Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 51 of 126
Found at i:15220215 original size:12 final size:12
Alignment explanation
Indices: 15220200--15220269 Score: 81
Period size: 12 Copynumber: 6.0 Consensus size: 12
15220190 AAATTATAGT
*
15220200 TTAAATTTGAAA
1 TTAAAATTGAAA
15220212 TTAAAATTGAAA
1 TTAAAATTGAAA
* *
15220224 TTACATTTGAAA
1 TTAAAATTGAAA
*
15220236 TGAAAATT-AAA
1 TTAAAATTGAAA
15220247 -TAAAATTGAAA
1 TTAAAATTGAAA
*
15220258 TTAAAGTTGAAA
1 TTAAAATTGAAA
15220270 AGAAAATTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
10 6 0.12
11 6 0.12
12 36 0.75
ACGTcount: A:0.54, C:0.01, G:0.10, T:0.34
Consensus pattern (12 bp):
TTAAAATTGAAA
Found at i:15220256 original size:34 final size:34
Alignment explanation
Indices: 15220213--15220280 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 34
15220203 AATTTGAAAT
* * *
15220213 TAAAATTGAAATTACATTTGAAATGAAAATTAAA
1 TAAAATTGAAATTAAAGTTGAAAAGAAAATTAAA
15220247 TAAAATTGAAATTAAAGTTGAAAAGAAAATTAAA
1 TAAAATTGAAATTAAAGTTGAAAAGAAAATTAAA
15220281 ATCCGAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.59, C:0.01, G:0.10, T:0.29
Consensus pattern (34 bp):
TAAAATTGAAATTAAAGTTGAAAAGAAAATTAAA
Found at i:15220389 original size:15 final size:16
Alignment explanation
Indices: 15220369--15220411 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
15220359 AATTTAAAAT
15220369 TAAAGTGTAATAAT-A
1 TAAAGTGTAATAATAA
* *
15220384 TAAAGTTTAA-ACTAA
1 TAAAGTGTAATAATAA
15220399 TAAAGTGTAATAA
1 TAAAGTGTAATAA
15220412 AATTTAATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
14 2 0.09
15 19 0.86
16 1 0.05
ACGTcount: A:0.53, C:0.02, G:0.12, T:0.33
Consensus pattern (16 bp):
TAAAGTGTAATAATAA
Found at i:15220543 original size:11 final size:11
Alignment explanation
Indices: 15220524--15220593 Score: 50
Period size: 11 Copynumber: 6.3 Consensus size: 11
15220514 ATTTAATTTT
*
15220524 AAATGAAATTA
1 AAATAAAATTA
*
15220535 AAATAAAATTG
1 AAATAAAATTA
*
15220546 AAATTAAATTA
1 AAATAAAATTA
* *
15220557 AAATTAAATGA
1 AAATAAAATTA
** *
15220568 AAGGAAATTTA
1 AAATAAAATTA
*
15220579 AAATTAAATTTA
1 AAA-TAAAATTA
15220591 AAA
1 AAA
15220594 ATTGGGGTAT
Statistics
Matches: 46, Mismatches: 12, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
11 36 0.78
12 10 0.22
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (11 bp):
AAATAAAATTA
Found at i:15220547 original size:17 final size:17
Alignment explanation
Indices: 15220527--15220565 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
15220517 TAATTTTAAA
15220527 TGAAATTAAAATAAAAT
1 TGAAATTAAAATAAAAT
*
15220544 TGAAATTAAATTAAAAT
1 TGAAATTAAAATAAAAT
15220561 T-AAAT
1 TGAAAT
15220566 GAAAGGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
TGAAATTAAAATAAAAT
Found at i:15220549 original size:22 final size:22
Alignment explanation
Indices: 15220524--15220588 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
15220514 ATTTAATTTT
*
15220524 AAATGAAATTAAAATAAAATTG
1 AAATGAAATTAAAATTAAATTG
*
15220546 AAATTAAATTAAAATTAAA-TG
1 AAATGAAATTAAAATTAAATTG
*
15220567 AAAGGAAATTTAAAATTAAATT
1 AAATGAAA-TTAAAATTAAATT
15220589 TAAAAATTGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
21 8 0.22
22 28 0.76
23 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (22 bp):
AAATGAAATTAAAATTAAATTG
Found at i:15220596 original size:13 final size:12
Alignment explanation
Indices: 15220513--15220593 Score: 55
Period size: 12 Copynumber: 7.2 Consensus size: 12
15220503 TTATACTTAC
* *
15220513 AATTTAATTTTA
1 AATTAAATTTAA
*
15220525 AATGAAA-TTAA
1 AATTAAATTTAA
* *
15220536 AA-TAAAATTGA
1 AATTAAATTTAA
15220547 AATTAAA-TTAA
1 AATTAAATTTAA
*
15220558 AATTAAA--TGA
1 AATTAAATTTAA
**
15220568 AAGGAAATTTAA
1 AATTAAATTTAA
15220580 AATTAAATTTAA
1 AATTAAATTTAA
15220592 AA
1 AA
15220594 ATTGGGGTAT
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
10 10 0.19
11 20 0.38
12 23 0.43
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (12 bp):
AATTAAATTTAA
Found at i:15220844 original size:11 final size:10
Alignment explanation
Indices: 15220833--15220955 Score: 97
Period size: 10 Copynumber: 12.0 Consensus size: 10
15220823 ATAATTAAAT
15220833 TTTAAAATAA
1 TTTAAAATAA
*
15220843 TTAAAACATAA
1 TTTAAA-ATAA
15220854 TTTAAAATAA
1 TTTAAAATAA
*
15220864 TTAAAATATAA
1 TTTAAA-ATAA
15220875 TTTAAAATAA
1 TTTAAAATAA
*
15220885 TTAAAACATAA
1 TTTAAA-ATAA
**
15220896 TTT-AAATTT
1 TTTAAAATAA
* *
15220905 TTTTAATTAA
1 TTTAAAATAA
*
15220915 ATTAAAATAA
1 TTTAAAATAA
15220925 -TTAAAATAA
1 TTTAAAATAA
* *
15220934 TTGAAATCAAAA
1 TTTAAA--ATAA
15220946 TTTAAAATAA
1 TTTAAAATAA
15220956 GTAAATTTTA
Statistics
Matches: 88, Mismatches: 18, Indels: 14
0.73 0.15 0.12
Matches are distributed among these distances:
9 14 0.16
10 42 0.48
11 24 0.27
12 8 0.09
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.38
Consensus pattern (10 bp):
TTTAAAATAA
Found at i:15220848 original size:9 final size:9
Alignment explanation
Indices: 15220820--15220940 Score: 75
Period size: 9 Copynumber: 12.6 Consensus size: 9
15220810 TATTTAATAA
15220820 AAAATAATT
1 AAAATAATT
*
15220829 -AAAT-TTT
1 AAAATAATT
15220836 AAAATAATT
1 AAAATAATT
15220845 AAAACATAATTT
1 -AAA-ATAA-TT
15220857 AAAATAATT
1 AAAATAATT
15220866 AAAATATAATTT
1 -AAA-ATAA-TT
15220878 AAAATAATT
1 AAAATAATT
15220887 AAAACATAATTT
1 -AAA-ATAA-TT
* **
15220899 AAATTTTTT
1 AAAATAATT
* *
15220908 TAATTAAATT
1 AAAAT-AATT
15220918 AAAATAATT
1 AAAATAATT
15220927 AAAATAATT
1 AAAATAATT
*
15220936 GAAAT
1 AAAAT
15220941 CAAAATTTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
7 2 0.02
8 8 0.09
9 29 0.33
10 23 0.26
11 21 0.24
12 6 0.07
ACGTcount: A:0.59, C:0.02, G:0.01, T:0.39
Consensus pattern (9 bp):
AAAATAATT
Found at i:15220857 original size:21 final size:21
Alignment explanation
Indices: 15220833--15220901 Score: 129
Period size: 21 Copynumber: 3.3 Consensus size: 21
15220823 ATAATTAAAT
15220833 TTTAAAATAATTAAAACATAA
1 TTTAAAATAATTAAAACATAA
*
15220854 TTTAAAATAATTAAAATATAA
1 TTTAAAATAATTAAAACATAA
15220875 TTTAAAATAATTAAAACATAA
1 TTTAAAATAATTAAAACATAA
15220896 TTTAAA
1 TTTAAA
15220902 TTTTTTTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (21 bp):
TTTAAAATAATTAAAACATAA
Found at i:15221004 original size:32 final size:32
Alignment explanation
Indices: 15220942--15221004 Score: 74
Period size: 32 Copynumber: 2.0 Consensus size: 32
15220932 AATTGAAATC
* ** *
15220942 AAAATTTAAAATAAGTAAATTTTATTTATAAA
1 AAAATTTAAAACAAGTAAATTAAATATATAAA
15220974 AAAATTTAAAACAA-TAAACTTAAATATATAA
1 AAAATTTAAAACAAGTAAA-TTAAATATATAA
15221005 TATAAAAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
31 4 0.15
32 22 0.85
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (32 bp):
AAAATTTAAAACAAGTAAATTAAATATATAAA
Found at i:15221025 original size:6 final size:6
Alignment explanation
Indices: 15221009--15221055 Score: 51
Period size: 7 Copynumber: 7.5 Consensus size: 6
15220999 ATATAATATA
*
15221009 AAAATT GAAATT AAAA-T AAAATTT AAAATT AAAGATT AAAGATT AAA
1 AAAATT AAAATT AAAATT AAAA-TT AAAATT AAA-ATT AAA-ATT AAA
15221056 TATGCATTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
5 5 0.14
6 13 0.36
7 18 0.50
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:15221029 original size:18 final size:18
Alignment explanation
Indices: 15220974--15221055 Score: 56
Period size: 18 Copynumber: 4.2 Consensus size: 18
15220964 TATTTATAAA
*
15220974 AAAATTTAAAACAATAAACTT
1 AAAA-TTAAAATAA-AAA-TT
*
15220995 AAATATATAATATAAAAATT
1 AAA-AT-TAAAATAAAAATT
* *
15221015 GAAATTAAAATAAAATTT
1 AAAATTAAAATAAAAATT
*
15221033 AAAATTAAAGATTAAAGATT
1 AAAATTAAA-A-TAAAAATT
15221053 AAA
1 AAA
15221056 TATGCATTTA
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
18 19 0.39
19 3 0.06
20 13 0.27
21 7 0.14
22 7 0.14
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.30
Consensus pattern (18 bp):
AAAATTAAAATAAAAATT
Found at i:15221267 original size:12 final size:12
Alignment explanation
Indices: 15221252--15221333 Score: 59
Period size: 12 Copynumber: 7.2 Consensus size: 12
15221242 AAAATACCAA
15221252 AAAAATTATATT
1 AAAAATTATATT
15221264 AAAAA-TAT-TT
1 AAAAATTATATT
* *
15221274 -TAAATT-TTTT
1 AAAAATTATATT
15221284 AAAATATTATATT
1 AAAA-ATTATATT
**
15221297 TCAAATTATATT
1 AAAAATTATATT
*
15221309 TAAAA-TA-ATT
1 AAAAATTATATT
*
15221319 AAAAATTATAAT
1 AAAAATTATATT
15221331 AAA
1 AAA
15221334 TTAAAATAAT
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
9 4 0.07
10 12 0.22
11 9 0.16
12 25 0.45
13 5 0.09
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (12 bp):
AAAAATTATATT
Found at i:15221296 original size:24 final size:26
Alignment explanation
Indices: 15221254--15221315 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 26
15221244 AATACCAAAA
15221254 AAATTATA-TTAAAA-A-TAT-TTT-
1 AAATTATATTTAAAATATTATATTTC
15221275 AAATT-T-TTTAAAATATTATATTTC
1 AAATTATATTTAAAATATTATATTTC
15221299 AAATTATATTTAAAATA
1 AAATTATATTTAAAATA
15221316 ATTAAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
20 7 0.21
21 6 0.18
22 3 0.09
23 3 0.09
24 5 0.15
25 1 0.03
26 9 0.26
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
AAATTATATTTAAAATATTATATTTC
Found at i:15221349 original size:10 final size:9
Alignment explanation
Indices: 15221308--15221348 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
15221298 CAAATTATAT
15221308 TTAAAATAA
1 TTAAAATAA
15221317 TT-AAA-AA
1 TTAAAATAA
*
15221324 TTATAATAAA
1 TTAAAAT-AA
15221334 TTAAAATAA
1 TTAAAATAA
15221343 TTAAAA
1 TTAAAA
15221349 AACCATTGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
7 4 0.15
8 5 0.19
9 10 0.37
10 8 0.30
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
TTAAAATAA
Found at i:15221412 original size:14 final size:12
Alignment explanation
Indices: 15221389--15221432 Score: 52
Period size: 14 Copynumber: 3.3 Consensus size: 12
15221379 ATTACCAATT
15221389 AAAAATAATTTAA
1 AAAAATAA-TTAA
15221402 AAAAGATAATTAA
1 AAAA-ATAATTAA
15221415 ATTAAAATAATTAA
1 A--AAAATAATTAA
15221429 AAAA
1 AAAA
15221433 CGATTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
12 3 0.11
13 9 0.32
14 13 0.46
15 3 0.11
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.27
Consensus pattern (12 bp):
AAAAATAATTAA
Found at i:15222919 original size:33 final size:31
Alignment explanation
Indices: 15222812--15222918 Score: 169
Period size: 31 Copynumber: 3.4 Consensus size: 31
15222802 TATGGTAAGA
*
15222812 TATATTTTAGAATTTTTTTAAATATATTTTT
1 TATATTTTCGAATTTTTTTAAATATATTTTT
*
15222843 TATATTTTCGAATTTTTTTAAATATATTTCT
1 TATATTTTCGAATTTTTTTAAATATATTTTT
*
15222874 TATATTTTCGAAATTTTTTTTACATATATTTTT
1 TATATTTTCG-AA-TTTTTTTAAATATATTTTT
15222907 TATATTTTCGAA
1 TATATTTTCGAA
15222919 AAAAATTTAG
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
31 39 0.56
32 4 0.06
33 27 0.39
ACGTcount: A:0.30, C:0.05, G:0.04, T:0.62
Consensus pattern (31 bp):
TATATTTTCGAATTTTTTTAAATATATTTTT
Found at i:15222997 original size:18 final size:20
Alignment explanation
Indices: 15222976--15223015 Score: 66
Period size: 18 Copynumber: 2.1 Consensus size: 20
15222966 TACATATATA
15222976 TTATATTTTC-AAAT-TTTT
1 TTATATTTTCGAAATATTTT
15222994 TTATATTTTCGAAATATTTT
1 TTATATTTTCGAAATATTTT
15223014 TT
1 TT
15223016 TACAAATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 10 0.50
19 4 0.20
20 6 0.30
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (20 bp):
TTATATTTTCGAAATATTTT
Found at i:15223593 original size:18 final size:18
Alignment explanation
Indices: 15223570--15223613 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
15223560 GATTCAGATT
*
15223570 TCGAGCCCGAGCACGAGC
1 TCGAGCCCGAGCACGACC
* *
15223588 TCGAGCTCGAGGACGACC
1 TCGAGCCCGAGCACGACC
15223606 TCGAGCCC
1 TCGAGCCC
15223614 CAATATCAAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.39, G:0.32, T:0.09
Consensus pattern (18 bp):
TCGAGCCCGAGCACGACC
Found at i:15223750 original size:90 final size:90
Alignment explanation
Indices: 15223599--15223792 Score: 379
Period size: 90 Copynumber: 2.2 Consensus size: 90
15223589 CGAGCTCGAG
15223599 GACGACCTCGAGCCCCAATATCAAGCATTCGGCTCGTCATCTTATTTGCCCCACCACCAATATCC
1 GACGACCTCGAGCCCCAATATCAAGCATTCGGCTCGTCATCTTATTTGCCCCACCACCAATATCC
15223664 TCGTTCCATGGAAAATATTTTTTAC
66 TCGTTCCATGGAAAATATTTTTTAC
15223689 GACGACCTCGAGCCCCAATATCAAGCATTCGGCTCGTCATCTTATTTGCCCCACCACCAATATCC
1 GACGACCTCGAGCCCCAATATCAAGCATTCGGCTCGTCATCTTATTTGCCCCACCACCAATATCC
15223754 TCGTTCCATGGAAAATATTTTTTAC
66 TCGTTCCATGGAAAATATTTTTTAC
*
15223779 GACGACCCCGAGCC
1 GACGACCTCGAGCC
15223793 TCAACATTCA
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 103 1.00
ACGTcount: A:0.25, C:0.34, G:0.14, T:0.27
Consensus pattern (90 bp):
GACGACCTCGAGCCCCAATATCAAGCATTCGGCTCGTCATCTTATTTGCCCCACCACCAATATCC
TCGTTCCATGGAAAATATTTTTTAC
Found at i:15224160 original size:30 final size:30
Alignment explanation
Indices: 15224126--15224183 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
15224116 TTTTCTTTTT
*
15224126 GTTTATTTTTTAAATTTAATTTGTAATTTC
1 GTTTATTTTTTAAATTTAATTTATAATTTC
15224156 GTTTATTTTTTAAATTTAATTTATAATT
1 GTTTATTTTTTAAATTTAATTTATAATT
15224184 ATTATTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (30 bp):
GTTTATTTTTTAAATTTAATTTATAATTTC
Found at i:15224206 original size:26 final size:27
Alignment explanation
Indices: 15224158--15224209 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
15224148 GTAATTTCGT
* *
15224158 TTATTTTTTAAATTTAATTTATAATTA
1 TTATTTTTTAAATATAATATATAATTA
*
15224185 TTATTTTTTCAATAT-ATATATAATT
1 TTATTTTTTAAATATAATATATAATT
15224210 TTTCAATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
TTATTTTTTAAATATAATATATAATTA
Found at i:15225290 original size:111 final size:112
Alignment explanation
Indices: 15225110--15225327 Score: 248
Period size: 110 Copynumber: 2.0 Consensus size: 112
15225100 TTTTTTTTAT
* * *
15225110 TTTTGGGTGTCGCCCATGAGTTGGCAAACACCTAAAAAATATATTTTTAAGACCTGAAAAGGGGA
1 TTTTGGGTGTCGCCAATGAGATGGCAAACACCTAAAAAATATATTTTTAAGACCTGAAAAAGGGA
* * **
15225175 TGTCGACCATGGGTTGGCA-ATCACCCAAAAATTATAATTTTTTAATCA
66 TGTCGACCATGGCTTGACAGA-CA-CCAAAAAAAATAATTTTTTAATCA
* * * * *
15225223 TTTTGGGTGTCGGCAATG-GATGG-ACAACACCTGAAAAA-ATATTTTT-GGATCTGAAAAAGTG
1 TTTTGGGTGTCGCCAATGAGATGGCA-AACACCTAAAAAATATATTTTTAAGACCTGAAAAAGGG
*
15225284 AGTGTCGATCATGGCTTGACAGACACCAAAAAAAATAATTTTTT
65 A-TGTCGACCATGGCTTGACAGACACCAAAAAAAATAATTTTTT
15225328 TATTCGTATT
Statistics
Matches: 89, Mismatches: 13, Indels: 9
0.80 0.12 0.08
Matches are distributed among these distances:
110 29 0.33
111 27 0.30
112 17 0.19
113 16 0.18
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (112 bp):
TTTTGGGTGTCGCCAATGAGATGGCAAACACCTAAAAAATATATTTTTAAGACCTGAAAAAGGGA
TGTCGACCATGGCTTGACAGACACCAAAAAAAATAATTTTTTAATCA
Found at i:15225328 original size:111 final size:112
Alignment explanation
Indices: 15225091--15225329 Score: 258
Period size: 111 Copynumber: 2.2 Consensus size: 112
15225081 GACAAACACC
* * *
15225091 AAAATATAATTTTTTTTATTTTTGGGTGTCGCCCATGAGTTGGCAAACACCTAAAAAATATATTT
1 AAAATATAATTTTTTTAATTTTTGGGTGTCGCCAATGAGATGGCAAACACCTAAAAAATATATTT
* * *
15225156 TTAAGACCTGAAAAGGGGATGTCGACCATGGGTTGGCAATCACCCAA
66 TTAAGACCTGAAAAAGGGATGTCGACCATGGCTTGACAATCACCCAA
* * *
15225203 AAATTATAA-TTTTTTAATCATTTTGGGTGTCGGCAATG-GATGG-ACAACACCTGAAAAA-ATA
1 AAAATATAATTTTTTTAAT--TTTTGGGTGTCGCCAATGAGATGGCA-AACACCTAAAAAATATA
* * * *
15225264 TTTTT-GGATCTGAAAAAGTGAGTGTCGATCATGGCTTGACAGA-CA-CCAA
63 TTTTTAAGACCTGAAAAAGGGA-TGTCGACCATGGCTTGACA-ATCACCCAA
*
15225313 AAAAAATAATTTTTTTA
1 AAAATATAATTTTTTTA
15225330 TTCGTATTTT
Statistics
Matches: 106, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
110 23 0.22
111 42 0.40
112 25 0.24
113 16 0.15
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (112 bp):
AAAATATAATTTTTTTAATTTTTGGGTGTCGCCAATGAGATGGCAAACACCTAAAAAATATATTT
TTAAGACCTGAAAAAGGGATGTCGACCATGGCTTGACAATCACCCAA
Found at i:15233016 original size:31 final size:30
Alignment explanation
Indices: 15232958--15233017 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 30
15232948 CTTAAAAGTT
15232958 AAAAAAAAAATTTGAGGCCCTTAAAAAAAA
1 AAAAAAAAAATTTGAGGCCCTTAAAAAAAA
15232988 AAAATAAATAAATTTG-GGCCCCTTAAAAAA
1 AAAA-AAA-AAATTTGAGG-CCCTTAAAAAA
15233018 TTGGACCCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 4 0.15
31 5 0.19
32 18 0.67
ACGTcount: A:0.58, C:0.12, G:0.10, T:0.20
Consensus pattern (30 bp):
AAAAAAAAAATTTGAGGCCCTTAAAAAAAA
Found at i:15233876 original size:9 final size:8
Alignment explanation
Indices: 15233853--15233900 Score: 55
Period size: 9 Copynumber: 5.9 Consensus size: 8
15233843 TATTAGTTTC
15233853 AAATTA-A
1 AAATTATA
15233860 AAA-TATA
1 AAATTATA
15233867 AAATATATA
1 AAAT-TATA
15233876 AAATTATA
1 AAATTATA
15233884 AAAGTTATAA
1 AAA-TTAT-A
15233894 AAATTAT
1 AAATTAT
15233901 TTCATATCCA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 2 0.06
7 7 0.19
8 7 0.19
9 16 0.44
10 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (8 bp):
AAATTATA
Found at i:15233883 original size:17 final size:17
Alignment explanation
Indices: 15233857--15233900 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
15233847 AGTTTCAAAT
*
15233857 TAAAAATATAAAA-TATA
1 TAAAATTATAAAAGT-TA
15233874 TAAAATTATAAAAGTTA
1 TAAAATTATAAAAGTTA
15233891 TAAAAATTAT
1 T-AAAATTAT
15233901 TTCATATCCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (17 bp):
TAAAATTATAAAAGTTA
Found at i:15240220 original size:93 final size:93
Alignment explanation
Indices: 15240059--15240242 Score: 316
Period size: 93 Copynumber: 2.0 Consensus size: 93
15240049 TAACTTTAAC
* *
15240059 AAACTTTTATTTTGGTTAACTTTTATTTTTAAAGAATGGGATTTATTCGATTCATTTGAATTGGT
1 AAACTTTTATTTTGGTTAACTTTTATTTTTAAAGAATAGGATTTATTCGATTCATTTGAATTGAT
15240124 TTGATTTGTGAAACATGTGGATAAACAT
66 TTGATTTGTGAAACATGTGGATAAACAT
* *
15240152 AAACTTTTATTTTGGTTAACTTTTATTTTTGACGAATAAGG-TTTATTCGATTCATTTGAATTGA
1 AAACTTTTATTTTGGTTAACTTTTATTTTTAAAGAAT-AGGATTTATTCGATTCATTTGAATTGA
15240216 TTTGATTTGTGAAACATGTGGATAAAC
65 TTTGATTTGTGAAACATGTGGATAAAC
15240243 CTGTTTATTT
Statistics
Matches: 86, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
93 84 0.98
94 2 0.02
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.46
Consensus pattern (93 bp):
AAACTTTTATTTTGGTTAACTTTTATTTTTAAAGAATAGGATTTATTCGATTCATTTGAATTGAT
TTGATTTGTGAAACATGTGGATAAACAT
Found at i:15240850 original size:9 final size:9
Alignment explanation
Indices: 15240810--15240851 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
15240800 GTTAACCAAA
15240810 TCGAGTTAT
1 TCGAGTTAT
**
15240819 TTTAGTTAT
1 TCGAGTTAT
*
15240828 TCGAATTAT
1 TCGAGTTAT
15240837 TCGAGTTAT
1 TCGAGTTAT
15240846 TCGAGT
1 TCGAGT
15240852 CGACTTGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.24, C:0.10, G:0.19, T:0.48
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:15241025 original size:19 final size:19
Alignment explanation
Indices: 15241000--15241043 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
15240990 ATAAAATAAA
15241000 CAAAATAATTTTCAAAATT
1 CAAAATAATTTTCAAAATT
* *
15241019 GAAAATAATTTTTAAAATT
1 CAAAATAATTTTCAAAATT
15241038 CAAAAT
1 CAAAAT
15241044 GTTTATAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (19 bp):
CAAAATAATTTTCAAAATT
Found at i:15242935 original size:25 final size:25
Alignment explanation
Indices: 15242904--15242956 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 25
15242894 TTTTGAAGTT
*
15242904 TGGCTCGTAAGAGCG-ATATTCTGTC
1 TGGCTCGTAAGAACGTA-ATTCTGTC
15242929 TGGCTCGTAAGAACGTAATTCTGTC
1 TGGCTCGTAAGAACGTAATTCTGTC
15242954 TGG
1 TGG
15242957 GTTCGTATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (25 bp):
TGGCTCGTAAGAACGTAATTCTGTC
Found at i:15244028 original size:13 final size:14
Alignment explanation
Indices: 15244003--15244035 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
15243993 TTTAATTTGT
15244003 ATTTATCTTTTTAG
1 ATTTATCTTTTTAG
15244017 ATTTAT-TTTTTAG
1 ATTTATCTTTTTAG
15244030 AGTTTA
1 A-TTTA
15244036 AATTGGATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.64
Consensus pattern (14 bp):
ATTTATCTTTTTAG
Found at i:15247513 original size:17 final size:18
Alignment explanation
Indices: 15247491--15247529 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
15247481 AGGCAACCCA
15247491 ATTTTTAATTTTT-TA-TT
1 ATTTTT-ATTTTTCTATTT
15247508 ATTTTTATTTTTCTATTT
1 ATTTTTATTTTTCTATTT
15247526 ATTT
1 ATTT
15247530 ATATATGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 8 0.40
18 6 0.30
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTTATTTTTCTATTT
Found at i:15248520 original size:6 final size:6
Alignment explanation
Indices: 15248487--15248586 Score: 71
Period size: 6 Copynumber: 16.8 Consensus size: 6
15248477 CTGAATCAAT
* * *
15248487 TTTAAA TTTTAAA TTTTAA TTT-AA TTTAAG TTTAAA TTT-AT TTTAAA
1 TTTAAA -TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* ** * * * *
15248534 TTTAAA CTTATT TTTGAG TTTAAG TTT-AT TTTAAA TTTAAA TTTAAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA
15248582 TTTAA
1 TTTAA
15248587 TTGAAAGTCC
Statistics
Matches: 74, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
5 13 0.18
6 49 0.66
7 12 0.16
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:15248524 original size:17 final size:17
Alignment explanation
Indices: 15248492--15248578 Score: 102
Period size: 17 Copynumber: 5.1 Consensus size: 17
15248482 TCAATTTTAA
*
15248492 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
* *
15248509 AATTTAAGTTTAAATTT
1 ATTTTAAATTTAAATTT
*
15248526 ATTTTAAATTTAAACTT
1 ATTTTAAATTTAAATTT
* * *
15248543 ATTTTTGAGTTTAAGTTT
1 A-TTTTAAATTTAAATTT
15248561 ATTTTAAATTTAAATTT
1 ATTTTAAATTTAAATTT
15248578 A
1 A
15248579 AAATTTAATT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
17 43 0.77
18 13 0.23
ACGTcount: A:0.37, C:0.01, G:0.05, T:0.57
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:15248562 original size:35 final size:34
Alignment explanation
Indices: 15248495--15248579 Score: 107
Period size: 35 Copynumber: 2.5 Consensus size: 34
15248485 ATTTTAAATT
* *
15248495 TTAAATTTTAATTTAATTTAAGTTTAAATTTATT
1 TTAAATTTAAACTTAATTTAAGTTTAAATTTATT
* * *
15248529 TTAAATTTAAACTTATTTTTGAGTTTAAGTTTATT
1 TTAAATTTAAACTTA-ATTTAAGTTTAAATTTATT
*
15248564 TTAAATTTAAATTTAA
1 TTAAATTTAAACTTAA
15248580 AATTTAATTG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
34 13 0.30
35 30 0.70
ACGTcount: A:0.38, C:0.01, G:0.05, T:0.56
Consensus pattern (34 bp):
TTAAATTTAAACTTAATTTAAGTTTAAATTTATT
Found at i:15250308 original size:28 final size:29
Alignment explanation
Indices: 15250277--15250502 Score: 117
Period size: 29 Copynumber: 7.9 Consensus size: 29
15250267 CTAAATTTCC
* *
15250277 AAAAATCAAAATTTTACCCTCGAACTTCA
1 AAAAATCACATTTTTACCCTCGAACTTCA
* * * *
15250306 AAAAATTACATTTTTGCCC-CTAAACTTCT
1 AAAAATCACATTTTTACCCTC-GAACTTCA
*
15250335 AAAAATCACATTTTTACCCT-GAACTTCC
1 AAAAATCACATTTTTACCCTCGAACTTCA
* * * *
15250363 AAAAATTACA-TTTT-CTCT-TAAATTCCAA
1 AAAAATCACATTTTTACCCTCGAACTT-C-A
* * *
15250391 AAAAATCACATTTTGACCC-CTAAACTTCC
1 AAAAATCACATTTTTACCCTC-GAACTTCA
* * * * * * **
15250420 AAAAATTATA-TCTTGCCCCCGAAATTTT
1 AAAAATCACATTTTTACCCTCGAACTTCA
* * *
15250448 AAAAATCACAATTTGACCCTCGAACTTCC
1 AAAAATCACATTTTTACCCTCGAACTTCA
* *
15250477 AAATATCACATTTTTA-CCTTGAACTT
1 AAAAATCACATTTTTACCCTCGAACTT
15250503 TCCCAAAATG
Statistics
Matches: 144, Mismatches: 43, Indels: 21
0.69 0.21 0.10
Matches are distributed among these distances:
26 7 0.05
27 5 0.03
28 51 0.35
29 74 0.51
30 3 0.02
31 4 0.03
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAAATCACATTTTTACCCTCGAACTTCA
Found at i:15250375 original size:57 final size:56
Alignment explanation
Indices: 15250265--15250490 Score: 215
Period size: 57 Copynumber: 4.0 Consensus size: 56
15250255 CCCAGAAGGT
* * * *
15250265 CCCTAAATTTCCAAAAATCAAAATTTTACCCTCGAACTTCAAAAAATTACATTTTTGC
1 CCCTAAA-TTCTAAAAATCACAATTTGACCCTCGAACTTCCAAAAATTACA-TTTTGC
* *
15250323 CCCTAAACTTCTAAAAATCACATTTTTACCCT-GAACTTCCAAAAATTACATTTT-C
1 CCCTAAA-TTCTAAAAATCACAATTTGACCCTCGAACTTCCAAAAATTACATTTTGC
* * * * * * *
15250378 TCTTAAATTCCAAAAAAATCACATTTTGACCC-CTAAACTTCCAAAAATTATATCTTGCC
1 CCCTAAATT-C-TAAAAATCACAATTTGACCCTC-GAACTTCCAAAAATTACATTTTG-C
* * * *
15250437 CCCGAAATTTTAAAAATCACAATTTGACCCTCGAACTTCCAAATATCACATTTT
1 CCCTAAATTCTAAAAATCACAATTTGACCCTCGAACTTCCAAAAATTACATTTT
15250491 TACCTTGAAC
Statistics
Matches: 138, Mismatches: 23, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
54 2 0.01
55 7 0.05
56 22 0.16
57 71 0.51
58 29 0.21
59 7 0.05
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.33
Consensus pattern (56 bp):
CCCTAAATTCTAAAAATCACAATTTGACCCTCGAACTTCCAAAAATTACATTTTGC
Found at i:15250548 original size:28 final size:30
Alignment explanation
Indices: 15250498--15250556 Score: 86
Period size: 28 Copynumber: 2.0 Consensus size: 30
15250488 TTTTACCTTG
*
15250498 AACTTTCCCAAAATGACATTTTACCCCTAA
1 AACTTTCCCAAAATGACATTTTAACCCTAA
*
15250528 AACTTT-CCAAAATTACA-TTTAACCCTAA
1 AACTTTCCCAAAATGACATTTTAACCCTAA
15250556 A
1 A
15250557 CCCTTCGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 11 0.41
29 10 0.37
30 6 0.22
ACGTcount: A:0.41, C:0.27, G:0.02, T:0.31
Consensus pattern (30 bp):
AACTTTCCCAAAATGACATTTTAACCCTAA
Found at i:15252101 original size:13 final size:14
Alignment explanation
Indices: 15252076--15252108 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
15252066 TTTAATTTGT
15252076 ATTTATCTTTTTAG
1 ATTTATCTTTTTAG
15252090 ATTTAT-TTTTTAG
1 ATTTATCTTTTTAG
15252103 AGTTTA
1 A-TTTA
15252109 AATTGGATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.24, C:0.03, G:0.09, T:0.64
Consensus pattern (14 bp):
ATTTATCTTTTTAG
Found at i:15253605 original size:18 final size:18
Alignment explanation
Indices: 15253562--15253605 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
15253552 TTCGAAATAG
*
15253562 TCAACGGTCAACGGTCAA
1 TCAACGGTCAACGGCCAA
* * *
15253580 TGATCGGTCAACGGCCGA
1 TCAACGGTCAACGGCCAA
15253598 TCAACGGT
1 TCAACGGT
15253606 AGATCAACGA
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (18 bp):
TCAACGGTCAACGGCCAA
Found at i:15260866 original size:14 final size:14
Alignment explanation
Indices: 15260828--15260867 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
15260818 CGAAAAAGTT
*
15260828 AATGGTCAACAGTC
1 AATGGTCAACGGTC
15260842 AATGGTCAACGGTC
1 AATGGTCAACGGTC
15260856 AATGGTCAACGG
1 AATGGTCAACGG
15260868 CCGGTCAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.33, C:0.20, G:0.28, T:0.20
Consensus pattern (14 bp):
AATGGTCAACGGTC
Found at i:15260879 original size:7 final size:7
Alignment explanation
Indices: 15260831--15260879 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
15260821 AAAAGTTAAT
15260831 GGTCAAC
1 GGTCAAC
* *
15260838 AGTCAAT
1 GGTCAAC
15260845 GGTCAAC
1 GGTCAAC
*
15260852 GGTCAAT
1 GGTCAAC
15260859 GGTCAAC
1 GGTCAAC
15260866 GG-C--C
1 GGTCAAC
15260870 GGTCAAC
1 GGTCAAC
15260877 GGT
1 GGT
15260880 TTTGACTTGA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
4 3 0.09
5 1 0.03
6 1 0.03
7 28 0.85
ACGTcount: A:0.27, C:0.24, G:0.31, T:0.18
Consensus pattern (7 bp):
GGTCAAC
Found at i:15263939 original size:14 final size:14
Alignment explanation
Indices: 15263920--15263964 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
15263910 CTACTAGACA
15263920 ATGAATAACTGTAT
1 ATGAATAACTGTAT
*
15263934 ATGAATAACTGTAA
1 ATGAATAACTGTAT
15263948 ATGAATAACTGTAT
1 ATGAATAACTGTAT
15263962 ATG
1 ATG
15263965 TAACCTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.33
Consensus pattern (14 bp):
ATGAATAACTGTAT
Found at i:15269593 original size:21 final size:20
Alignment explanation
Indices: 15269565--15269612 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
15269555 ATTTACTAGT
15269565 ATTTATATAATTTTTAAAAA
1 ATTTATATAATTTTTAAAAA
**
15269585 ATTTGATATTTTTTTTAAAAA
1 ATTT-ATATAATTTTTAAAAA
*
15269606 AATTATA
1 ATTTATA
15269613 CTTTTAGAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTTATATAATTTTTAAAAA
Found at i:15269617 original size:21 final size:21
Alignment explanation
Indices: 15269575--15269617 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
15269565 ATTTATATAA
*
15269575 TTTTTAAAAAATTTGATATTT
1 TTTTTAAAAAAATTGATATTT
*
15269596 TTTTTAAAAAAATT-ATACTT
1 TTTTTAAAAAAATTGATATTT
15269616 TT
1 TT
15269618 AGAAAAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (21 bp):
TTTTTAAAAAAATTGATATTT
Found at i:15282058 original size:19 final size:20
Alignment explanation
Indices: 15282022--15282074 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
15282012 TTTTTTTTTG
*
15282022 TTTTACTTTCTCCC-CAAAAT
1 TTTTACTTTC-CCCTCAAAAA
15282042 TTTTAC-TTCCCCTCAAAAA
1 TTTTACTTTCCCCTCAAAAA
*
15282061 TTGTACTTTCCCCT
1 TTTTACTTTCCCCT
15282075 AAACCTCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.10
19 13 0.45
20 13 0.45
ACGTcount: A:0.23, C:0.32, G:0.02, T:0.43
Consensus pattern (20 bp):
TTTTACTTTCCCCTCAAAAA
Found at i:15282111 original size:73 final size:70
Alignment explanation
Indices: 15281987--15282130 Score: 182
Period size: 73 Copynumber: 2.0 Consensus size: 70
15281977 TTTTGCTTAG
* * *** *
15281987 AAATTTTACTTCCCCCGAACCCCAATTTTTTTTTGTTTTACTTTCTCCCCAAAATTTTTACTTCC
1 AAATTGTACTTCCCCCAAACCCCAATTTTTTTTCCATTTACTTTCTCCCCAAAACTTTTACTTCC
15282052 CCTCAA
66 CC-CAA
*
15282058 AAATTGTACTTTCCCCTAAACCTCCAATTTTTTTTCCATTTACTTTC-CTCCCAAAACTTTTACT
1 AAATTGTAC-TTCCCCCAAACC-CCAATTTTTTTTCCATTTACTTTCTC-CCCAAAACTTTTACT
15282122 TCCCCCAA
63 TCCCCCAA
15282130 A
1 A
15282131 CCCCTACAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
71 8 0.13
72 15 0.24
73 40 0.63
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.42
Consensus pattern (70 bp):
AAATTGTACTTCCCCCAAACCCCAATTTTTTTTCCATTTACTTTCTCCCCAAAACTTTTACTTCC
CCCAA
Found at i:15282125 original size:53 final size:52
Alignment explanation
Indices: 15282043--15282174 Score: 137
Period size: 54 Copynumber: 2.5 Consensus size: 52
15282033 CCCCAAAATT
* * *
15282043 TTTAC-TTCCCCTCAAAAATTGTACTTTCCCCTAAACCTCC-A-ATTTTTTTTCCA
1 TTTACTTTCCCC-C-AAAATTTTAC-TTCCCCCAAACC-CCTACAATTTTTTTCCA
*
15282096 TTTACTTTCCTCCCAAAACTTTTACTTCCCCCAAACCCCTACAATTTTTTTCCT
1 TTTACTTTCC-CCCAAAA-TTTTACTTCCCCCAAACCCCTACAATTTTTTTCCA
*
15282150 TTTGCTTT-CCCCAAAATTTTACTTC
1 TTTACTTTCCCCCAAAATTTTACTTC
15282175 TCTTTAACCT
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
51 9 0.13
52 9 0.13
53 22 0.32
54 27 0.39
55 2 0.03
ACGTcount: A:0.23, C:0.33, G:0.02, T:0.42
Consensus pattern (52 bp):
TTTACTTTCCCCCAAAATTTTACTTCCCCCAAACCCCTACAATTTTTTTCCA
Found at i:15283271 original size:32 final size:32
Alignment explanation
Indices: 15283228--15283296 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
15283218 ATCGAAGAAA
* *
15283228 TATAATCCATTTTTCATTTCTAAATTTACCAT
1 TATAATCCATTTCTCATTTCTAAATTCACCAT
*
15283260 TATAATTCATTTCTCATTTCTAAATTCACCAT
1 TATAATCCATTTCTCATTTCTAAATTCACCAT
15283292 TATAA
1 TATAA
15283297 GGGTGAGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (32 bp):
TATAATCCATTTCTCATTTCTAAATTCACCAT
Found at i:15286960 original size:22 final size:22
Alignment explanation
Indices: 15286932--15286973 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
15286922 ATTTATAAGC
15286932 AGAATTAGTTCACAAACAATTT
1 AGAATTAGTTCACAAACAATTT
*
15286954 AGAATTAGTTCACCAACAAT
1 AGAATTAGTTCACAAACAAT
15286974 ACTAGCATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.45, C:0.17, G:0.10, T:0.29
Consensus pattern (22 bp):
AGAATTAGTTCACAAACAATTT
Found at i:15288368 original size:20 final size:19
Alignment explanation
Indices: 15288340--15288392 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
15288330 ATCGGTCCAA
*
15288340 TATCAATAATTTTTATATGG
1 TATCGATAATTTTTAT-TGG
**
15288360 TATCGATAAAAGTTTATTGG
1 TATCGAT-AATTTTTATTGG
15288380 TATCGAT-ATTTTT
1 TATCGATAATTTTT
15288393 GGCTCCAACG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 4 0.15
20 16 0.59
21 7 0.26
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (19 bp):
TATCGATAATTTTTATTGG
Found at i:15288852 original size:40 final size:40
Alignment explanation
Indices: 15288725--15288844 Score: 195
Period size: 40 Copynumber: 3.0 Consensus size: 40
15288715 TCCAAATAAA
*
15288725 TGAAAAGGATATTATTCGAAAGGATAATAAATGAAAAGGT
1 TGAAAAGGATATTATCCGAAAGGATAATAAATGAAAAGGT
* * *
15288765 TGAAAAGGATATTATCCGGAAGAATAATAAATGAAAAAGT
1 TGAAAAGGATATTATCCGAAAGGATAATAAATGAAAAGGT
*
15288805 TGAAAAGGATGTTATCCGAAAGGATAATAAATGAAAAGGT
1 TGAAAAGGATATTATCCGAAAGGATAATAAATGAAAAGGT
15288845 CAAAAAGGTA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 72 1.00
ACGTcount: A:0.50, C:0.04, G:0.23, T:0.23
Consensus pattern (40 bp):
TGAAAAGGATATTATCCGAAAGGATAATAAATGAAAAGGT
Found at i:15289744 original size:13 final size:13
Alignment explanation
Indices: 15289706--15289788 Score: 57
Period size: 13 Copynumber: 6.5 Consensus size: 13
15289696 ATATATGTAA
* *
15289706 ATGAAATGGTAAA
1 ATGAAATGGTTAT
*
15289719 ATGAAATGATTAT
1 ATGAAATGGTTAT
15289732 ATGAAATGGTTAT
1 ATGAAATGGTTAT
*
15289745 AACG-AATGGTTAT
1 -ATGAAATGGTTAT
*
15289758 A-GTAAATGATT-T
1 ATG-AAATGGTTAT
15289770 CATG-AATGGTTAT
1 -ATGAAATGGTTAT
*
15289783 GTGAAA
1 ATGAAA
15289789 AATATATGTA
Statistics
Matches: 55, Mismatches: 8, Indels: 14
0.71 0.10 0.18
Matches are distributed among these distances:
11 1 0.02
12 10 0.18
13 41 0.75
14 3 0.05
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.34
Consensus pattern (13 bp):
ATGAAATGGTTAT
Found at i:15289752 original size:26 final size:26
Alignment explanation
Indices: 15289706--15289758 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
15289696 ATATATGTAA
*
15289706 ATGAAATGGTAAAATGAAATGATTAT
1 ATGAAATGGTAAAACGAAATGATTAT
* *
15289732 ATGAAATGGTTATAACG-AATGGTTAT
1 ATGAAATGG-TAAAACGAAATGATTAT
15289758 A
1 A
15289759 GTAAATGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.45, C:0.02, G:0.21, T:0.32
Consensus pattern (26 bp):
ATGAAATGGTAAAACGAAATGATTAT
Found at i:15304851 original size:13 final size:14
Alignment explanation
Indices: 15304822--15304851 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
15304812 TTCAGTACAT
15304822 TGACATTTAACCTC
1 TGACATTTAACCTC
15304836 TGACATTTAA-CTC
1 TGACATTTAACCTC
15304849 TGA
1 TGA
15304852 TTGCGTTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:15309268 original size:15 final size:15
Alignment explanation
Indices: 15309248--15309276 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
15309238 GAATTAAAAA
15309248 TAAAAGAAATAGAAT
1 TAAAAGAAATAGAAT
15309263 TAAAAGAAATAGAA
1 TAAAAGAAATAGAA
15309277 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (15 bp):
TAAAAGAAATAGAAT
Found at i:15309277 original size:21 final size:21
Alignment explanation
Indices: 15309222--15309267 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
15309212 CGATCTAAGG
**
15309222 AAAAATAAAAGAAACGGAATT
1 AAAAATAAAAGAAATAGAATT
15309243 AAAAATAAAAGAAATAGAATT
1 AAAAATAAAAGAAATAGAATT
15309264 AAAA
1 AAAA
15309268 GAAATAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.72, C:0.02, G:0.11, T:0.15
Consensus pattern (21 bp):
AAAAATAAAAGAAATAGAATT
Found at i:15310094 original size:19 final size:19
Alignment explanation
Indices: 15310070--15310112 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
15310060 AAACATAAAT
15310070 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
15310089 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
15310108 TAAAT
1 TAAAT
15310113 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:15315744 original size:21 final size:21
Alignment explanation
Indices: 15315720--15315762 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
15315710 CTCAGTTTTA
*
15315720 TTTTGAAAATCCATAGTTTGC
1 TTTTGAAAATCCATAGATTGC
*
15315741 TTTTGAAAATCTATAGATTGC
1 TTTTGAAAATCCATAGATTGC
15315762 T
1 T
15315763 GCTGAAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (21 bp):
TTTTGAAAATCCATAGATTGC
Found at i:15315768 original size:21 final size:21
Alignment explanation
Indices: 15315723--15315774 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
15315713 AGTTTTATTT
* * **
15315723 TGAAAATCCATAGTTTGCTTT
1 TGAAAATCTATAGATTGCTGC
15315744 TGAAAATCTATAGATTGCTGC
1 TGAAAATCTATAGATTGCTGC
*
15315765 TGAAATTCTA
1 TGAAAATCTA
15315775 GAACATTAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (21 bp):
TGAAAATCTATAGATTGCTGC
Found at i:15317320 original size:21 final size:22
Alignment explanation
Indices: 15317296--15317342 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
15317286 CGATCTAAGG
*
15317296 AAAAATGAAAGA-AACAAAATT
1 AAAAATAAAAGACAACAAAATT
* *
15317317 AAAAATAAAAGACAATAGAATT
1 AAAAATAAAAGACAACAAAATT
15317339 AAAA
1 AAAA
15317343 GAAATAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.72, C:0.04, G:0.09, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGACAACAAAATT
Found at i:15317350 original size:15 final size:16
Alignment explanation
Indices: 15317322--15317351 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
15317312 AAATTAAAAA
15317322 TAAAAGACAATAGAAT
1 TAAAAGACAATAGAAT
15317338 TAAAAGA-AATAGAA
1 TAAAAGACAATAGAA
15317352 AATAGGGAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.67, C:0.03, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGACAATAGAAT
Found at i:15317355 original size:22 final size:22
Alignment explanation
Indices: 15317296--15317356 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
15317286 CGATCTAAGG
*
15317296 AAAAATGAAAGAAACA-A-AATT
1 AAAAATAAAAGAAA-ATAGAATT
*
15317317 AAAAATAAAAGACAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
*
15317339 AAAAGA-AATAGAAAATAG
1 AAAA-ATAAAAGAAAATAG
15317357 GGAAGTCGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 1 0.03
21 13 0.39
22 18 0.55
23 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.11, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:15318165 original size:19 final size:19
Alignment explanation
Indices: 15318141--15318183 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
15318131 AAACATAAAT
15318141 TAAATACAAAT-TTAAATAA
1 TAAATA-AAATCTTAAATAA
* *
15318160 TAAATAATATCTTAAATAT
1 TAAATAAAATCTTAAATAA
15318179 TAAAT
1 TAAAT
15318184 CCTAATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAATAAAATCTTAAATAA
Found at i:15318916 original size:16 final size:16
Alignment explanation
Indices: 15318892--15318924 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
15318882 GAAAAAAAAT
15318892 GGGCAATTACATTAAA
1 GGGCAATTACATTAAA
*
15318908 GGGCGATTACATTAAA
1 GGGCAATTACATTAAA
15318924 G
1 G
15318925 AAGATAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.12, G:0.24, T:0.24
Consensus pattern (16 bp):
GGGCAATTACATTAAA
Found at i:15322528 original size:29 final size:29
Alignment explanation
Indices: 15322486--15322566 Score: 126
Period size: 29 Copynumber: 2.8 Consensus size: 29
15322476 TCGTGAAAGA
* * *
15322486 GGTGGAGAATTTGTACGTTGAGAGTTCTT
1 GGTGAAGAACTTGTTCGTTGAGAGTTCTT
*
15322515 GGTGAAGAACTTGTTCGTTGAGAGTTTTT
1 GGTGAAGAACTTGTTCGTTGAGAGTTCTT
15322544 GGTGAAGAACTTGTTCGTTGAGA
1 GGTGAAGAACTTGTTCGTTGAGA
15322567 ATTCGTGTCT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.22, C:0.07, G:0.33, T:0.37
Consensus pattern (29 bp):
GGTGAAGAACTTGTTCGTTGAGAGTTCTT
Found at i:15328387 original size:23 final size:22
Alignment explanation
Indices: 15328344--15328407 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
15328334 TTATCCTTTT
15328344 ATTTTATAACAAAAACATATTTAAA
1 ATTTTAT-A-AAAAACATA-TTAAA
*
15328369 ATTTTATAAAAAACCTATTAAA
1 ATTTTATAAAAAACATATTAAA
* *
15328391 ATTCTATAAAAATCATA
1 ATTTTATAAAAAACATA
15328408 AAAATTATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 19 0.54
23 8 0.23
24 1 0.03
25 7 0.20
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (22 bp):
ATTTTATAAAAAACATATTAAA
Found at i:15328400 original size:10 final size:10
Alignment explanation
Indices: 15328377--15328430 Score: 51
Period size: 9 Copynumber: 5.6 Consensus size: 10
15328367 AAATTTTATA
*
15328377 AAAAACCTATT
1 AAAAATCTA-T
*
15328388 AAAATTCTAT
1 AAAAATCTAT
15328398 AAAAATC-AT
1 AAAAATCTAT
15328407 AAAAAT-TAT
1 AAAAATCTAT
15328416 AAAAAT-TAT
1 AAAAATCTAT
*
15328425 TAAAAT
1 AAAAAT
15328431 ATTAAATTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 24 0.63
10 7 0.18
11 7 0.18
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.31
Consensus pattern (10 bp):
AAAAATCTAT
Found at i:15328422 original size:9 final size:9
Alignment explanation
Indices: 15328395--15328466 Score: 65
Period size: 9 Copynumber: 7.9 Consensus size: 9
15328385 ATTAAAATTC
15328395 TATAAAAAT
1 TATAAAAAT
*
15328404 CATAAAAAT
1 TATAAAAAT
15328413 TATAAAAAT
1 TATAAAAAT
*
15328422 TATTAAAA-
1 TATAAAAAT
* *
15328430 TATTAAATT
1 TATAAAAAT
*
15328439 TGATATAAATT
1 T-ATA-AAAAT
*
15328450 TATAAAGAT
1 TATAAAAAT
15328459 TATAAAAA
1 TATAAAAA
15328467 AAATCCTAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
8 7 0.13
9 34 0.65
10 5 0.10
11 6 0.12
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (9 bp):
TATAAAAAT
Found at i:15328429 original size:18 final size:18
Alignment explanation
Indices: 15328384--15328465 Score: 60
Period size: 18 Copynumber: 4.4 Consensus size: 18
15328374 ATAAAAAACC
15328384 TATTAAAATTCTATAAAAAT
1 TATTAAAA-T-TATAAAAAT
* *
15328404 CATAAAAATTATAAAAAT
1 TATTAAAATTATAAAAAT
* *
15328422 TATTAAAA-TATTAAATT
1 TATTAAAATTATAAAAAT
* *
15328439 TGATATAAATTTATAAAGAT
1 T-AT-TAAAATTATAAAAAT
15328459 TA-TAAAA
1 TATTAAAA
15328466 AAAATCCTAA
Statistics
Matches: 48, Mismatches: 11, Indels: 9
0.71 0.16 0.13
Matches are distributed among these distances:
17 12 0.25
18 17 0.35
19 6 0.12
20 13 0.27
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (18 bp):
TATTAAAATTATAAAAAT
Found at i:15328958 original size:9 final size:9
Alignment explanation
Indices: 15328901--15329118 Score: 61
Period size: 10 Copynumber: 22.8 Consensus size: 9
15328891 TTTTATGATT
15328901 TTTTTAATAA
1 TTTTT-ATAA
15328911 TTTTTATAA
1 TTTTTATAA
*
15328920 GTTTATATGAA
1 -TTTTTAT-AA
*
15328931 -TTTTAT-T
1 TTTTTATAA
15328938 TTATTTATTAA
1 TT-TTTA-TAA
15328949 TTTTTATAA
1 TTTTTATAA
* *
15328958 TATTTATGA
1 TTTTTATAA
15328967 TTGTTTAATAA
1 TT-TTT-ATAA
* *
15328978 TTCTAATACA
1 TTTTTATA-A
15328988 TTTTTATCAA
1 TTTTTAT-AA
* *
15328998 ATTTTAAATA
1 TTTTTATA-A
15329008 TGTTTTATTAAA
1 T-TTTTA-T-AA
*
15329020 TTTTT-TTA
1 TTTTTATAA
**
15329028 TATAATATAA
1 T-TTTTATAA
*
15329038 TTCATTATAA
1 TT-TTTATAA
*
15329048 TTTATTAAAA
1 TTT-TTATAA
*
15329058 TTATTATAA
1 TTTTTATAA
*
15329067 -CTTTATAA
1 TTTTTATAA
15329075 TTTTTGATAA
1 TTTTT-ATAA
* *
15329085 GTTATATTAA
1 TTTTTA-TAA
*
15329095 TTTTAAT-A
1 TTTTTATAA
15329103 TTTTT-TAA
1 TTTTTATAA
15329111 TATTTTAT
1 T-TTTTAT
15329119 TTGAGTAAAT
Statistics
Matches: 150, Mismatches: 34, Indels: 48
0.65 0.15 0.21
Matches are distributed among these distances:
7 1 0.01
8 16 0.11
9 46 0.31
10 65 0.43
11 19 0.13
12 2 0.01
13 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.58
Consensus pattern (9 bp):
TTTTTATAA
Found at i:15328961 original size:19 final size:19
Alignment explanation
Indices: 15328903--15328964 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
15328893 TTATGATTTT
*
15328903 TTTAATAATTTTTATAAGT-
1 TTTATTAATTTTTATAA-TA
* **
15328922 TTATATGAA-TTTTATTTTA
1 TT-TATTAATTTTTATAATA
15328941 TTTATTAATTTTTATAATA
1 TTTATTAATTTTTATAATA
15328960 TTTAT
1 TTTAT
15328965 GATTGTTTAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 6 0.18
19 23 0.70
20 4 0.12
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (19 bp):
TTTATTAATTTTTATAATA
Found at i:15335714 original size:24 final size:24
Alignment explanation
Indices: 15335687--15335734 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
15335677 CAAGAATATG
*
15335687 AAAGGTTAAAAAAGATGAAAGGTT
1 AAAGGTCAAAAAAGATGAAAGGTT
***
15335711 AAAGGTCAAGGGAGATGAAAGGTT
1 AAAGGTCAAAAAAGATGAAAGGTT
15335735 GAACATCCAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.02, G:0.31, T:0.19
Consensus pattern (24 bp):
AAAGGTCAAAAAAGATGAAAGGTT
Found at i:15339359 original size:40 final size:40
Alignment explanation
Indices: 15339345--15339427 Score: 121
Period size: 40 Copynumber: 2.1 Consensus size: 40
15339335 AAAATGTGAC
* * * *
15339345 TTTGGAAAAGTTTGGGGGTTAAAATGTAAATTTGGAAAAG
1 TTTGGAAAAGTTTAGGAGTCAAAATGTAAATTTAGAAAAG
*
15339385 TTTGGAAAAGTTTAGGAGTCAAAATGTAATTTTAGAAAAG
1 TTTGGAAAAGTTTAGGAGTCAAAATGTAAATTTAGAAAAG
15339425 TTT
1 TTT
15339428 AGGGGTCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.39, C:0.01, G:0.25, T:0.35
Consensus pattern (40 bp):
TTTGGAAAAGTTTAGGAGTCAAAATGTAAATTTAGAAAAG
Found at i:15339408 original size:100 final size:99
Alignment explanation
Indices: 15339302--15339486 Score: 289
Period size: 100 Copynumber: 1.9 Consensus size: 99
15339292 AAGCTCGAGG
* * * *
15339302 GTCAAAATGAAATTTTGGAAAAGTTTAGGGGTTAAAATGTGACTTTGGAAAAGTTTGGGGGTTAA
1 GTCAAAATGAAATTTTAGAAAAGTTTAGGGGTCAAAATGTAACTTTGGAAAAGTTT-GGGGTCAA
15339367 AATGTAAATTTGGAAAAGTTTGGAAAAGTTTAGGA
65 AATGTAAATTTGGAAAAGTTTGGAAAAGTTTAGGA
* * *
15339402 GTCAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGTAATTTTGGAGAAGTTTGGGGTCAAA
1 GTCAAAATGAAATTTTAGAAAAGTTTAGGGGTCAAAATGTAACTTTGGAAAAGTTTGGGGTCAAA
*
15339467 ATGTAATTTTGGAAAAGTTT
66 ATGTAAATTTGGAAAAGTTT
15339487 AGGGGTTAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
99 27 0.35
100 50 0.65
ACGTcount: A:0.37, C:0.03, G:0.26, T:0.34
Consensus pattern (99 bp):
GTCAAAATGAAATTTTAGAAAAGTTTAGGGGTCAAAATGTAACTTTGGAAAAGTTTGGGGTCAAA
ATGTAAATTTGGAAAAGTTTGGAAAAGTTTAGGA
Found at i:15339433 original size:70 final size:70
Alignment explanation
Indices: 15339315--15339459 Score: 209
Period size: 70 Copynumber: 2.1 Consensus size: 70
15339305 AAAATGAAAT
* * * * * *
15339315 TTTGGAAAAGTTTAGGGGTTAAAATGTGACTTTGGAAAAGTTTGGGGGTTAAAATGTAAATTTGG
1 TTTGGAAAAGTTTAGGAGTCAAAATGTAACTTTAGAAAAGTTTAGGGGTCAAAATGTAAATTTGG
15339380 AAAAG
66 AAAAG
* *
15339385 TTTGGAAAAGTTTAGGAGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGTAATTTTGG
1 TTTGGAAAAGTTTAGGAGTCAAAATGTAACTTTAGAAAAGTTTAGGGGTCAAAATGTAAATTTGG
*
15339450 AGAAG
66 AAAAG
15339455 TTTGG
1 TTTGG
15339460 GGTCAAAATG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
70 66 1.00
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (70 bp):
TTTGGAAAAGTTTAGGAGTCAAAATGTAACTTTAGAAAAGTTTAGGGGTCAAAATGTAAATTTGG
AAAAG
Found at i:15339471 original size:29 final size:30
Alignment explanation
Indices: 15339300--15339520 Score: 230
Period size: 30 Copynumber: 7.1 Consensus size: 30
15339290 AAAAGCTCGA
*
15339300 GGGTCAAAATGAAATTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* * * *
15339330 GGGTTAAAATGTGACTTTGGAAAAGTTTGG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
*
15339360 GGGTTAAAATGTAAATTTGGAAAAGTTTGGAAAAGTTTAG
1 GGGTCAAAATGT-AA--T-------TTTGGAAAAGTTTAG
* *
15339400 GAGTCAAAATGTAATTTTAGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
*
15339430 GGGTCAAAATGTAATTTTGGAGAAGTTT-G
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
15339459 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
* * *
15339489 GGGTTAAAATGTAATTTTAGAAATGTTT-G
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAG
15339518 GGG
1 GGG
15339521 ACCTCTTGAG
Statistics
Matches: 162, Mismatches: 18, Indels: 23
0.80 0.09 0.11
Matches are distributed among these distances:
29 32 0.20
30 102 0.63
31 1 0.01
37 1 0.01
39 2 0.01
40 24 0.15
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.33
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTAG
Found at i:15339482 original size:59 final size:58
Alignment explanation
Indices: 15339385--15339520 Score: 200
Period size: 59 Copynumber: 2.3 Consensus size: 58
15339375 TTTGGAAAAG
*
15339385 TTTGGAAAAGTTTAGGAGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGTAAT
1 TTTGG-AAAGTTT-GGGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGTAAT
* *
15339445 TTTGGAGAAGTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTAGGGGTTAAAATGTAAT
1 TTTGGA-AAGTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGTAAT
*
15339504 TTTAGAAATGTTTGGGG
1 TTTGGAAA-GTTTGGGG
15339521 ACCTCTTGAG
Statistics
Matches: 70, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
58 2 0.03
59 57 0.81
60 11 0.16
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.35
Consensus pattern (58 bp):
TTTGGAAAGTTTGGGGTCAAAATGTAATTTTAGAAAAGTTTAGGGGTCAAAATGTAAT
Found at i:15339502 original size:129 final size:130
Alignment explanation
Indices: 15339275--15339518 Score: 357
Period size: 129 Copynumber: 1.9 Consensus size: 130
15339265 ACTCAGGATG
* *
15339275 AAAATGAAATTTTAGAAAAGCTCGAGGGTCAAAATGAAATTTTGGAAAAGTTTAGGGGTTAAAAT
1 AAAATGAAATTTTAGAAAAGCTAGAGGGTCAAAATGAAATTTTGGAAAAGTTTAGGGGTCAAAAT
* * *
15339340 GTGACTTTGGAAAAGTTTGGGGGTTAAAATGTAAATTTGGAAAAGTTTGGAAAAGTTTAGGAGTC
66 GTAACTTTGGAAAAGTTTAGGGGTTAAAATGTAAATTTAGAAAAGTTTGGAAAAGTTTAGGAGTC
* * * *
15339405 AAAATGTAATTTTAGAAAAGTTTAG-GGGTCAAAATGTAATTTTGGAGAAGTTT-GGGGTCAAAA
1 AAAATGAAATTTTAGAAAAG-CTAGAGGGTCAAAATGAAATTTTGGAAAAGTTTAGGGGTCAAAA
* * *
15339468 TGTAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTAGAAATGTTTGG
65 TGTAACTTTGGAAAAGTTTAGGGGTTAAAATGTAAATTTAGAAAAGTTTGG
15339519 GGACCTCTTG
Statistics
Matches: 101, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
129 54 0.53
130 45 0.45
131 2 0.02
ACGTcount: A:0.38, C:0.03, G:0.26, T:0.33
Consensus pattern (130 bp):
AAAATGAAATTTTAGAAAAGCTAGAGGGTCAAAATGAAATTTTGGAAAAGTTTAGGGGTCAAAAT
GTAACTTTGGAAAAGTTTAGGGGTTAAAATGTAAATTTAGAAAAGTTTGGAAAAGTTTAGGAGTC
Found at i:15340575 original size:11 final size:11
Alignment explanation
Indices: 15340540--15340577 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
15340530 ATGCAATGCT
15340540 TTTTTTTTGTA
1 TTTTTTTTGTA
**
15340551 TTGATTTTGTA
1 TTTTTTTTGTA
15340562 TTTTTTTTGTA
1 TTTTTTTTGTA
15340573 TTTTT
1 TTTTT
15340578 CGTGGGTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGTA
Found at i:15343607 original size:17 final size:17
Alignment explanation
Indices: 15343581--15343616 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
15343571 AAATAATTAC
*
15343581 AAGAATATGAAAGGTTA
1 AAGAAGATGAAAGGTTA
15343598 AAGAAGATGAAAGGTTA
1 AAGAAGATGAAAGGTTA
15343615 AA
1 AA
15343617 AGTCAAAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.25, T:0.19
Consensus pattern (17 bp):
AAGAAGATGAAAGGTTA
Found at i:15343980 original size:14 final size:14
Alignment explanation
Indices: 15343940--15343982 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 14
15343930 TTATGTCATT
*
15343940 TTTTATAAATATAT
1 TTTTATAAATATAC
15343954 TTGTTACATAAATATAC
1 TT-TT--ATAAATATAC
15343971 TTTTATAAATAT
1 TTTTATAAATAT
15343983 TTATATTAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
14 10 0.40
15 2 0.08
16 2 0.08
17 11 0.44
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.51
Consensus pattern (14 bp):
TTTTATAAATATAC
Found at i:15347742 original size:14 final size:15
Alignment explanation
Indices: 15347723--15347753 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
15347713 CATGTGTCTC
15347723 TATTTTTTAAT-ATT
1 TATTTTTTAATAATT
15347737 TATTTTTTAATAATT
1 TATTTTTTAATAATT
15347752 TA
1 TA
15347754 CTATACTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TATTTTTTAATAATT
Found at i:15348538 original size:15 final size:15
Alignment explanation
Indices: 15348503--15348541 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
15348493 ATTGACAGAG
15348503 ATAATAAAA-TATAC
1 ATAATAAAATTATAC
15348517 ATAATAAAATTATA-
1 ATAATAAAATTATAC
15348531 ATATATAAAAT
1 ATA-ATAAAAT
15348542 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATAAAATTATAC
Found at i:15351658 original size:21 final size:22
Alignment explanation
Indices: 15351616--15351660 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
15351606 AGTCCCGCTC
*
15351616 ATATTATTTTTTTTAAAATATTT
1 ATATTATTTATTTT-AAATATTT
15351639 ATATTATTTATTTT-AATATTT
1 ATATTATTTATTTTAAATATTT
15351660 A
1 A
15351661 ATAATTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.38
23 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATATTATTTATTTTAAATATTT
Found at i:15357009 original size:36 final size:36
Alignment explanation
Indices: 15356926--15357009 Score: 107
Period size: 36 Copynumber: 2.3 Consensus size: 36
15356916 TTGAATCTTC
* *
15356926 TCGATCGGGTTTGGGGTGTTACAAGTTCAGTCCATG
1 TCGATCGGGTTTGGGGTGTTACAAGGTCAGCCCATG
* * *
15356962 T-TAGCCTGGTTTGGGGTGTTACAAGGTCAGCCCATG
1 TCGA-TCGGGTTTGGGGTGTTACAAGGTCAGCCCATG
15356998 TCGATCGGGTTT
1 TCGATCGGGTTT
15357010 AGGGCACCAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
35 1 0.03
36 36 0.95
37 1 0.03
ACGTcount: A:0.15, C:0.18, G:0.33, T:0.33
Consensus pattern (36 bp):
TCGATCGGGTTTGGGGTGTTACAAGGTCAGCCCATG
Found at i:15359047 original size:10 final size:10
Alignment explanation
Indices: 15359032--15359056 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
15359022 ATAGGTTGGT
15359032 GTGTTGCAGA
1 GTGTTGCAGA
15359042 GTGTTGCAGA
1 GTGTTGCAGA
15359052 GTGTT
1 GTGTT
15359057 AGCTATATCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.08, G:0.40, T:0.36
Consensus pattern (10 bp):
GTGTTGCAGA
Found at i:15359696 original size:38 final size:38
Alignment explanation
Indices: 15359617--15359701 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 38
15359607 TGAGTCTATT
** *
15359617 CAGAATTGTGCCCGGAATTGTCACTACATGACGATATC
1 CAGAATTGTGCCCAAAATTGTCACTACATGACGATACC
* *
15359655 CAGAATTGTGCCCAAAATTGTCACTGCATGA-GCATGCC
1 CAGAATTGTGCCCAAAATTGTCACTACATGACG-ATACC
15359693 CAGAATTGT
1 CAGAATTGT
15359702 CGCTGTAGGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
37 1 0.02
38 40 0.98
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (38 bp):
CAGAATTGTGCCCAAAATTGTCACTACATGACGATACC
Found at i:15367116 original size:25 final size:25
Alignment explanation
Indices: 15367082--15367129 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
15367072 CCTTCCATCT
*
15367082 AACAATTCCTATAATTAGAGGCAGC
1 AACAAATCCTATAATTAGAGGCAGC
15367107 AACAAATCCTATAATTAGAGGCA
1 AACAAATCCTATAATTAGAGGCA
15367130 ATCATAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.23
Consensus pattern (25 bp):
AACAAATCCTATAATTAGAGGCAGC
Found at i:15369878 original size:12 final size:12
Alignment explanation
Indices: 15369861--15369885 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15369851 AGTACATATG
15369861 CTCTTTTTTTTT
1 CTCTTTTTTTTT
15369873 CTCTTTTTTTTT
1 CTCTTTTTTTTT
15369885 C
1 C
15369886 ATTTCTGTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
CTCTTTTTTTTT
Found at i:15377755 original size:11 final size:11
Alignment explanation
Indices: 15377739--15377768 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
15377729 TTGGAGCAAT
15377739 TTTTCTTTTTC
1 TTTTCTTTTTC
15377750 TTTTCTTTTTC
1 TTTTCTTTTTC
*
15377761 TCTTCTTT
1 TTTTCTTT
15377769 CTCATTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTCTTTTTC
Found at i:15405314 original size:79 final size:79
Alignment explanation
Indices: 15405178--15405330 Score: 245
Period size: 79 Copynumber: 1.9 Consensus size: 79
15405168 TTTATTTATG
*
15405178 TTGTCAGTTTAACTGACTAGAGCTGGGCTCACTTTTGCGACTTATCCGCTAAGCACTGGGTGCCA
1 TTGTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGACTTATCCGCTAAGCACTGGGTGCCA
15405243 AGACTTGACTGACC
66 AGACTTGACTGACC
**
15405257 TTGTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCT-AGCCACTGGGTGCC
1 TTGTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGACTTATCCGCTAAG-CACTGGGTGCC
* *
15405321 AGGATTTGAC
65 AAGACTTGAC
15405331 GGATATTTGT
Statistics
Matches: 68, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
78 2 0.03
79 66 0.97
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.30
Consensus pattern (79 bp):
TTGTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGACTTATCCGCTAAGCACTGGGTGCCA
AGACTTGACTGACC
Found at i:15420530 original size:328 final size:328
Alignment explanation
Indices: 15419948--15420544 Score: 998
Period size: 328 Copynumber: 1.8 Consensus size: 328
15419938 CACTAAATTT
* *
15419948 ATGGTCTTATATTGGTGTAAGGTTTAGGTATGTTTAAGGTACAATTTGGTATAGTTTGGACACTT
1 ATGGTCTTATATTGGTGCAAGGTTTAGGTATGTTTAAGGTACAATTTGGTATAGCTTGGACACTT
* *
15420013 GAAAATGTGCATTTAAGGTTAATTCACCATTGAGTCTCAAGACATCATGAATGTGTCTCGAGACC
66 GAAAATGTGCATTTAAGGTCAATTCACCATTGAGTCTCAAGACAGCATGAATGTGTCTCGAGACC
* *
15420078 ATAAGAGCAAAATTTTACCTTGTTGCTCAACCTACATGCTTAGTGTCTTGAGTCTTTTTAAGCTA
131 ATAAGAGCAAAATTTTACCTTGTTGCTCAACCTACATGCTTAGTGTCTTGAGTCTTGTCAAGCTA
* * * *
15420143 GTCTCGAGACAACCCAACTAAAGTCTCGAAACAAGTGGTCATTTTCTTTAGAAAAGAAAACATCA
196 GTCTCAAGACAACCCAACTAAAGTATCGAAACAAGTGGTCATTGTCTCTAGAAAAGAAAACATCA
*
15420208 AAGGTAAATGTTGATACATTGATGATATGACTTAATGATGTTTAGTTGTGTCTGCATGTGCTAAA
261 AAGCTAAATGTTGATACATTGATGATATGACTTAATGATGTTTAGTTGTGTCTGCATGTGCTAAA
15420273 CTG
326 CTG
* * **
15420276 ATGGTTTTATATTGGTGCAAGGTTTATGTATGTTTAAGGGTAC-ATTTTTTATAGCTTGGACACT
1 ATGGTCTTATATTGGTGCAAGGTTTAGGTATGTTTAA-GGTACAATTTGGTATAGCTTGGACACT
*
15420340 TGAAAATGTGCATTTAAGGTCAATTCACCATTGAGTCTTAAGACAGCATGAATGTGTCTCGAGAC
65 TGAAAATGTGCATTTAAGGTCAATTCACCATTGAGTCTCAAGACAGCATGAATGTGTCTCGAGAC
* *
15420405 CATAAGAGCAAAATTTTACCTTGTTGTTTAACCTACATGCTTAGTGTCTTGAGTCTTGTCAAGCT
130 CATAAGAGCAAAATTTTACCTTGTTGCTCAACCTACATGCTTAGTGTCTTGAGTCTTGTCAAGCT
* *
15420470 AGTCTTAAGACAACCCAACTAAAGTATCGAAACAAGTGGTCATTGTCTCTAGACAAGAAAACATC
195 AGTCTCAAGACAACCCAACTAAAGTATCGAAACAAGTGGTCATTGTCTCTAGAAAAGAAAACATC
15420535 AAAGCTAAAT
260 AAAGCTAAAT
15420545 TAGTTTTGCC
Statistics
Matches: 248, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
328 243 0.98
329 5 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (328 bp):
ATGGTCTTATATTGGTGCAAGGTTTAGGTATGTTTAAGGTACAATTTGGTATAGCTTGGACACTT
GAAAATGTGCATTTAAGGTCAATTCACCATTGAGTCTCAAGACAGCATGAATGTGTCTCGAGACC
ATAAGAGCAAAATTTTACCTTGTTGCTCAACCTACATGCTTAGTGTCTTGAGTCTTGTCAAGCTA
GTCTCAAGACAACCCAACTAAAGTATCGAAACAAGTGGTCATTGTCTCTAGAAAAGAAAACATCA
AAGCTAAATGTTGATACATTGATGATATGACTTAATGATGTTTAGTTGTGTCTGCATGTGCTAAA
CTG
Found at i:15422263 original size:6 final size:6
Alignment explanation
Indices: 15422252--15422277 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
15422242 TCATTTCTAG
15422252 TTCATT TTCATT TTCATT TTCATT TT
1 TTCATT TTCATT TTCATT TTCATT TT
15422278 GGAGAAAACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.69
Consensus pattern (6 bp):
TTCATT
Found at i:15422324 original size:57 final size:55
Alignment explanation
Indices: 15422254--15422381 Score: 186
Period size: 57 Copynumber: 2.3 Consensus size: 55
15422244 ATTTCTAGTT
* *
15422254 CATTT-TCATTTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGATTC
1 CATTTCTCATTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATG-TTC
*
15422309 CATTTCTCTATTTTCATTTTCATTTTAGAGAAAACCATAATCATTTCCAAATGTTC
1 CATTTCTC-ATTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATGTTC
15422365 CTATTTCTCCATTTTCA
1 C-ATTTCT-CATTTTCA
15422382 CCATTTTTAT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
55 5 0.08
56 6 0.09
57 54 0.82
58 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.05, T:0.45
Consensus pattern (55 bp):
CATTTCTCATTTTCATTTTCATTTTAGAGAAAACCACAATCATTTCCAAATGTTC
Found at i:15433839 original size:21 final size:22
Alignment explanation
Indices: 15433795--15433839 Score: 56
Period size: 25 Copynumber: 2.0 Consensus size: 22
15433785 TTCTTTTGTA
15433795 GCTGTCAAAGTTTGTTAATTAAATC
1 GCTGTCAAAGTTTG---ATTAAATC
15433820 GCTGTCAAAGTTTG-TTAAAT
1 GCTGTCAAAGTTTGATTAAAT
15433840 TCCAGCTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 6 0.30
25 14 0.70
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (22 bp):
GCTGTCAAAGTTTGATTAAATC
Found at i:15435674 original size:18 final size:19
Alignment explanation
Indices: 15435653--15435706 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
15435643 ATCTTCCTTC
*
15435653 TCTTCATTCTTCTCCTC-T
1 TCTTCCTTCTTCTCCTCAT
15435671 TCTTCCTTC-TCTTCCTCAT
1 TCTTCCTTCTTC-TCCTCAT
15435690 T-TTCCTTCTTCTCCTCA
1 TCTTCCTTCTTCTCCTCA
15435707 GGTTTTGCCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 2 0.06
18 26 0.81
19 4 0.12
ACGTcount: A:0.06, C:0.41, G:0.00, T:0.54
Consensus pattern (19 bp):
TCTTCCTTCTTCTCCTCAT
Found at i:15451655 original size:22 final size:22
Alignment explanation
Indices: 15451627--15451669 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
15451617 CACCAATAGT
15451627 TCTTCAAACACAAACTTTTATC
1 TCTTCAAACACAAACTTTTATC
**
15451649 TCTTCAAAGTCAAACTTTTAT
1 TCTTCAAACACAAACTTTTAT
15451670 TTGTCTACTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (22 bp):
TCTTCAAACACAAACTTTTATC
Found at i:15452363 original size:27 final size:25
Alignment explanation
Indices: 15452311--15452376 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
15452301 TTTCTGTTGT
* *
15452311 TTTTAATTTATTTTAAAATTATTTTA
1 TTTTAATTT-TTATAAAATTAGTTTA
15452337 TTTTGAATTTTTATAAAATTTAGTTTA
1 TTTT-AATTTTTATAAAA-TTAGTTTA
* *
15452364 GTTTAATGTTTAT
1 TTTTAATTTTTAT
15452377 TTGTTATATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 19 0.56
27 15 0.44
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (25 bp):
TTTTAATTTTTATAAAATTAGTTTA
Found at i:15452491 original size:19 final size:19
Alignment explanation
Indices: 15452447--15452493 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
15452437 GTTTAGTTTT
* *
15452447 AAATTTGTTATTTTATTGA
1 AAATTTATTATTTTATTAA
*
15452466 AATTTTATTATTTT-TTAA
1 AAATTTATTATTTTATTAA
15452484 CAAATTTATT
1 -AAATTTATT
15452494 GAAGATGGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (19 bp):
AAATTTATTATTTTATTAA
Found at i:15458476 original size:32 final size:33
Alignment explanation
Indices: 15458440--15458508 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 33
15458430 TTTGGCACCC
* *
15458440 AATGATC-GACACC-AAAAAACCCAAATTAAAAA
1 AATGATCAG-CACCAAAAAAACACAAATAAAAAA
15458472 AATGATCAGCACCTAAAAAAACACAAATAAAAAA
1 AATGATCAGCACC-AAAAAAACACAAATAAAAAA
15458506 AAT
1 AAT
15458509 TTTTTTTGGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.62, C:0.19, G:0.06, T:0.13
Consensus pattern (33 bp):
AATGATCAGCACCAAAAAAACACAAATAAAAAA
Found at i:15461857 original size:31 final size:30
Alignment explanation
Indices: 15461821--15461924 Score: 115
Period size: 29 Copynumber: 3.4 Consensus size: 30
15461811 ATTTAAGAAG
* *
15461821 TTAAATTATAATGTTGATATTGTAGTT-AAAT
1 TTAAATTATAA--ATGATATTGTAATTAAAAT
15461852 TTAAATTTATTAAATGATATTGTAATTAAAAT
1 TTAAA-TTA-TAAATGATATTGTAATTAAAAT
*
15461884 TTAAATT-TAAATGATATTGTAATTGAAAT
1 TTAAATTATAAATGATATTGTAATTAAAAT
*
15461913 TGAAATT-TAAAT
1 TTAAATTATAAAT
15461925 TGAAGTTGAA
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
29 32 0.48
31 19 0.29
32 12 0.18
33 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (30 bp):
TTAAATTATAAATGATATTGTAATTAAAAT
Found at i:15461903 original size:29 final size:28
Alignment explanation
Indices: 15461835--15461924 Score: 117
Period size: 29 Copynumber: 3.0 Consensus size: 28
15461825 ATTATAATGT
*
15461835 TGATATTGTAGTTAAATTTAAATTTATTAAA
1 TGATATTGTAATTAAATTTAAA--T-TTAAA
15461866 TGATATTGTAATTAAAATTTAAATTTAAA
1 TGATATTGTAATT-AAATTTAAATTTAAA
*
15461895 TGATATTGTAATTGAAATTGAAATTTAAA
1 TGATATTGTAATT-AAATTTAAATTTAAA
15461924 T
1 T
15461925 TGAAGTTGAA
Statistics
Matches: 55, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
29 33 0.60
30 1 0.02
31 12 0.22
32 9 0.16
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (28 bp):
TGATATTGTAATTAAATTTAAATTTAAA
Found at i:15462085 original size:29 final size:28
Alignment explanation
Indices: 15462026--15462183 Score: 157
Period size: 29 Copynumber: 5.7 Consensus size: 28
15462016 ATTTAAGTTG
* * *
15462026 AAGTTGAAATT-AACTACAAGTTAAAATT
1 AAGTTGAAATTAAAAT-TAAGTTGAAATT
15462054 AAGTTGAAATTAAAATTGAAGTTGAAATT
1 AAGTTGAAATTAAAATT-AAGTTGAAATT
15462083 AAGTTGAAATTAAAATTGAAGTTGAAATT
1 AAGTTGAAATTAAAATT-AAGTTGAAATT
** *
15462112 AAGTACAAGTTAAAATTAAGTTGAAATTT
1 AAGTTGAAATTAAAATTAAGTTGAAA-TT
*
15462141 AA---GAAATT-AAATTAA-ATGAAATT
1 AAGTTGAAATTAAAATTAAGTTGAAATT
*
15462164 AAGTTGAAAGTTGAAATTAA
1 AAGTTGAAA-TTAAAATTAA
15462184 ATGAGTGTTG
Statistics
Matches: 113, Mismatches: 9, Indels: 16
0.82 0.07 0.12
Matches are distributed among these distances:
23 4 0.04
24 5 0.04
25 7 0.06
26 8 0.07
27 2 0.02
28 27 0.24
29 60 0.53
ACGTcount: A:0.51, C:0.02, G:0.15, T:0.33
Consensus pattern (28 bp):
AAGTTGAAATTAAAATTAAGTTGAAATT
Found at i:15462088 original size:11 final size:11
Alignment explanation
Indices: 15462043--15462172 Score: 60
Period size: 11 Copynumber: 11.8 Consensus size: 11
15462033 AATTAACTAC
*
15462043 AAGTTAAAATT
1 AAGTTGAAATT
15462054 AAGTTGAAATT
1 AAGTTGAAATT
15462065 -A----AAATT
1 AAGTTGAAATT
15462071 GAAGTTGAAATT
1 -AAGTTGAAATT
15462083 AAGTTGAAATT
1 AAGTTGAAATT
* *
15462094 AAAATTGAAGTT
1 -AAGTTGAAATT
* * *
15462106 GAAATT-AAGTAC
1 -AAGTTGAAAT-T
*
15462118 AAGTTAAAATT
1 AAGTTGAAATT
15462129 AAGTTGAAATTT
1 AAGTTGAAA-TT
15462141 AAGAAATT-AAATT
1 AAG---TTGAAATT
*
15462154 AA-ATGAAATT
1 AAGTTGAAATT
15462164 AAGTTGAAA
1 AAGTTGAAA
15462173 GTTGAAATTA
Statistics
Matches: 93, Mismatches: 11, Indels: 30
0.69 0.08 0.22
Matches are distributed among these distances:
6 5 0.05
8 1 0.01
9 1 0.01
10 8 0.09
11 42 0.45
12 27 0.29
13 4 0.04
14 3 0.03
15 2 0.02
ACGTcount: A:0.52, C:0.01, G:0.15, T:0.33
Consensus pattern (11 bp):
AAGTTGAAATT
Found at i:15462129 original size:75 final size:69
Alignment explanation
Indices: 15462000--15462183 Score: 224
Period size: 75 Copynumber: 2.5 Consensus size: 69
15461990 ATATTTAAAT
*
15462000 TTAAATTGAAATTTAAATTTAAGTTGAAGTTGAAATTAACTACAAGTTAAAATTAAGTTGAAATT
1 TTAAATT-AAA-TGAAA-TTAAGTTGAAGTTGAAATTAACTACAAGTTAAAATTAAGTTGAAATT
*
15462065 AAAATTGAAG
63 -AAA--GAAA
* * *
15462075 TTGAAATTAAGTTGAAATTAAAATTGAAGTTGAAATTAAGTACAAGTTAAAATTAAGTTGAAATT
1 TT-AAATTAA-ATGAAATT-AAGTTGAAGTTGAAATTAACTACAAGTTAAAATTAAGTTGAAATT
*
15462140 TAAGAAA
63 AAAGAAA
15462147 TTAAATTAAATGAAATTAAGTTGAAAGTTGAAATTAA
1 TTAAATTAAATGAAATTAAGTTG-AAGTTGAAATTAA
15462184 ATGAGTGTTG
Statistics
Matches: 97, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
69 5 0.05
70 20 0.21
71 7 0.07
72 5 0.05
74 4 0.04
75 51 0.53
76 5 0.05
ACGTcount: A:0.49, C:0.02, G:0.14, T:0.35
Consensus pattern (69 bp):
TTAAATTAAATGAAATTAAGTTGAAGTTGAAATTAACTACAAGTTAAAATTAAGTTGAAATTAAA
GAAA
Found at i:15462168 original size:46 final size:45
Alignment explanation
Indices: 15461996--15462209 Score: 112
Period size: 46 Copynumber: 4.6 Consensus size: 45
15461986 TATGATATTT
* * * * * * **
15461996 AAATTTAAATTGAAATTTAAATTTAAGTTGAAGTTGAAATTAACTAC
1 AAATTAAAATTGAAATTGAAA-TGAAATT-AAGTTAAAATTAAGTTG
* * * *
15462043 AAGTTAAAATT-AAGTTGAAATTAAAATTGAAGTTGAAATTAAGTTG
1 AAATTAAAATTGAAATTGAAA-TGAAATT-AAGTTAAAATTAAGTTG
* * * *
15462089 AAATTAAAATTGAAGTTGAAATTAAGTACAAGTTAAAATTAAGTTG
1 AAATTAAAATTGAAATTGAAATGAAAT-TAAGTTAAAATTAAGTTG
* *
15462135 AAATTTAAGAAATT-AAATT-AAATGAAATTAAGTTGAAAGTTGAAATT-
1 AAA-TT-A-AAATTGAAATTGAAATGAAATTAAGTT-AAAATT-AAGTTG
* ***
15462182 AAATGAGTGTTGAAATTGAAATGAAATT
1 AAATTAAAATTGAAATTGAAATGAAATT
15462210 TGAATGAAAT
Statistics
Matches: 134, Mismatches: 24, Indels: 19
0.76 0.14 0.11
Matches are distributed among these distances:
44 2 0.01
45 6 0.04
46 77 0.57
47 35 0.26
48 9 0.07
49 5 0.04
ACGTcount: A:0.49, C:0.01, G:0.15, T:0.35
Consensus pattern (45 bp):
AAATTAAAATTGAAATTGAAATGAAATTAAGTTAAAATTAAGTTG
Found at i:15462180 original size:23 final size:23
Alignment explanation
Indices: 15462149--15462209 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
15462139 TTAAGAAATT
15462149 AAATT-AAATGAAATTA-AGTTG
1 AAATTGAAATGAAATTAGAGTTG
* * *
15462170 AAAGTTGAAATTAAATGAGTGTTG
1 AAA-TTGAAATGAAATTAGAGTTG
15462194 AAATTGAAATGAAATT
1 AAATTGAAATGAAATT
15462210 TGAATGAAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
21 3 0.09
22 2 0.06
23 20 0.62
24 7 0.22
ACGTcount: A:0.49, C:0.00, G:0.18, T:0.33
Consensus pattern (23 bp):
AAATTGAAATGAAATTAGAGTTG
Found at i:15462208 original size:5 final size:6
Alignment explanation
Indices: 15461870--15462260 Score: 122
Period size: 6 Copynumber: 67.5 Consensus size: 6
15461860 ATTAAATGAT
* * * * * *
15461870 ATTGTA ATTAAA ATTTAA ATTTAA A-TGAT ATTGTA ATTGAA ATTGAA
1 ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA
* * ** ** ** * *
15461917 ATTTAA ATTGAA GTTGAA AAAGAA AAAGAA AAAGAA ATTTAA A-TAAA
1 ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA
** * * * * * * *
15461964 ATT-AA ATACAA GTTTAA ATTTAT A-TGAT ATTTAA ATTTAA ATTGAA
1 ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA
* * * * * ** * *
15462010 ATTTAA ATTTAA GTTGAA GTTGAA ATT-AA CTACAA GTTAAA ATT-AA
1 ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA
* * * * *
15462056 GTTGAA ATTAAA ATTGAA GTTGAA ATT-AA GTTGAA ATTAAA ATTGAA
1 ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA
* * ** * * *
15462103 GTTGAA ATT-AA GTACAA GTTAAA ATT-AA GTTGAA ATTTAAGAA ATT-AA
1 ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA A-TT--GAA ATTGAA
* * *
15462151 ATT-AA A-TGAA ATT-AA GTTGAA AGTTGAA ATT-AA A-TGAGT GTTGAA
1 ATTGAA ATTGAA ATTGAA ATTGAA A-TTGAA ATTGAA ATTGA-A ATTGAA
*
15462196 ATTGAA A-TGAA ATTTG-A A-TGAA A-TGAA ATTAAA ATTGAA ATTGAA
1 ATTGAA ATTGAA A-TTGAA ATTGAA ATTGAA ATTGAA ATTGAA ATTGAA
15462241 ATTTG-A ATTGAA A-TGAA ATT
1 A-TTGAA ATTGAA ATTGAA ATT
15462261 TAAAATTTAA
Statistics
Matches: 294, Mismatches: 65, Indels: 52
0.72 0.16 0.13
Matches are distributed among these distances:
4 4 0.01
5 72 0.24
6 196 0.67
7 16 0.05
8 2 0.01
9 4 0.01
ACGTcount: A:0.50, C:0.01, G:0.14, T:0.35
Consensus pattern (6 bp):
ATTGAA
Found at i:15467950 original size:16 final size:16
Alignment explanation
Indices: 15467929--15467960 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
15467919 CCTCAAACTT
15467929 GAGTTTTTATTTGTCC
1 GAGTTTTTATTTGTCC
15467945 GAGTTTTTATTTGTCC
1 GAGTTTTTATTTGTCC
15467961 TCAAGTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.56
Consensus pattern (16 bp):
GAGTTTTTATTTGTCC
Found at i:15468214 original size:16 final size:15
Alignment explanation
Indices: 15468193--15468222 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
15468183 AATATATTTA
15468193 TTTTCTTTCTCTTTTT
1 TTTTCTTTCT-TTTTT
15468209 TTTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
15468223 GTGATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTTTCTTTTTT
Found at i:15469007 original size:21 final size:21
Alignment explanation
Indices: 15468968--15469014 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
15468958 CTCGCCTTCC
*
15468968 TCCTTGCGCTTCTTTTTCTTA
1 TCCTTGCGCTTCTTCTTCTTA
*
15468989 TCCTTGCGCTT-TCTCTTCTTG
1 TCCTTGCGCTTCT-TCTTCTTA
15469010 TCCTT
1 TCCTT
15469015 CGAATCAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.02, C:0.32, G:0.11, T:0.55
Consensus pattern (21 bp):
TCCTTGCGCTTCTTCTTCTTA
Found at i:15471206 original size:20 final size:20
Alignment explanation
Indices: 15471181--15471225 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
15471171 TGCATAAGAC
15471181 TAAAAAGA-AACAAGTAAAAG
1 TAAAAAGATAA-AAGTAAAAG
*
15471201 TAAAAAGATAAAAGTAAATG
1 TAAAAAGATAAAAGTAAAAG
15471221 TAAAA
1 TAAAA
15471226 TTGCATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (20 bp):
TAAAAAGATAAAAGTAAAAG
Found at i:15478682 original size:21 final size:21
Alignment explanation
Indices: 15478633--15478692 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
15478623 ATCGGCACAC
15478633 TCAGATGCATCCACAACAAAG
1 TCAGATGCATCCACAACAAAG
* * *
15478654 CCAAATGCATCCACATCAGAA-
1 TCAGATGCATCCACAACA-AAG
*
15478675 TCAGATGCAACCACAACA
1 TCAGATGCATCCACAACA
15478693 CTCATCAATG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.43, C:0.32, G:0.12, T:0.13
Consensus pattern (21 bp):
TCAGATGCATCCACAACAAAG
Found at i:15485328 original size:13 final size:13
Alignment explanation
Indices: 15485310--15485340 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
15485300 GCGTACGTCG
*
15485310 AGGATACTTGTGA
1 AGGATACTTGTAA
15485323 AGGATACTTGTAA
1 AGGATACTTGTAA
15485336 AGGAT
1 AGGAT
15485341 TGAGAGCCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (13 bp):
AGGATACTTGTAA
Found at i:15485482 original size:373 final size:362
Alignment explanation
Indices: 15484774--15485523 Score: 1016
Period size: 373 Copynumber: 2.0 Consensus size: 362
15484764 TACCAAGGCC
15484774 TGGAACAGTTCTGTTGTAGCCACATTAAAGCAGCTGAGCCTAGACTCACTCCTAGAATTCCTAAT
1 TGGAACAGTTCTGTTGTAGCCACATTAAAGCAGCTGAGCCTAGACTCACTCCTAGAATTCCTAAT
15484839 GTTTCCACCAATCATACAGGATTATGAGCCCTCATCAGAGGATGCTGACTTAGGGGACCAAGACC
66 GTTTCCACCAATCATACAGGATTATGAGCCCTCATCAGAGGATGCTGACTTAGGGGACCAAGACC
*
15484904 GATTGGTGCATCCCCTCCCATTACGTACGTCGAGGATACTTGTGAAGGATTGAGAGCCTGTTTGA
131 GATCGGTGCATCCCCTCCCATTACGTACGTCGAGGATACTTGTGAAGGATTGAGAGCCTGTTTGA
* * * * * *
15484969 AGATGATTTCACTGTTGGTCAAGAGGAGCATGCTGTTGAGAGGAATTTCGTGTGGGAGAGGAGGA
196 AGATGATTTCAATATTGGTCAAGAGGAACATGCTGTTGAGAGAAATTTCCTATGGGAGAGGAGGA
*
15485034 AACCCATGTTGATAATGAGAATGAGAAAGAAGAAGATGTCGAGGAAGAAAATGTTAAGAAAAAAG
261 AACCCATGTTGATAATGAGAATGAGAAAGAAAAAGATGTCGAGGAAGAAAA--TT--------AG
15485099 ATGCTGAGAAAGAATCAGCTGAAGACACTATCAATGCTGAGAAAATGT
316 AT-CTGAGAAAGAATCAGCTGAAGACACTATCAATGCTGAGAAAATGT
* * *
15485147 TGGAACAGTTTTGTTGTAGCCATATTAAAGCAGCTGAGCCTAGACTCACTCTTAGAATTCCTAAT
1 TGGAACAGTTCTGTTGTAGCCACATTAAAGCAGCTGAGCCTAGACTCACTCCTAGAATTCCTAAT
* *
15485212 GTTTCCACCAATCATACGGGATTATGAGCCCTCATCAGAGGATGCTGACTTAGGGGACCAAGATC
66 GTTTCCACCAATCATACAGGATTATGAGCCCTCATCAGAGGATGCTGACTTAGGGGACCAAGACC
* *
15485277 GATCGGTGGCGTCCCCTCCCATTGCGTACGTCGAGGATACTTGTGAAGGATACTTGTAAAGGATT
131 GATCGGT-GCATCCCCTCCCATTACGTACGTCGAGGATAC-T-T----G-----TG--AAGGATT
15485342 GAGAGCCTGTTTGAAGATGATTTCAATATTGGTCAAGAGGAACATGCTGTTGAGGAGAAATTTCC
182 GAGAGCCTGTTTGAAGATGATTTCAATATTGGTCAAGAGGAACATGCTGTTGA-GAGAAATTTCC
15485407 TATGGGAGAGGAGGAAACCCATGTTGATAATGAGAATGAGAAAGAAAAAGAT-TCCGAGGAAGAA
246 TATGGGAGAGGAGGAAACCCATGTTGATAATGAGAATGAGAAAGAAAAAGATGT-CGAGGAAGAA
15485471 AATGTTGAGAAAAAAGATGCTGAGAAAGAATCAGCTGAAGACACTATCAATGC
310 AA--TT--------AGAT-CTGAGAAAGAATCAGCTGAAGACACTATCAATGC
15485524 ACCCGAAGTT
Statistics
Matches: 345, Mismatches: 16, Indels: 17
0.91 0.04 0.04
Matches are distributed among these distances:
373 131 0.38
374 30 0.09
375 1 0.00
376 1 0.00
380 1 0.00
385 2 0.01
387 58 0.17
388 121 0.35
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (362 bp):
TGGAACAGTTCTGTTGTAGCCACATTAAAGCAGCTGAGCCTAGACTCACTCCTAGAATTCCTAAT
GTTTCCACCAATCATACAGGATTATGAGCCCTCATCAGAGGATGCTGACTTAGGGGACCAAGACC
GATCGGTGCATCCCCTCCCATTACGTACGTCGAGGATACTTGTGAAGGATTGAGAGCCTGTTTGA
AGATGATTTCAATATTGGTCAAGAGGAACATGCTGTTGAGAGAAATTTCCTATGGGAGAGGAGGA
AACCCATGTTGATAATGAGAATGAGAAAGAAAAAGATGTCGAGGAAGAAAATTAGATCTGAGAAA
GAATCAGCTGAAGACACTATCAATGCTGAGAAAATGT
Found at i:15485795 original size:12 final size:13
Alignment explanation
Indices: 15485778--15485806 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
15485768 AAAAGTGCAG
15485778 GAAGGAGG-AGAA
1 GAAGGAGGAAGAA
15485790 GAAGGAGGAAGAA
1 GAAGGAGGAAGAA
15485803 GAAG
1 GAAG
15485807 CATCGTGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (13 bp):
GAAGGAGGAAGAA
Found at i:15506914 original size:17 final size:17
Alignment explanation
Indices: 15506888--15506936 Score: 64
Period size: 19 Copynumber: 2.8 Consensus size: 17
15506878 ATAGTTTGCA
*
15506888 TGCATCTTTATTGTCAT
1 TGCATTTTTATTGTCAT
15506905 TGCATTTTTATTTTGTCAT
1 TGCATTTTTA--TTGTCAT
15506924 TGCATTTTT-TTGT
1 TGCATTTTTATTGT
15506937 TAATTTAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
16 4 0.14
17 9 0.31
19 16 0.55
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.61
Consensus pattern (17 bp):
TGCATTTTTATTGTCAT
Done.