Matches: 74, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
34 2 0.03
35 71 0.96
36 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (35 bp):
TCATCATTTGGCTGTATCTAGTCAAACTCTTCTCA
Found at i:622019 original size:13 final size:13
Alignment explanation
Indices: 622001--622025 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
621991 ACACAAAGTA
622001 TGTATCGATACAT
1 TGTATCGATACAT
622014 TGTATCGATACA
1 TGTATCGATACA
622026 CCATAAAATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:622022 original size:32 final size:33
Alignment explanation
Indices: 621981--622048 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
621971 GTAGCCAAAC
*
621981 TTGTATCGATACA-CA-AAGTATGTATCGATACA
1 TTGTATCGATACACCATAA-AATGTATCGATACA
622013 TTGTATCGATACACCATAAAATGTATCGATACA
1 TTGTATCGATACACCATAAAATGTATCGATACA
622046 TTG
1 TTG
622049 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACACCATAAAATGTATCGATACA
Found at i:623730 original size:166 final size:165
Alignment explanation
Indices: 623303--623730 Score: 465
Period size: 166 Copynumber: 2.6 Consensus size: 165
623293 AGTTTTCTTG
* *
623303 GTTTATAAATTTTAAAATTCATCAAATATTATTATTTAA-TCACCATTAAATCATTTTTGAAAAG
1 GTTTA-AAATTTTTAAATTCATCAAATATTATCATTTAATTCA-CATTAAATCATTTTTGAAAA-
* * *
623367 TTTATTTATTTTCATGAGTTTTTCATTTTTTCTCTTGAAATTCCTTTGTTTTTAAAAAACTAAGT
63 TTTATTTATTTTCATGAGTTTTTCATTTTTTCTCTTGAAATTCCTCTATATTTAAAAAACTAAGT
* * *
623432 TTTCTATTCTATAAAGGTTTTTGATGGGGTTTTTCTCG
128 TTTCTATTCTATAAAGGTTTTTCAAGGGGTTTTTCTCA
* * *
623470 GTCTGAAATTTTTAATATTCATCAAATATCATCATTTAATTCACATTAAATCATTTTTGAAAAAT
1 GTTTAAAATTTTTAA-ATTCATCAAATATTATCATTTAATTCACATTAAATCATTTTTG-AAAAT
* * * *
623535 TTATTTATTTTCATAATTTTTTCATTTTTTC-CTTGAAA-TGCTACTATATTTGAAAAACTGAA-
64 TTATTTATTTTCATGAGTTTTTCATTTTTTCTCTTGAAATTCCT-CTATATTTAAAAAACT-AAG
* * *
623597 TTTTTTA-TCTCATAAATG-TTTTCAAGGGAGTTTTTTTCA
127 TTTTCTATTCT-ATAAAGGTTTTTCAAGGG-GTTTTTCTCA
* * * * *
623636 GTTTAAAATTTTTATAATTCATCTAATATTGTCATTAAATTCTCATTAAATCAGTTTTGAGAAAT
1 GTTTAAAATTTTTA-AATTCATCAAATATTATCATTTAATTCACATTAAATCATTTTTGA-AAAT
* **
623701 TCAATTTATTTT-ATGAGTTTTGAATTTTTT
64 T-TATTTATTTTCATGAGTTTTTCATTTTTT
623731 AGTATATATT
Statistics
Matches: 220, Mismatches: 31, Indels: 21
0.81 0.11 0.08
Matches are distributed among these distances:
165 15 0.07
166 116 0.53
167 82 0.37
168 7 0.03
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.50
Consensus pattern (165 bp):
GTTTAAAATTTTTAAATTCATCAAATATTATCATTTAATTCACATTAAATCATTTTTGAAAATTT
ATTTATTTTCATGAGTTTTTCATTTTTTCTCTTGAAATTCCTCTATATTTAAAAAACTAAGTTTT
CTATTCTATAAAGGTTTTTCAAGGGGTTTTTCTCA
Found at i:624257 original size:15 final size:15
Alignment explanation
Indices: 624211--624249 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
624201 TTTTGCAAGC
*
624211 AAGAAAAAAAAGAGA
1 AAGAAAAAAAAGAAA
*
624226 GAGAAAAAAAAGAAA
1 AAGAAAAAAAAGAAA
624241 AAGAAAAAA
1 AAGAAAAAA
624250 TAAAAAAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAAGAAA
Found at i:625424 original size:142 final size:142
Alignment explanation
Indices: 625163--625439 Score: 407
Period size: 142 Copynumber: 2.0 Consensus size: 142
625153 ATTTTATCAC
* *
625163 TAAATAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCTTATGGTTTTTCGTAGAGATAT
1 TAAATAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTCCGTAGAGATAT
** * **
625228 AGAAATCTTCAAAACTTTTCATATCTATTTGGTTCTCCATTATGGTACAAAATGA-ATTTTTTAA
66 AGAAATCTTCAAAACTTTTCATATCTATTTAATTCTCCATTAAGGTACAAAATGAGATTTTCAAA
625292 AAATTAAAAAAT
131 AAATTAAAAAAT
* *
625304 TAAATAAAAATTATTATCTTAATTTTTTAAGATTTCTAATATTCCTATGGTTTTCCGTA-AGGGT
1 TAAAT-AAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTCCGTAGA-GAT
* *
625368 ATAGAAATCTTTAAAACTTTTCGTATCT-TTTCAATTCTCCATTAAGGTACAAAATGAGATTTTC
64 ATAGAAATCTTCAAAACTTTTCATATCTATTT-AATTCTCCATTAAGGTACAAAATGAGATTTTC
625432 AAAAAATT
128 AAAAAATT
625440 TAATACTATT
Statistics
Matches: 121, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
141 9 0.07
142 100 0.83
143 12 0.10
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (142 bp):
TAAATAAAATTATTATCTTAATTTTTCAAGATTTCTAATATTCCTATGGTTTTCCGTAGAGATAT
AGAAATCTTCAAAACTTTTCATATCTATTTAATTCTCCATTAAGGTACAAAATGAGATTTTCAAA
AAATTAAAAAAT
Found at i:625992 original size:157 final size:156
Alignment explanation
Indices: 625620--626228 Score: 670
Period size: 157 Copynumber: 3.9 Consensus size: 156
625610 ATAGGGTCCG
* * * * *
625620 CTTTTATACCGAAGATGGGTATTTAGGATAGTTTCATCCCTTCTATATTCCTTTTCAAGTCCTTA
1 CTTTTATACCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTA
* ** *
625685 AGGGGTATCGGGCACTTCTAAGTCGAAGGTATCCTCTAAAGTTATTTTCAGTAAGTTTTTTTTAG
66 AGGGGTATCGGGCACTTCTAAGTCGAAGGTATCCTCTAAGGGCATTTTCA-TAA--TTTTTTTAA
** *
625750 AATTGAGTCCTAGGTTGCCACTAAGTTCA
128 AACCGAGTCCTAGGTTGCCACCAAGTTCA
* * * * * * *
625779 CTTTTATACTGAAAGTGAGTATCTATGATAGGTTCATCTCATCTATAATCCTTTTTAAGTCCTTT
1 CTTTTATACCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTA
* * * *
625844 AGGGGTATCAGACACTTCTAAGTCGAAAGTATCCTCTAAGGGTATTTTCATAATTTTTTTCAAAA
66 AGGGGTATCGGGCACTTCTAAGTCGAAGGTATCCTCTAAGGGCATTTTCATAATTTTTTT-AAAA
**
625909 CCGAGTCCTAGGTTGCCACCAAGCCCA
130 CCGAGTCCTAGGTTGCCACCAAGTTCA
* * *
625936 CTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCATTTTTAAGTGCTTT
1 CTTTTATACCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGT-CCTT
** *
626001 AA-GGGTATTTGGCACTT-TAAAGGTCGAAGGTATCC-CATAGGGGCATTTTCATAATTTTTTTA
65 AAGGGGTATCGGGCACTTCT-AA-GTCGAAGGTATCCTC-TAAGGGCATTTTCATAATTTTTTTA
* * * ** **
626063 GAACTGAGTCCTAGGTTGTCACCGGGTTTG
127 AAACCGAGTCCTAGGTTGCCACCAAGTTCA
** * * * **
626093 CTTTTATGTCAAAGGTTGGTATTTAGGATAGGTTCATCCTATCTATAATTTTTTTTAAGTCCTTA
1 CTTTTATACCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTA
*
626158 AGGAGTATCGGGCACTTCTAAGTCGAAGGTAT-CT-TATAGGGACATTTTCATAATTTTTTTAAA
66 AGGGGTATCGGGCACTTCTAAGTCGAAGGTATCCTCTA-AGGG-CATTTTCATAATTTTTTTAAA
*
626221 ATCGAGTC
129 ACCGAGTC
626229 TTAATTTATC
Statistics
Matches: 378, Mismatches: 62, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
154 2 0.01
155 4 0.01
156 50 0.13
157 182 0.48
158 42 0.11
159 98 0.26
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (156 bp):
CTTTTATACCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCCTTTTTAAGTCCTTA
AGGGGTATCGGGCACTTCTAAGTCGAAGGTATCCTCTAAGGGCATTTTCATAATTTTTTTAAAAC
CGAGTCCTAGGTTGCCACCAAGTTCA
Found at i:626140 original size:314 final size:314
Alignment explanation
Indices: 625620--626228 Score: 743
Period size: 314 Copynumber: 1.9 Consensus size: 314
625610 ATAGGGTCCG
* * * *
625620 CTTTTATACCGAAGATGGGTATTTAGGATAGTTTCATCCCTTCTATATTCCTTTTCAAGTCCTTA
1 CTTTTATACCGAAGATGGGTATTTAGGATAGGTTCATCCCATCTATAATCATTTTCAAGTCCTTA
**
625685 AGGGGTATCGGGCACTTCTAAGTCGAAGGTATCCTCTAAAGTTATTTTCAGTAAGTTTTTTTTAG
66 AGGGGTATCGGGCACTTCTAAGTCGAAGGTATCCTCTAAAGGCATTTTCAGTAAG-TTTTTTTAG
* * * *
625750 AATTGAGTCCTAGGTTGCCACTAAGTTCACTTTTATACTGAAAGTGAGTATCTATGATAGGTTCA
130 AACTGAGTCCTAGGTTGCCACCAAGTTCACTTTTATACTCAAAGTGAGTATCTAGGATAGGTTCA
* *
625815 TCTCATCTATAATCCTTTTTAAGTCCTTTAGGGGTATCAGACACTTCTAAGTCGAAAGTATCCTC
195 TCTCATCTATAATCCTTTTTAAGTCCTTAAGGAGTATCAGACACTTCTAAGTCGAAAGTAT-CT-
*
625880 TA-AGGG-TATTTTCATAATTTTTTTCAAAACCGAGTCCTAGGTTGCCACCAAGCCCA
258 TATAGGGACATTTTCATAATTTTTTT-AAAACCGAGTCCTAGGTTGCCACCAAGCCCA
* * * *
625936 CTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCATCTATAATCATTTTTAAGTGCTTT
1 CTTTTATACCGAAGATGGGTATTTAGGATAGGTTCATCCCATCTATAATCATTTTCAAGT-CCTT
** **
626001 AA-GGGTATTTGGCACTT-TAAAGGTCGAAGGTATCC-CATAGGGGCATTTTCA-TAA-TTTTTT
65 AAGGGGTATCGGGCACTTCT-AA-GTCGAAGGTATCCTC-TAAAGGCATTTTCAGTAAGTTTTTT
* ** ** * *
626061 TAGAACTGAGTCCTAGGTTGTCACCGGGTTTGCTTTTAT-GTCAAAGGTTG-GTATTTAGGATAG
127 TAGAACTGAGTCCTAGGTTGCCACCAAGTTCACTTTTATACTCAAA-G-TGAGTATCTAGGATAG
** * * *
626124 GTTCATC-CTATCTATAATTTTTTTTAAGTCCTTAAGGAGTATCGGGCACTTCTAAGTCGAAGGT
190 GTTCATCTC-ATCTATAATCCTTTTTAAGTCCTTAAGGAGTATCAGACACTTCTAAGTCGAAAGT
*
626188 ATCTTATAGGGACATTTTCATAATTTTTTTAAAATCGAGTC
254 ATCTTATAGGGACATTTTCATAATTTTTTTAAAACCGAGTC
626229 TTAATTTATC
Statistics
Matches: 250, Mismatches: 34, Indels: 21
0.82 0.11 0.07
Matches are distributed among these distances:
312 2 0.01
313 21 0.08
314 124 0.50
315 3 0.01
316 72 0.29
317 28 0.11
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (314 bp):
CTTTTATACCGAAGATGGGTATTTAGGATAGGTTCATCCCATCTATAATCATTTTCAAGTCCTTA
AGGGGTATCGGGCACTTCTAAGTCGAAGGTATCCTCTAAAGGCATTTTCAGTAAGTTTTTTTAGA
ACTGAGTCCTAGGTTGCCACCAAGTTCACTTTTATACTCAAAGTGAGTATCTAGGATAGGTTCAT
CTCATCTATAATCCTTTTTAAGTCCTTAAGGAGTATCAGACACTTCTAAGTCGAAAGTATCTTAT
AGGGACATTTTCATAATTTTTTTAAAACCGAGTCCTAGGTTGCCACCAAGCCCA
Found at i:626370 original size:149 final size:146
Alignment explanation
Indices: 626193--626687 Score: 512
Period size: 149 Copynumber: 3.3 Consensus size: 146
626183 AAGGTATCTT
* * * * * * * *
626193 ATAGGGACATTTTCATAATTTTTTTAAAATCGAGTCTTAATTTATCACCTGGTCGCTTCTATACC
1 ATAGGGGCATTTTCATAATTTTTCTAAAACCAAGTCTTAATTTGTCACCTGGTTGCTTCCATGCC
**
626258 AAGAGTATGTATTAGGCGTAGGTTCATTTTTCCTTTTTAAGTCCTTTAGGGTTACAATGATACTT
66 -AGAGTATGTATTAGGCGTAGGTTCGCTTTTCCTTTTTAAGTCCTTTAGGGTTACAA-GATACTT
**
626323 TCATGTCAAAGCTATACTT
129 TCATGTCAAAG-TATACCC
* * * * * *
626342 ATAAGGGTATTTTCATAATTTTTCTAAAACCAAATCCTAATTTGTCGCCAGGTTGCTTCCATGCT
1 ATAGGGGCATTTTCATAATTTTTCTAAAACCAAGTCTTAATTTGTCACCTGGTTGCTTCCATGC-
* * * ** * *
626407 GAGGGTACGTATTAGGCGTAGGTTCGCTTTTCCTTTTTAAGTTTTTTAAGGTTACTAGGATACTT
65 CAGAGTATGTATTAGGCGTAGGTTCGCTTTTCCTTTTTAAGTCCTTTAGGGTTAC-AAGATACTT
626472 TCATGTCAAAAGTATACCC
129 TCATGTC-AAAGTATACCC
* * * * *
626491 ATAGGGGCATTTTCATAATTTTTCTAGAGCCAAGTCTTAATTTGTCA-TTGGGTTACTTCCATGT
1 ATAGGGGCATTTTCATAATTTTTCTAAAACCAAGTCTTAATTTGTCACCT-GGTTGCTTCCATGC
* * *
626555 C-GAGGATGCGTATTA-GTGTAGGTTTGCTTTTCCTTTTTAAGTCCTTTAGGGTTACCAAGATAC
65 CAGAGTAT--GTATTAGGCGTAGGTTCGCTTTTCCTTTTTAAGTCCTTTAGGGTTA-CAAGATAC
* *
626618 TTTCATATCGAAGGTATACCC
127 TTTCATGTC-AAAGTATACCC
* * *
626639 ATAGGGGCATTTTCAAAATTTTTC-AAGAACTAAGTCCTAATTTGTCACC
1 ATAGGGGCATTTTCATAATTTTTCTAA-AACCAAGTCTTAATTTGTCACC
626688 GAGTCACTTC
Statistics
Matches: 282, Mismatches: 55, Indels: 18
0.79 0.15 0.05
Matches are distributed among these distances:
147 4 0.01
148 98 0.35
149 175 0.62
150 5 0.02
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (146 bp):
ATAGGGGCATTTTCATAATTTTTCTAAAACCAAGTCTTAATTTGTCACCTGGTTGCTTCCATGCC
AGAGTATGTATTAGGCGTAGGTTCGCTTTTCCTTTTTAAGTCCTTTAGGGTTACAAGATACTTTC
ATGTCAAAGTATACCC
Found at i:626637 original size:148 final size:149
Alignment explanation
Indices: 626266--626719 Score: 529
Period size: 149 Copynumber: 3.1 Consensus size: 149
626256 CCAAGAGTAT
**
626266 GTATTAGGCGTAGGTTCATTTTTCCTTTTTAAGTCCTTTAGGGTTA-CAATGATACTTTCATGTC
1 GTATTAGGCGTAGGTTCGCTTTTCCTTTTTAAGTCCTTTAGGGTTACCAA-GATACTTTCATGTC
* ** * * * * *
626330 AAAGCTATACTTATAAGGGTATTTTCATAATTTTTCTAAAACCAAATCCTAATTTGTCGCCAGGT
65 AAAGGTATACCCATAGGGGCATTTTCATAATTTTTCTAGAACCAAGTCCTAATTTGTCACCAGGT
* *
626395 TGCTTCCATGCTGAGGGTAC
130 TACTTCCATGCTGAGGATAC
** * * *
626415 GTATTAGGCGTAGGTTCGCTTTTCCTTTTTAAGTTTTTTAAGGTTACTAGGATACTTTCATGTCA
1 GTATTAGGCGTAGGTTCGCTTTTCCTTTTTAAGTCCTTTAGGGTTACCAAGATACTTTCATGTCA
* * * ***
626480 AAAGTATACCCATAGGGGCATTTTCATAATTTTTCTAGAGCCAAGTCTTAATTTGTCATTGGGTT
66 AAGGTATACCCATAGGGGCATTTTCATAATTTTTCTAGAACCAAGTCCTAATTTGTCACCAGGTT
*
626545 ACTTCCATG-TCGAGGATGC
131 ACTTCCATGCT-GAGGATAC
* * * *
626564 GTATTA-GTGTAGGTTTGCTTTTCCTTTTTAAGTCCTTTAGGGTTACCAAGATACTTTCATATCG
1 GTATTAGGCGTAGGTTCGCTTTTCCTTTTTAAGTCCTTTAGGGTTACCAAGATACTTTCATGTCA
* * *
626628 AAGGTATACCCATAGGGGCATTTTCAAAATTTTTCAAGAACTAAGTCCTAATTTGTCACC-GAGT
66 AAGGTATACCCATAGGGGCATTTTCATAATTTTTCTAGAACCAAGTCCTAATTTGTCACCAG-GT
* * ** *
626692 CACTTCTATGCCAAAGATAC
130 TACTTCCATGCTGAGGATAC
626712 GTATTAGG
1 GTATTAGG
626720 TGTCTCTGGA
Statistics
Matches: 253, Mismatches: 47, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
147 1 0.00
148 123 0.49
149 128 0.51
150 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.39
Consensus pattern (149 bp):
GTATTAGGCGTAGGTTCGCTTTTCCTTTTTAAGTCCTTTAGGGTTACCAAGATACTTTCATGTCA
AAGGTATACCCATAGGGGCATTTTCATAATTTTTCTAGAACCAAGTCCTAATTTGTCACCAGGTT
ACTTCCATGCTGAGGATAC
Found at i:638392 original size:19 final size:19
Alignment explanation
Indices: 638368--638417 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
638358 AGCGATACAT
638368 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
638387 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
638406 TGTATCGATACA
1 TGTATCGATACA
638418 TTGTATCGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:638424 original size:13 final size:13
Alignment explanation
Indices: 638406--638430 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
638396 ACAACACTTA
638406 TGTATCGATACAT
1 TGTATCGATACAT
638419 TGTATCGATACA
1 TGTATCGATACA
638431 AATCGTTGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:641753 original size:7 final size:7
Alignment explanation
Indices: 641678--641739 Score: 90
Period size: 7 Copynumber: 8.7 Consensus size: 7
641668 GTGTAAAGAT
641678 ATAAAAA
1 ATAAAAA
641685 ATAATAAA
1 ATAA-AAA
641693 ATAACAAA
1 ATAA-AAA
641701 AT-AAAA
1 ATAAAAA
641707 ATAAAAA
1 ATAAAAA
*
641714 ACAAAAA
1 ATAAAAA
641721 ATAAAAA
1 ATAAAAA
641728 ATAAAAA
1 ATAAAAA
641735 ATAAA
1 ATAAA
641740 GAAAAAACAA
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
6 5 0.10
7 33 0.66
8 12 0.24
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.15
Consensus pattern (7 bp):
ATAAAAA
Found at i:641760 original size:18 final size:18
Alignment explanation
Indices: 641723--641761 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
641713 AACAAAAAAT
* *
641723 AAAAAATAAAAAATAAAG
1 AAAAAACAAAAAAGAAAG
*
641741 AAAAAACAAAAAAGAGAG
1 AAAAAACAAAAAAGAAAG
641759 AAA
1 AAA
641762 TCGAACGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.82, C:0.03, G:0.10, T:0.05
Consensus pattern (18 bp):
AAAAAACAAAAAAGAAAG
Found at i:642548 original size:91 final size:92
Alignment explanation
Indices: 642440--642743 Score: 320
Period size: 91 Copynumber: 3.3 Consensus size: 92
642430 TCACTACAAA
* * *
642440 GTATTGATGCATCACAAAACCTGATTTTCTTGAGGCAAGGATATCCAAACCACA-ATTCCTAATC
1 GTATTGATGCATCACAAAGCCTGATTTCCTTGAGGCAAGGATATCCAAACCACACATTCCCAATC
642504 ACGAT-CCC-TTCATCCAACCGCTAGATG
66 ACG-TCCCCATT-ATCCAACCGCTAGATG
* * * *
642531 GTATTAATGCATCACAAAGCCTGATTTCCTTG-GGGAAGGAATATTCAGA-CACACATTCCCAAT
1 GTATTGATGCATCACAAAGCCTGATTTCCTTGAGGCAAGG-ATATCCAAACCACACATTCCCAAT
* *
642594 TACGTCCCCATTATCCAACCGCTATATG
65 CACGTCCCCATTATCCAACCGCTAGATG
* * *
642622 GTATTGATGCATCACAAAGCCTGATTTCCTT-AGGGCAAGGATACCCAAACCACATATTCTCAAT
1 GTATTGATGCATCACAAAGCCTGATTTCCTTGA-GGCAAGGATATCCAAACCACACATTCCCAAT
** * * *
642686 CATAT-CCC-TTTTCCTCAAACACTAGATG
65 CACGTCCCCATTAT-C-CAACCGCTAGATG
* *
642714 ATATTGATGCATTACAAAGCCTGA-TTCCTT
1 GTATTGATGCATCACAAAGCCTGATTTCCTT
642744 TAGGGTAAAG
Statistics
Matches: 179, Mismatches: 25, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
90 14 0.08
91 111 0.62
92 54 0.30
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.28
Consensus pattern (92 bp):
GTATTGATGCATCACAAAGCCTGATTTCCTTGAGGCAAGGATATCCAAACCACACATTCCCAATC
ACGTCCCCATTATCCAACCGCTAGATG
Found at i:643301 original size:35 final size:35
Alignment explanation
Indices: 643250--643849 Score: 483
Period size: 35 Copynumber: 17.2 Consensus size: 35
643240 TCTTACCAAT
* * *
643250 AAACCCTTTTCATCATCATTTGGCCATATCTGGTC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
* * *
643285 AAACTCTTTTCCTCATCATTTAGCTGCATCTGGTC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
** * *
643320 AAACTCTTTTCATCATTGTTTAGCTACATTTGGTC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
** * **
643355 AAACTCTTTTCATCATTGTTTGGCTGCATCTAATC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
* * * * *
643390 AAACTCTTTACATTATTATTTGGATACATTTGGTC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
* * ** * * *
643425 AAACTGTTTTCATCATCGTTCAGTTGCATCTAGTC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
* * * *
643460 AAACCCTTTTCATCATCGTTTGGCTCCATCTAGTC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
* * *
643495 AAACTC-TTTCATCATCATTTGGTTACATTTGGTG
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
* * * *
643529 AAACCCTTTTCATCATCATATGGCTGCATCTAGTC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
* *
643564 AAACTC-TTTCATCATCATTTAGCTATATCTGGTC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
** ** *
643598 AAACTC-TTTCATCATTGTTTGGCTGTATCTAGTC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
* * *
643632 AAACTCTTTTCATCAT-AGTTGGCTACATTTGATC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
* * * * **
643666 AAACCCTTTTCATCTTCTATTTAGCTATATCTATTC
1 AAACTCTTTTCATCATC-ATTTGGCTACATCTGGTC
* * * *
643702 AAACTCTTTTTATCATCATTCGACTACATTTGGTC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
** **
643737 AAAC-CTTTTTCATCATCGCTTGGCTACATCTAATC
1 AAACTC-TTTTCATCATCATTTGGCTACATCTGGTC
* * * ** *
643772 AAACTTTTTTCATCATCGTTTGGTTGTATCTGGCC
1 AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
* ** *
643807 AAACT-TTTGTCATCATCGTTTGGCTGTATCTAGTC
1 AAACTCTTT-TCATCATCATTTGGCTACATCTGGTC
643842 AAACTCTT
1 AAACTCTT
643850 CTGGCTACAT
Statistics
Matches: 447, Mismatches: 110, Indels: 15
0.78 0.19 0.03
Matches are distributed among these distances:
34 114 0.26
35 305 0.68
36 28 0.06
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (35 bp):
AAACTCTTTTCATCATCATTTGGCTACATCTGGTC
Found at i:643923 original size:94 final size:94
Alignment explanation
Indices: 643757--643940 Score: 314
Period size: 94 Copynumber: 2.0 Consensus size: 94
643747 CATCATCGCT
643757 TGGCTACATCTAATCAAACTTTTTTCATCATCGTTTGGTTGTATCTGGCCAAACTTTTGTCATCA
1 TGGCTACATCTAATCAAACTTTTTTCATCATCGTTTGGTTGTATCTGGCCAAACTTTTGTCATCA
*
643822 TCGTTTGGCTGTATCTAGTCAAACTCTTC
66 TCATTTGGCTGTATCTAGTCAAACTCTTC
* * * *
643851 TGGCTACATCTGATTAAACTTTTTTCATCATCGTTTGGTTGTATGTGGCCAAACTTTTTTCATCA
1 TGGCTACATCTAATCAAACTTTTTTCATCATCGTTTGGTTGTATCTGGCCAAACTTTTGTCATCA
*
643916 TCATTTGGCTGTATCTGGTCAAACT
66 TCATTTGGCTGTATCTAGTCAAACT
643941 TTTTTCATCA
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
94 84 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (94 bp):
TGGCTACATCTAATCAAACTTTTTTCATCATCGTTTGGTTGTATCTGGCCAAACTTTTGTCATCA
TCATTTGGCTGTATCTAGTCAAACTCTTC
Found at i:644016 original size:35 final size:35
Alignment explanation
Indices: 643866--644010 Score: 175
Period size: 35 Copynumber: 4.1 Consensus size: 35
643856 ACATCTGATT
* * *
643866 AAACTTTTTTCATCATCGTTTGGTTGTATGTGGCC
1 AAACTTTTTTCATCATCGTTTGGCTGTATATGGTC
* *
643901 AAACTTTTTTCATCATCATTTGGCTGTATCTGGTC
1 AAACTTTTTTCATCATCGTTTGGCTGTATATGGTC
*** *
643936 AAACTTTTTTCATCATCGTTTGGCCAAATCTGGTC
1 AAACTTTTTTCATCATCGTTTGGCTGTATATGGTC
* *
643971 AAACTCTTCTT-ATCATCGTTTGGCTGTATATGGTT
1 AAACT-TTTTTCATCATCGTTTGGCTGTATATGGTC
644006 AAACT
1 AAACT
644011 CTTCTTGTTA
Statistics
Matches: 95, Mismatches: 14, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
35 91 0.96
36 4 0.04
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.43
Consensus pattern (35 bp):
AAACTTTTTTCATCATCGTTTGGCTGTATATGGTC
Found at i:644027 original size:35 final size:35
Alignment explanation
Indices: 643864--644044 Score: 143
Period size: 35 Copynumber: 5.2 Consensus size: 35
643854 CTACATCTGA
* * *
643864 TTAAACT-TTTTTCATCATCGTTTGGTTGTATGTGG
1 TTAAACTCTTCTT-ATCATCGTTTGGCTGTATATGG
** * * *
643899 CCAAACT-TTTTTCATCATCATTTGGCTGTATCTGG
1 TTAAACTCTTCTT-ATCATCGTTTGGCTGTATATGG
* * *** *
643934 TCAAACT-TTTTTCATCATCGTTTGGCCAAATCTGG
1 TTAAACTCTTCTT-ATCATCGTTTGGCTGTATATGG
*
643969 TCAAACTCTTCTTATCATCGTTTGGCTGTATATGG
1 TTAAACTCTTCTTATCATCGTTTGGCTGTATATGG
* * * *
644004 TTAAACTCTTCTTGTTATTGTTTGGTTGTATATGG
1 TTAAACTCTTCTTATCATCGTTTGGCTGTATATGG
644039 TTAAAC
1 TTAAAC
644045 CTGTTTTGTT
Statistics
Matches: 125, Mismatches: 20, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
35 121 0.97
36 4 0.03
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.46
Consensus pattern (35 bp):
TTAAACTCTTCTTATCATCGTTTGGCTGTATATGG
Found at i:644741 original size:22 final size:21
Alignment explanation
Indices: 644708--644752 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
644698 AAATTTTATA
* *
644708 TTTTTTAGAATTTTCTAAAAT
1 TTTTTTAAAATTTTCAAAAAT
*
644729 TTTTTTGAAAATTTTGAAAAAT
1 TTTTTT-AAAATTTTCAAAAAT
644751 TT
1 TT
644753 GCCGTGTATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (21 bp):
TTTTTTAAAATTTTCAAAAAT
Found at i:645815 original size:5 final size:5
Alignment explanation
Indices: 645807--645831 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
645797 GATTTTTGAA
645807 TATTT TATTT TATTT TATTT TATTT
1 TATTT TATTT TATTT TATTT TATTT
645832 GTTTTTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TATTT
Found at i:646611 original size:13 final size:13
Alignment explanation
Indices: 646590--646619 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
646580 CGATACATGG
*
646590 TACATTGTATCGA
1 TACAATGTATCGA
646603 TACAATGTATCGA
1 TACAATGTATCGA
646616 TACA
1 TACA
646620 TGATGAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:646612 original size:33 final size:33
Alignment explanation
Indices: 646575--646639 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
646565 CACCACTGTT
* *
646575 TGTATCGATACATGGT-ACATTGTATCGATACAA
1 TGTATCGATACATGATGA-ATTATATCGATACAA
646608 TGTATCGATACATGATGAATTATATCGATACA
1 TGTATCGATACATGATGAATTATATCGATACA
646640 TTGCTTCTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTATATCGATACAA
Found at i:649088 original size:13 final size:13
Alignment explanation
Indices: 649070--649094 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
649060 ATTTTACTAA
649070 GTATCGATACATT
1 GTATCGATACATT
649083 GTATCGATACAT
1 GTATCGATACAT
649095 AGAATTGGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:649156 original size:22 final size:22
Alignment explanation
Indices: 649130--649185 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
649120 TTTCACTGTT
*
649130 CATCACTATTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
649152 CATCACTGTTCATGTATCGATA
1 CATCACTGTTCATGTATCGATA
*
649174 CATTACTGTTCA
1 CATCACTGTTCA
649186 CTATTCATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.38
Consensus pattern (22 bp):
CATCACTGTTCATGTATCGATA
Found at i:649344 original size:33 final size:33
Alignment explanation
Indices: 649200--649352 Score: 104
Period size: 33 Copynumber: 4.5 Consensus size: 33
649190 TCATAACTGT
* * *
649200 ATCACTATCCATGTATCCATAAAAGCACTGTTC-
1 ATCACTATTCATGTATCGAT-AAATCACTGTTCG
* *
649233 ATCACTATTCATATATCGAT--A-CAGTGTATCG
1 ATCACTATTCATGTATCGATAAATCACTGT-TCG
* *
649264 AT-A-TATTGTGAATAGTATCGATATATCACTGTTCACG
1 ATCACTA-T-T-CAT-GTATCGATAAATCACTGTT--CG
649301 TATCACTATTCATGTATCGATAAAATCACTGTTC-
1 -ATCACTATTCATGTATCGAT-AAATCACTGTTCG
649335 ATCACTATTCATGTATCG
1 ATCACTATTCATGTATCG
649353 GTGGCAACTC
Statistics
Matches: 96, Mismatches: 9, Indels: 30
0.71 0.07 0.22
Matches are distributed among these distances:
29 7 0.07
30 5 0.05
31 3 0.03
32 2 0.02
33 42 0.44
35 3 0.03
36 13 0.14
37 14 0.15
38 3 0.03
39 2 0.02
40 2 0.02
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (33 bp):
ATCACTATTCATGTATCGATAAATCACTGTTCG
Found at i:649408 original size:33 final size:31
Alignment explanation
Indices: 649350--649438 Score: 126
Period size: 33 Copynumber: 2.8 Consensus size: 31
649340 TATTCATGTA
*
649350 TCGGTGGCAACTCTTCCTAAAGCCCACACAAG
1 TCGGTGGCAACCCTT-CTAAAGCCCACACAAG
649382 TCGGTGGCAACCACTCTCTAAAGCCCACACAAG
1 TCGGTGGCAACC-CT-TCTAAAGCCCACACAAG
*
649415 TCAGTGGCAACCCTTCT-AAGCCCA
1 TCGGTGGCAACCCTTCTAAAGCCCA
649439 ATATAGCTGG
Statistics
Matches: 53, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
30 7 0.13
31 3 0.06
32 13 0.25
33 29 0.55
34 1 0.02
ACGTcount: A:0.28, C:0.36, G:0.18, T:0.18
Consensus pattern (31 bp):
TCGGTGGCAACCCTTCTAAAGCCCACACAAG
Found at i:649489 original size:49 final size:48
Alignment explanation
Indices: 649431--649940 Score: 663
Period size: 49 Copynumber: 10.8 Consensus size: 48
649421 GCAACCCTTC
* * * *
649431 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
* *
649480 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
*
649528 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C-CA---T
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
* * *
649571 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
*
649620 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-C-CA---T
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
* * *
649663 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
*
649712 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCATCTT
*
649761 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCACCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
649809 TAAGTCCAAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--CTT
1 TAAGTCC-AATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
* *
649853 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC---T-CATCTT
*
649905 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTG
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTG
649941 ACATCCTTTT
Statistics
Matches: 410, Mismatches: 29, Indels: 41
0.85 0.06 0.09
Matches are distributed among these distances:
43 104 0.25
44 12 0.03
46 6 0.01
47 1 0.00
48 59 0.14
49 191 0.47
50 1 0.00
52 36 0.09
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.30
Consensus pattern (48 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCATCTT
Found at i:649656 original size:92 final size:92
Alignment explanation
Indices: 649479--649940 Score: 703
Period size: 92 Copynumber: 4.9 Consensus size: 92
649469 ACCTTCATCT
* * * * *
649479 TTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACC-TCACCTTTAAGTCCAATGTAGC
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
649543 TGGCCTTGACTCAGCACATTGGCACCA
66 TGGCCTTGACTCAGCACATTGGCACCA
649570 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
649635 TGGCCTTGACTCAGCACATTGGCACCA
66 TGGCCTTGACTCAGCACATTGGCACCA
649662 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
649727 TGGCCTTGACTCAGCACATTGGCACCTTCA
66 TGGCCTTGACTCAGCACATTGGCA-C--CA
* * * *
649757 TCTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC-TCACCTTTAAGTCCAAATG
1 ---TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCC-AATG
* *
649821 TAGCTGGCCTTGAATCAGCACATTGGCACCT
62 TAGCTGGCCTTGACTCAGCACATTGGCACCA
*
649852 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGT
1 TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC-TTT--ATCTTTAAGTCCAATGT
*
649917 AGCTGGCCTTGAATCAGCACATTG
63 AGCTGGCCTTGACTCAGCACATTG
649941 ACATCCTTTT
Statistics
Matches: 343, Mismatches: 16, Indels: 20
0.91 0.04 0.05
Matches are distributed among these distances:
91 39 0.11
92 176 0.51
93 1 0.00
94 1 0.00
95 32 0.09
96 10 0.03
97 13 0.04
98 71 0.21
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (92 bp):
TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTTTAAGTCCAATGTAGC
TGGCCTTGACTCAGCACATTGGCACCA
Found at i:649894 original size:43 final size:43
Alignment explanation
Indices: 649758--649896 Score: 206
Period size: 43 Copynumber: 3.1 Consensus size: 43
649748 GCACCTTCAT
649758 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGG-----CAC
649806 CTTTAAGTCCAAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCC-AATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
649850 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
649893 CTTT
1 CTTT
649897 TCCATCTTTA
Statistics
Matches: 88, Mismatches: 2, Indels: 7
0.91 0.02 0.07
Matches are distributed among these distances:
43 35 0.40
44 13 0.15
48 10 0.11
49 30 0.34
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.29
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:649928 original size:52 final size:55
Alignment explanation
Indices: 649850--650070 Score: 180
Period size: 52 Copynumber: 3.9 Consensus size: 55
649840 ACATTGGCAC
* *
649850 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC-TTTTC-CAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* *
649902 CTTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
* * * * * * *
649957 CTTTAAGCCCCATATCGTTGGCCGTGAATCAACATATTGGCATCTTTATCACTTTTCTCATCTTC
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATT-G-A-C---ATC-C-TTT-T--TC-TC
650022 AT
54 AT
* * *
650024 CTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA-CCTTT
1 CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTT
650071 ATCTTTAAGT
Statistics
Matches: 133, Mismatches: 21, Indels: 24
0.75 0.12 0.13
Matches are distributed among these distances:
52 38 0.29
53 2 0.02
54 5 0.04
55 32 0.24
56 1 0.01
57 1 0.01
58 4 0.03
59 1 0.01
60 1 0.01
61 4 0.03
62 1 0.01
63 3 0.02
64 2 0.02
66 3 0.02
67 35 0.26
ACGTcount: A:0.23, C:0.26, G:0.15, T:0.36
Consensus pattern (55 bp):
CTTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCTCAT
Found at i:650807 original size:13 final size:13
Alignment explanation
Indices: 650789--650826 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
650779 CATAAAGTGT
650789 TGTATCGATACAA
1 TGTATCGATACAA
650802 TGTATCGATACAA
1 TGTATCGATACAA
650815 TGTATCGATACA
1 TGTATCGATACA
650827 TATTTTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:650907 original size:13 final size:13
Alignment explanation
Indices: 650889--650913 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
650879 ATTACTCAAA
650889 TGTATCGATACAT
1 TGTATCGATACAT
650902 TGTATCGATACA
1 TGTATCGATACA
650914 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:650978 original size:52 final size:52
Alignment explanation
Indices: 650922--651046 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
650912 CACTGATCTT
*
650922 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
650974 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
651026 TGTATCGATACATGCAAGCAA
1 TGTATCGATACATGCAGGCAA
651047 CTTTTCATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:654658 original size:34 final size:35
Alignment explanation
Indices: 654595--654661 Score: 93
Period size: 36 Copynumber: 1.9 Consensus size: 35
654585 CTAAGTGATT
654595 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
*
654631 GAGAGGTTTCTATCTT-GGCTTTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
654662 TGTTGTAAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 8 0.28
36 12 0.41
37 9 0.31
ACGTcount: A:0.31, C:0.10, G:0.27, T:0.31
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:654992 original size:15 final size:16
Alignment explanation
Indices: 654972--655003 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
654962 TAATGCGCTA
654972 AGAAAATAAT-GAATT
1 AGAAAATAATCGAATT
654987 AGAAAATAATCGAATT
1 AGAAAATAATCGAATT
655003 A
1 A
655004 CAAGTTGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.59, C:0.03, G:0.12, T:0.25
Consensus pattern (16 bp):
AGAAAATAATCGAATT
Found at i:659150 original size:20 final size:21
Alignment explanation
Indices: 659114--659153 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
659104 TTACAAATTT
*
659114 CTTCATTTTTACTTCAAAATA
1 CTTCATTTTTACATCAAAATA
659135 CTTCATTTTT-CATCAAAAT
1 CTTCATTTTTACATCAAAAT
659154 CACCAACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.33, C:0.20, G:0.00, T:0.47
Consensus pattern (21 bp):
CTTCATTTTTACATCAAAATA
Found at i:661472 original size:13 final size:13
Alignment explanation
Indices: 661451--661480 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
661441 CGATACATGG
*
661451 TACATTGTATCGA
1 TACAATGTATCGA
661464 TACAATGTATCGA
1 TACAATGTATCGA
661477 TACA
1 TACA
661481 TGATGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:661478 original size:33 final size:33
Alignment explanation
Indices: 661436--661500 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
661426 TACCACTGTT
*
661436 TGTATCGATACATGGT-ACATTGTATCGATACAA
1 TGTATCGATACATGATGA-ATTGTATCGATACAA
661469 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGATGAATTGTATCGATACA
661501 TTGCTTCTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (33 bp):
TGTATCGATACATGATGAATTGTATCGATACAA
Found at i:663300 original size:153 final size:153
Alignment explanation
Indices: 663100--663379 Score: 443
Period size: 153 Copynumber: 1.8 Consensus size: 153
663090 ATTTTATCAC
* * * * *
663100 TAAATAAAATTATTATCTTAATTTTTTAAGATTTTTAATATTCCTATGATTTTCTGTAGGGGTAT
1 TAAATAAAATTATTATCTTAATTCTTAAAGATTTTTAATATTCCTATGATTTTCCGTAAGGATAT
* * * *
663165 AGAAATCTTCAAAACTTTTCGTATCTTTTCGGTTCTCCATTAAGGTACGAAATGAAATTTTCATA
66 AAAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTCCATTAAAGTACAAAATGAAATTTTCATA
663230 AATTAAAAAATTTAAATAAAAAT
131 AATTAAAAAATTTAAATAAAAAT
*
663253 TAAATAAAATTATTATCTTAATTCTTAAAGATTTTTAATATTCCTATGGTTTTCCGTAAGGATAT
1 TAAATAAAATTATTATCTTAATTCTTAAAGATTTTTAATATTCCTATGATTTTCCGTAAGGATAT
* * *
663318 AAAAATTTTCAAAACTTTTCATATCTTTTCGGTTCTCTATTAAAGTACAAAATGAGATTTTC
66 AAAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTCCATTAAAGTACAAAATGAAATTTTC
663380 GAAATTTACA
Statistics
Matches: 114, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
153 114 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.43
Consensus pattern (153 bp):
TAAATAAAATTATTATCTTAATTCTTAAAGATTTTTAATATTCCTATGATTTTCCGTAAGGATAT
AAAAATCTTCAAAACTTTTCATATCTTTTCGGTTCTCCATTAAAGTACAAAATGAAATTTTCATA
AATTAAAAAATTTAAATAAAAAT
Found at i:665276 original size:13 final size:13
Alignment explanation
Indices: 665258--665283 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
665248 AATTTTTTTG
665258 TGTATCGATACAT
1 TGTATCGATACAT
665271 TGTATCGATACAT
1 TGTATCGATACAT
665284 ATTTTGTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:665297 original size:32 final size:34
Alignment explanation
Indices: 665237--665301 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 34
665227 TACAAGCCAA
* *
665237 TGTATCGATACAATTTTTTTGTGTATCGATACAT
1 TGTATCGATACAATTATTTTGTGCATCGATACAT
665271 TGTATCGATAC-A-TATTTTGTGCATCGATACA
1 TGTATCGATACAATTATTTTGTGCATCGATACA
665302 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 17 0.59
33 1 0.03
34 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (34 bp):
TGTATCGATACAATTATTTTGTGCATCGATACAT
Found at i:665378 original size:20 final size:20
Alignment explanation
Indices: 665332--665405 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
665322 ATCCCAATGA
***
665332 CATGTATCGATACATCTTTTT
1 CATGTATCGATACAT-TGAAT
665353 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
665373 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
*
665393 TATGTATCGATAC
1 CATGTATCGATAC
665406 TTTTAAGGGT
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
19 2 0.04
20 29 0.63
21 15 0.33
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:665983 original size:39 final size:39
Alignment explanation
Indices: 665922--666030 Score: 110
Period size: 47 Copynumber: 2.6 Consensus size: 39
665912 TTTTCTTTTA
* *
665922 TTTCTCCCTTAATCAAAATAATTTTAACAAATTTGTACAT
1 TTTCCCCCTTAAT-AAAGTAATTTTAACAAATTTGTACAT
665962 TTTCCCCCTTAATAAAGTAATTCACGCATTTTAACAAATTTGTACAT
1 TTTCCCCCTTAATAAAG----T-A---ATTTTAACAAATTTGTACAT
*
666009 TCTCCCCCTTAATAAAGTAATT
1 TTTCCCCCTTAATAAAGTAATT
666031 CACGCATTCT
Statistics
Matches: 58, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
39 6 0.10
40 12 0.21
42 1 0.02
43 2 0.03
44 1 0.02
47 36 0.62
ACGTcount: A:0.35, C:0.21, G:0.05, T:0.39
Consensus pattern (39 bp):
TTTCCCCCTTAATAAAGTAATTTTAACAAATTTGTACAT
Found at i:665999 original size:47 final size:47
Alignment explanation
Indices: 665942--666038 Score: 185
Period size: 47 Copynumber: 2.1 Consensus size: 47
665932 AATCAAAATA
*
665942 ATTTTAACAAATTTGTACATTTTCCCCCTTAATAAAGTAATTCACGC
1 ATTTTAACAAATTTGTACATTCTCCCCCTTAATAAAGTAATTCACGC
665989 ATTTTAACAAATTTGTACATTCTCCCCCTTAATAAAGTAATTCACGC
1 ATTTTAACAAATTTGTACATTCTCCCCCTTAATAAAGTAATTCACGC
666036 ATT
1 ATT
666039 CTCCCCTTTA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.38
Consensus pattern (47 bp):
ATTTTAACAAATTTGTACATTCTCCCCCTTAATAAAGTAATTCACGC
Found at i:667420 original size:21 final size:20
Alignment explanation
Indices: 667391--667433 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
667381 GACTAGTGTG
* *
667391 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCGCGACCT
*
667412 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
667432 GG
1 GG
667434 TGGTGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.09, C:0.28, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:669985 original size:15 final size:15
Alignment explanation
Indices: 669965--669995 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
669955 ATTTCGTTTG
*
669965 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
669980 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
669995 G
1 G
669996 GACATTTTGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:673651 original size:21 final size:20
Alignment explanation
Indices: 673626--673678 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 20
673616 TACAAGCTAA
*
673626 TGTATCGATACAATTTTTTTG
1 TGTATCGATACAA-TATTTTG
673647 TGTATCGATAC-ATATTTTG
1 TGTATCGATACAATATTTTG
673666 TGTATCGATACAA
1 TGTATCGATACAA
673679 GTTTGGCTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 17 0.57
20 2 0.07
21 11 0.37
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.45
Consensus pattern (20 bp):
TGTATCGATACAATATTTTG
Found at i:673773 original size:20 final size:20
Alignment explanation
Indices: 673729--673784 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
673719 ACATCTTTTT
*
673729 CATGTATCGATACATTGCAA
1 CATGTATCGATACTTTGCAA
673749 CATGTATCGATACTTTG-AA
1 CATGTATCGATACTTTGCAA
* *
673768 TTATGTATAGATACTTT
1 -CATGTATCGATACTTT
673785 TAAGGGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (20 bp):
CATGTATCGATACTTTGCAA
Found at i:674413 original size:166 final size:167
Alignment explanation
Indices: 674074--674445 Score: 457
Period size: 167 Copynumber: 2.2 Consensus size: 167
674064 AATTAATCTT
* * *
674074 AAAAAATTAATTCATTTTCATGAGTTTTGAATTTTTTTCTTTGAAATTTCCCTTTCCCCGAAAAA
1 AAAAAATTAATTCATTTTCATGAGTTTTAAATTTTTTTCTTTGAAATTTCCATTTCCCCAAAAAA
* * *
674139 CGAGTTTCTTACTCCGTAAAGGTTTTTGAGAGGATTTTTCTTAGTTTATAATTTTTAAAATTCAT
66 CGAGTCTCTTACTCCATAAAGGTTTTCGAGAGGATTTTTCTTAGTTTATAATTTTTAAAATTCAT
* * *
674204 CAAATATCATCATTTAATTTATATTAAATCAGCTTTA
131 CAAATATCATCATTAAATCTACATTAAATCAGCTTTA
674241 AAAAAATT-ATTCATTTTCATGAGTTTTAAATTTTTTTCTTTGAAA-TTCTCATTTCCCCAAAAA
1 AAAAAATTAATTCATTTTCATGAGTTTTAAATTTTTTTCTTTGAAATTTC-CATTTCCCCAAAAA
* * * *
674304 ACTGAGTCTCTTACTCCATAAATGTTTTCGATAGGATTTTTTTTAGTTTATAATTTTTGAAATTC
65 AC-GAGTCTCTTACTCCATAAAGGTTTTCGAGAGGATTTTTCTTAGTTTATAATTTTTAAAATTC
** ** * * *
674369 ATTTAATATTGTTATTAAACTCT-CGTTAAATCAG-TTTC
129 ATCAAATATCATCATTAAA-TCTACATTAAATCAGCTTTA
* * *
674407 AAAAAATTCAATTTA-TTTCATGAATTTTTCAATTTTTTT
1 AAAAAATT-AATTCATTTTCATG-AGTTTTAAATTTTTTT
674446 GTATACATTA
Statistics
Matches: 176, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
165 3 0.02
166 61 0.35
167 92 0.52
168 20 0.11
ACGTcount: A:0.32, C:0.13, G:0.08, T:0.47
Consensus pattern (167 bp):
AAAAAATTAATTCATTTTCATGAGTTTTAAATTTTTTTCTTTGAAATTTCCATTTCCCCAAAAAA
CGAGTCTCTTACTCCATAAAGGTTTTCGAGAGGATTTTTCTTAGTTTATAATTTTTAAAATTCAT
CAAATATCATCATTAAATCTACATTAAATCAGCTTTA
Found at i:675002 original size:20 final size:20
Alignment explanation
Indices: 674957--675008 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
674947 AGGCCCAGAA
* *
674957 GTATCGATACATATTGCTTT
1 GTATCGATACATAATGCATT
*
674977 GCATCGATACATAAAT-CATT
1 GTATCGATACAT-AATGCATT
674997 GTATCGATACAT
1 GTATCGATACAT
675009 GAAACTGGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (20 bp):
GTATCGATACATAATGCATT
Found at i:681557 original size:33 final size:33
Alignment explanation
Indices: 681515--681645 Score: 203
Period size: 33 Copynumber: 4.0 Consensus size: 33
681505 TACAAGCTAT
*
681515 GTATCGATACATTTCTTCATGTATCGATACAAC
1 GTATAGATACATTTCTTCATGTATCGATACAAC
681548 GTATAGATACATTTCTTCATGTATCGATACAAC
1 GTATAGATACATTTCTTCATGTATCGATACAAC
*
681581 GTATAGATACATTTCTTCATGTATCGATACAAT
1 GTATAGATACATTTCTTCATGTATCGATACAAC
*
681614 GTATCGATACATTGTAC--CATGTATCGATACAA
1 GTATAGATACATT-T-CTTCATGTATCGATACAA
681646 ATAGTGATAG
Statistics
Matches: 93, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
33 91 0.98
34 1 0.01
35 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (33 bp):
GTATAGATACATTTCTTCATGTATCGATACAAC
Found at i:681617 original size:13 final size:13
Alignment explanation
Indices: 681599--681629 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
681589 ACATTTCTTC
681599 ATGTATCGATACA
1 ATGTATCGATACA
681612 ATGTATCGATACA
1 ATGTATCGATACA
*
681625 TTGTA
1 ATGTA
681630 CCATGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:682299 original size:16 final size:17
Alignment explanation
Indices: 682278--682312 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
682268 GTTTTCGTTT
682278 TTCT-CCCCTTAAAAAA
1 TTCTCCCCCTTAAAAAA
*
682294 TTCTCCCCCTTAAACAA
1 TTCTCCCCCTTAAAAAA
682311 TT
1 TT
682313 TTCTTCTCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (17 bp):
TTCTCCCCCTTAAAAAA
Found at i:690398 original size:13 final size:13
Alignment explanation
Indices: 690380--690410 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
690370 ACATTTCTTC
690380 ATGTATCGATACA
1 ATGTATCGATACA
690393 ATGTATCGATACA
1 ATGTATCGATACA
*
690406 TTGTA
1 ATGTA
690411 CCATGTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:693547 original size:52 final size:51
Alignment explanation
Indices: 693469--693617 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
693459 CAAAATATGA
693469 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
693521 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
693573 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
693618 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:693624 original size:13 final size:13
Alignment explanation
Indices: 693606--693630 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
693596 CAAAGATCAG
693606 TGTATCGATACAA
1 TGTATCGATACAA
693619 TGTATCGATACA
1 TGTATCGATACA
693631 TTTAAGTGAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:693708 original size:33 final size:33
Alignment explanation
Indices: 693671--693737 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
693661 AGTAGCTTAA
693671 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
693704 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
693737 A
1 A
693738 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:693711 original size:13 final size:13
Alignment explanation
Indices: 693693--693717 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
693683 CAAAAAAATA
693693 TGTATCGATACAT
1 TGTATCGATACAT
693706 TGTATCGATACA
1 TGTATCGATACA
693718 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:694039 original size:21 final size:19
Alignment explanation
Indices: 694013--694066 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
694003 CTGCCAGTTT
**
694013 CATGTATCGATACAATTTGTC
1 CATGTATCGATACAA--TGAA
*
694034 CATGTATTGATACAATGAA
1 CATGTATCGATACAATGAA
694053 CATGTATCGATACA
1 CATGTATCGATACA
694067 TTGTATCGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 15 0.52
21 14 0.48
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:694073 original size:13 final size:13
Alignment explanation
Indices: 694055--694079 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
694045 ACAATGAACA
694055 TGTATCGATACAT
1 TGTATCGATACAT
694068 TGTATCGATACA
1 TGTATCGATACA
694080 AAGCAGCATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:694095 original size:33 final size:32
Alignment explanation
Indices: 694036--694100 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
694026 AATTTGTCCA
* *
694036 TGTATTGATACAATGAACATGTATCGATACAT
1 TGTATCGATACAAAGAACATGTATCGATACAT
*
694068 TGTATCGATACAAAGCAGCATGTATCGATACAT
1 TGTATCGATACAAAG-AACATGTATCGATACAT
694101 CTGGGTGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (32 bp):
TGTATCGATACAAAGAACATGTATCGATACAT
Found at i:695184 original size:20 final size:20
Alignment explanation
Indices: 695161--695233 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
695151 ACAATTCAAA
695161 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
695181 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
695202 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
695222 GTATCGATACAT
1 GTATCGATACAT
695234 AAAAAAGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:695205 original size:21 final size:21
Alignment explanation
Indices: 695179--695254 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
695169 ACATGTTGCA
695179 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
695200 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
*
695220 ATGTATCGATACATAAAAAAG
1 ATGTATCGATACATGAAAAAG
695241 ATGTATCGATACAT
1 ATGTATCGATACAT
695255 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:695212 original size:41 final size:41
Alignment explanation
Indices: 695161--695254 Score: 179
Period size: 41 Copynumber: 2.3 Consensus size: 41
695151 ACAATTCAAA
*
695161 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
695202 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
695243 GTATCGATACAT
1 GTATCGATACAT
695255 TTCTTGGCAG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAAGAT
Done.