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 2 of 163
Found at i:503836 original size:9 final size:8
Alignment explanation
Indices: 503822--503847 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
503812 CGATTTAAAG
503822 AAAAAAAT
1 AAAAAAAT
503830 AAAAAAAT
1 AAAAAAAT
503838 AAAAAAAT
1 AAAAAAAT
503846 AA
1 AA
503848 GTTGCTTCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:514175 original size:20 final size:19
Alignment explanation
Indices: 514150--514188 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
514140 TAATTTTATA
514150 TTTAATAAAATAAATTATTT
1 TTTAATAAAATAAA-TATTT
* *
514170 TTTAATTATATAAATATTT
1 TTTAATAAAATAAATATTT
514189 AAATGTAAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAATAAAATAAATATTT
Found at i:520777 original size:15 final size:14
Alignment explanation
Indices: 520757--520809 Score: 52
Period size: 16 Copynumber: 3.4 Consensus size: 14
520747 CTTAAATGAA
520757 AAAATTAAAATAATT
1 AAAATTAAAA-AATT
520772 AAAATTTAAAAAATT
1 AAAA-TTAAAAAATT
*
520787 CAAACTTAAAAGAATTT
1 -AAAATTAAAA-AA-TT
520804 AAAATT
1 AAAATT
520810 TTCAAAACTT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
15 14 0.44
16 16 0.50
17 2 0.06
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (14 bp):
AAAATTAAAAAATT
Found at i:520780 original size:16 final size:15
Alignment explanation
Indices: 520756--520810 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
520746 CCTTAAATGA
*
520756 AAAAATTAAAATAATT
1 AAAATTTAAAA-AATT
520772 AAAATTTAAAAAATT
1 AAAATTTAAAAAATT
* *
520787 CAAACTTAAAAGAATTT
1 AAAATTTAAAA-AA-TT
520804 AAAATTT
1 AAAATTT
520811 TCAAAACTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 13 0.41
16 12 0.38
17 7 0.22
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (15 bp):
AAAATTTAAAAAATT
Found at i:528750 original size:20 final size:20
Alignment explanation
Indices: 528709--528755 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
528699 CTCAAACCTA
528709 AACTTGAACTCCCGAACTCG
1 AACTTGAACTCCCGAACTCG
528729 AACCTTGAA-TCCCGAA-TCCG
1 AA-CTTGAACTCCCGAACT-CG
528749 AACTTGA
1 AACTTGA
528756 GTTCAAGGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 6 0.24
20 13 0.52
21 6 0.24
ACGTcount: A:0.32, C:0.32, G:0.15, T:0.21
Consensus pattern (20 bp):
AACTTGAACTCCCGAACTCG
Found at i:528854 original size:14 final size:14
Alignment explanation
Indices: 528783--528854 Score: 60
Period size: 14 Copynumber: 5.3 Consensus size: 14
528773 GGGTTCCAAG
* *
528783 TTTGAAGTTTAGAA
1 TTTGAGGTTTAGGA
528797 TTTG-GGTTT-GGA
1 TTTGAGGTTTAGGA
528809 TTTGAGGTTTA-GA
1 TTTGAGGTTTAGGA
* * *
528822 GTTTAAAGTTTAAGA
1 -TTTGAGGTTTAGGA
*
528837 TTTGAGGTTTAGGG
1 TTTGAGGTTTAGGA
528851 TTTG
1 TTTG
528855 GAATTCAATG
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
12 6 0.13
13 11 0.24
14 27 0.59
15 2 0.04
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.46
Consensus pattern (14 bp):
TTTGAGGTTTAGGA
Found at i:536637 original size:30 final size:30
Alignment explanation
Indices: 536571--536638 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
536561 TTGTGCATCT
* *
536571 AATTTTTAATTTTTTATATTATTTTCATTT
1 AATTTTTAATATTTTATATTATTTTCATTA
*
536601 ATTTTTTAATATTTTA-A-TATTTTCATTGAA
1 AATTTTTAATATTTTATATTATTTTCATT--A
536631 AATTTTTA
1 AATTTTTA
536639 TATAATCATC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 10 0.31
29 1 0.03
30 21 0.66
ACGTcount: A:0.31, C:0.03, G:0.01, T:0.65
Consensus pattern (30 bp):
AATTTTTAATATTTTATATTATTTTCATTA
Found at i:540232 original size:31 final size:29
Alignment explanation
Indices: 540194--540256 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
540184 ATTGGATCTG
* *
540194 AATTTTAAAATTTAAAATATAAAGAGACTA
1 AATTTTTAAATGTAAAA-ATAAAGAGACTA
*
540224 AATTTTTAAATGTAAAAATATAGAGACTA
1 AATTTTTAAATGTAAAAATAAAGAGACTA
540253 AATT
1 AATT
540257 CTAAATTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 15 0.50
30 15 0.50
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (29 bp):
AATTTTTAAATGTAAAAATAAAGAGACTA
Found at i:552755 original size:14 final size:16
Alignment explanation
Indices: 552723--552755 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
552713 AAAATTTCAC
552723 AATTAAACCCCATAAT
1 AATTAAACCCCATAAT
552739 AATT-AACCCCA-AAT
1 AATTAAACCCCATAAT
552753 AAT
1 AAT
552756 AAGCTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 7 0.41
16 4 0.24
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (16 bp):
AATTAAACCCCATAAT
Found at i:555271 original size:388 final size:388
Alignment explanation
Indices: 554542--555289 Score: 1113
Period size: 388 Copynumber: 1.9 Consensus size: 388
554532 GGGAAATTAT
* *
554542 ACTGCTAATGGTTCTTTGCATTTCATTGCCTATGTTATGCTAAATGGACCTTGATAATGATACTT
1 ACTGCTAATGGTTCTTTACATTTCATTGCCTATGTTATACTAAATGGACCTTGATAATGATACTT
* * *
554607 TCGGGGATACTTCTGCCCCAGAAATCCATAAGGGCGAAAATCTACACGTGTTAAAGCTGTTTCTT
66 TCGGGGATACTTCTGCCCCAGAAATCCATAAGGACGAAAATCTACACGTGGTAAAGCCGTTTCTT
*
554672 GAGTTACATGTATAAATTATCATTTACGTAAAATGAGCATCAGTTCAACTTCGAATTTTCGAGTT
131 GAGTTACATGTATAAATTATCATTTACGTAAAATGAGCATCAGTTCAACTTCAAATTTTCGAGTT
**
554737 TTAAGTAGGATTTCATCAGGTATTAGGCCATCTTAAGGTAATGTTTGTATGCAAGGAATGCATTG
196 TTAAGTAGGATTTCATCAGGTATTAGGCCATCTTAAGGTAACATTTGTATGCAAGGAATGCATTG
* * *
554802 ATAAGGTTTTGTATTAAGATTTTGGAATCAGAAACATGAAGGAACTAGCTTTAGTACCCGAAAAC
261 ATAAGGTTTTGTATTAAAATTTTGGAACCAGAAACATGAAGGAACTAGCTTTAATACCCGAAAAC
*
554867 TCCATATTTCTGTGAGGCTTTTGATG-TTTAGAAGTAAACTTGTGCTTTGTGTCAGAAATTGC
326 TACATATTTCTGTGAGGCTTTTGATGTTTTAGAAGTAAACTTGTGCTTTGTGTCAGAAATTGC
* *
554929 ACTGCTAATGGTTCTTTACATTTCATTTCCTATGTTATACTAAATGGACCTTGATCATGATACTT
1 ACTGCTAATGGTTCTTTACATTTCATTGCCTATGTTATACTAAATGGACCTTGATAATGATACTT
* * * * * *
554994 TCCGGGGATTCTTCTGCCCCGGAAATCCATGAGGATGAAAATGTACACGTGGTGAAGCCGTTTCT
66 T-CGGGGATACTTCTGCCCCAGAAATCCATAAGGACGAAAATCTACACGTGGTAAAGCCGTTTCT
* *
555059 TGAGTTACATGTATAAATTCTCATTTATGTAAAATGAGCATCAGTTCAACTTCAAATTTTCGAGT
130 TGAGTTACATGTATAAATTATCATTTACGTAAAATGAGCATCAGTTCAACTTCAAATTTTCGAGT
* * * ** * * *
555124 TTTATGTAGGATTTCATCTGGTTTTAGGCTGTCTTAAGGTCACATTTGTTTGTAAGGAATGCATT
195 TTTAAGTAGGATTTCATCAGGTATTAGGCCATCTTAAGGTAACATTTGTATGCAAGGAATGCATT
* ** * * *
555189 GATAAGGTTTTGTATTAAAATTTTGGTACCTTAAACTTGAAGGAACTAGTTTTAATACTC-AAAC
260 GATAAGGTTTTGTATTAAAATTTTGGAACCAGAAACATGAAGGAACTAGCTTTAATACCCGAAA-
* * *
555253 ACTACGTATTTGTGTGAGGTTTTTGATGTTTTAGAAG
324 ACTACATATTTCTGTGAGGCTTTTGATGTTTTAGAAG
555290 CGAATTTGTG
Statistics
Matches: 319, Mismatches: 39, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
387 65 0.20
388 246 0.77
389 8 0.03
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (388 bp):
ACTGCTAATGGTTCTTTACATTTCATTGCCTATGTTATACTAAATGGACCTTGATAATGATACTT
TCGGGGATACTTCTGCCCCAGAAATCCATAAGGACGAAAATCTACACGTGGTAAAGCCGTTTCTT
GAGTTACATGTATAAATTATCATTTACGTAAAATGAGCATCAGTTCAACTTCAAATTTTCGAGTT
TTAAGTAGGATTTCATCAGGTATTAGGCCATCTTAAGGTAACATTTGTATGCAAGGAATGCATTG
ATAAGGTTTTGTATTAAAATTTTGGAACCAGAAACATGAAGGAACTAGCTTTAATACCCGAAAAC
TACATATTTCTGTGAGGCTTTTGATGTTTTAGAAGTAAACTTGTGCTTTGTGTCAGAAATTGC
Found at i:559625 original size:91 final size:90
Alignment explanation
Indices: 559422--559628 Score: 215
Period size: 91 Copynumber: 2.3 Consensus size: 90
559412 ATAAATCGAG
* *
559422 TTTCATTAAAACATCAAAAATTCAAATTCATAAAAATTAAACCGAAATAATCAAAATAACCCAAA
1 TTTCATTAAAACATC-AAAATTC-AATTCATAAAAATTAAACCGAAATAACCAAAAGAACCCAAA
* *
559487 ATTAATCATCATAACTAAAAGTTTAAA
64 ATTAATCATCATAAATAAAAGTTCAAA
* * * *
559514 TTTCATTATAATAT-ATAAATTCAATTCAT-AAAATTAAATCTAAATAACCAAAAGAATCCATCC
1 TTTCATTAAAACATCA-AAATTCAATTCATAAAAATTAAACCGAAATAACCAAAAGAA--C--CC
* * *
559577 AAAA-TGATGATGATAAATAAAAG-TCAAA
61 AAAATTAATCATCATAAATAAAAGTTCAAA
*
559605 TTTCATTAAAACATCGAAATTCAA
1 TTTCATTAAAACATCAAAATTCAA
559629 AATCATAATT
Statistics
Matches: 95, Mismatches: 14, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
89 23 0.24
90 8 0.08
91 31 0.33
92 27 0.28
93 6 0.06
ACGTcount: A:0.53, C:0.14, G:0.04, T:0.29
Consensus pattern (90 bp):
TTTCATTAAAACATCAAAATTCAATTCATAAAAATTAAACCGAAATAACCAAAAGAACCCAAAAT
TAATCATCATAAATAAAAGTTCAAA
Found at i:560969 original size:21 final size:20
Alignment explanation
Indices: 560945--560993 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
560935 CCCAAAAATA
560945 TTAATTATAATTTATACTAAT
1 TTAATTATAATTTA-ACTAAT
* * *
560966 TTAATATTTAATTTAATTTAT
1 TTAAT-TATAATTTAACTAAT
560987 TTAATTA
1 TTAATTA
560994 ATCCCTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 14 0.61
22 8 0.35
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAATTATAATTTAACTAAT
Found at i:561275 original size:22 final size:21
Alignment explanation
Indices: 561245--561290 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
561235 TCATTTAAAG
* *
561245 CTCCTCTCCCTCTCTCTTTCT
1 CTCCTCTCCCTCTCCCTCTCT
561266 CTCCTTCTCCCTCTCCCTCTCT
1 CTCC-TCTCCCTCTCCCTCTCT
561288 CTC
1 CTC
561291 TCTTACTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (21 bp):
CTCCTCTCCCTCTCCCTCTCT
Found at i:571876 original size:23 final size:23
Alignment explanation
Indices: 571850--571897 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
571840 GGATTCAATG
* *
571850 TTCACTTTGATACTCGAGTTTTT
1 TTCAATTTGATACTCGAGGTTTT
* *
571873 TTCAATTTGATGCTTGAGGTTTT
1 TTCAATTTGATACTCGAGGTTTT
571896 TT
1 TT
571898 ATCCCAGTTA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (23 bp):
TTCAATTTGATACTCGAGGTTTT
Found at i:577269 original size:29 final size:29
Alignment explanation
Indices: 577205--577273 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 29
577195 TTAATAAAAG
* *
577205 TAAAATTATATTTTATCCCTTTAAAATGA
1 TAAAATTATATTTAATCCCTTAAAAATGA
* *
577234 TAAAAATT-TGATTTAATTCCTTAAAAATTA
1 T-AAAATTAT-ATTTAATCCCTTAAAAATGA
577264 TAAAATTATA
1 TAAAATTATA
577274 GACTATTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
29 9 0.27
30 24 0.73
ACGTcount: A:0.46, C:0.07, G:0.03, T:0.43
Consensus pattern (29 bp):
TAAAATTATATTTAATCCCTTAAAAATGA
Found at i:586287 original size:31 final size:31
Alignment explanation
Indices: 586252--586318 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 31
586242 GGTTAGTAAG
586252 CTATTCAAAAGTTTTCATTTAAGTCACTAAA
1 CTATTCAAAAGTTTTCATTTAAGTCACTAAA
** * *
586283 CTATTTGAAAGTTTTTATTTAAGTCACTCAA
1 CTATTCAAAAGTTTTCATTTAAGTCACTAAA
586314 CTATT
1 CTATT
586319 AATTTTTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.34, C:0.15, G:0.07, T:0.43
Consensus pattern (31 bp):
CTATTCAAAAGTTTTCATTTAAGTCACTAAA
Found at i:593900 original size:33 final size:33
Alignment explanation
Indices: 593833--593901 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
593823 TGAATTTAAC
*
593833 TTTATTGGTTCATTTGTTGCATGAAAACCTAAT
1 TTTATTGGTTCATTTGTTGCATGAAAACCAAAT
593866 TTTATTGGTTCATTTGTTGCAT-AAAACCCAAAT
1 TTTATTGGTTCATTTGTTGCATGAAAA-CCAAAT
593899 TTT
1 TTT
593902 GATTTATTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 4 0.12
33 30 0.88
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (33 bp):
TTTATTGGTTCATTTGTTGCATGAAAACCAAAT
Found at i:594973 original size:13 final size:13
Alignment explanation
Indices: 594955--594983 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
594945 TGGATTTTTT
594955 TTAAATTAAGTTG
1 TTAAATTAAGTTG
594968 TTAAATTAAGTTG
1 TTAAATTAAGTTG
594981 TTA
1 TTA
594984 TCACTTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (13 bp):
TTAAATTAAGTTG
Found at i:600144 original size:15 final size:15
Alignment explanation
Indices: 600108--600145 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
600098 TTATATTCAA
600108 AATA-AAAGTAATAT
1 AATATAAAGTAATAT
*
600122 AGATATAAAGTAATTT
1 A-ATATAAAGTAATAT
600138 AATATAAA
1 AATATAAA
600146 ATTTATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 1 0.05
15 10 0.48
16 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.32
Consensus pattern (15 bp):
AATATAAAGTAATAT
Found at i:600242 original size:68 final size:66
Alignment explanation
Indices: 600163--600293 Score: 156
Period size: 66 Copynumber: 2.0 Consensus size: 66
600153 TATTATTATA
* * *
600163 TAAATTCATTTAATAAAAAGCT-TTTTAATAGAATTAGAGTTTTTATTTATAAGTGTGATAAATT
1 TAAATTCATTTAA-AAAAA--TATTTTAATAAAATTAAAGTTTTTATTTATAAATGTGATAAATT
600227 TTCT
63 TTCT
* * * * *
600231 TAAATTTATTTAAACAAATATTTTAGTAAAATTAAATTTTTTATTTATAAATGTGATATATTT
1 TAAATTCATTTAAAAAAATATTTTAATAAAATTAAAGTTTTTATTTATAAATGTGATAAATTT
600294 CTTTAATAGA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
65 1 0.02
66 37 0.69
67 4 0.07
68 12 0.22
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (66 bp):
TAAATTCATTTAAAAAAATATTTTAATAAAATTAAAGTTTTTATTTATAAATGTGATAAATTTTC
T
Found at i:606835 original size:34 final size:32
Alignment explanation
Indices: 606791--606864 Score: 87
Period size: 34 Copynumber: 2.2 Consensus size: 32
606781 CTAAACCTAG
* * *
606791 TAAAACCCTT-AAACCATAAAAATCTATAAGCCC
1 TAAAAACCTTAAAACC-TAAAAA-ATATAAACCC
606824 ATAAAAACCTTAAAACCTAAAAAATATAAACCC
1 -TAAAAACCTTAAAACCTAAAAAATATAAACCC
606857 TAAAAACC
1 TAAAAACC
606865 AAGAATCGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
32 8 0.22
33 8 0.22
34 15 0.42
35 5 0.14
ACGTcount: A:0.55, C:0.24, G:0.01, T:0.19
Consensus pattern (32 bp):
TAAAAACCTTAAAACCTAAAAAATATAAACCC
Found at i:606846 original size:16 final size:17
Alignment explanation
Indices: 606801--606864 Score: 51
Period size: 16 Copynumber: 3.8 Consensus size: 17
606791 TAAAACCCTT
*
606801 AAACCATAAAAATCTATA
1 AAACC-TAAAAACCTATA
**
606819 AGCCCATAAAAACCT-TA
1 AAACC-TAAAAACCTATA
*
606836 AAACCTAAAAA-ATATA
1 AAACCTAAAAACCTATA
*
606852 AACCCTAAAAACC
1 AAACCTAAAAACC
606865 AAGAATCGTA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
15 1 0.03
16 18 0.50
17 5 0.14
18 12 0.33
ACGTcount: A:0.58, C:0.23, G:0.02, T:0.17
Consensus pattern (17 bp):
AAACCTAAAAACCTATA
Found at i:611664 original size:20 final size:20
Alignment explanation
Indices: 611635--611672 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
611625 TCAAAACCCA
*
611635 AAACTTTAAATATTAAACTC
1 AAACTCTAAATATTAAACTC
*
611655 AAACTCTAAATCTTAAAC
1 AAACTCTAAATATTAAAC
611673 CCCAAATCCC
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:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (20 bp):
AAACTCTAAATATTAAACTC
Found at i:611913 original size:13 final size:13
Alignment explanation
Indices: 611864--611915 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
611854 AGGTTTAGGA
*
611864 TTTAGGGTTTGGG
1 TTTATGGTTTGGG
* * *
611877 TTTAAGTTTTGGT
1 TTTATGGTTTGGG
**
611890 TTTATATTTTGGG
1 TTTATGGTTTGGG
611903 TTTATGGTTTGGG
1 TTTATGGTTTGGG
611916 ATTCTAGATT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 31 1.00
ACGTcount: A:0.12, C:0.00, G:0.33, T:0.56
Consensus pattern (13 bp):
TTTATGGTTTGGG
Found at i:614325 original size:13 final size:13
Alignment explanation
Indices: 614307--614333 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
614297 CTCTTTTATA
614307 GTTAATGAATATT
1 GTTAATGAATATT
614320 GTTAATGAATATT
1 GTTAATGAATATT
614333 G
1 G
614334 ATCAACTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.19, T:0.44
Consensus pattern (13 bp):
GTTAATGAATATT
Found at i:618225 original size:22 final size:22
Alignment explanation
Indices: 618171--618226 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
618161 GCTGGGGAAA
* *
618171 CAGTAAGCTCACACAGTGCAAT
1 CAGTAGGCACACACAGTGCAAT
*
618193 CTAATAGGCACACACAGTGCAAT
1 C-AGTAGGCACACACAGTGCAAT
618216 CAGTAGGCACA
1 CAGTAGGCACA
618227 TGAAGTGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 10 0.34
23 19 0.66
ACGTcount: A:0.38, C:0.27, G:0.20, T:0.16
Consensus pattern (22 bp):
CAGTAGGCACACACAGTGCAAT
Found at i:618236 original size:22 final size:23
Alignment explanation
Indices: 618180--618226 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
618170 ACAGTAAGCT
618180 CACACAGTGCAATCTAATAGGCA
1 CACACAGTGCAATCTAATAGGCA
*
618203 CACACAGTGCAATC-AGTAGGCA
1 CACACAGTGCAATCTAATAGGCA
618225 CA
1 CA
618227 TGAAGTGCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.38, C:0.28, G:0.19, T:0.15
Consensus pattern (23 bp):
CACACAGTGCAATCTAATAGGCA
Found at i:618915 original size:26 final size:26
Alignment explanation
Indices: 618886--618941 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
618876 AGTTCGATTG
*
618886 AACTGATTTGTGTTGGTTCAAAAGTC
1 AACTGATTTGTATTGGTTCAAAAGTC
*
618912 AACTTATTTGTATTGGTTCAAAAGTC
1 AACTGATTTGTATTGGTTCAAAAGTC
618938 AACT
1 AACT
618942 AATTCAATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.30, C:0.12, G:0.18, T:0.39
Consensus pattern (26 bp):
AACTGATTTGTATTGGTTCAAAAGTC
Found at i:623402 original size:16 final size:16
Alignment explanation
Indices: 623381--623430 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
623371 TGATGGGGAT
623381 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
623397 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
623412 -TTATTTTGGTAATTA
1 ATTATTTTGATAATTA
623427 ATTA
1 ATTA
623431 GCTAGGTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 10 0.36
15 4 0.14
16 14 0.50
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:623651 original size:25 final size:25
Alignment explanation
Indices: 623607--623675 Score: 102
Period size: 25 Copynumber: 2.7 Consensus size: 25
623597 AAAAATATTT
*
623607 AAAATTTTATATTAATTTTTTATAACA
1 AAAAATTTAT-TTAA-TTTTTATAACA
623634 AAAAATTTATTTAATTTTTATAACA
1 AAAAATTTATTTAATTTTTATAACA
*
623659 AAAAATTTATTTTATTT
1 AAAAATTTATTTAATTT
623676 AATTTTTATC
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 27 0.68
26 4 0.10
27 9 0.22
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (25 bp):
AAAAATTTATTTAATTTTTATAACA
Found at i:625236 original size:30 final size:31
Alignment explanation
Indices: 625174--625249 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 31
625164 TTAAGTTAAG
*
625174 TTTAATATTTAAATTTTCAAAACTTAATTTT
1 TTTAATATTTAAATTTTCAAAACTTAACTTT
* ** *
625205 TTTACTATTT-AATTTTCAGTATTTAAC-TT
1 TTTAATATTTAAATTTTCAAAACTTAACTTT
*
625234 TTTAATTTATTAAATT
1 TTTAATAT-TTAAATT
625250 GCAACAATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
29 8 0.22
30 15 0.42
31 13 0.36
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.58
Consensus pattern (31 bp):
TTTAATATTTAAATTTTCAAAACTTAACTTT
Found at i:636535 original size:35 final size:36
Alignment explanation
Indices: 636485--636554 Score: 106
Period size: 35 Copynumber: 2.0 Consensus size: 36
636475 CAACTTTGTG
* * *
636485 CCCACATTCATCCATGTTCACATA-ATATATATATC
1 CCCACAGTCACCCATGTTCACATACATACATATATC
636520 CCCACAGTCACCCATGTTCACATACATACATATAT
1 CCCACAGTCACCCATGTTCACATACATACATATAT
636555 GTATGTATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
35 22 0.71
36 9 0.29
ACGTcount: A:0.34, C:0.31, G:0.04, T:0.30
Consensus pattern (36 bp):
CCCACAGTCACCCATGTTCACATACATACATATATC
Found at i:648425 original size:3 final size:3
Alignment explanation
Indices: 648406--648438 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
648396 TCTTTGGCCA
648406 TAT TAT ATAT T-T TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
648439 AATATATACT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 23 0.82
4 3 0.11
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:651823 original size:17 final size:17
Alignment explanation
Indices: 651801--651860 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
651791 ATTACTTTTT
651801 TAATCTTGATATGGTAA
1 TAATCTTGATATGGTAA
* * *
651818 TAATCTTAATTATTTGT-T
1 TAATCTTGA-TA-TGGTAA
651836 TGAATCTTGATATGGTAA
1 T-AATCTTGATATGGTAA
651854 TAATCTT
1 TAATCTT
651861 AATTATTTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 17 0.52
18 6 0.18
19 10 0.30
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (17 bp):
TAATCTTGATATGGTAA
Found at i:651842 original size:36 final size:36
Alignment explanation
Indices: 651790--651886 Score: 171
Period size: 36 Copynumber: 2.7 Consensus size: 36
651780 GCCATATTTG
651790 AATTACTTT-TTT-AATCTTGATATGGTAATAATCTT
1 AATTA-TTTGTTTGAATCTTGATATGGTAATAATCTT
651825 AATTATTTGTTTGAATCTTGATATGGTAATAATCTT
1 AATTATTTGTTTGAATCTTGATATGGTAATAATCTT
651861 AATTATTTGTTTGAATCTTGATATGG
1 AATTATTTGTTTGAATCTTGATATGG
651887 AGATTAATTT
Statistics
Matches: 60, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
34 3 0.05
35 8 0.13
36 49 0.82
ACGTcount: A:0.30, C:0.06, G:0.13, T:0.51
Consensus pattern (36 bp):
AATTATTTGTTTGAATCTTGATATGGTAATAATCTT
Found at i:651843 original size:19 final size:19
Alignment explanation
Indices: 651819--651879 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
651809 ATATGGTAAT
651819 AATCTTAATTATTTGTTTG
1 AATCTTAATTATTTGTTTG
* * *
651838 AATCTTGA-TA-TGGTAAT-
1 AATCTTAATTATTTGT-TTG
651855 AATCTTAATTATTTGTTTG
1 AATCTTAATTATTTGTTTG
651874 AATCTT
1 AATCTT
651880 GATATGGAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
17 10 0.31
18 6 0.19
19 16 0.50
ACGTcount: A:0.30, C:0.07, G:0.11, T:0.52
Consensus pattern (19 bp):
AATCTTAATTATTTGTTTG
Found at i:655244 original size:30 final size:31
Alignment explanation
Indices: 655186--655251 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
655176 TGATAGAAAA
*
655186 GGACTGTTTTGTCACATTTTCAAAAGTTGAG
1 GGACTATTTTGTCACATTTTCAAAAGTTGAG
*
655217 GGACTATTTTGTCATATTTTC-AAAGTTGAG
1 GGACTATTTTGTCACATTTTCAAAAGTTGAG
655247 GGACT
1 GGACT
655252 GAAATATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (31 bp):
GGACTATTTTGTCACATTTTCAAAAGTTGAG
Found at i:657651 original size:29 final size:30
Alignment explanation
Indices: 657617--657680 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
657607 AATTAAACTC
*
657617 TATTTTTTAT-TTAATAAAT-AAATAATTTTA
1 TATTTTTTATGAT-ATAAATAAAAT-ATTTTA
657647 -ATTTTTTATGATATAAATAAAATATTTTA
1 TATTTTTTATGATATAAATAAAATATTTTA
657676 TATTT
1 TATTT
657681 AAAATGATGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (30 bp):
TATTTTTTATGATATAAATAAAATATTTTA
Found at i:657830 original size:19 final size:20
Alignment explanation
Indices: 657798--657842 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
657788 CTTTTTTGTT
*
657798 AAAATAAAT-TTAAAAATAA
1 AAAATAAATATAAAAAATAA
*
657817 AAAATTAATATAAAAAAATAA
1 AAAATAAATAT-AAAAAATAA
657838 AAAAT
1 AAAAT
657843 CGAACCGAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 1 0.05
21 13 0.59
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (20 bp):
AAAATAAATATAAAAAATAA
Found at i:658548 original size:2 final size:2
Alignment explanation
Indices: 658541--658570 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
658531 AATACATAAT
658541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
658571 AGAGATTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:674102 original size:26 final size:27
Alignment explanation
Indices: 674046--674111 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 27
674036 TTGAGAATAT
*
674046 GCTATAGATAG-TTGATTTGAGAGGAA
1 GCTATGGATAGTTTGATTTGAGAGGAA
*
674072 ACTATGGATAGTTTGA-TTGAAGAGG-A
1 GCTATGGATAGTTTGATTTG-AGAGGAA
*
674098 GCTATGGGTAGTTT
1 GCTATGGATAGTTT
674112 TAGACATTGT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
26 25 0.74
27 9 0.26
ACGTcount: A:0.30, C:0.05, G:0.32, T:0.33
Consensus pattern (27 bp):
GCTATGGATAGTTTGATTTGAGAGGAA
Found at i:676301 original size:27 final size:27
Alignment explanation
Indices: 676244--676302 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
676234 AATCACAGCT
* * *
676244 TATTATGTTATAATATTGTGTATATTT
1 TATTATGTTATAATATTGTGTAAAGTA
*
676271 TATTATGTTATAAT-TGTGTTTAAAGTA
1 TATTATGTTATAATAT-TGTGTAAAGTA
676298 TATTA
1 TATTA
676303 GTTTTTATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (27 bp):
TATTATGTTATAATATTGTGTAAAGTA
Found at i:680623 original size:30 final size:32
Alignment explanation
Indices: 680578--680645 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 32
680568 ATCCTCTCAA
* *
680578 AATTTTTTGA-AAAAATTC-ATTAAA-CCCCT
1 AATTTTTTAATAAAAAATCAATTAAATCCCCT
*
680607 -ATTTTTTAATAAAAAATCAATTAAATCCTCT
1 AATTTTTTAATAAAAAATCAATTAAATCCCCT
680638 AATTTTTT
1 AATTTTTT
680646 TCGAAATGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
28 8 0.25
29 7 0.22
30 6 0.19
31 4 0.12
32 7 0.22
ACGTcount: A:0.41, C:0.13, G:0.01, T:0.44
Consensus pattern (32 bp):
AATTTTTTAATAAAAAATCAATTAAATCCCCT
Found at i:680644 original size:31 final size:30
Alignment explanation
Indices: 680587--680644 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
680577 AAATTTTTTG
*
680587 AAAAAATTCATTAAACCCCTATTTTTTAAT
1 AAAAAATTCATTAAACCCCTAATTTTTAAT
*
680617 AAAAAA-TCAATTAAATCCTCTAATTTTT
1 AAAAAATTC-ATTAAA-CCCCTAATTTTT
680645 TTCGAAATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.08
30 12 0.50
31 10 0.42
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.40
Consensus pattern (30 bp):
AAAAAATTCATTAAACCCCTAATTTTTAAT
Found at i:701710 original size:36 final size:36
Alignment explanation
Indices: 701663--701882 Score: 370
Period size: 36 Copynumber: 6.1 Consensus size: 36
701653 CCTATTACCC
*
701663 CCATCAACATCAGATGAAACCACTTTGTTCGTAGTA
1 CCATCAACATCAGATGAAACCACTTCGTTCGTAGTA
701699 CCATCAACATCAGATGAAACCACTTCGTTCGCT-GTA
1 CCATCAACATCAGATGAAACCACTTCGTTCG-TAGTA
* *
701735 CCATCAACATCAGAGGAAACCACTTCGTTCATAGTA
1 CCATCAACATCAGATGAAACCACTTCGTTCGTAGTA
* *
701771 CCATCAACATCAGATGAAACCACTTCGTTCGTTGCA
1 CCATCAACATCAGATGAAACCACTTCGTTCGTAGTA
701807 CCATCAACATCAGATGAAACCACTTCGTTCGTAGTA
1 CCATCAACATCAGATGAAACCACTTCGTTCGTAGTA
*
701843 CCATCAACATCAGATGAAACCACTTCATTCGTAGTA
1 CCATCAACATCAGATGAAACCACTTCGTTCGTAGTA
701879 CCAT
1 CCAT
701883 TTTTTATATC
Statistics
Matches: 172, Mismatches: 10, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
35 1 0.01
36 170 0.99
37 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.25
Consensus pattern (36 bp):
CCATCAACATCAGATGAAACCACTTCGTTCGTAGTA
Found at i:703846 original size:16 final size:16
Alignment explanation
Indices: 703825--703858 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
703815 AAAACCAAGG
703825 AAATCA-AAAGTAAAAT
1 AAATCAGAAA-TAAAAT
703841 AAATCAGAAATAAAAT
1 AAATCAGAAATAAAAT
703857 AA
1 AA
703859 CCTAAACATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 14 0.82
17 3 0.18
ACGTcount: A:0.71, C:0.06, G:0.06, T:0.18
Consensus pattern (16 bp):
AAATCAGAAATAAAAT
Found at i:704224 original size:14 final size:14
Alignment explanation
Indices: 704207--704237 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
704197 AGAAAATGGA
704207 AGAGAGAAAGAGAG
1 AGAGAGAAAGAGAG
704221 AGAGAGAAAGAGAG
1 AGAGAGAAAGAGAG
704235 AGA
1 AGA
704238 AAATAAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (14 bp):
AGAGAGAAAGAGAG
Found at i:704522 original size:17 final size:17
Alignment explanation
Indices: 704500--704533 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
704490 TAGGTCGAGC
704500 TCTAACTTGAACATCTA
1 TCTAACTTGAACATCTA
704517 TCTAACTTGAACATCTA
1 TCTAACTTGAACATCTA
704534 AAGCTCGAGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (17 bp):
TCTAACTTGAACATCTA
Found at i:708599 original size:45 final size:46
Alignment explanation
Indices: 708515--708602 Score: 110
Period size: 45 Copynumber: 1.9 Consensus size: 46
708505 TTTTAAAAAT
**
708515 TAAATTTAAAAATTATATAAATAAATATTTTCATAAAATATAATAA
1 TAAATTTAAAAATTATATAAATAAATATTTAAATAAAATATAATAA
*
708561 TAAA-TTAAAAATTATATTAATATTAATA-TTAAAT-AAATATAA
1 TAAATTTAAAAATTATA-TAA-ATAAATATTTAAATAAAATATAA
708603 ATATATTAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
45 20 0.54
46 11 0.30
47 6 0.16
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (46 bp):
TAAATTTAAAAATTATATAAATAAATATTTAAATAAAATATAATAA
Found at i:708608 original size:25 final size:24
Alignment explanation
Indices: 708580--708627 Score: 87
Period size: 25 Copynumber: 2.0 Consensus size: 24
708570 AATTATATTA
708580 ATATTAATATTAAATAAATATAAAT
1 ATATTAATATTAAATAAAT-TAAAT
708605 ATATTAATATTAAATAAATTAAA
1 ATATTAATATTAAATAAATTAAA
708628 AATCCCTCCG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (24 bp):
ATATTAATATTAAATAAATTAAAT
Found at i:710473 original size:28 final size:32
Alignment explanation
Indices: 710409--710471 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
710399 GTTAATTTTT
* *
710409 TAAAAAATTAATTTTATTCAATTTTGTAATAA
1 TAAAAAATTAAATTGATTCAATTTTGTAATAA
*
710441 TAAAAAATTAAATTGATTC-ATTTTATAATAA
1 TAAAAAATTAAATTGATTCAATTTTGTAATAA
710472 AATTCCTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (32 bp):
TAAAAAATTAAATTGATTCAATTTTGTAATAA
Found at i:717368 original size:25 final size:24
Alignment explanation
Indices: 717331--717380 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 24
717321 ATAAATTCCA
717331 AATATAAATAATA-AATAATAAAATG
1 AATATAAATAATATAA-AA-AAAATG
717356 AATATGAAA-AATATAAAAAAAATG
1 AATAT-AAATAATATAAAAAAAATG
717380 A
1 A
717381 TTAGTATTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 7 0.30
25 11 0.48
26 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (24 bp):
AATATAAATAATATAAAAAAAATG
Found at i:728928 original size:13 final size:13
Alignment explanation
Indices: 728910--728934 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
728900 AAATACGTTG
728910 ATTATGATTTTAT
1 ATTATGATTTTAT
728923 ATTATGATTTTA
1 ATTATGATTTTA
728935 AAGATTCATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (13 bp):
ATTATGATTTTAT
Found at i:729183 original size:31 final size:31
Alignment explanation
Indices: 729138--729214 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
729128 GATAATATAC
*
729138 TTTTTGTATCTTGAAT-TGGATAATT-AAGTTTA
1 TTTTAGTAT-TTGAATATGG-TAATTGAA-TTTA
*
729170 TTTTGGTATTTGAATATGGTAATTGAATTTA
1 TTTTAGTATTTGAATATGGTAATTGAATTTA
*
729201 TTTTAGTTTTTGAA
1 TTTTAGTATTTGAA
729215 CTTAAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
31 27 0.68
32 13 0.32
ACGTcount: A:0.27, C:0.01, G:0.17, T:0.55
Consensus pattern (31 bp):
TTTTAGTATTTGAATATGGTAATTGAATTTA
Found at i:741135 original size:21 final size:21
Alignment explanation
Indices: 741111--741153 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
741101 TACAAATCCG
741111 TTTCATATAAAAATGAAATTT
1 TTTCATATAAAAATGAAATTT
741132 TTTCATATAAAAATGAAATTT
1 TTTCATATAAAAATGAAATTT
741153 T
1 T
741154 ATATGGATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (21 bp):
TTTCATATAAAAATGAAATTT
Found at i:741473 original size:11 final size:11
Alignment explanation
Indices: 741456--741485 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
741446 GCCTACATTA
741456 AATTTTTATAT
1 AATTTTTATAT
*
741467 TATTTTTATAT
1 AATTTTTATAT
741478 AATTTTTA
1 AATTTTTA
741486 AATATATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
AATTTTTATAT
Found at i:741635 original size:30 final size:30
Alignment explanation
Indices: 741601--741665 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
741591 GCAACTTAAA
**
741601 AACAAATGTTTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
741631 AACAAATGCCTCTAAAATAATAACAAAATT
1 AACAAATGCCTCTAAAATAATAACAAAATT
741661 AACAA
1 AACAA
741666 TAAAATAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.58, C:0.14, G:0.03, T:0.25
Consensus pattern (30 bp):
AACAAATGCCTCTAAAATAATAACAAAATT
Found at i:744242 original size:21 final size:21
Alignment explanation
Indices: 744218--744274 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
744208 AAAAATAACA
* **
744218 GTAACAGTGAAATTATTTATT
1 GTAACAGTGAGATTAAATATT
744239 GTAAC-GATGAGATTAAATATT
1 GTAACAG-TGAGATTAAATATT
*
744260 ATAACAGTGAGATTA
1 GTAACAGTGAGATTA
744275 GAAACAATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 1 0.03
21 28 0.93
22 1 0.03
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (21 bp):
GTAACAGTGAGATTAAATATT
Found at i:751133 original size:3 final size:3
Alignment explanation
Indices: 751125--751181 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
751115 TTATGTAGCA
751125 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
751172 ATT ATT ATT A
1 ATT ATT ATT A
751182 AATTATATTT
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:751584 original size:22 final size:23
Alignment explanation
Indices: 751535--751584 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
751525 ATTATATTAT
751535 TAAATTATTACACAAGATTCAAC
1 TAAATTATTACACAAGATTCAAC
751558 TAAATTATTACAC-AGATATCAAC
1 TAAATTATTACACAAGAT-TCAAC
751581 -AAAT
1 TAAAT
751585 CGGTTCAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 8 0.31
23 18 0.69
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.30
Consensus pattern (23 bp):
TAAATTATTACACAAGATTCAAC
Found at i:756864 original size:19 final size:19
Alignment explanation
Indices: 756840--756876 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
756830 TCTTAATAAA
*
756840 TAATAATTTGATTTGAATG
1 TAATAATTTAATTTGAATG
756859 TAATAATTTAATTTGAAT
1 TAATAATTTAATTTGAAT
756877 ATGGACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.49
Consensus pattern (19 bp):
TAATAATTTAATTTGAATG
Found at i:762289 original size:2 final size:2
Alignment explanation
Indices: 762240--762277 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
762230 CATGTAACAA
762240 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
762278 GCACGTATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:766731 original size:18 final size:18
Alignment explanation
Indices: 766708--766748 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
766698 TAGTATATAA
766708 TATATTAAT-TATTATCAT
1 TATATTAATAT-TTATCAT
*
766726 TATATTAATATTTATTAT
1 TATATTAATATTTATCAT
766744 TATAT
1 TATAT
766749 GGATTGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTAATATTTATCAT
Found at i:767510 original size:27 final size:27
Alignment explanation
Indices: 767471--767523 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
767461 AAAAAATACT
*
767471 TGACACCAGTGGAGGAACACCAAGTGG
1 TGACACCAATGGAGGAACACCAAGTGG
* *
767498 TGACACCAATGGAGGAATATCAAGTG
1 TGACACCAATGGAGGAACACCAAGTG
767524 ACGGCATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.19, G:0.30, T:0.15
Consensus pattern (27 bp):
TGACACCAATGGAGGAACACCAAGTGG
Found at i:767764 original size:21 final size:20
Alignment explanation
Indices: 767735--767773 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
767725 AAGAAAAAAG
*
767735 AGAAAGGAAGAAGGAGAAGA
1 AGAAAGGAAAAAGGAGAAGA
*
767755 AGAAAGGGAAAAATGAGAA
1 AGAAA-GGAAAAAGGAGAA
767774 AGAAAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.03
Consensus pattern (20 bp):
AGAAAGGAAAAAGGAGAAGA
Found at i:767773 original size:35 final size:32
Alignment explanation
Indices: 767712--767775 Score: 83
Period size: 35 Copynumber: 1.9 Consensus size: 32
767702 AACTAAAATT
767712 GAAGGAAAAAAGAAAGAAAAAAGAGAAAGGAA
1 GAAGGAAAAAAGAAAGAAAAAAGAGAAAGGAA
* *
767744 GAAGGAGAAGAAGAAAGGGAAAAATGAGAAAG
1 GAAGGA-AAAAAGAAA--GAAAAAAGAGAAAG
767776 AAAAAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 6 0.22
33 8 0.30
35 13 0.48
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.02
Consensus pattern (32 bp):
GAAGGAAAAAAGAAAGAAAAAAGAGAAAGGAA
Found at i:768304 original size:94 final size:95
Alignment explanation
Indices: 768127--768404 Score: 399
Period size: 94 Copynumber: 3.0 Consensus size: 95
768117 TTTACTTTAA
* * *
768127 TTTAATTTTTGCTCGTTAGTAATTTTATTTTGTTGTTAGTAGT--AGTAAGTAAAAAATATTGTT
1 TTTAAATTTTACTAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGAGTAAGTAAAAAATATTGTT
*
768190 CATATTTATTGATTTAAAATTTAATAATG-
66 CATATTTATTGATTTAAAATTAAATAATGT
*
768219 TTTAAATTTTACTAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGAGTAAGTAAAAAATATTATT
1 TTTAAATTTTACTAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGAGTAAGTAAAAAATATTGTT
768284 CATATTTATTGATTTAAAATTAAATAATGT
66 CATATTTATTGATTTAAAATTAAATAATGT
** * * *
768314 TTTAAA--AAATTAGTTAGTAATTTTATTTTTTTGTTAGTAAGTAGTAGTAAATAAAAAATATTG
1 TTTAAATTTTACTAGTTAGTAATTTTATTTTGTTGTTAGT-AGTAG-AGTAAGTAAAAAATATTG
768377 TTCATATTTATTGATTTAAAA--AAATAAT
64 TTCATATTTATTGATTTAAAATTAAATAAT
768405 ATAATATTTT
Statistics
Matches: 170, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
92 40 0.24
93 35 0.21
94 52 0.31
95 43 0.25
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.49
Consensus pattern (95 bp):
TTTAAATTTTACTAGTTAGTAATTTTATTTTGTTGTTAGTAGTAGAGTAAGTAAAAAATATTGTT
CATATTTATTGATTTAAAATTAAATAATGT
Found at i:768634 original size:16 final size:16
Alignment explanation
Indices: 768589--768638 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
768579 TAAACCTAAT
*
768589 TAATTAATTACCAAAA
1 TAATTAATTATCAAAA
*
768605 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
768619 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
768635 TAAT
1 TAAT
768639 ACTCCATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 2 0.07
16 12 0.44
17 3 0.11
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:787468 original size:14 final size:14
Alignment explanation
Indices: 787449--787475 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
787439 TCAAATTAAG
787449 CTTTAATTTTTATA
1 CTTTAATTTTTATA
787463 CTTTAATTTTTAT
1 CTTTAATTTTTAT
787476 CATTTGGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (14 bp):
CTTTAATTTTTATA
Found at i:797014 original size:3 final size:3
Alignment explanation
Indices: 797008--797057 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
796998 TTATATTATT
* * *
797008 ATA ATA ATA ACA TTA A-A ATTA ACA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
797053 ATA AT
1 ATA AT
797058 TTCTCTTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 35 0.90
4 2 0.05
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:800898 original size:18 final size:18
Alignment explanation
Indices: 800885--800920 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
800875 TTATTTTATA
800885 AAAAAATTAAATTTTTAC
1 AAAAAATTAAATTTTTAC
*
800903 AATAAATTAAATTATTTA
1 AAAAAATTAAATT-TTTA
800921 ATTATAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
AAAAAATTAAATTTTTAC
Found at i:800900 original size:19 final size:18
Alignment explanation
Indices: 800878--800921 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
800868 TGTAATTTTA
800878 TTTTATAAAAAAATTAAAT
1 TTTTA-AAAAAAATTAAAT
* *
800897 TTTTACAATAAATTAAAT
1 TTTTAAAAAAAATTAAAT
800915 TATTTAA
1 T-TTTAA
800922 TTATAAGGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
TTTTAAAAAAAATTAAAT
Found at i:815705 original size:25 final size:26
Alignment explanation
Indices: 815670--815719 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
815660 AAAACTTGGA
815670 AAAAATATTTAT-TTTTTTGAATTTTT
1 AAAAATATTTATATTTTTT-AATTTTT
815696 AAAAAT-TTTATGATTTTTTAATTT
1 AAAAATATTTAT-ATTTTTTAATTT
815720 ATGATTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.23
26 11 0.50
27 6 0.27
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (26 bp):
AAAAATATTTATATTTTTTAATTTTT
Found at i:815774 original size:40 final size:40
Alignment explanation
Indices: 815699--815774 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
815689 AATTTTTAAA
* *
815699 AATTTTATGATTTTTTAATTTATGATTTTTTGTTTTCTAT
1 AATTTTAAGATTTTTTAATTTATGATTTTTAGTTTTCTAT
**
815739 AATTTTAAGATTTTTTTTTTTATG-TTTTATAGTTTT
1 AATTTTAAGATTTTTTAATTTATGATTTT-TAGTTTT
815775 AAATTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 4 0.13
40 27 0.87
ACGTcount: A:0.22, C:0.01, G:0.08, T:0.68
Consensus pattern (40 bp):
AATTTTAAGATTTTTTAATTTATGATTTTTAGTTTTCTAT
Found at i:815901 original size:41 final size:41
Alignment explanation
Indices: 815856--815985 Score: 113
Period size: 41 Copynumber: 3.1 Consensus size: 41
815846 ATGTATTCAA
815856 ACATATGGATTGAATTTCAAAATTATGATATTAATTTTCTT
1 ACATATGGATTGAATTTCAAAATTATGATATTAATTTTCTT
* * * * **
815897 ACATAT--TTTCAAAATTCAAATATATAT-ATATATATATATTCAA
1 ACATATGGATT-GAATTTCAAA-AT-TATGATAT-TA-ATTTTCTT
* * *
815940 ACATATGGATTGATTTTCAAAACTATGATATTAAATTTCTT
1 ACATATGGATTGAATTTCAAAATTATGATATTAATTTTCTT
815981 ACATA
1 ACATA
815986 CTTTCAAAAT
Statistics
Matches: 66, Mismatches: 15, Indels: 16
0.68 0.15 0.16
Matches are distributed among these distances:
39 2 0.03
40 8 0.12
41 21 0.32
42 10 0.15
43 16 0.24
44 7 0.11
45 2 0.03
ACGTcount: A:0.42, C:0.09, G:0.06, T:0.43
Consensus pattern (41 bp):
ACATATGGATTGAATTTCAAAATTATGATATTAATTTTCTT
Found at i:815967 original size:84 final size:84
Alignment explanation
Indices: 815849--816011 Score: 290
Period size: 84 Copynumber: 1.9 Consensus size: 84
815839 CAAATACATG
* * *
815849 TATTCAAACATATGGATTGAATTTCAAAATTATGATATTAATTTTCTTACATATTTTCAAAATTC
1 TATTCAAACATATGGATTGAATTTCAAAACTATGATATTAAATTTCTTACATACTTTCAAAATTC
815914 AAATATATATATATATATA
66 AAATATATATATATATATA
*
815933 TATTCAAACATATGGATTGATTTTCAAAACTATGATATTAAATTTCTTACATACTTTCAAAATTC
1 TATTCAAACATATGGATTGAATTTCAAAACTATGATATTAAATTTCTTACATACTTTCAAAATTC
815998 AAATATATATATAT
66 AAATATATATATAT
816012 TCAAATATAT
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
84 75 1.00
ACGTcount: A:0.42, C:0.10, G:0.05, T:0.43
Consensus pattern (84 bp):
TATTCAAACATATGGATTGAATTTCAAAACTATGATATTAAATTTCTTACATACTTTCAAAATTC
AAATATATATATATATATA
Found at i:820433 original size:20 final size:21
Alignment explanation
Indices: 820394--820433 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
820384 ATAACACAGT
*
820394 TAATATTTTGGAACAATTTATA
1 TAATATTTT-GAAAAATTTATA
820416 TAATATTTT-AAAAATTTA
1 TAATATTTTGAAAAATTTA
820434 AGTACCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (21 bp):
TAATATTTTGAAAAATTTATA
Found at i:828350 original size:112 final size:112
Alignment explanation
Indices: 828180--828403 Score: 421
Period size: 112 Copynumber: 2.0 Consensus size: 112
828170 TTATTCATTG
828180 CTCACTTTTTCTTAGTGATGTGGTATGGTTATGTTAACTCTCAAGTCTTTTAACGGCTAGTTTAC
1 CTCACTTTTTCTTAGTGATGTGGTATGGTTATGTTAACTCTCAAGTCTTTTAACGGCTAGTTTAC
828245 CATTGAGGTTGAAAAGTGTTTTTGATATGTTTGATAATGTTTACCAT
66 CATTGAGGTTGAAAAGTGTTTTTGATATGTTTGATAATGTTTACCAT
* *
828292 CTCACTTTTTCTTAGTGATGTGGTATGGTTATGTTATCTCTCAAGTGTTTTAACGGCTAGTTTAC
1 CTCACTTTTTCTTAGTGATGTGGTATGGTTATGTTAACTCTCAAGTCTTTTAACGGCTAGTTTAC
*
828357 CATTGAGGTTGAAAAGTGTTTTTGATATGTTTGATAATGTTTGCCAT
66 CATTGAGGTTGAAAAGTGTTTTTGATATGTTTGATAATGTTTACCAT
828404 TGCTGTCAAA
Statistics
Matches: 109, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
112 109 1.00
ACGTcount: A:0.22, C:0.12, G:0.21, T:0.45
Consensus pattern (112 bp):
CTCACTTTTTCTTAGTGATGTGGTATGGTTATGTTAACTCTCAAGTCTTTTAACGGCTAGTTTAC
CATTGAGGTTGAAAAGTGTTTTTGATATGTTTGATAATGTTTACCAT
Found at i:832174 original size:16 final size:14
Alignment explanation
Indices: 832143--832183 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
832133 ATTTGAAGAA
832143 TATTA-TTTAAAAT
1 TATTATTTTAAAAT
*
832156 TATTATTTTAAAAA
1 TATTATTTTAAAAT
832170 T-TTATTATTAAAAT
1 TATTATT-TTAAAAT
832184 AAAATTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTATTTTAAAAT
Found at i:832288 original size:17 final size:18
Alignment explanation
Indices: 832251--832289 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
832241 ATTTTATATT
**
832251 AATATTTTAATAAATTTA
1 AATATTTTAATAAATAAA
832269 AATATTTTAA-AAATAAA
1 AATATTTTAATAAATAAA
832286 AATA
1 AATA
832290 AAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATTTTAATAAATAAA
Found at i:832642 original size:28 final size:28
Alignment explanation
Indices: 832602--832655 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
832592 TAAAATAATG
*
832602 ATGGATGAGTGGTTAAATTTGGATAACT
1 ATGGATGAGTGGTTAAATGTGGATAACT
*
832630 ATGGAT-AGATGGTTAAGTGTGGATAA
1 ATGGATGAG-TGGTTAAATGTGGATAA
832656 TGGTAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 2 0.09
28 21 0.91
ACGTcount: A:0.33, C:0.02, G:0.31, T:0.33
Consensus pattern (28 bp):
ATGGATGAGTGGTTAAATGTGGATAACT
Found at i:837374 original size:11 final size:11
Alignment explanation
Indices: 837360--837384 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
837350 AACCAAATTT
837360 TTTTTAATAAA
1 TTTTTAATAAA
837371 TTTTTAATAAA
1 TTTTTAATAAA
837382 TTT
1 TTT
837385 AATAAATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTTAATAAA
Found at i:841699 original size:21 final size:22
Alignment explanation
Indices: 841658--841701 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
841648 AAAATAAAAA
841658 ATATATTTTTAATTGATATTTC
1 ATATATTTTTAATTGATATTTC
841680 ATATATTTTATAATT-A-ATTTC
1 ATATATTTT-TAATTGATATTTC
841701 A
1 A
841702 AGTAAAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 6 0.29
22 10 0.48
23 5 0.24
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (22 bp):
ATATATTTTTAATTGATATTTC
Found at i:843124 original size:30 final size:32
Alignment explanation
Indices: 843061--843125 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
843051 AAATTATAAC
****
843061 ATATAATAATTTCAATAAATGAAGTTGTCTAT
1 ATATAATAATTTCAATAAATGAAAAAATCTAT
843093 ATATAA-AATTTCAATAAATGAAAAAAT-TAT
1 ATATAATAATTTCAATAAATGAAAAAATCTAT
843123 ATA
1 ATA
843126 AAATTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 6 0.21
31 17 0.59
32 6 0.21
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (32 bp):
ATATAATAATTTCAATAAATGAAAAAATCTAT
Found at i:848243 original size:190 final size:191
Alignment explanation
Indices: 847920--848297 Score: 636
Period size: 190 Copynumber: 2.0 Consensus size: 191
847910 GATAAGTCAC
847920 CTTTACTACTACTCTATAAACTTGCACATGAGATTTTCACCCCATACAGCTCCTCGTTCAATTCT
1 CTTTACTACTACTCTATAAACTTGCACATGAGATTTTCACCCCATACAGCTCCTCGTTCAATTCT
* *
847985 TTCAAAGTTTTTAGGTCCTTTTCCTCATTCAAGAATCTCTTCTTTTCTTCCACTCTGTCTCGAAG
66 TTCAAAGTTATTAGGTCCTTTTCCTCATTCAAGAATCTCTTCCTTTCTTCCACTCTGTCTCGAAG
* *
848050 AGTAATGAGGACAAATTCAATTATGTTTTCATGTTCCAATTGAACAC-TTGCATTTTTCAT
131 AGTAATGAGGACAAATTCAATCACGTTTTCATGTTCCAATTGAACACTTTGCATTTTTCAT
* * *
848110 CTTTACTGCTACTCTATAGAA-TCT-CACATGAGATTTTCACCCCATACGGTTCCTCGTTCAATT
1 CTTTACTACTACTCTATA-AACT-TGCACATGAGATTTTCACCCCATACAGCTCCTCGTTCAATT
* *
848173 CTTTCAAAGTTATTAGGTCCTTTTCCTCGTTCGAGAATCTCTTCCTTTCTTCCACTCTGTCTCGA
64 CTTTCAAAGTTATTAGGTCCTTTTCCTCATTCAAGAATCTCTTCCTTTCTTCCACTCTGTCTCGA
848238 AGAGTAATGAGGACAAATTCAATCACGTTTTCATGTTCCAATTGAACACTTTGCATTTTT
129 AGAGTAATGAGGACAAATTCAATCACGTTTTCATGTTCCAATTGAACACTTTGCATTTTT
848298 ATTATTCTCA
Statistics
Matches: 176, Mismatches: 9, Indels: 5
0.93 0.05 0.03
Matches are distributed among these distances:
190 163 0.93
191 13 0.07
ACGTcount: A:0.24, C:0.25, G:0.12, T:0.39
Consensus pattern (191 bp):
CTTTACTACTACTCTATAAACTTGCACATGAGATTTTCACCCCATACAGCTCCTCGTTCAATTCT
TTCAAAGTTATTAGGTCCTTTTCCTCATTCAAGAATCTCTTCCTTTCTTCCACTCTGTCTCGAAG
AGTAATGAGGACAAATTCAATCACGTTTTCATGTTCCAATTGAACACTTTGCATTTTTCAT
Found at i:849120 original size:12 final size:12
Alignment explanation
Indices: 849087--849145 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
849077 ATTCATGAAC
849087 AAGCTCGTTTAT
1 AAGCTCGTTTAT
* *
849099 -TGACTTGTTTAT
1 AAG-CTCGTTTAT
849111 AAGCTCGTTTATT
1 AAGCTCGTTTA-T
*
849124 AA-TTCGTTTAT
1 AAGCTCGTTTAT
849135 -AGCTCGTTTAT
1 AAGCTCGTTTAT
849146 TTATTAATGA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
10 1 0.03
11 10 0.27
12 22 0.59
13 4 0.11
ACGTcount: A:0.22, C:0.14, G:0.15, T:0.49
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:849142 original size:23 final size:24
Alignment explanation
Indices: 849087--849146 Score: 88
Period size: 24 Copynumber: 2.5 Consensus size: 24
849077 ATTCATGAAC
*
849087 AAGCTCGTTTATTGACTTGTTTAT
1 AAGCTCGTTTATTGAATTGTTTAT
849111 AAGCTCGTTTATT-AATTCGTTTAT
1 AAGCTCGTTTATTGAATT-GTTTAT
849135 -AGCTCGTTTATT
1 AAGCTCGTTTATT
849147 TATTAATGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
23 15 0.44
24 19 0.56
ACGTcount: A:0.22, C:0.13, G:0.15, T:0.50
Consensus pattern (24 bp):
AAGCTCGTTTATTGAATTGTTTAT
Found at i:849310 original size:23 final size:23
Alignment explanation
Indices: 849273--849338 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
849263 GTTCATGAAT
* *
849273 ATGTTCGTGACCATGTTCGTTTA
1 ATGTTCATGAACATGTTCGTTTA
*
849296 ATGTTCATGAACATGTTCGATTA
1 ATGTTCATGAACATGTTCGTTTA
* *
849319 A-GTTAAGTGAATATGTTCGT
1 ATGTTCA-TGAACATGTTCGT
849339 GAACATTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.11
23 32 0.89
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (23 bp):
ATGTTCATGAACATGTTCGTTTA
Found at i:849676 original size:26 final size:26
Alignment explanation
Indices: 849615--849679 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
849605 AGAAATATTA
** *
849615 AATTAACATCGATTAAATTTTAATTC
1 AATTAACATTAATTAAATCTTAATTC
* *
849641 AATCAACATTAATTAAATCTTAATTT
1 AATTAACATTAATTAAATCTTAATTC
849667 AATTAACATTAAT
1 AATTAACATTAAT
849680 ATTAATTATC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.46, C:0.11, G:0.02, T:0.42
Consensus pattern (26 bp):
AATTAACATTAATTAAATCTTAATTC
Found at i:849685 original size:21 final size:21
Alignment explanation
Indices: 849672--849716 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
849662 AATTTAATTA
*
849672 ACATTAATATTAATTATCAGT
1 ACATTAATATTAATTATAAGT
*
849693 ACATTAATATTAATTATCAGT
1 ACATTAATATTAATTATAAGT
849714 ACA
1 ACA
849717 ACAAAACGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.44, C:0.11, G:0.04, T:0.40
Consensus pattern (21 bp):
ACATTAATATTAATTATAAGT
Found at i:859091 original size:10 final size:10
Alignment explanation
Indices: 859076--859107 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
859066 GAAATTTTTT
859076 GACTCGATTC
1 GACTCGATTC
859086 GACTCGATTC
1 GACTCGATTC
*
859096 GATTCGATTC
1 GACTCGATTC
859106 GA
1 GA
859108 AAAAATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (10 bp):
GACTCGATTC
Found at i:863366 original size:24 final size:22
Alignment explanation
Indices: 863315--863366 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
863305 ATTTAATTTG
863315 GTCCTTAATTATTTATTTTAGT
1 GTCCTTAATTATTTATTTTAGT
**
863337 ACCCTTAA-TATTTATATTACTAGT
1 GTCCTTAATTATTTAT-TT--TAGT
863361 GTCCTT
1 GTCCTT
863367 TTCTCTAATC
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
21 7 0.30
22 8 0.35
24 8 0.35
ACGTcount: A:0.25, C:0.15, G:0.08, T:0.52
Consensus pattern (22 bp):
GTCCTTAATTATTTATTTTAGT
Found at i:864632 original size:14 final size:14
Alignment explanation
Indices: 864613--864639 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
864603 GAATAGGTTG
864613 TTAATTAATTAAAT
1 TTAATTAATTAAAT
864627 TTAATTAATTAAA
1 TTAATTAATTAAA
864640 AATTTTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
TTAATTAATTAAAT
Found at i:867983 original size:2 final size:2
Alignment explanation
Indices: 867976--868000 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
867966 TTTATTTGAG
867976 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 A
868001 GTATTAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:868981 original size:13 final size:15
Alignment explanation
Indices: 868956--868989 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
868946 AAAATCAATG
868956 TATTTTTCAGAAATC
1 TATTTTTCAGAAATC
868971 -ATTTTTC-GAAATC
1 TATTTTTCAGAAATC
868984 TATTTT
1 TATTTT
868990 CAATGAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (15 bp):
TATTTTTCAGAAATC
Found at i:870686 original size:2 final size:2
Alignment explanation
Indices: 870642--870675 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
870632 AAATTTCACT
870642 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
870676 ATTTTTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:871447 original size:25 final size:29
Alignment explanation
Indices: 871420--871473 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
871410 TACCCATATA
871420 ATAT-AAAAAT-AATTAATTACGAAAAAT
1 ATATAAAAAATAAATTAATTACGAAAAAT
*
871447 ATATAAAAAATAAATTAATTATGAAAA
1 ATATAAAAAATAAATTAATTACGAAAA
871474 TGGGTATTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 4 0.17
28 6 0.25
29 14 0.58
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.30
Consensus pattern (29 bp):
ATATAAAAAATAAATTAATTACGAAAAAT
Found at i:873811 original size:59 final size:61
Alignment explanation
Indices: 873731--873857 Score: 179
Period size: 59 Copynumber: 2.1 Consensus size: 61
873721 TTAAATATTA
873731 TTTTATAATTTTTAGAATTAGAATTAAAATAAAAAAAT-TGTAAACATT-AAGAGCTAAATT
1 TTTTATAATTTTTAGAATTAGAATTAAAATAAAAAAATATGTAAACATTGAAG-GCTAAATT
* * * *
873791 TTTTA-AATTTTTAGATTTAGAATTAAACTAATAGAATATGTAAACATTGGAAGGCTAAATT
1 TTTTATAATTTTTAGAATTAGAATTAAAATAAAAAAATATGTAAACATT-GAAGGCTAAATT
873852 TTTTAT
1 TTTTAT
873858 TAGACTAGAA
Statistics
Matches: 59, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
59 28 0.47
60 15 0.25
61 13 0.22
62 3 0.05
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (61 bp):
TTTTATAATTTTTAGAATTAGAATTAAAATAAAAAAATATGTAAACATTGAAGGCTAAATT
Found at i:874918 original size:21 final size:22
Alignment explanation
Indices: 874887--874930 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
874877 ATGCTTATGA
874887 AAGTCATAAACCTATGCTATAT
1 AAGTCATAAACCTATGCTATAT
*
874909 AAGTC-TAAACCTATGTTATAT
1 AAGTCATAAACCTATGCTATAT
874930 A
1 A
874931 TAAATATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (22 bp):
AAGTCATAAACCTATGCTATAT
Found at i:876524 original size:2 final size:2
Alignment explanation
Indices: 876517--876580 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
876507 TAAATGTTGG
876517 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
876559 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
876581 TTATTGGTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:882527 original size:189 final size:189
Alignment explanation
Indices: 882286--882640 Score: 527
Period size: 189 Copynumber: 1.9 Consensus size: 189
882276 GCATCCTGAA
* * * *
882286 ATTTCTGGGAATTCGACTATTGGGCAATGGCTGAGATCTAGATCACGAAGGGAATCCGTCTTGAT
1 ATTTCTGGGAATTCGACTATTGGACAATGACTAAGATCTAGAACACGAAGGGAATCCGTCTTGAT
* * *
882351 CGATACAGTTTTTACCTTTGAGCCACTCATAGCTAAG-GTCTGAAGATTACCTAGAGAGTCGAAA
66 CGATACAGTTTTTACCCTTGAGCCACTCATAGCTAAGATTC-GAAGATTACCTAGAAAGTCGAAA
882415 GACAAGCACACCTCTTCAATTTGAGTTCCAGATAAGTATAATTTTTTTAAACCTCTTGGG
130 GACAAGCACACCTCTTCAATTTGAGTTCCAGATAAGTATAATTTTTTTAAACCTCTTGGG
* *
882475 ATTTC-GGGAAATTTGACTATTGGACAATGATTAAGAT-TCAGAACACGAAGGGAATCCGTCTTG
1 ATTTCTGGG-AATTCGACTATTGGACAATGACTAAGATCT-AGAACACGAAGGGAATCCGTCTTG
* * * * *
882538 ATCGATACATTTTTTACCCTTGAGTCACTCATATCTAAGATTCGAAGATTACTTAGAAAGTCGAG
64 ATCGATACAGTTTTTACCCTTGAGCCACTCATAGCTAAGATTCGAAGATTACCTAGAAAGTCGAA
*
882603 AGACAGGCACACCTCTTCAATTTGAGTTCCAGATAAGT
129 AGACAAGCACACCTCTTCAATTTGAGTTCCAGATAAGT
882641 CCAATTCTAT
Statistics
Matches: 148, Mismatches: 15, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
188 4 0.03
189 142 0.96
190 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (189 bp):
ATTTCTGGGAATTCGACTATTGGACAATGACTAAGATCTAGAACACGAAGGGAATCCGTCTTGAT
CGATACAGTTTTTACCCTTGAGCCACTCATAGCTAAGATTCGAAGATTACCTAGAAAGTCGAAAG
ACAAGCACACCTCTTCAATTTGAGTTCCAGATAAGTATAATTTTTTTAAACCTCTTGGG
Found at i:894057 original size:189 final size:188
Alignment explanation
Indices: 893736--894191 Score: 533
Period size: 189 Copynumber: 2.4 Consensus size: 188
893726 CTTTTGAATG
* * * *
893736 CTTGAGCCGCTCATCTTTAA-GTCTTGAAGATTACTGAGAGAGTCTAA-AGACAAGGACGCTTCT
1 CTTGAGCCACTCATATTTAAGGTC-TGAAGATTACT-AGAGAGTC-AAGAGACAAGGACACCTCT
* * * * *
893799 TTAATTTGAGTCCCAGATAAATCTAATTCTCTTAAGCATCCTGGAATTTCTGGGAATTCGAGAAT
63 TCAATTTGAGTTCCAGATAAATCTAATTCTCTTAAACATCCTGGAATTTCTGGGAATTCAACAAT
* * *
893864 TGGGCAACCACTGAGATCCAGATTATGAAGGGATTCCATCTTGATCGATACATTTTTTACC
128 TGGGCAACCACTAAGATCCAGATCACGAAGGGATTCCATCTTGATCGATACATTTTTTACC
*
893925 TTTGAGCCACTCATATTTAAGGTCTGAAGATTACCTAGAGAGTCAAGAGACAAGGACACCTCTTC
1 CTTGAGCCACTCATATTTAAGGTCTGAAGATTA-CTAGAGAGTCAAGAGACAAGGACACCTCTTC
* * ** * * * *
893990 AATTTGAGTTCCAGATAAATCTAATTTTGTTAAATTTCTTGGGATTTC-GGGAAATTTAACTATT
65 AATTTGAGTTCCAGATAAATCTAATTCTCTTAAACATCCTGGAATTTCTGGG-AATTCAACAATT
*** * * *
894054 GGGCAATGGCTAAGATTCAGCTCACGAAGGGATTCCATCTTGATGGATACATTTTTTACC
129 GGGCAACCACTAAGATCCAGATCACGAAGGGATTCCATCTTGATCGATACATTTTTTACC
* * * * *
894114 CTTGAGCCACTCATATTTAAGATCTCAAGATTATTTGGAGAGTCGAGAGAC-AGGCACACCTCTT
1 CTTGAGCCACTCATATTTAAGGTCTGAAGATTA-CTAGAGAGTCAAGAGACAAGG-ACACCTCTT
894178 CAATTTGAGTTCCA
64 CAATTTGAGTTCCA
894192 CGTAAGTTCA
Statistics
Matches: 228, Mismatches: 34, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
188 8 0.04
189 215 0.94
190 5 0.02
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (188 bp):
CTTGAGCCACTCATATTTAAGGTCTGAAGATTACTAGAGAGTCAAGAGACAAGGACACCTCTTCA
ATTTGAGTTCCAGATAAATCTAATTCTCTTAAACATCCTGGAATTTCTGGGAATTCAACAATTGG
GCAACCACTAAGATCCAGATCACGAAGGGATTCCATCTTGATCGATACATTTTTTACC
Found at i:894220 original size:189 final size:189
Alignment explanation
Indices: 893736--894250 Score: 531
Period size: 189 Copynumber: 2.7 Consensus size: 189
893726 CTTTTGAATG
* * * * *
893736 CTTGAGCCGCTCATCTTTAAG-TCTTGAAGATTA-CTGAGAGAGTCTAA-AGACAAGGACGCTTC
1 CTTGAGCCACTCATATTTAAGATC-TCAAGATTACCT-AGAGAGTC-AAGAGACAAGGACACCTC
* * ** * * * * * **
893798 TTTAATTTGAGTCCCAGATAAATCTAATTCTCTTAAGCATCCTGGAATTTCTGGG-AATTCGAGA
63 TTCAATTTGAGTTCCAGATAAATCTAATGATCTTAAACTTCTTGGGATTTC-GGGAAATTCAACC
* *** * * * * *
893862 ATTGGGCAACCACTGAGATCCAGATTATGAAGGGATTCCATCTTGATCGATACATTTTTTACC
127 ACTGGGCAATGGCTAAGATTCAGCTCACGAAGGGATTCCATCTTGATCGATACATTTTTTACC
* * *
893925 TTTGAGCCACTCATATTTAAGGTCTGAAGATTACCTAGAGAGTCAAGAGACAAGGACACCTCTTC
1 CTTGAGCCACTCATATTTAAGATCTCAAGATTACCTAGAGAGTCAAGAGACAAGGACACCTCTTC
** * * * * *
893990 AATTTGAGTTCCAGATAAATCTAATTTTGTTAAATTTCTTGGGATTTCGGGAAATTTAACTATTG
66 AATTTGAGTTCCAGATAAATCTAATGATCTTAAACTTCTTGGGATTTCGGGAAATTCAACCACTG
*
894055 GGCAATGGCTAAGATTCAGCTCACGAAGGGATTCCATCTTGATGGATACATTTTTTACC
131 GGCAATGGCTAAGATTCAGCTCACGAAGGGATTCCATCTTGATCGATACATTTTTTACC
** * *
894114 CTTGAGCCACTCATATTTAAGATCTCAAGATTATTTGGAGAGTCGAGAGAC-AGGCACACCTCTT
1 CTTGAGCCACTCATATTTAAGATCTCAAGATTACCTAGAGAGTCAAGAGACAAGG-ACACCTCTT
* * *
894178 CAATTTGAGTTCCACG-TAAGT-TCAATGATCTTAAGCTTCTTGGGATTTCTGGAAATTCAACCA
65 CAATTTGAGTTCCA-GATAAATCT-AATGATCTTAAACTTCTTGGGATTTCGGGAAATTCAACCA
894241 CTGGGCAATG
128 CTGGGCAATG
894251 ACAAAGAGCT
Statistics
Matches: 275, Mismatches: 44, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
188 9 0.03
189 261 0.95
190 5 0.02
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (189 bp):
CTTGAGCCACTCATATTTAAGATCTCAAGATTACCTAGAGAGTCAAGAGACAAGGACACCTCTTC
AATTTGAGTTCCAGATAAATCTAATGATCTTAAACTTCTTGGGATTTCGGGAAATTCAACCACTG
GGCAATGGCTAAGATTCAGCTCACGAAGGGATTCCATCTTGATCGATACATTTTTTACC
Found at i:899841 original size:28 final size:28
Alignment explanation
Indices: 899809--899872 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
899799 AATTTACAAA
* *
899809 AATTAGATCAAATCAAAAATACA-TATAT
1 AATTACATAAAATCAAAAATA-AGTATAT
*
899837 AATTACATAAAATCAAAGATAATGTATAT
1 AATTACATAAAATCAAAAATAA-GTATAT
899866 AATTACA
1 AATTACA
899873 CATTAAACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 18 0.58
29 12 0.39
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (28 bp):
AATTACATAAAATCAAAAATAAGTATAT
Found at i:904365 original size:55 final size:55
Alignment explanation
Indices: 904300--904410 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
904290 AAAATGTTTA
904300 AGTATGAAACAATAGATTCAAATCAAGAAATGGAAACTGGTTAATTAGAGTTTGG
1 AGTATGAAACAATAGATTCAAATCAAGAAATGGAAACTGGTTAATTAGAGTTTGG
*
904355 AGTATGAAACAATAGATTCAAATCAAGAAATGGAAACTGGTTGATTAGAGTTTGG
1 AGTATGAAACAATAGATTCAAATCAAGAAATGGAAACTGGTTAATTAGAGTTTGG
904410 A
1 A
904411 TTTTCTGCAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.43, C:0.07, G:0.23, T:0.27
Consensus pattern (55 bp):
AGTATGAAACAATAGATTCAAATCAAGAAATGGAAACTGGTTAATTAGAGTTTGG
Found at i:905019 original size:8 final size:9
Alignment explanation
Indices: 904993--905023 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
904983 GAATTAAATA
904993 ATTCGAGTT
1 ATTCGAGTT
905002 ATTCGAGTT
1 ATTCGAGTT
905011 ATT-GAGTT
1 ATTCGAGTT
905019 ATTCG
1 ATTCG
905024 GAGCGATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.45
Consensus pattern (9 bp):
ATTCGAGTT
Found at i:905684 original size:23 final size:25
Alignment explanation
Indices: 905658--905703 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
905648 CCAATTAGGG
905658 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
905681 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
905704 TGGATCAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:906816 original size:14 final size:14
Alignment explanation
Indices: 906799--906831 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
906789 ATTATTTGCA
906799 TTTTTAATTTAATT
1 TTTTTAATTTAATT
*
906813 TTTTTATTTTAATT
1 TTTTTAATTTAATT
906827 TTTTT
1 TTTTT
906832 CCCTTCTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTAATTTAATT
Found at i:909645 original size:14 final size:14
Alignment explanation
Indices: 909628--909657 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
909618 TCATGTTTTT
909628 AAAAAAATTGAAAA
1 AAAAAAATTGAAAA
*
909642 AAAATAATTGAAAA
1 AAAAAAATTGAAAA
909656 AA
1 AA
909658 TTGAAAAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAAAATTGAAAA
Found at i:910687 original size:13 final size:13
Alignment explanation
Indices: 910671--910729 Score: 50
Period size: 14 Copynumber: 4.4 Consensus size: 13
910661 AAAAGTCGAA
910671 AAGAAAAAAAATG
1 AAGAAAAAAAATG
910684 AAGAAAAAAAGAATTG
1 AAG-AAAAAA-AA-TG
910700 AA-AAAAAAAA-G
1 AAGAAAAAAAATG
* *
910711 AAAAATAAAAAAAG
1 AAGAA-AAAAAATG
910725 AAGAA
1 AAGAA
910730 GATAAAAGTG
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
11 3 0.08
12 2 0.05
13 11 0.28
14 17 0.44
15 2 0.05
16 4 0.10
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (13 bp):
AAGAAAAAAAATG
Found at i:910690 original size:11 final size:11
Alignment explanation
Indices: 910669--910736 Score: 52
Period size: 11 Copynumber: 6.2 Consensus size: 11
910659 AAAAAAGTCG
910669 AAAAGAA-AAA
1 AAAAGAAGAAA
*
910679 AAATGAAGAAA
1 AAAAGAAGAAA
910690 AAAAGAATTGAAA
1 AAAAGAA--GAAA
*
910703 AAAAAAAGAAA
1 AAAAGAAGAAA
*
910714 AATA-AA-AAA
1 AAAAGAAGAAA
*
910723 AGAAGAAGATAA
1 AAAAGAAGA-AA
910735 AA
1 AA
910737 GTGTTTTGAG
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
9 5 0.11
10 10 0.22
11 17 0.38
12 3 0.07
13 10 0.22
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.07
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:910691 original size:14 final size:13
Alignment explanation
Indices: 910655--910722 Score: 50
Period size: 14 Copynumber: 4.8 Consensus size: 13
910645 TTATTATTTT
*
910655 AAAAAAAAAAGTCG
1 AAAAAAAAAAAT-G
910669 AAAAGAAAAAAAATG
1 -AAA-AAAAAAAATG
910684 AAGAAAAAAAGAATTG
1 AA-AAAAAAA-AA-TG
910700 -AAAAAAAAAA-G
1 AAAAAAAAAAATG
910711 AAAAATAAAAAA
1 AAAAA-AAAAAA
910723 AGAAGAAGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
11 1 0.02
12 4 0.09
13 8 0.17
14 15 0.33
15 8 0.17
16 10 0.22
ACGTcount: A:0.79, C:0.01, G:0.12, T:0.07
Consensus pattern (13 bp):
AAAAAAAAAAATG
Found at i:910708 original size:30 final size:31
Alignment explanation
Indices: 910668--910726 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
910658 AAAAAAAGTC
*
910668 GAAAAGAAAAAA-AATGAAGAAAAAAAGAATT
1 GAAAAGAAAAAAGAA-AAAGAAAAAAAGAATT
*
910699 GAAAA-AAAAAAGAAAAATAAAAAAAGAA
1 GAAAAGAAAAAAGAAAAAGAAAAAAAGAA
910727 GAAGATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 18 0.72
31 7 0.28
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.07
Consensus pattern (31 bp):
GAAAAGAAAAAAGAAAAAGAAAAAAAGAATT
Found at i:910710 original size:16 final size:16
Alignment explanation
Indices: 910655--910712 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
910645 TTATTATTTT
*
910655 AAAAAAAAAAG--TCG
1 AAAAAAAAAAGAATTG
910669 AAAAGAAAAAA-AA-TG
1 AAAA-AAAAAAGAATTG
*
910684 AAGAAAAAAAGAATTG
1 AAAAAAAAAAGAATTG
910700 AAAAAAAAAAGAA
1 AAAAAAAAAAGAA
910713 AAATAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 10 0.28
15 12 0.33
16 14 0.39
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.07
Consensus pattern (16 bp):
AAAAAAAAAAGAATTG
Found at i:910723 original size:14 final size:16
Alignment explanation
Indices: 910703--910736 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
910693 AGAATTGAAA
910703 AAAAAAAGAA-AA-AT
1 AAAAAAAGAAGAAGAT
910717 AAAAAAAGAAGAAGAT
1 AAAAAAAGAAGAAGAT
910733 AAAA
1 AAAA
910737 GTGTTTTGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 10 0.56
15 2 0.11
16 6 0.33
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAAAAAGAAGAAGAT
Found at i:911789 original size:23 final size:25
Alignment explanation
Indices: 911763--911808 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
911753 CCAATTAGGG
911763 AATTAT-TGTTTAG-ATTTAATTCT
1 AATTATCTGTTTAGAATTTAATTCT
*
911786 AATTATCTTTTTAGAATTTAATT
1 AATTATCTGTTTAGAATTTAATT
911809 TGGATCCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 6 0.30
25 8 0.40
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.57
Consensus pattern (25 bp):
AATTATCTGTTTAGAATTTAATTCT
Found at i:924762 original size:58 final size:59
Alignment explanation
Indices: 924693--924838 Score: 192
Period size: 58 Copynumber: 2.5 Consensus size: 59
924683 AATTTTAATG
* *
924693 ATTATTATTAAATATAATTTAATAAAAATATTAAT-TAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAAT-ATGTAATTTAATAATATTTTTAACATA
* *
924751 ATTATTATTAAATACAATTTAAT-AAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATATGTAATTTAATAATATTTTTAACATA
*
924809 ATTATTATTAAAATATGAA-TTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTTAATAAAAAT
924839 TATAATATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
56 2 0.03
57 19 0.25
58 40 0.52
59 9 0.12
60 7 0.09
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATATGTAATTTAATAATATTTTTAACATA
Found at i:924841 original size:25 final size:24
Alignment explanation
Indices: 924812--924862 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
924802 TAATATAATT
*
924812 ATTATTAAAATATGA-ATTAGTAAAA
1 ATTA-TAAAATATAATATTAG-AAAA
*
924837 ATTATAATATATAATATTAGAAAA
1 ATTATAAAATATAATATTAGAAAA
924861 AT
1 AT
924863 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:936976 original size:27 final size:26
Alignment explanation
Indices: 936924--936976 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
936914 TGATCCCAAT
* * *
936924 TAAAGTTTAAAGGATATCTAATTAAA
1 TAAAGTCTAAAGGATAACTAAATAAA
*
936950 TAAAGTCTAATAGGTTAACTAAATAAA
1 TAAAGTCTAA-AGGATAACTAAATAAA
936977 GTGATAAAGC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.51, C:0.06, G:0.11, T:0.32
Consensus pattern (26 bp):
TAAAGTCTAAAGGATAACTAAATAAA
Found at i:940475 original size:189 final size:188
Alignment explanation
Indices: 940155--940645 Score: 856
Period size: 189 Copynumber: 2.6 Consensus size: 188
940145 TGGTAAGGAT
* *
940155 ACTTCTTCAATTTGAGTACTAGATAGATTTAAGCTTATTAAGCTTCTTGGAATTTCTGGAAAATT
1 ACTTCTTCAATTTGAGTACTAGATAGGTTTAAGCTTATTAAGCTTCTTGGAATTTCTGGAAATTT
940220 AATCATTGGGCAATGACTAAGATCCAATTCATGAAGGGATTCCAACTTGATCGATGCAGTTTTGA
66 AATCATTGGGCAATGACTAAGATCCAATTCATGAA-GGATTCCAACTTGATCGATGCAGTTTTGA
* *
940285 CCGCTGTGCCACTCATATTTAGGTCCTGAAGATTACATAGAGAGTCGGAAGGCAATGGC
130 CCGCTGAGCCACTCATATTTAGGTCCTGAAGATTACATAGAGAGTCGGAAGGCAATGAC
940344 ACTTCTTCAATTTGAGTACTAGATAGGTTTAAGCTTATTAAGCTTCTTGGAATTTCTGGAAATTT
1 ACTTCTTCAATTTGAGTACTAGATAGGTTTAAGCTTATTAAGCTTCTTGGAATTTCTGGAAATTT
*
940409 AATCATTGGGCAATGACTAAGATCCAATTTATGAAGAGATTCCAACTTGATCGATGCAGTTTTGA
66 AATCATTGGGCAATGACTAAGATCCAATTCATGAAG-GATTCCAACTTGATCGATGCAGTTTTGA
*
940474 CCGCTGAGCCACTCATATTTAGGTTCTGAAGATTACATAGAGAGTCGGAAGGCAATGAC
130 CCGCTGAGCCACTCATATTTAGGTCCTGAAGATTACATAGAGAGTCGGAAGGCAATGAC
* *
940533 ACTTCTTCAATTTGAGTACTAGATAGGTTTAAGCTGATTAAGCTTCTTGGGATTTCTGGAAATTT
1 ACTTCTTCAATTTGAGTACTAGATAGGTTTAAGCTTATTAAGCTTCTTGGAATTTCTGGAAATTT
* * *
940598 AATCATTGGACAATCACTAAGATCCAATTCACGAAGGAATTCCAACTT
66 AATCATTGGGCAATGACTAAGATCCAATTCATGAAGG-ATTCCAACTT
940646 TGAAATATTG
Statistics
Matches: 288, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
188 2 0.01
189 286 0.99
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (188 bp):
ACTTCTTCAATTTGAGTACTAGATAGGTTTAAGCTTATTAAGCTTCTTGGAATTTCTGGAAATTT
AATCATTGGGCAATGACTAAGATCCAATTCATGAAGGATTCCAACTTGATCGATGCAGTTTTGAC
CGCTGAGCCACTCATATTTAGGTCCTGAAGATTACATAGAGAGTCGGAAGGCAATGAC
Done.