Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 136 of 198
Found at i:43393151 original size:15 final size:15
Alignment explanation
Indices: 43393133--43393163 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
43393123 GGGTTTTAAG
*
43393133 TTTAGGTTTATGGTT
1 TTTAGGTTTAGGGTT
43393148 TTTAGGTTTAGGGTT
1 TTTAGGTTTAGGGTT
43393163 T
1 T
43393164 GGGGTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.00, G:0.29, T:0.58
Consensus pattern (15 bp):
TTTAGGTTTAGGGTT
Found at i:43393173 original size:43 final size:43
Alignment explanation
Indices: 43393068--43393393 Score: 327
Period size: 43 Copynumber: 7.5 Consensus size: 43
43393058 AAGTTAAGGT
* * *
43393068 TTTAGGGTTTAGGGTTTTTAAGTTTAGGGTTTAGGGTTTTTAAG
1 TTTAGGGTTTGGGGTTTTTAAGTTTA-GGTTTATGGTTTTTAGG
* *
43393112 TTTAAGGTTTAGGG-TTTTAAGTTTAGGTTTATGGTTTTTAGG
1 TTTAGGGTTTGGGGTTTTTAAGTTTAGGTTTATGGTTTTTAGG
*
43393154 TTTAGGGTTTGGGGTTTTTAAGTTAAAGG-TTATGGTTTTTAGG
1 TTTAGGGTTTGGGGTTTTTAAGTT-TAGGTTTATGGTTTTTAGG
* * * * *
43393197 TTTACGGTTTGAGGTTTTTAAGTTAAGGGTTAGGGTTTTTAGG
1 TTTAGGGTTTGGGGTTTTTAAGTTTAGGTTTATGGTTTTTAGG
* * * * *
43393240 GTTAGTGTTTGAGGTTTTTTTAGTTTAGGGTTTATAGTTTTTAGG
1 TTTAGGGTTTG-GGGTTTTTAAGTTTA-GGTTTATGGTTTTTAGG
* * * *
43393285 TTTAAGGTTTAGGGTTTTTAGGTTTAGGGTTTGTGGTTTTTAGG
1 TTTAGGGTTTGGGGTTTTTAAGTTTA-GGTTTATGGTTTTTAGG
* * *
43393329 TTTAGGGTTTGAGGG-TTTTAAGTTAAGGGTTAGCGGGTTTTTAGG
1 TTTAGGGTTTG-GGGTTTTTAAGTTTAGGTTTA--TGGTTTTTAGG
* *
43393374 TTTGGGGTTT-GTGTTTTTAA
1 TTTAGGGTTTGGGGTTTTTAA
43393394 ATTAAGGGTT
Statistics
Matches: 236, Mismatches: 37, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
42 31 0.13
43 83 0.35
44 79 0.33
45 43 0.18
ACGTcount: A:0.17, C:0.01, G:0.32, T:0.50
Consensus pattern (43 bp):
TTTAGGGTTTGGGGTTTTTAAGTTTAGGTTTATGGTTTTTAGG
Found at i:43393288 original size:15 final size:15
Alignment explanation
Indices: 43393262--43393316 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
43393252 GGTTTTTTTA
43393262 GTTTAGGGTTTATAG
1 GTTTAGGGTTTATAG
*
43393277 TTTTTA-GGTTTA-AG
1 -GTTTAGGGTTTATAG
*
43393291 GTTTAGGGTTTTTAG
1 GTTTAGGGTTTATAG
43393306 GTTTAGGGTTT
1 GTTTAGGGTTT
43393317 GTGGTTTTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 4 0.12
14 7 0.21
15 19 0.56
16 4 0.12
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (15 bp):
GTTTAGGGTTTATAG
Found at i:43394022 original size:18 final size:18
Alignment explanation
Indices: 43393999--43394038 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
43393989 GACTTAGAAA
* *
43393999 AGGATACATATAAGGGTT
1 AGGATACATAAAAGGGCT
43394017 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
43394035 AGGA
1 AGGA
43394039 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.07, G:0.30, T:0.20
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:43395992 original size:12 final size:12
Alignment explanation
Indices: 43395941--43395984 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
43395931 ATTAAATATG
43395941 AATTTGAGA-GA
1 AATTTGAGAGGA
43395952 AATTTG-GAAGGA
1 AATTTGAG-AGGA
43395964 AA-TTGAGAGGA
1 AATTTGAGAGGA
43395975 AATTTGAGAG
1 AATTTGAGAG
43395985 AAGATTTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.03
11 16 0.55
12 12 0.41
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (12 bp):
AATTTGAGAGGA
Found at i:43404762 original size:16 final size:18
Alignment explanation
Indices: 43404726--43404763 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
43404716 ACAAAATGTC
*
43404726 AAATTATTTATAATAATA
1 AAATCATTTATAATAATA
43404744 AAATCATTTA-AAT-ATA
1 AAATCATTTATAATAATA
43404760 AAAT
1 AAAT
43404764 TGCTTTGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 3 0.16
18 9 0.47
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (18 bp):
AAATCATTTATAATAATA
Found at i:43409785 original size:33 final size:33
Alignment explanation
Indices: 43409747--43409852 Score: 133
Period size: 33 Copynumber: 3.2 Consensus size: 33
43409737 CCGGAAGTAA
*
43409747 TGGAGTACGGCGGTGGATACGGGCCTAGAGAAG
1 TGGAGTACGACGGTGGATACGGGCCTAGAGAAG
* ** *
43409780 TGGAGTACGATGGTACATACGGGCCGAGAGAAG
1 TGGAGTACGACGGTGGATACGGGCCTAGAGAAG
* *
43409813 TGGAGTACGACAGTGGATACGGG-CTAGCAGGAG
1 TGGAGTACGACGGTGGATACGGGCCTAG-AGAAG
43409846 TGGAGTA
1 TGGAGTA
43409853 TTGTGGTGGA
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
32 3 0.05
33 58 0.95
ACGTcount: A:0.27, C:0.14, G:0.42, T:0.16
Consensus pattern (33 bp):
TGGAGTACGACGGTGGATACGGGCCTAGAGAAG
Found at i:43409883 original size:66 final size:66
Alignment explanation
Indices: 43409747--43409886 Score: 151
Period size: 66 Copynumber: 2.1 Consensus size: 66
43409737 CCGGAAGTAA
* * *
43409747 TGGAGTACGGCGGTGGATACGGGCCTAGAGAAGTGGAGTACGATGGTACATACGGGCCGAGAGAA
1 TGGAGTACGACAGTGGATACGGGCCTAGAGAAGTGGAGTACGATGGTACATACGAGCCGAGAGAA
*
43409812 G
66 C
* * ** *
43409813 TGGAGTACGACAGTGGATACGGG-CTAGCAGGAGTGGAGTATTG-TGGTGGATACGAGCCGGGAT
1 TGGAGTACGACAGTGGATACGGGCCTAG-AGAAGTGGAGTA-CGATGGTACATACGAGCCGAGA-
43409876 G-AC
63 GAAC
43409879 TGGAGTAC
1 TGGAGTAC
43409887 TGAGGTGGTA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
65 4 0.06
66 56 0.90
67 2 0.03
ACGTcount: A:0.26, C:0.14, G:0.42, T:0.18
Consensus pattern (66 bp):
TGGAGTACGACAGTGGATACGGGCCTAGAGAAGTGGAGTACGATGGTACATACGAGCCGAGAGAA
C
Found at i:43411925 original size:14 final size:16
Alignment explanation
Indices: 43411891--43411929 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
43411881 AAAATCAAAT
*
43411891 AAAATTACATTATATA
1 AAAATCACATTATATA
43411907 AAAATCACATTA-A-A
1 AAAATCACATTATATA
43411921 AAAATCACA
1 AAAATCACA
43411930 AAACACTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.45
15 1 0.05
16 11 0.50
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATCACATTATATA
Found at i:43412183 original size:104 final size:103
Alignment explanation
Indices: 43411889--43412353 Score: 484
Period size: 106 Copynumber: 4.5 Consensus size: 103
43411879 TAAAAATCAA
* * * *
43411889 ATAAAATTACATTATATAAAAATCACATTA-AAAAAATCACAAAACACTAAACTAAACACTAACA
1 ATAAAATTAC-TTTTTTAAAAATTACATTACTAAAAATCACAAAACACTAAACTAAACACTAACA
*
43411953 ATTTATATAACCTAATCATCAATTACTAACAAAATAACT
65 ATTTATATAACCTAATCATAAATTACTAACAAAATAACT
* * *
43411992 ATAAAATTACCTTTTTTATTTAAATTGCTTTACTAAAAATCACAAAACACTAAACTAAACACTAA
1 ATAAAATTA-CTTTTTTA--AAAATTACATTACTAAAAATCACAAAACACTAAACTAAACACTAA
*
43412057 CAATTTATATAACCTAATCATAAATTACTAACAAAATAATT
63 CAATTTATATAACCTAATCATAAATTACTAACAAAATAACT
*
43412098 ATAAAATTACTTTTTTAAAAATTACATTACTTAAAAATCACAAAACCCTAAACTAAACACTAACA
1 ATAAAATTACTTTTTTAAAAATTACATTAC-TAAAAATCACAAAACACTAAACTAAACACTAACA
* * *
43412163 A-TT-TATAATCTAGTCCCATAAATTACTAACAAAATAAAT
65 ATTTATATAACCTAAT--CATAAATTACTAACAAAATAACT
******* *
43412202 AACTACAACATTTAAAAAAAAAAAGAAATTACATTACTAAAAAATAACAAAACAC---A--AAAC
1 -A-TA-AA-A-TT-ACTTTTTTAA-AAATTACATTACT-AAAAATCACAAAACACTAAACTAAAC
*
43412262 ACTAACAA-TT-TATAACCTAATCATAAACTACTAACAAAATAACT
58 ACTAACAATTTATATAACCTAATCATAAATTACTAACAAAATAACT
**
43412306 ATAAAATTA-TTATTTTTTAAATTACATTACTAAAAACTCACAAAACAC
1 ATAAAATTACTT-TTTTAAAAATTACATTACTAAAAA-TCACAAAACAC
43412354 AACAATTTAT
Statistics
Matches: 307, Mismatches: 38, Indels: 40
0.80 0.10 0.10
Matches are distributed among these distances:
96 5 0.02
97 23 0.07
98 1 0.00
99 2 0.01
100 1 0.00
101 2 0.01
102 11 0.04
103 27 0.09
104 78 0.25
105 17 0.06
106 104 0.34
107 2 0.01
108 2 0.01
109 2 0.01
110 4 0.01
111 26 0.08
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.29
Consensus pattern (103 bp):
ATAAAATTACTTTTTTAAAAATTACATTACTAAAAATCACAAAACACTAAACTAAACACTAACAA
TTTATATAACCTAATCATAAATTACTAACAAAATAACT
Found at i:43412700 original size:21 final size:23
Alignment explanation
Indices: 43412674--43412716 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
43412664 TTTTTCTTTC
*
43412674 TTTCTTCTTC-TTCT-TCTTTTT
1 TTTCTTCTCCTTTCTCTCTTTTT
43412695 TTTCTTCTCCTTTCTCTCTTTT
1 TTTCTTCTCCTTTCTCTCTTTT
43412717 CTTCCCCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 4 0.21
23 6 0.32
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTCTTCTCCTTTCTCTCTTTTT
Found at i:43412708 original size:31 final size:29
Alignment explanation
Indices: 43412661--43412720 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 29
43412651 TACATTACCT
43412661 TTTTTTTTCTTTCTTTCT-TCTTCTTCTTC
1 TTTTTTTTCTTTCTTTCTCTCTT-TTCTTC
43412690 TTTTTTTTCTTCTCCTTTCTCTCTTTTCTTC
1 TTTTTTTTCTT-T-CTTTCTCTCTTTTCTTC
43412721 CCCACACACC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 11 0.39
30 1 0.04
31 12 0.43
32 4 0.14
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (29 bp):
TTTTTTTTCTTTCTTTCTCTCTTTTCTTC
Found at i:43412709 original size:28 final size:29
Alignment explanation
Indices: 43412661--43412719 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
43412651 TACATTACCT
*
43412661 TTTTTTTTCTTTCTTTCTTCT-TCTTCTTC
1 TTTTTTTTCTTTCTCTCTTCTCTCTT-TTC
43412690 TTTTTTTTC-TTCTC-CTTTCTCTCTTTTC
1 TTTTTTTTCTTTCTCTC-TTCTCTCTTTTC
43412718 TT
1 TT
43412720 CCCCACACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 1 0.04
28 13 0.48
29 13 0.48
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (29 bp):
TTTTTTTTCTTTCTCTCTTCTCTCTTTTC
Found at i:43413073 original size:20 final size:21
Alignment explanation
Indices: 43413043--43413082 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
43413033 TATATATAAA
43413043 AATATTTTTTTAAAATAAAAT
1 AATATTTTTTTAAAATAAAAT
*
43413064 AATA-TTTTTTAAAGTAAAA
1 AATATTTTTTTAAAATAAAA
43413083 AAGATTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (21 bp):
AATATTTTTTTAAAATAAAAT
Found at i:43413083 original size:21 final size:19
Alignment explanation
Indices: 43413038--43413083 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
43413028 CCCGATATAT
43413038 ATAAAAATATTTTTTTAAA
1 ATAAAAATATTTTTTTAAA
43413057 AT-AAAATAATATTTTTTAAA
1 ATAAAAAT-AT-TTTTTTAAA
*
43413077 GTAAAAA
1 ATAAAAA
43413084 AGATTATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.22
19 4 0.17
20 10 0.43
21 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
ATAAAAATATTTTTTTAAA
Found at i:43415829 original size:36 final size:37
Alignment explanation
Indices: 43415789--43415873 Score: 136
Period size: 39 Copynumber: 2.3 Consensus size: 37
43415779 TTCGTTTGCT
*
43415789 TTACTGCTTTCGATTAGAA-TCAGGGAAAATTCTGGC
1 TTACTGCTTTCGATTAGAATTCAGGGAAAATTCTGGA
43415825 TTACTGCTTTCGATTAGAATTTTCAGGGAAAATTCTGGA
1 TTACTGCTTTCGATTAGAA--TTCAGGGAAAATTCTGGA
43415864 TTACTGCTTT
1 TTACTGCTTT
43415874 GCTTTACTGT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
36 19 0.42
39 26 0.58
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (37 bp):
TTACTGCTTTCGATTAGAATTCAGGGAAAATTCTGGA
Found at i:43418482 original size:13 final size:13
Alignment explanation
Indices: 43418464--43418520 Score: 69
Period size: 13 Copynumber: 4.4 Consensus size: 13
43418454 CAAATTTTTT
43418464 AAAAGCACTTCTC
1 AAAAGCACTTCTC
*
43418477 AAAAGCACTTCTT
1 AAAAGCACTTCTC
*
43418490 AAAAGCACTTTTC
1 AAAAGCACTTCTC
* * *
43418503 TACAGCACTTTTC
1 AAAAGCACTTCTC
43418516 AAAAG
1 AAAAG
43418521 TAATGAAGAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 37 1.00
ACGTcount: A:0.39, C:0.25, G:0.09, T:0.28
Consensus pattern (13 bp):
AAAAGCACTTCTC
Found at i:43418509 original size:26 final size:25
Alignment explanation
Indices: 43418460--43418520 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
43418450 CACTCAAATT
43418460 TTTTAAAAGCACTTCTCAAAAGCAC
1 TTTTAAAAGCACTTCTCAAAAGCAC
* * *
43418485 TTCTTAAAAGCACTTTTCTACAGCAC
1 TT-TTAAAAGCACTTCTCAAAAGCAC
43418511 TTTTCAAAAG
1 TTTT-AAAAG
43418521 TAATGAAGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.13
26 27 0.87
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (25 bp):
TTTTAAAAGCACTTCTCAAAAGCAC
Found at i:43424235 original size:50 final size:50
Alignment explanation
Indices: 43424086--43424332 Score: 228
Period size: 50 Copynumber: 4.8 Consensus size: 50
43424076 GATAATAACA
* * ** * * *
43424086 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * ** * *
43424135 TACCAATGCCATATCCCAGATATGGTCTTGCATGGGAGTTCTTATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
43424185 TGCCCATGCCATGTCCCAGACATGATCTTACAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
43424235 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
*
43424291 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
43424333 TTACCCAAAT
Statistics
Matches: 160, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
48 1 0.01
49 35 0.22
50 78 0.49
53 5 0.03
56 41 0.26
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:43424704 original size:30 final size:30
Alignment explanation
Indices: 43424670--43424733 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
43424660 CCTTGACTCG
* *
43424670 AACTTTGGAAAAATTATAATTTTGCCCCTA
1 AACTTTGGAAAAATTACAATTTTGCCCCAA
* * * *
43424700 AACTTTTGCATAATTACACTTTTGCCCCAA
1 AACTTTGGAAAAATTACAATTTTGCCCCAA
43424730 AACT
1 AACT
43424734 CAGAAATTAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.34, C:0.22, G:0.08, T:0.36
Consensus pattern (30 bp):
AACTTTGGAAAAATTACAATTTTGCCCCAA
Found at i:43433403 original size:38 final size:38
Alignment explanation
Indices: 43433361--43433459 Score: 103
Period size: 38 Copynumber: 2.6 Consensus size: 38
43433351 CGAATACAAT
* *
43433361 AATTATAATTACCATAATTATAATAATGTTTGA-CAAAA
1 AATTATAATTACCATAATTATAATAATATTCGATC-AAA
* * **
43433399 AATTACAATTA-CAGTAATTAAAATAATATTCGATCCTA
1 AATTATAATTACCA-TAATTATAATAATATTCGATCAAA
*
43433437 AATTATAATTACAATAATTATAA
1 AATTATAATTACCATAATTATAA
43433460 CAAAGATTTC
Statistics
Matches: 49, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
37 2 0.04
38 45 0.92
39 2 0.04
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (38 bp):
AATTATAATTACCATAATTATAATAATATTCGATCAAA
Found at i:43436624 original size:11 final size:11
Alignment explanation
Indices: 43436594--43436637 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
43436584 AAACTAATCC
43436594 TCTCTCAATTAT
1 TCTCTCAATT-T
*
43436606 TTTCTCAATTT
1 TCTCTCAATTT
43436617 TCTCTCAATTT
1 TCTCTCAATTT
*
43436628 GCTCTCAATT
1 TCTCTCAATT
43436638 CCCTTCCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.20, C:0.25, G:0.02, T:0.52
Consensus pattern (11 bp):
TCTCTCAATTT
Found at i:43436745 original size:15 final size:16
Alignment explanation
Indices: 43436721--43436751 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
43436711 TCTTATTTTT
43436721 AATT-ATTTTTAAAAA
1 AATTAATTTTTAAAAA
43436736 AATTAATTTTTAAAAA
1 AATTAATTTTTAAAAA
43436752 TTTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTAATTTTTAAAAA
Found at i:43437876 original size:7 final size:7
Alignment explanation
Indices: 43437864--43437889 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
43437854 TAGTCGATTG
43437864 GTATTTA
1 GTATTTA
43437871 GTATTTA
1 GTATTTA
43437878 GTATTTA
1 GTATTTA
43437885 GTATT
1 GTATT
43437890 ATGTATATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (7 bp):
GTATTTA
Found at i:43438560 original size:18 final size:18
Alignment explanation
Indices: 43438537--43438579 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
43438527 TGCCAGGTGC
*
43438537 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTATAT
43438555 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
43438573 GTTTCCT
1 GTATCCT
43438580 TTTTCGAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:43439068 original size:8 final size:7
Alignment explanation
Indices: 43439047--43439080 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
43439037 AAACTAATTT
43439047 ATTAAAA
1 ATTAAAA
43439054 ATTAAAA
1 ATTAAAA
43439061 ATTAAAA
1 ATTAAAA
* *
43439068 ATTTATA
1 ATTAAAA
43439075 ATTAAA
1 ATTAAA
43439081 TTTATAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
ATTAAAA
Found at i:43439281 original size:127 final size:127
Alignment explanation
Indices: 43439133--43439379 Score: 440
Period size: 127 Copynumber: 1.9 Consensus size: 127
43439123 ACCGGAAGCA
*
43439133 TTTTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAA
1 TTTTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACCTACTGTAGCAA
* *
43439198 AAGCGCGTCCATGAGGGCGCGATTTCAGAAATTCTTCTAATAAAGCATCCTGCTTGAAGCGT
66 AAGCGCGTCCACGAGGGCGCGACTTCAGAAATTCTTCTAATAAAGCATCCTGCTTGAAGCGT
*
43439260 TTTTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACCTACTGTAGCAA
1 TTTTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACCTACTGTAGCAA
* *
43439325 AAGCGCGTCCACGTGGGCGCGACTTCAGAAATTCTTCTGATAAAGCATCCTGCTT
66 AAGCGCGTCCACGAGGGCGCGACTTCAGAAATTCTTCTAATAAAGCATCCTGCTT
43439380 TGATTTTATC
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 114 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.32
Consensus pattern (127 bp):
TTTTTTTATACTATTTACTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACCTACTGTAGCAA
AAGCGCGTCCACGAGGGCGCGACTTCAGAAATTCTTCTAATAAAGCATCCTGCTTGAAGCGT
Found at i:43439412 original size:127 final size:125
Alignment explanation
Indices: 43439152--43439412 Score: 330
Period size: 127 Copynumber: 2.1 Consensus size: 125
43439142 ACTATTTACT
* *
43439152 CAGAAACGTCAACTCGAAATTATTTTTCCAGGACCTACTGTAGCAAAAGCGCGTCCATGAGGGCG
1 CAGAAACGTCAACTCGAAATTATTTTTCCAAGACCTACTGTAGCAAAAGCGCGTCCACGAGGGCG
* * * * *** *
43439217 CGATTTCAGAAATTCTTCTAATAAAGCATCCTGCTTGAAGCGTTTTTTTTATACTATTTGCT
66 CGACTTCAGAAATTCTTCTAATAAAGCATCCTGCTTGAA--GTTTTTTTAAAACCATAAACA
*
43439279 CAGAAACGTCAACTCGAAATTATTTTTCCAAGACCTACTGTAGCAAAAGCGCGTCCACGTGGGCG
1 CAGAAACGTCAACTCGAAATTATTTTTCCAAGACCTACTGTAGCAAAAGCGCGTCCACGAGGGCG
*
43439344 CGACTTCAGAAATTCTTCTGATAAAGCATCCTGCTTTG-A-TTTTATCTTAAAAACCCATAAACA
66 CGACTTCAGAAATTCTTCTAATAAAGCATCCTGC-TTGAAGTTTT-T-TT-AAAA-CCATAAACA
43439407 C-GAAAC
1 CAGAAAC
43439413 CTAATCTAAT
Statistics
Matches: 117, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
124 4 0.03
125 1 0.01
126 2 0.02
127 102 0.87
128 8 0.07
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (125 bp):
CAGAAACGTCAACTCGAAATTATTTTTCCAAGACCTACTGTAGCAAAAGCGCGTCCACGAGGGCG
CGACTTCAGAAATTCTTCTAATAAAGCATCCTGCTTGAAGTTTTTTTAAAACCATAAACA
Found at i:43440221 original size:22 final size:22
Alignment explanation
Indices: 43440190--43440249 Score: 57
Period size: 26 Copynumber: 2.5 Consensus size: 22
43440180 AAAACAGAAT
*
43440190 ATAATGTTTATCATAAAGATAA
1 ATAATATTTATCATAAAGATAA
* *
43440212 ATAATATTTAATTAAAATAAAGTTAA
1 ATAATATTT-A-T--CATAAAGATAA
43440238 ATAATATTTATC
1 ATAATATTTATC
43440250 TTAATAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
22 8 0.27
23 1 0.03
24 2 0.07
25 1 0.03
26 18 0.60
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (22 bp):
ATAATATTTATCATAAAGATAA
Found at i:43440439 original size:30 final size:29
Alignment explanation
Indices: 43440405--43440475 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
43440395 AATAAATTTC
* *
43440405 AAATTTTTATTTCAACTT-TTTTACTTTAAA
1 AAATTTTTAATT-AACTTATCTTA-TTTAAA
* *
43440435 AAATTATGTAATTAACTTATCTTATTTAAT
1 AAATT-TTTAATTAACTTATCTTATTTAAA
43440465 AAATTTTTAAT
1 AAATTTTTAAT
43440476 ATTTCACTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
29 5 0.15
30 20 0.59
31 9 0.26
ACGTcount: A:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (29 bp):
AAATTTTTAATTAACTTATCTTATTTAAA
Found at i:43441991 original size:31 final size:30
Alignment explanation
Indices: 43441956--43442055 Score: 76
Period size: 31 Copynumber: 3.1 Consensus size: 30
43441946 TCTAAAATTA
43441956 AAAATTAAAATA-TATTTAACACTTTATTTCT
1 AAAATTAAAA-ACTATTTAA-ACTTTATTTCT
* * *
43441987 AAAATTAAGATTAAAATTATTTTATACTTTATTTTT
1 AAAATT---A--AAAACTA-TTTAAACTTTATTTCT
*
43442023 AAAACTAAAAACTATTTAAACCTTTATTTCT
1 AAAATTAAAAACTATTTAAA-CTTTATTTCT
43442054 AA
1 AA
43442056 GCTTAACTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
30 5 0.09
31 23 0.42
33 1 0.02
34 1 0.02
35 1 0.02
36 20 0.36
37 4 0.07
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (30 bp):
AAAATTAAAAACTATTTAAACTTTATTTCT
Found at i:43442016 original size:36 final size:38
Alignment explanation
Indices: 43441941--43442033 Score: 127
Period size: 36 Copynumber: 2.5 Consensus size: 38
43441931 TAAATATATA
43441941 TTATTTCTAAAATTAAAAATTAAAATATATTTAACACT
1 TTATTTCTAAAATTAAAAATTAAAATATATTTAACACT
* * *
43441979 TTATTTCTAAAATT-AAGATTAAAAT-TATTTTATACT
1 TTATTTCTAAAATTAAAAATTAAAATATATTTAACACT
* *
43442015 TTATTTTTAAAACTAAAAA
1 TTATTTCTAAAATTAAAAA
43442034 CTATTTAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
36 21 0.44
37 13 0.27
38 14 0.29
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.45
Consensus pattern (38 bp):
TTATTTCTAAAATTAAAAATTAAAATATATTTAACACT
Found at i:43445780 original size:3 final size:3
Alignment explanation
Indices: 43445774--43445813 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
43445764 CAGTAGTAGT
*
43445774 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGG AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
43445814 TTGTATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:43448101 original size:27 final size:27
Alignment explanation
Indices: 43448071--43448140 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
43448061 AATAATCAAT
*
43448071 TCAATATCCAACAATGTTAAAACATA-A
1 TCAATATCCAACAAT-TCAAAACATATA
* *
43448098 TCAATATCTAACAAATTCAAGACATATA
1 TCAATATCCAAC-AATTCAAAACATATA
*
43448126 TCAAAATCCAACAAT
1 TCAATATCCAACAAT
43448141 CTAAAATTTG
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
27 22 0.61
28 14 0.39
ACGTcount: A:0.51, C:0.20, G:0.03, T:0.26
Consensus pattern (27 bp):
TCAATATCCAACAATTCAAAACATATA
Found at i:43449945 original size:23 final size:23
Alignment explanation
Indices: 43449879--43449945 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 23
43449869 AATATGTTTT
43449879 TATAAAGTTACCATGACTTAAAA
1 TATAAAGTTACCATGACTTAAAA
* *
43449902 TAT--A-TTGATCATGA-TT---T
1 TATAAAGTT-ACCATGACTTAAAA
43449919 TATAAAGTTACCATGACTTAAAA
1 TATAAAGTTACCATGACTTAAAA
43449942 TATA
1 TATA
43449946 TTGCCCAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 16
0.62 0.08 0.31
Matches are distributed among these distances:
17 3 0.09
19 7 0.22
20 8 0.25
21 7 0.22
23 7 0.22
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.37
Consensus pattern (23 bp):
TATAAAGTTACCATGACTTAAAA
Found at i:43458739 original size:218 final size:218
Alignment explanation
Indices: 43458352--43458797 Score: 718
Period size: 218 Copynumber: 2.0 Consensus size: 218
43458342 CCTATTCATT
* *
43458352 TCGTTCATTTTTATTCAAACAGACAATTCATTTCTAGTTTCAACGAGTTAGCGGATGGACCGATT
1 TCGTTCA-ATTTATTCAAACAGACAATTCATTTCTAGTTTCAACGAGTTAGCGGAGGGACCGATT
43458417 GAACATATGTAGTTGAGGCTCAAATGATTTATAATTAAATTCTGGCTTTTCGCTTATTAATTATA
65 GAACATATGTAGTTGAGGCTCAAATGATTTATAATTAAATTCTGGCTTTTCGCTTATTAATTATA
*
43458482 AATGCATTTAGTCACGAAGTCATTCCACTATAGTATCGTGATTGAGTTCTCCTCAACAACATACC
130 AATGCATTTAGTCACGAAGTCAGTCCACTATAGTATCGTGATTGAGTTCTCCTCAACAACATACC
43458547 ATTACT-AAAGCAACTACTCAATGC
195 ATTA-TGAAAGCAACTACTCAATGC
*
43458571 TCGTTCAATTTATTCAAACACG-CAATTCATTTCTGGTTTCAACGAGTTAGCGGAGGGACCGATT
1 TCGTTCAATTTATTCAAACA-GACAATTCATTTCTAGTTTCAACGAGTTAGCGGAGGGACCGATT
* * * * *
43458635 GGACATATGTAGTTGAGGCTCAAATGATTTATATTTAAGTTTTGGCTTTTCGTTTATTAATTATA
65 GAACATATGTAGTTGAGGCTCAAATGATTTATAATTAAATTCTGGCTTTTCGCTTATTAATTATA
* *
43458700 AACT-CATTTAGTCACGAAGTCAGTCCACTATAGTATCGTGATTGAGTTCTCCTTAACGACATAC
130 AA-TGCATTTAGTCACGAAGTCAGTCCACTATAGTATCGTGATTGAGTTCTCCTCAACAACATAC
*
43458764 CATTATGAAAGCAACTACTTAATGC
194 CATTATGAAAGCAACTACTCAATGC
*
43458789 TCGTCCAAT
1 TCGTTCAAT
43458798 GACCTTGTCA
Statistics
Matches: 211, Mismatches: 13, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
217 1 0.00
218 201 0.95
219 9 0.04
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (218 bp):
TCGTTCAATTTATTCAAACAGACAATTCATTTCTAGTTTCAACGAGTTAGCGGAGGGACCGATTG
AACATATGTAGTTGAGGCTCAAATGATTTATAATTAAATTCTGGCTTTTCGCTTATTAATTATAA
ATGCATTTAGTCACGAAGTCAGTCCACTATAGTATCGTGATTGAGTTCTCCTCAACAACATACCA
TTATGAAAGCAACTACTCAATGC
Found at i:43470423 original size:101 final size:101
Alignment explanation
Indices: 43470288--43470495 Score: 391
Period size: 101 Copynumber: 2.1 Consensus size: 101
43470278 GAAATACAAT
*
43470288 ATTTTTTTGTTTATATATTTTTTAATATTTTATATTTTCATTTAATTTCTAACTTTCCTCTTTTC
1 ATTTCTTTGTTTATATATTTTTTAATATTTTATATTTTCATTTAATTTCTAACTTTCCTCTTTTC
43470353 TTCTTACTCTCTTGAGAAGATTTCAGATATTTTTTTA
66 TTCTTACTCTCTTGAGAAGATTTCAGATA-TTTTTTA
43470390 ATTTCTTTGTTTATATA-TTTTTAATATTTTATATTTTCATTTAATTTCTAACTTTCCTCTTTTC
1 ATTTCTTTGTTTATATATTTTTTAATATTTTATATTTTCATTTAATTTCTAACTTTCCTCTTTTC
43470454 TTCTTACTCTCTTGAGAAGATTTCAGATATTTTTTA
66 TTCTTACTCTCTTGAGAAGATTTCAGATATTTTTTA
43470490 ATTTCT
1 ATTTCT
43470496 AATTATTATT
Statistics
Matches: 105, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
100 13 0.12
101 76 0.72
102 16 0.15
ACGTcount: A:0.23, C:0.12, G:0.05, T:0.60
Consensus pattern (101 bp):
ATTTCTTTGTTTATATATTTTTTAATATTTTATATTTTCATTTAATTTCTAACTTTCCTCTTTTC
TTCTTACTCTCTTGAGAAGATTTCAGATATTTTTTA
Found at i:43470528 original size:101 final size:100
Alignment explanation
Indices: 43470298--43470530 Score: 364
Period size: 101 Copynumber: 2.3 Consensus size: 100
43470288 ATTTTTTTGT
43470298 TTATATATTTTTTAATATTTTATATTTTCATTTAATTTCTAACTTTCCTCTTTTCTTCTTACTCT
1 TTATATA-TTTTTAATATTTTATATTTTCATTTAATTTCTAACTTTCCTCTTTTCTTCTTACTCT
**
43470363 CTTGAGAAGATTTCAGATATTTTTTTAATTTCTTTGT
65 CTTGAGAAGATTTCAGATATTTTTTTAATTTC-TTAA
43470400 TTATATATTTTTAATATTTTATATTTTCATTTAATTTCTAACTTTCCTCTTTTCTTCTTACTCTC
1 TTATATATTTTTAATATTTTATATTTTCATTTAATTTCTAACTTTCCTCTTTTCTTCTTACTCTC
43470465 TTGAGAAGATTTCAGATA-TTTTTTAATTTC-TAA
66 TTGAGAAGATTTCAGATATTTTTTTAATTTCTTAA
*
43470498 TTAT-TATTTCTAGTAATTTTTTAATATTTTCAT
1 TTATATATTT-T--TAATATTTT-ATATTTTCAT
43470531 AATCTGATTT
Statistics
Matches: 124, Mismatches: 3, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
97 5 0.04
98 6 0.05
100 20 0.16
101 86 0.69
102 7 0.06
ACGTcount: A:0.24, C:0.12, G:0.04, T:0.59
Consensus pattern (100 bp):
TTATATATTTTTAATATTTTATATTTTCATTTAATTTCTAACTTTCCTCTTTTCTTCTTACTCTC
TTGAGAAGATTTCAGATATTTTTTTAATTTCTTAA
Found at i:43471199 original size:5 final size:5
Alignment explanation
Indices: 43471189--43471233 Score: 72
Period size: 5 Copynumber: 9.0 Consensus size: 5
43471179 AATAAGGAAA
* *
43471189 GATAT GATAT GATAT GATAT GATAT GACAT GACAT GATAT GATAT
1 GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT GATAT
43471234 TATGCTAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.40, C:0.04, G:0.20, T:0.36
Consensus pattern (5 bp):
GATAT
Found at i:43472121 original size:66 final size:66
Alignment explanation
Indices: 43471989--43472122 Score: 171
Period size: 66 Copynumber: 2.0 Consensus size: 66
43471979 ACGAAAGCTC
** *
43471989 AGACAAATCCCCTAAAAGGGGTTATTAAACCAAGAGGAGAACATAAAAAAATAGAGTAGAACAAG
1 AGACAAATCCCCTAAAAGGGGTTATTAAACCAAGAAAAGAACATAAAAAAATAGAGGAGAACAAG
43472054 G
66 G
* * * * * *
43472055 AGACAAGTCCCCTAAAAGGGGTTATTAAACCAATAAAAGGACATCAGAAAACT-GAGGAGAATAA
1 AGACAAATCCCCTAAAAGGGGTTATTAAACCAAGAAAAGAACAT-AAAAAAATAGAGGAGAACAA
43472119 GG
65 GG
43472121 AG
1 AG
43472123 GATGACGACC
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 52 0.90
67 6 0.10
ACGTcount: A:0.49, C:0.14, G:0.22, T:0.14
Consensus pattern (66 bp):
AGACAAATCCCCTAAAAGGGGTTATTAAACCAAGAAAAGAACATAAAAAAATAGAGGAGAACAAG
G
Found at i:43482521 original size:22 final size:23
Alignment explanation
Indices: 43482496--43482553 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
43482486 ATAAAAACAT
* *
43482496 AATAAAATATTTTCT-AAAATTA
1 AATATAATATTTTATAAAAATTA
* *
43482518 AATATAATAATTAATAAAAATTA
1 AATATAATATTTTATAAAAATTA
43482541 AATATAATATTTT
1 AATATAATATTTT
43482554 TCATTAGAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
22 11 0.38
23 18 0.62
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATAATATTTTATAAAAATTA
Found at i:43484845 original size:21 final size:21
Alignment explanation
Indices: 43484819--43484870 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
43484809 GTGGTGGTGG
* *
43484819 TGAGATTAGTTACTGTAACAA
1 TGAGATTAGATACTATAACAA
* *
43484840 TGAGATTAGATATTATATCAA
1 TGAGATTAGATACTATAACAA
43484861 TGAGATTAGA
1 TGAGATTAGA
43484871 AATAGCGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (21 bp):
TGAGATTAGATACTATAACAA
Found at i:43491053 original size:3 final size:3
Alignment explanation
Indices: 43491027--43491102 Score: 98
Period size: 3 Copynumber: 24.7 Consensus size: 3
43491017 TATACATAAA
* * * *
43491027 TAT TAT ATAT AAT TAT TAT AAT TAT TAAC CAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT
43491074 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
43491103 AATAAAGTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
3 59 0.94
4 4 0.06
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:43491653 original size:12 final size:12
Alignment explanation
Indices: 43491636--43491666 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
43491626 GAAGTAGGGG
43491636 AGAAAAAGCGAA
1 AGAAAAAGCGAA
*
43491648 AGAAAAAGGGAA
1 AGAAAAAGCGAA
43491660 AGAAAAA
1 AGAAAAA
43491667 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGCGAA
Found at i:43492431 original size:37 final size:37
Alignment explanation
Indices: 43492363--43492452 Score: 112
Period size: 37 Copynumber: 2.4 Consensus size: 37
43492353 ATGTGTGGAA
*
43492363 TTGAATCGAATAT-TGACTTGAAAATGGAAAAGTGAATT
1 TTGAATCGAAT-TGTGACTTGAAAATGAAAAAGTGAA-T
*
43492401 TTGAATCGAATTGTGA-TTGAAAGTGAAAAAGTGAAT
1 TTGAATCGAATTGTGACTTGAAAATGAAAAAGTGAAT
* *
43492437 TTGAATTGAAATGTGA
1 TTGAATCGAATTGTGA
43492453 ATTTGGAGTC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
36 15 0.32
37 18 0.38
38 14 0.30
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.32
Consensus pattern (37 bp):
TTGAATCGAATTGTGACTTGAAAATGAAAAAGTGAAT
Found at i:43495200 original size:27 final size:27
Alignment explanation
Indices: 43495170--43495307 Score: 161
Period size: 27 Copynumber: 5.1 Consensus size: 27
43495160 TCGATATCTG
* * * *
43495170 GACCAAAATACCCTCAAAGGATAAAAT
1 GACCGAAATACCCACATAGGGTAAAAT
43495197 GACCGAAATACCCACATAGGGTAAAAT
1 GACCGAAATACCCACATAGGGTAAAAT
* * *
43495224 GACTGAAATGCCCCCATAGGGTAAAAT
1 GACCGAAATACCCACATAGGGTAAAAT
**
43495251 GACAAAAATACCCACATAGGGTAAAAT
1 GACCGAAATACCCACATAGGGTAAAAT
* *
43495278 GACCGTAATACCC-CTGTAGGGTAAAAT
1 GACCGAAATACCCAC-ATAGGGTAAAAT
43495305 GAC
1 GAC
43495308 AGTAATGCCC
Statistics
Matches: 95, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
26 1 0.01
27 94 0.99
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (27 bp):
GACCGAAATACCCACATAGGGTAAAAT
Found at i:43495273 original size:54 final size:54
Alignment explanation
Indices: 43495170--43495308 Score: 179
Period size: 54 Copynumber: 2.6 Consensus size: 54
43495160 TCGATATCTG
* * * * **
43495170 GACCAAAATACCCTCAAAGGATAAAATGACCGAAATACCCACATAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAATGACAAAAATACCCACATAGGGTAAAAT
* *
43495224 GACTGAAATGCCCCCATAGGGTAAAATGACAAAAATACCCACATAGGGTAAAAT
1 GACCGAAATACCCCCATAGGGTAAAATGACAAAAATACCCACATAGGGTAAAAT
* **
43495278 GACCGTAATACCCCTGTAGGGTAAAATGACA
1 GACCGAAATACCCCCATAGGGTAAAATGACA
43495309 GTAATGCCCT
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 72 1.00
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.17
Consensus pattern (54 bp):
GACCGAAATACCCCCATAGGGTAAAATGACAAAAATACCCACATAGGGTAAAAT
Found at i:43495426 original size:24 final size:24
Alignment explanation
Indices: 43495374--43495428 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
43495364 TTTATGGTTA
43495374 AATGACTAATTTGTCTATGTTTGG
1 AATGACTAATTTGTCTATGTTTGG
* * *
43495398 TATGATTAATTTGTCTGTGATTT-G
1 AATGACTAATTTGTCTATG-TTTGG
43495422 AATGACT
1 AATGACT
43495429 GATTCTGAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.25, C:0.07, G:0.20, T:0.47
Consensus pattern (24 bp):
AATGACTAATTTGTCTATGTTTGG
Found at i:43495662 original size:32 final size:32
Alignment explanation
Indices: 43495619--43495808 Score: 154
Period size: 32 Copynumber: 5.9 Consensus size: 32
43495609 ATGGCTGCCA
*
43495619 ATCATAGT-ACCGTTATTGATGGCTTTGTGCAG
1 ATCATA-TCACCGTTACTGATGGCTTTGTGCAG
* * *
43495651 ATCATATTACCGTTACCT-ATGGCTGTGTGCTG
1 ATCATATCACCGTTA-CTGATGGCTTTGTGCAG
* * * *
43495683 ATCATGTCACTGTTACTGATAG-TTGTGTGCCG
1 ATCATATCACCGTTACTGATGGCTT-TGTGCAG
* * *
43495715 ATCATATCACTGCTACTGATGGCTTTGTGCCG
1 ATCATATCACCGTTACTGATGGCTTTGTGCAG
* * * *
43495747 ATCATGTTACCATTACTGATGGCTGTGTGTCAG
1 ATCATATCACCGTTACTGATGGCTTTGTG-CAG
* * *
43495780 -TCATATCACTGCTACTGATAGCTTTGTGC
1 ATCATATCACCGTTACTGATGGCTTTGTGC
43495809 CAATCACATT
Statistics
Matches: 126, Mismatches: 26, Indels: 13
0.76 0.16 0.08
Matches are distributed among these distances:
31 5 0.04
32 116 0.92
33 5 0.04
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.37
Consensus pattern (32 bp):
ATCATATCACCGTTACTGATGGCTTTGTGCAG
Found at i:43495712 original size:64 final size:64
Alignment explanation
Indices: 43495635--43495814 Score: 175
Period size: 64 Copynumber: 2.8 Consensus size: 64
43495625 GTACCGTTAT
* * * * * **
43495635 TGATGGCTTTGTGCAGATCATATTACCGTTACCT-ATGGCTGTGTGCTGATCATGTCACTGTTAC
1 TGATAGCTGTGTGCAGATCATATCACCGCTA-CTGATGGCTGTGTGCCGATCATGTCACCATTAC
* * * * *
43495699 TGATAGTTGTGTGCCGATCATATCACTGCTACTGATGGCTTTGTGCCGATCATGTTACCATTAC
1 TGATAGCTGTGTGCAGATCATATCACCGCTACTGATGGCTGTGTGCCGATCATGTCACCATTAC
* * * * *
43495763 TGATGGCTGTGTGTCAG-TCATATCACTGCTACTGATAGCTTTGTGCCAATCA
1 TGATAGCTGTGTG-CAGATCATATCACCGCTACTGATGGCTGTGTGCCGATCA
43495815 CATTATTATA
Statistics
Matches: 97, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
63 2 0.02
64 93 0.96
65 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (64 bp):
TGATAGCTGTGTGCAGATCATATCACCGCTACTGATGGCTGTGTGCCGATCATGTCACCATTAC
Found at i:43495789 original size:96 final size:96
Alignment explanation
Indices: 43495635--43495814 Score: 249
Period size: 96 Copynumber: 1.9 Consensus size: 96
43495625 GTACCGTTAT
* * * *
43495635 TGATGGCTTTGTGCAGATCATATTACCGTTACCTATGGCTGTGTGCTGATCATGTCACTGTTACT
1 TGATGGCTTTGTGCAGATCATATTACCATTACCTATGGCTGTGTGCAGATCATATCACTGCTACT
*
43495700 GATAG-TTGTGTGCCGATCATATCACTGCTAC
66 GATAGCTT-TGTGCCAATCATATCACTGCTAC
* *
43495731 TGATGGCTTTGTGCCGATCATGTTACCATTA-CTGATGGCTGTGTGTCAG-TCATATCACTGCTA
1 TGATGGCTTTGTGCAGATCATATTACCATTACCT-ATGGCTGTGTG-CAGATCATATCACTGCTA
43495794 CTGATAGCTTTGTGCCAATCA
64 CTGATAGCTTTGTGCCAATCA
43495815 CATTATTATA
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
95 2 0.03
96 68 0.92
97 4 0.05
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (96 bp):
TGATGGCTTTGTGCAGATCATATTACCATTACCTATGGCTGTGTGCAGATCATATCACTGCTACT
GATAGCTTTGTGCCAATCATATCACTGCTAC
Found at i:43497231 original size:266 final size:272
Alignment explanation
Indices: 43496729--43497251 Score: 641
Period size: 273 Copynumber: 1.9 Consensus size: 272
43496719 ATTTTGGATT
* * ** * *
43496729 GTTATGGAATTTTTTAATTTGTTTGGAATTCTTGTCTTTAAAGTGTTAGATATATTTAAATTGTT
1 GTTATGGAAATTTTTAATTTATTCAGAATTCTTATCTTTAAAGTATTAGATATATTTAAATTGTT
* * * * * * * *
43496794 TTGAGATTGTTATGTTTAATTTATTTGTATTGTTATTTAATTCCTTTTGTTAATTTACATTTATT
66 GTGAAATTATTATGTTCAACTTATTTGGATTATTATTTAATTACTTTTGTTAATTTACATTTATT
* * * * *
43496859 TATTGTTATTTATGAATAATTTTTATTTAAAATTAATTTTTTTGGCTTGATTTTATATTATTTTG
131 TATTATTAATTATAAATAAATTTTATTTAAAATT-ATTTTTTTGGCTTGATTCTATATTATTTT-
* ** *
43496924 CATATTTGGATTTGAATTTTTGCAGCTCCAGATATCCGACATATAATTGAAAATGTTAAATTTGG
194 CATATTTGGATTCGAATTTTTGCAAATCCAGATATCCGACATATAATTGAAAATGTGAAATTTGG
43496989 ATTTTTTGCAAATA
259 ATTTTTTGCAAATA
* *
43497003 GTTAT-GAAATTTTTAATTTATTCAGAATTCTTATGTTT-AAGTTATTAGGTATATTTAAATTGT
1 GTTATGGAAATTTTTAATTTATTCAGAATTCTTATCTTTAAAG-TATTAGATATATTTAAATTGT
* * *
43497066 TGTGAAATTATTATGTTCAACTTGTTTGGCTTATTATTTAATTACTTTT-TT-ATTTTCATTTAT
65 TGTGAAATTATTATGTTCAACTTATTTGGATTATTATTTAATTACTTTTGTTAATTTACATTTAT
*
43497129 TTATTATTAATTATAAATAAATTTTATTT-AAA-T-TTTTTTT-GTTTGATTCTATATTATTTT-
130 TTATTATTAATTATAAATAAATTTTATTTAAAATTATTTTTTTGGCTTGATTCTATATTATTTTC
* * * *
43497189 ATGGATTTGGATTCGGATTTTTGCAAATTCGGATATCCGACATATGATTGAAAATGTGAAATT
195 AT--ATTTGGATTCGAATTTTTGCAAATCCAGATATCCGACATATAATTGAAAATGTGAAATT
43497252 CAAAATTTTT
Statistics
Matches: 213, Mismatches: 33, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
264 2 0.01
266 69 0.32
267 7 0.03
269 1 0.00
270 3 0.01
271 36 0.17
272 5 0.02
273 85 0.40
274 5 0.02
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.53
Consensus pattern (272 bp):
GTTATGGAAATTTTTAATTTATTCAGAATTCTTATCTTTAAAGTATTAGATATATTTAAATTGTT
GTGAAATTATTATGTTCAACTTATTTGGATTATTATTTAATTACTTTTGTTAATTTACATTTATT
TATTATTAATTATAAATAAATTTTATTTAAAATTATTTTTTTGGCTTGATTCTATATTATTTTCA
TATTTGGATTCGAATTTTTGCAAATCCAGATATCCGACATATAATTGAAAATGTGAAATTTGGAT
TTTTTGCAAATA
Found at i:43497676 original size:14 final size:14
Alignment explanation
Indices: 43497657--43497695 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
43497647 TTATTTCATT
*
43497657 GAAAATGACTTCTG
1 GAAAATGACTTCTA
* *
43497671 GAAAATTATTTCTA
1 GAAAATGACTTCTA
43497685 GAAAATGACTT
1 GAAAATGACTT
43497696 ACTTTTCTAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.33
Consensus pattern (14 bp):
GAAAATGACTTCTA
Found at i:43497863 original size:315 final size:310
Alignment explanation
Indices: 43497287--43497902 Score: 943
Period size: 315 Copynumber: 2.0 Consensus size: 310
43497277 TCTGGAGGAT
* * * *
43497287 AATGATATTTAAATCGGATTCAGATTTAGATACTATTAGACTCCGTTTGTTTCACTAAAAATGAC
1 AATGATATTTAAATCGGATTCAAATTTAGATACTATTAGACCCCATTTATTTCACTAAAAATGAC
* *
43497352 TTTCAGAAAATTATTTCTAGAAAAGACTTACTTTCTGGAAAAATTAATATTTTTTAGTGTTTGGA
66 TTTCAGAAAATTATTTCTAGAAAAGACTTACTTTCTGAAAAAACTAATATTTTTTAGTGTTTGGA
*
43497417 TGAACCTGTGTAAAATATTTTCTGTTGTTTGGCATATTTTCTGAAAATATTTCGTAAAAGTTGTT
131 TGAACCTGTGTAAAATATTTTCTGTTGTTTGGCATATTTTCTGAAAATATTTCATAAAAGTTGTT
* *
43497482 TCCAATTAAACAAACATACATTTAAGATTTTCTTATCTTTTCATTATTTAATTGAGTTGATTTTA
196 TCCAATGAAACAAACATACATTTAAGATTTTCTTATATTTTCATTATTTAATTGAGTTGATTTTA
* *
43497547 TATCTATAAATTTATATTTTACATTGTTTTTGTATATAATAAAATGTGATTGGA
261 TATCTAT--A--TATATTTTACATTGCTTTTGCATATAATAAAATGTGATTGGA
* * * * *
43497601 AATGATATTTAAATCGGCTTCAAATTTGGATACTATTAGGCCCCATTTATTTCATTGAAAATGAC
1 AATGATATTTAAATCGGATTCAAATTTAGATACTATTAGACCCCATTTATTTCACTAAAAATGAC
* * *
43497666 -TTCTGGAAAATTATTTCTAGAAAATGACTTACTTTTCT-AAAAAACTAATCTTTTTTTGTGTTT
66 TTTC-AGAAAATTATTTCTAGAAAA-GACTTAC-TTTCTGAAAAAACTAATATTTTTTAGTGTTT
43497729 GGATGAACCTGTGTAAAATATTTTCTGTTGTTTGGCATA-TTTCTTGAAAATATTTCATAAAAGT
128 GGATGAACCTGTGTAAAATATTTTCTGTTGTTTGGCATATTTTC-TGAAAATATTTCATAAAAGT
*
43497793 TGTTTCCAATGAAACAAACATACATTTGAGATTTTCTTATATTTTCATTATTTAATTGAGTTTG-
192 TGTTTCCAATGAAACAAACATACATTTAAGATTTTCTTATATTTTCATTATTTAATTGAG-TTGA
43497857 TTTTATATCTATATATATTTTACATTGCTTTTGCATATAATAAAAT
256 TTTTATATCTATATATATTTTACATTGCTTTTGCATATAATAAAAT
43497903 TATTTTATTA
Statistics
Matches: 277, Mismatches: 20, Indels: 13
0.89 0.06 0.04
Matches are distributed among these distances:
311 31 0.11
313 4 0.01
314 79 0.29
315 155 0.56
316 8 0.03
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.45
Consensus pattern (310 bp):
AATGATATTTAAATCGGATTCAAATTTAGATACTATTAGACCCCATTTATTTCACTAAAAATGAC
TTTCAGAAAATTATTTCTAGAAAAGACTTACTTTCTGAAAAAACTAATATTTTTTAGTGTTTGGA
TGAACCTGTGTAAAATATTTTCTGTTGTTTGGCATATTTTCTGAAAATATTTCATAAAAGTTGTT
TCCAATGAAACAAACATACATTTAAGATTTTCTTATATTTTCATTATTTAATTGAGTTGATTTTA
TATCTATATATATTTTACATTGCTTTTGCATATAATAAAATGTGATTGGA
Found at i:43498081 original size:29 final size:29
Alignment explanation
Indices: 43498048--43498131 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 29
43498038 TTAAAATTTG
* *
43498048 AAAAGTAGAGGGACTAAATTCTTGAAAAT
1 AAAAGTAAAGGGACTAAATTCTTAAAAAT
*
43498077 AAAAGTACAAGGACTAACTAAATTCTTAAAAAT
1 AAAAGTA-AAGG---GACTAAATTCTTAAAAAT
*
43498110 AAAAGTATAGGGACTAAATTCT
1 AAAAGTAAAGGGACTAAATTCT
43498132 AAATTTGTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
29 17 0.37
30 3 0.07
32 3 0.07
33 23 0.50
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (29 bp):
AAAAGTAAAGGGACTAAATTCTTAAAAAT
Found at i:43498102 original size:33 final size:33
Alignment explanation
Indices: 43498060--43498126 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
43498050 AAGTAGAGGG
*
43498060 ACTAAATTCTTGAAAATAAAAGTACAAGGACTA
1 ACTAAATTCTTAAAAATAAAAGTACAAGGACTA
* *
43498093 ACTAAATTCTTAAAAATAAAAGTATAGGGACTA
1 ACTAAATTCTTAAAAATAAAAGTACAAGGACTA
43498126 A
1 A
43498127 ATTCTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.25
Consensus pattern (33 bp):
ACTAAATTCTTAAAAATAAAAGTACAAGGACTA
Found at i:43498344 original size:39 final size:39
Alignment explanation
Indices: 43498291--43498379 Score: 94
Period size: 39 Copynumber: 2.3 Consensus size: 39
43498281 ATGAATGTTC
* *
43498291 AATAATATTT-AAAATTATAATAT-TTTATATTA-ATATATT
1 AATAAT-TTTAAAAATAAGAATATATTT-TATTATATATA-T
*
43498330 AATAATTTTAAAAATAAGAATATATTTTATTATCTATAT
1 AATAATTTTAAAAATAAGAATATATTTTATTATATATAT
*
43498369 AATAATATTAA
1 AATAATTTTAA
43498380 GGTTTATTTA
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
38 3 0.07
39 33 0.77
40 7 0.16
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (39 bp):
AATAATTTTAAAAATAAGAATATATTTTATTATATATAT
Found at i:43502134 original size:12 final size:12
Alignment explanation
Indices: 43502117--43502141 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43502107 CTTGAAATGC
43502117 CTTCTCTTCACT
1 CTTCTCTTCACT
43502129 CTTCTCTTCACT
1 CTTCTCTTCACT
43502141 C
1 C
43502142 CTTTCTGCTG
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:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (12 bp):
CTTCTCTTCACT
Found at i:43502777 original size:17 final size:17
Alignment explanation
Indices: 43502755--43502789 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
43502745 AACCAGTTAA
43502755 TGCCATTCCAAAAACAC
1 TGCCATTCCAAAAACAC
43502772 TGCCATTCCAAAAACAC
1 TGCCATTCCAAAAACAC
43502789 T
1 T
43502790 CATTCTCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.34, G:0.06, T:0.20
Consensus pattern (17 bp):
TGCCATTCCAAAAACAC
Found at i:43504064 original size:24 final size:24
Alignment explanation
Indices: 43504035--43504095 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
43504025 ATAAGTAACA
43504035 TATAAAAACATAATAAAATA-TTTT
1 TATAAAAACA-AATAAAATATTTTT
** *
43504059 TATAAAATTAAATATAATATTTTT
1 TATAAAAACAAATAAAATATTTTT
*
43504083 TATTAAAA-AAATA
1 TATAAAAACAAATA
43504096 TCTACTTTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 13 0.42
24 18 0.58
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
TATAAAAACAAATAAAATATTTTT
Found at i:43504094 original size:23 final size:22
Alignment explanation
Indices: 43504046--43504096 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 22
43504036 ATAAAAACAT
*
43504046 AATAAAATATTTTTATAAAATTA
1 AATATAATATTTTTATAAAA-TA
43504069 AATATAATATTTTTTATTAAAA-A
1 AATATAATA-TTTTTA-TAAAATA
43504092 AATAT
1 AATAT
43504097 CTACTTTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 14 0.56
24 6 0.24
25 5 0.20
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
AATATAATATTTTTATAAAATA
Found at i:43508795 original size:3 final size:3
Alignment explanation
Indices: 43508777--43508820 Score: 56
Period size: 3 Copynumber: 15.0 Consensus size: 3
43508767 ATCATTATTG
*
43508777 TAT TA- TAT TA- TAT TAT TATT TAC TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT
43508821 ATTCATATGC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
2 4 0.11
3 29 0.81
4 3 0.08
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:43513863 original size:7 final size:7
Alignment explanation
Indices: 43513851--43513901 Score: 74
Period size: 6 Copynumber: 7.9 Consensus size: 7
43513841 TGAGTCGTAA
43513851 AAAAATG
1 AAAAATG
43513858 AAAAATG
1 AAAAATG
43513865 -AAAATG
1 AAAAATG
43513871 AAAAATG
1 AAAAATG
43513878 AAAAAT-
1 AAAAATG
43513884 AAAAAT-
1 AAAAATG
43513890 AAAAAT-
1 AAAAATG
43513896 AAAAAT
1 AAAAAT
43513902 AGAGAGGCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 24 0.56
7 19 0.44
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (7 bp):
AAAAATG
Found at i:43513870 original size:13 final size:12
Alignment explanation
Indices: 43513852--43513901 Score: 64
Period size: 13 Copynumber: 3.9 Consensus size: 12
43513842 GAGTCGTAAA
43513852 AAAATGAAAAATG
1 AAAAT-AAAAATG
43513865 AAAATGAAAAATG
1 AAAAT-AAAAATG
*
43513878 AAAAATAAAAATA
1 -AAAATAAAAATG
43513891 AAAATAAAAAT
1 AAAATAAAAAT
43513902 AGAGAGGCTA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
12 11 0.31
13 19 0.54
14 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAATAAAAATG
Found at i:43514912 original size:44 final size:44
Alignment explanation
Indices: 43514839--43515432 Score: 545
Period size: 44 Copynumber: 13.4 Consensus size: 44
43514829 ATACTGGTGG
* *
43514839 TGAAGTAGATCGAAGATAGTGGATATTGTCTTCATGTATTGACA
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATTGACA
** * ***
43514883 TGAAGTAGATCGAAGATAACAGATCTTGTCTTCCA--TACTGGTGG
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTT-CATGTA-TTGACA
* * *
43514927 TAAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATTGACA
* * *
43514971 TGAAGTAGAT-TATAGATAGTGGATCTTGTCTTTATGTATTGACA
1 TGAAGTAGATCGA-AGATAGTAGATCTTGTCTTCATGTATTGACA
* *** * ***
43515015 TGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGGTGG
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTA-TTGACA
* *
43515060 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATTGACA
* * *
43515104 TGAAGTAGATC-AGAGATAGTGGATCTTATCTTCATGTATTAACA
1 TGAAGTAGATCGA-AGATAGTAGATCTTGTCTTCATGTATTGACA
* * * *** * ***
43515148 TTAATTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGGTGG
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTA-TTGACA
* *
43515193 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATTGACA
* * * *** * ***
43515237 TGAAGTAGATCGAAAATAGCAGATTTTGTCTTCCCATACTGGTGG
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTA-TTGACA
*
43515282 TGAAGTAGATCGAAGATAATAGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATTGACA
*
43515326 TGAAGTAGATC-AGAGATAGTGGATCTTGTCTTCATGTATTGACA
1 TGAAGTAGATCGA-AGATAGTAGATCTTGTCTTCATGTATTGACA
* * * *
43515370 TGAAGTAGATCAAAGATAGCAGATCATGTCTTCCTGTATTAGTAGC-
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATT-G-A-CA
43515416 -GAAGTAGATCGAAGATA
1 TGAAGTAGATCGAAGATA
43515433 ACAAGTCTTA
Statistics
Matches: 436, Mismatches: 98, Indels: 31
0.77 0.17 0.05
Matches are distributed among these distances:
43 7 0.02
44 305 0.70
45 122 0.28
46 1 0.00
47 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (44 bp):
TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATTGACA
Found at i:43515112 original size:133 final size:132
Alignment explanation
Indices: 43514839--43515435 Score: 763
Period size: 133 Copynumber: 4.5 Consensus size: 132
43514829 ATACTGGTGG
*
43514839 TGAAGTAGATCGAAGATAGTGGATATTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAACA
1 TGAAGTAGATC-AAGATAGTGGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAACA
*
43514904 GATCTTGTCTT-CCATACTGGTGGTAAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTG
65 GATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTG
43514968 ACA
130 ACA
* * *
43514971 TGAAGTAGATTATAGATAGTGGATCTTGTCTTTATGTATTGACATGAAGTAGATCGAAGATAGCA
1 TGAAGTAGATCA-AGATAGTGGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAACA
43515036 GATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTG
65 GATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTG
43515101 ACA
130 ACA
* * * * *
43515104 TGAAGTAGATCAGAGATAGTGGATCTTATCTTCATGTATTAACATTAATTAGATCGAAGATAGCA
1 TGAAGTAGATCA-AGATAGTGGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAACA
43515169 GATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTG
65 GATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTG
43515234 ACA
130 ACA
* ** * *** * *** *
43515237 TGAAGTAGATCGAAAATAGCAGATTTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAAT
1 TGAAGTAGATC-AAGATAGTGGATCTTGTCTTCATGTA-TTGACATGAAGTAGATCGAAGATAAC
*** * *** *
43515302 AGATCTTGTCTTCATGTA-TTGACATGAAGTAGATC-AGAGATAGTGGATCTTGTCTTCATGTAT
64 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGA-AGATAATGGATCTTGTCTTCATGTAT
43515365 TGACA
128 TGACA
** * *
43515370 TGAAGTAGATCAAAGATAGCAGATCATGTCTTCCTGTATTAGTAGC--GAAGTAGATCGAAGATA
1 TGAAGTAGATC-AAGATAGTGGATCTTGTCTTCATGTATT-G-A-CATGAAGTAGATCGAAGATA
43515433 ACA
62 ACA
43515436 AGTCTTATCC
Statistics
Matches: 410, Mismatches: 47, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
131 1 0.00
132 72 0.18
133 304 0.74
134 33 0.08
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (132 bp):
TGAAGTAGATCAAGATAGTGGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAACAG
ATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGA
CA
Found at i:43515197 original size:89 final size:89
Alignment explanation
Indices: 43514806--43515358 Score: 614
Period size: 89 Copynumber: 6.2 Consensus size: 89
43514796 GCAGGTTGAA
* * *
43514806 AAGATAGCAGATATTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAGTGGATATTGTCTT
1 AAGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTT
43514871 CATGTATTGACATGAAGTAGATCG
66 CATGTATTGACATGAAGTAGATCG
* *
43514895 AAGATAACAGATCTTGTCTT-CCATACTGGTGGTAAAGTAGATCGAAGATAATGGATCTTGTCTT
1 AAGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTT
*
43514959 CATGTATTGACATGAAGTAGAT-T
66 CATGTATTGACATGAAGTAGATCG
** **** * *** ***
43514982 ATAGATAGTGGATCTTGTCTTTATGTA-TTGACATGAAGTAGATCGAAGATAGCAGATCTTGTCT
1 A-AGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCT
*** * ***
43515046 TCCCATACTGGTGGTGAAGTAGATCG
65 TCATGTA-TTGACATGAAGTAGATCG
*** *** * *** * *
43515072 AAGATAATGGATCTTGTCTTCATGTA-TTGACATGAAGTAGATC-AGAGATAGTGGATCTTATCT
1 AAGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGA-AGATAATGGATCTTGTCT
* * *
43515135 TCATGTATTAACATTAATTAGATCG
65 TCATGTATTGACATGAAGTAGATCG
43515160 AAGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTT
1 AAGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTT
43515225 CATGTATTGACATGAAGTAGATCG
66 CATGTATTGACATGAAGTAGATCG
* * *
43515249 AAAATAGCAGATTTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATAGATCTTGTCTT
1 AAGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTT
43515314 CATGTATTGACATGAAGTAGATC-
66 CATGTATTGACATGAAGTAGATCG
**
43515337 AGAGATAGTGGATCTTGTCTTC
1 A-AGATAGCAGATCTTGTCTTC
43515359 ATGTATTGAC
Statistics
Matches: 391, Mismatches: 65, Indels: 16
0.83 0.14 0.03
Matches are distributed among these distances:
87 1 0.00
88 145 0.37
89 243 0.62
90 2 0.01
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.33
Consensus pattern (89 bp):
AAGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAATGGATCTTGTCTT
CATGTATTGACATGAAGTAGATCG
Found at i:43515420 original size:89 final size:86
Alignment explanation
Indices: 43514839--43515432 Score: 469
Period size: 89 Copynumber: 6.7 Consensus size: 86
43514829 ATACTGGTGG
* * ***
43514839 TGAAGTAGATCGAAGATAGTGGATATTGTCTTCATGTATTGACATGAAGTAGATCGAAGATAACA
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATTGAC--GAAGTAGATCGAAGATAGTG
* ***
43514904 GATCTTGTCTTCCA--TACTGGTGG
64 GATCTTGTCTT-CATGTA-TTGACA
* * * *
43514927 TAAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGAT-TATAGATAGT
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATTGAC--GAAGTAGATCGA-AGATAGT
*
43514991 GGATCTTGTCTTTATGTATTGACA
63 GGATCTTGTCTTCATGTATTGACA
* * ** ** *
43515015 TGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGATAAT
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTT--CAT-GTATTGACGAAGTAGATCGAAGATAGT
43515080 GGATCTTGTCTTCATGTATTGACA
63 GGATCTTGTCTTCATGTATTGACA
* * * * * *
43515104 TGAAGTAGATC-AGAGATAGTGGATCTTATCTTCATGTATTAACATTAATTAGATCGAAGATAGC
1 TGAAGTAGATCGA-AGATAGTAGATCTTGTCTTCATGTATTGAC--GAAGTAGATCGAAGATAGT
* *** * ***
43515168 AGATCTTGTCTTCCCATACTGGTGG
63 GGATCTTGTCTTCATGTA-TTGACA
* * * **
43515193 TGAAGTAGATCGAAGATAATGGATCTTGTCTTCATGTATTGACATGAAGTAGATCGAAAATAGCA
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATTGAC--GAAGTAGATCGAAGATAGTG
* *** * ***
43515258 GATTTTGTCTTCCCATACTGGTGG
64 GATCTTGTCTTCATGTA-TTGACA
*
43515282 TGAAGTAGATCGAAGATAATAGATCTTGTCTTCATGTATTGACATGAAGTAGATC-AGAGATAGT
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATTGAC--GAAGTAGATCGA-AGATAGT
43515346 GGATCTTGTCTTCATGTATTGACA
63 GGATCTTGTCTTCATGTATTGACA
* * * *
43515370 TGAAGTAGATCAAAGATAGCAGATCATGTCTTCCTGTATTAGTAGCGAAGTAGATCGAAGATA
1 TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATT-G-A-CGAAGTAGATCGAAGATA
43515433 ACAAGTCTTA
Statistics
Matches: 420, Mismatches: 69, Indels: 33
0.80 0.13 0.06
Matches are distributed among these distances:
86 2 0.00
87 5 0.01
88 165 0.39
89 237 0.56
90 7 0.02
91 4 0.01
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (86 bp):
TGAAGTAGATCGAAGATAGTAGATCTTGTCTTCATGTATTGACGAAGTAGATCGAAGATAGTGGA
TCTTGTCTTCATGTATTGACA
Found at i:43515545 original size:44 final size:42
Alignment explanation
Indices: 43515438--43515855 Score: 291
Period size: 44 Copynumber: 9.8 Consensus size: 42
43515428 AGATAACAAG
* *
43515438 TCTTATCCCCCTGAAGTTGCAGTGG-GCAGATTGAAGAA-ATCA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGA-T-AA-AACA-CAGA
*
43515481 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGA-TAAAA-CACAGA
* * ** *
43515525 TCTTATCTCTCTGAAGTTGCAGTAGAGCGGATCGCATC-CAG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGAT-AAAACACAGA
* * * * * *
43515566 TCTTATCTCTCTAAAGTTACAGTGGAGCAGACAGAAGAAATCA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGATA-AA-ACA-CAGA
* * * *
43515610 TCCTATCTCCCTAAAATTGCAGTGGAGCAGATTAAAACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGA-TAAAA-CACAGA
* * ** *
43515654 TCTTATCTCTCTGAAGTTGCAGTAGAGCGGATCGCATC-CAG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGAT-AAAACACAGA
* * *
43515695 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAATAAATCA-A
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGATA-AA-ACA-CAGA
*
43515739 TCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGA-TAAAA-CACAGA
* * ** *
43515783 TCTTATCTCTCTGAAGTTGCAGTAGAGCGGATCGCATC-CAG-
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGAT-AAAACACAGA
*
43515824 TCTTATCTCCCTGAAGTTGCAGTGGAGTGGAT
1 TCTTATCTCCCTGAAGTTGCAGTGGAGCGGAT
43515856 TAAAGATAGT
Statistics
Matches: 298, Mismatches: 54, Indels: 48
0.75 0.14 0.12
Matches are distributed among these distances:
41 86 0.29
42 11 0.04
43 39 0.13
44 160 0.54
45 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (42 bp):
TCTTATCTCCCTGAAGTTGCAGTGGAGCGGATAAAACACAGA
Found at i:43515593 original size:85 final size:85
Alignment explanation
Indices: 43515484--43515859 Score: 343
Period size: 85 Copynumber: 4.4 Consensus size: 85
43515474 AAATCAATCC
*
43515484 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTA
* *
43515549 GAGCGGATCGCATCCAGTCT
66 GAGCAGATCGAATCCAGTCT
* * * * * * * * *
43515569 TATCTCTCTAAAGTTACAGTGGAGCAGA-CAGAAGA-AATCA-ATCCTATCTCCCTAAAATTGCA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTA-AA-ACCA-CAGATCTTATCTCCCTGAAGTTGCA
* ** *
43515631 GTGGAGCAGATTAAAACCACAGATCT
63 GTAGAGCAGA-TCGAATC-CAG-TCT
* * *** * *
43515657 TATCTCTCTGAAGTTGCAGTAGAGCGGA-TCGCATC-CAG-TCTTATCTCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTA
* * *
43515719 GAGCAGA-CAGAATAAATCAATCC
66 GAGCAGATC-GAAT---CCAGTCT
*
43515742 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTA
* *
43515807 GAGCGGATCGCATCCAGTCT
66 GAGCAGATCGAATCCAGTCT
*
43515827 TATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAA
43515860 GATAGTAAAT
Statistics
Matches: 227, Mismatches: 48, Indels: 32
0.74 0.16 0.10
Matches are distributed among these distances:
84 3 0.01
85 147 0.65
86 12 0.05
87 6 0.03
88 58 0.26
89 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.26
Consensus pattern (85 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCACAGATCTTATCTCCCTGAAGTTGCAGTA
GAGCAGATCGAATCCAGTCT
Found at i:43515630 original size:129 final size:129
Alignment explanation
Indices: 43515436--43515850 Score: 733
Period size: 129 Copynumber: 3.2 Consensus size: 129
43515426 GAAGATAACA
* **
43515436 AGTCTTATCCCCCTGAAGTTGCAGTGG-GCAGATTGAAGAAATCAATCCTATCTCCCTGAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTG
43515500 CAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCGGATCGCATCC
66 CAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCGGATCGCATCC
* * * * *
43515564 AGTCTTATCTCTCTAAAGTTACAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTAAAATTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTG
*
43515629 CAGTGGAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCGGATCGCATCC
66 CAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCGGATCGCATCC
*
43515693 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAATAAATCAATCCTATCTCCCTGAAGTTG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTG
43515758 CAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCGGATCGCATCC
66 CAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCGGATCGCATCC
43515822 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
1 AGTCTTATCTCCCTGAAGTTGCAGTGGAG
43515851 TGGATTAAAG
Statistics
Matches: 270, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
128 23 0.09
129 247 0.91
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (129 bp):
AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACAGAAGAAATCAATCCTATCTCCCTGAAGTTG
CAGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCGGATCGCATCC
Found at i:43517202 original size:3 final size:3
Alignment explanation
Indices: 43517191--43517228 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
43517181 ATCATTATTG
43517191 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
43517229 ATTCATATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 32 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:43519371 original size:17 final size:17
Alignment explanation
Indices: 43519330--43519376 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
43519320 ATTTTGGAAC
43519330 TTTTTATATTTTTATAAT
1 TTTTTA-ATTTTTATAAT
43519348 TTCTTTAATTTTTA-AAT
1 TT-TTTAATTTTTATAAT
43519365 TATTTT-ATTTTT
1 T-TTTTAATTTTT
43519377 TCACATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
16 6 0.22
17 7 0.26
18 10 0.37
19 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTTTAATTTTTATAAT
Found at i:43519377 original size:17 final size:17
Alignment explanation
Indices: 43519330--43519377 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 17
43519320 ATTTTGGAAC
43519330 TTTTTATATTTTTATAAT
1 TTTTTAT-TTTTTATAAT
*
43519348 TTCTTTAATTTTTA-AAT
1 TT-TTTATTTTTTATAAT
43519365 TATTTTATTTTTT
1 T-TTTTATTTTTT
43519378 CACATTTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 13 0.50
18 9 0.35
19 4 0.15
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTATTTTTTATAAT
Found at i:43520028 original size:19 final size:19
Alignment explanation
Indices: 43520004--43520146 Score: 82
Period size: 19 Copynumber: 7.4 Consensus size: 19
43519994 TAATATTCTC
*
43520004 ATTAAAAATCATGAAAATT
1 ATTAAAAATCATAAAAATT
43520023 ATTAAAAATCA-ATAAAATAT
1 ATTAAAAATCATA-AAAAT-T
* * *
43520043 ATTTAAGATAT-ATTATAATT
1 A-TTAA-AAATCATAAAAATT
*
43520063 AATTAAAAAT-ATAAAAAAT
1 -ATTAAAAATCATAAAAATT
**
43520082 CGTAAAAATCATAAAAACTT
1 ATTAAAAATCATAAAAA-TT
43520102 A-TAAAAATTCATAAAAATT
1 ATTAAAAA-TCATAAAAATT
*
43520121 -TATAACTAAT-ATAAAAATT
1 AT-TAA-AAATCATAAAAATT
*
43520140 ACTAAAA
1 ATTAAAA
43520147 TTTTATAGAA
Statistics
Matches: 96, Mismatches: 15, Indels: 27
0.70 0.11 0.20
Matches are distributed among these distances:
18 8 0.08
19 52 0.54
20 21 0.22
21 12 0.12
22 3 0.03
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (19 bp):
ATTAAAAATCATAAAAATT
Found at i:43520108 original size:20 final size:19
Alignment explanation
Indices: 43520085--43520146 Score: 63
Period size: 20 Copynumber: 3.2 Consensus size: 19
43520075 AAAAAATCGT
43520085 AAAAATCATAAAAACTTATA
1 AAAAATCATAAAAA-TTATA
*
43520105 AAAATTCATAAAAATTTATA
1 AAAAATCATAAAAA-TTATA
**
43520125 ACTAAT-ATAAAAATTACTA
1 AAAAATCATAAAAATTA-TA
43520144 AAA
1 AAA
43520147 TTTTATAGAA
Statistics
Matches: 34, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
18 3 0.09
19 10 0.29
20 21 0.62
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAAATCATAAAAATTATA
Found at i:43520120 original size:10 final size:10
Alignment explanation
Indices: 43520073--43520125 Score: 56
Period size: 10 Copynumber: 5.4 Consensus size: 10
43520063 AATTAAAAAT
*
43520073 ATAAAAAATC
1 ATAAAAATTC
*
43520083 GTAAAAA-TC
1 ATAAAAATTC
43520092 ATAAAAACTT-
1 ATAAAAA-TTC
43520102 ATAAAAATTC
1 ATAAAAATTC
*
43520112 ATAAAAATTT
1 ATAAAAATTC
43520122 ATAA
1 ATAA
43520126 CTAATATAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 10 0.27
10 26 0.70
11 1 0.03
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.28
Consensus pattern (10 bp):
ATAAAAATTC
Found at i:43522035 original size:19 final size:19
Alignment explanation
Indices: 43521985--43522045 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
43521975 TTTTTTAAAG
* *
43521985 TTTTATAATTATTGATAAG-
1 TTTTATAA-TATTTATATGT
43522004 TTTTAT-A-ATTTATATGT
1 TTTTATAATATTTATATGT
43522021 TTTTATAATATTTAT-TGGT
1 TTTTATAATATTTATAT-GT
43522040 TTTTAT
1 TTTTAT
43522046 GCTTTTTTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
16 7 0.19
17 6 0.17
18 3 0.08
19 20 0.56
ACGTcount: A:0.30, C:0.00, G:0.08, T:0.62
Consensus pattern (19 bp):
TTTTATAATATTTATATGT
Found at i:43526080 original size:29 final size:29
Alignment explanation
Indices: 43526048--43526139 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 29
43526038 CATTTAATTG
43526048 TTAAACATATTTTTATTATTGTATTATTA
1 TTAAACATATTTTTATTATTGTATTATTA
* * *
43526077 TTAAAGATA---TAAGTA-T-TATTATTA
1 TTAAACATATTTTTATTATTGTATTATTA
* * * *
43526101 TTCAACATATTTTTATTATAGGATTATTG
1 TTAAACATATTTTTATTATTGTATTATTA
43526130 TTAAACATAT
1 TTAAACATAT
43526140 ATATGCATAC
Statistics
Matches: 47, Mismatches: 11, Indels: 10
0.69 0.16 0.15
Matches are distributed among these distances:
24 15 0.32
25 1 0.02
26 4 0.09
27 4 0.09
29 23 0.49
ACGTcount: A:0.38, C:0.04, G:0.07, T:0.51
Consensus pattern (29 bp):
TTAAACATATTTTTATTATTGTATTATTA
Found at i:43529737 original size:18 final size:18
Alignment explanation
Indices: 43529714--43529748 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
43529704 AACACCCATT
43529714 TTTTTTACTTAATTTTAG
1 TTTTTTACTTAATTTTAG
**
43529732 TTTTTTTTTTAATTTTA
1 TTTTTTACTTAATTTTA
43529749 TCTTCACCCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (18 bp):
TTTTTTACTTAATTTTAG
Found at i:43534985 original size:22 final size:22
Alignment explanation
Indices: 43534963--43535042 Score: 112
Period size: 22 Copynumber: 3.7 Consensus size: 22
43534953 AAATTAAATC
* *
43534963 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTGC-ATATCATATCT
43534986 TCTAAGATTGCATATCATATCT
1 TCTAAGATTGCATATCATATCT
43535008 TCTAAGATTGCATATCATA---
1 TCTAAGATTGCATATCATATCT
43535027 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
43535043 CTTGAAGATT
Statistics
Matches: 55, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
19 16 0.29
22 29 0.53
23 10 0.18
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (22 bp):
TCTAAGATTGCATATCATATCT
Found at i:43535053 original size:17 final size:19
Alignment explanation
Indices: 43534989--43535042 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
43534979 CATATCTTCT
*
43534989 AAGATTGCATATCATATCTTCT
1 AAGATTGCATATCATA---TCG
*
43535011 AAGATTGCATATCATATCT
1 AAGATTGCATATCATATCG
43535030 AAGATTGCATATC
1 AAGATTGCATATC
43535043 CTTGAAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
19 16 0.50
22 16 0.50
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (19 bp):
AAGATTGCATATCATATCG
Found at i:43535896 original size:50 final size:50
Alignment explanation
Indices: 43535802--43536028 Score: 152
Period size: 50 Copynumber: 4.5 Consensus size: 50
43535792 TTCTGCTCCG
* * * * * * * *
43535802 CTGCAATGCCAGGGAAACAAGATTCGCTACCTT-TAGCTTTAATCTGTTCTA
1 CTGCAACGCCAAGGAAATAAGATTCGC--CGTTGTGGCTTCAATCTATTCCA
* * * * * **
43535853 CTGTAACGCCAAGGAGATAAGATTTGTCGTTGTGGCTTTAATCTATTTAA
1 CTGCAACGCCAAGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCCA
* ** * * * *
43535903 CTGCAATGTTAAGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCA
1 CTGCAACGCCAAGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCCA
* *
43535953 CTACACCGCC-AGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCA
1 CTGCAACGCCAAGGAAA-TAAGATTCGCCGTTGTGGCTTCAATCTATTCCA
* * * * *
43536003 CTGTAATGCCAAAGAGATAGGATTCG
1 CTGCAACGCCAAGGAAATAAGATTCG
43536029 TTGCCCACAG
Statistics
Matches: 131, Mismatches: 42, Indels: 7
0.73 0.23 0.04
Matches are distributed among these distances:
49 9 0.07
50 98 0.75
51 24 0.18
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.30
Consensus pattern (50 bp):
CTGCAACGCCAAGGAAATAAGATTCGCCGTTGTGGCTTCAATCTATTCCA
Found at i:43535924 original size:101 final size:100
Alignment explanation
Indices: 43535814--43535999 Score: 232
Period size: 100 Copynumber: 1.9 Consensus size: 100
43535804 GCAATGCCAG
* * * ** *
43535814 GGAAACAAGATTCGCTACCT-TTAGCTTTAATCTGTTCTACTGTAACGCCAAGGAGA-TAAGATT
1 GGAAACAAGATTCGC--CCTCGTAGCTTCAATCTGTTCCACTACAACGCC-AGGAAAGTAAGATT
* * *
43535877 TGTCGTTGTGGCTTTAATCTATTTAACTGCAATGTTAA
63 CGCCGTTGTGGCTTCAATCTATTTAACTGCAATGTTAA
* *
43535915 GGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTACACCGCCAGGAAAGTAAGATTCGC
1 GGAAACAAGATTCGCCCTCGTAGCTTCAATCTGTTCCACTACAACGCCAGGAAAGTAAGATTCGC
43535980 CGTTGTGGCTTCAATCTATT
66 CGTTGTGGCTTCAATCTATT
43536000 CCACTGTAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
99 7 0.10
100 50 0.69
101 15 0.21
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (100 bp):
GGAAACAAGATTCGCCCTCGTAGCTTCAATCTGTTCCACTACAACGCCAGGAAAGTAAGATTCGC
CGTTGTGGCTTCAATCTATTTAACTGCAATGTTAA
Found at i:43536241 original size:168 final size:168
Alignment explanation
Indices: 43535962--43536346 Score: 594
Period size: 168 Copynumber: 2.3 Consensus size: 168
43535952 ACTACACCGC
* ** *
43535962 CAGGAAAGTAAGATTCGCCGTTGTGGCTTCAATCTATTCCACTGTAATGCCAAAGAGATAGGATT
1 CAGGAAAGTAAGATTCGCCGTTTTGGCTTCAATCTATTTAACTGCAATGCCAAAGAGATAGGATT
** *
43536027 CGTTGCCCACAGCTTTAATCCACTCCACTTCAGCTAATCTAAGTCTTAACGCCAAGGAGATAAGA
66 CACTGCCCACAGCTTCAATCCACTCCACTTCAGCTAATCTAAGTCTTAACGCCAAGGAGATAAGA
43536092 TTCGCTGCCCTCAGCTTTAATCTACTCCGCTATAAAGT
131 TTCGCTGCCCTCAGCTTTAATCTACTCCGCTATAAAGT
* *
43536130 CAGGAAAGTAAGATTCACCGTTTTGGCTTCAATCTATTTAACTACAATGCCAAAGAGATAGGATT
1 CAGGAAAGTAAGATTCGCCGTTTTGGCTTCAATCTATTTAACTGCAATGCCAAAGAGATAGGATT
* * * *
43536195 CACTGCCTACAGCTTCAATCCACTTCACTTCAGCT-ATTTCAAGTCTTAACGCCAGGGAGATAAG
66 CACTGCCCACAGCTTCAATCCACTCCACTTCAGCTAATCT-AAGTCTTAACGCCAAGGAGATAAG
* *
43536259 ATTCGCTGCCCTCAGCTTTAATCTGCTCCGCTATAACGT
130 ATTCGCTGCCCTCAGCTTTAATCTACTCCGCTATAAAGT
*
43536298 CAAGG-AAGTAAGATTCGCCGTTTTGGCTTCAATCTATTTGACTGCAATG
1 C-AGGAAAGTAAGATTCGCCGTTTTGGCTTCAATCTATTTAACTGCAATG
43536347 TCAGGGAACT
Statistics
Matches: 197, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
167 3 0.02
168 191 0.97
169 3 0.02
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (168 bp):
CAGGAAAGTAAGATTCGCCGTTTTGGCTTCAATCTATTTAACTGCAATGCCAAAGAGATAGGATT
CACTGCCCACAGCTTCAATCCACTCCACTTCAGCTAATCTAAGTCTTAACGCCAAGGAGATAAGA
TTCGCTGCCCTCAGCTTTAATCTACTCCGCTATAAAGT
Found at i:43536360 original size:50 final size:50
Alignment explanation
Indices: 43536296--43536482 Score: 198
Period size: 50 Copynumber: 3.7 Consensus size: 50
43536286 CCGCTATAAC
* ** * *
43536296 GTCAAGGAAGTAAGATTCGCCGTTTTGGCTTCAATCTATTTGACTGCAAT
1 GTCAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTATTTAACTGCAAT
* * * * * *
43536346 GTCAGGGAACTAAGATTCGTCATCGTAGCTTCAATCTATTCAACTACACT
1 GTCAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTATTTAACTGCAAT
* * *
43536396 G-CTAGGGAAGTAAGATTCGCTGTTGTGGCTTCAATCTATTTAACTGCAAT
1 GTC-AGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTATTTAACTGCAAT
* *
43536446 GT-AGGAGAAATAAGATTCACCGTCGTAGCTTCAATCT
1 GTCAGG-GAAGTAAGATTCGCCGTCGTAGCTTCAATCT
43536483 GTTCCACTAC
Statistics
Matches: 109, Mismatches: 25, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
49 4 0.04
50 105 0.96
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (50 bp):
GTCAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTATTTAACTGCAAT
Found at i:43536405 original size:100 final size:100
Alignment explanation
Indices: 43536301--43536535 Score: 328
Period size: 100 Copynumber: 2.4 Consensus size: 100
43536291 ATAACGTCAA
* * * * *
43536301 GGAAGTAAGATTCGCCGTTTTGGCTTCAATCTATTTGACTGCAATGTCAGG-GAACTAAGATTCG
1 GGAAGTAAGATTCGCTGTTGTGGCTTCAATCTATTTAACTGCAATGT-AGGAGAAATAAGATTCA
* * *
43536365 TCATCGTAGCTTCAATCTATTCAACTACACTGCTAG
65 CCATCGTAGCTTCAATCTATTCAACTACACCGCCAG
43536401 GGAAGTAAGATTCGCTGTTGTGGCTTCAATCTATTTAACTGCAATGTAGGAGAAATAAGATTCAC
1 GGAAGTAAGATTCGCTGTTGTGGCTTCAATCTATTTAACTGCAATGTAGGAGAAATAAGATTCAC
* * *
43536466 CGTCGTAGCTTCAATCTGTTCCACTACACCGCCAG
66 CATCGTAGCTTCAATCTATTCAACTACACCGCCAG
* * *
43536501 GGAAATAAGATTCACTGTTGTGGCTTTAATCTATT
1 GGAAGTAAGATTCGCTGTTGTGGCTTCAATCTATT
43536536 CCACTCTAAT
Statistics
Matches: 120, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
99 3 0.03
100 117 0.98
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (100 bp):
GGAAGTAAGATTCGCTGTTGTGGCTTCAATCTATTTAACTGCAATGTAGGAGAAATAAGATTCAC
CATCGTAGCTTCAATCTATTCAACTACACCGCCAG
Found at i:43536506 original size:50 final size:50
Alignment explanation
Indices: 43536323--43536536 Score: 178
Period size: 50 Copynumber: 4.3 Consensus size: 50
43536313 CGCCGTTTTG
** * * * * ** *
43536323 GCTTCAATCTATTTGACTGCAATGTCAGGGAACTAAGATTCGTCATCGTA
1 GCTTCAATCTATTCAACTACACTGCCAGGGAAATAAGATTCACCGTCGTA
* * * * * *
43536373 GCTTCAATCTATTCAACTACACTGCTAGGGAAGTAAGATTCGCTGTTGTG
1 GCTTCAATCTATTCAACTACACTGCCAGGGAAATAAGATTCACCGTCGTA
* * * *
43536423 GCTTCAATCTATTTAACTGCAATG-TAGGAGAAATAAGATTCACCGTCGTA
1 GCTTCAATCTATTCAACTACACTGCCAGG-GAAATAAGATTCACCGTCGTA
* * * * * *
43536473 GCTTCAATCTGTTCCACTACACCGCCAGGGAAATAAGATTCACTGTTGTG
1 GCTTCAATCTATTCAACTACACTGCCAGGGAAATAAGATTCACCGTCGTA
*
43536523 GCTTTAATCTATTC
1 GCTTCAATCTATTC
43536537 CACTCTAATG
Statistics
Matches: 130, Mismatches: 32, Indels: 4
0.78 0.19 0.02
Matches are distributed among these distances:
49 4 0.03
50 123 0.95
51 3 0.02
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (50 bp):
GCTTCAATCTATTCAACTACACTGCCAGGGAAATAAGATTCACCGTCGTA
Found at i:43536540 original size:50 final size:50
Alignment explanation
Indices: 43536373--43536536 Score: 195
Period size: 50 Copynumber: 3.3 Consensus size: 50
43536363 CGTCATCGTA
* *
43536373 GCTTCAATCTATTCAACTACACTGCTAGGGAAGTAAGATTCGCTGTTGTG
1 GCTTCAATCTATTCAACTACACTGCTAGGGAAATAAGATTCACTGTTGTG
* * * * * *
43536423 GCTTCAATCTATTTAACTGCAATG-TAGGAGAAATAAGATTCACCGTCGTA
1 GCTTCAATCTATTCAACTACACTGCTAGG-GAAATAAGATTCACTGTTGTG
* * * *
43536473 GCTTCAATCTGTTCCACTACACCGCCAGGGAAATAAGATTCACTGTTGTG
1 GCTTCAATCTATTCAACTACACTGCTAGGGAAATAAGATTCACTGTTGTG
*
43536523 GCTTTAATCTATTC
1 GCTTCAATCTATTC
43536537 CACTCTAATG
Statistics
Matches: 92, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
49 4 0.04
50 85 0.92
51 3 0.03
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (50 bp):
GCTTCAATCTATTCAACTACACTGCTAGGGAAATAAGATTCACTGTTGTG
Found at i:43539650 original size:9 final size:9
Alignment explanation
Indices: 43539631--43539663 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
43539621 ATGCAAAGCT
43539631 AATGC-ATG
1 AATGCAATG
43539639 AATGCAATG
1 AATGCAATG
*
43539648 AATGCCATG
1 AATGCAATG
43539657 AATGCAA
1 AATGCAA
43539664 AAGAAGAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 5 0.23
9 17 0.77
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.21
Consensus pattern (9 bp):
AATGCAATG
Found at i:43541616 original size:3 final size:3
Alignment explanation
Indices: 43541608--43541637 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
43541598 TGATCAAGAA
43541608 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
43541638 GAAAAGATAA
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):
AAT
Found at i:43542605 original size:23 final size:22
Alignment explanation
Indices: 43542575--43542641 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
43542565 AAATTAAATC
*
43542575 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTGC-AAATCATATCT
*
43542598 TCTAAGATTGCAGATCATATCT
1 TCTAAGATTGCAAATCATATCT
* *
43542620 TTTAAGATTGCATATCATATCT
1 TCTAAGATTGCAAATCATATCT
43542642 AAGATTGCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 30 0.75
23 10 0.25
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (22 bp):
TCTAAGATTGCAAATCATATCT
Found at i:43542635 original size:17 final size:17
Alignment explanation
Indices: 43542613--43542664 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
43542603 GATTGCAGAT
43542613 CATATCTTTTAAGATTG
1 CATATCTTTTAAGATTG
*
43542630 CATATCATATCTAAGATTG
1 CATATC-T-TTTAAGATTG
* *
43542649 CATATCCTTGAAGATT
1 CATATCTTTTAAGATT
43542665 ATGTTTCCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
17 13 0.45
18 1 0.03
19 15 0.52
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (17 bp):
CATATCTTTTAAGATTG
Found at i:43542646 original size:19 final size:19
Alignment explanation
Indices: 43542598--43542654 Score: 78
Period size: 22 Copynumber: 2.8 Consensus size: 19
43542588 AATCATATCT
*
43542598 TCTAAGATTGCAGATCATA
1 TCTAAGATTGCATATCATA
43542617 TCTTTTAAGATTGCATATCATA
1 TC---TAAGATTGCATATCATA
43542639 TCTAAGATTGCATATC
1 TCTAAGATTGCATATC
43542655 CTTGAAGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
19 16 0.47
22 18 0.53
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.39
Consensus pattern (19 bp):
TCTAAGATTGCATATCATA
Found at i:43543903 original size:33 final size:33
Alignment explanation
Indices: 43543866--43543943 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 33
43543856 TGGCCCTGCC
*** *
43543866 ATGGTCTTACATTCATTGTGCCATAACCCAGTT
1 ATGGTCTTACATTCAAAATGCCATAACCCAGCT
* *
43543899 ATGGTCTTATCA-TCAAAATGTCATAGCCCAGCT
1 ATGGTCTTA-CATTCAAAATGCCATAACCCAGCT
43543932 ATGGTCTTACAT
1 ATGGTCTTACAT
43543944 ATAAACACTG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
32 2 0.05
33 33 0.89
34 2 0.05
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (33 bp):
ATGGTCTTACATTCAAAATGCCATAACCCAGCT
Found at i:43544025 original size:101 final size:101
Alignment explanation
Indices: 43543818--43544079 Score: 348
Period size: 101 Copynumber: 2.6 Consensus size: 101
43543808 GTTTCTTTTG
* * * * * ** * *
43543818 TGCCATAGTCCAACTATGGTCTTACATAT--GCATTGCCATGGCCCTGCCATGGTCTTACATTCA
1 TGCCATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTCCA
* * *
43543881 TTGTGCCATAACCCAGTTATGGTCTTATCATCAAAA
66 TAGTGCCATAACCCACTTATGATCTTATCATCAAAA
* * *
43543917 TGTCATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATAGTCCTACGTCCA
1 TGCCATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTCCA
* *
43543982 TAGTGTCATAACCCACTTATGATCTTATCATCAGAA
66 TAGTGCCATAACCCACTTATGATCTTATCATCAAAA
*
43544018 TGCCATAGCTCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGT
1 TGCCATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGT
43544080 TTGAATAATT
Statistics
Matches: 140, Mismatches: 21, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
99 26 0.19
101 114 0.81
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (101 bp):
TGCCATAGCCCAGCTATGGTCTTACATATAAACACTGCCATGGTCCAACCATGGTCTTACGTCCA
TAGTGCCATAACCCACTTATGATCTTATCATCAAAA
Found at i:43545943 original size:111 final size:111
Alignment explanation
Indices: 43545745--43545961 Score: 371
Period size: 111 Copynumber: 2.0 Consensus size: 111
43545735 TCCCGAAAGC
43545745 TTTATAACCAATACTTCTCCCTAACAGTCTAAATACCACTACATTCTCCATACTCTTGTCAATCA
1 TTTATAACCAATACTTCTCCCTAACAGTCTAAATACCACTACATTCTCCATACTCTTGTCAATCA
* *
43545810 AACTGTGAACTCTATCAAGAAACCTAATCTCGAGATATGGGACAGG
66 AACTATGAACACTATCAAGAAACCTAATCTCGAGATATGGGACAGG
*
43545856 TTTATAACCAATACTTCTCCCTAACAGTCTAAATACTACTACATTCTCCATACTCTTGTCAATCA
1 TTTATAACCAATACTTCTCCCTAACAGTCTAAATACCACTACATTCTCCATACTCTTGTCAATCA
* * * *
43545921 ACCTATGAACACTCTTAGGAAACCTAATCTCGAGATATGGG
66 AACTATGAACACTATCAAGAAACCTAATCTCGAGATATGGG
43545962 CCCTCCTTAG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 99 1.00
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (111 bp):
TTTATAACCAATACTTCTCCCTAACAGTCTAAATACCACTACATTCTCCATACTCTTGTCAATCA
AACTATGAACACTATCAAGAAACCTAATCTCGAGATATGGGACAGG
Found at i:43547347 original size:5 final size:5
Alignment explanation
Indices: 43547339--43547377 Score: 78
Period size: 5 Copynumber: 7.8 Consensus size: 5
43547329 AGTTAAATCT
43547339 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
43547378 TACCAAATCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 34 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTTA
Found at i:43548678 original size:5 final size:5
Alignment explanation
Indices: 43548668--43548725 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
43548658 ATATACTAAA
* * *
43548668 ATATG ATATG ATATGAG ATATG ACATA ATATG ATATG AAATCTG ATATG
1 ATATG ATATG ATAT--G ATATG ATATG ATATG ATATG --ATATG ATATG
43548717 ATATG ATAT
1 ATATG ATAT
43548726 TTTATAAGTT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 34 0.79
7 9 0.21
ACGTcount: A:0.43, C:0.03, G:0.17, T:0.36
Consensus pattern (5 bp):
ATATG
Found at i:43548701 original size:22 final size:22
Alignment explanation
Indices: 43548673--43548725 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
43548663 CTAAAATATG
*
43548673 ATATGATATGAGATATGACATA
1 ATATGATATGAAATATGACATA
* * *
43548695 ATATGATATGAAATCTGATATG
1 ATATGATATGAAATATGACATA
43548717 ATATGATAT
1 ATATGATAT
43548726 TTTATAAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.43, C:0.04, G:0.17, T:0.36
Consensus pattern (22 bp):
ATATGATATGAAATATGACATA
Found at i:43548714 original size:27 final size:27
Alignment explanation
Indices: 43548647--43548717 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
43548637 ATAGGGGTAG
43548647 GATATGAAA-CGATAT-ACTAAAATAT
1 GATATGAAATCGATATGACTAAAATAT
* * *
43548672 GATATGATATGAGATATGAC-ATAATAT
1 GATATGAAAT-CGATATGACTAAAATAT
43548699 GATATGAAATCTGATATGA
1 GATATGAAATC-GATATGA
43548718 TATGATATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
25 8 0.22
27 27 0.73
28 2 0.05
ACGTcount: A:0.46, C:0.06, G:0.17, T:0.31
Consensus pattern (27 bp):
GATATGAAATCGATATGACTAAAATAT
Found at i:43552840 original size:13 final size:13
Alignment explanation
Indices: 43552816--43552841 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
43552806 ACAGATATAC
43552816 AAATGTCATATTA
1 AAATGTCATATTA
43552829 AAATGTCATATTA
1 AAATGTCATATTA
43552842 CCAGAAACAT
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:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
AAATGTCATATTA
Found at i:43552873 original size:18 final size:18
Alignment explanation
Indices: 43552852--43552917 Score: 50
Period size: 18 Copynumber: 3.8 Consensus size: 18
43552842 CCAGAAACAT
43552852 ATATCAGATCAGAATGTC
1 ATATCAGATCAGAATGTC
** *
43552870 ATAT--TTTCA-AAAG-C
1 ATATCAGATCAGAATGTC
*
43552884 ATATGTCAGATCAAAATGTC
1 ATA--TCAGATCAGAATGTC
43552904 ATATCAGATCAGAA
1 ATATCAGATCAGAA
43552918 CAAATCCTAC
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
14 4 0.11
15 3 0.09
16 4 0.11
18 17 0.49
19 3 0.09
20 4 0.11
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.29
Consensus pattern (18 bp):
ATATCAGATCAGAATGTC
Found at i:43552873 original size:34 final size:34
Alignment explanation
Indices: 43552828--43552907 Score: 108
Period size: 34 Copynumber: 2.4 Consensus size: 34
43552818 ATGTCATATT
43552828 AAAATGTCATATTACCAGAAA-CATATATCAGATC
1 AAAATGTCATATTACCA-AAAGCATATATCAGATC
* ** *
43552862 AGAATGTCATATTTTCAAAAGCATATGTCAGATC
1 AAAATGTCATATTACCAAAAGCATATATCAGATC
43552896 AAAATGTCATAT
1 AAAATGTCATAT
43552908 CAGATCAGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
33 3 0.08
34 37 0.93
ACGTcount: A:0.44, C:0.15, G:0.11, T:0.30
Consensus pattern (34 bp):
AAAATGTCATATTACCAAAAGCATATATCAGATC
Found at i:43564242 original size:3 final size:3
Alignment explanation
Indices: 43564234--43564283 Score: 57
Period size: 3 Copynumber: 17.0 Consensus size: 3
43564224 AGAATTTTTC
* * * *
43564234 TCT TCT TCT TCT CCT T-T TCT TTT TCT TCT TTT TCT TCT TCT TCC TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
43564281 TCT
1 TCT
43564284 CTTTTTTCTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:43564264 original size:9 final size:9
Alignment explanation
Indices: 43564228--43564295 Score: 52
Period size: 9 Copynumber: 7.4 Consensus size: 9
43564218 CACTCTAGAA
43564228 TTTTTC-TC
1 TTTTTCTTC
*
43564236 TTCTTCTTC
1 TTTTTCTTC
**
43564245 TCCTT-TTC
1 TTTTTCTTC
43564253 TTTTTCTTC
1 TTTTTCTTC
43564262 TTTTTCTTC
1 TTTTTCTTC
43564271 TTCTTCCTCTTC
1 TT-TT--TCTTC
43564283 TCTTTT-TTC
1 T-TTTTCTTC
43564292 TTTT
1 TTTT
43564296 ACTGCCCAAC
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
8 14 0.28
9 24 0.48
10 3 0.06
12 8 0.16
13 1 0.02
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (9 bp):
TTTTTCTTC
Found at i:43566261 original size:50 final size:50
Alignment explanation
Indices: 43566200--43566391 Score: 269
Period size: 50 Copynumber: 3.9 Consensus size: 50
43566190 GATAATAACA
* * ** *
43566200 TGCCAAAGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCGG
*
43566250 TGCCAGCGCCATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCGG
* * *
43566300 TGCCAACTCTATGTCCCAAACATGGTCTTACATGAGACCTCTTATCTCGG
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCGG
* * *
43566350 TGCCAATGCCATGTCCCAGACAT-GTCTTACATGAGACCTCTT
1 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTT
43566392 TACCCAAATT
Statistics
Matches: 128, Mismatches: 14, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
49 19 0.15
50 109 0.85
ACGTcount: A:0.22, C:0.31, G:0.20, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTTATCTCGG
Found at i:43580870 original size:13 final size:13
Alignment explanation
Indices: 43580854--43580878 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43580844 AATTATAAAT
43580854 GTAAATAAAATAA
1 GTAAATAAAATAA
43580867 GTAAATAAAATA
1 GTAAATAAAATA
43580879 CCAAAATGAA
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:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
GTAAATAAAATAA
Found at i:43588100 original size:22 final size:23
Alignment explanation
Indices: 43588074--43588117 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
43588064 CATCACAATA
*
43588074 GTATCCCCACATTCACA-GTTTT
1 GTATCCCCACATGCACATGTTTT
43588096 GTATCCCCACATGCACATGTTT
1 GTATCCCCACATGCACATGTTT
43588118 ACATATGACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.23, C:0.32, G:0.11, T:0.34
Consensus pattern (23 bp):
GTATCCCCACATGCACATGTTTT
Found at i:43588406 original size:41 final size:41
Alignment explanation
Indices: 43588321--43588419 Score: 117
Period size: 41 Copynumber: 2.4 Consensus size: 41
43588311 TGTGGGCATG
* ** * *
43588321 TTTGCAGATAAACTACCACTAGGCTGTGGGTGGACAACATA
1 TTTGCAGATAAACTGCCACTAGGCTGTGAATGCACAACAAA
* * *
43588362 TTTGCAGATAAACTGCCACTAGGTTGTGAATGCATAGCAAA
1 TTTGCAGATAAACTGCCACTAGGCTGTGAATGCACAACAAA
*
43588403 TTTGTAGATAAACTGCC
1 TTTGCAGATAAACTGCC
43588420 TTTTTTGTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.27
Consensus pattern (41 bp):
TTTGCAGATAAACTGCCACTAGGCTGTGAATGCACAACAAA
Found at i:43592989 original size:5 final size:5
Alignment explanation
Indices: 43592979--43593012 Score: 61
Period size: 5 Copynumber: 7.0 Consensus size: 5
43592969 TGATTTAATT
43592979 ATTAA ATTAA ATTAA ATTAA ATTAA ATT-A ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
43593013 CTAATTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 24 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (5 bp):
ATTAA
Found at i:43592999 original size:15 final size:14
Alignment explanation
Indices: 43592975--43593012 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
43592965 AAAATGATTT
43592975 AATT-ATTAAATTA
1 AATTAATTAAATTA
43592988 AATTAAATTAAATTA
1 AATT-AATTAAATTA
43593003 AATTAATTAA
1 AATTAATTAA
43593013 CTAATTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 4 0.17
14 6 0.26
15 13 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
AATTAATTAAATTA
Found at i:43593063 original size:17 final size:18
Alignment explanation
Indices: 43593041--43593077 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
43593031 AATAGAAAAT
43593041 AATTAT-AGGGTTGGATA
1 AATTATAAGGGTTGGATA
*
43593058 AATTATAAGTGTTGGATA
1 AATTATAAGGGTTGGATA
43593076 AA
1 AA
43593078 AGTCCAAACA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.35
Consensus pattern (18 bp):
AATTATAAGGGTTGGATA
Found at i:43601573 original size:20 final size:21
Alignment explanation
Indices: 43601540--43601586 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
43601530 TTTAAGATTA
*
43601540 TAAAAAATATAAAAA-TA-TT
1 TAAAAAATAGAAAAATTATTT
43601559 TAAAATAATAGAAAAATTATTT
1 TAAAA-AATAGAAAAATTATTT
43601581 TAAAAA
1 TAAAAA
43601587 TTATAATAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.21
20 9 0.38
21 3 0.12
22 7 0.29
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (21 bp):
TAAAAAATAGAAAAATTATTT
Found at i:43601662 original size:20 final size:21
Alignment explanation
Indices: 43601629--43601683 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 21
43601619 AAATTTATTT
*
43601629 AAAATAGTATAAAATCACAAA
1 AAAATATTATAAAATCACAAA
* *
43601650 AAAATATTA-AAAATTACAAG
1 AAAATATTATAAAATCACAAA
*
43601670 AAAATATTCTAAAA
1 AAAATATTATAAAA
43601684 AATTCTCTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.24
Consensus pattern (21 bp):
AAAATATTATAAAATCACAAA
Found at i:43602485 original size:16 final size:16
Alignment explanation
Indices: 43602409--43602487 Score: 65
Period size: 16 Copynumber: 4.9 Consensus size: 16
43602399 ATGTATAATA
*
43602409 AAACAAAATA-AAAAGA
1 AAAC-AAATAGAAAAGG
*
43602425 AAAGAAATAGTAAAA-G
1 AAACAAATAG-AAAAGG
*
43602441 AAACAAGATAG-AAACG
1 AAACAA-ATAGAAAAGG
43602457 AAACAGAATAGAAAAGG
1 AAACA-AATAGAAAAGG
*
43602474 AAACAAAAAGAAAA
1 AAACAAATAGAAAA
43602488 AGGGAAAAAG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
15 8 0.15
16 26 0.50
17 18 0.35
ACGTcount: A:0.72, C:0.06, G:0.15, T:0.06
Consensus pattern (16 bp):
AAACAAATAGAAAAGG
Found at i:43607256 original size:16 final size:17
Alignment explanation
Indices: 43607227--43607264 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
43607217 CATAAAAATA
*
43607227 AAATTAATAAAAATTT-
1 AAATTAACAAAAATTTG
*
43607243 AAATTAACACAAATTTG
1 AAATTAACAAAAATTTG
43607260 AAATT
1 AAATT
43607265 GAAATTCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.58, C:0.05, G:0.03, T:0.34
Consensus pattern (17 bp):
AAATTAACAAAAATTTG
Found at i:43608531 original size:53 final size:53
Alignment explanation
Indices: 43608473--43608589 Score: 182
Period size: 53 Copynumber: 2.2 Consensus size: 53
43608463 CACTAAAATA
* * *
43608473 AATTAA-ATTAAATTAAATAAAAGTTAGAATATTATCTAGGTCGTTCGTCTTTC
1 AATTAATATTAAA-TAAATAAAAGTTAGAACATTATCTAGATCATTCGTCTTTC
*
43608526 AATTAATATTAAATAAATAAAAGTTTGAACATTATCTAGATCATTCGTCTTTC
1 AATTAATATTAAATAAATAAAAGTTAGAACATTATCTAGATCATTCGTCTTTC
43608579 AATTAATATTA
1 AATTAATATTA
43608590 TTTTGCAGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
53 53 0.90
54 6 0.10
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (53 bp):
AATTAATATTAAATAAATAAAAGTTAGAACATTATCTAGATCATTCGTCTTTC
Found at i:43612296 original size:18 final size:18
Alignment explanation
Indices: 43612263--43612315 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
43612253 ATTCACCTAA
*
43612263 ACCCAATCCAAACCCAAGT
1 ACCCAA-CCCAACCCAAGT
** *
43612282 ATTCAACCCAACCCAATT
1 ACCCAACCCAACCCAAGT
43612300 ACCCAACCCAACCCAA
1 ACCCAACCCAACCCAA
43612316 TCATAAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.42, C:0.45, G:0.02, T:0.11
Consensus pattern (18 bp):
ACCCAACCCAACCCAAGT
Found at i:43612439 original size:9 final size:9
Alignment explanation
Indices: 43612419--43612458 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
43612409 GTAGTGATTC
43612419 AATTCGGTT
1 AATTCGGTT
* *
43612428 AATTTGGGT
1 AATTCGGTT
43612437 AATTCGGTT
1 AATTCGGTT
43612446 AATTCGGTT
1 AATTCGGTT
43612455 AATT
1 AATT
43612459 TTTAACCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Done.