Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 98600468
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: 98600468
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 273 characters in sequence are not A, C, G, or T
File 68 of 325
Found at i:18215738 original size:141 final size:141
Alignment explanation
Indices: 18215466--18215746 Score: 422
Period size: 141 Copynumber: 2.0 Consensus size: 141
18215456 GATTTTATGA
18215466 GATGAATGTGAACATGCATATACGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
1 GATGAATGTGAACATGCATATACGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
* * * * *
18215531 TATACGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACTTGCATATGTGTGATAAGGTCGA
66 TATACGTGATAAGGCAGAATGGCCAATGTGATGAACGTGAACTTACATATGTGTGAGAAGGCCGA
18215596 ATGGCCAATGT
131 ATGGCCAATGT
*
18215607 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
1 GATGAATGTGAACATGCATATACGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
* * * * *
18215672 TATATGTGATAAGGTAGAATGGCCAATGTGATGAACGTGGAAGTGTATATATGTG-GCGAA-GCC
66 TATACGTGATAAGGCAGAATGGCCAATGTGATGAACGT-GAACT-TACATATGTGTGAGAAGGCC
*
18215735 GAATGGCTAATG
129 GAATGGCCAATG
18215747 CGAAACGTGT
Statistics
Matches: 126, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
141 111 0.88
142 7 0.06
143 8 0.06
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (141 bp):
GATGAATGTGAACATGCATATACGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAACATGCA
TATACGTGATAAGGCAGAATGGCCAATGTGATGAACGTGAACTTACATATGTGTGAGAAGGCCGA
ATGGCCAATGT
Found at i:18215741 original size:47 final size:47
Alignment explanation
Indices: 18215466--18215706 Score: 419
Period size: 47 Copynumber: 5.1 Consensus size: 47
18215456 GATTTTATGA
*
18215466 GATGAATGTGAACATGCATATACGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
*
18215513 GATGAATGTGAACATGCATATACGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
* * *
18215560 GATGAATGTGAACTTGCATATGTGTGATAAGGTCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
18215607 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
**
18215654 GATGAATGTGAACATGCATATATGTGATAAGGTAGAATGGCCAATGT
1 GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
18215701 GATGAA
1 GATGAA
18215707 CGTGGAAGTG
Statistics
Matches: 185, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 185 1.00
ACGTcount: A:0.34, C:0.12, G:0.28, T:0.26
Consensus pattern (47 bp):
GATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCAATGT
Found at i:18218575 original size:40 final size:40
Alignment explanation
Indices: 18218462--18218584 Score: 149
Period size: 40 Copynumber: 3.1 Consensus size: 40
18218452 TTGGCTCGGT
** * ** *
18218462 TATAATAACCCGCACGAATGCCTTCGGGA-CTTAACCCGGT
1 TATAATAACTAGCACAAATGCCTTC-GGATCTTAGTCCGGA
* *
18218502 TATAATAACTTGCACAATTGCCTTCGGATCTTAGTCCGGA
1 TATAATAACTAGCACAAATGCCTTCGGATCTTAGTCCGGA
*
18218542 TATAGTAACTAGCACAAATGCCTTCGGATCTTAGTCCGGA
1 TATAATAACTAGCACAAATGCCTTCGGATCTTAGTCCGGA
18218582 TAT
1 TAT
18218585 CATCCGAATA
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
39 3 0.04
40 69 0.96
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (40 bp):
TATAATAACTAGCACAAATGCCTTCGGATCTTAGTCCGGA
Found at i:18224118 original size:27 final size:28
Alignment explanation
Indices: 18224057--18224126 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
18224047 AAATTTGTAC
* *
18224057 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGAATATAT
18224085 AGCACTAAGTGTGCGAG-CTGAATATAT
1 AGCACTAAGTGTGCGAGTCTGAATATAT
*
18224112 GGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
18224127 TGATCGAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGAATATAT
Found at i:18232119 original size:27 final size:28
Alignment explanation
Indices: 18232058--18232127 Score: 106
Period size: 27 Copynumber: 2.5 Consensus size: 28
18232048 AAATTTGTAC
* *
18232058 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTCTGAATATAT
18232086 AGCACTAAGTGTGCGAG-CTGAATATAT
1 AGCACTAAGTGTGCGAGTCTGAATATAT
*
18232113 GGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
18232128 TGATCGAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 22 0.56
28 17 0.44
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTCTGAATATAT
Found at i:18238389 original size:12 final size:12
Alignment explanation
Indices: 18238372--18238397 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
18238362 TTAGTTTAAC
18238372 TATATTCATGAT
1 TATATTCATGAT
18238384 TATATTCATGAT
1 TATATTCATGAT
18238396 TA
1 TA
18238398 CTTCTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.50
Consensus pattern (12 bp):
TATATTCATGAT
Found at i:18244566 original size:51 final size:51
Alignment explanation
Indices: 18244492--18244612 Score: 131
Period size: 51 Copynumber: 2.4 Consensus size: 51
18244482 CCAAACTTAT
* * * *
18244492 TTCATACTTCATCCAGA-ATTATTACTTTGATAT-TCTGGCTTCAATAAGAAC
1 TTCATATTTCATCCGGATATTATTACTTT-AT-TCTCTAGCTTCAACAAGAAC
* *
18244543 TTCATATTTCATCCGGATA-TATTACTTTATTGCTCTAGTTTCAACAAGAGC
1 TTCATATTTCATCCGGATATTATTACTTTATT-CTCTAGCTTCAACAAGAAC
*
18244594 TTCATATTTCATCTGGATA
1 TTCATATTTCATCCGGATA
18244613 ACTTAGTTGT
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
49 1 0.02
50 2 0.03
51 56 0.93
52 1 0.02
ACGTcount: A:0.29, C:0.19, G:0.11, T:0.41
Consensus pattern (51 bp):
TTCATATTTCATCCGGATATTATTACTTTATTCTCTAGCTTCAACAAGAAC
Found at i:18261042 original size:25 final size:25
Alignment explanation
Indices: 18261014--18261076 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 25
18261004 AAGTAATATG
18261014 CCACAAAGACTTTCCAGATTA-TACA
1 CCACAAAGACTTTCCAGA-TAGTACA
*
18261039 CCACAAA-AGCTTCCCAGATAGTACA
1 CCACAAAGA-CTTTCCAGATAGTACA
18261064 CCACAAAGACTTT
1 CCACAAAGACTTT
18261077 ACAAAGAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
24 3 0.09
25 29 0.88
26 1 0.03
ACGTcount: A:0.40, C:0.30, G:0.10, T:0.21
Consensus pattern (25 bp):
CCACAAAGACTTTCCAGATAGTACA
Found at i:18261122 original size:25 final size:25
Alignment explanation
Indices: 18261062--18261122 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
18261052 CCAGATAGTA
*
18261062 CACCACAAAGACTTTACAAAGAATT
1 CACCACAAAGGCTTTACAAAGAATT
* * *
18261087 CACCATAAAGGCTTTATAGAGAATT
1 CACCACAAAGGCTTTACAAAGAATT
*
18261112 CGCCACAAAGG
1 CACCACAAAGG
18261123 TTTGTTTGGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.20
Consensus pattern (25 bp):
CACCACAAAGGCTTTACAAAGAATT
Found at i:18290354 original size:26 final size:26
Alignment explanation
Indices: 18290323--18290430 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
18290313 TGAAATGCCC
*
18290323 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
18290349 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
18290375 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
18290401 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
18290427 ATCA
1 ATCA
18290431 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:18297508 original size:26 final size:26
Alignment explanation
Indices: 18297478--18297585 Score: 207
Period size: 26 Copynumber: 4.2 Consensus size: 26
18297468 TGAAATTCCC
18297478 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
18297504 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
18297530 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
18297556 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
18297582 ATCA
1 ATCA
18297586 ATTTGTATCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:18298238 original size:44 final size:45
Alignment explanation
Indices: 18298167--18298253 Score: 113
Period size: 44 Copynumber: 2.0 Consensus size: 45
18298157 TCTTATCTTT
* * * *
18298167 GCTGAGCAGGAGCGGAGCAGATCAAATTTTAGCAGATCTTATCCC
1 GCTGAGCAGGAGCGGAACAGATCAAATTTCAGCAAATCCTATCCC
* *
18298212 GCTG-GCAGGAGTGGAACAGATTAAATTTCAGCAAATCCTATC
1 GCTGAGCAGGAGCGGAACAGATCAAATTTCAGCAAATCCTATC
18298254 TCCCTAAGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 32 0.89
45 4 0.11
ACGTcount: A:0.31, C:0.21, G:0.25, T:0.23
Consensus pattern (45 bp):
GCTGAGCAGGAGCGGAACAGATCAAATTTCAGCAAATCCTATCCC
Found at i:18298413 original size:43 final size:43
Alignment explanation
Indices: 18298243--18298552 Score: 177
Period size: 43 Copynumber: 7.0 Consensus size: 43
18298233 TAAATTTCAG
* **
18298243 CAAATCCTATCTCCCTAAGCAATATTGGAGTGGATCGAAAATTA
1 CAAATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAAAA-TA
* * *
18298287 CAGATCTTATCTCCCTAAGCAATAGTGGAGCAAATC-AAAGATA
1 CAAATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAAA-ATA
** * * * *
18298330 GTGAGTCTTAAC-CCCTAAGCAATAG-GGTAACAGA-CTGAAAATA
1 -CAAATCCTATCTCCCTAAGCAATAGTGG-AGCAGATC-GAAAATA
* * *
18298373 CAAATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAAATGG
1 CAAATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAAAAT-A
*
18298417 CAAGCTTTATCTTCTTATCTCCCTAAGCAATAGTGGAGCAAATC-AAAGATA
1 CAA-----ATC--C-TATCTCCCTAAGCAATAGTGGAGCAGATCGAAA-ATA
** * * * * *
18298468 GTGAGTCTTAAC-CCCTAAGTAATAG-GGTAACAGA-CTGAAAATA
1 -CAAATCCTATCTCCCTAAGCAATAGTGG-AGCAGATC-GAAAATA
* *
18298511 CAAATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAAAT
1 CAAATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAAAAT
18298553 GGCAAGCTTT
Statistics
Matches: 198, Mismatches: 43, Indels: 51
0.68 0.15 0.17
Matches are distributed among these distances:
42 16 0.08
43 89 0.45
44 55 0.28
47 2 0.01
49 3 0.02
51 4 0.02
52 29 0.15
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (43 bp):
CAAATCCTATCTCCCTAAGCAATAGTGGAGCAGATCGAAAATA
Found at i:18298483 original size:138 final size:138
Alignment explanation
Indices: 18298291--18298566 Score: 543
Period size: 138 Copynumber: 2.0 Consensus size: 138
18298281 AAATTACAGA
18298291 TCTTATCTCCCTAAGCAATAGTGGAGCAAATCAAAGATAGTGAGTCTTAACCCCTAAGCAATAGG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAAATCAAAGATAGTGAGTCTTAACCCCTAAGCAATAGG
18298356 GTAACAGACTGAAAATACAAATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAAATGGCAAG
66 GTAACAGACTGAAAATACAAATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAAATGGCAAG
18298421 CTTTATCT
131 CTTTATCT
*
18298429 TCTTATCTCCCTAAGCAATAGTGGAGCAAATCAAAGATAGTGAGTCTTAACCCCTAAGTAATAGG
1 TCTTATCTCCCTAAGCAATAGTGGAGCAAATCAAAGATAGTGAGTCTTAACCCCTAAGCAATAGG
18298494 GTAACAGACTGAAAATACAAATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAAATGGCAAG
66 GTAACAGACTGAAAATACAAATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAAATGGCAAG
18298559 CTTTATCT
131 CTTTATCT
18298567 CCTTGAGCAG
Statistics
Matches: 137, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 137 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (138 bp):
TCTTATCTCCCTAAGCAATAGTGGAGCAAATCAAAGATAGTGAGTCTTAACCCCTAAGCAATAGG
GTAACAGACTGAAAATACAAATCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAAATGGCAAG
CTTTATCT
Found at i:18298639 original size:44 final size:44
Alignment explanation
Indices: 18298429--18298866 Score: 139
Period size: 44 Copynumber: 9.9 Consensus size: 44
18298419 AGCTTTATCT
* * * **
18298429 TCTTATCTCCCTAAGCAATAGTGGAGCAAATCAAAGA-TAGTGA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTACAGA
* * * * * *
18298472 GTCTTAAC-CCCTAAGTAATAG-GGTAACAGA-CTGAA-AATACAAA
1 -TCTTATCTCCCTAAGCAGTAGTGG-AGCAGATC-GAAGATTACAGA
* * * * * **
18298515 TCCTATTTCCCTAAGCAATAGTGGAGCGGATCGAAAATGGCA-A
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTACAGA
* * * * *
18298558 GCTTTATCTCCTTGAGCAGCAGTGGAGCA-AGCTGAAGATTACAGA
1 TC-TTATCTCCCTAAGCAGTAGTGGAGCAGATC-GAAGATTACAGA
* * * *
18298603 TCTTATCTCTCTAAGCAGCAGCGGAGCAGATCGAAGACGATGAGCAG-
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCG-A-A-GATTA-CAGA
* * * ** * * * *
18298650 GCTTTAACTCCCTAAGTAGTAG-GGTAAAAGGCTGGAGGATTACAATA
1 TC-TTATCTCCCTAAGCAGTAGTGG-AGCA-GATCGAAGATTAC-AGA
*
18298697 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGA-TAGCAAA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTA-CAGA
* * ** * * * *
18298741 CCTTATCTCTCTGAAGTTGCAG-AGAGCAGGTTGAAG-TTACA-A
1 TCTTATCTCCCT-AAGCAGTAGTGGAGCAGATCGAAGATTACAGA
* ** * * * *
18298783 GTCTTATCTCTCTGAAGCCA-TAGCAGAGCATATTGAAGATAATAGA
1 -TCTTATCTCCCT-AAG-CAGTAGTGGAGCAGATCGAAGATTACAGA
*
18298829 TCTTATCTCCCTAAGCAGTAGTGAAGCAGATCGAAGAT
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
18298867 ACCAAACCTT
Statistics
Matches: 285, Mismatches: 79, Indels: 60
0.67 0.19 0.14
Matches are distributed among these distances:
42 9 0.03
43 65 0.23
44 118 0.41
45 33 0.12
46 26 0.09
47 10 0.04
48 21 0.07
49 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (44 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGATTACAGA
Found at i:18304585 original size:16 final size:16
Alignment explanation
Indices: 18304564--18304594 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18304554 TTATTTAAAC
18304564 TTTAAAATTATTATTT
1 TTTAAAATTATTATTT
*
18304580 TTTAAATTTATTATT
1 TTTAAAATTATTATT
18304595 CAAATAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTAAAATTATTATTT
Found at i:18314612 original size:47 final size:48
Alignment explanation
Indices: 18314558--18314761 Score: 172
Period size: 47 Copynumber: 4.3 Consensus size: 48
18314548 GTAAGATATA
18314558 TCTGGGACAT-GCATCAGCCAC-ATTACGAGAGCCAGTGTAAGACCATG
1 TCTGGGACATGGCATC-GCCACGATTACGAGAGCCAGTGTAAGACCATG
* * *
18314605 TCTGGGACATGGCATCGGCACGGA-TATGCGAG---GTGTAAGACCATG
1 TCTGGGACATGGCATCGCCAC-GATTACGAGAGCCAGTGTAAGACCATG
* * * * * *
18314650 TCTGGGACATAGAATCGGCCTCGATTTCGATAGTCAGTGTAAGACCATG
1 TCTGGGACATGGCATC-GCCACGATTACGAGAGCCAGTGTAAGACCATG
* **** *
18314699 TCTGGGAAATGGCATCGATTTGA-T-GGATGAGCCAGTGTAAGACCATG
1 TCTGGGACATGGCATCGCCACGATTACGA-GAGCCAGTGTAAGACCATG
*
18314746 TCTAGGACATGGCATC
1 TCTGGGACATGGCATC
18314762 AGCATTCTAC
Statistics
Matches: 126, Mismatches: 22, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
45 29 0.23
46 9 0.07
47 46 0.37
48 15 0.12
49 27 0.21
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (48 bp):
TCTGGGACATGGCATCGCCACGATTACGAGAGCCAGTGTAAGACCATG
Found at i:18316324 original size:12 final size:12
Alignment explanation
Indices: 18316307--18316334 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
18316297 TGGTCATCAA
18316307 ATGACAAGTCTT
1 ATGACAAGTCTT
18316319 ATGACAAGTCTT
1 ATGACAAGTCTT
18316331 ATGA
1 ATGA
18316335 ATGTGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (12 bp):
ATGACAAGTCTT
Found at i:18318367 original size:44 final size:44
Alignment explanation
Indices: 18318296--18318379 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
18318286 CATGTATCGT
* *
18318296 ATCCATTATGAACTCGGACCAATTCAACGAGTTCAGATGCTAGC
1 ATCCATTATGAACTCGGACCAACTCAACGAGCTCAGATGCTAGC
*
18318340 ATCCA-TAGTGAACTCGGACTAACTCAACGAGCTCAGATGC
1 ATCCATTA-TGAACTCGGACCAACTCAACGAGCTCAGATGC
18318380 CTCATATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (44 bp):
ATCCATTATGAACTCGGACCAACTCAACGAGCTCAGATGCTAGC
Found at i:18323520 original size:93 final size:93
Alignment explanation
Indices: 18323407--18323579 Score: 319
Period size: 93 Copynumber: 1.9 Consensus size: 93
18323397 CCGCCCATAA
* *
18323407 ACGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTC
1 ACGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
18323472 AACGAGTTCGGATGCCTAGTTACATCTC
66 AACGAGTTCGGATGCCTAGTTACATCTC
*
18323500 ACGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
1 ACGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
18323565 AACGAGTTCGGATGC
66 AACGAGTTCGGATGC
18323580 TCAACCATCC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 77 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (93 bp):
ACGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTC
AACGAGTTCGGATGCCTAGTTACATCTC
Found at i:18323576 original size:46 final size:46
Alignment explanation
Indices: 18323409--18323576 Score: 209
Period size: 46 Copynumber: 3.6 Consensus size: 46
18323399 GCCCATAAAC
* * *
18323409 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
* * *
18323455 GAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-TCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCATAAGT
18323502 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
18323548 GAACTCGGACTCAACTCAACGAGTTCGGA
1 GAACTCGGACTCAACTCAACGAGTTCGGA
18323577 TGCTCAACCA
Statistics
Matches: 104, Mismatches: 9, Indels: 18
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 56 0.54
47 29 0.28
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGT
Found at i:18333761 original size:46 final size:44
Alignment explanation
Indices: 18333621--18333761 Score: 108
Period size: 46 Copynumber: 3.0 Consensus size: 44
18333611 GCCCATAAGC
* *
18333621 GAACTCGGACTCAACTCAACAAGTTCGGATGCCTAGTTA-CATCTCA-C
1 GAACTCGGACTCAACTCAACGAGTTCGGATGCC-A---ACCATCT-AGT
* * * * *
18333668 GAACTCGTACTCAACTCAATGAGTTCGGACATTCGCATCCAT-AAGT
1 GAACTCGGACTCAACTCAACGAGTTCGG--ATGC-CAACCATCTAGT
18333714 GAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCTAGT
1 GAACTCGGACTCAACTCAACGAGTTCGGATGC-CAACCAT-CTAGT
18333760 GA
1 GA
18333762 CATGTCACTT
Statistics
Matches: 74, Mismatches: 13, Indels: 15
0.73 0.13 0.15
Matches are distributed among these distances:
44 9 0.12
45 1 0.01
46 31 0.42
47 28 0.38
49 4 0.05
50 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (44 bp):
GAACTCGGACTCAACTCAACGAGTTCGGATGCCAACCATCTAGT
Found at i:18336113 original size:26 final size:26
Alignment explanation
Indices: 18336082--18336189 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
18336072 TGAAATGCCC
*
18336082 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
18336108 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
18336134 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
18336160 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
18336186 ATCA
1 ATCA
18336190 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:18344210 original size:26 final size:26
Alignment explanation
Indices: 18344179--18344286 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
18344169 TGAAATGCCC
*
18344179 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
18344205 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
18344231 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
18344257 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
18344283 ATCA
1 ATCA
18344287 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:18357997 original size:16 final size:16
Alignment explanation
Indices: 18357976--18358007 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
18357966 ACTAAGTTCG
18357976 ATTCATGGTTTATATA
1 ATTCATGGTTTATATA
18357992 ATTCATGGTTTATATA
1 ATTCATGGTTTATATA
18358008 TTTGGGTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.12, T:0.50
Consensus pattern (16 bp):
ATTCATGGTTTATATA
Found at i:18361432 original size:11 final size:12
Alignment explanation
Indices: 18361406--18361438 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
18361396 TAAATATATA
*
18361406 TTTTGTAACACT
1 TTTTATAACACT
18361418 TTTTATAACAC-
1 TTTTATAACACT
18361429 TTTTATAACA
1 TTTTATAACA
18361439 TATTTTACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (12 bp):
TTTTATAACACT
Found at i:18362514 original size:20 final size:20
Alignment explanation
Indices: 18362477--18362516 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
18362467 TAAATTTTCT
* *
18362477 AAAATTTTAAATATATTAAA
1 AAAATTTTAAAAAAATTAAA
18362497 AAAATTTTAAAAAAATTAAA
1 AAAATTTTAAAAAAATTAAA
18362517 TTTGCCTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATTTTAAAAAAATTAAA
Found at i:18362636 original size:17 final size:17
Alignment explanation
Indices: 18362548--18362677 Score: 61
Period size: 17 Copynumber: 7.4 Consensus size: 17
18362538 TTAAATATGT
*
18362548 TTTAAAATTATAATATA
1 TTTAAAATTTTAATATA
*
18362565 TTTAAATATATTAA-A-A
1 TTTAAA-ATTTTAATATA
*
18362581 TTTCAAAA-TTTATTATA
1 TTT-AAAATTTTAATATA
* * *
18362598 TTCAACATTTTCTTTAACATA
1 TTTAA-A--AT-TTTAATATA
18362619 TTTAAAATTTTAATATA
1 TTTAAAATTTTAATATA
** * *
18362636 TTTACATTTTTTAATTTT
1 TTTA-AAATTTTAATATA
*
18362654 TTTTAAATTTTAA-ATA
1 TTTAAAATTTTAATATA
18362670 TATTAAAA
1 T-TTAAAA
18362678 AAAATTCTCT
Statistics
Matches: 81, Mismatches: 21, Indels: 22
0.65 0.17 0.18
Matches are distributed among these distances:
15 3 0.04
16 10 0.12
17 38 0.47
18 18 0.22
20 1 0.01
21 11 0.14
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAAAATTTTAATATA
Found at i:18362683 original size:21 final size:21
Alignment explanation
Indices: 18362658--18362721 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
18362648 AATTTTTTTT
18362658 AAATTTTAAATATATTAAAAA
1 AAATTTTAAATATATTAAAAA
** **
18362679 AAATTCTCTTTACCTATTAAAAA
1 AAATT-T-TAAATATATTAAAAA
* *
18362702 ATATATTAAATATATTAAAA
1 AAATTTTAAATATATTAAAA
18362722 GTTTAAAATA
Statistics
Matches: 31, Mismatches: 10, Indels: 4
0.69 0.22 0.09
Matches are distributed among these distances:
21 15 0.48
22 2 0.06
23 14 0.45
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTTTAAATATATTAAAAA
Found at i:18362913 original size:72 final size:72
Alignment explanation
Indices: 18362733--18362883 Score: 241
Period size: 72 Copynumber: 2.1 Consensus size: 72
18362723 TTTAAAATAT
* * * *
18362733 ATTTTTAAAAAATACATTGAATATATTAAAATTTTAAAATTGGTTATACTTAAACATTTTTTAAT
1 ATTTTT-AAAAATATATTAAAAATATTAAAATATTAAAATTGGTTATACTTAAACATTTTTTAAT
18362798 ATATTTAA
65 ATATTTAA
*
18362806 TTTTTTAAAAATATATTAAAAATATTAAAATATTAAAATTGGTTATACTT-AACATTTTTTAATA
1 ATTTTTAAAAATATATTAAAAATATTAAAATATTAAAATTGGTTATACTTAAACATTTTTTAATA
18362870 TATTTAA
66 TATTTAA
18362877 ATTTTTA
1 ATTTTTA
18362884 TTAAGTTTTA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
71 27 0.38
72 40 0.56
73 5 0.07
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (72 bp):
ATTTTTAAAAATATATTAAAAATATTAAAATATTAAAATTGGTTATACTTAAACATTTTTTAATA
TATTTAA
Found at i:18362988 original size:18 final size:17
Alignment explanation
Indices: 18362942--18362980 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
18362932 AAAATATATA
* *
18362942 TTAAGTATATTAAAATT
1 TTAAATATATTAAACTT
18362959 TTAAATATATTAAACTT
1 TTAAATATATTAAACTT
18362976 TTAAA
1 TTAAA
18362981 ATTAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TTAAATATATTAAACTT
Found at i:18363010 original size:42 final size:41
Alignment explanation
Indices: 18362941--18363021 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 41
18362931 AAAAATATAT
*
18362941 ATTAAGTATATTAAAATTTTAAATATA-TTAAACTTTTAAA
1 ATTAAGTATATTAAAATTTTAAATATATTTAAAATTTTAAA
* * *
18362981 ATTAATTATACTTAACATTTTTTAATATATTTAAAATTTTA
1 ATTAAGTATA-TTAA-AATTTTAAATATATTTAAAATTTTA
18363022 GAAAACTTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 9 0.26
41 4 0.12
42 11 0.32
43 10 0.29
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (41 bp):
ATTAAGTATATTAAAATTTTAAATATATTTAAAATTTTAAA
Found at i:18363014 original size:19 final size:20
Alignment explanation
Indices: 18362982--18363020 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
18362972 ACTTTTAAAA
*
18362982 TTAATTATACTTAACATTTT
1 TTAATTATACTTAAAATTTT
*
18363002 TTAA-TATATTTAAAATTTT
1 TTAATTATACTTAAAATTTT
18363021 AGAAAACTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTAATTATACTTAAAATTTT
Found at i:18370322 original size:52 final size:52
Alignment explanation
Indices: 18370252--18370359 Score: 207
Period size: 52 Copynumber: 2.1 Consensus size: 52
18370242 TTTCCCAGAA
*
18370252 CTTTCCAAAGTTTTCGGTTTAGTCCCGAACCATTTCTAAAGCATGTTTTGGG
1 CTTTCCAAAGTTCTCGGTTTAGTCCCGAACCATTTCTAAAGCATGTTTTGGG
18370304 CTTTCCAAAGTTCTCGGTTTAGTCCCGAACCATTTCTAAAGCATGTTTTGGG
1 CTTTCCAAAGTTCTCGGTTTAGTCCCGAACCATTTCTAAAGCATGTTTTGGG
18370356 CTTT
1 CTTT
18370360 GTAAACCCAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (52 bp):
CTTTCCAAAGTTCTCGGTTTAGTCCCGAACCATTTCTAAAGCATGTTTTGGG
Found at i:18376859 original size:13 final size:13
Alignment explanation
Indices: 18376843--18376867 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18376833 CAACCGTGTG
18376843 AGGGACACGGCCT
1 AGGGACACGGCCT
18376856 AGGGACACGGCC
1 AGGGACACGGCC
18376868 ATGTGGCCTG
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:0.24, C:0.32, G:0.40, T:0.04
Consensus pattern (13 bp):
AGGGACACGGCCT
Found at i:18380829 original size:21 final size:21
Alignment explanation
Indices: 18380787--18380827 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
18380777 TTATTTCACT
18380787 ATTTTAAATATAAAATATTTA
1 ATTTTAAATATAAAATATTTA
*
18380808 ATTTTATATTATAAAATATT
1 ATTTTA-AATATAAAATATT
18380828 AAAAATCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTAAATATAAAATATTTA
Found at i:18383154 original size:17 final size:17
Alignment explanation
Indices: 18383127--18383159 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
18383117 TTGTATTTTA
18383127 TGAATTGTG-AATAAAG
1 TGAATTGTGAAATAAAG
18383143 TGAATATGTGAAATAAA
1 TGAAT-TGTGAAATAAA
18383160 CATGTAGTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 4 0.27
18 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.21, T:0.30
Consensus pattern (17 bp):
TGAATTGTGAAATAAAG
Found at i:18387034 original size:6 final size:6
Alignment explanation
Indices: 18387025--18387064 Score: 62
Period size: 6 Copynumber: 6.3 Consensus size: 6
18387015 ATTGAAATTG
18387025 AAATAA AAATAA AAATAA AAATAA AAATGAA AAGATAA AA
1 AAATAA AAATAA AAATAA AAATAA AAAT-AA AA-ATAA AA
18387065 GGATTCAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 22 0.69
7 8 0.25
8 2 0.06
ACGTcount: A:0.80, C:0.00, G:0.05, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:18393068 original size:9 final size:9
Alignment explanation
Indices: 18393031--18393071 Score: 55
Period size: 9 Copynumber: 4.4 Consensus size: 9
18393021 AGGAAAGTCC
*
18393031 ATTAGGTTA
1 ATTAGTTTA
18393040 AGTTAGTTTA
1 A-TTAGTTTA
*
18393050 GTTAGTTTA
1 ATTAGTTTA
18393059 ATTAGTTTA
1 ATTAGTTTA
18393068 ATTA
1 ATTA
18393072 AAATATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (9 bp):
ATTAGTTTA
Found at i:18393416 original size:5 final size:5
Alignment explanation
Indices: 18393406--18393446 Score: 73
Period size: 5 Copynumber: 8.2 Consensus size: 5
18393396 TAGTGTTCTA
*
18393406 AATTT AATTT AATTT AATTT AATTT AATTT AATTT ATTTT A
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT AATTT A
18393447 GTGTAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
AATTT
Found at i:18395341 original size:25 final size:25
Alignment explanation
Indices: 18395313--18395399 Score: 77
Period size: 25 Copynumber: 3.5 Consensus size: 25
18395303 AGTTCGTCAC
* *
18395313 AAAGGCTTTACATAGAGTTTACCAT
1 AAAGGCTTTACAAAGAGTTTACCAA
* * * *
18395338 AAAGACGTTATAAAGAGTTTTCCAA
1 AAAGGCTTTACAAAGAGTTTACCAA
* *
18395363 AAAGG-TCTTACAAAGAGTTTGCCAC
1 AAAGGCT-TTACAAAGAGTTTACCAA
*
18395388 AAAGGCCTTACA
1 AAAGGCTTTACA
18395400 GGTAATCCAT
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
25 48 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.26
Consensus pattern (25 bp):
AAAGGCTTTACAAAGAGTTTACCAA
Found at i:18413450 original size:39 final size:39
Alignment explanation
Indices: 18413392--18413542 Score: 187
Period size: 39 Copynumber: 3.9 Consensus size: 39
18413382 TCATATGTAA
* *
18413392 TCAGTAACAATCAGTTATTCAGTATAGTAATTTAGTCT-T
1 TCAGTAACTATCAATTATTCAGTATAGTAATTTAGT-TAT
* * ** *
18413431 TCAGTAACTATCAAATATTCATTGCAGTAGTTTAGTTAT
1 TCAGTAACTATCAATTATTCAGTATAGTAATTTAGTTAT
* *
18413470 TCAATAACTATCAATTATTCAATATAGTAATTTAGTTAT
1 TCAGTAACTATCAATTATTCAGTATAGTAATTTAGTTAT
* *
18413509 TTAGTAACTATCAATTATTCAGTATAGTAGTTTA
1 TCAGTAACTATCAATTATTCAGTATAGTAATTTA
18413543 CCCCTATTAA
Statistics
Matches: 94, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
38 1 0.01
39 93 0.99
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (39 bp):
TCAGTAACTATCAATTATTCAGTATAGTAATTTAGTTAT
Found at i:18413538 original size:78 final size:78
Alignment explanation
Indices: 18413396--18413542 Score: 206
Period size: 78 Copynumber: 1.9 Consensus size: 78
18413386 ATGTAATCAG
* * * *
18413396 TAACAATCAGTTATTCAGTATAGTAATTTAGTCTTTCAGTAACTATCAAATATTCATTGCAGTAG
1 TAACAATCAATTATTCAATATAGTAATTTAGTCTTTCAGTAACTATCAAATATTCAGTACAGTAG
18413461 TTTAGTTATTCAA
66 TTTAGTTATTCAA
* * * *
18413474 TAACTATCAATTATTCAATATAGTAATTTAGT-TATTTAGTAACTATCAATTATTCAGTATAGTA
1 TAACAATCAATTATTCAATATAGTAATTTAGTCT-TTCAGTAACTATCAAATATTCAGTACAGTA
18413538 GTTTA
65 GTTTA
18413543 CCCCTATTAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
77 1 0.02
78 59 0.98
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (78 bp):
TAACAATCAATTATTCAATATAGTAATTTAGTCTTTCAGTAACTATCAAATATTCAGTACAGTAG
TTTAGTTATTCAA
Found at i:18413689 original size:47 final size:47
Alignment explanation
Indices: 18413597--18413700 Score: 129
Period size: 47 Copynumber: 2.2 Consensus size: 47
18413587 CCAACACACT
* ** *
18413597 AGTACGACACTTAGTACCTCATCGGCTTTGCCGAAGAAAACAGTAAC
1 AGTACGACACTTAGTACCTCATCGGATTAACCAAAGAAAACAGTAAC
* * *
18413644 AGTACGATACTTAGTACCTCATCGGATTAAACCAAAG-TAATAGTAAC
1 AGTACGACACTTAGTACCTCATCGGATT-AACCAAAGAAAACAGTAAC
18413691 AGTACGACAC
1 AGTACGACAC
18413701 ACAAGGTGCC
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 43 0.90
48 5 0.10
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (47 bp):
AGTACGACACTTAGTACCTCATCGGATTAACCAAAGAAAACAGTAAC
Found at i:18413743 original size:44 final size:44
Alignment explanation
Indices: 18413685--18413776 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
18413675 CCAAAGTAAT
* *
18413685 AGTAACAGTACGACACACA-AGGTGCCTCATTGACTCAAAGTCGA
1 AGTAACAGAACGACACACATA-GTGCCTCATCGACTCAAAGTCGA
* ** *
18413729 AGTACCAGAACGACACTTATAGTGCCTCATCGACTCAAGGTCGA
1 AGTAACAGAACGACACACATAGTGCCTCATCGACTCAAAGTCGA
18413773 AGTA
1 AGTA
18413777 TCCCTAAGCA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 40 0.98
45 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.21, T:0.20
Consensus pattern (44 bp):
AGTAACAGAACGACACACATAGTGCCTCATCGACTCAAAGTCGA
Found at i:18414894 original size:30 final size:28
Alignment explanation
Indices: 18414839--18414900 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 28
18414829 GTTATTTAAT
18414839 TAATAAATATCTTTTACTTAATAATAAA
1 TAATAAATATCTTTTACTTAATAATAAA
18414867 TAATAAATATCTATTTACTTAAATAATAAA
1 TAATAAATATCT-TTTACTT-AATAATAAA
18414897 TAAT
1 TAAT
18414901 TTAAATCCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 12 0.38
29 7 0.22
30 13 0.41
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (28 bp):
TAATAAATATCTTTTACTTAATAATAAA
Found at i:18434385 original size:47 final size:46
Alignment explanation
Indices: 18434315--18434479 Score: 167
Period size: 46 Copynumber: 3.5 Consensus size: 46
18434305 TTTGCGTGCT
18434315 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
* * * *
18434361 AATGTAAGACCATGTCTGGGACATGGCATC-G--ATATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACATT---ATGAGAGCC
* * * *
18434409 AGTGTAAGACATGTTTGGGAAATGCATCGGCCTCATGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATG-AGAGCC
*
18434455 AGTGTAAGACATGTTTGGGACATGC
1 AGTGTAAGACATGTCTGGGACATGC
18434480 GGCGGCTACG
Statistics
Matches: 97, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
45 4 0.04
46 42 0.43
47 29 0.30
48 20 0.21
49 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
Found at i:18434459 original size:46 final size:46
Alignment explanation
Indices: 18434315--18434575 Score: 176
Period size: 47 Copynumber: 5.6 Consensus size: 46
18434305 TTTGCGTGCT
* *
18434315 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCATGATGAGAGCC
* *** * * *
18434361 AATGTAAGACCATGTCTGGGACATGGCATCGATATTGA-GACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCG-GCCTCATGATGAGAGCC
* *
18434409 AGTGTAAGACATGTTTGGGAAATGCATCGGCCTCATGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCATGATG-AGAGCC
* ** * * *
18434455 AGTGTAAGACATGTTTGGGACATGCGGCGG-CT-ACGA-GATGTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCATGATGA-GAGCC
* * * * *
18434499 AGTGTAAGGCCATGTTTGGGACATGGCATCGACTTAATG--GATGAGCC
1 AGTGTAA-GACATGTCTGGGACAT-GCATCGGCCTCATGATGA-GAGCC
*
18434546 AGTGTAAGACCATGTCTAGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
18434576 AGTATTACAC
Statistics
Matches: 168, Mismatches: 35, Indels: 23
0.74 0.15 0.10
Matches are distributed among these distances:
42 1 0.01
43 1 0.01
44 12 0.07
45 19 0.11
46 52 0.31
47 59 0.35
48 23 0.14
49 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTCATGATGAGAGCC
Found at i:18436637 original size:20 final size:21
Alignment explanation
Indices: 18436614--18436660 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
18436604 TAATAGGAAA
*
18436614 ATGTTTTCTTTATTTTG-AAG
1 ATGTTTTATTTATTTTGCAAG
* *
18436634 ATGTCTTATTTTTTTTGCAAG
1 ATGTTTTATTTATTTTGCAAG
18436655 A-GTTTT
1 ATGTTTT
18436661 TACTCATCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.19, C:0.06, G:0.15, T:0.60
Consensus pattern (21 bp):
ATGTTTTATTTATTTTGCAAG
Found at i:18441270 original size:69 final size:69
Alignment explanation
Indices: 18441177--18441336 Score: 166
Period size: 69 Copynumber: 2.3 Consensus size: 69
18441167 TTCATAGTTA
* * * * * * **
18441177 AGCTATGGTCTTATAGCTTGAAATC-CCTGTGTTTACTATCCCAATAGACTTTATTTTTTGCCAA
1 AGCTATGGTCTTACAGCTTAAAATCATC-ATGTTTACTATCCCAATAAACTCTATTAGTTGCCAA
18441241 AGCT-G
65 AG-TAG
* *
18441246 AGCTATGGTCTTACA-CTTTAAAATCATCATGTTTACTATCCCATTAAACTCTATTAGTTGCCAT
1 AGCTATGGTCTTACAGC-TTAAAATCATCATGTTTACTATCCCAATAAACTCTATTAGTTGCCAA
18441310 AGTAG
65 AGTAG
18441315 AGCTATGGTCTTA-AGCCTTAAA
1 AGCTATGGTCTTACAG-CTTAAA
18441337 CCTATTTGAG
Statistics
Matches: 76, Mismatches: 10, Indels: 10
0.79 0.10 0.10
Matches are distributed among these distances:
68 3 0.04
69 71 0.93
70 2 0.03
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (69 bp):
AGCTATGGTCTTACAGCTTAAAATCATCATGTTTACTATCCCAATAAACTCTATTAGTTGCCAAA
GTAG
Found at i:18450264 original size:29 final size:29
Alignment explanation
Indices: 18450231--18450362 Score: 201
Period size: 29 Copynumber: 4.6 Consensus size: 29
18450221 GTGACGAGAT
18450231 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
18450260 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
18450289 TGGCACTAAGTGTGCGTGCTGGAAATATT
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
** *
18450318 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* **
18450347 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
18450363 AGTTCGGAGG
Statistics
Matches: 94, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 94 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:18457685 original size:29 final size:29
Alignment explanation
Indices: 18457652--18457781 Score: 183
Period size: 29 Copynumber: 4.6 Consensus size: 29
18457642 GTGACGAGAT
18457652 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
18457681 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
*
18457710 TGGCACTAA--GTGCGTGCTGGAAATATT
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
** *
18457737 TGGCACTAAGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAATATA
* **
18457766 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
18457782 AGTTCGGAGG
Statistics
Matches: 90, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
27 26 0.29
29 64 0.71
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAATATA
Found at i:18457730 original size:56 final size:57
Alignment explanation
Indices: 18457652--18457772 Score: 181
Period size: 56 Copynumber: 2.1 Consensus size: 57
18457642 GTGACGAGAT
** *
18457652 TGGCACTAAGTGTGCGTGCTGGAAATATATGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAG-GTGCGTGCTGGAAATATATGGCACTAAGTGTGCAAGCTGGAAAAATA
*
18457710 TGGCACTAA-GTGCGTGCTGGAAATATTTGGCACTAAGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGGTGCGTGCTGGAAATATATGGCACTAAGTGTGCAAGCTGGAAAAATA
*
18457766 CGGCACT
1 TGGCACT
18457773 GGGTGTGCGA
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
56 49 0.84
58 9 0.16
ACGTcount: A:0.29, C:0.16, G:0.30, T:0.26
Consensus pattern (57 bp):
TGGCACTAAGGTGCGTGCTGGAAATATATGGCACTAAGTGTGCAAGCTGGAAAAATA
Found at i:18465025 original size:17 final size:17
Alignment explanation
Indices: 18464993--18465028 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
18464983 TTAAGACTTA
*
18464993 TTTTATTTTTGGTTAGT
1 TTTTATTTTTAGTTAGT
*
18465010 TTTTATTTTTATTTAGT
1 TTTTATTTTTAGTTAGT
18465027 TT
1 TT
18465029 AATTAGGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.00, G:0.11, T:0.75
Consensus pattern (17 bp):
TTTTATTTTTAGTTAGT
Found at i:18471607 original size:49 final size:50
Alignment explanation
Indices: 18471428--18471624 Score: 243
Period size: 50 Copynumber: 3.9 Consensus size: 50
18471418 ATCTATTGTG
** *
18471428 AGGTCACAAGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAACTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAA-TT
* * * * * **
18471479 CGATCACGTGTGTAGTACTAAGTGCAGGATACTATGTGTATCAGATGGTT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATT
* * *
18471529 AGGTCACGTGTGTAGTACTAAGTGGAGGCTACTACGTGTACCAGATAATT
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATT
* *
18471579 -GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
1 AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATA
18471625 GCTTTGGCTA
Statistics
Matches: 123, Mismatches: 23, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
49 41 0.33
50 44 0.36
51 38 0.31
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.28
Consensus pattern (50 bp):
AGGTCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATAATT
Found at i:18484672 original size:30 final size:30
Alignment explanation
Indices: 18484636--18484697 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
18484626 AACTCTGTAA
18484636 ACCACTCATTCATCATCTGGAAGAAGGCTT
1 ACCACTCATTCATCATCTGGAAGAAGGCTT
18484666 ACCACTCATTCATCATCTGGAAGAAGGCTT
1 ACCACTCATTCATCATCTGGAAGAAGGCTT
18484696 AC
1 AC
18484698 TTAGTCTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (30 bp):
ACCACTCATTCATCATCTGGAAGAAGGCTT
Found at i:18495122 original size:37 final size:37
Alignment explanation
Indices: 18495072--18495146 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
18495062 TTTAACTGAT
*
18495072 ACACAATGTTGCTCACACAAGCTTCAGAGATTCCACA
1 ACACAATGCTGCTCACACAAGCTTCAGAGATTCCACA
18495109 ACACAATGCTGCTCACACAAGCTTCAGAGATTCCACA
1 ACACAATGCTGCTCACACAAGCTTCAGAGATTCCACA
18495146 A
1 A
18495147 TTTAAACGAC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.36, C:0.31, G:0.13, T:0.20
Consensus pattern (37 bp):
ACACAATGCTGCTCACACAAGCTTCAGAGATTCCACA
Found at i:18495850 original size:11 final size:10
Alignment explanation
Indices: 18495801--18495851 Score: 57
Period size: 11 Copynumber: 4.7 Consensus size: 10
18495791 CACAATAGTC
18495801 CTCTCACAATT
1 CTCTCA-AATT
*
18495812 CTATCTAAATT
1 CTCTC-AAATT
18495823 CTCTCCAAATT
1 CTCT-CAAATT
18495834 CTCTCAAATTT
1 CTCTCAAA-TT
18495845 CTCTCAA
1 CTCTCAA
18495852 TTTTTGTCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 4 0.11
11 29 0.83
12 2 0.06
ACGTcount: A:0.29, C:0.31, G:0.00, T:0.39
Consensus pattern (10 bp):
CTCTCAAATT
Found at i:18495861 original size:21 final size:22
Alignment explanation
Indices: 18495844--18495883 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
18495834 CTCTCAAATT
18495844 TCTCTC-AATTTTTGTCAAAGC
1 TCTCTCTAATTTTTGTCAAAGC
18495865 TCTCTCTAATTTTTG-CAAA
1 TCTCTCTAATTTTTGTCAAA
18495884 ATAGCTCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (22 bp):
TCTCTCTAATTTTTGTCAAAGC
Found at i:18497034 original size:7 final size:7
Alignment explanation
Indices: 18497014--18497056 Score: 68
Period size: 7 Copynumber: 6.0 Consensus size: 7
18497004 CATAATAAAA
18497014 TAGTCATT
1 TAGT-ATT
*
18497022 TCGTATT
1 TAGTATT
18497029 TAGTATT
1 TAGTATT
18497036 TAGTATT
1 TAGTATT
18497043 TAGTATT
1 TAGTATT
18497050 TAGTATT
1 TAGTATT
18497057 ACCTATATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
7 30 0.91
8 3 0.09
ACGTcount: A:0.26, C:0.05, G:0.14, T:0.56
Consensus pattern (7 bp):
TAGTATT
Found at i:18498319 original size:130 final size:129
Alignment explanation
Indices: 18498111--18498487 Score: 611
Period size: 127 Copynumber: 2.9 Consensus size: 129
18498101 ATTTGTAGAA
18498111 TTTTTTTATATAGTTTC-ATATAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACT
1 TTTTTTTATATAGTTTCAAT-TAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACT
* *
18498175 TTTTTTTAATTTTATTAAAATAAATATTCTTTTAAATTAGGCAATATTTTTTATTATTTTTATA-
65 TTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATA-TTTTTATTATTTTTATAG
18498239 T
129 T
*
18498240 TTAATTTTTATATAGTTTCAATTAATAAAATAAAAGTT-TTTTTAATATTTTAATTATACTTTAC
1 TT--TTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC
*
18498304 TTTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTTGCCAATA-TTTTATTATTTTTATAG
64 TTTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATAG
18498368 T
129 T
*
18498369 TTTTTTTATATAGTTTTAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTAC-T
1 TTTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTT
* *
18498433 TTTTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGCCAATAATTTTTATTA
66 TTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAAT-ATTTTTATTA
18498488 AAATAAATGT
Statistics
Matches: 232, Mismatches: 9, Indels: 14
0.91 0.04 0.05
Matches are distributed among these distances:
127 75 0.32
128 42 0.18
129 13 0.06
130 69 0.30
131 31 0.13
132 2 0.01
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.56
Consensus pattern (129 bp):
TTTTTTTATATAGTTTCAATTAATAAAATAAAAGTTGTTTTTAATATTTTAATTGTACTTTACTT
TTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTAGCCAATATTTTTATTATTTTTATAGT
Found at i:18498352 original size:64 final size:64
Alignment explanation
Indices: 18498283--18498487 Score: 160
Period size: 64 Copynumber: 3.2 Consensus size: 64
18498273 AAGTTTTTTT
18498283 AATATTTTAATTATACTTTACTTTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTTGCC
1 AATATTTTAATTATACTTTACTTTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTTGCC
** * * *
18498347 AATATTTT-ATTATTTTTATAGTTTTTTTTATATAGTTTTAATTAATAAAATAAAAG-T-TGTT-
1 AATATTTTAATTATACTT-TA-CTTTTTTT-TA-A-TTTT-A-T--TAAAATAAATGTTCTTTTA
18498408 --TTT---
57 AATTTGCC
* * * *
18498411 AATATTTTAATTGTACTTTAC-TTTTTTTAATTTTAATACAATAAATGTTCTTTTAAATTAGCC
1 AATATTTTAATTATACTTTACTTTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTTGCC
*
18498474 AATAATTTTTATTA
1 AAT-ATTTTAATTA
18498488 AAATAAATGT
Statistics
Matches: 106, Mismatches: 16, Indels: 38
0.66 0.10 0.24
Matches are distributed among these distances:
55 9 0.08
56 1 0.01
57 3 0.03
58 1 0.01
59 4 0.04
60 3 0.03
61 2 0.02
62 6 0.06
63 10 0.09
64 28 0.26
65 13 0.12
66 2 0.02
67 4 0.04
68 4 0.04
69 1 0.01
70 4 0.04
71 1 0.01
72 10 0.09
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.56
Consensus pattern (64 bp):
AATATTTTAATTATACTTTACTTTTTTTTAATTTTATTAAAATAAATGTTCTTTTAAATTTGCC
Found at i:18498516 original size:39 final size:38
Alignment explanation
Indices: 18498441--18498525 Score: 100
Period size: 39 Copynumber: 2.2 Consensus size: 38
18498431 CTTTTTTTAA
* *
18498441 TTTTAATACAATAAATGTTCTTTTAAATTAGCCAATAAT
1 TTTTAATAAAATAAATGTTATTTTAAATTAGCCAAT-AT
* * *
18498480 TTTTATTAAAATAAATGTTATTTTGAA-TACGGCAATAT
1 TTTTAATAAAATAAATGTTATTTTAAATTA-GCCAATAT
18498518 TTTTAATA
1 TTTTAATA
18498526 TTTTTAGTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
38 11 0.28
39 28 0.72
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.46
Consensus pattern (38 bp):
TTTTAATAAAATAAATGTTATTTTAAATTAGCCAATAT
Found at i:18501861 original size:125 final size:126
Alignment explanation
Indices: 18501564--18501871 Score: 496
Period size: 126 Copynumber: 2.5 Consensus size: 126
18501554 AGTCTAAGGC
* * * *
18501564 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCATATAGGAGCTTTTTTCCGTAATTTTGTTGAC
1 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCATGTGGGAGCTTTTTTCTGTAATTTTGCTGAC
* * *
18501629 AGTGCATCCTTCTTGAAGCATTTTTGACATTGTTTGTTCAGAAACATCTTCTCAAAATTAT
66 AGTGCATCCTTCTTGAAGCATTTTTGACACTATTCGTTCAGAAACATCTTCTCAAAATTAT
18501690 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCATGTGGGAGCTTTTTTCTGTAATTTTGCTGAC
1 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCATGTGGGAGCTTTTTTCTGTAATTTTGCTGAC
*
18501755 AGTGCATCCTTCTTGAAGCGTTTTTGACACTATTCGTTCCAG-AACATCTTCTCAAAATTA-
66 AGTGCATCCTTCTTGAAGCATTTTTGACACTATTCGTT-CAGAAACATCTTCTCAAAATTAT
*
18501815 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCACGTGGGAGCTTTTTT-TCGTAATT
1 TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCATGTGGGAGCTTTTTTCT-GTAATT
18501872 AATAGTTAAT
Statistics
Matches: 171, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
124 1 0.01
125 54 0.32
126 113 0.66
127 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.38
Consensus pattern (126 bp):
TTTTTCAGATACTACTGTAGCAAAAGAGCGTCCATGTGGGAGCTTTTTTCTGTAATTTTGCTGAC
AGTGCATCCTTCTTGAAGCATTTTTGACACTATTCGTTCAGAAACATCTTCTCAAAATTAT
Found at i:18506291 original size:28 final size:28
Alignment explanation
Indices: 18506193--18506291 Score: 69
Period size: 28 Copynumber: 3.4 Consensus size: 28
18506183 GAGTTAACTG
* * *
18506193 GGCCTTAGCCCATATCAATATTAATC-T
1 GGCCATAGCCCATATCAGTATCAATCTT
* *
18506220 GCGCCATAGCCCCT-TACAGTATCAGGGTATACTG
1 G-GCCATAGCCCATAT-CAGTATCA----AT-CTT
18506254 GGCC-TAGCCCATATCAGTATCAATCTT
1 GGCCATAGCCCATATCAGTATCAATCTT
18506281 GGCCATAGCCC
1 GGCCATAGCCC
18506292 TATTACAAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 19
0.68 0.09 0.23
Matches are distributed among these distances:
27 8 0.15
28 24 0.44
32 17 0.31
33 5 0.09
34 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.26
Consensus pattern (28 bp):
GGCCATAGCCCATATCAGTATCAATCTT
Found at i:18506316 original size:60 final size:60
Alignment explanation
Indices: 18506189--18506327 Score: 158
Period size: 60 Copynumber: 2.3 Consensus size: 60
18506179 ATCAGAGTTA
* * *
18506189 ACTGGGCCTTAGCCCATATCAATATTAATCTGCGCCATAGCCCCTTACAGTATCAGGGTAT
1 ACTGGGCC-TAGCCCATATCAATATCAATCTGCGCCATAGCCCATTACAGTATCAGGATAT
* *
18506250 ACTGGGCCTAGCCCATATCAGTATCAATCTTG-GCCATAGCCCTATTACAAGT-TGA-GATAT
1 ACTGGGCCTAGCCCATATCAATATCAATC-TGCGCCATAGCCC-ATTAC-AGTATCAGGATAT
* *
18506310 ATTGGGCCTTGCCCATAT
1 ACTGGGCCTAGCCCATAT
18506328 TAACACAGTT
Statistics
Matches: 68, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
60 49 0.72
61 16 0.24
62 3 0.04
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (60 bp):
ACTGGGCCTAGCCCATATCAATATCAATCTGCGCCATAGCCCATTACAGTATCAGGATAT
Found at i:18517564 original size:2 final size:2
Alignment explanation
Indices: 18517557--18517585 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18517547 CTTTTAAATT
18517557 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18517586 GTATGTGTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18518713 original size:128 final size:128
Alignment explanation
Indices: 18518264--18518694 Score: 639
Period size: 128 Copynumber: 3.4 Consensus size: 128
18518254 TGAAGATTCA
* * * * *
18518264 CTAAAACAAAGGCAATATCCGATGTTTGGAAATGCGGGGAATAGGGCCCTATCGTGTTGGGTTTC
1 CTAAAAC-AAGGCAATATTCGATGTTTGGAAATTCGAGGAATAGTGCCCTATCGTGCTGGGTTTC
*
18518329 GATTTCCCGTTTGTTTAAAATAATCGAATATTCCTTTAGAATTTTACTCGTGTTTTTCCAAACG
65 GATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTTACTCGTGTTTTTCCAAACG
** *
18518393 CTAAAACAATACAATATTCGATGTTTGGAAATTCGAGGAATAGTGCCCTATCGTGCTGGGTTTTG
1 CTAAAACAAGGCAATATTCGATGTTTGGAAATTCGAGGAATAGTGCCCTATCGTGCTGGGTTTCG
18518458 ATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTTACTCGTGTTTTTCCAAACG
66 ATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTTACTCGTGTTTTTCCAAACG
* *
18518521 CTAAAACAAGGCAATATTCGATGTTTGGAAATTCGGGGAATAGTGCCCTATCGTGCTAGGTTTCG
1 CTAAAACAAGGCAATATTCGATGTTTGGAAATTCGAGGAATAGTGCCCTATCGTGCTGGGTTTCG
* * ** * *
18518586 ATTTCCCCGTTTGTCCAAAATAATCGAATATTCCTTTGGAATTTCGCTCGTG-TTTTCTAAATG
66 ATTT-CCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTTACTCGTGTTTTTCCAAACG
* * * * *
18518649 CTAAAGCGAGGCAATGTTCAATGTTTGGAAATTCGAGGAATCGTGC
1 CTAAAACAAGGCAATATTCGATGTTTGGAAATTCGAGGAATAGTGC
18518695 TTTACCATTC
Statistics
Matches: 275, Mismatches: 26, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
128 225 0.82
129 50 0.18
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (128 bp):
CTAAAACAAGGCAATATTCGATGTTTGGAAATTCGAGGAATAGTGCCCTATCGTGCTGGGTTTCG
ATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTTACTCGTGTTTTTCCAAACG
Found at i:18520228 original size:19 final size:19
Alignment explanation
Indices: 18520204--18520249 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
18520194 CTTTCTTTCC
18520204 TTTGCATT-CATCCCATGCA
1 TTTGCATTGCATCCCAT-CA
**
18520223 TTTGCATTGCATTGCATCA
1 TTTGCATTGCATCCCATCA
18520242 TTTGCATT
1 TTTGCATT
18520250 AGATTTTCCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.43
Consensus pattern (19 bp):
TTTGCATTGCATCCCATCA
Found at i:18521934 original size:89 final size:90
Alignment explanation
Indices: 18521782--18521957 Score: 327
Period size: 89 Copynumber: 2.0 Consensus size: 90
18521772 TGATTTGTCA
*
18521782 AGGATGGTAGAACAAGATGAGAAATAGATCCTACCTTACAAAGGGGCAATGGACATCGCGAACCT
1 AGGATGGTAGAACAAGATGAGAAATAGATCCTACCTTAAAAAGGGGCAATGGACATCGCGAACCT
18521847 AAGAGAAGAAAAGAGGTAAAGAGTC
66 AAGAGAAGAAAAGAGGTAAAGAGTC
*
18521872 AGGATGGTAGAACAAGATGAGAAAT-GATCCTACCTTAAAAAGGGGCAATGGACATCGTGAACCT
1 AGGATGGTAGAACAAGATGAGAAATAGATCCTACCTTAAAAAGGGGCAATGGACATCGCGAACCT
18521936 AAGAGAAGAAAAGAGGTAAAGA
66 AAGAGAAGAAAAGAGGTAAAGA
18521958 TCAAAGCCTA
Statistics
Matches: 84, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
89 59 0.70
90 25 0.30
ACGTcount: A:0.44, C:0.13, G:0.28, T:0.15
Consensus pattern (90 bp):
AGGATGGTAGAACAAGATGAGAAATAGATCCTACCTTAAAAAGGGGCAATGGACATCGCGAACCT
AAGAGAAGAAAAGAGGTAAAGAGTC
Found at i:18522427 original size:7 final size:7
Alignment explanation
Indices: 18522410--18522439 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
18522400 ATGCATATAT
18522410 AAAAC-A
1 AAAACAA
18522416 AAAACAA
1 AAAACAA
18522423 AAAACAA
1 AAAACAA
18522430 AAAACAA
1 AAAACAA
18522437 AAA
1 AAA
18522440 GATTATATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAACAA
Found at i:18524245 original size:64 final size:64
Alignment explanation
Indices: 18524173--18524364 Score: 312
Period size: 64 Copynumber: 3.0 Consensus size: 64
18524163 TCATTCATAA
* * *
18524173 CACATCTAGTTAGGAGCATTTGATTCATTTTGATCATAGTATCCTAATTATTTAACATAAGTAT
1 CACATCTAGTTAGGAGCATTTAATTCATTTTGATCATAGTATCCTAATTATTTGACATAAGCAT
* *
18524237 CACATCTAGTTAGGAGCATTTAATTCATTTCGGTCATAGTATCCTAATTATTTGACATAAGCAT
1 CACATCTAGTTAGGAGCATTTAATTCATTTTGATCATAGTATCCTAATTATTTGACATAAGCAT
* * *
18524301 CACATCTAGTTAGGAGCATTTAATTCATTTTGATCATAGCATCCTAGTCATTTGACATAAGCAT
1 CACATCTAGTTAGGAGCATTTAATTCATTTTGATCATAGTATCCTAATTATTTGACATAAGCAT
18524365 AGCCATACAG
Statistics
Matches: 118, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
64 118 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.38
Consensus pattern (64 bp):
CACATCTAGTTAGGAGCATTTAATTCATTTTGATCATAGTATCCTAATTATTTGACATAAGCAT
Found at i:18524572 original size:89 final size:88
Alignment explanation
Indices: 18524410--18525202 Score: 708
Period size: 89 Copynumber: 9.0 Consensus size: 88
18524400 GCGACATCGA
* * * * **
18524410 TGAAAATTGTAGATCTTGTCTCCCTAAACAGT--AGTGGAGCAAATTGAAGA-AGCAAGCCTTAA
1 TGAAGATTGTAGATCTTGTCTCCCT-GA-AGTACAGTGGAACAGATCAAAGACAGCAAGCCTTAA
* * *
18524472 CCCCTTAAGTAGTAAGGTAATAGGC
64 CCCCCTAAGTAGTAGGGTAACAGGC
* * * * *
18524497 TAAAGATT-TCAGATCTTGTCTCCCTGAAGTTACAGTGGAATAGATCAAAGACGGCGAGCTTTAA
1 TGAAGATTGT-AGATCTTGTCTCCCTGAAG-TACAGTGGAACAGATCAAAGACAGCAAGCCTTAA
*
18524561 CCCCCTAAGTAGTAAGGTAACAGGC
64 CCCCCTAAGTAGTAGGGTAACAGGC
* * ** * *
18524586 TGAAGATTGTAGATCTTGTTCTCCCT-AAATAGTAGTGGAGTAGATCGAAGAAAGCAAGCCTTAA
1 TGAAGATTGTAGATCTTG-TCTCCCTGAAGTA-CAGTGGAACAGATCAAAGACAGCAAGCCTTAA
* *
18524650 CCCTCTAAGTAGTAGGGTAATAGGC
64 CCCCCTAAGTAGTAGGGTAACAGGC
* * * *
18524675 TGAAGATTGTAAATCTTGTCTCCCTAAACAGT--AGTGGAGCAAATCAAAGA-AGCAAGCCTTAA
1 TGAAGATTGTAGATCTTGTCTCCCT-GA-AGTACAGTGGAACAGATCAAAGACAGCAAGCCTTAA
18524737 CCCCCTAAGTAGTAGGGTAACAGGC
64 CCCCCTAAGTAGTAGGGTAACAGGC
** * * * ***
18524762 TGAAGATTCCAGATCTTTTCTCTCTGAAGCTGCAGTGGAACAGATCAAAGACAATGAGCCTTAAC
1 TGAAGATTGTAGATCTTGTCTCCCTGAAG-TACAGTGGAACAGATCAAAGACAGCAAGCCTTAAC
18524827 CCCCT-A--AGTAGGGTAACAGGC
65 CCCCTAAGTAGTAGGGTAACAGGC
* * * * * * *
18524848 TAAATATTGTAGATCTTGTCCCCCT-AAATAGTAGTGGAGA-AAATCGAAGA-AGCAAGCCTTAA
1 TGAAGATTGTAGATCTTGTCTCCCTGAAGTA-CAGTGGA-ACAGATCAAAGACAGCAAGCCTTAA
** *
18524910 CCTACTAAGTAGTAGGGTAATAGGC
64 CCCCCTAAGTAGTAGGGTAACAGGC
* * * *
18524935 TGAAGATTGCAGATCTTGTCTCCCTGAAGCTGCAGTGGAACAGATCAAAGACGGCGAGCCTTAAC
1 TGAAGATTGTAGATCTTGTCTCCCTGAAG-TACAGTGGAACAGATCAAAGACAGCAAGCCTTAAC
**
18525000 CCCCTAAGTAGTAGGGTAACAGAA
65 CCCCTAAGTAGTAGGGTAACAGGC
* * *
18525024 TGAAGATTGTAGATCTTGCCTCCCT-AA--ACAGTAGTGAAGCAAATCGAAGA-AGCAAGCCTTA
1 TGAAGATTGTAGATCTTGTCTCCCTGAAGTACAGT-G-GAA-CAGATCAAAGACAGCAAGCCTTA
*
18525085 ACCCCCTAAGTAGTAGGGTAACGGGC
63 ACCCCCTAAGTAGTAGGGTAACAGGC
* ** * * * ** *
18525111 TGAAGATTGCAGATCTTACCT-CCTAGAAGTTGCAGTGGAATAGATCAAAGACGGTGAGCCTTGA
1 TGAAGATTGTAGATCTTGTCTCCCT-GAAG-TACAGTGGAACAGATCAAAGACAGCAAGCCTTAA
*
18525175 -CCCCTAAGCAGTAGGGTAACAGGC
64 CCCCCTAAGTAGTAGGGTAACAGGC
18525199 TGAA
1 TGAA
18525203 AATCACAGAT
Statistics
Matches: 574, Mismatches: 99, Indels: 65
0.78 0.13 0.09
Matches are distributed among these distances:
84 14 0.02
85 25 0.04
86 43 0.07
87 166 0.29
88 117 0.20
89 193 0.34
90 10 0.02
91 6 0.01
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (88 bp):
TGAAGATTGTAGATCTTGTCTCCCTGAAGTACAGTGGAACAGATCAAAGACAGCAAGCCTTAACC
CCCTAAGTAGTAGGGTAACAGGC
Found at i:18524768 original size:176 final size:176
Alignment explanation
Indices: 18524410--18525199 Score: 834
Period size: 176 Copynumber: 4.5 Consensus size: 176
18524400 GCGACATCGA
* * * * * * * **
18524410 TGAAAATTGTAGATCTTGTCTCCCTAAACA-GTAGTGGAGCAAATTGAAG-AAGCAAGCCTTAAC
1 TGAAGATTGCAGATCTTGTCTCCCTGAAGATGCAGTGGAACAGATCAAAGAAAGCAAGCCTTAAC
* * * *
18524473 CCCTTAAGTAGTAAGGTAATAGGCTAAAGATT-TCAGATCTTGTCTCCCT-GA-AGTTACAGTGG
66 CCCCTAAGTAGTAGGGTAACAGGCTAAAGATTGT-AGATCTTGTCTCCCTAAACAG-T--AGTGG
** * * * * *
18524535 AATAGATCAAAGACGGCGAGCTTTAACCCCCTAAGTAGTAAGGTAACAGGC
127 AGCAAATCAAAGA-AGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
* * ** *
18524586 TGAAGATTGTAGATCTTGTTCTCCCT-AA-ATAGTAGTGGAGTAGATCGAAGAAAGCAAGCCTTA
1 TGAAGATTGCAGATCTTG-TCTCCCTGAAGAT-GCAGTGGAACAGATCAAAGAAAGCAAGCCTTA
* * * *
18524649 ACCCTCTAAGTAGTAGGGTAATAGGCTGAAGATTGTAAATCTTGTCTCCCTAAACAGTAGTGGAG
64 ACCCCCTAAGTAGTAGGGTAACAGGCTAAAGATTGTAGATCTTGTCTCCCTAAACAGTAGTGGAG
18524714 CAAATCAAAGAAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
129 CAAATCAAAGAAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
* * * *
18524762 TGAAGATTCCAGATCTTTTCTCTCTGAAGCTGCAGTGGAACAGATCAAAGACAATG--AGCCTTA
1 TGAAGATTGCAGATCTTGTCTCCCTGAAGATGCAGTGGAACAGATCAAAGA-AA-GCAAGCCTTA
* * *
18524825 ACCCCCT-A--AGTAGGGTAACAGGCTAAATATTGTAGATCTTGTCCCCCTAAATAGTAGTGGAG
64 ACCCCCTAAGTAGTAGGGTAACAGGCTAAAGATTGTAGATCTTGTCTCCCTAAACAGTAGTGGAG
* * ** *
18524887 AAAATCGAAGAAGCAAGCCTTAACCTACTAAGTAGTAGGGTAATAGGC
129 CAAATCAAAGAAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
* ** *
18524935 TGAAGATTGCAGATCTTGTCTCCCTGAAGCTGCAGTGGAACAGATCAAAGACGGCGAGCCTTAAC
1 TGAAGATTGCAGATCTTGTCTCCCTGAAGATGCAGTGGAACAGATCAAAGAAAGCAAGCCTTAAC
** * * *
18525000 CCCCTAAGTAGTAGGGTAACAGAATGAAGATTGTAGATCTTGCCTCCCTAAACAGTAGTGAAGCA
66 CCCCTAAGTAGTAGGGTAACAGGCTAAAGATTGTAGATCTTGTCTCCCTAAACAGTAGTGGAGCA
* *
18525065 AATCGAAGAAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACGGGC
131 AATCAAAGAAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
** * * ** ** *
18525111 TGAAGATTGCAGATCTTACCT-CCTAGAAGTTGCAGTGGAATAGATCAAAGACGGTGAGCCTTGA
1 TGAAGATTGCAGATCTTGTCTCCCT-GAAGATGCAGTGGAACAGATCAAAGAAAGCAAGCCTTAA
*
18525175 -CCCCTAAGCAGTAGGGTAACAGGCT
65 CCCCCTAAGTAGTAGGGTAACAGGCT
18525200 GAAAATCACA
Statistics
Matches: 532, Mismatches: 65, Indels: 35
0.84 0.10 0.06
Matches are distributed among these distances:
171 1 0.00
173 153 0.29
174 1 0.00
175 33 0.06
176 241 0.45
177 41 0.08
178 57 0.11
179 3 0.01
180 2 0.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (176 bp):
TGAAGATTGCAGATCTTGTCTCCCTGAAGATGCAGTGGAACAGATCAAAGAAAGCAAGCCTTAAC
CCCCTAAGTAGTAGGGTAACAGGCTAAAGATTGTAGATCTTGTCTCCCTAAACAGTAGTGGAGCA
AATCAAAGAAGCAAGCCTTAACCCCCTAAGTAGTAGGGTAACAGGC
Found at i:18525833 original size:20 final size:20
Alignment explanation
Indices: 18525784--18525833 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
18525774 GCGCCACAAC
18525784 CACGC-CCAC-GCCCCCGTA
1 CACGCGCCACGGCCCCCGTA
*
18525802 CGC-CAGCACACGGCCCCCGTA
1 CACGC-GC-CACGGCCCCCGTA
18525823 CACGCGCCACG
1 CACGCGCCACG
18525834 CATTCCATAC
Statistics
Matches: 25, Mismatches: 2, Indels: 8
0.71 0.06 0.23
Matches are distributed among these distances:
17 1 0.04
18 2 0.08
19 1 0.04
20 7 0.28
21 13 0.52
22 1 0.04
ACGTcount: A:0.18, C:0.56, G:0.22, T:0.04
Consensus pattern (20 bp):
CACGCGCCACGGCCCCCGTA
Found at i:18527194 original size:2 final size:2
Alignment explanation
Indices: 18527187--18527211 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18527177 CTTTTAAATT
18527187 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
18527212 GTGTGTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18527216 original size:2 final size:2
Alignment explanation
Indices: 18527211--18527260 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
18527201 TATATATATA
18527211 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
18527253 TG TG TG TG
1 TG TG TG TG
18527261 CGCGCGCTTT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:18528235 original size:127 final size:128
Alignment explanation
Indices: 18527922--18528367 Score: 569
Period size: 128 Copynumber: 3.5 Consensus size: 128
18527912 TGAAGATTCA
** *
18527922 CTAAAACAAAGGCAAT-TCTGATGTTTGGAAATGCGGGGAATAGGGCCCTATCGTGCTGGGTTTC
1 CTAAAAC-AAGGCAATATCTGATGTTTGGAAATTTGGGGAATAGTGCCCTATCGTGCTGGGTTTC
* *
18527986 GATTTCCCGTTTGTTCATAATAATCGAATATTCCTTTAGAATTTTACTCGTGTTTTTTCAAACG
65 GATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTTACTCGTGTTTTTCCAAACG
* * * *
18528050 CTAAAACAATGCAAGATTTGATGTTTGGAAA-TTCGGGAATAGTGCCCTATCGTGCTGGGTTTCG
1 CTAAAACAAGGCAATATCTGATGTTTGGAAATTTGGGGAATAGTGCCCTATCGTGCTGGGTTTCG
* * *
18528114 ATTT-CCGTTTGTTCAAAATAATCAAATACTCCTTTAGAATTTTACTCGTGTTTTTCCAAATG
66 ATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTTACTCGTGTTTTTCCAAACG
* * *
18528176 TTAAAACAAGGCAATATCCGATGTTTAGAAATTTGGGGAATAGTGCCCTATCGTGCTGGGTTTCG
1 CTAAAACAAGGCAATATCTGATGTTTGGAAATTTGGGGAATAGTGCCCTATCGTGCTGGGTTTCG
* * * *
18528241 ATTTCCCCGTTTGTTCAAAATAATCGAATATTCCTTTGGAATTTTGCTCGTG-TTTTCTAAATG
66 ATTT-CCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTTACTCGTGTTTTTCCAAACG
* * * * * * * * * *
18528304 CTAAAGCGAA-GCAATGTTTAATGTTTGGAAATTCGAGGAATCGTGTCCTACCGTGTTGGGTTTC
1 CTAAAAC-AAGGCAATATCTGATGTTTGGAAATTTGGGGAATAGTGCCCTATCGTGCTGGGTTTC
18528368 AGTTTTTCGT
Statistics
Matches: 276, Mismatches: 37, Indels: 10
0.85 0.11 0.03
Matches are distributed among these distances:
126 78 0.28
127 75 0.27
128 79 0.29
129 44 0.16
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (128 bp):
CTAAAACAAGGCAATATCTGATGTTTGGAAATTTGGGGAATAGTGCCCTATCGTGCTGGGTTTCG
ATTTCCCGTTTGTTCAAAATAATCGAATATTCCTTTAGAATTTTACTCGTGTTTTTCCAAACG
Found at i:18538823 original size:49 final size:49
Alignment explanation
Indices: 18538746--18539014 Score: 193
Period size: 49 Copynumber: 5.6 Consensus size: 49
18538736 GAATGTGTGT
* * * **
18538746 TAGTGTAAGATCTGTCTGGGATAGGGCATGGGCATAGATAAGTGAGAGC
1 TAGTGTAAGACCTGTCTGGGACATGGCATCAGCATAGATAAGTGAGAGC
*
18538795 TAGTGTAAGACCTGTCTGGGACATGGCATCAGCCTCAAGAT-A-TGCA-AGC
1 TAGTGTAAGACCTGTCTGGGACATGGCATCAGCAT--AGATAAGTG-AGAGC
* * * ** * * * *
18538844 TAGTGTAAGACCTGTTTAGGACATGGTATTGGC-T---TGAG-GTGTGT
1 TAGTGTAAGACCTGTCTGGGACATGGCATCAGCATAGATAAGTGAGAGC
* * *
18538888 TAGCGTAAGACCTGTCTGGGACATGGCATCAACAAAGATAAGTGAGAGC
1 TAGTGTAAGACCTGTCTGGGACATGGCATCAGCATAGATAAGTGAGAGC
* * * *
18538937 CAGTGTAAGACCTGTCT-GGACATGGCATCAGCCTCGATGTA-TGTA-AG-
1 TAGTGTAAGACCTGTCTGGGACATGGCATCAGCATAGAT-AAGTG-AGAGC
*
18538984 TCAGTATAAGACCTGTCTGGGACATGGCATC
1 T-AGTGTAAGACCTGTCTGGGACATGGCATC
18539015 TATAACATCT
Statistics
Matches: 170, Mismatches: 35, Indels: 30
0.72 0.15 0.13
Matches are distributed among these distances:
43 1 0.01
44 29 0.17
48 40 0.24
49 94 0.55
50 2 0.01
51 4 0.02
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (49 bp):
TAGTGTAAGACCTGTCTGGGACATGGCATCAGCATAGATAAGTGAGAGC
Found at i:18543096 original size:40 final size:40
Alignment explanation
Indices: 18543032--18543107 Score: 116
Period size: 40 Copynumber: 1.9 Consensus size: 40
18543022 TGCAGTACCT
*
18543032 TATGGTGTGTAGGAATGGACGGGTCGATTTTATCCCCATA
1 TATGGTGTGCAGGAATGGACGGGTCGATTTTATCCCCATA
* **
18543072 TATGGTGTGCAGGGATGGGTGGGTCGATTTTATCCC
1 TATGGTGTGCAGGAATGGACGGGTCGATTTTATCCC
18543108 TACATGGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.18, C:0.14, G:0.34, T:0.33
Consensus pattern (40 bp):
TATGGTGTGCAGGAATGGACGGGTCGATTTTATCCCCATA
Found at i:18548180 original size:18 final size:18
Alignment explanation
Indices: 18548157--18548196 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
18548147 CTAGACTGAG
*
18548157 TTGGGTGAGCAACGAGTT
1 TTGGGTGACCAACGAGTT
*
18548175 TTGGGTGACCGACGAGTT
1 TTGGGTGACCAACGAGTT
18548193 TTGG
1 TTGG
18548197 TTTCGGAGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.12, G:0.40, T:0.30
Consensus pattern (18 bp):
TTGGGTGACCAACGAGTT
Found at i:18550259 original size:40 final size:38
Alignment explanation
Indices: 18550195--18550282 Score: 115
Period size: 40 Copynumber: 2.3 Consensus size: 38
18550185 TACAGTACCT
18550195 TATGGTGTGTAAGGATGGACGGGTCGATTTTATCCCCATA
1 TATGGTGTGTAAGGATGGACGGGTCGATTTTAT-CCC-TA
* *
18550235 TATGGTGTGTAGGGATAGG-TGGGTCGATTTTATCCCTA
1 TATGGTGTGTAAGGAT-GGACGGGTCGATTTTATCCCTA
*
18550273 CATGGTGTGT
1 TATGGTGTGT
18550283 TGGGTTGGAC
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
38 11 0.25
39 3 0.07
40 28 0.64
41 2 0.05
ACGTcount: A:0.19, C:0.12, G:0.33, T:0.35
Consensus pattern (38 bp):
TATGGTGTGTAAGGATGGACGGGTCGATTTTATCCCTA
Found at i:18556221 original size:19 final size:19
Alignment explanation
Indices: 18556197--18556233 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
18556187 TAGTCTTAAA
*
18556197 ATAAAATAAAAGTAAAAAC
1 ATAAAATAAAAATAAAAAC
18556216 ATAAAATAAAAATAAAAA
1 ATAAAATAAAAATAAAAA
18556234 AAATTTAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.78, C:0.03, G:0.03, T:0.16
Consensus pattern (19 bp):
ATAAAATAAAAATAAAAAC
Found at i:18562278 original size:13 final size:13
Alignment explanation
Indices: 18562259--18562311 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
18562249 GCTTGGCAGG
*
18562259 GACACGCCTGTGT
1 GACACGCCCGTGT
*
18562272 TACACGCCCGTGT
1 GACACGCCCGTGT
*
18562285 GACACGCCCATGT
1 GACACGCCCGTGT
18562298 GACACGCCCGTGT
1 GACACGCCCGTGT
18562311 G
1 G
18562312 TGATTGCCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 35 1.00
ACGTcount: A:0.17, C:0.36, G:0.28, T:0.19
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:18570748 original size:39 final size:38
Alignment explanation
Indices: 18570713--18570831 Score: 123
Period size: 39 Copynumber: 3.1 Consensus size: 38
18570703 TTCTTCGGAA
* *
18570713 TACAACCGGATATAACCACACGCACGAATGCCTTCGGG
1 TACAACCGGATATAACAACTCGCACGAATGCCTTCGGG
* * *
18570751 T-CTTAGCCCGGATATAACGACTCGCACAAATGCCTTCGGG
1 TAC--A-ACCGGATATAACAACTCGCACGAATGCCTTCGGG
* * *
18570791 TATTAGCCGGATATAACAACTTGCACGAATGCCTTCGGG
1 TA-CAACCGGATATAACAACTCGCACGAATGCCTTCGGG
18570830 TA
1 TA
18570832 TTAGCCCGGA
Statistics
Matches: 67, Mismatches: 9, Indels: 9
0.79 0.11 0.11
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
39 33 0.49
40 32 0.48
ACGTcount: A:0.29, C:0.28, G:0.22, T:0.22
Consensus pattern (38 bp):
TACAACCGGATATAACAACTCGCACGAATGCCTTCGGG
Found at i:18570832 original size:39 final size:40
Alignment explanation
Indices: 18570718--18570884 Score: 198
Period size: 40 Copynumber: 4.2 Consensus size: 40
18570708 CGGAATACAA
* * *
18570718 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACAACTCGCACGAATGCCTTCGGGTATTAGC
* *
18570758 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAG-
1 CCGGATATAACAACTCGCACGAATGCCTTCGGGTATTAGC
*
18570797 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGC
1 CCGGATATAACAACTCGCACGAATGCCTTCGGGTATTAGC
* * *
18570837 CCGGATA-AAGTC-ACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA--CAACTCGCACGAA-TGCCTTCGGGTATTAGC
18570877 CCGGATAT
1 CCGGATAT
18570885 CATTCAATTG
Statistics
Matches: 112, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
39 40 0.36
40 71 0.63
41 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACAACTCGCACGAATGCCTTCGGGTATTAGC
Found at i:18570836 original size:79 final size:79
Alignment explanation
Indices: 18570718--18570884 Score: 221
Period size: 79 Copynumber: 2.1 Consensus size: 79
18570708 CGGAATACAA
* * *
18570718 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAA-CGACTCGCACAAAT
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATA-AAGC-ACTAGCACAAAT
*
18570782 GCCTTCGGGTATT-AG
64 GCCTTCGGGTATTAAC
** *
18570797 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGCCCGGATAAAGTCACTAGCACAATTG
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATAAAG-CACTAGCACAAATG
*
18570862 CCTTCGGGTCTTAAC
65 CCTTCGGGTATTAAC
18570877 CCGGATAT
1 CCGGATAT
18570885 CATTCAATTG
Statistics
Matches: 77, Mismatches: 8, Indels: 5
0.86 0.09 0.06
Matches are distributed among these distances:
78 2 0.03
79 65 0.84
80 10 0.13
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (79 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATAAAGCACTAGCACAAATGC
CTTCGGGTATTAAC
Found at i:18578763 original size:40 final size:40
Alignment explanation
Indices: 18578718--18578885 Score: 198
Period size: 40 Copynumber: 4.2 Consensus size: 40
18578708 CGGAATACAA
*
18578718 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
18578758 CCGGATATAACGACTCGCACAAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* **
18578798 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGC
1 CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
* * *
18578838 CCGGATA-AAGTCACTA-GCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATATAA-CCAC-ACGCACGAA-TGCCTTCGGGTATTAGC
18578878 CCGGATAT
1 CCGGATAT
18578886 CATTCAATTG
Statistics
Matches: 112, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
39 4 0.04
40 108 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACACGCACGAATGCCTTCGGGTATTAGC
Found at i:18578858 original size:80 final size:80
Alignment explanation
Indices: 18578718--18578885 Score: 232
Period size: 80 Copynumber: 2.1 Consensus size: 80
18578708 CGGAATACAA
* * *
18578718 CCGGATATAACCACACGCACGAATGCCTTCGGGTCTTAGCCCGGATATAACGACTCGCACAAATG
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
*
18578783 CCTTCGGGTATTAGC
66 CCTTCGGGTATTAAC
** *
18578798 CCGGATATAACAACTTGCACGAATGCCTTCGGGTATTAGCCCGGATA-AA-GTCACTAGCACAAT
1 CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACG--ACTAGCACAAA
*
18578861 TGCCTTCGGGTCTTAAC
64 TGCCTTCGGGTATTAAC
18578878 CCGGATAT
1 CCGGATAT
18578886 CATTCAATTG
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
78 1 0.01
79 2 0.03
80 75 0.96
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (80 bp):
CCGGATATAACAACACGCACGAATGCCTTCGGGTATTAGCCCGGATATAACGACTAGCACAAATG
CCTTCGGGTATTAAC
Found at i:18581964 original size:47 final size:48
Alignment explanation
Indices: 18581908--18582005 Score: 189
Period size: 48 Copynumber: 2.1 Consensus size: 48
18581898 CACTTGTGAA
18581908 CTTTCATTGTA-TTTTTTATTCGTTCAAGTGTTTTCCTTGTATTTGTG
1 CTTTCATTGTATTTTTTTATTCGTTCAAGTGTTTTCCTTGTATTTGTG
18581955 CTTTCATTGTATTTTTTTATTCGTTCAAGTGTTTTCCTTGTATTTGTG
1 CTTTCATTGTATTTTTTTATTCGTTCAAGTGTTTTCCTTGTATTTGTG
18582003 CTT
1 CTT
18582006 AATTGGCGAA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 11 0.22
48 39 0.78
ACGTcount: A:0.12, C:0.13, G:0.14, T:0.60
Consensus pattern (48 bp):
CTTTCATTGTATTTTTTTATTCGTTCAAGTGTTTTCCTTGTATTTGTG
Found at i:18583050 original size:13 final size:13
Alignment explanation
Indices: 18583032--18583056 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18583022 GCACGACTCA
18583032 CACGGGCGTGTCG
1 CACGGGCGTGTCG
18583045 CACGGGCGTGTC
1 CACGGGCGTGTC
18583057 CCTGCCGAGC
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:0.08, C:0.32, G:0.44, T:0.16
Consensus pattern (13 bp):
CACGGGCGTGTCG
Found at i:18598948 original size:40 final size:39
Alignment explanation
Indices: 18598904--18599004 Score: 175
Period size: 40 Copynumber: 2.5 Consensus size: 39
18598894 CTTGCTCAAC
18598904 TGCCTTCAGGACTTAGCCCGGATATAGTAACTCGCACAAA
1 TGCCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAA
18598944 TGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAA
1 TGCCTTC-GGACTTAGCCCGGATATAGTAACTCGCACAAA
18598984 TGCCTTCGAGACTTAGCCCGG
1 TGCCTTCG-GACTTAGCCCGG
18599005 TTATCATCCG
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
39 1 0.02
40 58 0.98
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.23
Consensus pattern (39 bp):
TGCCTTCGGACTTAGCCCGGATATAGTAACTCGCACAAA
Found at i:18600177 original size:8 final size:8
Alignment explanation
Indices: 18600164--18600193 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
18600154 ACCTCTTCAA
18600164 CCTTTCTT
1 CCTTTCTT
18600172 CCTTTCTT
1 CCTTTCTT
18600180 CCTTTCTTT
1 CCTTTC-TT
18600189 CCTTT
1 CCTTT
18600194 GATTTTTCGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 14 0.67
9 7 0.33
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (8 bp):
CCTTTCTT
Found at i:18602382 original size:26 final size:26
Alignment explanation
Indices: 18602353--18602406 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
18602343 TCCTCTCTTA
*
18602353 AGCCATATAA-CAGGAAGCTTACAAAG
1 AGCCAT-TAATCAGGAAGCTCACAAAG
18602379 AGCCATTAATCAGGAAGCTCACAAAG
1 AGCCATTAATCAGGAAGCTCACAAAG
18602405 AG
1 AG
18602407 ACTATAAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 3 0.12
26 23 0.88
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.15
Consensus pattern (26 bp):
AGCCATTAATCAGGAAGCTCACAAAG
Found at i:18604072 original size:16 final size:17
Alignment explanation
Indices: 18604051--18604086 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
18604041 ATTAATTCTA
18604051 AATTCATTTGTGA-ATT
1 AATTCATTTGTGACATT
18604067 AATTCATTTGTGACATT
1 AATTCATTTGTGACATT
18604084 AAT
1 AAT
18604087 GGTGTGATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.47
Consensus pattern (17 bp):
AATTCATTTGTGACATT
Found at i:18605342 original size:17 final size:16
Alignment explanation
Indices: 18605322--18605379 Score: 57
Period size: 17 Copynumber: 3.6 Consensus size: 16
18605312 ATTTTAATAG
18605322 ATTTAATATTTAATTTA
1 ATTTAATATTT-ATTTA
*
18605339 ATTTAATACTTATATTA
1 ATTTAATATTTAT-TTA
* *
18605356 ATATCAT-TTTA-TTA
1 ATTTAATATTTATTTA
18605370 ATTTAATATT
1 ATTTAATATT
18605380 AAAGTGATTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 8 0.24
15 2 0.06
16 5 0.15
17 18 0.55
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTAATATTTATTTA
Found at i:18605514 original size:58 final size:61
Alignment explanation
Indices: 18605365--18605522 Score: 155
Period size: 58 Copynumber: 2.6 Consensus size: 61
18605355 AATATCATTT
*
18605365 TATTAATTTAATATTAAAGTGATTATCTTAATATTAATTTAATATTTATCTTATAGATAAATATT
1 TATTAATTTAATATTAAAGTGATTA----AAT-TTAATCTAATATTTATCTTATAGATAAATATT
*
18605430 C
61 A
* * *
18605431 TGTTAATTTAATAGATTTAA-T-ATTAAATTTAATCTAATATTTATC-T-T-GATAAGTATTA
1 TATTAATTTAAT--ATTAAAGTGATTAAATTTAATCTAATATTTATCTTATAGATAAATATTA
* *
18605489 TATTAATTTAATATAAAAGTGATTAAGTTTAATC
1 TATTAATTTAATATTAAAGTGATTAAATTTAATC
18605523 ATAGTTGAAC
Statistics
Matches: 79, Mismatches: 9, Indels: 16
0.76 0.09 0.15
Matches are distributed among these distances:
56 4 0.05
57 1 0.01
58 32 0.41
59 1 0.01
60 1 0.01
61 16 0.20
62 3 0.04
66 15 0.19
67 1 0.01
68 5 0.06
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (61 bp):
TATTAATTTAATATTAAAGTGATTAAATTTAATCTAATATTTATCTTATAGATAAATATTA
Found at i:18605625 original size:39 final size:39
Alignment explanation
Indices: 18605574--18605649 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
18605564 TGGGTCATTA
*
18605574 TTTTTCATATTTACAACTTGACCCTAAAGTTTAGAGATT
1 TTTTTCATATTTACAACTTGACCCTAAAATTTAGAGATT
*
18605613 TTTTTTATATTTACAACTTGACCCTAAAATTTAGAGA
1 TTTTTCATATTTACAACTTGACCCTAAAATTTAGAGA
18605650 AATCAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.43
Consensus pattern (39 bp):
TTTTTCATATTTACAACTTGACCCTAAAATTTAGAGATT
Found at i:18607291 original size:2 final size:2
Alignment explanation
Indices: 18607281--18607311 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18607271 GTTAATTTTT
*
18607281 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18607312 TTAAAGGCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:18615261 original size:16 final size:16
Alignment explanation
Indices: 18615240--18615288 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 16
18615230 ATATTAAGTC
18615240 ATATAATAAATTATTA
1 ATATAATAAATTATTA
18615256 ATATAAT---TTATTA
1 ATATAATAAATTATTA
* *
18615269 TTTTAATAAATTATTTA
1 ATATAATAAATTA-TTA
18615286 ATA
1 ATA
18615289 GTTCAATTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 7
0.69 0.11 0.19
Matches are distributed among these distances:
13 11 0.44
16 10 0.40
17 4 0.16
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATAATAAATTATTA
Found at i:18615332 original size:14 final size:14
Alignment explanation
Indices: 18615264--18615342 Score: 52
Period size: 14 Copynumber: 5.4 Consensus size: 14
18615254 TAATATAATT
*
18615264 TATTATTTTAATAA
1 TATTATTTAAATAA
18615278 -ATTATTTAATAGTTCAA
1 TATTATTTAA-A--T-AA
* *
18615295 TTTTATTTTAATAA
1 TATTATTTAAATAA
*
18615309 TAATTTTTTAAATAA
1 T-ATTATTTAAATAA
* *
18615324 TATTATTTACATAT
1 TATTATTTAAATAA
18615338 TATTA
1 TATTA
18615343 AAAATATTCA
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
13 8 0.16
14 19 0.38
15 12 0.24
16 1 0.02
17 3 0.06
18 7 0.14
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.56
Consensus pattern (14 bp):
TATTATTTAAATAA
Found at i:18615811 original size:13 final size:11
Alignment explanation
Indices: 18615776--18615806 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
18615766 ATTGAAAACA
18615776 ATTTTATAAAAT
1 ATTTT-TAAAAT
18615788 ATTTTTAAAAT
1 ATTTTTAAAAT
18615799 ATTTTTAA
1 ATTTTTAA
18615807 GAAATCTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.74
12 5 0.26
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (11 bp):
ATTTTTAAAAT
Found at i:18643560 original size:14 final size:14
Alignment explanation
Indices: 18643534--18643572 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
18643524 TCATAAACCT
*
18643534 TAAACCCTTAATCA
1 TAAACCCTAAATCA
*
18643548 TATACCCTAAATCA
1 TAAACCCTAAATCA
18643562 TAAACCCTAAA
1 TAAACCCTAAA
18643573 CTATAATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCCTAAATCA
Found at i:18644006 original size:23 final size:22
Alignment explanation
Indices: 18643976--18644023 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
18643966 GTTTAAGATT
* *
18643976 TTTTAAGGTTTAGGAGTTTAGTG
1 TTTTAAGGATTA-GAGATTAGTG
*
18643999 TTTTAAGGATTATAGATTAGTG
1 TTTTAAGGATTAGAGATTAGTG
18644021 TTT
1 TTT
18644024 ATGATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (22 bp):
TTTTAAGGATTAGAGATTAGTG
Found at i:18644175 original size:41 final size:41
Alignment explanation
Indices: 18644065--18644240 Score: 282
Period size: 41 Copynumber: 4.3 Consensus size: 41
18644055 GTTATATGAC
*
18644065 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGTTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
18644106 TTTTAGCGGCGTTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCG-TTTTACCAAAAGCGCCGCTAATGCTCTGGT
*
18644148 TTTTAGCAGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
* * * *
18644189 TTTTAGCGGTGTTTTACCAAAAACGCCGCTATTGCTCT-AT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
18644229 TTTTAGCGGCGT
1 TTTTAGCGGCGT
18644241 CAAAAACGCC
Statistics
Matches: 126, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
40 12 0.10
41 75 0.60
42 39 0.31
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.35
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:18645267 original size:31 final size:31
Alignment explanation
Indices: 18645222--18645301 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
18645212 AACTATTGGT
*
18645222 AATTTTT-TT-TTTGGTCACCCAACTACTTG
1 AATTTTTCTTCTTTGGTCACCCAAATACTTG
* * *
18645251 ACTTTTTCTTCTTTGGTCGCCCAAATATTTG
1 AATTTTTCTTCTTTGGTCACCCAAATACTTG
*
18645282 AAGTTTTC-TCTTTTGGTCAC
1 AATTTTTCTTC-TTTGGTCAC
18645302 TGACCGTTAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
29 6 0.15
30 4 0.10
31 31 0.76
ACGTcount: A:0.17, C:0.21, G:0.12, T:0.49
Consensus pattern (31 bp):
AATTTTTCTTCTTTGGTCACCCAAATACTTG
Found at i:18647883 original size:37 final size:38
Alignment explanation
Indices: 18647833--18647911 Score: 142
Period size: 37 Copynumber: 2.1 Consensus size: 38
18647823 TTCATCAGAA
18647833 GAAAGAATTATGGGGAGGAAGAGAGTGAAATTA-TTTT
1 GAAAGAATTATGGGGAGGAAGAGAGTGAAATTATTTTT
*
18647870 GAAAGAATTATGGGGAGGAAGAGAGTGTAATTATTTTT
1 GAAAGAATTATGGGGAGGAAGAGAGTGAAATTATTTTT
18647908 GAAA
1 GAAA
18647912 AGTTTCAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 32 0.80
38 8 0.20
ACGTcount: A:0.41, C:0.00, G:0.32, T:0.28
Consensus pattern (38 bp):
GAAAGAATTATGGGGAGGAAGAGAGTGAAATTATTTTT
Found at i:18653419 original size:25 final size:25
Alignment explanation
Indices: 18653391--18653440 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
18653381 AAAAATCATG
18653391 TATT-ATTAATTTTAAAAATAATTTA
1 TATTAATTAATTTTAAAAAT-ATTTA
*
18653416 TATTAATTATTTTTAAAAATATTTA
1 TATTAATTAATTTTAAAAATATTTA
18653441 AAATGTACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TATTAATTAATTTTAAAAATATTTA
Found at i:18656196 original size:8 final size:9
Alignment explanation
Indices: 18656173--18656214 Score: 52
Period size: 8 Copynumber: 4.8 Consensus size: 9
18656163 TTCAGATATG
18656173 ATTTTAAAT
1 ATTTTAAAT
18656182 GATTTTAAA-
1 -ATTTTAAAT
18656191 ATTTTAAA-
1 ATTTTAAAT
*
18656199 ATTATAAAT
1 ATTTTAAAT
18656208 ATTTTAA
1 ATTTTAA
18656215 TTTTGAATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
8 15 0.52
9 6 0.21
10 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (9 bp):
ATTTTAAAT
Found at i:18658854 original size:29 final size:29
Alignment explanation
Indices: 18658812--18658868 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
18658802 TATCGTCCCA
18658812 ACGGATTATTGACCGCCTCCCGACATACG
1 ACGGATTATTGACCGCCTCCCGACATACG
18658841 ACGGATTATTGACCGCCTCCCGACATAC
1 ACGGATTATTGACCGCCTCCCGACATAC
18658869 CAATGTCGGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.35, G:0.19, T:0.21
Consensus pattern (29 bp):
ACGGATTATTGACCGCCTCCCGACATACG
Found at i:18660113 original size:132 final size:131
Alignment explanation
Indices: 18659866--18660136 Score: 463
Period size: 132 Copynumber: 2.1 Consensus size: 131
18659856 TCTGAGCAAG
* * *
18659866 TATTTATAGATTACATGTATTATGATCTAACTAAATTCTTGAAATAAAAGTACTAAATTGCAAAT
1 TATTTATAGATTACATGTATTATGACCTAACTAAATTATAGAAATAAAAGTACTAAATTGCAAAT
* *
18659931 TTGTGAAGAGTACATAGACTTATGATATATTTTTAACCTTTATACTCAAAACATTTATTATTAAT
66 TTGTGAAGAGTACATAGACTTATGACATATTTTTAACATTTATACTCAAAACATTTATTATTAAT
18659996 A
131 A
18659997 TATTTATAGATTACATGTATTATGACCTAACTAAATTATAGAAAATAAAAGTACTAAATTGCAAA
1 TATTTATAGATTACATGTATTATGACCTAACTAAATTATAG-AAATAAAAGTACTAAATTGCAAA
*
18660062 TTTGTGAAGAGTACATAGACTTATGACATA-TTTTAACATTTATCCTACAAAACATTTATTATTA
65 TTTGTGAAGAGTACATAGACTTATGACATATTTTTAACATTTATACT-CAAAACATTTATTATTA
18660126 ATA
129 ATA
18660129 TATTTATA
1 TATTTATA
18660137 ATTGTAATAA
Statistics
Matches: 132, Mismatches: 6, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
131 52 0.39
132 80 0.61
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (131 bp):
TATTTATAGATTACATGTATTATGACCTAACTAAATTATAGAAATAAAAGTACTAAATTGCAAAT
TTGTGAAGAGTACATAGACTTATGACATATTTTTAACATTTATACTCAAAACATTTATTATTAAT
A
Found at i:18660402 original size:36 final size:39
Alignment explanation
Indices: 18660328--18660402 Score: 95
Period size: 36 Copynumber: 2.0 Consensus size: 39
18660318 AATATGTATG
*
18660328 TTTAATAATATTGAAAAATATAATATTTTATATTAATAT
1 TTTAATAATATTGAAAAATATAATATTTTATATCAATAT
*
18660367 TTTAATAAT-TTTAAAAATA-AA-A-TTTATTATCAATAT
1 TTTAATAATATTGAAAAATATAATATTTTA-TATCAATAT
18660403 AATAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
35 4 0.12
36 9 0.27
37 2 0.06
38 9 0.27
39 9 0.27
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (39 bp):
TTTAATAATATTGAAAAATATAATATTTTATATCAATAT
Found at i:18663352 original size:2 final size:2
Alignment explanation
Indices: 18663335--18663367 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
18663325 ACCTATGTTC
*
18663335 AT AT -T AT AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18663368 TATTTAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
AT
Found at i:18667084 original size:5 final size:5
Alignment explanation
Indices: 18667066--18667159 Score: 138
Period size: 5 Copynumber: 19.2 Consensus size: 5
18667056 ATAAAATATA
* * * *
18667066 ATTAT A-TA- ATTAT ATTAT ATTGT ATTGT ATTGT ATTGT ATTAT ATTAT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT
18667114 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
18667160 ATTAAAGAAT
Statistics
Matches: 85, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
3 1 0.01
4 4 0.05
5 80 0.94
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (5 bp):
ATTAT
Found at i:18667248 original size:26 final size:25
Alignment explanation
Indices: 18667183--18667254 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 25
18667173 AGAAAAAAAT
* *
18667183 AGAAAAAAAAAGG-GAAAGAAACAA
1 AGAAAAAGAAAGGAGAAAGAAAGAA
* *
18667207 AG-AAACGAAACAGAGAAAGAATAGAA
1 AGAAAAAGAAA-GGAGAAAGAA-AGAA
*
18667233 AGAAAAAGAAAGGAGAACGAAA
1 AGAAAAAGAAAGGAGAAAGAAA
18667255 AGAAGGAGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
23 6 0.16
24 3 0.08
25 8 0.22
26 13 0.35
27 7 0.19
ACGTcount: A:0.69, C:0.06, G:0.24, T:0.01
Consensus pattern (25 bp):
AGAAAAAGAAAGGAGAAAGAAAGAA
Found at i:18667249 original size:17 final size:17
Alignment explanation
Indices: 18667183--18667264 Score: 50
Period size: 15 Copynumber: 5.0 Consensus size: 17
18667173 AGAAAAAAAT
*
18667183 AGAAAAAAAAAGG-GAA
1 AGAAAAAGAAAGGAGAA
*
18667199 AGAAACAAAGAAACGA-AA
1 AG-AA-AAAGAAAGGAGAA
* *
18667217 CAGAGAAAG-AA-TAGAA
1 -AGAAAAAGAAAGGAGAA
18667233 AGAAAAAGAAAGGAGAA
1 AGAAAAAGAAAGGAGAA
*
18667250 CG-AAAAG-AAGGAGAA
1 AGAAAAAGAAAGGAGAA
18667265 TTAAAGATTT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
15 16 0.31
16 13 0.25
17 11 0.21
18 10 0.19
19 2 0.04
ACGTcount: A:0.68, C:0.05, G:0.26, T:0.01
Consensus pattern (17 bp):
AGAAAAAGAAAGGAGAA
Found at i:18670020 original size:55 final size:54
Alignment explanation
Indices: 18669920--18670040 Score: 143
Period size: 55 Copynumber: 2.2 Consensus size: 54
18669910 CCCGTGTGGG
* * * **
18669920 CCCACACGGCCCAAAATAGCCTTGGCTGTGCGGATTACACGGCCTGGCTTAGAAT
1 CCCACAC-GCCCAAAATAGCCTTGGCTGTGCGAATCACACAGCCTGGCCCAGAAT
* * * *
18669975 CCCACATGCCCTAAAATGGCCTTGGTTGTGTGAATCACACAGCCTGGCCCAGAAT
1 CCCACACGCCC-AAAATAGCCTTGGCTGTGCGAATCACACAGCCTGGCCCAGAAT
18670030 CCCACACGCCC
1 CCCACACGCCC
18670041 GTGTGGTTCA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
54 4 0.07
55 51 0.93
ACGTcount: A:0.24, C:0.35, G:0.22, T:0.19
Consensus pattern (54 bp):
CCCACACGCCCAAAATAGCCTTGGCTGTGCGAATCACACAGCCTGGCCCAGAAT
Found at i:18673725 original size:31 final size:31
Alignment explanation
Indices: 18673690--18673751 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
18673680 TGAATTTGAA
18673690 AGAAAATAATGGAAGAATTTTGTTTTCTTTC
1 AGAAAATAATGGAAGAATTTTGTTTTCTTTC
18673721 AGAAAATAATGGAAGAATTTTGTTTTCTTTC
1 AGAAAATAATGGAAGAATTTTGTTTTCTTTC
18673752 TTTCACCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.06, G:0.16, T:0.42
Consensus pattern (31 bp):
AGAAAATAATGGAAGAATTTTGTTTTCTTTC
Found at i:18678784 original size:21 final size:22
Alignment explanation
Indices: 18678737--18678787 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
18678727 ATTTATACTT
18678737 TTTTATATTTACTTTTTAAAGAA
1 TTTTATATTTAC-TTTTAAAGAA
*
18678760 -TTTATATTTA-TTTTAAATAA
1 TTTTATATTTACTTTTAAAGAA
18678780 TTTTATAT
1 TTTTATAT
18678788 CTTTGCTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 9 0.35
21 7 0.27
22 10 0.38
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (22 bp):
TTTTATATTTACTTTTAAAGAA
Found at i:18680240 original size:13 final size:13
Alignment explanation
Indices: 18680222--18680256 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
18680212 CAAAAACAAC
18680222 TTAATAAGCTTAA
1 TTAATAAGCTTAA
18680235 TTAAT-AGACTTAA
1 TTAATAAG-CTTAA
18680248 TTAATAAGC
1 TTAATAAGC
18680257 ACATTTAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 2 0.10
13 16 0.80
14 2 0.10
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (13 bp):
TTAATAAGCTTAA
Done.