Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold424
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: 270792
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.33
Warning! 10530 characters in sequence are not A, C, G, or T
Found at i:970 original size:14 final size:15
Alignment explanation
Indices: 953--985 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
943 ACCTTGATGT
953 ATGATAT-AGTTAAA
1 ATGATATAAGTTAAA
*
967 ATGATATAATTTAAA
1 ATGATATAAGTTAAA
982 ATGA
1 ATGA
986 ATTTGTAGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (15 bp):
ATGATATAAGTTAAA
Found at i:1057 original size:17 final size:17
Alignment explanation
Indices: 1027--1063 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1017 ATGAAGAAAT
*
1027 ATTATAATAGTAATAAC
1 ATTATAATAATAATAAC
*
1044 ATTATTATAATAATAAC
1 ATTATAATAATAATAAC
1061 ATT
1 ATT
1064 GACATTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (17 bp):
ATTATAATAATAATAAC
Found at i:1192 original size:30 final size:29
Alignment explanation
Indices: 1151--1218 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 29
1141 ATGATTTTTT
* * *
1151 AAAAA-AAATAAACATATCATGAAAATATC
1 AAAAATAAATAAACAAATAAT-AAAATAAC
*
1180 AAAAATAAATAAAGAAATAATAAAATAAC
1 AAAAATAAATAAACAAATAATAAAATAAC
1209 AATAAATAAA
1 AA-AAATAAA
1219 AATAATATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.72, C:0.06, G:0.03, T:0.19
Consensus pattern (29 bp):
AAAAATAAATAAACAAATAATAAAATAAC
Found at i:1648 original size:15 final size:15
Alignment explanation
Indices: 1628--1666 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
1618 TAAAATTTCA
1628 TCCAAATTAAAAACT
1 TCCAAATTAAAAACT
1643 TCCAAATTAAAAACT
1 TCCAAATTAAAAACT
*
1658 TTCAAATTA
1 TCCAAATTA
1667 TTATCTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (15 bp):
TCCAAATTAAAAACT
Found at i:4085 original size:21 final size:22
Alignment explanation
Indices: 4043--4085 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
4033 TTCATGACAA
*
4043 AAACAAAGAGAAACACTTACCG
1 AAACAAAGAGAAACACTAACCG
*
4065 AAACAAAGA-AAGCACTAACCG
1 AAACAAAGAGAAACACTAACCG
4086 CGTGCGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.56, C:0.23, G:0.14, T:0.07
Consensus pattern (22 bp):
AAACAAAGAGAAACACTAACCG
Found at i:5374 original size:51 final size:50
Alignment explanation
Indices: 5243--5665 Score: 388
Period size: 51 Copynumber: 8.8 Consensus size: 50
5233 AGGGTTTGTC
* * *
5243 GCTTTAATCTGCTCCACTACAATTTCAGAGAAAT-A-ATAT-T-A--GTA
1 GCTTTAATCTGCTCCACTACAACTTCAGGGAAATAAGATTTGTAACTGTA
* ** * *
5287 GCTTTAATCTGCTCCATTGTAATTTTCA-GGAGATAAGATTTGTAACTCGTA
1 GCTTTAATCTGCTCCACTACAA-CTTCAGGGAAATAAGATTTGTAACT-GTA
* *
5338 GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTG--A---TA
1 GCTTTAATCTGCTCCACTACAACTTCAGGGAAATAAGATTTGTAACTGTA
* * *
5383 TCTTTAATCTGCTCCGCTACAACTTCAGGGAGATAAGATTTGTAACTTGTA
1 GCTTTAATCTGCTCCACTACAACTTCAGGGAAATAAGATTTGTAAC-TGTA
* *
5434 GCTTTAATCTGCTCCACTACAACTTTAGAGAAATAAGA--T-T-A--GTA
1 GCTTTAATCTGCTCCACTACAACTTCAGGGAAATAAGATTTGTAACTGTA
* ** *
5478 GCTTTAATCTGCTCCACTATAACTTTTGGGAGATAAGATTTGTAACTCGTA
1 GCTTTAATCTGCTCCACTACAACTTCAGGGAAATAAGATTTGTAACT-GTA
* *
5529 GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTG--A---TA
1 GCTTTAATCTGCTCCACTACAACTTCAGGGAAATAAGATTTGTAACTGTA
* * *
5574 TCTTTAATCTGCTCCTCTACAACTTCAGGGAGATAAGATTTGTAACTTGTA
1 GCTTTAATCTGCTCCACTACAACTTCAGGGAAATAAGATTTGTAAC-TGTA
* * * *
5625 GCTTTAATCTGTTCCATTGCAACTGCAGGGAAATAAGATTT
1 GCTTTAATCTGCTCCACTACAACTTCAGGGAAATAAGATTT
5666 TCTATCTTTA
Statistics
Matches: 308, Mismatches: 43, Indels: 49
0.77 0.11 0.12
Matches are distributed among these distances:
44 60 0.19
45 84 0.27
46 4 0.01
47 5 0.02
48 3 0.01
49 3 0.01
50 4 0.01
51 145 0.47
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (50 bp):
GCTTTAATCTGCTCCACTACAACTTCAGGGAAATAAGATTTGTAACTGTA
Found at i:5435 original size:96 final size:95
Alignment explanation
Indices: 5238--5713 Score: 621
Period size: 96 Copynumber: 5.0 Consensus size: 95
5228 GGTACAGGGT
* * * * * * * *
5238 TTGTCGCTTTAATCTGCTCCACTACAATTTCAGAGAAATAATATTAGTAGCTTTAATCTGCTCCA
1 TTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGTATCTTTAATCTGCTCCA
* * *
5303 TTGTAATTTTCA-GGAGATAAGATTTGTAAC
66 CTATAA-CTTCAGGGAGATAAGATTTGTAAC
*
5333 TCGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGATATCTTTAATCTGCTCC
1 TTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTG-TATCTTTAATCTGCTCC
* *
5398 GCTACAACTTCAGGGAGATAAGATTTGTAAC
65 ACTATAACTTCAGGGAGATAAGATTTGTAAC
* * * * * *
5429 TTGTAGCTTTAATCTGCTCCACTACAACTTTAGAGAAATAAGATTAGTAGCTTTAATCTGCTCCA
1 TTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGTATCTTTAATCTGCTCCA
**
5494 CTATAACTTTTGGGAGATAAGATTTGTAAC
66 CTATAACTTCAGGGAGATAAGATTTGTAAC
*
5524 TCGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGATATCTTTAATCTGCTCC
1 TTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTG-TATCTTTAATCTGCTCC
* *
5589 TCTACAACTTCAGGGAGATAAGATTTGTAAC
65 ACTATAACTTCAGGGAGATAAGATTTGTAAC
* * * *
5620 TTGTAGCTTTAATCTGTTCCATTGCAACTGCAGGGAAATAAGATTTTCTATCTTTAATCTGCTCT
1 TTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGA-TTTGTATCTTTAATCTGCTCC
* * *
5685 GCTGTAACTTCAAGGAGATAAGATTTGTA
65 ACTATAACTTCAGGGAGATAAGATTTGTA
5714 GCTTCAATCT
Statistics
Matches: 332, Mismatches: 45, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
95 127 0.38
96 202 0.61
97 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (95 bp):
TTGTAGCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTTGTATCTTTAATCTGCTCCA
CTATAACTTCAGGGAGATAAGATTTGTAAC
Found at i:5502 original size:44 final size:45
Alignment explanation
Indices: 5243--5842 Score: 435
Period size: 44 Copynumber: 12.9 Consensus size: 45
5233 AGGGTTTGTC
* * * *
5243 GCTTTAATCTGCTCCACTACAATTTCAGAGAAATAATA-TTAGTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTAGTA
* * * *
5287 GCTTTAATCTGCTCCATTGTAATTTTCA-GGAGATAAGATTTGTAACTCGTA
1 GCTTTAATCTGCTCCACTGCAA-CTTCAGGGAAATAAGA-TT-T-A---GTA
*
5338 GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTT-GATA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTAG-TA
* * * *
5383 TCTTTAATCTGCTCCGCTACAACTTCAGGGAGATAAGATTTGTAACTTGTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TT-T-A---GTA
* * *
5434 GCTTTAATCTGCTCCACTACAACTTTAGAGAAATAAGA-TTAGTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTAGTA
** ** *
5478 GCTTTAATCTGCTCCACTATAACTTTTGGGAGATAAGATTTGTAACTCGTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TT-T-A---GTA
*
5529 GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTT-GATA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTAG-TA
* * * *
5574 TCTTTAATCTGCTCCTCTACAACTTCAGGGAGATAAGATTTGTAACTTGTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGA-TT-T-A---GTA
* * * **
5625 GCTTTAATCTGTTCCATTGCAACTGCAGGGAAATAAGATTTTCTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTAGTA
* ** * * *
5670 TCTTTAATCTGCTCTGCTGTAACTTCAAGGAGATAAGATTT-GTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTAGTA
* * ** * * *
5714 GCTTCAATCTACTCTGCTGCAATTTTAGGGAGATAAGATTTA-TA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTAGTA
* *
5758 GCTTCAATCTACTCCACTGCAACTTCA-GGAAGATAAGATTT-GTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAA-ATAAGATTTAGTA
* * * *
5802 GTTTTAATCTGCTCCATTGCAAATTCAGGGAGATAAGATTT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTT
5843 GCCACGATGA
Statistics
Matches: 447, Mismatches: 73, Indels: 72
0.76 0.12 0.12
Matches are distributed among these distances:
43 3 0.01
44 168 0.38
45 112 0.25
46 6 0.01
47 5 0.01
48 3 0.01
49 4 0.01
50 10 0.02
51 134 0.30
52 2 0.00
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (45 bp):
GCTTTAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTAGTA
Found at i:5567 original size:191 final size:191
Alignment explanation
Indices: 5238--5713 Score: 740
Period size: 191 Copynumber: 2.5 Consensus size: 191
5228 GGTACAGGGT
* *
5238 TTGTCGCTTTAATCTGCTCCACTACAA-TTTCAGAGAAATAATATTAGTAGCTTTAATCTGCTCC
1 TTGTAGCTTTAATCTGCTCCACTACAACTTT-AGAGAAATAAGATTAGTAGCTTTAATCTGCTCC
*
5302 ATTGTAA-TTTTCAGGAGATAAGATTTGTAACTCGTAGCTTTAATCTGTTCCACTGCAACTTCAG
65 ACTGTAACTTTT-AGGAGATAAGATTTGTAACTCGTAGCTTTAATCTGTTCCACTGCAACTTCAG
5366 GGAAATAAGATTTGATATCTTTAATCTGCTCCGCTACAACTTCAGGGAGATAAGATTTGTAAC
129 GGAAATAAGATTTGATATCTTTAATCTGCTCCGCTACAACTTCAGGGAGATAAGATTTGTAAC
5429 TTGTAGCTTTAATCTGCTCCACTACAACTTTAGAGAAATAAGATTAGTAGCTTTAATCTGCTCCA
1 TTGTAGCTTTAATCTGCTCCACTACAACTTTAGAGAAATAAGATTAGTAGCTTTAATCTGCTCCA
* *
5494 CTATAACTTTTGGGAGATAAGATTTGTAACTCGTAGCTTTAATCTGTTCCACTGCAACTTCAGGG
66 CTGTAACTTTTAGGAGATAAGATTTGTAACTCGTAGCTTTAATCTGTTCCACTGCAACTTCAGGG
*
5559 AAATAAGATTTGATATCTTTAATCTGCTCCTCTACAACTTCAGGGAGATAAGATTTGTAAC
131 AAATAAGATTTGATATCTTTAATCTGCTCCGCTACAACTTCAGGGAGATAAGATTTGTAAC
* * * ** * ** * *
5620 TTGTAGCTTTAATCTGTTCCATTGCAACTGCAGGGAAATAAGATTTTCTATCTTTAATCTGCTCT
1 TTGTAGCTTTAATCTGCTCCACTACAACTTTAGAGAAATAAGA-TTAGTAGCTTTAATCTGCTCC
* **
5685 GCTGTAACTTCAAGGAGATAAGATTTGTA
65 ACTGTAACTTTTAGGAGATAAGATTTGTA
5714 GCTTCAATCT
Statistics
Matches: 261, Mismatches: 21, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
191 213 0.82
192 48 0.18
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.36
Consensus pattern (191 bp):
TTGTAGCTTTAATCTGCTCCACTACAACTTTAGAGAAATAAGATTAGTAGCTTTAATCTGCTCCA
CTGTAACTTTTAGGAGATAAGATTTGTAACTCGTAGCTTTAATCTGTTCCACTGCAACTTCAGGG
AAATAAGATTTGATATCTTTAATCTGCTCCGCTACAACTTCAGGGAGATAAGATTTGTAAC
Found at i:15759 original size:17 final size:17
Alignment explanation
Indices: 15729--15765 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
15719 ATGAAGAAAT
*
15729 ATTATAATAGTAATAAC
1 ATTATAATAATAATAAC
*
15746 ATTATTATAATAATAAC
1 ATTATAATAATAATAAC
15763 ATT
1 ATT
15766 GACATTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (17 bp):
ATTATAATAATAATAAC
Found at i:15915 original size:30 final size:29
Alignment explanation
Indices: 15871--15930 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 29
15861 ACATATCATG
*
15871 AAAATATCAAAAATAAATAAT-AAAATAAT
1 AAAATAACAAAAATAAA-AATAAAAATAAT
15900 AAAATAACAAGAAATAAAAATAAAAATAAT
1 AAAATAACAA-AAATAAAAATAAAAATAAT
15930 A
1 A
15931 TAATGATGAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.75, C:0.03, G:0.02, T:0.20
Consensus pattern (29 bp):
AAAATAACAAAAATAAAAATAAAAATAAT
Found at i:16041 original size:12 final size:12
Alignment explanation
Indices: 16007--16041 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
15997 AGAAAAAAGT
16007 AATAAACAAATA
1 AATAAACAAATA
*
16019 AATGAACAAATA
1 AATAAACAAATA
*
16031 AATAAATAAAT
1 AATAAACAAAT
16042 CAACTTGTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (12 bp):
AATAAACAAATA
Found at i:16139 original size:141 final size:142
Alignment explanation
Indices: 15976--16258 Score: 550
Period size: 141 Copynumber: 2.0 Consensus size: 142
15966 AAGAATATAA
15976 ACAATTTAATTTTTAAGTGTAAGAAAAAAGTAATAAACAAATAAATGAACAAATAAATAAATAAA
1 ACAATTTAATTTTTAAGTGTAAGAAAAAAGTAATAAACAAATAAATGAACAAATAAATAAATAAA
16041 TCAACTTGTAGAAAGGTTGAAATTAAATAAATAGAGAGCTTAATTGAAATTTTAATGAAATTAAG
66 TCAACTTGTAGAAAGGTTGAAATTAAATAAATAGAGAGCTTAATTGAAATTTTAATGAAATTAAG
16106 GGGTATAAATTG
131 GGGTATAAATTG
16118 ACAATTTAA-TTTTAAGTGTAAGAAAAAAGTAATAAACAAATAAATGAACAAATAAATAAATAAA
1 ACAATTTAATTTTTAAGTGTAAGAAAAAAGTAATAAACAAATAAATGAACAAATAAATAAATAAA
*
16182 TCAACTTGTAGAAAGGTTGAAATTAAATAAATAGAGGGCTTAATTGAAATTTTAATGAAATTAAG
66 TCAACTTGTAGAAAGGTTGAAATTAAATAAATAGAGAGCTTAATTGAAATTTTAATGAAATTAAG
16247 GGGTATAAATTG
131 GGGTATAAATTG
16259 TAAATAAATA
Statistics
Matches: 140, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
141 131 0.94
142 9 0.06
ACGTcount: A:0.52, C:0.04, G:0.14, T:0.29
Consensus pattern (142 bp):
ACAATTTAATTTTTAAGTGTAAGAAAAAAGTAATAAACAAATAAATGAACAAATAAATAAATAAA
TCAACTTGTAGAAAGGTTGAAATTAAATAAATAGAGAGCTTAATTGAAATTTTAATGAAATTAAG
GGGTATAAATTG
Found at i:16182 original size:12 final size:12
Alignment explanation
Indices: 16148--16182 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
16138 AGAAAAAAGT
16148 AATAAACAAATA
1 AATAAACAAATA
*
16160 AATGAACAAATA
1 AATAAACAAATA
*
16172 AATAAATAAAT
1 AATAAACAAAT
16183 CAACTTGTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.20
Consensus pattern (12 bp):
AATAAACAAATA
Found at i:16652 original size:8 final size:9
Alignment explanation
Indices: 16631--16662 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
16621 AATCAAATGG
*
16631 AAAAAAAAG
1 AAAAAAAAT
16640 AAAAAAAAT
1 AAAAAAAAT
16649 AAAAAAAAT
1 AAAAAAAAT
16658 AAAAA
1 AAAAA
16663 TATGGCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.91, C:0.00, G:0.03, T:0.06
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:18984 original size:28 final size:30
Alignment explanation
Indices: 18949--19010 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
18939 TAATAATGGT
* *
18949 AAATTTTTAGTATAATTT-TTTAAAA-TATA
1 AAATTTTGA-TATAATTTATTAAAAATTATA
*
18978 AAATTTTGATTTAATTTATTAAAAATTATA
1 AAATTTTGATATAATTTATTAAAAATTATA
19008 AAA
1 AAA
19011 ATATAATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.25
29 14 0.50
30 7 0.25
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
AAATTTTGATATAATTTATTAAAAATTATA
Found at i:19020 original size:30 final size:28
Alignment explanation
Indices: 18961--19020 Score: 66
Period size: 30 Copynumber: 2.1 Consensus size: 28
18951 ATTTTTAGTA
* * * *
18961 TAATTTTTTAAAATATAAAATTTTGATT
1 TAATTTTTAAAAATATAAAAATATAATT
18989 TAATTTATTAAAAATTATAAAAATATAATT
1 TAATTT-TTAAAAA-TATAAAAATATAATT
19019 TA
1 TA
19021 TTAAAATGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 6 0.23
29 6 0.23
30 14 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (28 bp):
TAATTTTTAAAAATATAAAAATATAATT
Found at i:22111 original size:44 final size:44
Alignment explanation
Indices: 22063--22653 Score: 168
Period size: 44 Copynumber: 13.1 Consensus size: 44
22053 AAGGTATATG
*
22063 ATTTGTCACTTCAATCTGCTCTAATGCAACTTCAGCGAAATAA-A
1 ATTTGT-ACTTCAATCTGCTCCAATGCAACTTCAGCGAAATAAGA
* * * *
22107 ATTTGTAACTTCAATCTGCTCCACTGCAATTTCAGGGAGATAAGA
1 ATTTGT-ACTTCAATCTGCTCCAATGCAACTTCAGCGAAATAAGA
** * * * * * *
22152 A-TTGTAGCTTCAATCAACTCCATTACTACTTAAGGGAGATAAG-
1 ATTTGTA-CTTCAATCTGCTCCAATGCAACTTCAGCGAAATAAGA
* * * * * *
22195 ATTTGTAGCTTGTAGCTTTAATTTGTTCCACTACAACTTCAGAGAAATAGGA
1 ATTTGTA-C-T-T--C---AATCTGCTCCAATGCAACTTCAGCGAAATAAGA
* * * * * ** ** *
22247 CTCGCTATGGTAGATTTAATCTGAC-CCATTACAACTTCAAAGGTAT-AGG
1 AT---T-T-GTA-CTTCAATCTG-CTCCAATGCAACTTCAGCGAAATAAGA
* * * * *
22296 ATTTGTCGCTTCAATTTGCTCTATTGCAACTTCAGCGAGATAAG-
1 ATTTGT-ACTTCAATCTGCTCCAATGCAACTTCAGCGAAATAAGA
* * * *
22340 ATTTGTAGCTTCAATCTGCTCCACTGCAATTTCAGAGAGATAAG-
1 ATTTGTA-CTTCAATCTGCTCCAATGCAACTTCAGCGAAATAAGA
* * * *
22384 ATTTGTTGCTTCAATCTGCTCCACTGCTACTTCAAG-GAGATAAG-
1 ATTTG-TACTTCAATCTGCTCCAATGCAACTTC-AGCGAAATAAGA
* * * * * * * *
22428 ATCTGTAACTTTAATATGCTTCACTGCAACTTTAGGGAGATAAG-
1 ATTTGT-ACTTCAATCTGCTCCAATGCAACTTCAGCGAAATAAGA
* * * * *
22472 ATTTGTAACTTCAATATGCTCCACTGCCACTTCAGGGAGATAAG-
1 ATTTGT-ACTTCAATCTGCTCCAATGCAACTTCAGCGAAATAAGA
* * * * * *
22516 ATTTATAACTTCAATCTGCTCCATTGTAACTTTAGGGAGATAAG-
1 ATTTGT-ACTTCAATCTGCTCCAATGCAACTTCAGCGAAATAAGA
* * * * * *
22560 ATTTGTAACTCCAATTTGCTCCACTACAACTTCAGGGAGATAAG-
1 ATTTGT-ACTTCAATCTGCTCCAATGCAACTTCAGCGAAATAAGA
* * * * * *
22604 ATTTGTAGCCTC-ATCTTGCTCCATTGCATCTTTAGGGAGATAAG-
1 ATTTGTA-CTTCAATC-TGCTCCAATGCAACTTCAGCGAAATAAGA
22648 ATTTGT
1 ATTTGT
22654 TATATTCAAT
Statistics
Matches: 434, Mismatches: 86, Indels: 54
0.76 0.15 0.09
Matches are distributed among these distances:
43 9 0.02
44 358 0.82
45 9 0.02
46 2 0.00
48 1 0.00
49 2 0.00
50 22 0.05
51 22 0.05
52 1 0.00
55 2 0.00
56 2 0.00
57 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (44 bp):
ATTTGTACTTCAATCTGCTCCAATGCAACTTCAGCGAAATAAGA
Found at i:22290 original size:233 final size:233
Alignment explanation
Indices: 21898--22438 Score: 737
Period size: 233 Copynumber: 2.3 Consensus size: 233
21888 TCTACTTCGT
* * * * ** *
21898 TGCAACTTCAAAGAGATAAG-ATTCCTAGCTTTAATCTGCTCCACTGCTACTTCAAGGAGATAAG
1 TGCAATTTCAGAGAGATAAGAATT-GTAGCTTCAATCAACTCCACTACTACTTCAAGGAGATAAG
* * * *
21962 ATTTGTAACTTGTAACTTTATTCTGTTCCACTGCAACTTTAGGGAAATAAGACTCGTTATGGTAG
65 ATTTGTAACTTGTAACTTTATTCTGTTCCACTACAACTTCAGAGAAATAAGACTCGCTATGGTAG
* *
22027 ATTTAATCCGACCCACTGCAACTCCAAAGGTATATGATTTGTCACTTCAATCTGCTCTAATGCAA
130 ATTTAATCCGACCCACTACAACTCCAAAGGTATAGGATTTGTCACTTCAATCTGCTCTAATGCAA
22092 CTTCAGCGAAATAAAATTTGTAACTTCAATCTGCTCCAC
195 CTTCAGCGAAATAAAATTTGTAACTTCAATCTGCTCCAC
* *
22131 TGCAATTTCAGGGAGATAAGAATTGTAGCTTCAATCAACTCCATTACTACTT-AAGGGAGATAAG
1 TGCAATTTCAGAGAGATAAGAATTGTAGCTTCAATCAACTCCACTACTACTTCAA-GGAGATAAG
* * *
22195 ATTTGTAGCTTGTAGCTTTAATT-TGTTCCACTACAACTTCAGAGAAATAGGACTCGCTATGGTA
65 ATTTGTAACTTGTAACTTT-ATTCTGTTCCACTACAACTTCAGAGAAATAAGACTCGCTATGGTA
* * * * * *
22259 GATTTAATCTGACCCATTACAACTTCAAAGGTATAGGATTTGTCGCTTCAATTTGCTCTATTGCA
129 GATTTAATCCGACCCACTACAACTCCAAAGGTATAGGATTTGTCACTTCAATCTGCTCTAATGCA
* * *
22324 ACTTCAGCGAGATAAGATTTGTAGCTTCAATCTGCTCCAC
194 ACTTCAGCGAAATAAAATTTGTAACTTCAATCTGCTCCAC
* * ** *
22364 TGCAATTTCAGAGAGATAAGATTTGTTGCTTCAATCTGCTCCACTGCTACTTCAAGGAGATAAGA
1 TGCAATTTCAGAGAGATAAGAATTGTAGCTTCAATCAACTCCACTACTACTTCAAGGAGATAAGA
*
22429 TCTGTAACTT
66 TTTGTAACTT
22439 TAATATGCTT
Statistics
Matches: 268, Mismatches: 36, Indels: 8
0.86 0.12 0.03
Matches are distributed among these distances:
232 2 0.01
233 258 0.96
234 8 0.03
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (233 bp):
TGCAATTTCAGAGAGATAAGAATTGTAGCTTCAATCAACTCCACTACTACTTCAAGGAGATAAGA
TTTGTAACTTGTAACTTTATTCTGTTCCACTACAACTTCAGAGAAATAAGACTCGCTATGGTAGA
TTTAATCCGACCCACTACAACTCCAAAGGTATAGGATTTGTCACTTCAATCTGCTCTAATGCAAC
TTCAGCGAAATAAAATTTGTAACTTCAATCTGCTCCAC
Found at i:22395 original size:88 final size:88
Alignment explanation
Indices: 22062--22653 Score: 474
Period size: 88 Copynumber: 6.6 Consensus size: 88
22052 AAAGGTATAT
* * * * * * * *
22062 GATTTGTCACTTCAATCTGCTCTAATGCAACTTCAGCGAAATAAAATTTGTAACTTCAATCTGCT
1 GATTTGTAACTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAACTTCAATTTGCT
*
22127 CCACTGCAATTTCAGGGAGATAA
66 CCACTGCAACTTCAGGGAGATAA
* * ** * * * * *
22150 GAATTGTAGCTTCAATCAACTCCATTACTACTTAAGGGAGATAAGATTTGTAGCTTGTAGCTTTA
1 GATTTGTAACTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTA------A-CTTCA
* * * * *
22215 ATTTGTTCCACTACAACTTCAGAGAAATAG
59 ATTTGCTCCACTGCAACTTCAGGGAGATAA
* * * * * * * **
22245 GACTCGCTATGGTAGA-TTTAATCTGAC-CCATTACAACTTCAAAGG-TATAGGATTTGTCGCTT
1 GA-T---T-T-GTA-ACTTCAATCTG-CTCCACTGCAACTT-TAGGGAGATAAGATTTGTAACTT
* * *
22307 CAATTTGCTCTATTGCAACTTCAGCGAGATAA
57 CAATTTGCTCCACTGCAACTTCAGGGAGATAA
* * ** *
22339 GATTTGTAGCTTCAATCTGCTCCACTGCAA-TTTCAGAGAGATAAGATTTGTTGCTTCAATCTGC
1 GATTTGTAACTTCAATCTGCTCCACTGCAACTTT-AGGGAGATAAGATTTGTAACTTCAATTTGC
* *
22403 TCCACTGCTACTTCAAGGAGATAA
65 TCCACTGCAACTTCAGGGAGATAA
* * * * *
22427 GATCTGTAACTTTAATATGCTTCACTGCAACTTTAGGGAGATAAGATTTGTAACTTCAATATGCT
1 GATTTGTAACTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAACTTCAATTTGCT
*
22492 CCACTGCCACTTCAGGGAGATAA
66 CCACTGCAACTTCAGGGAGATAA
* * * *
22515 GATTTATAACTTCAATCTGCTCCATTGTAACTTTAGGGAGATAAGATTTGTAACTCCAATTTGCT
1 GATTTGTAACTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAACTTCAATTTGCT
*
22580 CCACTACAACTTCAGGGAGATAA
66 CCACTGCAACTTCAGGGAGATAA
* * * *
22603 GATTTGTAGCCTC-ATCTTGCTCCATTGCATCTTTAGGGAGATAAGATTTGT
1 GATTTGTAACTTCAATC-TGCTCCACTGCAACTTTAGGGAGATAAGATTTGT
22654 TATATTCAAT
Statistics
Matches: 399, Mismatches: 83, Indels: 44
0.76 0.16 0.08
Matches are distributed among these distances:
87 8 0.02
88 289 0.72
89 4 0.01
90 1 0.00
93 1 0.00
94 30 0.08
95 29 0.07
99 1 0.00
100 1 0.00
101 30 0.08
102 5 0.01
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (88 bp):
GATTTGTAACTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTAACTTCAATTTGCT
CCACTGCAACTTCAGGGAGATAA
Found at i:22469 original size:132 final size:131
Alignment explanation
Indices: 22320--22693 Score: 432
Period size: 132 Copynumber: 2.8 Consensus size: 131
22310 TTTGCTCTAT
* *
22320 TGCAACTTCAGCGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCAATTTCAGAGAGATAAGA
1 TGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGC-ATTTCAGGGAGATAAGA
* ** *
22385 TTTGTTGCTTCAATCTGCTCCACTGCT-ACTTCAAGGAGATAAGATCTGTAACTTTAATATGCTT
65 TTTGTTACTTCAATCTGCTCCACTG-TAACTTCAAGGAGATAAGATCTGTAACTCCAATATGCTC
22449 CAC
129 CAC
* * * *
22452 TGCAACTTTAGGGAGATAAGATTTGTAACTTCAATATGCTCCACTGCCACTTCAGGGAGATAAGA
1 TGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTG-CATTTCAGGGAGATAAGA
* * * * * * *
22517 TTTATAACTTCAATCTGCTCCATTGTAACTTTAGGGAGATAAGATTTGTAACTCCAATTTGCTCC
65 TTTGTTACTTCAATCTGCTCCACTGTAACTTCAAGGAGATAAGATCTGTAACTCCAATATGCTCC
22582 AC
130 AC
* * * *
22584 TACAACTTCAGGGAGATAAGATTTGTAGCCTC-ATCTTGCTCCATTGCATCTTTAGGGAGATAAG
1 TGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATC-TGCTCCACTGCAT-TTCAGGGAGATAAG
* * *
22648 ATTTGTTATATTCAATCTAAC-CCATTGTAACTTCAAGG-GTATAAGA
64 ATTTGTTA-CTTCAATCT-GCTCCACTGTAACTTCAAGGAG-ATAAGA
22694 ATTGTGGTTT
Statistics
Matches: 204, Mismatches: 31, Indels: 13
0.82 0.12 0.05
Matches are distributed among these distances:
131 5 0.02
132 168 0.82
133 30 0.15
134 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (131 bp):
TGCAACTTCAGGGAGATAAGATTTGTAGCTTCAATCTGCTCCACTGCATTTCAGGGAGATAAGAT
TTGTTACTTCAATCTGCTCCACTGTAACTTCAAGGAGATAAGATCTGTAACTCCAATATGCTCCA
C
Found at i:34185 original size:19 final size:21
Alignment explanation
Indices: 34161--34201 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
34151 TAAGCGAATT
*
34161 TTAACAA-AATTATTA-TTAA
1 TTAACAACAATAATTACTTAA
34180 TTAACAACAATAATTACTTAA
1 TTAACAACAATAATTACTTAA
34201 T
1 T
34202 AATGTTAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 7 0.37
21 5 0.26
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (21 bp):
TTAACAACAATAATTACTTAA
Found at i:34250 original size:20 final size:20
Alignment explanation
Indices: 34214--34251 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
34204 TGTTAGTAAT
*
34214 ATCAATAATTAAAAATAAGG
1 ATCAATAATAAAAAATAAGG
34234 ATCAA-AATAAAATAATAA
1 ATCAATAATAAAA-AATAA
34252 AAAATTAGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (20 bp):
ATCAATAATAAAAAATAAGG
Found at i:34442 original size:29 final size:30
Alignment explanation
Indices: 34385--34442 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 30
34375 GAATAAAGGA
*
34385 CTAAATTAAAAATATAACAAAACTAAAAGC
1 CTAAATTAAAAAGATAACAAAACTAAAAGC
* * *
34415 CTAAATTATAAAGA-AACGAAACTTAAAG
1 CTAAATTAAAAAGATAACAAAACTAAAAG
34443 GATTAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.21
Consensus pattern (30 bp):
CTAAATTAAAAAGATAACAAAACTAAAAGC
Found at i:38585 original size:11 final size:11
Alignment explanation
Indices: 38535--38592 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
38525 TTTTAAAGTA
38535 AAAATAAAAA-
1 AAAATAAAAAT
*
38545 AGAATAGAAAAT
1 AAAATA-AAAAT
*
38557 AAAATAAAAGGGT
1 AAAATAAAA--AT
*
38570 AAAATTAAAAT
1 AAAATAAAAAT
38581 AAAATAAAAAT
1 AAAATAAAAAT
38592 A
1 A
38593 TAGGGACCAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
10 5 0.13
11 19 0.50
12 5 0.13
13 9 0.24
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:40133 original size:94 final size:95
Alignment explanation
Indices: 40016--40469 Score: 480
Period size: 94 Copynumber: 4.8 Consensus size: 95
40006 GCTCCATTGT
* * * * *
40016 AACTTCAAGGAAATAAGATTCGTTGTTGTAATTTCAATCCGACCCACTGTAACTTCAAGGGTATA
1 AACTTCAGGGAGATAAGATTCGTTATGGTAATTTCAATCCGACCCACTGCAACTTCAAGGGTATA
40081 GGATTTGTAG-TCTC-ATCTTGCTC-ACTAC
66 GGATTTGTAGCT-TCAATCTTGCTCTACTAC
* *
40109 AACTTCAGGGAGATAAAGATTCGTTATGGTAACTTCAATCCGACCCACTGCAACTTCAGGGGTAT
1 AACTTCAGGGAGAT-AAGATTCGTTATGGTAATTTCAATCCGACCCACTGCAACTTCAAGGGTAT
* * * * *
40174 AAGATTTGTAACTTCAATC-TACT-TCACCAT
65 AGGATTTGTAGCTTCAATCTTGCTCT-ACTAC
* * * *
40204 AACTTCAGGGAGATAAGATTCGCTATGGTAATTTCAATTCGA--CACAGCAACTTCAAAGGTATA
1 AACTTCAGGGAGATAAGATTCGTTATGGTAATTTCAATCCGACCCACTGCAACTTCAAGGGTATA
*
40267 GGATTTGTAGCTTCAAT-TTGCTCTACTGC
66 GGATTTGTAGCTTCAATCTTGCTCTACTAC
* * * * *
40296 AACTTTAGGGAGATAAGATTCATTATGGTAGA-TTCAATACGACCCACTACAATTTCAAGGGTAT
1 AACTTCAGGGAGATAAGATTCGTTATGGTA-ATTTCAATCCGACCCACTGCAACTTCAAGGGTAT
* *
40360 AGGATCTGTAGCTTC-ATCTTGCTCTACTGC
65 AGGATTTGTAGCTTCAATCTTGCTCTACTAC
* ** * * * * * *
40390 AACTTCAGAGAGATAAGATTCACTATGGTGGA-TGCAATCTGACCCACTACAACTTTAAGGGTGT
1 AACTTCAGGGAGATAAGATTCGTTATGGT-AATTTCAATCCGACCCACTGCAACTTCAAGGGTAT
*
40454 AAGATTTGTAGCTTCA
65 AGGATTTGTAGCTTCA
40470 CTGATCTGTT
Statistics
Matches: 303, Mismatches: 45, Indels: 24
0.81 0.12 0.06
Matches are distributed among these distances:
92 74 0.24
93 16 0.05
94 192 0.63
95 21 0.07
ACGTcount: A:0.31, C:0.20, G:0.19, T:0.31
Consensus pattern (95 bp):
AACTTCAGGGAGATAAGATTCGTTATGGTAATTTCAATCCGACCCACTGCAACTTCAAGGGTATA
GGATTTGTAGCTTCAATCTTGCTCTACTAC
Found at i:40341 original size:186 final size:187
Alignment explanation
Indices: 40015--40418 Score: 471
Period size: 186 Copynumber: 2.2 Consensus size: 187
40005 TGCTCCATTG
* * * * * * * *
40015 TAACTTCAAGGAAATAAGATTCGTTGTTGTAATTTCAATCCGACCCACTGTAACTTCAAGGGTAT
1 TAACTTCAGGGAGATAAGATTCGCTATGGTAATTTCAATCCGA-CCACAGCAACTTCAAAGGTAT
*
40080 AGGATTTGTAGTCTCATCTTGCTCACTACAACTTCAGGGAGATAAAGATTCGTTATGGTAACTTC
65 AGGATTTGTAGTCTCATCTTGCTCACTACAACTTCAGGGAGATAAAGATTCATTATGGTAACTTC
* * * *
40145 AATCCGACCCACTGCAACTTCAGGGGTATAAGATTTGTAACTTCAATC-TACT-TCACCA
130 AATACGACCCACTACAACTTCAAGGGTATAAGATCTGTAACTTC-ATCTTACTCT-ACCA
*
40203 TAACTTCAGGGAGATAAGATTCGCTATGGTAATTTCAATTCGA-CACAGCAACTTCAAAGGTATA
1 TAACTTCAGGGAGATAAGATTCGCTATGGTAATTTCAATCCGACCACAGCAACTTCAAAGGTATA
* *
40267 GGATTTGTAG-CTTCAAT-TTGCTCTACTGCAACTTTAGGGAGAT-AAGATTCATTATGGTAGA-
66 GGATTTGTAGTC-TC-ATCTTGCTC-ACTACAACTTCAGGGAGATAAAGATTCATTATGGTA-AC
* * * * **
40328 TTCAATACGACCCACTACAATTTCAAGGGTATAGGATCTGTAGCTTCATCTTGCTCTACTG
127 TTCAATACGACCCACTACAACTTCAAGGGTATAAGATCTGTAACTTCATCTTACTCTACCA
* * *
40389 CAACTTCAGAGAGATAAGATTCACTATGGT
1 TAACTTCAGGGAGATAAGATTCGCTATGGT
40419 GGATGCAATC
Statistics
Matches: 185, Mismatches: 25, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
185 4 0.02
186 123 0.66
187 21 0.11
188 37 0.20
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (187 bp):
TAACTTCAGGGAGATAAGATTCGCTATGGTAATTTCAATCCGACCACAGCAACTTCAAAGGTATA
GGATTTGTAGTCTCATCTTGCTCACTACAACTTCAGGGAGATAAAGATTCATTATGGTAACTTCA
ATACGACCCACTACAACTTCAAGGGTATAAGATCTGTAACTTCATCTTACTCTACCA
Found at i:65589 original size:2 final size:2
Alignment explanation
Indices: 65582--65618 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
65572 AGTGTTCTAG
65582 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT G
65619 AGGTCTTGGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.51, T:0.49
Consensus pattern (2 bp):
GT
Found at i:65934 original size:6 final size:6
Alignment explanation
Indices: 65923--65950 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
65913 GGATTTAAAA
65923 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTT
65951 TCCTACAAGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTAT
Found at i:68318 original size:12 final size:11
Alignment explanation
Indices: 68289--68327 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
68279 TAACCACATA
*
68289 AATAATAAAAT
1 AATAATACAAT
*
68300 AATAATACTAT
1 AATAATACAAT
68311 AATGAATACAAT
1 AAT-AATACAAT
68323 AATAA
1 AATAA
68328 AAATGGTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 14 0.58
12 10 0.42
ACGTcount: A:0.64, C:0.05, G:0.03, T:0.28
Consensus pattern (11 bp):
AATAATACAAT
Found at i:68682 original size:11 final size:11
Alignment explanation
Indices: 68607--68689 Score: 51
Period size: 11 Copynumber: 7.2 Consensus size: 11
68597 AACAGGGGAC
* *
68607 TAAATTAAAAC
1 TAAAATAAAAA
* *
68618 TATAATAAAATT
1 TAAAATAAAA-A
*
68630 TAAAGTAAAAA
1 TAAAATAAAAA
68641 T-AAATAAGAACA
1 TAAAATAA-AA-A
*
68653 TAAAATAAAAGGG
1 TAAAATAAAA--A
*
68666 TAAAATTAAAA
1 TAAAATAAAAA
68677 TAAAATAAAAA
1 TAAAATAAAAA
68688 TA
1 TA
68690 TACGACCAAA
Statistics
Matches: 55, Mismatches: 12, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
10 5 0.09
11 23 0.42
12 12 0.22
13 15 0.27
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.24
Consensus pattern (11 bp):
TAAAATAAAAA
Found at i:82592 original size:18 final size:19
Alignment explanation
Indices: 82571--82630 Score: 61
Period size: 20 Copynumber: 3.2 Consensus size: 19
82561 ATGCATATGG
82571 AAATTATAAAGTATATA-A
1 AAATTATAAAGTATATATA
*
82589 AAA-TATATATGTATATATA
1 AAATTATA-AAGTATATATA
* *
82608 TAAATTGTAAAATATATATA
1 -AAATTATAAAGTATATATA
82628 AAA
1 AAA
82631 AAAATATATG
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
17 4 0.12
18 11 0.32
19 4 0.12
20 12 0.35
21 3 0.09
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (19 bp):
AAATTATAAAGTATATATA
Found at i:82713 original size:2 final size:2
Alignment explanation
Indices: 82706--82731 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
82696 GCACCAGCTT
82706 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
82732 ATTGAATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:83609 original size:5 final size:5
Alignment explanation
Indices: 83599--83630 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
83589 CCGTATGTAA
83599 AAAAT AAAAT -AAAT -AAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
83631 GTAGACTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:89867 original size:87 final size:88
Alignment explanation
Indices: 89753--89928 Score: 345
Period size: 87 Copynumber: 2.0 Consensus size: 88
89743 ATACACTTGC
89753 CATTTCAGCATCCATAGAACCCAAAACCTTCAAACAAGCAAGTAAATTTCCCCACTGGAATGAGG
1 CATTTCAGCATCCATAGAACCCAAAACCTTCAAACAAGCAAGTAAATTTCCCCACTGGAATGAGG
89818 CAATGCTAGCTGAGATTAATGCA
66 CAATGCTAGCTGAGATTAATGCA
89841 CATTTCAGCA-CCATAGAACCCAAAACCTTCAAACAAGCAAGTAAATTTCCCCACTGGAATGAGG
1 CATTTCAGCATCCATAGAACCCAAAACCTTCAAACAAGCAAGTAAATTTCCCCACTGGAATGAGG
89905 CAATGCTAGCTGAGATTAATGCA
66 CAATGCTAGCTGAGATTAATGCA
89928 C
1 C
89929 TTGAGCAGAA
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 78 0.89
88 10 0.11
ACGTcount: A:0.38, C:0.26, G:0.16, T:0.21
Consensus pattern (88 bp):
CATTTCAGCATCCATAGAACCCAAAACCTTCAAACAAGCAAGTAAATTTCCCCACTGGAATGAGG
CAATGCTAGCTGAGATTAATGCA
Found at i:96134 original size:6 final size:6
Alignment explanation
Indices: 96123--96158 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
96113 ATCCTATTTC
96123 ATTTTT ATTTTT ATTTTT ATTTTT ATCCTTTT ATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT AT--TTTT ATTT
96159 CATCCTTGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
6 22 0.79
8 6 0.21
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (6 bp):
ATTTTT
Found at i:99520 original size:19 final size:19
Alignment explanation
Indices: 99496--99534 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
99486 TAAGGCTGTA
* *
99496 TATGTAAATATATTTGTTT
1 TATGTAAAGAGATTTGTTT
99515 TATGTAAAGAGATTTGTTT
1 TATGTAAAGAGATTTGTTT
99534 T
1 T
99535 CTATTAAAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (19 bp):
TATGTAAAGAGATTTGTTT
Found at i:107115 original size:3 final size:3
Alignment explanation
Indices: 107107--107258 Score: 304
Period size: 3 Copynumber: 50.7 Consensus size: 3
107097 CCACTCATCT
107107 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
107155 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
107203 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
107251 TAA TAA TA
1 TAA TAA TA
107259 TTTTAATCCT
Statistics
Matches: 149, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 149 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:107930 original size:15 final size:14
Alignment explanation
Indices: 107906--107942 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 14
107896 ATTCATTTGC
107906 TTTCTTTTATTTTA
1 TTTCTTTTATTTTA
107920 TTTCATTTTATTTTA
1 TTTC-TTTTATTTTA
107935 TTTACTTT
1 TTT-CTTT
107943 ATGTTGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.19
15 16 0.76
16 1 0.05
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTCTTTTATTTTA
Found at i:108256 original size:17 final size:17
Alignment explanation
Indices: 108234--108266 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
108224 TCTTTTAATT
108234 TAATAATAAATAATAAC
1 TAATAATAAATAATAAC
108251 TAATAATAAATAATAA
1 TAATAATAAATAATAA
108267 ATATCTTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TAATAATAAATAATAAC
Found at i:108269 original size:21 final size:21
Alignment explanation
Indices: 108245--108287 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
108235 AATAATAAAT
108245 AATAACTAATAATAAATAATA
1 AATAACTAATAATAAATAATA
* * * *
108266 AATATCTTATACTAATTAATA
1 AATAACTAATAATAAATAATA
108287 A
1 A
108288 GCAAATTAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.58, C:0.07, G:0.00, T:0.35
Consensus pattern (21 bp):
AATAACTAATAATAAATAATA
Found at i:110569 original size:44 final size:44
Alignment explanation
Indices: 110506--111043 Score: 355
Period size: 44 Copynumber: 12.1 Consensus size: 44
110496 TATCATGGAG
* * *
110506 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTAAAGCCACA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * *
110550 AATCTTATCTCCCTAAAGTTACAATGGAGCAGATTGAAGATAGCA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTA-CA
* * * * * *
110595 AATCTTATCTCTCTGAAGTTGCCGTAGAGTAGATTAAAGATACA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * * **
110639 AACCTTATCTCTCTGAAA-TTGTAGTGAAACAGATTGAAA-CGGCA
1 AATCTTATCTCCCT-AAAGTTGCAGTGGAGCAGATT-AAAGCTACA
* ** *
110683 ATTCTTATCTCCCT-GGGTTGCAGTGGAGTAGATTAAAGCTACA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * *
110726 AATCTTATTTCCCTGAAA-CTGCAGTGGAACAGATTAAAGCTACAAATTTA
1 AATCTTATCTCCCT-AAAGTTGCAGTGGAGCAGATTAAAGCTAC------A
* * * * ** *
110776 AATATTATCTCCCTAAAGTTACAGTGGAGTAGATTGAATATACG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * ** * *
110820 AGTCTCATGTCTTTAAAGTTGCAGTGGAGTAGATTAAAGTTACA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * *
110864 AATCTTATCTCCCTGAAGTTGCAGTAGAGCAGATTGAAGTTACA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * * * * * *
110908 AATCTCATCTCCCTGAATTTGTAGTGAAGTAGATTGAAGATACG
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * ** *
110952 AGTCTCATCTCCCCGAAGTTGTAGTGGAGCAGATTAAAGCTACA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
* * * * * * * *
110996 AGTCTAATCTCTCTTAAGTTACAGTAGAGCAGATTGAAGCAACA
1 AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
111040 AATC
1 AATC
111044 CTATACCTTT
Statistics
Matches: 380, Mismatches: 100, Indels: 28
0.75 0.20 0.06
Matches are distributed among these distances:
42 3 0.01
43 28 0.07
44 274 0.72
45 41 0.11
49 3 0.01
50 31 0.08
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCTACA
Found at i:110726 original size:87 final size:89
Alignment explanation
Indices: 110451--111066 Score: 379
Period size: 88 Copynumber: 6.9 Consensus size: 89
110441 ATCAATGAAA
* * * * *
110451 CTACAAATCCTATAC-CCCTGAAGTTGCAGTGGGACGGATTGAAGTTATCATGGAGAATCTTATC
1 CTACAAATCTTAT-CTCCCTGAAATTGCAGTGGAACAGATTGAAG--A-CA-GCA-AATCTTATC
* *
110515 TCCCTGAAGTTGCAGTGGAGCAAATTAAAG
60 TCCCTGAAGTTGCAGTGGAGTAGATTAAAG
* * * * * *
110545 CCACAAATCTTATCTCCCT-AAAGTTACAATGGAGCAGATTGAAGATAGCAAATCTTATCTCTCT
1 CTACAAATCTTATCTCCCTGAAA-TTGCAGTGGAACAGATTGAAGACAGCAAATCTTATCTCCCT
* *
110609 GAAGTTGCCGTAGAGTAGATTAAAG
65 GAAGTTGCAGTGGAGTAGATTAAAG
* * * * * * *
110634 ATACAAACCTTATCTCTCTGAAATTGTAGTGAAACAGATTGAA-ACGGCAATTCTTATCTCCCTG
1 CTACAAATCTTATCTCCCTGAAATTGCAGTGGAACAGATTGAAGACAGCAAATCTTATCTCCCTG
*
110698 -GGTTGCAGTGGAGTAGATTAAAG
66 AAGTTGCAGTGGAGTAGATTAAAG
* * * ** *
110721 CTACAAATCTTATTTCCCTGAAACTGCAGTGGAACAGATTAAAGCTACAAATTTAAATATTATCT
1 CTACAAATCTTATCTCCCTGAAATTGCAGTGGAACAGATTGAAG--AC--A-GCAAATCTTATCT
* * * *
110786 CCCTAAAGTTACAGTGGAGTAGATTGAAT
61 CCCTGAAGTTGCAGTGGAGTAGATTAAAG
* * * * * * * ** * **
110815 ATACGAGTCTCATGT-CTTTAAAGTTGCAGTGGAGTAGATTAAAGTTA-CAAATCTTATCTCCCT
1 CTACAAATCTTATCTCCCTGAAA-TTGCAGTGGAACAGATTGAAGACAGCAAATCTTATCTCCCT
* * *
110878 GAAGTTGCAGTAGAGCAGATTGAAG
65 GAAGTTGCAGTGGAGTAGATTAAAG
* * * * * * * * * *
110903 TTACAAATCTCATCTCCCTGAATTTGTAGT-GAAGTAGATTGAAGATA-CGAGTCTCATCTCCCC
1 CTACAAATCTTATCTCCCTGAAATTGCAGTGGAA-CAGATTGAAGACAGCAAATCTTATCTCCCT
* *
110966 GAAGTTGTAGTGGAGCAGATTAAAG
65 GAAGTTGCAGTGGAGTAGATTAAAG
* * * * * * * * * * **
110991 CTACAAGTCTAATCTCTCTTAAGTTACAGTAGAGCAGATTGAAG-CAACAAATCCTATAC-CTTT
1 CTACAAATCTTATCTCCCTGAAATTGCAGTGGAACAGATTGAAGACAGCAAATCTTAT-CTCCCT
111054 GAAGTTGCAGTGG
65 GAAGTTGCAGTGG
111067 GTTAGAATGA
Statistics
Matches: 401, Mismatches: 105, Indels: 38
0.74 0.19 0.07
Matches are distributed among these distances:
87 58 0.14
88 163 0.41
89 71 0.18
90 8 0.02
91 1 0.00
92 1 0.00
93 21 0.05
94 78 0.19
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (89 bp):
CTACAAATCTTATCTCCCTGAAATTGCAGTGGAACAGATTGAAGACAGCAAATCTTATCTCCCTG
AAGTTGCAGTGGAGTAGATTAAAG
Found at i:110996 original size:132 final size:131
Alignment explanation
Indices: 110556--111043 Score: 431
Period size: 132 Copynumber: 3.7 Consensus size: 131
110546 CACAAATCTT
* * * * * * *
110556 ATCTCCCTAAAGTTACAATGGAGCAGATTGAAGATAGCAAATCTTATCTCTCTGAAGTTGCCGTA
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTA-CAAATCTTATCTCCCTGAAGTTGCAGTA
* * * * ** ** * *
110621 GAGTAGATTAAAGATACAAACCTTATCTCTCTGAAATTGTAGTGAAACAGATTGAAACGGCAATT
65 GAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAATTGTAGTGAAGTAGATTGAAA-TACGAGT
*
110686 CTT
129 CTC
* * * ** *
110689 ATCTCCCTG-GGTTGCAGTGGAGTAGATTAAAGCTACAAATCTTATTTCCCTGAAACTGCAGTGG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTAG
* * ** *
110753 AACAGATTAAAGCTACAAATTTAAATATTATCTCCCT-AAAGTTACAGTGGAGTAGATTGAATAT
66 AGCAGATTAAAGCTAC------AAATCTTATCTCCCTGAAA-TTGTAGTGAAGTAGATTGAA-AT
110817 ACGAGTCTC
123 ACGAGTCTC
* ** * * *
110826 ATGTCTTTAAAGTTGCAGTGGAGTAGATTAAAGTTACAAATCTTATCTCCCTGAAGTTGCAGTAG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTAG
* * * *
110891 AGCAGATTGAAGTTACAAATCTCATCTCCCTGAATTTGTAGTGAAGTAGATTGAAGATACGAGTC
66 AGCAGATTAAAGCTACAAATCTTATCTCCCTGAAATTGTAGTGAAGTAGATTGAA-ATACGAGTC
110956 TC
130 TC
* * * * * * *
110958 ATCTCCCCGAAGTTGTAGTGGAGCAGATTAAAGCTACAAGTCTAATCTCTCTTAAGTTACAGTAG
1 ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTAG
* *
111023 AGCAGATTGAAGCAACAAATC
66 AGCAGATTAAAGCTACAAATC
111044 CTATACCTTT
Statistics
Matches: 281, Mismatches: 64, Indels: 21
0.77 0.17 0.06
Matches are distributed among these distances:
131 36 0.13
132 132 0.47
133 10 0.04
136 3 0.01
137 37 0.13
138 63 0.22
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (131 bp):
ATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCTTATCTCCCTGAAGTTGCAGTAG
AGCAGATTAAAGCTACAAATCTTATCTCCCTGAAATTGTAGTGAAGTAGATTGAAATACGAGTCT
C
Found at i:113073 original size:12 final size:11
Alignment explanation
Indices: 113054--113093 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
113044 TTACAAAATT
113054 TTATTTATTTA
1 TTATTTATTTA
113065 TTCATTTATTTA
1 TT-ATTTATTTA
113077 TTACTTTATTT-
1 TTA-TTTATTTA
113088 TTATTT
1 TTATTT
113094 TTATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.11
11 6 0.22
12 18 0.67
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (11 bp):
TTATTTATTTA
Found at i:114087 original size:19 final size:19
Alignment explanation
Indices: 114060--114096 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
114050 TCCATTCTTC
* *
114060 ATTTTAAAATAAAAAGTTG
1 ATTTAAAAAAAAAAAGTTG
114079 ATTTAAAAAAAAAAAGTT
1 ATTTAAAAAAAAAAAGTT
114097 TTCGACAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.32
Consensus pattern (19 bp):
ATTTAAAAAAAAAAAGTTG
Found at i:120518 original size:13 final size:13
Alignment explanation
Indices: 120500--120524 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
120490 ATTAAATGGA
120500 TATTATTATTATT
1 TATTATTATTATT
120513 TATTATTATTAT
1 TATTATTATTAT
120525 GCTCTATTTG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TATTATTATTATT
Found at i:121142 original size:2 final size:2
Alignment explanation
Indices: 121137--121163 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
121127 ATAAAAAATT
121137 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
121164 TGCATTGAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:124301 original size:50 final size:50
Alignment explanation
Indices: 124182--124305 Score: 126
Period size: 50 Copynumber: 2.5 Consensus size: 50
124172 TTGTCGCTTC
* * * *
124182 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTAGTAGCTTATAGCTTT
1 AATCTGATCCACTGCAACTTCAGGGAAATAAGA-TAGTAGCTTATAGATTT
* * * * *
124233 AGTGTGTTCCACTACAACTTCAGGGAAAT-AGA-AGTTGCTATAGTAGATTT
1 AATCTGATCCACTGCAACTTCAGGGAAATAAGATAGTAGCT-TA-TAGATTT
124283 AATCTGATCCACTGCAACTTCAG
1 AATCTGATCCACTGCAACTTCAG
124306 AGGTATAAGA
Statistics
Matches: 59, Mismatches: 12, Indels: 5
0.78 0.16 0.07
Matches are distributed among these distances:
48 6 0.10
49 2 0.03
50 28 0.47
51 23 0.39
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (50 bp):
AATCTGATCCACTGCAACTTCAGGGAAATAAGATAGTAGCTTATAGATTT
Found at i:124465 original size:89 final size:90
Alignment explanation
Indices: 124283--125263 Score: 715
Period size: 89 Copynumber: 10.8 Consensus size: 90
124273 TAGTAGATTT
* * * * *
124283 AATCTGATCCACTGCAACTTCAGAG-GTATAAGATT-TGTCGCTTCAAGCTACTTCACTGCAACT
1 AATCTGCTCCACTGCAACTTCAGAGAG-ATAAGATTATGTAGCTTTAATCTACTCCACTGCAACT
*** *
124346 TCAGGGAGATAAGGCCTG-TAACTTC
65 TCAGGGAGATAAGATTTGCTATCTTC
* * * * * *
124371 AATCTGCTCCACTGCAACTTCAGAGAGATAAGCTTCAT-TACCTTCAATCTGCTCCACTACCACT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATT-ATGTAGCTTTAATCTACTCCACTGCAACT
* * *
124435 TTAGGGAGATAAGATTTGTTA-CTTT
65 TCAGGGAGATAAGATTTGCTATCTTC
* * * *
124460 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTGTAGCTTTAATCTATTCCACTA
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGA--T-T-A--TGTAGCTTTAATCTACTCCACTG
* * * *
124525 CAACTTTAGGGAAATGAGATTAGCTATCTTC
60 CAACTTCAGGGAGATAAGATTTGCTATCTTC
* * * * * *
124556 AATCTACTCTACTTCAACTTCAGAGAAATAAGATT-TGTAGCTTTAA-CTTCCTCCAATGCAACT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTATGTAGCTTTAATC-TACTCCACTGCAACT
*
124619 TCAGGGAGATGAA-ATTTG-TGA-CTTT
65 TCAGGGAGAT-AAGATTTGCT-ATCTTC
** * * * *
124644 AATCTTTTCCACTGCCACTTCAGA-AGCATAGGATTTGTGACTTGTAACTTTAATCTATTCCACT
1 AATCTGCTCCACTGCAACTTCAGAGAG-ATAAGA--T-T-A--TGTAGCTTTAATCTACTCCACT
* * * *
124708 GTAACTTTAGGGAAATAAGATTCGC-ATCTTC
59 GCAACTTCAGGGAGATAAGATTTGCTATCTTC
* * * * * * *
124739 AACCTGCTCCATTGCAACTTCAGGGAGATAAGATT-TATAGCTTTAATCTACACTACTGTAACTT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTATGTAGCTTTAATCTACTCCACTGCAACTT
* *
124803 CAGAGAGATAAGATTTACTATCTTC
66 CAGGGAGATAAGATTTGCTATCTTC
** * * * * * *
124828 AATCTTTTCCATTGCAACTTCA-AGCAAATAAGA-TATATAGCTTTAATCTGCTCTACTCCAACT
1 AATCTGCTCCACTGCAACTTCAGAG-AGATAAGATTATGTAGCTTTAATCTACTCCACTGCAACT
*
124891 TCAGAGAGATAAGATTTGCTATCTTC
65 TCAGGGAGATAAGATTTGCTATCTTC
** * * * * * **
124917 AATCTTTTCCACTGCAACTTCAGGGAGATAAGATTTTCTATCTTCAATCTTTTCCACTGCAACTT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTATGTAGCTTTAATCTACTCCACTGCAACTT
** * *
124982 CAGATAGATAAGATTT-ATAAT-TTT
66 CAGGGAGATAAGATTTGCT-ATCTTC
** * * ** *
125006 AATCTGCTATACTGCAACTTCAGAGAGATAAGATT-TGATATCTTCAATCTGTTCCACTGCAGCT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTATG-TAGCTTTAATCTACTCCACTGCAACT
*
125070 TCAGGGAGATAAGATTT-ATATCTTC
65 TCAGGGAGATAAGATTTGCTATCTTC
* * * * **
125095 AATCTACCCCACTGCCACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGTTCCACTG
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGA--T-T-A--TGTAGCTTTAATCTACTCCACTG
* * *
125160 CAACTTCAGGGAAATAAGATTCGCTATCTTT
60 CAACTTCAGGGAGATAAGATTTGCTATCTTC
* * * * *
125191 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-TGTATCTTTAATATACTCTACTGCAACTT
1 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTATGTAGCTTTAATCTACTCCACTGCAACTT
125255 CAGGGAGAT
66 CAGGGAGAT
125264 GAAATTCGTG
Statistics
Matches: 716, Mismatches: 134, Indels: 85
0.77 0.14 0.09
Matches are distributed among these distances:
87 1 0.00
88 102 0.14
89 346 0.48
90 46 0.06
91 3 0.00
92 4 0.01
93 3 0.00
94 5 0.01
95 135 0.19
96 71 0.10
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.34
Consensus pattern (90 bp):
AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTATGTAGCTTTAATCTACTCCACTGCAACTT
CAGGGAGATAAGATTTGCTATCTTC
Found at i:124657 original size:184 final size:183
Alignment explanation
Indices: 124432--125213 Score: 468
Period size: 184 Copynumber: 4.3 Consensus size: 183
124422 CTCCACTACC
* * * *
124432 ACTTTAGGGAGATAAGATTTGTTACTTTAATCTGCTCCACTGCAACTTTAGGGAG-ATAAGATTT
1 ACTTCAGGGAGATAAGATTTGTGACTTTAATCTGCTCCACTGCAACTTCA-GAAGCATAAGATTT
* * *
124496 ATAACTTGTAGCTTTAATCTATTCCACTACAACTTTAGGGAAATGAGATTAGCTATCTTCAATCT
65 ATAACTTGTAACTTTAATCTATTCCACTACAACTTTAGGGAAATAAGATTAGC-ATCTTCAACCT
* *
124561 ACTCTACTT-CAACTTCAGAGAAATAAGATTTGTAGCTTTAACTTCCTCCAATGCA
129 ACTCCA-TTGCAACTTCAGAGAAATAAGATTTATAGCTTTAACTTCCTCCAATGCA
** * *
124616 ACTTCAGGGAGATGAA-ATTTGTGACTTTAATCTTTTCCACTGCCACTTCAGAAGCATAGGATTT
1 ACTTCAGGGAGAT-AAGATTTGTGACTTTAATCTGCTCCACTGCAACTTCAGAAGCATAAGATTT
* * ** * *
124680 GTGACTTGTAACTTTAATCTATTCCACTGTAACTTTAGGGAAATAAGATTCGCATCTTCAACCTG
65 ATAACTTGTAACTTTAATCTATTCCACTACAACTTTAGGGAAATAAGATTAGCATCTTCAACCTA
* * * * *
124745 CTCCATTGCAACTTCAGGGAGATAAGATTTATAGCTTTAATCTACACT--ACTGTA
130 CTCCATTGCAACTTCAGAGAAATAAGATTTATAGCTTTAA-CTTC-CTCCAATGCA
* * * ** *
124799 ACTTCAGAGAGATAAGATTTACT-ATCTTCAATCTTTTCCATTGCAACTTC--AAGCAAATAAGA
1 ACTTCAGGGAGATAAGATTT-GTGA-CTTTAATCTGCTCCACTGCAACTTCAGAAGC--ATAAGA
* ** * * * * * *
124861 --TAT-A----TAGCTTTAATCTGCTCTACTCCAACTTCAGAGAGATAAGATTTGCTATCTTCAA
62 TTTATAACTTGTAACTTTAATCTATTCCACTACAACTTTAGGGAAATAAGATTAGC-ATCTTCAA
* ** * * * * * * * *
124919 TCTTTTCCACTGCAACTTCAGGGAGATAAGATTTTCTATCTTCAATCTT-TTCCACTGCA
126 CCTACTCCATTGCAACTTCAGAGAAATAAGA-TTTATAGCTTTAA-CTTCCTCCAATGCA
** * * * **
124978 ACTTCAGATAGATAAGATTTATAATTTTAATCTGCTATACTGCAACTTCAGAGAG-ATAAGATTT
1 ACTTCAGGGAGATAAGATTTGTGACTTTAATCTGCTCCACTGCAACTTCAGA-AGCATAAGATTT
* * * * * * * *
125042 GAT-A----T--CTTCAATCTGTTCCACTGCAGCTTCAGGGAGATAAGATTTA-TATCTTCAATC
65 -ATAACTTGTAACTTTAATCTATTCCACTACAACTTTAGGGAAATAAGA-TTAGCATCTTCAACC
* * * * * *
125099 TACCCCACTGCCACTTCAGGGAGATAAGATTTGTAACTTGTAGCTTTAATCTGT--TCCACTGCA
128 TACTCCATTGCAACTTCAGAGAAATAAGA-TT-T-A----TAGCTTTAA-CT-TCCTCCAATGCA
* *
125162 ACTTCAGGGAAATAAGATTCGCT-ATCTTTAATCTGCTCCACTGCAACTTCAG
1 ACTTCAGGGAGATAAGATTTG-TGA-CTTTAATCTGCTCCACTGCAACTTCAG
125214 GGAGATAAGA
Statistics
Matches: 484, Mismatches: 83, Indels: 61
0.77 0.13 0.10
Matches are distributed among these distances:
177 36 0.07
178 98 0.20
179 70 0.14
180 4 0.01
181 7 0.01
182 10 0.02
183 67 0.14
184 162 0.33
185 30 0.06
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (183 bp):
ACTTCAGGGAGATAAGATTTGTGACTTTAATCTGCTCCACTGCAACTTCAGAAGCATAAGATTTA
TAACTTGTAACTTTAATCTATTCCACTACAACTTTAGGGAAATAAGATTAGCATCTTCAACCTAC
TCCATTGCAACTTCAGAGAAATAAGATTTATAGCTTTAACTTCCTCCAATGCA
Found at i:124971 original size:134 final size:133
Alignment explanation
Indices: 124337--125223 Score: 531
Period size: 140 Copynumber: 6.5 Consensus size: 133
124327 AAGCTACTTC
* *** * *
124337 ACTGCAACTTCAGGGAGATAAGGCCTG-TAACTTCAATCTGCTCCACTGCAACTTCAGAGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
* * * ** * * * * * * *
124401 AGCTTCAT-TACCTTCAATCTGCTCCACTACCACTTTAGGGAGATAAGATTTGTTA-CTTTAATC
66 AGATT-TTCTATCTTCAATCTTTTCCACTGCAACTTCA-AGAAATAAGATAT-ATAGCTTTAATC
*
124464 TGCTCC
128 TGCTCT
* * * ** * *
124470 ACTGCAACTTTAGGGAGATAAGATTT-ATAACTTGTAGCTTTAATCTATTCCACTACAACTTTAG
1 ACTGCAACTTCAGAGAGATAAGATTTGAT-A----T--CTTCAATCTGCTCCACTGCAACTTCAG
* * ** ** * * * *
124534 GGAAATGAGATTAGCTATCTTCAATCTACTCTACTTCAACTTCAGAGAAATAAGATTTGTAGCTT
59 GGAGATAAGATTTTCTATCTTCAATCTTTTCCACTGCAACTTCA-AGAAATAAGATATATAGCTT
* *
124599 TAA-CTTCCTCC
123 TAATC-TGCTCT
* * * ** * *
124610 AATGCAACTTCAGGGAGATGAA-ATTTG-TGA-CTTTAATCTTTTCCACTGCCACTTCA-GAAGC
1 ACTGCAACTTCAGAGAGAT-AAGATTTGAT-ATCTTCAATCTGCTCCACTGCAACTTCAGGGAG-
* * * * * * * ** *
124671 ATAGGATTTGTGACTTGTAACTTTAATCTATTCCACTGTAACTTTAGGGAAATAAGAT-TCGCAT
63 ATAAGATTT-T--C---TATCTTCAATCTTTTCCACTGCAACTTCA-AGAAATAAGATAT-ATAG
* * *
124735 CTTCAACCTGCTCC
120 CTTTAATCTGCTCT
* * * * * * * * *
124749 ATTGCAACTTCAGGGAGATAAGATTT-ATAGCTTTAATCTACACTACTGTAACTTCAGAGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
* *
124813 AGATTTACTATCTTCAATCTTTTCCATTGCAACTTCAAGCAAATAAGATATATAGCTTTAATCTG
66 AGATTTTCTATCTTCAATCTTTTCCACTGCAACTTCAAG-AAATAAGATATATAGCTTTAATCTG
124878 CTCT
130 CTCT
* * **
124882 ACTCCAACTTCAGAGAGATAAGATTTGCTATCTTCAATCTTTTCCACTGCAACTTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
* **
124947 AGATTTTCTATCTTCAATCTTTTCCACTGCAACTTC-AGATAGATAAGATTTATAATTTTAATCT
66 AGATTTTCTATCTTCAATCTTTTCCACTGCAACTTCAAGA-A-ATAAGATATATAGCTTTAATCT
*
125011 GCTAT
129 GCTCT
* *
125016 ACTGCAACTTCAGAGAGATAAGATTTGATATCTTCAATCTGTTCCACTGCAGCTTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
* *** * * * *
125081 AGA-TTTATATCTTCAATCTACCCCACTGCCACTTCAGGGAGATAAGATTTGTAACTTGTAGCTT
66 AGATTTTCTATCTTCAATCTTTTCCACTGCAACTTCA-AGAAATAAGA----T-A--TATAGCTT
* *
125145 TAATCTGTTCC
123 TAATCTGCTCT
* * * * *
125156 ACTGCAACTTCAGGGAAATAAGATTCGCTATCTTTAATCTGCTCCACTGCAACTTCAGGGAGATA
1 ACTGCAACTTCAGAGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
125221 AGA
66 AGA
125224 CTTGTATCTT
Statistics
Matches: 597, Mismatches: 117, Indels: 73
0.76 0.15 0.09
Matches are distributed among these distances:
132 4 0.01
133 154 0.26
134 152 0.25
135 2 0.00
136 2 0.00
137 1 0.00
138 4 0.01
139 100 0.17
140 176 0.29
141 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.15, T:0.33
Consensus pattern (133 bp):
ACTGCAACTTCAGAGAGATAAGATTTGATATCTTCAATCTGCTCCACTGCAACTTCAGGGAGATA
AGATTTTCTATCTTCAATCTTTTCCACTGCAACTTCAAGAAATAAGATATATAGCTTTAATCTGC
TCT
Found at i:125158 original size:51 final size:47
Alignment explanation
Indices: 124177--125263 Score: 568
Period size: 44 Copynumber: 23.7 Consensus size: 47
124167 AGAAATTGTC
* * *
124177 GCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTAGTAGCTTATA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTA-C---TA
* * * * * * *
124228 GCTTTAGTGTGTTCCACTACAACTTCAGGGAAAT-AGAAGTTGCTATAGTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG-A-TT--TGTACTA
* * *
124278 GATTTAATCTGATCCACTGCAACTTCAGAGG-TATAAGATTTGT-C--
1 GCTTTAATCTGCTCCACTGCAACTTCAG-GGAGATAAGATTTGTACTA
* * * * ***
124322 GCTTCAAGCTACTTCACTGCAACTTCAGGGAGATAAGGCCTGTA--A
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * * * *
124367 -CTTCAATCTGCTCCACTGCAACTTCAGAGAGATAAG-CTT-CATTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * * * *
124411 CCTTCAATCTGCTCCACTACCACTTTAGGGAGATAAGATTTGT--TA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* *
124456 -CTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTATAACTTGTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-AC---TA
** * * * * *
124506 GCTTTAATCTATTCCACTACAACTTTAGGGAAATGAGATTAG--CTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * * * * * *
124551 TCTTCAATCTACTCTACTTCAACTTCAGAGAAATAAGATTTG---TA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * *
124595 GCTTTAA-CTTCCTCCAATGCAACTTCAGGGAGATGAA-ATTTGT--GA
1 GCTTTAATC-TGCTCCACTGCAACTTCAGGGAGAT-AAGATTTGTACTA
** * * *
124640 -CTTTAATCTTTTCCACTGCCACTTCA-GAAGCATAGGATTTGTGACTTGTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAG-ATAAGATTTGT-AC---TA
* ** * * * *
124690 ACTTTAATCTATTCCACTGTAACTTTAGGGAAATAAGATTCG--C-A
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * * *
124734 TCTTCAACCTGCTCCATTGCAACTTCAGGGAGATAAGA-TT-TA-TA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * * * *
124778 GCTTTAATCTACACTACTGTAACTTCAGAGAGATAAGA-TT-TACTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * ** * * * * *
124823 TCTTCAATCTTTTCCATTGCAACTTCAAGCAAATAAGA--TATA-TA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * *
124867 GCTTTAATCTGCTCTACTCCAACTTCAGAGAGATAAGATTTG--CTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * **
124912 TCTTCAATCTTTTCCACTGCAACTTCAGGGAGATAAGATTT-T-CTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * ** **
124957 TCTTCAATCTTTTCCACTGCAACTTCAGATAGATAAGA-TT-TA-TA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
** ** *
125001 ATTTTAATCTGCTATACTGCAACTTCAGAGAGATAAGATTTG-A-TA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * * *
125046 TCTTCAATCTGTTCCACTGCAGCTTCAGGGAGATAAGA-TT-TA-TA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * * * *
125090 TCTTCAATCTACCCCACTGCCACTTCAGGGAGATAAGATTTGTAACTTGTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGT-AC---TA
* * *
125141 GCTTTAATCTGTTCCACTGCAACTTCAGGGAAATAAGATTCG--CTA
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* *
125186 TCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTA-T-
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
* * *
125231 -CTTTAATATACTCTACTGCAACTTCAGGGAGAT
1 GCTTTAATCTGCTCCACTGCAACTTCAGGGAGAT
125264 GAAATTCGTG
Statistics
Matches: 806, Mismatches: 173, Indels: 121
0.73 0.16 0.11
Matches are distributed among these distances:
42 1 0.00
43 10 0.01
44 357 0.44
45 254 0.32
46 5 0.01
47 3 0.00
48 3 0.00
49 2 0.00
50 33 0.04
51 132 0.16
52 4 0.00
54 2 0.00
ACGTcount: A:0.30, C:0.21, G:0.16, T:0.33
Consensus pattern (47 bp):
GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGTACTA
Found at i:128874 original size:33 final size:33
Alignment explanation
Indices: 128828--128928 Score: 184
Period size: 33 Copynumber: 3.1 Consensus size: 33
128818 TGGTACCAAG
128828 GATGGTCACCCTTTTCTTCTTCCTCAATATTGT
1 GATGGTCACCCTTTTCTTCTTCCTCAATATTGT
* *
128861 GATGGTCATCCTTTTCTTCTTCCTTAATATTGT
1 GATGGTCACCCTTTTCTTCTTCCTCAATATTGT
128894 GATGGTCACCCTTTTCTTCTTCCTCAATATTGT
1 GATGGTCACCCTTTTCTTCTTCCTCAATATTGT
128927 GA
1 GA
128929 CAATGGAATG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 64 1.00
ACGTcount: A:0.16, C:0.25, G:0.13, T:0.47
Consensus pattern (33 bp):
GATGGTCACCCTTTTCTTCTTCCTCAATATTGT
Found at i:133306 original size:19 final size:20
Alignment explanation
Indices: 133284--133326 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
133274 GGTCTTTTTG
* *
133284 TGAAATTTAATGCATATG-A
1 TGAAATGTAATGCACATGAA
133303 TGAAATGTAATGCACATGAA
1 TGAAATGTAATGCACATGAA
133323 TGAA
1 TGAA
133327 TGCAAAAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (20 bp):
TGAAATGTAATGCACATGAA
Found at i:135521 original size:23 final size:23
Alignment explanation
Indices: 135479--135522 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
135469 TGGTATTAAT
*
135479 AATAAAATAAATAAAGTAATACA
1 AATAAAATAAATAAAATAATACA
135502 AATAAAA-AAATAAAAATAATA
1 AATAAAATAAAT-AAAATAATA
135523 TTTTATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.20
Consensus pattern (23 bp):
AATAAAATAAATAAAATAATACA
Found at i:135589 original size:66 final size:66
Alignment explanation
Indices: 135519--137077 Score: 3118
Period size: 66 Copynumber: 23.6 Consensus size: 66
135509 AAATAAAAAT
135519 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
135584 A
66 A
135585 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
135650 A
66 A
135651 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
135716 A
66 A
135717 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
135782 A
66 A
135783 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
135848 A
66 A
135849 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
135914 A
66 A
135915 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
135980 A
66 A
135981 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136046 A
66 A
136047 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136112 A
66 A
136113 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136178 A
66 A
136179 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136244 A
66 A
136245 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136310 A
66 A
136311 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136376 A
66 A
136377 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136442 A
66 A
136443 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136508 A
66 A
136509 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136574 A
66 A
136575 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136640 A
66 A
136641 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136706 A
66 A
136707 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136772 A
66 A
136773 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136838 A
66 A
136839 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136904 A
66 A
136905 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
136970 A
66 A
136971 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
137036 A
66 A
137037 AATATTTTATGAAATTATATATTAATATAATAATAAAATTA
1 AATATTTTATGAAATTATATATTAATATAATAATAAAATTA
137078 CACTATCATA
Statistics
Matches: 1493, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 1493 1.00
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (66 bp):
AATATTTTATGAAATTATATATTAATATAATAATAAAATTAGATAAATTCATCATTTAATCCTTT
A
Found at i:141369 original size:131 final size:132
Alignment explanation
Indices: 141214--141487 Score: 541
Period size: 131 Copynumber: 2.1 Consensus size: 132
141204 ATAACAATTA
141214 GTAATAAAAAATTTATTTGTCCGAATGAACAATTTAAAGGTGAAAAAGAGTTATGGATGGAAGTA
1 GTAATAAAAAATTTATTTGTCCGAATGAACAATTTAAAGGTGAAAAAGAGTTATGGATGGAAGTA
141279 AATTTTGTATAAAAGAAAATTTACCTTTTAACTTTTATAATATTTTTTTTATTTAATATAAAATT
66 AATTTTGTATAAAAGAAAATTTACCTTTTAACTTTTATAATATTTTTTTTATTTAATATAAAATT
141344 TT
131 TT
141346 GTAATAAAAAA-TTATTTGTCCGAATGAACAATTTAAAGGTGAAAAAGAGTTATGGATGGAAGTA
1 GTAATAAAAAATTTATTTGTCCGAATGAACAATTTAAAGGTGAAAAAGAGTTATGGATGGAAGTA
141410 AATTTTGTATAAAAGAAAATTTACCTTTTAACTTTTATAATATTTTTTTTATTTAATATAAAATT
66 AATTTTGTATAAAAGAAAATTTACCTTTTAACTTTTATAATATTTTTTTTATTTAATATAAAATT
141475 TT
131 TT
141477 GTAATAAAAAA
1 GTAATAAAAAA
141488 ATATCTCTCC
Statistics
Matches: 142, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
131 131 0.92
132 11 0.08
ACGTcount: A:0.43, C:0.04, G:0.12, T:0.41
Consensus pattern (132 bp):
GTAATAAAAAATTTATTTGTCCGAATGAACAATTTAAAGGTGAAAAAGAGTTATGGATGGAAGTA
AATTTTGTATAAAAGAAAATTTACCTTTTAACTTTTATAATATTTTTTTTATTTAATATAAAATT
TT
Found at i:144552 original size:22 final size:21
Alignment explanation
Indices: 144524--144574 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
144514 TTTGAATAAA
*
144524 TTTTTTAAAATTTTTTTGAATT
1 TTTTTTAAAA-TTTGTTGAATT
*
144546 TTTTTTAAAATTTGTTGATTT
1 TTTTTTAAAATTTGTTGAATT
144567 TTTTTTAA
1 TTTTTTAA
144575 TTTTATAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 17 0.63
22 10 0.37
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (21 bp):
TTTTTTAAAATTTGTTGAATT
Found at i:147370 original size:6 final size:6
Alignment explanation
Indices: 147328--147368 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
147318 AATAGTGATA
*
147328 ATAATG ATAATG ATAATG ATAATG ATAATG ATAATA ATAAT
1 ATAATG ATAATG ATAATG ATAATG ATAATG ATAATG ATAAT
147369 AACAACAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (6 bp):
ATAATG
Found at i:150605 original size:46 final size:46
Alignment explanation
Indices: 150547--150911 Score: 278
Period size: 46 Copynumber: 8.0 Consensus size: 46
150537 TGTAATTAAG
* * *
150547 GTGTATAAATGTTGTTAATAG-AGATGTTAAAGTGCTGCAAATTGAA
1 GTGTTTAAATGTTGTAAATTGAAG-TGTTAAAGTGCTGCAAATTGAA
* *
150593 GTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGTTACAAATTGAA
1 GTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGAA
* * * *
150639 GTATTTAAATGCTGTGAATTGAAGTGTTAAAGTGATGCAAATTGAA
1 GTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGAA
* *
150685 GTGTTTAAATGTTGTAAATTGAAGTGTTTTAAGTACTGCAAATTGAA
1 GTGTTTAAATGTTGTAAATTGAAGTG-TTAAAGTGCTGCAAATTGAA
* * ** * * *
150732 TTGTATAGTTGCTTG-AAATTG-AGATGTT-TA-T-CATTG-TAATTGAG
1 GTGTTTAAATG-TTGTAAATTGAAG-TGTTAAAGTGC--TGCAAATTGAA
* * * * * * *
150776 GTGTATAAATGTTGTTAATTG-GGATGTTAAAGTGTTGTAAGTTGAG
1 GTGTTTAAATGTTGTAAATTGAAG-TGTTAAAGTGCTGCAAATTGAA
* * * * ** *
150822 GTGTTTAAATGCTGTAAACTGAAGTGTTTAATTGCTATAAATTGAG
1 GTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGAA
* * * * *
150868 GTGCTCAAATGATGTAAATTGAAGTGTTTAAGTGCTACAAATTG
1 GTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTGCAAATTG
150912 TGGTGTACAA
Statistics
Matches: 259, Mismatches: 48, Indels: 24
0.78 0.15 0.07
Matches are distributed among these distances:
43 4 0.02
44 26 0.10
45 6 0.02
46 185 0.71
47 35 0.14
48 3 0.01
ACGTcount: A:0.33, C:0.04, G:0.24, T:0.39
Consensus pattern (46 bp):
GTGTTTAAATGTTGTAAATTGAAGTGTTAAAGTGCTGCAAATTGAA
Found at i:150848 original size:23 final size:23
Alignment explanation
Indices: 150573--150903 Score: 212
Period size: 23 Copynumber: 14.4 Consensus size: 23
150563 AATAGAGATG
*
150573 TTAAAGTGCTGCAAATTGAAGTGT
1 TTAAA-TGCTGTAAATTGAAGTGT
*
150597 TTAAATGTTGTAAATTGAAGTG-
1 TTAAATGCTGTAAATTGAAGTGT
* ** *
150619 TTAAAGTGTTACAAATTGAAGTAT
1 TTAAA-TGCTGTAAATTGAAGTGT
*
150643 TTAAATGCTGTGAATTGAAGTG-
1 TTAAATGCTGTAAATTGAAGTGT
* *
150665 TTAAAGTGATGCAAATTGAAGTGT
1 TTAAA-TGCTGTAAATTGAAGTGT
*
150689 TTAAATGTTGTAAATTGAAGTGTT
1 TTAAATGCTGTAAATTGAAGTG-T
* * * *
150713 TTAAGTACTGCAAATTGAATTGT
1 TTAAATGCTGTAAATTGAAGTGT
* **
150736 ATAGTTGCT-TGAAATTG-AGATGT
1 TTAAATGCTGT-AAATTGAAG-TGT
* *
150759 TTATCAT--TGT-AATTGAGGTGT
1 TTA-AATGCTGTAAATTGAAGTGT
* * * *
150780 ATAAATGTTGTTAATTG-GGATG-
1 TTAAATGCTGTAAATTGAAG-TGT
* * *
150802 TTAAAGTGTTGTAAGTTGAGGTGT
1 TTAAA-TGCTGTAAATTGAAGTGT
*
150826 TTAAATGCTGTAAACTGAAGTGT
1 TTAAATGCTGTAAATTGAAGTGT
* * * *
150849 TTAATTGCTATAAATTGAGGTGC
1 TTAAATGCTGTAAATTGAAGTGT
* *
150872 TCAAATGATGTAAATTGAAGTGT
1 TTAAATGCTGTAAATTGAAGTGT
*
150895 TTAAGTGCT
1 TTAAATGCT
150904 ACAAATTGTG
Statistics
Matches: 237, Mismatches: 53, Indels: 35
0.73 0.16 0.11
Matches are distributed among these distances:
20 2 0.01
21 10 0.04
22 22 0.09
23 162 0.68
24 41 0.17
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.39
Consensus pattern (23 bp):
TTAAATGCTGTAAATTGAAGTGT
Found at i:150923 original size:46 final size:46
Alignment explanation
Indices: 150817--150925 Score: 139
Period size: 46 Copynumber: 2.4 Consensus size: 46
150807 GTGTTGTAAG
* * * * *
150817 TTGAGGTGTTTAAATGCTGTAAACTGAAGTGTTTAATTGCTATAAA
1 TTGAGGTGCTCAAATGATGTAAACTGAAGTGTTTAAGTGCTACAAA
*
150863 TTGAGGTGCTCAAATGATGTAAATTGAAGTGTTTAAGTGCTACAAA
1 TTGAGGTGCTCAAATGATGTAAACTGAAGTGTTTAAGTGCTACAAA
*
150909 TTGTGGTG-TACAAATGA
1 TTGAGGTGCT-CAAATGA
150926 GTCTAAAATT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
45 1 0.02
46 54 0.98
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (46 bp):
TTGAGGTGCTCAAATGATGTAAACTGAAGTGTTTAAGTGCTACAAA
Found at i:153892 original size:44 final size:42
Alignment explanation
Indices: 153570--154385 Score: 383
Period size: 44 Copynumber: 18.7 Consensus size: 42
153560 GGCTTTAATT
* *
153570 TGCTCCA-TCGCAACTTCAGGGAGATAAGATTTGCCAACTTCAGTC
1 TGCTCCACT-GCAACTTCAGGGAGATAAGACTTG-C-TCTT-AGTC
* *
153615 TGC-CTCACTGCAATTTCA-GGAGGATAAGACTTACTTTGCTTAGTC
1 TGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGC--T-CTTAGTC
* * * *
153660 TGCTCCACTGTAACTTCAGGGAGATAAGATTTGATGC-GA-TC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCT-CTTAGTC
* * * * * *
153701 TGCT-CTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTCTTAGTC
** ** * * * * * *
153744 CACTCCACTATAATTTTAGGGAGATAGGA-TTGTTGGCTTTAATT
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCT--C-TTAGTC
* * * *
153788 TGCTCCACTGCAACTTCAGAGAGATCAGCCTTACCATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTT-GC-TCTT-AGTC
* *
153833 TGCCCCACTGCAACTTCA-AGAGGATAAGACTTGCTTACTTAGTC
1 TGCTCCACTGCAACTTCAGGGA-GATAAGACTTGC-T-CTTAGTC
* * * *
153877 TGCTCCACTGTAACTTCAGGGAGATAAGACTAGATGC-GA-TC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCT-CTTAGTC
* * * * * *
153918 TGCT-CTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTCTTAGTC
* * * * * * *
153961 CGTTCCAATGCAAGTTCAGGGAGATAGGATTATCGGCT-TTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACT-T--GCTCTTAGTC
* *
154005 TGCTCCACTGTAACTTCAAGGAGATAAGACTTGCCATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTG-C-TCTT-AGTC
*
154050 TGCCCCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTTAGTC
1 TGCTCCACTGCAACTTCAGGGA-GATAAGACTTGC-T-CTTAGTC
* * * *
154094 TGCTCTACTGTAACTTCAGGGAGATAAGACTAGCTGC-GA-TC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCT-CTTAGTC
* * * * ** * * *
154135 TGCT-CTCTGCAACTTTAGAGAGATAATATCCGAGGTTTTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGA--CTTGCTCTTAGTC
* * * * *
154178 TGCTCCAATGCAACTTCAAGGAGATAGGATTATCGGCT-TTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACT-T--GCTCTTAGTC
* * * *
154222 TGTTCCACTACAACTTCAGGGAGATAAGATTATCGGCT-TTAATC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACT-T--GCTCTTAGTC
*
154266 TGCTCCACTGTAACTTCAGGGAGATAAGACTTGCCATCTTCAGTC
1 TGCTCCACTGCAACTTCAGGGAGATAAGACTTG-C-TCTT-AGTC
* *
154311 TGCCCCACTGCAACTTCA-GGAGGATAAGACTTGCTTATTTAGTC
1 TGCTCCACTGCAACTTCAGGGA-GATAAGACTTGC-T-CTTAGTC
*
154355 TGCTCCACTGTAACTTCAGGGAGATAAGACT
1 TGCTCCACTGCAACTTCAGGGAGATAAGACT
154386 AGATGCGATA
Statistics
Matches: 590, Mismatches: 130, Indels: 103
0.72 0.16 0.13
Matches are distributed among these distances:
40 60 0.10
41 25 0.04
42 18 0.03
43 26 0.04
44 293 0.50
45 159 0.27
46 8 0.01
47 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (42 bp):
TGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTCTTAGTC
Found at i:153936 original size:217 final size:217
Alignment explanation
Indices: 153558--154341 Score: 1022
Period size: 217 Copynumber: 3.6 Consensus size: 217
153548 CACTCCACTG
* * * * * *
153558 TCGGCTTTAATTTGCTCCA-TCGCAACTTCAGGGAGATAAGATTTGCCAACTTCAGTCTGCCTCA
1 TCGGCTTTAATCTGCTCCACT-GCAACTTCAGAGAGATAAGACTTACCATCTTCAGTCTGCCCCA
* * * *
153622 CTGCAATTTCAGGAGGATAAGACTTACTTTGCTTAGTCTGCTCCACTGTAACTTCAGGGAGATAA
65 CTGCAACTTCAAGAGGATAAGACTTGC-TTACTTAGTCTGCTCCACTGTAACTTCAGGGAGATAA
* * * *
153687 GATTTGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCACTCCAC
129 GACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCAA
** * * *
153752 TATAATTTTAGGGAGATAGGATTG
194 TGCAACTTCAGGGAGATAGGATTA
* * * *
153776 TTGGCTTTAATTTGCTCCACTGCAACTTCAGAGAGATCAGCCTTACCATCTTCAGTCTGCCCCAC
1 TCGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTTACCATCTTCAGTCTGCCCCAC
153841 TGCAACTTCAAGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGA
66 TGCAACTTCAAGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGA
*
153906 CTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGTTCCAATG
131 CTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCAATG
*
153971 CAAGTTCAGGGAGATAGGATTA
196 CAACTTCAGGGAGATAGGATTA
* *
153993 TCGGCTTTAATCTGCTCCACTGTAACTTCA-AGGAGATAAGACTTGCCATCTTCAGTCTGCCCCA
1 TCGGCTTTAATCTGCTCCACTGCAACTTCAGA-GAGATAAGACTTACCATCTTCAGTCTGCCCCA
* *
154057 CTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTCTACTGTAACTTCAGGGAGATAAG
65 CTGCAACTTCAAGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAG
* * * * *
154122 ACTAGCTGCGATCTGCTCTCTGCAACTTTAGAGAGATAATATCCGAGGTTTTAATCTGCTCCAAT
130 ACTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCAAT
*
154187 GCAACTTCAAGGAGATAGGATTA
195 GCAACTTCAGGGAGATAGGATTA
* * * * ** * * *
154210 TCGGCTTTAATCTGTTCCACTACAACTTCAGGGAGATAAGA-TTATCGGCTTTAATCTGCTCCAC
1 TCGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTTACCATCTTCAGTCTGCCCCAC
* * * * *
154274 TGTAACTTC-AGGGAGATAAGACTTGC-CATCTTCAGTCTGCCCCACTGCAACTTCA-GGAGGAT
66 TGCAACTTCAAGAG-GATAAGACTTGCTTA-CTT-AGTCTGCTCCACTGTAACTTCAGGGA-GAT
154336 AAGACT
127 AAGACT
154342 TGCTTATTTA
Statistics
Matches: 503, Mismatches: 56, Indels: 15
0.88 0.10 0.03
Matches are distributed among these distances:
215 3 0.01
216 43 0.09
217 378 0.75
218 78 0.16
219 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (217 bp):
TCGGCTTTAATCTGCTCCACTGCAACTTCAGAGAGATAAGACTTACCATCTTCAGTCTGCCCCAC
TGCAACTTCAAGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGA
CTAGATGCGATCTGCTCTCTGCAACTTCAGAGAGATAAGATCTGAGGTTTTAATCCGCTCCAATG
CAACTTCAGGGAGATAGGATTA
Found at i:154096 original size:89 final size:88
Alignment explanation
Indices: 153563--154385 Score: 418
Period size: 89 Copynumber: 9.4 Consensus size: 88
153553 CACTGTCGGC
* * * * *
153563 TTTAATTTGCTCCA-TCGCAACTTCAGGGAGATAAGATTTGCCAACTTCAGTCTGCCTCACTGCA
1 TTTAATCTGCTCCACT-GTAACTTCAGGGAGATAAGACTTGCCAGCTTCAGTCTGCCCCACTGCA
* *
153627 ATTTCAGGAG-GATAAGACTTACTT
65 ACTTCAGGAGAGATAAGACTTGC-T
* * * * *
153651 TGCTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGATTTG--A--TGC-GATCTG-CTCTCTG
1 T--TTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGCCAGCTTCAG-TCTGCCCCACTG
* *
153710 CAACTTCA-GAGAGATAAGATCTGAGGT
63 CAACTTCAGGAGAGATAAGA-CT-TGCT
** * * * * *** * * * *
153737 TTTAATCCACTCCACTATAATTTTAGGGAGATAGGA-TTGTTGGCTTTAATTTGCTCCACTGCAA
1 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGCCAGCTTCAGTCTGCCCCACTGCAA
* * *
153801 CTTCA-GAGAGATCAGCCTTACCAT
66 CTTCAGGAGAGATAAGACTT-GC-T
* * * * * * *
153825 CTTCAGTCTGCCCCACTGCAACTTCA-AGAGGATAAGACTTGCTTA-CTT-AGTCTGCTCCACTG
1 -TTTAATCTGCTCCACTGTAACTTCAGGGA-GATAAGACTTGC-CAGCTTCAGTCTGCCCCACTG
* * *
153887 TAACTTCAGG-GAGATAAGACTAG-A
63 CAACTTCAGGAGAGATAAGACTTGCT
*** * * * * * * * ** *
153911 TGCGATCTGCT-CTCTGCAACTTCAGAGAGATAAGA-TCTG--AGGTTTTAATCCGTTCCAATGC
1 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACT-TGCCA-GCTTCAGTCTGCCCCACTGC
* * *
153972 AAGTTCAGG-GAGATAGGATTATCGGC-
64 AACTTCAGGAGAGATAAGACT-T--GCT
* *
153998 TTTAATCTGCTCCACTGTAACTTCAAGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAA
1 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGCCAGCTTCAGTCTGCCCCACTGCAA
154063 CTTCAGGAG-GATAAGACTTGCT
66 CTTCAGGAGAGATAAGACTTGCT
* * * * *
154085 TACTTAGTCTGCTCTACTGTAACTTCAGGGAGATAAGAC-T---AGCTGC-GATCTG-CTCTCTG
1 T--TTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGCCAGCTTCAG-TCTGCCCCACTG
* * ** *
154144 CAACTTTA-GAGAGATAATATCCGAGGT
63 CAACTTCAGGAGAGATAAGA--CTTGCT
* * * * ** * * * ** *
154171 TTTAATCTGCTCCAATGCAACTTCAAGGAGATAGGA-TTATCGGCTTTAATCTGTTCCACTACAA
1 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGCCAGCTTCAGTCTGCCCCACTGCAA
*
154235 CTTCAGG-GAGATAAGATTATCGGC-
66 CTTCAGGAGAGATAAGACT-T--GCT
*
154259 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAA
1 TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGCCAGCTTCAGTCTGCCCCACTGCAA
154324 CTTCAGGAG-GATAAGACTTGCTT
66 CTTCAGGAGAGATAAGACTTGC-T
*
154347 ATTTAGTCTGCTCCACTGTAACTTCAGGGAGATAAGACT
1 -TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACT
154386 AGATGCGATA
Statistics
Matches: 549, Mismatches: 130, Indels: 111
0.69 0.16 0.14
Matches are distributed among these distances:
81 1 0.00
83 9 0.02
84 128 0.23
85 39 0.07
86 18 0.03
87 23 0.04
88 101 0.18
89 184 0.34
90 44 0.08
91 2 0.00
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (88 bp):
TTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGACTTGCCAGCTTCAGTCTGCCCCACTGCAA
CTTCAGGAGAGATAAGACTTGCT
Found at i:154111 original size:261 final size:258
Alignment explanation
Indices: 153829--154387 Score: 734
Period size: 261 Copynumber: 2.1 Consensus size: 258
153819 TACCATCTTC
* * * * * *
153829 AGTCTGCCCCACTGCAACTTCA-AGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGTAACTT
1 AGTCTGCTCCACTGTAACTTCAGGGA-GATAAGACTAGC-TAC-GA-TCTGCT-CACTGCAACTT
* * *
153893 CAGGGAGATAAGA-CTA-GATGCGATCTGCTCTC-TGCAACTTC-AGAGAGATAAGATCTGA-GG
61 CAGAGAGATAAGACCGAGGATGCAATCTGCTC-CATGCAACTTCAAG-GAGATAAGAT-T-ACGG
* * * *
153953 TTTTAATCCGTTCCAATGCAAGTTCAGGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGTAA
122 CTTTAATCCGTTCCAATACAACTTCAGGGAGATAAGATTATCGGCTTTAATCTGCTCCACTGTAA
154018 CTTCAAGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTG
187 CTTCAAGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTG
154083 CTTACTT
252 CTTACTT
* * * *
154090 AGTCTGCTCTACTGTAACTTCAGGGAGATAAGACTAGCTGCGATCTGCTCTCTGCAACTTTAGAG
1 AGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGCTACGATCTGCTCACTGCAACTTCAGAG
* * ** *
154155 AGATAATATCCGAGGTTTTAATCTGCTCCAATGCAACTTCAAGGAGATAGGATTATCGGCTTTAA
66 AGATAAGA-CCGAGGATGCAATCTGCTCC-ATGCAACTTCAAGGAGATAAGATTA-CGGCTTTAA
* * *
154220 TCTGTTCCACTACAACTTCAGGGAGATAAGATTATCGGCTTTAATCTGCTCCACTGTAACTTCAG
128 TCCGTTCCAATACAACTTCAGGGAGATAAGATTATCGGCTTTAATCTGCTCCACTGTAACTTCAA
*
154285 GGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTATT
193 GGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACT
154350 T
258 T
154351 AGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAG
1 AGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAG
154388 ATGCGATATG
Statistics
Matches: 262, Mismatches: 27, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
257 19 0.07
258 6 0.02
259 5 0.02
260 13 0.05
261 215 0.82
262 4 0.02
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (258 bp):
AGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTAGCTACGATCTGCTCACTGCAACTTCAGAG
AGATAAGACCGAGGATGCAATCTGCTCCATGCAACTTCAAGGAGATAAGATTACGGCTTTAATCC
GTTCCAATACAACTTCAGGGAGATAAGATTATCGGCTTTAATCTGCTCCACTGTAACTTCAAGGA
GATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGAGGATAAGACTTGCTTACTT
Found at i:178802 original size:17 final size:15
Alignment explanation
Indices: 178765--178796 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
178755 ATTTTCATTT
178765 TATT-ATTTAAAATA
1 TATTAATTTAAAATA
178779 TATTAATTTAAAATA
1 TATTAATTTAAAATA
178794 TAT
1 TAT
178797 ATTAATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATTAATTTAAAATA
Found at i:197784 original size:16 final size:16
Alignment explanation
Indices: 197751--197810 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
197741 ACAAATGTAT
*
197751 AAATATATATAATATA
1 AAATATATAAAATATA
197767 AAATATATAAAAGT-TA
1 AAATATATAAAA-TATA
* * *
197783 AAAGAGATAAAATAAA
1 AAATATATAAAATATA
*
197799 AAAAATATAAAA
1 AAATATATAAAA
197811 CGTATGTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
15 1 0.03
16 34 0.94
17 1 0.03
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (16 bp):
AAATATATAAAATATA
Found at i:199508 original size:45 final size:45
Alignment explanation
Indices: 199452--199610 Score: 180
Period size: 45 Copynumber: 3.6 Consensus size: 45
199442 ATAAGACTTG
*
199452 TATCTTTGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGT
1 TATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGT
* ** ** ** *
199497 TATCTTCGATCTACTTCGCCACTGATATGGGAAGACAAGATCTGC
1 TATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGT
*
199542 TATCTTCGATCTACTTCA-TGCCAATACATGAAGACAAGATCTGCT
1 TATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTG-T
*
199587 T-TCTTCGATC-GCTTCCACTGCCAA
1 TATCTTCGATCTACTT-CACTGCCAA
199611 CCAGGGAGAT
Statistics
Matches: 92, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
43 3 0.03
44 29 0.32
45 60 0.65
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.31
Consensus pattern (45 bp):
TATCTTCGATCTACTTCACTGCCAATACAGGAAGACAAGATCTGT
Found at i:199780 original size:132 final size:132
Alignment explanation
Indices: 199620--199871 Score: 353
Period size: 132 Copynumber: 1.9 Consensus size: 132
199610 ACCAGGGAGA
** ** *
199620 TAGAATTACTGGCTTCAATATACTCCACTGTAACTTCAGAGAGGTAAAATTTACCATCTTTGATC
1 TAGAATTACTGGCTTCAATATACTCCACTGTAACCACAGAGAGGTAAAATCCACCATCCTTGATC
* * *
199685 TGCTCCACTACTGCTT-GAGGAGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCTAGGG
66 TGCTCCACTACTACTTAG-GGAGACAAGATCTGAAATATTCAATCTATTCAACTGCTGCCTAGGG
199749 AAG
130 AAG
* * * *
199752 TAGAATTACTGGCTTCACTGTACTCCACTGTAACCACAGGGAGGTAAAATCCGCCATCCTTGATC
1 TAGAATTACTGGCTTCAATATACTCCACTGTAACCACAGAGAGGTAAAATCCACCATCCTTGATC
* * *
199817 TGCTCCACTACTACTTAGGGAGATAAGATCTGTAATATTCAATCTGTTCAACTGC
66 TGCTCCACTACTACTTAGGGAGACAAGATCTGAAATATTCAATCTATTCAACTGC
199872 AATGTCGGGG
Statistics
Matches: 104, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
132 103 0.99
133 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (132 bp):
TAGAATTACTGGCTTCAATATACTCCACTGTAACCACAGAGAGGTAAAATCCACCATCCTTGATC
TGCTCCACTACTACTTAGGGAGACAAGATCTGAAATATTCAATCTATTCAACTGCTGCCTAGGGA
AG
Found at i:199913 original size:50 final size:50
Alignment explanation
Indices: 199854--200521 Score: 448
Period size: 50 Copynumber: 13.4 Consensus size: 50
199844 ATCTGTAATA
* *
199854 TTCAATCTGTTCAACTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGC
1 TTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* * *** *** * * *
199904 TTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCTGCCGTTGTGGC
1 TTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* * * *
199954 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCATCGTAGC
1 TTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* * * * * * *** * * *
200004 TTCAATTTGTTCTATTGCACT-GCTAAGGAAGTAAGATCCACCGTTGTGGC
1 TTCAATCTGTTCAACTGCAATATC-AGGGAAACCAGATCCGCCGTCGTAGC
* * * *
200054 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCACCGTCGTAGC
1 TTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* * * * *** * * *
200104 TTCAATCTGTTCCACTGCACT-GCTAAGGAAGTAAGATCCGTCGTTGTGGC
1 TTCAATCTGTTCAACTGCAATATC-AGGGAAACCAGATCCGCCGTCGTAGC
* * * * *
200154 TTTAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCACCGTCGTAGC
1 TTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* * * *** * ** * *
200204 TTCAATCTGTTCCACTGCACT-GCTA-GGAAGTAAGATCCACTATTGTGGC
1 TTCAATCTGTTCAACTGCAATATC-AGGGAAACCAGATCCGCCGTCGTAGC
* * *
200253 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
1 TTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* * * *** * * *
200303 TTCAATCTGTTCCACTGCACTA-CTAAGGAAGTAAGATCCACCGTTGTGGC
1 TTCAATCTGTTCAACTGCAATATC-AGGGAAACCAGATCCGCCGTCGTAGC
* * * *
200353 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCCGTCGTAGC
1 TTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
* * * *** * * *
200403 TTCAATCTGTTCCACTGCACTA-CTAAGGAAGTAAGATCCGTCGTTGTGGC
1 TTCAATCTGTTCAACTGCAATATC-AGGGAAACCAGATCCGCCGTCGTAGC
* * * *
200453 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCCGTCGTAGC
1 TTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
*
200503 TTCAATCTGTTCCACTGCA
1 TTCAATCTGTTCAACTGCA
200522 TTGCTAAGGA
Statistics
Matches: 443, Mismatches: 164, Indels: 22
0.70 0.26 0.03
Matches are distributed among these distances:
49 39 0.09
50 400 0.90
51 4 0.01
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (50 bp):
TTCAATCTGTTCAACTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGC
Found at i:199973 original size:100 final size:100
Alignment explanation
Indices: 199854--200540 Score: 1054
Period size: 100 Copynumber: 6.9 Consensus size: 100
199844 ATCTGTAATA
* * * * *
199854 TTCAATCTGTTCAACTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
* * **
199919 CGCACCG-TCAGGGAAGTAAGATCTGCCGTTGTGGC
66 TGCACCGCT-AAGGAAGTAAGATCCACCGTTGTGGC
* * * *
199954 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCATCGTAGCTTCAATTTGTTCTAT
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
*
200019 TGCACTGCTAAGGAAGTAAGATCCACCGTTGTGGC
66 TGCACCGCTAAGGAAGTAAGATCCACCGTTGTGGC
*
200054 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
* **
200119 TGCACTGCTAAGGAAGTAAGATCCGTCGTTGTGGC
66 TGCACCGCTAAGGAAGTAAGATCCACCGTTGTGGC
* *
200154 TTTAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
* **
200219 TGCACTGCT-AGGAAGTAAGATCCACTATTGTGGC
66 TGCACCGCTAAGGAAGTAAGATCCACCGTTGTGGC
200253 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
**
200318 TGCACTACTAAGGAAGTAAGATCCACCGTTGTGGC
66 TGCACCGCTAAGGAAGTAAGATCCACCGTTGTGGC
*
200353 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
** **
200418 TGCACTACTAAGGAAGTAAGATCCGTCGTTGTGGC
66 TGCACCGCTAAGGAAGTAAGATCCACCGTTGTGGC
*
200453 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
**
200518 TGCATTGCTAAGGAAGTAAGATC
66 TGCACCGCTAAGGAAGTAAGATC
200541 TATGGTTCCG
Statistics
Matches: 549, Mismatches: 36, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
99 92 0.17
100 456 0.83
101 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (100 bp):
TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
TGCACCGCTAAGGAAGTAAGATCCACCGTTGTGGC
Found at i:200418 original size:299 final size:300
Alignment explanation
Indices: 199854--200540 Score: 1135
Period size: 299 Copynumber: 2.3 Consensus size: 300
199844 ATCTGTAATA
* * * * *
199854 TTCAATCTGTTCAACTGCAATGTCGGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
* * * ** *
199919 CGCACCG-TCAGGGAAGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGA
66 TGCACTGCT-AAGGAAGTAAGATCCACCATTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGA
* * * *
199983 AACCAGATCCGCCATCGTAGCTTCAATTTGTTCTATTGCACTGCTAAGGAAGTAAGATCCACCGT
130 AACCAGATCCGCCATCGTAGCTTCAATCTGTTCCACTGCACTACTAAGGAAGTAAGATCCACCGT
200048 TGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTG
195 TGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTG
*
200113 TTCCACTGCACTGCTAAGGAAGTAAGATCCGTCGTTGTGGC
260 TTCCACTGCACTACTAAGGAAGTAAGATCCGTCGTTGTGGC
* *
200154 TTTAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
*
200219 TGCACTGCT-AGGAAGTAAGATCCACTATTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAA
66 TGCACTGCTAAGGAAGTAAGATCCACCATTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAA
*
200283 ACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACTGCACTACTAAGGAAGTAAGATCCACCGTT
131 ACCAGATCCGCCATCGTAGCTTCAATCTGTTCCACTGCACTACTAAGGAAGTAAGATCCACCGTT
**
200348 GTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGT
196 GTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGT
200413 TCCACTGCACTACTAAGGAAGTAAGATCCGTCGTTGTGGC
261 TCCACTGCACTACTAAGGAAGTAAGATCCGTCGTTGTGGC
*
200453 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCTGCCGTCGTAGCTTCAATCTGTTCCAC
1 TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
*
200518 TGCATTGCTAAGGAAGTAAGATC
66 TGCACTGCTAAGGAAGTAAGATC
200541 TATGGTTCCG
Statistics
Matches: 359, Mismatches: 26, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
299 282 0.79
300 76 0.21
301 1 0.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (300 bp):
TTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCAC
TGCACTGCTAAGGAAGTAAGATCCACCATTGTGGCTTCAATCTTTTTAATTGCAATATCAGGGAA
ACCAGATCCGCCATCGTAGCTTCAATCTGTTCCACTGCACTACTAAGGAAGTAAGATCCACCGTT
GTGGCTTCAATCTTTTTAATTGCAATATCAGGGAAACCAGATCCACCGTCGTAGCTTCAATCTGT
TCCACTGCACTACTAAGGAAGTAAGATCCGTCGTTGTGGC
Found at i:201802 original size:7 final size:7
Alignment explanation
Indices: 201783--201824 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
201773 TTAGCCTCTC
201783 CATTTTT
1 CATTTTT
201790 -ACTTTTT
1 CA-TTTTT
201797 CATTTTT
1 CATTTTT
201804 CATTTTT
1 CATTTTT
201811 C-TCTTTT
1 CAT-TTTT
201818 CATTTTT
1 CATTTTT
201825 TCACATCACT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
6 2 0.06
7 27 0.87
8 2 0.06
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (7 bp):
CATTTTT
Found at i:201807 original size:21 final size:21
Alignment explanation
Indices: 201783--201824 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
201773 TTAGCCTCTC
201783 CATTTTTACT-TTTTCATTTTT
1 CATTTTT-CTCTTTTCATTTTT
201804 CATTTTTCTCTTTTCATTTTT
1 CATTTTTCTCTTTTCATTTTT
201825 TCACATCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.71
Consensus pattern (21 bp):
CATTTTTCTCTTTTCATTTTT
Found at i:211846 original size:86 final size:84
Alignment explanation
Indices: 211701--211868 Score: 257
Period size: 86 Copynumber: 2.0 Consensus size: 84
211691 ATTTAAATCC
* * *
211701 TTTAAAACATTATAAAGATATAAACTATTAAAATAGTAAATTTACATTTTAGCTTTTATAAATAA
1 TTTAAAAAATTATAAAGATATAAACTATTAAAATAGTAAAATTACATTTTAGCTCTTATAAA-AA
211766 TATACAACTTAATATCTGCAT
65 TATACAACTTAAT-TCTGCAT
*
211787 TTTAAAAAATTATAAAGATATAAGCTATTAAAAT-GATAAAATTACATTTTAGCTCTTATAAAAA
1 TTTAAAAAATTATAAAGATATAAACTATTAAAATAG-TAAAATTACATTTTAGCTCTTATAAAAA
*
211851 TATGCAACTTAATTCTGC
65 TATACAACTTAATTCTGC
211869 TTTGCTACTT
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
84 5 0.07
85 15 0.20
86 56 0.74
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.38
Consensus pattern (84 bp):
TTTAAAAAATTATAAAGATATAAACTATTAAAATAGTAAAATTACATTTTAGCTCTTATAAAAAT
ATACAACTTAATTCTGCAT
Found at i:212379 original size:22 final size:20
Alignment explanation
Indices: 212354--212405 Score: 50
Period size: 22 Copynumber: 2.4 Consensus size: 20
212344 ATTTTAAACC
212354 TTAAATCAATAATTCAATAAAA
1 TTAAATCAAT-ATT-AATAAAA
*
212376 TTAAAATTCAATATTAATAATA
1 TT-AAA-TCAATATTAATAAAA
212398 TATAAATC
1 T-TAAATC
212406 GTTTGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 12 0.46
23 7 0.27
24 5 0.19
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.37
Consensus pattern (20 bp):
TTAAATCAATATTAATAAAA
Found at i:213162 original size:31 final size:31
Alignment explanation
Indices: 213087--213163 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
213077 GTAACATTTC
*
213087 ATAGTTAGGTGACCAAAAAAAAAATTTACTA
1 ATAGTTAGGTGACTAAAAAAAAAATTTACTA
*
213118 ATAGTTAGGTGACTAAAAAAGAAATTTACTA
1 ATAGTTAGGTGACTAAAAAAAAAATTTACTA
213149 ATAGTT-GGCTGACTA
1 ATAGTTAGG-TGACTA
213164 CTAGCATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 2 0.05
31 41 0.95
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.29
Consensus pattern (31 bp):
ATAGTTAGGTGACTAAAAAAAAAATTTACTA
Found at i:213375 original size:16 final size:15
Alignment explanation
Indices: 213334--213376 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
213324 ATTTTATTCT
213334 AATTATAATTATTGA
1 AATTATAATTATTGA
*
213349 AA-TATATATTATTTA
1 AATTATA-ATTATTGA
213364 CAATTATAATTAT
1 -AATTATAATTAT
213377 ATTTGTGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
14 4 0.17
15 9 0.38
16 7 0.29
17 4 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (15 bp):
AATTATAATTATTGA
Found at i:213888 original size:238 final size:239
Alignment explanation
Indices: 213458--213935 Score: 949
Period size: 238 Copynumber: 2.0 Consensus size: 239
213448 AAATTTAAGA
213458 AAAAACTTATATATATAATATAATATCATATCAAACATATACATTTGTAGAATGTAATAAAAGTT
1 AAAAACTTATATATATAATATAATATCATATCAAACATATACATTTGTAGAATGTAATAAAAGTT
213523 GTGAGGGAATTCAAACATTCATTAGATTACGAAGAAAATAGAAATAATGATAACGGATAATGTAA
66 GTGAGGGAATTCAAACATTCATTAGATTACGAAGAAAATAGAAATAATGATAACGGATAATGTAA
213588 TATTTAATCCCTGAATTTAATAATTTTTCACTTTAGTTCTTAAAGGTTTATTTGGCCAACATTAA
131 TATTTAATCCCTGAATTTAATAATTTTTCACTTTAGTTCTTAAAGGTTTATTTGGCCAACATTAA
213653 TCCTGGAATTAGATAAACTTTCTCAATTTGGTTCCTGAGCTTAG
196 TCCTGGAATTAGATAAACTTTCTCAATTTGGTTCCTGAGCTTAG
213697 AAAAACTTATA-ATATAATATAATATCATATCAAACATATACATTTGTAGAATGTAATAAAAGTT
1 AAAAACTTATATATATAATATAATATCATATCAAACATATACATTTGTAGAATGTAATAAAAGTT
213761 GTGAGGGAATTCAAACATTCATTAGATTACGAAGAAAATAGAAATAATGATAACGGATAATGTAA
66 GTGAGGGAATTCAAACATTCATTAGATTACGAAGAAAATAGAAATAATGATAACGGATAATGTAA
213826 TATTTAATCCCTGAATTTAATAATTTTTCACTTTAGTTCTTAAAGGTTTATTTGGCCAACATTAA
131 TATTTAATCCCTGAATTTAATAATTTTTCACTTTAGTTCTTAAAGGTTTATTTGGCCAACATTAA
213891 TCCTGGAATTAGATAAACTTTCTCAATTTGGTTCCTGAGCTTAG
196 TCCTGGAATTAGATAAACTTTCTCAATTTGGTTCCTGAGCTTAG
213935 A
1 A
213936 TTCCTTTAAG
Statistics
Matches: 239, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
238 228 0.95
239 11 0.05
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (239 bp):
AAAAACTTATATATATAATATAATATCATATCAAACATATACATTTGTAGAATGTAATAAAAGTT
GTGAGGGAATTCAAACATTCATTAGATTACGAAGAAAATAGAAATAATGATAACGGATAATGTAA
TATTTAATCCCTGAATTTAATAATTTTTCACTTTAGTTCTTAAAGGTTTATTTGGCCAACATTAA
TCCTGGAATTAGATAAACTTTCTCAATTTGGTTCCTGAGCTTAG
Found at i:218279 original size:39 final size:37
Alignment explanation
Indices: 218235--218324 Score: 94
Period size: 39 Copynumber: 2.4 Consensus size: 37
218225 GAATTTAATA
*
218235 AAAATATATTTTTATTTTTATTTTTTAATTTTTAATTTT
1 AAAATATATTTTTACTTTTA-TTTTT-ATTTTTAATTTT
* *
218274 AAAATAT-TTTAAAATACTTTTATTTTTATTTTTATTTTT
1 AAAATATATTT---TTACTTTTATTTTTATTTTTAATTTT
218313 AAAAT-TATTTTT
1 AAAATATATTTTT
218325 TGGTGTTTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
36 1 0.02
38 4 0.09
39 26 0.60
40 5 0.12
41 7 0.16
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (37 bp):
AAAATATATTTTTACTTTTATTTTTATTTTTAATTTT
Found at i:220725 original size:31 final size:31
Alignment explanation
Indices: 220687--220745 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
220677 CGTTTGTTCA
*
220687 GGACTAAAATTTTA-AAATTCAAAAAGTACAT
1 GGACT-AAATTTAACAAATTCAAAAAGTACAT
220718 GGACTAAATTTAACAAATTCAAAAAGTA
1 GGACTAAATTTAACAAATTCAAAAAGTA
220746 TAGATACTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.53, C:0.10, G:0.10, T:0.27
Consensus pattern (31 bp):
GGACTAAATTTAACAAATTCAAAAAGTACAT
Found at i:225669 original size:8 final size:9
Alignment explanation
Indices: 225648--225673 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
225638 GTGGTGGAAG
225648 AAAAAGAAC
1 AAAAAGAAC
225657 AAAAAGAAC
1 AAAAAGAAC
225666 AAAAAGAA
1 AAAAAGAA
225674 AATGAAAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.81, C:0.08, G:0.12, T:0.00
Consensus pattern (9 bp):
AAAAAGAAC
Found at i:225687 original size:15 final size:15
Alignment explanation
Indices: 225645--225694 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
225635 GTGGTGGTGG
*
225645 AAGAAAAAGAACAAA
1 AAGAAAAAGAAGAAA
225660 AAGAACAAA-AAGAAA
1 AAGAA-AAAGAAGAAA
* *
225675 ATGAAAAAGAAGAAG
1 AAGAAAAAGAAGAAA
225690 AAGAA
1 AAGAA
225695 GCACATCCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 3 0.10
15 23 0.79
16 3 0.10
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (15 bp):
AAGAAAAAGAAGAAA
Found at i:225695 original size:9 final size:9
Alignment explanation
Indices: 225644--225695 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
225634 GGTGGTGGTG
225644 GAAGAAAAA
1 GAAGAAAAA
*
225653 GAACAAAAA
1 GAAGAAAAA
*
225662 GAACAAAAA
1 GAAGAAAAA
225671 GAAAATGAAAAA
1 G--AA-GAAAAA
*
225683 GAAGAAGAA
1 GAAGAAAAA
225692 GAAG
1 GAAG
225696 CACATCCATA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
9 27 0.73
10 2 0.05
11 2 0.05
12 6 0.16
ACGTcount: A:0.73, C:0.04, G:0.21, T:0.02
Consensus pattern (9 bp):
GAAGAAAAA
Found at i:230327 original size:20 final size:20
Alignment explanation
Indices: 230289--230327 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
230279 TCATGTCATC
*
230289 ATCTAAAAATAATATATATA
1 ATCTAAAAATAATAAATATA
230309 ATCTAAAAATTAA-AAATAT
1 ATCTAAAAA-TAATAAATAT
230328 TATAATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
ATCTAAAAATAATAAATATA
Found at i:231078 original size:85 final size:85
Alignment explanation
Indices: 230929--231088 Score: 212
Period size: 85 Copynumber: 1.9 Consensus size: 85
230919 TTCACCATAA
* * *** * * *
230929 GTAAGATAATGTCAGAGATCATGTTAGAATCCAATTTTGGATGATTTTGTGACATACCGGCAACA
1 GTAAGACAATGTCAGAGATCATGTCAGAATCCAATTTCAAATGATTCTATGACATACCGACAACA
230994 ACACAAGTATTTCAAAATAC
66 ACACAAGTATTTCAAAATAC
* * *
231014 GTAAGACAATGTTAGAGATCATGTCAGAATCCAATTTCAAATGATTCTATGACGTACCTACAACA
1 GTAAGACAATGTCAGAGATCATGTCAGAATCCAATTTCAAATGATTCTATGACATACCGACAACA
*
231079 ACATAAGTAT
66 ACACAAGTAT
231089 GTGTAGTGTT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
85 63 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (85 bp):
GTAAGACAATGTCAGAGATCATGTCAGAATCCAATTTCAAATGATTCTATGACATACCGACAACA
ACACAAGTATTTCAAAATAC
Found at i:233296 original size:26 final size:26
Alignment explanation
Indices: 233263--233315 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 26
233253 AAAATTTATA
233263 TATAAAA-TAAAACAATATTTTTATTT
1 TATAAAATTAAAA-AATATTTTTATTT
*
233289 TATAAAATTAAAATATATTTTTATTT
1 TATAAAATTAAAAAATATTTTTATTT
233315 T
1 T
233316 TATTTTATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
TATAAAATTAAAAAATATTTTTATTT
Found at i:241400 original size:31 final size:31
Alignment explanation
Indices: 241333--241400 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
241323 TTAATAGCTC
* * * *
241333 AGTGACTTAAATGAAAAGTTTTAAATAGTTT
1 AGTGATTTAAATGAAAACTTTCAAATAATTT
241364 AGTGATTTAAATGAAAACTTTCAAATAATTT
1 AGTGATTTAAATGAAAACTTTCAAATAATTT
241395 AGTGAT
1 AGTGAT
241401 CATTTTGTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.43, C:0.04, G:0.15, T:0.38
Consensus pattern (31 bp):
AGTGATTTAAATGAAAACTTTCAAATAATTT
Found at i:245093 original size:17 final size:17
Alignment explanation
Indices: 245068--245100 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
245058 ATAATATTTT
*
245068 ATAATAAATATATTTAA
1 ATAAAAAATATATTTAA
245085 ATAAAAAATATATTTA
1 ATAAAAAATATATTTA
245101 TGTTGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
ATAAAAAATATATTTAA
Found at i:252274 original size:28 final size:28
Alignment explanation
Indices: 252239--252293 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
252229 GATACTCAAA
252239 CTTGGCTCCCTTGAGAAATAAAGCTCAG
1 CTTGGCTCCCTTGAGAAATAAAGCTCAG
* *
252267 CTTGGCTCCTTTGAGAAATCAAGCTCA
1 CTTGGCTCCCTTGAGAAATAAAGCTCA
252294 ACTTAACTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.27
Consensus pattern (28 bp):
CTTGGCTCCCTTGAGAAATAAAGCTCAG
Found at i:262877 original size:25 final size:25
Alignment explanation
Indices: 262843--262897 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
262833 TAGACAGAGC
*
262843 TTAAATTATTATTATTATGTTGATT
1 TTAAATTATTATTATTATGTGGATT
262868 TTAAATTATTATTATTATGTGGATT
1 TTAAATTATTATTATTATGTGGATT
262893 TTAAA
1 TTAAA
262898 AGTTGTCAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.56
Consensus pattern (25 bp):
TTAAATTATTATTATTATGTGGATT
Done.