Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr1
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: 106989029
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3754247 characters in sequence are not A, C, G, or T
File 171 of 322
Found at i:55840264 original size:13 final size:14
Alignment explanation
Indices: 55840236--55840264 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
55840226 AGATATTCTT
55840236 TTTCTAAATAAAGA
1 TTTCTAAATAAAGA
55840250 TTTCTAAAT-AAGA
1 TTTCTAAATAAAGA
55840263 TT
1 TT
55840265 GAATCGAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
TTTCTAAATAAAGA
Found at i:55840315 original size:16 final size:14
Alignment explanation
Indices: 55840283--55840335 Score: 65
Period size: 14 Copynumber: 3.7 Consensus size: 14
55840273 ATCGATACCT
55840283 TTTGCATTCATGCA
1 TTTGCATTCATGCA
55840297 TTTGCATCTCATAGCA
1 TTTGCAT-TCAT-GCA
55840313 TTT-CATTGCAT-CA
1 TTTGCATT-CATGCA
55840326 TTTGCATTCA
1 TTTGCATTCA
55840336 AAATTATAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
13 7 0.20
14 12 0.34
15 10 0.29
16 6 0.17
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:55843916 original size:44 final size:44
Alignment explanation
Indices: 55843868--55845458 Score: 1809
Period size: 44 Copynumber: 36.2 Consensus size: 44
55843858 GATTTCAGCA
55843868 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
* * * *
55843912 TGGCATCCCTATGTTTATAGGGAA-TAGATCGAAGATAGCAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAAG-TTGAAGATAGCAGATT
* * * * * ** * **
55843956 TGACA-CTCTTGTGCTTACAGCGAAGTAGATCGAAGATTTCAGCA--
1 TGGCATC-CCTGTGTTTATAGGGAACAAG-TTGAAGATAGCAG-ATT
* *
55844000 TGGCATCTCTGTGTTTATAGGGAACAAGTTGAAGATAGCATATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
* *
55844044 TGGCATCCCTGTGTTTATAGGGAAC-AGATCGAAGATAGCAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAAG-TTGAAGATAGCAGATT
* * * * * * **
55844088 TGACA-CTCTTGTGCTTACAGCGAAGC-AGATCGAAGATTTCAGCA--
1 TGGCATC-CCTGTGTTTATAGGGAA-CAAG-TTGAAGATAGCAG-ATT
55844132 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
* * * * *
55844176 TGGCATCCCTTTGTTTATCGGGAAC-AGCTCGAAGATATCAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAAG-TTGAAGATAGCAGATT
** * * * * * * **
55844220 T-AAAACTCTTGTGATTACAGCGAAGC-AGATCGAAGATTTCAGCA--
1 TGGCATC-CCTGTGTTTATAGGGAA-CAAG-TTGAAGATAGCAG-ATT
55844264 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
* * * *
55844308 TGGCATCCCTTTGTTTATAGGGAAC-AGATCGAAGATATCAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAAG-TTGAAGATAGCAGATT
** * * * * * **
55844352 TAACA-CTCTTGTGATTACAGCGAAGC-AGATCGAAGATTTCAGCA--
1 TGGCATC-CCTGTGTTTATAGGGAA-CAAG-TTGAAGATAGCAG-ATT
55844396 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
* * * *
55844440 TGGCATCCCTATGTTTATAGGGAA-TAGATCGAAGATAGCAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAAG-TTGAAGATAGCAGATT
* * * * * * ***
55844484 TGACA-CTCTTGTGCTTACAGCGAAGC-AGATCGAAGATTTTAGCA--
1 TGGCATC-CCTGTGTTTATAGGGAA-CAAG-TTGAAGATAGCAG-ATT
55844528 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55844572 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55844616 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55844660 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55844704 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55844748 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55844792 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55844836 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55844880 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55844924 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55844968 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55845012 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55845056 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55845100 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
* ** *
55845144 TGGCATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
* * * * * * **
55845188 TGACATTCCTGTGATTACAGCGAAGC-AGATCGAAGATTTCAGCA--
1 TGGCATCCCTGTGTTTATAGGGAA-CAAG-TTGAAGATAGCAG-ATT
55845232 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
* * *
55845276 TGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
* * * * ** * ** **
55845320 TGACATTCCTATGCTTATAGCAAAGC-AGATCGAAGATTTCA-ACA
1 TGGCATCCCTGTGTTTATAGGGAA-CAAG-TTGAAGATAGCAGATT
* * *
55845364 TGACATCCCTATGTTTATAGGGAACAAATTGAAGATAGCAGATT
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
* * * * *
55845408 TGGCATCCCTGTGCTTATAGGGAACAAATCGAAGATAACAGATC
1 TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
55845452 TGGCATC
1 TGGCATC
55845459 TCCATTTCGA
Statistics
Matches: 1334, Mismatches: 163, Indels: 100
0.84 0.10 0.06
Matches are distributed among these distances:
42 6 0.00
43 89 0.07
44 1131 0.85
45 102 0.08
46 6 0.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (44 bp):
TGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATAGCAGATT
Found at i:55846055 original size:19 final size:19
Alignment explanation
Indices: 55846031--55846128 Score: 155
Period size: 19 Copynumber: 5.2 Consensus size: 19
55846021 AATCTTTAAG
55846031 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55846050 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
55846069 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
55846086 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
55846105 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
55846126 GAT
1 GAT
55846129 CTTGTAATCT
Statistics
Matches: 73, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
17 17 0.23
19 47 0.64
21 9 0.12
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:55846061 original size:36 final size:35
Alignment explanation
Indices: 55846021--55846128 Score: 103
Period size: 36 Copynumber: 2.9 Consensus size: 35
55846011 ATGGAAATAT
55846021 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATGC
55846057 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATGC
* *
55846093 AATCCTAGATATGATATGCAATCTTGAAGATATGAT
1 AAT-CT--TTAAGATATGCAATCTT--AGATATGAT
55846129 CTTGTAATCT
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 27 0.45
37 1 0.02
38 7 0.12
40 10 0.17
41 6 0.10
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATGC
Found at i:55850767 original size:33 final size:33
Alignment explanation
Indices: 55850730--55850816 Score: 111
Period size: 33 Copynumber: 2.6 Consensus size: 33
55850720 GTATCCACCT
** * *
55850730 CAGTACTCTGCTCCTTCCGGCCCGTACCAATCG
1 CAGTACTCCACTCCTCCCGACCCGTACCAATCG
* *
55850763 CAGTACTCCACTCCTCCCGACCCGTATCAATTG
1 CAGTACTCCACTCCTCCCGACCCGTACCAATCG
*
55850796 CCGTACTCCACTCCTCCCGAC
1 CAGTACTCCACTCCTCCCGAC
55850817 TCAAGTTCAT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 47 1.00
ACGTcount: A:0.17, C:0.46, G:0.14, T:0.23
Consensus pattern (33 bp):
CAGTACTCCACTCCTCCCGACCCGTACCAATCG
Found at i:55854300 original size:27 final size:27
Alignment explanation
Indices: 55854243--55854314 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
55854233 CCCCACCATT
**
55854243 TGCGCCTCTGAGATAGGCACAATCATT
1 TGCGCCTCTGAGATAGGCACAATCAGC
* * *
55854270 TGCGCCTCTGAGATAGGCTCGATTAGC
1 TGCGCCTCTGAGATAGGCACAATCAGC
* *
55854297 TGCGCCTCTCAGGTAGGC
1 TGCGCCTCTGAGATAGGC
55854315 GCAACCTGTA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (27 bp):
TGCGCCTCTGAGATAGGCACAATCAGC
Found at i:55861640 original size:28 final size:28
Alignment explanation
Indices: 55861608--55861677 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 28
55861598 ATAGTAAGTC
55861608 CGCACACTTAGTGCT-TA-ATAGTCAAACT
1 CGCACACTTAGTGCTATACA-A-TCAAACT
*
55861636 CGCACACTTAGTGCTATACAATTAAACT
1 CGCACACTTAGTGCTATACAATCAAACT
55861664 CGCACACTTAGTGC
1 CGCACACTTAGTGC
55861678 CAATCTCATT
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 35 0.90
29 3 0.08
30 1 0.03
ACGTcount: A:0.31, C:0.27, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATACAATCAAACT
Found at i:55866727 original size:34 final size:34
Alignment explanation
Indices: 55866662--55866747 Score: 93
Period size: 34 Copynumber: 2.5 Consensus size: 34
55866652 CTGAGGTGAT
**
55866662 CTGTTATAAGCATATTACTTGCTACTTTATTAAA
1 CTGTTATAAGCATATTACTTGCTACCGTATTAAA
* **
55866696 CTGTTATAAGCATATTGA-TTGCTGCCGTATTACT
1 CTGTTATAAGCATATT-ACTTGCTACCGTATTAAA
*
55866730 CTGTTAAAAGCATTATTA
1 CTGTTATAAGCA-TATTA
55866748 AATGTTATCA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
34 39 0.89
35 5 0.11
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (34 bp):
CTGTTATAAGCATATTACTTGCTACCGTATTAAA
Found at i:55867336 original size:12 final size:12
Alignment explanation
Indices: 55867321--55867350 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
55867311 ATGATTGAAC
55867321 TCATATTGAGCT
1 TCATATTGAGCT
55867333 TCATATTGAGCT
1 TCATATTGAGCT
55867345 TCATAT
1 TCATAT
55867351 CTCACTATCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (12 bp):
TCATATTGAGCT
Found at i:55867493 original size:23 final size:21
Alignment explanation
Indices: 55867454--55867496 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
55867444 TTTATTAAAA
55867454 ATATTTTAAGATTATTATTTG
1 ATATTTTAAGATTATTATTTG
*
55867475 ATATTTTTAGACTTAATTATTT
1 ATATTTTAAGA-TT-ATTATTT
55867497 TATTTTCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 10 0.53
22 2 0.11
23 7 0.37
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.58
Consensus pattern (21 bp):
ATATTTTAAGATTATTATTTG
Found at i:55867500 original size:21 final size:20
Alignment explanation
Indices: 55867454--55867502 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
55867444 TTTATTAAAA
55867454 ATATTTTAAGATTATTATTT
1 ATATTTTAAGATTATTATTT
*
55867474 GATATTTTTAGACTTAATTATTT
1 -ATATTTTAAGA-TT-ATTATTT
55867497 -TATTTT
1 ATATTTT
55867503 CAACTGTGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 16 0.64
22 2 0.08
23 7 0.28
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (20 bp):
ATATTTTAAGATTATTATTT
Found at i:55877171 original size:21 final size:22
Alignment explanation
Indices: 55877134--55877174 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
55877124 AAATAGGGAG
55877134 AAAACAACAAGAAAATAGCATT
1 AAAACAACAAGAAAATAGCATT
*
55877156 AAAATAACAA-AAAATAGCA
1 AAAACAACAAGAAAATAGCA
55877175 ATTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.68, C:0.12, G:0.07, T:0.12
Consensus pattern (22 bp):
AAAACAACAAGAAAATAGCATT
Found at i:55877784 original size:19 final size:17
Alignment explanation
Indices: 55877733--55877799 Score: 62
Period size: 19 Copynumber: 3.6 Consensus size: 17
55877723 AATGAATTAT
*
55877733 AATTAAAACTATTTATAA
1 AATTAAAA-TAATTATAA
* *
55877751 TATTAAAACATAATTTTAAA
1 AATT-AAA-ATAATTAT-AA
55877771 AATATAAAATAATTATAA
1 AAT-TAAAATAATTATAA
55877789 AATTAAAATAA
1 AATTAAAATAA
55877800 AGATATTGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
17 8 0.20
18 8 0.20
19 15 0.38
20 8 0.20
21 1 0.03
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (17 bp):
AATTAAAATAATTATAA
Found at i:55882295 original size:21 final size:20
Alignment explanation
Indices: 55882256--55882295 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
55882246 TCAAAATTGG
*
55882256 AATAAAAATAATAATAGATT
1 AATAAAAAAAATAATAGATT
*
55882276 AATAAATAAAAATTATAGAT
1 AATAAA-AAAAATAATAGAT
55882296 CGTAATTAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (20 bp):
AATAAAAAAAATAATAGATT
Found at i:55882871 original size:18 final size:17
Alignment explanation
Indices: 55882845--55882880 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
55882835 AACATAATTG
*
55882845 ATTTCTAATATTATCAAA
1 ATTTATAATATT-TCAAA
55882863 ATTTATAATATTTCAAA
1 ATTTATAATATTTCAAA
55882880 A
1 A
55882881 GGGGAGAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTATAATATTTCAAA
Found at i:55890618 original size:44 final size:44
Alignment explanation
Indices: 55890568--55890655 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
55890558 TACTCTTTTG
*
55890568 CCCTTGCTATTTACTATTTTACCTTTTTATTACTAGTATAAATA
1 CCCTTGCTATTTACTATTTTACCTTTCTATTACTAGTATAAATA
55890612 CCCTTGCTATTTACTATTTTACCTTTCTATTACTAGTATAAATA
1 CCCTTGCTATTTACTATTTTACCTTTCTATTACTAGTATAAATA
55890656 GAAAGTTTTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.27, C:0.19, G:0.05, T:0.49
Consensus pattern (44 bp):
CCCTTGCTATTTACTATTTTACCTTTCTATTACTAGTATAAATA
Found at i:55892692 original size:33 final size:33
Alignment explanation
Indices: 55892655--55892720 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
55892645 CTTTTCGTTA
55892655 TTGATTAATTGCCCCTACTTGTGAAAGTTTGGT
1 TTGATTAATTGCCCCTACTTGTGAAAGTTTGGT
55892688 TTGATTAATTGCCCCTACTTGTGAAAGTTTGGT
1 TTGATTAATTGCCCCTACTTGTGAAAGTTTGGT
55892721 CGGATTTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.42
Consensus pattern (33 bp):
TTGATTAATTGCCCCTACTTGTGAAAGTTTGGT
Found at i:55897357 original size:6 final size:6
Alignment explanation
Indices: 55897346--55897379 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
55897336 TAAAATATTG
*
55897346 ATGGCA ATGGCA ATGGCA CTGGCA ATGGCA ATGG
1 ATGGCA ATGGCA ATGGCA ATGGCA ATGGCA ATGG
55897380 AGATTGGATG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.35, T:0.18
Consensus pattern (6 bp):
ATGGCA
Found at i:55898874 original size:26 final size:25
Alignment explanation
Indices: 55898820--55898871 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
55898810 TTGAATATTA
*
55898820 TTTAATATTTTTTCATTTATGTAAT
1 TTTAATATTTTTTCATTTATATAAT
55898845 TTTAATTATTTTTT-ATTT-TATAAT
1 TTTAA-TATTTTTTCATTTATATAAT
55898869 TTT
1 TTT
55898872 TTATAACAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 8 0.32
25 9 0.36
26 8 0.32
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (25 bp):
TTTAATATTTTTTCATTTATATAAT
Found at i:55904501 original size:40 final size:40
Alignment explanation
Indices: 55904445--55904586 Score: 178
Period size: 40 Copynumber: 3.5 Consensus size: 40
55904435 GCACAAGGCT
* * * * *
55904445 TTCGGGTCTTAACCCGGATATGGTCACTAGCATAAATGCC
1 TTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGCC
55904485 TTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGCC
1 TTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGCC
* * *
55904525 TTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAGCC
1 TTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAATGCC
*
55904566 TTCGGGACTTAGCCCGAATAT
1 TTCGGGACTTAGCCCGGATAT
55904587 CATTCGAGTA
Statistics
Matches: 88, Mismatches: 11, Indels: 5
0.85 0.11 0.05
Matches are distributed among these distances:
39 3 0.03
40 56 0.64
41 26 0.30
42 3 0.03
ACGTcount: A:0.25, C:0.25, G:0.24, T:0.26
Consensus pattern (40 bp):
TTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGCC
Found at i:55907447 original size:125 final size:125
Alignment explanation
Indices: 55907171--55908550 Score: 1564
Period size: 125 Copynumber: 11.2 Consensus size: 125
55907161 TAAAGCCAAG
* ** * * * * *
55907171 CAGGAACTACTGCAGAAAAAGAGTGTTCATGTGGGAGCTTTTTTCAGTAATTTTGCTGATAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTT-AGTAATTTTTCTGACAATGC
* * * ** *
55907236 ATCCTGCTTGAAGCAG-TTTTGAAACTATTTTTTTAGGACCGTCTTCTCAAAATTATTTTTT
65 ATCCTACTTGAAGC-GTTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
* *
55907297 CAGGAACTACTATAGAAAAAGAGCATCCACGTGGGAGCTTGTTTTAGTAATTTTTCTGACAATAC
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTT-TTTTAGTAATTTTTCTGACAATGC
55907362 ATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTC-TCTCAAAATTATTTTTT
65 ATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
* *
55907422 CAGGAACTACTATAGAAAAAGAGCATCCACGTGGGAGCTTGTTTTAGTAATTTTTCTGACAATAC
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTT-TTTTAGTAATTTTTCTGACAATGC
55907487 ATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTC-TCTCAAAATTATTTTTT
65 ATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
* *
55907547 CAGGAACTACTATAGAAAAAGAGCATCCACGTGGGAGCTTGTTTTAGTAATTTTTCTGACAATAC
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTT-TTTTAGTAATTTTTCTGACAATGC
55907612 ATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTC-TCTCAAAATTATTTTTT
65 ATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
* *
55907672 CAGGAACTACTATAGAAAAAGAGCATCCACGTGGGAGCTTGTTTTAGTAATTTTTCTGACAATAC
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTT-TTTTAGTAATTTTTCTGACAATGC
55907737 ATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTC-TCTCAAAATTATTTTTT
65 ATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
* * * * *
55907797 CAGGAACTACTGTA-AAAAAAAGCATCTATGTGGGAGCTTTTGTTAATAATTTTGT-TGACAGTG
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTT-TTAGTAATTTT-TCTGACAATG
* ** * *
55907860 CATCTTGTTTGAAGCATTTTTGACACTATTTTTT-AGAA-TCGTCTTCTCAAAATT-TTTTTT
64 CATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACT-GTCTTCTCAAAATTATTTTTT
* * *
55907920 -AAGAACTACTGTAGAAAAAGAGCATCCATGTGGGAGCTTTTTTAGTAGTTTTTCTGA-AAGTGC
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTAGTAATTTTTCTGACAA-TGC
* * *
55907983 ATCCTGCTTGAAGCGTTTTTGACACTATTTTTTCAGAACCGTCTTCTCAAAATTATTTTTT
65 ATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
* * * * * * *
55908044 CAGCAACTACTATAGAAAAAGAGCGTCCACGTGGGAGCTTTTTTAGTACTTTTGCTGACAGTGTA
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTAGTAATTTTTCTGACAATGCA
* * * * * *
55908109 TACTACTTTAAGCATTTTT-ACATTATTTTTTCATAA-TAGTCTTCTCAAAATTATTTTCT
66 TCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACT-GTCTTCTCAAAATTATTTTTT
** * *
55908168 CAAAAACTATTGTAGAAAAAGAGCTTCCACGTGGGAGCTTTTTTCAGTAATTTTGT-TGACAATG
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTT-AGTAATTTT-TCTGACAATG
** * * * * *
55908232 CATCCTACTTGAAATGTTTTTCACACTATTTTTTTAGAACCGTCTTCTTAAAATTATTTTTT
64 CATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
* * * * *
55908294 CAGG-A--AC--T--------A-C-TCCACGTGGGAGCTTTTTTAGTACTTTTGCTAATAGTGCA
1 CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTAGTAATTTTTCTGACAATGCA
* * * * ** * *
55908344 TACTACTTGAAGTGTTTTTTACATTATTTTTTCAAAACCATCTTTTCAAAATTATTCTTT
66 TCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
* * * * *
55908404 CAGAAACTACTGTAGAAAAAGAGCGA-CCACGT-GGAGCTTTTTTCAGTACTTTTGCTTACACTG
1 CAGGAACTACTGTAGAAAAAGAGC-ATCCACGTGGGAGCTTTTTT-AGTAATTTTTCTGACAATG
* * * ** ** * *
55908467 AATCTTGCTTGAAGATTTTTTTTCACTATTTTTTCAGAACCGTCTTCTCAAAATTAATTTTTTT
64 CATCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAATT-A-TTTTTT
* *
55908531 TAGAAACTACTGTAGAAAAA
1 CAGGAACTACTGTAGAAAAA
55908551 AAAAACAAAC
Statistics
Matches: 1105, Mismatches: 110, Indels: 77
0.86 0.09 0.06
Matches are distributed among these distances:
110 68 0.06
111 20 0.02
112 1 0.00
113 3 0.00
115 1 0.00
121 3 0.00
122 58 0.05
123 59 0.05
124 170 0.15
125 572 0.52
126 122 0.11
127 28 0.03
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (125 bp):
CAGGAACTACTGTAGAAAAAGAGCATCCACGTGGGAGCTTTTTTAGTAATTTTTCTGACAATGCA
TCCTACTTGAAGCGTTTTTGACACTATTTTTTCAAAACTGTCTTCTCAAAATTATTTTTT
Found at i:55908350 original size:110 final size:111
Alignment explanation
Indices: 55908193--55908414 Score: 295
Period size: 110 Copynumber: 2.0 Consensus size: 111
55908183 AAAAAGAGCT
* * *
55908193 TCCACGTGGGAGCTTTTTTCAGTAATTTTGTTGACAATGCATCCTACTTGAAATGTTTTTCACAC
1 TCCACGTGGGAGCTTTTTTCAGTAATTTTGCTAACAATGCATACTACTTGAAATGTTTTTCACAC
* * * * *
55908258 TATTTTTTTAGAACCGTCTTCTT-AAAATTATTTTTTCAGGAACTAC
66 TATTTTTTCAAAACCATCTT-TTCAAAATTATTCTTTCAGAAACTAC
* * * * * *
55908304 TCCACGTGGGAGCTTTTTT-AGTACTTTTGCTAATAGTGCATACTACTTGAAGTGTTTTTTACAT
1 TCCACGTGGGAGCTTTTTTCAGTAATTTTGCTAACAATGCATACTACTTGAAATGTTTTTCACAC
55908368 TATTTTTTCAAAACCATCTTTTCAAAATTATTCTTTCAGAAACTAC
66 TATTTTTTCAAAACCATCTTTTCAAAATTATTCTTTCAGAAACTAC
55908414 T
1 T
55908415 GTAGAAAAAG
Statistics
Matches: 96, Mismatches: 14, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
109 2 0.02
110 75 0.78
111 19 0.20
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.44
Consensus pattern (111 bp):
TCCACGTGGGAGCTTTTTTCAGTAATTTTGCTAACAATGCATACTACTTGAAATGTTTTTCACAC
TATTTTTTCAAAACCATCTTTTCAAAATTATTCTTTCAGAAACTAC
Found at i:55908496 original size:235 final size:236
Alignment explanation
Indices: 55908069--55908529 Score: 637
Period size: 235 Copynumber: 2.0 Consensus size: 236
55908059 AAAAAGAGCG
* * *
55908069 TCCACGTGGGAGCTTTTTTAGTACTTTTGCTGACAGTGTATACTACTTTAAGCATTTTTACATTA
1 TCCACGTGGGAGCTTTTTTAGTACTTTTGCTAACAGTGCATACTACTTGAAGCATTTTTACATTA
* * * **
55908134 TTTTTTCATAATAGTCTTCTCAAAATTATTTTCTCAAAAACTATTGTAGAAAAAGAGCTTCCACG
66 TTTTTTCAAAACAGTCTTCTCAAAATTATTTTCTCAAAAACTACTGTAGAAAAAGAGCGACCACG
*
55908199 TGGGAGCTTTTTTCAGTAATTTTGTTGACAATGCATCCTACTTGAAATGTTTTTCACACTATTTT
131 TGGGAGCTTTTTTCAGTAATTTTGTTGACAATGAATCCTACTTGAAATGTTTTTCACACTATTTT
* *
55908264 TTTAGAACCGTCTTCTTAAAATT-ATTTTTTCAGGAACTAC
196 TTCAGAACCGTCTTCTCAAAATTAATTTTTTCAGGAACTAC
* **
55908304 TCCACGTGGGAGCTTTTTTAGTACTTTTGCTAATAGTGCATACTACTTGAAGTGTTTTTTACATT
1 TCCACGTGGGAGCTTTTTTAGTACTTTTGCTAACAGTGCATACTACTTGAAG-CATTTTTACATT
* *
55908369 ATTTTTTCAAAACCA-TCTTTTCAAAATTATTCTT-TCAGAAACTACTGTAGAAAAAGAGCGACC
65 ATTTTTTCAAAA-CAGTCTTCTCAAAATTATT-TTCTCAAAAACTACTGTAGAAAAAGAGCGACC
* * * * **
55908432 ACGT-GGAGCTTTTTTCAGTACTTTTGCTT-ACACTGAATCTTGCTTGAAGAT-TTTTTTTCACT
128 ACGTGGGAGCTTTTTTCAGTAATTTTG-TTGACAATGAATCCTACTTGAA-ATGTTTTTCACACT
55908494 ATTTTTTCAGAACCGTCTTCTCAAAATTAATTTTTT
191 ATTTTTTCAGAACCGTCTTCTCAAAATTAATTTTTT
55908530 TTAGAAACTA
Statistics
Matches: 198, Mismatches: 22, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
235 119 0.60
236 76 0.38
237 3 0.02
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (236 bp):
TCCACGTGGGAGCTTTTTTAGTACTTTTGCTAACAGTGCATACTACTTGAAGCATTTTTACATTA
TTTTTTCAAAACAGTCTTCTCAAAATTATTTTCTCAAAAACTACTGTAGAAAAAGAGCGACCACG
TGGGAGCTTTTTTCAGTAATTTTGTTGACAATGAATCCTACTTGAAATGTTTTTCACACTATTTT
TTCAGAACCGTCTTCTCAAAATTAATTTTTTCAGGAACTAC
Found at i:55908692 original size:34 final size:34
Alignment explanation
Indices: 55908654--55908749 Score: 135
Period size: 34 Copynumber: 2.9 Consensus size: 34
55908644 TAAAAGACTC
55908654 TAAACCTTAATTTAATTAATTTTCTTAAAAACCA
1 TAAACCTTAATTTAATTAATTTTCTTAAAAACCA
* * *
55908688 TAAACCTTAATTTAATTAATTTACTT-AAACCCC
1 TAAACCTTAATTTAATTAATTTTCTTAAAAACCA
55908721 TAAAACC-TAATTTAATTAATTTT-TTAAAA
1 T-AAACCTTAATTTAATTAATTTTCTTAAAA
55908750 GATTTTAAAC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
32 2 0.04
33 24 0.43
34 30 0.54
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (34 bp):
TAAACCTTAATTTAATTAATTTTCTTAAAAACCA
Found at i:55909515 original size:10 final size:9
Alignment explanation
Indices: 55909418--55909540 Score: 59
Period size: 8 Copynumber: 14.4 Consensus size: 9
55909408 GTCAAGTGAA
*
55909418 AAAAATGAT
1 AAAAATTAT
*
55909427 AAAAA-AAT
1 AAAAATTAT
*
55909435 AAAAATCAAT
1 AAAAAT-TAT
*
55909445 AAAATTTAT
1 AAAAATTAT
55909454 -AAAATTAT
1 AAAAATTAT
* *
55909462 -TAAATTTT
1 AAAAATTAT
*
55909470 AAAAAATAT
1 AAAAATTAT
55909479 AAAAATTATT
1 AAAAATTA-T
55909489 AAAAATTA-
1 AAAAATTAT
* *
55909497 GAAGA--A-
1 AAAAATTAT
55909503 AAAAATTAT
1 AAAAATTAT
55909512 -AAAATATAT
1 AAAAAT-TAT
*
55909521 AGAAATTA-
1 AAAAATTAT
55909529 AAAAATTA-
1 AAAAATTAT
55909537 AAAA
1 AAAA
55909541 TTTTTATAAA
Statistics
Matches: 89, Mismatches: 16, Indels: 19
0.72 0.13 0.15
Matches are distributed among these distances:
6 4 0.04
8 40 0.45
9 24 0.27
10 21 0.24
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:55909846 original size:32 final size:32
Alignment explanation
Indices: 55909810--55909879 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
55909800 ATGTCCATTG
55909810 GTAAATAATGTGCCTCGTTAAAACCTTACTAA
1 GTAAATAATGTGCCTCGTTAAAACCTTACTAA
*
55909842 GTAAATAATGTGCCTCGTTAAAACCTTTCTAA
1 GTAAATAATGTGCCTCGTTAAAACCTTACTAA
55909874 GATAAA
1 G-TAAA
55909880 AACCCTATGG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 32 0.89
33 4 0.11
ACGTcount: A:0.39, C:0.17, G:0.13, T:0.31
Consensus pattern (32 bp):
GTAAATAATGTGCCTCGTTAAAACCTTACTAA
Found at i:55931694 original size:36 final size:35
Alignment explanation
Indices: 55931639--55931717 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 35
55931629 CCCTCCAAAT
*
55931639 CACACCAATGCTCATAAGAGCTAATCCAACAAAAA
1 CACACCAATGCTCAAAAGAGCTAATCCAACAAAAA
* * **
55931674 CACACCAGATGCTCAAAAGAGCTAGTCCCACCGAAA
1 CACACCA-ATGCTCAAAAGAGCTAATCCAACAAAAA
55931710 CACACCAA
1 CACACCAA
55931718 ATAGAAAGTA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
35 8 0.21
36 30 0.79
ACGTcount: A:0.44, C:0.33, G:0.11, T:0.11
Consensus pattern (35 bp):
CACACCAATGCTCAAAAGAGCTAATCCAACAAAAA
Found at i:55934425 original size:17 final size:17
Alignment explanation
Indices: 55934400--55934435 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55934390 TTGAATTTTG
55934400 GGCTCACATGCCCATGT
1 GGCTCACATGCCCATGT
* *
55934417 GGCTGACATGCCCGTGT
1 GGCTCACATGCCCATGT
55934434 GG
1 GG
55934436 TCCTCATGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.22
Consensus pattern (17 bp):
GGCTCACATGCCCATGT
Found at i:55938338 original size:41 final size:41
Alignment explanation
Indices: 55938293--55938375 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
55938283 GCCTAATAAT
*
55938293 CCACATGCCCAACTTGGGCTAACCCATGTGGCCCACACGAC
1 CCACATGCCCAACTTGGCCTAACCCATGTGGCCCACACGAC
* *
55938334 CCACATGCCCAACTTGGCCTAGCCCATGTGGCCCATACGAC
1 CCACATGCCCAACTTGGCCTAACCCATGTGGCCCACACGAC
55938375 C
1 C
55938376 ATACTCAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.23, C:0.42, G:0.19, T:0.16
Consensus pattern (41 bp):
CCACATGCCCAACTTGGCCTAACCCATGTGGCCCACACGAC
Found at i:55940762 original size:43 final size:43
Alignment explanation
Indices: 55940700--55940784 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
55940690 GGGAATTGAG
* *
55940700 GAGAGATCTTCAGTCTTGATGATGAATCTGGCTTCTGAGATGT
1 GAGAGATCTTCAGTCTTGATGATGAATCCGGCGTCTGAGATGT
* *
55940743 GAGAGATCTTCAGTTTTGATGATGAATCCGTCGTCTGAGATG
1 GAGAGATCTTCAGTCTTGATGATGAATCCGGCGTCTGAGATG
55940785 GATCAATCGG
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:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (43 bp):
GAGAGATCTTCAGTCTTGATGATGAATCCGGCGTCTGAGATGT
Found at i:55940951 original size:13 final size:13
Alignment explanation
Indices: 55940933--55940959 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
55940923 GCTCGGTAGG
55940933 GACACGCCCGTGT
1 GACACGCCCGTGT
55940946 GACACGCCCGTGT
1 GACACGCCCGTGT
55940959 G
1 G
55940960 CGATTACTTC
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:0.15, C:0.37, G:0.33, T:0.15
Consensus pattern (13 bp):
GACACGCCCGTGT
Found at i:55948798 original size:40 final size:39
Alignment explanation
Indices: 55948739--55948870 Score: 149
Period size: 40 Copynumber: 3.3 Consensus size: 39
55948729 CATTTGAATG
* *
55948739 ATATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTG-TT
* * *
55948779 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGTT
* * * *
55948819 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGT-GTT
55948859 ATATCC-GGCTAA
1 ATATCCGGGCTAA
55948871 ATTCCGAAGA
Statistics
Matches: 76, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
39 6 0.08
40 68 0.89
41 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.28
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGTT
Found at i:55951850 original size:295 final size:295
Alignment explanation
Indices: 55951320--55951913 Score: 1188
Period size: 295 Copynumber: 2.0 Consensus size: 295
55951310 ACTGTCGAAC
55951320 CCAAAGGAACTAAAAGTACTAGTAATGACTGTCTTTTTATTATCTAGCCTAAGAATAAAGAGGTT
1 CCAAAGGAACTAAAAGTACTAGTAATGACTGTCTTTTTATTATCTAGCCTAAGAATAAAGAGGTT
55951385 TTGTTTTAATTAACTAATTATCTAAACTAAGAACTCACAGAGAAAAGAATTGGGGAATTGCTTTT
66 TTGTTTTAATTAACTAATTATCTAAACTAAGAACTCACAGAGAAAAGAATTGGGGAATTGCTTTT
55951450 GGGAAAAATCGATTGACTTAAGACAATAACTAAGGACAAATCCACCTAGACTTTACTTGTTATTC
131 GGGAAAAATCGATTGACTTAAGACAATAACTAAGGACAAATCCACCTAGACTTTACTTGTTATTC
55951515 TGGCTCCGAATGTATTCATTCAACTTGCTCCGTAGAGATCCCTAAGTTATGTTATTATCCCTATT
196 TGGCTCCGAATGTATTCATTCAACTTGCTCCGTAGAGATCCCTAAGTTATGTTATTATCCCTATT
55951580 CAAGACTAATAACGTCTAATCCCTAGATTGAATAA
261 CAAGACTAATAACGTCTAATCCCTAGATTGAATAA
55951615 CCAAAGGAACTAAAAGTACTAGTAATGACTGTCTTTTTATTATCTAGCCTAAGAATAAAGAGGTT
1 CCAAAGGAACTAAAAGTACTAGTAATGACTGTCTTTTTATTATCTAGCCTAAGAATAAAGAGGTT
55951680 TTGTTTTAATTAACTAATTATCTAAACTAAGAACTCACAGAGAAAAGAATTGGGGAATTGCTTTT
66 TTGTTTTAATTAACTAATTATCTAAACTAAGAACTCACAGAGAAAAGAATTGGGGAATTGCTTTT
55951745 GGGAAAAATCGATTGACTTAAGACAATAACTAAGGACAAATCCACCTAGACTTTACTTGTTATTC
131 GGGAAAAATCGATTGACTTAAGACAATAACTAAGGACAAATCCACCTAGACTTTACTTGTTATTC
55951810 TGGCTCCGAATGTATTCATTCAACTTGCTCCGTAGAGATCCCTAAGTTATGTTATTATCCCTATT
196 TGGCTCCGAATGTATTCATTCAACTTGCTCCGTAGAGATCCCTAAGTTATGTTATTATCCCTATT
55951875 CAAGACTAATAACGTCTAATCCCTAGATTGAATAA
261 CAAGACTAATAACGTCTAATCCCTAGATTGAATAA
55951910 CCAA
1 CCAA
55951914 GACTTTTCTC
Statistics
Matches: 299, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
295 299 1.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (295 bp):
CCAAAGGAACTAAAAGTACTAGTAATGACTGTCTTTTTATTATCTAGCCTAAGAATAAAGAGGTT
TTGTTTTAATTAACTAATTATCTAAACTAAGAACTCACAGAGAAAAGAATTGGGGAATTGCTTTT
GGGAAAAATCGATTGACTTAAGACAATAACTAAGGACAAATCCACCTAGACTTTACTTGTTATTC
TGGCTCCGAATGTATTCATTCAACTTGCTCCGTAGAGATCCCTAAGTTATGTTATTATCCCTATT
CAAGACTAATAACGTCTAATCCCTAGATTGAATAA
Found at i:55954220 original size:16 final size:16
Alignment explanation
Indices: 55954201--55954232 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55954191 AATTGTTTTA
55954201 TTACAAAATTTCACTT
1 TTACAAAATTTCACTT
*
55954217 TTACATAATTTCACTT
1 TTACAAAATTTCACTT
55954233 ACTCCATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.19, G:0.00, T:0.47
Consensus pattern (16 bp):
TTACAAAATTTCACTT
Found at i:55954518 original size:50 final size:50
Alignment explanation
Indices: 55954443--55954671 Score: 246
Period size: 50 Copynumber: 4.6 Consensus size: 50
55954433 CTGGTACGCA
* * *
55954443 TAGTAGCCTACACTTAGTATTACACATGAGACCTATCAATCTAGTACATG
1 TAGTAGCCTGCACTTAGTACTACACATGAGACCTATCAATCTAGTACACG
* * * *
55954493 TAGTAGCCTGCACTTAGTACTACACACGAGACTTAACCATCT-GATACACG
1 TAGTAGCCTGCACTTAGTACTACACATGAGACCTATCAATCTAG-TACACG
* * ** * ** *
55954543 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTAA-CGGGTACACA
1 TAGTAGCCTGCACTTAGTACTACACATGAGA-CCTA-TCAATCTAGTACACG
* * *
55954594 TAGTAGCCTGTACTTTGTACTACACATGCGACCTATCAATCTAGTACACG
1 TAGTAGCCTGCACTTAGTACTACACATGAGACCTATCAATCTAGTACACG
*
55954644 TAGTAGCCTGCACTTAGTGCTACACATG
1 TAGTAGCCTGCACTTAGTACTACACATG
55954672 TGACTCACAA
Statistics
Matches: 146, Mismatches: 28, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
49 4 0.03
50 105 0.72
51 35 0.24
52 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (50 bp):
TAGTAGCCTGCACTTAGTACTACACATGAGACCTATCAATCTAGTACACG
Found at i:55954618 original size:101 final size:101
Alignment explanation
Indices: 55954493--55954674 Score: 267
Period size: 101 Copynumber: 1.8 Consensus size: 101
55954483 CTAGTACATG
* *
55954493 TAGTAGCCTGCACTTAGTACTACACACGAGACTTAACCATCT-GATACACGTAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACTACACACGAGACCTAACAATCTAG-TACACGTAGTAGCCTGCACT
55954557 TAGTACTACACACGTGATCGAAGTTAACGGGTACACA
65 TAGTACTACACACGTGATCGAAGTTAACGGGTACACA
* * * * *
55954594 TAGTAGCCTGTACTTTGTACTACACATGCGACCTATCAATCTAGTACACGTAGTAGCCTGCACTT
1 TAGTAGCCTGCACTTAGTACTACACACGAGACCTAACAATCTAGTACACGTAGTAGCCTGCACTT
* *
55954659 AGTGCTACACATGTGA
66 AGTACTACACACGTGA
55954675 CTCACAATGA
Statistics
Matches: 71, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 70 0.99
102 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (101 bp):
TAGTAGCCTGCACTTAGTACTACACACGAGACCTAACAATCTAGTACACGTAGTAGCCTGCACTT
AGTACTACACACGTGATCGAAGTTAACGGGTACACA
Found at i:55963360 original size:17 final size:19
Alignment explanation
Indices: 55963333--55963377 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
55963323 ATCTAAATTT
*
55963333 GGGTCGTGTGGG-CCACAC
1 GGGTAGTGTGGGCCCACAC
55963351 GGGT-GTGTGGGCCCACAC
1 GGGTAGTGTGGGCCCACAC
55963369 GGGTAGTGT
1 GGGTAGTGT
55963378 ACACGAGCGT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.28
18 14 0.56
19 4 0.16
ACGTcount: A:0.11, C:0.22, G:0.47, T:0.20
Consensus pattern (19 bp):
GGGTAGTGTGGGCCCACAC
Found at i:55963772 original size:40 final size:40
Alignment explanation
Indices: 55963710--55963786 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
55963700 ATGGTACCAT
** * * *
55963710 TTGGTGTGTAGGGTTGGATGGGTTGATTTTATTCCCATAC
1 TTGGTGTGTAGGGCAGGATGGGTCGATTCTATCCCCATAC
55963750 TTGGTGTGTAGGGCCAGG-TGGGTCGATTCTATCCCCA
1 TTGGTGTGTAGGG-CAGGATGGGTCGATTCTATCCCCA
55963787 CATGGTGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
40 29 0.94
41 2 0.06
ACGTcount: A:0.14, C:0.16, G:0.34, T:0.36
Consensus pattern (40 bp):
TTGGTGTGTAGGGCAGGATGGGTCGATTCTATCCCCATAC
Found at i:55967537 original size:11 final size:11
Alignment explanation
Indices: 55967521--55967551 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
55967511 ATCATTCAAA
55967521 GAATTTTATAT
1 GAATTTTATAT
55967532 GAATTTTATAT
1 GAATTTTATAT
55967543 GAATTTTAT
1 GAATTTTAT
55967552 GGGTATTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (11 bp):
GAATTTTATAT
Found at i:55968234 original size:22 final size:22
Alignment explanation
Indices: 55968206--55968249 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
55968196 TTCTATTGAA
55968206 AATAGACTAATTAAGAATTTAC
1 AATAGACTAATTAAGAATTTAC
55968228 AATAGACTAATTAAGAATTTAC
1 AATAGACTAATTAAGAATTTAC
55968250 TCATATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (22 bp):
AATAGACTAATTAAGAATTTAC
Found at i:55968967 original size:48 final size:50
Alignment explanation
Indices: 55968842--55968975 Score: 166
Period size: 50 Copynumber: 2.7 Consensus size: 50
55968832 AAAAGGGTAA
* *
55968842 AATGTCGATGTCATGTCCCAAGCATGGTCTTACACTGGCTCTCATACATC
1 AATGTCGATGTCATGTCCCAAGCATGGTCTTACACTGACACTCATACATC
* * *
55968892 AGTGTCGATGCCATGTCCCAGGCATGGTCTTACACTGACACAT-ATA-A-C
1 AATGTCGATGTCATGTCCCAAGCATGGTCTTACACTGACAC-TCATACATC
* * *
55968940 AATGCCGATGTCATGTTCCAAACATGGTCTTACACT
1 AATGTCGATGTCATGTCCCAAGCATGGTCTTACACT
55968976 TGCTCGCATA
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
48 31 0.43
49 1 0.01
50 39 0.54
51 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (50 bp):
AATGTCGATGTCATGTCCCAAGCATGGTCTTACACTGACACTCATACATC
Found at i:55969003 original size:48 final size:48
Alignment explanation
Indices: 55968847--55969071 Score: 172
Period size: 48 Copynumber: 4.6 Consensus size: 48
55968837 GGTAAAATGT
* * * *
55968847 CGATGTCATGTCCCA-AGCATGGTCTTACACTGGCTCTCATACATCAGT-GT
1 CGATGCCATGTTCCAGA-CATGGTCTTACACTGGCTCGCATA-AT--GTAGC
* * * * ** **
55968897 CGATGCCATGTCCCAGGCATGGTCTTACACTGACACATATAA-CAATGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCGCATAATGTA-GC
* * * *
55968945 CGATGTCATGTTCCAAACATGGTCTTACACTTGCTCGCATATTG-AGGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCGCATAATGTA-GC
* * * *
55968993 TGATGCCATGTCCCAGACATGGTCTTATACTGGCTCTCATAATGTAGC
1 CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCGCATAATGTAGC
55969041 CGATGCCATG-TCCTAGACATGGTCTTACACT
1 CGATGCCATGTTCC-AGACATGGTCTTACACT
55969072 AGAACACATA
Statistics
Matches: 137, Mismatches: 32, Indels: 14
0.75 0.17 0.08
Matches are distributed among these distances:
47 2 0.01
48 99 0.72
49 2 0.01
50 34 0.25
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (48 bp):
CGATGCCATGTTCCAGACATGGTCTTACACTGGCTCGCATAATGTAGC
Found at i:55969051 original size:96 final size:98
Alignment explanation
Indices: 55968842--55969024 Score: 255
Period size: 98 Copynumber: 1.9 Consensus size: 98
55968832 AAAAGGGTAA
* * * *
55968842 AATGTCGATGTCATGTCCCAAGCATGGTCTTACACTGGCTCTCATACATCAGTGTCGATGCCATG
1 AATGCCGATGTCATGTTCCAAACATGGTCTTACACTGGCTCGCATACATCAGTGTCGATGCCATG
*
55968907 TCCCAGGCATGGTCTTACACTGACACATATAAC
66 TCCCAGACATGGTCTTACACTGACACATATAAC
* * *
55968940 AATGCCGATGTCATGTTCCAAACATGGTCTTACACTTGCTCGCATA-TTGAG-G-CTGATGCCAT
1 AATGCCGATGTCATGTTCCAAACATGGTCTTACACTGGCTCGCATACATCAGTGTC-GATGCCAT
*
55969002 GTCCCAGACATGGTCTTATACTG
65 GTCCCAGACATGGTCTTACACTG
55969025 GCTCTCATAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
95 1 0.01
96 30 0.40
97 3 0.04
98 41 0.55
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (98 bp):
AATGCCGATGTCATGTTCCAAACATGGTCTTACACTGGCTCGCATACATCAGTGTCGATGCCATG
TCCCAGACATGGTCTTACACTGACACATATAAC
Found at i:55969061 original size:96 final size:96
Alignment explanation
Indices: 55968842--55969071 Score: 234
Period size: 96 Copynumber: 2.4 Consensus size: 96
55968832 AAAAGGGTAA
* * * * * * * *
55968842 AATGTCGATGTCATGTCCCAAGCATGGTCTTACACTGGCTCTCATACATCAGTG-TCGATGCCAT
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTTGCTCGCATA-TTGAG-GCT-GATGCCAT
*
55968906 GTCCCAGGCATGGTCTTACACTGACACATATAAC
63 GTCCCAGACATGGTCTTACACTGACACATATAAC
*
55968940 AATGCCGATGTCATGTTCCAAACATGGTCTTACACTTGCTCGCATATTGAGGCTGATGCCATGTC
1 AATGCCGATGCCATGTTCCAAACATGGTCTTACACTTGCTCGCATATTGAGGCTGATGCCATGTC
* * *
55969005 CCAGACATGGTCTTATACTGGCTC-TCATAA-
66 CCAGACATGGTCTTACACTGACACAT-ATAAC
** *
55969035 TGTAGCCGATGCCATG-TCCTAGACATGGTCTTACACT
1 AAT-GCCGATGCCATGTTCC-AAACATGGTCTTACACT
55969072 AGAACACATA
Statistics
Matches: 113, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
95 5 0.04
96 63 0.56
97 4 0.04
98 41 0.36
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (96 bp):
AATGCCGATGCCATGTTCCAAACATGGTCTTACACTTGCTCGCATATTGAGGCTGATGCCATGTC
CCAGACATGGTCTTACACTGACACATATAAC
Found at i:55969082 original size:96 final size:96
Alignment explanation
Indices: 55968897--55969114 Score: 226
Period size: 96 Copynumber: 2.3 Consensus size: 96
55968887 ACATCAGTGT
* *
55968897 CGATGCCATGTCCCAGGCATGGTCTTACACTGACACATATAACAATGCCGATGTCATGTTCCAAA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACACATATAACAATGCCGATGCCATGTTCCAAA
* ** * ** **
55968962 CATGGTCTTACACTTGCTCGCATATTGAGGC
66 CATGGTCTTACACTAGAACACATATCAACAC
* * * * **
55968993 TGATGCCATGTCCCAGACATGGTCTTATACTGGCTC-TCATAA-TGTAGCCGATGCCATG-TCCT
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACACAT-ATAACAAT-GCCGATGCCATGTTCC-
*
55969055 AGACATGGTCTTACACTAGAACACATATCAACAC
63 AAACATGGTCTTACACTAGAACACATATCAACAC
*
55969089 CGATGCCATGTCCCAAACATGGTCTT
1 CGATGCCATGTCCCAGACATGGTCTT
55969115 TTGCTAGCAC
Statistics
Matches: 100, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
95 5 0.05
96 95 0.95
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.27
Consensus pattern (96 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACACATATAACAATGCCGATGCCATGTTCCAAA
CATGGTCTTACACTAGAACACATATCAACAC
Found at i:55969092 original size:48 final size:48
Alignment explanation
Indices: 55968897--55969134 Score: 187
Period size: 48 Copynumber: 5.0 Consensus size: 48
55968887 ACATCAGTGT
*
55968897 CGATGCCATGTCCCAGGCATGGTCTTACACT-G-ACACATAT-AACAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAC-A--C
* * * * * * ** **
55968945 CGATGTCATGTTCCAAACATGGTCTTACACTTGCTCGCATATTGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACAC
* * * * * ** *
55968993 TGATGCCATGTCCCAGACATGGTCTTATACTGGCTCTCATAATGTA-GC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACAT-ATCAACAC
* *
55969041 CGATGCCATGTCCTAGACATGGTCTTACACTAGAACACATATCAACAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACAC
* ***
55969089 CGATGCCATGTCCCAAACATGGTCTTTTGCTAGCACACATATCAAC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAAC
55969135 CAAATGTCTT
Statistics
Matches: 151, Mismatches: 34, Indels: 10
0.77 0.17 0.05
Matches are distributed among these distances:
47 3 0.02
48 137 0.91
49 4 0.03
50 6 0.04
51 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.18, T:0.27
Consensus pattern (48 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCACACATATCAACAC
Found at i:55969130 original size:144 final size:144
Alignment explanation
Indices: 55968848--55969130 Score: 351
Period size: 144 Copynumber: 2.0 Consensus size: 144
55968838 GTAAAATGTC
* *
55968848 GATGTCATGTCCCAAGCATGGTCTTACACTGGCTCTCATACATCAGTGTCGATGCCATGTCCCAG
1 GATGCCATGTCCCAAGCATGGTCTTACACTGGCTCTCATACAT-AGTGCCGATGCCATGTCCCAG
* * * *
55968913 GCATGGTCTTACACTGACACATATAACAATGCCGATGTCATGTTCCAAACATGGTCTTACACTTG
65 ACATGGTCTTACACTGACACATATAACAA-GCCGATGCCATGTCCCAAACATGGTCTTACACTAG
* *
55968978 CTCGCATATTGAGGCT
129 CACACATATTGAGGCT
* *
55968994 GATGCCATGTCCC-AGACATGGTCTTATACTGGCTCTCATA-AT-GTAGCCGATGCCATGTCCTA
1 GATGCCATGTCCCAAG-CATGGTCTTACACTGGCTCTCATACATAGT-GCCGATGCCATGTCCCA
***
55969056 GACATGGTCTTACACTAGAACACATATCAAC-A-CCGATGCCATGTCCCAAACATGGTCTTTTGC
64 GACATGGTCTTACACT-G-ACACATAT-AACAAGCCGATGCCATGTCCCAAACATGGTCTTACAC
55969119 TAGCACACATAT
126 TAGCACACATAT
55969131 CAACCAAATG
Statistics
Matches: 119, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
143 2 0.02
144 65 0.55
145 5 0.04
146 44 0.37
147 3 0.03
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.28
Consensus pattern (144 bp):
GATGCCATGTCCCAAGCATGGTCTTACACTGGCTCTCATACATAGTGCCGATGCCATGTCCCAGA
CATGGTCTTACACTGACACATATAACAAGCCGATGCCATGTCCCAAACATGGTCTTACACTAGCA
CACATATTGAGGCT
Found at i:55972751 original size:19 final size:19
Alignment explanation
Indices: 55972708--55972744 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
55972698 TCCAAACACT
55972708 AGAAAAGTAAATCATTTTC
1 AGAAAAGTAAATCATTTTC
55972727 AGAAAAGTAAATCATTTT
1 AGAAAAGTAAATCATTTT
55972745 TCAAAAATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (19 bp):
AGAAAAGTAAATCATTTTC
Found at i:55975904 original size:43 final size:43
Alignment explanation
Indices: 55975850--55975931 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
55975840 GAGTTTTTAG
* * *
55975850 AATAAGTTTTAAATTCCTTCTTGGCAGCCAAATAGACACCGGC
1 AATAAGCTTTAAATTCCCTCTTAGCAGCCAAATAGACACCGGC
*
55975893 AATAAGCTTTAAATTCCCTCTTAGCAGCCGAATAGACAC
1 AATAAGCTTTAAATTCCCTCTTAGCAGCCAAATAGACAC
55975932 TAACAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.34, C:0.24, G:0.15, T:0.27
Consensus pattern (43 bp):
AATAAGCTTTAAATTCCCTCTTAGCAGCCAAATAGACACCGGC
Found at i:55976400 original size:53 final size:49
Alignment explanation
Indices: 55976316--55976417 Score: 150
Period size: 53 Copynumber: 2.0 Consensus size: 49
55976306 AATTTAGACA
* *
55976316 CATTTATTTAGACTAAACTATATTAACTTAATTAAATAGTTAGCAGCTT
1 CATTTATTTAGACTAAACTATATTAACTTAATTAAATAGCTAGAAGCTT
55976365 CATTTATTTAGACTAAACTATATTAATTAACTTAATTAAATAGCTAGAAGCTT
1 CATTTATTTAGACTAAAC--TA-T-ATTAACTTAATTAAATAGCTAGAAGCTT
55976418 TAGAACGCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
49 18 0.38
51 2 0.04
52 1 0.02
53 26 0.55
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (49 bp):
CATTTATTTAGACTAAACTATATTAACTTAATTAAATAGCTAGAAGCTT
Found at i:55976975 original size:20 final size:21
Alignment explanation
Indices: 55976938--55976981 Score: 72
Period size: 20 Copynumber: 2.1 Consensus size: 21
55976928 CAAATAAACC
55976938 AATACCAAGATAAAAAATAGA
1 AATACCAAGATAAAAAATAGA
*
55976959 AATACCGAGAT-AAAAATAGA
1 AATACCAAGATAAAAAATAGA
55976979 AAT
1 AAT
55976982 CGGTCTTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.64, C:0.09, G:0.11, T:0.16
Consensus pattern (21 bp):
AATACCAAGATAAAAAATAGA
Found at i:55983048 original size:18 final size:18
Alignment explanation
Indices: 55983025--55983065 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
55983015 TTAAATTCTC
*
55983025 TCTTTTTCAATCTCTTTT
1 TCTTTTTCAATCTCTTAT
*
55983043 TCTTTTTCAATTTCTTAT
1 TCTTTTTCAATCTCTTAT
55983061 TCTTT
1 TCTTT
55983066 CATTTCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.12, C:0.20, G:0.00, T:0.68
Consensus pattern (18 bp):
TCTTTTTCAATCTCTTAT
Found at i:55984938 original size:42 final size:41
Alignment explanation
Indices: 55984891--55984976 Score: 102
Period size: 42 Copynumber: 2.1 Consensus size: 41
55984881 GAGTTTTTAG
* * * *
55984891 AATAAG-TTTTAATTCCCTCTTGGTAGCCACATAAACACCAGC
1 AATAAGCTTTAAATTCCATC-TGGCAGCCA-ATAAACACCAAC
*
55984933 AATAAGCTTTAAATTCCATCTGGCAGCCAATAGACACCAAC
1 AATAAGCTTTAAATTCCATCTGGCAGCCAATAAACACCAAC
55984974 AAT
1 AAT
55984977 TTTGTCGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
41 13 0.34
42 14 0.37
43 11 0.29
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.26
Consensus pattern (41 bp):
AATAAGCTTTAAATTCCATCTGGCAGCCAATAAACACCAAC
Found at i:55985186 original size:63 final size:63
Alignment explanation
Indices: 55985114--55985240 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
55985104 ATTCCAGCTG
*
55985114 AATAGTCACCTACAAGCATTAACAAACACATTAAAATCAAGCTTAAATTAAGACATAATTATA
1 AATAGTCACCTACAAGCATTAACAAACACATTAAAATCAAGCTTAAACTAAGACATAATTATA
*
55985177 AATAGTCACCTACAAGCATTAACAAACACATTAAAATCAAGTTTAAACTAAGACATAATTATA
1 AATAGTCACCTACAAGCATTAACAAACACATTAAAATCAAGCTTAAACTAAGACATAATTATA
55985240 A
1 A
55985241 CACATATTTA
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.51, C:0.17, G:0.06, T:0.25
Consensus pattern (63 bp):
AATAGTCACCTACAAGCATTAACAAACACATTAAAATCAAGCTTAAACTAAGACATAATTATA
Found at i:55985560 original size:11 final size:11
Alignment explanation
Indices: 55985544--55985570 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
55985534 GCAACTAAAA
55985544 CAAAATAAATT
1 CAAAATAAATT
55985555 CAAAATAAATT
1 CAAAATAAATT
55985566 CAAAA
1 CAAAA
55985571 CGAGCAAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (11 bp):
CAAAATAAATT
Found at i:55986145 original size:10 final size:10
Alignment explanation
Indices: 55986132--55986231 Score: 75
Period size: 10 Copynumber: 10.3 Consensus size: 10
55986122 TTTTGATGCA
55986132 TTTTATAAAT
1 TTTTATAAAT
*
55986142 TTTT-TATGAT
1 TTTTATA-AAT
*
55986152 TTTTATAAAA
1 TTTTATAAAT
*
55986162 TTTTA-CAAT
1 TTTTATAAAT
*
55986171 TTTTATAATT
1 TTTTATAAAT
55986181 TTTTAT-AAT
1 TTTTATAAAT
*
55986190 TTTTA-ATAT
1 TTTTATAAAT
*
55986199 TTTAAT-AAT
1 TTTTATAAAT
*
55986208 TTTTATTAAAA
1 TTTTA-TAAAT
*
55986219 TTTAATAAAT
1 TTTTATAAAT
55986229 TTT
1 TTT
55986232 ATTTATTTTT
Statistics
Matches: 68, Mismatches: 15, Indels: 14
0.70 0.15 0.14
Matches are distributed among these distances:
9 28 0.41
10 32 0.47
11 8 0.12
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (10 bp):
TTTTATAAAT
Found at i:55986153 original size:19 final size:18
Alignment explanation
Indices: 55986131--55986212 Score: 76
Period size: 19 Copynumber: 4.4 Consensus size: 18
55986121 TTTTTGATGC
*
55986131 ATTTTATAAATTTTTTATG
1 ATTTT-TAAATTTTTTATA
** *
55986150 ATTTTTATAAAATTTTACA
1 ATTTTTA-AATTTTTTATA
55986169 ATTTTTATAATTTTTTATA
1 ATTTTTA-AATTTTTTATA
*
55986188 ATTTTT-AATATTTTAATA
1 ATTTTTAAAT-TTTTTATA
55986206 ATTTTTA
1 ATTTTTA
55986213 TTAAAATTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
17 3 0.06
18 15 0.29
19 34 0.65
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (18 bp):
ATTTTTAAATTTTTTATA
Found at i:55986154 original size:9 final size:9
Alignment explanation
Indices: 55986132--55986213 Score: 76
Period size: 9 Copynumber: 8.7 Consensus size: 9
55986122 TTTTGATGCA
55986132 TTTTATAAATT
1 TTTTAT-AA-T
*
55986143 TTTTATGAT
1 TTTTATAAT
*
55986152 TTTTATAAAA
1 TTTTAT-AAT
*
55986162 TTTTACAAT
1 TTTTATAAT
55986171 TTTTATAATT
1 TTTTATAA-T
55986181 TTTTATAAT
1 TTTTATAAT
55986190 TTTTA-ATAT
1 TTTTATA-AT
*
55986199 TTTAATAAT
1 TTTTATAAT
55986208 TTTTAT
1 TTTTAT
55986214 TAAAATTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
8 1 0.02
9 35 0.59
10 17 0.29
11 6 0.10
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (9 bp):
TTTTATAAT
Found at i:55986181 original size:28 final size:28
Alignment explanation
Indices: 55986142--55986243 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 28
55986132 TTTTATAAAT
*
55986142 TTTTTATGATTTTTATAAAATTTTACA-A
1 TTTTTATAATTTTTATAAAATTTTA-ATA
*
55986170 TTTTTATAATTTTT-TATAATTTTTAATA
1 TTTTTATAATTTTTATA-AAATTTTAATA
*
55986198 TTTTAATAATTTTTATTAAAA-TTTAATAA
1 TTTTTATAATTTTTA-TAAAATTTTAAT-A
* *
55986227 ATTTTATTTATTTTTAT
1 TTTTTA-TAATTTTTAT
55986244 TTTTATCATT
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
27 3 0.05
28 40 0.66
29 8 0.13
30 10 0.16
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.63
Consensus pattern (28 bp):
TTTTTATAATTTTTATAAAATTTTAATA
Found at i:55990485 original size:22 final size:23
Alignment explanation
Indices: 55990456--55990530 Score: 84
Period size: 22 Copynumber: 3.3 Consensus size: 23
55990446 CTGTTGTTTG
*
55990456 TTTTTTTTTCTCTTATAATTCAA
1 TTTTTTTGTCTCTTATAATTCAA
*
55990479 TTTTTTTTGTCTCTGTA-AATT-GA
1 -TTTTTTTGTCTCT-TATAATTCAA
55990502 TTTTTTTGTCTC-TATAATTCAA
1 TTTTTTTGTCTCTTATAATTCAA
*
55990524 ATTTTTT
1 TTTTTTT
55990531 AGTTCATGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
20 2 0.05
21 4 0.09
22 19 0.43
23 1 0.02
24 16 0.36
25 2 0.05
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.64
Consensus pattern (23 bp):
TTTTTTTGTCTCTTATAATTCAA
Found at i:55990491 original size:24 final size:24
Alignment explanation
Indices: 55990456--55990530 Score: 88
Period size: 23 Copynumber: 3.3 Consensus size: 24
55990446 CTGTTGTTTG
55990456 TTTTTTTT-TCTCTTATAATTCAA
1 TTTTTTTTGTCTCTTATAATTCAA
*
55990479 TTTTTTTTGTCTCTGTA-AATT-GA
1 TTTTTTTTGTCTCT-TATAATTCAA
55990502 -TTTTTTTGTCTC-TATAATTCAA
1 TTTTTTTTGTCTCTTATAATTCAA
*
55990524 ATTTTTT
1 TTTTTTT
55990531 AGTTCATGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
20 2 0.04
21 4 0.09
22 13 0.29
23 15 0.33
24 9 0.20
25 2 0.04
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.64
Consensus pattern (24 bp):
TTTTTTTTGTCTCTTATAATTCAA
Found at i:55990529 original size:45 final size:46
Alignment explanation
Indices: 55990391--55990530 Score: 160
Period size: 45 Copynumber: 3.1 Consensus size: 46
55990381 GTATTTCGTC
* * * *
55990391 TTTTTTATCCCTGTAATTTGAATTTTTGGTC-CTTATAATTCTAAT
1 TTTTTTGTCCCTGTAATTTGATTTTTTTGTCTCTTATAATTCAAAT
* ** * *
55990436 TTGTTTGTCCCTGTTGTTTG-TTTTTTTTTCTCTTATAATTCAATT
1 TTTTTTGTCCCTGTAATTTGATTTTTTTGTCTCTTATAATTCAAAT
* *
55990481 TTTTTTGTCTCTGTAAATTGATTTTTTTGTCTC-TATAATTCAAAT
1 TTTTTTGTCCCTGTAATTTGATTTTTTTGTCTCTTATAATTCAAAT
55990526 TTTTT
1 TTTTT
55990531 AGTTCATGTA
Statistics
Matches: 77, Mismatches: 16, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
44 7 0.09
45 59 0.77
46 11 0.14
ACGTcount: A:0.18, C:0.12, G:0.09, T:0.61
Consensus pattern (46 bp):
TTTTTTGTCCCTGTAATTTGATTTTTTTGTCTCTTATAATTCAAAT
Found at i:55995399 original size:25 final size:25
Alignment explanation
Indices: 55995365--55995484 Score: 195
Period size: 25 Copynumber: 4.8 Consensus size: 25
55995355 CTCTTTTAAT
* *
55995365 AACTGAGGCAAAGCCTTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTTGATA
*
55995390 AACTAGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTTGATA
55995415 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTTGATA
* *
55995440 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTTGATA
55995465 AACTGGGGCAAAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
55995485 AGCACTTCCT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 89 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTTGATA
Found at i:55995747 original size:27 final size:27
Alignment explanation
Indices: 55995688--55995830 Score: 184
Period size: 27 Copynumber: 5.4 Consensus size: 27
55995678 AGGGGCAAAT
* *
55995688 GGTAATTTTACCC-A-A-GGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
55995712 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* * * *
55995739 GATATTTCTACCCTACAAGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
55995766 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
55995793 CGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
55995820 GGTAATTCTAC
1 GGTAATTCTAC
55995831 AAATTGAGAG
Statistics
Matches: 102, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
24 12 0.12
25 1 0.01
26 1 0.01
27 88 0.86
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:55995879 original size:81 final size:80
Alignment explanation
Indices: 55995700--55995961 Score: 203
Period size: 81 Copynumber: 3.2 Consensus size: 80
55995690 TAATTTTACC
* * * ** **
55995700 CAAGGGTATCTCGGTAATTCTACCCTATAGGGGTATTTCGATATTTCTACCCTACAAGGGTATTT
1 CAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCGGTAATTCTA-CAAATTAGGGTATTT
* **
55995765 TGGTAA-TTCTAC-CCT
65 TGATAATTTC-ACAAAT
* * *
55995780 ACAGGGGTATTTCCGTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACAAATTGAGAGTATT
1 -CAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACAAATT-AGGGTATT
55995845 TTGATAATTTCACAAAT
64 TTGATAATTTCACAAAT
* * * * *
55995862 CAAGGGTATTTTGGTAATTTTACAAGCC-A-A-GGGTATTTTGGTAATTTTACAAACTAGGGGTA
1 CAAGGGTATTTCGGTAATTCTAC---CCTATAGGGGTATTTCGGTAATTCTACAAATTA-GGGTA
* *
55995924 TTTT-AGTAATTTTACAAAC
62 TTTTGA-TAATTTCACAAAT
* *
55995943 CAGGGGTATTTTGGTAATT
1 CAAGGGTATTTCGGTAATT
55995962 TTACTGATCG
Statistics
Matches: 149, Mismatches: 24, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
80 4 0.03
81 137 0.92
82 5 0.03
83 1 0.01
84 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (80 bp):
CAAGGGTATTTCGGTAATTCTACCCTATAGGGGTATTTCGGTAATTCTACAAATTAGGGTATTTT
GATAATTTCACAAAT
Found at i:55995962 original size:81 final size:81
Alignment explanation
Indices: 55995840--55996582 Score: 410
Period size: 81 Copynumber: 9.2 Consensus size: 81
55995830 CAAATTGAGA
* * * *
55995840 GTATTTT-GATAATTTCACAAATCAAGGGTATTTTGGTAATTTTACAAGCCAAGGGTATTTTGGT
1 GTATTTTAG-TAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAGTCGAGGGTATTTTGGT
* *
55995904 AATTTTACAAACTAGGG
65 AATTTTATAAACCAGGG
* *
55995921 GTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTAC-TGATCGAGGGTATTTTGGT
1 GTATTTTAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAG-TCGAGGGTATTTTGGT
* *
55995985 AATTTTGTAAACCAAGG
65 AATTTTATAAACCAGGG
* **** ** * *****
55996002 GTATTTTAGTAATTTTATAAATC-GAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACAGT
1 GTATTTTAGTAATTTTACAAATCAG-GGGTATTTTGGTAATTTTACAAGTCGAGGGTATTTTGGT
* * **
55996066 AATTCTGTAAA-TTGAGG
65 AATTTTATAAACCAG-GG
*** * * * **** ***
55996083 GTAAAATGGTAATTCTATAAATC-GAGGGTAAAACGGTAATTCTGTA-AA-TCGAGGGTGA-AAC
1 GTATTTTAGTAATTTTACAAATCAG-GGGTATTTTGGTAATT-T-TACAAGTCGAGGGT-ATTTT
* * *
55996144 GATAATTCTATAAATCGAGGG
62 GGTAATTTTATAAA-CCAGGG
* *** * * *
55996165 TGAAACGT--TAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAGCCAAGGGTATTTTGGT
1 -GTATTTTAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAGTCGAGGGTATTTTGGT
* *
55996228 AATTTTACAAACCAGGA
65 AATTTTATAAACCAGGG
* * * *
55996245 GTATTTTAGTAATTATACAAACCA-GGATATTTTGGTAATTTTAC-TGATCGAGGGTATTTTGGT
1 GTATTTTAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAG-TCGAGGGTATTTTGGT
* *
55996308 AATTTTGTAAACCAAGG
65 AATTTTATAAACCAGGG
* **** ***
55996325 GTATTTTAGTAATTTTATAAATC-GAGGGTAAAACGGTAATTCTGTA-AA-TCGAGGGTGA-AAC
1 GTATTTTAGTAATTTTACAAATCAG-GGGTATTTTGGTAATT-T-TACAAGTCGAGGGT-ATTTT
* * *
55996386 GATAATTCTATAAATCGAGGG
62 GGTAATTTTATAAA-CCAGGG
* *** * * *
55996407 TGAAACGT--TAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAGCCAAGGGTATTTTGGT
1 -GTATTTTAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAGTCGAGGGTATTTTGGT
* *
55996470 AATTTTACAAACCAGGA
65 AATTTTATAAACCAGGG
* * * *
55996487 GTATTTTAGTAATTATACAAACCA-GGATATTTTGGTAATTTTAC-TGATCGAGGGTATTTTGGT
1 GTATTTTAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAG-TCGAGGGTATTTTGGT
* **
55996550 AATTTTGTAAACCAATG
65 AATTTTATAAACCAGGG
*
55996567 GTATTTCAGTAATTTT
1 GTATTTTAGTAATTTT
55996583 GTAAATTAAG
Statistics
Matches: 499, Mismatches: 130, Indels: 67
0.72 0.19 0.10
Matches are distributed among these distances:
79 12 0.02
80 143 0.29
81 318 0.64
82 15 0.03
83 11 0.02
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (81 bp):
GTATTTTAGTAATTTTACAAATCAGGGGTATTTTGGTAATTTTACAAGTCGAGGGTATTTTGGTA
ATTTTATAAACCAGGG
Found at i:55996017 original size:27 final size:27
Alignment explanation
Indices: 55995811--55996582 Score: 309
Period size: 27 Copynumber: 28.7 Consensus size: 27
55995801 TACCCTATAG
* * ***
55995811 GGGTATTTCGGTAATTCTACAAATTGA
1 GGGTATTTTGGTAATTTTACAAACCAA
* * * *
55995838 GAGTATTTTGATAATTTCACAAATCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
*
55995865 GGGTATTTTGGTAATTTTACAAGCCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
55995892 GGGTATTTTGGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
55995919 GGGTATTTTAGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
** * *
55995946 GGGTATTTTGGTAATTTTACTGATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
**
55995973 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* * * *
55996000 GGGTATTTTAGTAATTTTATAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
**** ** * *
55996027 GGGTAAAACGGTAATTTTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
***** * ** ***
55996054 GGGTAAAACAGTAATTCTGTAAATTGA
1 GGGTATTTTGGTAATTTTACAAACCAA
*** * * * *
55996081 GGGTAAAATGGTAATTCTATAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
**** * ** * *
55996108 GGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
*** * * * * *
55996135 GGGTGA-AACGATAATTCTATAAATCGA
1 GGGT-ATTTTGGTAATTTTACAAACCAA
*** * * * *
55996162 GGGTGA-AACGTTAATTTCACAAATCAG
1 GGGT-ATTTTGGTAATTTTACAAACCAA
*
55996189 GGGTATTTTGGTAATTTTACAAGCCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
55996216 GGGTATTTTGGTAATTTTACAAACC-A
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
55996242 GGAGTATTTTAGTAATTATACAAACC-A
1 GG-GTATTTTGGTAATTTTACAAACCAA
* ** * *
55996269 GGATATTTTGGTAATTTTACTGATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
**
55996296 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* * * *
55996323 GGGTATTTTAGTAATTTTATAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
**** * ** * *
55996350 GGGTAAAACGGTAATTCTGTAAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
*** * * * * *
55996377 GGGTGA-AACGATAATTCTATAAATCGA
1 GGGT-ATTTTGGTAATTTTACAAACCAA
*** * * * *
55996404 GGGTGA-AACGTTAATTTCACAAATCAG
1 GGGT-ATTTTGGTAATTTTACAAACCAA
*
55996431 GGGTATTTTGGTAATTTTACAAGCCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
55996458 GGGTATTTTGGTAATTTTACAAACC-A
1 GGGTATTTTGGTAATTTTACAAACCAA
* *
55996484 GGAGTATTTTAGTAATTATACAAACC-A
1 GG-GTATTTTGGTAATTTTACAAACCAA
* ** * *
55996511 GGATATTTTGGTAATTTTACTGATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
**
55996538 GGGTATTTTGGTAATTTTGTAAACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
* **
55996565 TGGTATTTCAGTAATTTT
1 GGGTATTTTGGTAATTTT
55996583 GTAAATTAAG
Statistics
Matches: 611, Mismatches: 126, Indels: 16
0.81 0.17 0.02
Matches are distributed among these distances:
26 42 0.07
27 567 0.93
28 2 0.00
ACGTcount: A:0.33, C:0.09, G:0.21, T:0.36
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:55996376 original size:242 final size:242
Alignment explanation
Indices: 55996091--55996676 Score: 1028
Period size: 242 Copynumber: 2.4 Consensus size: 242
55996081 GGGTAAAATG
*
55996091 GTAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTGAAACGATAATTCTATA
1 GTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTGAAACGATAATTCTATA
55996156 AATCGAGGGTGAAACGTTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAGCCAAGGGTA
66 AATCGAGGGTGAAACGTTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAGCCAAGGGTA
55996221 TTTTGGTAATTTTACAAACCAGGAGTATTTTAGTAATTATACAAACCAGGATATTTTGGTAATTT
131 TTTTGGTAATTTTACAAACCAGGAGTATTTTAGTAATTATACAAACCAGGATATTTTGGTAATTT
*
55996286 TACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTA
196 TACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCA
55996333 GTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTGAAACGATAATTCTATA
1 GTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTGAAACGATAATTCTATA
55996398 AATCGAGGGTGAAACGTTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAGCCAAGGGTA
66 AATCGAGGGTGAAACGTTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAGCCAAGGGTA
55996463 TTTTGGTAATTTTACAAACCAGGAGTATTTTAGTAATTATACAAACCAGGATATTTTGGTAATTT
131 TTTTGGTAATTTTACAAACCAGGAGTATTTTAGTAATTATACAAACCAGGATATTTTGGTAATTT
*
55996528 TACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAATGGTATTTCA
196 TACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCA
* ** * * * *
55996575 GTAATTTTGTAAATTAAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATGGTAATTCTATA
1 GTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTGAAACGATAATTCTATA
* * * * * *
55996640 AATTGAGGGTAAAACGGTAATTTTATAAATCAAGGGT
66 AATCGAGGGTGAAACGTTAATTTCACAAATCAGGGGT
55996677 GAAACGTTAA
Statistics
Matches: 328, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
242 328 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (242 bp):
GTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTGAAACGATAATTCTATA
AATCGAGGGTGAAACGTTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAGCCAAGGGTA
TTTTGGTAATTTTACAAACCAGGAGTATTTTAGTAATTATACAAACCAGGATATTTTGGTAATTT
TACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTCA
Found at i:55996596 original size:27 final size:27
Alignment explanation
Indices: 55996537--55996676 Score: 84
Period size: 27 Copynumber: 5.2 Consensus size: 27
55996527 TTACTGATCG
* **
55996537 AGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTCGGTAATTTTGTAAATTA
* *
55996564 ATGGTATTTCAGTAATTTTGTAAATTA
1 AGGGTATTTCGGTAATTTTGTAAATTA
*** * *
55996591 AGGGTAAAACGGTAATTCTGTAAATTG
1 AGGGTATTTCGGTAATTTTGTAAATTA
** * * *
55996618 AGGGTAAAAT-GGTAATTCTATAAATTG
1 AGGGT-ATTTCGGTAATTTTGTAAATTA
*** * *
55996645 AGGGTAAAACGGTAATTTTATAAATCA
1 AGGGTATTTCGGTAATTTTGTAAATTA
55996672 AGGGT
1 AGGGT
55996677 GAAACGTTAA
Statistics
Matches: 93, Mismatches: 18, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
26 3 0.03
27 87 0.94
28 3 0.03
ACGTcount: A:0.36, C:0.06, G:0.22, T:0.36
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTGTAAATTA
Found at i:55996681 original size:27 final size:27
Alignment explanation
Indices: 55996575--55997162 Score: 320
Period size: 27 Copynumber: 21.8 Consensus size: 27
55996565 TGGTATTTCA
* * *
55996575 GTAATTTTGTAAATTAAGGGTAAAACG
1 GTAATTCTATAAATCAAGGGTAAAACG
* ** *
55996602 GTAATTCTGTAAATTGAGGGTAAAATG
1 GTAATTCTATAAATCAAGGGTAAAACG
**
55996629 GTAATTCTATAAATTGAGGGTAAAACG
1 GTAATTCTATAAATCAAGGGTAAAACG
* *
55996656 GTAATTTTATAAATCAAGGGTGAAACG
1 GTAATTCTATAAATCAAGGGTAAAACG
* ** **
55996683 TTAATTCTATAAATTGAGGGTAAAATA
1 GTAATTCTATAAATCAAGGGTAAAACG
* *
55996710 GTAATTCTGTAAATCAAGGGTAAAATG
1 GTAATTCTATAAATCAAGGGTAAAACG
55996737 GTAATTCTATAAATCAAGGGTAAAACG
1 GTAATTCTATAAATCAAGGGTAAAACG
* *
55996764 GTAATTCTATAAATCAAAGGTGAAACG
1 GTAATTCTATAAATCAAGGGTAAAACG
* * *
55996791 ATAATTCTATAAATCGAGGGTGAAACG
1 GTAATTCTATAAATCAAGGGTAAAACG
* * * ****
55996818 TTAATT-TCAAAAATCAGGGGTATTTTG
1 GTAATTCT-ATAAATCAAGGGTAAAACG
* * * * * ***
55996845 AT-ATTTTACAAATCGAGAGTATTTCG
1 GTAATTCTATAAATCAAGGGTAAAACG
* * * * *****
55996871 ATAATTTTACAAA-CAGGGAGTATTTTA
1 GTAATTCTATAAATCAAGG-GTAAAACG
* * * * * ****
55996898 GAAATTGTACAAACCAGGGGTATTTTG
1 GTAATTCTATAAATCAAGGGTAAAACG
* * * ****
55996925 GTAATTTTACT-GATCGAGGGTATTTTG
1 GTAATTCTA-TAAATCAAGGGTAAAACG
* * * * *** *
55996952 GTAATTTTGTAAACCAATGGTATTTCA
1 GTAATTCTATAAATCAAGGGTAAAACG
* * *
55996979 GTAATTTTGTAAATTAAGGGTAAAACG
1 GTAATTCTATAAATCAAGGGTAAAACG
* ** *
55997006 GTAATTCTGTAAATTGAGGGTAAAATG
1 GTAATTCTATAAATCAAGGGTAAAACG
**
55997033 GTAATTCTATAAATTGAGGGTAAAACG
1 GTAATTCTATAAATCAAGGGTAAAACG
* *
55997060 GTAATTTTATAAATCAAGGGTGAAACG
1 GTAATTCTATAAATCAAGGGTAAAACG
* ** *
55997087 TTAATTCTATAAATTGAGGGTAAAATG
1 GTAATTCTATAAATCAAGGGTAAAACG
*
55997114 GTAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTCTATAAATCAAGGGTAAAACG
* *
55997141 GTAATTTTGTAAATCAAGGGTA
1 GTAATTCTATAAATCAAGGGTA
55997163 CTTTGGTAAT
Statistics
Matches: 460, Mismatches: 94, Indels: 14
0.81 0.17 0.02
Matches are distributed among these distances:
26 23 0.05
27 432 0.94
28 5 0.01
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (27 bp):
GTAATTCTATAAATCAAGGGTAAAACG
Found at i:55997173 original size:54 final size:54
Alignment explanation
Indices: 55996010--55997162 Score: 357
Period size: 54 Copynumber: 21.4 Consensus size: 54
55996000 GGGTATTTTA
* * * * * *
55996010 GTAATTTTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * ** *
55996064 GTAATTCTGTAAATTGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * * * * * * *
55996118 GTAATTCTGTAAATCGAGGGTGAAACGATAATTCTATAAATCGAGGGTGAAACG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * * * *** * * ** ****
55996172 TTAATTTCACAAATCAGGGGTATTTTGGTAATTTTACAAGCCAAGGGTATTTTG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * *** * * * * * ****
55996226 GTAATTTTACAAA-CCAGGAGTATTTTAGTAATTATACAAA-CCAGGATATTTTG
1 GTAATTTTATAAATCAAGG-GTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * *** * * * *****
55996279 GTAATTTTACT-GATCGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTA
1 GTAATTTTA-TAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * * * *
55996333 GTAATTTTATAAATCGAGGGTAAAACGGTAATTCTGTAAATCGAGGGTGAAACG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * * * * * * * ****
55996387 ATAATTCTATAAATCGAGGGTGAAACGTTAATT-TCACAAATCAGGGGTATTTTG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCT-ATAAATCAAGGGTAAAACG
* ** *** * * * *****
55996441 GTAATTTTACAAGCCAAGGGTATTTTGGTAATTTTACAAA-CCAGGAGTATTTTA
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGG-GTAAAACG
* * * * *** * * * ****
55996495 GTAATTATACAAA-CCAGGATATTTTGGTAATTTTACT-GATCGAGGGTATTTTG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTA-TAAATCAAGGGTAAAACG
* * * ** * * * *
55996548 GTAATTTTGTAAACCAATGGT-ATTTCAGTAATTTTGTAAATTAAGGGTAAAACG
1 GTAATTTTATAAATCAAGGGTAAAAT-GGTAATTCTATAAATCAAGGGTAAAACG
* * ** **
55996602 GTAATTCTGTAAATTGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAACG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * * ** **
55996656 GTAATTTTATAAATCAAGGGTGAAACGTTAATTCTATAAATTGAGGGTAAAATA
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* *
55996710 GTAATTCTGTAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * * * * * *
55996764 GTAATTCTATAAATCAAAGGTGAAACGATAATTCTATAAATCGAGGGTGAAACG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * * * *** * * * * * ***
55996818 TTAATTTCAAAAATCAGGGGTATTTTGAT-ATTTTACAAATCGAGAGTATTTCG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * * *** * * * * * * ****
55996871 ATAATTTTACAAA-CAGGGAGTATTTTAGAAATTGTACAAACCAGGGGTATTTTG
1 GTAATTTTATAAATCAAGG-GTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * *** * * * * *** *
55996925 GTAATTTTACT-GATCGAGGGTATTTTGGTAATTTTGTAAACCAATGGTATTTCA
1 GTAATTTTA-TAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * * * ** *
55996979 GTAATTTTGTAAATTAAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* ** * * *
55997033 GTAATTCTATAAATTGAGGGTAAAACGGTAATTTTATAAATCAAGGGTGAAACG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
* * ** *
55997087 TTAATTCTATAAATTGAGGGTAAAATGGTAATTCTGTAAATCAAGGGTAAAACG
1 GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
*
55997141 GTAATTTTGTAAATCAAGGGTA
1 GTAATTTTATAAATCAAGGGTA
55997163 CTTTGGTAAT
Statistics
Matches: 843, Mismatches: 237, Indels: 38
0.75 0.21 0.03
Matches are distributed among these distances:
52 5 0.01
53 123 0.15
54 709 0.84
55 6 0.01
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.34
Consensus pattern (54 bp):
GTAATTTTATAAATCAAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAACG
Found at i:55997187 original size:81 final size:81
Alignment explanation
Indices: 55996575--55997162 Score: 446
Period size: 81 Copynumber: 7.3 Consensus size: 81
55996565 TGGTATTTCA
* * *
55996575 GTAATTTTGTAAATTAAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATGGTAATTCTATA
1 GTAATTTTATAAATCAAGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTATA
**
55996640 AATTGAGGGTAAAACG
66 AATCAAGGGTAAAACG
* * * *
55996656 GTAATTTTATAAATCAAGGGTGAAACGTTAATTCTATAAATTGAGGGTAAAATAGTAATTCTGTA
1 GTAATTTTATAAATCAAGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTATA
*
55996721 AATCAAGGGTAAAATG
66 AATCAAGGGTAAAACG
* ** * * * *
55996737 GTAATTCTATAAATCAAGGGTAAAACGGTAATTCTATAAATCAAAGGTGAAACGATAATTCTATA
1 GTAATTTTATAAATCAAGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTATA
* *
55996802 AATCGAGGGTGAAACG
66 AATCAAGGGTAAAACG
* * * * **** * * * * * ** * * *
55996818 TTAATTTCAAAAATCAGGGGTATTTTGAT-ATTTTACAAATCGAGAGT-ATTTCGATAATTTTAC
1 GTAATTTTATAAATCAAGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAAT-GGTAATTCTAT
* *****
55996881 AAA-CAGGGAGTATTTTA
65 AAATCAAGG-GTAAAACG
* * * * * **** * * * *** * *
55996898 GAAATTGTACAAACCAGGGGTATTTTGGTAATTTTACT-GATCGAGGGTATTTTGGTAATTTTGT
1 GTAATTTTATAAATCAAGGGTAAAACGGTAATTCTA-TAAATTGAGGGTAAAATGGTAATTCTAT
* * *** *
55996962 AAACCAATGGTATTTCA
65 AAATCAAGGGTAAAACG
* * *
55996979 GTAATTTTGTAAATTAAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAATGGTAATTCTATA
1 GTAATTTTATAAATCAAGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTATA
**
55997044 AATTGAGGGTAAAACG
66 AATCAAGGGTAAAACG
* * *
55997060 GTAATTTTATAAATCAAGGGTGAAACGTTAATTCTATAAATTGAGGGTAAAATGGTAATTCTGTA
1 GTAATTTTATAAATCAAGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTATA
55997125 AATCAAGGGTAAAACG
66 AATCAAGGGTAAAACG
*
55997141 GTAATTTTGTAAATCAAGGGTA
1 GTAATTTTATAAATCAAGGGTA
55997163 CTTTGGTAAT
Statistics
Matches: 393, Mismatches: 107, Indels: 14
0.76 0.21 0.03
Matches are distributed among these distances:
79 4 0.01
80 50 0.13
81 333 0.85
82 6 0.02
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (81 bp):
GTAATTTTATAAATCAAGGGTAAAACGGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTATA
AATCAAGGGTAAAACG
Found at i:56000020 original size:29 final size:27
Alignment explanation
Indices: 56000002--56000071 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
55999992 ATATTAAGTC
56000002 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTCAGTGCTATATAATCAACT
*
56000029 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTCAGTGCTATATAATC-AACT
*
56000057 CGCACACTTAGTGCT
1 CGCACACTCAGTGCT
56000072 GTACAATTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 22 0.54
28 19 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTCAGTGCTATATAATCAACT
Found at i:56000065 original size:28 final size:28
Alignment explanation
Indices: 56000002--56000099 Score: 135
Period size: 28 Copynumber: 3.5 Consensus size: 28
55999992 ATATTAAGTC
*
56000002 CGCACACTCAGTGCTATATAATC-AACT
1 CGCACACTTAGTGCTATATAATCAAACT
56000029 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
56000057 CGCACACTTAGTGCTGTACAATTTAAACC
1 CGCACACTTAGTGCTATATAA-TCAAACT
56000086 CGCACACTTAGTGC
1 CGCACACTTAGTGC
56000100 CAATCTCATG
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
27 22 0.34
28 23 0.36
29 19 0.30
ACGTcount: A:0.32, C:0.29, G:0.13, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:56002974 original size:24 final size:25
Alignment explanation
Indices: 56002947--56002998 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
56002937 GCCTAACCTC
*
56002947 TTTTAATAACCGA-GGCAAAGCCCT
1 TTTTAATAAACGAGGGCAAAGCCCT
* *
56002971 TTTTGATAAACTAGGGCAAAGCCCT
1 TTTTAATAAACGAGGGCAAAGCCCT
56002996 TTT
1 TTT
56002999 CGGTAAACTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (25 bp):
TTTTAATAAACGAGGGCAAAGCCCT
Found at i:56002992 original size:25 final size:25
Alignment explanation
Indices: 56002960--56003048 Score: 126
Period size: 25 Copynumber: 3.6 Consensus size: 25
56002950 TAATAACCGA
* *
56002960 GGCAAAGCCCTTTTTGATAAACTAG
1 GGCAAAGCCCTTTTTGGTAAACTGG
*
56002985 GGCAAAGCCCTTTTCGGTAAACTGG
1 GGCAAAGCCCTTTTTGGTAAACTGG
*
56003010 GGCAAAG-CTTTTTTCGGTAAACTGG
1 GGCAAAGCCCTTTTT-GGTAAACTGG
56003035 GGCAAAGCCCTTTT
1 GGCAAAGCCCTTTT
56003049 AGCACTTCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
24 5 0.09
25 46 0.82
26 5 0.09
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (25 bp):
GGCAAAGCCCTTTTTGGTAAACTGG
Found at i:56003312 original size:27 final size:27
Alignment explanation
Indices: 56003268--56003448 Score: 233
Period size: 27 Copynumber: 6.7 Consensus size: 27
56003258 TTTTACCCAA
* * *
56003268 GGGTATCTCGGTAATTCTACCCTATAG
1 GGGTATTTCGATAATTCTACCCTACAG
* * *
56003295 GAGTATTTCGATATTTCTACCCTACAA
1 GGGTATTTCGATAATTCTACCCTACAG
* *
56003322 GGGTATTTTGGTAA-TCTACCCTACAG
1 GGGTATTTCGATAATTCTACCCTACAG
56003348 GGGTATTTC-AGTAATTCTACCCTACAG
1 GGGTATTTCGA-TAATTCTACCCTACAG
56003375 GGGTATTTCGATAATTCTACCCTACAG
1 GGGTATTTCGATAATTCTACCCTACAG
*
56003402 GGGTATTT-TAGTAATTCTACCCTACAG
1 GGGTATTTCGA-TAATTCTACCCTACAG
*
56003429 GGGTATTTCAATAATTCTAC
1 GGGTATTTCGATAATTCTAC
56003449 AAATCGAGAG
Statistics
Matches: 134, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
26 23 0.17
27 109 0.81
28 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (27 bp):
GGGTATTTCGATAATTCTACCCTACAG
Found at i:56003366 original size:80 final size:81
Alignment explanation
Indices: 56003268--56003448 Score: 283
Period size: 80 Copynumber: 2.2 Consensus size: 81
56003258 TTTTACCCAA
* * * * *
56003268 GGGTATCTCGGTAATTCTACCCTATAGGAGTATTTCGATATTTCTACCCTACAAGGGTATTTTGG
1 GGGTATTTCAGTAATTCTACCCTACAGGAGTATTTCGATAATTCTACCCTACAAGGGTATTTTAG
56003333 TAA-TCTACCCTACAG
66 TAATTCTACCCTACAG
* *
56003348 GGGTATTTCAGTAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTTAG
1 GGGTATTTCAGTAATTCTACCCTACAGGAGTATTTCGATAATTCTACCCTACAAGGGTATTTTAG
56003413 TAATTCTACCCTACAG
66 TAATTCTACCCTACAG
*
56003429 GGGTATTTCAATAATTCTAC
1 GGGTATTTCAGTAATTCTAC
56003449 AAATCGAGAG
Statistics
Matches: 92, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
80 61 0.66
81 31 0.34
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.35
Consensus pattern (81 bp):
GGGTATTTCAGTAATTCTACCCTACAGGAGTATTTCGATAATTCTACCCTACAAGGGTATTTTAG
TAATTCTACCCTACAG
Found at i:56003463 original size:81 final size:80
Alignment explanation
Indices: 56003279--56003471 Score: 246
Period size: 80 Copynumber: 2.4 Consensus size: 80
56003269 GGTATCTCGG
** * * *
56003279 TAATTCTACCCTATAGGAGTATTTCGATATTTCTACCCTACAAGGGTATTTTGGTAATCTACCCT
1 TAATTCTACAATACAGGAGTATTTCGATAATTCTACCCTACAAGGGTATTTTAGTAATCTACCCT
*
56003344 ACAGGGGTATTTCAG
66 ACAGGGGTATTTCAA
** * *
56003359 TAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTTAGTAATTCTACCC
1 TAATTCTACAATACAGGAGTATTTCGATAATTCTACCCTACAAGGGTATTTTAGTAA-TCTACCC
56003424 TACAGGGGTATTTCAA
65 TACAGGGGTATTTCAA
*
56003440 TAATTCTACAA-ATC-GAGAGTATTTCCATAATT
1 TAATTCTACAATA-CAG-GAGTATTTCGATAATT
56003472 TCACAAATCA
Statistics
Matches: 100, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
80 54 0.54
81 46 0.46
ACGTcount: A:0.28, C:0.20, G:0.16, T:0.36
Consensus pattern (80 bp):
TAATTCTACAATACAGGAGTATTTCGATAATTCTACCCTACAAGGGTATTTTAGTAATCTACCCT
ACAGGGGTATTTCAA
Found at i:56003498 original size:81 final size:81
Alignment explanation
Indices: 56003279--56003498 Score: 209
Period size: 81 Copynumber: 2.7 Consensus size: 81
56003269 GGTATCTCGG
** * * * ** * *
56003279 TAATTCTACCCTATAGGAGTATTTCGATATTTCTACCCTACAAGGGTATTTTGGTAA-TCTACCC
1 TAATTCTACAATACAGGAGTATTTCCATAATTCTACAATACAGGGGTATTTTGATAATTCTACCC
*
56003343 TACAGGGGTATTTCAG
66 TACAGGGGTATTTCAA
** * * **
56003359 TAATTCTACCCTACAGGGGTATTTCGATAATTCTACCCTACAGGGGTATTTT-AGTAATTCTACC
1 TAATTCTACAATACAGGAGTATTTCCATAATTCTACAATACAGGGGTATTTTGA-TAATTCTACC
56003423 CTACAGGGGTATTTCAA
65 CTACAGGGGTATTTCAA
56003440 TAATTCTACAA-ATC-GAGAGTATTTCCATAATT-TCACAA-ATCAGGGGTATTTTGATAATT
1 TAATTCTACAATA-CAG-GAGTATTTCCATAATTCT-ACAATA-CAGGGGTATTTTGATAATT
56003499 TTACAAGCCA
Statistics
Matches: 121, Mismatches: 12, Indels: 13
0.83 0.08 0.09
Matches are distributed among these distances:
80 55 0.45
81 65 0.54
82 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (81 bp):
TAATTCTACAATACAGGAGTATTTCCATAATTCTACAATACAGGGGTATTTTGATAATTCTACCC
TACAGGGGTATTTCAA
Found at i:56003518 original size:27 final size:27
Alignment explanation
Indices: 56003426--56003571 Score: 107
Period size: 27 Copynumber: 5.4 Consensus size: 27
56003416 TTCTACCCTA
** * *
56003426 CAGGGGTATTTCAATAATTCTACAAAT
1 CAGGGGTATTTTGATAATTTTACAAAC
* ** * *
56003453 C-GAGAGTATTTCCATAATTTCACAAAT
1 CAG-GGGTATTTTGATAATTTTACAAAC
*
56003480 CAGGGGTATTTTGATAATTTTACAAGC
1 CAGGGGTATTTTGATAATTTTACAAAC
* * *
56003507 CAGGGGTATTTTGGTAATTTTACTAAT
1 CAGGGGTATTTTGATAATTTTACAAAC
* **
56003534 C-GAGGGTATTTTGGTAATTTTTTAAAC
1 CAG-GGGTATTTTGATAATTTTACAAAC
*
56003561 CAAGGGTATTT
1 CAGGGGTATTT
56003572 CAGTAATTTT
Statistics
Matches: 96, Mismatches: 19, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
26 2 0.02
27 93 0.97
28 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (27 bp):
CAGGGGTATTTTGATAATTTTACAAAC
Found at i:56003581 original size:54 final size:54
Alignment explanation
Indices: 56003348--56003581 Score: 145
Period size: 54 Copynumber: 4.3 Consensus size: 54
56003338 TACCCTACAG
* ** * * ** *
56003348 GGGTATTTCAGTAATTCTAC-CCTACAGGGGTATTTCGATAATTCTACCCTA-CAG
1 GGGTATTTCAGTAATTTTACAAAT-CAGGGGTATTTTGATAATTTTA-CAAACCAA
* * ** ** * * *
56003402 GGGTATTTTAGTAATTCTAC-CCTACAGGGGTATTTCAATAATTCTACAAATCGA
1 GGGTATTTCAGTAATTTTACAAAT-CAGGGGTATTTTGATAATTTTACAAACCAA
* * * *
56003456 GAGTATTTCCA-TAATTTCACAAATCAGGGGTATTTTGATAATTTTACAAGCCAG
1 GGGTATTT-CAGTAATTTTACAAATCAGGGGTATTTTGATAATTTTACAAACCAA
** * * **
56003510 GGGTATTTTGGTAATTTTACTAATC-GAGGGTATTTTGGTAATTTTTTAAACCAA
1 GGGTATTTCAGTAATTTTACAAATCAG-GGGTATTTTGATAATTTTACAAACCAA
56003564 GGGTATTTCAGTAATTTT
1 GGGTATTTCAGTAATTTT
56003582 GTAAATTGAG
Statistics
Matches: 144, Mismatches: 31, Indels: 10
0.78 0.17 0.05
Matches are distributed among these distances:
53 3 0.02
54 139 0.97
55 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (54 bp):
GGGTATTTCAGTAATTTTACAAATCAGGGGTATTTTGATAATTTTACAAACCAA
Found at i:56003605 original size:54 final size:54
Alignment explanation
Indices: 56003547--56003775 Score: 190
Period size: 54 Copynumber: 4.2 Consensus size: 54
56003537 GGGTATTTTG
* * *** * *
56003547 GTAATTTTTTAAACCAAGGGTATTTCAGTAATTTTGTAAATTGAGGGTAAAACA
1 GTAATTCTATAAACCAAGGGTAAAACAGTAATTTTGTAAATCGAGGGAAAAACA
* * * **
56003601 GTAATTCTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGAAAAATG
1 GTAATTCTATAAACCAAGGGTAAAACAGTAATTTTGTAAATCGAGGGAAAAACA
* * * ** *
56003655 GTAATTCTATAAATCGAGGGTAAAAC-GATAATTCTGTAAATCGAGGGTGAAACG
1 GTAATTCTATAAACCAAGGGTAAAACAG-TAATTTTGTAAATCGAGGGAAAAACA
* * ** * * * * **
56003709 GTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAATG
1 GTAATTCTATAAACCAAGGGTAAAACAGTAATTTTGTAAATCGAGGGAAAAACA
56003763 GTAATTCTATAAA
1 GTAATTCTATAAA
56003776 TCGAGAGTAT
Statistics
Matches: 152, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 150 0.99
55 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (54 bp):
GTAATTCTATAAACCAAGGGTAAAACAGTAATTTTGTAAATCGAGGGAAAAACA
Found at i:56003631 original size:81 final size:81
Alignment explanation
Indices: 56003546--56003780 Score: 249
Period size: 81 Copynumber: 2.9 Consensus size: 81
56003536 AGGGTATTTT
* * ** * * *
56003546 GGTAATTTTTTAAACCAAGGG-TATTTCAGTAATTTTGTAAATTGAGGGTAAAAC-AGTAATTCT
1 GGTAATTTTGTAAACCAAGGGAAAAAT-AGTAATTCTATAAATCGAGGGTAAAACGA-TAATTCT
56003609 ATAAATCGAGGGTAAAAC
64 ATAAATCGAGGGTAAAAC
* * * *
56003627 GGTAATTTTGTAAATCGAGGGAAAAATGGTAATTCTATAAATCGAGGGTAAAACGATAATTCTGT
1 GGTAATTTTGTAAACCAAGGGAAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTAT
*
56003692 AAATCGAGGGTGAAAC
66 AAATCGAGGGTAAAAC
* * * * * * * * *
56003708 GGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAATGGTAATTCTAT
1 GGTAATTTTGTAAACCAAGGGAAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTAT
56003773 AAATCGAG
66 AAATCGAG
56003781 AGTATTTTGG
Statistics
Matches: 133, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
81 130 0.98
82 3 0.02
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.30
Consensus pattern (81 bp):
GGTAATTTTGTAAACCAAGGGAAAAATAGTAATTCTATAAATCGAGGGTAAAACGATAATTCTAT
AAATCGAGGGTAAAAC
Found at i:56003795 original size:27 final size:27
Alignment explanation
Indices: 56003574--56003780 Score: 279
Period size: 27 Copynumber: 7.7 Consensus size: 27
56003564 GGGTATTTCA
* * * **
56003574 GTAATTTTGTAAATTGAGGGTAAAACA
1 GTAATTCTATAAATCGAGGGTAAAATG
*
56003601 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
* * *
56003628 GTAATTTTGTAAATCGAGGGAAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
56003655 GTAATTCTATAAATCGAGGGTAAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
* * * *
56003682 ATAATTCTGTAAATCGAGGGTGAAACG
1 GTAATTCTATAAATCGAGGGTAAAATG
56003709 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
*
56003736 GTAATTCTATAAATCAAGGGTAAAATG
1 GTAATTCTATAAATCGAGGGTAAAATG
56003763 GTAATTCTATAAATCGAG
1 GTAATTCTATAAATCGAG
56003781 AGTATTTTGG
Statistics
Matches: 159, Mismatches: 21, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 159 1.00
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.29
Consensus pattern (27 bp):
GTAATTCTATAAATCGAGGGTAAAATG
Found at i:56003814 original size:27 final size:27
Alignment explanation
Indices: 56003761--56003814 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
56003751 AAGGGTAAAA
* *
56003761 TGGTAATTCTATAAATCGAGAGTATTT
1 TGGTAATTCTACAAATCGAGAGCATTT
* * *
56003788 TGGTAATTTTACAAATTGAGGGCATTT
1 TGGTAATTCTACAAATCGAGAGCATTT
56003815 CAGGAATTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.31, C:0.07, G:0.20, T:0.41
Consensus pattern (27 bp):
TGGTAATTCTACAAATCGAGAGCATTT
Found at i:56003995 original size:12 final size:12
Alignment explanation
Indices: 56003978--56004004 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
56003968 TTACTACACA
56003978 ATCAAACAACTT
1 ATCAAACAACTT
56003990 ATCAAACAACTT
1 ATCAAACAACTT
56004002 ATC
1 ATC
56004005 GCGGCCCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (12 bp):
ATCAAACAACTT
Found at i:56007807 original size:19 final size:20
Alignment explanation
Indices: 56007783--56007820 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
56007773 GCTCGAATTA
*
56007783 TAAAA-TTAATTTTATTTTT
1 TAAAATTTAAATTTATTTTT
56007802 TAAAATTTAAATTTATTTT
1 TAAAATTTAAATTTATTTT
56007821 AATTATATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TAAAATTTAAATTTATTTTT
Found at i:56014860 original size:29 final size:29
Alignment explanation
Indices: 56014822--56014913 Score: 98
Period size: 29 Copynumber: 3.1 Consensus size: 29
56014812 TATAGATAAG
*
56014822 TATAGGGGTTTTGTTATTTATATATAATA
1 TATATGGGTTTTGTTATTTATATATAATA
* *
56014851 TATATGGGTTTTGGTGTTATATATATAATA
1 TATATGGGTTTTGTTATT-TATATATAATA
**
56014881 TATATGTGCGGGTT-TTA-TTATATATAATA
1 TATATG-G-GTTTTGTTATTTATATATAATA
56014910 TATA
1 TATA
56014914 CACATTTATA
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
29 30 0.57
30 18 0.34
31 2 0.04
32 3 0.06
ACGTcount: A:0.32, C:0.01, G:0.17, T:0.50
Consensus pattern (29 bp):
TATATGGGTTTTGTTATTTATATATAATA
Found at i:56014876 original size:30 final size:29
Alignment explanation
Indices: 56014822--56014886 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
56014812 TATAGATAAG
* *
56014822 TATAGGGGTTTTGTTATTTATATATAATA
1 TATATGGGTTTTGGTATTTATATATAATA
*
56014851 TATATGGGTTTTGGTGTTATATATATAATA
1 TATATGGGTTTTGGTATT-TATATATAATA
56014881 TATATG
1 TATATG
56014887 TGCGGGTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 15 0.47
30 17 0.53
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (29 bp):
TATATGGGTTTTGGTATTTATATATAATA
Found at i:56015319 original size:18 final size:18
Alignment explanation
Indices: 56015295--56015345 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
56015285 TATTATGGAA
*
56015295 AATTGTATTAATTTGGTG
1 AATTGTATTAATTTGATG
*
56015313 -ATCTGTATTAATATGATG
1 AAT-TGTATTAATTTGATG
56015331 AATTGTATTAATTTG
1 AATTGTATTAATTTG
56015346 TCAAACTGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 2 0.07
18 24 0.86
19 2 0.07
ACGTcount: A:0.31, C:0.02, G:0.18, T:0.49
Consensus pattern (18 bp):
AATTGTATTAATTTGATG
Found at i:56016037 original size:17 final size:17
Alignment explanation
Indices: 56016013--56016099 Score: 102
Period size: 17 Copynumber: 5.1 Consensus size: 17
56016003 TGGAGCATGG
*
56016013 ACTATTATTTTGCATGA
1 ACTATTATTTTGTATGA
* * *
56016030 ATTGTTATTTGGTATGA
1 ACTATTATTTTGTATGA
56016047 ACTATTATTTTGTATGA
1 ACTATTATTTTGTATGA
* * *
56016064 ACTATCATTTGGTAAGA
1 ACTATTATTTTGTATGA
*
56016081 ACTATTATTTTATATGA
1 ACTATTATTTTGTATGA
56016098 AC
1 AC
56016100 AAATGTTTGG
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
17 56 1.00
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (17 bp):
ACTATTATTTTGTATGA
Found at i:56016097 original size:34 final size:34
Alignment explanation
Indices: 56016013--56016099 Score: 120
Period size: 34 Copynumber: 2.6 Consensus size: 34
56016003 TGGAGCATGG
* * * * *
56016013 ACTATTATTTTGCATGAATTGTTATTTGGTATGA
1 ACTATTATTTTGTATGAACTATCATTTGGTAAGA
56016047 ACTATTATTTTGTATGAACTATCATTTGGTAAGA
1 ACTATTATTTTGTATGAACTATCATTTGGTAAGA
*
56016081 ACTATTATTTTATATGAAC
1 ACTATTATTTTGTATGAAC
56016100 AAATGTTTGG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.31, C:0.08, G:0.14, T:0.47
Consensus pattern (34 bp):
ACTATTATTTTGTATGAACTATCATTTGGTAAGA
Found at i:56025533 original size:2 final size:2
Alignment explanation
Indices: 56025526--56025550 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
56025516 TGTGACATCT
56025526 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
56025551 GAAAATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:56029565 original size:19 final size:19
Alignment explanation
Indices: 56029543--56029580 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
56029533 TCACTATCAC
56029543 CCACCGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
* *
56029562 CCACTGTAATTAAATTTGT
1 CCACCGTAATCAAATTTGT
56029581 TATTAACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.37
Consensus pattern (19 bp):
CCACCGTAATCAAATTTGT
Found at i:56030210 original size:18 final size:18
Alignment explanation
Indices: 56030187--56030223 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
56030177 TGTAGTTTAG
*
56030187 TATTCAATTTATTCGAAT
1 TATTCAAGTTATTCGAAT
56030205 TATTCAAGTTATTCGAAT
1 TATTCAAGTTATTCGAAT
56030223 T
1 T
56030224 CGAAAACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.49
Consensus pattern (18 bp):
TATTCAAGTTATTCGAAT
Found at i:56030257 original size:18 final size:18
Alignment explanation
Indices: 56030215--56030257 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
56030205 TATTCAAGTT
**
56030215 ATTCGAATTCGAAAACCAA
1 ATTC-AATTCGAAAAAAAA
*
56030234 ACTCAATTCGAAAAAAAA
1 ATTCAATTCGAAAAAAAA
56030252 ATTCAA
1 ATTCAA
56030258 GTTGACTCGA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.53, C:0.19, G:0.07, T:0.21
Consensus pattern (18 bp):
ATTCAATTCGAAAAAAAA
Found at i:56033142 original size:21 final size:21
Alignment explanation
Indices: 56033116--56033161 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
56033106 TATATAAATA
*
56033116 AATTTAGCA-TCAATTTAATTC
1 AATTTA-CACTCAATTGAATTC
*
56033137 AATTTATACTCAATTGAATTC
1 AATTTACACTCAATTGAATTC
56033158 AATT
1 AATT
56033162 CACATCTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 21 0.95
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (21 bp):
AATTTACACTCAATTGAATTC
Found at i:56045401 original size:79 final size:81
Alignment explanation
Indices: 56045265--56045449 Score: 227
Period size: 79 Copynumber: 2.3 Consensus size: 81
56045255 TTGAATGATG
* *
56045265 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
56045329 TGTGCGAGATACTA-A
66 TGTGCGAGATACTATA
* * * **
56045344 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
56045406 ATTGTGCGAGTTACTATA
64 ATTGTGCGAGATACTATA
* *
56045424 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
56045450 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 57 0.63
80 33 0.36
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCAAT
TGTGCGAGATACTATA
Found at i:56045463 original size:40 final size:40
Alignment explanation
Indices: 56045266--56045449 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
56045256 TGAATGATGT
* * * *
56045266 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* * *
56045306 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
56045346 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* *
56045384 TCCGGGTTAAGTCCCGAAGGCAATTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
56045425 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
56045450 AACGAGTAGC
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
39 35 0.28
40 79 0.64
41 10 0.08
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:56045471 original size:79 final size:79
Alignment explanation
Indices: 56045318--56045472 Score: 199
Period size: 79 Copynumber: 2.0 Consensus size: 79
56045308 GGACTAAGAT
* * **
56045318 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
56045383 ATCCGGGTTAAGTC
66 ATCCGGGTTAAGTC
* *
56045397 CCGAAGGCAATTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCAATTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
*
56045460 TATATCC-GGTTAA
63 TAAATCCGGGTTAA
56045473 ATTCCGAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
78 2 0.03
79 39 0.59
80 25 0.38
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCAATTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAGTC
Found at i:56047562 original size:17 final size:18
Alignment explanation
Indices: 56047529--56047563 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
56047519 AAAACCCCAA
56047529 ATATAGAAAAACTTAAGG
1 ATATAGAAAAACTTAAGG
56047547 ATATAGAAAAAC-TAAGG
1 ATATAGAAAAACTTAAGG
56047564 CCAAAAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.57, C:0.06, G:0.17, T:0.20
Consensus pattern (18 bp):
ATATAGAAAAACTTAAGG
Found at i:56049009 original size:48 final size:48
Alignment explanation
Indices: 56048953--56049172 Score: 237
Period size: 48 Copynumber: 4.6 Consensus size: 48
56048943 TGTGTGCTAG
* * *
56048953 TGTAAGACCATGTATGGGACATGGCATCGGCCATGATATAAGAGCCAA
1 TGTAAGACCATGTCTGGGACATGGCATCAGCCATGATATGAGAGCCAA
* * * *
56049001 TGTAAGACCATGTTTGGAACATGGCATCAGCAAT-ATAATGAGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCAGCCATGAT-ATGAGAGCCAA
* ** * * *
56049049 TGTAATACCATGTCTAAGACATGGCATCAG-CATTGATATGTGCGCTAA
1 TGTAAGACCATGTCTGGGACATGGCATCAGCCA-TGATATGAGAGCCAA
* * * *
56049097 TGTAAGACCATGTCTGGGACATGGCATCAGCCTTGACATGTGAGCCAG
1 TGTAAGACCATGTCTGGGACATGGCATCAGCCATGATATGAGAGCCAA
* *
56049145 TGTAAGACCATGTTTGGAACATGGCATC
1 TGTAAGACCATGTCTGGGACATGGCATC
56049173 GACAATTCAC
Statistics
Matches: 142, Mismatches: 26, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
47 3 0.02
48 136 0.96
49 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (48 bp):
TGTAAGACCATGTCTGGGACATGGCATCAGCCATGATATGAGAGCCAA
Found at i:56051446 original size:22 final size:22
Alignment explanation
Indices: 56051418--56051463 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
56051408 CACTAGAGAG
56051418 TGCGTATCTACTGAAGCCATCA
1 TGCGTATCTACTGAAGCCATCA
*
56051440 TGCGTATCTATTGAAGCCATCA
1 TGCGTATCTACTGAAGCCATCA
56051462 TG
1 TG
56051464 TGCAAGAGAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (22 bp):
TGCGTATCTACTGAAGCCATCA
Found at i:56056529 original size:25 final size:28
Alignment explanation
Indices: 56056477--56056530 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 28
56056467 TTATCACTAT
* *
56056477 TATGTGTTGAATGATTGATTTTGCATAA
1 TATGTGTTGAATGATTGATTATGAATAA
56056505 TATG-GTTGAAT-A-TGATTATGAATAA
1 TATGTGTTGAATGATTGATTATGAATAA
56056530 T
1 T
56056531 GTATGATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 12 0.50
26 1 0.04
27 7 0.29
28 4 0.17
ACGTcount: A:0.33, C:0.02, G:0.20, T:0.44
Consensus pattern (28 bp):
TATGTGTTGAATGATTGATTATGAATAA
Found at i:56056678 original size:48 final size:48
Alignment explanation
Indices: 56056619--56056891 Score: 304
Period size: 48 Copynumber: 5.7 Consensus size: 48
56056609 TATGTGTGGT
*
56056619 AGTGTAAGACCATGTCTAGGACATGGCATTGGCCACGATATGAGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGATATGAGAGCC
* * * * *
56056667 AATGTAAGACCATGT-TTGGAACATGGCATCGACAATG-TAATGAGAGCC
1 AGTGTAAGACCATGTCTAGG-ACATGGCATCGGCCACGAT-ATGAGAGCC
*
56056715 AGTGTAAGACCATGTCTAGGACATGGCGTCGGCCAC-ATCATGAGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGAT-ATGAGAGCC
* * * * * *
56056763 AGTGTAAGACCATGTCTGGGACATGGCATCGG-TATTGAGACGAGAGCT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCA-CGATATGAGAGCC
* * * *
56056811 AGTGTAAGACCATGTCTAGGACATAGCATCGGCCTCGACATGTGAGCC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGATATGAGAGCC
*
56056859 AGTGTAAGACCATGT-TTGGAACATGGCATCGGC
1 AGTGTAAGACCATGTCTAGG-ACATGGCATCGGC
56056892 AATTCACCCT
Statistics
Matches: 186, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
47 8 0.04
48 174 0.94
49 4 0.02
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.22
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGATATGAGAGCC
Found at i:56056787 original size:96 final size:97
Alignment explanation
Indices: 56056619--56056894 Score: 398
Period size: 96 Copynumber: 2.9 Consensus size: 97
56056609 TATGTGTGGT
* *
56056619 AGTGTAAGACCATGTCTAGGACATGGCATTGGCCACGAT-ATGAGAGCCAATGTAAGACCATGTT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGATCATGAGAGCCAGTGTAAGACCATGTT
* *
56056683 TGGAACATGGCATCGACAATGTA-ATGAGAGCC
66 TGGAACATGGCATCGGCAATG-AGACGAGAGCC
* *
56056715 AGTGTAAGACCATGTCTAGGACATGGCGTCGGCCAC-ATCATGAGAGCCAGTGTAAGACCATGTC
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGATCATGAGAGCCAGTGTAAGACCATGTT
* * * *
56056779 TGGGACATGGCATCGGTATTGAGACGAGAGCT
66 TGGAACATGGCATCGGCAATGAGACGAGAGCC
* * *
56056811 AGTGTAAGACCATGTCTAGGACATAGCATCGGCCTCGA-CATGTGAGCCAGTGTAAGACCATGTT
1 AGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGATCATGAGAGCCAGTGTAAGACCATGTT
56056875 TGGAACATGGCATCGGCAAT
66 TGGAACATGGCATCGGCAAT
56056895 TCACCCTCTT
Statistics
Matches: 159, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
95 3 0.02
96 155 0.97
97 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.22
Consensus pattern (97 bp):
AGTGTAAGACCATGTCTAGGACATGGCATCGGCCACGATCATGAGAGCCAGTGTAAGACCATGTT
TGGAACATGGCATCGGCAATGAGACGAGAGCC
Found at i:56059272 original size:62 final size:62
Alignment explanation
Indices: 56059189--56059306 Score: 182
Period size: 62 Copynumber: 1.9 Consensus size: 62
56059179 GGTTGTGTGG
** *
56059189 TTTTATACCACAAAAAGTGAGTTGCACGGCCTAGGCATGCGCCCGTGTCCCTGGCCATTTGA
1 TTTTATACCACAAAAAGTGAGTCACACGGCCTAGGCATACGCCCGTGTCCCTGGCCATTTGA
* * *
56059251 TTTTATACCACAAATAGTGAGTCACATGGCCTAGGCGTACGCCCGTGTCCCTGGCC
1 TTTTATACCACAAAAAGTGAGTCACACGGCCTAGGCATACGCCCGTGTCCCTGGCC
56059307 CATGTGAACC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 50 1.00
ACGTcount: A:0.22, C:0.29, G:0.24, T:0.25
Consensus pattern (62 bp):
TTTTATACCACAAAAAGTGAGTCACACGGCCTAGGCATACGCCCGTGTCCCTGGCCATTTGA
Found at i:56076770 original size:35 final size:35
Alignment explanation
Indices: 56076716--56076786 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
56076706 TTTCGTTGCC
* *
56076716 ATAGAACTTTTACTGATGTTATGCTTTTGTTTCTT
1 ATAGAACTTTCACTAATGTTATGCTTTTGTTTCTT
56076751 ATAGAACTTTCACTAATGTTATGCTTTTGTTTCTT
1 ATAGAACTTTCACTAATGTTATGCTTTTGTTTCTT
56076786 A
1 A
56076787 ACTTTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.52
Consensus pattern (35 bp):
ATAGAACTTTCACTAATGTTATGCTTTTGTTTCTT
Found at i:56099446 original size:40 final size:40
Alignment explanation
Indices: 56099372--56099543 Score: 224
Period size: 40 Copynumber: 4.3 Consensus size: 40
56099362 GATAATCGGA
* * * *
56099372 CTAAGATCCGAAGGCATTCGTGCGAGTTGCTATATCCAGG
1 CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGG
* * * *
56099412 CTATGTCCCGAAGGCATTTATGCTAG-TGATTATATCCGGG
1 CTAAGACCCGAAGGCATTTGTGCGAGTTG-TTATATCCGGG
*
56099452 CTAAGACCCGAAGGCATTTGTGCGAGTTGCTATATCCGGG
1 CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGG
56099492 CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCC-GG
1 CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGG
56099531 CTAA-ATCCCGAAG
1 CTAAGA-CCCGAAG
56099544 ATACTTGGGT
Statistics
Matches: 115, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
38 1 0.01
39 15 0.13
40 97 0.84
41 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (40 bp):
CTAAGACCCGAAGGCATTTGTGCGAGTTGTTATATCCGGG
Found at i:56099811 original size:22 final size:22
Alignment explanation
Indices: 56099771--56099812 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
56099761 GAATGTGCAT
*
56099771 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
56099793 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
56099813 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:56102120 original size:34 final size:34
Alignment explanation
Indices: 56102082--56102149 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
56102072 CTATTATAAG
56102082 TGCGGATCAGCTGACCACTTTATCAAGGAATGCC
1 TGCGGATCAGCTGACCACTTTATCAAGGAATGCC
*
56102116 TGCGGATCAGCTGACCACTTTATCAAGGATTGCC
1 TGCGGATCAGCTGACCACTTTATCAAGGAATGCC
56102150 CGAGACTGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (34 bp):
TGCGGATCAGCTGACCACTTTATCAAGGAATGCC
Found at i:56107557 original size:40 final size:40
Alignment explanation
Indices: 56107478--56107654 Score: 205
Period size: 40 Copynumber: 4.5 Consensus size: 40
56107468 CGGATGATAA
* * ** * *
56107478 CCGGACTAAGATCCGAAGGCATTCGTGTGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGGTGCTATAT
* * * *
56107518 CCGGGCTATGTCCCGAAGGCATTTATGCTA-GTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGGTG-CTATAT
*
56107558 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGGTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGGTGCTATAT
* *
56107598 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCGAGGTGCTATAT
*
56107638 CCGGCCTAAGA-CCGAAG
1 CCGGGCTAAGACCCGAAG
56107655 ATACTTGGGT
Statistics
Matches: 118, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
39 8 0.07
40 107 0.91
41 3 0.03
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCGAGGTGCTATAT
Found at i:56107616 original size:80 final size:79
Alignment explanation
Indices: 56107478--56107654 Score: 230
Period size: 80 Copynumber: 2.2 Consensus size: 79
56107468 CGGATGATAA
* * * *
56107478 CCGGACTAAGATCCGAAGGCATTCGTGTGAGTTGCTATATCCGGGCTATGTCCCGAAGGCATTTA
1 CCGGACTAAGA-CCGAAGGCATTCGTGCGAGGTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
* *
56107543 TGCTAG-TGATTATAT
65 TGCGAGTTG-CTATAT
* * *
56107558 CCGGGCTAAGACCCGAAGGCATTTGTGCGAGGTGCTATATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGACTAAGA-CCGAAGGCATTCGTGCGAGGTGCTATATCCGGGCTAAGACCCGAAGGCATTTA
56107623 TGCGAGTTGCTATAT
65 TGCGAGTTGCTATAT
*
56107638 CCGGCCTAAGACCGAAG
1 CCGGACTAAGACCGAAG
56107655 ATACTTGGGT
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
79 6 0.07
80 77 0.91
81 2 0.02
ACGTcount: A:0.24, C:0.23, G:0.29, T:0.25
Consensus pattern (79 bp):
CCGGACTAAGACCGAAGGCATTCGTGCGAGGTGCTATATCCGGGCTAAGACCCGAAGGCATTTAT
GCGAGTTGCTATAT
Found at i:56107877 original size:136 final size:136
Alignment explanation
Indices: 56107649--56107898 Score: 482
Period size: 136 Copynumber: 1.8 Consensus size: 136
56107639 CGGCCTAAGA
*
56107649 CCGAAGATACTTGGGTTTGGAAGTGAGCGATCTTGCTGTAATAATTTCAATTAATACGTTCATAA
1 CCGAAGATACTTGGGTTTGGAAGTGAGCGACCTTGCTGTAATAATTTCAATTAATACGTTCATAA
*
56107714 AATCCAAACGATAAGGTATGTTTCGTATATGCATCGGAAAAGTCGATTCTGTTGTTATATCTGGC
66 AATCCAAACGATAAGGGATGTTTCGTATATGCATCGGAAAAGTCGATTCTGTTGTTATATCTGGC
56107779 TAAATC
131 TAAATC
56107785 CCGAAGATACTTGGGTTTGGAAGTGAGCGACCTTGCTGTAATAATTTCAATTAATACGTTCATAA
1 CCGAAGATACTTGGGTTTGGAAGTGAGCGACCTTGCTGTAATAATTTCAATTAATACGTTCATAA
56107850 AATCCAAACGATAAGGGATGTTTCGTATATGCATCGGAAAAGTCGATTC
66 AATCCAAACGATAAGGGATGTTTCGTATATGCATCGGAAAAGTCGATTC
56107899 GTTTTAAATA
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 112 1.00
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Consensus pattern (136 bp):
CCGAAGATACTTGGGTTTGGAAGTGAGCGACCTTGCTGTAATAATTTCAATTAATACGTTCATAA
AATCCAAACGATAAGGGATGTTTCGTATATGCATCGGAAAAGTCGATTCTGTTGTTATATCTGGC
TAAATC
Found at i:56108058 original size:22 final size:22
Alignment explanation
Indices: 56108018--56108059 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
56108008 GAACGTGCAT
*
56108018 ATATGAAGTTATTCATTTAGCC
1 ATATGAAGTTATACATTTAGCC
56108040 ATATGAATGTTATAC-TTTAG
1 ATATGAA-GTTATACATTTAG
56108060 TCAAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (22 bp):
ATATGAAGTTATACATTTAGCC
Found at i:56110801 original size:26 final size:26
Alignment explanation
Indices: 56110766--56110817 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
56110756 ACTATTCAAT
56110766 ATAAAGAAAATCATAACAGGGAAAGA
1 ATAAAGAAAATCATAACAGGGAAAGA
*
56110792 ATAAAGAAAATCATAAGAGGGAAAGA
1 ATAAAGAAAATCATAACAGGGAAAGA
56110818 GGTGAAACTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.62, C:0.06, G:0.21, T:0.12
Consensus pattern (26 bp):
ATAAAGAAAATCATAACAGGGAAAGA
Found at i:56111169 original size:6 final size:6
Alignment explanation
Indices: 56111135--56111219 Score: 68
Period size: 6 Copynumber: 14.3 Consensus size: 6
56111125 AACAAAATTG
* * * *
56111135 AAATGA AAATAA AAATCA AAAGAA AAATAA GAAT-A AAATAAA TAAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAAT-AA -AAATAA
* * *
56111184 AAATAA AAATAA GAAT-- AAATAA AAAGAA AAAGAA AA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AA
56111220 TAGGAGGATT
Statistics
Matches: 64, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
4 3 0.05
5 4 0.06
6 50 0.78
7 3 0.05
8 4 0.06
ACGTcount: A:0.78, C:0.01, G:0.07, T:0.14
Consensus pattern (6 bp):
AAATAA
Found at i:56111195 original size:31 final size:30
Alignment explanation
Indices: 56111140--56111219 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 30
56111130 AATTGAAATG
*
56111140 AAAAT-AAAAATCAAAAGAAAAATAAGAAT
1 AAAATAAAAAATAAAAAGAAAAATAAGAAT
*
56111169 AAAATAAATAAATAAAAATAAAAATAAGAAT
1 AAAATAAA-AAATAAAAAGAAAAATAAGAAT
*
56111200 -AAAT-AAAAAGAAAAAGAAAA
1 AAAATAAAAAATAAAAAGAAAA
56111220 TAGGAGGATT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
28 12 0.27
29 7 0.16
30 6 0.13
31 20 0.44
ACGTcount: A:0.79, C:0.01, G:0.06, T:0.14
Consensus pattern (30 bp):
AAAATAAAAAATAAAAAGAAAAATAAGAAT
Done.