Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
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: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 176 of 210
Found at i:58485758 original size:15 final size:15
Alignment explanation
Indices: 58485738--58485794 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
58485728 CCTAATGCAT
58485738 CTAACCCCTAAACCC
1 CTAACCCCTAAACCC
58485753 CTAACCCTCT-AACCC
1 CTAACCC-CTAAACCC
* * *
58485768 CTAAACCTTAAATCC
1 CTAACCCCTAAACCC
*
58485783 C-AACCCTTAAAC
1 CTAACCCCTAAAC
58485795 TATAATCACT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
14 10 0.29
15 23 0.66
16 2 0.06
ACGTcount: A:0.35, C:0.46, G:0.00, T:0.19
Consensus pattern (15 bp):
CTAACCCCTAAACCC
Found at i:58485774 original size:8 final size:7
Alignment explanation
Indices: 58485738--58485771 Score: 50
Period size: 8 Copynumber: 4.6 Consensus size: 7
58485728 CCTAATGCAT
58485738 CTAACCC
1 CTAACCC
58485745 CTAAACCC
1 CT-AACCC
58485753 CTAACCC
1 CTAACCC
58485760 TCTAACCC
1 -CTAACCC
58485768 CTAA
1 CTAA
58485772 ACCTTAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 11 0.44
8 14 0.56
ACGTcount: A:0.32, C:0.50, G:0.00, T:0.18
Consensus pattern (7 bp):
CTAACCC
Found at i:58485872 original size:298 final size:295
Alignment explanation
Indices: 58485312--58486478 Score: 1537
Period size: 298 Copynumber: 4.0 Consensus size: 295
58485302 AATATATTTG
*
58485312 ATTTATTATTATCTCTTTTACAATTATTTAAGAACATATTTAAAATATAAATTAAAAAATAATTA
1 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATTA
* * * * * * * *
58485377 ATCTAAACTCAAAACCTTAACCCGACCCGTGAATCCCTAAACCTTAAATCCTTAACTCT-TAACC
66 ATCTAAACCCAAAACCCTAACCCGACCCCTGAATCCCT-AACTTTTAACCCCTAAATCTCTAACC
* * *
58485441 CATAACGTCTAACCCCAAACCCCTAACCCTTAAACCTTAAATCCCAACCCTTAAACCATAATCCC
130 C----C-T-AAACCCCTAACCCCTAACCCCTAAACCTTAAATCCCAACCCTTAAACCATAAT-CC
* *
58485506 TAATCCATAATCCCTAAATTCATACTCCTTAAACCTTAAAATA-TGAACTCCTAAACCAACCTTA
188 TAATCCATAATCCCTAAATCCATACTCCCTAAACCTTAAAATAGT-AACTCCTAAACCAACCTTA
58485570 AATCTTAAATAAATCATATACCCTAAACAAAAAACCCTAAACAA
252 AATCTTAAATAAATCATATACCCTAAACAAAAAACCCTAAACAA
58485614 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATTA
1 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATTA
* *
58485679 ATCTAAATCCAAAACCCTAACTCGACCCCTGAATCCCTAACTTTTAACCCCT-AATGCATCTAAC
66 ATCTAAACCCAAAACCCTAACCCGACCCCTGAATCCCTAACTTTTAACCCCTAAAT-C-TCTAAC
*
58485743 CCCTAAACCCCTAACCCTCTAACCCCTAAACCTTAAATCCCAACCCTTAAACTATAATCACTAAT
129 CCCTAAACCCCTAACCC-CTAACCCCTAAACCTTAAATCCCAACCCTTAAACCATAATC-CTAAT
* *
58485808 CCAGAATCCCTAAATCCATACTCTCTAAACCTTAAAATA-TGAACTCCTAAACCAACCTTAAATC
192 CCATAATCCCTAAATCCATACTCCCTAAACCTTAAAATAGT-AACTCCTAAACCAACCTTAAATC
58485872 TTAAATAAATCATATACCCTAAACAAAAAACCCTAAACAA
256 TTAAATAAATCATATACCCTAAACAAAAAACCCTAAACAA
* *
58485912 ATTTATTATTATCTCTTTTACAATTATATAAGAAAATATTTAAAATATAAATT-CAAAA-AATTA
1 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATTA
* * * * * * *
58485975 ATCTACACGCCCAAAATCCTAACTCAAGCCCTAAATCCCT-A-----AA-CCCTAAATCCCTAA-
66 ATCTA-A-ACCCAAAACCCTAACCCGACCCCTGAATCCCTAACTTTTAACCCCTAAATCTCTAAC
* * * ** * *
58486032 CTCTTAATCCCTAACGTCTAACCCTTAAACCTTAAATCTCAACCCTTAAACCATAATCTCTAATC
129 CCCTAAACCCCTAACCCCTAACCCCTAAACCTTAAATCCCAACCCTTAAACCATAATC-CTAATC
* * *
58486097 CATAATCCCTAAA-CCATACTCCCTAAAACTTAAAATAGTAACTCCTAAACTAGCCTTAAATCTT
193 CATAATCCCTAAATCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCAACCTTAAATCTT
58486161 AAATAAATCATATACCCTAAACAAAAAACCCTAAACAA
258 AAATAAATCATATACCCTAAACAAAAAACCCTAAACAA
58486199 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATTA
1 ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATTA
* * *
58486264 ATCTAAACCCAAAACCCTAACCCGACCACTGAATCCCTAACTTTTAACCCCTCACTCATCTAACC
66 ATCTAAACCCAAAACCCTAACCCGACCCCTGAATCCCTAACTTTTAACCCCTAAATC-TCTAACC
* *
58486329 CCTAAACCCATAAATCCCTAACCCCTAAACCTTAAATCCCAACCC-T------T-A----AA-CC
130 CCTAAACCCCT-AACCCCTAACCCCTAAACCTTAAATCCCAACCCTTAAACCATAATCCTAATCC
**
58486381 ATAATCCCT-AATCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCGGCCTTAAATCTTA
194 ATAATCCCTAAATCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCAACCTTAAATCTTA
* *
58486445 AATAAATCATATACCCTAAACCAAAAACACTAAA
259 AATAAATCATATACCCTAAACAAAAAACCCTAAA
58486479 TTATAGTGAT
Statistics
Matches: 775, Mismatches: 68, Indels: 63
0.86 0.08 0.07
Matches are distributed among these distances:
282 2 0.00
283 92 0.12
284 2 0.00
287 160 0.21
288 63 0.08
289 23 0.03
290 5 0.01
291 5 0.01
292 5 0.01
293 2 0.00
294 7 0.01
295 4 0.01
296 19 0.02
297 46 0.06
298 222 0.29
299 1 0.00
300 2 0.00
301 11 0.01
302 98 0.13
303 6 0.01
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.28
Consensus pattern (295 bp):
ATTTATTATTATCTCTTTTACAATTATATAAGAACATATTTAAAATATAAATTAAAAAATAATTA
ATCTAAACCCAAAACCCTAACCCGACCCCTGAATCCCTAACTTTTAACCCCTAAATCTCTAACCC
CTAAACCCCTAACCCCTAACCCCTAAACCTTAAATCCCAACCCTTAAACCATAATCCTAATCCAT
AATCCCTAAATCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAACCAACCTTAAATCTTAAA
TAAATCATATACCCTAAACAAAAAACCCTAAACAA
Found at i:58486023 original size:7 final size:8
Alignment explanation
Indices: 58486003--58486031 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
58485993 CTAACTCAAG
58486003 CCCTAAAT
1 CCCTAAAT
58486011 CCCTAAA-
1 CCCTAAAT
58486018 CCCTAAAT
1 CCCTAAAT
58486026 CCCTAA
1 CCCTAA
58486032 CTCTTAATCC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.38, C:0.41, G:0.00, T:0.21
Consensus pattern (8 bp):
CCCTAAAT
Found at i:58486023 original size:15 final size:15
Alignment explanation
Indices: 58486003--58486045 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
58485993 CTAACTCAAG
58486003 CCCTAAATCCCTAAA
1 CCCTAAATCCCTAAA
58486018 CCCTAAATCCCT-AA
1 CCCTAAATCCCTAAA
* *
58486032 CTCTTAATCCCTAA
1 CCCTAAATCCCTAA
58486046 CGTCTAACCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.26
Consensus pattern (15 bp):
CCCTAAATCCCTAAA
Found at i:58486042 original size:14 final size:14
Alignment explanation
Indices: 58486003--58486046 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
58485993 CTAACTCAAG
58486003 CCCTAAATCCCTAAA
1 CCCTAAATCCCT-AA
58486018 CCCTAAATCCCTAA
1 CCCTAAATCCCTAA
* *
58486032 CTCTTAATCCCTAA
1 CCCTAAATCCCTAA
58486046 C
1 C
58486047 GTCTAACCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.34, C:0.41, G:0.00, T:0.25
Consensus pattern (14 bp):
CCCTAAATCCCTAA
Found at i:58486058 original size:21 final size:20
Alignment explanation
Indices: 58486014--58486108 Score: 64
Period size: 21 Copynumber: 4.5 Consensus size: 20
58486004 CCTAAATCCC
* *
58486014 TAAACCCTAAATCCCTAACTCT
1 TAAACCCT-AA-CTCTAACCCT
*
58486036 TAATCCCTAACGTCTAACCCT
1 TAAACCCTAAC-TCTAACCCT
* *
58486057 TAAACCTTAAATCTCAACCCT
1 TAAACCCTAACTCT-AACCCT
* * *
58486078 TAAACCATAATCTCTAATCCA
1 TAAACCCTAA-CTCTAACCCT
*
58486099 TAATCCCTAA
1 TAAACCCTAA
58486109 ACCATACTCC
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 4 0.07
21 44 0.76
22 10 0.17
ACGTcount: A:0.37, C:0.34, G:0.01, T:0.28
Consensus pattern (20 bp):
TAAACCCTAACTCTAACCCT
Found at i:58486099 original size:14 final size:14
Alignment explanation
Indices: 58486078--58486123 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
58486068 TCTCAACCCT
*
58486078 TAAACCATAATCTC
1 TAAACCATAATCCC
*
58486092 TAATCCATAATCCC
1 TAAACCATAATCCC
*
58486106 TAAACCATACTCCC
1 TAAACCATAATCCC
58486120 TAAA
1 TAAA
58486124 ACTTAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.41, C:0.33, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCATAATCCC
Found at i:58486378 original size:21 final size:22
Alignment explanation
Indices: 58486323--58486391 Score: 97
Period size: 21 Copynumber: 3.2 Consensus size: 22
58486313 CCTCACTCAT
58486323 CTAACCCCTAAACCCATAAATCC
1 CTAACCCCTAAA-CCATAAATCC
*
58486346 CTAACCCCTAAACCTTAAATCC
1 CTAACCCCTAAACCATAAATCC
*
58486368 C-AACCCTTAAACCAT-AATCC
1 CTAACCCCTAAACCATAAATCC
58486388 CTAA
1 CTAA
58486392 TCCATACTCC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 6 0.14
21 14 0.33
22 10 0.24
23 12 0.29
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (22 bp):
CTAACCCCTAAACCATAAATCC
Found at i:58486395 original size:585 final size:573
Alignment explanation
Indices: 58485312--58486478 Score: 1665
Period size: 585 Copynumber: 2.0 Consensus size: 573
58485302 AATATATTTG
* *
58485312 ATTTATTATTATCTCTTTTACAATTATTTAAGAACATATTTAAAATATAAATTAAAAAATAATTA
1 ATTTATTATTATCTCTTTTACAATTATATAAGAAAATATTTAAAATATAAATTAAAAAATAATTA
* * * * *
58485377 ATCTAAACTCAAAACCTTAACCCGACCCGTGAATCCCTAAACCTTAAATCCTTAACTCTTAACCC
66 ATCTAAACCCAAAACCTTAACCCAACCCGTAAATCCCTAAACCCTAAATCCCTAACTCTTAACCC
58485442 ATAACGTCTAACCCCAAACCCCTAACCCTTAAACCTTAAATCCCAACCCTTAAACCATAATCCCT
131 ATAACG-CT-----------CCTAACCCTTAAACCTTAAATCCCAACCCTTAAACCATAATCCCT
* * *
58485507 AATCCATAATCCCTAAATTCATACTCCTTAAACCTTAAAATATGAACTCCTAAACCAACCTTAAA
184 AATCCATAATCCCTAAATCCATACTCCCTAAAACTTAAAATATGAACTCCTAAACCAACCTTAAA
58485572 TCTTAAATAAATCATATACCCTAAACAAAAAACCCTAAACAAATTTATTATTATCTCTTTTACAA
249 TCTTAAATAAATCATATACCCTAAACAAAAAACCCTAAACAAATTTATTATTATCTCTTTTACAA
* *
58485637 TTATATAAGAACATATTTAAAATATAAATTAAAAAATAATTAATCTAAATCCAAAACCCTAACTC
314 TTATATAAGAACATATTTAAAATATAAATTAAAAAATAATTAATCTAAACCCAAAACCCTAACCC
* *
58485702 GACCCCTGAATCCCTAACTTTTAACCCCTAATGCATCTAACCCCTAAACCCCTAACCCTCTAACC
379 GACCACTGAATCCCTAACTTTTAACCCCTAATGCATCTAACCCCTAAACCCATAACCCTCTAACC
*
58485767 CCTAAACCTTAAATCCCAACCCTTAAACTATAATCACTAATCCAGAATCCCTAAATCCATACTCT
444 CCTAAACCTTAAATCCCAACCCTTAAAC------CA-TAAT-C---A---CT-AATCCATACTCC
58485832 CTAAACCTTAAAATA-TGAACTCCTAAACCAACCTTAAATCTTAAATAAATCATATACCCTAAAC
494 CTAAACCTTAAAATAGT-AACTCCTAAACCAACCTTAAATCTTAAATAAATCATATACCCTAAAC
*
58485896 AAAAAACCCTAAACAA
558 AAAAAACACTAAACAA
*
58485912 ATTTATTATTATCTCTTTTACAATTATATAAGAAAATATTTAAAATATAAATT-CAAAA-AATTA
1 ATTTATTATTATCTCTTTTACAATTATATAAGAAAATATTTAAAATATAAATTAAAAAATAATTA
* *
58485975 ATCTACACGCCCAAAATCC-TAACTCAAGCCC-TAAATCCCTAAACCCTAAATCCCTAACTCTTA
66 ATCTA-A-ACCCAAAA-CCTTAACCCAA-CCCGTAAATCCCTAAACCCTAAATCCCTAACTCTTA
* *
58486038 ATCCC-TAACG-T-CTAACCCTTAAACCTTAAATCTCAACCCTTAAACCATAATCTCTAATCCAT
127 A-CCCATAACGCTCCTAACCCTTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAATCCAT
* *
58486100 AATCCCTAAA-CCATACTCCCTAAAACTTAAAATA-GTAACTCCTAAACTAGCCTTAAATCTTAA
191 AATCCCTAAATCCATACTCCCTAAAACTTAAAATATG-AACTCCTAAACCAACCTTAAATCTTAA
58486163 ATAAATCATATACCCTAAACAAAAAACCCTAAACAAATTTATTATTATCTCTTTTACAATTATAT
255 ATAAATCATATACCCTAAACAAAAAACCCTAAACAAATTTATTATTATCTCTTTTACAATTATAT
58486228 AAGAACATATTTAAAATATAAATTAAAAAATAATTAATCTAAACCCAAAACCCTAACCCGACCAC
320 AAGAACATATTTAAAATATAAATTAAAAAATAATTAATCTAAACCCAAAACCCTAACCCGACCAC
* *
58486293 TGAATCCCTAACTTTTAACCCCTCACT-CATCTAACCCCTAAACCCATAAATCC-CTAACCCCTA
385 TGAATCCCTAACTTTTAACCCCT-AATGCATCTAACCCCTAAACCCAT-AACCCTCTAACCCCTA
*
58486356 AACCTTAAATCCCAACCCTTAAACCATAATCCCTAATCCATACTCCCTAAACCTTAAAATAGTAA
448 AACCTTAAATCCCAACCCTTAAACCATAATCACTAATCCATACTCCCTAAACCTTAAAATAGTAA
** *
58486421 CTCCTAAACCGGCCTTAAATCTTAAATAAATCATATACCCTAAACCAAAAACACTAAA
513 CTCCTAAACCAACCTTAAATCTTAAATAAATCATATACCCTAAACAAAAAACACTAAA
58486479 TTATAGTGAT
Statistics
Matches: 529, Mismatches: 29, Indels: 48
0.87 0.05 0.08
Matches are distributed among these distances:
570 82 0.16
571 3 0.01
577 1 0.00
578 4 0.01
579 2 0.00
584 1 0.00
585 249 0.47
586 65 0.12
598 11 0.02
599 5 0.01
600 98 0.19
601 8 0.02
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.28
Consensus pattern (573 bp):
ATTTATTATTATCTCTTTTACAATTATATAAGAAAATATTTAAAATATAAATTAAAAAATAATTA
ATCTAAACCCAAAACCTTAACCCAACCCGTAAATCCCTAAACCCTAAATCCCTAACTCTTAACCC
ATAACGCTCCTAACCCTTAAACCTTAAATCCCAACCCTTAAACCATAATCCCTAATCCATAATCC
CTAAATCCATACTCCCTAAAACTTAAAATATGAACTCCTAAACCAACCTTAAATCTTAAATAAAT
CATATACCCTAAACAAAAAACCCTAAACAAATTTATTATTATCTCTTTTACAATTATATAAGAAC
ATATTTAAAATATAAATTAAAAAATAATTAATCTAAACCCAAAACCCTAACCCGACCACTGAATC
CCTAACTTTTAACCCCTAATGCATCTAACCCCTAAACCCATAACCCTCTAACCCCTAAACCTTAA
ATCCCAACCCTTAAACCATAATCACTAATCCATACTCCCTAAACCTTAAAATAGTAACTCCTAAA
CCAACCTTAAATCTTAAATAAATCATATACCCTAAACAAAAAACACTAAACAA
Found at i:58486814 original size:41 final size:41
Alignment explanation
Indices: 58486755--58486951 Score: 299
Period size: 41 Copynumber: 4.8 Consensus size: 41
58486745 AAAATATTTC
* *
58486755 TAGCGGCGCTT-TTCCAAAAATGCCACTAAAGCCCCCAGCAT
1 TAGCGGCGCTTCTT-CAAAAACGCCGCTAAAGCCCCCAGCAT
58486796 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCCAGCAT
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCCAGCAT
* * *
58486837 TAGCGGCGATTCTTCAAAAACGCCGCTAAAACCCCCAGAAT
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCCAGCAT
*
58486878 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTCAGCAT
1 TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCCAGCAT
*
58486919 TAGCGGCGCCTT-TTCAAAAACGCCCCTAAAGCC
1 TAGCGGCG-CTTCTTCAAAAACGCCGCTAAAGCC
58486952 ACGAAAGGTA
Statistics
Matches: 144, Mismatches: 10, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
41 139 0.97
42 5 0.03
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (41 bp):
TAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCCCAGCAT
Found at i:58488003 original size:87 final size:88
Alignment explanation
Indices: 58487882--58488056 Score: 343
Period size: 87 Copynumber: 2.0 Consensus size: 88
58487872 AATTTATATA
58487882 ATTATATATTAATTAATCAAATATTTAAAATAATGTATCTATATTTTATTAATTTTAGTCTTTTT
1 ATTATATATTAATTAATCAAATATTTAAAATAATGTATCTATATTTTATTAATTTTAGTCTTTTT
58487947 AATTATTTATTATGTTATAAGGT
66 AATTATTTATTATGTTATAAGGT
58487970 ATTATATATT-ATTAATCAAATATTTAAAATAATGTATCTATATTTTATTAATTTTAGTCTTTTT
1 ATTATATATTAATTAATCAAATATTTAAAATAATGTATCTATATTTTATTAATTTTAGTCTTTTT
58488034 AATTATTTATTATGTTATAAGGT
66 AATTATTTATTATGTTATAAGGT
58488057 CTACTGAATA
Statistics
Matches: 87, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 77 0.89
88 10 0.11
ACGTcount: A:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (88 bp):
ATTATATATTAATTAATCAAATATTTAAAATAATGTATCTATATTTTATTAATTTTAGTCTTTTT
AATTATTTATTATGTTATAAGGT
Found at i:58492055 original size:45 final size:45
Alignment explanation
Indices: 58492004--58492171 Score: 192
Period size: 45 Copynumber: 3.7 Consensus size: 45
58491994 ATCAACACCA
* * *
58492004 GTACATAGTCCCTATTGTATGTATATGGCATGATAGCCAAGACCG
1 GTACATAGTACCTATTGTATGTATATGGCATGATAGCCAACACTG
* * * *
58492049 GTACATAGTACCTATTTTATTTATATGGCATGAAAACCAACACTG
1 GTACATAGTACCTATTGTATGTATATGGCATGATAGCCAACACTG
* * * **
58492094 GTAAATAGTATCTGTTGTATGTATACAGCATGATAGCCAACACTG
1 GTACATAGTACCTATTGTATGTATATGGCATGATAGCCAACACTG
* * * *
58492139 GTACATACTACTTGTTGTATTTATATGGCATGA
1 GTACATAGTACCTATTGTATGTATATGGCATGA
58492172 AATTTGGCAC
Statistics
Matches: 100, Mismatches: 23, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
45 100 1.00
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (45 bp):
GTACATAGTACCTATTGTATGTATATGGCATGATAGCCAACACTG
Found at i:58492192 original size:90 final size:90
Alignment explanation
Indices: 58491990--58492208 Score: 249
Period size: 90 Copynumber: 2.4 Consensus size: 90
58491980 GTTAAAGTAA
* ** * ** *
58491990 GAAAATCAACACCAGTACATAGTCCCTATTGTATGTATATGGCATGATAGCCAAGACCGGTACAT
1 GAAAACCAACACCAGTACATAGTATCTGTTGTATGTATACAGCATGATAGCCAACACCGGTACAT
* *
58492055 AGTACCTATTTTATTTATATGGCAT
66 ACTACCTATTGTATTTATATGGCAT
** * *
58492080 GAAAACCAACACTGGTAAATAGTATCTGTTGTATGTATACAGCATGATAGCCAACACTGGTACAT
1 GAAAACCAACACCAGTACATAGTATCTGTTGTATGTATACAGCATGATAGCCAACACCGGTACAT
* *
58492145 ACTACTTGTTGTATTTATATGGCAT
66 ACTACCTATTGTATTTATATGGCAT
***** *
58492170 GAAATTTGGCACCAGTACATAGTATTTGTTGTATGTATA
1 GAAAACCAACACCAGTACATAGTATCTGTTGTATGTATA
58492209 TTCTAATTAT
Statistics
Matches: 105, Mismatches: 24, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
90 105 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (90 bp):
GAAAACCAACACCAGTACATAGTATCTGTTGTATGTATACAGCATGATAGCCAACACCGGTACAT
ACTACCTATTGTATTTATATGGCAT
Found at i:58495914 original size:16 final size:17
Alignment explanation
Indices: 58495887--58495921 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
58495877 AGAGAGTTGA
58495887 GAGAGAGGATGAGAGAT
1 GAGAGAGGATGAGAGAT
*
58495904 GAGAG-GGATGAGGGAT
1 GAGAGAGGATGAGAGAT
58495920 GA
1 GA
58495922 TTGAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.37, C:0.00, G:0.51, T:0.11
Consensus pattern (17 bp):
GAGAGAGGATGAGAGAT
Found at i:58499793 original size:20 final size:20
Alignment explanation
Indices: 58499768--58499805 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
58499758 ACCCCCTTTA
58499768 TTAACATAAA-AATTTAAATT
1 TTAACA-AAATAATTTAAATT
58499788 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
58499806 CTAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAACAAAATAATTTAAATT
Found at i:58506470 original size:16 final size:15
Alignment explanation
Indices: 58506435--58506472 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
58506425 TAAGAGAGTT
58506435 GAGA-GAGAGGGTGA
1 GAGATGAGAGGGTGA
58506449 GAGATGAGAGGGATGA
1 GAGATGAGAGGG-TGA
*
58506465 GGGATGAG
1 GAGATGAG
58506473 GGATGATTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 7 0.33
16 10 0.48
ACGTcount: A:0.34, C:0.00, G:0.55, T:0.11
Consensus pattern (15 bp):
GAGATGAGAGGGTGA
Found at i:58507514 original size:17 final size:17
Alignment explanation
Indices: 58507492--58507524 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
58507482 CACTAACATT
*
58507492 AAAATGCAATGACAATA
1 AAAATGCAACGACAATA
58507509 AAAATGCAACGACAAT
1 AAAATGCAACGACAAT
58507525 GCTCACTAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.58, C:0.15, G:0.12, T:0.15
Consensus pattern (17 bp):
AAAATGCAACGACAATA
Found at i:58507559 original size:43 final size:42
Alignment explanation
Indices: 58507512--58507641 Score: 117
Period size: 43 Copynumber: 3.1 Consensus size: 42
58507502 GACAATAAAA
*
58507512 ATGCAACGACAATGCTCACTAACAAAATGAAAATTACAGTTAC
1 ATGCAACGACAATG-TCACTAATAAAATGAAAATTACAGTTAC
* * * * * *
58507555 ATGCAATG-C-ATG-AAC-ATTAAAATG-CAATGACAGTAAAC
1 ATGCAACGACAATGTCACTAATAAAATGAAAATTACAGT-TAC
* *
58507593 ATGCAACGACAATGTTCACTAATAAGATGAAAATTACAGCTAC
1 ATGCAACGACAATG-TCACTAATAAAATGAAAATTACAGTTAC
58507636 ATGCAA
1 ATGCAA
58507642 TGCTTGAATA
Statistics
Matches: 65, Mismatches: 15, Indels: 14
0.69 0.16 0.15
Matches are distributed among these distances:
37 8 0.12
38 16 0.25
39 3 0.05
40 3 0.05
41 3 0.05
42 3 0.05
43 22 0.34
44 7 0.11
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.22
Consensus pattern (42 bp):
ATGCAACGACAATGTCACTAATAAAATGAAAATTACAGTTAC
Found at i:58507577 original size:38 final size:39
Alignment explanation
Indices: 58507529--58507649 Score: 93
Period size: 38 Copynumber: 3.0 Consensus size: 39
58507519 GACAATGCTC
*
58507529 ACTAACAAAATGAAAATTACAGTTACATGCAATGCATGA
1 ACTAATAAAATGAAAATTACAGTTACATGCAATGCATGA
* * * * * *
58507568 AC-ATTAAAATG-CAATGACAGTAAACATGCAACGACAATGTTC
1 ACTAATAAAATGAAAATTACAGT-TACATGCAATG-C-ATG--A
* * *
58507610 ACTAATAAGATGAAAATTACAGCTACATGCAATGCTTGA
1 ACTAATAAAATGAAAATTACAGTTACATGCAATGCATGA
58507649 A
1 A
58507650 TACTACAGCT
Statistics
Matches: 59, Mismatches: 16, Indels: 14
0.66 0.18 0.16
Matches are distributed among these distances:
37 8 0.14
38 16 0.27
39 4 0.07
40 3 0.05
41 2 0.03
42 3 0.05
43 16 0.27
44 7 0.12
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (39 bp):
ACTAATAAAATGAAAATTACAGTTACATGCAATGCATGA
Found at i:58507612 original size:81 final size:81
Alignment explanation
Indices: 58507477--58507649 Score: 267
Period size: 81 Copynumber: 2.1 Consensus size: 81
58507467 GTATTGTCCC
58507477 CAATGCACT-AACATTAAAATGCAATGACAATAAAAATGCAACGACAATGCTCACTAACAAAATG
1 CAATGCA-TGAACATTAAAATGCAATGACAATAAAAATGCAACGACAATGCTCACTAACAAAATG
*
58507541 AAAATTACAGTTACATG
65 AAAATTACAGCTACATG
* * * * *
58507558 CAATGCATGAACATTAAAATGCAATGACAGTAAACATGCAACGACAATGTTCACTAATAAGATGA
1 CAATGCATGAACATTAAAATGCAATGACAATAAAAATGCAACGACAATGCTCACTAACAAAATGA
58507623 AAATTACAGCTACATG
66 AAATTACAGCTACATG
*
58507639 CAATGCTTGAA
1 CAATGCATGAA
58507650 TACTACAGCT
Statistics
Matches: 84, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
80 1 0.01
81 83 0.99
ACGTcount: A:0.47, C:0.18, G:0.13, T:0.22
Consensus pattern (81 bp):
CAATGCATGAACATTAAAATGCAATGACAATAAAAATGCAACGACAATGCTCACTAACAAAATGA
AAATTACAGCTACATG
Found at i:58512591 original size:50 final size:50
Alignment explanation
Indices: 58512468--58512660 Score: 192
Period size: 50 Copynumber: 3.7 Consensus size: 50
58512458 GGTAAAGAAA
* *
58512468 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGAATCATTGAGACTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGG---CATCGAG---ATGAGAGG
*
58512524 TCCCATC-TAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAGAGG
1 TCCCA-CGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
* * * **
58512574 TCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCA-CTGATATGAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATC-GAGATGAGAGG
* * **
58512624 TCCCAAGTAAGACCATATCTGGGATGTGGCATTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
58512661 GTATAGGAAA
Statistics
Matches: 119, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
49 2 0.02
50 79 0.66
53 6 0.05
56 32 0.27
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (50 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGG
Found at i:58512659 original size:100 final size:104
Alignment explanation
Indices: 58512474--58512660 Score: 238
Period size: 100 Copynumber: 1.8 Consensus size: 104
58512464 GAAATCCCAT
* * ** *
58512474 GTAAGACCATGTCTGGGACATGGCATTGGAATCATTGAGACTATGAGAGGTCCCATCTAAGACCA
1 GTAAGACCATGTCTGGGACATGGCATTGG-AGCACT-AGACTATGAGAACTCCCAACTAAGACCA
* *
58512539 TGTCTGGGACATGGCGTTGGCATCGAGATGAGAGGTCCCCC
64 TATCTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCCC
*
58512580 GTAAGACCATGTCTGGGACATGGCA-TGG-GCACT-GA-TATGAGAACTCCCAAGTAAGACCATA
1 GTAAGACCATGTCTGGGACATGGCATTGGAGCACTAGACTATGAGAACTCCCAACTAAGACCATA
**
58512641 TCTGGGATGTGGCATTGGCA
66 TCTGGGACATGGCATTGGCA
58512661 GTATAGGAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
100 38 0.54
101 2 0.03
103 3 0.04
105 3 0.04
106 25 0.35
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (104 bp):
GTAAGACCATGTCTGGGACATGGCATTGGAGCACTAGACTATGAGAACTCCCAACTAAGACCATA
TCTGGGACATGGCATTGGCATCGAGATGAGAGGTCCCCC
Found at i:58512708 original size:49 final size:50
Alignment explanation
Indices: 58512463--58512709 Score: 176
Period size: 50 Copynumber: 4.8 Consensus size: 50
58512453 ATTTGGGTAA
* * * *
58512463 AGAAATCCCATGTAAGACCATGTCTGGGACATGGCATTGGAATCATTGAGACTATG
1 AGAACTCCCAAGTAAGACCATGTCTGGGACATGGCATTGG---CACT--GA-TAGG
** ** * * *
58512519 AGAGGTCCCATCTAAGACCATGTCTGGGACATGGCGTTGGCA-TCGAGATG
1 AGAACTCCCAAGTAAGACCATGTCTGGGACATGGCATTGGCACT-GATAGG
** ** * *
58512569 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACTGATATG
1 AGAACTCCCAAGTAAGACCATGTCTGGGACATGGCATTGGCACTGATAGG
* ** *
58512619 AGAACTCCCAAGTAAGACCATATCTGGGATGTGGCATTGGCAGT-ATAGG
1 AGAACTCCCAAGTAAGACCATGTCTGGGACATGGCATTGGCACTGATAGG
* * * *
58512668 A-AACATCCCATGTAATACCATGCCTGGGACATGGCTTTGGCA
1 AGAAC-TCCCAAGTAAGACCATGTCTGGGACATGGCATTGGCA
58512710 TGTTATTATT
Statistics
Matches: 160, Mismatches: 29, Indels: 11
0.80 0.14 0.05
Matches are distributed among these distances:
48 3 0.02
49 35 0.22
50 80 0.50
51 3 0.02
52 1 0.01
53 2 0.01
56 36 0.22
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (50 bp):
AGAACTCCCAAGTAAGACCATGTCTGGGACATGGCATTGGCACTGATAGG
Found at i:58515356 original size:22 final size:23
Alignment explanation
Indices: 58515313--58515369 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
58515303 GATCAGGAAA
*
58515313 TGCTCCTGTAATATCCCAAAAAT
1 TGCTACTGTAATATCCCAAAAAT
*
58515336 TGCTACTGTAATACCCCAAAAAT
1 TGCTACTGTAATATCCCAAAAAT
* *
58515359 TACTACAGTAA
1 TGCTACTGTAA
58515370 GAAAGTAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.28
Consensus pattern (23 bp):
TGCTACTGTAATATCCCAAAAAT
Found at i:58522381 original size:55 final size:50
Alignment explanation
Indices: 58522314--58522499 Score: 178
Period size: 50 Copynumber: 3.6 Consensus size: 50
58522304 AGAGATTCAG
* * * *
58522314 TGTAAGATCATGTATGGGACATGGCATTGGCATCATTGAGACTTGAGAGGTCCCA
1 TGTAAGACCATGTCTAGGACATGGCATTGGCA-C--CGAGA--TGAGAGGTCCCA
* *
58522369 TGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGGTCCCC
1 TGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
* * * * **
58522419 CGTAAGACCATGTCTAGGACATGGCATTGGCA--GTACAGGAAACATCCCA
1 TGTAAGACCATGTCTAGGACATGGCATTGGCACCG-AGATGAGAGGTCCCA
* *
58522468 TGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TGTAAGACCATGTCTAGGACATGGCATTGGCA
58522500 TGTTATTATC
Statistics
Matches: 113, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 38 0.34
50 41 0.36
52 4 0.04
54 1 0.01
55 28 0.25
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
TGTAAGACCATGTCTAGGACATGGCATTGGCACCGAGATGAGAGGTCCCA
Found at i:58522492 original size:49 final size:49
Alignment explanation
Indices: 58522364--58522499 Score: 157
Period size: 49 Copynumber: 2.8 Consensus size: 49
58522354 ACTTGAGAGG
* * * * **
58522364 TCCCATGTAAGACCATGTCTAGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA-CGACAGGAAACA
**
58522414 TCCCCCGTAAGACCATGTCTAGGACATGGCATTGGCA-GTACAGGAAACA
1 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACG-ACAGGAAACA
* *
58522463 TCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCA
58522500 TGTTATTATC
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
48 1 0.01
49 38 0.52
50 34 0.47
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.21
Consensus pattern (49 bp):
TCCCATGTAAGACCATGTCTAGGACATGGCATTGGCACGACAGGAAACA
Found at i:58525989 original size:21 final size:21
Alignment explanation
Indices: 58525963--58526005 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
58525953 GAACATGAGA
58525963 TAGTAAAGCTCCCAGGATCTT
1 TAGTAAAGCTCCCAGGATCTT
58525984 TAGTAAAGCTCCCAGGATCTT
1 TAGTAAAGCTCCCAGGATCTT
58526005 T
1 T
58526006 CATTTTGGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (21 bp):
TAGTAAAGCTCCCAGGATCTT
Found at i:58526791 original size:21 final size:21
Alignment explanation
Indices: 58526753--58526792 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
58526743 TTCTGGTATG
**
58526753 GATGCATTTGACTTTGTTGTC
1 GATGCATTTGACGGTGTTGTC
*
58526774 GATGCATTTGAGGGTGTTG
1 GATGCATTTGACGGTGTTG
58526793 ATCGTAGTTA
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:0.15, C:0.10, G:0.33, T:0.42
Consensus pattern (21 bp):
GATGCATTTGACGGTGTTGTC
Found at i:58528110 original size:17 final size:16
Alignment explanation
Indices: 58528079--58528112 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
58528069 AAATATAATG
58528079 AAATAAAAACAAACAA
1 AAATAAAAACAAACAA
*
58528095 AAATAAACATCAAACAA
1 AAATAAA-AACAAACAA
58528112 A
1 A
58528113 TGCCATCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.76, C:0.15, G:0.00, T:0.09
Consensus pattern (16 bp):
AAATAAAAACAAACAA
Found at i:58529423 original size:56 final size:51
Alignment explanation
Indices: 58529357--58529639 Score: 232
Period size: 50 Copynumber: 5.7 Consensus size: 51
58529347 ATTTGGGTAA
* * *
58529357 AGAGATCCCATGTAAGACCATGTATGGGACATGGCATTGACATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACATC--CGAG---ATG
*
58529413 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCCGAGATG
* *
58529463 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGCCAT-CGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCCGAGATG
* * * * *
58529513 AGAGGTCCC-------ACCATGTCTAGGACATGGCATGGGCA-CCAATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCCGAGATG
** * * ** *
58529556 AGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTAGTAC-A-A-G
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACA-TCCGAGATG
* **
58529605 AAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGC
58529640 TTTGGCATGT
Statistics
Matches: 191, Mismatches: 25, Indels: 29
0.78 0.10 0.12
Matches are distributed among these distances:
43 34 0.18
49 31 0.16
50 81 0.42
51 1 0.01
52 1 0.01
53 3 0.02
55 1 0.01
56 39 0.20
ACGTcount: A:0.29, C:0.21, G:0.28, T:0.22
Consensus pattern (51 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCCGAGATG
Found at i:58529466 original size:50 final size:50
Alignment explanation
Indices: 58529410--58529646 Score: 240
Period size: 50 Copynumber: 4.9 Consensus size: 50
58529400 CATTGAGATT
58529410 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* * *
58529460 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGCCATCGAG
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
* * * *
58529510 ATGAGAGGTCCC-------ACCATGTCTAGGACATGGCATGGGCACCAAT
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
** * * * *
58529553 ATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGTA--GTAC
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AG
* * ** *
58529602 AAGAAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
58529647 TGTTATTATC
Statistics
Matches: 152, Mismatches: 27, Indels: 17
0.78 0.14 0.09
Matches are distributed among these distances:
43 34 0.22
49 38 0.25
50 80 0.53
ACGTcount: A:0.28, C:0.22, G:0.28, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAG
Found at i:58531187 original size:27 final size:27
Alignment explanation
Indices: 58531157--58531210 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
58531147 CTGGGATCCC
58531157 CAACATGAATATTCAACATTATACTAA
1 CAACATGAATATTCAACATTATACTAA
58531184 CAACATGAATATTCAACATTATACTAA
1 CAACATGAATATTCAACATTATACTAA
58531211 GTGTTCACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.30
Consensus pattern (27 bp):
CAACATGAATATTCAACATTATACTAA
Found at i:58534168 original size:20 final size:20
Alignment explanation
Indices: 58534140--58534194 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
58534130 GTACGGTAAA
*
58534140 TATCGATACCCATGTTCCAG
1 TATCAATACCCATGTTCCAG
*
58534160 TATCAATACACATGTTCCAG
1 TATCAATACCCATGTTCCAG
*
58534180 TATCAATACCTATGT
1 TATCAATACCCATGT
58534195 ACTTGTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (20 bp):
TATCAATACCCATGTTCCAG
Found at i:58536188 original size:68 final size:68
Alignment explanation
Indices: 58536079--58536217 Score: 251
Period size: 68 Copynumber: 2.0 Consensus size: 68
58536069 TTGCAAAACA
* *
58536079 AAATTGAAAGAGAAGAGCTTGGGGAGCAATGGACAACAAAACAAAGCTTAAAGGAAAAGTATATT
1 AAATTGAAAGAGAAGAGCTTGGGGAACAAGGGACAACAAAACAAAGCTTAAAGGAAAAGTATATT
58536144 GTG
66 GTG
*
58536147 AAATTGAAAGAGAAGAGCTTGGGGAACAAGGGACAACAAAACAAAGCTTAAAGGAAAATTATATT
1 AAATTGAAAGAGAAGAGCTTGGGGAACAAGGGACAACAAAACAAAGCTTAAAGGAAAAGTATATT
58536212 GTG
66 GTG
58536215 AAA
1 AAA
58536218 CTATATATGG
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.49, C:0.09, G:0.25, T:0.17
Consensus pattern (68 bp):
AAATTGAAAGAGAAGAGCTTGGGGAACAAGGGACAACAAAACAAAGCTTAAAGGAAAAGTATATT
GTG
Found at i:58538778 original size:47 final size:46
Alignment explanation
Indices: 58538724--58538816 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 46
58538714 TCACATGCAA
58538724 CTACTTATCTCACAGATTCTGCAAAACGACCCTTAAATGCTCGTTGT
1 CTACTTATCTCACAGATTCTGCAAAACGA-CCTTAAATGCTCGTTGT
58538771 CTACTTATCTCACAGATTCTGCAAAACGACCTTAAATGCTCGTTGT
1 CTACTTATCTCACAGATTCTGCAAAACGACCTTAAATGCTCGTTGT
58538817 GATCATCCTT
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 17 0.37
47 29 0.63
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.32
Consensus pattern (46 bp):
CTACTTATCTCACAGATTCTGCAAAACGACCTTAAATGCTCGTTGT
Found at i:58540312 original size:56 final size:56
Alignment explanation
Indices: 58540234--58540359 Score: 182
Period size: 56 Copynumber: 2.2 Consensus size: 56
58540224 TAGCAACCGC
* *
58540234 TACCCTCTATTTTCTTCTAAGGGATTTCTCCTTCCAAAAATGACTCTCCAACCGTG
1 TACCCTCTATTTTCTTCTAAGGGATTTCTCCTACAAAAAATGACTCTCCAACCGTG
* * *
58540290 TACCCTCTATTTT-TGTTTAAGGGATTTCTCCTACAAAAAATGACTCTCCAACTGTT
1 TACCCTCTATTTTCT-TCTAAGGGATTTCTCCTACAAAAAATGACTCTCCAACCGTG
*
58540346 TACCCCCTATTTTC
1 TACCCTCTATTTTC
58540360 AGTTTTTATT
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
55 1 0.02
56 61 0.98
ACGTcount: A:0.24, C:0.29, G:0.10, T:0.38
Consensus pattern (56 bp):
TACCCTCTATTTTCTTCTAAGGGATTTCTCCTACAAAAAATGACTCTCCAACCGTG
Found at i:58541476 original size:36 final size:36
Alignment explanation
Indices: 58541412--58541485 Score: 85
Period size: 36 Copynumber: 2.1 Consensus size: 36
58541402 AGAAGAGCAC
** * *
58541412 ATCAGTCAAAATAGATCTGAAAGACTGCTGAATTGA
1 ATCAGTCAAAATAGATCCAAAAGACTGCTAAACTGA
* * *
58541448 ATCAGTTAGAATAGATCCAAAAGGCTGCTAAACTGA
1 ATCAGTCAAAATAGATCCAAAAGACTGCTAAACTGA
58541484 AT
1 AT
58541486 AGAGTTTACT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.24
Consensus pattern (36 bp):
ATCAGTCAAAATAGATCCAAAAGACTGCTAAACTGA
Found at i:58562653 original size:27 final size:27
Alignment explanation
Indices: 58562614--58562862 Score: 342
Period size: 27 Copynumber: 9.2 Consensus size: 27
58562604 ATTCATGGGC
*
58562614 AAAATGACTGAAATACCCTCAAAGGGT
1 AAAATGACCGAAATACCCTCAAAGGGT
* *
58562641 AAAATGACCGAAATTCCCTCGAAGGGT
1 AAAATGACCGAAATACCCTCAAAGGGT
*
58562668 AAAATGACCGAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCCTCAAAGGGT
* *
58562695 AAAATAACCGAAATACCCTCGAAGGGT
1 AAAATGACCGAAATACCCTCAAAGGGT
58562722 AAAAATGACC-AAATACCCTCAAAGGGT
1 -AAAATGACCGAAATACCCTCAAAGGGT
* *
58562749 GAACTGACCGAAATACCCTCAAAGGGT
1 AAAATGACCGAAATACCCTCAAAGGGT
*
58562776 AAAATGACCGAAATACCCGTGAAA-GGT
1 AAAATGACCGAAATACCC-TCAAAGGGT
*
58562803 AAAATGACCGAAATACCC-CTAAAAGGT
1 AAAATGACCGAAATACCCTC-AAAGGGT
* *
58562830 AAAATGACCGAAATACCCCCATAGGGT
1 AAAATGACCGAAATACCCTCAAAGGGT
58562857 AAAATG
1 AAAATG
58562863 GCTATTATAC
Statistics
Matches: 201, Mismatches: 15, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
26 10 0.05
27 178 0.89
28 13 0.06
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (27 bp):
AAAATGACCGAAATACCCTCAAAGGGT
Found at i:58563282 original size:30 final size:28
Alignment explanation
Indices: 58563220--58563315 Score: 140
Period size: 28 Copynumber: 3.4 Consensus size: 28
58563210 ACTGCATTGT
58563220 ACTGATTACTGTATTGGGCTAAGGCCCAC
1 ACTG-TTACTGTATTGGGCTAAGGCCCAC
58563249 ACTGTTACTGTATTGGGCTAAGGCTCACAC
1 ACTGTTACTGTATTGGGCTAAGGC-C-CAC
* *
58563279 ACTGTTACTGTAATAGGCTAAGGCCCAC
1 ACTGTTACTGTATTGGGCTAAGGCCCAC
58563307 ACTG-TACTG
1 ACTGTTACTG
58563316 ATACTGTACA
Statistics
Matches: 63, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
27 5 0.08
28 27 0.43
29 6 0.10
30 25 0.40
ACGTcount: A:0.25, C:0.24, G:0.23, T:0.28
Consensus pattern (28 bp):
ACTGTTACTGTATTGGGCTAAGGCCCAC
Found at i:58565870 original size:20 final size:20
Alignment explanation
Indices: 58565847--58565904 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
58565837 ATGTGTAATT
58565847 AGGGGTACCGAAGTACAATC
1 AGGGGTACCGAAGTACAATC
* * *
58565867 AGGGGCA-CGTATGTACAATT
1 AGGGGTACCG-AAGTACAATC
*
58565887 AAGGGTACCGAAGTACAA
1 AGGGGTACCGAAGTACAA
58565905 ATAGGTGCAC
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.36, C:0.17, G:0.29, T:0.17
Consensus pattern (20 bp):
AGGGGTACCGAAGTACAATC
Found at i:58565887 original size:40 final size:40
Alignment explanation
Indices: 58565827--58565925 Score: 137
Period size: 40 Copynumber: 2.5 Consensus size: 40
58565817 TCACACTAAA
* * *
58565827 AGGGGCACATATGTGTAATTAGGGGTACCGAAGTAC-AAT
1 AGGGGCACGTATGTGCAATTAAGGGTACCGAAGTACAAAT
*
58565866 CAGGGGCACGTATGTACAATTAAGGGTACCGAAGTACAAAT
1 -AGGGGCACGTATGTGCAATTAAGGGTACCGAAGTACAAAT
*
58565907 AGGTGCACGTATGTGCAAT
1 AGGGGCACGTATGTGCAAT
58565926 CAGTCATTAG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
40 49 0.94
41 3 0.06
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.22
Consensus pattern (40 bp):
AGGGGCACGTATGTGCAATTAAGGGTACCGAAGTACAAAT
Found at i:58566802 original size:12 final size:12
Alignment explanation
Indices: 58566774--58566813 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
58566764 ACTCGATTTC
*
58566774 TTTTCAAGCTCT
1 TTTTCAATCTCT
* *
58566786 CTTTCAATTTCT
1 TTTTCAATCTCT
58566798 TTTTCAATCTCT
1 TTTTCAATCTCT
58566810 TTTT
1 TTTT
58566814 GCTTTTCACT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.15, C:0.23, G:0.03, T:0.60
Consensus pattern (12 bp):
TTTTCAATCTCT
Found at i:58567763 original size:15 final size:15
Alignment explanation
Indices: 58567743--58567801 Score: 59
Period size: 14 Copynumber: 4.0 Consensus size: 15
58567733 AGACTTTTCA
58567743 CTTCTTTTTTTTCTT
1 CTTCTTTTTTTTCTT
* *
58567758 CTTC-TTTTTTACTC
1 CTTCTTTTTTTTCTT
* *
58567772 CTT-TTTTTTTGCTCA
1 CTTCTTTTTTTTCT-T
58567787 CTTCTTTTTTTTCTT
1 CTTCTTTTTTTTCTT
58567802 TTTTTTTGAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
14 19 0.54
15 7 0.20
16 9 0.26
ACGTcount: A:0.03, C:0.22, G:0.02, T:0.73
Consensus pattern (15 bp):
CTTCTTTTTTTTCTT
Found at i:58567814 original size:18 final size:17
Alignment explanation
Indices: 58567793--58567838 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
58567783 CTCACTTCTT
*
58567793 TTTTTTCTTTTTTTTTGA
1 TTTTTT-TTTTATTTTGA
*
58567811 TTTTTTTTTGAATTTTGA
1 TTTTTTTTT-TATTTTGA
58567829 TTTTTTTTTT
1 TTTTTTTTTT
58567839 GTGATACTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
17 3 0.12
18 21 0.88
ACGTcount: A:0.09, C:0.02, G:0.07, T:0.83
Consensus pattern (17 bp):
TTTTTTTTTTATTTTGA
Found at i:58569370 original size:20 final size:20
Alignment explanation
Indices: 58569347--58569393 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
58569337 GGGTTAAAAT
*
58569347 TGAGCTGAATTGATCTCGAA-
1 TGAGCTGAATTGAGCTC-AAG
*
58569367 TGAGCTGACTTGAGCTCAAG
1 TGAGCTGAATTGAGCTCAAG
58569387 TGAGCTG
1 TGAGCTG
58569394 GAAACGAGCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 2 0.08
20 22 0.92
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCAAG
Found at i:58587062 original size:27 final size:28
Alignment explanation
Indices: 58587005--58587080 Score: 86
Period size: 28 Copynumber: 2.8 Consensus size: 28
58586995 ATTAATTCAG
*
58587005 CTAAAACATATTAAAAAT-ATGTAATAGA
1 CTAAGACATATT-AAAATCATGTAATAGA
*
58587033 CTAAGACATATTAAAATCATGTACTA-A
1 CTAAGACATATTAAAATCATGTAATAGA
*
58587060 CTATGACATATTTAAAA-CATG
1 CTAAGACATA-TTAAAATCATG
58587081 CATTAAAATT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
27 19 0.44
28 24 0.56
ACGTcount: A:0.50, C:0.12, G:0.08, T:0.30
Consensus pattern (28 bp):
CTAAGACATATTAAAATCATGTAATAGA
Found at i:58587318 original size:35 final size:34
Alignment explanation
Indices: 58587231--58587329 Score: 125
Period size: 35 Copynumber: 3.0 Consensus size: 34
58587221 TGAACTGGTC
*
58587231 GATCGTCGTAACTTGTTAAAGCATCTTAGAGC-T
1 GATCGTCGTAACTTGTTAAAGCATCTTGGAGCTT
* * *
58587264 --TC-TTGGAGCTTGTTAAAGCATCTTGGAGCTT
1 GATCGTCGTAACTTGTTAAAGCATCTTGGAGCTT
58587295 GGATCGTCGTAACTTGTTAAAGCATCTTGGAGCTT
1 -GATCGTCGTAACTTGTTAAAGCATCTTGGAGCTT
58587330 CTTGGCACGA
Statistics
Matches: 54, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
30 23 0.43
31 3 0.06
34 2 0.04
35 26 0.48
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (34 bp):
GATCGTCGTAACTTGTTAAAGCATCTTGGAGCTT
Found at i:58601363 original size:11 final size:12
Alignment explanation
Indices: 58601336--58601364 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
58601326 ACAACAAGAA
58601336 CATTCAAATATT
1 CATTCAAATATT
58601348 CATTCAAATA-T
1 CATTCAAATATT
58601359 CATTCA
1 CATTCA
58601365 CCATTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 7 0.41
12 10 0.59
ACGTcount: A:0.41, C:0.21, G:0.00, T:0.38
Consensus pattern (12 bp):
CATTCAAATATT
Found at i:58601497 original size:12 final size:12
Alignment explanation
Indices: 58601480--58601507 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
58601470 TTTGATGCGA
58601480 AACGTACGCACG
1 AACGTACGCACG
58601492 AACGTACGCACG
1 AACGTACGCACG
58601504 AACG
1 AACG
58601508 AGATTTGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.36, C:0.32, G:0.25, T:0.07
Consensus pattern (12 bp):
AACGTACGCACG
Found at i:58603096 original size:243 final size:243
Alignment explanation
Indices: 58602668--58603470 Score: 1281
Period size: 243 Copynumber: 3.3 Consensus size: 243
58602658 AATTCATACA
* * * * * *
58602668 TGTGAATAGCAGAGGATATTGCTCTTTCATTAAACATTCTCTTTCCCAAGTAGCCTCTT-TTGTA
1 TGTGAATATCCGAGGATACTGCTATTTCATTAAACTTTCTCTTTCCCAAGTAGCCTCTTCCT-TA
* * * *
58602732 TTATGATTTCTCCAT-ATTGCTTTTAGCAAAGGAATCCT-TCTATTTCTAACCTTTTTCACCTTT
65 TTATGATTTCTCCATAATT-CTTTAAGCAAAGGAATCCTCT-TATTTCTAATCTCTTTCACTTTT
*
58602795 CTTGCCAAGGTACGTATGGGCTCTTCCTCATAACACAGATTTTGTTCTACCTCTAACTCTTCAAA
128 CTTGCCAAGGTACGAATGGGCTCTTCCTCATAACACAGATTTTGTTCTACCTCTAACTCTTCAAA
58602860 CTACACAACATGGTCTGGATTTGATCTATATCTTCTCAGCCCATTTGTACC
193 CTACACAACATGGTCTGGATTTGATCTATATCTTCTCAGCCCATTTGTACC
* *
58602911 TGTGAATATCCGAGAATACTGCTATTTCATTAAACTTTCTCTTTCCCAAGTATCCTCTTCCTTAT
1 TGTGAATATCCGAGGATACTGCTATTTCATTAAACTTTCTCTTTCCCAAGTAGCCTCTTCCTTAT
*
58602976 TATGATTTCTCTATAATTCTTTAAGCAAAGGAATCCTCTTATTTCTAATCTCTTTCACTTTTCTT
66 TATGATTTCTCCATAATTCTTTAAGCAAAGGAATCCTCTTATTTCTAATCTCTTTCACTTTTCTT
58603041 GCCAAGGTACGAATGGGCTCTTCCTCATAACACAGATTTTGTTCTACCTCTAACTCTTCAAACTA
131 GCCAAGGTACGAATGGGCTCTTCCTCATAACACAGATTTTGTTCTACCTCTAACTCTTCAAACTA
58603106 CACAACATGGTCTGGATTTGATCTATATCTTCTCAGCCCATTTGTACC
196 CACAACATGGTCTGGATTTGATCTATATCTTCTCAGCCCATTTGTACC
*
58603154 TGTGAATATCCGAGGATACTGCTATTTCATTAAACTTTCTCTTTCCCAAGTATCCTCTTCCTTAT
1 TGTGAATATCCGAGGATACTGCTATTTCATTAAACTTTCTCTTTCCCAAGTAGCCTCTTCCTTAT
58603219 TATGATTTCTCCATAATTCTTTAAGCAAAGGAATCCTCTTATTTCTAATCTCTTTCACTTTTCTT
66 TATGATTTCTCCATAATTCTTTAAGCAAAGGAATCCTCTTATTTCTAATCTCTTTCACTTTTCTT
*
58603284 GCCAAGGTACGAATGGGCTCTTCCTCATAACACAGATTTGGTTCTACCTCTAACTCTT-AAATCT
131 GCCAAGGTACGAATGGGCTCTTCCTCATAACACAGATTTTGTTCTACCTCTAACTCTTCAAA-CT
* * * **
58603348 ACACAACATGGTCTAGATTTAATCTATATCTTCTCAGCCTATTCATACC
195 ACACAACATGGTCTGGATTTGATCTATATCTTCTCAGCCCATTTGTACC
* * * * * * * *
58603397 TGTGAATATCTGAGGATATTTCTCTTTCGTTAAACTTTCTCTTTCCGAAGTAGCCTATTCCATAT
1 TGTGAATATCCGAGGATACTGCTATTTCATTAAACTTTCTCTTTCCCAAGTAGCCTCTTCCTTAT
58603462 TATGATTTC
66 TATGATTTC
58603471 ATTATATAAT
Statistics
Matches: 525, Mismatches: 31, Indels: 8
0.93 0.05 0.01
Matches are distributed among these distances:
242 3 0.01
243 517 0.98
244 5 0.01
ACGTcount: A:0.25, C:0.24, G:0.11, T:0.40
Consensus pattern (243 bp):
TGTGAATATCCGAGGATACTGCTATTTCATTAAACTTTCTCTTTCCCAAGTAGCCTCTTCCTTAT
TATGATTTCTCCATAATTCTTTAAGCAAAGGAATCCTCTTATTTCTAATCTCTTTCACTTTTCTT
GCCAAGGTACGAATGGGCTCTTCCTCATAACACAGATTTTGTTCTACCTCTAACTCTTCAAACTA
CACAACATGGTCTGGATTTGATCTATATCTTCTCAGCCCATTTGTACC
Found at i:58606376 original size:19 final size:20
Alignment explanation
Indices: 58606344--58606382 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
58606334 CAAGCTGACT
58606344 TTAGCTCAATTTCAGATCCA
1 TTAGCTCAATTTCAGATCCA
*
58606364 TTAGCTC-ATTTCAGCTCCA
1 TTAGCTCAATTTCAGATCCA
58606383 ATCAGCTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.26, C:0.28, G:0.10, T:0.36
Consensus pattern (20 bp):
TTAGCTCAATTTCAGATCCA
Found at i:58606389 original size:20 final size:19
Alignment explanation
Indices: 58606346--58606391 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
58606336 AGCTGACTTT
*
58606346 AGCTCAATTTCAGATCCATT
1 AGCTC-ATTTCAGATCCATC
*
58606366 AGCTCATTTCAGCTCCAATC
1 AGCTCATTTCAGATCC-ATC
58606386 AGCTCA
1 AGCTCA
58606392 CTTGAGCTCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.28, C:0.30, G:0.11, T:0.30
Consensus pattern (19 bp):
AGCTCATTTCAGATCCATC
Found at i:58608803 original size:6 final size:6
Alignment explanation
Indices: 58608792--58608889 Score: 51
Period size: 6 Copynumber: 16.0 Consensus size: 6
58608782 CCAATCGCAT
* * *
58608792 GAAAAA GAAAAA -AAGAA GAAAGA GAAAAA GAAAATA -AAAAT GAAAATAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAA-A GAAAAA G-AAA-AA
* ** *
58608841 GAAAACA -AAAGTA GAAAAA GAAAGT G-AAAA GAAAAT GAGAAAA GAAAAA
1 GAAAA-A GAAA-AA GAAAAA GAAAAA GAAAAA GAAAAA GA-AAAA GAAAAA
58608890 CAAGAAAATG
Statistics
Matches: 68, Mismatches: 14, Indels: 20
0.67 0.14 0.20
Matches are distributed among these distances:
5 7 0.10
6 43 0.63
7 16 0.24
8 2 0.03
ACGTcount: A:0.74, C:0.01, G:0.18, T:0.06
Consensus pattern (6 bp):
GAAAAA
Found at i:58608856 original size:13 final size:13
Alignment explanation
Indices: 58608817--58608888 Score: 57
Period size: 13 Copynumber: 5.7 Consensus size: 13
58608807 AAGAAAGAGA
58608817 AAAAGAAAA-TA-
1 AAAAGAAAAGTAG
58608828 AAAATGAAAA-TAAG
1 AAAA-GAAAAGT-AG
*
58608842 AAAACAAAAGTAG
1 AAAAGAAAAGTAG
58608855 AAAA-AGAAAGT-G
1 AAAAGA-AAAGTAG
58608867 AAAAGAAAA-TGAG
1 AAAAGAAAAGT-AG
58608880 AAAAGAAAA
1 AAAAGAAAA
58608889 ACAAGAAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 14
0.78 0.01 0.21
Matches are distributed among these distances:
11 5 0.10
12 15 0.29
13 27 0.52
14 5 0.10
ACGTcount: A:0.74, C:0.01, G:0.17, T:0.08
Consensus pattern (13 bp):
AAAAGAAAAGTAG
Found at i:58608882 original size:38 final size:38
Alignment explanation
Indices: 58608810--58608888 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
58608800 AAAAAAGAAG
58608810 AAAGAGAAAAAGAAAATAAAAATGAAAATAAGAAAACA
1 AAAGAGAAAAAGAAAATAAAAATGAAAATAAGAAAACA
* * * *
58608848 AAAGTAGAAAAAGAAAGTGAAAA-GAAAATGAGAAAAGA
1 AAAG-AGAAAAAGAAAATAAAAATGAAAATAAGAAAACA
58608886 AAA
1 AAA
58608889 ACAAGAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 20 0.56
39 16 0.44
ACGTcount: A:0.73, C:0.01, G:0.18, T:0.08
Consensus pattern (38 bp):
AAAGAGAAAAAGAAAATAAAAATGAAAATAAGAAAACA
Found at i:58608896 original size:39 final size:39
Alignment explanation
Indices: 58608814--58608897 Score: 98
Period size: 39 Copynumber: 2.2 Consensus size: 39
58608804 AAGAAGAAAG
* **
58608814 AGAAAAAGAAAATAAAAATGAAAATAAGAAAACAAAAGT
1 AGAAAAAGAAAATAAAAATGAAAATAAGAAAAAAAAACA
* * *
58608853 AGAAAAAGAAAGTGAAAA-GAAAATGAGAAAAGAAAAACA
1 AGAAAAAGAAAATAAAAATGAAAATAAGAAAA-AAAAACA
58608892 AGAAAA
1 AGAAAA
58608898 TGTGACAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 12 0.32
39 26 0.68
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (39 bp):
AGAAAAAGAAAATAAAAATGAAAATAAGAAAAAAAAACA
Found at i:58617146 original size:10 final size:10
Alignment explanation
Indices: 58617131--58617158 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
58617121 AGGTGGTGCG
58617131 ATGGTGGTTA
1 ATGGTGGTTA
58617141 ATGGTGGTTA
1 ATGGTGGTTA
58617151 ATGGTGGT
1 ATGGTGGT
58617159 GAAACAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.00, G:0.43, T:0.39
Consensus pattern (10 bp):
ATGGTGGTTA
Found at i:58620475 original size:26 final size:26
Alignment explanation
Indices: 58620444--58620590 Score: 149
Period size: 27 Copynumber: 5.5 Consensus size: 26
58620434 GAAGCCCATT
*
58620444 AGGACTATCTAAGGTGGAAGTCTGCA
1 AGGACTATCTAATGTGGAAGTCTGCA
* *
58620470 ATGACTATCTAATGTGGGAAGTCTGCC
1 AGGACTATCTAATGT-GGAAGTCTGCA
**
58620497 AGGACTATC-ATATGTGGAAGTCCACA
1 AGGACTATCTA-ATGTGGAAGTCTGCA
58620523 AGGACTATCTAATGTGGAAAGT-T-CA
1 AGGACTATCTAATGTGG-AAGTCTGCA
*
58620548 CCAGGACTATTTAATGTGTGAAGTCTGTCA
1 --AGGACTATCTAATGTG-GAAGTCTG-CA
58620578 A-GACTATCTAATG
1 AGGACTATCTAATG
58620591 CAGGAAGCCC
Statistics
Matches: 101, Mismatches: 10, Indels: 19
0.78 0.08 0.15
Matches are distributed among these distances:
25 2 0.02
26 37 0.37
27 57 0.56
28 3 0.03
30 2 0.02
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.28
Consensus pattern (26 bp):
AGGACTATCTAATGTGGAAGTCTGCA
Found at i:58620490 original size:53 final size:53
Alignment explanation
Indices: 58620400--58620612 Score: 189
Period size: 53 Copynumber: 4.0 Consensus size: 53
58620390 CGTTACCATA
* * * **
58620400 AATGTGGATAGTCTGTCAAGACTATTTAAAGTTGGAAGCCCATTAGGACTATCT
1 AATGTGGA-AGTCTGTCAAGACTATCTAATGTGGGAAGCCCACCAGGACTATCT
* * **
58620454 AAGGTGGAAGTCTG-CAATGACTATCTAATGTGGGAAGTCTGCCAGGACTATC-
1 AATGTGGAAGTCTGTCAA-GACTATCTAATGTGGGAAGCCCACCAGGACTATCT
** * ** *
58620506 ATATGTGGAAGTC-CACAAGGACTATCTAATGTGGAAAGTTCACCAGGACTATTT
1 A-ATGTGGAAGTCTGTCAA-GACTATCTAATGTGGGAAGCCCACCAGGACTATCT
** * *
58620560 AATGTGTGAAGTCTGTCAAGACTATCTAATGCAGGAAGCCCATCAAGACTATC
1 AATGTG-GAAGTCTGTCAAGACTATCTAATGTGGGAAGCCCACCAGGACTATC
58620613 ATTATAACAC
Statistics
Matches: 126, Mismatches: 27, Indels: 12
0.76 0.16 0.07
Matches are distributed among these distances:
52 4 0.03
53 79 0.63
54 40 0.32
55 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.27
Consensus pattern (53 bp):
AATGTGGAAGTCTGTCAAGACTATCTAATGTGGGAAGCCCACCAGGACTATCT
Found at i:58621714 original size:27 final size:27
Alignment explanation
Indices: 58621684--58621924 Score: 410
Period size: 27 Copynumber: 8.9 Consensus size: 27
58621674 TTCATACTTC
*
58621684 GCCACAAAGGCTTTCATTTCGTGATTT
1 GCCACAAAGGCTTTCATTTCATGATTT
58621711 GCCACAAAGGCTTTCATTTCATGATTT
1 GCCACAAAGGCTTTCATTTCATGATTT
*
58621738 TCCACAAAGGCTTTCATTTCATGATTT
1 GCCACAAAGGCTTTCATTTCATGATTT
*
58621765 TCCACAAAGGCTTTCATTTCATGATTT
1 GCCACAAAGGCTTTCATTTCATGATTT
*
58621792 TCCACAAAGGCTTTCATTTCATGATTT
1 GCCACAAAGGCTTTCATTTCATGATTT
58621819 GCCACAAAGGCTTTCATTTCATGATTT
1 GCCACAAAGGCTTTCATTTCATGATTT
58621846 GCCACAAAGGCTTTCATTTCATGATTT
1 GCCACAAAGGCTTTCATTTCATGATTT
*
58621873 GCTACAAAGGCTTTCATTTCATGATTT
1 GCCACAAAGGCTTTCATTTCATGATTT
* * *
58621900 TCCATAAAGGCTTTCATTTCCTGAT
1 GCCACAAAGGCTTTCATTTCATGAT
58621925 GAGTTTACGA
Statistics
Matches: 206, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 206 1.00
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (27 bp):
GCCACAAAGGCTTTCATTTCATGATTT
Found at i:58622271 original size:25 final size:25
Alignment explanation
Indices: 58622237--58622288 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
58622227 TGACAAATAG
58622237 CTATACTCAAACTTTACATACTTAA
1 CTATACTCAAACTTTACATACTTAA
58622262 CTATACTCAAACTTTACATACTTAA
1 CTATACTCAAACTTTACATACTTAA
58622287 CT
1 CT
58622289 TGTCAGACTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.37
Consensus pattern (25 bp):
CTATACTCAAACTTTACATACTTAA
Found at i:58622990 original size:21 final size:21
Alignment explanation
Indices: 58622965--58623004 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
58622955 ATAATAATGC
58622965 ATTGA-GACAAATGTGTTGTTG
1 ATTGATGACAAA-GTGTTGTTG
58622986 ATTGATGACAAAGTGTTGT
1 ATTGATGACAAAGTGTTGT
58623005 CATTAACATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.30, C:0.05, G:0.28, T:0.38
Consensus pattern (21 bp):
ATTGATGACAAAGTGTTGTTG
Found at i:58624734 original size:27 final size:27
Alignment explanation
Indices: 58624677--58624791 Score: 104
Period size: 27 Copynumber: 4.3 Consensus size: 27
58624667 GTTCCCAAGG
* * ** *
58624677 ACTATCTAATGTGGAAAGTCAACCAGG
1 ACTATCTAATGTGGGAAGTCCATTAGA
* * *
58624704 ACTATTTAATGTTGGAAGTCCATTATA
1 ACTATCTAATGTGGGAAGTCCATTAGA
* * * *
58624731 ACTATCTAATGAGGGAAGTTCGTTAGG
1 ACTATCTAATGTGGGAAGTCCATTAGA
* *
58624758 ACTATCTAATGTGGGAAGTCCATTGGG
1 ACTATCTAATGTGGGAAGTCCATTAGA
58624785 ACTATCT
1 ACTATCT
58624792 TTTATGAAGG
Statistics
Matches: 69, Mismatches: 19, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (27 bp):
ACTATCTAATGTGGGAAGTCCATTAGA
Found at i:58625982 original size:15 final size:16
Alignment explanation
Indices: 58625964--58625997 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
58625954 AAATTAAATT
*
58625964 AATTAAC-TAGATGCA
1 AATTAACTTAAATGCA
58625979 AATTAACTTAAATGCA
1 AATTAACTTAAATGCA
58625995 AAT
1 AAT
58625998 AAGAGGAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (16 bp):
AATTAACTTAAATGCA
Found at i:58633485 original size:18 final size:19
Alignment explanation
Indices: 58633458--58633495 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
58633448 ATCTAAACTC
*
58633458 TTTTCTTTTTCTTTTTCAT
1 TTTTCTTTTTCTTGTTCAT
58633477 TTTTC-TTTTCTTGTTCAT
1 TTTTCTTTTTCTTGTTCAT
58633495 T
1 T
58633496 CACTCTCGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.05, C:0.16, G:0.03, T:0.76
Consensus pattern (19 bp):
TTTTCTTTTTCTTGTTCAT
Found at i:58641238 original size:27 final size:28
Alignment explanation
Indices: 58641208--58641267 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
58641198 ACTTTGGACA
* *
58641208 ACATTAA-AACATGCAATAAAATTAGAC
1 ACATTAATAACATGCAATAAAATAAAAC
*
58641235 ACATTAATAACATGCATTAAAATAAAAC
1 ACATTAATAACATGCAATAAAATAAAAC
58641263 ACATT
1 ACATT
58641268 TATCACAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 7 0.24
28 22 0.76
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (28 bp):
ACATTAATAACATGCAATAAAATAAAAC
Found at i:58648196 original size:82 final size:83
Alignment explanation
Indices: 58648090--58648255 Score: 325
Period size: 82 Copynumber: 2.0 Consensus size: 83
58648080 ACAATGAAAT
58648090 TAGTAGGAAAAATAAATTTATCGAATCTTACAAAAACATCCTCGATCTTTCCTTCGGGATATGCT
1 TAGTAGGAAAAATAAATTTATCGAATCTTACAAAAACATCCTCGATCTTTCCTTCGGGATATGCT
58648155 AAAGATCGATCCACTAGC
66 AAAGATCGATCCACTAGC
58648173 TAGTAGG-AAAATAAATTTATCGAATCTTACAAAAACATCCTCGATCTTTCCTTCGGGATATGCT
1 TAGTAGGAAAAATAAATTTATCGAATCTTACAAAAACATCCTCGATCTTTCCTTCGGGATATGCT
58648237 AAAGATCGATCCACTAGC
66 AAAGATCGATCCACTAGC
58648255 T
1 T
58648256 GAAGCGTCAT
Statistics
Matches: 83, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
82 76 0.92
83 7 0.08
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Consensus pattern (83 bp):
TAGTAGGAAAAATAAATTTATCGAATCTTACAAAAACATCCTCGATCTTTCCTTCGGGATATGCT
AAAGATCGATCCACTAGC
Found at i:58652209 original size:23 final size:23
Alignment explanation
Indices: 58652183--58652266 Score: 105
Period size: 23 Copynumber: 3.7 Consensus size: 23
58652173 GCTGATTCAG
58652183 TGGAAGCCTTTGTGGCTATTCTA
1 TGGAAGCCTTTGTGGCTATTCTA
* * *
58652206 TGGAAGCCTTTATGGCTATTTTG
1 TGGAAGCCTTTGTGGCTATTCTA
* *
58652229 CGGAAGCCTTTGTGGCTGTTCTA
1 TGGAAGCCTTTGTGGCTATTCTA
* *
58652252 AGGAAGCCCTTGTGG
1 TGGAAGCCTTTGTGG
58652267 TTGTTCTGAT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.17, C:0.18, G:0.30, T:0.36
Consensus pattern (23 bp):
TGGAAGCCTTTGTGGCTATTCTA
Found at i:58659015 original size:9 final size:9
Alignment explanation
Indices: 58659001--58659026 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
58658991 CAATTCCTCC
58659001 TTTATTTTT
1 TTTATTTTT
58659010 TTTATTTTT
1 TTTATTTTT
58659019 TTTATTTT
1 TTTATTTT
58659027 CGAATCTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTATTTTT
Found at i:58659450 original size:52 final size:52
Alignment explanation
Indices: 58659394--58659962 Score: 1093
Period size: 52 Copynumber: 10.9 Consensus size: 52
58659384 TATGCACATA
58659394 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
58659446 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
58659498 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
58659550 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
58659602 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
58659654 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
58659706 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
58659758 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
58659810 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
58659862 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
* * * * *
58659914 TTTGAGCTTTAGCCGAGCTAGAAATGAGATCTTAAGCTGTTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTA
58659963 CGTTTCCTTA
Statistics
Matches: 512, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 512 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
Found at i:58669212 original size:40 final size:40
Alignment explanation
Indices: 58669168--58669248 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
58669158 TAGTCGAAAG
58669168 ATAACCAATGAGAGAGACAATACTTAGGAAGAATCCACCT
1 ATAACCAATGAGAGAGACAATACTTAGGAAGAATCCACCT
58669208 ATAACCAATGAGAGAGACAATACTTAGGAAGAATCCACCT
1 ATAACCAATGAGAGAGACAATACTTAGGAAGAATCCACCT
58669248 A
1 A
58669249 GACTTCTATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.46, C:0.20, G:0.17, T:0.17
Consensus pattern (40 bp):
ATAACCAATGAGAGAGACAATACTTAGGAAGAATCCACCT
Found at i:58677923 original size:25 final size:26
Alignment explanation
Indices: 58677866--58677924 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
58677856 TATAAAAGAA
* *
58677866 AATTTT-AAGATAAATAATATACATG
1 AATTTTAAAAATAAATAATAAACATG
**
58677891 AAACTTAAAAATAAA-AATAAACATG
1 AATTTTAAAAATAAATAATAAACATG
58677916 AATTTTAAA
1 AATTTTAAA
58677925 TTAAATGTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
25 20 0.74
26 7 0.26
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (26 bp):
AATTTTAAAAATAAATAATAAACATG
Found at i:58678441 original size:3 final size:3
Alignment explanation
Indices: 58678427--58678526 Score: 96
Period size: 3 Copynumber: 33.0 Consensus size: 3
58678417 TAACATTATG
* * * *
58678427 AAT AAT AGT AAT AAT AAT AAT ACT AAT AAT AAT GAA- AGT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * *
58678472 AAT AAT AAT AAAT AAT AGT ACA- AAT AAT AAT AAT AGT ATT AAT AAT
1 AAT AAT AAT -AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
58678518 AAT AAT AAT
1 AAT AAT AAT
58678527 GATAGCAACA
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
2 2 0.02
3 74 0.91
4 5 0.06
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:58680183 original size:44 final size:43
Alignment explanation
Indices: 58680089--58680335 Score: 164
Period size: 44 Copynumber: 5.7 Consensus size: 43
58680079 ATCATTTTAA
* * * *
58680089 TCTGCTCCGCTGCAACTTCAGGGAGATAGGATT-TATAACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGT-TTA-TTCAG
* * *
58680133 TTTGCTCTATTGCAACTTCAGGGAGATAAGATTGGTTTATTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTTTATTCAG
* *
58680177 TCTGCTCCACTGCATA-TTCAGGGAGATAAGACCTG---ATGC-G
1 TCTGCTCCACTGCA-ACTTCAGGGAGATAAGA-TTGTTTATTCAG
* * * * ** * * *
58680217 ATCTACTCTATTGCAACTTCAGAGAGATAAGATTCATCATTTTAA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTTTA-TTCAG
* * * * *
58680262 TCCGCTCCACTACAACTTCAGGGAGATAGGATTGGTTTCTTCTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-GTTTATTCAG
*
58680306 TCTGCTCCACTACAACTTCAGGGAGATAAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG
58680336 TCTTGTAACT
Statistics
Matches: 154, Mismatches: 37, Indels: 24
0.72 0.17 0.11
Matches are distributed among these distances:
40 3 0.02
41 28 0.18
43 1 0.01
44 116 0.75
45 5 0.03
46 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.31
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTTTATTCAG
Found at i:58680269 original size:85 final size:87
Alignment explanation
Indices: 58680057--58680289 Score: 233
Period size: 85 Copynumber: 2.7 Consensus size: 87
58680047 TGTTCTACCA
* * * * *
58680057 CAACTTTAGAGAGGTAAGATCCATCATTTTAATCTGCTCCGCTGCAACTTCAGGGAGATAGGATT
1 CAACTTCAGAGAGATAAGATTCATCATTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-T
* * * *
58680122 TATAACTTCAATTTGCTCTATTG
65 CATAACTGCAATCTACTCTATTG
* ** *
58680145 CAACTTCAGGGAGATAAGATTGGT--TTATTCAGTCTGCTCCACTGCATA-TTCAGGGAGATAAG
1 CAACTTCAGAGAGATAAGATTCATCATT-TT-AATCTGCTCCACTGCA-ACTTCAGGGAGATAAG
* * *
58680207 A-CCTGA-TGCGATCTACTCTATTG
63 ATCATAACTGCAATCTACTCTATTG
* *
58680230 CAACTTCAGAGAGATAAGATTCATCATTTTAATCCGCTCCACTACAACTTCAGGGAGATA
1 CAACTTCAGAGAGATAAGATTCATCATTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
58680290 GGATTGGTTT
Statistics
Matches: 117, Mismatches: 22, Indels: 15
0.76 0.14 0.10
Matches are distributed among these distances:
84 1 0.01
85 59 0.50
86 6 0.05
87 4 0.03
88 46 0.39
89 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.31
Consensus pattern (87 bp):
CAACTTCAGAGAGATAAGATTCATCATTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATC
ATAACTGCAATCTACTCTATTG
Found at i:58681504 original size:172 final size:171
Alignment explanation
Indices: 58681284--58681734 Score: 650
Period size: 172 Copynumber: 2.6 Consensus size: 171
58681274 TGTTCTACCA
* * *
58681284 CAACTTTAGAGAGGTAAGATCCATCATTTTAATCTGCTCCGCTGCAACTTCAGGGAGATAGGATT
1 CAACTTCAGAGAGATAAGAT-CATCATTTTAATCTGCTCC-ATGCAACTTCAGGGAGATAGGATT
* * * *
58681349 TATAACTTCAATTTGCTCTATTGCAACTTCAGGGAGATAAGATTGGTTTATTCAGTCTGCTTCGC
64 GATAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAGTCTGCTTCGC
58681414 TGCACGTTTAGGGAGATAAGACCTGATGCGATCTACTCTATTG
129 TGCACGTTTAGGGAGATAAGACCTGATGCGATCTACTCTATTG
**
58681457 CAACTTCAGAGAGATAAGATCAATCATTTTAATCTGCTCCATGCAACTTCAAAGAGATAGGATTG
1 CAACTTCAGAGAGATAAGATC-ATCATTTTAATCTGCTCCATGCAACTTCAGGGAGATAGGATTG
* ** ***
58681522 GTTTCTTTTGTCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAGTCTGCTTCGCT
65 ATAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAGTCTGCTTCGCT
58681587 GCACGTTTAGGGAGATAAGACCTGATGCGATCTACTCTATTG
130 GCACGTTTAGGGAGATAAGACCTGATGCGATCTACTCTATTG
* *
58681629 CAACTTCAGAGAGATAAGATTCATCATTTTAATCCGCTCCACTACAACTTCAGGGAGATAGGATT
1 CAACTTCAGAGAGATAAGA-TCATCATTTTAATCTGCTCCA-TGCAACTTCAGGGAGATAGGATT
* ** ** *
58681694 GGTTTCTTCTGTCTGCTCCACTACAACTTCAGGGAGATAAG
64 GATAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
58681735 TCTTGTAACT
Statistics
Matches: 254, Mismatches: 21, Indels: 6
0.90 0.07 0.02
Matches are distributed among these distances:
172 157 0.62
173 97 0.38
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (171 bp):
CAACTTCAGAGAGATAAGATCATCATTTTAATCTGCTCCATGCAACTTCAGGGAGATAGGATTGA
TAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAGTCTGCTTCGCTG
CACGTTTAGGGAGATAAGACCTGATGCGATCTACTCTATTG
Found at i:58681506 original size:43 final size:43
Alignment explanation
Indices: 58681455--58681563 Score: 114
Period size: 43 Copynumber: 2.5 Consensus size: 43
58681445 TCTACTCTAT
58681455 TGCAACTTCAGAGAGATAAGAT-CAATCATTTTAATCTGCTCCA-
1 TGCAACTTCAGAGAGATAAGATGCAATC-TTTT-ATCTGCTCCAC
* * *** *
58681498 TGCAACTTCAAAGAGATAGGATTGGTTTCTTTTGTCTGCTCCAC
1 TGCAACTTCAGAGAGATAAGA-TGCAATCTTTTATCTGCTCCAC
*
58681542 TGCAACTTCAGGGAGATAAGAT
1 TGCAACTTCAGAGAGATAAGAT
58681564 TGGTTTATTC
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
43 29 0.54
44 23 0.43
45 2 0.04
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.31
Consensus pattern (43 bp):
TGCAACTTCAGAGAGATAAGATGCAATCTTTTATCTGCTCCAC
Found at i:58681558 original size:44 final size:44
Alignment explanation
Indices: 58681489--58681734 Score: 168
Period size: 44 Copynumber: 5.7 Consensus size: 44
58681479 ATCATTTTAA
** * *
58681489 TCTGCTCCA-TGCAACTTCAAAGAGATAGGATTGGTTTCTTTTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTG
* *
58681532 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTATTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTG
* * * * * *
58681576 TCTGCTTCGCTGC-ACGTTTAGGGAGATAAGACCT-G---ATGC-G
1 TCTGCTCCACTGCAAC-TTCAGGGAGATAAGA-TTGGTTTCTTCTG
* * * * ** **
58681616 ATCTACTCTATTGCAACTTCAGAGAGATAAGATTCATCATT-TT-AA
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGT--TTCTTCTG
* * *
58681661 TCCGCTCCACTACAACTTCAGGGAGATAGGATTGGTTTCTTCTG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTG
*
58681705 TCTGCTCCACTACAACTTCAGGGAGATAAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG
58681735 TCTTGTAACT
Statistics
Matches: 154, Mismatches: 35, Indels: 27
0.71 0.16 0.12
Matches are distributed among these distances:
40 2 0.01
41 24 0.16
42 4 0.03
43 13 0.08
44 109 0.71
45 2 0.01
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGGTTTCTTCTG
Found at i:58691021 original size:25 final size:25
Alignment explanation
Indices: 58690987--58691037 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
58690977 CTCCGAGATG
*
58690987 TTGTCCCTCCTTGGTGTAGCTACTA
1 TTGTCCCTCCTCGGTGTAGCTACTA
* *
58691012 TTGTCGCTCCTCGGTGTAGTTACTA
1 TTGTCCCTCCTCGGTGTAGCTACTA
58691037 T
1 T
58691038 CTCTTTTAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (25 bp):
TTGTCCCTCCTCGGTGTAGCTACTA
Found at i:58693587 original size:3 final size:3
Alignment explanation
Indices: 58693573--58693690 Score: 132
Period size: 3 Copynumber: 39.0 Consensus size: 3
58693563 TAACATTATG
* * * *
58693573 AAT AAT AGT AAT AAT AAT AAT ACT AAT AAT AAT GAA- AGT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT
* * *
58693618 AAT AAT AAT AAAT AAT AGT ACA- AAT AAT AAT AAT AGT ATT AAT AAT
1 AAT AAT AAT -AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT
58693664 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
58693691 GATAGCAATA
Statistics
Matches: 99, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
2 2 0.02
3 92 0.93
4 5 0.05
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:58710943 original size:85 final size:84
Alignment explanation
Indices: 58710786--58711107 Score: 398
Period size: 85 Copynumber: 3.8 Consensus size: 84
58710776 ATCCTTTACT
* * * * * * * *
58710786 CGGTGGATTCATCACTTAGCAACCACC-ATAAATTCAGTGATAC-AGGAATCAACACATAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAAC
* *
58710849 CCCTTTCACAATTAAGGATT
66 CCCTTTCACAATTAA-AATA
*
58710869 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCACTTAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAAC
* *
58710934 CCCATTCACAATTAAAAAA
66 CCCTTTCACAATTAAAATA
* * * *
58710953 CGGTGGATTCAGCACATAGCAACCACCATTATATTCAACGATACGGGGAATCAGCACTTAGCAAC
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAAC
58711018 CCCTTTCACAATTAAAAATA
66 CCCTTTCACAATT-AAAATA
* * * * *
58711038 CGGTGGGATCAGCACTTAGCAACCACCTTTAGAGTT-AATAATTCAGGGAATCAGCACTTAGCAA
1 CGGTGGAATCAGCACTTAGCAACCACCTTTATA-TTCAATGATACGGGGAATCAGCACTTAGCAA
58711102 CCCCTT
65 CCCCTT
58711108 GGGGAATCAA
Statistics
Matches: 208, Mismatches: 27, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
83 25 0.12
84 87 0.42
85 94 0.45
86 2 0.01
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (84 bp):
CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAAC
CCCTTTCACAATTAAAATA
Found at i:58710973 original size:84 final size:84
Alignment explanation
Indices: 58710786--58711107 Score: 400
Period size: 84 Copynumber: 3.8 Consensus size: 84
58710776 ATCCTTTACT
* * * * * * *
58710786 CGGTGGATTCATCACTTAGCAACCACC-ATAAATTCAGTGATAC-AGGAATCAACACATAGCAAC
1 CGGTGGATTCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAAC
* **
58710849 CCCTTTCACAATTAAGGATT
66 CCCTTTCACAATTAA-AAAA
* *
58710869 CGGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCACTTAGCAAC
1 CGGTGGATTCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAAC
*
58710934 CCCATTCACAATTAAAAAA
66 CCCTTTCACAATTAAAAAA
* * *
58710953 CGGTGGATTCAGCACATAGCAACCACCATTATATTCAACGATACGGGGAATCAGCACTTAGCAAC
1 CGGTGGATTCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAAC
58711018 CCCTTTCACAATTAAAAATA
66 CCCTTTCACAATTAAAAA-A
* * * *
58711038 CGGTGGGA-TCAGCACTTAGCAACCACCTTTAGAGTT-AATAATTCAGGGAATCAGCACTTAGCA
1 CGGT-GGATTCAGCACTTAGCAACCACCTTTATA-TTCAATGATACGGGGAATCAGCACTTAGCA
58711101 ACCCCTT
64 ACCCCTT
58711108 GGGGAATCAA
Statistics
Matches: 210, Mismatches: 24, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
83 25 0.12
84 92 0.44
85 88 0.42
86 5 0.02
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.23
Consensus pattern (84 bp):
CGGTGGATTCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACTTAGCAAC
CCCTTTCACAATTAAAAAA
Found at i:58711063 original size:169 final size:167
Alignment explanation
Indices: 58710786--58711105 Score: 453
Period size: 169 Copynumber: 1.9 Consensus size: 167
58710776 ATCCTTTACT
* * **
58710786 CGGTGGATTCATCACTTAGCAACCACCATAAATTCAGTGATACAGGAATCAACACATAGCAACCC
1 CGGTGGATTCAGCACATAGCAACCACCATAAATTCAACGATACAGGAATCAACACATAGCAACCC
** * * * * *
58710851 CTTTCACAATTAAGGATTCGGTGGAATCAGCACTTAGCAACCACCTTTATA-TTCAGTGATACGG
66 CTTTCACAATTAAAAATACGGTGGAATCAGCACTTAGCAACCACCTTTAGAGTT-AATAATACAG
58710915 GGAATCAGCACTTAGCAACCCCATTCACAATTAAAAAA
130 GGAATCAGCACTTAGCAACCCCATTCACAATTAAAAAA
* * * *
58710953 CGGTGGATTCAGCACATAGCAACCACCATTATATTCAACGATACGGGGAATCAGCACTTAGCAAC
1 CGGTGGATTCAGCACATAGCAACCACCA-TAAATTCAACGATAC-AGGAATCAACACATAGCAAC
* *
58711018 CCCTTTCACAATTAAAAATACGGTGGGATCAGCACTTAGCAACCACCTTTAGAGTTAATAATTCA
64 CCCTTTCACAATTAAAAATACGGTGGAATCAGCACTTAGCAACCACCTTTAGAGTTAATAATACA
58711083 GGGAATCAGCACTTAGCAACCCC
129 GGGAATCAGCACTTAGCAACCCC
58711106 TTGGGGAATC
Statistics
Matches: 133, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
167 26 0.20
168 12 0.09
169 93 0.70
170 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.23
Consensus pattern (167 bp):
CGGTGGATTCAGCACATAGCAACCACCATAAATTCAACGATACAGGAATCAACACATAGCAACCC
CTTTCACAATTAAAAATACGGTGGAATCAGCACTTAGCAACCACCTTTAGAGTTAATAATACAGG
GAATCAGCACTTAGCAACCCCATTCACAATTAAAAAA
Found at i:58711112 original size:26 final size:26
Alignment explanation
Indices: 58711083--58711133 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
58711073 TAATAATTCA
*
58711083 GGGAATCAGCACTTAGCAACCCCTTG
1 GGGAATCAACACTTAGCAACCCCTTG
*
58711109 GGGAATCAACATTTAGCAACCCCTT
1 GGGAATCAACACTTAGCAACCCCTT
58711134 TTTATTCAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (26 bp):
GGGAATCAACACTTAGCAACCCCTTG
Found at i:58718588 original size:85 final size:84
Alignment explanation
Indices: 58718443--58718743 Score: 318
Period size: 85 Copynumber: 3.6 Consensus size: 84
58718433 TCCGTTACTT
* * * * * * *
58718443 GGTGGATTCATCACTTCGCAACCACC-ATAAATTCATTGATATGGGGAATCAGCACATAGCAACC
1 GGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAACC
** **
58718507 TCTTTCACAATTAAGGATTT
66 -CTTTCACAATTAAAAATAC
*
58718527 GGTGGAATCAGCACTTAGCAACCACCTTTATATTCAGTGATACGGGGAATCAGCATC-TAGCAAC
1 GGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCA-CATAGCAA-
*
58718591 CCCATTCACAATTAAAAATAC
64 CCCTTTCACAATTAAAAATAC
* * * * * * * * *
58718612 GATGGATTCAGCACATAGCAAGCACCATTATGTTCAACGATACGGGGAATCAACACTTAGCAACC
1 GGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAACC
58718677 CTTTTCACAATTAAAAATAC
66 C-TTTCACAATTAAAAATAC
* * * *
58718697 GGTGGGATCAGCACTTAGCAACCACCTTTATAGTCAATAATTCGGGG
1 GGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGG
58718744 CCCCTCGGGG
Statistics
Matches: 179, Mismatches: 33, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
84 27 0.15
85 149 0.83
86 3 0.02
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (84 bp):
GGTGGAATCAGCACTTAGCAACCACCTTTATATTCAATGATACGGGGAATCAGCACATAGCAACC
CTTTCACAATTAAAAATAC
Found at i:58718612 original size:42 final size:42
Alignment explanation
Indices: 58718485--58718719 Score: 147
Period size: 43 Copynumber: 5.5 Consensus size: 42
58718475 TCATTGATAT
* * * ** **
58718485 GGGGAATCAGCACATAGCAACCTCTTTCACAATTAAGGATTT
1 GGGGAATCAGCACTTAGCAACCCCATTCACAATTAAAAATAC
* * ***
58718527 GGTGGAATCAGCACTTAGCAACCACC-TTTA-TATTCAGTGATAC
1 GG-GGAATCAGCACTTAGCAACC-CCATTCACAATT-AAAAATAC
58718570 GGGGAATCAGCA-TCTAGCAACCCCATTCACAATTAAAAATAC
1 GGGGAATCAGCACT-TAGCAACCCCATTCACAATTAAAAATAC
* * * * ** **
58718612 GATGGATTCAGCACATAGCAAGCACCATT-A-TGTTCAACGATAC
1 G-GGGAATCAGCACTTAGCAA-CCCCATTCACAATT-AAAAATAC
* **
58718655 GGGGAATCAACACTTAGCAACCCTTTTCACAATTAAAAATAC
1 GGGGAATCAGCACTTAGCAACCCCATTCACAATTAAAAATAC
*
58718697 GGTGGGATCAGCACTTAGCAACC
1 GG-GGAATCAGCACTTAGCAACC
58718720 ACCTTTATAG
Statistics
Matches: 146, Mismatches: 34, Indels: 25
0.71 0.17 0.12
Matches are distributed among these distances:
41 7 0.05
42 58 0.40
43 74 0.51
44 7 0.05
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (42 bp):
GGGGAATCAGCACTTAGCAACCCCATTCACAATTAAAAATAC
Found at i:58723358 original size:19 final size:17
Alignment explanation
Indices: 58723318--58723368 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 17
58723308 AATTAGAATG
*
58723318 TAAAAATTAAACTAAAA
1 TAAAAATTAAAATAAAA
*
58723335 CAAAAATATAAAAATAAAA
1 TAAAAAT-T-AAAATAAAA
58723354 T-AAAA-TAAAATAAAA
1 TAAAAATTAAAATAAAA
58723369 ATGGATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 9 0.31
16 1 0.03
17 6 0.21
18 5 0.17
19 8 0.28
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (17 bp):
TAAAAATTAAAATAAAA
Found at i:58725748 original size:28 final size:28
Alignment explanation
Indices: 58725632--58725775 Score: 123
Period size: 28 Copynumber: 5.2 Consensus size: 28
58725622 TGCCACAAGA
* * *
58725632 GCTTTCATTT-CATA-ATCCACCACACAG
1 GCTTCCATTTCCATAGAT-CACCATAAAG
**
58725659 GCTTCCATTT-CATAGATCACCATAACT
1 GCTTCCATTTCCATAGATCACCATAAAG
* * ** *
58725686 GCTTCCCTTTCCATAGATCGCCGCAAAT
1 GCTTCCATTTCCATAGATCACCATAAAG
* * * **
58725714 ACCTCCATTTGCATAGATTGCCATAAAG
1 GCTTCCATTTCCATAGATCACCATAAAG
58725742 GCTTCCATTTCCATAGATCACCATAAAG
1 GCTTCCATTTCCATAGATCACCATAAAG
58725770 GCTTCC
1 GCTTCC
58725776 CTATTCCTGG
Statistics
Matches: 92, Mismatches: 23, Indels: 3
0.78 0.19 0.03
Matches are distributed among these distances:
27 28 0.30
28 64 0.70
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (28 bp):
GCTTCCATTTCCATAGATCACCATAAAG
Found at i:58731775 original size:17 final size:17
Alignment explanation
Indices: 58731753--58731785 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
58731743 AAATGAGGGG
58731753 ATCTTTTAAGAACTAAA
1 ATCTTTTAAGAACTAAA
58731770 ATCTTTTAAGAACTAA
1 ATCTTTTAAGAACTAA
58731786 GTCACGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
ATCTTTTAAGAACTAAA
Found at i:58741134 original size:24 final size:24
Alignment explanation
Indices: 58741105--58741156 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
58741095 TGAAAATTAC
*
58741105 CTCCCTTACCTTGAAGTTCAACAA
1 CTCCCTTACCTTGAACTTCAACAA
58741129 CTCCCTTACCTTGAACTTCAACAA
1 CTCCCTTACCTTGAACTTCAACAA
58741153 CTCC
1 CTCC
58741157 GTATGGATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.38, G:0.06, T:0.29
Consensus pattern (24 bp):
CTCCCTTACCTTGAACTTCAACAA
Found at i:58748011 original size:28 final size:28
Alignment explanation
Indices: 58747944--58748071 Score: 132
Period size: 28 Copynumber: 4.6 Consensus size: 28
58747934 CGTGTTTCAA
* *
58747944 GCCACACAGGCTTCCATTT-CATAGATC
1 GCCACAAAGGCTTCCCTTTCCATAGATC
* * *
58747971 TCCATAAATGCTTCCCTTTCCATAGATC
1 GCCACAAAGGCTTCCCTTTCCATAGATC
* * *
58747999 GCCACAAAGGCTTCCCTTTCTATAGGTT
1 GCCACAAAGGCTTCCCTTTCCATAGATC
* * * * *
58748027 GCAACAAAGGTTTCCCTTACCATAAATT
1 GCCACAAAGGCTTCCCTTTCCATAGATC
58748055 GCCACAAAGGCTTCCCT
1 GCCACAAAGGCTTCCCT
58748072 ATTCTTGGCG
Statistics
Matches: 81, Mismatches: 19, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
27 14 0.17
28 67 0.83
ACGTcount: A:0.27, C:0.31, G:0.13, T:0.29
Consensus pattern (28 bp):
GCCACAAAGGCTTCCCTTTCCATAGATC
Found at i:58755749 original size:7 final size:7
Alignment explanation
Indices: 58755737--58755768 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
58755727 TTGCAATGGG
58755737 ATATGTT
1 ATATGTT
58755744 ATATGTT
1 ATATGTT
58755751 ATATGTT
1 ATATGTT
58755758 ATATGTT
1 ATATGTT
58755765 ATAT
1 ATAT
58755769 AATATGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (7 bp):
ATATGTT
Found at i:58757442 original size:3 final size:3
Alignment explanation
Indices: 58757434--58757471 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
58757424 GGAGACTGCA
58757434 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
58757472 AGAAATTGTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:58763385 original size:22 final size:21
Alignment explanation
Indices: 58763345--58763386 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
58763335 AATTTATGAT
**
58763345 AATAAATTTATAATTTTAATG
1 AATAAATTTATAAGATTAATG
58763366 AATATAATTTATAAGATTAAT
1 AATA-AATTTATAAGATTAAT
58763387 ATTAAGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (21 bp):
AATAAATTTATAAGATTAATG
Found at i:58766385 original size:27 final size:27
Alignment explanation
Indices: 58766355--58766413 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
58766345 AGAAGGCCAC
58766355 CATTGGCGCCTCTCTATGAGGCACCTT
1 CATTGGCGCCTCTCTATGAGGCACCTT
58766382 CATTGGCGCCTCTCTATGAGGCACCTT
1 CATTGGCGCCTCTCTATGAGGCACCTT
58766409 CATTG
1 CATTG
58766414 ACGGCTACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.15, C:0.32, G:0.22, T:0.31
Consensus pattern (27 bp):
CATTGGCGCCTCTCTATGAGGCACCTT
Found at i:58781759 original size:2 final size:2
Alignment explanation
Indices: 58781735--58781774 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
58781725 GATACGTTTA
*
58781735 AT AT TT AT AT AT -T A- AT AT A- AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58781774 A
1 A
58781775 GAGAGAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58781779 original size:2 final size:2
Alignment explanation
Indices: 58781774--58781798 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
58781764 ATATATATAT
58781774 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
58781799 AAGGAATGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:58782175 original size:29 final size:29
Alignment explanation
Indices: 58782133--58782198 Score: 132
Period size: 29 Copynumber: 2.3 Consensus size: 29
58782123 GCGAAGAAGG
58782133 ATTTTATTTTATTCGCAATTAGTATTTCT
1 ATTTTATTTTATTCGCAATTAGTATTTCT
58782162 ATTTTATTTTATTCGCAATTAGTATTTCT
1 ATTTTATTTTATTCGCAATTAGTATTTCT
58782191 ATTTTATT
1 ATTTTATT
58782199 CGCTCCAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.61
Consensus pattern (29 bp):
ATTTTATTTTATTCGCAATTAGTATTTCT
Found at i:58783210 original size:11 final size:12
Alignment explanation
Indices: 58783185--58783220 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 12
58783175 TTTTTTAATA
58783185 TTATTTAATTTT
1 TTATTTAATTTT
58783197 TTATTTAATTTT
1 TTATTTAATTTT
58783209 TATAATTTAATT
1 T-T-ATTTAATT
58783221 AATATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 13 0.59
13 1 0.05
14 8 0.36
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (12 bp):
TTATTTAATTTT
Found at i:58783229 original size:31 final size:31
Alignment explanation
Indices: 58783168--58783229 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
58783158 GTAAGGATTA
* * *
58783168 ATTTCATTTTTTTAATATTATTTAATTTTTT
1 ATTTAATTTTTATAATATTAATTAATTTTTT
58783199 ATTTAATTTTTATAAT-TTAATTAATATTTTT
1 ATTTAATTTTTATAATATTAATTAAT-TTTTT
58783230 TATAATAGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (31 bp):
ATTTAATTTTTATAATATTAATTAATTTTTT
Found at i:58784757 original size:18 final size:18
Alignment explanation
Indices: 58784734--58784776 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
58784724 TGCCAAATGC
** *
58784734 GTATCCTAACTTTTATGT
1 GTATCCTAACCCTTATAT
58784752 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
58784770 GTATCCT
1 GTATCCT
58784777 TTTTTCACTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.09, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:58786109 original size:9 final size:9
Alignment explanation
Indices: 58786083--58786157 Score: 77
Period size: 9 Copynumber: 8.4 Consensus size: 9
58786073 CATGTGGTAA
58786083 AAAAATTAT
1 AAAAATTAT
58786092 AAAAA--AT
1 AAAAATTAT
58786099 AAAAATTAT
1 AAAAATTAT
58786108 AAAAATTATT
1 AAAAATTA-T
**
58786118 AAATTTTAAT
1 AAAAATT-AT
58786128 AAAAATTAT
1 AAAAATTAT
58786137 -AAAA-TATT
1 AAAAATTA-T
58786145 AAAAATTAT
1 AAAAATTAT
58786154 AAAA
1 AAAA
58786158 TTTGTAAAAN
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
7 9 0.16
8 5 0.09
9 26 0.47
10 14 0.25
11 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
AAAAATTAT
Found at i:58786121 original size:17 final size:16
Alignment explanation
Indices: 58786083--58786157 Score: 77
Period size: 17 Copynumber: 4.8 Consensus size: 16
58786073 CATGTGGTAA
*
58786083 AAAAATTATAAAAAAT
1 AAAAATTATAAAAATT
58786099 AAAAATTATAAAAATT
1 AAAAATTATAAAAATT
* *
58786115 ATTAAATT-T--TAA-T
1 A-AAAATTATAAAAATT
58786128 AAAAATTATAAAATATT
1 AAAAATTATAAAA-ATT
58786145 AAAAATTATAAAA
1 AAAAATTATAAAA
58786158 TTTGTAAAAN
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
12 5 0.10
13 3 0.06
14 2 0.04
15 1 0.02
16 18 0.38
17 19 0.40
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAAATTATAAAAATT
Found at i:58786148 original size:37 final size:36
Alignment explanation
Indices: 58786090--58786160 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 36
58786080 TAAAAAAATT
*
58786090 ATAAAAAATAAAAATTATAAAAATTATTAAATTTTA
1 ATAAAAAATAAAAATTATAAAAATTATAAAATTTTA
*
58786126 ATAAAAATTATAAAA-TATTAAAAATTATAAAATTT
1 ATAAAAAATA-AAAATTA-TAAAAATTATAAAATTT
58786161 GTAAAANNNN
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 11 0.35
37 20 0.65
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (36 bp):
ATAAAAAATAAAAATTATAAAAATTATAAAATTTTA
Found at i:58786150 original size:29 final size:29
Alignment explanation
Indices: 58786096--58786151 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 29
58786086 AATTATAAAA
*
58786096 AATAAAAATTATAAAAATTATTAAATTTT
1 AATAAAAATTATAAAAATTATAAAATTTT
58786125 AATAAAAATTATAAAATATTA-AAAATT
1 AATAAAAATTATAAAA-ATTATAAAATT
58786152 ATAAAATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (29 bp):
AATAAAAATTATAAAAATTATAAAATTTT
Found at i:58788198 original size:5 final size:5
Alignment explanation
Indices: 58788188--58788213 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
58788178 CAATGCAAAC
58788188 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
58788214 AATTCTAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:58794681 original size:11 final size:11
Alignment explanation
Indices: 58794665--58794690 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
58794655 TGGACATGCA
58794665 TGGAACACACG
1 TGGAACACACG
58794676 TGGAACACACG
1 TGGAACACACG
58794687 TGGA
1 TGGA
58794691 GGATATAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.23, G:0.31, T:0.12
Consensus pattern (11 bp):
TGGAACACACG
Found at i:58797107 original size:40 final size:41
Alignment explanation
Indices: 58797050--58797139 Score: 94
Period size: 42 Copynumber: 2.2 Consensus size: 41
58797040 TCCTTGTAGG
* * *
58797050 CGCGATTTGTGTCCACGTAAGC-AAATCGTGCTGACGTGGA
1 CGCGATTTGTGTACACGTAACCGAAATCGCGCTGACGTGGA
** *
58797090 CGCGATTTGCTG-ACACGTCCCCTGACATCGCGCTGACGTGGA
1 CGCGATTTG-TGTACACGTAACC-GAAATCGCGCTGACGTGGA
58797132 CGCGATTT
1 CGCGATTT
58797140 AGGGAAAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
40 15 0.37
41 2 0.05
42 24 0.59
ACGTcount: A:0.19, C:0.28, G:0.29, T:0.24
Consensus pattern (41 bp):
CGCGATTTGTGTACACGTAACCGAAATCGCGCTGACGTGGA
Found at i:58798392 original size:30 final size:29
Alignment explanation
Indices: 58798326--58798392 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
58798316 CCTATGTCCC
* * **
58798326 CCTATGTTCCTGAGAACTTGAAAGCCCAT
1 CCTATCTTCCTGACAACTCCAAAGCCCAT
*
58798355 CCATATCTTCCTGACAACTCCAAAGGCCATT
1 CC-TATCTTCCTGACAACTCCAAAGCCCA-T
58798386 CCTATCT
1 CCTATCT
58798393 CCCCTACGTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
29 2 0.06
30 26 0.84
31 3 0.10
ACGTcount: A:0.27, C:0.33, G:0.12, T:0.28
Consensus pattern (29 bp):
CCTATCTTCCTGACAACTCCAAAGCCCAT
Found at i:58804621 original size:21 final size:21
Alignment explanation
Indices: 58804580--58804621 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
58804570 CCAAGCTCAA
*
58804580 TTTTAGCTCAATTTTAGTTTG
1 TTTTAGCTCAAGTTTAGTTTG
58804601 TTTTAGCTCGAAGTTTA-TTTG
1 TTTTAGCTC-AAGTTTAGTTTG
58804622 CTGGAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.55
Consensus pattern (21 bp):
TTTTAGCTCAAGTTTAGTTTG
Found at i:58812071 original size:20 final size:18
Alignment explanation
Indices: 58812046--58812129 Score: 57
Period size: 20 Copynumber: 4.4 Consensus size: 18
58812036 TTCCTATATC
58812046 AAATTCTATTATCAATCCAT
1 AAATTC-ATTATCAAT-CAT
*
58812066 AAATTCA-TATCAATTTCAC
1 AAATTCATTATCAA--TCAT
*
58812085 ATAATTCATT-TCAAT-TT
1 A-AATTCATTATCAATCAT
58812102 CAAATTCTATTATCAATCAT
1 -AAATTC-ATTATCAATCAT
*
58812122 AAACTCAT
1 AAATTCAT
58812130 ACTAAATTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 14 0.27
20 18 0.35
21 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.40
Consensus pattern (18 bp):
AAATTCATTATCAATCAT
Found at i:58812076 original size:31 final size:30
Alignment explanation
Indices: 58812041--58812138 Score: 75
Period size: 31 Copynumber: 3.4 Consensus size: 30
58812031 ATTCATTCCT
58812041 ATATCAAATTCTATTATCAATCCATAAATTC
1 ATATCAAATTCTATTATCAAT-CATAAATTC
* *
58812072 ATATCAATTTC-A-CAT-AATTCAT---TTC
1 ATATCAAATTCTATTATCAA-TCATAAATTC
* *
58812097 AATTTCAAATTCTATTATCAATCATAAACTC
1 -ATATCAAATTCTATTATCAATCATAAATTC
58812128 ATA-CTAAATTC
1 ATATC-AAATTC
58812139 ACGTATTTCA
Statistics
Matches: 51, Mismatches: 7, Indels: 19
0.66 0.09 0.25
Matches are distributed among these distances:
25 3 0.06
26 9 0.18
27 1 0.02
28 11 0.22
29 6 0.12
30 9 0.18
31 12 0.24
ACGTcount: A:0.41, C:0.19, G:0.00, T:0.40
Consensus pattern (30 bp):
ATATCAAATTCTATTATCAATCATAAATTC
Found at i:58812080 original size:57 final size:56
Alignment explanation
Indices: 58812019--58812130 Score: 179
Period size: 57 Copynumber: 2.0 Consensus size: 56
58812009 TAGCATATAC
* *
58812019 CAATTTCACATAATTCATTCCTATATCAAATTCTATTATCAATCCATAAATTCATAT
1 CAATTTCACATAATTCATTCCAATATCAAATTCTATTATCAAT-CATAAACTCATAT
* *
58812076 CAATTTCACATAATTCATTTCAATTTCAAATTCTATTATCAATCATAAACTCATA
1 CAATTTCACATAATTCATTCCAATATCAAATTCTATTATCAATCATAAACTCATA
58812131 CTAAATTCAC
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
56 11 0.22
57 40 0.78
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.40
Consensus pattern (56 bp):
CAATTTCACATAATTCATTCCAATATCAAATTCTATTATCAATCATAAACTCATAT
Found at i:58812149 original size:56 final size:57
Alignment explanation
Indices: 58812023--58812172 Score: 187
Period size: 56 Copynumber: 2.6 Consensus size: 57
58812013 ATATACCAAT
* * * * *
58812023 TTCACATAATTCATTCCTATATCAAATTCTATTATCAATCCATAAATTCATATCAAT
1 TTCACATAATTCATTTCAATTTCAAATTCTATTATCAATCCATAAACTCATATCAAA
58812080 TTCACATAATTCATTTCAATTTCAAATTCTATTATCAAT-CATAAACTCATA-CTAAA
1 TTCACATAATTCATTTCAATTTCAAATTCTATTATCAATCCATAAACTCATATC-AAA
* * * * *
58812136 TTCACGTATTTCATTTCAGTTTCATACTCTATTATCA
1 TTCACATAATTCATTTCAATTTCAAATTCTATTATCA
58812173 TTTTATAAGA
Statistics
Matches: 82, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
55 1 0.01
56 45 0.55
57 36 0.44
ACGTcount: A:0.36, C:0.21, G:0.01, T:0.42
Consensus pattern (57 bp):
TTCACATAATTCATTTCAATTTCAAATTCTATTATCAATCCATAAACTCATATCAAA
Found at i:58812632 original size:31 final size:30
Alignment explanation
Indices: 58812592--58812650 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
58812582 AAATCATTCA
*
58812592 CATTCACATTCACATATTCATACTCTGTAAT
1 CATTCACATTCACATA-TCACACTCTGTAAT
* * *
58812623 CATTTACATTTACCTATCACACTCTGTA
1 CATTCACATTCACATATCACACTCTGTA
58812651 CACTATACTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 11 0.46
31 13 0.54
ACGTcount: A:0.31, C:0.27, G:0.03, T:0.39
Consensus pattern (30 bp):
CATTCACATTCACATATCACACTCTGTAAT
Found at i:58815153 original size:25 final size:25
Alignment explanation
Indices: 58815105--58815153 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
58815095 CATAATTGAA
* * *
58815105 ATGAAATGGATTGATTTTGTATATT
1 ATGAAATAGATTGATTATGAATATT
*
58815130 ATGAAATATATTGATTATGAATAT
1 ATGAAATAGATTGATTATGAATAT
58815154 ATGTGTATTG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.16, T:0.45
Consensus pattern (25 bp):
ATGAAATAGATTGATTATGAATATT
Found at i:58815658 original size:42 final size:43
Alignment explanation
Indices: 58815549--58815676 Score: 206
Period size: 43 Copynumber: 3.0 Consensus size: 43
58815539 TATGTGATTG
*
58815549 ATATTGAAATGACAAAGATGAGAAATGAA-TATGAGATGAGAAA
1 ATATTGAAATGACAAATATGAGAAAT-AATTATGAGATGAGAAA
* *
58815592 ATATTGAAATGACAATTACGAGAAATAATTATGAGATGAGAAA
1 ATATTGAAATGACAAATATGAGAAATAATTATGAGATGAGAAA
58815635 ATATTG-AATGACAAATATGAGAAATAATTATGAGATGAGAAA
1 ATATTGAAATGACAAATATGAGAAATAATTATGAGATGAGAAA
58815677 TGAAATATGA
Statistics
Matches: 79, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
42 36 0.46
43 43 0.54
ACGTcount: A:0.52, C:0.03, G:0.20, T:0.24
Consensus pattern (43 bp):
ATATTGAAATGACAAATATGAGAAATAATTATGAGATGAGAAA
Found at i:58817390 original size:18 final size:19
Alignment explanation
Indices: 58817358--58817397 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
58817348 TTCTATTTTC
58817358 TAAAATAAATATAATGAAT
1 TAAAATAAATATAATGAAT
* *
58817377 TAAATTAAAT-TAATTAAT
1 TAAAATAAATATAATGAAT
58817395 TAA
1 TAA
58817398 TTTCCCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TAAAATAAATATAATGAAT
Found at i:58818159 original size:22 final size:22
Alignment explanation
Indices: 58818120--58818161 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
58818110 AATATAATAA
**
58818120 TACTCATAATGTTTTTTTATAG
1 TACTCATAATGTCATTTTATAG
58818142 TACTCATAATGTCATTTTAT
1 TACTCATAATGTCATTTTAT
58818162 TATATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (22 bp):
TACTCATAATGTCATTTTATAG
Done.