Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 147 of 163
Found at i:40003396 original size:17 final size:17
Alignment explanation
Indices: 40003356--40003421 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
40003346 GCCCAGTGAG
*
40003356 ATAAATTTAGATTTATT
1 ATAAATTTAAATTTATT
* *
40003373 TTGAATTTAAATTTGCA-T
1 ATAAATTTAAATTT--ATT
40003391 A-AAATTTAAATTTATT
1 ATAAATTTAAATTTATT
40003407 ATAAATTTAAATTTA
1 ATAAATTTAAATTTA
40003422 AAATTAAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
15 1 0.03
16 2 0.05
17 35 0.88
18 1 0.03
19 1 0.03
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.50
Consensus pattern (17 bp):
ATAAATTTAAATTTATT
Found at i:40003490 original size:27 final size:28
Alignment explanation
Indices: 40003436--40003490 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 28
40003426 TAAATGTCCA
*
40003436 GTCCATATTACAAAGGCCCAAATTAAAG
1 GTCCATATTACAAAGGCCCAAATGAAAG
40003464 GTCCA-ATTACAAAGG-CCAAATAGAAAG
1 GTCCATATTACAAAGGCCCAAAT-GAAAG
40003491 CCTAATTGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 6 0.24
27 14 0.56
28 5 0.20
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.18
Consensus pattern (28 bp):
GTCCATATTACAAAGGCCCAAATGAAAG
Found at i:40005389 original size:58 final size:59
Alignment explanation
Indices: 40005267--40005516 Score: 371
Period size: 59 Copynumber: 4.3 Consensus size: 59
40005257 CTTGAACTGT
* * *
40005267 CCAAAAATTACCATTTGACCCCCGAAC-TTCTAAAATCCCA-TTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
*
40005324 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* ** * *
40005383 CC-AAAATTACCATTTTACCTCTGAACTTTCTAAAATCCCATTTTTAACCCTGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* *
40005441 CCAAAAATTACCATTTTGCCCCCAAACTTTCCAAAATCCTATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
*
40005500 CCAAAAATTATCATTTT
1 CCAAAAATTACCATTTT
40005517 GCCCTCGAAA
Statistics
Matches: 174, Mismatches: 16, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
57 24 0.14
58 66 0.38
59 84 0.48
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.33
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
Found at i:40005472 original size:117 final size:116
Alignment explanation
Indices: 40005267--40005525 Score: 403
Period size: 117 Copynumber: 2.2 Consensus size: 116
40005257 CTTGAACTGT
*
40005267 CCAAAAATTACCATTTGACCCCCGAACTTCTAAAATCCCATTTTAACCCCGATTTCACCAAAAAT
1 CCAAAAATTACCATTTTACCCCCGAACTTCTAAAATCCCATTTTAACCCCGATTTCACCAAAAAT
*
40005332 TACCATTTTACCCCTAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
66 TACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* * *
40005383 CC-AAAATTACCATTTTACCTCTGAACTTTCTAAAATCCCATTTTTAACCCTGATTTCACCAAAA
1 CCAAAAATTACCATTTTACCCCCGAAC-TTCTAAAATCCCA-TTTTAACCCCGATTTCACCAAAA
* *
40005447 ATTACCATTTTGCCCCCAAACTTTCCAAAATCCTATTTTTAACCCCGATTTCA
64 ATTACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
* * *
40005500 CCAAAAATTATCATTTTGCCCTCGAA
1 CCAAAAATTACCATTTTACCCCCGAA
40005526 AGTCAAAAAT
Statistics
Matches: 128, Mismatches: 12, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
115 21 0.16
116 15 0.12
117 74 0.58
118 18 0.14
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.32
Consensus pattern (116 bp):
CCAAAAATTACCATTTTACCCCCGAACTTCTAAAATCCCATTTTAACCCCGATTTCACCAAAAAT
TACCATTTTACCCCCAAACTTTCCAAAATCCCATTTTTAACCCCGATTTCA
Found at i:40007914 original size:43 final size:43
Alignment explanation
Indices: 40007850--40008080 Score: 275
Period size: 43 Copynumber: 5.3 Consensus size: 43
40007840 ATTTGTTAAT
* *
40007850 TTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTC
* ** *
40007893 TTTAGCGGCGTTTGTTAGAAAAGCATCGCTAAACACCATGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTC
* * *
40007936 TTTAGCGACATTTGTGAAAAAAGCGCCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTC
* * * *
40007979 TTTAGCGGAGTTTGTGAGAAAAGCACCGCTCTTAAAGATCATGTTT
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCG--C-TAAAGACCATGTTC
* *
40008025 TTTAGTGGCGTTTGTGCA-AAAAGCGTCGCTAAAGACCATGTTC
1 TTTAGCGGCGTTTGTG-AGAAAAGCGCCGCTAAAGACCATGTTC
*
40008068 TTTAGTGGCGTTT
1 TTTAGCGGCGTTT
40008081 TTCCTTATAA
Statistics
Matches: 158, Mismatches: 26, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
43 121 0.77
44 1 0.01
45 1 0.01
46 34 0.22
47 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGACCATGTTC
Found at i:40007999 original size:86 final size:88
Alignment explanation
Indices: 40007850--40008072 Score: 306
Period size: 86 Copynumber: 2.5 Consensus size: 88
40007840 ATTTGTTAAT
** * *
40007850 TTTAGCGACGTTTGTGGGAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTGTTAGAAAA
1 TTTAGCGACGTTTGTGAAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGAGTTTGTGAGAAAA
*
40007915 GCATCG-C-TAAACACCATGTTC
66 GCACCGCCTTAAACACCATGTTC
*
40007936 TTTAGCGACATTTGTGAAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGAGTTTGTGAGAAAA
1 TTTAGCGACGTTTGTGAAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGAGTTTGTGAGAAAA
* * *
40008001 GCACCGCTCTTAAAGATCATGTTT
66 GCACCGC-CTTAAACACCATGTTC
* * * *
40008025 TTTAGTGGCGTTTGTGCAAAAAGCGTCGCTAAAGACCATGTTCTTTAG
1 TTTAGCGACGTTTGTGAAAAAAGCGCCGCTAAAGACCATGTTCTTTAG
40008073 TGGCGTTTTT
Statistics
Matches: 120, Mismatches: 14, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
86 65 0.54
88 1 0.01
89 54 0.45
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.30
Consensus pattern (88 bp):
TTTAGCGACGTTTGTGAAAAAAGCGCCGCTAAAGACCATGTTCTTTAGCGGAGTTTGTGAGAAAA
GCACCGCCTTAAACACCATGTTC
Found at i:40015057 original size:29 final size:30
Alignment explanation
Indices: 40015025--40015081 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
40015015 TGGTTTATTA
40015025 TGCAATTGTATACATG-AATTTTGATTTTG
1 TGCAATTGTATACATGAAATTTTGATTTTG
* *
40015054 TGCAATTTTATATATGAAATTTTGATTT
1 TGCAATTGTATACATGAAATTTTGATTT
40015082 GATCCATTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.30, C:0.05, G:0.14, T:0.51
Consensus pattern (30 bp):
TGCAATTGTATACATGAAATTTTGATTTTG
Found at i:40015308 original size:29 final size:30
Alignment explanation
Indices: 40015276--40015334 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
40015266 TCATGTGTAT
* *
40015276 AATTGTAC-TAAATTAAAGTTCATATATAC
1 AATTGCACATAAATCAAAGTTCATATATAC
*
40015305 AATTGCACATTAAATCAAAGTTCATGTATA
1 AATTGCACA-TAAATCAAAGTTCATATATA
40015335 ATTTCTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 7 0.28
31 18 0.72
ACGTcount: A:0.44, C:0.12, G:0.08, T:0.36
Consensus pattern (30 bp):
AATTGCACATAAATCAAAGTTCATATATAC
Found at i:40015337 original size:29 final size:27
Alignment explanation
Indices: 40015271--40015337 Score: 71
Period size: 31 Copynumber: 2.3 Consensus size: 27
40015261 GAGTTTCATG
* *
40015271 TGTATAATTGTACTAAATTAAAGTTCA
1 TGTATAATTGCACTAAATCAAAGTTCA
*
40015298 TATATACAATTGCACATTAAATCAAAGTTCA
1 TGTAT--AATTGCAC--TAAATCAAAGTTCA
40015329 TGTATAATT
1 TGTATAATT
40015338 TCTAATTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
27 4 0.12
29 11 0.34
31 17 0.53
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (27 bp):
TGTATAATTGCACTAAATCAAAGTTCA
Found at i:40019127 original size:16 final size:16
Alignment explanation
Indices: 40019086--40019119 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
40019076 TATATATATA
40019086 TATATATTTA-A-AAT
1 TATATATTTATAGAAT
40019100 TATATATTTATAGAAT
1 TATATATTTATAGAAT
40019116 TATA
1 TATA
40019120 ACTTTATATC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 1 0.06
16 7 0.39
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
TATATATTTATAGAAT
Found at i:40020792 original size:20 final size:18
Alignment explanation
Indices: 40020745--40020796 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 18
40020735 GGAGAAAAAC
40020745 AAAAGAAAATAAAAAATA
1 AAAAGAAAATAAAAAATA
*
40020763 AAGAAAAAAATTAAAAAATA
1 AA-AAGAAAA-TAAAAAATA
40020783 TAAAAGAAAA-AAAA
1 -AAAAGAAAATAAAA
40020797 TTACTCAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 6 0.21
19 6 0.21
20 15 0.52
21 2 0.07
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.12
Consensus pattern (18 bp):
AAAAGAAAATAAAAAATA
Found at i:40027570 original size:61 final size:62
Alignment explanation
Indices: 40027483--40027656 Score: 180
Period size: 62 Copynumber: 2.8 Consensus size: 62
40027473 AAAAAAAAAA
* *
40027483 TTGGTGTTGGCCATTGC-ATGGACGACACTCCTTTTTAATCTGATAAAAAAA-ATC-AAA-TTT
1 TTGGTGTTGGTCA-TGCAATGGACGACACTCCTTTTT-ATCAGATAAAAAAATATCAAAATTTT
* * * *
40027543 TTGGATGTTGGTCATGCAATGGCCGACACCCCTTTTTGTCAGATAAAAAAATTTCAAAATTTT
1 TTGG-TGTTGGTCATGCAATGGACGACACTCCTTTTTATCAGATAAAAAAATATCAAAATTTT
* * *
40027606 TTGGTATT-GTCCATGCAATGGTCGACACTACCTTTTT-TCAGATACAAAAAT
1 TTGGTGTTGGT-CATGCAATGGACGACACT-CCTTTTTATCAGATAAAAAAAT
40027657 TTTAAAAAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
60 19 0.20
61 29 0.30
62 35 0.36
63 14 0.14
ACGTcount: A:0.30, C:0.18, G:0.17, T:0.35
Consensus pattern (62 bp):
TTGGTGTTGGTCATGCAATGGACGACACTCCTTTTTATCAGATAAAAAAATATCAAAATTTT
Found at i:40027785 original size:130 final size:123
Alignment explanation
Indices: 40027660--40027910 Score: 292
Period size: 130 Copynumber: 2.0 Consensus size: 123
40027650 CAAAAATTTT
* * * * *
40027660 AAAAAAA-ATTTGTGTT-AGCCATGCCATGACCGACACC-TCTTTTTTGTCAGATAATAAATTCT
1 AAAAAAATATTTGTGTTGA-CAATGCAATGACCGACACCTTC-TTTTTGTAAAATAAAAAATTC-
* * *
40027722 AATTTTTTTTTGTGTTGGTCATGGTCATGCCATGGCCAACACCCCTTTTTTTATTTGGTAAAAAA
63 AAATTTTTTTTG-G-T-GT--TGGCCATGCCATGACCAACACCCC-TTTTTTATTTGGTAAAAAA
40027787 TC
122 TC
* **
40027789 AAAAAAATTTTTGTGTTGACAATGCAATGGTCGACACCTTCTTTTTGTAAAATAAAAAATTCAAA
1 AAAAAAATATTTGTGTTGACAATGCAATGACCGACACCTTCTTTTTGTAAAATAAAAAATTCAAA
*
40027854 TTTTTTTTGGTGTTGGCCATGCCATGACCGACACCCCTTTTTTATTTGGTAAAAAAT
66 TTTTTTTTGGTGTTGGCCATGCCATGACCAACACCCCTTTTTTATTTGGTAAAAAAT
40027911 TAATTTTTTT
Statistics
Matches: 107, Mismatches: 12, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
123 20 0.19
124 21 0.20
126 2 0.02
127 1 0.01
128 1 0.01
129 18 0.17
130 41 0.38
131 3 0.03
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (123 bp):
AAAAAAATATTTGTGTTGACAATGCAATGACCGACACCTTCTTTTTGTAAAATAAAAAATTCAAA
TTTTTTTTGGTGTTGGCCATGCCATGACCAACACCCCTTTTTTATTTGGTAAAAAATC
Found at i:40027896 original size:62 final size:63
Alignment explanation
Indices: 40027540--40027896 Score: 171
Period size: 62 Copynumber: 5.6 Consensus size: 63
40027530 AAAAATCAAA
* * * *
40027540 TTTTTGGATGTTGGTCATGCAATGGCCGACACCCC-TTTTTGTCAGATAAAAAAATTTCAAAA--
1 TTTTTGG-TGTTGGCCATGCCATGACCGACACCCCTTTTTTGTAAGAT-AAAAAA-TTCAAAATT
40027602 T
63 T
* * * ** * * * *
40027603 TTTTTGGTATTGTCCATGCAATGGTCGACACTACC-TTTTT-TCAGATACAAAAATTTTAAAA-A
1 TTTTTGGTGTTGGCCATGCCATGACCGACAC-CCCTTTTTTGTAAGATA-AAAAA-TTCAAAATT
*
40027665 A
63 T
** * * * * * *
40027666 AATTT-GTGTTAGCCATGCCATGACCGACACCTCTTTTTTGTCAGATAATAAATTCTAATTTT
1 TTTTTGGTGTTGGCCATGCCATGACCGACACCCCTTTTTTGTAAGATAAAAAATTCAAAATTT
* * * * *
40027728 TTTTTGTGTTGGTCATGGTCATGCCATGGCCAACACCCCTTTTTT-TATTTGGTAAAAAA-TCAA
1 TTTTTG-G-T-GT--TGGCCATGCCATGACCGACACCCCTTTTTTGTA--AGATAAAAAATTCAA
***
40027791 AAAAA
59 AATTT
* * * ** * *
40027796 TTTTT-GTGTTGACAATGCAATGGTCGACA-CCTTCTTTTTGTAAAATAAAAAATTC-AAATTT
1 TTTTTGGTGTTGGCCATGCCATGACCGACACCCCT-TTTTTGTAAGATAAAAAATTCAAAATTT
40027857 TTTTTGGTGTTGGCCATGCCATGACCGACACCCCTTTTTT
1 TTTTTGGTGTTGGCCATGCCATGACCGACACCCCTTTTTT
40027897 ATTTGGTAAA
Statistics
Matches: 217, Mismatches: 58, Indels: 39
0.69 0.18 0.12
Matches are distributed among these distances:
61 24 0.11
62 114 0.53
63 29 0.13
64 3 0.01
65 2 0.01
66 3 0.01
67 1 0.00
68 34 0.16
69 7 0.03
ACGTcount: A:0.29, C:0.18, G:0.15, T:0.38
Consensus pattern (63 bp):
TTTTTGGTGTTGGCCATGCCATGACCGACACCCCTTTTTTGTAAGATAAAAAATTCAAAATTT
Found at i:40027907 original size:62 final size:63
Alignment explanation
Indices: 40027483--40027911 Score: 167
Period size: 62 Copynumber: 6.8 Consensus size: 63
40027473 AAAAAAAAAA
* * *
40027483 TTGGTGTTGGCCATTG-CATGGA-CGACACTCCTTTTTAATCT-GATAAAAAAAATC-AAA---T
1 TTGGTGTTGGCCA-TGCCAT-GACCGACACCCCTTTTTTAT-TAGAT-AAAAAATTCAAAATTTT
40027541 TT
62 TT
* * * * *
40027543 TTGGATGTTGGTCATGCAATGGCCGACACCCC-TTTTTGTCAGATAAAAAAATTTCAAAA--TTT
1 TTGG-TGTTGGCCATGCCATGACCGACACCCCTTTTTTATTAGAT-AAAAAA-TTCAAAATTTTT
40027605 T
63 T
* * * ** * * * ****
40027606 TTGGTATTGTCCATGCAATGGTCGACACTACC-TTTTT-TCAGATACAAAAATTTTAAAA-AAAA
1 TTGGTGTTGGCCATGCCATGACCGACAC-CCCTTTTTTATTAGATA-AAAAA-TTCAAAATTTTT
40027668 T
63 T
* * * * * * *
40027669 TT-GTGTTAGCCATGCCATGACCGACACCTCTTTTTTGTCAGATAATAAATTCTAATTTTTTT
1 TTGGTGTTGGCCATGCCATGACCGACACCCCTTTTTTATTAGATAAAAAATTCAAAATTTTTT
* * * * * **
40027731 TTGTGTTGGTCATGGTCATGCCATGGCCAACACCCCTTTTTTTATTTGGTAAAAAA-TCAAAAAA
1 TTG-G-T-GT--TGGCCATGCCATGACCGACACCCC-TTTTTTATTAGATAAAAAATTCAAAATT
*
40027795 ATTT
60 TTTT
* * * ** * *
40027799 TT-GTGTTGACAATGCAATGGTCGACACCTTCTTTTTGTA--AAATAAAAAATTC-AAATTTTTT
1 TTGGTGTTGGCCATGCCATGACCGACACC-CCTTTTT-TATTAGATAAAAAATTCAAAATTTTTT
* *
40027860 TTGGTGTTGGCCATGCCATGACCGACACCCCTTTTTTATTTGGTAAAAAATT
1 TTGGTGTTGGCCATGCCATGACCGACACCCCTTTTTTATTAGATAAAAAATT
40027912 AATTTTTTTT
Statistics
Matches: 273, Mismatches: 70, Indels: 50
0.69 0.18 0.13
Matches are distributed among these distances:
60 24 0.09
61 47 0.17
62 125 0.46
63 27 0.10
64 3 0.01
65 2 0.01
66 3 0.01
68 28 0.10
69 14 0.05
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (63 bp):
TTGGTGTTGGCCATGCCATGACCGACACCCCTTTTTTATTAGATAAAAAATTCAAAATTTTTT
Found at i:40028796 original size:30 final size:30
Alignment explanation
Indices: 40028756--40028853 Score: 106
Period size: 30 Copynumber: 3.3 Consensus size: 30
40028746 AAATAATAAT
* *
40028756 AATTAGAATATACAGGAAATTAGGAAGTAA
1 AATTAAAATATACAGGAAATTAGAAAGTAA
*
40028786 AATTAAAATATACAGGAAATTAGAAATTAA
1 AATTAAAATATACAGGAAATTAGAAAGTAA
* * * * * *
40028816 ATTTAAAATAAAAACGAAATTATAAATTAA
1 AATTAAAATATACAGGAAATTAGAAAGTAA
*
40028846 ATTTAAAA
1 AATTAAAA
40028854 AGTAAACGGA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 60 1.00
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (30 bp):
AATTAAAATATACAGGAAATTAGAAAGTAA
Found at i:40029928 original size:19 final size:20
Alignment explanation
Indices: 40029906--40029943 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
40029896 CGAATTTAGT
40029906 TAAAAAA-ATTTCGAAAATC
1 TAAAAAATATTTCGAAAATC
40029925 TAAAAAATATTTCGAAAAT
1 TAAAAAATATTTCGAAAAT
40029944 TTATTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.58, C:0.08, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAAATATTTCGAAAATC
Found at i:40030035 original size:20 final size:20
Alignment explanation
Indices: 40030012--40030049 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40030002 AAACATTTCG
*
40030012 AAAATAGAAAAAATATATAA
1 AAAATACAAAAAATATATAA
*
40030032 AAAATTCAAAAAATATAT
1 AAAATACAAAAAATATAT
40030050 CTTACATCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (20 bp):
AAAATACAAAAAATATATAA
Found at i:40031351 original size:84 final size:84
Alignment explanation
Indices: 40031258--40031891 Score: 900
Period size: 84 Copynumber: 7.5 Consensus size: 84
40031248 AAATCAACAC
* *
40031258 TAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGATAAATAATATATTATC
1 TAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGATAAATAATGTATTGTC
40031323 AAATCAATACATTATTTGA
66 AAATCAATACATTATTTGA
**
40031342 TAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTT-AGTAAATAATGTATTGT
1 TAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGA-TAAATAATGTATTGT
40031406 CAAATCAATACATTATTTGA
65 CAAATCAATACATTATTTGA
* *
40031426 TTAAAATTGTAATATAATAATAA-TTTTT-TTTAAATATGAAAATTTGATAAATAATGTATTATC
1 TAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGATAAATAATGTATTGTC
40031489 AAATCAATACATTATTTGA
66 AAATCAATACATTATTTGA
* * *
40031508 TAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAG-TAAATAATGTATTAT
1 TAAAAATTGTAATATAATAATAATTTTTTATTTAAATA-TGAAAATTTGATAAATAATGTATTGT
* *
40031572 CAAATCAACATATTATTTGA
65 CAAATCAATACATTATTTGA
*
40031592 TAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAATTTTGATAAATAATGTATTGTC
1 TAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGATAAATAATGTATTGTC
* *
40031657 AAATCAACATATTATTTGA
66 AAATCAATACATTATTTGA
* * *
40031676 TAAAAATTGTAATATAATAATAATTTTTCATTTAAATATTTAAAATTAG-TAAATAATGTATTGT
1 TAAAAATTGTAATATAATAATAATTTTTTATTTAAATA-TGAAAATTTGATAAATAATGTATTGT
*
40031740 CAAATCAACACATTATTTGA
65 CAAATCAATACATTATTTGA
* * * *
40031760 TAAAAATTATAATATAATAATAATTTGTAATTTAAATATAAAAATTTGATAAATAATGTATTGTC
1 TAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGATAAATAATGTATTGTC
*
40031825 AAATAAACATAATATTTGATTTATTTGA
66 AAAT---C--AATA---CA-TTATTTGA
*
40031853 TATAAATTGTAATATAATAATAATCTTTTTATTTAAATA
1 TAAAAATTGTAATATAATAATAAT-TTTTTATTTAAATA
40031892 ATGTTAGATT
Statistics
Matches: 499, Mismatches: 33, Indels: 26
0.89 0.06 0.05
Matches are distributed among these distances:
82 71 0.14
83 27 0.05
84 339 0.68
85 15 0.03
87 1 0.00
89 3 0.01
92 1 0.00
93 30 0.06
94 12 0.02
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.44
Consensus pattern (84 bp):
TAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGATAAATAATGTATTGTC
AAATCAATACATTATTTGA
Found at i:40031717 original size:168 final size:168
Alignment explanation
Indices: 40031180--40031891 Score: 1041
Period size: 168 Copynumber: 4.2 Consensus size: 168
40031170 ATTTAAAATC
* * * *
40031180 TGATAAATATTGTAATATAATATTAATTCTTGATTTAAATATTTAAAATTAGTAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
40031245 GTCAAATCAACAC---------TAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAA
66 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAA
* *
40031301 ATTTGATAAATAATATATTATCAAATCAATACATTATT
131 ATTTGATAAATAATGTATTATCAAATCAACACATTATT
*
40031339 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAATTTAGTAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
* *
40031404 GTCAAATCAATACATTATTTGATTAAAATTGTAATATAATAATAA-TTTTT-TTTAAATATGAAA
66 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAA
*
40031467 ATTTGATAAATAATGTATTATCAAATCAATACATTATT
131 ATTTGATAAATAATGTATTATCAAATCAACACATTATT
40031505 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
* *
40031570 ATCAAATCAACATATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAA
66 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAA
* * *
40031635 TTTTGATAAATAATGTATTGTCAAATCAACATATTATT
131 ATTTGATAAATAATGTATTATCAAATCAACACATTATT
*
40031673 TGATAAAAATTGTAATATAATAATAATTTTTCATTTAAATATTTAAAATTAGTAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
* * * *
40031738 GTCAAATCAACACATTATTTGATAAAAATTATAATATAATAATAATTTGTAATTTAAATATAAAA
66 GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAA
* * *
40031803 ATTTGATAAATAATGTATTGTCAAATAAACATAATATTTGATTTATT
131 ATTTGATAAATAATGTATTATCAAAT---C--AACA---CA-TTATT
*
40031850 TGATATAAATTGTAATATAATAATAATCTTTTTATTTAAATA
1 TGATAAAAATTGTAATATAATAATAAT-TTTTTATTTAAATA
40031892 ATGTTAGATT
Statistics
Matches: 503, Mismatches: 29, Indels: 23
0.91 0.05 0.04
Matches are distributed among these distances:
159 72 0.14
166 155 0.31
167 10 0.02
168 217 0.43
171 1 0.00
173 3 0.01
176 1 0.00
177 31 0.06
178 13 0.03
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (168 bp):
TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
GTCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAA
ATTTGATAAATAATGTATTATCAAATCAACACATTATT
Found at i:40031780 original size:334 final size:331
Alignment explanation
Indices: 40031180--40031891 Score: 1058
Period size: 334 Copynumber: 2.1 Consensus size: 331
40031170 ATTTAAAATC
* * * *
40031180 TGATAAATATTGTAATATAATATTAATTCTTGATTTAAATATTTAAAATTAGTAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
* *
40031245 GTCAAATCAACACTAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGATAA
66 ATCAAATCAACAATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGATAA
* *
40031310 ATAATATATTATCAAATCAATACATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTT
131 ATAATATATTATCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTCATTT
* * * *
40031375 AAATATTTAAATTTAGTAAATAATGTATTGTCAAATCAATACATTATTTGATTAAAATTGTAATA
196 AAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTATAATA
* *
40031440 TAATAATAATTT-T-TTTTAAATATGAAAATTTGATAAATAATGTATTATCAAAT-C-AATA-CA
261 TAATAATAATTTGTAATTTAAATATAAAAATTTGATAAATAATGTATTATCAAATACAAATATCA
40031500 -TTATT
326 TTTATT
40031505 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
1 TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
40031570 ATCAAATCAACATATTATTTGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAA
66 ATCAAATCAAC-----A----ATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAA
* * * *
40031635 TTTTGATAAATAATGTATTGTCAAATCAACATATTATTTGATAAAAATTGTAATATAATAATAAT
122 ATTTGATAAATAATATATTATCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAAT
40031700 TTTTCATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAA
187 TTTTCATTTAAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAA
*
40031765 ATTATAATATAATAATAATTTGTAATTTAAATATAAAAATTTGATAAATAATGTATTGTCAAATA
252 ATTATAATATAATAATAATTTGTAATTTAAATATAAAAATTTGATAAATAATGTATTATCAAAT-
*
40031830 AACATAATATTTGATTTATT
316 -ACA-AATA--TCATTTATT
*
40031850 TGATATAAATTGTAATATAATAATAATCTTTTTATTTAAATA
1 TGATAAAAATTGTAATATAATAATAAT-TTTTTATTTAAATA
40031892 ATGTTAGATT
Statistics
Matches: 345, Mismatches: 21, Indels: 21
0.89 0.05 0.05
Matches are distributed among these distances:
325 71 0.21
330 1 0.00
334 184 0.53
335 1 0.00
336 37 0.11
339 1 0.00
341 4 0.01
344 1 0.00
345 31 0.09
346 14 0.04
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (331 bp):
TGATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATTTAAAATTAGTAAATAATGTATT
ATCAAATCAACAATAAAAATTGTAATATAATAATAATTTTTTATTTAAATATGAAAATTTGATAA
ATAATATATTATCAAATCAACACATTATTTGATAAAAATTGTAATATAATAATAATTTTTCATTT
AAATATTTAAAATTAGTAAATAATGTATTGTCAAATCAACACATTATTTGATAAAAATTATAATA
TAATAATAATTTGTAATTTAAATATAAAAATTTGATAAATAATGTATTATCAAATACAAATATCA
TTTATT
Found at i:40035177 original size:22 final size:22
Alignment explanation
Indices: 40035152--40035198 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
40035142 ATAAATCTTT
*
40035152 TTAAATATTACA-ATAATACAAA
1 TTAAAT-TTACAGATAAAACAAA
*
40035174 TTAAATTTACAGATAAAATAAA
1 TTAAATTTACAGATAAAACAAA
40035196 TTA
1 TTA
40035199 TAAATAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.34
Consensus pattern (22 bp):
TTAAATTTACAGATAAAACAAA
Found at i:40035869 original size:61 final size:59
Alignment explanation
Indices: 40035786--40036052 Score: 205
Period size: 61 Copynumber: 4.4 Consensus size: 59
40035776 GGAATAGCCG
* * * * *
40035786 ACACCAAAAAAATTTAATTTTTTACCAAACAAAAAAGGGGTGTCAATCATGGCACGACCA
1 ACACCAAAAAAATTTAAATTTTTACCAGAC-AAAAAGGGGTGTCGACCATGGCATGACCA
**** * *
40035846 ACACCAAAAAAATTTTAAATTTTTTATTTCACAAAAAGGAGGTGTCGACCATTGCATGGCCA
1 ACACCAAAAAAA-TTTAAA-TTTTTACCAGACAAAAAGG-GGTGTCGACCATGGCATGACCA
* * * ***
40035908 ACA-CAAAAAAAATTAATTTTTTTACCAGATAAAAAAGGGGGTGTCGACCATGGCATGGTTA
1 ACACCAAAAAAATTTAA-ATTTTTACCAGA-CAAAAA-GGGGTGTCGACCATGGCATGACCA
** * * * ** *
40035969 ACA-CAAAAAAATCGAAATTTTTATCTGACAAAAAGAGGATGTCGGTCATGGCATGATCA
1 ACACCAAAAAAATTTAAATTTTTACCAGACAAAAAG-GGGTGTCGACCATGGCATGACCA
*
40036028 ACACCAAAAAATTTTGAAATTTTTA
1 ACACCAAAAAAATTT-AAATTTTTA
40036053 ATCTGAAAAA
Statistics
Matches: 163, Mismatches: 35, Indels: 17
0.76 0.16 0.08
Matches are distributed among these distances:
58 1 0.01
59 26 0.16
60 40 0.25
61 66 0.40
62 30 0.18
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.26
Consensus pattern (59 bp):
ACACCAAAAAAATTTAAATTTTTACCAGACAAAAAGGGGTGTCGACCATGGCATGACCA
Found at i:40039000 original size:31 final size:32
Alignment explanation
Indices: 40038950--40039017 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
40038940 AATTATTGGG
*
40038950 TAATTTGCATTTTACATCATTGAA-CTTC-ATCT
1 TAATTTGCATATTACATCATT-AACCTTCAAT-T
*
40038982 TAATTTTCATATT-CATCATTAACCTTCAATT
1 TAATTTGCATATTACATCATTAACCTTCAATT
40039013 TAATT
1 TAATT
40039018 AAATTACATC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 2 0.06
31 17 0.53
32 13 0.41
ACGTcount: A:0.31, C:0.18, G:0.03, T:0.49
Consensus pattern (32 bp):
TAATTTGCATATTACATCATTAACCTTCAATT
Found at i:40051170 original size:16 final size:17
Alignment explanation
Indices: 40051151--40051182 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
40051141 TTTCCCAACC
40051151 TATTTTTTATT-TATTA
1 TATTTTTTATTGTATTA
40051167 TATTTTTTATTGTATT
1 TATTTTTTATTGTATT
40051183 TCTATTTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (17 bp):
TATTTTTTATTGTATTA
Found at i:40060569 original size:224 final size:223
Alignment explanation
Indices: 40060180--40060622 Score: 814
Period size: 224 Copynumber: 2.0 Consensus size: 223
40060170 TATGTTCGAT
*
40060180 TGTCAAGGAAATATTTTTACTTTATTTTGGCTATCATCAGTTGAGATTTTTGTATGTGCACTTCT
1 TGTCAAGGAAATATTTTTACTTTATTTTGCCTATCATCAGTTGAGATTTTTGTATGTGCACTTCT
40060245 TCAACTTTCATATCAGAAGTTTGATGAAGTACTTCAACAAAATGGATGATGGCAGTTAACTGTTT
66 TCAACTTTCATATCAGAAGTTTGATGAAGTACTTCAACAAAATGGATGATGGCAGTTAACTGTTT
*
40060310 GAGCTCGTAAGGGATTTTCATCATAACCAAGAGAATGTTGTGTCTAAATCAATCAAAATTTTGCT
131 GAGCTCGTAAGGGATTTTCATCATAACCAAGAGAATGTTGTGTCCAAATCAATCAAAATTTTGCT
40060375 AACCTCTAATATCAATAAACTTCTCTAA
196 AACCTCTAATATCAATAAACTTCTCTAA
*
40060403 TGTCAAGGAAATATTTTTACTTTATTTTGCCCTATCATTAGTTGAGATTTTTGTATGTGCACTTC
1 TGTCAAGGAAATATTTTTACTTTATTTTG-CCTATCATCAGTTGAGATTTTTGTATGTGCACTTC
*
40060468 TTCAACTTTCATATCAGAAGTTTGATGAAGTACTTCAACAAAATGGATGATGGTAGTTAACTGTT
65 TTCAACTTTCATATCAGAAGTTTGATGAAGTACTTCAACAAAATGGATGATGGCAGTTAACTGTT
*
40060533 TGAGCTCGTAAGGGATTTTCATCATAACCAAGAGAATTTTGTGTCCAAATCAATCAAAATTTTGC
130 TGAGCTCGTAAGGGATTTTCATCATAACCAAGAGAATGTTGTGTCCAAATCAATCAAAATTTTGC
* *
40060598 TAATCTCTAATATCTATAAACTTCT
195 TAACCTCTAATATCAATAAACTTCT
40060623 TTAGGAACTA
Statistics
Matches: 212, Mismatches: 7, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
223 29 0.14
224 183 0.86
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (223 bp):
TGTCAAGGAAATATTTTTACTTTATTTTGCCTATCATCAGTTGAGATTTTTGTATGTGCACTTCT
TCAACTTTCATATCAGAAGTTTGATGAAGTACTTCAACAAAATGGATGATGGCAGTTAACTGTTT
GAGCTCGTAAGGGATTTTCATCATAACCAAGAGAATGTTGTGTCCAAATCAATCAAAATTTTGCT
AACCTCTAATATCAATAAACTTCTCTAA
Found at i:40073447 original size:15 final size:16
Alignment explanation
Indices: 40073431--40073472 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
40073421 AAAGAAAAAG
40073431 AAAGGAAAGGAAGAGA
1 AAAGGAAAGGAAGAGA
*
40073447 AAAGG-AAGGAAG-GT
1 AAAGGAAAGGAAGAGA
*
40073461 TAAGGAAAGGAA
1 AAAGGAAAGGAA
40073473 ATGATATGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 5 0.22
15 13 0.57
16 5 0.22
ACGTcount: A:0.57, C:0.00, G:0.38, T:0.05
Consensus pattern (16 bp):
AAAGGAAAGGAAGAGA
Found at i:40077637 original size:5 final size:5
Alignment explanation
Indices: 40077627--40077653 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
40077617 AGGTTATGTA
40077627 TTTCT TTTCT TTTCT TTTCT TTTCT TT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TT
40077654 AACTTGTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:40078771 original size:17 final size:20
Alignment explanation
Indices: 40078744--40078782 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
40078734 CCATTAGCAG
40078744 TATACTAAAT-A-TTTTTTT
1 TATACTAAATAAGTTTTTTT
40078762 TATA-TAAATAAGTTTTTTT
1 TATACTAAATAAGTTTTTTT
40078781 TA
1 TA
40078783 ATTGTTAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (20 bp):
TATACTAAATAAGTTTTTTT
Found at i:40081858 original size:6 final size:6
Alignment explanation
Indices: 40081847--40081892 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
40081837 ATCTAATTTC
40081847 ACCACT ACCACT ACCACT ACCACT ACCACT ACCACT ACCACT ACCA
1 ACCACT ACCACT ACCACT ACCACT ACCACT ACCACT ACCACT ACCA
40081893 GTGGTCTCCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.35, C:0.50, G:0.00, T:0.15
Consensus pattern (6 bp):
ACCACT
Found at i:40084401 original size:16 final size:17
Alignment explanation
Indices: 40084366--40084399 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
40084356 CGAAATTAAA
40084366 TTATAATTTTTAGTAAT
1 TTATAATTTTTAGTAAT
40084383 TTAT-ATTTTTA-TAAT
1 TTATAATTTTTAGTAAT
40084398 TT
1 TT
40084400 TAAAATATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 7 0.41
17 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (17 bp):
TTATAATTTTTAGTAAT
Found at i:40099174 original size:2 final size:2
Alignment explanation
Indices: 40099167--40099192 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40099157 AGGCCTCCAA
40099167 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40099193 TTTAAAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40101892 original size:21 final size:21
Alignment explanation
Indices: 40101868--40101910 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
40101858 ACACCATTCC
40101868 AAACAACAAAACAAAAAATAA
1 AAACAACAAAACAAAAAATAA
* * *
40101889 AAACAATACAACAAAAATTAA
1 AAACAACAAAACAAAAAATAA
40101910 A
1 A
40101911 TAAACGAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.77, C:0.14, G:0.00, T:0.09
Consensus pattern (21 bp):
AAACAACAAAACAAAAAATAA
Found at i:40113881 original size:10 final size:9
Alignment explanation
Indices: 40113874--40113957 Score: 57
Period size: 9 Copynumber: 9.2 Consensus size: 9
40113864 ATTTAAAATT
*
40113874 ATTAAAAAA
1 ATTATAAAA
40113883 ATTATAAAA
1 ATTATAAAA
* *
40113892 ATCATAAAC
1 ATTATAAAA
40113901 ATTATAGAAA
1 ATTATA-AAA
40113911 A--ATAAAA
1 ATTATAAAA
40113918 A-TATAAAA
1 ATTATAAAA
40113926 ATTTATTAAAA
1 A-TTA-TAAAA
* *
40113937 TATTTTAAAT
1 -ATTATAAAA
*
40113947 TTTATAAAA
1 ATTATAAAA
40113956 AT
1 AT
40113958 AAAGAAAACT
Statistics
Matches: 58, Mismatches: 11, Indels: 12
0.72 0.14 0.15
Matches are distributed among these distances:
7 4 0.07
8 10 0.17
9 27 0.47
10 9 0.16
11 7 0.12
12 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (9 bp):
ATTATAAAA
Found at i:40120170 original size:30 final size:31
Alignment explanation
Indices: 40120136--40120344 Score: 254
Period size: 30 Copynumber: 7.0 Consensus size: 31
40120126 AAAAAAGCTC
*
40120136 AGGGGTCAAAATGTGATTTTGGAAAA-TTTG
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTTG
* *
40120166 AGGGGTTAAAATGTGATTTTGGAAAAGTTTG
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTTG
*
40120197 A-GGGTTAAAATGTAATTTTGGAAAAGTTTG
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTTG
**
40120227 -GGGGTCAAAATGTAATTTTAAAAAAGTTTG
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTTG
* *
40120257 -GAGGTTAAAATGTAATTTTGG-AAAGTTT-
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTTG
* *
40120285 A-GGGTCAAAATATAATTTTGAAAAAGTTTG
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTTG
* *
40120315 A-GGGTCAAAATGTAATTTTTGAAAGGTTTG
1 AGGGGTCAAAATGTAATTTTGGAAAAGTTTG
40120345 GGGACCTCTT
Statistics
Matches: 157, Mismatches: 17, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
28 16 0.10
29 14 0.09
30 122 0.78
31 5 0.03
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.35
Consensus pattern (31 bp):
AGGGGTCAAAATGTAATTTTGGAAAAGTTTG
Found at i:40120327 original size:88 final size:90
Alignment explanation
Indices: 40120138--40120333 Score: 281
Period size: 88 Copynumber: 2.2 Consensus size: 90
40120128 AAAAGCTCAG
* ** * * *
40120138 GGGTCAAAATGTGATTTTGGAAAATTTGAGGGGTTAAAATGTGATTTTGGAAAAGTTTGAGGGTT
1 GGGTCAAAATGTAATTTTAAAAAATTTGAGAGGTTAAAATGTAATTTTGGAAAAGTTTGAGGGTC
* * *
40120203 AAAATGTAATTTTGGAAAAGTTTGG
66 AAAATATAATTTTGAAAAAGTTTGA
40120228 GGGTCAAAATGTAATTTTAAAAAAGTTTG-GAGGTTAAAATGTAATTTTGG-AAAGTTT-AGGGT
1 GGGTCAAAATGTAATTTTAAAAAA-TTTGAGAGGTTAAAATGTAATTTTGGAAAAGTTTGAGGGT
40120290 CAAAATATAATTTTGAAAAAGTTTGA
65 CAAAATATAATTTTGAAAAAGTTTGA
40120316 GGGTCAAAATGTAATTTT
1 GGGTCAAAATGTAATTTT
40120334 TGAAAGGTTT
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
88 45 0.47
89 7 0.07
90 40 0.42
91 4 0.04
ACGTcount: A:0.37, C:0.02, G:0.26, T:0.36
Consensus pattern (90 bp):
GGGTCAAAATGTAATTTTAAAAAATTTGAGAGGTTAAAATGTAATTTTGGAAAAGTTTGAGGGTC
AAAATATAATTTTGAAAAAGTTTGA
Found at i:40122206 original size:49 final size:49
Alignment explanation
Indices: 40122124--40122796 Score: 467
Period size: 49 Copynumber: 13.7 Consensus size: 49
40122114 ATGTTTCTAG
* * * *
40122124 GGTACCGGGTTCGCCGTTGCGG-TTGTAACCTTTCCCTCCATATCTTCGT
1 GGTACTGGATTCGCCGTTGCGGCTT-AAATCTTTCCCTCCATATCTTCGT
* ** * * *
40122173 GCTACTGGATTCGCCGTTATGGCTTAAATCTTTCCCTTCAT-GCTTCCGA
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTCCATATCTT-CGT
* * * * * *
40122222 GGTACAAGG-TTCGCCATTACGACTTAAACCTTTCTCTCCATATCCTT-GT
1 GGTAC-TGGATTCGCCGTTGCGGCTTAAATCTTTCCCTCCATAT-CTTCGT
* * * * *
40122271 GGTATTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT-GCTTCTGA
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTCCATATCTTC-GT
* ** * * *
40122320 GGTACAAGG-TTCGTTGTTGCGACTTAAACCTTTCCTTCCATATCTTCGT
1 GGTAC-TGGATTCGCCGTTGCGGCTTAAATCTTTCCCTCCATATCTTCGT
* * * * * * *
40122369 GGTACTAGATTCGGCATTACGGCTTAAATCTTTCCCT--TTATGATTCTGA
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTCCATAT-CTTC-GT
** * * * *
40122418 GGTAC-AAAGTTCGCCATTGCGACTTAAACCTTTCCCTCTATATCTTCGT
1 GGTACTGGA-TTCGCCGTTGCGGCTTAAATCTTTCCCTCCATATCTTCGT
* * * * * *
40122467 GGTATTGGATTCGCCGTTGCGGCTTAGATATTTCCCTTCAT-GCTTCTGA
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTCCATATCTTC-GT
* * *
40122516 GGTACAAGG-TTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGT
1 GGTAC-TGGATTCGCCGTTGCGGCTTAAATCTTTCCCTCCATATCTTCGT
* * * * * *
40122565 AGTACTAGATTCACCGTTGCGGCTTAAATCTTTCCCTTCAT-GCTTCTGA
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTCCATATCTTC-GT
* * * * *
40122614 GGTACAAGG-TTCTCCGTTACGACTTAAACCTTTCCCTCCATATCTTCGT
1 GGTAC-TGGATTCGCCGTTGCGGCTTAAATCTTTCCCTCCATATCTTCGT
* * * *
40122663 AGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCAT-GCTTCTGA
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTCCATATCTTC-GT
* * * * * * *
40122712 GGTGCAAGG-TCCGCCGTTGCGACTTAAACCTTTCCCTTCAAATCTTCGT
1 GGTAC-TGGATTCGCCGTTGCGGCTTAAATCTTTCCCTCCATATCTTCGT
40122761 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC
1 GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCC
40122797 ATAATATCTG
Statistics
Matches: 470, Mismatches: 125, Indels: 58
0.72 0.19 0.09
Matches are distributed among these distances:
47 6 0.01
48 27 0.06
49 401 0.85
50 30 0.06
51 6 0.01
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (49 bp):
GGTACTGGATTCGCCGTTGCGGCTTAAATCTTTCCCTCCATATCTTCGT
Found at i:40122282 original size:98 final size:98
Alignment explanation
Indices: 40122131--40122863 Score: 993
Period size: 98 Copynumber: 7.5 Consensus size: 98
40122121 TAGGGTACCG
* * * **
40122131 GGTTCGCCGTTGCG-GTTGTAACCTTTCCCTCCATATCTTCGTGCTACTGGATTCGCCGTTATGG
1 GGTTCGCCGTTGCGACTT-AAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGCCGTTGCGG
*
40122195 CTTAAATCTTTCCCTTCATGCTTCCGAGGTACAA
65 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * * * *
40122229 GGTTCGCCATTACGACTTAAACCTTTCTCTCCATATCCTT-GTGGTATTAGATTCGCCGTTGCGG
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATAT-CTTCGTGGTACTGGATTCGCCGTTGCGG
40122293 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
65 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
** * * * * *
40122327 GGTTCGTTGTTGCGACTTAAACCTTTCCTTCCATATCTTCGTGGTACTAGATTCGGCATTACGGC
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGCCGTTGCGGC
* *
40122392 TTAAATCTTTCCCTTTATGATTCTGAGGTACAA
66 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * * *
40122425 AGTTCGCCATTGCGACTTAAACCTTTCCCTCTATATCTTCGTGGTATTGGATTCGCCGTTGCGGC
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGCCGTTGCGGC
* *
40122490 TTAGATATTTCCCTTCATGCTTCTGAGGTACAA
66 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * *
40122523 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTAGTACTAGATTCACCGTTGCGGC
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGCCGTTGCGGC
40122588 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
66 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * *
40122621 GGTTCTCCGTTACGACTTAAACCTTTCCCTCCATATCTTCGTAGTACTGGATTCGCCGTTGCGGC
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGCCGTTGCGGC
*
40122686 TTAAATCTTTCCCTTCATGCTTCTGAGGTGCAA
66 TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
* * *
40122719 GGTCCGCCGTTGCGACTTAAACCTTTCCCTTCAAATCTTCGTGGTACTGGATTCGCCGTTGCGGC
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGCCGTTGCGGC
* * * * * **
40122784 TTAAATCTTTCCCATAATATCTGCTAAGGTACCG
66 TTAAATCTTTCCCTTCAT-GCTTCTGAGGTACAA
* * ** *
40122818 GGTCCGCCGTTGCGACCTCGACCTTTCCCTTCATATCTTCGTGGTA
1 GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTA
40122864 ATGAAACCTG
Statistics
Matches: 561, Mismatches: 70, Indels: 7
0.88 0.11 0.01
Matches are distributed among these distances:
97 3 0.01
98 502 0.89
99 56 0.10
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.36
Consensus pattern (98 bp):
GGTTCGCCGTTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTGGATTCGCCGTTGCGGC
TTAAATCTTTCCCTTCATGCTTCTGAGGTACAA
Found at i:40124738 original size:3 final size:3
Alignment explanation
Indices: 40124727--40124757 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
40124717 TTTCTTTTTT
40124727 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
40124758 TCTTTTAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:40127978 original size:28 final size:29
Alignment explanation
Indices: 40127945--40127999 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
40127935 TTGTCATGCC
40127945 ATTTCATA-AAAATGCAAAGGATCATAAT
1 ATTTCATAGAAAATGCAAAGGATCATAAT
40127973 ATTTCATAGAAAATGCAAAGGATCATA
1 ATTTCATAGAAAATGCAAAGGATCATA
40128000 CATCAATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.49, C:0.11, G:0.13, T:0.27
Consensus pattern (29 bp):
ATTTCATAGAAAATGCAAAGGATCATAAT
Found at i:40128929 original size:30 final size:30
Alignment explanation
Indices: 40128895--40128960 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
40128885 TGAAATCTTA
40128895 GAAAAGCTCGAGGGTTAAAATGTGATTTTG
1 GAAAAGCTCGAGGGTTAAAATGTGATTTTG
** *
40128925 GAAAATTTTGAGGGTTAAAATGTGATTTTG
1 GAAAAGCTCGAGGGTTAAAATGTGATTTTG
40128955 GAAAAG
1 GAAAAG
40128961 TTTAGGGGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (30 bp):
GAAAAGCTCGAGGGTTAAAATGTGATTTTG
Found at i:40128988 original size:29 final size:30
Alignment explanation
Indices: 40128906--40129012 Score: 146
Period size: 30 Copynumber: 3.6 Consensus size: 30
40128896 AAAAGCTCGA
* *
40128906 GGGTTAAAATGTGATTTTGGAAAA-TTTTG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
*
40128935 AGGGTTAAAATGTGATTTTGGAAAAGTTTAG
1 -GGGTTAAAATGTAATTTTGGAAAAGTTTAG
*
40128966 GGGTTAAAATATAATTTT-GAAAAGTTTAG
1 GGGTTAAAATGTAATTTTGGAAAAGTTTAG
*
40128995 GGGTCAAAATGTAATTTT
1 GGGTTAAAATGTAATTTT
40129013 TAAAAGGTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
29 27 0.38
30 40 0.56
31 4 0.06
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (30 bp):
GGGTTAAAATGTAATTTTGGAAAAGTTTAG
Found at i:40129017 original size:29 final size:29
Alignment explanation
Indices: 40128906--40129026 Score: 138
Period size: 30 Copynumber: 4.1 Consensus size: 29
40128896 AAAAGCTCGA
* *
40128906 GGGTTAAAATGTGATTTTGGAAAA-TTTTG
1 GGGTTAAAATGTAATTTT-GAAAAGTTTAG
*
40128935 AGGGTTAAAATGTGATTTTGGAAAAGTTTAG
1 -GGGTTAAAATGTAATTTT-GAAAAGTTTAG
*
40128966 GGGTTAAAATATAATTTTGAAAAGTTTAG
1 GGGTTAAAATGTAATTTTGAAAAGTTTAG
* *
40128995 GGGTCAAAATGTAATTTTTAAAAGGTTT-G
1 GGGTTAAAATGTAATTTTGAAAA-GTTTAG
40129024 GGG
1 GGG
40129027 ATGTTTTGAG
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
29 35 0.42
30 44 0.53
31 4 0.05
ACGTcount: A:0.35, C:0.01, G:0.27, T:0.37
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTGAAAAGTTTAG
Found at i:40129805 original size:13 final size:12
Alignment explanation
Indices: 40129788--40129812 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40129778 TTAAAAGTAA
40129788 ATTTTTTATTTC
1 ATTTTTTATTTC
40129800 ATTTTTTATTTC
1 ATTTTTTATTTC
40129812 A
1 A
40129813 AAAAACAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTTTTATTTC
Found at i:40130625 original size:21 final size:21
Alignment explanation
Indices: 40130600--40130666 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
40130590 AGAGTTTTAA
40130600 TAAATAATAAATAAATAATAT
1 TAAATAATAAATAAATAATAT
*
40130621 TAAATTAAAATAATATAAAT-ATTT
1 TAAA-T--AATAA-ATAAATAATAT
* *
40130645 TAAAAAATTCAATAAATAATAT
1 TAAATAA-TAAATAAATAATAT
40130667 AAACAGACCT
Statistics
Matches: 36, Mismatches: 4, Indels: 11
0.71 0.08 0.22
Matches are distributed among these distances:
21 12 0.33
22 6 0.17
24 12 0.33
25 6 0.17
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (21 bp):
TAAATAATAAATAAATAATAT
Found at i:40130632 original size:24 final size:22
Alignment explanation
Indices: 40130596--40130666 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 22
40130586 ATATAGAGTT
40130596 TTAATAAATAATAAATAAATAATA
1 TTAA-AAA-AATAAATAAATAATA
*
40130620 TTAAATTAAAATAATATAAAT-ATT
1 TTAAA--AAAATAA-ATAAATAATA
* *
40130644 TTAAAAAATTCAATAAATAATA
1 TTAAAAAAATAAATAAATAATA
40130666 T
1 T
40130667 AAACAGACCT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
21 6 0.15
22 8 0.21
23 1 0.03
24 16 0.41
25 8 0.21
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (22 bp):
TTAAAAAAATAAATAAATAATA
Found at i:40136140 original size:8 final size:8
Alignment explanation
Indices: 40136127--40136156 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
40136117 TGTTCCTGTT
40136127 TTTTTAAA
1 TTTTTAAA
40136135 TTTTTAAA
1 TTTTTAAA
40136143 TTTTTAAA
1 TTTTTAAA
*
40136151 ATTTTA
1 TTTTTA
40136157 GTCCTGGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TTTTTAAA
Found at i:40136949 original size:20 final size:20
Alignment explanation
Indices: 40136907--40136960 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
40136897 GAAAATATAG
*
40136907 ATTTTGAAATTTTTATAAGT
1 ATTTTGAAATTTTTAAAAGT
*
40136927 ATTTT-AAATTTTTAAAAATT
1 ATTTTGAAATTTTT-AAAAGT
*
40136947 ATTTTGTAATTTTT
1 ATTTTGAAATTTTT
40136961 GTTGAGAGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.28
20 14 0.48
21 7 0.24
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (20 bp):
ATTTTGAAATTTTTAAAAGT
Found at i:40137382 original size:13 final size:13
Alignment explanation
Indices: 40137364--40137388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40137354 TTTCTTCCTT
40137364 TCTTTCCTTTTTA
1 TCTTTCCTTTTTA
40137377 TCTTTCCTTTTT
1 TCTTTCCTTTTT
40137389 CACATTTTCT
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:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (13 bp):
TCTTTCCTTTTTA
Found at i:40139392 original size:24 final size:25
Alignment explanation
Indices: 40139365--40139412 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
40139355 TTTAATCTCA
* *
40139365 TTATGTGATATATGTAA-ATATTTT
1 TTATGTGACATATATAAGATATTTT
*
40139389 TTATGTTACATATATAAGATATTT
1 TTATGTGACATATATAAGATATTT
40139413 CTAAAAATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.52
Consensus pattern (25 bp):
TTATGTGACATATATAAGATATTTT
Found at i:40140647 original size:22 final size:21
Alignment explanation
Indices: 40140622--40140689 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
40140612 AAATTTATAT
40140622 TGTTGTTTTGATTTTTTTTTAC
1 TGTT-TTTTGATTTTTTTTTAC
*
40140644 TGTTTTGGTG-TTGTTTTTTTAC
1 TGTTTT-TTGATT-TTTTTTTAC
*
40140666 --TATTTTGA-TTTTTTTTAC
1 TGTTTTTTGATTTTTTTTTAC
40140684 TGTTTT
1 TGTTTT
40140690 GGTGCTATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 12
0.70 0.08 0.23
Matches are distributed among these distances:
18 9 0.24
19 3 0.08
20 6 0.16
21 4 0.11
22 15 0.41
ACGTcount: A:0.09, C:0.04, G:0.15, T:0.72
Consensus pattern (21 bp):
TGTTTTTTGATTTTTTTTTAC
Found at i:40140710 original size:23 final size:23
Alignment explanation
Indices: 40140673--40140751 Score: 104
Period size: 23 Copynumber: 3.4 Consensus size: 23
40140663 TACTATTTTG
* * * *
40140673 ATTTTTTTTACTGTTTTGGTGCT
1 ATTTTTGTTATTGTTTTGTTGTT
40140696 ATTTTTGTTATTGTTTTGTTGTT
1 ATTTTTGTTATTGTTTTGTTGTT
*
40140719 ATTTTTGTTGTTGTTTTGTTTGTT
1 ATTTTTGTTATTGTTTTG-TTGTT
40140743 ATTTTTGTT
1 ATTTTTGTT
40140752 GTTTGAATGT
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 36 0.72
24 14 0.28
ACGTcount: A:0.08, C:0.03, G:0.18, T:0.72
Consensus pattern (23 bp):
ATTTTTGTTATTGTTTTGTTGTT
Found at i:40140712 original size:12 final size:12
Alignment explanation
Indices: 40140697--40140754 Score: 66
Period size: 12 Copynumber: 4.9 Consensus size: 12
40140687 TTTGGTGCTA
*
40140697 TTTTTGTTATTG
1 TTTTTGTTGTTG
*
40140709 -TTTTGTTGTTA
1 TTTTTGTTGTTG
40140720 TTTTTGTTGTTG
1 TTTTTGTTGTTG
*
40140732 -TTTTGTTTGTTA
1 TTTTTG-TTGTTG
40140744 TTTTTGTTGTT
1 TTTTTGTTGTT
40140755 TGAATGTTAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
11 14 0.36
12 20 0.51
13 5 0.13
ACGTcount: A:0.05, C:0.00, G:0.19, T:0.76
Consensus pattern (12 bp):
TTTTTGTTGTTG
Found at i:40140713 original size:41 final size:41
Alignment explanation
Indices: 40140624--40140713 Score: 128
Period size: 40 Copynumber: 2.2 Consensus size: 41
40140614 ATTTATATTG
* *
40140624 TTGTTTTGATTTTTTTTTACTGTTTTGGTGTTGTTTTTTTA
1 TTGTTTTGATTTTTTTTTACTGTTTTGGTGCTATTTTTTTA
* *
40140665 CTATTTTGA-TTTTTTTTACTGTTTTGGTGCTATTTTTGTTA
1 TTGTTTTGATTTTTTTTTACTGTTTTGGTGCTATTTTT-TTA
40140706 TTGTTTTG
1 TTGTTTTG
40140714 TTGTTATTTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 26 0.62
41 16 0.38
ACGTcount: A:0.09, C:0.04, G:0.17, T:0.70
Consensus pattern (41 bp):
TTGTTTTGATTTTTTTTTACTGTTTTGGTGCTATTTTTTTA
Found at i:40140749 original size:24 final size:23
Alignment explanation
Indices: 40140684--40140754 Score: 106
Period size: 23 Copynumber: 3.0 Consensus size: 23
40140674 TTTTTTTTAC
* * *
40140684 TGTTTTGGTGCTATTTTTGTTAT
1 TGTTTTGTTGTTATTTTTGTTGT
40140707 TGTTTTGTTGTTATTTTTGTTGT
1 TGTTTTGTTGTTATTTTTGTTGT
40140730 TGTTTTGTTTGTTATTTTTGTTGT
1 TGTTTTG-TTGTTATTTTTGTTGT
40140754 T
1 T
40140755 TGAATGTTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
23 27 0.61
24 17 0.39
ACGTcount: A:0.06, C:0.01, G:0.21, T:0.72
Consensus pattern (23 bp):
TGTTTTGTTGTTATTTTTGTTGT
Found at i:40140756 original size:20 final size:21
Alignment explanation
Indices: 40140726--40140768 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
40140716 GTTATTTTTG
**
40140726 TTGTTGTTTTGTTTGTTATTT
1 TTGTTGTTTTGAATGTTATTT
40140747 TTGTTG-TTTGAATGTTATTT
1 TTGTTGTTTTGAATGTTATTT
40140767 TT
1 TT
40140769 TATGCGTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.00, G:0.19, T:0.72
Consensus pattern (21 bp):
TTGTTGTTTTGAATGTTATTT
Found at i:40140762 original size:24 final size:24
Alignment explanation
Indices: 40140695--40140762 Score: 68
Period size: 24 Copynumber: 2.9 Consensus size: 24
40140685 GTTTTGGTGC
* **
40140695 TATTTTTGTTATTGTTTTG-TTGT
1 TATTTTTGTTGTTGTAATGTTTGT
**
40140718 TATTTTTGTTGTTGTTTTGTTTGT
1 TATTTTTGTTGTTGTAATGTTTGT
40140742 TATTTTTGTTGTT-TGAATGTT
1 TATTTTTGTTGTTGT-AATGTT
40140763 ATTTTTTATG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
23 19 0.47
24 21 0.52
ACGTcount: A:0.09, C:0.00, G:0.19, T:0.72
Consensus pattern (24 bp):
TATTTTTGTTGTTGTAATGTTTGT
Found at i:40141940 original size:17 final size:19
Alignment explanation
Indices: 40141901--40141940 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
40141891 ATTATACATG
40141901 ATATTTTAGATTCAAATTT
1 ATATTTTAGATTCAAATTT
*
40141920 -TATTTT-GATT-TAATTT
1 ATATTTTAGATTCAAATTT
40141936 ATATT
1 ATATT
40141941 GATTTGTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 5 0.26
17 8 0.42
18 6 0.32
ACGTcount: A:0.33, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
ATATTTTAGATTCAAATTT
Found at i:40143661 original size:18 final size:18
Alignment explanation
Indices: 40143638--40143673 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40143628 ATTAACTCAT
40143638 AGTACTTTCTCTTTTTTC
1 AGTACTTTCTCTTTTTTC
40143656 AGTACTTTCTCTTTTTTC
1 AGTACTTTCTCTTTTTTC
40143674 TTACATGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.06, T:0.61
Consensus pattern (18 bp):
AGTACTTTCTCTTTTTTC
Found at i:40148264 original size:6 final size:6
Alignment explanation
Indices: 40148245--40148313 Score: 65
Period size: 6 Copynumber: 12.2 Consensus size: 6
40148235 GACTTTATGT
* * * *
40148245 TTTAAT TTTGAA TTTAAA -TTAAT TTTTAA TTT--A TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
40148290 TTT-AT TTTAAA TTTAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA T
40148314 CAAATTATGA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
4 4 0.08
5 8 0.16
6 39 0.76
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (6 bp):
TTTAAA
Found at i:40148268 original size:17 final size:17
Alignment explanation
Indices: 40148255--40148319 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 17
40148245 TTTAATTTTG
* *
40148255 AATTTAAATTAATTTTT
1 AATTTAAATTAAATTTA
*
40148272 AATTT-ATTTAAATTTA
1 AATTTAAATTAAATTTA
**
40148288 AATTTATTTTAAATTTA
1 AATTTAAATTAAATTTA
*
40148305 AATTTAAATCAAATT
1 AATTTAAATTAAATT
40148320 ATGAAAATAT
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
16 13 0.32
17 27 0.68
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
AATTTAAATTAAATTTA
Found at i:40148290 original size:27 final size:28
Alignment explanation
Indices: 40148245--40148313 Score: 86
Period size: 27 Copynumber: 2.4 Consensus size: 28
40148235 GACTTTATGT
* *
40148245 TTTAATTTTGAATTTAAATTAATTTTTAA
1 TTTAA-TTTAAATTTAAATTAATTTTAAA
*
40148274 TTT-ATTTAAATTTAAATTTATTTTAAA
1 TTTAATTTAAATTTAAATTAATTTTAAA
40148301 TTTAAATTTAAAT
1 TTT-AATTTAAAT
40148314 CAAATTATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 23 0.66
28 1 0.03
29 11 0.31
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (28 bp):
TTTAATTTAAATTTAAATTAATTTTAAA
Found at i:40148291 original size:16 final size:17
Alignment explanation
Indices: 40148244--40148310 Score: 73
Period size: 17 Copynumber: 4.0 Consensus size: 17
40148234 GGACTTTATG
* *
40148244 TTTTAATTTTGAATTTA
1 TTTTAAATTTAAATTTA
** * *
40148261 AATTAATTTTTAATTTA
1 TTTTAAATTTAAATTTA
40148278 -TTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
40148294 TTTTAAATTTAAATTTA
1 TTTTAAATTTAAATTTA
40148311 AATCAAATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
16 13 0.30
17 30 0.70
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (17 bp):
TTTTAAATTTAAATTTA
Found at i:40148309 original size:33 final size:33
Alignment explanation
Indices: 40148245--40148310 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
40148235 GACTTTATGT
* * * *
40148245 TTTAATTTTGAATTTAAATTAATTTTTAATTTA
1 TTTAAATTTAAATTTAAATTAAATTTAAATTTA
**
40148278 TTTAAATTTAAATTTATTTTAAATTTAAATTTA
1 TTTAAATTTAAATTTAAATTAAATTTAAATTTA
40148311 AATCAAATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (33 bp):
TTTAAATTTAAATTTAAATTAAATTTAAATTTA
Found at i:40148321 original size:27 final size:28
Alignment explanation
Indices: 40148245--40148339 Score: 72
Period size: 27 Copynumber: 3.4 Consensus size: 28
40148235 GACTTTATGT
* * * *
40148245 TTTAATTTTGAATTTAAATTAATTTTTAA
1 TTTAAATTTAAATTCAAATT-ATTTTAAA
*
40148274 TTT--ATTTAAATTTAAATTTATTTTAAA
1 TTTAAATTTAAATTCAAA-TTATTTTAAA
**
40148301 TTTAAATTTAAA-TCAAATTA-TGAAAA
1 TTTAAATTTAAATTCAAATTATTTTAAA
40148327 TATTAAATTTAAA
1 T-TTAAATTTAAA
40148340 CATTAAAATT
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
26 5 0.09
27 35 0.62
28 6 0.11
29 10 0.18
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (28 bp):
TTTAAATTTAAATTCAAATTATTTTAAA
Found at i:40150237 original size:29 final size:28
Alignment explanation
Indices: 40150201--40150410 Score: 153
Period size: 29 Copynumber: 7.2 Consensus size: 28
40150191 CCTGAACTCA
*
40150201 CCAAAATTACCATTTTACCCCCAAACTTT
1 CCAAAATTACCATTTTAACCCC-AACTTT
* * *
40150230 CTAAAATTA-CATTTGTAACCCCGATTTT
1 CCAAAATTACCATTT-TAACCCCAACTTT
*
40150258 ACCAAAAATTACCATTTT-ACCCTAAACTTT
1 -CC-AAAATTACCATTTTAACCC-CAACTTT
*
40150288 CCAAAATT-CCATTTTTAACCCCGA-TTT
1 CCAAAATTACCA-TTTTAACCCCAACTTT
* *
40150315 CACCAAAATTATCATTTTACCCCCGAACTTT
1 --CCAAAATTACCATTTTAACCCC-AACTTT
* *
40150346 CCAAAATT-CCATTTTAACCTCGA-TTT
1 CCAAAATTACCATTTTAACCCCAACTTT
* *
40150372 CACCAAAAATTACCATTTTACCCCCGAACCTT
1 --CC-AAAATTACCATTTTAACCCC-AACTTT
40150404 CCAAAAT
1 CCAAAAT
40150411 CTCATTTTTA
Statistics
Matches: 142, Mismatches: 21, Indels: 36
0.71 0.11 0.18
Matches are distributed among these distances:
26 3 0.02
27 7 0.05
28 32 0.23
29 61 0.43
30 28 0.20
31 9 0.06
32 2 0.01
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (28 bp):
CCAAAATTACCATTTTAACCCCAACTTT
Found at i:40150294 original size:58 final size:59
Alignment explanation
Indices: 40150198--40150423 Score: 318
Period size: 58 Copynumber: 3.9 Consensus size: 59
40150188 GTCCCTGAAC
* * *
40150198 TCACC-AAAATTACCATTTTACCCCCAAACTTTCTAAAATTACATTTGTAACCCCGATT
1 TCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATT
* *
40150256 TTACCAAAAATTACCATTTTA-CCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATT
1 TCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATT
* * *
40150314 TCACC-AAAATTATCATTTTACCCCCGAACTTTCCAAAATTCCA-TTTTAACCTCGATT
1 TCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATT
* *
40150371 TCACCAAAAATTACCATTTTACCCCCGAACCTTCCAAAA-TCTCATTTTTAACC
1 TCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTC-CATTTTTAACC
40150424 TCTATTTTTT
Statistics
Matches: 151, Mismatches: 12, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
57 34 0.23
58 94 0.62
59 23 0.15
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.34
Consensus pattern (59 bp):
TCACCAAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATT
Found at i:40160035 original size:76 final size:76
Alignment explanation
Indices: 40159909--40160572 Score: 1076
Period size: 76 Copynumber: 8.7 Consensus size: 76
40159899 GAGCATCAAC
* * * *
40159909 ATCATTTTCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATATCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
*
40159974 GTAAGAGCAAT
66 GTAAGAGCAAG
* * *
40159985 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTAAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
40160050 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
40160061 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTGTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
40160126 GTAAGAGCAAG
66 GTAAGAGCAAG
* * *
40160137 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTGTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
40160202 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
40160213 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
40160278 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
40160289 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
40160354 GTAAGAGCAAG
66 GTAAGAGCAAG
* * * *
40160365 ATCATTTCCTATCCTCATGAAATTGAAGTAGAGTTGAATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
40160430 GTAAGAGCAAG
66 GTAAGAGCAAG
* *
40160441 ATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
*
40160506 GTAAGAGCGAG
66 GTAAGAGCAAG
* * *
40160517 ATCATCTCCTATCCTCTTGAAATTGAAGTAGAGCCGGATATCAAGACTTTATCTCT
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCT
40160573 CTGAAGCTAT
Statistics
Matches: 551, Mismatches: 37, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
76 551 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Consensus pattern (76 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAG
Found at i:40160306 original size:228 final size:228
Alignment explanation
Indices: 40159743--40160572 Score: 1275
Period size: 228 Copynumber: 3.6 Consensus size: 228
40159733 ATCAATCAAC
*
40159743 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTCGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
* * *
40159808 GTAAGAGCAAGATTATTTTCTATCCTCTTGAAATTGAAGT-AAGCTGGATATCAAGTCTTTATCT
66 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTA--T
*
40159872 CTCTGAAATTGAAGTAAGAGCAAGACAGAGCATCAACATCATTTTCTATCCTCTTGAAATTGAAG
129 CTCTGAAATTGAAGT-A-AG--AG-CA-AG-------ATCATTTCCTATCCTCTTGAAATTGAAG
* *
40159937 TAGAGTTGGATAACAAGTCTTTATATCTGAAATTGAAGTAAGAGCAAT
181 TAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
* *
40159985 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTAAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
*
40160050 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAATCTGTATCT
66 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCT
* * *
40160115 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCA
131 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACA
* *
40160180 AATCTGTATCTCTGAAATTGAAGTAAGAGCAAG
196 AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
*
40160213 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
40160278 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCT
66 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCT
* *
40160343 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCATGAAATTGAAGTAGAGTTGAATAACA
131 CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACA
40160408 AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
196 AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
* * *
40160441 ATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
* * * * * *
40160506 GTAAGAGCGAGATCATCTCCTATCCTCTTGAAATTGAAGTAGAGCCGGATATCAAGACTTTATCT
66 GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCT
40160571 CT
131 CT
40160573 CTGAAGCTAT
Statistics
Matches: 553, Mismatches: 34, Indels: 16
0.92 0.06 0.03
Matches are distributed among these distances:
228 409 0.74
235 2 0.00
236 2 0.00
237 2 0.00
239 2 0.00
240 1 0.00
241 16 0.03
242 100 0.18
243 19 0.03
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (228 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
GTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTGTATCT
CTGAAATTGAAGTAAGAGCAAGATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACA
AGTCTTTATCTCTGAAATTGAAGTAAGAGCAAG
Found at i:40160868 original size:6 final size:6
Alignment explanation
Indices: 40160849--40160932 Score: 84
Period size: 6 Copynumber: 14.2 Consensus size: 6
40160839 GACTTTATGT
* * *
40160849 TTTAAT TTTGAA TTTAAA -TTAAA TTTAAA TTT-AT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
40160895 TTCAACTA TTTAAA TTT-AT TTTAAA TTTAAA TTTAAA T
1 TTTAA--A TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
40160933 CAAATTATAC
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
5 13 0.20
6 46 0.72
8 5 0.08
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:40160875 original size:11 final size:12
Alignment explanation
Indices: 40160849--40160932 Score: 84
Period size: 11 Copynumber: 7.1 Consensus size: 12
40160839 GACTTTATGT
* *
40160849 TTTAATTTTGAA
1 TTTAAATTTAAA
40160861 TTTAAA-TTAAA
1 TTTAAATTTAAA
*
40160872 TTTAAATTT-AT
1 TTTAAATTTAAA
40160883 TTTAAATTTAAA
1 TTTAAATTTAAA
*
40160895 TTCAACTATTTAAA
1 TTTAA--ATTTAAA
*
40160909 TTT-ATTTTAAA
1 TTTAAATTTAAA
40160920 TTTAAATTTAAA
1 TTTAAATTTAAA
40160932 T
1 T
40160933 CAAATTATAC
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
11 29 0.49
12 20 0.34
13 1 0.02
14 9 0.15
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:40160879 original size:17 final size:17
Alignment explanation
Indices: 40160859--40160938 Score: 76
Period size: 17 Copynumber: 4.9 Consensus size: 17
40160849 TTTAATTTTG
40160859 AATTTAAATTAAATTTA
1 AATTTAAATTAAATTTA
**
40160876 AATTTATTTTAAATTTA
1 AATTTAAATTAAATTTA
* *
40160893 AA-TTCAACT--ATTTA
1 AATTTAAATTAAATTTA
**
40160907 AATTTATTTTAAATTTA
1 AATTTAAATTAAATTTA
*
40160924 AATTTAAATCAAATT
1 AATTTAAATTAAATT
40160939 ATACAAATAT
Statistics
Matches: 47, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
14 7 0.15
15 3 0.06
16 3 0.06
17 34 0.72
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTAAATTAAATTTA
Found at i:40160909 original size:31 final size:28
Alignment explanation
Indices: 40160853--40160932 Score: 115
Period size: 31 Copynumber: 2.7 Consensus size: 28
40160843 TTATGTTTTA
*
40160853 ATTTTGAATTTAAATTAAATTTAAATTT
1 ATTTTAAATTTAAATTAAATTTAAATTT
40160881 ATTTTAAATTTAAATTCAACTATTTAAATTT
1 ATTTTAAATTTAAATT-AA--ATTTAAATTT
40160912 ATTTTAAATTTAAATTTAAAT
1 ATTTTAAATTTAAA-TTAAAT
40160933 CAAATTATAC
Statistics
Matches: 47, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
28 15 0.32
29 4 0.09
31 26 0.55
32 2 0.04
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.53
Consensus pattern (28 bp):
ATTTTAAATTTAAATTAAATTTAAATTT
Found at i:40162275 original size:25 final size:23
Alignment explanation
Indices: 40162148--40162297 Score: 164
Period size: 23 Copynumber: 6.4 Consensus size: 23
40162138 ACGGAACAAG
* *
40162148 CAGAGAGTAC-CAAAGTACTAA-
1 CAGAGAGCACACAAAGTGCTAAT
*
40162169 CAGAGAGCACA-TAAGTGCTGGGCAA-
1 CAGAGAGCACACAAAGTGCT----AAT
* *
40162194 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
40162217 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
40162240 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
40162263 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
40162286 AACAGAGAGCAC
1 --CAGAGAGCAC
40162298 GAGACGTGCT
Statistics
Matches: 111, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
21 15 0.14
22 2 0.02
23 66 0.59
25 22 0.20
26 6 0.05
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:40162306 original size:25 final size:25
Alignment explanation
Indices: 40162166--40162318 Score: 128
Period size: 23 Copynumber: 6.4 Consensus size: 25
40162156 ACCAAAGTAC
* **
40162166 TAACAGAGAGCACATA-AGTGCTGGG
1 TAACAGAGAGCACACACAGTGCT-AA
* * * *
40162191 CAACAGAGAGTACACAAAGTACTAA
1 TAACAGAGAGCACACACAGTGCTAA
*
40162216 T--CAGAGAGCACACAAAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
*
40162239 T--CAGAGAGCACACAAAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
40162262 T--CAGAGAGCACACACAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
*
40162285 TAACAGAGAGCACGAGAC-GTGCT-A
1 TAACAGAGAGCAC-ACACAGTGCTAA
40162309 -AACAGAGAGC
1 TAACAGAGAGC
40162319 GCGCTAGTGT
Statistics
Matches: 113, Mismatches: 11, Indels: 10
0.84 0.08 0.07
Matches are distributed among these distances:
23 76 0.67
24 1 0.01
25 28 0.25
26 8 0.07
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.12
Consensus pattern (25 bp):
TAACAGAGAGCACACACAGTGCTAA
Found at i:40167750 original size:23 final size:23
Alignment explanation
Indices: 40167678--40167804 Score: 118
Period size: 23 Copynumber: 5.4 Consensus size: 23
40167668 ACGGAACAAG
* *
40167678 CAGAGAGTAC-CAAAGTACTAA-
1 CAGAGAGCACACAAAGTGCTAAT
*
40167699 CAGAGAGCACA-TAAGTGCTGGGCAA-
1 CAGAGAGCACACAAAGTGCT----AAT
* *
40167724 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
40167747 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
40167770 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
40167793 AACAGAGAGCAC
1 --CAGAGAGCAC
40167805 GAGACGTGCT
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
21 15 0.17
22 2 0.02
23 43 0.49
25 22 0.25
26 6 0.07
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.13
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:40167774 original size:46 final size:45
Alignment explanation
Indices: 40167678--40167824 Score: 138
Period size: 48 Copynumber: 3.2 Consensus size: 45
40167668 ACGGAACAAG
*
40167678 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACATAAGTGCTGGGCAA
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCT--G-AA
40167724 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AA
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACA-AAAGTGCTGAA
* * * * * *
40167769 TCAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAA
1 -CAGAGAGTACACAAAGTACTAAT--CAGAGAGCAC-AAAAGTGCTGAA
40167818 CAGAGAG
1 CAGAGAG
40167825 CGCGCTAGTG
Statistics
Matches: 87, Mismatches: 6, Indels: 14
0.81 0.06 0.13
Matches are distributed among these distances:
45 2 0.02
46 30 0.34
47 11 0.13
48 34 0.39
49 10 0.11
ACGTcount: A:0.43, C:0.20, G:0.24, T:0.12
Consensus pattern (45 bp):
CAGAGAGTACACAAAGTACTAATCAGAGAGCACAAAAGTGCTGAA
Found at i:40167813 original size:25 final size:25
Alignment explanation
Indices: 40167696--40167825 Score: 105
Period size: 23 Copynumber: 5.4 Consensus size: 25
40167686 ACCAAAGTAC
* **
40167696 TAACAGAGAGCACATA-AGTGCTGGG
1 TAACAGAGAGCACACACAGTGCT-AA
* * * *
40167721 CAACAGAGAGTACACAAAGTACTAA
1 TAACAGAGAGCACACACAGTGCTAA
*
40167746 T--CAGAGAGCACACAAAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
40167769 T--CAGAGAGCACACACAGTGCTAA
1 TAACAGAGAGCACACACAGTGCTAA
*
40167792 TAACAGAGAGCACGAGAC-GTGCT-A
1 TAACAGAGAGCAC-ACACAGTGCTAA
40167816 -AACAGAGAGC
1 TAACAGAGAGC
40167826 GCGCTAGTGT
Statistics
Matches: 90, Mismatches: 11, Indels: 10
0.81 0.10 0.09
Matches are distributed among these distances:
23 53 0.59
24 1 0.01
25 28 0.31
26 8 0.09
ACGTcount: A:0.42, C:0.21, G:0.25, T:0.12
Consensus pattern (25 bp):
TAACAGAGAGCACACACAGTGCTAA
Found at i:40167819 original size:23 final size:23
Alignment explanation
Indices: 40167722--40167825 Score: 111
Period size: 23 Copynumber: 4.4 Consensus size: 23
40167712 AGTGCTGGGC
* * *
40167722 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
40167745 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
40167768 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
40167792 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
40167816 AACAGAGAGC
1 AACAGAGAGC
40167826 GCGCTAGTGT
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
23 51 0.71
24 2 0.03
25 16 0.22
26 3 0.04
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:40170555 original size:34 final size:34
Alignment explanation
Indices: 40170512--40170630 Score: 116
Period size: 34 Copynumber: 3.3 Consensus size: 34
40170502 GTCCTTTCGC
40170512 TTTTTTTATTTGTTTCAATTTAGTCCTTTTTTGT
1 TTTTTTTATTTGTTTCAATTTAGTCCTTTTTTGT
* * *
40170546 TTTTTTTATTAT-TTAT-AATTTTGCCCGGTAATTTTAATTT
1 TTTTTTTATT-TGTT-TCAATTTAGTCC--T--TTTT--TGT
40170586 CTTTTTTTATTTGTTTCAATTTAGTCCTTTTTTGT
1 -TTTTTTTATTTGTTTCAATTTAGTCCTTTTTTGT
40170621 TTTTTTTATT
1 TTTTTTTATT
40170631 ATTTGTAATT
Statistics
Matches: 68, Mismatches: 6, Indels: 22
0.71 0.06 0.23
Matches are distributed among these distances:
34 30 0.44
35 4 0.06
36 1 0.01
37 4 0.06
38 4 0.06
39 1 0.01
40 4 0.06
41 20 0.29
ACGTcount: A:0.15, C:0.08, G:0.08, T:0.69
Consensus pattern (34 bp):
TTTTTTTATTTGTTTCAATTTAGTCCTTTTTTGT
Found at i:40170593 original size:75 final size:75
Alignment explanation
Indices: 40170511--40170665 Score: 301
Period size: 75 Copynumber: 2.1 Consensus size: 75
40170501 GGTCCTTTCG
40170511 CTTTTTTTATTTGTTTCAATTTAGTCCTTTTTTGTTTTTTTTATTATTTATAATTTTGCCCGGTA
1 CTTTTTTTATTTGTTTCAATTTAGTCCTTTTTTGTTTTTTTTATTATTTATAATTTTGCCCGGTA
40170576 ATTTTAATTT
66 ATTTTAATTT
*
40170586 CTTTTTTTATTTGTTTCAATTTAGTCCTTTTTTGTTTTTTTTATTATTTGTAATTTTGCCCGGTA
1 CTTTTTTTATTTGTTTCAATTTAGTCCTTTTTTGTTTTTTTTATTATTTATAATTTTGCCCGGTA
40170651 ATTTTAATTT
66 ATTTTAATTT
40170661 CTTTT
1 CTTTT
40170666 CAATTTGATC
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 79 1.00
ACGTcount: A:0.16, C:0.10, G:0.08, T:0.66
Consensus pattern (75 bp):
CTTTTTTTATTTGTTTCAATTTAGTCCTTTTTTGTTTTTTTTATTATTTATAATTTTGCCCGGTA
ATTTTAATTT
Found at i:40171067 original size:58 final size:58
Alignment explanation
Indices: 40170912--40171173 Score: 364
Period size: 59 Copynumber: 4.5 Consensus size: 58
40170902 GTCCCTGAAC
* *
40170912 TCACCAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTGTAACCCCGATT
1 TCACCAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATT
*
40170970 TCACCAAAAATTACCATTTTACCCTCAAACTTTCCAAAATTCCATTTTTAACCCCGATT
1 TCACC-AAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATT
* *
40171029 TCACCAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCCAATT
1 TCACCAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATT
* * *
40171087 TCACCAAAAATTACCATTTTACCCCCGAACCTTCCAAAA-TCTCATTTTTAACCTCGATTT
1 TCACC-AAAATTACCATTTTACCCTCGAACTTTCCAAAATTC-CATTTTTAACCCCGA-TT
** ** *
40171147 TTTCCAAAATTACTTTTTTGCCCTCGA
1 TCACCAAAATTACCATTTTACCCTCGA
40171174 GAGTCAAAAA
Statistics
Matches: 183, Mismatches: 17, Indels: 7
0.88 0.08 0.03
Matches are distributed among these distances:
58 62 0.34
59 116 0.63
60 5 0.03
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.35
Consensus pattern (58 bp):
TCACCAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATT
Found at i:40171122 original size:117 final size:118
Alignment explanation
Indices: 40170912--40171173 Score: 384
Period size: 117 Copynumber: 2.2 Consensus size: 118
40170902 GTCCCTGAAC
* *
40170912 TCACCAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTGTAACCCCGATTTCACCAA
1 TCACCAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTGTAACCCCAATTTCACCAA
* *
40170977 AAATTACCATTTTACCCTCAAACTTTCCAAAAT-TCCATTTTTAACCCCGA-TT
66 AAATTACCATTTTACCCCCAAACCTTCCAAAATCT-CATTTTTAACCCCGATTT
* *
40171029 TCACCAAAATTACCATTTTACCCTCGAACTTTCTAAAATTCCATTTTTAACCCCAATTTCACCAA
1 TCACCAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTGTAACCCCAATTTCACCAA
* *
40171094 AAATTACCATTTTACCCCCGAACCTTCCAAAATCTCATTTTTAACCTCGATTT
66 AAATTACCATTTTACCCCCAAACCTTCCAAAATCTCATTTTTAACCCCGATTT
** ** *
40171147 TTTCCAAAATTACTTTTTTGCCCTCGA
1 TCACCAAAATTACCATTTTACCCTCGA
40171174 GAGTCAAAAA
Statistics
Matches: 130, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
117 105 0.81
118 25 0.19
ACGTcount: A:0.31, C:0.31, G:0.03, T:0.35
Consensus pattern (118 bp):
TCACCAAAATTACCATTTTACCCTCGAACTTTCCAAAATTCCATTTGTAACCCCAATTTCACCAA
AAATTACCATTTTACCCCCAAACCTTCCAAAATCTCATTTTTAACCCCGATTT
Found at i:40173452 original size:24 final size:26
Alignment explanation
Indices: 40173415--40173463 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
40173405 TATTGACCAA
40173415 CTTTATTA-TCTTTTAAAATTAAGTC
1 CTTTATTATTCTTTTAAAATTAAGTC
*
40173440 CTTT-TTATTTTTTTAAAATTAAGT
1 CTTTATTATTCTTTTAAAATTAAGT
40173464 TTTTCTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 3 0.14
25 19 0.86
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (26 bp):
CTTTATTATTCTTTTAAAATTAAGTC
Found at i:40175401 original size:13 final size:13
Alignment explanation
Indices: 40175383--40175408 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40175373 ATTTGATATA
40175383 AATTTAATATTAT
1 AATTTAATATTAT
40175396 AATTTAATATTAT
1 AATTTAATATTAT
40175409 GTCAAATCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTAATATTAT
Found at i:40175493 original size:17 final size:17
Alignment explanation
Indices: 40175458--40175493 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
40175448 TAGAAGTATA
*
40175458 TTTGAATTTATTAATTT
1 TTTGAATTTATGAATTT
40175475 TTTGAGATTTATGAATTT
1 TTTGA-ATTTATGAATTT
40175493 T
1 T
40175494 GAAAATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (17 bp):
TTTGAATTTATGAATTT
Found at i:40176124 original size:30 final size:30
Alignment explanation
Indices: 40176090--40176150 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
40176080 AATTTGAATT
*
40176090 TTTCGAATCGAATCGAATCAAGTTAAAAAA
1 TTTCGAATCAAATCGAATCAAGTTAAAAAA
* * * *
40176120 TTTCGAGTCAAATCGAGTCGAGTTAACAAA
1 TTTCGAATCAAATCGAATCAAGTTAAAAAA
40176150 T
1 T
40176151 CCTATTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (30 bp):
TTTCGAATCAAATCGAATCAAGTTAAAAAA
Found at i:40176758 original size:47 final size:49
Alignment explanation
Indices: 40176707--40176805 Score: 139
Period size: 47 Copynumber: 2.1 Consensus size: 49
40176697 AAATATATAA
* *
40176707 AAATTTAATTTAATAATTATCTCAATAATT-TT-TATTAATTTAATATT
1 AAATTAAATTAAATAATTATCTCAATAATTATTATATTAATTTAATATT
* * *
40176754 AAATTAAATTAAATATTTATTTTAATAATTATTATATTAATTTAATATT
1 AAATTAAATTAAATAATTATCTCAATAATTATTATATTAATTTAATATT
40176803 AAA
1 AAA
40176806 GTGATTAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
47 25 0.56
48 2 0.04
49 18 0.40
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (49 bp):
AAATTAAATTAAATAATTATCTCAATAATTATTATATTAATTTAATATT
Found at i:40176798 original size:5 final size:6
Alignment explanation
Indices: 40176739--40176804 Score: 50
Period size: 6 Copynumber: 11.0 Consensus size: 6
40176729 CAATAATTTT
* *
40176739 TATTAA T-TTAA TATTAA -ATTAA -ATTAAA TATTTA TTTTAA TAATTATTA
1 TATTAA TATTAA TATTAA TATTAA TATT-AA TATTAA TATTAA T-ATTA--A
40176788 TATTAA T-TTAA TATTAA
1 TATTAA TATTAA TATTAA
40176805 AGTGATTAAG
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
5 18 0.37
6 19 0.39
7 6 0.12
8 4 0.08
9 2 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TATTAA
Found at i:40178160 original size:17 final size:18
Alignment explanation
Indices: 40178140--40178182 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
40178130 TTTTTAAGTA
40178140 ATAATTATAATTAAAT-T
1 ATAATTATAATTAAATGT
**
40178157 ATAATTATTTTTAAATGT
1 ATAATTATAATTAAATGT
40178175 ATAATTAT
1 ATAATTAT
40178183 CACCGTTCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
ATAATTATAATTAAATGT
Found at i:40197373 original size:13 final size:13
Alignment explanation
Indices: 40197355--40197388 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
40197345 TGGAACAATC
40197355 ATATTCGATATAT
1 ATATTCGATATAT
40197368 ATATTCGATATAT
1 ATATTCGATATAT
40197381 ATATTCGA
1 ATATTCGA
40197389 ACACGGATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (13 bp):
ATATTCGATATAT
Found at i:40198741 original size:7 final size:8
Alignment explanation
Indices: 40198717--40198748 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
40198707 GGATATTTTG
40198717 TTTAATTT
1 TTTAATTT
40198725 TTTAATTT
1 TTTAATTT
40198733 TTTAATTT
1 TTTAATTT
*
40198741 TTAAATTT
1 TTTAATTT
40198749 GTATTATTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTAATTT
Found at i:40213594 original size:2 final size:2
Alignment explanation
Indices: 40213548--40213578 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
40213538 AAAATTTTTA
40213548 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
40213579 ATTAACTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:40218997 original size:32 final size:32
Alignment explanation
Indices: 40218961--40219023 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
40218951 TAATGGAAAA
*
40218961 CATGAGTTAAGGGTTTTTTTGACGATTATGCC
1 CATGAGTTAAGGGTATTTTTGACGATTATGCC
*
40218993 CATGAGTTGAGGGTATTTTTGACGATTATGC
1 CATGAGTTAAGGGTATTTTTGACGATTATGC
40219024 TTTTTCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.40
Consensus pattern (32 bp):
CATGAGTTAAGGGTATTTTTGACGATTATGCC
Found at i:40220902 original size:12 final size:13
Alignment explanation
Indices: 40220876--40220910 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
40220866 ATATTTTATT
40220876 ATTTTTAAAACTA
1 ATTTTTAAAACTA
40220889 ATTTTTAAAA-TA
1 ATTTTTAAAACTA
*
40220901 ATATTTAAAA
1 ATTTTTAAAA
40220911 ATATATGTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (13 bp):
ATTTTTAAAACTA
Found at i:40226872 original size:21 final size:20
Alignment explanation
Indices: 40226848--40226912 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 20
40226838 GTTTTATGCG
40226848 TTTAATTTTTATTTAATATGT
1 TTTAATTTTTATTTAATAT-T
*
40226869 TTTAATTATTATAATTAAT-TT
1 TTTAATT-TT-TATTTAATATT
*
40226890 TTTAA--TTTATTTAATATA
1 TTTAATTTTTATTTAATATT
40226908 TTTAA
1 TTTAA
40226913 AATATATTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
17 7 0.18
18 8 0.21
21 13 0.34
22 3 0.08
23 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTAATTTTTATTTAATATT
Found at i:40226902 original size:9 final size:9
Alignment explanation
Indices: 40226883--40226931 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
40226873 ATTATTATAA
40226883 TTAATTT-T
1 TTAATTTAT
40226891 TTAATTTAT
1 TTAATTTAT
*
40226900 TTAATATAT
1 TTAATTTAT
**
40226909 TTAAAATAT
1 TTAATTTAT
40226918 ATTAATTTAT
1 -TTAATTTAT
40226928 TTAA
1 TTAA
40226932 CAATTCAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
8 7 0.20
9 21 0.60
10 7 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
TTAATTTAT
Found at i:40226928 original size:19 final size:19
Alignment explanation
Indices: 40226882--40226931 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
40226872 AATTATTATA
**
40226882 ATTAATTT-TTTAATTTAT
1 ATTAATTTATTTAAAATAT
*
40226900 -TTAATATATTTAAAATAT
1 ATTAATTTATTTAAAATAT
40226918 ATTAATTTATTTAA
1 ATTAATTTATTTAA
40226932 CAATTCAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 6 0.23
18 8 0.31
19 12 0.46
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTAATTTATTTAAAATAT
Found at i:40242085 original size:30 final size:30
Alignment explanation
Indices: 40242013--40242092 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 30
40242003 CTCTAAATTT
* *
40242013 TACATCAACTTTAATTTACTGTGTAATTGTA
1 TACATAAATTTTAATTTA-TGTGTAATTGTA
*
40242044 TACATAAATTTTAATTT-TGTGTAATTTTA
1 TACATAAATTTTAATTTATGTGTAATTGTA
* *
40242073 TATATGAAATTTTGATTTAT
1 TACAT-AAATTTTAATTTAT
40242093 TCAATTCTCA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
29 15 0.36
30 11 0.26
31 16 0.38
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (30 bp):
TACATAAATTTTAATTTATGTGTAATTGTA
Found at i:40251138 original size:14 final size:15
Alignment explanation
Indices: 40251100--40251140 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
40251090 TTTAAGTGGG
40251100 TTTAATATTTTCTAAA
1 TTTAATATTTT-TAAA
*
40251116 CTT-ATATTTTT-AA
1 TTTAATATTTTTAAA
40251129 TTTAATATTTTT
1 TTTAATATTTTT
40251141 GTTCAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 4 0.18
14 9 0.41
15 7 0.32
16 2 0.09
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTAATATTTTTAAA
Found at i:40273310 original size:23 final size:23
Alignment explanation
Indices: 40273283--40273327 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40273273 GAATTTGGGA
40273283 ATTGAA-TTTGATAATTTTTTTAT
1 ATTGAATTTTGA-AATTTTTTTAT
*
40273306 ATTGAATTTTGAATTTTTTTTA
1 ATTGAATTTTGAAATTTTTTTA
40273328 ATTTTTATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (23 bp):
ATTGAATTTTGAAATTTTTTTAT
Found at i:40280917 original size:15 final size:14
Alignment explanation
Indices: 40280886--40280927 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
40280876 TTAATATTAA
*
40280886 TTATTTTTAAGATT
1 TTATTTTTAAAATT
40280900 TTATTTTGTAAAATT
1 TTATTTT-TAAAATT
40280915 TTATTTTTCAAAA
1 TTATTTTT-AAAA
40280928 ACTTTCACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 17 0.68
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (14 bp):
TTATTTTTAAAATT
Found at i:40282571 original size:24 final size:26
Alignment explanation
Indices: 40282544--40282591 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
40282534 TATCACAATA
*
40282544 TATTTTTTAAAT-TATA-ATATATCT
1 TATTTATTAAATATATATATATATCT
*
40282568 TATTTATTATATATATATATATAT
1 TATTTATTAAATATATATATATAT
40282592 ATAATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 10 0.50
25 4 0.20
26 6 0.30
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTTATTAAATATATATATATATCT
Found at i:40283299 original size:21 final size:19
Alignment explanation
Indices: 40283274--40283312 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
40283264 TGAATAACTT
40283274 AAATTATTTAATTCAAAATTA
1 AAATT-TTTAATT-AAAATTA
*
40283295 AAATTTTTTATTAAAATT
1 AAATTTTTAATTAAAATT
40283313 TTCGAATCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTTTAATTAAAATTA
Found at i:40286064 original size:25 final size:23
Alignment explanation
Indices: 40286028--40286077 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 23
40286018 TAGTAATGAT
*
40286028 AAAATTATATTTTAACCTTTTAAAA
1 AAAATTATA-TTTAA-CTATTAAAA
40286053 AAAATT-TGATTTAACTATTAAAA
1 AAAATTAT-ATTTAACTATTAAAA
40286076 AA
1 AA
40286078 TAACAAAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 10 0.43
24 6 0.26
25 7 0.30
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (23 bp):
AAAATTATATTTAACTATTAAAA
Found at i:40287957 original size:17 final size:17
Alignment explanation
Indices: 40287928--40287960 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40287918 TTTATAATTT
40287928 ATAACACATTAAAAAAA
1 ATAACACATTAAAAAAA
40287945 ATAA-ACATATAAAAAA
1 ATAACACAT-TAAAAAA
40287961 TATATAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.09, G:0.00, T:0.18
Consensus pattern (17 bp):
ATAACACATTAAAAAAA
Found at i:40291021 original size:16 final size:16
Alignment explanation
Indices: 40291000--40291030 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40290990 TTATTTTCTA
40291000 TTTCTTTTAGTTTTAT
1 TTTCTTTTAGTTTTAT
*
40291016 TTTCTTTTATTTTTA
1 TTTCTTTTAGTTTTA
40291031 ATTCTGTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTCTTTTAGTTTTAT
Found at i:40293179 original size:8 final size:8
Alignment explanation
Indices: 40293166--40293216 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
40293156 AACCCAATTA
40293166 TTTTTATT
1 TTTTTATT
40293174 TTTTTATT
1 TTTTTATT
*
40293182 TTTTT-CT
1 TTTTTATT
* *
40293189 ATCTTATT
1 TTTTTATT
40293197 TTATTTATT
1 TT-TTTATT
*
40293206 TATTTATT
1 TTTTTATT
40293214 TTT
1 TTT
40293217 GTTCAGGAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
7 4 0.12
8 23 0.70
9 6 0.18
ACGTcount: A:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTATT
Found at i:40294094 original size:106 final size:106
Alignment explanation
Indices: 40293903--40294094 Score: 255
Period size: 106 Copynumber: 1.8 Consensus size: 106
40293893 CGTTAGACTG
* * *
40293903 AGTAACCGGGGTGGAGTGCTTGGTTGTCATTTCACTTCGAGTCAAAAGGGCTAATGCATTCTACA
1 AGTAACCGGGATGGAGTGCTTGGGTGTCATTTCACTTCGAGTCAAAAGGGCTAATGCATTCTAAA
*
40293968 ACAAAAAAAAGAGAAGAAAAAATTGAGAGCATGTTGGGCTC
66 AAAAAAAAAAGAGAAGAAAAAATTGAGAGCATGTTGGGCTC
* * * * *
40294009 AGTAATCGGGATGGAGTGCTTGGGTGTCATTTCATTTCGCGTCAAAA-GGTTCAATGTATTCTTA
1 AGTAACCGGGATGGAGTGCTTGGGTGTCATTTCACTTCGAGTCAAAAGGGCT-AATGCATTC-TA
40294073 AAGAAAAAAAAAAG-GAA-AAAAA
64 AA-AAAAAAAAAAGAGAAGAAAAA
40294095 TCACAAAATA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
105 3 0.04
106 55 0.74
107 6 0.08
108 10 0.14
ACGTcount: A:0.37, C:0.13, G:0.25, T:0.25
Consensus pattern (106 bp):
AGTAACCGGGATGGAGTGCTTGGGTGTCATTTCACTTCGAGTCAAAAGGGCTAATGCATTCTAAA
AAAAAAAAAAGAGAAGAAAAAATTGAGAGCATGTTGGGCTC
Found at i:40294685 original size:19 final size:19
Alignment explanation
Indices: 40294663--40294707 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40294653 TTATATTAGG
40294663 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
40294682 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
40294701 ATTTAAT
1 ATTTAAT
40294708 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:40295535 original size:16 final size:16
Alignment explanation
Indices: 40295514--40295544 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40295504 CTATTTTCTA
40295514 TTTCTTTTAGTTTTAT
1 TTTCTTTTAGTTTTAT
*
40295530 TTTCTTTTATTTTTA
1 TTTCTTTTAGTTTTA
40295545 ATTCTGTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTCTTTTAGTTTTAT
Found at i:40312347 original size:20 final size:18
Alignment explanation
Indices: 40312297--40312348 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
40312287 CTACAAGATA
40312297 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
40312314 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
40312334 AATATTAAATTAATA
1 AATATTAAATTAATA
40312349 AAATACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:40319205 original size:54 final size:54
Alignment explanation
Indices: 40319092--40319206 Score: 167
Period size: 54 Copynumber: 2.1 Consensus size: 54
40319082 AGTAATTACA
* * *
40319092 TATTTGTTTATCTAGTTTATTAATAAAGATATTACTATTATTATTTTCAGTCTT
1 TATTTGTTTATCTAGTTTATTAAAAAAGATATTACTATTATTATTTTCAATATT
* ** *
40319146 CATTTGTTTATCTAGTTTATTAAAAAAGATATTGTTATTATTATTTTTAATATT
1 TATTTGTTTATCTAGTTTATTAAAAAAGATATTACTATTATTATTTTCAATATT
40319200 TATTTGT
1 TATTTGT
40319207 GGGTACTAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.57
Consensus pattern (54 bp):
TATTTGTTTATCTAGTTTATTAAAAAAGATATTACTATTATTATTTTCAATATT
Found at i:40320671 original size:2 final size:2
Alignment explanation
Indices: 40320664--40320706 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
40320654 TAAGGGACTA
40320664 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40320706 A
1 A
40320707 AAGGGAAAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40322324 original size:30 final size:31
Alignment explanation
Indices: 40322290--40322358 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
40322280 TATTATAGAT
* *
40322290 ATTTTTTAATTATTTA-ATGAT-ATTTTAATA
1 ATTTTTTAATCATTTACA-CATAATTTTAATA
* *
40322320 ATTTTTTAGTCATTTACACATAATTTTGATA
1 ATTTTTTAATCATTTACACATAATTTTAATA
40322351 ATTTTTTA
1 ATTTTTTA
40322359 CCCCGAATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.58
Consensus pattern (31 bp):
ATTTTTTAATCATTTACACATAATTTTAATA
Found at i:40331160 original size:18 final size:17
Alignment explanation
Indices: 40331128--40331161 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
40331118 CACAAAGGGG
40331128 AAGAAAAAAACAGAAGA
1 AAGAAAAAAACAGAAGA
*
40331145 AAGAAAGAAAAGAGAAG
1 AAGAAA-AAAACAGAAG
40331162 GGGTGGGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.74, C:0.03, G:0.24, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAACAGAAGA
Found at i:40331705 original size:17 final size:18
Alignment explanation
Indices: 40331675--40331718 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
40331665 TTCCTTTGTA
* *
40331675 ATTTATTATTTTTATATT
1 ATTTATTATGTTTATATC
40331693 ATTT-TTATGTTTATATC
1 ATTTATTATGTTTATATC
40331710 ATTTATTAT
1 ATTTATTAT
40331719 TTCTAAAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.68
Consensus pattern (18 bp):
ATTTATTATGTTTATATC
Found at i:40331769 original size:20 final size:21
Alignment explanation
Indices: 40331746--40331784 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40331736 TTATTCAATA
40331746 AATAAAATT-GTTATTTTTTT
1 AATAAAATTAGTTATTTTTTT
*
40331766 AATAAAATTATTTATTTTT
1 AATAAAATTAGTTATTTTT
40331785 AACTTTGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (21 bp):
AATAAAATTAGTTATTTTTTT
Found at i:40334182 original size:9 final size:9
Alignment explanation
Indices: 40334165--40334196 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
40334155 TTTGTTTTTT
40334165 AATATAAAAA
1 AATA-AAAAA
40334175 AATAAAAAA
1 AATAAAAAA
40334184 AATAAAAAA
1 AATAAAAAA
40334193 AATA
1 AATA
40334197 TTGGTGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 18 0.82
10 4 0.18
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (9 bp):
AATAAAAAA
Found at i:40335699 original size:12 final size:12
Alignment explanation
Indices: 40335684--40335713 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
40335674 CTCTCCTCCT
40335684 TCCTCCAAGAAC
1 TCCTCCAAGAAC
40335696 TCCTCCAAGAAC
1 TCCTCCAAGAAC
40335708 TCCTCC
1 TCCTCC
40335714 GCATCCTCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.27, C:0.47, G:0.07, T:0.20
Consensus pattern (12 bp):
TCCTCCAAGAAC
Done.