Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr8
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70076365
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3341059 characters in sequence are not A, C, G, or T
File 121 of 210
Found at i:40726255 original size:28 final size:27
Alignment explanation
Indices: 40726200--40726255 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
40726190 TTTAAAATAC
* *
40726200 TTTTAAAATAATTTTTTTTGTTTTTTT
1 TTTTAAAATAATTTTTTATGTTTATTT
40726227 TTTTAAAATAATTTTTTAATGTTTATTT
1 TTTTAAAATAATTTTTT-ATGTTTATTT
40726255 T
1 T
40726256 AAAAATGGGC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.70
Consensus pattern (27 bp):
TTTTAAAATAATTTTTTATGTTTATTT
Found at i:40729796 original size:3 final size:3
Alignment explanation
Indices: 40729788--40729824 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
40729778 TGAGTTAAAA
40729788 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
40729825 TTTAGTATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40729854 original size:12 final size:13
Alignment explanation
Indices: 40729837--40729873 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
40729827 TAGTATAGTA
40729837 AAAAGAAGA-AAG
1 AAAAGAAGAGAAG
40729849 AAAAGAA-AGAAG
1 AAAAGAAGAGAAG
40729861 AAAAGAAGGAGAA
1 AAAAGAA-GAGAA
40729874 CGCACCGCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 1 0.05
12 17 0.77
14 4 0.18
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (13 bp):
AAAAGAAGAGAAG
Found at i:40732346 original size:483 final size:483
Alignment explanation
Indices: 40731440--40732401 Score: 1924
Period size: 483 Copynumber: 2.0 Consensus size: 483
40731430 CAGGTTAGGC
40731440 ACTTCACTTTTGATCACCGATTTATCATCCAACAACGATCCCAAACTCAAATGTGGTGATGTTTA
1 ACTTCACTTTTGATCACCGATTTATCATCCAACAACGATCCCAAACTCAAATGTGGTGATGTTTA
40731505 TCTTTTGTGTCGACATGTACCTAGGATGTTTAGTTGATAGCTATTTTGTGGATGGATAGTAAATG
66 TCTTTTGTGTCGACATGTACCTAGGATGTTTAGTTGATAGCTATTTTGTGGATGGATAGTAAATG
40731570 AGGTTATAAGTGTAATGTTGGTTTAGTATTTATGTAAACATGTGTTTGTGTTTGAAGCCATAGTA
131 AGGTTATAAGTGTAATGTTGGTTTAGTATTTATGTAAACATGTGTTTGTGTTTGAAGCCATAGTA
40731635 TGGTATGGTGAATTGAAGCAATGCTTGAAATATGCAGATGAATTATATTATGATTTTTTTTAAAT
196 TGGTATGGTGAATTGAAGCAATGCTTGAAATATGCAGATGAATTATATTATGATTTTTTTTAAAT
40731700 GTTTGAAAATGAATGATTTAATTACGGTTACTTGGTAATACTCCGAAACCCTATTCCGACGACGG
261 GTTTGAAAATGAATGATTTAATTACGGTTACTTGGTAATACTCCGAAACCCTATTCCGACGACGG
40731765 ATACGGGTTAGGGGTGTTACAGAAGGTCCGCACCAGAGGCGAATCTAGCGGGACTAACAAGGGCC
326 ATACGGGTTAGGGGTGTTACAGAAGGTCCGCACCAGAGGCGAATCTAGCGGGACTAACAAGGGCC
40731830 CTAGCCCCCCTAAAATGTAAAATTGTTATTTAGGCCTTTAAATTTTTTAAAAGAATTTAAATTTG
391 CTAGCCCCCCTAAAATGTAAAATTGTTATTTAGGCCTTTAAATTTTTTAAAAGAATTTAAATTTG
40731895 TAAAAGTAAAATTACTCTTTCACCACCT
456 TAAAAGTAAAATTACTCTTTCACCACCT
40731923 ACTTCACTTTTGATCACCGATTTATCATCCAACAACGATCCCAAACTCAAATGTGGTGATGTTTA
1 ACTTCACTTTTGATCACCGATTTATCATCCAACAACGATCCCAAACTCAAATGTGGTGATGTTTA
40731988 TCTTTTGTGTCGACATGTACCTAGGATGTTTAGTTGATAGCTATTTTGTGGATGGATAGTAAATG
66 TCTTTTGTGTCGACATGTACCTAGGATGTTTAGTTGATAGCTATTTTGTGGATGGATAGTAAATG
40732053 AGGTTATAAGTGTAATGTTGGTTTAGTATTTATGTAAACATGTGTTTGTGTTTGAAGCCATAGTA
131 AGGTTATAAGTGTAATGTTGGTTTAGTATTTATGTAAACATGTGTTTGTGTTTGAAGCCATAGTA
40732118 TGGTATGGTGAATTGAAGCAATGCTTGAAATATGCAGATGAATTATATTATGATTTTTTTTAAAT
196 TGGTATGGTGAATTGAAGCAATGCTTGAAATATGCAGATGAATTATATTATGATTTTTTTTAAAT
40732183 GTTTGAAAATGAATGATTTAATTACGGTTACTTGGTAATACTCCGAAACCCTATTCCGACGACGG
261 GTTTGAAAATGAATGATTTAATTACGGTTACTTGGTAATACTCCGAAACCCTATTCCGACGACGG
40732248 ATACGGGTTAGGGGTGTTACAGAAGGTCCGCACCAGAGGCGAATCTAGCGGGACTAACAAGGGCC
326 ATACGGGTTAGGGGTGTTACAGAAGGTCCGCACCAGAGGCGAATCTAGCGGGACTAACAAGGGCC
40732313 CTAGCCCCCCTAAAATGTAAAATTGTTATTTAGGCCTTTAAATTTTTTAAAAGAATTTAAATTTG
391 CTAGCCCCCCTAAAATGTAAAATTGTTATTTAGGCCTTTAAATTTTTTAAAAGAATTTAAATTTG
40732378 TAAAAGTAAAATTACTCTTTCACC
456 TAAAAGTAAAATTACTCTTTCACC
40732402 CCCTTAAAAT
Statistics
Matches: 479, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
483 479 1.00
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.35
Consensus pattern (483 bp):
ACTTCACTTTTGATCACCGATTTATCATCCAACAACGATCCCAAACTCAAATGTGGTGATGTTTA
TCTTTTGTGTCGACATGTACCTAGGATGTTTAGTTGATAGCTATTTTGTGGATGGATAGTAAATG
AGGTTATAAGTGTAATGTTGGTTTAGTATTTATGTAAACATGTGTTTGTGTTTGAAGCCATAGTA
TGGTATGGTGAATTGAAGCAATGCTTGAAATATGCAGATGAATTATATTATGATTTTTTTTAAAT
GTTTGAAAATGAATGATTTAATTACGGTTACTTGGTAATACTCCGAAACCCTATTCCGACGACGG
ATACGGGTTAGGGGTGTTACAGAAGGTCCGCACCAGAGGCGAATCTAGCGGGACTAACAAGGGCC
CTAGCCCCCCTAAAATGTAAAATTGTTATTTAGGCCTTTAAATTTTTTAAAAGAATTTAAATTTG
TAAAAGTAAAATTACTCTTTCACCACCT
Found at i:40734353 original size:10 final size:11
Alignment explanation
Indices: 40734331--40734362 Score: 55
Period size: 11 Copynumber: 2.8 Consensus size: 11
40734321 CTTTTAGCTG
40734331 AATTTTTTAAA
1 AATTTTTTAAA
40734342 AATTTTTTAAA
1 AATTTTTTAAA
40734353 AATATTTTTA
1 AAT-TTTTTA
40734363 GTGTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
AATTTTTTAAA
Found at i:40735860 original size:18 final size:17
Alignment explanation
Indices: 40735837--40735875 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
40735827 CATAATTAAG
*
40735837 AAAAATCATAACAAATAA
1 AAAAATCAGAACAAA-AA
*
40735855 AAAAATCAGAAGAAAAA
1 AAAAATCAGAACAAAAA
40735872 AAAA
1 AAAA
40735876 GAAAATTTAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.77, C:0.08, G:0.05, T:0.10
Consensus pattern (17 bp):
AAAAATCAGAACAAAAA
Found at i:40740858 original size:27 final size:26
Alignment explanation
Indices: 40740809--40740868 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
40740799 TTGTACTTAA
40740809 ATTTAAATTTTTTTTCCTAATTTGAT
1 ATTTAAATTTTTTTTCCTAATTTGAT
*
40740835 ATTTAAGATTTTTTTATCC-GATTTGAT
1 ATTTAA-ATTTTTTT-TCCTAATTTGAT
*
40740862 ATCTAAA
1 ATTTAAA
40740869 CTTGTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 7 0.23
27 20 0.67
28 3 0.10
ACGTcount: A:0.30, C:0.08, G:0.07, T:0.55
Consensus pattern (26 bp):
ATTTAAATTTTTTTTCCTAATTTGAT
Found at i:40741331 original size:103 final size:104
Alignment explanation
Indices: 40741218--40741424 Score: 391
Period size: 103 Copynumber: 2.0 Consensus size: 104
40741208 TTAAAAACCC
40741218 AAAATAAAATAAATTCATTATGTTAAAATAAATAAAACTAAAATTAATTGAACATTT-AAATACA
1 AAAATAAAATAAATTCATTATGTTAAAATAAATAAAACTAAAATTAATTGAACATTTAAAATAC-
40741282 AAAAGAAAAACGAAGAAATTTTATGTTA-CTGCCACTTGT
65 AAAAGAAAAACGAAGAAATTTTATGTTACCTGCCACTTGT
40741321 AAAATAAAATAAATTCATTATGTTAAAATAAATAAAACTAAAATTAATTGAACATTTAAAATACA
1 AAAATAAAATAAATTCATTATGTTAAAATAAATAAAACTAAAATTAATTGAACATTTAAAATACA
40741386 AAAGAAAAACGAAGAAATTTTATGTTACCTGCCACTTGT
66 AAAGAAAAACGAAGAAATTTTATGTTACCTGCCACTTGT
40741425 TGGTCATACA
Statistics
Matches: 102, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
103 85 0.83
104 17 0.17
ACGTcount: A:0.53, C:0.09, G:0.08, T:0.30
Consensus pattern (104 bp):
AAAATAAAATAAATTCATTATGTTAAAATAAATAAAACTAAAATTAATTGAACATTTAAAATACA
AAAGAAAAACGAAGAAATTTTATGTTACCTGCCACTTGT
Found at i:40743435 original size:26 final size:26
Alignment explanation
Indices: 40743368--40743427 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
40743358 TATTTTCTCG
*
40743368 AAATTTTACCAGGGCAAAATCATCAA
1 AAATTTTACCAGGGTAAAATCATCAA
* *
40743394 AAAATTTACCGGGGTAAAATCATC-A
1 AAATTTTACCAGGGTAAAATCATCAA
40743419 AAATTTTAC
1 AAATTTTAC
40743428 TAAGGGTAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 9 0.30
26 21 0.70
ACGTcount: A:0.45, C:0.17, G:0.12, T:0.27
Consensus pattern (26 bp):
AAATTTTACCAGGGTAAAATCATCAA
Found at i:40745584 original size:87 final size:87
Alignment explanation
Indices: 40745405--40745584 Score: 222
Period size: 87 Copynumber: 2.1 Consensus size: 87
40745395 CAAACTTTTC
* * * * * **
40745405 AAAAAAAGTAATTAAGTTCCTTTTTTTTTTATACTTAATTGGGTACTTGAATTTTTAAAATGCAT
1 AAAAAAAGCAATTAAG-TCCTTTTTTTTTTACACTCAATTGAGTACTTGAACTTTTAAAATAAAT
*
40745470 AAAAAAGCCCCTCAAACTTTAAA
65 AAAAAAGCCCATCAAACTTTAAA
*
40745493 AAAAAGAAGCAATTAAG-CCTTTTTTTTTTGCACTCAATTGAGTACTTGAACTTTTAAAATAAAT
1 AAAAA-AAGCAATTAAGTCCTTTTTTTTTTACACTCAATTGAGTACTTGAACTTTTAAAATAAAT
* *
40745557 TAAAAAGGCCAT-AAA-TTTAAA
65 AAAAAAGCCCATCAAACTTTAAA
40745578 AAAAAAA
1 AAAAAAA
40745585 TTAAGCTCCT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
84 2 0.03
85 11 0.14
86 3 0.04
87 49 0.61
88 5 0.06
89 10 0.12
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (87 bp):
AAAAAAAGCAATTAAGTCCTTTTTTTTTTACACTCAATTGAGTACTTGAACTTTTAAAATAAATA
AAAAAGCCCATCAAACTTTAAA
Found at i:40745689 original size:20 final size:20
Alignment explanation
Indices: 40745653--40745690 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40745643 CAAAGACTCT
**
40745653 TTGATCGTTAACTTTAATAG
1 TTGATCGTTAAAGTTAATAG
40745673 TTGATCGTTAAAGTTAAT
1 TTGATCGTTAAAGTTAAT
40745691 TGCCCCTAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (20 bp):
TTGATCGTTAAAGTTAATAG
Found at i:40745788 original size:30 final size:29
Alignment explanation
Indices: 40745752--40745856 Score: 81
Period size: 30 Copynumber: 3.6 Consensus size: 29
40745742 ACATGTGACA
40745752 AAAAAAATATATAAAAAAATAATAAAAGTT
1 AAAAAAATATATAAAAAAATAATAAAA-TT
* *** *
40745782 AAAAAAA-ATTATTAAATTTTAATAAAAAAT
1 AAAAAAATA-TATAAAAAAATAAT-AAAATT
* *
40745812 AAAAAAATAT-TTAAAAAATATTAAAATCGT
1 AAAAAAATATATAAAAAAATAATAAAAT--T
40745842 AAAAAAAT-TATAAAA
1 AAAAAAATATATAAAA
40745857 TATTTTAAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
28 4 0.07
29 10 0.17
30 39 0.67
31 5 0.09
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.28
Consensus pattern (29 bp):
AAAAAAATATATAAAAAAATAATAAAATT
Found at i:40745837 original size:19 final size:19
Alignment explanation
Indices: 40745804--40745866 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
40745794 TAAATTTTAA
**
40745804 TAAAAAATAAAAAAATATT
1 TAAAAAATATTAAAATATT
**
40745823 TAAAAAATATTAAAATCGT
1 TAAAAAATATTAAAATATT
*
40745842 AAAAAAAT-TATAAAATATTT
1 TAAAAAATAT-TAAAATA-TT
40745862 TAAAA
1 TAAAA
40745867 TTTTATAAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
18 1 0.03
19 28 0.82
20 5 0.15
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAAAATATTAAAATATT
Found at i:40745856 original size:10 final size:10
Alignment explanation
Indices: 40745753--40745894 Score: 66
Period size: 10 Copynumber: 14.3 Consensus size: 10
40745743 CATGTGACAA
40745753 AAAAAATATAT
1 AAAAAAT-TAT
40745764 AAAAAA--AT
1 AAAAAATTAT
*
40745772 AATAAAAGTTAA
1 AA-AAAA-TTAT
40745784 AAAAAATTAT
1 AAAAAATTAT
* **
40745794 TAAATTTTAAT
1 AAAAAATT-AT
40745805 AAAAAA-TA-
1 AAAAAATTAT
*
40745813 AAAAAATATTT
1 AAAAAAT-TAT
40745824 AAAAAA-TAT
1 AAAAAATTAT
*
40745833 -TAAAATCGTA-
1 AAAAAAT--TAT
40745843 AAAAAATTAT
1 AAAAAATTAT
* *
40745853 AAAATATTTT
1 AAAAAATTAT
**
40745863 AAAATTTTAT
1 AAAAAATTAT
*
40745873 -AAAAATCAT
1 AAAAAATTAT
40745882 AAAAAATTAT
1 AAAAAATTAT
40745892 AAA
1 AAA
40745895 TTGCATCAAA
Statistics
Matches: 97, Mismatches: 20, Indels: 29
0.66 0.14 0.20
Matches are distributed among these distances:
8 14 0.14
9 15 0.15
10 37 0.38
11 28 0.29
12 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:40745891 original size:19 final size:19
Alignment explanation
Indices: 40745823--40745894 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
40745813 AAAAAATATT
* *
40745823 TAAAAAA-TATTAAAATCG
1 TAAAAAATTATAAAAATCA
**
40745841 TAAAAAAATTATAAAATATTT
1 T-AAAAAATTATAAAA-ATCA
**
40745862 TAAAATTTTATAAAAATCA
1 TAAAAAATTATAAAAATCA
40745881 TAAAAAATTATAAA
1 TAAAAAATTATAAA
40745895 TTGCATCAAA
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
18 1 0.02
19 20 0.48
20 18 0.43
21 3 0.07
ACGTcount: A:0.62, C:0.03, G:0.01, T:0.33
Consensus pattern (19 bp):
TAAAAAATTATAAAAATCA
Found at i:40746276 original size:53 final size:51
Alignment explanation
Indices: 40746175--40746272 Score: 121
Period size: 52 Copynumber: 1.9 Consensus size: 51
40746165 ATATATATTA
40746175 TAATTTTTTTTACGAATTTTATAAAATTTTACAATTTTTTAATAAATTTGG
1 TAATTTTTTTTACGAATTTTATAAAATTTTACAATTTTTTAATAAATTTGG
* *
40746226 TAATTTTTTCTT-CTAACTTTTAATAAAA-TTTA-AATATTTTTATTAAA
1 TAATTTTTT-TTACGAA-TTTT-ATAAAATTTTACAAT-TTTTTAATAAA
40746273 ATTTAATCAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
51 15 0.37
52 20 0.49
53 6 0.15
ACGTcount: A:0.37, C:0.05, G:0.03, T:0.55
Consensus pattern (51 bp):
TAATTTTTTTTACGAATTTTATAAAATTTTACAATTTTTTAATAAATTTGG
Found at i:40746693 original size:88 final size:89
Alignment explanation
Indices: 40746579--40746744 Score: 219
Period size: 88 Copynumber: 1.9 Consensus size: 89
40746569 ATTATGGGTG
* * * *
40746579 GTTCAAGTACCCAATTGAGTGGAAAAAAAAT-CAGGGGATTAATTGC-TTTTGTGAAAAAGTTTG
1 GTTCAAGTACCCAATTGAATGG-AAAAAAATGCAAGGGATTAATTGCTTTTTGTGAAAAAATTTA
40746642 AGGGCCTTTTTGATGCTTTTTAAAA
65 AGGGCCTTTTTGATGCTTTTTAAAA
* * * * *
40746667 GTTCAAGTACTCAATTGAATGTAAAAAAATGCAAGGGCTTAATTTCTTTTTTTGAAAAAATTTAA
1 GTTCAAGTACCCAATTGAATGGAAAAAAATGCAAGGGATTAATTGCTTTTTGTGAAAAAATTTAA
*
40746732 GGGTCTTTTTGAT
66 GGGCCTTTTTGAT
40746745 ATTTAAAGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
87 8 0.12
88 31 0.47
89 27 0.41
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.37
Consensus pattern (89 bp):
GTTCAAGTACCCAATTGAATGGAAAAAAATGCAAGGGATTAATTGCTTTTTGTGAAAAAATTTAA
GGGCCTTTTTGATGCTTTTTAAAA
Found at i:40751795 original size:42 final size:41
Alignment explanation
Indices: 40751692--40751838 Score: 125
Period size: 43 Copynumber: 3.5 Consensus size: 41
40751682 TGTGATATCG
* * * * *
40751692 TGTAAGACCTTGTCTGGGACATTAGCATCAATTAGAGATTACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGA-TA-TGATTACC
* *
40751735 TGTAAGACCATGTTTGGGACATTGGCATCGTATATGATTTCC
1 TGTAAGACCATGTCTGGGACATTGGCATCG-ATATGATTACC
* * * *
40751777 TGTAAGACCCTGTCTGGGATAGTGGCATCGATATTTGATAACAC
1 TGTAAGACCATGTCTGGGACATTGGCATCGATA--TGATTAC-C
*
40751821 -GTAAGACCATATCTGGGA
1 TGTAAGACCATGTCTGGGA
40751839 TATGGAATTG
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
41 3 0.04
42 31 0.36
43 49 0.58
44 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATGATTACC
Found at i:40752738 original size:55 final size:56
Alignment explanation
Indices: 40752672--40752784 Score: 219
Period size: 55 Copynumber: 2.0 Consensus size: 56
40752662 TAGACAAAAC
40752672 TTAGTGAATTCTTCTTATCAAGGTTGAGTCAGAATCATTACCAG-TTGGACTTGAA
1 TTAGTGAATTCTTCTTATCAAGGTTGAGTCAGAATCATTACCAGCTTGGACTTGAA
40752727 TTAGTGAATTCTTCTTATCAAGGTTGAGTCAGAATCATTACCAGCTTGGACTTGAA
1 TTAGTGAATTCTTCTTATCAAGGTTGAGTCAGAATCATTACCAGCTTGGACTTGAA
40752783 TT
1 TT
40752785 GCTAAGATTG
Statistics
Matches: 57, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 44 0.77
56 13 0.23
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.37
Consensus pattern (56 bp):
TTAGTGAATTCTTCTTATCAAGGTTGAGTCAGAATCATTACCAGCTTGGACTTGAA
Found at i:40754314 original size:42 final size:41
Alignment explanation
Indices: 40754211--40754357 Score: 125
Period size: 43 Copynumber: 3.5 Consensus size: 41
40754201 TGTGATATCG
* * * * *
40754211 TGTAAGACCTTGTCTGGGACATTAGCATCAATTAGAGATTACG
1 TGTAAGACCATGTCTGGGACATTGGCATCGA-TA-TGATTACC
* *
40754254 TGTAAGACCATGTTTGGGACATTGGCATCGTATATGATTTCC
1 TGTAAGACCATGTCTGGGACATTGGCATCG-ATATGATTACC
* * * *
40754296 TGTAAGACCCTGTCTGGGATAGTGGCATCGATATTTGATAACAC
1 TGTAAGACCATGTCTGGGACATTGGCATCGATA--TGATTAC-C
*
40754340 -GTAAGACCATATCTGGGA
1 TGTAAGACCATGTCTGGGA
40754358 TATGGAATTG
Statistics
Matches: 85, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
41 3 0.04
42 31 0.36
43 49 0.58
44 2 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (41 bp):
TGTAAGACCATGTCTGGGACATTGGCATCGATATGATTACC
Found at i:40755218 original size:24 final size:24
Alignment explanation
Indices: 40755191--40755236 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
40755181 ATGAGATAGC
40755191 ATATTTAGCTTAAAAGATTAAGAG
1 ATATTTAGCTTAAAAGATTAAGAG
40755215 ATATTTAGCTTAAAAGATTAAG
1 ATATTTAGCTTAAAAGATTAAG
40755237 TGATGTTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (24 bp):
ATATTTAGCTTAAAAGATTAAGAG
Found at i:40756408 original size:21 final size:22
Alignment explanation
Indices: 40756382--40756423 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
40756372 AACAGAATTT
*
40756382 ATGATGATGTTTGAC-TATGAG
1 ATGATGATGTATGACTTATGAG
40756403 ATGATGATGTATGACTTATGA
1 ATGATGATGTATGACTTATGA
40756424 TTGTGAAGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.31, C:0.05, G:0.26, T:0.38
Consensus pattern (22 bp):
ATGATGATGTATGACTTATGAG
Found at i:40763871 original size:17 final size:17
Alignment explanation
Indices: 40763845--40763887 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
40763835 AGCTAAAAAC
* *
40763845 ATTTGATGAGCTTGCAG
1 ATTTGGTGAGCTAGCAG
*
40763862 ATTTGGTGAGCTAGCAT
1 ATTTGGTGAGCTAGCAG
*
40763879 CTTTGGTGA
1 ATTTGGTGA
40763888 CCTCGCACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.21, C:0.12, G:0.30, T:0.37
Consensus pattern (17 bp):
ATTTGGTGAGCTAGCAG
Found at i:40767389 original size:43 final size:43
Alignment explanation
Indices: 40767194--40767385 Score: 260
Period size: 43 Copynumber: 4.5 Consensus size: 43
40767184 AGGTCATAAC
*
40767194 CTTTAGCGGCGCTTATTCCACAAACGCCGCTAAAGCTCATGTT
1 CTTTAGCGGCGCTTATTCCACAAACGCCGCTAAAGGTCATGTT
* * * * *
40767237 CTTTAGCAGCACTTATCCCACAAACGCCACTAAAGGTCATGCT
1 CTTTAGCGGCGCTTATTCCACAAACGCCGCTAAAGGTCATGTT
40767280 CTTTAGCGGCGCTTATTCCACAAACGCCGCTAAAGGTCATGTT
1 CTTTAGCGGCGCTTATTCCACAAACGCCGCTAAAGGTCATGTT
* * *
40767323 CTTTGGCGGCGCTTA-TCTCAAAAACGCCGCTAAATGTCATGTT
1 CTTTAGCGGCGCTTATTC-CACAAACGCCGCTAAAGGTCATGTT
* * *
40767366 CTTTAGAGGTGCTTTTTCCA
1 CTTTAGCGGCGCTTATTCCA
40767386 AAAATGCCAC
Statistics
Matches: 129, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
42 2 0.02
43 125 0.97
44 2 0.02
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (43 bp):
CTTTAGCGGCGCTTATTCCACAAACGCCGCTAAAGGTCATGTT
Found at i:40767703 original size:5 final size:5
Alignment explanation
Indices: 40767693--40767718 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
40767683 CGTCCTACTT
40767693 TCTGC TCTGC TCTGC TCTGC TCTGC T
1 TCTGC TCTGC TCTGC TCTGC TCTGC T
40767719 TCCCTCGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.38, G:0.19, T:0.42
Consensus pattern (5 bp):
TCTGC
Found at i:40773865 original size:20 final size:20
Alignment explanation
Indices: 40773840--40773877 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40773830 AGTAATGCAT
*
40773840 TTTTAAAAAATAATTACACA
1 TTTTAAAAAATAAATACACA
40773860 TTTTAAAAAATAAATACA
1 TTTTAAAAAATAAATACA
40773878 TCAATATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.34
Consensus pattern (20 bp):
TTTTAAAAAATAAATACACA
Found at i:40774372 original size:107 final size:107
Alignment explanation
Indices: 40774187--40774384 Score: 247
Period size: 107 Copynumber: 1.9 Consensus size: 107
40774177 CATATAAATT
* * * * *
40774187 ACCAAACCATCAAACCCCTAAATCCAATCCCCACTATACTATAAGCCTTAACCCTAAATCTTAAA
1 ACCAAACCACCAAACCCCAAAATCCAATCCACACTATACTATAAGCATTAACCCAAAATCTTAAA
* *
40774252 CCCCAAACTATAAACCCTAAACCCATCAATTAACCATAAAAC
66 CCCCAAACCATAAACACTAAACCCATCAATTAACCATAAAAC
* *
40774294 ACCAAACCACCAAACCCCAAAATCCAATCCATACTATATCGTA-AA-CATTAACCGAAAATCTTA
1 ACCAAACCACCAAACCCCAAAATCCAATCCACACTATA-C-TATAAGCATTAACCCAAAATCTTA
* ** *
40774357 AATCTTAAACCATAAACATTAAACCCAT
64 AACCCCAAACCATAAACACTAAACCCAT
40774385 AAACCATAAA
Statistics
Matches: 76, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
107 71 0.93
108 3 0.04
109 2 0.03
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.20
Consensus pattern (107 bp):
ACCAAACCACCAAACCCCAAAATCCAATCCACACTATACTATAAGCATTAACCCAAAATCTTAAA
CCCCAAACCATAAACACTAAACCCATCAATTAACCATAAAAC
Found at i:40774460 original size:14 final size:13
Alignment explanation
Indices: 40774437--40774485 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
40774427 AAAATTGGCC
*
40774437 AAACCTTAAAGTCT
1 AAACCATAAA-TCT
40774451 AAACCATAAATCAT
1 AAACCATAAATC-T
40774465 AAACCAT-AATCCT
1 AAACCATAAAT-CT
40774478 AAACCATA
1 AAACCATA
40774486 TCTTTGGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 13 0.42
14 18 0.58
ACGTcount: A:0.51, C:0.24, G:0.02, T:0.22
Consensus pattern (13 bp):
AAACCATAAATCT
Found at i:40774480 original size:13 final size:13
Alignment explanation
Indices: 40774449--40774485 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
40774439 ACCTTAAAGT
40774449 CTAAACCATAAATC
1 CTAAACCAT-AATC
*
40774463 ATAAACCATAATC
1 CTAAACCATAATC
40774476 CTAAACCATA
1 CTAAACCATA
40774486 TCTTTGGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (13 bp):
CTAAACCATAATC
Found at i:40775207 original size:87 final size:88
Alignment explanation
Indices: 40775058--40775223 Score: 208
Period size: 87 Copynumber: 1.9 Consensus size: 88
40775048 TAATTGAGGG
* * * * * *
40775058 ATATAGCTGCGTTTTTAGGTAAGCGCCGCTAACGCCTCTATAGGTCAAGCCGGAACGATGCGTTT
1 ATATAGCGGCGTTTTCAGGTAAGCGCCGCTAACGCCGCTATAGCTCAAGACGAAACGATGCGTTT
*
40775123 TG-GTTAAAATTTTTAAGCTGAT
66 CGAGTTAAAATTTTTAAGCTGAT
* * * * *
40775145 ATATAGCGGCGTTTTCGGGTAAGCGCCGCTGACGGCGCTATAGCTTAAGACGAAACGTTGCGTTT
1 ATATAGCGGCGTTTTCAGGTAAGCGCCGCTAACGCCGCTATAGCTCAAGACGAAACGATGCGTTT
*
40775210 CGATTTAAAATTTT
66 CGAGTTAAAATTTT
40775224 CCGGCATTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
87 55 0.85
88 10 0.15
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (88 bp):
ATATAGCGGCGTTTTCAGGTAAGCGCCGCTAACGCCGCTATAGCTCAAGACGAAACGATGCGTTT
CGAGTTAAAATTTTTAAGCTGAT
Found at i:40779152 original size:39 final size:39
Alignment explanation
Indices: 40779098--40779174 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 39
40779088 ACCTTTGTTG
* * *
40779098 GAGGGTTCGCATGGGGTAGCGAACTAGTCTTCGCATCTA
1 GAGGGTTCGCATGGGGCAACGAACTAGTCTTCACATCTA
*
40779137 GAGGGTTCGCATGGGGCAACGAACTGGTCTTCACATCT
1 GAGGGTTCGCATGGGGCAACGAACTAGTCTTCACATCT
40779175 GGTTGTGAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.21, C:0.22, G:0.32, T:0.25
Consensus pattern (39 bp):
GAGGGTTCGCATGGGGCAACGAACTAGTCTTCACATCTA
Found at i:40780532 original size:17 final size:17
Alignment explanation
Indices: 40780520--40780640 Score: 82
Period size: 17 Copynumber: 7.0 Consensus size: 17
40780510 TAGTGACTTT
40780520 GCAACTTTGGTGAGCTC
1 GCAACTTTGGTGAGCTC
*
40780537 GCAACTTTGATGAGCTC
1 GCAACTTTGGTGAGCTC
*
40780554 GTAGA-TTTGGTGAGCTC
1 GCA-ACTTTGGTGAGCTC
* ** *
40780571 ACATTTTTGGTAAGCTC
1 GCAACTTTGGTGAGCTC
* * * *
40780588 ACAGCTTTGTTGAGCTT
1 GCAACTTTGGTGAGCTC
** *
40780605 GCATTTTTTAGTGAGCTC
1 GCA-ACTTTGGTGAGCTC
*
40780623 GCATCTTTGGGTGAGCTC
1 GCAACTTT-GGTGAGCTC
40780641 AGAGATGTGC
Statistics
Matches: 80, Mismatches: 20, Indels: 7
0.75 0.19 0.07
Matches are distributed among these distances:
17 59 0.74
18 21 0.26
ACGTcount: A:0.18, C:0.19, G:0.26, T:0.36
Consensus pattern (17 bp):
GCAACTTTGGTGAGCTC
Found at i:40784926 original size:24 final size:24
Alignment explanation
Indices: 40784899--40784944 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
40784889 GTAATATCAT
*
40784899 GCATA-ACATGCTCATATACAGATA
1 GCATATACATGCTC-TAAACAGATA
*
40784923 GCATATATATGCTCTAAACAGA
1 GCATATACATGCTCTAAACAGA
40784945 ACAGATATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.41, C:0.20, G:0.13, T:0.26
Consensus pattern (24 bp):
GCATATACATGCTCTAAACAGATA
Found at i:40797860 original size:10 final size:10
Alignment explanation
Indices: 40797845--40797881 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
40797835 ATATTAATAA
40797845 TTAATTAATC
1 TTAATTAATC
40797855 TTAATTAA-C
1 TTAATTAATC
40797864 TTAATTAAT-
1 TTAATTAATC
40797873 TATAATTAA
1 T-TAATTAA
40797882 CTAACTTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 10 0.40
10 15 0.60
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (10 bp):
TTAATTAATC
Found at i:40797869 original size:19 final size:19
Alignment explanation
Indices: 40797845--40797902 Score: 66
Period size: 19 Copynumber: 3.0 Consensus size: 19
40797835 ATATTAATAA
40797845 TTAATTAATCTTAATTAAC
1 TTAATTAATCTTAATTAAC
40797864 TTAATTAAT-TATAATTAAC
1 TTAATTAATCT-TAATTAAC
*
40797883 -TAACTTTAATCATAATTAAC
1 TTAA--TTAATCTTAATTAAC
40797903 AAAATTGGTG
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 4 0.12
19 17 0.50
20 13 0.38
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (19 bp):
TTAATTAATCTTAATTAAC
Found at i:40797881 original size:23 final size:23
Alignment explanation
Indices: 40797842--40797888 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
40797832 CTTATATTAA
* *
40797842 TAATTAATTAATCTTAATTAACT
1 TAATTAATTAATATTAACTAACT
40797865 TAATTAATT-ATAATTAACTAACT
1 TAATTAATTAAT-ATTAACTAACT
40797888 T
1 T
40797889 TAATCATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 2 0.10
23 19 0.90
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATTAATTAATATTAACTAACT
Found at i:40798970 original size:15 final size:15
Alignment explanation
Indices: 40798938--40798971 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
40798928 GATTTCAACA
* *
40798938 GAATGTGATTCTTTG
1 GAATGTGATTATTAG
40798953 GAATGTGATTATTAG
1 GAATGTGATTATTAG
40798968 GAAT
1 GAAT
40798972 ATTACTTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.26, T:0.41
Consensus pattern (15 bp):
GAATGTGATTATTAG
Found at i:40805686 original size:13 final size:13
Alignment explanation
Indices: 40805624--40805689 Score: 82
Period size: 13 Copynumber: 5.1 Consensus size: 13
40805614 GTTTTGGCAA
40805624 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
40805637 TG-TTGTAGAAAAG
1 TGCTT-TTGAAAAG
40805650 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
40805663 TG-TTGTGGAAAAG
1 TGCTT-TTGAAAAG
40805676 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
40805689 T
1 T
40805690 TTGGTTTAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
12 4 0.09
13 37 0.82
14 4 0.09
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:40805700 original size:26 final size:26
Alignment explanation
Indices: 40805624--40805689 Score: 123
Period size: 26 Copynumber: 2.5 Consensus size: 26
40805614 GTTTTGGCAA
40805624 TGCTTTTGAAAAGTGTTGTAGAAAAG
1 TGCTTTTGAAAAGTGTTGTAGAAAAG
*
40805650 TGCTTTTGAAAAGTGTTGTGGAAAAG
1 TGCTTTTGAAAAGTGTTGTAGAAAAG
40805676 TGCTTTTGAAAAGT
1 TGCTTTTGAAAAGT
40805690 TTGGTTTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.36
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGTTGTAGAAAAG
Found at i:40813157 original size:17 final size:17
Alignment explanation
Indices: 40813135--40813167 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40813125 AAAATACCAT
40813135 ATTGGAGTTCGGCCTAA
1 ATTGGAGTTCGGCCTAA
*
40813152 ATTGGAGTTTGGCCTA
1 ATTGGAGTTCGGCCTA
40813168 TCCGTATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.33
Consensus pattern (17 bp):
ATTGGAGTTCGGCCTAA
Found at i:40815524 original size:7 final size:7
Alignment explanation
Indices: 40815486--40815510 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
40815476 TTGCTTCTTC
40815486 TTTTCCT
1 TTTTCCT
40815493 TTTTCCT
1 TTTTCCT
40815500 TTTTCCT
1 TTTTCCT
40815507 TTTT
1 TTTT
40815511 TTTTTTTTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTCCT
Found at i:40838370 original size:20 final size:19
Alignment explanation
Indices: 40838327--40838374 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
40838317 TGTCAGTCTT
*
40838327 ATGAATAGGAGATCAAATC
1 ATGAATAGTAGATCAAATC
* *
40838346 GTGAATAGTAGAGTCAAGTC
1 ATGAATAGTAGA-TCAAATC
40838366 ATGAATAGT
1 ATGAATAGT
40838375 GGTAATATGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (19 bp):
ATGAATAGTAGATCAAATC
Found at i:40840259 original size:70 final size:69
Alignment explanation
Indices: 40840143--40840711 Score: 485
Period size: 70 Copynumber: 8.1 Consensus size: 69
40840133 AACATATCCT
* *
40840143 TCCAAAATAGTCAGCGTGAGCTC-AAGCTCCCAACTGTAATCCAAAGGCTCTCTGATTCAATATC
1 TCCAAAATAGT-AACGCGAGC-CAAAGCTCCCAACTGTAATCCAAAGGCTCTCTGATTCAATATC
40840207 GCGACC
64 GCGACC
* *
40840213 TCTAAAATAGTCAACGCGAGCCAAAGCTCCCAACTGTAATCTAAAGGCTCGT-TGATTCAATATC
1 TCCAAAATAGT-AACGCGAGCCAAAGCTCCCAACTGTAATCCAAAGGCTC-TCTGATTCAATATC
*
40840277 GCGGCC
64 GCGACC
* *
40840283 TCCAAAACAATAAGCGCGAGCTC-AAGCTCCCAACTGTAATCCAAAGGCT-TGCTGATTCAATAT
1 TCCAAAATAGTAA-CGCGAGC-CAAAGCTCCCAACTGTAATCCAAAGGCTCT-CTGATTCAATAT
*
40840346 CGCAACC
63 CGCGACC
* * * * * * * * *
40840353 TTCAAAACAGTAA-GCATAAGCTAAAGCTACTAACTG-ATATGCAAAGGCTCGCTAATTCAATAT
1 TCCAAAATAGTAACGC--GAGCCAAAGCTCCCAACTGTA-ATCCAAAGGCTCTCTGATTCAATAT
* *
40840416 CACGGCC
63 CGCGACC
* ** * *
40840423 TCCAAAATAGTTAGCGCGAGCCAAAGCTCCCAGTTGTAATCCAAAGGCTCGCTGATTTAATATCG
1 TCCAAAATAG-TAACGCGAGCCAAAGCTCCCAACTGTAATCCAAAGGCTCTCTGATTCAATATCG
*
40840488 CAACC
65 CGACC
* * * * * * *
40840493 TCCAAAACAGTTAGCACGAGCCAAAGCTCCTAATTGTAATCCAAATGCT-TGTTGATTCAATATC
1 TCCAAAATAG-TAACGCGAGCCAAAGCTCCCAACTGTAATCCAAAGGCTCT-CTGATTCAATATC
40840557 GCGACC
64 GCGACC
* * * * *
40840563 TCCAAAATAGTCAATGTGAGCTC-AAGCTCCTAGCTGTAATCCAAAGACTCGT-TGATTCAATAT
1 TCCAAAATAGT-AACGCGAGC-CAAAGCTCCCAACTGTAATCCAAAGGCTC-TCTGATTCAATAT
*
40840626 CGCGTCC
63 CGCGACC
* * * * *
40840633 TCCAAAATAGTAAGCACGAG-CAAAGCTCCCAACTG-ATATGCAAAGGCTCACTTATTCAAAATC
1 TCCAAAATAGTAA-CGCGAGCCAAAGCTCCCAACTGTA-ATCCAAAGGCTCTCTGATTCAATATC
**
40840696 GAAACC
64 GCGACC
*
40840702 TCTAAAATAG
1 TCCAAAATAG
40840712 CTCACAGATT
Statistics
Matches: 405, Mismatches: 71, Indels: 47
0.77 0.14 0.09
Matches are distributed among these distances:
68 5 0.01
69 50 0.12
70 341 0.84
71 6 0.01
72 3 0.01
ACGTcount: A:0.34, C:0.27, G:0.17, T:0.23
Consensus pattern (69 bp):
TCCAAAATAGTAACGCGAGCCAAAGCTCCCAACTGTAATCCAAAGGCTCTCTGATTCAATATCGC
GACC
Found at i:40840399 original size:140 final size:140
Alignment explanation
Indices: 40840143--40840681 Score: 624
Period size: 140 Copynumber: 3.9 Consensus size: 140
40840133 AACATATCCT
* * *
40840143 TCCAAAATAGTCAGCGTGAGCTCAAGCTCCCAACTGTAATCCAAAGGCTCTCTGATTCAATATCG
1 TCCAAAATAGTAAGCGCGAGCTCAAGCTCCCAACTGTAATCCAAAGGCTCGCTGATTCAATATCG
* * * *
40840208 CGACCTCTAAAATAGTCAA-CGCGAGCCAAAGCTCCCAACTGTAAT-CTAAAGGCTCGTTGATTC
66 CAACCTCCAAAACAGT-AAGCACGAGCCAAAGCTCCCAACTGTAATGC-AAAGGCTCGTTGATTC
40840271 AATATCGCGGCC
129 AATATCGCGGCC
* * *
40840283 TCCAAAACAATAAGCGCGAGCTCAAGCTCCCAACTGTAATCCAAAGGCTTGCTGATTCAATATCG
1 TCCAAAATAGTAAGCGCGAGCTCAAGCTCCCAACTGTAATCCAAAGGCTCGCTGATTCAATATCG
* ** * * * * *
40840348 CAACCTTCAAAACAGTAAGCATAAGCTAAAGCTACTAACTG-ATATGCAAAGGCTCGCTAATTCA
66 CAACCTCCAAAACAGTAAGCACGAGCCAAAGCTCCCAACTGTA-ATGCAAAGGCTCGTTGATTCA
*
40840412 ATATCACGGCC
130 ATATCGCGGCC
* ** *
40840423 TCCAAAATAGTTAGCGCGAGC-CAAAGCTCCCAGTTGTAATCCAAAGGCTCGCTGATTTAATATC
1 TCCAAAATAGTAAGCGCGAGCTC-AAGCTCCCAACTGTAATCCAAAGGCTCGCTGATTCAATATC
* * * * * *
40840487 GCAACCTCCAAAACAGTTAGCACGAGCCAAAGCTCCTAATTGTAATCCAAATGCTTGTTGATTCA
65 GCAACCTCCAAAACAGTAAGCACGAGCCAAAGCTCCCAACTGTAATGCAAAGGCTCGTTGATTCA
*
40840552 ATATCGCGACC
130 ATATCGCGGCC
* * * * * *
40840563 TCCAAAATAGTCAA-TGTGAGCTCAAGCTCCTAGCTGTAATCCAAAGACTCGTTGATTCAATATC
1 TCCAAAATAGT-AAGCGCGAGCTCAAGCTCCCAACTGTAATCCAAAGGCTCGCTGATTCAATATC
** *
40840627 GCGTCCTCCAAAATAGTAAGCACGAG-CAAAGCTCCCAACTG-ATATGCAAAGGCTC
65 GCAACCTCCAAAACAGTAAGCACGAGCCAAAGCTCCCAACTGTA-ATGCAAAGGCTC
40840682 ACTTATTCAA
Statistics
Matches: 334, Mismatches: 57, Indels: 17
0.82 0.14 0.04
Matches are distributed among these distances:
138 1 0.00
139 26 0.08
140 303 0.91
141 4 0.01
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (140 bp):
TCCAAAATAGTAAGCGCGAGCTCAAGCTCCCAACTGTAATCCAAAGGCTCGCTGATTCAATATCG
CAACCTCCAAAACAGTAAGCACGAGCCAAAGCTCCCAACTGTAATGCAAAGGCTCGTTGATTCAA
TATCGCGGCC
Found at i:40840551 original size:210 final size:210
Alignment explanation
Indices: 40840174--40840708 Score: 625
Period size: 210 Copynumber: 2.6 Consensus size: 210
40840164 TCAAGCTCCC
* *
40840174 AACTGTAATCCAAAGGCTCTCTGATTCAATATCGCGACCTCTAAAATAGTCAA-CGCGAGCCAAA
1 AACTGTAATCCAAAGGCTCGCTGATTCAATATCGCGACCTCCAAAATAGT-AAGCGCGAGCCAAA
* * ** *
40840238 GCTCCCAACTGTAATCTAAAGGCTCGTTGATTCAATATCGCGGCCTCCAAAACAATAAGCGCGAG
65 GCTCCCAACTGTAATCCAAAGGCTCGCTGATTCAATATCGCAACCTCCAAAACAATAAGCACGAG
*
40840303 CTCAAGCTCCCAACTGTAATCCAAAGGCTTGCTGATTCAATATCGCAACCTTCAAAACAGT-AA-
130 CTCAAGCTCCCAACTGTAATCCAAAGGCTTGCTGATTCAATATCGCAACCTCCAAAACAGTCAAT
40840366 GCATAAGCTAAAGCTACT
195 G--TAAGCTAAAGCTACT
* * * * *
40840384 AACTG-ATATGCAAAGGCTCGCTAATTCAATATCACGGCCTCCAAAATAGTTAGCGCGAGCCAAA
1 AACTGTA-ATCCAAAGGCTCGCTGATTCAATATCGCGACCTCCAAAATAGTAAGCGCGAGCCAAA
** * * *
40840448 GCTCCCAGTTGTAATCCAAAGGCTCGCTGATTTAATATCGCAACCTCCAAAACAGTTAGCACGAG
65 GCTCCCAACTGTAATCCAAAGGCTCGCTGATTCAATATCGCAACCTCCAAAACAATAAGCACGAG
* * * * * *
40840513 C-CAAAGCTCCTAATTGTAATCCAAATGCTTGTTGATTCAATATCGCGACCTCCAAAATAGTCAA
130 CTC-AAGCTCCCAACTGTAATCCAAAGGCTTGCTGATTCAATATCGCAACCTCCAAAACAGTCAA
* * *
40840577 TGTGAGCTCAAGCTCCT
194 TGTAAGCTAAAGCTACT
* * * * *
40840594 AGCTGTAATCCAAAGACTCGTTGATTCAATATCGCGTCCTCCAAAATAGTAAGCACGAG-CAAAG
1 AACTGTAATCCAAAGGCTCGCTGATTCAATATCGCGACCTCCAAAATAGTAAGCGCGAGCCAAAG
* * * * * *
40840658 CTCCCAACTG-ATATGCAAAGGCTCACTTATTCAAAATCGAAACCTCTAAAA
66 CTCCCAACTGTA-ATCCAAAGGCTCGCTGATTCAATATCGCAACCTCCAAAA
40840709 TAGCTCACAG
Statistics
Matches: 273, Mismatches: 45, Indels: 15
0.82 0.14 0.05
Matches are distributed among these distances:
208 1 0.00
209 48 0.18
210 220 0.81
211 3 0.01
212 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.23
Consensus pattern (210 bp):
AACTGTAATCCAAAGGCTCGCTGATTCAATATCGCGACCTCCAAAATAGTAAGCGCGAGCCAAAG
CTCCCAACTGTAATCCAAAGGCTCGCTGATTCAATATCGCAACCTCCAAAACAATAAGCACGAGC
TCAAGCTCCCAACTGTAATCCAAAGGCTTGCTGATTCAATATCGCAACCTCCAAAACAGTCAATG
TAAGCTAAAGCTACT
Found at i:40844568 original size:19 final size:20
Alignment explanation
Indices: 40844544--40844582 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
40844534 AAATAAACAT
40844544 TAAAAAA-TTATTTTAAAAA
1 TAAAAAATTTATTTTAAAAA
40844563 TAAAAAATTTTATTTTAAAA
1 TAAAAAA-TTTATTTTAAAA
40844583 GTATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAAATTTATTTTAAAAA
Found at i:40844607 original size:8 final size:7
Alignment explanation
Indices: 40844590--40844623 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
40844580 AAAGTATTTT
*
40844590 AAAATTA
1 AAAAATA
40844597 AAAAATA
1 AAAAATA
40844604 AAAAAT-
1 AAAAATA
40844610 AAAAATA
1 AAAAATA
40844617 AAAAATA
1 AAAAATA
40844624 TATATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
6 6 0.24
7 19 0.76
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAAATA
Found at i:40844613 original size:13 final size:13
Alignment explanation
Indices: 40844597--40844623 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
40844587 TTTAAAATTA
40844597 AAAAATAAAAAAT
1 AAAAATAAAAAAT
40844610 AAAAATAAAAAAT
1 AAAAATAAAAAAT
40844623 A
1 A
40844624 TATATTATTA
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATAAAAAAT
Found at i:40845052 original size:31 final size:28
Alignment explanation
Indices: 40844995--40845062 Score: 82
Period size: 31 Copynumber: 2.3 Consensus size: 28
40844985 ATCAACAATT
*
40844995 AATTAATTTAAAAAAAATAAAAATAAAA
1 AATTAAATTAAAAAAAATAAAAATAAAA
*
40845023 AATTAAATTAACAAAATATATAAACATAAAA
1 AATTAAATTAA-AAAA-A-ATAAAAATAAAA
*
40845054 GATTAAATT
1 AATTAAATT
40845063 TAGCATAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 10 0.29
29 4 0.12
30 1 0.03
31 19 0.56
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (28 bp):
AATTAAATTAAAAAAAATAAAAATAAAA
Found at i:40846387 original size:22 final size:24
Alignment explanation
Indices: 40846351--40846415 Score: 66
Period size: 23 Copynumber: 2.8 Consensus size: 24
40846341 TCAAACAATT
40846351 TTTAG-AATACAATTTTTATT-TAA
1 TTTAGAAATA-AATTTTTATTATAA
* *
40846374 TTTA-AAATTAATTTTT-TTATTA
1 TTTAGAAATAAATTTTTATTATAA
40846396 TTTAGAAATAAATATTTTAT
1 TTTAGAAATAAAT-TTTTAT
40846416 ATTTAAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
21 2 0.06
22 13 0.38
23 14 0.41
24 4 0.12
25 1 0.03
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (24 bp):
TTTAGAAATAAATTTTTATTATAA
Found at i:40846389 original size:23 final size:25
Alignment explanation
Indices: 40846362--40846421 Score: 72
Period size: 23 Copynumber: 2.5 Consensus size: 25
40846352 TTAGAATACA
*
40846362 ATTTTTATTTAATTTA-AAATTAAT
1 ATTTTTATTTAATTTAGAAATAAAT
*
40846386 TTTTTTA-TT-ATTTAGAAATAAAT
1 ATTTTTATTTAATTTAGAAATAAAT
40846409 ATTTTATATTTAA
1 ATTTT-TATTTAA
40846422 AATGGTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 5 0.17
23 13 0.45
24 8 0.28
25 2 0.07
26 1 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTTTTATTTAATTTAGAAATAAAT
Found at i:40846413 original size:24 final size:23
Alignment explanation
Indices: 40846363--40846424 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
40846353 TAGAATACAA
*
40846363 TTTTTATTTAATTTAAAATTAATT
1 TTTTTA-TTAATTTAAAATAAATT
40846387 TTTTTATT-ATTTAGAAATAAA-T
1 TTTTTATTAATTTA-AAATAAATT
*
40846409 ATTTTA-T-ATTTAAAAT
1 TTTTTATTAATTTAAAAT
40846425 GGTAAAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
20 4 0.11
21 6 0.17
22 11 0.31
23 8 0.23
24 6 0.17
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
TTTTTATTAATTTAAAATAAATT
Found at i:40847414 original size:21 final size:21
Alignment explanation
Indices: 40847383--40847439 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
40847373 TCAGAATGTT
* *
40847383 AGTCCTATGAATAGTGGGGTCA
1 AGTCC-ATGAACAGTGGAGTCA
40847405 AGTCCATGAACAGTGGAGTCA
1 AGTCCATGAACAGTGGAGTCA
*
40847426 A-ACCATGAACAGTG
1 AGTCCATGAACAGTG
40847440 ATAATATGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
20 12 0.38
21 15 0.47
22 5 0.16
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (21 bp):
AGTCCATGAACAGTGGAGTCA
Found at i:40852587 original size:22 final size:20
Alignment explanation
Indices: 40852562--40852610 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
40852552 TTAATCAAAG
40852562 TTTTATTTTAAATT-TTTATGCA
1 TTTTATTTT-AATTATTTA--CA
*
40852584 TTTTAATTTAATTATTTACA
1 TTTTATTTTAATTATTTACA
40852604 TTTTATT
1 TTTTATT
40852611 ACTTTAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 8 0.33
21 4 0.17
22 12 0.50
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (20 bp):
TTTTATTTTAATTATTTACA
Found at i:40855930 original size:42 final size:42
Alignment explanation
Indices: 40855884--40856249 Score: 302
Period size: 42 Copynumber: 8.6 Consensus size: 42
40855874 CATATGCCAC
*
40855884 TGTCCCAGACAGGGTCTTACACGAAATCAAATATAATGCCGA
1 TGTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGA
* * * * *
40855926 TGTCCCAGACATGGTCTTATACATAAATCTCAAAT-CGATGCCAA
1 TGTCCCAGACAGGGTCTTACAC-GAAA--TCAAATATGATGCCGA
* * *
40855970 CGTCCCAGAC-GTGGTCTTACATGTAATC-AATATCGATGCC-A
1 TGTCCCAGACAG-GGTCTTACACGAAATCAAATAT-GATGCCGA
40856011 CTGTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGA
1 -TGTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGA
* * * * *
40856054 TGTCCCAGACATGGTCTTATACATAAATCTCAAAT-CGATGCCAA
1 TGTCCCAGACAGGGTCTTACAC-GAAA--TCAAATATGATGCCGA
* * *
40856098 CGTCCCAGAC-GTGGTCTTACATGTAATC-AATATCGATGCC-A
1 TGTCCCAGACAG-GGTCTTACACGAAATCAAATAT-GATGCCGA
40856139 CTGTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGA
1 -TGTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGA
* * * * * *
40856182 TGTCCTAGACACGGTCTTATACATAAATCTCAAAT-CGATGCCAA
1 TGTCCCAGACAGGGTCTTACAC-GAAA--TCAAATATGATGCCGA
*
40856226 CGTCCCAGAC-GTGGTCTTACACGA
1 TGTCCCAGACAG-GGTCTTACACGA
40856250 TAACACATAT
Statistics
Matches: 258, Mismatches: 42, Indels: 47
0.74 0.12 0.14
Matches are distributed among these distances:
40 6 0.02
41 6 0.02
42 129 0.50
43 28 0.11
44 71 0.28
45 18 0.07
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (42 bp):
TGTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGA
Found at i:40855986 original size:86 final size:83
Alignment explanation
Indices: 40855877--40856249 Score: 357
Period size: 86 Copynumber: 4.4 Consensus size: 83
40855867 AAAATTTCAT
*
40855877 ATGCCACTGTCCCAGACAG-GGTCTTACACGAAATCAAATATAATGCCGATGTCCCAGACATGGT
1 ATGCCAC-GTCCCAGAC-GTGGTCTTACACGAAATCAAATATGATGCCGATGTCCCAGACATGGT
40855941 CTTATACATAAATCTCAAATCG
64 CTTATACATAAA--TCAAATCG
* * *
40855963 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATC-AATATCGATGCC-ACTGTCCCAGACAGGG
1 ATGCC-ACGTCCCAGACGTGGTCTTACACGAAATCAAATAT-GATGCCGA-TGTCCCAGACATGG
* * *
40856026 TCTTACAC-GAAATCAAATATG
63 TCTTATACATAAATCAAAT-CG
* * * * * * * *
40856047 ATGCCGATGTCCCAGACATGGTCTTATACATAAATCTCAAAT-CGATGCCAACGTCCCAGACGTG
1 ATGCC-ACGTCCCAGACGTGGTCTTACAC-GAAA--TCAAATATGATGCCGATGTCCCAGACATG
*
40856111 GTC-T-TACATGTAATCAATATCG
62 GTCTTATACAT-AAATCAA-ATCG
* *
40856133 ATGCCACTGTCCCAGACAG-GGTCTTACACGAAATCAAATATGATGCCGATGTCCTAGACACGGT
1 ATGCCAC-GTCCCAGAC-GTGGTCTTACACGAAATCAAATATGATGCCGATGTCCCAGACATGGT
40856197 CTTATACATAAATCTCAAATCG
64 CTTATACATAAA--TCAAATCG
40856219 ATGCCAACGTCCCAGACGTGGTCTTACACGA
1 ATGCC-ACGTCCCAGACGTGGTCTTACACGA
40856250 TAACACATAT
Statistics
Matches: 232, Mismatches: 33, Indels: 44
0.75 0.11 0.14
Matches are distributed among these distances:
83 12 0.05
84 46 0.20
85 21 0.09
86 137 0.59
87 13 0.06
88 3 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.24
Consensus pattern (83 bp):
ATGCCACGTCCCAGACGTGGTCTTACACGAAATCAAATATGATGCCGATGTCCCAGACATGGTCT
TATACATAAATCAAATCG
Found at i:40856105 original size:128 final size:128
Alignment explanation
Indices: 40855877--40856246 Score: 713
Period size: 128 Copynumber: 2.9 Consensus size: 128
40855867 AAAATTTCAT
*
40855877 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAATATAATGCCGATGTCCCAGACATGGTC
1 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGATGTCCCAGACATGGTC
40855942 TTATACATAAATCTCAAATCGATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAATATCG
66 TTATACATAAATCTCAAATCGATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAATATCG
40856005 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGATGTCCCAGACATGGTC
1 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGATGTCCCAGACATGGTC
40856070 TTATACATAAATCTCAAATCGATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAATATCG
66 TTATACATAAATCTCAAATCGATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAATATCG
* *
40856133 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGATGTCCTAGACACGGTC
1 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGATGTCCCAGACATGGTC
40856198 TTATACATAAATCTCAAATCGATGCCAACGTCCCAGACGTGGTCTTACA
66 TTATACATAAATCTCAAATCGATGCCAACGTCCCAGACGTGGTCTTACA
40856247 CGATAACACA
Statistics
Matches: 239, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
128 239 1.00
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (128 bp):
ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAATATGATGCCGATGTCCCAGACATGGTC
TTATACATAAATCTCAAATCGATGCCAACGTCCCAGACGTGGTCTTACATGTAATCAATATCG
Found at i:40858698 original size:18 final size:18
Alignment explanation
Indices: 40858677--40858717 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
40858667 AAGCACCATT
*
40858677 GCACTATGGACCACCACC
1 GCACTATAGACCACCACC
*
40858695 GCACTATAGACCACCACT
1 GCACTATAGACCACCACC
40858713 GCACT
1 GCACT
40858718 TGGCCAATTC
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:0.29, C:0.41, G:0.15, T:0.15
Consensus pattern (18 bp):
GCACTATAGACCACCACC
Found at i:40864213 original size:12 final size:12
Alignment explanation
Indices: 40864196--40864220 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40864186 AAACTCTTAA
40864196 AATAAAAACCCT
1 AATAAAAACCCT
40864208 AATAAAAACCCT
1 AATAAAAACCCT
40864220 A
1 A
40864221 TTATTAGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.24, G:0.00, T:0.16
Consensus pattern (12 bp):
AATAAAAACCCT
Found at i:40864473 original size:21 final size:21
Alignment explanation
Indices: 40864449--40864494 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
40864439 TAACTTTTTG
40864449 ATTTAGT-TATTAAAAT-TTTCA
1 ATTTAGTGTA-TAAAATATTT-A
40864470 ATTTAGTGTATAAAATATTTA
1 ATTTAGTGTATAAAATATTTA
40864491 ATTT
1 ATTT
40864495 TGAAAAACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (21 bp):
ATTTAGTGTATAAAATATTTA
Found at i:40865148 original size:164 final size:165
Alignment explanation
Indices: 40864973--40865301 Score: 651
Period size: 164 Copynumber: 2.0 Consensus size: 165
40864963 TTGATGAGTA
40864973 TTTTTTTCGATATATTAAAATTTACATATAGTGAGATTTAAATCCATCCACTGATATTTTTAAAA
1 TTTTTTTCGATATATTAAAATTTACATATAGTGAGATTTAAATCCATCCACTGATATTTTTAAAA
40865038 TATTTTTTTATCACTCCAACCTATGCTTTATTTTTTATGAGTATTTTATAATTAAAATTTATTTA
66 TATTTTTTTATCACTCCAACCTATGCTTTATTTTTTATGAGTATTTTATAATTAAAATTTATTTA
40865103 ATATCATTATTTGATATTTATAAA-ATTTTTATAT
131 ATATCATTATTTGATATTTATAAATATTTTTATAT
40865137 TTTTTTTCGATATATTAAAATTTACATATAGTGAGATTTAAATCCATCCACTGATATTTTTAAAA
1 TTTTTTTCGATATATTAAAATTTACATATAGTGAGATTTAAATCCATCCACTGATATTTTTAAAA
40865202 TATTTTTTTATCACTCCAACCTATGCTTTATTTTTTATGAGTATTTTATAATTAAAATTTATTTA
66 TATTTTTTTATCACTCCAACCTATGCTTTATTTTTTATGAGTATTTTATAATTAAAATTTATTTA
40865267 ATATCATTATTTGATATTTATAAATATTTTTATAT
131 ATATCATTATTTGATATTTATAAATATTTTTATAT
40865302 ACAAATAGCA
Statistics
Matches: 164, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
164 154 0.94
165 10 0.06
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.51
Consensus pattern (165 bp):
TTTTTTTCGATATATTAAAATTTACATATAGTGAGATTTAAATCCATCCACTGATATTTTTAAAA
TATTTTTTTATCACTCCAACCTATGCTTTATTTTTTATGAGTATTTTATAATTAAAATTTATTTA
ATATCATTATTTGATATTTATAAATATTTTTATAT
Found at i:40867227 original size:37 final size:37
Alignment explanation
Indices: 40867167--40867276 Score: 112
Period size: 37 Copynumber: 3.0 Consensus size: 37
40867157 GGATGTATAG
* * * * * *
40867167 CTCTTCAGAGCACATGACCTGTTATCTGTTGCATTAA
1 CTCTTCGGAGCACTTGGCATGTTATCAGTTGGATTAA
* * * * *
40867204 CTCTTTGTAGCATTTGGCGTGTTATCAGTTGGATTAG
1 CTCTTCGGAGCACTTGGCATGTTATCAGTTGGATTAA
*
40867241 CTCTTCGGAGCACTTGGCATGTTATCGGTTGGATTA
1 CTCTTCGGAGCACTTGGCATGTTATCAGTTGGATTA
40867277 CTTGTGTACT
Statistics
Matches: 58, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (37 bp):
CTCTTCGGAGCACTTGGCATGTTATCAGTTGGATTAA
Found at i:40874034 original size:2 final size:2
Alignment explanation
Indices: 40874029--40874063 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
40874019 ATTTTTTTCT
40874029 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
40874064 CTTCAAAATC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40874662 original size:29 final size:30
Alignment explanation
Indices: 40874603--40874677 Score: 75
Period size: 29 Copynumber: 2.5 Consensus size: 30
40874593 TGGATAATAG
*
40874603 AAGAATAGTTTAGGTGACACTTACGACAAA
1 AAGAATAGTTTAGGTGACACTTACGAAAAA
40874633 AAGAA-AGTTTAGGT-ACCAACTTA-GAAAAA
1 AAGAATAGTTTAGGTGA-C-ACTTACGAAAAA
* *
40874662 AATGTATAATTTAGGT
1 AA-GAATAGTTTAGGT
40874678 ACTAATTTGT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
28 1 0.03
29 17 0.45
30 12 0.32
31 8 0.21
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.27
Consensus pattern (30 bp):
AAGAATAGTTTAGGTGACACTTACGAAAAA
Found at i:40875186 original size:128 final size:129
Alignment explanation
Indices: 40874958--40875214 Score: 507
Period size: 128 Copynumber: 2.0 Consensus size: 129
40874948 ACCTTGTCGT
40874958 CATCGATTAGTCCTTGACCACATATAAATAATTAATTAATTAATAATAAATAATATGTAATTTTG
1 CATCGATTAGTCCTTGACCACATATAAATAATTAATTAATTAATAATAAATAATATGTAATTTTG
40875023 TTAAGATTAATATAAATAATTTATAAAAAGTAGTATATAATTTAGTTAATA-TTAGTAGGTTGA
66 TTAAGATTAATATAAATAATTTATAAAAAGTAGTATATAATTTAGTTAATATTTAGTAGGTTGA
40875086 CATCGATTAGTCCTTGACCACATATAAATAATTAATTAATTAATAATAAATAATATGTAATTTTG
1 CATCGATTAGTCCTTGACCACATATAAATAATTAATTAATTAATAATAAATAATATGTAATTTTG
40875151 TTAAGATTAATATAAATAATTTATAAAAAGTAGTATATAATTTAGTTAATATTTAGTAGGTTGA
66 TTAAGATTAATATAAATAATTTATAAAAAGTAGTATATAATTTAGTTAATATTTAGTAGGTTGA
40875215 AATGTAAGAA
Statistics
Matches: 128, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
128 116 0.91
129 12 0.09
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.40
Consensus pattern (129 bp):
CATCGATTAGTCCTTGACCACATATAAATAATTAATTAATTAATAATAAATAATATGTAATTTTG
TTAAGATTAATATAAATAATTTATAAAAAGTAGTATATAATTTAGTTAATATTTAGTAGGTTGA
Found at i:40879369 original size:22 final size:20
Alignment explanation
Indices: 40879344--40879387 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
40879334 CTCTATTTTT
40879344 TTACCATTTTATTATTATATTG
1 TTACCATTTTATT-TT-TATTG
*
40879366 TTACTATTTTATTTTTATTG
1 TTACCATTTTATTTTTATTG
40879386 TT
1 TT
40879388 TGAATATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 2 0.10
22 12 0.57
ACGTcount: A:0.23, C:0.07, G:0.05, T:0.66
Consensus pattern (20 bp):
TTACCATTTTATTTTTATTG
Found at i:40879449 original size:30 final size:30
Alignment explanation
Indices: 40879413--40879475 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
40879403 ATTTATTTTA
40879413 TTGTTAATTTTGTTATTATTTT-AAAGACAT
1 TTGTTAATTTTGTTATTATTTTAAAAG-CAT
40879443 TTGTTAATTTTGTTATTATTTTAAAAGCAT
1 TTGTTAATTTTGTTATTATTTTAAAAGCAT
40879473 TTG
1 TTG
40879476 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.29, C:0.03, G:0.11, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAAGCAT
Found at i:40879595 original size:20 final size:20
Alignment explanation
Indices: 40879570--40879609 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40879560 CGTAAAATGA
*
40879570 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
40879590 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
40879610 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:40879599 original size:34 final size:35
Alignment explanation
Indices: 40879555--40879621 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
40879545 CAGTAAAATA
*
40879555 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
40879589 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
40879622 CTGCTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:40879679 original size:55 final size:55
Alignment explanation
Indices: 40879595--40879704 Score: 211
Period size: 55 Copynumber: 2.0 Consensus size: 55
40879585 TTACTTTTCT
40879595 GTAAAATGATTTACTGGAAAATATTTTCTGCTGTTTGGTAAATCTGTGTAAAATA
1 GTAAAATGATTTACTGGAAAATATTTTCTGCTGTTTGGTAAATCTGTGTAAAATA
*
40879650 GTAAAATGATTTACTGGAAAATATTTTCTGGTGTTTGGTAAATCTGTGTAAAATA
1 GTAAAATGATTTACTGGAAAATATTTTCTGCTGTTTGGTAAATCTGTGTAAAATA
40879705 TTTTCTGCTG
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (55 bp):
GTAAAATGATTTACTGGAAAATATTTTCTGCTGTTTGGTAAATCTGTGTAAAATA
Found at i:40879735 original size:32 final size:31
Alignment explanation
Indices: 40879657--40879741 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 31
40879647 ATAGTAAAAT
* *
40879657 GATTTACTGGAAAATATTTTCTGGTGTTTGGTA
1 GATTT-CT-GAAAATATTTTCTGCTGTTTGGCA
* * *
40879690 AATCTGTGTAAAATATTTTCTGCTGTTTGGCA
1 GATTTCTG-AAAATATTTTCTGCTGTTTGGCA
40879722 GATTTCCTGAAAATATTTTC
1 GATTT-CTGAAAATATTTTC
40879742 CGGAAAAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
31 1 0.02
32 36 0.86
33 5 0.12
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.45
Consensus pattern (31 bp):
GATTTCTGAAAATATTTTCTGCTGTTTGGCA
Found at i:40879961 original size:40 final size:39
Alignment explanation
Indices: 40879916--40880042 Score: 109
Period size: 40 Copynumber: 3.2 Consensus size: 39
40879906 ACAAGTATTG
40879916 AATAATTATAAATTGCTTCGAAACCAGAATGAGTACTAGA
1 AATAA-TATAAATTGCTTCGAAACCAGAATGAGTACTAGA
* * * * * * *
40879956 AATAATAT-TATT--ATCCAAATACATAATTAATGGTAC-ACA
1 AATAATATAAATTGCTTCGAAA-CCAGAA-TGA--GTACTAGA
40879995 ACATAATATAAATTGCTTCGAAACCAGAATGAGTACTAGA
1 A-ATAATATAAATTGCTTCGAAACCAGAATGAGTACTAGA
40880035 AATAATAT
1 AATAATAT
40880043 TATTATCCAA
Statistics
Matches: 64, Mismatches: 14, Indels: 19
0.66 0.14 0.20
Matches are distributed among these distances:
36 5 0.08
37 4 0.06
38 5 0.08
39 17 0.27
40 19 0.30
41 5 0.08
42 4 0.06
43 5 0.08
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.29
Consensus pattern (39 bp):
AATAATATAAATTGCTTCGAAACCAGAATGAGTACTAGA
Found at i:40880007 original size:79 final size:79
Alignment explanation
Indices: 40879917--40880090 Score: 321
Period size: 79 Copynumber: 2.2 Consensus size: 79
40879907 CAAGTATTGA
40879917 ATAATTATAAATTGCTTCGAAACCAGAATGAGTACTAGAAATAATATTATTATCCAAATACATAA
1 ATAA-TATAAATTGCTTCGAAACCAGAATGAGTACTAGAAATAATATTATTATCCAAATACATAA
40879982 TTAATGGTACACAAC
65 TTAATGGTACACAAC
40879997 ATAATATAAATTGCTTCGAAACCAGAATGAGTACTAGAAATAATATTATTATCCAAATACATAAT
1 ATAATATAAATTGCTTCGAAACCAGAATGAGTACTAGAAATAATATTATTATCCAAATACATAAT
40880062 TAATGGTACACAAC
66 TAATGGTACACAAC
40880076 ATAATAATAACATTG
1 ATAAT-ATAA-ATTG
40880091 TCCAAGTGAA
Statistics
Matches: 92, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
79 80 0.87
80 8 0.09
81 4 0.04
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (79 bp):
ATAATATAAATTGCTTCGAAACCAGAATGAGTACTAGAAATAATATTATTATCCAAATACATAAT
TAATGGTACACAAC
Found at i:40880163 original size:72 final size:72
Alignment explanation
Indices: 40880046--40880189 Score: 243
Period size: 72 Copynumber: 2.0 Consensus size: 72
40880036 ATAATATTAT
*
40880046 TATCCAAATACATAATTAATGGTACACAACATAATAATAACATTGTCCAAGTGAATAATATTACA
1 TATCCAAATACATAATTAATGGTACACAACATAATAAGAACATTGTCCAAGTGAATAATATTACA
*
40880111 TCACATA
66 CCACATA
* * *
40880118 TATCCAAATACATAATTAATGGTACACCACATAGTAAGAACATTGTCCAAGTGCATAATATTACA
1 TATCCAAATACATAATTAATGGTACACAACATAATAAGAACATTGTCCAAGTGAATAATATTACA
40880183 CCACATA
66 CCACATA
40880190 AATGTATCAA
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.45, C:0.19, G:0.08, T:0.28
Consensus pattern (72 bp):
TATCCAAATACATAATTAATGGTACACAACATAATAAGAACATTGTCCAAGTGAATAATATTACA
CCACATA
Found at i:40886340 original size:12 final size:12
Alignment explanation
Indices: 40886323--40886355 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
40886313 AAACCAAATC
*
40886323 AAGGGAGAACGA
1 AAGGGAGAACAA
40886335 AAGGGAGAACAA
1 AAGGGAGAACAA
40886347 AAGGGAGAA
1 AAGGGAGAA
40886356 GGGAGAACGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.55, C:0.06, G:0.39, T:0.00
Consensus pattern (12 bp):
AAGGGAGAACAA
Found at i:40888066 original size:153 final size:156
Alignment explanation
Indices: 40887782--40888090 Score: 480
Period size: 153 Copynumber: 2.0 Consensus size: 156
40887772 CAGCAGACCT
* * *
40887782 AGGGTGGATTTGGATGGGTGATTGGGTGCGGTGCGGTGCGGTGCGTTTACTTTACTTTTTGTCTC
1 AGGGTGGATTTGGATGGGCGATTGGGTGCGGTGCGGTGCGGT--GTTAACTTTACTTTTTGTCCC
* * * *
40887847 ACGCTACAGTATTGCTACAGTATCTAATCTCACCATCACCGTTGTTTTTACACTAACCGCAGGTA
64 ACGCTACAGTATTGCTACAGTATCTAATCTCACCACCACCGCTATTTTTACACTAACCGCAAGTA
*
40887912 AACGTACCGCCCATCCAAACTCACCCTA
129 AACGCACCGCCCATCCAAACTCACCCTA
*
40887940 AGGGTGGGTTTGGATGGGCGATTGGGTGCGGTGCGGTGC-GT-TTAAC-TTACTTTTTGTCCCAC
1 AGGGTGGATTTGGATGGGCGATTGGGTGCGGTGCGGTGCGGTGTTAACTTTACTTTTTGTCCCAC
*
40888002 GCTACAGTATTGCTACAGTATCTAATCTCACCGCCACCGCTATTTTTACACTAACCGCAAGTAAA
66 GCTACAGTATTGCTACAGTATCTAATCTCACCACCACCGCTATTTTTACACTAACCGCAAGTAAA
*
40888067 CGCACTGCCCATCCAAACTCACCC
131 CGCACCGCCCATCCAAACTCACCC
40888091 CTAGTCCCAA
Statistics
Matches: 140, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
153 97 0.69
154 4 0.03
157 2 0.01
158 37 0.26
ACGTcount: A:0.21, C:0.26, G:0.23, T:0.29
Consensus pattern (156 bp):
AGGGTGGATTTGGATGGGCGATTGGGTGCGGTGCGGTGCGGTGTTAACTTTACTTTTTGTCCCAC
GCTACAGTATTGCTACAGTATCTAATCTCACCACCACCGCTATTTTTACACTAACCGCAAGTAAA
CGCACCGCCCATCCAAACTCACCCTA
Found at i:40900378 original size:39 final size:39
Alignment explanation
Indices: 40900330--40900405 Score: 152
Period size: 39 Copynumber: 1.9 Consensus size: 39
40900320 AAACTTCTGG
40900330 AGTATCTTCTTTAAATATTACTTCTGAGACAAACTAAGT
1 AGTATCTTCTTTAAATATTACTTCTGAGACAAACTAAGT
40900369 AGTATCTTCTTTAAATATTACTTCTGAGACAAACTAA
1 AGTATCTTCTTTAAATATTACTTCTGAGACAAACTAA
40900406 CTCTGCCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.38
Consensus pattern (39 bp):
AGTATCTTCTTTAAATATTACTTCTGAGACAAACTAAGT
Found at i:40904924 original size:59 final size:61
Alignment explanation
Indices: 40904835--40904958 Score: 198
Period size: 59 Copynumber: 2.1 Consensus size: 61
40904825 TTTTATTATG
40904835 CCAATATCTCGATACCCATATCTTTGACTTTCCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATCTCGATACCCATATCTTTGACTTTCCAATATTTGATACCCATATCTTTGACTTT
* * * *
40904896 CCAATAT-TTGATACCCATA-CTTTGACTTTCTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATCTCGATACCCATATCTTTGACTTTCCAATATTTGATACCCATATCTTTGACTTT
40904955 CCAA
1 CCAA
40904959 AAATATGGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
59 41 0.69
60 11 0.19
61 7 0.12
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.43
Consensus pattern (61 bp):
CCAATATCTCGATACCCATATCTTTGACTTTCCAATATTTGATACCCATATCTTTGACTTT
Found at i:40904932 original size:29 final size:30
Alignment explanation
Indices: 40904835--40904958 Score: 196
Period size: 30 Copynumber: 4.1 Consensus size: 30
40904825 TTTTATTATG
*
40904835 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
40904866 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
40904896 CCAATATTTGATACCCATA-CTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
40904925 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
40904955 CCAA
1 CCAA
40904959 AAATATGGAT
Statistics
Matches: 86, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
29 27 0.31
30 52 0.60
31 7 0.08
ACGTcount: A:0.27, C:0.24, G:0.06, T:0.43
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:40908774 original size:21 final size:20
Alignment explanation
Indices: 40908736--40908779 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
40908726 TATAAAGTAT
* *
40908736 ATTTTATTTTATTTATTATG
1 ATTTTATTTTATTCATTAGG
*
40908756 ATTTTCTTTATATTCATTAGG
1 ATTTTATTT-TATTCATTAGG
40908777 ATT
1 ATT
40908780 GGAGATAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.25, C:0.05, G:0.07, T:0.64
Consensus pattern (20 bp):
ATTTTATTTTATTCATTAGG
Found at i:40915244 original size:30 final size:31
Alignment explanation
Indices: 40915189--40915254 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 31
40915179 TATAGTCTAT
*
40915189 ATTTTTATAATTTTTAAAGGATTAAA-TCAA
1 ATTTTTATAATTTTTAAAGGATTAAAGTAAA
* *
40915219 ATTTTTATAA-TTTTAGAGGGGTTAAAGTAAA
1 ATTTTTATAATTTTTA-AAGGATTAAAGTAAA
40915250 ATTTT
1 ATTTT
40915255 ACCTTTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.16
30 18 0.58
31 8 0.26
ACGTcount: A:0.39, C:0.02, G:0.12, T:0.47
Consensus pattern (31 bp):
ATTTTTATAATTTTTAAAGGATTAAAGTAAA
Found at i:40916414 original size:3 final size:3
Alignment explanation
Indices: 40916406--40916435 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
40916396 AATTAAATCC
40916406 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40916436 GTATCACCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40922424 original size:95 final size:95
Alignment explanation
Indices: 40922261--40922439 Score: 358
Period size: 95 Copynumber: 1.9 Consensus size: 95
40922251 AGGATGGAAT
40922261 AAGTATTAATAGCAAAAAGAAAATACTCAAGTTTTTAATTTTTGTAAATTATATTAAAAAAATAA
1 AAGTATTAATAGCAAAAAGAAAATACTCAAGTTTTTAATTTTTGTAAATTATATTAAAAAAATAA
40922326 AAGCATTAAATGTTAAAATTAATTTTATCC
66 AAGCATTAAATGTTAAAATTAATTTTATCC
40922356 AAGTATTAATAGCAAAAAGAAAATACTCAAGTTTTTAATTTTTGTAAATTATATTAAAAAAATAA
1 AAGTATTAATAGCAAAAAGAAAATACTCAAGTTTTTAATTTTTGTAAATTATATTAAAAAAATAA
40922421 AAGCATTAAATGTTAAAAT
66 AAGCATTAAATGTTAAAAT
40922440 GACAATTTTA
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 84 1.00
ACGTcount: A:0.51, C:0.06, G:0.08, T:0.36
Consensus pattern (95 bp):
AAGTATTAATAGCAAAAAGAAAATACTCAAGTTTTTAATTTTTGTAAATTATATTAAAAAAATAA
AAGCATTAAATGTTAAAATTAATTTTATCC
Found at i:40922969 original size:10 final size:10
Alignment explanation
Indices: 40922939--40922973 Score: 56
Period size: 9 Copynumber: 3.7 Consensus size: 10
40922929 GTTTACCCAC
40922939 AATTAAAAC-
1 AATTAAAACA
40922948 AATTAAAA-A
1 AATTAAAACA
40922957 AATTAAAACA
1 AATTAAAACA
40922967 AATTAAA
1 AATTAAA
40922974 CACTGACCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.23
Consensus pattern (10 bp):
AATTAAAACA
Found at i:40925402 original size:6 final size:6
Alignment explanation
Indices: 40925391--40925417 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
40925381 AGTAAATGTA
40925391 GTGAGG GTGAGG GTGAGG GTGAGG GTG
1 GTGAGG GTGAGG GTGAGG GTGAGG GTG
40925418 GTGAGGTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.67, T:0.19
Consensus pattern (6 bp):
GTGAGG
Found at i:40925434 original size:51 final size:51
Alignment explanation
Indices: 40925357--40925468 Score: 179
Period size: 51 Copynumber: 2.2 Consensus size: 51
40925347 TAATAAAGGT
* * *
40925357 GGTGAGGATGGTGACGTTGTTGGTAGTAAATGTAGTGAGGGTGAGGGTGAG
1 GGTGAGGGTGGTGACGTTGTTAGTAGTAAATATAGTGAGGGTGAGGGTGAG
* *
40925408 GGTGAGGGTGGTGAGGTTGTTAGTAGTAAATATGGTGAGGGTGAGGGTGAG
1 GGTGAGGGTGGTGACGTTGTTAGTAGTAAATATAGTGAGGGTGAGGGTGAG
40925459 GGTGAGGGTG
1 GGTGAGGGTG
40925469 AGGGTGAGGG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 56 1.00
ACGTcount: A:0.21, C:0.01, G:0.52, T:0.27
Consensus pattern (51 bp):
GGTGAGGGTGGTGACGTTGTTAGTAGTAAATATAGTGAGGGTGAGGGTGAG
Found at i:40925452 original size:6 final size:6
Alignment explanation
Indices: 40925441--40925486 Score: 83
Period size: 6 Copynumber: 7.7 Consensus size: 6
40925431 TAGTAAATAT
*
40925441 GGTGAG GGTGAG GGTGAG GGTGAG GGTGAG GGTGAG GGAGAG GGTG
1 GGTGAG GGTGAG GGTGAG GGTGAG GGTGAG GGTGAG GGTGAG GGTG
40925487 GTGAGGTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.17, C:0.00, G:0.67, T:0.15
Consensus pattern (6 bp):
GGTGAG
Found at i:40929073 original size:28 final size:28
Alignment explanation
Indices: 40929020--40929080 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
40929010 TAGTATGATA
*
40929020 AATAATATAAATGATAATATTGT-AAAT
1 AATAATATAAATGATAATAATGTAAAAT
40929047 AATAATAATAAATGATAATACAT-TAAAAT
1 AATAAT-ATAAATGATAATA-ATGTAAAAT
40929076 AATAA
1 AATAA
40929081 AGAAAATGAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 6 0.20
28 14 0.47
29 10 0.33
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.33
Consensus pattern (28 bp):
AATAATATAAATGATAATAATGTAAAAT
Found at i:40929866 original size:15 final size:16
Alignment explanation
Indices: 40929846--40929882 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
40929836 TTTCCGTTTG
40929846 TAAAAAA-AATGAAA-A
1 TAAAAAATAAT-AAAGA
40929861 TAAAAAATAATAAAGA
1 TAAAAAATAATAAAGA
40929877 TAAAAA
1 TAAAAA
40929883 CGAAACGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (16 bp):
TAAAAAATAATAAAGA
Found at i:40930737 original size:44 final size:43
Alignment explanation
Indices: 40930687--40931286 Score: 494
Period size: 44 Copynumber: 13.7 Consensus size: 43
40930677 GGTGGCTTAA
* * * *
40930687 ATCTGCTTCACTATTGCTTAGGAAGATAAGATTCGCCGTCTTCG
1 ATCTGCTTCACTACTGCTTAGGGAGATAGGA-TCACCGTCTTCG
* * ** *
40930731 ATCTGCTCCACTATTGCTTAGGGAGATAGGATCTACCAACTTTG
1 ATCTGCTTCACTACTGCTTAGGGAGATAGGATC-ACCGTCTTCG
* * *
40930775 ACCTGC-TCTACTACTGCTTAAGGAGATAGGATCTACCATCTTCG
1 ATCTGCTTC-ACTACTGCTTAGGGAGATAGGATC-ACCGTCTTCG
* * * * * **
40930819 ACCTGCTCCACTACTGCTTAGGGAGATAGGACTGA-TGGCTTAA
1 ATCTGCTTCACTACTGCTTAGGGAGATAGGA-TCACCGTCTTCG
* * *
40930862 ATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCG
1 ATCTGCTTCACTACTGCTTAGGGAGATAGGA-TCACCGTCTTCG
** * *
40930906 ATCTGCTTCACTACTGCTTAGGGAGATAAAATCTACCATCTTTG
1 ATCTGCTTCACTACTGCTTAGGGAGATAGGATC-ACCGTCTTCG
* * *
40930950 ACCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCG
1 ATCTGCTTCACTACTGCTTAGGGAGATAGGATC-ACCGTCTTCG
* * * ** **
40930994 ACCTGCTCCACTACTGCTTAGGGAGATATGA-C-TGGTGGCTTAA
1 ATCTGCTTCACTACTGCTTAGGGAGATAGGATCACCGT--CTTCG
* * *
40931037 ATCTACTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTCG
1 ATCTGCTTCACTACTGCTTAGGGAGATAGGA-TCACCGTCTTCG
* *
40931081 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCG
1 ATCTGCTTCACTACTGCTTAGGGAGATAGGATC-ACCGTCTTCG
* * ** **
40931125 AACTGC-TCTACTACTACTTAGGGAGATAGGA-C-TGGTGGCTTAA
1 ATCTGCTTC-ACTACTGCTTAGGGAGATAGGATCACCGT--CTTCG
* * *
40931168 ATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCG
1 ATCTGCTTCACTACTGCTTAGGGAGATAGGA-TCACCGTCTTCG
* * *
40931212 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATATTCG
1 ATCTGCTTCACTACTGCTTAGGGAGATAGGATC-ACCGTCTTCG
* * *
40931256 ACCTGCTCCACTACTACTTAGGGAGATAGGA
1 ATCTGCTTCACTACTGCTTAGGGAGATAGGA
40931287 CTTGATATGA
Statistics
Matches: 450, Mismatches: 86, Indels: 40
0.78 0.15 0.07
Matches are distributed among these distances:
41 2 0.00
43 99 0.22
44 341 0.76
45 4 0.01
46 4 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (43 bp):
ATCTGCTTCACTACTGCTTAGGGAGATAGGATCACCGTCTTCG
Found at i:40930893 original size:175 final size:175
Alignment explanation
Indices: 40930602--40931286 Score: 874
Period size: 175 Copynumber: 3.9 Consensus size: 175
40930592 TGGATGCGAT
* * * * * * *
40930602 CTGCTCTACTATTGCTT-AGAGAGATAAGATCTACAATCTTCAACCTACTCCACTGCTACTCT-G
1 CTGCTCTACTACTGCTTAAG-GAGATAGGATCTACCATCTTCGACCTGCTCCACTACTGCT-TAG
*
40930665 GGAGATAGGACTGGTGGCTTAAATCTGCTTCACTATTGCTTAGGAAGATAAGATTCGCCGTCTTC
64 GGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTC
* *
40930730 GATCTGCTCCACTATTGCTTAGGGAGATAGGATCTACCAACTTTGAC
129 GATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGAC
40930777 CTGCTCTACTACTGCTTAAGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGGG
1 CTGCTCTACTACTGCTTAAGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGGG
*
40930842 AGATAGGACTGATGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCGA
66 AGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCGA
* **
40930907 TCTGCTTCACTACTGCTTAGGGAGATAAAATCTACCATCTTTGAC
131 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGAC
* *
40930952 CTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGGG
1 CTGCTCTACTACTGCTTAAGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGGG
* * *
40931017 AGATATGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTCGA
66 AGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCGA
* *
40931082 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAA
131 TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGAC
* * ***** ** * * *
40931127 CTGCTCTACTACTACTTAGGGAGATAGGA-CTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGA
1 CTGCTCTACTACTGCTTAAGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGGG
* * ** * ** * * * * * *
40931191 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAGGA-TCTACCATATTC
66 AGATAGGACT-GGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTC-GCCGTCTTC
* *
40931255 GACCTGCTCCACTACTACTTAGGGAGATAGGA
129 GATCTGCTCCACTACTGCTTAGGGAGATAGGA
40931287 CTTGATATGA
Statistics
Matches: 454, Mismatches: 52, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
174 36 0.08
175 416 0.92
176 2 0.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (175 bp):
CTGCTCTACTACTGCTTAAGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTGCTTAGGG
AGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTCGA
TCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTTGAC
Found at i:40931284 original size:131 final size:131
Alignment explanation
Indices: 40930687--40931288 Score: 653
Period size: 131 Copynumber: 4.6 Consensus size: 131
40930677 GGTGGCTTAA
* * * * * * * * *
40930687 ATCTGCTTCACTATTGCTTAGGAAGATAAGAT-TCGCCGTCTTCGATCTGCTCCACTATTGCTTA
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCT-ACCATCTTCGACCTGCTCCACTACTACTTA
***** ** * * *
40930751 GGGAGATAGGATCTACCAACTTTGACCTGC-TCTACTACTGCTTAAGG-AGATAGGA-TCTACCA
65 GGGAGATAGGA-CTGGTGGCTTAAATCTGCTTC-ACTACTGCTT-AGGAAGATAAGATTC-ACCG
40930813 TCTTCG
126 TCTTCG
* * ** * * *
40930819 ACCTGCTCCACTACTGCTTAGGGAGATAGGA-CT--GATGGCTTAAATCTGCTTCACTACTGCTT
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCAT--CTTCGACCTGCTCCACTACTACTT
* * * ** * ** * * *
40930881 AGGAAGATAAGATTCGCCGTCTTCGATCTGCTTCACTACTGCTTAGGGAGATAA-AATCTACCAT
64 AGGGAGATAGGACT-GGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTC-ACCGT
*
40930945 CTTTG
127 CTTCG
* *
40930950 ACCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTGCTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTACTTAG
* *
40931015 GGAGATATGACTGGTGGCTTAAATCTACTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTC
66 GGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTC
40931080 G
131 G
* *
40931081 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGAACTGCTCTACTACTACTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTACTTAG
*
40931146 GGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCGCCGTCTTC
66 GGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTC
40931211 G
131 G
*
40931212 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATATTCGACCTGCTCCACTACTACTTAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTACTTAG
40931277 GGAGATAGGACT
66 GGAGATAGGACT
40931289 TGATATGATG
Statistics
Matches: 410, Mismatches: 49, Indels: 23
0.85 0.10 0.05
Matches are distributed among these distances:
129 1 0.00
130 5 0.01
131 337 0.82
132 65 0.16
134 2 0.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.30
Consensus pattern (131 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAGGATCTACCATCTTCGACCTGCTCCACTACTACTTAG
GGAGATAGGACTGGTGGCTTAAATCTGCTTCACTACTGCTTAGGAAGATAAGATTCACCGTCTTC
G
Found at i:40931787 original size:107 final size:107
Alignment explanation
Indices: 40931601--40931817 Score: 416
Period size: 107 Copynumber: 2.0 Consensus size: 107
40931591 TCAGATTGCC
40931601 TCCACTGTAATCTTCAAAGTTAAGTCCACTTGTAATTTTGGGACTTAAAATTTGAACCATCCTCC
1 TCCACTGTAATCTTCAAAGTTAAGTCCACTTGTAATTTTGGGACTTAAAATTTGAACCATCCTCC
*
40931666 TCCCACTGTAATTCAAGGGTAGAAAGATCTGGCTTTTCTCAA
66 TCCCACTGTAATTCAAGGGTAGAAAAATCTGGCTTTTCTCAA
*
40931708 TCCACTGTAATCTTCAAGGTTAAGTCCACTTGTAATTTTGGGACTTAAAATTTGAACCATCCTCC
1 TCCACTGTAATCTTCAAAGTTAAGTCCACTTGTAATTTTGGGACTTAAAATTTGAACCATCCTCC
40931773 TCCCACTGTAATTCAAGGGTAGAAAAATCTGGCTTTTCTCAA
66 TCCCACTGTAATTCAAGGGTAGAAAAATCTGGCTTTTCTCAA
40931815 TCC
1 TCC
40931818 TCTGCTATCA
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (107 bp):
TCCACTGTAATCTTCAAAGTTAAGTCCACTTGTAATTTTGGGACTTAAAATTTGAACCATCCTCC
TCCCACTGTAATTCAAGGGTAGAAAAATCTGGCTTTTCTCAA
Found at i:40932664 original size:75 final size:80
Alignment explanation
Indices: 40932562--40932818 Score: 218
Period size: 86 Copynumber: 3.1 Consensus size: 80
40932552 TTGTACTTTT
** *
40932562 AGCGGCGTTTGTGATAAAAGCGCCGCTAAAG-A-T-ATT-G-CGTTCGTGGGAAAAACGCAGCTA
1 AGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGCAGTCATTAGACGTTCGTGGGAAAAACGCAGCTA
40932622 AAGGTCATGGTCTTC
66 AAGGTCATGGTCTTC
* * * * *
40932637 AGCGGCGTTTGTGGGAGAAGTGTCGCTAAAGGTCATGGTCTTTAGCGACGTTTGTGGGAAAAGCG
1 AGCGGCGTTTGTGGGAGAAGCGCCGCTAAA-G-CA--GTCATTA--GACGTTCGTGGGAAAAACG
* * *
40932702 CCGTTAAAGGTCATGGTCTTT
60 CAGCTAAAGGTCATGGTCTTC
* * * *
40932723 AGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGGTCATAGTCTTTAGCCGCGTTTGTGGGAAAAGCG
1 AGCGGCGTTTGTGGGAGAAGCGCCGCTAAA-G-C--AGTCATTAG--ACGTTCGTGGGAAAAACG
* *
40932788 CCGCTAAAGGTCATGGTCTTT
60 CAGCTAAAGGTCATGGTCTTC
40932809 AGCGGCGTTT
1 AGCGGCGTTT
40932819 AGTTATAAAA
Statistics
Matches: 152, Mismatches: 15, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
75 25 0.16
76 1 0.01
78 1 0.01
81 1 0.01
82 2 0.01
84 1 0.01
85 1 0.01
86 119 0.78
88 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.33, T:0.26
Consensus pattern (80 bp):
AGCGGCGTTTGTGGGAGAAGCGCCGCTAAAGCAGTCATTAGACGTTCGTGGGAAAAACGCAGCTA
AAGGTCATGGTCTTC
Found at i:40932665 original size:43 final size:43
Alignment explanation
Indices: 40932598--40932818 Score: 334
Period size: 43 Copynumber: 5.1 Consensus size: 43
40932588 TAAAGATATT
* * * *
40932598 GCGTTCGTGGGAAAAACGCAGCTAAAGGTCATGGTCTTCAGCG
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCG
* * *
40932641 GCGTTTGTGGGAGAAGTGTCGCTAAAGGTCATGGTCTTTAGCG
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCG
* *
40932684 ACGTTTGTGGGAAAAGCGCCGTTAAAGGTCATGGTCTTTAGCG
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCG
* * *
40932727 GCGTTTGTGGGAGAAGCGCCGCTAAAGGTCATAGTCTTTAGCC
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCG
40932770 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCG
1 GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCG
40932813 GCGTTT
1 GCGTTT
40932819 AGTTATAAAA
Statistics
Matches: 158, Mismatches: 20, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 158 1.00
ACGTcount: A:0.21, C:0.18, G:0.34, T:0.27
Consensus pattern (43 bp):
GCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCG
Found at i:40932940 original size:22 final size:22
Alignment explanation
Indices: 40932912--40932954 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
40932902 TAGCGGCGCT
*
40932912 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
40932934 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
40932955 GTTTTGTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.42, C:0.28, G:0.21, T:0.09
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:40934082 original size:13 final size:13
Alignment explanation
Indices: 40934064--40934088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40934054 TGTAATCAGT
40934064 AAAATTTTCATAA
1 AAAATTTTCATAA
40934077 AAAATTTTCATA
1 AAAATTTTCATA
40934089 TGAATTCTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
AAAATTTTCATAA
Found at i:40936762 original size:316 final size:315
Alignment explanation
Indices: 40936190--40936818 Score: 1051
Period size: 316 Copynumber: 2.0 Consensus size: 315
40936180 GTAGAAGAGC
* *
40936190 TGTAGCCATTTGGTTCACGAATTAGCCTGAGGTTTTAAAGGCACATGGTCGTGTGGTGGACATGT
1 TGTAGCCATTTGGTTCACGAACTAGCCTGAGGTTTTAAAGGCACATAGTCGTGTGGTGGACATGT
* *
40936255 GGTCGACCTATGTAGAAGACCATGTGGCCCTAATCCTACACACGATAAGCACTAATTCACTTGGG
66 GGTCCACCTATGTAGAAGACCATGTGGCCCTAATCCTACACACGATAAGCACTAATTCACTTAGG
* * * *
40936320 AACGATCACATGCCTTTCATCAGAGTTCTGATTGACGTTCCTCACGATCAAACCTGATCTAATAC
131 AAAGATCACACGACTTTCATCAGAGTTCTGATTGACGTTCCTCACGATCAAACCTGATCCAATAC
** * *
40936385 ACTTAAATTCGATCCTTCAAAAATATGTACACAATTAGTTATTAATGTCAAGATTGACGAGATTT
196 ACTTAAATTCGATCCTTCAAAAATATGTACACAATTAGCGATTAACGTCAAGAATGACGAGATTT
* *
40936450 GCAAAAGATTTATCAAGGTTTCAAATAGATCGATTGATCGAATTAAAGATTAAGT
261 GCAAAAGATCTATCAAGATTTCAAATAGATCGATTGATCGAATTAAAGATTAAGT
* *
40936505 TGTAGCCATTTGGTTCACGAACTAGCCTGAGGTTTTAAGAGGCACATAGTCGTGTGGTTGCCATG
1 TGTAGCCATTTGGTTCACGAACTAGCCTGAGGTTTTAA-AGGCACATAGTCGTGTGGTGGACATG
* *
40936570 TGGTCCACCTATGTAGAAGACCGTGTGGCCCTAATCCTACACACGATAAGCACTGATTCACTTAG
65 TGGTCCACCTATGTAGAAGACCATGTGGCCCTAATCCTACACACGATAAGCACTAATTCACTTAG
*
40936635 GAAAGATCACACGACTTTCATCAGAGTTCTGATTGACGTTCCTCACGATCAAACCTGATCCGATA
130 GAAAGATCACACGACTTTCATCAGAGTTCTGATTGACGTTCCTCACGATCAAACCTGATCCAATA
* *
40936700 CACTTAAATTCGATCCTTCAGACATATGTACACAATTAGCGATTAACGTCAAGAATGACGAGATT
195 CACTTAAATTCGATCCTTCAAAAATATGTACACAATTAGCGATTAACGTCAAGAATGACGAGATT
*
40936765 TGCAAAAGATCTATCAATATTTCAAATAGATCGATTGATCGAATTAAAGATTAA
260 TGCAAAAGATCTATCAAGATTTCAAATAGATCGATTGATCGAATTAAAGATTAA
40936819 AGGTTGGAGA
Statistics
Matches: 291, Mismatches: 22, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
315 37 0.13
316 254 0.87
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (315 bp):
TGTAGCCATTTGGTTCACGAACTAGCCTGAGGTTTTAAAGGCACATAGTCGTGTGGTGGACATGT
GGTCCACCTATGTAGAAGACCATGTGGCCCTAATCCTACACACGATAAGCACTAATTCACTTAGG
AAAGATCACACGACTTTCATCAGAGTTCTGATTGACGTTCCTCACGATCAAACCTGATCCAATAC
ACTTAAATTCGATCCTTCAAAAATATGTACACAATTAGCGATTAACGTCAAGAATGACGAGATTT
GCAAAAGATCTATCAAGATTTCAAATAGATCGATTGATCGAATTAAAGATTAAGT
Found at i:40937849 original size:16 final size:15
Alignment explanation
Indices: 40937797--40937849 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 15
40937787 TTATAAAAGA
*
40937797 AAAAGAATAAAAAAAT
1 AAAAGAA-AAAAAATT
*
40937813 AAAGAGAAAAATAATGT
1 AAA-AGAAAAAAAAT-T
40937830 AAAAGAAAAAAAATT
1 AAAAGAAAAAAAATT
40937845 CAAAA
1 -AAAA
40937850 TAATTTTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 1 0.03
16 22 0.71
17 8 0.26
ACGTcount: A:0.75, C:0.02, G:0.09, T:0.13
Consensus pattern (15 bp):
AAAAGAAAAAAAATT
Found at i:40938657 original size:5 final size:5
Alignment explanation
Indices: 40938642--40938671 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
40938632 TTCCATTTGC
*
40938642 TCTTT TTTTT TCTTT TCTTT TCTTT TCTTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT
40938672 CTGTATTGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:40955992 original size:28 final size:28
Alignment explanation
Indices: 40955958--40956027 Score: 81
Period size: 29 Copynumber: 2.5 Consensus size: 28
40955948 TAGTATATAT
40955958 AAATTTTAGGGGGAG-GGGAAGGGAGTAA
1 AAATTTTAGGGGGAGTGGG-AGGGAGTAA
* **
40955986 AAGTTTTAGGGAAAAGTGGGAGGGAGTAA
1 AAATTTTAGGG-GGAGTGGGAGGGAGTAA
40956015 AAATTTT-GGGGGA
1 AAATTTTAGGGGGA
40956028 AAATAAAAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
27 1 0.03
28 13 0.38
29 17 0.50
30 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.43, T:0.21
Consensus pattern (28 bp):
AAATTTTAGGGGGAGTGGGAGGGAGTAA
Found at i:40957914 original size:20 final size:20
Alignment explanation
Indices: 40957889--40957928 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40957879 CAGAAAATGA
*
40957889 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
40957909 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
40957929 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:40957944 original size:14 final size:15
Alignment explanation
Indices: 40957868--40957944 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
40957858 GATTGGCAGT
**
40957868 AAAATG-TTTTCCAG
1 AAAATGATTTTCTGG
40957882 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
40957896 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
40957916 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
40957931 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
40957945 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.42
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:40958039 original size:20 final size:20
Alignment explanation
Indices: 40958014--40958090 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
40958004 TTCAGGAAAG
40958014 TTGTTTTTACATATATTAAA
1 TTGTTTTTACATATATTAAA
*
40958034 TTGTTTTTACATATATATTAA
1 TTGTTTTTACATATAT-TAAA
** *
40958055 TAAATTTTT--ATATTTTAAA
1 T-TGTTTTTACATATATTAAA
40958074 TTGTTTTTACATATATT
1 TTGTTTTTACATATATT
40958091 GCAATGATTT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
18 5 0.11
19 4 0.09
20 27 0.60
21 4 0.09
22 5 0.11
ACGTcount: A:0.34, C:0.04, G:0.04, T:0.58
Consensus pattern (20 bp):
TTGTTTTTACATATATTAAA
Found at i:40958232 original size:15 final size:15
Alignment explanation
Indices: 40958212--40958242 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
40958202 TAAAGCCAAG
40958212 GATGTGATTGATGAT
1 GATGTGATTGATGAT
40958227 GATGTGATTGATGAT
1 GATGTGATTGATGAT
40958242 G
1 G
40958243 TTAATATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.39
Consensus pattern (15 bp):
GATGTGATTGATGAT
Found at i:40960550 original size:27 final size:27
Alignment explanation
Indices: 40960512--40960569 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
40960502 TAAAGCATTG
* *
40960512 AAGGTCAGATGCTATTGTATTGGTGTT
1 AAGGTCAAATGCTACTGTATTGGTGTT
40960539 AAGGTCAAATGCTACTGTATTGGTGTT
1 AAGGTCAAATGCTACTGTATTGGTGTT
40960566 AAGG
1 AAGG
40960570 CTGCAATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.09, G:0.29, T:0.36
Consensus pattern (27 bp):
AAGGTCAAATGCTACTGTATTGGTGTT
Found at i:40960843 original size:13 final size:13
Alignment explanation
Indices: 40960825--40960850 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40960815 CCAGAAACTG
40960825 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
40960838 ATTTGCAGAAAAC
1 ATTTGCAGAAAAC
40960851 TCCCATTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.23
Consensus pattern (13 bp):
ATTTGCAGAAAAC
Found at i:40961026 original size:14 final size:14
Alignment explanation
Indices: 40961007--40961036 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40960997 AACAAAACTA
40961007 GCAGAGAAGATGAG
1 GCAGAGAAGATGAG
*
40961021 GCAGAGATGATGAG
1 GCAGAGAAGATGAG
40961035 GC
1 GC
40961037 TGCAATCGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.10, G:0.43, T:0.10
Consensus pattern (14 bp):
GCAGAGAAGATGAG
Found at i:40961094 original size:24 final size:24
Alignment explanation
Indices: 40961059--40961104 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
40961049 GGTGAAGAGA
*
40961059 GTGAAGAGAGGAGCTGTGGAAAGG
1 GTGAAGAAAGGAGCTGTGGAAAGG
40961083 GTGAAGAAAGGAGCTGTGGAAA
1 GTGAAGAAAGGAGCTGTGGAAA
40961105 TGGTTTCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.37, C:0.04, G:0.46, T:0.13
Consensus pattern (24 bp):
GTGAAGAAAGGAGCTGTGGAAAGG
Found at i:40962380 original size:45 final size:44
Alignment explanation
Indices: 40962314--40962402 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
40962304 GGAATTGAGG
40962314 TGTAATGGAATAGAGACGTAATAGTAATTCAAT-TGTTTGGTTGAA
1 TGTAATGGAATAGAGACGTAATAGT-ATTC-ATGTGTTTGGTTGAA
*
40962359 TGTAATGGAATAGA-ACTGTAATAGTATTCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGAC-GTAATAGTATTCATGTGTTTGGTTGAA
40962403 CGGAATGATG
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
43 1 0.02
44 18 0.44
45 22 0.54
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (44 bp):
TGTAATGGAATAGAGACGTAATAGTATTCATGTGTTTGGTTGAA
Found at i:40965135 original size:12 final size:12
Alignment explanation
Indices: 40965120--40965153 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
40965110 ACTTAACAGA
40965120 AACCAAAACATG
1 AACCAAAACATG
40965132 AACCAAAACATG
1 AACCAAAACATG
40965144 AACCAAAACA
1 AACCAAAACA
40965154 ATAGAGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.62, C:0.26, G:0.06, T:0.06
Consensus pattern (12 bp):
AACCAAAACATG
Found at i:40965620 original size:20 final size:19
Alignment explanation
Indices: 40965592--40965650 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
40965582 AAACAGGAAA
*
40965592 AAATTTGGAAGAAGAAACAG
1 AAATCTGGAAGAAGAAA-AG
*
40965612 AAATCTGGAGAAAAGAAAAG
1 AAATCTGGA-AGAAGAAAAG
*
40965632 AAATGT-G-AGAAGAAAAG
1 AAATCTGGAAGAAGAAAAG
40965649 AA
1 AA
40965651 GCGTACCGTA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
17 11 0.32
19 1 0.03
20 15 0.44
21 7 0.21
ACGTcount: A:0.59, C:0.03, G:0.25, T:0.12
Consensus pattern (19 bp):
AAATCTGGAAGAAGAAAAG
Found at i:40965646 original size:17 final size:18
Alignment explanation
Indices: 40965601--40965650 Score: 57
Period size: 17 Copynumber: 2.7 Consensus size: 18
40965591 AAAATTTGGA
40965601 AGAAGAAACAGAAATCTGG
1 AGAAGAAA-AGAAATCTGG
*
40965620 AGAAAAGAAAAGAAATGT-G
1 AG--AAGAAAAGAAATCTGG
40965639 AGAAGAAAAGAA
1 AGAAGAAAAGAA
40965651 GCGTACCGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 10 0.36
19 5 0.18
20 7 0.25
21 6 0.21
ACGTcount: A:0.62, C:0.04, G:0.26, T:0.08
Consensus pattern (18 bp):
AGAAGAAAAGAAATCTGG
Found at i:40965647 original size:22 final size:21
Alignment explanation
Indices: 40965603--40965650 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
40965593 AATTTGGAAG
40965603 AAGAAACAGAAATCTGGAGAA
1 AAGAAACAGAAATCTGGAGAA
*
40965624 AAGAAA-AGAAATGTGAGAAGAA
1 AAGAAACAGAAATCTG-G-AGAA
40965646 AAGAA
1 AAGAA
40965651 GCGTACCGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 8 0.33
21 7 0.29
22 9 0.38
ACGTcount: A:0.62, C:0.04, G:0.25, T:0.08
Consensus pattern (21 bp):
AAGAAACAGAAATCTGGAGAA
Found at i:40967455 original size:17 final size:17
Alignment explanation
Indices: 40967433--40967488 Score: 67
Period size: 17 Copynumber: 3.3 Consensus size: 17
40967423 TCGTACATTG
*
40967433 ACACAAATCGCATATAA
1 ACACAACTCGCATATAA
* * *
40967450 ACACAACTCACAAATAG
1 ACACAACTCGCATATAA
*
40967467 ACACAGCTCGCATATAA
1 ACACAACTCGCATATAA
40967484 ACACA
1 ACACA
40967489 TATATGTATA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.50, C:0.29, G:0.07, T:0.14
Consensus pattern (17 bp):
ACACAACTCGCATATAA
Found at i:40969401 original size:25 final size:25
Alignment explanation
Indices: 40969372--40969434 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
40969362 GTAGAATAGT
* *
40969372 AAGCTCCTCCGAGCTGAATAACGGG
1 AAGCTCATCCGAGCTAAATAACGGG
* **
40969397 GAGCTCATGTGAGCTAAATAACGGG
1 AAGCTCATCCGAGCTAAATAACGGG
*
40969422 AAGCTCATGCGAG
1 AAGCTCATCCGAG
40969435 TTGAGCATCG
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.30, C:0.22, G:0.30, T:0.17
Consensus pattern (25 bp):
AAGCTCATCCGAGCTAAATAACGGG
Found at i:40976156 original size:17 final size:17
Alignment explanation
Indices: 40976134--40976169 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
40976124 TTAGAAAATA
40976134 GGCCCATACGCCCATGT
1 GGCCCATACGCCCATGT
* *
40976151 GGCCCATATGCCCGTGT
1 GGCCCATACGCCCATGT
40976168 GG
1 GG
40976170 ACTACATAGC
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:0.36, G:0.31, T:0.19
Consensus pattern (17 bp):
GGCCCATACGCCCATGT
Found at i:40981379 original size:26 final size:26
Alignment explanation
Indices: 40981343--40981401 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
40981333 GTAAGTGTTT
40981343 TGAAACTGATACATGCTATGATATTC
1 TGAAACTGATACATGCTATGATATTC
* ** *
40981369 TGAAACTGATATATTTTATGATATTT
1 TGAAACTGATACATGCTATGATATTC
40981395 TGAAACT
1 TGAAACT
40981402 ACTATAGGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.41
Consensus pattern (26 bp):
TGAAACTGATACATGCTATGATATTC
Found at i:40985759 original size:17 final size:17
Alignment explanation
Indices: 40985727--40985760 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40985717 GTTTTTTCCC
*
40985727 TTTTTGTTCACTTTTGG
1 TTTTTGTTCACCTTTGG
*
40985744 TTTTTGTTCCCCTTTGG
1 TTTTTGTTCACCTTTGG
40985761 CCGAGTCTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.03, C:0.18, G:0.18, T:0.62
Consensus pattern (17 bp):
TTTTTGTTCACCTTTGG
Found at i:41000779 original size:15 final size:14
Alignment explanation
Indices: 41000759--41000804 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 14
41000749 AGAGCTGATG
41000759 GGCCAGTCAAAACT
1 GGCCAGTCAAAACT
*
41000773 AGGCCAGTCAAAGCT
1 -GGCCAGTCAAAACT
41000788 GGACCAGTCAAAACT
1 GG-CCAGTCAAAACT
41000803 GG
1 GG
41000805 GGCATGCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 2 0.07
15 26 0.93
ACGTcount: A:0.35, C:0.26, G:0.26, T:0.13
Consensus pattern (14 bp):
GGCCAGTCAAAACT
Done.