Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 159 of 193
Found at i:49094390 original size:178 final size:179
Alignment explanation
Indices: 49094079--49094418 Score: 605
Period size: 179 Copynumber: 1.9 Consensus size: 179
49094069 AGAACATCCT
49094079 AAAATTACTATTTTACCCCCGAACATCCAAAAATTACCATTTTCCCCCCAAATTTCCAAAAATCA
1 AAAATTACTATTTTACCCCCGAACATCCAAAAATTACCATTTTCCCCCCAAATTTCCAAAAATCA
49094144 CATTTCCAACTTCAAATTTTTCCAAAAGTTCAATTTTAATCCCAAATTTCTCCCAAATTTCAATT
66 CATTTCCAACTTCAAATTTTTCCAAAAGTTCAATTTTAATCCCAAATTTCTCCCAAATTTCAATT
49094209 TTGATCCCCAAATTCCTCGAAAATTACATTTTTACCCCCAAACTTTTCC
131 TTGATCCCCAAATTCCTCGAAAATTACATTTTTACCCCCAAACTTTTCC
*
49094258 AAAATTAC-ATTTTTACCCCCGAACATCCAAAAATTACCATTTTGCCCCCAAATTTCCAAAAATC
1 AAAATTACTA-TTTTACCCCCGAACATCCAAAAATTACCATTTTCCCCCCAAATTTCCAAAAATC
* *
49094322 ACATTTCCAACTTCAAA-TTTTCCAAAAGTTCGATTTTAATCCCAAATTTC-CCCTAAATTTTAA
65 ACATTTCCAACTTCAAATTTTTCCAAAAGTTCAATTTTAATCCCAAATTTCTCCC-AAATTTCAA
*
49094385 TTTTGATCCCCAAATTCCTCGAAAATTATATTTT
129 TTTTGATCCCCAAATTCCTCGAAAATTACATTTT
49094419 CATCCCGAAT
Statistics
Matches: 155, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
177 3 0.02
178 74 0.48
179 78 0.50
ACGTcount: A:0.35, C:0.27, G:0.03, T:0.35
Consensus pattern (179 bp):
AAAATTACTATTTTACCCCCGAACATCCAAAAATTACCATTTTCCCCCCAAATTTCCAAAAATCA
CATTTCCAACTTCAAATTTTTCCAAAAGTTCAATTTTAATCCCAAATTTCTCCCAAATTTCAATT
TTGATCCCCAAATTCCTCGAAAATTACATTTTTACCCCCAAACTTTTCC
Found at i:49095712 original size:20 final size:21
Alignment explanation
Indices: 49095687--49095725 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
49095677 AAAAAATTCT
49095687 ATTAATTCAATTAA-TATTAA
1 ATTAATTCAATTAACTATTAA
*
49095707 ATTAATTCGATTAACTATT
1 ATTAATTCAATTAACTATT
49095726 TAAACACTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (21 bp):
ATTAATTCAATTAACTATTAA
Found at i:49100511 original size:23 final size:23
Alignment explanation
Indices: 49100467--49100511 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
49100457 TAGGGGAATT
* * *
49100467 TTTATAAAAGATTTGTTTTAATA
1 TTTATAAAAGAATTATTATAATA
*
49100490 TTTATAAAATAATTATTATAAT
1 TTTATAAAAGAATTATTATAAT
49100512 TAAAATAAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTATAAAAGAATTATTATAATA
Found at i:49101374 original size:23 final size:22
Alignment explanation
Indices: 49101344--49101386 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
49101334 ACATTTGAAT
49101344 TTAAATTTGAAAAAGTAAAAAGA
1 TTAAATTTGAAAAA-TAAAAAGA
*
49101367 TTAAATTTTAAAAATAAAAA
1 TTAAATTTGAAAAATAAAAA
49101387 TATATAGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (22 bp):
TTAAATTTGAAAAATAAAAAGA
Found at i:49112694 original size:13 final size:13
Alignment explanation
Indices: 49112676--49112700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49112666 AGATCACAGT
49112676 TTGTACTTGTTGC
1 TTGTACTTGTTGC
49112689 TTGTACTTGTTG
1 TTGTACTTGTTG
49112701 AAGTATAGTG
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:0.08, C:0.12, G:0.24, T:0.56
Consensus pattern (13 bp):
TTGTACTTGTTGC
Found at i:49114207 original size:32 final size:32
Alignment explanation
Indices: 49114171--49114253 Score: 96
Period size: 32 Copynumber: 2.6 Consensus size: 32
49114161 TAACAAAGAA
*
49114171 TTATAACTATTTAAGTA-ATATTACTTGAATAG
1 TTATATCTATTTAAG-AGATATTACTTGAATAG
* * * * *
49114203 TTATATTTATTTATGAGGTCTTACTTGAATGG
1 TTATATCTATTTAAGAGATATTACTTGAATAG
49114235 TTATATCTATTTAAGAGAT
1 TTATATCTATTTAAGAGAT
49114254 GTAATTATTT
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 1 0.02
32 40 0.98
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.47
Consensus pattern (32 bp):
TTATATCTATTTAAGAGATATTACTTGAATAG
Found at i:49117627 original size:52 final size:51
Alignment explanation
Indices: 49117547--49117834 Score: 418
Period size: 52 Copynumber: 5.6 Consensus size: 51
49117537 GTAAATGCAA
49117547 AAGGTCCGATGACTA--TGTCATCGTGAGTATATGAATACTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT-CTTTACGGATTAT
*
49117597 AAGATCCGATGACTATGTGTCATCGTGAGTATATGAATCATTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATC-TTTACGGATTAT
* * * *
49117649 AAGGTCCGATGAATATGTATTATCGTAAGTATATGAATTCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAA-TCTTTACGGATTAT
* * *
49117701 AAGGTCCGATGACTATATGTCGTCGTGAGTATATGGATCCTTTACGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAAT-CTTTACGGATTAT
* *
49117753 AAGGTCCGATGACTATGTGTCATCATGAGTATATGAATCTTTTTCGGATTAT
1 AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATC-TTTACGGATTAT
*
49117805 AAGGTCCGATGACAATGTGTCATCGTGAGT
1 AAGGTCCGATGACTATGTGTCATCGTGAGT
49117835 TACCAAATGC
Statistics
Matches: 212, Mismatches: 20, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
50 14 0.07
51 3 0.01
52 193 0.91
53 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (51 bp):
AAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCTTTACGGATTAT
Found at i:49120764 original size:2 final size:2
Alignment explanation
Indices: 49120757--49120788 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
49120747 CTTATCCTTT
49120757 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49120789 GCTAAGCCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49122205 original size:23 final size:23
Alignment explanation
Indices: 49122175--49122218 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
49122165 AAAATTTTGA
**
49122175 TTTAATATTTTAAAAATTATATT
1 TTTAATATCGTAAAAATTATATT
49122198 TTTAATATCGTAAAAATTATA
1 TTTAATATCGTAAAAATTATA
49122219 ATTTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
TTTAATATCGTAAAAATTATATT
Found at i:49122223 original size:22 final size:22
Alignment explanation
Indices: 49122165--49122225 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
49122155 TAAAAATGAT
* * **
49122165 AAAATTTTGATTTAATATTTTA
1 AAAATTATAATTTAATATCGTA
*
49122187 AAAATTATATTTTTAATATCGTA
1 AAAATTATA-ATTTAATATCGTA
49122210 AAAATTATAATTTAAT
1 AAAATTATAATTTAAT
49122226 TTTAACCCCT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 13 0.41
23 19 0.59
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (22 bp):
AAAATTATAATTTAATATCGTA
Found at i:49127027 original size:3 final size:3
Alignment explanation
Indices: 49127019--49127059 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
49127009 CTATTTTTGC
49127019 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
49127060 CTTCTATCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:49138813 original size:16 final size:17
Alignment explanation
Indices: 49138783--49138814 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49138773 AGATGATTAT
49138783 ATAAAAAATTCTAATAA
1 ATAAAAAATTCTAATAA
49138800 ATAAAAAATT-TAATA
1 ATAAAAAATTCTAATA
49138815 TTTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (17 bp):
ATAAAAAATTCTAATAA
Found at i:49139254 original size:25 final size:27
Alignment explanation
Indices: 49139214--49139264 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
49139204 TTAAATACGT
*
49139214 AATTTTTACATATATA-TATGTTATAG
1 AATTTCTACATATATAGTATGTTATAG
49139240 AATTTCTA-ATATATAGTTATGTTAT
1 AATTTCTACATATATAG-TATGTTAT
49139265 TAGTTATTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 7 0.32
26 7 0.32
27 8 0.36
ACGTcount: A:0.37, C:0.04, G:0.08, T:0.51
Consensus pattern (27 bp):
AATTTCTACATATATAGTATGTTATAG
Found at i:49140535 original size:16 final size:16
Alignment explanation
Indices: 49140516--49140569 Score: 72
Period size: 16 Copynumber: 3.4 Consensus size: 16
49140506 AAAATAGAGG
49140516 TGTAATGGAATAAAAC
1 TGTAATGGAATAAAAC
*
49140532 TGTAATAGAATAAAAC
1 TGTAATGGAATAAAAC
* **
49140548 TGTAATGAAATAGGAC
1 TGTAATGGAATAAAAC
49140564 TGTAAT
1 TGTAAT
49140570 TAGTAATTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAAAAC
Found at i:49140808 original size:58 final size:59
Alignment explanation
Indices: 49140739--49140893 Score: 192
Period size: 58 Copynumber: 2.6 Consensus size: 59
49140729 AATTTTAATG
* *
49140739 ATTATTATTAAATATAATTTAATAAAAATATTA-ATTAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATA-TAATTTAATAATATTTTTAACATA
* *
49140797 ATTATTATTAAATACAATTTAAT-AAAATAATATATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTTTTAACATA
* *
49140855 ATTATTATTAAAATATGAA-TTAGTAAAAATTATAATATA
1 ATTATTATT-AAATAT-AATTTAATAAAAATAAT-ATATA
49140894 TAATATTAGA
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
57 20 0.24
58 41 0.49
59 9 0.11
60 9 0.11
61 5 0.06
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATATAATTTAATAATATTTTTAACATA
Found at i:49140887 original size:25 final size:24
Alignment explanation
Indices: 49140858--49140908 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
49140848 TAATATAATT
*
49140858 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
49140883 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
49140907 AT
1 AT
49140909 AATATATAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 14 0.61
25 9 0.39
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.37
Consensus pattern (24 bp):
ATTATAAAATATAATATTAGAAAA
Found at i:49146890 original size:31 final size:30
Alignment explanation
Indices: 49146833--49146900 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
49146823 ATCTTTATAA
* **
49146833 TTTTTAAAAAATTAAGTTAAATTTTTATTAT
1 TTTTTAAAAAATAAAAATAAATTTTTATT-T
49146864 TTTTTAAAAAATAAAAATATAA-TTTTATTT
1 TTTTTAAAAAATAAAAATA-AATTTTTATTT
*
49146894 TTATTAA
1 TTTTTAA
49146901 TTTAAAATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 7 0.22
31 23 0.72
32 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (30 bp):
TTTTTAAAAAATAAAAATAAATTTTTATTT
Found at i:49146940 original size:85 final size:84
Alignment explanation
Indices: 49146780--49146949 Score: 204
Period size: 83 Copynumber: 2.0 Consensus size: 84
49146770 GTTTGTAAAA
* ** * **
49146780 TTTTTAATAATAAAAATATAATTTTATTATTTTAATAATTTATATCTTTATAATTTTTAAAAAAT
1 TTTTTAAAAATAAAAATATAATTTTATTATTTTAATAATTTATAAATTTAAAATAATTAAAAAAT
*
49146845 TAAGTTAAATTTTTATTAT
66 TAAATTAAATTTTTATTAT
*
49146864 TTTTTAAAAAATAAAAATATAATTTTA-T-TTTTATTAATTTA-AAATTTAAAATAATTAAAAAA
1 TTTTT-AAAAATAAAAATATAATTTTATTATTTTAATAATTTATAAATTTAAAATAATTAAAAAA
*
49146926 TTTAAATATAAAATTTT-TTAT
65 -TTAAAT-TAAATTTTTATTAT
49146947 TTT
1 TTT
49146950 AAGAAAATCG
Statistics
Matches: 74, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
82 16 0.22
83 24 0.32
84 14 0.19
85 20 0.27
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (84 bp):
TTTTTAAAAATAAAAATATAATTTTATTATTTTAATAATTTATAAATTTAAAATAATTAAAAAAT
TAAATTAAATTTTTATTAT
Found at i:49150806 original size:13 final size:13
Alignment explanation
Indices: 49150790--49150814 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49150780 AAAATCTAAA
49150790 TAAAAAAATCCAC
1 TAAAAAAATCCAC
49150803 TAAAAAAATCCA
1 TAAAAAAATCCA
49150815 AATAACAAAA
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:0.64, C:0.20, G:0.00, T:0.16
Consensus pattern (13 bp):
TAAAAAAATCCAC
Found at i:49160824 original size:22 final size:21
Alignment explanation
Indices: 49160799--49160841 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 21
49160789 TATGGCTTTG
49160799 ATTAATTAACATACCTTTTTTT
1 ATTAATTAACATA-CTTTTTTT
49160821 ATTAATTAACATACTTTTTTT
1 ATTAATTAACATACTTTTTTT
49160842 GACTGACCCC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTAATTAACATACTTTTTTT
Found at i:49161803 original size:92 final size:92
Alignment explanation
Indices: 49161617--49161804 Score: 231
Period size: 92 Copynumber: 2.0 Consensus size: 92
49161607 AAAATTTCTC
* * **
49161617 TTTTCATGATTTATTATTTCTTTTTTAAAAATTTAAATTTCTTTTTTTTGGTGCCATATAATATG
1 TTTTAATGATTTATTATTTATTTTTTAAAAATTTAAATTTCTTTTTAGTGGTGCCATATAATATG
*
49161682 GCACCACTTCTCCAACAAATTTCATTT
66 GCACCACTTCTCCAACAAATGTCATTT
*
49161709 TTTTAATGATTTATTATTTATTTTTTAAAAATTT-AATTT-TTTTTAGTGGTGTCATATTAA-AT
1 TTTTAATGATTTATTATTTATTTTTTAAAAATTTAAATTTCTTTTTAGTGGTGCCATA-TAATAT
* *
49161771 GACATCACCACTTCTCTAA-AACATGTCATTT
65 G---GCACCACTTCTCCAACAA-ATGTCATTT
49161802 TTT
1 TTT
49161805 CTTTTTATTT
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
90 17 0.20
91 8 0.10
92 34 0.41
93 24 0.29
ACGTcount: A:0.29, C:0.13, G:0.07, T:0.52
Consensus pattern (92 bp):
TTTTAATGATTTATTATTTATTTTTTAAAAATTTAAATTTCTTTTTAGTGGTGCCATATAATATG
GCACCACTTCTCCAACAAATGTCATTT
Found at i:49161817 original size:4 final size:4
Alignment explanation
Indices: 49161808--49161848 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
49161798 ATTTTTTCTT
*
49161808 TTTA TTTA TTTA TTTA -TTA TTTG TTTA -TTA TTTA TTT- TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
49161849 AAAAATTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 9 0.28
4 23 0.72
ACGTcount: A:0.22, C:0.00, G:0.02, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:49161829 original size:11 final size:11
Alignment explanation
Indices: 49161808--49161844 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
49161798 ATTTTTTCTT
49161808 TTTATTTATTTA
1 TTTA-TTATTTA
*
49161820 TTTATTATTTG
1 TTTATTATTTA
49161831 TTTATTATTTA
1 TTTATTATTTA
49161842 TTT
1 TTT
49161845 TTTAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 19 0.83
12 4 0.17
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.76
Consensus pattern (11 bp):
TTTATTATTTA
Found at i:49161829 original size:15 final size:13
Alignment explanation
Indices: 49161798--49161848 Score: 57
Period size: 15 Copynumber: 3.6 Consensus size: 13
49161788 AAAACATGTC
*
49161798 ATTTTTTCTTTTT
1 ATTTTTTATTTTT
49161811 ATTTATTTATTTATT
1 ATTT-TTTATTT-TT
49161826 ATTTGTTTATTATTT
1 ATTT-TTTATT-TTT
49161841 ATTTTTTA
1 ATTTTTTA
49161849 AAAAATTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
13 4 0.12
14 10 0.30
15 18 0.55
16 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (13 bp):
ATTTTTTATTTTT
Found at i:49163222 original size:16 final size:17
Alignment explanation
Indices: 49163196--49163234 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
49163186 TCAAATTAAC
49163196 TAAATTAATTTTC-CAAT
1 TAAA-TAATTTTCTCAAT
49163213 TAAATAATTTTCTCAAT
1 TAAATAATTTTCTCAAT
*
49163230 CAAAT
1 TAAAT
49163235 TCTAATTCCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.44, C:0.13, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATAATTTTCTCAAT
Found at i:49164313 original size:25 final size:25
Alignment explanation
Indices: 49164279--49164329 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
49164269 CATTTCGTCC
49164279 TTGCGAAAATGATGAATAGTCTTGG
1 TTGCGAAAATGATGAATAGTCTTGG
49164304 TTGCGAAAATGATGAATAGTCTTGG
1 TTGCGAAAATGATGAATAGTCTTGG
49164329 T
1 T
49164330 CCTGAAGTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.33
Consensus pattern (25 bp):
TTGCGAAAATGATGAATAGTCTTGG
Found at i:49165759 original size:29 final size:27
Alignment explanation
Indices: 49165722--49165778 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 27
49165712 TTATAATAGA
49165722 TTTTTAATTTTTCTATAATTTTTAAAAC
1 TTTTTAATTTTTCTAT-ATTTTTAAAAC
* *
49165750 TTTTATAATTTTTTTATATTTTTATAAC
1 TTTT-TAATTTTTCTATATTTTTAAAAC
49165778 T
1 T
49165779 AATATTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 15 0.58
29 11 0.42
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (27 bp):
TTTTTAATTTTTCTATATTTTTAAAAC
Found at i:49175024 original size:2 final size:2
Alignment explanation
Indices: 49175019--49175078 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
49175009 TTTTAACCCC
49175019 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
49175061 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
49175079 CTCGAACTTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49175605 original size:2 final size:2
Alignment explanation
Indices: 49175598--49175631 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
49175588 AATCCCAACC
*
49175598 TA TA TA TA TA TA TA TA TA T- TA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49175632 CAAATCTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49177328 original size:26 final size:26
Alignment explanation
Indices: 49177290--49177339 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
49177280 AATTTATTTT
*
49177290 TATTTTATATTATAATATTATTATAA
1 TATTTAATATTATAATATTATTATAA
* *
49177316 TATTTAATTTTATCATATTATTAT
1 TATTTAATATTATAATATTATTAT
49177340 TTTTATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (26 bp):
TATTTAATATTATAATATTATTATAA
Found at i:49186018 original size:19 final size:19
Alignment explanation
Indices: 49185961--49186020 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 19
49185951 TGCATACTTG
49185961 GCACACGAAGTGCATCCT-
1 GCACACGAAGTGCATCCTA
* *
49185979 G-ACACAAAAGAATGTAT-CTA
1 GCACAC-GAAG--TGCATCCTA
49185999 GCACACGAAGTGCATCCTA
1 GCACACGAAGTGCATCCTA
49186018 GCA
1 GCA
49186021 TATAATCTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 11
0.68 0.09 0.23
Matches are distributed among these distances:
17 4 0.12
18 8 0.25
19 8 0.25
20 8 0.25
21 4 0.12
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.17
Consensus pattern (19 bp):
GCACACGAAGTGCATCCTA
Found at i:49198642 original size:27 final size:28
Alignment explanation
Indices: 49198593--49198646 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
49198583 GTATATTAAA
49198593 TTTATAATATTTTTATAATATTAGTTTTG
1 TTTATAATATTTTTATAATATTA-TTTTG
49198622 TTTA-AAT-TTTTTAATAA-ATTATTTT
1 TTTATAATATTTTT-ATAATATTATTTT
49198647 AAAATATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 4 0.17
27 9 0.38
28 7 0.29
29 4 0.17
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTATAATATTTTTATAATATTATTTTG
Found at i:49202709 original size:30 final size:30
Alignment explanation
Indices: 49202668--49202733 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
49202658 ATCACAGAAC
* *
49202668 ATGTGGAGGGTGTCTTATAACCACTTGGAA
1 ATGTGGAGGGTGTCTTAGAACCACTTGAAA
* *
49202698 ATGTGGCGGGTGTCTTAGAACCATTTGAAA
1 ATGTGGAGGGTGTCTTAGAACCACTTGAAA
49202728 ATGTGG
1 ATGTGG
49202734 GAAGTGTCTT
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:0.26, C:0.12, G:0.32, T:0.30
Consensus pattern (30 bp):
ATGTGGAGGGTGTCTTAGAACCACTTGAAA
Found at i:49202741 original size:30 final size:30
Alignment explanation
Indices: 49202668--49202743 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
49202658 ATCACAGAAC
* * * *
49202668 ATGTGGAGGGTGTCTTATAACCACTTGGAA
1 ATGTGGCGAGTGTCTTAGAACCACTTGAAA
* *
49202698 ATGTGGCGGGTGTCTTAGAACCATTTGAAA
1 ATGTGGCGAGTGTCTTAGAACCACTTGAAA
49202728 ATGTGG-GAAGTGTCTT
1 ATGTGGCG-AGTGTCTT
49202744 GTTAACGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 1 0.03
30 39 0.98
ACGTcount: A:0.25, C:0.12, G:0.32, T:0.32
Consensus pattern (30 bp):
ATGTGGCGAGTGTCTTAGAACCACTTGAAA
Found at i:49203274 original size:13 final size:13
Alignment explanation
Indices: 49203236--49203279 Score: 61
Period size: 14 Copynumber: 3.2 Consensus size: 13
49203226 ATATTTGTTT
*
49203236 TAATATATGATAAA
1 TAATATATTAT-AA
49203250 TAATAGTATTATAA
1 TAATA-TATTATAA
49203264 TAATATATTATAA
1 TAATATATTATAA
49203277 TAA
1 TAA
49203280 AAAAATAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.39
14 12 0.43
15 5 0.18
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (13 bp):
TAATATATTATAA
Found at i:49207602 original size:25 final size:23
Alignment explanation
Indices: 49207577--49207623 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
49207567 ACCAATTATT
*
49207577 ATTAT-TTTGTAACTGTCCTGCC
1 ATTATATTTGTAACTCTCCTGCC
*
49207599 ATTATATTTGTAACTCTCTTGCC
1 ATTATATTTGTAACTCTCCTGCC
49207622 AT
1 AT
49207624 AATGTTTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.21, C:0.21, G:0.11, T:0.47
Consensus pattern (23 bp):
ATTATATTTGTAACTCTCCTGCC
Found at i:49208019 original size:11 final size:12
Alignment explanation
Indices: 49207992--49208025 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
49207982 TTATTTGTTT
*
49207992 TTAAATTTATTA
1 TTAAATTTATAA
49208004 TTAAATTTA-AA
1 TTAAATTTATAA
49208015 TTAAATTTATA
1 TTAAATTTATA
49208026 TTTTTTTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAATTTATAA
Found at i:49210764 original size:17 final size:18
Alignment explanation
Indices: 49210744--49210787 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
49210734 TTTTTCTTAT
49210744 AATTAATTTTAAAAT-AA
1 AATTAATTTTAAAATCAA
*
49210761 AATTAA-TTT-ATATCAA
1 AATTAATTTTAAAATCAA
49210777 AATTAATTTTA
1 AATTAATTTTA
49210788 TTTTGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 3 0.13
16 11 0.48
17 9 0.39
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTAATTTTAAAATCAA
Found at i:49211600 original size:22 final size:20
Alignment explanation
Indices: 49211548--49211601 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
49211538 TAATTTTTAT
*
49211548 ATTTTTATATAAAATAATAA
1 ATTTATATATAAAATAATAA
*
49211568 CTTATATTATATAAAATTTAATAA
1 ATT-TA-TATATAAAA--TAATAA
49211592 ATTTATATAT
1 ATTTATATAT
49211602 CCGCATCGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 2 0.07
21 1 0.04
22 14 0.52
23 2 0.07
24 8 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTATATATAAAATAATAA
Found at i:49216441 original size:6 final size:6
Alignment explanation
Indices: 49216418--49216460 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
49216408 AATTCATATG
* * * *
49216418 ACTTTC AATTCC AATTTC ACTTTC ACATTC ACTTTC ACTTTC A
1 ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC ACTTTC A
49216461 ATTTTGATCA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.26, C:0.30, G:0.00, T:0.44
Consensus pattern (6 bp):
ACTTTC
Found at i:49216441 original size:18 final size:17
Alignment explanation
Indices: 49216418--49216463 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 17
49216408 AATTCATATG
49216418 ACTTTCAATTCCAATTTC
1 ACTTTCAATT-CAATTTC
*
49216436 ACTTTCACATTCACTTTC
1 ACTTTCA-ATTCAATTTC
49216454 ACTTTCAATT
1 ACTTTCAATT
49216464 TTGATCACAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.46
Consensus pattern (17 bp):
ACTTTCAATTCAATTTC
Found at i:49218430 original size:41 final size:40
Alignment explanation
Indices: 49218382--49218482 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
49218372 TCGACCTTGA
** *
49218382 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
49218422 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
49218460 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
49218483 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:49221088 original size:16 final size:15
Alignment explanation
Indices: 49221067--49221117 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
49221057 ACCTAATCTA
49221067 AAAATAAGAAGAAAAG
1 AAAATAA-AAGAAAAG
*
49221083 AAAATAAAAGGAAAAT
1 AAAATAAAA-GAAAAG
49221099 AAAAT-AAAGTAAAAG
1 AAAATAAAAG-AAAAG
49221114 AAAA
1 AAAA
49221118 GAAACTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 1 0.03
15 13 0.42
16 17 0.55
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (15 bp):
AAAATAAAAGAAAAG
Found at i:49221118 original size:11 final size:10
Alignment explanation
Indices: 49221078--49221117 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
49221068 AAATAAGAAG
49221078 AAAAGAAAAT
1 AAAAGAAAAT
49221088 AAAAGGAAAAT
1 AAAA-GAAAAT
* *
49221099 AAAATAAAGT
1 AAAAGAAAAT
49221109 AAAAGAAAA
1 AAAAGAAAA
49221118 GAAACTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.10
Consensus pattern (10 bp):
AAAAGAAAAT
Found at i:49226802 original size:3 final size:3
Alignment explanation
Indices: 49226794--49226821 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
49226784 AGATGACGGC
49226794 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
49226822 CTTGTTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:49229888 original size:26 final size:26
Alignment explanation
Indices: 49229859--49229914 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
49229849 ATTAAAATTA
49229859 ATTTAATAATG-AAATTATAAATTAAT
1 ATTTAATAA-GAAAATTATAAATTAAT
**
49229885 ATTTTTTAAGAAAAATTATAAATTAAT
1 ATTTAATAAG-AAAATTATAAATTAAT
49229912 ATT
1 ATT
49229915 GAGATATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 1 0.04
26 7 0.27
27 18 0.69
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.45
Consensus pattern (26 bp):
ATTTAATAAGAAAATTATAAATTAAT
Found at i:49231992 original size:10 final size:11
Alignment explanation
Indices: 49231977--49232021 Score: 58
Period size: 10 Copynumber: 4.3 Consensus size: 11
49231967 AGTTCAAAAC
49231977 TAAAAAAA-GT
1 TAAAAAAATGT
*
49231987 TAAAAAAATAT
1 TAAAAAAATGT
*
49231998 TATAAAAAT-T
1 TAAAAAAATGT
49232008 TAAAAAAATGT
1 TAAAAAAATGT
49232019 TAA
1 TAA
49232022 TATTTATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
10 17 0.57
11 13 0.43
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (11 bp):
TAAAAAAATGT
Found at i:49232064 original size:30 final size:28
Alignment explanation
Indices: 49231993--49232065 Score: 69
Period size: 30 Copynumber: 2.5 Consensus size: 28
49231983 AAGTTAAAAA
* *
49231993 AATA-TTATAAAAATTTAAAAAAATGTT
1 AATATTTATAAAATTTTAAAAAAATGTC
49232020 AATATTTATTTAAAATTTTAAAAAAAAT-TC
1 AATATTTA--TAAAATTTT-AAAAAAATGTC
49232050 AATACATTTATAAAAT
1 AAT--ATTTATAAAAT
49232066 AATTTTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 4 0.11
28 3 0.08
30 18 0.47
31 8 0.21
32 5 0.13
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (28 bp):
AATATTTATAAAATTTTAAAAAAATGTC
Found at i:49232087 original size:21 final size:23
Alignment explanation
Indices: 49232063--49232104 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
49232053 ACATTTATAA
49232063 AATAATTTT-TAT-AAATATTTG
1 AATAATTTTATATAAAATATTTG
49232084 AATAATTTTATATAAAATATT
1 AATAATTTTATATAAAATATT
49232105 CAAATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 3 0.16
23 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
AATAATTTTATATAAAATATTTG
Found at i:49232490 original size:9 final size:10
Alignment explanation
Indices: 49232470--49232494 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
49232460 TTATAAAAAC
49232470 TTTTAAATTT
1 TTTTAAATTT
49232480 TTTTAAATTT
1 TTTTAAATTT
49232490 TTTTA
1 TTTTA
49232495 TTGACATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (10 bp):
TTTTAAATTT
Found at i:49233402 original size:3 final size:3
Alignment explanation
Indices: 49233394--49233421 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
49233384 TTTGATTCGC
49233394 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
49233422 CATTTAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:49234484 original size:23 final size:23
Alignment explanation
Indices: 49234441--49234489 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
49234431 AAATTTAAAT
* *
49234441 TTCGAGTTAATCGAATCGAGTTA
1 TTCGAGTCAATCGAATCGAGTAA
49234464 TTCGAGTCAACTCGAAT-GAGTAA
1 TTCGAGTCAA-TCGAATCGAGTAA
49234487 TTC
1 TTC
49234490 AAGTTTCGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (23 bp):
TTCGAGTCAATCGAATCGAGTAA
Found at i:49236714 original size:20 final size:21
Alignment explanation
Indices: 49236650--49236717 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
49236640 TAATCAACAA
49236650 CAAACCCAAACCCTTATGAAC
1 CAAACCCAAACCCTTATGAAC
49236671 CAAACCCAAACCCTTATGAAC
1 CAAACCCAAACCCTTATGAAC
* * *
49236692 CAAACTCAAA-CCTTTTGACC
1 CAAACCCAAACCCTTATGAAC
49236712 CAAACC
1 CAAACC
49236718 AAGTGAACCA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
20 13 0.30
21 30 0.70
ACGTcount: A:0.41, C:0.38, G:0.04, T:0.16
Consensus pattern (21 bp):
CAAACCCAAACCCTTATGAAC
Found at i:49244449 original size:39 final size:40
Alignment explanation
Indices: 49244390--49244470 Score: 128
Period size: 39 Copynumber: 2.0 Consensus size: 40
49244380 TATCATGCGG
* *
49244390 ACTGTAATATTTAGAAATTTAA-TTTTTTAATCCGTATTC
1 ACTGCAATATTTAAAAATTTAATTTTTTTAATCCGTATTC
49244429 ACTGCAATATTTAAAAATTTAATTTTTTTTAATCCGTATTC
1 ACTGCAATATTTAAAAATTTAA-TTTTTTTAATCCGTATTC
49244470 A
1 A
49244471 GCTCTTGTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
39 20 0.53
41 18 0.47
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (40 bp):
ACTGCAATATTTAAAAATTTAATTTTTTTAATCCGTATTC
Found at i:49252005 original size:14 final size:15
Alignment explanation
Indices: 49251988--49252016 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49251978 TTTTTATAAA
49251988 CAAGT-TGATATATC
1 CAAGTCTGATATATC
49252002 CAAGTCTGATATATC
1 CAAGTCTGATATATC
49252017 TTTCCTTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (15 bp):
CAAGTCTGATATATC
Found at i:49253276 original size:22 final size:22
Alignment explanation
Indices: 49253251--49253351 Score: 68
Period size: 22 Copynumber: 5.2 Consensus size: 22
49253241 ACATTTAATG
49253251 TTTCAATTTATCAAACTTATTT
1 TTTCAATTTATCAAACTTATTT
* *
49253273 TTTC-A---AT---ACTTAATG
1 TTTCAATTTATCAAACTTATTT
49253288 TTTCAATTTATCAAACTTATTT
1 TTTCAATTTATCAAACTTATTT
* *
49253310 TTTC-A---AT---ACTTAATG
1 TTTCAATTTATCAAACTTATTT
49253325 TTTCAATTTATCAAACTTATTT
1 TTTCAATTTATCAAACTTATTT
49253347 TTTCA
1 TTTCA
49253352 GTATTTAATG
Statistics
Matches: 57, Mismatches: 8, Indels: 28
0.61 0.09 0.30
Matches are distributed among these distances:
15 20 0.35
16 2 0.04
18 4 0.07
19 4 0.07
21 2 0.04
22 25 0.44
ACGTcount: A:0.32, C:0.14, G:0.02, T:0.52
Consensus pattern (22 bp):
TTTCAATTTATCAAACTTATTT
Found at i:49253286 original size:37 final size:37
Alignment explanation
Indices: 49253228--49253369 Score: 232
Period size: 37 Copynumber: 3.9 Consensus size: 37
49253218 AATATTTCCG
* * *
49253228 AACTTA-TTTTTAAACATTTAATGTTTCAATTTATCA
1 AACTTATTTTTTCAATACTTAATGTTTCAATTTATCA
49253264 AACTTATTTTTTCAATACTTAATGTTTCAATTTATCA
1 AACTTATTTTTTCAATACTTAATGTTTCAATTTATCA
49253301 AACTTATTTTTTCAATACTTAATGTTTCAATTTATCA
1 AACTTATTTTTTCAATACTTAATGTTTCAATTTATCA
* *
49253338 AACTTATTTTTTCAGTATTTAATGTTTCAATT
1 AACTTATTTTTTCAATACTTAATGTTTCAATT
49253370 CATCCCTAAA
Statistics
Matches: 100, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
36 6 0.06
37 94 0.94
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.52
Consensus pattern (37 bp):
AACTTATTTTTTCAATACTTAATGTTTCAATTTATCA
Found at i:49254089 original size:31 final size:31
Alignment explanation
Indices: 49254046--49254123 Score: 138
Period size: 31 Copynumber: 2.5 Consensus size: 31
49254036 AATTTTTTTG
*
49254046 TTAGTCCCTGTACTTAGATAAAATTCGAAAC
1 TTAGGCCCTGTACTTAGATAAAATTCGAAAC
49254077 TTAGGCCCTGTACTTAGATAAAATTCGAAAC
1 TTAGGCCCTGTACTTAGATAAAATTCGAAAC
*
49254108 TTAGGCCCTATACTTA
1 TTAGGCCCTGTACTTA
49254124 AAAAGCTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (31 bp):
TTAGGCCCTGTACTTAGATAAAATTCGAAAC
Found at i:49255750 original size:20 final size:20
Alignment explanation
Indices: 49255725--49255766 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
49255715 ATCATTATTG
*
49255725 TTATAAAAAAGAAAATAAAA
1 TTATAAAAAAAAAAATAAAA
*
49255745 TTATAAAAAAAAAAATCAAA
1 TTATAAAAAAAAAAATAAAA
49255765 TT
1 TT
49255767 TCACAATGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.71, C:0.02, G:0.02, T:0.24
Consensus pattern (20 bp):
TTATAAAAAAAAAAATAAAA
Found at i:49261005 original size:6 final size:7
Alignment explanation
Indices: 49260989--49261017 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
49260979 TATTAATTTC
49260989 AAAATTA
1 AAAATTA
49260996 AAAATTA
1 AAAATTA
49261003 AAAATT-
1 AAAATTA
49261009 AAAATTA
1 AAAATTA
49261016 AA
1 AA
49261018 GTCCCAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (7 bp):
AAAATTA
Found at i:49261012 original size:13 final size:14
Alignment explanation
Indices: 49260989--49261017 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
49260979 TATTAATTTC
49260989 AAAATTAAAAATTA
1 AAAATTAAAAATTA
49261003 AAAATT-AAAATTA
1 AAAATTAAAAATTA
49261016 AA
1 AA
49261018 GTCCCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATTAAAAATTA
Found at i:49267179 original size:31 final size:31
Alignment explanation
Indices: 49267144--49267221 Score: 84
Period size: 31 Copynumber: 2.5 Consensus size: 31
49267134 ACTTAGTGGT
* * * * *
49267144 CAAGTTCAAGGGCTAATGTGGACTTACTTGC
1 CAAGTTCAAAGGCCAATATAGACCTACTTGC
49267175 CAAGTTCAAAGGCCAATATAGACCTACTTGC
1 CAAGTTCAAAGGCCAATATAGACCTACTTGC
* * *
49267206 TAAGTTTAGAGGCCAA
1 CAAGTTCAAAGGCCAA
49267222 AAGTTATATT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.32, C:0.21, G:0.22, T:0.26
Consensus pattern (31 bp):
CAAGTTCAAAGGCCAATATAGACCTACTTGC
Found at i:49296279 original size:17 final size:18
Alignment explanation
Indices: 49296231--49296280 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
49296221 GATTTTATAA
*
49296231 TTAA-AATTAAAATTTTTT
1 TTAATAATT-AAATTTATT
49296249 TTAATAA-TATAATTTATT
1 TTAATAATTA-AATTTATT
49296267 TT-ATAATTAAATTT
1 TTAATAATTAAATTT
49296281 GTATCAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 10 0.36
18 16 0.57
19 2 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTAATAATTAAATTTATT
Found at i:49301394 original size:38 final size:38
Alignment explanation
Indices: 49301352--49301433 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 38
49301342 TAAACTTAAA
49301352 TTTTTTGTAATTTTTCAGATTTTTAAAATTTT-AAGGATT
1 TTTTTTGTAATTTTT--GATTTTTAAAATTTTAAAGGATT
* * * *
49301391 TTTTATTTTTATTTTTGATTTTTTATATTTTAAAGGATT
1 TTTT-TTGTAATTTTTGATTTTTAAAATTTTAAAGGATT
49301430 TTTT
1 TTTT
49301434 ACTTTTTTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
38 13 0.35
39 15 0.41
40 9 0.24
ACGTcount: A:0.24, C:0.01, G:0.09, T:0.66
Consensus pattern (38 bp):
TTTTTTGTAATTTTTGATTTTTAAAATTTTAAAGGATT
Found at i:49302766 original size:19 final size:19
Alignment explanation
Indices: 49302742--49302780 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
49302732 TATGCTAGAC
*
49302742 TACTCTTAAATAGGGACTT
1 TACTCTTAAATAGAGACTT
49302761 TACTCTTAAATAGAGACTT
1 TACTCTTAAATAGAGACTT
49302780 T
1 T
49302781 TCCTCCTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.13, T:0.38
Consensus pattern (19 bp):
TACTCTTAAATAGAGACTT
Found at i:49304052 original size:25 final size:25
Alignment explanation
Indices: 49304024--49304120 Score: 108
Period size: 25 Copynumber: 3.9 Consensus size: 25
49304014 GGGAGTTCAC
* *
49304024 CACAAAAGCTTTTTAGAGAATTCGT
1 CACAAAAGCTTTCTAGAGAGTTCGT
* * *
49304049 CACAAAGGCTTTCTAGAGAGTTTGC
1 CACAAAAGCTTTCTAGAGAGTTCGT
*
49304074 CACAAAGGCTTTCTAGAGAGTTC-T
1 CACAAAAGCTTTCTAGAGAGTTCGT
49304098 C-CAAAAAGGCTTTCTAGAGAGTT
1 CAC-AAAA-GCTTTCTAGAGAGTT
49304121 TGCCACAAGG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
23 1 0.02
24 4 0.06
25 57 0.92
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.29
Consensus pattern (25 bp):
CACAAAAGCTTTCTAGAGAGTTCGT
Found at i:49304070 original size:50 final size:49
Alignment explanation
Indices: 49303982--49304120 Score: 143
Period size: 50 Copynumber: 2.8 Consensus size: 49
49303972 CCACGAAGGC
* * * * * *
49303982 CTTTTTAAAGAATTCACCACAAGGGTTTTATAGGGAGTTCACCACAAAAG
1 CTTTTTAGAGAATTC-TCACAAAGGCTTTCTAGAGAGTTCACCACAAAAG
** *
49304032 CTTTTTAGAGAATTCGTCACAAAGGCTTTCTAGAGAGTTTGCCACAAAGG
1 CTTTTTAGAGAATTC-TCACAAAGGCTTTCTAGAGAGTTCACCACAAAAG
* * *
49304082 CTTTCTAGAGAGTTCTCCAAAAAGGCTTTCTAGAGAGTT
1 CTTTTTAGAGAATTCT-CACAAAGGCTTTCTAGAGAGTT
49304121 TGCCACAAGG
Statistics
Matches: 75, Mismatches: 13, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
49 1 0.01
50 74 0.99
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (49 bp):
CTTTTTAGAGAATTCTCACAAAGGCTTTCTAGAGAGTTCACCACAAAAG
Found at i:49304110 original size:75 final size:74
Alignment explanation
Indices: 49303998--49304135 Score: 170
Period size: 75 Copynumber: 1.9 Consensus size: 74
49303988 AAAGAATTCA
* * * * *
49303998 CCACAAGGGTTTTATAGGGAGTTCACCACAAAAGCTTTTTAGAGAATTCGTCACAAAGGCTTTCT
1 CCACAAAGGCTTTATAGAGAGTTCACCACAAAAGCTTTCTAGAGAATTCGCCAC-AAGGCTTTCT
49304063 AGAGAGTTTG
65 AGAGAGTTTG
* * * *
49304073 CCACAAAGGCTTTCTAGAGAGTTCTCCA-AAAAGGCTTTCTAGAGAGTTTGCCACAAGGCTTTC
1 CCACAAAGGCTTTATAGAGAGTTCACCACAAAA-GCTTTCTAGAGAATTCGCCACAAGGCTTTC
49304136 CAGGTAACCT
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
74 13 0.25
75 40 0.75
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (74 bp):
CCACAAAGGCTTTATAGAGAGTTCACCACAAAAGCTTTCTAGAGAATTCGCCACAAGGCTTTCTA
GAGAGTTTG
Found at i:49304121 original size:50 final size:50
Alignment explanation
Indices: 49304023--49304135 Score: 167
Period size: 50 Copynumber: 2.3 Consensus size: 50
49304013 AGGGAGTTCA
* * *
49304023 CCACAAAAGCTTTTTAGAGAATTCGTCACAAAGGCTTTCTAGAGAGTTTG
1 CCACAAAGGCTTTCTAGAGAATTCGTCAAAAAGGCTTTCTAGAGAGTTTG
*
49304073 CCACAAAGGCTTTCTAGAGAGTTC-TCCAAAAAGGCTTTCTAGAGAGTTTG
1 CCACAAAGGCTTTCTAGAGAATTCGT-CAAAAAGGCTTTCTAGAGAGTTTG
49304123 CCAC-AAGGCTTTC
1 CCACAAAGGCTTTC
49304136 CAGGTAACCT
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
49 10 0.17
50 48 0.83
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.28
Consensus pattern (50 bp):
CCACAAAGGCTTTCTAGAGAATTCGTCAAAAAGGCTTTCTAGAGAGTTTG
Found at i:49304135 original size:24 final size:24
Alignment explanation
Indices: 49304053--49304135 Score: 123
Period size: 25 Copynumber: 3.4 Consensus size: 24
49304043 ATTCGTCACA
49304053 AAGGCTTTCTAGAGAGTTTGCCAC
1 AAGGCTTTCTAGAGAGTTTGCCAC
*
49304077 AAAGGCTTTCTAGAGAGTTCT-CCAAA
1 -AAGGCTTTCTAGAGAGTT-TGCC-AC
49304103 AAGGCTTTCTAGAGAGTTTGCCAC
1 AAGGCTTTCTAGAGAGTTTGCCAC
49304127 AAGGCTTTC
1 AAGGCTTTC
49304136 CAGGTAACCT
Statistics
Matches: 53, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
24 11 0.21
25 40 0.75
26 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (24 bp):
AAGGCTTTCTAGAGAGTTTGCCAC
Found at i:49304377 original size:44 final size:44
Alignment explanation
Indices: 49304314--49304424 Score: 213
Period size: 44 Copynumber: 2.5 Consensus size: 44
49304304 TAGCTTTTTC
49304314 TTGTGTTTACTGTCCCGTCGAACTACATTTCGCCATATTGATCT
1 TTGTGTTTACTGTCCCGTCGAACTACATTTCGCCATATTGATCT
49304358 TTGTGTTTACTGTCCCGTCGAACTACATTTCGCCATATTGATCT
1 TTGTGTTTACTGTCCCGTCGAACTACATTTCGCCATATTGATCT
*
49304402 TTGTGTTTACTGTCCCGACGAAC
1 TTGTGTTTACTGTCCCGTCGAAC
49304425 ATCATCAAAG
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
44 66 1.00
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (44 bp):
TTGTGTTTACTGTCCCGTCGAACTACATTTCGCCATATTGATCT
Found at i:49329087 original size:34 final size:34
Alignment explanation
Indices: 49329049--49329122 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 34
49329039 CCTTTCATCT
* *
49329049 TTTAACCCTCCAT-TTTCCTTAACTTCCTTTGACC
1 TTTAACCCTCCATCTTT-CTTAACCTCCCTTGACC
* *
49329083 TTTAACCTTCCATCTTTCTTAACCTCCCTTGATC
1 TTTAACCCTCCATCTTTCTTAACCTCCCTTGACC
49329117 TTTAAC
1 TTTAAC
49329123 TTTTCATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 32 0.91
35 3 0.09
ACGTcount: A:0.19, C:0.34, G:0.03, T:0.45
Consensus pattern (34 bp):
TTTAACCCTCCATCTTTCTTAACCTCCCTTGACC
Found at i:49339067 original size:14 final size:14
Alignment explanation
Indices: 49339018--49339067 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
49339008 CAACAAAATC
49339018 AAAATTATTTGAAA
1 AAAATTATTTGAAA
* *
49339032 AAAAATATTTACCTAAA
1 AAAATTATTT---GAAA
49339049 AAAATTATTTGAAA
1 AAAATTATTTGAAA
49339063 AAAAT
1 AAAAT
49339068 ATGAAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 17 0.59
17 12 0.41
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (14 bp):
AAAATTATTTGAAA
Found at i:49339560 original size:11 final size:11
Alignment explanation
Indices: 49339528--49339560 Score: 52
Period size: 10 Copynumber: 3.2 Consensus size: 11
49339518 CTCCTGGATC
49339528 AAAA-AAATTA
1 AAAATAAATTA
49339538 AAAATAAA-TA
1 AAAATAAATTA
49339548 AAAATAAATTA
1 AAAATAAATTA
49339559 AA
1 AA
49339561 GAAACAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.67
11 7 0.33
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAATAAATTA
Found at i:49344504 original size:151 final size:151
Alignment explanation
Indices: 49344229--49344529 Score: 512
Period size: 151 Copynumber: 2.0 Consensus size: 151
49344219 CTAAACTCAT
* * *
49344229 TTCCACACACCTCTCTTTTTCATCTTCATCTTCTTCCTTTTTTATTCCAATATATTTAGTTACAA
1 TTCCACACACCTCTCTTCTTCATCTTCATCTTCTTCCCTTTTGATTCCAATATATTTAGTTACAA
* * * *
49344294 ATCTGTCTCAAAGCTTGAATCTTTGAAACTCATTAACCCAAAAAAACTTAACGGGAAGAAGATAT
66 ATCTATCTCAAAGCTTGAATATTTGAAACCCATTAACCCAAAAAAACTTAACGGAAAGAAGATAT
49344359 TGGAATCAAAGATATTGAATC
131 TGGAATCAAAGATATTGAATC
* *
49344380 TTCCACACACCTCTCTTCTTCATCTTCATCTTCTTCCCTTTTGATTCCAATATCTTTCGTTACAA
1 TTCCACACACCTCTCTTCTTCATCTTCATCTTCTTCCCTTTTGATTCCAATATATTTAGTTACAA
*
49344445 ATCTATCTCAATGCTTGAATATTTGAAACCCATTAACCCAAAAAAACTTAACGGAAAGAAGATAT
66 ATCTATCTCAAAGCTTGAATATTTGAAACCCATTAACCCAAAAAAACTTAACGGAAAGAAGATAT
49344510 TGGAATCAAAGATATTGAAT
131 TGGAATCAAAGATATTGAAT
49344530 TTTTGGGTTA
Statistics
Matches: 140, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
151 140 1.00
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (151 bp):
TTCCACACACCTCTCTTCTTCATCTTCATCTTCTTCCCTTTTGATTCCAATATATTTAGTTACAA
ATCTATCTCAAAGCTTGAATATTTGAAACCCATTAACCCAAAAAAACTTAACGGAAAGAAGATAT
TGGAATCAAAGATATTGAATC
Found at i:49344835 original size:29 final size:30
Alignment explanation
Indices: 49344795--49344868 Score: 98
Period size: 29 Copynumber: 2.5 Consensus size: 30
49344785 ACAAAATGCT
49344795 AACATAAGTGACTAAAACGTAACATT-T-CA
1 AACATAAGTGACTAAAACGTAAC-TTGTGCA
*
49344824 AACATAAGTGACTAAAATGTAACTTGTGGCA
1 AACATAAGTGACTAAAACGTAACTTGT-GCA
*
49344855 AACAAAAGTGACTA
1 AACATAAGTGACTA
49344869 TTTTTACAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 2 0.05
29 23 0.57
31 15 0.38
ACGTcount: A:0.47, C:0.15, G:0.15, T:0.23
Consensus pattern (30 bp):
AACATAAGTGACTAAAACGTAACTTGTGCA
Found at i:49345156 original size:19 final size:19
Alignment explanation
Indices: 49345128--49345173 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
49345118 TTTCAAAAAT
49345128 AATA-TTTAAAAATACATA
1 AATATTTTAAAAATACATA
* *
49345146 AATATTTTAAAAATGCTTA
1 AATATTTTAAAAATACATA
*
49345165 AAAATTTTA
1 AATATTTTA
49345174 CATTGCATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.39
Consensus pattern (19 bp):
AATATTTTAAAAATACATA
Found at i:49346851 original size:26 final size:26
Alignment explanation
Indices: 49346822--49346874 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
49346812 AAAAGTAACA
* *
49346822 AAACTGTCACTG-TTTAATCCACTTGT
1 AAACTG-CACTGCTTGAAACCACTTGT
49346848 AAACTGCACTGCTTGAAACCACTTGT
1 AAACTGCACTGCTTGAAACCACTTGT
49346874 A
1 A
49346875 TTCCACCGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 5 0.21
26 19 0.79
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.32
Consensus pattern (26 bp):
AAACTGCACTGCTTGAAACCACTTGT
Found at i:49348014 original size:30 final size:31
Alignment explanation
Indices: 49347943--49348014 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
49347933 TTCAGAATAA
49347943 TAGTGACTGTTTTGTCACTTTTCGATAACGT
1 TAGTGACTGTTTTGTCACTTTTCGATAACGT
*
49347974 TAGCGACTGTTTTGTCACATTTTC-A-AA-GT
1 TAGTGACTGTTTTGTCAC-TTTTCGATAACGT
49348003 TGAGTGACTGTT
1 T-AGTGACTGTT
49348015 GTGTTAAATG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
29 3 0.08
30 11 0.30
31 18 0.49
32 5 0.14
ACGTcount: A:0.21, C:0.15, G:0.21, T:0.43
Consensus pattern (31 bp):
TAGTGACTGTTTTGTCACTTTTCGATAACGT
Found at i:49348789 original size:30 final size:30
Alignment explanation
Indices: 49348753--49348818 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 30
49348743 TAGTTTATAT
*
49348753 TTTTATAATTTTTAA-AG-AATTAAATCAAAA
1 TTTTATAA-TTTTAAGAGAAATAAAAT-AAAA
49348783 TTTTATAATTTTAAGAGAAATAAAATAAAA
1 TTTTATAATTTTAAGAGAAATAAAATAAAA
49348813 TTTTAT
1 TTTTAT
49348819 TTTTACTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 6 0.18
30 20 0.61
31 7 0.21
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.44
Consensus pattern (30 bp):
TTTTATAATTTTAAGAGAAATAAAATAAAA
Found at i:49348846 original size:83 final size:82
Alignment explanation
Indices: 49348720--49348877 Score: 180
Period size: 82 Copynumber: 1.9 Consensus size: 82
49348710 TTTTAGGGGT
* * * * *
49348720 TAAAATTAAATTTTAATTTTTAATAGTTTATATTTTTATAATTTTTAAAGAA-TTAAATCAA-AA
1 TAAAATAAAATTTTAATTTTTAATAGTTTA-AATTTTAAAAATTTTAAAAAACTTAAAT-AATAA
49348783 TTTTATAATTTTAAGAGAAA
64 TTTT-TAATTTTAAGAGAAA
*
49348803 TAAAATAAAATTTT-ATTTTTACT-GATTTAAAATTTTAAAAATTTTAAAAAACTTAAATAATAA
1 TAAAATAAAATTTTAATTTTTAATAG-TTT-AAATTTTAAAAATTTTAAAAAACTTAAATAATAA
*
49348866 TTTTTCATTTTA
64 TTTTTAATTTTA
49348878 GGAGGGTCAG
Statistics
Matches: 64, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
81 1 0.02
82 37 0.58
83 26 0.41
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (82 bp):
TAAAATAAAATTTTAATTTTTAATAGTTTAAATTTTAAAAATTTTAAAAAACTTAAATAATAATT
TTTAATTTTAAGAGAAA
Found at i:49355411 original size:13 final size:12
Alignment explanation
Indices: 49355393--49355422 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
49355383 AGGTATGCAA
49355393 AAAAAAAAAAAGG
1 AAAAAAAAAAA-G
49355406 AAAAAAAAAAAG
1 AAAAAAAAAAAG
49355418 AAAAA
1 AAAAA
49355423 CAAATCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:49359441 original size:31 final size:31
Alignment explanation
Indices: 49359357--49359448 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 31
49359347 AAATTTAGGT
* * * *
49359357 ATTAGAAAAAAGTGTCAAGTTTGAGTACCAA
1 ATTAAAAAAAAGTATCAAATTTAAGTACCAA
49359388 ATTAGACAAAAAA--AT---ATTTAAGTACCAA
1 ATTA-A-AAAAAAGTATCAAATTTAAGTACCAA
*
49359416 ATTAAAAAAAAGTATCAAATTTAAGTGCCAA
1 ATTAAAAAAAAGTATCAAATTTAAGTACCAA
49359447 AT
1 AT
49359449 ATTATATTAA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
26 6 0.12
27 1 0.02
28 17 0.35
31 19 0.39
33 6 0.12
ACGTcount: A:0.52, C:0.10, G:0.12, T:0.26
Consensus pattern (31 bp):
ATTAAAAAAAAGTATCAAATTTAAGTACCAA
Found at i:49361606 original size:2 final size:2
Alignment explanation
Indices: 49361599--49361627 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
49361589 TATGGAAGAA
49361599 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
49361628 AATGTTACCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:49364432 original size:17 final size:17
Alignment explanation
Indices: 49364402--49364435 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49364392 ATTTTGGCCC
**
49364402 TTTAAATTTTTAAAAAA
1 TTTAAATTAGTAAAAAA
49364419 TTTAAATTAGTAAAAAA
1 TTTAAATTAGTAAAAAA
49364436 AAAATTGTAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
TTTAAATTAGTAAAAAA
Found at i:49369655 original size:14 final size:14
Alignment explanation
Indices: 49369626--49369664 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
49369616 TGTTGTCTCA
*
49369626 TTGTTGG-TGTTGG
1 TTGTTGGTTGCTGG
49369639 TTGTTGGTTGCTGG
1 TTGTTGGTTGCTGG
*
49369653 TTGCTGGTTGCT
1 TTGTTGGTTGCT
49369665 CATTTGTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 7 0.30
14 16 0.70
ACGTcount: A:0.00, C:0.08, G:0.41, T:0.51
Consensus pattern (14 bp):
TTGTTGGTTGCTGG
Found at i:49370504 original size:20 final size:20
Alignment explanation
Indices: 49370460--49370506 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
49370450 TGGTTCTTCA
*
49370460 ATTTAAAAATTAAAAAAACT
1 ATTTAAAAATTAAAAAAAAT
*
49370480 -CTTAAAAA-TAAAAAATAAT
1 ATTTAAAAATTAAAAAA-AAT
49370499 ATTTAAAA
1 ATTTAAAA
49370507 GTTATTTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
18 7 0.32
19 9 0.41
20 6 0.27
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (20 bp):
ATTTAAAAATTAAAAAAAAT
Found at i:49373877 original size:23 final size:23
Alignment explanation
Indices: 49373839--49373887 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
49373829 GTAATAAATG
49373839 TTTTATAATATAAAAAATGAATA
1 TTTTATAATATAAAAAATGAATA
*
49373862 TTTTCATAATAT-AAAAATGAGTA
1 TTTT-ATAATATAAAAAATGAATA
49373885 TTT
1 TTT
49373888 GTTTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (23 bp):
TTTTATAATATAAAAAATGAATA
Found at i:49388797 original size:31 final size:29
Alignment explanation
Indices: 49388762--49388827 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
49388752 ATTTTAAAAC
* *
49388762 TATACGCGAATTTTAGTTTAATGTGTAATTT
1 TATACACGAATTTTAATTT--TGTGTAATTT
* *
49388793 TATACATGCATTTTAATTTTGTGTAATTT
1 TATACACGAATTTTAATTTTGTGTAATTT
49388822 TATACA
1 TATACA
49388828 TGAAAATTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.52
31 15 0.48
ACGTcount: A:0.30, C:0.08, G:0.12, T:0.50
Consensus pattern (29 bp):
TATACACGAATTTTAATTTTGTGTAATTT
Found at i:49388842 original size:29 final size:29
Alignment explanation
Indices: 49388783--49388841 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
49388773 TTTAGTTTAA
* *
49388783 TGTGTAATTTTATACATGCATTTTAATTT
1 TGTGTAATTTTATACATGAAATTTAATTT
*
49388812 TGTGTAATTTTATACATGAAAATTTGATTT
1 TGTGTAATTTTATACATG-AAATTTAATTT
49388842 GATCTAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.69
30 8 0.31
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.53
Consensus pattern (29 bp):
TGTGTAATTTTATACATGAAATTTAATTT
Found at i:49390197 original size:72 final size:76
Alignment explanation
Indices: 49390111--49390260 Score: 191
Period size: 79 Copynumber: 2.0 Consensus size: 76
49390101 TCCCGCAAAA
* * *
49390111 CCCAACGGACGAGACAAATT-AAA-AT-G-GCTCCCTTGCATCTCCCAACAATCACAAAATTTAA
1 CCCAAAGGACGAGACAAATTCAAAGATAGAGCCCCCTTACATCTCCCAACAATCACAAAATTTAA
*
49390172 AATCTAGATTC
66 AATCGAGATTC
**
49390183 CCCAAAGGACGAGACAAATTCAAATGATCAGACGCCCCCTTACATCTCCCAACTGTCACAAAATT
1 CCCAAAGGACGAGACAAATTCAAA-GAT-AGA-GCCCCCTTACATCTCCCAACAATCACAAAATT
49390248 TAAAATCGAGATT
63 TAAAATCGAGATT
49390261 GACCACATCT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
72 19 0.29
73 3 0.05
75 2 0.03
77 1 0.02
79 40 0.62
ACGTcount: A:0.39, C:0.28, G:0.12, T:0.21
Consensus pattern (76 bp):
CCCAAAGGACGAGACAAATTCAAAGATAGAGCCCCCTTACATCTCCCAACAATCACAAAATTTAA
AATCGAGATTC
Found at i:49390354 original size:70 final size:71
Alignment explanation
Indices: 49390232--49390447 Score: 310
Period size: 70 Copynumber: 3.0 Consensus size: 71
49390222 TTACATCTCC
* * *
49390232 CAACTGTCACAAAATTTAAAATCGAGATTGACCACATCTAAACAACGTTGTTTTCTTTTCCTCTA
1 CAACGGTCACAAAATTTAAAATC--CA--GACCATATCTAAACAACGTTGTTTTCTTTTCCTCTA
49390297 TCAACTGTTG
62 TCAACTGTTG
*
49390307 CAACGGTCACAAAATTTAAAATCCAGA-CATATCTAAACAACGTTGTTTTCTTTTCCTCCATCAA
1 CAACGGTCACAAAATTTAAAATCCAGACCATATCTAAACAACGTTGTTTTCTTTTCCTCTATCAA
49390371 CTGTTG
66 CTGTTG
49390377 CAACGGTCACAAAATTTAAAATCCAGATTCCCCATATCTAAACAAC-TTGTTTTCTTTTCCTCTA
1 CAACGGTCACAAAATTTAAAATCCAGA----CCATATCTAAACAACGTTGTTTTCTTTTCCTCTA
49390441 TCAACTG
62 TCAACTG
49390448 CTTCTATCCA
Statistics
Matches: 131, Mismatches: 5, Indels: 11
0.89 0.03 0.07
Matches are distributed among these distances:
70 68 0.52
71 2 0.02
73 1 0.01
74 24 0.18
75 36 0.27
ACGTcount: A:0.32, C:0.25, G:0.09, T:0.34
Consensus pattern (71 bp):
CAACGGTCACAAAATTTAAAATCCAGACCATATCTAAACAACGTTGTTTTCTTTTCCTCTATCAA
CTGTTG
Found at i:49391187 original size:32 final size:32
Alignment explanation
Indices: 49391151--49391231 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
49391141 TTGTGAGATT
* *
49391151 ATTAAGATTTTCAAAAAATTTAAGAGAGCTTA
1 ATTAAAATTTTCAAAAAATTTAAGAGAGCATA
*
49391183 ATTAAAATTTTCAAAAAATTTAAGAGGGCATA
1 ATTAAAATTTTCAAAAAATTTAAGAGAGCATA
*
49391215 ATTAAAATTTTCTAAAA
1 ATTAAAATTTTCAAAAA
49391232 TGTAAGGAGT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 45 1.00
ACGTcount: A:0.49, C:0.06, G:0.10, T:0.35
Consensus pattern (32 bp):
ATTAAAATTTTCAAAAAATTTAAGAGAGCATA
Found at i:49392754 original size:156 final size:156
Alignment explanation
Indices: 49392470--49392783 Score: 556
Period size: 156 Copynumber: 2.0 Consensus size: 156
49392460 TAAAGAGTGC
* *
49392470 ACAAAGGATGGGACCATTCGCTTCTCGGTTAGTAGGCAAAACACCCAGTTCCATACGCTCTATGA
1 ACAAAGGATGGGACCATTCGCTTCTCGATTAGTAGGCAAAACACCCAGCTCCATACGCTCTATGA
*
49392535 AGAAGCTTGATTACAACAACTCTTGCAAAATAAAAAAATCTACCAAAGATGATCCTTCTAATACC
66 AGAAGCCTGATTACAACAACTCTTGCAAAATAAAAAAATCTACCAAAGATGATCCTTCTAATACC
49392600 AAAGACAGGTATAGACTAACTTGACT
131 AAAGACAGGTATAGACTAACTTGACT
* * * *
49392626 ACAAAGGATGGGACCATTCGCTTCTCGATTAGTAGGCAAAGCACCTAGCTGCATACGCTTTATGA
1 ACAAAGGATGGGACCATTCGCTTCTCGATTAGTAGGCAAAACACCCAGCTCCATACGCTCTATGA
*
49392691 AGAAGCCTGATTACAACAACTCTTGCAAAGTAAAAAAATCTACCAAAGATGATCCTTCTAATACC
66 AGAAGCCTGATTACAACAACTCTTGCAAAATAAAAAAATCTACCAAAGATGATCCTTCTAATACC
49392756 AAAGACAGGTATAGACTAACTTGACT
131 AAAGACAGGTATAGACTAACTTGACT
49392782 AC
1 AC
49392784 TACTTGAATA
Statistics
Matches: 150, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
156 150 1.00
ACGTcount: A:0.38, C:0.22, G:0.17, T:0.24
Consensus pattern (156 bp):
ACAAAGGATGGGACCATTCGCTTCTCGATTAGTAGGCAAAACACCCAGCTCCATACGCTCTATGA
AGAAGCCTGATTACAACAACTCTTGCAAAATAAAAAAATCTACCAAAGATGATCCTTCTAATACC
AAAGACAGGTATAGACTAACTTGACT
Found at i:49393735 original size:224 final size:220
Alignment explanation
Indices: 49393448--49393888 Score: 702
Period size: 224 Copynumber: 2.0 Consensus size: 220
49393438 TTTAAACAAG
*
49393448 TTTTTTGAATTATGAGTGAAGGTAAGCTGTCTGTTTTTTCAGCTAAGTAACTTGTTCAGCAGAGC
1 TTTTTTGAATTATGAGTGAAGGTAAGCTGACTGTTTTTTCAGCTAAGTAACTTGTTCAGCAGAGC
* * *
49393513 TGCAAAAGGAATTATTGAGTGAGCAGAAATTACAATTTATCTGTGTAATACAATATAGTTGTTTC
66 TGCAAAAGGAATTATTGAGTGAGAAGAAATTACAATTTATCCGAGTAATACAATATAGTTGTTTC
* * ***
49393578 TCAAATCTTCTTTTCTATATATCTTCAAGTACCCTATGTATATGTTATAGGGTATTGGATTTCAG
131 TCAAATCTTCTTTTCTATATATCTTCAAGTACCCTATGCATATGTTATAGGGTATTGAATCGAAG
49393643 ATGACAAAATAAATAATTGAACTTA
196 ATGACAAAATAAATAATTGAACTTA
49393668 TTTTTTGAATTATGAGTGAAGGTAGCTAAGCTGACTGTTTTTTCAGCTAAGTAACTTGTTCAGCA
1 TTTTTTGAATTATGAGTGAA-G--G-TAAGCTGACTGTTTTTTCAGCTAAGTAACTTGTTCAGCA
* *
49393733 GAGCTGCAAAAGGAATTATTGAGTGAGAAGAAATTGCAATTTATCCGAGTAATGCAATATAGTTG
62 GAGCTGCAAAAGGAATTATTGAGTGAGAAGAAATTACAATTTATCCGAGTAATACAATATAGTTG
* ***
49393798 TTTCTCACATCTTCTTTTCTATATATCTTCAAGTATTGTATGCATATGTTATAGGGTATTGAATC
127 TTTCTCAAATCTTCTTTTCTATATATCTTCAAGTACCCTATGCATATGTTATAGGGTATTGAATC
*
49393863 GAAGATGACAAAATACATAATTGAAC
192 GAAGATGACAAAATAAATAATTGAAC
49393889 CTCCCTTTAA
Statistics
Matches: 201, Mismatches: 16, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
220 20 0.10
221 1 0.00
223 1 0.00
224 179 0.89
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.37
Consensus pattern (220 bp):
TTTTTTGAATTATGAGTGAAGGTAAGCTGACTGTTTTTTCAGCTAAGTAACTTGTTCAGCAGAGC
TGCAAAAGGAATTATTGAGTGAGAAGAAATTACAATTTATCCGAGTAATACAATATAGTTGTTTC
TCAAATCTTCTTTTCTATATATCTTCAAGTACCCTATGCATATGTTATAGGGTATTGAATCGAAG
ATGACAAAATAAATAATTGAACTTA
Found at i:49395625 original size:295 final size:295
Alignment explanation
Indices: 49394271--49396006 Score: 2292
Period size: 295 Copynumber: 5.9 Consensus size: 295
49394261 GGTCTTGCTA
* *
49394271 CCTGAGTATTATAGTGCACTAAAGTTAGGAAATAAAA-GATTAACCGACTTCATAGAGTTGGTGA
1 CCTGAGTATTATAGTGCACTAAAGTTAGGAAATAAAATG-TTAACCGACTTCATAGAGTTGATGT
* *
49394335 AACATTACTTGTAGGTCTTAAGTCCTCCTCT-GT--ATTG-----GGCTCGTCGAGTTCCCAATA
65 AACATTACTTGTAGGTCTTAAGT-CTTCTGTAGTGGATTGTATTAGGCTCGTCGAGTT-CCAATA
* ** * * * * * *
49394392 AGTGGAATCAAAGCAAGTGTTTCGGGATCATCACTAATGGAGGAAGTTTTGGTAAGCATTGGGAG
128 AGTGGTATCAAAGCAAGCATTCCGAGATCGTCACTAGTGGAGGAAGTTTCGGTAAGCATTGGGCG
* * *
49394457 TTTGCATTGGTTGGTGTGTCATAAAGGCATTAAGGGGAGATTCTACCGGTAAACAGTCAGGGACT
193 TTTACATTGGTTGGTGTGGCATAAAGGCATTAAGGGGAGACTCTACCGGTAAACAGTCAGGGACT
* * *
49394522 GCGAAGCTTATTGGTCAGGTATATGGTCGATCCTGTCG
258 GCGAAGCTTATTGGTCAGATATATGGTCGGTCCTGCCG
* * * * *
49394560 CCTGAGTATTATAATGCACTAAAGTTAGGAAATAAAAGGTTAATCGACTTTATAGAGTTGGTGTA
1 CCTGAGTATTATAGTGCACTAAAGTTAGGAAATAAAATGTTAACCGACTTCATAGAGTTGATGTA
* * * *
49394625 ACATTACTTATAGGTCTTAAATCTTCTGTAGTGGA-TGTATTAGGTTCGTCAAGTTCCTAATAAG
66 ACATTACTTGTAGGTCTTAAGTCTTCTGTAGTGGATTGTATTAGGCTCGTCGAGTTCC-AATAAG
* * * * *
49394689 TGGTATCGAAGCAAGCATTCCGAGATTGTCACTAGTGGAGGAAGTTTCGGCAAGCACTAGGCGTT
130 TGGTATCAAAGCAAGCATTCCGAGATCGTCACTAGTGGAGGAAGTTTCGGTAAGCATTGGGCGTT
* * *
49394754 TACATTGGTTGATGT-G-----A--CATTAA-GGGAGACTCTACAGGTAAACAGTCAAGGACTGC
195 TACATTGGTTGGTGTGGCATAAAGGCATTAAGGGGAGACTCTACCGGTAAACAGTCAGGGACTGC
* **
49394810 GAAGCTTATTGGTCAGATGTATGAACGGTCCTGCCG
260 GAAGCTTATTGGTCAGATATATGGTCGGTCCTGCCG
* * *
49394846 CTTGAGTATTATTATAGTGCACTAAAGTTAGGAAATAAAATGTTAACTGACTTCATAGAGTTGGT
1 CCTGAG---TATTATAGTGCACTAAAGTTAGGAAATAAAATGTTAACCGACTTCATAGAGTTGAT
* * * *
49394911 GTAATATTAC--GTAAG---TAAGTCTTTTGTAGTGGA-TGTATTAGGCTCGTTGAGTTCCCAAT
63 GTAACATTACTTGTAGGTCTTAAGTCTTCTGTAGTGGATTGTATTAGGCTCGTCGAGTT-CCAAT
* * ** * *
49394970 AAGTAGTATCAAAGCAAGCGTTTTGAGATCGTTA-TTGTTGGAGGAAGTTTCGGTAAGCATTGGG
127 AAGTGGTATCAAAGCAAGCATTCCGAGATCGTCACTAG-TGGAGGAAGTTTCGGTAAGCATTGGG
* * **
49395034 CGTTTACATTGGTTGGTGTGGCATAAAGGCATTAAGTGAAGACTCTATTGGTAAACAGTCAGGGA
191 CGTTTACATTGGTTGGTGTGGCATAAAGGCATTAAGGGGAGACTCTACCGGTAAACAGTCAGGGA
* * *
49395099 CTGCGAAGCTTATTGGTCAGATATATAGTCGATCCTGCCA
256 CTGCGAAGCTTATTGGTCAGATATATGGTCGGTCCTGCCG
*
49395139 CCTGAGTATTATAGTGCACTAAAGTTAGGAAATAAAATGTTAACCGATTTCATAGAGTTGATGT-
1 CCTGAGTATTATAGTGCACTAAAGTTAGGAAATAAAATGTTAACCGACTTCATAGAGTTGATGTA
* *
49395203 -CATTACTTGTAGGTCTTAAGTCTTCTGTAGT-GATTGTATTCGGCTCATCGAGTTACCAATAAG
66 ACATTACTTGTAGGTCTTAAGTCTTCTGTAGTGGATTGTATTAGGCTCGTCGAGTT-CCAATAAG
* *
49395266 TGGTATCAAAGCAAGCATTCCGAGATCGTCACTAGTGGAGGAAGTTTCGATAAGCATTGGGTGTT
130 TGGTATCAAAGCAAGCATTCCGAGATCGTCACTAGTGGAGGAAGTTTCGGTAAGCATTGGGCGTT
*
49395331 TACATTGGTTGGTGTGGCATAAAGGCATTAAGGGGAGACTCTACCGGTAAATAGTCAGGGACTGC
195 TACATTGGTTGGTGTGGCATAAAGGCATTAAGGGGAGACTCTACCGGTAAACAGTCAGGGACTGC
* * *
49395396 GAAGCTTATTAGTCAAATATATGGTCGGTCCTGCTG
260 GAAGCTTATTGGTCAGATATATGGTCGGTCCTGCCG
*
49395432 TCTGAGTATTATAGTGCACTAAAGTTAGGAAATAAAATGTTAACCGACTTCATAGAGTTGATGTA
1 CCTGAGTATTATAGTGCACTAAAGTTAGGAAATAAAATGTTAACCGACTTCATAGAGTTGATGTA
* *
49395497 ACATTACTTGTAGGTCTTAAGTCTTCTGTAGT-GATTGTATTCGGCTCATCGAGTTACCAATAAG
66 ACATTACTTGTAGGTCTTAAGTCTTCTGTAGTGGATTGTATTAGGCTCGTCGAGTT-CCAATAAG
* *
49395561 TGGTATCAAAGCAAGCATTCCGAGATCGTCACTAGTGGAGGAAGTTTCGATAAGCATTGGGTGTT
130 TGGTATCAAAGCAAGCATTCCGAGATCGTCACTAGTGGAGGAAGTTTCGGTAAGCATTGGGCGTT
*
49395626 TACATTGGTTGGTGTGGCATAAAGGCATTAAGGGGAGACTCTACCGGTAAATAGTCAGGGACTGC
195 TACATTGGTTGGTGTGGCATAAAGGCATTAAGGGGAGACTCTACCGGTAAACAGTCAGGGACTGC
*
49395691 GAAGCTTATTGGTCGGATATATGGTCGGTCCTGCCG
260 GAAGCTTATTGGTCAGATATATGGTCGGTCCTGCCG
* *
49395727 CCTGAGTATTATAGTGCACTAAATTTAGGAAATAAAATGTTAACCGACTTTATAGAGTTGATGTA
1 CCTGAGTATTATAGTGCACTAAAGTTAGGAAATAAAATGTTAACCGACTTCATAGAGTTGATGTA
* *
49395792 ACATTTACTTGTAGGTCTTAAGTCCTCTGTAGTGGATT-TATTGGGCTCGTCGAGTTCTCAATAA
66 ACA-TTACTTGTAGGTCTTAAGTCTTCTGTAGTGGATTGTATTAGGCTCGTCGAGTTC-CAATAA
* * * * * * *
49395856 GTAGTATCATAGCAAGCCTTTCGGGATCGTCACTAGTGGAGGAAGTTTAGGTAAGCATTGGACGT
129 GTGGTATCAAAGCAAGCATTCCGAGATCGTCACTAGTGGAGGAAGTTTCGGTAAGCATTGGGCGT
* * ** * * *
49395921 TTACATTGGTTGGTGTGGCATAAAGGCATTAAGGGAAAACTCTATTGATAAACAATCAGGGACTA
194 TTACATTGGTTGGTGTGGCATAAAGGCATTAAGGGGAGACTCTACCGGTAAACAGTCAGGGACTG
*
49395986 CGAAGCTTATTGGTTAGATAT
259 CGAAGCTTATTGGTCAGATAT
49396007 GAAAATTTGA
Statistics
Matches: 1277, Mismatches: 134, Indels: 65
0.87 0.09 0.04
Matches are distributed among these distances:
283 2 0.00
284 104 0.08
285 3 0.00
286 65 0.05
287 9 0.01
288 10 0.01
289 142 0.11
290 63 0.05
291 1 0.00
292 8 0.01
293 308 0.24
294 4 0.00
295 372 0.29
296 182 0.14
297 4 0.00
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (295 bp):
CCTGAGTATTATAGTGCACTAAAGTTAGGAAATAAAATGTTAACCGACTTCATAGAGTTGATGTA
ACATTACTTGTAGGTCTTAAGTCTTCTGTAGTGGATTGTATTAGGCTCGTCGAGTTCCAATAAGT
GGTATCAAAGCAAGCATTCCGAGATCGTCACTAGTGGAGGAAGTTTCGGTAAGCATTGGGCGTTT
ACATTGGTTGGTGTGGCATAAAGGCATTAAGGGGAGACTCTACCGGTAAACAGTCAGGGACTGCG
AAGCTTATTGGTCAGATATATGGTCGGTCCTGCCG
Found at i:49398182 original size:46 final size:44
Alignment explanation
Indices: 49398127--49398221 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 44
49398117 GGTTCGCTGT
* *
49398127 AATGAAATAGAGCTGTAATCAGTATTTCA-ATTGTTTGGTTGAATGG
1 AATGAAATAGAGCTATAAT-AGTA-TTCATA-TGTTTGGTTGAATAG
* * *
49398173 AATGGAATAGGGCTATAATAGTATTCTTATGTTTGGTTGAATAG
1 AATGAAATAGAGCTATAATAGTATTCATATGTTTGGTTGAATAG
49398217 AATGA
1 AATGA
49398222 TACTGTAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
44 21 0.50
45 5 0.12
46 16 0.38
ACGTcount: A:0.34, C:0.05, G:0.24, T:0.37
Consensus pattern (44 bp):
AATGAAATAGAGCTATAATAGTATTCATATGTTTGGTTGAATAG
Found at i:49401139 original size:11 final size:11
Alignment explanation
Indices: 49401123--49401155 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
49401113 AGTATTGAGG
49401123 GAAAAATAATT
1 GAAAAATAATT
*
49401134 GAAAAATAATG
1 GAAAAATAATT
49401145 GAAAAATAATT
1 GAAAAATAATT
49401156 TTGTGAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (11 bp):
GAAAAATAATT
Found at i:49417842 original size:15 final size:15
Alignment explanation
Indices: 49417822--49417857 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
49417812 ACCATTAAGC
49417822 CCAAACCCAATTGAA
1 CCAAACCCAATTGAA
49417837 CCAAACCCAATTGAA
1 CCAAACCCAATTGAA
49417852 CCAAAC
1 CCAAAC
49417858 TCAAACCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.36, G:0.06, T:0.11
Consensus pattern (15 bp):
CCAAACCCAATTGAA
Found at i:49417916 original size:7 final size:7
Alignment explanation
Indices: 49417904--49417963 Score: 50
Period size: 7 Copynumber: 8.7 Consensus size: 7
49417894 TGACCGACTA
49417904 TTGACCG
1 TTGACCG
*
49417911 TTGACCA
1 TTGACCG
*
49417918 TTGATCG
1 TTGACCG
49417925 TTGACCG
1 TTGACCG
**
49417932 TTGA-TT
1 TTGACCG
*
49417938 TTGACTG
1 TTGACCG
*
49417945 TTGATCG
1 TTGACCG
*
49417952 TTGACTG
1 TTGACCG
49417959 TTGAC
1 TTGAC
49417964 TTTTTCCGAA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
6 4 0.10
7 37 0.90
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.40
Consensus pattern (7 bp):
TTGACCG
Found at i:49417936 original size:14 final size:14
Alignment explanation
Indices: 49417904--49417962 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
49417894 TGACCGACTA
* *
49417904 TTGACCGTTGACCA
1 TTGATCGTTGACCG
49417918 TTGATCGTTGACCG
1 TTGATCGTTGACCG
* *
49417932 TTGAT-TTTGACTG
1 TTGATCGTTGACCG
*
49417945 TTGATCGTTGACTG
1 TTGATCGTTGACCG
49417959 TTGA
1 TTGA
49417963 CTTTTTCCGA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
13 11 0.28
14 28 0.72
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (14 bp):
TTGATCGTTGACCG
Found at i:49419055 original size:19 final size:17
Alignment explanation
Indices: 49419020--49419058 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
49419010 TTATATTATT
*
49419020 TTATTTTATTTTTATTA
1 TTATTTTATTTTGATTA
49419037 TTATTTTGATTTTGGATTA
1 TTATTTT-ATTTT-GATTA
49419056 TTA
1 TTA
49419059 ATATACTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (17 bp):
TTATTTTATTTTGATTA
Found at i:49421509 original size:21 final size:20
Alignment explanation
Indices: 49421483--49421525 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
49421473 TTATATTTAA
49421483 ATAAATTATTAATATTTATTT
1 ATAAATTATTAATATTT-TTT
* *
49421504 ATAAATTTTTTATATTTTTT
1 ATAAATTATTAATATTTTTT
49421524 AT
1 AT
49421526 TTAATTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (20 bp):
ATAAATTATTAATATTTTTT
Found at i:49424314 original size:24 final size:24
Alignment explanation
Indices: 49424280--49424326 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
49424270 TAATTTTTAT
* *
49424280 TTTTTTTAAAATTATAAAATAATA
1 TTTTTTAAAAATTAGAAAATAATA
49424304 TTTTTTAAAAATTAGAAAATAAT
1 TTTTTTAAAAATTAGAAAATAAT
49424327 TAAAAATGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (24 bp):
TTTTTTAAAAATTAGAAAATAATA
Found at i:49424812 original size:22 final size:22
Alignment explanation
Indices: 49424786--49424831 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
49424776 ATTAAATAAA
49424786 ATAAAAAAATAGTTAA-AAATTT
1 ATAAAAAAATA-TTAATAAATTT
*
49424808 ATAAATAAATATTAATAAATTT
1 ATAAAAAAATATTAATAAATTT
49424830 AT
1 AT
49424832 TTAAACATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
ATAAAAAAATATTAATAAATTT
Found at i:49424936 original size:22 final size:21
Alignment explanation
Indices: 49424911--49424992 Score: 64
Period size: 22 Copynumber: 4.0 Consensus size: 21
49424901 TAAATATGAG
49424911 AATTATTTATATTTATTTATA
1 AATTATTTATATTTATTTATA
* * *
49424932 CAATTAATTATAGTTA--AATA
1 -AATTATTTATATTTATTTATA
* *
49424952 AATTATTAATATTTATTTACA
1 AATTATTTATATTTATTTATA
49424973 AATT-TTTCATATATT-TTTAT
1 AATTATTT-ATAT-TTATTTAT
49424993 TTAATTTAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
19 12 0.26
20 5 0.11
21 14 0.30
22 15 0.33
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (21 bp):
AATTATTTATATTTATTTATA
Found at i:49426533 original size:2 final size:2
Alignment explanation
Indices: 49426526--49426557 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
49426516 TATCAGAAAA
49426526 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
49426558 TTTAACTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:49429815 original size:13 final size:13
Alignment explanation
Indices: 49429797--49429833 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
49429787 CTTAGATTTA
49429797 AAGTTTTAACATT
1 AAGTTTTAACATT
49429810 AAGTTTTAA-ATT
1 AAGTTTTAACATT
*
49429822 AAATTTT-ACATT
1 AAGTTTTAACATT
49429834 TTAATTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
11 1 0.05
12 12 0.55
13 9 0.41
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (13 bp):
AAGTTTTAACATT
Found at i:49429974 original size:41 final size:40
Alignment explanation
Indices: 49429890--49429977 Score: 104
Period size: 41 Copynumber: 2.1 Consensus size: 40
49429880 TCAAGCTTCA
* * * * * *
49429890 TTTAGATTTTAGATTTGGATTTTAAACTTATTTTTTATTTT
1 TTTA-ATTTTAGATTTAGACTTTAAAATTAATTGTTATATT
49429931 TTTAATTTTAGATTTTAGACTTTAAAATTAATTGTTATATT
1 TTTAATTTTAGA-TTTAGACTTTAAAATTAATTGTTATATT
49429972 TTTAAT
1 TTTAAT
49429978 GAGGTTTTAG
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
40 8 0.20
41 32 0.80
ACGTcount: A:0.30, C:0.02, G:0.08, T:0.60
Consensus pattern (40 bp):
TTTAATTTTAGATTTAGACTTTAAAATTAATTGTTATATT
Found at i:49431473 original size:29 final size:26
Alignment explanation
Indices: 49431413--49431483 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 26
49431403 GAATTGGAGG
*
49431413 AGGGATTAAAATTTT-AAATCAAGTAT
1 AGGGATT-AAATTTTAAAATAAAGTAT
*
49431439 AAGGATTCAATATTTTAAAATTAAAGTAT
1 AGGGATT-AA-ATTTTAAAA-TAAAGTAT
49431468 AGGGATTAAATTTTAA
1 AGGGATTAAATTTTAA
49431484 TTTTCAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
26 8 0.21
27 12 0.32
28 5 0.13
29 13 0.34
ACGTcount: A:0.46, C:0.03, G:0.14, T:0.37
Consensus pattern (26 bp):
AGGGATTAAATTTTAAAATAAAGTAT
Found at i:49434279 original size:30 final size:30
Alignment explanation
Indices: 49434245--49434374 Score: 163
Period size: 30 Copynumber: 4.3 Consensus size: 30
49434235 TAACCCTGGG
* *
49434245 GTTGGTCAGCAACTCATCAGCTATCCCGGA
1 GTTGGTCAGCAACACATCAGCAATCCCGGA
* * *
49434275 GTTGGTCAGCAACACATCAACAATCCTGGT
1 GTTGGTCAGCAACACATCAGCAATCCCGGA
* *
49434305 GTTGGTCAGCAACTA-ATTAGCTATCCCGGA
1 GTTGGTCAGCAAC-ACATCAGCAATCCCGGA
* *
49434335 GTTGGTCAGCAACACATCAGCAATCCAGGT
1 GTTGGTCAGCAACACATCAGCAATCCCGGA
49434365 GTTGGTCAGC
1 GTTGGTCAGC
49434375 TCATGGGTGT
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 1 0.01
30 82 0.98
31 1 0.01
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (30 bp):
GTTGGTCAGCAACACATCAGCAATCCCGGA
Found at i:49434332 original size:60 final size:60
Alignment explanation
Indices: 49434239--49434374 Score: 227
Period size: 60 Copynumber: 2.3 Consensus size: 60
49434229 CCTCAATAAC
* *
49434239 CCTGGGGTTGGTCAGCAACTCATCAGCTATCCCGGAGTTGGTCAGCAACACATCAACAAT
1 CCTGGTGTTGGTCAGCAACTAATCAGCTATCCCGGAGTTGGTCAGCAACACATCAACAAT
* *
49434299 CCTGGTGTTGGTCAGCAACTAATTAGCTATCCCGGAGTTGGTCAGCAACACATCAGCAAT
1 CCTGGTGTTGGTCAGCAACTAATCAGCTATCCCGGAGTTGGTCAGCAACACATCAACAAT
*
49434359 CCAGGTGTTGGTCAGC
1 CCTGGTGTTGGTCAGC
49434375 TCATGGGTGT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (60 bp):
CCTGGTGTTGGTCAGCAACTAATCAGCTATCCCGGAGTTGGTCAGCAACACATCAACAAT
Found at i:49439550 original size:18 final size:17
Alignment explanation
Indices: 49439507--49439559 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
49439497 TAAAATACGC
*
49439507 TCTCTCTCTTTTGTTCTT
1 TCTCTCTC-TTTGTTATT
49439525 TCAT-TCTCTTTGTTATT
1 TC-TCTCTCTTTGTTATT
49439542 TACTCTCTCTTT-TTATT
1 T-CTCTCTCTTTGTTATT
49439559 T
1 T
49439560 TATAACACGT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.52
18 14 0.45
19 1 0.03
ACGTcount: A:0.08, C:0.23, G:0.04, T:0.66
Consensus pattern (17 bp):
TCTCTCTCTTTGTTATT
Found at i:49444476 original size:21 final size:21
Alignment explanation
Indices: 49444451--49444502 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
49444441 GAGTTTGTAA
*
49444451 TATCGGTAGATGGATATATTG
1 TATCGGTAGATGGAAATATTG
* *
49444472 TATCGGTAGTTGGAAATGTTG
1 TATCGGTAGATGGAAATATTG
*
49444493 TTTCGGTAGA
1 TATCGGTAGA
49444503 ACATTCTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.38
Consensus pattern (21 bp):
TATCGGTAGATGGAAATATTG
Found at i:49447943 original size:31 final size:31
Alignment explanation
Indices: 49447901--49447991 Score: 96
Period size: 31 Copynumber: 2.9 Consensus size: 31
49447891 TATAAAATTG
*
49447901 TCACTAAACTATTCAAAATTTTTCATTTAAA
1 TCACTTAACTATTCAAAATTTTTCATTTAAA
* ** *
49447932 TCA-TTGGACTATTCAAAAAATTTCATTTAAG
1 TCACTT-AACTATTCAAAATTTTTCATTTAAA
*
49447963 TCACTTAACTATTCATAAGTTTTT-ATTTA
1 TCACTTAACTATTCA-AAATTTTTCATTTA
49447992 CGTCATTAGA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
30 1 0.02
31 40 0.83
32 7 0.15
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.44
Consensus pattern (31 bp):
TCACTTAACTATTCAAAATTTTTCATTTAAA
Found at i:49452782 original size:27 final size:27
Alignment explanation
Indices: 49452744--49452798 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
49452734 CAAACTCCAG
*
49452744 AGTAAGTCCAATACGAGTACTTGTGCT
1 AGTAAGTCCAATACGAGTACTTCTGCT
49452771 AGTAAGTCCAATACGAGTACTTCTGCT
1 AGTAAGTCCAATACGAGTACTTCTGCT
49452798 A
1 A
49452799 TATGGGCATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (27 bp):
AGTAAGTCCAATACGAGTACTTCTGCT
Found at i:49457697 original size:12 final size:12
Alignment explanation
Indices: 49457677--49457714 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
49457667 CGCAGCACCA
*
49457677 TCACCAGCCCCGT
1 TCACGAGCCCC-T
49457690 T-ACGAGCCCCT
1 TCACGAGCCCCT
49457701 TCACGAGCCCCT
1 TCACGAGCCCCT
49457713 TC
1 TC
49457715 TTCCTCACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 2 0.09
12 20 0.87
13 1 0.04
ACGTcount: A:0.16, C:0.50, G:0.16, T:0.18
Consensus pattern (12 bp):
TCACGAGCCCCT
Found at i:49457865 original size:15 final size:15
Alignment explanation
Indices: 49457784--49457864 Score: 108
Period size: 15 Copynumber: 5.4 Consensus size: 15
49457774 GGGGACCCTC
*
49457784 TGCTGAAGGATCCGA
1 TGCTGAAGGACCCGA
* *
49457799 GGCTGAAGAACCCGA
1 TGCTGAAGGACCCGA
49457814 TGCTGAAGGACCCGA
1 TGCTGAAGGACCCGA
* *
49457829 TGCTGATGGACCTGA
1 TGCTGAAGGACCCGA
*
49457844 TGCTGATGGACCCGA
1 TGCTGAAGGACCCGA
49457859 TGCTGA
1 TGCTGA
49457865 TTACGGTGGT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 58 1.00
ACGTcount: A:0.25, C:0.23, G:0.33, T:0.19
Consensus pattern (15 bp):
TGCTGAAGGACCCGA
Found at i:49463484 original size:6 final size:6
Alignment explanation
Indices: 49463469--49463509 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
49463459 TGAAGATTCT
* * *
49463469 GATGAC GATGAA GATGAC GATGAG GATGAG GATGAG GATGA
1 GATGAG GATGAG GATGAG GATGAG GATGAG GATGAG GATGA
49463510 CGATTCCGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.37, C:0.05, G:0.41, T:0.17
Consensus pattern (6 bp):
GATGAG
Found at i:49463484 original size:12 final size:12
Alignment explanation
Indices: 49463469--49463513 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
49463459 TGAAGATTCT
*
49463469 GATGACGATGAA
1 GATGACGATGAG
49463481 GATGACGATGAG
1 GATGACGATGAG
*
49463493 GATGAGGATGAG
1 GATGACGATGAG
49463505 GATGACGAT
1 GATGACGAT
49463514 TCCGATGAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.36, C:0.07, G:0.40, T:0.18
Consensus pattern (12 bp):
GATGACGATGAG
Done.