Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 141 of 213
Found at i:42149022 original size:27 final size:27
Alignment explanation
Indices: 42148990--42149044 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
42148980 GTTTATAAAT
*
42148990 TTTTAAAATTTATATTTTAATGTGTAA
1 TTTTAAAATTTATATTTTAATGTATAA
* *
42149017 TTTTAAATTTTATGTTTTAATGTATAA
1 TTTTAAAATTTATATTTTAATGTATAA
42149044 T
1 T
42149045 GATTGAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTTAAAATTTATATTTTAATGTATAA
Found at i:42149248 original size:13 final size:12
Alignment explanation
Indices: 42149210--42149241 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
42149200 CCGCATGTAT
42149210 TAATTTTTTATA
1 TAATTTTTTATA
*
42149222 TTATTTTTTATA
1 TAATTTTTTATA
42149234 TAATTTTT
1 TAATTTTT
42149242 AAATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
TAATTTTTTATA
Found at i:42149502 original size:11 final size:11
Alignment explanation
Indices: 42149463--42149503 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
42149453 ACAATAACAA
42149463 CAAAATAGTAG
1 CAAAATAGTAG
* *
42149474 CAACATAATAG
1 CAAAATAGTAG
*
42149485 TAAAATAGTAG
1 CAAAATAGTAG
42149496 CAAAATAG
1 CAAAATAG
42149504 AGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:42149511 original size:22 final size:22
Alignment explanation
Indices: 42149464--42149511 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
42149454 CAATAACAAC
* *
42149464 AAAATAGTAGCAACATAATAGT
1 AAAATAGTAGCAAAATAAGAGT
42149486 AAAATAGTAGCAAAATAGAGAG-
1 AAAATAGTAGCAAAATA-AGAGT
42149508 AAAA
1 AAAA
42149512 CAAATAAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 20 0.87
23 3 0.13
ACGTcount: A:0.60, C:0.06, G:0.17, T:0.17
Consensus pattern (22 bp):
AAAATAGTAGCAAAATAAGAGT
Found at i:42150077 original size:40 final size:40
Alignment explanation
Indices: 42149989--42150114 Score: 96
Period size: 40 Copynumber: 3.1 Consensus size: 40
42149979 ATTTTCCGCG
* ** * *
42149989 AAATCGCGTCCACATCAGCGCGATGTCAGGGTACGT-GTCAGG
1 AAATCGCGTCCACATCAGCGCGAT-T-TGCTTACGTGGACA-C
*
42150031 ACATCGCGTCCACATCAGCGCGATTTGCTTACGTGGACAC
1 AAATCGCGTCCACATCAGCGCGATTTGCTTACGTGGACAC
* ** *
42150071 AAATCGC-ACCTACGAGGA-CGCGATTTGCTTAAGTGGACAC
1 AAATCGCGTCC-AC-ATCAGCGCGATTTGCTTACGTGGACAC
42150111 AAAT
1 AAAT
42150115 AGCGCCTACG
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
39 2 0.03
40 39 0.56
41 6 0.09
42 23 0.33
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.21
Consensus pattern (40 bp):
AAATCGCGTCCACATCAGCGCGATTTGCTTACGTGGACAC
Found at i:42150147 original size:40 final size:40
Alignment explanation
Indices: 42150049--42150147 Score: 162
Period size: 40 Copynumber: 2.5 Consensus size: 40
42150039 TCCACATCAG
*
42150049 CGCGATTTGCTTACGTGGACACAAATCGCACCTACGAGGA
1 CGCGATTTGCTTACGTGGACACAAATAGCACCTACGAGGA
* *
42150089 CGCGATTTGCTTAAGTGGACACAAATAGCGCCTACGAGGA
1 CGCGATTTGCTTACGTGGACACAAATAGCACCTACGAGGA
*
42150129 CGCGATTTGCTGACGTGGA
1 CGCGATTTGCTTACGTGGA
42150148 TGAACAGTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 54 1.00
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.21
Consensus pattern (40 bp):
CGCGATTTGCTTACGTGGACACAAATAGCACCTACGAGGA
Found at i:42162664 original size:12 final size:12
Alignment explanation
Indices: 42162647--42162685 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
42162637 CGCCTTAGCA
*
42162647 CCTAGGCGCTCG
1 CCTAGGCGCTTG
42162659 CCTAGGCGCTTG
1 CCTAGGCGCTTG
42162671 CCTAGGCGCTTG
1 CCTAGGCGCTTG
42162683 CCT
1 CCT
42162686 TGACATCACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.08, C:0.38, G:0.31, T:0.23
Consensus pattern (12 bp):
CCTAGGCGCTTG
Found at i:42170346 original size:25 final size:26
Alignment explanation
Indices: 42170297--42170347 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
42170287 AGGTATAATT
**
42170297 ACGTTTATATATTTCACTCTTAATTTC
1 ACGTTTATATATAGCACTC-TAATTTC
42170324 ACGTTTATATATAGCACTC-AATTT
1 ACGTTTATATATAGCACTCTAATTT
42170348 TTTCACTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
27 17 0.77
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (26 bp):
ACGTTTATATATAGCACTCTAATTTC
Found at i:42172306 original size:7 final size:7
Alignment explanation
Indices: 42172296--42172324 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
42172286 ATTATATAAT
42172296 GTGCATG
1 GTGCATG
42172303 GTGCATG
1 GTGCATG
42172310 GTGCATG
1 GTGCATG
42172317 GTGCATG
1 GTGCATG
42172324 G
1 G
42172325 AAACATGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.45, T:0.28
Consensus pattern (7 bp):
GTGCATG
Found at i:42173677 original size:187 final size:186
Alignment explanation
Indices: 42173342--42173690 Score: 531
Period size: 187 Copynumber: 1.9 Consensus size: 186
42173332 AACGCAGAGT
*
42173342 TTGGTCTTAAGGTACACTAGCATTAGTGGCGCTTATACGAAAACGCCGCTAAAGCATAGTATTAG
1 TTGGTCTTAAGGTACACTAACATTAGTGGCGCTTATACGAAAACGCCGCTAAAGCATAGTATTAG
* *
42173407 CGGCGAGTAGAGAAAGCGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTATAT
66 CGGCGAGTAGAGAAAACGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACAT
*
42173472 TAGGATTAGTGGCGCTTAT-TGGAAAACACCGCAAAATATTAACCAAAACGTGCGCA
131 TACGATTAGTGGCGCTTATAT-GAAAACACCGCAAAATATTAACCAAAACGTGCGCA
* * * * * *
42173528 TTGGTCTTAATGTATAGTAACATTAGTGGCGCTTATGCTAAAACGCCGCTAAAGTATAGTATTAG
1 TTGGTCTTAAGGTACACTAACATTAGTGGCGCTTATACGAAAACGCCGCTAAAGCATAGTATTAG
* * *
42173593 CGGCGAGTACTTA-AAAACGCCGCAATCTTTCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTAC
66 CGGCGAGTA--GAGAAAACGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTAC
*
42173657 ATTACGATTAGTGGCGCTTATATGAAAACGCCGC
129 ATTACGATTAGTGGCGCTTATATGAAAACACCGC
42173691 TAAAGCATAG
Statistics
Matches: 146, Mismatches: 14, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
186 67 0.46
187 77 0.53
188 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.27
Consensus pattern (186 bp):
TTGGTCTTAAGGTACACTAACATTAGTGGCGCTTATACGAAAACGCCGCTAAAGCATAGTATTAG
CGGCGAGTAGAGAAAACGCCGCAATATTTCTTAACCAAAACGCAGAGTTTGGTCTTGAGGTACAT
TACGATTAGTGGCGCTTATATGAAAACACCGCAAAATATTAACCAAAACGTGCGCA
Found at i:42173821 original size:73 final size:74
Alignment explanation
Indices: 42173709--42173862 Score: 202
Period size: 73 Copynumber: 2.1 Consensus size: 74
42173699 AGTATTAGCA
* * * *
42173709 GCGCGTATTGTAAAGTGCCACAAAATATGAACCAAAACGCAGAG-TTTGGTCTTGCGGTATACTA
1 GCGCTTATTGGAAAATGCCACAAAATATGAACCAAAACGCAGAGCTTTGGTCTTGAGGTATACTA
*
42173773 GGATTAGTG
66 GCATTAGTG
* * * * * *
42173782 GCGCTTATTGGAAAATGCCGCAAAATATTAACCAAAACGCTGCGCTTTGGTCTTGATGTATAGTA
1 GCGCTTATTGGAAAATGCCACAAAATATGAACCAAAACGCAGAGCTTTGGTCTTGAGGTATACTA
42173847 GCATTAGTG
66 GCATTAGTG
42173856 GCGCTTA
1 GCGCTTA
42173863 AGCTAAAATG
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
73 37 0.54
74 32 0.46
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (74 bp):
GCGCTTATTGGAAAATGCCACAAAATATGAACCAAAACGCAGAGCTTTGGTCTTGAGGTATACTA
GCATTAGTG
Found at i:42173834 original size:300 final size:298
Alignment explanation
Indices: 42173322--42174108 Score: 1157
Period size: 300 Copynumber: 2.6 Consensus size: 298
42173312 CCGCAATACA
* * * * *
42173322 TCTTAACGAAAACGCAGAGTTTGGTCTTAAGGTACACTAGCATTAGTGGCGCTTATACGAAAACG
1 TCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTAG-ATTAGTGGCGCTTATATGAAAACG
* ** * *
42173387 CCGCTAAAGCATAGTATTAGCGGCGAGTAGAG-AAAGCGCCGCAATATTTCTTAACCAAAACGCA
65 CCGCTAAAGCATAGTATTAGCGGCGCGTATTGTAAAGCGCCGCAA-A-ATATTAACCAAAACGCA
* *
42173451 GAGTTTGGTCTTGAGGTATATTAGGATTAGTGGCGCTTATTGGAAAACACCGCAAAATATTAACC
128 GAGTTTGGTCTTGAGGTATACTAGGATTAGTGGCGCTTATTGGAAAACGCCGCAAAATATTAACC
*
42173516 AAAACGTGCGCATTGGTCTTAATGTATAGTAACATTAGTGGCGCTTATGCTAAAACGCCGCTAAA
193 AAAACGTGCGCATTGGTCTTAATGTATAGTAACATTAGTGGCGCTTAAGCTAAAACGCCGCTAAA
* * * *
42173581 GTATAGTATTAGCGGCGAGTACTTAAAAACGCCGCAATCTT
258 GTATAGTATTAGCAGCGAGTACTGAAAAACACAGCAATCTT
42173622 TCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTACGATTAGTGGCGCTTATATGAAAACG
1 TCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTA-GATTAGTGGCGCTTATATGAAAACG
* * * *
42173687 CCGCTAAAGCATAGTATTAGCAGCGCGTATTGTAAAGTGCCACAAAATATGAACCAAAACGCAGA
65 CCGCTAAAGCATAGTATTAGCGGCGCGTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGA
* *
42173752 GTTTGGTCTTGCGGTATACTAGGATTAGTGGCGCTTATTGGAAAATGCCGCAAAATATTAACCAA
130 GTTTGGTCTTGAGGTATACTAGGATTAGTGGCGCTTATTGGAAAACGCCGCAAAATATTAACCAA
* * * *
42173817 AACGCTGCGCTTTGGTCTTGATGTATAGTAGCATTAGTGGCGCTTAAGCTAAAATGCCGCTAAAG
195 AACG-TGCGCATTGGTCTTAATGTATAGTAACATTAGTGGCGCTTAAGCTAAAACGCCGCTAAAG
*
42173882 TATAGTATTAGCAGCGAGTACTGAAAAGCACAGCAATCTT
259 TATAGTATTAGCAGCGAGTACTGAAAAACACAGCAATCTT
*
42173922 TCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTAGGATTAGTGGCGCTTATTTGAAAACG
1 TCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTA-GATTAGTGGCGCTTATATGAAAACG
* * *
42173987 CCGCTAAAGCAAAGTATTAGCGGCACGTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGC
65 CCGCTAAAGCATAGTATTAGCGGCGCGTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGA
* *
42174052 GCTTTGGTCTTGATGTATACTAGCAGTT-GTGGCGCTTA-TGGTAAAACGCCGCTAAAA
130 G-TTTGGTCTTGAGGTATACTAGGA-TTAGTGGCGCTTATTGG-AAAACGCCGC-AAAA
42174109 CATATTATTA
Statistics
Matches: 439, Mismatches: 41, Indels: 12
0.89 0.08 0.02
Matches are distributed among these distances:
299 81 0.18
300 302 0.69
301 50 0.11
302 6 0.01
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.26
Consensus pattern (298 bp):
TCTTAACCAAAACGCAGAGTTTGGTGTTGAGGTACATTAGATTAGTGGCGCTTATATGAAAACGC
CGCTAAAGCATAGTATTAGCGGCGCGTATTGTAAAGCGCCGCAAAATATTAACCAAAACGCAGAG
TTTGGTCTTGAGGTATACTAGGATTAGTGGCGCTTATTGGAAAACGCCGCAAAATATTAACCAAA
ACGTGCGCATTGGTCTTAATGTATAGTAACATTAGTGGCGCTTAAGCTAAAACGCCGCTAAAGTA
TAGTATTAGCAGCGAGTACTGAAAAACACAGCAATCTT
Found at i:42173871 original size:74 final size:73
Alignment explanation
Indices: 42173709--42173876 Score: 194
Period size: 74 Copynumber: 2.3 Consensus size: 73
42173699 AGTATTAGCA
* * * * *
42173709 GCGCGTATTGTAAAGTGCCACAAAATATGAACCAAAACGCAGAGTTTGGTCTTGCGGTATACTAG
1 GCGCTTATAGTAAAATGCCGCAAAATATGAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAG
*
42173774 GATTAGTG
66 CATTAGTG
* * * * * * *
42173782 GCGCTTATTGGAAAATGCCGCAAAATATTAACCAAAACGCTGCGCTTTGGTCTTGATGTATAGTA
1 GCGCTTATAGTAAAATGCCGCAAAATATGAACCAAAACGCAGAG-TTTGGTCTTGAGGTATACTA
42173847 GCATTAGTG
65 GCATTAGTG
42173856 GCGCTTA-AGCTAAAATGCCGC
1 GCGCTTATAG-TAAAATGCCGC
42173877 TAAAGTATAG
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
73 38 0.47
74 42 0.52
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (73 bp):
GCGCTTATAGTAAAATGCCGCAAAATATGAACCAAAACGCAGAGTTTGGTCTTGAGGTATACTAG
CATTAGTG
Found at i:42174100 original size:113 final size:113
Alignment explanation
Indices: 42173798--42174124 Score: 365
Period size: 114 Copynumber: 2.9 Consensus size: 113
42173788 ATTGGAAAAT
* *
42173798 GCCGCAAAATATTAACCAAAACGCTGCGCTTTGGTCTTGATGTATAGTAGCATTAGTGGCGCTTA
1 GCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGCATTAGTGGCGCTTA
* * * *
42173863 AGCTAAAATGCCGCTAAAGTATAGTATTAGCAGCGAGTACTGAAAAGC
66 TGCTAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTACTGAAAAGC
* * ** * * * * * * *
42173911 ACAGCAATCTTTCTTAACCAAAACGCAGAG-TTTGGTGTTGAGGTACATTAGGATTAGTGGCGCT
1 GCCGCAA--AATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGCATTAGTGGCGCT
* * * *
42173975 TAT-TTGAAAACGCCGCTAAAGCAAAGTATTAGCGGC-ACGTATTGTAAAGC
64 TATGCT-AAAACGCCGCTAAAGCATAGTATTAGCGGCGA-GTACTGAAAAGC
42174025 GCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGCAGTT-GTGGCGCTT
1 GCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGCA-TTAGTGGCGCTT
* * *
42174089 ATGGTAAAACGCCGCTAAAACATATTATTAGCGGCG
65 ATGCTAAAACGCCGCTAAAGCATAGTATTAGCGGCG
42174125 CGTTGTGGAA
Statistics
Matches: 171, Mismatches: 35, Indels: 15
0.77 0.16 0.07
Matches are distributed among these distances:
112 17 0.10
113 63 0.37
114 75 0.44
115 16 0.09
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.26
Consensus pattern (113 bp):
GCCGCAAAATATTAACCAAAACGCAGCGCTTTGGTCTTGATGTATACTAGCATTAGTGGCGCTTA
TGCTAAAACGCCGCTAAAGCATAGTATTAGCGGCGAGTACTGAAAAGC
Found at i:42174180 original size:16 final size:17
Alignment explanation
Indices: 42174146--42174220 Score: 127
Period size: 16 Copynumber: 4.5 Consensus size: 17
42174136 CACCGCTAGA
42174146 TTATTATATAATGTAGT
1 TTATTATATAATGTAGT
*
42174163 TTATTATAT-ATTTAGT
1 TTATTATATAATGTAGT
42174179 TTATTATAT-ATGTAGT
1 TTATTATATAATGTAGT
42174195 TTATTATATAATGTAGT
1 TTATTATATAATGTAGT
42174212 TTATTATAT
1 TTATTATAT
42174221 TATATAATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
16 30 0.55
17 25 0.45
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.57
Consensus pattern (17 bp):
TTATTATATAATGTAGT
Found at i:42174183 original size:33 final size:33
Alignment explanation
Indices: 42174146--42174220 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
42174136 CACCGCTAGA
*
42174146 TTATTATATAATGTAGTTTATTATAT-ATTTAGT
1 TTATTATAT-ATGTAGTTTATTATATAATGTAGT
42174179 TTATTATATATGTAGTTTATTATATAATGTAGT
1 TTATTATATATGTAGTTTATTATATAATGTAGT
42174212 TTATTATAT
1 TTATTATAT
42174221 TATATAATTT
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
32 16 0.40
33 24 0.60
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.57
Consensus pattern (33 bp):
TTATTATATATGTAGTTTATTATATAATGTAGT
Found at i:42176349 original size:3 final size:3
Alignment explanation
Indices: 42176341--42176366 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
42176331 CCATTGTTAA
42176341 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
42176367 CACTACATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:42177382 original size:24 final size:24
Alignment explanation
Indices: 42177355--42177401 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
42177345 AGACAACTTA
* *
42177355 CATAATACATAGCATACATAACTG
1 CATAATACAAAACATACATAACTG
*
42177379 CATAATACAAAACTTACATAACT
1 CATAATACAAAACATACATAACT
42177402 TAAATATCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.26
Consensus pattern (24 bp):
CATAATACAAAACATACATAACTG
Found at i:42177401 original size:9 final size:9
Alignment explanation
Indices: 42177349--42177752 Score: 308
Period size: 9 Copynumber: 46.0 Consensus size: 9
42177339 TATCTTAGAC
42177349 AACTTACAT
1 AACTTACAT
42177358 AA--TACAT
1 AACTTACAT
* *
42177365 AGCATACAT
1 AACTTACAT
*
42177374 AAC-TGCAT
1 AACTTACAT
*
42177382 AA--TACAA
1 AACTTACAT
42177389 AACTTACAT
1 AACTTACAT
*
42177398 AACTTAAAT
1 AACTTACAT
* *
42177407 ATCTTACAC
1 AACTTACAT
42177416 AACTTACAT
1 AACTTACAT
*
42177425 AACCTACAT
1 AACTTACAT
**
42177434 AA-TATATTT
1 AACT-TACAT
42177443 AACTTACAT
1 AACTTACAT
42177452 AACTTACAT
1 AACTTACAT
42177461 AACTTACAT
1 AACTTACAT
*
42177470 AA--TACAA
1 AACTTACAT
42177477 AACTTACAT
1 AACTTACAT
*
42177486 AACTTAAAT
1 AACTTACAT
* *
42177495 ATCTTACAC
1 AACTTACAT
42177504 AACTTACAT
1 AACTTACAT
*
42177513 AACCTACAT
1 AACTTACAT
42177522 AA--TACATTT
1 AACTTACA--T
42177531 AACTTACAT
1 AACTTACAT
*
42177540 AACTTACGT
1 AACTTACAT
42177549 AACTTACAT
1 AACTTACAT
*
42177558 AA--TACAA
1 AACTTACAT
42177565 AAC-TACAT
1 AACTTACAT
*
42177573 AACTTAAAT
1 AACTTACAT
* *
42177582 ATCTTACAC
1 AACTTACAT
42177591 AACTTACAT
1 AACTTACAT
*
42177600 AACCTACAT
1 AACTTACAT
42177609 AA--TACATTT
1 AACTTACA--T
42177618 AACTTACAT
1 AACTTACAT
42177627 AACTTACAT
1 AACTTACAT
*
42177636 AA--TACAA
1 AACTTACAT
42177643 AACTTACAT
1 AACTTACAT
*
42177652 AACTTAAAT
1 AACTTACAT
* *
42177661 ATCTTACAC
1 AACTTACAT
42177670 AACTTACAT
1 AACTTACAT
*
42177679 AACCTACAT
1 AACTTACAT
42177688 AA--TACATTT
1 AACTTACA--T
*
42177697 AACTTATAT
1 AACTTACAT
*
42177706 AACTTATAT
1 AACTTACAT
42177715 AACTTACAT
1 AACTTACAT
*
42177724 AA-TAACTTAT
1 AACTTAC--AT
*
42177734 ACACGTACAT
1 A-ACTTACAT
42177744 AACTTACAT
1 AACTTACAT
42177753 TTAACTTACC
Statistics
Matches: 314, Mismatches: 53, Indels: 56
0.74 0.13 0.13
Matches are distributed among these distances:
7 41 0.13
8 16 0.05
9 236 0.75
10 7 0.02
11 12 0.04
12 2 0.01
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:42177477 original size:88 final size:88
Alignment explanation
Indices: 42177360--42177727 Score: 596
Period size: 88 Copynumber: 4.3 Consensus size: 88
42177350 ACTTACATAA
* * *
42177360 TACATAGCATACATAAC-TGCATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
1 TACATAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
*
42177424 TAACCTACATAATATATTTAACT
66 TAACCTACATAATACATTTAACT
42177447 TACATAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
1 TACATAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
42177512 TAACCTACATAATACATTTAACT
66 TAACCTACATAATACATTTAACT
*
42177535 TACATAACTTACGTAACTTACATAATACAAAAC-TACATAACTTAAATATCTTACACAACTTACA
1 TACATAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
42177599 TAACCTACATAATAC-----A-T
66 TAACCTACATAATACATTTAACT
42177616 T---TAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
1 TACATAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
42177678 TAACCTACATAATACATTTAACT
66 TAACCTACATAATACATTTAACT
* *
42177701 TATATAACTTATATAACTTACATAATA
1 TACATAACTTACATAACTTACATAATA
42177728 ACTTATACAC
Statistics
Matches: 263, Mismatches: 7, Indels: 21
0.90 0.02 0.07
Matches are distributed among these distances:
78 28 0.11
79 46 0.17
81 2 0.01
82 1 0.00
84 1 0.00
85 2 0.01
87 61 0.23
88 122 0.46
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (88 bp):
TACATAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
TAACCTACATAATACATTTAACT
Found at i:42177645 original size:166 final size:172
Alignment explanation
Indices: 42177360--42177727 Score: 588
Period size: 166 Copynumber: 2.2 Consensus size: 172
42177350 ACTTACATAA
* * *
42177360 TACATAGCATACATAAC-TGCATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
1 TACATAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
42177424 TAACCTACATAATATATTTAACTTACATAACTTACATAACTTACATAATACAAAACTTACATAAC
66 TAACCTACATAATATA--TAACTT--ATAACTTACATAACTTACATAATACAAAACTTACATAAC
42177489 TTAAATATCTTACACAACTTACATAACCTACATAATACATTTAACT
127 TTAAATATCTTACACAACTTACATAACCTACATAATACATTTAACT
*
42177535 TACATAACTTACGTAACTTACATAATACAAAAC-TACATAACTTAAATATCTTACACAACTTACA
1 TACATAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
*
42177599 TAACCTACAT-A-ATA-CA-TT-TAACTTACATAACTTACATAATACAAAACTTACATAACTTAA
66 TAACCTACATAATATATAACTTATAACTTACATAACTTACATAATACAAAACTTACATAACTTAA
42177659 ATATCTTACACAACTTACATAACCTACATAATACATTTAACT
131 ATATCTTACACAACTTACATAACCTACATAATACATTTAACT
* *
42177701 TATATAACTTATATAACTTACATAATA
1 TACATAACTTACATAACTTACATAATA
42177728 ACTTATACAC
Statistics
Matches: 184, Mismatches: 8, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
166 108 0.59
169 2 0.01
170 1 0.01
173 3 0.02
174 1 0.01
175 55 0.30
176 14 0.08
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (172 bp):
TACATAACTTACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACA
TAACCTACATAATATATAACTTATAACTTACATAACTTACATAATACAAAACTTACATAACTTAA
ATATCTTACACAACTTACATAACCTACATAATACATTTAACT
Found at i:42183222 original size:21 final size:21
Alignment explanation
Indices: 42183196--42183266 Score: 81
Period size: 21 Copynumber: 3.4 Consensus size: 21
42183186 CTACAACTTA
*
42183196 AAGCAGAGGCGGCAGTGAGGG
1 AAGCAGAGGCTGCAGTGAGGG
*
42183217 AAGCAGCA-GTTGCAGTGAGGG
1 AAGCAG-AGGCTGCAGTGAGGG
** *
42183238 AAGCAGAGGCTGCAACGAGAG
1 AAGCAGAGGCTGCAGTGAGGG
42183259 AAGCAGAG
1 AAGCAGAG
42183267 CAGAGCAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
20 1 0.02
21 40 0.95
22 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.44, T:0.07
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGTGAGGG
Found at i:42183692 original size:42 final size:42
Alignment explanation
Indices: 42183584--42183827 Score: 296
Period size: 42 Copynumber: 5.8 Consensus size: 42
42183574 GTTTTTGTAT
* *
42183584 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTTAG-A
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* * *
42183625 AAAAACGCCGCTAAAGACCATGTTCTTTAGTGGTGCCTAGAA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* * *
42183667 AAAAACGCCGTTAAAGTCCAAGTTCTTTAGCGGCGCTTA-ATA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGA-A
* *
42183709 AAAAATGCCGCTAAAGACCTTGTTCTTTAGCGGCGCTTA-ATA
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGA-A
* * * *
42183751 AAAAATGCCGCTAAAGACCTTGTTCTTTAGAGGCGCTTAGAT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
* * *
42183793 AAAAACGCCGTTAAAGATCATGCTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCG
42183828 TTTATTATTA
Statistics
Matches: 176, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
41 36 0.20
42 139 0.79
43 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.26
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
Found at i:42183808 original size:126 final size:125
Alignment explanation
Indices: 42183584--42183869 Score: 351
Period size: 126 Copynumber: 2.3 Consensus size: 125
42183574 GTTTTTGTAT
* * * *
42183584 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTTAGAAAAAACGCCGCTAAAGACCATGTT
1 AAAAATGCCGCTAAAGACCTTGTTCTTTAGCGGCGCTTAGAAAAAACGCCGCTAAAGACCATGTT
* * *
42183649 CTTTAGTGGTGCCTAGAAAAAAACGCCGTTAAAG-TCCAAGTTCTTTAGCGGCGCTTAATA
66 CTTTAGAGGCGCCTAGAAAAAAACGCCGTTAAAGAT-CAAGCTCTTTAGCGGCGCTTAATA
* * *
42183709 AAAAATGCCGCTAAAGACCTTGTTCTTTAGCGGCGCTTAATAAAAAATGCCGCTAAAGACCTTGT
1 AAAAATGCCGCTAAAGACCTTGTTCTTTAGCGGCGCTT-AGAAAAAACGCCGCTAAAGACCATGT
* * * * *
42183774 TCTTTAGAGGCGCTTAGATAAAAACGCCGTTAAAGATCATGCTCTTTAGCGGCGTTTATTA
65 TCTTTAGAGGCGCCTAGAAAAAAACGCCGTTAAAGATCAAGCTCTTTAGCGGCGCTTAATA
** * * *
42183835 TTAAGTGCCGCTAAAGAACATGGTT-TTTAGCGGCG
1 AAAAATGCCGCTAAAG-ACCTTGTTCTTTAGCGGCG
42183870 TTTTTGTTTG
Statistics
Matches: 138, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
125 34 0.25
126 97 0.70
127 7 0.05
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (125 bp):
AAAAATGCCGCTAAAGACCTTGTTCTTTAGCGGCGCTTAGAAAAAACGCCGCTAAAGACCATGTT
CTTTAGAGGCGCCTAGAAAAAAACGCCGTTAAAGATCAAGCTCTTTAGCGGCGCTTAATA
Found at i:42183850 original size:42 final size:42
Alignment explanation
Indices: 42183584--42183869 Score: 292
Period size: 42 Copynumber: 6.8 Consensus size: 42
42183574 GTTTTTGTAT
* * * *
42183584 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGACGCTT-AGA
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAATA
* * * *
42183625 AAAAACGCCGCTAAAGACCATGTTCTTTAGTGGTGCCTAGA-A
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTA-ATA
* * * *
42183667 AAAAACGCCGTTAAAGTCCAAGTTCTTTAGCGGCGCTTAATA
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAATA
*
42183709 AAAAATGCCGCTAAAGACCTTGTTCTTTAGCGGCGCTTAATA
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAATA
* *
42183751 AAAAATGCCGCTAAAGACCTTGTTCTTTAGAGGCGCTTAGAT-
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTA-ATA
* * * * * *
42183793 AAAAACGCCGTTAAAGATCATGCTCTTTAGCGGCGTTTATTA
1 AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAATA
** * *
42183835 TTAAGTGCCGCTAAAGAACATGGTT-TTTAGCGGCG
1 AAAAATGCCGCTAAAGACCAT-GTTCTTTAGCGGCG
42183870 TTTTTGTTTG
Statistics
Matches: 207, Mismatches: 32, Indels: 11
0.83 0.13 0.04
Matches are distributed among these distances:
41 35 0.17
42 167 0.81
43 5 0.02
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (42 bp):
AAAAATGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAATA
Found at i:42190142 original size:20 final size:20
Alignment explanation
Indices: 42190117--42190159 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
42190107 ATTTTCTCGA
42190117 ATGTCCATGGCCTGACGTCC
1 ATGTCCATGGCCTGACGTCC
42190137 ATGTCCATGGCCTGACGTCC
1 ATGTCCATGGCCTGACGTCC
42190157 ATG
1 ATG
42190160 ATATAGTGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.16, C:0.33, G:0.26, T:0.26
Consensus pattern (20 bp):
ATGTCCATGGCCTGACGTCC
Found at i:42191777 original size:390 final size:391
Alignment explanation
Indices: 42191058--42191820 Score: 1048
Period size: 390 Copynumber: 2.0 Consensus size: 391
42191048 TAACTAATCC
** * * *
42191058 TGAGCATCCCTGGGACTCTCACTCGATCTTGCTATTTCTTTGACTTTTCCCTTGACGATCGACCT
1 TGAGCATCCCCAGGACTCTCACTCGATCTTGCTATTCCTTTGAATTTGCCCTTGACGATCGACCT
* * * * * * * *
42191123 TTTGTAAGATAATTTGAGTTGGTCGCTTAGTTTACGGATGATGGAGGCCCCCGTGGATGGTTGTG
66 TTTATAAGACAATCTGAGCTGATCGCTCAGTTTACGAATGAAGGAGGCCCCCGTGGATGGTTGTG
* * * * *
42191188 CGAGCACGAACATATCTTATAGATCATCGTGATAGGGCTCAAAGTTGTCATCCTTCGTAGCCTCG
131 CGAGCACAAACACATCTTATAGATAATCGTGATAGGGCTCAAAGTCGTCATCCTTCGTAGCCTCA
* * ** *
42191253 TCATCCTCCTCCTCTCCTGCTTCATATTCTTTCTATTCCTCCTAGGATACGTTTTCCTCAGATGA
196 TCATCCTCCTCCTCTCCTACTTCATATTCTTTCTATTCCTCCTAGGATACATTGCCCTCAGATAA
42191318 ATCACTCAATTTGTCAGGCCATTGTATGCTTTCTGCCCCCTGACTCGCCATAAATGTGTCACACC
261 ATCACTCAATTTGTCAGGCCATTGTATGCTTTCTGCCCCCTGACTCGCCATAAATGTGTCACACC
*
42191383 CCAACATCAGCGGATCCGA-GAAAAAGGGTAACTAGGCATG-ATGTTACCTATTTTAACTTTTCC
326 CCAACATCAACGGATCCGAGGAAAAA-GGTAACTAGGCATGCATGTTACCTATTTTAACTTTTCC
42191446 CT
390 CT
* *
42191448 TGAGCATCCCCAGGACTCTCACTTGATCTTGTTATTCCTTTGAATTTGCCCTTGACGATCGACCT
1 TGAGCATCCCCAGGACTCTCACTCGATCTTGCTATTCCTTTGAATTTGCCCTTGACGATCGACCT
*
42191513 TTTATAAGACAGTCTGAGCTGATCGCTCAGTTTACGAATGACAGG-GGCCCCCGTGGATGGTTGT
66 TTTATAAGACAATCTGAGCTGATCGCTCAGTTTACGAATGA-AGGAGGCCCCCGTGGATGGTTGT
* * ** *
42191577 GCGAGCGCAAACACATCTTATATATAATCGTGATAGGGCTTGAAGTCGTC-TTCTTCCGTAGCCT
130 GCGAGCACAAACACATCTTATAGATAATCGTGATAGGGCTCAAAGTCGTCATCCTT-CGTAGCCT
* * * ** * * *
42191641 CATCATCGTCCTTCTCTCTTACTTTGTCTTCTTTCTATTCCTCCTTGGCTACATTGCCCTCAGAT
194 CATCATCCTCCTCCTCTCCTACTTCATATTCTTTCTATTCCTCCTAGGATACATTGCCCTCAGAT
** * * *
42191706 AAATCACTTGATTTTTTAGGTCATTGTATGCTTTCTGCCCCCTGACTCGCCATAAATGTGTCACA
259 AAATCACTCAATTTGTCAGGCCATTGTATGCTTTCTGCCCCCTGACTCGCCATAAATGTGTCACA
* *
42191771 CCCCAACATCAATGGATCTGAGGAAAAAGGTAACTAGGCATGCATGTTAC
324 CCCCAACATCAACGGATCCGAGGAAAAAGGTAACTAGGCATGCATGTTAC
42191821 ATGTTTTGGT
Statistics
Matches: 322, Mismatches: 47, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
389 4 0.01
390 303 0.94
391 15 0.05
ACGTcount: A:0.22, C:0.26, G:0.19, T:0.33
Consensus pattern (391 bp):
TGAGCATCCCCAGGACTCTCACTCGATCTTGCTATTCCTTTGAATTTGCCCTTGACGATCGACCT
TTTATAAGACAATCTGAGCTGATCGCTCAGTTTACGAATGAAGGAGGCCCCCGTGGATGGTTGTG
CGAGCACAAACACATCTTATAGATAATCGTGATAGGGCTCAAAGTCGTCATCCTTCGTAGCCTCA
TCATCCTCCTCCTCTCCTACTTCATATTCTTTCTATTCCTCCTAGGATACATTGCCCTCAGATAA
ATCACTCAATTTGTCAGGCCATTGTATGCTTTCTGCCCCCTGACTCGCCATAAATGTGTCACACC
CCAACATCAACGGATCCGAGGAAAAAGGTAACTAGGCATGCATGTTACCTATTTTAACTTTTCCC
T
Found at i:42205785 original size:39 final size:39
Alignment explanation
Indices: 42205690--42205947 Score: 273
Period size: 39 Copynumber: 6.6 Consensus size: 39
42205680 TTGAATGCTG
*
42205690 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTA-AGTGAC-AATA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGA-T-ACTAA-A
* *
42205729 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCGAAGGCATTTGTGCGAGATACTAAA
* *
42205769 TCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
* * *
42205808 TCCGGGTTAAGTCCGAA-GCATTTATGCGAGTTACTAAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
* *
42205846 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGT-CCGAAGGCATTTGTGCGAGATACTAAA
*
42205886 TCCGGGTTAAGTCCGAA-GCA-TTGTGCGA-ATTACTATAA
1 TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGA-TACTA-AA
*
42205924 -CCGGGCTATGTCCGAAGGCATTTG
1 TCCGGGCTAAGTCCGAAGGCATTTG
42205948 AACGAGGAGC
Statistics
Matches: 194, Mismatches: 14, Indels: 22
0.84 0.06 0.10
Matches are distributed among these distances:
37 27 0.14
38 40 0.21
39 71 0.37
40 45 0.23
41 10 0.05
42 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGCTAAGTCCGAAGGCATTTGTGCGAGATACTAAA
Found at i:42205865 original size:78 final size:78
Alignment explanation
Indices: 42205690--42205947 Score: 332
Period size: 78 Copynumber: 3.3 Consensus size: 78
42205680 TTGAATGCTG
* * **
42205690 TCCGGGCTAAGTCCCGAAGGC--TTGTGCTAAGTGAC-AATATCCGGACTAAGATCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAA-ATCCGGGTTAAG-TCCGAA-GCAT
* *
42205752 TTGTGCGAGATACTAAT
62 TTGTGCGAGTTACTAAA
*
42205769 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGCATTTAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGCATTTGT
42205833 GCGAGTTACTAAA
66 GCGAGTTACTAAA
*
42205846 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGCA-TTGT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGCATTTGT
*
42205910 GCGAATTACTATAA
66 GCGAGTTACTA-AA
*
42205924 -CCGGGCTATGT-CCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
42205948 AACGAGGAGC
Statistics
Matches: 162, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
76 13 0.08
77 50 0.31
78 65 0.40
79 26 0.16
80 8 0.05
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.26
Consensus pattern (78 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCGAAGCATTTGT
GCGAGTTACTAAA
Found at i:42209746 original size:25 final size:26
Alignment explanation
Indices: 42209718--42209766 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
42209708 CAACAAAACT
*
42209718 AAAATCTAACCTAAAAA-GAAAAGGG
1 AAAATCTAAACTAAAAATGAAAAGGG
42209743 AAAATCTAAACTAAAAATGAAAAG
1 AAAATCTAAACTAAAAATGAAAAG
42209767 AAAAAGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.63, C:0.10, G:0.12, T:0.14
Consensus pattern (26 bp):
AAAATCTAAACTAAAAATGAAAAGGG
Found at i:42211846 original size:13 final size:13
Alignment explanation
Indices: 42211830--42211881 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
42211820 TTTAAACCAA
42211830 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
42211843 ACTTCTCAAAAAGT
1 ACTTTTC-AAAAGC
* *
42211857 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
42211870 ACTTTTCAAAAG
1 ACTTTTCAAAAG
42211882 TAATGAAGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.31
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:42212394 original size:16 final size:16
Alignment explanation
Indices: 42212373--42212405 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
42212363 CTTCAAACAC
42212373 TATTTCATTGTCATTT
1 TATTTCATTGTCATTT
42212389 TATTTCATTGTCATTT
1 TATTTCATTGTCATTT
42212405 T
1 T
42212406 TTAAAGTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.18, C:0.12, G:0.06, T:0.64
Consensus pattern (16 bp):
TATTTCATTGTCATTT
Found at i:42214207 original size:54 final size:54
Alignment explanation
Indices: 42214113--42214215 Score: 127
Period size: 54 Copynumber: 1.9 Consensus size: 54
42214103 AATATTTACT
* *
42214113 AAATTTAAAACTTAATTTGAATAAAAAATTTAAACTCCAATACAAAAAATTATC
1 AAATTTAAAACTTAATTTGAATAAAAAATTAAAACCCCAATACAAAAAATTATC
* * * * *
42214167 AAATTTAAAATTTAACTTT-ATTTAAGAATTAAAACCCCAATATAAAAAA
1 AAATTTAAAACTTAA-TTTGAATAAAAAATTAAAACCCCAATACAAAAAA
42214216 AATTTGTGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
54 38 0.93
55 3 0.07
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (54 bp):
AAATTTAAAACTTAATTTGAATAAAAAATTAAAACCCCAATACAAAAAATTATC
Found at i:42222730 original size:27 final size:27
Alignment explanation
Indices: 42222700--42222796 Score: 122
Period size: 27 Copynumber: 3.3 Consensus size: 27
42222690 ATCAACGCAC
42222700 AGCAACCCCTCGGGGGAATCAGCACTT
1 AGCAACCCCTCGGGGGAATCAGCACTT
*
42222727 AGCAACCACCAAATGGGTCGAGGAATCAGCACTT
1 AGCAACC-CC---TCGG--G-GGAATCAGCACTT
42222761 AGCAACCCCTCGGGGGAATCAGCACTT
1 AGCAACCCCTCGGGGGAATCAGCACTT
42222788 AGCAACCCC
1 AGCAACCCC
42222797 CTTTCACATT
Statistics
Matches: 61, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
27 29 0.48
28 3 0.05
30 3 0.05
31 3 0.05
33 3 0.05
34 20 0.33
ACGTcount: A:0.30, C:0.33, G:0.24, T:0.13
Consensus pattern (27 bp):
AGCAACCCCTCGGGGGAATCAGCACTT
Found at i:42222765 original size:61 final size:60
Alignment explanation
Indices: 42222662--42222794 Score: 191
Period size: 61 Copynumber: 2.2 Consensus size: 60
42222652 GGTGCATTCC
*
42222662 GCACTTAGC-ACCACCAATGAATCGGGGAATCAACGCACAGCAACCCCTCGGGGGAATCA
1 GCACTTAGCAACCACCAATGAATCGAGGAATCAACGCACAGCAACCCCTCGGGGGAATCA
**
42222721 GCACTTAGCAACCACCAAATGGGTCGAGGAATC-A-GCACTTAGCAACCCCTCGGGGGAATCA
1 GCACTTAGCAACCACC-AATGAATCGAGGAATCAACGCAC--AGCAACCCCTCGGGGGAATCA
42222782 GCACTTAGCAACC
1 GCACTTAGCAACC
42222795 CCCTTTCACA
Statistics
Matches: 67, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
59 13 0.19
60 7 0.10
61 47 0.70
ACGTcount: A:0.32, C:0.32, G:0.23, T:0.14
Consensus pattern (60 bp):
GCACTTAGCAACCACCAATGAATCGAGGAATCAACGCACAGCAACCCCTCGGGGGAATCA
Found at i:42222836 original size:43 final size:42
Alignment explanation
Indices: 42222775--42222913 Score: 161
Period size: 43 Copynumber: 3.5 Consensus size: 42
42222765 ACCCCTCGGG
42222775 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCC-TTCACATTTAAAATACGGT
* **
42222818 GGAATCAGCACTTAGCAA-CCAC--CA-A--T-AGGTA-GG-
1 GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGT
42222851 GGAATCAGCACTTAGCAACCCCCTTCCACATTTAAAATACGGT
1 GGAATCAGCACTTAGCAACCCCCTT-CACATTTAAAATACGGT
*
42222894 GGAACCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
42222914 ACCAATAGGT
Statistics
Matches: 79, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
33 18 0.23
34 5 0.06
35 3 0.04
36 1 0.01
37 2 0.03
38 2 0.03
39 2 0.03
40 1 0.01
41 3 0.04
42 5 0.06
43 37 0.47
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (42 bp):
GGAATCAGCACTTAGCAACCCCCTTCACATTTAAAATACGGT
Found at i:42222860 original size:33 final size:33
Alignment explanation
Indices: 42222818--42222946 Score: 132
Period size: 33 Copynumber: 3.6 Consensus size: 33
42222808 AAAATACGGT
42222818 GGAATCAGCACTTAGCAACCACCAATAGGTAGG
1 GGAATCAGCACTTAGCAACCACCAATAGGTAGG
* **
42222851 GGAATCAGCACTTAGCAACCCCCTTCCACATTTAAAATACGG
1 GGAATCAGCACTTAGCAA---CC-ACCA-A--T-AGGTA-GG
*
42222893 TGGAACCAGCACTTAGCAACCACCAATAGGTAGG
1 -GGAATCAGCACTTAGCAACCACCAATAGGTAGG
42222927 GGAATCAGCACTTAGCAACC
1 GGAATCAGCACTTAGCAACC
42222947 CCTTTATATG
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
33 37 0.47
34 2 0.03
35 3 0.04
36 3 0.04
37 3 0.04
38 2 0.03
39 3 0.04
40 3 0.04
41 3 0.04
42 2 0.03
43 17 0.22
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.17
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATAGGTAGG
Found at i:42222868 original size:76 final size:76
Alignment explanation
Indices: 42222773--42222948 Score: 334
Period size: 76 Copynumber: 2.3 Consensus size: 76
42222763 CAACCCCTCG
* *
42222773 GGGGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCCACATTTAAAATACGGTGGAACCAGCACTTAGCAACC
42222838 ACCAATAGGTA
66 ACCAATAGGTA
42222849 GGGGAATCAGCACTTAGCAACCCCCTTCCACATTTAAAATACGGTGGAACCAGCACTTAGCAACC
1 GGGGAATCAGCACTTAGCAACCCCCTTCCACATTTAAAATACGGTGGAACCAGCACTTAGCAACC
42222914 ACCAATAGGTA
66 ACCAATAGGTA
42222925 GGGGAATCAGCACTTAGCAACCCC
1 GGGGAATCAGCACTTAGCAACCCC
42222949 TTTATATGCA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
76 98 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (76 bp):
GGGGAATCAGCACTTAGCAACCCCCTTCCACATTTAAAATACGGTGGAACCAGCACTTAGCAACC
ACCAATAGGTA
Found at i:42223317 original size:30 final size:30
Alignment explanation
Indices: 42223283--42223340 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
42223273 CCACCCAACT
*
42223283 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATAACAATTTTGCCCCCAAAC
* * * *
42223313 TTTTGCATAATAACATTTTTGTCCCCAA
1 TTTTGAAAAATAACAATTTTGCCCCCAA
42223341 GCTCGGAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATAACAATTTTGCCCCCAAAC
Found at i:42226877 original size:19 final size:19
Alignment explanation
Indices: 42226849--42226885 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42226839 TGGCTAAGAA
42226849 ATTTTATAAAATATGCATC
1 ATTTTATAAAATATGCATC
* *
42226868 ATTTTTTAAAGTATGCAT
1 ATTTTATAAAATATGCAT
42226886 TGACATGTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (19 bp):
ATTTTATAAAATATGCATC
Found at i:42226984 original size:23 final size:22
Alignment explanation
Indices: 42226941--42226983 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
42226931 ATGATGATTG
42226941 ATATGATGAGATTGATATTTTC
1 ATATGATGAGATTGATATTTTC
*
42226963 ATATGTATGTGATT-ATATTTT
1 ATATG-ATGAGATTGATATTTT
42226984 TTTTATCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.30, C:0.02, G:0.16, T:0.51
Consensus pattern (22 bp):
ATATGATGAGATTGATATTTTC
Found at i:42230692 original size:37 final size:37
Alignment explanation
Indices: 42230620--42230697 Score: 102
Period size: 37 Copynumber: 2.1 Consensus size: 37
42230610 TATTACGAAA
* * * *
42230620 TCTTACTCGGACATAATCTCCACACGAAGTTATCGGG
1 TCTTACCCGGACAAAATCCCCACACGAAGTCATCGGG
* *
42230657 TCTTACCCGGACAAAATCCCCACGCGTAGTCATCGGG
1 TCTTACCCGGACAAAATCCCCACACGAAGTCATCGGG
42230694 TCTT
1 TCTT
42230698 TAGAGCTCGG
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.26
Consensus pattern (37 bp):
TCTTACCCGGACAAAATCCCCACACGAAGTCATCGGG
Found at i:42230942 original size:47 final size:47
Alignment explanation
Indices: 42230816--42231105 Score: 454
Period size: 47 Copynumber: 6.1 Consensus size: 47
42230806 CCCTTCGGGA
* * * * * *
42230816 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
42230863 CCTGTCACATATATATACACTTCCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42230912 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42230959 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42231006 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
42231055 CTTATCTCATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
42231102 CTTA
1 CTTA
42231106 CTATCATTTC
Statistics
Matches: 226, Mismatches: 13, Indels: 8
0.91 0.05 0.03
Matches are distributed among these distances:
47 142 0.63
49 84 0.37
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42231020 original size:96 final size:96
Alignment explanation
Indices: 42230816--42231105 Score: 453
Period size: 96 Copynumber: 3.0 Consensus size: 96
42230806 CCCTTCGGGA
* * * * * * *
42230816 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATAT
*
42230879 ACACTTCCACATTCATCACATCGGCCATTAGGC
64 ACACTTTCACATTCATCACATCGGCCATTAGGC
42230912 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
42230975 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
*
42231006 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
42231071 ACTTTCACATTCATCACATCGGCCATTAGGC
66 ACTTTCACATTCATCACATCGGCCATTAGGC
42231102 CTTA
1 CTTA
42231106 CTATCATTTC
Statistics
Matches: 181, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
94 46 0.25
95 1 0.01
96 134 0.74
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (96 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAC
ACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:42231074 original size:143 final size:143
Alignment explanation
Indices: 42230816--42231105 Score: 490
Period size: 143 Copynumber: 2.0 Consensus size: 143
42230806 CCCTTCGGGA
* * * * *
42230816 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCACATATATATAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATATAC
42230881 ACTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
42230946 TCGGCCATTAGGC
131 TCGGCCATTAGGC
* * *
42230959 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATATAC
* *
42231024 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCTCATATATACACTTTCACATTCATCACA
66 ACTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
42231089 TCGGCCATTAGGC
131 TCGGCCATTAGGC
42231102 CTTA
1 CTTA
42231106 CTATCATTTC
Statistics
Matches: 137, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
143 137 1.00
ACGTcount: A:0.28, C:0.31, G:0.09, T:0.32
Consensus pattern (143 bp):
CTTATCACATATATACACTTTCACATCCATCACATCGGCCACTAGGCCCTATCACATATATATAC
ACTTCCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:42248838 original size:18 final size:17
Alignment explanation
Indices: 42248805--42248846 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
42248795 GTGTGAATCC
*
42248805 AAACTAATATATTAATT
1 AAACTAATAAATTAATT
42248822 AAACTAATTAAATTAATT
1 AAACTAA-TAAATTAATT
*
42248840 AACCTAA
1 AAACTAA
42248847 CTAACCTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.36
Consensus pattern (17 bp):
AAACTAATAAATTAATT
Found at i:42253404 original size:39 final size:39
Alignment explanation
Indices: 42253149--42253401 Score: 382
Period size: 39 Copynumber: 6.5 Consensus size: 39
42253139 CATGTTTTTA
42253149 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* * *
42253188 AGAATTGT-AGTATATGCTTGAATTTTATATGATTATATG
1 AGTATTGTGA-TATATGCTTGAATGTTATGTGATTATATG
42253227 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* *
42253266 AGTATTGCGATATATTCTTGAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* * * *
42253305 AGTATTGCGATATGTGCTTGAACGTTATGTAATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
*
42253344 AGTATTGTGATATATGCTTAAATGTTATGTGATTATATG
1 AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
* *
42253383 TGTAATGTGATATATGCTT
1 AGTATTGTGATATATGCTT
42253402 AAAAGTGAAC
Statistics
Matches: 193, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
38 1 0.01
39 191 0.99
40 1 0.01
ACGTcount: A:0.29, C:0.04, G:0.21, T:0.45
Consensus pattern (39 bp):
AGTATTGTGATATATGCTTGAATGTTATGTGATTATATG
Found at i:42270601 original size:45 final size:47
Alignment explanation
Indices: 42270515--42270603 Score: 119
Period size: 45 Copynumber: 1.9 Consensus size: 47
42270505 TGAGCCATGT
* *
42270515 AACAGGAAGCTTATCCGGGCTATAACAGGAAACTCATAAGAGTTTAA
1 AACAGGAAGCTTATCCGAGCTATAACAGGAAACTCAGAAGAGTTTAA
* * *
42270562 AACAGGAAGCTTAT-TGAGCT-TAACAGGTAACTCCGAAGAGTT
1 AACAGGAAGCTTATCCGAGCTATAACAGGAAACTCAGAAGAGTT
42270604 ATTATTAGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
45 19 0.51
46 4 0.11
47 14 0.38
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.22
Consensus pattern (47 bp):
AACAGGAAGCTTATCCGAGCTATAACAGGAAACTCAGAAGAGTTTAA
Found at i:42272809 original size:56 final size:56
Alignment explanation
Indices: 42272712--42272890 Score: 245
Period size: 55 Copynumber: 3.2 Consensus size: 56
42272702 GCGCACTCTT
* * *
42272712 ATGAATTGCCCTTGTGGTGAATTCT-AAAAAGAGTAGCCTTTGTGGCAAACTCTTGA
1 ATGAA-TGGCCTTGTGGTGAATTCTGAAAAAGAGTAGCCTTTGTGGAAAAATCTTGA
* *
42272768 ATGATTGGCCTTGTGGTGAATTCTGAAAAAAAGTAGCCTTTGTGGAAAAATCTTGA
1 ATGAATGGCCTTGTGGTGAATTCTGAAAAAGAGTAGCCTTTGTGGAAAAATCTTGA
* * * * *
42272824 ATGAATGGCCTTGTGGTGAATTTTG-AAAAGAGTAACTTTTATGGAAAATTCTTGA
1 ATGAATGGCCTTGTGGTGAATTCTGAAAAAGAGTAGCCTTTGTGGAAAAATCTTGA
42272879 ATGAATGGCCTT
1 ATGAATGGCCTT
42272891 TTGGCGATAA
Statistics
Matches: 110, Mismatches: 12, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
55 55 0.50
56 55 0.50
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.34
Consensus pattern (56 bp):
ATGAATGGCCTTGTGGTGAATTCTGAAAAAGAGTAGCCTTTGTGGAAAAATCTTGA
Found at i:42272907 original size:56 final size:55
Alignment explanation
Indices: 42272712--42272910 Score: 227
Period size: 56 Copynumber: 3.6 Consensus size: 55
42272702 GCGCACTCTT
* * * * *
42272712 ATGAATTGCCCTTGTGGTGAATTCTAAAAAGAGTAGCCTTTGTGGCAAACTCTTGA
1 ATGAA-TGGCCTTGTGGTGAATTATGAAAAGAGTAGCCTTTGTGGAAAAATCTTGA
* * *
42272768 ATGATTGGCCTTGTGGTGAATTCTGAAAAAAAGTAGCCTTTGTGGAAAAATCTTGA
1 ATGAATGGCCTTGTGGTGAATTATG-AAAAGAGTAGCCTTTGTGGAAAAATCTTGA
* * * * *
42272824 ATGAATGGCCTTGTGGTGAATTTTGAAAAGAGTAACTTTTATGGAAAATTCTTGA
1 ATGAATGGCCTTGTGGTGAATTATGAAAAGAGTAGCCTTTGTGGAAAAATCTTGA
* * *
42272879 ATGAATGGCCTTTTGGCGATAATATGAAAAGA
1 ATGAATGGCCTTGTGGTGA-ATTATGAAAAGA
42272911 AAAGACTTTG
Statistics
Matches: 124, Mismatches: 17, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
55 60 0.48
56 64 0.52
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (55 bp):
ATGAATGGCCTTGTGGTGAATTATGAAAAGAGTAGCCTTTGTGGAAAAATCTTGA
Found at i:42272920 original size:111 final size:109
Alignment explanation
Indices: 42272712--42272940 Score: 253
Period size: 111 Copynumber: 2.1 Consensus size: 109
42272702 GCGCACTCTT
* * * *
42272712 ATGAATTGCCCTTGTGGTGAATTCTAAAAAGAGTAGCCTTTGTGGCAAACTCTTGAATGATTGGC
1 ATGAA-TGCCCTTGTGGTGAATTCTAAAAAGAGTAACCTTTATGGAAAACTCTTGAATGAATGGC
* * * * *
42272777 CTTGTGGTGAATTCTGAAAAAAAGTAGCCTTTGTGGAAAAATCTTGA
65 CTTGTGGCGAAATATGAAAAAAAG-AGACTTTGTGGAAAAATC-TAA
* * * * *
42272824 ATGAATGGCCTTGTGGTGAATTTTGAAAAGAGTAACTTTTATGGAAAATTCTTGAATGAATGGCC
1 ATGAATGCCCTTGTGGTGAATTCTAAAAAGAGTAACCTTTATGGAAAACTCTTGAATGAATGGCC
* **
42272889 TTTTGGCGATAATATGAAAAGAAA-AGACTTTGTGGCGAAATCTAA
66 TTGTGGCGA-AATATGAAAA-AAAGAGACTTTGTGGAAAAATCTAA
42272934 ATGAATG
1 ATGAATG
42272941 ATCTTTGTAG
Statistics
Matches: 98, Mismatches: 17, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
110 9 0.09
111 73 0.74
112 13 0.13
113 3 0.03
ACGTcount: A:0.33, C:0.11, G:0.24, T:0.32
Consensus pattern (109 bp):
ATGAATGCCCTTGTGGTGAATTCTAAAAAGAGTAACCTTTATGGAAAACTCTTGAATGAATGGCC
TTGTGGCGAAATATGAAAAAAAGAGACTTTGTGGAAAAATCTAA
Found at i:42274524 original size:23 final size:23
Alignment explanation
Indices: 42274465--42274553 Score: 88
Period size: 23 Copynumber: 3.9 Consensus size: 23
42274455 ATATCATACT
* * *
42274465 GAAGTTCTAGTAACAGAAGCACC
1 GAAGTACTAGTAATAGAAGTACC
* *
42274488 GCAGTGCTAGTAATAGAAGTACC
1 GAAGTACTAGTAATAGAAGTACC
* * *
42274511 GAAGTACTAATAATAAAATTACC
1 GAAGTACTAGTAATAGAAGTACC
* *
42274534 AAAGTACTAGTAATTGAAGT
1 GAAGTACTAGTAATAGAAGT
42274554 CCCCTGTGGG
Statistics
Matches: 52, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.43, C:0.15, G:0.19, T:0.24
Consensus pattern (23 bp):
GAAGTACTAGTAATAGAAGTACC
Found at i:42275056 original size:17 final size:17
Alignment explanation
Indices: 42275031--42275064 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42275021 TCAATTTTCA
*
42275031 ATTTTCATATTATGGCT
1 ATTTCCATATTATGGCT
42275048 ATTTCCATATTATGGCT
1 ATTTCCATATTATGGCT
42275065 TATATAGACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.12, T:0.50
Consensus pattern (17 bp):
ATTTCCATATTATGGCT
Found at i:42280712 original size:9 final size:9
Alignment explanation
Indices: 42280698--42280750 Score: 79
Period size: 9 Copynumber: 5.9 Consensus size: 9
42280688 ATTATGCCTA
42280698 ACCAAATTG
1 ACCAAATTG
*
42280707 ACCAAATTT
1 ACCAAATTG
**
42280716 ATAAAATTG
1 ACCAAATTG
42280725 ACCAAATTG
1 ACCAAATTG
42280734 ACCAAATTG
1 ACCAAATTG
42280743 ACCAAATT
1 ACCAAATT
42280751 TATATAAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.47, C:0.19, G:0.08, T:0.26
Consensus pattern (9 bp):
ACCAAATTG
Found at i:42293232 original size:41 final size:41
Alignment explanation
Indices: 42293187--42293335 Score: 183
Period size: 41 Copynumber: 3.6 Consensus size: 41
42293177 ACCTCAGTGC
*
42293187 ATCATCGGATAAACCAAAGTAAATATACTAGCACATAGTAT
1 ATCATCGAATAAACCAAAGTAAATATACTAGCACATAGTAT
* *
42293228 ATCATCGAATAAA-CAGAAATAAATATACTAGCACATAGTGT
1 ATCATCGAATAAACCA-AAGTAAATATACTAGCACATAGTAT
** * * *
42293269 ATCATCGAATAAACTGAAGTAAATATATTGGCACATAGTAC
1 ATCATCGAATAAACCAAAGTAAATATACTAGCACATAGTAT
** *
42293310 ATCATCGGTTACACCAAAGTAAATAT
1 ATCATCGAATAAACCAAAGTAAATAT
42293336 GATGGCATAA
Statistics
Matches: 91, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
40 2 0.02
41 89 0.98
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.26
Consensus pattern (41 bp):
ATCATCGAATAAACCAAAGTAAATATACTAGCACATAGTAT
Found at i:42293355 original size:82 final size:82
Alignment explanation
Indices: 42293184--42293371 Score: 193
Period size: 82 Copynumber: 2.3 Consensus size: 82
42293174 GGCACCTCAG
* * *
42293184 TGCATCATCGGATAAACCAAAGTAAATATACTAGCACATAGTATATCATCGAATAAACAGAAATA
1 TGCATCATCGAATAAACCGAAGTAAATATACTAGCACATAGTACATCATCGAATAAACAGAAATA
* *
42293249 AATATACTAGCACATAG
66 AATATACTAGCACAAAA
* * * * ** * *
42293266 TGTATCATCGAATAAACTGAAGTAAATATATTGGCACATAGTACATCATCGGTTACACCA-AAGT
1 TGCATCATCGAATAAACCGAAGTAAATATACTAGCACATAGTACATCATCGAATA-AACAGAAAT
* *
42293330 AAATATGA-TGGCATAAAA
65 AAATAT-ACTAGCACAAAA
42293348 TGCATCATC-AGATAAACCGAAGTA
1 TGCATCATCGA-ATAAACCGAAGTA
42293372 TAAACTCGTA
Statistics
Matches: 86, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
81 1 0.01
82 81 0.94
83 4 0.05
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.24
Consensus pattern (82 bp):
TGCATCATCGAATAAACCGAAGTAAATATACTAGCACATAGTACATCATCGAATAAACAGAAATA
AATATACTAGCACAAAA
Found at i:42293371 original size:41 final size:40
Alignment explanation
Indices: 42293186--42293371 Score: 113
Period size: 41 Copynumber: 4.5 Consensus size: 40
42293176 CACCTCAGTG
* * * * *
42293186 CATCATCGGATAAACCAAAGTAAATATACTAGCACATAGTA
1 CATCATC-GATAAACCGAAGTAAATATATTGGCACAAAATA
* * * * * * * *
42293227 TATCATCGAATAAACAGAAATAAATATACTAGCACATAGTG
1 CATCATCG-ATAAACCGAAGTAAATATATTGGCACAAAATA
* * * *
42293268 TATCATCGAATAAACTGAAGTAAATATATTGGCACATAGTA
1 CATCATCG-ATAAACCGAAGTAAATATATTGGCACAAAATA
* * * * *
42293309 CATCATCGGTTACACCAAAGTAAATATGA-TGGCATAAAATG
1 CATCATC-GATAAACCGAAGTAAATAT-ATTGGCACAAAATA
42293350 CATCATCAGATAAACCGAAGTA
1 CATCATC-GATAAACCGAAGTA
42293372 TAAACTCGTA
Statistics
Matches: 119, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
40 1 0.01
41 116 0.97
42 2 0.02
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (40 bp):
CATCATCGATAAACCGAAGTAAATATATTGGCACAAAATA
Found at i:42305858 original size:309 final size:309
Alignment explanation
Indices: 42305299--42305920 Score: 1208
Period size: 309 Copynumber: 2.0 Consensus size: 309
42305289 CACCCCAATG
42305299 AATTTTCAGAGAATCGTCTTAAACTTATCCCATGCTTGCCCCAAAGTCTCTATTGGATCTTGCTT
1 AATTTTCAGAGAATCGTCTTAAACTTATCCCATGCTTGCCCCAAAGTCTCTATTGGATCTTGCTT
42305364 GAAATCAAACAATTCCTAGGCATGGAGGACTGCCGTCATTGGTATGTTTCGGCTCAAGAATAGTT
66 GAAATCAAACAATTCCTAGGCATGGAGGACTGCCGTCATTGGTATGTTTCGGCTCAAGAATAGTT
42305429 ACACAAATTCATCCCAAGTAGTGAAGGCTTCCAACCACACCTTGGCTTCACCTCCAAGAACAAAA
131 ACACAAATTCATCCCAAGTAGTGAAGGCTTCCAACCACACCTTGGCTTCACCTCCAAGAACAAAA
*
42305494 GGGGTTAATAATAAATTGATCACTTCATTTGACACCCTCGAATAAGCAATTGTGTTGTATAAACA
196 GGGGTTAATAATAAATTGATCACTTCATTTGACACACTCGAATAAGCAATTGTGTTGTATAAACA
42305559 TTTGAATTGTTGAAGGAACATTATTGGATGCAATACTTCGCTGTTACAA
261 TTTGAATTGTTGAAGGAACATTATTGGATGCAATACTTCGCTGTTACAA
42305608 AATTTTCAGAGAATCGTCTTAAACTTATCCCATGCTTGCCCCAAAGTCTCTATTGGATCTTGCTT
1 AATTTTCAGAGAATCGTCTTAAACTTATCCCATGCTTGCCCCAAAGTCTCTATTGGATCTTGCTT
42305673 GAAATCAAACAATTCCTAGGCATGGAGGACTGCCGTCATTGGTATGTTTCGGCTCAAGAATAGTT
66 GAAATCAAACAATTCCTAGGCATGGAGGACTGCCGTCATTGGTATGTTTCGGCTCAAGAATAGTT
*
42305738 ACACAAATTCATCCCAAGTAGTGAAGGCTTCCAACCACACCTTGGCTTCACCTCTAAGAACAAAA
131 ACACAAATTCATCCCAAGTAGTGAAGGCTTCCAACCACACCTTGGCTTCACCTCCAAGAACAAAA
* *
42305803 GGGGTTAATAATAAATTGATCACTTCATTTGACACATTCGAATAAGCAATTGTGTTGTATAAACG
196 GGGGTTAATAATAAATTGATCACTTCATTTGACACACTCGAATAAGCAATTGTGTTGTATAAACA
42305868 TTTGAATTGTTGAAGGAACATTATTGGATGCAATACTTCGCTGTTACAA
261 TTTGAATTGTTGAAGGAACATTATTGGATGCAATACTTCGCTGTTACAA
42305917 AATT
1 AATT
42305921 GAAGTGTAAT
Statistics
Matches: 309, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
309 309 1.00
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.31
Consensus pattern (309 bp):
AATTTTCAGAGAATCGTCTTAAACTTATCCCATGCTTGCCCCAAAGTCTCTATTGGATCTTGCTT
GAAATCAAACAATTCCTAGGCATGGAGGACTGCCGTCATTGGTATGTTTCGGCTCAAGAATAGTT
ACACAAATTCATCCCAAGTAGTGAAGGCTTCCAACCACACCTTGGCTTCACCTCCAAGAACAAAA
GGGGTTAATAATAAATTGATCACTTCATTTGACACACTCGAATAAGCAATTGTGTTGTATAAACA
TTTGAATTGTTGAAGGAACATTATTGGATGCAATACTTCGCTGTTACAA
Found at i:42311369 original size:30 final size:30
Alignment explanation
Indices: 42311326--42311590 Score: 419
Period size: 30 Copynumber: 8.9 Consensus size: 30
42311316 TTATTTATTT
*
42311326 CCGAATTGA-TTGTATATGGGTATACATTG
1 CCGAATTGATTTGTATATGGATATACATTG
*
42311355 CCGAATTGATTTGTATATGGATATACATTA
1 CCGAATTGATTTGTATATGGATATACATTG
* *
42311385 CCGAATTGATTTGTATATGGATATACGTTA
1 CCGAATTGATTTGTATATGGATATACATTG
* *
42311415 CCGAATTGATTTGTATATAGATATACGTTG
1 CCGAATTGATTTGTATATGGATATACATTG
42311445 CCGAATTGATTTGTATATGGATATACATTG
1 CCGAATTGATTTGTATATGGATATACATTG
42311475 CCGAATTGATTTGTATATGGATATACATTG
1 CCGAATTGATTTGTATATGGATATACATTG
* *
42311505 CCAAATTGACTTGTATATGGATATACATTG
1 CCGAATTGATTTGTATATGGATATACATTG
* *
42311535 CCGAATTGATTTGTATATAGATAGACATTG
1 CCGAATTGATTTGTATATGGATATACATTG
42311565 CCGAATTGATTTGTATAT-G-TATACAT
1 CCGAATTGATTTGTATATGGATATACAT
42311591 ATATATTGCC
Statistics
Matches: 221, Mismatches: 14, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
28 6 0.03
29 10 0.05
30 205 0.93
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (30 bp):
CCGAATTGATTTGTATATGGATATACATTG
Found at i:42318607 original size:10 final size:10
Alignment explanation
Indices: 42318592--42318639 Score: 53
Period size: 10 Copynumber: 4.5 Consensus size: 10
42318582 GAAAAAAGTG
42318592 AGAAAGAAAA
1 AGAAAGAAAA
42318602 AGAAAGAAAA
1 AGAAAGAAAA
42318612 CCAGAAA-AAAA
1 --AGAAAGAAAA
42318623 AGGAAAGAAAGA
1 A-GAAAGAAA-A
42318635 AGAAA
1 AGAAA
42318640 AAATGAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
9 1 0.03
10 14 0.42
11 11 0.33
12 7 0.21
ACGTcount: A:0.75, C:0.04, G:0.21, T:0.00
Consensus pattern (10 bp):
AGAAAGAAAA
Found at i:42318641 original size:22 final size:21
Alignment explanation
Indices: 42318592--42318642 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
42318582 GAAAAAAGTG
*
42318592 AGAAAGAAAAAGAAAGAAAACC
1 AGAAAAAAAAAGAAAGAAAA-C
*
42318614 AGAAAAAAAAGGAAAGAAAGA-
1 AGAAAAAAAAAGAAAGAAA-AC
42318635 AGAAAAAA
1 AGAAAAAA
42318643 TGAGTAACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 8 0.31
22 17 0.65
23 1 0.04
ACGTcount: A:0.76, C:0.04, G:0.20, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAAAGAAAGAAAAC
Found at i:42330165 original size:138 final size:138
Alignment explanation
Indices: 42329953--42330643 Score: 924
Period size: 138 Copynumber: 5.1 Consensus size: 138
42329943 TAGAAAAACG
42329953 AATTATA-TACTTTCCAAAAGAATATTAATTTT-A--TCTTTTATATTTTGACCGAAATTAATTA
1 AATTATATTA-TTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTA
* * *
42330014 ATATAACTATTTATATTAATAAATTTGATAAAATATATACAATTAATAATATGTATGAATCAAAT
65 ATATAACTGTTTATATTAATAAATTTGATAAAATATATACAATTAATATTTTGTATGAATCAAAT
42330079 TCATATATT
130 TCATATATT
* * * *
42330088 AATTATATTATTTCCATAAGAATATTAATTTTCATGTGTTTTATATTTTGATCAAAATTAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
** * *
42330153 TATAGTTTTTTATATTAATAAA-TTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAAT
66 TATAACTGTTTATATTAATAAATTTGA-TAAAATATATACAATTAATATTTTGTATGAATCAAAT
42330217 TCATATATT
130 TCATATATT
* * *
42330226 AATTATATCATTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTTA
1 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * * *
42330291 TGTAACTGTATATATTAATAAATTCGGTAAAATAT-TGACAATTAATATTTTGTTTGAATCAAAT
66 TATAACTGTTTATATTAATAAATTTGATAAAATATAT-ACAATTAATATTTTGTATGAATCAAAT
42330355 TCATATATT
130 TCATATATT
* * * * *
42330364 AATTATATTCTTTTCAAAAGAATATTAATTTTCATATCTTTTATATTATGACCGAAATTAATAAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * *
42330429 TATAACCGTTCATATTAATAAATTTTG-CAAAATATATAAAATTAATATTTTGTATGAATCAAAT
66 TATAACTGTTTATATTAATAAA-TTTGATAAAATATATACAATTAATATTTTGTATGAATCAAAT
42330493 TCATATATT
130 TCATATATT
* * *
42330502 AATTATATTCTTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCTAAATCAATTAA
1 AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
* * * * *
42330567 TATAATTGTTTATA-T--T---TTCGGTAAAATATATACAGTTAATATTTTGTATTAATCAAATT
66 TATAACTGTTTATATTAATAAATTTGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
42330626 CATATATT
131 CATATATT
42330634 AATTAT-TTAT
1 AATTATATTAT
42330644 ATATCTATAT
Statistics
Matches: 489, Mismatches: 57, Indels: 24
0.86 0.10 0.04
Matches are distributed among these distances:
131 6 0.01
132 48 0.10
135 29 0.06
136 3 0.01
137 5 0.01
138 393 0.80
139 5 0.01
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (138 bp):
AATTATATTATTTCCAAAAGAATATTAATTTTCATGTCTTTTATATTTTGACCGAAATTAATTAA
TATAACTGTTTATATTAATAAATTTGATAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:42337987 original size:138 final size:138
Alignment explanation
Indices: 42337155--42337969 Score: 1168
Period size: 138 Copynumber: 5.9 Consensus size: 138
42337145 AAAAAGAAAC
* * **
42337155 TATATTCTTTCCAAAAGAATATTAATTTCCACGCCTTTTATATTTTGACAAAAATTAATTAATAT
1 TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
* * * * ** * *
42337220 AATTATTTATGTTATTAATTTCGGTAAAATGTATACAATTATTATTTTGTATGAATCAAATTCAT
66 AATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAATTCAT
42337285 ATATTAAT
131 ATATTAAT
* *
42337293 TATATTCTTTCCAAAAGAATATTAATTTTCATGCCTTTTATATTTTGACCGAAATTAATTAATAT
1 TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
* *
42337358 AACTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCCAATTCAT
66 AATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAATTCAT
42337423 ATATTAAT
131 ATATTAAT
* * * * * *
42337431 TATTTTCTTTCC-AAAGAATTTTAATTTCCATTTCTTTCATATTTTGACCAAAATTAATTAATGT
1 TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
* * * *
42337495 AATTTTTTATATTAATAAATTTGGTAAAACATATACAATTAGTATTTTGTATGAATCAAATTCAT
66 AATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAATTCAT
42337560 ATATTAAT
131 ATATTAAT
* * * *
42337568 TATATTCTTTCCAAAAGAATACTAATTTTCATGTCTTTTATATTTTGATCGAAATTAATTAATCT
1 TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
* *
42337633 AATAGTTTATATTAATAAATTCGGTAAAA-ATATATATAATTAATATTTTGCATGAATCAAATTC
66 AATTGTTTATATTAATAAATTCGGTAAAACATATA-A-AATTAATATTTTGTATGAATCAAATTC
42337697 ATATATTAAT
129 ATATATTAAT
* * * * * *
42337707 TATTTTCTTTGC-AAAGAATAATAATTTTCACGTCTTTTATATTTTGACCGAAATTAATTAATGT
1 TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
* * *
42337771 AATTGTTTATATTAATAAATTTGGTAAAATATATAAAATTAATATTTTGTATTAATCAAATTCAT
66 AATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAATTCAT
42337836 ATATTAAT
131 ATATTAAT
* * * *
42337844 TACATTCTTTCCAAAAGAATATTAATTCCCATTTCTTTTAAATTTTGACCGAAATTAATTAATAT
1 TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
* *
42337909 AACTGTTTATATTAATAAATTCAGTAAAACATATAAAATTAATATTTTGTATGAATCAAAT
66 AATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAAT
42337970 AGAGAACATA
Statistics
Matches: 604, Mismatches: 68, Indels: 10
0.89 0.10 0.01
Matches are distributed among these distances:
137 172 0.28
138 382 0.63
139 50 0.08
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (138 bp):
TATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACCGAAATTAATTAATAT
AATTGTTTATATTAATAAATTCGGTAAAACATATAAAATTAATATTTTGTATGAATCAAATTCAT
ATATTAAT
Found at i:42355093 original size:27 final size:27
Alignment explanation
Indices: 42355063--42355240 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42355053 ATATTGAGTC
* * * *
42355063 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42355090 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42355117 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42355145 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42355172 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42355199 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42355226 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42355241 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42355202 original size:82 final size:81
Alignment explanation
Indices: 42355084--42355239 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42355074 TGCTATATAA
* *
42355084 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42355149 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42355166 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42355230 CACTTAGTGC
65 CACTTAGTGC
42355240 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42363170 original size:27 final size:27
Alignment explanation
Indices: 42363140--42363317 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
42363130 ATATTGAGTC
* * * *
42363140 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
42363167 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42363194 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42363222 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42363249 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42363276 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42363303 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42363318 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42363279 original size:82 final size:81
Alignment explanation
Indices: 42363161--42363316 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
42363151 TGCTATATAA
* *
42363161 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
42363226 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
42363243 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
42363307 CACTTAGTGC
65 CACTTAGTGC
42363317 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:42366832 original size:10 final size:10
Alignment explanation
Indices: 42366817--42366847 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
42366807 ATTAATTTTT
42366817 ATATTATATA
1 ATATTATATA
42366827 ATATTATATA
1 ATATTATATA
*
42366837 ATATAATATA
1 ATATTATATA
42366847 A
1 A
42366848 AAATAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (10 bp):
ATATTATATA
Found at i:42366833 original size:15 final size:15
Alignment explanation
Indices: 42366801--42366845 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
42366791 TTTTATTTAA
*
42366801 TATATAAT-TAATTTT
1 TATATAATATAA-TAT
*
42366816 TATATTATATAATAT
1 TATATAATATAATAT
42366831 TATATAATATAATAT
1 TATATAATATAATAT
42366846 AAAAATAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 23 0.88
16 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATATAATATAATAT
Found at i:42370372 original size:21 final size:21
Alignment explanation
Indices: 42370346--42370386 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42370336 AATTATTTCC
42370346 TTTATTT-AGTGTTATTTTATT
1 TTTATTTGA-TGTTATTTTATT
*
42370367 TTTATTTGATTTTATTTTAT
1 TTTATTTGATGTTATTTTAT
42370387 AGTTTTTACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (21 bp):
TTTATTTGATGTTATTTTATT
Found at i:42380050 original size:29 final size:29
Alignment explanation
Indices: 42380013--42380204 Score: 122
Period size: 29 Copynumber: 6.6 Consensus size: 29
42380003 CAATGGTTGT
*
42380013 AACCGTCCCTTTTCATATTCGATGGTCGA
1 AACCATCCCTTTTCATATTCGATGGTCGA
* * *
42380042 AACCATCCCTTTTCATTAATCAATGGTTC-T
1 AACCATCCCTTTTCA-TATTCGATGG-TCGA
*
42380072 CACCATCCCTTTTCATAGTT-GATGGTC-A
1 AACCATCCCTTTTCATA-TTCGATGGTCGA
* * *
42380100 TCACCATCCCTTTTCATTAATCGATAGTCGA
1 -AACCATCCCTTTTCA-TATTCGATGGTCGA
* * ** *
42380131 AGCTATCATTTTTCATATTCGATAGTCGA
1 AACCATCCCTTTTCATATTCGATGGTCGA
** * * *
42380160 TGCTATCCCTTTTCACACTT-GATGGTCGT
1 AACCATCCCTTTTCATA-TTCGATGGTCGA
* *
42380189 CACCACCCCTTTTCAT
1 AACCATCCCTTTTCAT
42380205 CGTTGATGAT
Statistics
Matches: 128, Mismatches: 27, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
28 2 0.02
29 80 0.62
30 43 0.34
31 3 0.02
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.38
Consensus pattern (29 bp):
AACCATCCCTTTTCATATTCGATGGTCGA
Found at i:42380096 original size:59 final size:59
Alignment explanation
Indices: 42380003--42380121 Score: 170
Period size: 59 Copynumber: 2.0 Consensus size: 59
42379993 GTGTGCTAAA
* *
42380003 CAATGGTTGTAACCGTCCCTTTTCATATTCGATGGTCGA-AACCATCCCTTTTCATTAAT
1 CAATGGTTCTAACCATCCCTTTTCATATTCGATGGTC-ATAACCATCCCTTTTCATTAAT
* *
42380062 CAATGGTTCTCACCATCCCTTTTCATAGTT-GATGGTCATCACCATCCCTTTTCATTAAT
1 CAATGGTTCTAACCATCCCTTTTCATA-TTCGATGGTCATAACCATCCCTTTTCATTAAT
42380121 C
1 C
42380122 GATAGTCGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
58 1 0.02
59 51 0.94
60 2 0.04
ACGTcount: A:0.23, C:0.28, G:0.12, T:0.38
Consensus pattern (59 bp):
CAATGGTTCTAACCATCCCTTTTCATATTCGATGGTCATAACCATCCCTTTTCATTAAT
Found at i:42400642 original size:19 final size:18
Alignment explanation
Indices: 42400611--42400648 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
42400601 TATTTATTTG
42400611 TATTTTTTCTCTT-TTTT
1 TATTTTTTCTCTTCTTTT
42400628 TATTTTTTCCTTCTTCTTTT
1 TATTTTTT-C-TCTTCTTTT
42400648 T
1 T
42400649 CTAAAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.44
18 1 0.06
19 4 0.22
20 5 0.28
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (18 bp):
TATTTTTTCTCTTCTTTT
Found at i:42408071 original size:21 final size:22
Alignment explanation
Indices: 42408031--42408071 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
42408021 ATTTATTTGA
*
42408031 TATTTTATATGTAATTTGTTAT
1 TATTTTATATCTAATTTGTTAT
*
42408053 TATTTTA-ATCTAGTTTGTT
1 TATTTTATATCTAATTTGTT
42408072 TAAACTTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.24, C:0.02, G:0.10, T:0.63
Consensus pattern (22 bp):
TATTTTATATCTAATTTGTTAT
Found at i:42412284 original size:40 final size:40
Alignment explanation
Indices: 42412225--42412492 Score: 473
Period size: 40 Copynumber: 6.7 Consensus size: 40
42412215 GAGCATTGGA
*
42412225 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
42412265 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
42412305 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
42412345 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
42412385 ATATATCCGGGCTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
42412425 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
42412465 ATATGTTCGGGCTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
42412493 ATGTGTTTGC
Statistics
Matches: 219, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 219 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:42423424 original size:40 final size:40
Alignment explanation
Indices: 42423365--42423695 Score: 583
Period size: 40 Copynumber: 8.3 Consensus size: 40
42423355 GAGTTATATA
*
42423365 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
42423405 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
*
42423445 AATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
*
42423485 TATCCGGGCTAAGTTCCGAAGAGCATTCATGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
*
42423525 TATCCGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
*
42423565 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
*
42423605 T-TCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
* *
42423644 TATCCGGGCTAAGTTCCGAAAAGCATTCGTGCTAGTGATA
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
42423684 TATCCGGGCTAA
1 TATCCGGGCTAA
42423696 ACCTCGAAGG
Statistics
Matches: 279, Mismatches: 11, Indels: 2
0.96 0.04 0.01
Matches are distributed among these distances:
39 39 0.14
40 240 0.86
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
Found at i:42423767 original size:28 final size:27
Alignment explanation
Indices: 42423727--42423883 Score: 143
Period size: 28 Copynumber: 5.6 Consensus size: 27
42423717 GAGTTATGAG
* * *
42423727 GCACTGTGTGTGCAAGTTCTTCAACCGA
1 GCACTATGTGTGCGAGTTCTT-AATCGA
* * * * *
42423755 GCACTATGTGTGCCAGATCAGTAGTTGA
1 GCACTATGTGTGCGAGTTC-TTAATCGA
42423783 GGCACTATGTGTGCGAGTTCTTCAATCGA
1 -GCACTATGTGTGCGAGTTCTT-AATCGA
** *
42423812 GCACTATGTGTGCGAGATTGGTAATTGA
1 GCACTATGTGTGCGAG-TTCTTAATCGA
42423840 GGCACTATGTGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTC-TTAATCGA
*
42423869 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
42423884 AATCAGTCAG
Statistics
Matches: 104, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
28 57 0.55
29 47 0.45
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (27 bp):
GCACTATGTGTGCGAGTTCTTAATCGA
Found at i:42423790 original size:29 final size:28
Alignment explanation
Indices: 42423755--42423883 Score: 118
Period size: 29 Copynumber: 4.5 Consensus size: 28
42423745 CTTCAACCGA
* *
42423755 GCACTATGTGTGCCAGATCAGTAGTTGAG
1 GCACTATGTGTGCGAGATC-GTAATTGAG
* * *
42423784 GCACTATGTGTGCGAGTTCTTCAATCGA-
1 GCACTATGTGTGCGAGATCGT-AATTGAG
*
42423812 GCACTATGTGTGCGAGATTGGTAATTGAG
1 GCACTATGTGTGCGAGA-TCGTAATTGAG
* * *
42423841 GCACTATGTGTGCGAGTTCTTTAATCGA-
1 GCACTATGTGTGCGAGATC-GTAATTGAG
*
42423869 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
42423884 AATCAGTCAG
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
28 37 0.45
29 45 0.55
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGTAATTGAG
Found at i:42423813 original size:57 final size:57
Alignment explanation
Indices: 42423723--42423911 Score: 247
Period size: 57 Copynumber: 3.3 Consensus size: 57
42423713 GCTGGAGTTA
* * * *
42423723 TGAGGCACTGTGTGTGCAAGTTCTTCAACCGAGCACTATGTGTGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAGT
** *
42423780 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATTGGTAAT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAGT
* * *
42423837 TGAGGCACTATGTGTGCGAGTTCTTTAATCGAGCGCTATGTGTGCGAAATCAGTCAG-
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGT-AGT
* *
42423894 TG-GGCACTGTGTATGCGA
1 TGAGGCACTATGTGTGCGA
42423912 AGTGTGTTTC
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
56 14 0.12
57 101 0.87
58 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (57 bp):
TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAGT
Found at i:42427484 original size:48 final size:48
Alignment explanation
Indices: 42427413--42427750 Score: 577
Period size: 48 Copynumber: 7.0 Consensus size: 48
42427403 CAAGATAAAT
* *
42427413 ATATATATGTGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* * *
42427461 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATTTATATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
42427509 ATAGGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
42427557 ATATGTATATGTGGTAAAGCCGAATGGCTACTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
* *
42427605 ATATTTATATGTGGTAAAGCGGAATGGCTAGTGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
42427653 ATATGTATATGTGGTAAAGCCGAATGGCTAATGTGAAATATGTATGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
*
42427701 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTAGGAG
1 ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
42427749 AT
1 AT
42427751 GTGTGTATAT
Statistics
Matches: 271, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 271 1.00
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (48 bp):
ATATGTATATGTGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAG
Found at i:42427949 original size:37 final size:37
Alignment explanation
Indices: 42427891--42427993 Score: 170
Period size: 37 Copynumber: 2.8 Consensus size: 37
42427881 GGAAATATAT
*
42427891 TCCGGGTAAGACCCGACGACTACGTGTGGAGATTATG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
* *
42427928 TCCGAGTAAGACCCGATGACTACGTGTGGAGATTTTG
1 TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
*
42427965 TCCGGGTAAGACCCGATAACTACGTGTGG
1 TCCGGGTAAGACCCGATGACTACGTGTGG
42427994 GGACTATTCG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.24, C:0.21, G:0.31, T:0.23
Consensus pattern (37 bp):
TCCGGGTAAGACCCGATGACTACGTGTGGAGATTATG
Found at i:42429340 original size:40 final size:40
Alignment explanation
Indices: 42429281--42429572 Score: 458
Period size: 40 Copynumber: 7.3 Consensus size: 40
42429271 GAGTTATATA
* * *
42429281 TATCCGGGCTAAGTCCCGAAGAGCATTCATACTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
*
42429321 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTACTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
* ** *
42429361 AATCCGATCTAAGTTTCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
*
42429401 TATCCGGGCTAAGTTTCGAAGAGCATTCGTGCTAGTGATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
* *
42429441 TATCCGGGCTAAGTTCCAAAGAGCATTCGTGCTAGTAATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
*
42429481 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTAATG
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
* *
42429521 TATCCGGGCTAAGTTCCGAAAAGCATTCGTGCTAGTGATA
1 TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
42429561 TATCCGGGCTAA
1 TATCCGGGCTAA
42429573 ACCTCGAAGG
Statistics
Matches: 233, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 233 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTAAGTTCCGAAGAGCATTCGTGCTAGTGATG
Found at i:42429644 original size:28 final size:27
Alignment explanation
Indices: 42429604--42429760 Score: 143
Period size: 28 Copynumber: 5.6 Consensus size: 27
42429594 GAGTTATGAG
* * *
42429604 GCACTGTGTGTGCAAGTTCTTCAACCGA
1 GCACTATGTGTGCGAGTTCTT-AATCGA
* * * * *
42429632 GCACTATGTGTGCCAGATCAGTAGTTGA
1 GCACTATGTGTGCGAGTTC-TTAATCGA
42429660 GGCACTATGTGTGCGAGTTCTTCAATCGA
1 -GCACTATGTGTGCGAGTTCTT-AATCGA
** *
42429689 GCACTATGTGTGCGAGATTGGTAATTGA
1 GCACTATGTGTGCGAG-TTCTTAATCGA
42429717 GGCACTATGTGTGCGAGTTCTTTAATCGA
1 -GCACTATGTGTGCGAGTTC-TTAATCGA
*
42429746 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
42429761 AATCAGTCAG
Statistics
Matches: 104, Mismatches: 19, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
28 57 0.55
29 47 0.45
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (27 bp):
GCACTATGTGTGCGAGTTCTTAATCGA
Found at i:42429667 original size:29 final size:28
Alignment explanation
Indices: 42429632--42429760 Score: 118
Period size: 29 Copynumber: 4.5 Consensus size: 28
42429622 CTTCAACCGA
* *
42429632 GCACTATGTGTGCCAGATCAGTAGTTGAG
1 GCACTATGTGTGCGAGATC-GTAATTGAG
* * *
42429661 GCACTATGTGTGCGAGTTCTTCAATCGA-
1 GCACTATGTGTGCGAGATCGT-AATTGAG
*
42429689 GCACTATGTGTGCGAGATTGGTAATTGAG
1 GCACTATGTGTGCGAGA-TCGTAATTGAG
* * *
42429718 GCACTATGTGTGCGAGTTCTTTAATCGA-
1 GCACTATGTGTGCGAGATC-GTAATTGAG
*
42429746 GCGCTATGTGTGCGA
1 GCACTATGTGTGCGA
42429761 AATCAGTCAG
Statistics
Matches: 82, Mismatches: 14, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
28 37 0.45
29 45 0.55
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (28 bp):
GCACTATGTGTGCGAGATCGTAATTGAG
Found at i:42429690 original size:57 final size:57
Alignment explanation
Indices: 42429600--42429788 Score: 247
Period size: 57 Copynumber: 3.3 Consensus size: 57
42429590 GCTGGAGTTA
* * * *
42429600 TGAGGCACTGTGTGTGCAAGTTCTTCAACCGAGCACTATGTGTGCCAGATCAGTAGT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAGT
** *
42429657 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATTGGTAAT
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAGT
* * *
42429714 TGAGGCACTATGTGTGCGAGTTCTTTAATCGAGCGCTATGTGTGCGAAATCAGTCAG-
1 TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGT-AGT
* *
42429771 TG-GGCACTGTGTATGCGA
1 TGAGGCACTATGTGTGCGA
42429789 AGTGTGTTTC
Statistics
Matches: 116, Mismatches: 15, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
56 14 0.12
57 101 0.87
58 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (57 bp):
TGAGGCACTATGTGTGCGAGTTCTTCAATCGAGCACTATGTGTGCGAGATCAGTAGT
Found at i:42433540 original size:40 final size:40
Alignment explanation
Indices: 42433481--42433748 Score: 464
Period size: 40 Copynumber: 6.7 Consensus size: 40
42433471 GAGCATTGGA
*
42433481 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
42433521 ATATATCCGGGCTAGGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
42433561 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
42433601 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
42433641 ATATATCCGGGCTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
42433681 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
42433721 ATATGTTCGGGCTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
42433749 ATGTGTTTGC
Statistics
Matches: 218, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 218 1.00
ACGTcount: A:0.30, C:0.20, G:0.28, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:42442102 original size:40 final size:40
Alignment explanation
Indices: 42442043--42442310 Score: 473
Period size: 40 Copynumber: 6.7 Consensus size: 40
42442033 GAGCATTGGA
*
42442043 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
42442083 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
42442123 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
42442163 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
42442203 ATATATCCGGGCTAAAACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
42442243 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
42442283 ATATGTTCGGGCTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
42442311 ATGTGTTTGC
Statistics
Matches: 219, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 219 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:42448145 original size:17 final size:17
Alignment explanation
Indices: 42448119--42448156 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
42448109 ATAGAATAGA
42448119 ATAATAATATAAAATAT
1 ATAATAATATAAAATAT
* *
42448136 ATAATGATATAATATAT
1 ATAATAATATAAAATAT
42448153 -TAAT
1 ATAAT
42448157 TTAATAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATAATAATATAAAATAT
Found at i:42449102 original size:32 final size:34
Alignment explanation
Indices: 42449028--42449102 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 34
42449018 CCACTACATA
*
42449028 ATATGGTAATATAGTATATAATTATTACTAAAAG
1 ATATGGTAATATAGTATATAATTAGTACTAAAAG
42449062 ATAT--TAATATA-T-TATAGATT-GTACTAAAAG
1 ATATGGTAATATAGTATATA-ATTAGTACTAAAAG
42449092 ATATGGTAATA
1 ATATGGTAATA
42449103 CCACATATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
30 17 0.46
31 4 0.11
32 12 0.32
34 4 0.11
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.39
Consensus pattern (34 bp):
ATATGGTAATATAGTATATAATTAGTACTAAAAG
Found at i:42449257 original size:58 final size:57
Alignment explanation
Indices: 42449152--42449261 Score: 125
Period size: 58 Copynumber: 1.9 Consensus size: 57
42449142 TTTGATATAA
* * * *
42449152 TATTACAAATTATAATAATATATATTATGTATTCTTAGTATAGCATATGATATAGTAT
1 TATTACAAATTATAATAATATATATTATATATTATTAATAAAGCATAT-ATATAGTAT
* *
42449210 TATTACATAA-TATAATAATATATTTTATAT-TTATTAATACAATCATATATAT
1 TATTACA-AATTATAATAATATATATTATATATTATTAATA-AAGCATATATAT
42449262 GACATTAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
57 11 0.25
58 31 0.70
59 2 0.05
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (57 bp):
TATTACAAATTATAATAATATATATTATATATTATTAATAAAGCATATATATAGTAT
Found at i:42449795 original size:21 final size:21
Alignment explanation
Indices: 42449756--42449795 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42449746 AACTCTTAAT
* * *
42449756 ATATTATATTATATGATATGG
1 ATATAATATTACATAATATGG
42449777 ATATAATATTACATAATAT
1 ATATAATATTACATAATAT
42449796 AATATAACAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (21 bp):
ATATAATATTACATAATATGG
Found at i:42449797 original size:15 final size:17
Alignment explanation
Indices: 42449777--42449814 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
42449767 TATGATATGG
*
42449777 ATATAATATTAC-A-TA
1 ATATAATATAACAATTA
42449792 ATATAATATAACAATTA
1 ATATAATATAACAATTA
42449809 ATATAA
1 ATATAA
42449815 CTTTTAATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 11 0.55
16 1 0.05
17 8 0.40
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (17 bp):
ATATAATATAACAATTA
Found at i:42463256 original size:5 final size:5
Alignment explanation
Indices: 42463248--42463285 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
42463238 AGAAGAGAAC
42463248 GGGAA GGGAA GGGAA -GGAA GGGAA GGGAA -GGAA GGGAA
1 GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA GGGAA
42463286 AAAAGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 8 0.26
5 23 0.74
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (5 bp):
GGGAA
Found at i:42463266 original size:14 final size:14
Alignment explanation
Indices: 42463249--42463285 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
42463239 GAAGAGAACG
42463249 GGAAGGGAAGGGAA
1 GGAAGGGAAGGGAA
42463263 GGAAGGGAAGGGAA
1 GGAAGGGAAGGGAA
42463277 GGAAGGGAA
1 GGAAGGGAA
42463286 AAAAGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (14 bp):
GGAAGGGAAGGGAA
Found at i:42463268 original size:9 final size:10
Alignment explanation
Indices: 42463248--42463285 Score: 62
Period size: 9 Copynumber: 4.0 Consensus size: 10
42463238 AGAAGAGAAC
42463248 GGGAAGGGAA
1 GGGAAGGGAA
42463258 GGGAA-GGAA
1 GGGAAGGGAA
42463267 GGGAAGGGAA
1 GGGAAGGGAA
42463277 -GGAAGGGAA
1 GGGAAGGGAA
42463286 AAAAGAAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 18 0.67
10 9 0.33
ACGTcount: A:0.42, C:0.00, G:0.58, T:0.00
Consensus pattern (10 bp):
GGGAAGGGAA
Found at i:42467685 original size:9 final size:9
Alignment explanation
Indices: 42467672--42467729 Score: 71
Period size: 9 Copynumber: 6.4 Consensus size: 9
42467662 TTTGGTTAAA
*
42467672 AATTAACCA
1 AATTAACCG
*
42467681 AATTACCCG
1 AATTAACCG
*
42467690 AATTAATCG
1 AATTAACCG
*
42467699 AATTACCCG
1 AATTAACCG
42467708 AATTAACCG
1 AATTAACCG
*
42467717 ACTTAACCG
1 AATTAACCG
42467726 AATT
1 AATT
42467730 CCCCGAATTC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 40 1.00
ACGTcount: A:0.41, C:0.24, G:0.09, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:42467695 original size:18 final size:18
Alignment explanation
Indices: 42467672--42467757 Score: 84
Period size: 18 Copynumber: 4.8 Consensus size: 18
42467662 TTTGGTTAAA
*
42467672 AATTAACCAAATTACCCG
1 AATTAACCGAATTACCCG
*
42467690 AATTAATCGAATTACCCG
1 AATTAACCGAATTACCCG
* *
42467708 AATTAACCGACTTAACCG
1 AATTAACCGAATTACCCG
**
42467726 AATTCCCCGAATT-CCTCG
1 AATTAACCGAATTACC-CG
**
42467744 AATTGCCCGAATTA
1 AATTAACCGAATTA
42467758 TATGTTTTTT
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
17 1 0.02
18 55 0.98
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:42467711 original size:27 final size:27
Alignment explanation
Indices: 42467672--42467757 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 27
42467662 TTTGGTTAAA
* * *
42467672 AATTAACCAAATTACCCGAATTAATCG
1 AATTACCCGAATTACCCGAATTAACCG
* *
42467699 AATTACCCGAATTAACCGACTTAACCG
1 AATTACCCGAATTACCCGAATTAACCG
* **
42467726 AATTCCCCGAATT-CCTCGAATTGCCCG
1 AATTACCCGAATTACC-CGAATTAACCG
42467753 AATTA
1 AATTA
42467758 TATGTTTTTT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
26 1 0.02
27 46 0.98
ACGTcount: A:0.36, C:0.28, G:0.10, T:0.26
Consensus pattern (27 bp):
AATTACCCGAATTACCCGAATTAACCG
Found at i:42467735 original size:9 final size:9
Alignment explanation
Indices: 42467723--42467756 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
42467713 ACCGACTTAA
42467723 CCGAATTCC
1 CCGAATTCC
42467732 CCGAATTCC
1 CCGAATTCC
* *
42467741 TCGAATTGC
1 CCGAATTCC
42467750 CCGAATT
1 CCGAATT
42467757 ATATGTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (9 bp):
CCGAATTCC
Found at i:42472460 original size:24 final size:24
Alignment explanation
Indices: 42472401--42472464 Score: 69
Period size: 24 Copynumber: 2.7 Consensus size: 24
42472391 AAATTTGTAT
* * *
42472401 TTTATTTATATTTATTGATTATAA
1 TTTATTTATATTTATTAAATAAAA
42472425 TTAATATTTAT-TTT-TTAAATAAAA
1 TT--TATTTATATTTATTAAATAAAA
42472449 TTTATTTATATTTATT
1 TTTATTTATATTTATT
42472465 GTAAAACCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
22 7 0.21
23 3 0.09
24 13 0.39
25 3 0.09
26 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTATTTATATTTATTAAATAAAA
Found at i:42486958 original size:26 final size:27
Alignment explanation
Indices: 42486929--42486988 Score: 88
Period size: 26 Copynumber: 2.3 Consensus size: 27
42486919 TTTACCCTAG
*
42486929 TAAAATTTTTGACAATTTT-ACCCCGA
1 TAAAATTTTTGACAATTTTGACCCCAA
*
42486955 TAAAA-TTTTGACAATTTTGCCCCCAA
1 TAAAATTTTTGACAATTTTGACCCCAA
42486981 TAAAATTT
1 TAAAATTT
42486989 CGAGAAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
25 13 0.43
26 15 0.50
27 2 0.07
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (27 bp):
TAAAATTTTTGACAATTTTGACCCCAA
Found at i:42489950 original size:23 final size:26
Alignment explanation
Indices: 42489917--42489967 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
42489907 ATAGTAATAA
*
42489917 GACAACA-TTTTAAAAA-TAATATAT
1 GACAACATTTTTAAAAACAAATATAT
42489941 GACAA-ATTTTTAAAAACAAATATAT
1 GACAACATTTTTAAAAACAAATATAT
42489966 GA
1 GA
42489968 TAATAAATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 1 0.04
24 14 0.58
25 9 0.38
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (26 bp):
GACAACATTTTTAAAAACAAATATAT
Found at i:42494646 original size:18 final size:18
Alignment explanation
Indices: 42494625--42494687 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
42494615 AAAAAACTAC
*
42494625 ATATATTTTAATTTTTTT
1 ATATATTTTAAATTTTTT
*
42494643 ATATATTTTGAAAGTTTTT
1 ATATATTTT-AAATTTTTT
*
42494662 ATAT-TTTTAAATTTTAT
1 ATATATTTTAAATTTTTT
42494679 -TATATTTTA
1 ATATATTTTA
42494688 TTATTTGTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
16 3 0.08
17 12 0.31
18 13 0.33
19 11 0.28
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (18 bp):
ATATATTTTAAATTTTTT
Found at i:42494666 original size:17 final size:17
Alignment explanation
Indices: 42494639--42494686 Score: 60
Period size: 17 Copynumber: 2.7 Consensus size: 17
42494629 ATTTTAATTT
42494639 TTTTATATATTTTGAAAG
1 TTTT-TATATTTTGAAAG
* *
42494657 TTTTTATATTTTTAAAT
1 TTTTTATATTTTGAAAG
42494674 TTTATTATATTTT
1 TTT-TTATATTTT
42494687 ATTATTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 14 0.52
18 13 0.48
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (17 bp):
TTTTTATATTTTGAAAG
Found at i:42503690 original size:21 final size:21
Alignment explanation
Indices: 42503630--42503707 Score: 81
Period size: 21 Copynumber: 3.7 Consensus size: 21
42503620 AAATTAAATC
* *
42503630 TCTAAGATTTCA-AAATCATA
1 TCTAAGATTGCATATATCATA
42503650 TCTTCCAAGATTGC--ATATCATA
1 TC-T--AAGATTGCATATATCATA
*
42503672 TTTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
42503693 TCTAAGATTGCATAT
1 TCTAAGATTGCATAT
42503708 CCTTGAAGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 8 0.16
20 2 0.04
21 24 0.49
22 8 0.16
23 7 0.14
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.38
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:42505550 original size:13 final size:13
Alignment explanation
Indices: 42505532--42505608 Score: 91
Period size: 13 Copynumber: 5.9 Consensus size: 13
42505522 AGTTCTTCAT
42505532 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
42505545 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* * *
42505558 TGTTTTTCAAAAG
1 TGCTTTTGAGAAG
*
42505571 TACTTTTGAGAAG
1 TGCTTTTGAGAAG
* * *
42505584 TACTTTTTAAAAG
1 TGCTTTTGAGAAG
42505597 TGCTTTTGAGAA
1 TGCTTTTGAGAA
42505609 ATTTGATTGT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 52 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.42
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:42505877 original size:19 final size:20
Alignment explanation
Indices: 42505833--42505882 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
42505823 ATTAATTATT
*
42505833 TATAAAATTTAATTAGAATA
1 TATAAAATATAATTAGAATA
*
42505853 TATAAAATATATTTA-AATA
1 TATAAAATATAATTAGAATA
*
42505872 T-TTAAATATAA
1 TATAAAATATAA
42505883 AATTAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 8 0.31
19 5 0.19
20 13 0.50
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TATAAAATATAATTAGAATA
Found at i:42510674 original size:18 final size:19
Alignment explanation
Indices: 42510635--42510675 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
42510625 AAAAATTACA
*
42510635 AAAATTCAAAATAATTTCT
1 AAAATTCAAAATAATTTAT
*
42510654 AAAATTTAAAAT-ATTTAT
1 AAAATTCAAAATAATTTAT
42510672 AAAA
1 AAAA
42510676 AAATTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAATTCAAAATAATTTAT
Found at i:42510676 original size:19 final size:20
Alignment explanation
Indices: 42510634--42510686 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 20
42510624 CAAAAATTAC
*
42510634 AAAAATTCAAAATAATTTCT
1 AAAAATTCAAAATAATTTAT
*
42510654 -AAAATTTAAAAT-ATTTAT
1 AAAAATTCAAAATAATTTAT
42510672 AAAAAAATTCAAAAT
1 --AAAAATTCAAAAT
42510687 TTAAATTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.19
19 11 0.41
21 11 0.41
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAT
Found at i:42510713 original size:28 final size:28
Alignment explanation
Indices: 42510653--42510713 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
42510643 AAATAATTTC
42510653 TAAAATTTAAAATATTTATAAAAAAATT
1 TAAAATTTAAAATATTTATAAAAAAATT
* * * *
42510681 CAAAATTT-AAATTTTTTTTAAAAAATT
1 TAAAATTTAAAATATTTATAAAAAAATT
42510708 ATAAAA
1 -TAAAA
42510714 AATTAAAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (28 bp):
TAAAATTTAAAATATTTATAAAAAAATT
Found at i:42510714 original size:10 final size:10
Alignment explanation
Indices: 42510699--42510762 Score: 71
Period size: 10 Copynumber: 6.5 Consensus size: 10
42510689 AAATTTTTTT
42510699 TAAAAAATTA
1 TAAAAAATTA
42510709 TAAAAAATTA
1 TAAAAAATTA
*
42510719 -AAAAAATTC
1 TAAAAAATTA
42510728 TAAAAAATATA
1 TAAAAAAT-TA
*
42510739 TAAAGAAAGT-
1 TAAA-AAATTA
42510749 TAAAAAATTA
1 TAAAAAATTA
42510759 -AAAA
1 TAAAA
42510763 TTTTCTAGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
9 16 0.35
10 21 0.46
11 6 0.13
12 3 0.07
ACGTcount: A:0.70, C:0.02, G:0.03, T:0.25
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:42510714 original size:29 final size:28
Alignment explanation
Indices: 42510654--42510721 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
42510644 AATAATTTCT
*
42510654 AAAATTTAAAATATTTATAAAAAAATTC
1 AAAATTTAAAATATTTATAAAAAAATTA
* * * *
42510682 AAAATTTAAATTTTTTTTAAAAAATTATA
1 AAAATTTAAAATATTTATAAAAAAAT-TA
*
42510711 AAAAATTAAAA
1 AAAATTTAAAA
42510722 AAATTCTAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.38
Consensus pattern (28 bp):
AAAATTTAAAATATTTATAAAAAAATTA
Found at i:42510722 original size:19 final size:18
Alignment explanation
Indices: 42510700--42510762 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 18
42510690 AATTTTTTTT
42510700 AAAAAATTATAAAAAATTA
1 AAAAAATT-TAAAAAATTA
42510719 AAAAAATTCTAAAAAATATA
1 AAAAAATT-TAAAAAAT-TA
*
42510739 TAAAGAAAGTTAAAAAATTA
1 -AAA-AAATTTAAAAAATTA
42510759 AAAA
1 AAAA
42510763 TTTTCTAGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
18 1 0.03
19 19 0.49
20 4 0.10
21 11 0.28
22 4 0.10
ACGTcount: A:0.71, C:0.02, G:0.03, T:0.24
Consensus pattern (18 bp):
AAAAAATTTAAAAAATTA
Found at i:42511256 original size:17 final size:18
Alignment explanation
Indices: 42511230--42511279 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
42511220 AAATATTTTA
42511230 AAAAATTATAAAAACACT
1 AAAAATTATAAAAACACT
*
42511248 AAAAA-TATAAAAACATT
1 AAAAATTATAAAAACACT
*
42511265 AAAATTTTATAAAAA
1 AAAA-ATTATAAAAA
42511280 ATATAGAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 15 0.54
18 5 0.18
19 8 0.29
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAATTATAAAAACACT
Found at i:42511349 original size:22 final size:22
Alignment explanation
Indices: 42511276--42511349 Score: 64
Period size: 22 Copynumber: 3.4 Consensus size: 22
42511266 AAATTTTATA
* *
42511276 AAAAATATAGA-AAAATATCTT
1 AAAATTATAGATAAAATATATT
* *
42511297 AAAATTTATAAAT-AAATAAATAT
1 AAAA-TTATAGATAAAATATAT-T
*
42511320 AAAA-TATAGATAAAATTTATT
1 AAAATTATAGATAAAATATATT
42511341 AAAATTATA
1 AAAATTATA
42511350 AATTTTTTTT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
21 15 0.37
22 21 0.51
23 5 0.12
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (22 bp):
AAAATTATAGATAAAATATATT
Found at i:42511461 original size:35 final size:35
Alignment explanation
Indices: 42511422--42511492 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
42511412 AAAAATGTGA
42511422 AAAAAATTATAAGATTTAAAGTTATTATCTCCACT
1 AAAAAATTATAAGATTTAAAGTTATTATCTCCACT
42511457 AAAAAATTATAAGATTTAAAGTTATTATCTCCACT
1 AAAAAATTATAAGATTTAAAGTTATTATCTCCACT
42511492 A
1 A
42511493 TGTTTAATGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (35 bp):
AAAAAATTATAAGATTTAAAGTTATTATCTCCACT
Found at i:42517066 original size:33 final size:32
Alignment explanation
Indices: 42517029--42517207 Score: 110
Period size: 33 Copynumber: 5.4 Consensus size: 32
42517019 TGGCCCTGCC
* * *
42517029 ATGGTCTTACATTCATAGTGCCATAACCCAATT
1 ATGGTCTTACA-TCAGAATGCCATAACCCAACT
*
42517062 ATGGTCTTATCATCAGAATGCCATAGCCCAACT
1 ATGGTCTTA-CATCAGAATGCCATAACCCAACT
* * *** *
42517095 ATGGTCTTACGTAT-AAACACCGCCATGGTCCAACC
1 ATGGTCTTAC--ATCAGA-A-TGCCATAACCCAACT
* * *
42517130 ATGGTCTTACGTCCATAGTGCCATAACCCAA-T
1 ATGGTCTTACAT-CAGAATGCCATAACCCAACT
* * *
42517162 CATGGTCTTATCATCGGAATGCCATAGCCCAGCT
1 -ATGGTCTTA-CATCAGAATGCCATAACCCAACT
*
42517196 GTGGTCTTACAT
1 ATGGTCTTACAT
42517208 ATAAACATTG
Statistics
Matches: 112, Mismatches: 24, Indels: 21
0.71 0.15 0.13
Matches are distributed among these distances:
32 4 0.04
33 77 0.69
34 8 0.07
35 23 0.21
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.28
Consensus pattern (32 bp):
ATGGTCTTACATCAGAATGCCATAACCCAACT
Found at i:42517154 original size:101 final size:101
Alignment explanation
Indices: 42517027--42517242 Score: 333
Period size: 101 Copynumber: 2.1 Consensus size: 101
42517017 CATGGCCCTG
* * *
42517027 CCATGGTCTTACATTCATAGTGCCATAACCCAATTATGGTCTTATCATCAGAATGCCATAGCCCA
1 CCATGGTCTTACGTCCATAGTGCCATAACCCAATCATGGTCTTATCATCAGAATGCCATAGCCCA
* *
42517092 ACTATGGTCTTACGTATAAACACCGCCATGGTCCAA
66 ACTATGGTCTTACATATAAACACCGCCATGGTCAAA
*
42517128 CCATGGTCTTACGTCCATAGTGCCATAACCCAATCATGGTCTTATCATCGGAATGCCATAGCCCA
1 CCATGGTCTTACGTCCATAGTGCCATAACCCAATCATGGTCTTATCATCAGAATGCCATAGCCCA
* * ** *
42517193 GCTGTGGTCTTACATATAAACATTGCGATGGTCAAA
66 ACTATGGTCTTACATATAAACACCGCCATGGTCAAA
42517229 CCATGGTCTTACGT
1 CCATGGTCTTACGT
42517243 TTGAATAATT
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
101 104 1.00
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (101 bp):
CCATGGTCTTACGTCCATAGTGCCATAACCCAATCATGGTCTTATCATCAGAATGCCATAGCCCA
ACTATGGTCTTACATATAAACACCGCCATGGTCAAA
Found at i:42525653 original size:47 final size:47
Alignment explanation
Indices: 42525581--42526205 Score: 1040
Period size: 47 Copynumber: 13.2 Consensus size: 47
42525571 TTTAGGATTC
*
42525581 TATGTGATAAGGCCTAATGGCCGATGTGATAAATGTGAAAGTGTATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* *
42525628 TATGTGATAAGGCCTAATAGTCGATGTGATGAATGTGAAAGTGTATATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
42525677 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
*
42525726 TATGTGATAAGGCCTAATGGCCGATGTGATAAATGTGAAAGTGTATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
42525773 TATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
42525822 TATGTGATAA-GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
42525868 TATGTGATAAGG-CTAAT-GCCGATGTGATAAATGTGAAAGTGTATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
42525913 TATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
42525960 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
42526007 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
42526054 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
42526101 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
* * * * * * *
42526148 TATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA
1 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
42526195 AATGTGATAAG
1 TATGTGATAAG
42526206 TCCCGAAGGG
Statistics
Matches: 549, Mismatches: 22, Indels: 14
0.94 0.04 0.02
Matches are distributed among these distances:
45 39 0.07
46 24 0.04
47 348 0.63
48 31 0.06
49 107 0.19
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
Found at i:42526380 original size:37 final size:37
Alignment explanation
Indices: 42526324--42526402 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
42526314 CCGAGCTCTA
* * *
42526324 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
42526361 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
42526398 AAGAC
1 AAGAC
42526403 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Done.