Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 115 of 145
Found at i:38293158 original size:41 final size:41
Alignment explanation
Indices: 38293036--38293160 Score: 205
Period size: 41 Copynumber: 3.0 Consensus size: 41
38293026 CTGAGTTTTG
* *
38293036 AGGGCATTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTA
1 AGGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
*
38293077 AGGGCTTTAGCGGCGTTTTTGAAGAAGCGCTGCTAATGCTC
1 AGGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
* *
38293118 AGGGCTTTAGCGGCGTTTATGAGGAAGCGCCGCTAATGCTC
1 AGGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
38293159 AG
1 AG
38293161 ATTTATCATA
Statistics
Matches: 78, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 78 1.00
ACGTcount: A:0.22, C:0.20, G:0.33, T:0.26
Consensus pattern (41 bp):
AGGGCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTC
Found at i:38295101 original size:17 final size:17
Alignment explanation
Indices: 38295076--38295115 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
38295066 TCACTGGACT
*
38295076 GAAACCCTAGATGAGAA
1 GAAATCCTAGATGAGAA
38295093 GAAATCCTAGATGAGAA
1 GAAATCCTAGATGAGAA
38295110 GAAATC
1 GAAATC
38295116 GGAGGAAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.47, C:0.15, G:0.23, T:0.15
Consensus pattern (17 bp):
GAAATCCTAGATGAGAA
Found at i:38296252 original size:114 final size:114
Alignment explanation
Indices: 38296052--38299594 Score: 7007
Period size: 114 Copynumber: 31.1 Consensus size: 114
38296042 ATGTTCATCT
38296052 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38296117 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38296166 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38296231 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38296280 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38296345 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38296394 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38296459 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38296508 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38296573 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38296622 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38296687 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38296736 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38296801 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38296850 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38296915 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38296964 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38297029 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38297078 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38297143 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38297192 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38297257 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38297306 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38297371 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38297420 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38297485 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38297534 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38297599 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38297648 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38297713 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38297762 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38297827 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38297876 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38297941 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38297990 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38298055 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38298104 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38298169 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38298218 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38298283 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38298332 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38298397 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38298446 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38298511 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38298560 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38298625 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38298674 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38298739 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38298788 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38298853 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38298902 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38298967 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38299016 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38299081 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38299130 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38299195 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38299244 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38299309 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
38299358 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
38299423 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
** * *
38299472 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTACAAAGTGAGATGTTTTATCGCTGTAAT
1 AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
* *
38299537 TGATGTGTATAAATGTTGTTAATTGATATG-TTAAGGTGCTGCAAATTGA
66 TGAGGTGTATAAATGTTGTTAATTGATATGTTTAA-GTGCTGCAAATTTA
*
38299586 AGTGTTTAA
1 AGTTTTTAA
38299595 ATTTAACTTG
Statistics
Matches: 3421, Mismatches: 7, Indels: 2
1.00 0.00 0.00
Matches are distributed among these distances:
113 4 0.00
114 3417 1.00
ACGTcount: A:0.30, C:0.06, G:0.22, T:0.42
Consensus pattern (114 bp):
AGTTTTTAAGTGCTGCAAATTGAAGTGTTTAAGTGCTGTAAATTGAGATATTTTATCGCTGTAAT
TGAGGTGTATAAATGTTGTTAATTGATATGTTTAAGTGCTGCAAATTTA
Found at i:38300258 original size:43 final size:43
Alignment explanation
Indices: 38300211--38300653 Score: 602
Period size: 43 Copynumber: 10.3 Consensus size: 43
38300201 TTTTCGTGAC
* * * * *
38300211 CTTTAGTGGCGTTTTTGGGAAAAGCACCACTAAAGGTTTTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
* * **
38300254 CTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGG-CGTGAC
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
* * * * *
38300296 CTTTAGTGGCGTTTTTGGGAAAAGCACCACTAAAGGTTTTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
*
38300339 CTTTAGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
*
38300382 CTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
* *
38300425 CTTTAGCAGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
* * * *
38300468 CTTTAGCGGCGTTTGCGGGAGAAGCGTCGCTAAAGGTCCTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
*
38300511 CTTTAGCGGCGTTT-TCGGGAGAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGT-GGGAAAAGCGCCGCTAAAGGTCTTGGT
* * *
38300554 TTTTAGCGGCGTTTGCGGGAGAAGCGCCGCTAAAGGTCTTGGT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
* **
38300597 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTAAT
1 CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
38300640 CTTTAGCGGCGTTT
1 CTTTAGCGGCGTTT
38300654 TTTCCGGCGC
Statistics
Matches: 355, Mismatches: 42, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
42 33 0.09
43 322 0.91
ACGTcount: A:0.19, C:0.19, G:0.33, T:0.28
Consensus pattern (43 bp):
CTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGT
Found at i:38303196 original size:21 final size:20
Alignment explanation
Indices: 38303173--38303242 Score: 56
Period size: 19 Copynumber: 3.5 Consensus size: 20
38303163 TTTCAATACA
38303173 TTTTTATAAAATTTTACAA-
1 TTTTTATAAAATTTTACAAT
* *
38303192 TATTTA-AATAATTTATTAGAAT
1 TTTTTATAA-AA-TT-TTACAAT
*
38303214 TTTCTTATAAAA-TTTATAAT
1 TTT-TTATAAAATTTTACAAT
38303234 TTTTTATAA
1 TTTTTATAA
38303243 TTTTTATAAC
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
18 2 0.05
19 13 0.32
20 11 0.27
21 6 0.15
22 2 0.05
23 5 0.12
24 2 0.05
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.54
Consensus pattern (20 bp):
TTTTTATAAAATTTTACAAT
Found at i:38303246 original size:9 final size:9
Alignment explanation
Indices: 38303226--38303303 Score: 77
Period size: 9 Copynumber: 8.3 Consensus size: 9
38303216 TCTTATAAAA
38303226 TTTATAATTT
1 TTTATAA-TT
38303236 TTTATAATT
1 TTTATAATT
38303245 TTTATAACTT
1 TTTATAA-TT
*
38303255 TATATCAATT
1 TTTAT-AATT
* *
38303265 TTCAGAATT
1 TTTATAATT
38303274 TTTATAATT
1 TTTATAATT
38303283 TTTGAT-ATT
1 TTT-ATAATT
*
38303292 TTTATCATT
1 TTTATAATT
38303301 TTT
1 TTT
38303304 TGAAAAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
8 2 0.03
9 35 0.60
10 19 0.33
11 2 0.03
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTATAATT
Found at i:38304367 original size:2 final size:2
Alignment explanation
Indices: 38304360--38304386 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38304350 CTTTTATAAT
38304360 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
38304387 TTGGATCCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38305520 original size:17 final size:17
Alignment explanation
Indices: 38305483--38305520 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
38305473 GTTAAAATGT
*
38305483 AATTTTATTATTTTAAT
1 AATTTTATTATTTTAAA
38305500 AATTTATATTA-TTTAAA
1 AATTT-TATTATTTTAAA
38305517 AATT
1 AATT
38305521 AAATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTTTATTATTTTAAA
Found at i:38305799 original size:12 final size:12
Alignment explanation
Indices: 38305778--38305812 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
38305768 TCTTTTAAAG
38305778 TTACAAATATAA
1 TTACAAATATAA
*
38305790 TTACAGATATAA
1 TTACAAATATAA
*
38305802 TTACAATTATA
1 TTACAAATATA
38305813 GCTATAGATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.51, C:0.09, G:0.03, T:0.37
Consensus pattern (12 bp):
TTACAAATATAA
Found at i:38310573 original size:66 final size:66
Alignment explanation
Indices: 38310459--38310594 Score: 236
Period size: 66 Copynumber: 2.1 Consensus size: 66
38310449 GCAACCTCAC
* * *
38310459 TTCTCTCCAGTGCTTGATTATCGAAAATTGCCCAAACCTGAAGACTCTTCCGGGAAACAATATGC
1 TTCTCTCCAGTGCTTGACTATCGAAAATTGCCCAAACCTCAAGACTCTTCCAGGAAACAATATGC
38310524 T
66 T
*
38310525 TTCTCTCCAGTGCTTGACTATCGAAAATTGCCCAAACCTCAAGTCTCTTCCAGGAAACAATATGC
1 TTCTCTCCAGTGCTTGACTATCGAAAATTGCCCAAACCTCAAGACTCTTCCAGGAAACAATATGC
38310590 T
66 T
38310591 TTCT
1 TTCT
38310595 TCGCTTTTCG
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (66 bp):
TTCTCTCCAGTGCTTGACTATCGAAAATTGCCCAAACCTCAAGACTCTTCCAGGAAACAATATGC
T
Found at i:38311967 original size:25 final size:25
Alignment explanation
Indices: 38311933--38311984 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
38311923 CTCGATGATA
38311933 GTTAAGCTAGAGTTATGTATTTATT
1 GTTAAGCTAGAGTTATGTATTTATT
*
38311958 GTTACGCTAGAGTTATGTATTTATT
1 GTTAAGCTAGAGTTATGTATTTATT
38311983 GT
1 GT
38311985 GATAATGTAG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.06, G:0.21, T:0.48
Consensus pattern (25 bp):
GTTAAGCTAGAGTTATGTATTTATT
Found at i:38314107 original size:93 final size:93
Alignment explanation
Indices: 38313930--38314304 Score: 470
Period size: 93 Copynumber: 4.0 Consensus size: 93
38313920 TGATTGTCCA
* * * * ** * *
38313930 CCAAAATTCTCTACATCTCTTGAGATGGAAATCATAGGCAAGGCATTTACTGCACAAGAACTATC
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTCTC
* * *
38313995 TAT-AGTTTGCATCAAGGCAGTCTTTTCT
66 T-TCATTTTGTATCAGGGCAGTCTTTTCT
* * * *
38314023 CCAACATTCTCCACATCTCTTGGGTTGGAAGTTATAGGCAAAGCATTTACCCCACAGGCACTCTC
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTCTC
38314088 TTCATTTTGTATCAGGGCAGTCTTTTCT
66 TTCATTTTGTATCAGGGCAGTCTTTTCT
* * * * *
38314116 GCAACATTCTCCATATCTCTCGGGATGGAAATTATAGGCAAAGCATTTGCCCCACAAGCACTAC-
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACT-CT
38314180 CTTCATTTTGTATCAGGGCAGTCTTTTCT
65 CTTCATTTTGTATCAGGGCAGTCTTTTCT
* *
38314209 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTAACCAACAAGCAC-CAT
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTC-T
* *
38314273 CTTCATTTTGTA-CTGGGTCATTCTTTTCT
65 CTTCATTTTGTATCAGGG-CAGTCTTTTCT
38314302 CCA
1 CCA
38314305 GCTGGTATTT
Statistics
Matches: 246, Mismatches: 31, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
91 1 0.00
92 5 0.02
93 239 0.97
94 1 0.00
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (93 bp):
CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTCTC
TTCATTTTGTATCAGGGCAGTCTTTTCT
Found at i:38317632 original size:21 final size:20
Alignment explanation
Indices: 38317606--38317660 Score: 83
Period size: 21 Copynumber: 2.6 Consensus size: 20
38317596 AACAGCGGTG
*
38317606 GCGGTGAGATTAGTTACTGTA
1 GCGGTGATATTAG-TACTGTA
38317627 GCGGTGATATTGAGTACTGTA
1 GCGGTGATATT-AGTACTGTA
38317648 GCGGTGATATTAG
1 GCGGTGATATTAG
38317661 AAACAATGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.24, C:0.09, G:0.35, T:0.33
Consensus pattern (20 bp):
GCGGTGATATTAGTACTGTA
Found at i:38317937 original size:22 final size:22
Alignment explanation
Indices: 38317886--38317937 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
38317876 TTTTATAGTT
*
38317886 ATAATTAAATATTTTTTATAACA
1 ATAA-TAAATATTATTTATAACA
* *
38317909 ATGATAAATATTATTT-TCACAA
1 ATAATAAATATTATTTATAAC-A
38317931 ATAATAA
1 ATAATAA
38317938 CATTATACTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
21 3 0.12
22 18 0.75
23 3 0.12
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (22 bp):
ATAATAAATATTATTTATAACA
Found at i:38327471 original size:497 final size:497
Alignment explanation
Indices: 38326537--38327530 Score: 1988
Period size: 497 Copynumber: 2.0 Consensus size: 497
38326527 TTAGGTTATT
38326537 ACACAGAGGAATGGAAAAAATTGTAGAAAACCAAACAATTATACAATATTTGCCTTATGTAACGC
1 ACACAGAGGAATGGAAAAAATTGTAGAAAACCAAACAATTATACAATATTTGCCTTATGTAACGC
38326602 ATTGGGATTATTTAGCCATTACGTTCACAGAAGCAATAACCGTAAATGGACCAGAACAATTGGGG
66 ATTGGGATTATTTAGCCATTACGTTCACAGAAGCAATAACCGTAAATGGACCAGAACAATTGGGG
38326667 AATATTTAAGTCCCTAAAAGGGCCAACTATATCAGAGTAATTATGTTGGAGTTGAGTCGTATAAC
131 AATATTTAAGTCCCTAAAAGGGCCAACTATATCAGAGTAATTATGTTGGAGTTGAGTCGTATAAC
38326732 TTCTCATCTATTATGGCTTGGGCCTTTTATGGTAGTTATTGGTGCACAAACCCCCTTTTTTTCTA
196 TTCTCATCTATTATGGCTTGGGCCTTTTATGGTAGTTATTGGTGCACAAACCCCCTTTTTTTCTA
38326797 TATTTTCAAAGAAAGAGAATTAGTATATGATTTATTTGAAACTGCCACCTATATGACAATGATGC
261 TATTTTCAAAGAAAGAGAATTAGTATATGATTTATTTGAAACTGCCACCTATATGACAATGATGC
38326862 ATAATTATTTTCGTATCGGAGGAGTGGCGGCCGATCTACCTTATGGCTGAATAGATAAATGTTTT
326 ATAATTATTTTCGTATCGGAGGAGTGGCGGCCGATCTACCTTATGGCTGAATAGATAAATGTTTT
38326927 GATTTCTATAATTATTTCTTAACAGGAATTGTTGAATATCAAAAACTTATTTCGCGAAATCCTAT
391 GATTTCTATAATTATTTCTTAACAGGAATTGTTGAATATCAAAAACTTATTTCGCGAAATCCTAT
38326992 TTTTTAGAACGAGTTAAAGGGATAGGCGTTATTGGTGGAGAA
456 TTTTTAGAACGAGTTAAAGGGATAGGCGTTATTGGTGGAGAA
38327034 ACACAGAGGAATGGAAAAAATTGTAGAAAACCAAACAATTATACAATATTTGCCTTATGTAACGC
1 ACACAGAGGAATGGAAAAAATTGTAGAAAACCAAACAATTATACAATATTTGCCTTATGTAACGC
38327099 ATTGGGATTATTTAGCCATTACGTTCACAGAAGCAATAACCGTAAATGGACCAGAACAATTGGGG
66 ATTGGGATTATTTAGCCATTACGTTCACAGAAGCAATAACCGTAAATGGACCAGAACAATTGGGG
38327164 AATATTTAAGTCCCTAAAAGGGCCAACTATATCAGAGTAATTATGTTGGAGTTGAGTCGTATAAC
131 AATATTTAAGTCCCTAAAAGGGCCAACTATATCAGAGTAATTATGTTGGAGTTGAGTCGTATAAC
38327229 TTCTCATCTATTATGGCTTGGGCCTTTTATGGTAGTTATTGGTGCACAAACCCCCTTTTTTTCTA
196 TTCTCATCTATTATGGCTTGGGCCTTTTATGGTAGTTATTGGTGCACAAACCCCCTTTTTTTCTA
38327294 TATTTTCAAAGAAAGAGAATTAGTATATGATTTATTTGAAACTGCCACCTATATGACAATGATGC
261 TATTTTCAAAGAAAGAGAATTAGTATATGATTTATTTGAAACTGCCACCTATATGACAATGATGC
38327359 ATAATTATTTTCGTATCGGAGGAGTGGCGGCCGATCTACCTTATGGCTGAATAGATAAATGTTTT
326 ATAATTATTTTCGTATCGGAGGAGTGGCGGCCGATCTACCTTATGGCTGAATAGATAAATGTTTT
38327424 GATTTCTATAATTATTTCTTAACAGGAATTGTTGAATATCAAAAACTTATTTCGCGAAATCCTAT
391 GATTTCTATAATTATTTCTTAACAGGAATTGTTGAATATCAAAAACTTATTTCGCGAAATCCTAT
38327489 TTTTTAGAACGAGTTAAAGGGATAGGCGTTATTGGTGGAGAA
456 TTTTTAGAACGAGTTAAAGGGATAGGCGTTATTGGTGGAGAA
38327531 GAAGCAATAA
Statistics
Matches: 497, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
497 497 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (497 bp):
ACACAGAGGAATGGAAAAAATTGTAGAAAACCAAACAATTATACAATATTTGCCTTATGTAACGC
ATTGGGATTATTTAGCCATTACGTTCACAGAAGCAATAACCGTAAATGGACCAGAACAATTGGGG
AATATTTAAGTCCCTAAAAGGGCCAACTATATCAGAGTAATTATGTTGGAGTTGAGTCGTATAAC
TTCTCATCTATTATGGCTTGGGCCTTTTATGGTAGTTATTGGTGCACAAACCCCCTTTTTTTCTA
TATTTTCAAAGAAAGAGAATTAGTATATGATTTATTTGAAACTGCCACCTATATGACAATGATGC
ATAATTATTTTCGTATCGGAGGAGTGGCGGCCGATCTACCTTATGGCTGAATAGATAAATGTTTT
GATTTCTATAATTATTTCTTAACAGGAATTGTTGAATATCAAAAACTTATTTCGCGAAATCCTAT
TTTTTAGAACGAGTTAAAGGGATAGGCGTTATTGGTGGAGAA
Found at i:38328591 original size:29 final size:29
Alignment explanation
Indices: 38328525--38328580 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
38328515 CACGTTATCC
* *
38328525 AAATGCTTTTTAATTTAGACAACGTGTCT
1 AAATGCATTTGAATTTAGACAACGTGTCT
* *
38328554 AGATGCATTTGAATTTGGACAACGTGT
1 AAATGCATTTGAATTTAGACAACGTGT
38328581 TCAAATTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (29 bp):
AAATGCATTTGAATTTAGACAACGTGTCT
Found at i:38328796 original size:147 final size:148
Alignment explanation
Indices: 38328621--38328915 Score: 583
Period size: 147 Copynumber: 2.0 Consensus size: 148
38328611 TTACTCTTTT
38328621 TATTAATTTATATATTTAAAAAATTTAAAATTTTATATATTTTTAGTTTCAAAATAATAAAAACA
1 TATTAATTTATATATTTAAAAAATTTAAAATTTTATATATTTTTAGTTTCAAAATAATAAAAACA
38328686 ACCTAATGTTTTATTAAAATCTAAAAATATATAATTTATATATTCTTTATTTCTTTATCATGATA
66 ACCTAATGTTTTATTAAAATCTAAAAATATATAATTTATATATTCTTTATTTCTTTATCATGATA
38328751 TCAATTTTGTTTCTTCTG
131 TCAATTTTGTTTCTTCTG
38328769 TATTAATTTA-ATATTTAAAAAATTTAAAATTTTATATATTTTTAGTTTCAAAATAATAAAAACA
1 TATTAATTTATATATTTAAAAAATTTAAAATTTTATATATTTTTAGTTTCAAAATAATAAAAACA
38328833 ACCTAATGTTTTATTAAAATCTAAAAATATATAATTTATATATTCTTTATTTCTTTATCATGATA
66 ACCTAATGTTTTATTAAAATCTAAAAATATATAATTTATATATTCTTTATTTCTTTATCATGATA
38328898 TCAATTTTGTTTCTTCTG
131 TCAATTTTGTTTCTTCTG
38328916 AAATATAATA
Statistics
Matches: 147, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
147 137 0.93
148 10 0.07
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.49
Consensus pattern (148 bp):
TATTAATTTATATATTTAAAAAATTTAAAATTTTATATATTTTTAGTTTCAAAATAATAAAAACA
ACCTAATGTTTTATTAAAATCTAAAAATATATAATTTATATATTCTTTATTTCTTTATCATGATA
TCAATTTTGTTTCTTCTG
Found at i:38329043 original size:25 final size:26
Alignment explanation
Indices: 38329015--38329066 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
38329005 GCTTGGTTTC
*
38329015 TGTAGTATATAATATATATAG-ATTT
1 TGTAGTATATAATATATAAAGTATTT
*
38329040 TGTAGTATATATTATATAAAGTATTT
1 TGTAGTATATAATATATAAAGTATTT
38329066 T
1 T
38329067 CAAATAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (26 bp):
TGTAGTATATAATATATAAAGTATTT
Found at i:38331711 original size:10 final size:10
Alignment explanation
Indices: 38331698--38331762 Score: 53
Period size: 10 Copynumber: 6.6 Consensus size: 10
38331688 TTTTATGATT
38331698 TTTTTTATCA
1 TTTTTTATCA
*
38331708 -TTTTTATAA
1 TTTTTTATCA
* *
38331717 GTTTATATCA
1 TTTTTTATCA
* * *
38331727 ATTTTCATAA
1 TTTTTTATCA
38331737 TTTTTTAT-A
1 TTTTTTATCA
38331746 TTTTTTTATCA
1 -TTTTTTATCA
38331757 TTTTTT
1 TTTTTT
38331763 GAAAAAAAAT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
9 9 0.21
10 33 0.77
11 1 0.02
ACGTcount: A:0.25, C:0.06, G:0.02, T:0.68
Consensus pattern (10 bp):
TTTTTTATCA
Found at i:38334531 original size:17 final size:17
Alignment explanation
Indices: 38334511--38334544 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38334501 TATTCATATA
* *
38334511 GTTCTCTTATTTAGATG
1 GTTCTCATAGTTAGATG
38334528 GTTCTCATAGTTAGATG
1 GTTCTCATAGTTAGATG
38334545 CAAAATCAGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.47
Consensus pattern (17 bp):
GTTCTCATAGTTAGATG
Found at i:38335876 original size:19 final size:17
Alignment explanation
Indices: 38335852--38335894 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
38335842 AAAAAATATT
38335852 TAAAAATTCATATTTTTGA
1 TAAAAATTCAT-TTTTT-A
*
38335871 TAAAAATACATTTTTTA
1 TAAAAATTCATTTTTTA
38335888 -AAAAATT
1 TAAAAATT
38335895 TATTAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 1 0.05
18 5 0.23
19 10 0.45
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAAAATTCATTTTTTA
Found at i:38345526 original size:30 final size:29
Alignment explanation
Indices: 38345490--38345552 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 29
38345480 TCCTTCTTTC
*
38345490 GCAAACCCAACTCCGTAAGGAGAAATGCT
1 GCAAACCCAACTCCATAAGGAGAAATGCT
38345519 AGCAAACCCAACTCCATAAGGAGAAATGCT
1 -GCAAACCCAACTCCATAAGGAGAAATGCT
38345549 GCAA
1 GCAA
38345553 CATATACAAC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.41, C:0.27, G:0.19, T:0.13
Consensus pattern (29 bp):
GCAAACCCAACTCCATAAGGAGAAATGCT
Found at i:38348779 original size:48 final size:49
Alignment explanation
Indices: 38348702--38348800 Score: 191
Period size: 48 Copynumber: 2.0 Consensus size: 49
38348692 TACATACAGT
38348702 TACAAAAATAAGAATAAGACATGTATATATACTTCAGGTTTATAAAATA
1 TACAAAAATAAGAATAAGACATGTATATATACTTCAGGTTTATAAAATA
38348751 TACAAAAATAA-AATAAGACATGTATATATACTTCAGGTTTATAAAATA
1 TACAAAAATAAGAATAAGACATGTATATATACTTCAGGTTTATAAAATA
38348799 TA
1 TA
38348801 AGAGTATGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
48 39 0.78
49 11 0.22
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (49 bp):
TACAAAAATAAGAATAAGACATGTATATATACTTCAGGTTTATAAAATA
Found at i:38348915 original size:3 final size:3
Alignment explanation
Indices: 38348907--38348949 Score: 68
Period size: 3 Copynumber: 14.0 Consensus size: 3
38348897 GAAATAAAAC
*
38348907 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TGA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
38348950 CATTATTGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:38350824 original size:2 final size:2
Alignment explanation
Indices: 38350817--38350842 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38350807 CAGATCCAAA
38350817 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
38350843 GGTCCAAGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38354533 original size:35 final size:35
Alignment explanation
Indices: 38354493--38354572 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
38354483 AATTTTTTTG
*
38354493 TAATTTTTATAAGTTTATATCAATTTTAATACTTT
1 TAATTTTTATAAGTTTATATCAATTTTAATACCTT
* ** *
38354528 TAATTTTTTTATTTTTATATTAATTTTAATACCTT
1 TAATTTTTATAAGTTTATATCAATTTTAATACCTT
38354563 T--TTTTTATAA
1 TAATTTTTATAA
38354573 AATTTTACAA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
33 7 0.18
35 31 0.82
ACGTcount: A:0.31, C:0.05, G:0.01, T:0.62
Consensus pattern (35 bp):
TAATTTTTATAAGTTTATATCAATTTTAATACCTT
Found at i:38354654 original size:21 final size:22
Alignment explanation
Indices: 38354613--38354656 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38354603 AATTTTATAA
* *
38354613 TTTATTAAATTTATTAGAATTT
1 TTTATAAAATTTATTAAAATTT
38354635 TTTATAAAATTTA-TAAAATTT
1 TTTATAAAATTTATTAAAATTT
38354656 T
1 T
38354657 ATAATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTATAAAATTTATTAAAATTT
Found at i:38354662 original size:29 final size:28
Alignment explanation
Indices: 38354605--38354695 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
38354595 TTGTTATTAA
* *
38354605 TTTTAT-AATTTATTAAATTTATTAGAATT
1 TTTTATAAATTTA-TAAAATT-TTATAATT
38354634 TTTTATAAAATTTATAAAATTTTATAATT
1 TTTTAT-AAATTTATAAAATTTTATAATT
* *
38354663 TTTTATAACTTTATATCAATTTTCATAATT
1 TTTTATAAATTTATA-AAATTTT-ATAATT
38354693 TTT
1 TTT
38354696 AATATTTTTA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
28 8 0.15
29 25 0.46
30 15 0.28
31 6 0.11
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTTATAAATTTATAAAATTTTATAATT
Found at i:38354704 original size:19 final size:19
Alignment explanation
Indices: 38354605--38354745 Score: 71
Period size: 19 Copynumber: 7.4 Consensus size: 19
38354595 TTGTTATTAA
38354605 TTTTATAATTTATT-A-AAT
1 TTTTATAATTT-TTAATAAT
* * *
38354623 TTATTAGAATTTTTTATAAA
1 TT-TTATAATTTTTAATAAT
* *
38354643 ATTTATAAAATTTT-ATAATT
1 TTTTAT-AATTTTTAATAA-T
*
38354663 TTTTATAA-CTTTATATCAAT
1 TTTTATAATTTTTA-AT-AAT
*
38354683 TTTCATAATTTTTAAT-A-
1 TTTTATAATTTTTAATAAT
* *
38354700 TTTT-TAATATCTAATAAT
1 TTTTATAATTTTTAATAAT
* *
38354718 TTTTATAATTTTTTATCAT
1 TTTTATAATTTTTAATAAT
38354737 TTTTCATAA
1 TTTT-ATAA
38354746 AAGATATTAT
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
16 9 0.10
17 4 0.04
18 12 0.13
19 32 0.34
20 30 0.32
21 6 0.06
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (19 bp):
TTTTATAATTTTTAATAAT
Found at i:38354730 original size:10 final size:10
Alignment explanation
Indices: 38354605--38354745 Score: 74
Period size: 10 Copynumber: 13.8 Consensus size: 10
38354595 TTGTTATTAA
38354605 TTTTATAATT
1 TTTTATAATT
*
38354615 TATTA-AATT
1 TTTTATAATT
* *
38354624 TATTAGAATT
1 TTTTATAATT
*
38354634 TTTTATAA-A
1 TTTTATAATT
* **
38354643 ATTTATAAAA
1 TTTTATAATT
38354653 TTTTATAATT
1 TTTTATAATT
*
38354663 TTTTATAACT
1 TTTTATAATT
*
38354673 TTATATCAA-T
1 TTTTAT-AATT
*
38354683 TTTCATAATT
1 TTTTATAATT
*
38354693 TTTAAT-ATT
1 TTTTATAATT
38354702 TTTAATATCTAATAAT
1 TTT--TA--TAAT--T
38354718 TTTTATAATT
1 TTTTATAATT
*
38354728 TTTTATCATT
1 TTTTATAATT
*
38354738 TTTCATAA
1 TTTTATAA
38354746 AAGATATTAT
Statistics
Matches: 103, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
9 24 0.23
10 63 0.61
11 3 0.03
12 4 0.04
13 1 0.01
14 4 0.04
16 4 0.04
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.58
Consensus pattern (10 bp):
TTTTATAATT
Found at i:38361923 original size:66 final size:66
Alignment explanation
Indices: 38361817--38362015 Score: 353
Period size: 66 Copynumber: 3.0 Consensus size: 66
38361807 GCAACCTCAC
* *
38361817 TTCTCTCCAGTGCTTGACTATCGGAAATTGCCCAAACCTCAAGACTCTTCCGGGAAACAATATGC
1 TTCTCTCCAGCGCTTGACTATCGCAAATTGCCCAAACCTCAAGACTCTTCCGGGAAACAATATGC
38361882 T
66 T
*
38361883 TTCTCTCCAGCGCTTGACTATCGCAAATTGCCCACACCTCAAGACTCTTCCGGGAAACAATATGC
1 TTCTCTCCAGCGCTTGACTATCGCAAATTGCCCAAACCTCAAGACTCTTCCGGGAAACAATATGC
38361948 T
66 T
* *
38361949 TTCTCTCCAGCGCTTGACTATTGCAAATTGCCCAAACCTCAAGACTCTTCCAGGAAACAATATGC
1 TTCTCTCCAGCGCTTGACTATCGCAAATTGCCCAAACCTCAAGACTCTTCCGGGAAACAATATGC
38362014 T
66 T
38362015 T
1 T
38362016 CCTTCGCTTT
Statistics
Matches: 127, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
66 127 1.00
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (66 bp):
TTCTCTCCAGCGCTTGACTATCGCAAATTGCCCAAACCTCAAGACTCTTCCGGGAAACAATATGC
T
Found at i:38364454 original size:30 final size:30
Alignment explanation
Indices: 38364418--38364476 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
38364408 TCCTTCTTTT
*
38364418 GCAAACCCAACTCCGTAAGGAGAAATGCTC
1 GCAAACCCAACTCCATAAGGAGAAATGCTC
38364448 GCAAACCCAACTCCATAAGGAGAAATGCT
1 GCAAACCCAACTCCATAAGGAGAAATGCT
38364477 GAAACATATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.39, C:0.29, G:0.19, T:0.14
Consensus pattern (30 bp):
GCAAACCCAACTCCATAAGGAGAAATGCTC
Found at i:38366922 original size:2 final size:2
Alignment explanation
Indices: 38366917--38366953 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
38366907 TCCAAAAAAG
38366917 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38366954 ATAACCTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38371940 original size:93 final size:93
Alignment explanation
Indices: 38371773--38372147 Score: 495
Period size: 93 Copynumber: 4.0 Consensus size: 93
38371763 TGATTGTCCA
* * * * * * *
38371773 CCAAAATTCTCTACATCTCTTGAGATGGAAATCATAGGCAAGGCATTTACCGCACAAGAACTATC
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTCTC
* * *
38371838 TTTAGTTTGTATCAAGGCAGTCTTTTCT
66 TTCATTTTGTATCAGGGCAGTCTTTTCT
* * * *
38371866 CCAACATTCTCCACATCTCTTGGGTTGGAAGTTATAGGCATAGCATTTACCCCACAAGCACTCTC
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTCTC
38371931 TTCATTTTGTATCAGGGCAGTCTTTTCT
66 TTCATTTTGTATCAGGGCAGTCTTTTCT
* * *
38371959 GCAACATTCTCCATATCTCTTGGGATGGAAATTATAGGCAAAGCATTTACCCCACAAGCACTAC-
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACT-CT
*
38372023 CTTCATTTTGTATCAGGGCAGTCTTTTCC
65 CTTCATTTTGTATCAGGGCAGTCTTTTCT
* *
38372052 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTAACCAACAAGCAC-CAT
1 CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTC-T
* * *
38372116 CTTCATTTTTTA-CTGGGTCACTCTTTTCT
65 CTTCATTTTGTATCAGGG-CAGTCTTTTCT
38372145 CCA
1 CCA
38372148 GCTGGTATTT
Statistics
Matches: 249, Mismatches: 29, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
91 1 0.00
92 4 0.02
93 243 0.98
94 1 0.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (93 bp):
CCAACATTCTCCACATCTCTTGGGATGGAAATCATAGGCAAAGCATTTACCCCACAAGCACTCTC
TTCATTTTGTATCAGGGCAGTCTTTTCT
Found at i:38388579 original size:14 final size:16
Alignment explanation
Indices: 38388560--38388591 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
38388550 TGCCTTTCTG
38388560 ATTA-TTTTAA-ATAA
1 ATTATTTTTAATATAA
38388574 ATTATTTTTAATATAA
1 ATTATTTTTAATATAA
38388590 AT
1 AT
38388592 GCGTTGCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.25
15 6 0.38
16 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTATTTTTAATATAA
Found at i:38393427 original size:22 final size:22
Alignment explanation
Indices: 38393402--38393471 Score: 140
Period size: 22 Copynumber: 3.2 Consensus size: 22
38393392 TAAGACAAGT
38393402 AAAGAAATTATTACAGGAGATG
1 AAAGAAATTATTACAGGAGATG
38393424 AAAGAAATTATTACAGGAGATG
1 AAAGAAATTATTACAGGAGATG
38393446 AAAGAAATTATTACAGGAGATG
1 AAAGAAATTATTACAGGAGATG
38393468 AAAG
1 AAAG
38393472 GGAAAGGTTG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.21
Consensus pattern (22 bp):
AAAGAAATTATTACAGGAGATG
Found at i:38395471 original size:2 final size:2
Alignment explanation
Indices: 38395466--38395502 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
38395456 ACACACACAC
38395466 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38395503 NNNNNNNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38406291 original size:2 final size:2
Alignment explanation
Indices: 38406286--38406314 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38406276 TAAAAATTTA
38406286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38406315 CATTCGTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38406320 original size:196 final size:196
Alignment explanation
Indices: 38406106--38406462 Score: 597
Period size: 196 Copynumber: 1.8 Consensus size: 196
38406096 ATAACATTTC
* ** *
38406106 ATATATATATACACATTCGTTTAAACATTTATCACCTGTTGAACCAAATGAAATAACATCGAATG
1 ATATATATATACACATTCGTTTAAACATTTACCACCCATTGAACCAAATGAAATAACATCGAATA
* * * *
38406171 CTTGGGAAAATGCTCACACAAGCTGTGACTGTAATTGTATATGCTCACATGAACTATGAAATGGG
66 CTCGGAAAAATGCTCACACAAGCTGTGACTGTAATTGTATATGCTCACACGAACTATAAAATGGG
* *
38406236 CCTGCTCACACGAGTTGTGGGTCAAGATGTTTATATATCATAAAAATTTAATATATATATATATA
131 CCTACTCACACGAGTTGTGGGCCAAGATGTTTATATATCATAAAAATTTAATATATATATATATA
38406301 T
196 T
*
38406302 ATATATATATATACATTCGTTTAAACATTTACCACCCATTGAACCAAATGAAATAACATCGAATA
1 ATATATATATACACATTCGTTTAAACATTTACCACCCATTGAACCAAATGAAATAACATCGAATA
38406367 CTCGGAAAAATGCTCACACAAGCTGTGACTGTAATTGTATATGCTCACACGAACTATAAAATGGG
66 CTCGGAAAAATGCTCACACAAGCTGTGACTGTAATTGTATATGCTCACACGAACTATAAAATGGG
* *
38406432 TCTACTCACACGAGTTGTGGGCCAGGATGTT
131 CCTACTCACACGAGTTGTGGGCCAAGATGTT
38406463 AGGCTACACG
Statistics
Matches: 148, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
196 148 1.00
ACGTcount: A:0.36, C:0.17, G:0.16, T:0.31
Consensus pattern (196 bp):
ATATATATATACACATTCGTTTAAACATTTACCACCCATTGAACCAAATGAAATAACATCGAATA
CTCGGAAAAATGCTCACACAAGCTGTGACTGTAATTGTATATGCTCACACGAACTATAAAATGGG
CCTACTCACACGAGTTGTGGGCCAAGATGTTTATATATCATAAAAATTTAATATATATATATATA
T
Found at i:38407692 original size:173 final size:173
Alignment explanation
Indices: 38407403--38407749 Score: 694
Period size: 173 Copynumber: 2.0 Consensus size: 173
38407393 CAAGAGATGA
38407403 AAGGGAAAGGTTGAAGAGCCTTTCCTTTATGCAAAAACTAATAAGAAATGAATCAGCGAGACAAC
1 AAGGGAAAGGTTGAAGAGCCTTTCCTTTATGCAAAAACTAATAAGAAATGAATCAGCGAGACAAC
38407468 CCAACAACCACTCAGTACATCGAAGAATAATAAAAGAGAATCGCTGTGAATGACGATATTTAAGG
66 CCAACAACCACTCAGTACATCGAAGAATAATAAAAGAGAATCGCTGTGAATGACGATATTTAAGG
38407533 AGCGCAAATATATTCGGTAGCGACTCTTCTTCCACAATTATTG
131 AGCGCAAATATATTCGGTAGCGACTCTTCTTCCACAATTATTG
38407576 AAGGGAAAGGTTGAAGAGCCTTTCCTTTATGCAAAAACTAATAAGAAATGAATCAGCGAGACAAC
1 AAGGGAAAGGTTGAAGAGCCTTTCCTTTATGCAAAAACTAATAAGAAATGAATCAGCGAGACAAC
38407641 CCAACAACCACTCAGTACATCGAAGAATAATAAAAGAGAATCGCTGTGAATGACGATATTTAAGG
66 CCAACAACCACTCAGTACATCGAAGAATAATAAAAGAGAATCGCTGTGAATGACGATATTTAAGG
38407706 AGCGCAAATATATTCGGTAGCGACTCTTCTTCCACAATTATTG
131 AGCGCAAATATATTCGGTAGCGACTCTTCTTCCACAATTATTG
38407749 A
1 A
38407750 GTAAGAGACT
Statistics
Matches: 174, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
173 174 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.23
Consensus pattern (173 bp):
AAGGGAAAGGTTGAAGAGCCTTTCCTTTATGCAAAAACTAATAAGAAATGAATCAGCGAGACAAC
CCAACAACCACTCAGTACATCGAAGAATAATAAAAGAGAATCGCTGTGAATGACGATATTTAAGG
AGCGCAAATATATTCGGTAGCGACTCTTCTTCCACAATTATTG
Found at i:38413048 original size:46 final size:46
Alignment explanation
Indices: 38412981--38413075 Score: 163
Period size: 46 Copynumber: 2.1 Consensus size: 46
38412971 AGGTTAATAT
*
38412981 TTATTTATTTTTTTAGATAATTCTAAAGAGTTTTATTAGGATTCAA
1 TTATTTATTTTCTTAGATAATTCTAAAGAGTTTTATTAGGATTCAA
* *
38413027 TTATTTATTTTCTTAGATAATTTTAAAGAGTTTTATTAGGGTTCAA
1 TTATTTATTTTCTTAGATAATTCTAAAGAGTTTTATTAGGATTCAA
38413073 TTA
1 TTA
38413076 CTCTTGTCTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.32, C:0.04, G:0.12, T:0.53
Consensus pattern (46 bp):
TTATTTATTTTCTTAGATAATTCTAAAGAGTTTTATTAGGATTCAA
Found at i:38413575 original size:22 final size:22
Alignment explanation
Indices: 38413550--38413597 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
38413540 TCAAAAACAC
*
38413550 TTTTCATCGGTTTCGTCAATTT
1 TTTTCATCGGTTTCATCAATTT
*
38413572 TTTTCATCGGTTTCATCGATTT
1 TTTTCATCGGTTTCATCAATTT
38413594 TTTT
1 TTTT
38413598 TAAAAAAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.12, C:0.17, G:0.12, T:0.58
Consensus pattern (22 bp):
TTTTCATCGGTTTCATCAATTT
Found at i:38414248 original size:30 final size:31
Alignment explanation
Indices: 38414200--38414261 Score: 117
Period size: 30 Copynumber: 2.0 Consensus size: 31
38414190 AAGCGATGAA
38414200 AAAGTTGCAAACTCAATTCGAACATCGCATG
1 AAAGTTGCAAACTCAATTCGAACATCGCATG
38414231 AAAGTTGCAAA-TCAATTCGAACATCGCATG
1 AAAGTTGCAAACTCAATTCGAACATCGCATG
38414261 A
1 A
38414262 CCCAGATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 20 0.65
31 11 0.35
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (31 bp):
AAAGTTGCAAACTCAATTCGAACATCGCATG
Found at i:38422197 original size:3 final size:3
Alignment explanation
Indices: 38422185--38422245 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
38422175 AATGAAAACC
*
38422185 ATA A-A ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
38422232 ATA ATA ATA ATA AT
1 ATA ATA ATA ATA AT
38422246 GAAAGTCAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:38431935 original size:23 final size:23
Alignment explanation
Indices: 38431881--38431925 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
38431871 AATTTACTTC
38431881 AAATATATAAT--TTATATATTT
1 AAATATATAATGGTTATATATTT
38431902 AAATATATAATGGTTATAT-TTT
1 AAATATATAATGGTTATATATTT
38431924 AA
1 AA
38431926 TATTTTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 11 0.50
22 5 0.23
23 6 0.27
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
AAATATATAATGGTTATATATTT
Found at i:38432094 original size:22 final size:23
Alignment explanation
Indices: 38432066--38432113 Score: 71
Period size: 22 Copynumber: 2.1 Consensus size: 23
38432056 AGTTGATTGC
* *
38432066 ATTAAAGGATGAGAGG-TGAAGT
1 ATTAAAGGATGAAAGGAGGAAGT
38432088 ATTAAAGGATGAAAGGAGGAAGT
1 ATTAAAGGATGAAAGGAGGAAGT
38432111 ATT
1 ATT
38432114 TTCGAAACCT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.23
Consensus pattern (23 bp):
ATTAAAGGATGAAAGGAGGAAGT
Found at i:38433302 original size:26 final size:25
Alignment explanation
Indices: 38433247--38433302 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 25
38433237 TTTTAGGGAT
**
38433247 AATTTTTTAGAATTAAAATTCCGCC
1 AATTTTTTAGAATTAAAATTCAACC
* * *
38433272 TATTTTTTAGAATTCAAATTTAACTC
1 AATTTTTTAGAATTAAAATTCAAC-C
38433298 AATTT
1 AATTT
38433303 CTACCACATA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
25 19 0.79
26 5 0.21
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.46
Consensus pattern (25 bp):
AATTTTTTAGAATTAAAATTCAACC
Found at i:38434829 original size:1 final size:1
Alignment explanation
Indices: 38434825--38434855 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
38434815 ATAAAAACAT
38434825 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38434856 CAAGCTCTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:38440833 original size:25 final size:26
Alignment explanation
Indices: 38440805--38440862 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
38440795 AAAAAAAGAG
*
38440805 AAAATTTTAAAGAACATAAAA-GAAA
1 AAAATATTAAAGAACATAAAACGAAA
* ** *
38440830 AAAAAATTAAATTACTTAAAACGAAA
1 AAAATATTAAAGAACATAAAACGAAA
38440856 AAAATAT
1 AAAATAT
38440863 AGAAATCAAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.22
Consensus pattern (26 bp):
AAAATATTAAAGAACATAAAACGAAA
Found at i:38444785 original size:16 final size:18
Alignment explanation
Indices: 38444758--38444790 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38444748 TATAATTCGG
38444758 TTGAGAAAATT-ATTTAA
1 TTGAGAAAATTAATTTAA
38444775 TTGAG-AAATTAATTTA
1 TTGAGAAAATTAATTTA
38444791 TTTAGCAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (18 bp):
TTGAGAAAATTAATTTAA
Found at i:38446153 original size:28 final size:29
Alignment explanation
Indices: 38446100--38446155 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
38446090 CGCGAAAAAT
*
38446100 GGCCCATTCCGGTAAATAATTAAAAAACC
1 GGCCCATTCCAGTAAATAATTAAAAAACC
*
38446129 GGCCCATTTCAGTAAAT-ATTGAAAAAA
1 GGCCCATTCCAGTAAATAATT-AAAAAA
38446156 AGGGCTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.23
Consensus pattern (29 bp):
GGCCCATTCCAGTAAATAATTAAAAAACC
Found at i:38447604 original size:21 final size:20
Alignment explanation
Indices: 38447556--38447605 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
38447546 TTTTAAAATA
38447556 TTTTTAAAATTCTTTTTTAT
1 TTTTTAAAATTCTTTTTTAT
*
38447576 TTTTTAAAATT-TTTTTGTGT
1 TTTTTAAAATTCTTTTT-TAT
38447596 TTATTTAAAA
1 TT-TTTAAAA
38447606 AACGGGTTGG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 15 0.56
21 7 0.26
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (20 bp):
TTTTTAAAATTCTTTTTTAT
Found at i:38449697 original size:24 final size:24
Alignment explanation
Indices: 38449663--38449714 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
38449653 TTTCTAGAAG
*
38449663 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAGTATAATAT
*
38449687 ATTTAGCATTTATTAGTATAATTT
1 ATTTAGCATTTATTAGTATAATAT
38449711 ATTT
1 ATTT
38449715 GACCTATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.56
Consensus pattern (24 bp):
ATTTAGCATTTATTAGTATAATAT
Found at i:38450777 original size:25 final size:27
Alignment explanation
Indices: 38450744--38450793 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
38450734 ATTATGATAT
* *
38450744 GCAAGTAAAA-AT-AATAAGAGTCACA
1 GCAAATAAAAGATAAATAAAAGTCACA
38450769 GCAAATAAAAGATAAATAAAAGTCA
1 GCAAATAAAAGATAAATAAAAGTCA
38450794 AATTAATTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 9 0.43
26 2 0.10
27 10 0.48
ACGTcount: A:0.60, C:0.10, G:0.14, T:0.16
Consensus pattern (27 bp):
GCAAATAAAAGATAAATAAAAGTCACA
Found at i:38451221 original size:10 final size:10
Alignment explanation
Indices: 38451192--38451222 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
38451182 ATATGTAAGT
*
38451192 ATGTATATAT
1 ATGTATATAA
38451202 ATGTATATAA
1 ATGTATATAA
38451212 ATGTATATAA
1 ATGTATATAA
38451222 A
1 A
38451223 AATTATGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.48, C:0.00, G:0.10, T:0.42
Consensus pattern (10 bp):
ATGTATATAA
Found at i:38451320 original size:33 final size:33
Alignment explanation
Indices: 38451256--38451321 Score: 91
Period size: 33 Copynumber: 2.0 Consensus size: 33
38451246 AAAAAATATA
*
38451256 TAAAAATATGTGTATATATATTTTTACAAAAGT
1 TAAAAATATGTGTATATATATTTATACAAAAGT
38451289 TAAAAATATGTACGTATATATA-TTATA-AAAAGT
1 TAAAAATATGT--GTATATATATTTATACAAAAGT
38451322 ATGTATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 17 0.57
34 4 0.13
35 9 0.30
ACGTcount: A:0.48, C:0.03, G:0.09, T:0.39
Consensus pattern (33 bp):
TAAAAATATGTGTATATATATTTATACAAAAGT
Found at i:38451328 original size:18 final size:18
Alignment explanation
Indices: 38451302--38451342 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
38451292 AAATATGTAC
38451302 GTATATATATTATAAAAA
1 GTATATATATTATAAAAA
*
38451320 GTATGTATATTATAAAAA
1 GTATATATATTATAAAAA
38451338 -TATAT
1 GTATAT
38451343 GCATGTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.41
Consensus pattern (18 bp):
GTATATATATTATAAAAA
Found at i:38451471 original size:26 final size:27
Alignment explanation
Indices: 38451420--38451471 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
38451410 TAATAAGGTA
*
38451420 AGTAATAATAAATACAATAATAGTAAT
1 AGTAATAATAAATAAAATAATAGTAAT
*
38451447 AGTAATATTAAA-AAAATAATAGTAA
1 AGTAATAATAAATAAAATAATAGTAA
38451472 AAATAATGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.29
Consensus pattern (27 bp):
AGTAATAATAAATAAAATAATAGTAAT
Found at i:38452125 original size:2 final size:2
Alignment explanation
Indices: 38452120--38452160 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
38452110 TATATATATA
38452120 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
38452161 ACGATTAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:38452549 original size:13 final size:13
Alignment explanation
Indices: 38452531--38452557 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
38452521 TTTTCTGATT
38452531 TGATGCTTTGGGC
1 TGATGCTTTGGGC
38452544 TGATGCTTTGGGC
1 TGATGCTTTGGGC
38452557 T
1 T
38452558 ATTAGGGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.15, G:0.37, T:0.41
Consensus pattern (13 bp):
TGATGCTTTGGGC
Found at i:38463517 original size:1 final size:1
Alignment explanation
Indices: 38463513--38463538 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
38463503 AAATTTTTCC
38463513 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
38463539 GCCAATATGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:38463570 original size:100 final size:102
Alignment explanation
Indices: 38463371--38463572 Score: 347
Period size: 100 Copynumber: 2.0 Consensus size: 102
38463361 TAAGATATAA
*
38463371 AGAGTGATCAACTTTTCTCCACAAAACAGGCAAATTTTTCCTCTTTTTTCTTTTTTTTTTTTTTT
1 AGAGGGATCAACTTTTCTCCACAAAACAGGCAAATTTTTCCTCTTTTTTCTTTTTTTTTTTTTTT
*
38463436 TTTTTCAATATGCAGAGTTTGTCTATGGTCTCAAGTT
66 TTTTCCAATATGCAGAGTTTGTCTATGGTCTCAAGTT
*
38463473 AGAGGGATC-ACTTTTCTCCCCAAAACAGGCAAATTTTTCCT-TTTTTT-TTTTTTTTTTTTTTT
1 AGAGGGATCAACTTTTCTCCACAAAACAGGCAAATTTTTCCTCTTTTTTCTTTTTTTTTTTTTTT
38463535 TTTTGCCAATATGCAGAGTTTGTCTATGGTCTCAAGTT
66 TTTT-CCAATATGCAGAGTTTGTCTATGGTCTCAAGTT
38463573 TGTTGATGAA
Statistics
Matches: 96, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
99 19 0.20
100 38 0.40
101 31 0.32
102 8 0.08
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.50
Consensus pattern (102 bp):
AGAGGGATCAACTTTTCTCCACAAAACAGGCAAATTTTTCCTCTTTTTTCTTTTTTTTTTTTTTT
TTTTCCAATATGCAGAGTTTGTCTATGGTCTCAAGTT
Found at i:38463640 original size:12 final size:13
Alignment explanation
Indices: 38463618--38463654 Score: 58
Period size: 12 Copynumber: 2.9 Consensus size: 13
38463608 TTTGATATTG
38463618 TTCTCTTTTTTTT
1 TTCTCTTTTTTTT
38463631 TTCT-TTTTTTTT
1 TTCTCTTTTTTTT
*
38463643 TTCCCTTTTTTT
1 TTCTCTTTTTTT
38463655 ACTATTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
TTCTCTTTTTTTT
Found at i:38465589 original size:15 final size:16
Alignment explanation
Indices: 38465569--38465606 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
38465559 GAAAAATTAT
38465569 AAACTAAATAAATA-A
1 AAACTAAATAAATACA
38465584 AAACT-AATAAATACA
1 AAACTAAATAAATACA
*
38465599 TAACTAAA
1 AAACTAAA
38465607 AGGTAACACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 8 0.40
15 10 0.50
16 2 0.10
ACGTcount: A:0.68, C:0.11, G:0.00, T:0.21
Consensus pattern (16 bp):
AAACTAAATAAATACA
Found at i:38466349 original size:20 final size:20
Alignment explanation
Indices: 38466320--38466360 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 20
38466310 TGACTATCTT
38466320 AGTAAAAAATTCC-ACAAAA
1 AGTAAAAAATTCCAACAAAA
38466339 AGTACAAAAATTCCAACAAAA
1 AGTA-AAAAATTCCAACAAAA
38466360 A
1 A
38466361 AAAAAGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 4 0.20
20 9 0.45
21 7 0.35
ACGTcount: A:0.63, C:0.17, G:0.05, T:0.15
Consensus pattern (20 bp):
AGTAAAAAATTCCAACAAAA
Found at i:38466981 original size:52 final size:52
Alignment explanation
Indices: 38466922--38467091 Score: 331
Period size: 52 Copynumber: 3.3 Consensus size: 52
38466912 AAATTATTTA
*
38466922 TATTTAAAAAATCTCTATATTTTTAAAAAAAATAGTTTCTTTCTATATAAAT
1 TATTTAAAAAATCTCTATATTTTTTAAAAAAATAGTTTCTTTCTATATAAAT
38466974 TATTTAAAAAATCTCTATATTTTTTAAAAAAATAGTTTCTTTCTATATAAAT
1 TATTTAAAAAATCTCTATATTTTTTAAAAAAATAGTTTCTTTCTATATAAAT
38467026 TATTTAAAAAATCTCTATATTTTTTAAAAAAATAGTTTCTTTCTATATAAAT
1 TATTTAAAAAATCTCTATATTTTTTAAAAAAATAGTTTCTTTCTATATAAAT
38467078 TATTTAAAAAATCT
1 TATTTAAAAAATCT
38467092 NNNNNNNNNA
Statistics
Matches: 117, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 117 1.00
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.47
Consensus pattern (52 bp):
TATTTAAAAAATCTCTATATTTTTTAAAAAAATAGTTTCTTTCTATATAAAT
Found at i:38466990 original size:24 final size:24
Alignment explanation
Indices: 38466963--38467045 Score: 66
Period size: 24 Copynumber: 3.3 Consensus size: 24
38466953 ATAGTTTCTT
38466963 TCTATATAAATTATTTAAAAAATC
1 TCTATATAAATTATTTAAAAAATC
38466987 TCTATAT---TT-TTTAAAAAAATAGTTTC
1 TCTATATAAATTATTT--AAAAA-A---TC
38467013 TTTCTATATAAATTATTTAAAAAATC
1 --TCTATATAAATTATTTAAAAAATC
38467039 TCTATAT
1 TCTATAT
38467046 TTTTTAAAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 24
0.66 0.00 0.34
Matches are distributed among these distances:
20 3 0.06
21 2 0.04
22 5 0.11
23 1 0.02
24 14 0.30
26 4 0.09
28 7 0.15
29 1 0.02
30 5 0.11
31 2 0.04
32 3 0.06
ACGTcount: A:0.43, C:0.08, G:0.01, T:0.47
Consensus pattern (24 bp):
TCTATATAAATTATTTAAAAAATC
Found at i:38469619 original size:21 final size:21
Alignment explanation
Indices: 38469595--38469635 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
38469585 TTATGTGTTA
38469595 ACCTCTTGGAA-TACAGTGCAG
1 ACCT-TTGGAATTACAGTGCAG
38469616 ACCTTTGGAATTTACAGTGC
1 ACCTTTGGAA-TTACAGTGC
38469636 TATAGATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 4 0.22
22 8 0.44
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (21 bp):
ACCTTTGGAATTACAGTGCAG
Found at i:38469953 original size:27 final size:27
Alignment explanation
Indices: 38469915--38469991 Score: 120
Period size: 27 Copynumber: 2.9 Consensus size: 27
38469905 TAGTATTGGC
38469915 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
38469942 GCCTACCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
38469969 GCC-ATTCTGAGAGGCGCCAATGG
1 GCCTA-TCTGGGAGGCGCCAATGG
38469992 GCCGGGCCGG
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.17, C:0.25, G:0.39, T:0.19
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:38475264 original size:4 final size:4
Alignment explanation
Indices: 38475257--38475300 Score: 52
Period size: 4 Copynumber: 10.5 Consensus size: 4
38475247 TAGTATTAGA
* *
38475257 ATTT ATTT ATAT ATTTT ATTT ATTT ATTT ATAT ATTTT ATTT AT
1 ATTT ATTT ATTT A-TTT ATTT ATTT ATTT ATTT A-TTT ATTT AT
38475301 AATATATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
4 28 0.82
5 6 0.18
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:38475276 original size:13 final size:13
Alignment explanation
Indices: 38475258--38475345 Score: 54
Period size: 13 Copynumber: 7.5 Consensus size: 13
38475248 AGTATTAGAA
38475258 TTTATTTATATAT
1 TTTATTTATATAT
38475271 TTTA--T-T-TA-
1 TTTATTTATATAT
38475279 TTTATTTATATAT
1 TTTATTTATATAT
38475292 TTTATTTATA-A-
1 TTTATTTATATAT
* * *
38475303 TATATTAAAATAT
1 TTTATTTATATAT
*
38475316 TATA-TTA-ATA-
1 TTTATTTATATAT
38475326 -TTATTTATATAT
1 TTTATTTATATAT
38475338 TTCTATTT
1 TT-TATTT
38475346 CATTTGCATT
Statistics
Matches: 58, Mismatches: 5, Indels: 23
0.67 0.06 0.27
Matches are distributed among these distances:
8 4 0.07
9 4 0.07
10 5 0.09
11 15 0.26
12 6 0.10
13 19 0.33
14 5 0.09
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATTTATATAT
Found at i:38475305 original size:16 final size:17
Alignment explanation
Indices: 38475275--38475308 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
38475265 ATATATTTTA
*
38475275 TTTATTTATTTATATAT
1 TTTATTTATTAATATAT
38475292 TTTATTTA-TAATATAT
1 TTTATTTATTAATATAT
38475308 T
1 T
38475309 AAAATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTATTTATTAATATAT
Found at i:38475344 original size:17 final size:16
Alignment explanation
Indices: 38475259--38475344 Score: 50
Period size: 17 Copynumber: 5.1 Consensus size: 16
38475249 GTATTAGAAT
38475259 TTATTTATATATTTTA
1 TTATTTATATATTTTA
*
38475275 TTTATTTATTTATATATT-
1 -TTATTTA--TATATTTTA
*
38475293 TTATTTATAATATATTA
1 TTATTTAT-ATATTTTA
** **
38475310 AAATATTATAT-TAATA
1 TTAT-TTATATATTTTA
38475326 TTATTTATATATTTCTA
1 TTATTTATATATTT-TA
38475343 TT
1 TT
38475345 TCATTTGCAT
Statistics
Matches: 54, Mismatches: 8, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
15 7 0.13
16 14 0.26
17 22 0.41
18 4 0.07
19 7 0.13
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (16 bp):
TTATTTATATATTTTA
Found at i:38478521 original size:17 final size:16
Alignment explanation
Indices: 38478499--38478532 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
38478489 TTAATTAAGC
38478499 TTAGGTAATTATATTAA
1 TTAGGT-ATTATATTAA
*
38478516 TTAGGTTTTATATTAA
1 TTAGGTATTATATTAA
38478532 T
1 T
38478533 AATTTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (16 bp):
TTAGGTATTATATTAA
Found at i:38483785 original size:22 final size:20
Alignment explanation
Indices: 38483733--38483785 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
38483723 AAAATGTATG
38483733 AAATTATTAAATATTAAAAAA
1 AAATT-TTAAATATTAAAAAA
*
38483754 ACAA-TATAAATATTTTAAAAAA
1 A-AATTTTAAATA--TTAAAAAA
38483776 AAATTTTAAA
1 AAATTTTAAA
38483786 AATAATATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
20 6 0.23
21 4 0.15
22 16 0.62
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTTTAAATATTAAAAAA
Found at i:38486002 original size:22 final size:20
Alignment explanation
Indices: 38485950--38486002 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
38485940 AAAATGTATG
38485950 AAATTATTAAATATTAAAAAA
1 AAATT-TTAAATATTAAAAAA
*
38485971 ACAA-TATAAATATTTTAAAAAA
1 A-AATTTTAAATA--TTAAAAAA
38485993 AAATTTTAAA
1 AAATTTTAAA
38486003 AATAATATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
20 6 0.23
21 4 0.15
22 16 0.62
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTTTAAATATTAAAAAA
Found at i:38487687 original size:456 final size:455
Alignment explanation
Indices: 38486830--38487727 Score: 1760
Period size: 456 Copynumber: 2.0 Consensus size: 455
38486820 AAGCTGAGTT
38486830 TTGTTTACTATAGGGAGGTAAGGTTTTCTTCTTTTAGCTTCGTTTTTTAACCAAACGTCGAACTC
1 TTGTTTACTATAGGGAGGTAAGGTTTTCTTCTTTTAGCTTCGTTTTTTAACCAAACGTCGAACTC
*
38486895 TGTTGATAGTAACTTTAAACTGGTTTACGCTTGTGAAAAAAATGGTCTCTGTACCTTATAGATTT
66 TGTTGATAGTAACTTTAAACTGGTTTACGCTTGTGAAAAAAATGGTCTCTGTACCTTATAGATCT
38486960 ATGTTTTCTTGATTGCCACTGATTGTTTTAGAGTCTAGAGTTGCAATGATTTTGTCTCATTAATT
131 ATGTTTTCTTGATTGCCACTGATTGTTTTAGAGTCTAGAGTTGCAATGATTTTGTCTCATTAATT
38487025 TTTTTTCCAAATTTCTTGATTTTCCTTTAAAATCTGGTTGTTCTCTATAATAAATTGTGCAAGTG
196 TTTTTTCCAAATTTCTTGATTTTCCTTTAAAATCTGGTTGTTCTCTATAATAAATTGTGCAAGTG
38487090 ACGATAAAGATAGACAGGGACATCAGTACCCATTGGAGGATGATGAGTTGTCTAAAATGGGAATC
261 ACGATAAAGATAGACAGGGACATCAGTACCCATTGGAGGATGATGAGTTGTCTAAAATGGGAATC
38487155 TCTCTGATGCACAAAACTAATTGGTTTTATTTCATGCATGAGTTTCTTTTTCATGATTTGATAAA
326 TCTCTGATGCACAAAACTAATTGGTTTTATTTCATGCATGAGTTTCTTTTTCATGATTTGATAAA
*
38487220 ATTTGTACAAAATTTTAGATGAAAGGTTTCTAAGGAGTATTTTGGTGTATGCACAAAACTAATCC
391 ATTTATACAAAATTTTAGATGAAAGGTTTCTAAGGAGTATTTTGGTGTATGCACAAAACTAATCC
38487285 TTGTTTACTATAGGGAGGTAAGGTTTTCTTCTTTTAGCTTCGTTTTTTAACCAAACGTCGAACTC
1 TTGTTTACTATAGGGAGGTAAGGTTTTCTTCTTTTAGCTTCGTTTTTTAACCAAACGTCGAACTC
38487350 TGTTGATAGTAACTTTAAACTGGTTTACGCTTGTGAAAAAAATGGTCTCTGTACCTTATAGATCT
66 TGTTGATAGTAACTTTAAACTGGTTTACGCTTGTGAAAAAAATGGTCTCTGTACCTTATAGATCT
38487415 ATGTTTTCTTGATTGCCACTGATTGTTTTAGAGTCTAGAGTTGCAATGATTTTGTCTCATTAATT
131 ATGTTTTCTTGATTGCCACTGATTGTTTTAGAGTCTAGAGTTGCAATGATTTTGTCTCATTAA-T
*
38487480 TTTTTTTCCAAATTTCTTGTTTTTCCTTTAAAATCTGGTTGTTCTCTATAATAAATTGTGCAAGT
195 TTTTTTTCCAAATTTCTTGATTTTCCTTTAAAATCTGGTTGTTCTCTATAATAAATTGTGCAAGT
38487545 GACGATAAAGATAGACAGGGACATCAGTACCCATTGGAGGATGATGAGTTGTCTAAAATGGGAAT
260 GACGATAAAGATAGACAGGGACATCAGTACCCATTGGAGGATGATGAGTTGTCTAAAATGGGAAT
38487610 CTCTCTGATGCACAAAACTAATTGGTTTTATTTCATGCATGAGTTTCTTTTTCATGATTTGATAA
325 CTCTCTGATGCACAAAACTAATTGGTTTTATTTCATGCATGAGTTTCTTTTTCATGATTTGATAA
38487675 AATTTATACAAAATTTTAGATGAAAGGTTTCTAAGGAGTATTTTGGTGTATGC
390 AATTTATACAAAATTTTAGATGAAAGGTTTCTAAGGAGTATTTTGGTGTATGC
38487728 TTAATCCATT
Statistics
Matches: 439, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
455 192 0.44
456 247 0.56
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (455 bp):
TTGTTTACTATAGGGAGGTAAGGTTTTCTTCTTTTAGCTTCGTTTTTTAACCAAACGTCGAACTC
TGTTGATAGTAACTTTAAACTGGTTTACGCTTGTGAAAAAAATGGTCTCTGTACCTTATAGATCT
ATGTTTTCTTGATTGCCACTGATTGTTTTAGAGTCTAGAGTTGCAATGATTTTGTCTCATTAATT
TTTTTTCCAAATTTCTTGATTTTCCTTTAAAATCTGGTTGTTCTCTATAATAAATTGTGCAAGTG
ACGATAAAGATAGACAGGGACATCAGTACCCATTGGAGGATGATGAGTTGTCTAAAATGGGAATC
TCTCTGATGCACAAAACTAATTGGTTTTATTTCATGCATGAGTTTCTTTTTCATGATTTGATAAA
ATTTATACAAAATTTTAGATGAAAGGTTTCTAAGGAGTATTTTGGTGTATGCACAAAACTAATCC
Found at i:38490921 original size:77 final size:80
Alignment explanation
Indices: 38490788--38490941 Score: 224
Period size: 77 Copynumber: 1.9 Consensus size: 80
38490778 ATGATTATTG
* *
38490788 TTATTGTTATTTAAAATTTAATAAGATTATTAATATTAATATTAATAATAAATAATTTAATTATA
1 TTATTGTTATTTAAAATTTAATAAG--TATT-ATATTAATATCAATAATAAATAATTTAATCATA
*
38490853 TTTAAATATAATAATTAA
63 TTTAAACATAATAATTAA
*
38490871 TTATTGTTATTTAAATTTTAATAAG-A-T-TATTAATATCAATAATAAATAATTTAATCATATTT
1 TTATTGTTATTTAAAATTTAATAAGTATTATATTAATATCAATAATAAATAATTTAATCATATTT
38490933 AAACATAAT
66 AAACATAAT
38490942 TTTTATTAAA
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
77 41 0.61
79 1 0.01
80 1 0.01
83 24 0.36
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (80 bp):
TTATTGTTATTTAAAATTTAATAAGTATTATATTAATATCAATAATAAATAATTTAATCATATTT
AAACATAATAATTAA
Found at i:38498646 original size:32 final size:31
Alignment explanation
Indices: 38498593--38498652 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
38498583 TAAAAAAAAG
* * *
38498593 TAAATTAACTAAAATTTAAAAATTAAAAGGT
1 TAAATTAACTAAAAATAAAAAATAAAAAGGT
*
38498624 TAAATTATTCTAAAAATAAAAAATAAAAA
1 TAAATTA-ACTAAAAATAAAAAATAAAAA
38498653 TAGTAAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 7 0.29
32 17 0.71
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (31 bp):
TAAATTAACTAAAAATAAAAAATAAAAAGGT
Found at i:38507800 original size:50 final size:50
Alignment explanation
Indices: 38507742--38507844 Score: 170
Period size: 50 Copynumber: 2.1 Consensus size: 50
38507732 AGTAGGATTG
* *
38507742 TTTCCGAACTACGTTAACAAACGATTGTGTGCAAATCTCTTCTTACCTTC
1 TTTCCGAACTACGTTAACAAACAATTGTGTGCAAATCTCTTCTTACCTAC
* *
38507792 TTTCCGAACTACGTTGACAAACAATTGTGTGCAAATCTTTTCTTACCTAC
1 TTTCCGAACTACGTTAACAAACAATTGTGTGCAAATCTCTTCTTACCTAC
38507842 TTT
1 TTT
38507845 GATTTTCGTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.26, C:0.24, G:0.12, T:0.38
Consensus pattern (50 bp):
TTTCCGAACTACGTTAACAAACAATTGTGTGCAAATCTCTTCTTACCTAC
Found at i:38510567 original size:14 final size:14
Alignment explanation
Indices: 38510538--38510566 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
38510528 CAATATTTAC
38510538 TTATTTTGAAATTT
1 TTATTTTGAAATTT
38510552 TTATTTT-AAATTT
1 TTATTTTGAAATTT
38510565 TT
1 TT
38510567 TTCTCAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (14 bp):
TTATTTTGAAATTT
Found at i:38512551 original size:948 final size:948
Alignment explanation
Indices: 38510830--38512728 Score: 3798
Period size: 948 Copynumber: 2.0 Consensus size: 948
38510820 ACAAATTTAT
38510830 AAAACATTATAGGACTAGAAAATTGATTTTTAAGTAATTGTTTTCTCATTTTATTATAATTTTTT
1 AAAACATTATAGGACTAGAAAATTGATTTTTAAGTAATTGTTTTCTCATTTTATTATAATTTTTT
38510895 AATATTGCTTTTTGGAAAAGAAATTTAATTGGTGATGAATAGCAGAAGAAATTAATATGAAAATT
66 AATATTGCTTTTTGGAAAAGAAATTTAATTGGTGATGAATAGCAGAAGAAATTAATATGAAAATT
38510960 CAAAAATCATGTTATACATAAAAGGCAAATCAACATGTAATTTTGGACATAGAAATGATTATAGG
131 CAAAAATCATGTTATACATAAAAGGCAAATCAACATGTAATTTTGGACATAGAAATGATTATAGG
38511025 CTGAGTTAACTATAAGTCTGCTTCGTGTCATTTTAATAACTATGCCAACAAAACTAATATATCAT
196 CTGAGTTAACTATAAGTCTGCTTCGTGTCATTTTAATAACTATGCCAACAAAACTAATATATCAT
38511090 TTTATTATCCTGATTTCGATAAAAGAAATTGCTACCAAACATAACCAAAGCCAAGTCATACCGAC
261 TTTATTATCCTGATTTCGATAAAAGAAATTGCTACCAAACATAACCAAAGCCAAGTCATACCGAC
38511155 AAAAAACCTGAACCCAGATAAAATGTCGGAGAGAATGCCACTATCATGGGCATAGATCTCATTGT
326 AAAAAACCTGAACCCAGATAAAATGTCGGAGAGAATGCCACTATCATGGGCATAGATCTCATTGT
38511220 CAAACGTTAGCCACCAAGACAGAATAAGTGAAATGATGTGTTTTAACAGCTATCAACGATCTTGT
391 CAAACGTTAGCCACCAAGACAGAATAAGTGAAATGATGTGTTTTAACAGCTATCAACGATCTTGT
38511285 TGAATCCATTTGATCAGACGTAGACAAAAAGAATTGATAAAGCCACAAGAGATTCGAGAAAAACG
456 TGAATCCATTTGATCAGACGTAGACAAAAAGAATTGATAAAGCCACAAGAGATTCGAGAAAAACG
38511350 AGTAACCGTGAAACTAGAAGAACATGAGTCATTCCCCAAAGGAAAAACCGTTAGTTTCATTATTA
521 AGTAACCGTGAAACTAGAAGAACATGAGTCATTCCCCAAAGGAAAAACCGTTAGTTTCATTATTA
38511415 TTCTGAGCAGTCCACTTAATTTGAAAAAGGATAGTCGATAAGGGTGGCAGGGGATAAAAGGATGA
586 TTCTGAGCAGTCCACTTAATTTGAAAAAGGATAGTCGATAAGGGTGGCAGGGGATAAAAGGATGA
38511480 AAGGTTAAGGAGGTGGGTGATGAAATAAGAGGAAGTCAAGGAAAGAAAAGATGAGTGGGGAGAAG
651 AAGGTTAAGGAGGTGGGTGATGAAATAAGAGGAAGTCAAGGAAAGAAAAGATGAGTGGGGAGAAG
38511545 GAGGAGGTCGACAAGGAGGTGGCGTTGAAACAAGCTCCAACGTCTCTCCAGCAAAAAGGAGGAAA
716 GAGGAGGTCGACAAGGAGGTGGCGTTGAAACAAGCTCCAACGTCTCTCCAGCAAAAAGGAGGAAA
38511610 GGCACAAAGAAAAATAAATTTTTAATAAATTTTCAAACATAAATAATTAACATATTTTTTTTAAT
781 GGCACAAAGAAAAATAAATTTTTAATAAATTTTCAAACATAAATAATTAACATATTTTTTTTAAT
38511675 ATTTACATTATATTTAGTTTTCATATTTATTATAAATTAGAAAATGAATGGCATTATACTCGAGC
846 ATTTACATTATATTTAGTTTTCATATTTATTATAAATTAGAAAATGAATGGCATTATACTCGAGC
38511740 TTTAACTATCGAAACTCAAACTCGAAGAATATAAAAAG
911 TTTAACTATCGAAACTCAAACTCGAAGAATATAAAAAG
38511778 AAAACATTATAGGACTAGAAAATTGATTTTTAAGTAATTGTTTTCTCATTTTATTATAATTTTTT
1 AAAACATTATAGGACTAGAAAATTGATTTTTAAGTAATTGTTTTCTCATTTTATTATAATTTTTT
38511843 AATATTGCTTTTTGGAAAAGAAATTTAATTGGTGATGAATAGCAGAAGAAATTAATATGAAAATT
66 AATATTGCTTTTTGGAAAAGAAATTTAATTGGTGATGAATAGCAGAAGAAATTAATATGAAAATT
38511908 CAAAAATCATGTTATACATAAAAGGCAAATCAACATGTAATTTTGGACATAGAAATGATTATAGG
131 CAAAAATCATGTTATACATAAAAGGCAAATCAACATGTAATTTTGGACATAGAAATGATTATAGG
38511973 CTGAGTTAACTATAAGTCTGCTTCGTGTCATTTTAATAACTATGCCAACAAAACTAATATATCAT
196 CTGAGTTAACTATAAGTCTGCTTCGTGTCATTTTAATAACTATGCCAACAAAACTAATATATCAT
38512038 TTTATTATCCTGATTTCGATAAAAGAAATTGCTACCAAACATAACCAAAGCCAAGTCATACCGAC
261 TTTATTATCCTGATTTCGATAAAAGAAATTGCTACCAAACATAACCAAAGCCAAGTCATACCGAC
38512103 AAAAAACCTGAACCCAGATAAAATGTCGGAGAGAATGCCACTATCATGGGCATAGATCTCATTGT
326 AAAAAACCTGAACCCAGATAAAATGTCGGAGAGAATGCCACTATCATGGGCATAGATCTCATTGT
38512168 CAAACGTTAGCCACCAAGACAGAATAAGTGAAATGATGTGTTTTAACAGCTATCAACGATCTTGT
391 CAAACGTTAGCCACCAAGACAGAATAAGTGAAATGATGTGTTTTAACAGCTATCAACGATCTTGT
38512233 TGAATCCATTTGATCAGACGTAGACAAAAAGAATTGATAAAGCCACAAGAGATTCGAGAAAAACG
456 TGAATCCATTTGATCAGACGTAGACAAAAAGAATTGATAAAGCCACAAGAGATTCGAGAAAAACG
38512298 AGTAACCGTGAAACTAGAAGAACATGAGTCATTCCCCAAAGGAAAAACCGTTAGTTTCATTATTA
521 AGTAACCGTGAAACTAGAAGAACATGAGTCATTCCCCAAAGGAAAAACCGTTAGTTTCATTATTA
38512363 TTCTGAGCAGTCCACTTAATTTGAAAAAGGATAGTCGATAAGGGTGGCAGGGGATAAAAGGATGA
586 TTCTGAGCAGTCCACTTAATTTGAAAAAGGATAGTCGATAAGGGTGGCAGGGGATAAAAGGATGA
38512428 AAGGTTAAGGAGGTGGGTGATGAAATAAGAGGAAGTCAAGGAAAGAAAAGATGAGTGGGGAGAAG
651 AAGGTTAAGGAGGTGGGTGATGAAATAAGAGGAAGTCAAGGAAAGAAAAGATGAGTGGGGAGAAG
38512493 GAGGAGGTCGACAAGGAGGTGGCGTTGAAACAAGCTCCAACGTCTCTCCAGCAAAAAGGAGGAAA
716 GAGGAGGTCGACAAGGAGGTGGCGTTGAAACAAGCTCCAACGTCTCTCCAGCAAAAAGGAGGAAA
38512558 GGCACAAAGAAAAATAAATTTTTAATAAATTTTCAAACATAAATAATTAACATATTTTTTTTAAT
781 GGCACAAAGAAAAATAAATTTTTAATAAATTTTCAAACATAAATAATTAACATATTTTTTTTAAT
38512623 ATTTACATTATATTTAGTTTTCATATTTATTATAAATTAGAAAATGAATGGCATTATACTCGAGC
846 ATTTACATTATATTTAGTTTTCATATTTATTATAAATTAGAAAATGAATGGCATTATACTCGAGC
38512688 TTTAACTATCGAAACTCAAACTCGAAGAATATAAAAAG
911 TTTAACTATCGAAACTCAAACTCGAAGAATATAAAAAG
38512726 AAA
1 AAA
38512729 GGCTTAGTTT
Statistics
Matches: 951, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
948 951 1.00
ACGTcount: A:0.41, C:0.13, G:0.18, T:0.28
Consensus pattern (948 bp):
AAAACATTATAGGACTAGAAAATTGATTTTTAAGTAATTGTTTTCTCATTTTATTATAATTTTTT
AATATTGCTTTTTGGAAAAGAAATTTAATTGGTGATGAATAGCAGAAGAAATTAATATGAAAATT
CAAAAATCATGTTATACATAAAAGGCAAATCAACATGTAATTTTGGACATAGAAATGATTATAGG
CTGAGTTAACTATAAGTCTGCTTCGTGTCATTTTAATAACTATGCCAACAAAACTAATATATCAT
TTTATTATCCTGATTTCGATAAAAGAAATTGCTACCAAACATAACCAAAGCCAAGTCATACCGAC
AAAAAACCTGAACCCAGATAAAATGTCGGAGAGAATGCCACTATCATGGGCATAGATCTCATTGT
CAAACGTTAGCCACCAAGACAGAATAAGTGAAATGATGTGTTTTAACAGCTATCAACGATCTTGT
TGAATCCATTTGATCAGACGTAGACAAAAAGAATTGATAAAGCCACAAGAGATTCGAGAAAAACG
AGTAACCGTGAAACTAGAAGAACATGAGTCATTCCCCAAAGGAAAAACCGTTAGTTTCATTATTA
TTCTGAGCAGTCCACTTAATTTGAAAAAGGATAGTCGATAAGGGTGGCAGGGGATAAAAGGATGA
AAGGTTAAGGAGGTGGGTGATGAAATAAGAGGAAGTCAAGGAAAGAAAAGATGAGTGGGGAGAAG
GAGGAGGTCGACAAGGAGGTGGCGTTGAAACAAGCTCCAACGTCTCTCCAGCAAAAAGGAGGAAA
GGCACAAAGAAAAATAAATTTTTAATAAATTTTCAAACATAAATAATTAACATATTTTTTTTAAT
ATTTACATTATATTTAGTTTTCATATTTATTATAAATTAGAAAATGAATGGCATTATACTCGAGC
TTTAACTATCGAAACTCAAACTCGAAGAATATAAAAAG
Found at i:38520690 original size:13 final size:13
Alignment explanation
Indices: 38520669--38520717 Score: 53
Period size: 13 Copynumber: 3.7 Consensus size: 13
38520659 TTTAGCATTG
*
38520669 TATTATTATTATT
1 TATTTTTATTATT
*
38520682 TATTTTTATCATT
1 TATTTTTATTATT
* *
38520695 TATTTTCATTTTAT
1 TATTTTTATTAT-T
38520709 TATTTTTAT
1 TATTTTTAT
38520718 ATCCATATGC
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
13 20 0.69
14 9 0.31
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTTTTATTATT
Found at i:38520694 original size:27 final size:27
Alignment explanation
Indices: 38520651--38520717 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
38520641 AAGGTTTTTT
*
38520651 TTATATTA--TTTAGCATTGTATTATT-A
1 TTATATTATTTTTATCATT-TATT-TTCA
38520677 TTAT-TTATTTTTATCATTTATTTTCA
1 TTATATTATTTTTATCATTTATTTTCA
*
38520703 TTTTATTATTTTTAT
1 TTATATTATTTTTAT
38520718 ATCCATATGC
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
25 5 0.14
26 12 0.34
27 18 0.51
ACGTcount: A:0.25, C:0.04, G:0.03, T:0.67
Consensus pattern (27 bp):
TTATATTATTTTTATCATTTATTTTCA
Found at i:38520710 original size:37 final size:36
Alignment explanation
Indices: 38520648--38520717 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
38520638 AAAAAGGTTT
38520648 TTTTTATATTATTTAGCATTGTATTATTATTATTTA
1 TTTTTATATTATTTAGCATTGTATTATTATTATTTA
* * *
38520684 TTTTTATCATTTATTT-TCATTTTATTATTTTTAT
1 TTTTTAT-A-TTATTTAGCATTGTATTATTATTAT
38520718 ATCCATATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 7 0.24
37 16 0.55
38 6 0.21
ACGTcount: A:0.24, C:0.04, G:0.03, T:0.69
Consensus pattern (36 bp):
TTTTTATATTATTTAGCATTGTATTATTATTATTTA
Found at i:38520868 original size:94 final size:94
Alignment explanation
Indices: 38520759--38521218 Score: 893
Period size: 94 Copynumber: 4.9 Consensus size: 94
38520749 ATGTATGTAT
*
38520759 TGTTTTGTATATAATGCACGTATATTGGTACATATTTTATACATAGTTTATTATTTTATTTCATC
1 TGTTTTGTATATAATGCACGTATATTTGTACATATTTTATACATAGTTTATTATTTTATTTCATC
38520824 ACTTTTATATACATATATATATTTCTATA
66 ACTTTTATATACATATATATATTTCTATA
38520853 TGTTTTGTATATAATGCACGTATATTTGTACATATTTTATACATAGTTTATTATTTTATTTCATC
1 TGTTTTGTATATAATGCACGTATATTTGTACATATTTTATACATAGTTTATTATTTTATTTCATC
38520918 ACTTTTATATACATATATATATTTCTATA
66 ACTTTTATATACATATATATATTTCTATA
38520947 TGTTTTGTATATAATGCACGTATATTTGTACATATTTTATACATAGTTTATTATTTTATTTCATC
1 TGTTTTGTATATAATGCACGTATATTTGTACATATTTTATACATAGTTTATTATTTTATTTCATC
38521012 ACTTTTATATACATATATATATTTCTATA
66 ACTTTTATATACATATATATATTTCTATA
38521041 TGTTTTGTATATAATGCACGTATATTTGTACATATTTTATACATAGTTTATTATTTTATTTCATC
1 TGTTTTGTATATAATGCACGTATATTTGTACATATTTTATACATAGTTTATTATTTTATTTCATC
38521106 ACTTTTATATACATATATATATTTCTATA
66 ACTTTTATATACATATATATATTTCTATA
38521135 TGTTTTGTATATAATGCACGTATATTTGTACATATTTTATACATAGTTTATTATTTTATTTCATC
1 TGTTTTGTATATAATGCACGTATATTTGTACATATTTTATACATAGTTTATTATTTTATTTCATC
**
38521200 ACTAATATATACATATATA
66 ACTTTTATATACATATATA
38521219 CATATTTTTT
Statistics
Matches: 363, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
94 363 1.00
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (94 bp):
TGTTTTGTATATAATGCACGTATATTTGTACATATTTTATACATAGTTTATTATTTTATTTCATC
ACTTTTATATACATATATATATTTCTATA
Found at i:38522857 original size:31 final size:29
Alignment explanation
Indices: 38522822--38522893 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
38522812 CGGCTTAGTA
*
38522822 ACTAAAATGTTACAATACAATAACATAAGTG
1 ACTAAAATGTAACAATAC-A-AACATAAGTG
* * *
38522853 ACTAAAATGTAACATTTCAAATATAAGTG
1 ACTAAAATGTAACAATACAAACATAAGTG
38522882 ACTAAAATGTAA
1 ACTAAAATGTAA
38522894 TTTGAGGCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 21 0.57
30 1 0.03
31 15 0.41
ACGTcount: A:0.51, C:0.11, G:0.10, T:0.28
Consensus pattern (29 bp):
ACTAAAATGTAACAATACAAACATAAGTG
Found at i:38535481 original size:37 final size:37
Alignment explanation
Indices: 38535413--38535488 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 37
38535403 TATATTTTTT
*
38535413 ATTAAATTATATTTAATAATAATTATGTTAAAATATA
1 ATTAAATTATATTTAATAATAATTATATTAAAATATA
* *
38535450 ATTAAATTAT-TTATATTAATAATCT-TATTAAAATTTA
1 ATTAAATTATATT-TAATAATAAT-TATATTAAAATATA
38535487 AT
1 AT
38535489 AACAATAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 2 0.06
37 31 0.91
38 1 0.03
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (37 bp):
ATTAAATTATATTTAATAATAATTATATTAAAATATA
Found at i:38536594 original size:4 final size:4
Alignment explanation
Indices: 38536573--38536610 Score: 51
Period size: 4 Copynumber: 9.5 Consensus size: 4
38536563 TCAAAATAAT
*
38536573 AATA AA-A AAGTA AGTA AATA AATA AATA AATA AATA AA
1 AATA AATA AA-TA AATA AATA AATA AATA AATA AATA AA
38536611 GAAAATGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.83
5 2 0.07
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (4 bp):
AATA
Found at i:38536728 original size:51 final size:51
Alignment explanation
Indices: 38536643--38536777 Score: 141
Period size: 51 Copynumber: 2.6 Consensus size: 51
38536633 ATATAAAAAG
* * *
38536643 ATATATAAGTATGTACATATATGTATGTATATAAAAAT-TATAAAAAAATAT
1 ATATATAAGTATGTATATATAT-TATGAAAATAAAAATATATAAAAAAATAT
* * * *
38536694 ATATATAAGTATGTATATATATTCATGAAAATAAAAAATATGTATATAGATAT
1 ATATATAAGTATGTATATATATT-ATGAAAAT-AAAAATATATAAAAAAATAT
*
38536747 ATATAT-AGATATGTATATAAATTAT-AAAATA
1 ATATATAAG-TATGTATATATATTATGAAAATA
38536778 TAAGAAAAAA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
50 2 0.03
51 32 0.44
52 10 0.14
53 28 0.39
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (51 bp):
ATATATAAGTATGTATATATATTATGAAAATAAAAATATATAAAAAAATAT
Found at i:38536751 original size:12 final size:12
Alignment explanation
Indices: 38536731--38536765 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
38536721 AAAATAAAAA
38536731 ATATGTATATAG
1 ATATGTATATAG
*
38536743 ATATATATATAG
1 ATATGTATATAG
38536755 ATATGTATATA
1 ATATGTATATA
38536766 AATTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (12 bp):
ATATGTATATAG
Found at i:38536925 original size:35 final size:34
Alignment explanation
Indices: 38536885--38536977 Score: 91
Period size: 35 Copynumber: 2.7 Consensus size: 34
38536875 AGAAGTATGT
*
38536885 ATATGTACATATATATATATAAATA-AGTTATAAAA
1 ATATGTACGTATATATATATAAATATA-TTAT-AAA
* * * *
38536920 ATATGTATGTGTATATGTATATATATATTATAAA
1 ATATGTACGTATATATATATAAATATATTATAAA
*
38536954 A-ATGTACGTATAATGTATATAAAT
1 ATATGTACGTAT-ATATATATAAAT
38536978 TATGAAGTAT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
33 8 0.17
34 13 0.28
35 24 0.52
36 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (34 bp):
ATATGTACGTATATATATATAAATATATTATAAA
Found at i:38537810 original size:11 final size:10
Alignment explanation
Indices: 38537785--38537818 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
38537775 TAATATTTCG
*
38537785 AAAAAAATAA
1 AAAAAAACAA
38537795 AAAAAAACAA
1 AAAAAAACAA
38537805 AGAAAAAACAA
1 A-AAAAAACAA
38537816 AAA
1 AAA
38537819 TAAGAAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.88, C:0.06, G:0.03, T:0.03
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:38538306 original size:16 final size:16
Alignment explanation
Indices: 38538281--38538318 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
38538271 TTGAATTACT
*
38538281 ATTACGCCTCTATTCC
1 ATTACACCTCTATTCC
38538297 ATTACACCTCTATTCC
1 ATTACACCTCTATTCC
38538313 ATTACA
1 ATTACA
38538319 GCGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.26, C:0.34, G:0.03, T:0.37
Consensus pattern (16 bp):
ATTACACCTCTATTCC
Found at i:38544469 original size:59 final size:60
Alignment explanation
Indices: 38544382--38544500 Score: 222
Period size: 59 Copynumber: 2.0 Consensus size: 60
38544372 GAAATTTTGG
*
38544382 AATGTTTTTATATATTTAAAAAATTTTAATTTTGAATTTTAAATTGTTTATATTTTATAA
1 AATGTTTTTAAATATTTAAAAAATTTTAATTTTGAATTTTAAATTGTTTATATTTTATAA
38544442 AATGTTTTTAAAT-TTTAAAAAATTTTAATTTTGAATTTTAAATTGTTTATATTTTATAA
1 AATGTTTTTAAATATTTAAAAAATTTTAATTTTGAATTTTAAATTGTTTATATTTTATAA
38544501 TTTTTATTTT
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
59 46 0.79
60 12 0.21
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (60 bp):
AATGTTTTTAAATATTTAAAAAATTTTAATTTTGAATTTTAAATTGTTTATATTTTATAA
Found at i:38544497 original size:16 final size:15
Alignment explanation
Indices: 38544463--38544514 Score: 56
Period size: 16 Copynumber: 3.5 Consensus size: 15
38544453 ATTTTAAAAA
*
38544463 ATTTT-AATTTTGA-
1 ATTTTAAATTTTTAT
38544476 ATTTTAAATTGTTTAT
1 ATTTTAAATT-TTTAT
38544492 ATTTTATAATTTTTAT
1 ATTTTA-AATTTTTAT
38544508 -TTTTAAA
1 ATTTTAAA
38544515 AAATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
13 5 0.15
14 6 0.18
15 8 0.24
16 11 0.32
17 4 0.12
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (15 bp):
ATTTTAAATTTTTAT
Found at i:38544526 original size:59 final size:57
Alignment explanation
Indices: 38544385--38544518 Score: 202
Period size: 59 Copynumber: 2.4 Consensus size: 57
38544375 ATTTTGGAAT
*
38544385 GTTTTTATATATTTAAAAAATTTTAATTTTGAATTTTAAATTGTTTATATTTTATAAAA
1 GTTTTTAAAT-TTTAAAAAATTTTAATTTTGAATTTTAAATTGTTTATATTTTAT-AAA
38544444 TGTTTTTAAATTTTAAAAAATTTTAATTTTGAATTTTAAATTGTTTATATTTTAT-AA
1 -GTTTTTAAATTTTAAAAAATTTTAATTTTGAATTTTAAATTGTTTATATTTTATAAA
*
38544501 -TTTTT-ATTTTTAAAAAAT
1 GTTTTTAAATTTTAAAAAAT
38544519 ATGATTTTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
54 12 0.17
55 5 0.07
57 2 0.03
59 44 0.61
60 9 0.12
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (57 bp):
GTTTTTAAATTTTAAAAAATTTTAATTTTGAATTTTAAATTGTTTATATTTTATAAA
Found at i:38544541 original size:26 final size:24
Alignment explanation
Indices: 38544501--38544551 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 24
38544491 TATTTTATAA
*
38544501 TTTTTATTTTTAAAAAATATGATT
1 TTTTTATTTTTAAAAAATATAATT
38544525 TTTTTATATTTTAAAAAATTATAATT
1 TTTTTAT-TTTTAAAAAA-TATAATT
38544551 T
1 T
38544552 GAAAATTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 7 0.29
25 10 0.42
26 7 0.29
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTTTATTTTTAAAAAATATAATT
Found at i:38549636 original size:20 final size:18
Alignment explanation
Indices: 38549602--38549638 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
38549592 ATTGAATTAT
38549602 TCACAAGATTTATTTAAG
1 TCACAAGATTTATTTAAG
38549620 TCACTAAGATGTTATTTAA
1 TCAC-AAGAT-TTATTTAA
38549639 AAAAAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.41
Consensus pattern (18 bp):
TCACAAGATTTATTTAAG
Found at i:38558422 original size:2 final size:2
Alignment explanation
Indices: 38558415--38558444 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
38558405 GTAGGGACGT
38558415 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
38558445 TGGGACACTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38565155 original size:43 final size:43
Alignment explanation
Indices: 38565094--38565178 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
38565084 ATATCCAAGC
*
38565094 CAAGGGTGGCAACAATAGTTTAATTATATCGAGTGACCATAGT
1 CAAGGATGGCAACAATAGTTTAATTATATCGAGTGACCATAGT
* * *
38565137 CAAGGATGGCGACAATAGTTTAATTATATTGCGTGACCATAG
1 CAAGGATGGCAACAATAGTTTAATTATATCGAGTGACCATAG
38565179 GATAGACAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (43 bp):
CAAGGATGGCAACAATAGTTTAATTATATCGAGTGACCATAGT
Found at i:38577796 original size:12 final size:12
Alignment explanation
Indices: 38577773--38577807 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
38577763 GAACTTTCTT
38577773 TTTTTAATATATA
1 TTTTTAA-ATATA
38577786 TTTTTAAATATA
1 TTTTTAAATATA
38577798 TTTATTAAAT
1 TTT-TTAAAT
38577808 TACATTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTTAAATATA
Found at i:38578870 original size:22 final size:22
Alignment explanation
Indices: 38578812--38578870 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
38578802 CATTTATATC
*
38578812 ATAATTTCCAAAATTTAAATTT
1 ATAATTTCCATAATTTAAATTT
** * *
38578834 ATAA-ACCCCTGAATTTTAATTT
1 ATAATTTCCAT-AATTTAAATTT
38578856 ATAATTTCCATAATT
1 ATAATTTCCATAATT
38578871 AAGCCACCAA
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
21 2 0.07
22 22 0.81
23 3 0.11
ACGTcount: A:0.41, C:0.14, G:0.02, T:0.44
Consensus pattern (22 bp):
ATAATTTCCATAATTTAAATTT
Found at i:38583946 original size:20 final size:20
Alignment explanation
Indices: 38583913--38583983 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 20
38583903 AATATTTAAG
*
38583913 ATAATGCATAATAAAATAAA
1 ATAATACATAATAAAATAAA
*
38583933 ATAATACATGATAAAAGCATTACAAA
1 ATAATACATAAT-AAA--A-T--AAA
38583959 ATAATACATAATAAAATAAA
1 ATAATACATAATAAAATAAA
38583979 ATAAT
1 ATAAT
38583984 GTAAAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
20 18 0.43
21 3 0.07
22 1 0.02
23 2 0.05
24 1 0.02
25 3 0.07
26 14 0.33
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.25
Consensus pattern (20 bp):
ATAATACATAATAAAATAAA
Found at i:38584894 original size:12 final size:12
Alignment explanation
Indices: 38584877--38584901 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38584867 TTCAATCACC
38584877 TTTCAATATTTT
1 TTTCAATATTTT
38584889 TTTCAATATTTT
1 TTTCAATATTTT
38584901 T
1 T
38584902 CTTTGTACTG
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:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTCAATATTTT
Found at i:38585826 original size:18 final size:20
Alignment explanation
Indices: 38585799--38585845 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
38585789 TTCATTTATT
*
38585799 TATTTATTTATATGTC-CA-
1 TATTTTTTTATATGTCTCAG
38585817 TATTTTTTTA-ATGTCTCAG
1 TATTTTTTTATATGTCTCAG
38585836 T-TTTTTTTAT
1 TATTTTTTTAT
38585846 TTACTTGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
17 5 0.20
18 19 0.76
19 1 0.04
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.64
Consensus pattern (20 bp):
TATTTTTTTATATGTCTCAG
Found at i:38585939 original size:21 final size:20
Alignment explanation
Indices: 38585908--38585952 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
38585898 TTGCTCATAT
*
38585908 TATTTTTATTCATATTAT-CA
1 TATTTTTATTC-CATTATGCA
38585928 TATTTATTATTCCATTATGCA
1 TATTT-TTATTCCATTATGCA
38585949 TATT
1 TATT
38585953 AACACCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.29, C:0.11, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTTTTATTCCATTATGCA
Found at i:38586224 original size:107 final size:107
Alignment explanation
Indices: 38585980--38586310 Score: 443
Period size: 107 Copynumber: 3.1 Consensus size: 107
38585970 AAGGAAAATT
*
38585980 TTTCTAAA-TAAGGCAATGTTTTGCGTTTGGAAGTTCGAGAAAACGTGCCCTAATGTGCTGGGTT
1 TTTC-AAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTT
** * *
38586044 TCGATTTTTTTTGTTCGACCAAATAGCCAAATATCCTTTTAAAA
65 TCGA-TTTTTCCGTCCGACCAAATAGCCAAATATCATTTTAAAA
* * * * *
38586088 TTTTAAAGTAAGGAAATGTTTTGCATTTGGAAATTCGAGAAAACATGCCCTAATGTGCTAGGTTT
1 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
*
38586153 CGATTTTTCCGTCCGACCATATAGCCAAATATCATTTTAAAA
66 CGATTTTTCCGTCCGACCAAATAGCCAAATATCATTTTAAAA
*
38586195 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATATGCTGGGTTT
1 TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
* ** * * * *
38586260 CGATTTCT-CGT-TTAGCCAAATAGCCAAATACCCTCTTAAAG
66 CGATTTTTCCGTCCGA-CCAAATAGCCAAATATCATTTTAAAA
38586301 TTTCAAAGTA
1 TTTCAAAGTA
38586311 TGGGTTTTGG
Statistics
Matches: 196, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
105 1 0.01
106 34 0.17
107 103 0.53
108 58 0.30
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (107 bp):
TTTCAAAGTAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTT
CGATTTTTCCGTCCGACCAAATAGCCAAATATCATTTTAAAA
Found at i:38589832 original size:33 final size:33
Alignment explanation
Indices: 38589794--38590050 Score: 210
Period size: 33 Copynumber: 7.8 Consensus size: 33
38589784 GGAGTAGAAA
* * *
38589794 CTGATGGGGTGGGTTATGTTGAAGGGGTACAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* * *** *
38589827 TTGATGGGGAGGGTGATGTTGAAGGAAAATGAA-
1 CTGATGGGGAGGGTGATGTAGAAGGGGTA-CAAG
* **
38589860 ATGATGATGAGGGTGATGTAGAAGGGGTACAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* * * * * *
38589893 TTGATAGGAAGGGTGATGTTGAAGGAGTAGAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
** ** *
38589926 CTGATATGGAAAGTGATGTAGAAGAGGTACAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* * * *
38589959 CTGATGAGGTGGGTAATGTAGATGGGGTACAAG
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* * *
38589992 CTGTTGGGGAAGGTGATGTAGAAGGGGTACAAA
1 CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
* *
38590025 CTGTTGGGGAGGGTGATGTTGAAGGG
1 CTGATGGGGAGGGTGATGTAGAAGGG
38590051 TAGAAGGTGA
Statistics
Matches: 173, Mismatches: 49, Indels: 4
0.77 0.22 0.02
Matches are distributed among these distances:
32 2 0.01
33 169 0.98
34 2 0.01
ACGTcount: A:0.30, C:0.04, G:0.43, T:0.24
Consensus pattern (33 bp):
CTGATGGGGAGGGTGATGTAGAAGGGGTACAAG
Found at i:38589914 original size:99 final size:98
Alignment explanation
Indices: 38589804--38590049 Score: 237
Period size: 99 Copynumber: 2.5 Consensus size: 98
38589794 CTGATGGGGT
* * *
38589804 GGGTTATGTTGAAGGGGTACAAGTTGATGGGGAGGGTGATGTTGAAGG-AAAATGAAATGATGAT
1 GGGTGATGTTGAAGGGGTACAAGCTGATGGGGAGGGTGATGTTGAAGGTAAAA-G--ATGATGAG
* *
38589868 GAGGGTGATGTAGAAGGGGTACAAGTTGAT-AGGAA
63 GAGGGTAATGTAGAAGGGGTACAAGCTGATGAGGAA
* * ** ** * * *
38589903 GGGTGATGTTGAAGGAGTAGAAGCTGATATGGAAAGTGATGTAGAAGAGGTACAAGCTGATGAGG
1 GGGTGATGTTGAAGGGGTACAAGCTGATGGGGAGGGTGATGTTG-A-AGGTAAAAGATGATGAGG
* * * *
38589968 TGGGTAATGTAGATGGGGTACAAGCTGTTGGGGAA
64 AGGGTAATGTAGAAGGGGTACAAGCTGATGAGGAA
* * *
38590003 -GGTGATGTAGAAGGGGTACAAACTGTTGGGGAGGGTGATGTTGAAGG
1 GGGTGATGTTGAAGGGGTACAAGCTGATGGGGAGGGTGATGTTGAAGG
38590050 GTAGAAGGTG
Statistics
Matches: 115, Mismatches: 28, Indels: 10
0.75 0.18 0.07
Matches are distributed among these distances:
97 3 0.03
98 1 0.01
99 99 0.86
100 5 0.04
101 4 0.03
102 3 0.03
ACGTcount: A:0.30, C:0.04, G:0.42, T:0.24
Consensus pattern (98 bp):
GGGTGATGTTGAAGGGGTACAAGCTGATGGGGAGGGTGATGTTGAAGGTAAAAGATGATGAGGAG
GGTAATGTAGAAGGGGTACAAGCTGATGAGGAA
Found at i:38589942 original size:66 final size:66
Alignment explanation
Indices: 38589773--38590056 Score: 234
Period size: 66 Copynumber: 4.3 Consensus size: 66
38589763 GCTGGGAAGA
** * ** ** * * * *
38589773 GTGATGTTGGTGGAGTAGAAACTGATGGGGTGGGTTATGTTGAAGGGGTACAAGTTGATGGGGAG
1 GTGATGTTGAAGGAGTAGAAGCTGATATGGAAGGTGATGTAGAAGGGGTACAAGCTGATAGGGAG
38589838 G
66 G
** * * * *
38589839 GTGATGTTGAAGGAAAATGAA-ATGATGAT-GAGGGTGATGTAGAAGGGGTACAAGTTGATAGGA
1 GTGATGTTGAAGGAGTA-GAAGCTGAT-ATGGAAGGTGATGTAGAAGGGGTACAAGCTGATAGGG
38589902 AGG
64 AGG
* * *
38589905 GTGATGTTGAAGGAGTAGAAGCTGATATGGAAAGTGATGTAGAAGAGGTACAAGCTGAT-GAGGT
1 GTGATGTTGAAGGAGTAGAAGCTGATATGGAAGGTGATGTAGAAGGGGTACAAGCTGATAG-GGA
38589969 GG
65 GG
* * * * * * ** * * *
38589971 GTAATGTAGATGGGGTACAAGCTGTTGGGGAAGGTGATGTAGAAGGGGTACAAACTGTTGGGGAG
1 GTGATGTTGAAGGAGTAGAAGCTGATATGGAAGGTGATGTAGAAGGGGTACAAGCTGATAGGGAG
38590036 G
66 G
38590037 GTGATGTTGAAGG-GTAGAAG
1 GTGATGTTGAAGGAGTAGAAG
38590057 GTGACGAGGA
Statistics
Matches: 174, Mismatches: 38, Indels: 13
0.77 0.17 0.06
Matches are distributed among these distances:
65 12 0.07
66 158 0.91
67 4 0.02
ACGTcount: A:0.30, C:0.04, G:0.43, T:0.24
Consensus pattern (66 bp):
GTGATGTTGAAGGAGTAGAAGCTGATATGGAAGGTGATGTAGAAGGGGTACAAGCTGATAGGGAG
G
Found at i:38595016 original size:22 final size:22
Alignment explanation
Indices: 38594986--38595028 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
38594976 ACAGCAGAAC
* *
38594986 AGGTTTTTAGCGGCGTTTTTTT
1 AGGTCTTTAGCGGCGCTTTTTT
38595008 AGGTCTTTAGCGGCGCTTTTT
1 AGGTCTTTAGCGGCGCTTTTT
38595029 AACGCCACTA
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:0.09, C:0.14, G:0.28, T:0.49
Consensus pattern (22 bp):
AGGTCTTTAGCGGCGCTTTTTT
Found at i:38595171 original size:42 final size:42
Alignment explanation
Indices: 38595122--38595284 Score: 238
Period size: 42 Copynumber: 3.9 Consensus size: 42
38595112 TTACATAAAA
38595122 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAA-
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAT
* * *
38595163 AATGCGCCGCTAAAGATCATGTTCTTTAGTGGCGCTTACAAAT
1 AA-ACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAT
* ** *
38595206 AAACGCCGCTAAAGAACATAATCTTTAGCAGCGCTTAGAAAT
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAT
*
38595248 AAACGCCGCTAAATATCATGTTCTTTAGCGGCGCTTA
1 AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTA
38595285 NNNNNNNNNN
Statistics
Matches: 105, Mismatches: 15, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
41 2 0.02
42 101 0.96
43 2 0.02
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAAT
Found at i:38595217 original size:84 final size:85
Alignment explanation
Indices: 38595100--38595284 Score: 257
Period size: 84 Copynumber: 2.2 Consensus size: 85
38595090 ACGTCGCTAA
* * ** *
38595100 CTTTTGTGGCGCTTACATAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAAA-A
1 CTTTAGTGGCGCTTACA-AAAAAAACGCCGCTAAAGAACATAATCTTTAGCAGCGCTTAGAAATA
*
38595164 ATGCGCCGCTAAAGATCATGTT
65 A-ACGCCGCTAAAGATCATGTT
*
38595186 CTTTAGTGGCGCTTAC-AAATAAACGCCGCTAAAGAACATAATCTTTAGCAGCGCTTAGAAATAA
1 CTTTAGTGGCGCTTACAAAAAAAACGCCGCTAAAGAACATAATCTTTAGCAGCGCTTAGAAATAA
*
38595250 ACGCCGCTAAATATCATGTT
66 ACGCCGCTAAAGATCATGTT
*
38595270 CTTTAGCGGCGCTTA
1 CTTTAGTGGCGCTTA
38595285 NNNNNNNNNN
Statistics
Matches: 89, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
84 72 0.81
85 2 0.02
86 15 0.17
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (85 bp):
CTTTAGTGGCGCTTACAAAAAAAACGCCGCTAAAGAACATAATCTTTAGCAGCGCTTAGAAATAA
ACGCCGCTAAAGATCATGTT
Found at i:38595487 original size:18 final size:18
Alignment explanation
Indices: 38595464--38595501 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
38595454 TTTAGCGGCG
38595464 CTTATTTCACAAATGCCA
1 CTTATTTCACAAATGCCA
38595482 CTTATTTCACAAATGCCA
1 CTTATTTCACAAATGCCA
38595500 CT
1 CT
38595502 GTTTTGATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (18 bp):
CTTATTTCACAAATGCCA
Found at i:38613300 original size:42 final size:42
Alignment explanation
Indices: 38613171--38613399 Score: 259
Period size: 42 Copynumber: 5.4 Consensus size: 42
38613161 ACGTCGCTAA
* * *
38613171 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATATT
1 CTTTAGCGGCGCTT--AGGAAAAAACGCCGCTAAAGATCATGTT
* * *
38613215 CTTTAGCGGCACTAAGGAAATAAACGCCGCTAAAGATCGTGTT
1 CTTTAGCGGCGCTTAGGAAA-AAACGCCGCTAAAGATCATGTT
*
38613258 CTTTAGCGGCGCTTATGAAAAAACGCCGCTAAAGATCATGTT
1 CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
*
38613300 CTTTAGCGGCGCTTAGGAAGAAAACGCCGCTAAA-AGTAATGTT
1 CTTTAGCGGCGCTTAGGAA-AAAACGCCGCTAAAGA-TCATGTT
* * *
38613343 CTATAGCGGTGCTT-GGTCAAAAACGCCGCTAAA-AGT-AGTGTT
1 CTTTAGCGGCGCTTAGG-AAAAAACGCCGCTAAAGA-TCA-TGTT
38613385 CTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTA
38613400 TTTCACAAAC
Statistics
Matches: 162, Mismatches: 17, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
41 1 0.01
42 80 0.49
43 70 0.43
44 11 0.07
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (42 bp):
CTTTAGCGGCGCTTAGGAAAAAACGCCGCTAAAGATCATGTT
Found at i:38613325 original size:85 final size:86
Alignment explanation
Indices: 38613171--38613399 Score: 263
Period size: 85 Copynumber: 2.7 Consensus size: 86
38613161 ACGTCGCTAA
* * * *
38613171 CTTTTGCGGCGCTTACAGAAAAAAACGCCGCTAAAGATCATATTCTTTAGCGGCACTAAGGAAAT
1 CTTTAGCGGCGCTTA-AGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAAT
**
38613236 AAACGCCGCT-AAAGATCGTGTT
65 AAACGCCGCTAAAAG-TAATGTT
*
38613258 CTTTAGCGGCGCTTATG-AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAGA-
1 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAA-AT
38613321 AAACGCCGCTAAAAGTAATGTT
65 AAACGCCGCTAAAAGTAATGTT
* * * **
38613343 CTATAGCGGTGCTT-GGTCAAAAACGCCGCTAAA-AGT-AGTGTTCTTTAGCGGCGCTTA
1 CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGA-TCA-TGTTCTTTAGCGGCGCTTA
38613400 TTTCACAAAC
Statistics
Matches: 126, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
84 3 0.02
85 103 0.82
86 6 0.05
87 14 0.11
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.25
Consensus pattern (86 bp):
CTTTAGCGGCGCTTAAGAAAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGGAAATA
AACGCCGCTAAAAGTAATGTT
Found at i:38613565 original size:112 final size:113
Alignment explanation
Indices: 38613367--38613591 Score: 427
Period size: 112 Copynumber: 2.0 Consensus size: 113
38613357 GGTCAAAAAC
38613367 GCCGCTAAAAGTAGTGTTCTTTAGCGGCGCTTATTTCACAAACGCCACTATTTGATATGACTTTT
1 GCCGCTAAAAGTAGTGTTCTTTAGCGGCGCTTATTTCACAAACGCCACTATTTGATATGACTTTT
38613432 AGAGGTGCTTTTTTAAAAAACGCCA-CTAATTTTGGGATTTTTTTTAAA
66 AGAGGTGCTTTTTTAAAAAACGCCACCT-ATTTTGGGATTTTTTTTAAA
38613480 GCCGCTAAAA-TAGTGTTCTTTAGCGGCGCTTATTTCACAAACGCCACTATTTGATATGACTTTT
1 GCCGCTAAAAGTAGTGTTCTTTAGCGGCGCTTATTTCACAAACGCCACTATTTGATATGACTTTT
38613544 AGAGGTGCTTTTTTAAAAAACGCCACCTATTTTGGGATTTTTTTTAAA
66 AGAGGTGCTTTTTTAAAAAACGCCACCTATTTTGGGATTTTTTTTAAA
38613592 ATAAAATTTT
Statistics
Matches: 111, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
112 99 0.89
113 12 0.11
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (113 bp):
GCCGCTAAAAGTAGTGTTCTTTAGCGGCGCTTATTTCACAAACGCCACTATTTGATATGACTTTT
AGAGGTGCTTTTTTAAAAAACGCCACCTATTTTGGGATTTTTTTTAAA
Found at i:38613713 original size:19 final size:19
Alignment explanation
Indices: 38613689--38613725 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
38613679 AATATTTCAA
38613689 ATTAAATGACTA-AAATAAT
1 ATTAAATGA-TATAAATAAT
38613708 ATTAAATGATATAAATAA
1 ATTAAATGATATAAATAA
38613726 AAGTGAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.32
Consensus pattern (19 bp):
ATTAAATGATATAAATAAT
Found at i:38613998 original size:21 final size:21
Alignment explanation
Indices: 38613972--38614040 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
38613962 GCTTCTTTCG
* *
38613972 CTGCTTTTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
**
38613993 CTGCTTCTCTCGCTATAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* **
38614014 CTGCTTCCCTCGCTGCCTCCT
1 CTGCTTCTCTCGCTGCAGCCT
38614035 CTGCTT
1 CTGCTT
38614041 TAAGTTGTTG
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.03, C:0.42, G:0.17, T:0.38
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Done.