Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 132263754
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: 132263754
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 372 characters in sequence are not A, C, G, or T
File 126 of 433
Found at i:38604463 original size:44 final size:45
Alignment explanation
Indices: 38604403--38604510 Score: 119
Period size: 47 Copynumber: 2.4 Consensus size: 45
38604393 GCAGTCAACA
* ** ***
38604403 ATTCATCTGCTTGACCAGTGGCTTA-ACAGTGTATTCTAGTCAGC
1 ATTCATCTGCTCGACCAACGGCTTATACAACATATTCTAGTCAGC
* *
38604447 ATTCATCTGCTCGACCAACGGTTTATTCACAACATATTCTAGTCGGC
1 ATTCATCTGCTCGACCAACGGCTTA-T-ACAACATATTCTAGTCAGC
38604494 ATTCATCTGCTCGACCA
1 ATTCATCTGCTCGACCA
38604511 TTGGTTTATC
Statistics
Matches: 53, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 21 0.40
47 32 0.60
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (45 bp):
ATTCATCTGCTCGACCAACGGCTTATACAACATATTCTAGTCAGC
Found at i:38604497 original size:47 final size:47
Alignment explanation
Indices: 38604434--38604531 Score: 153
Period size: 47 Copynumber: 2.1 Consensus size: 47
38604424 CTTAACAGTG
38604434 TATTCTAGTCAGCATTCATCTGCTCGACCAACGGTTTATTC-ACAACA
1 TATTCTAGTCAGCATTCATCTGCTCGACCAACGGTTTA-TCGACAACA
* **
38604481 TATTCTAGTCGGCATTCATCTGCTCGACCATTGGTTTATCGACAACA
1 TATTCTAGTCAGCATTCATCTGCTCGACCAACGGTTTATCGACAACA
38604528 TATT
1 TATT
38604532 AGTAGCTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 2 0.04
47 45 0.96
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.35
Consensus pattern (47 bp):
TATTCTAGTCAGCATTCATCTGCTCGACCAACGGTTTATCGACAACA
Found at i:38604654 original size:91 final size:91
Alignment explanation
Indices: 38604481--38604664 Score: 233
Period size: 91 Copynumber: 2.0 Consensus size: 91
38604471 ATTCACAACA
* * * * * *
38604481 TATTCTAGTCGGCATTCATCTGCTCGACCATTGGTTTATCGACAACATATTAGTAGCTTTTATAT
1 TATTCTAGTAGACAGTCATCTGCTCAACCAATGGTTTATCGACAACATATTAGCAGCTTTTATAT
* **
38604546 GCACAAATGGATAGTTCATCCACCAG
66 ACACAAACAGATAGTTCATCCACCAG
* * * *
38604572 TATTCTAGTAGACAGTCATCTGTTCAACCAATGGTTTATCTACAACGTATTAGCAGCTTTTATCT
1 TATTCTAGTAGACAGTCATCTGCTCAACCAATGGTTTATCGACAACATATTAGCAGCTTTTATAT
* *
38604637 ACACAGACAGATGGTTCATCCACCAG
66 ACACAAACAGATAGTTCATCCACCAG
38604663 TA
1 TA
38604665 AATTTATCAT
Statistics
Matches: 78, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
91 78 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (91 bp):
TATTCTAGTAGACAGTCATCTGCTCAACCAATGGTTTATCGACAACATATTAGCAGCTTTTATAT
ACACAAACAGATAGTTCATCCACCAG
Found at i:38605658 original size:20 final size:18
Alignment explanation
Indices: 38605621--38605723 Score: 84
Period size: 20 Copynumber: 5.3 Consensus size: 18
38605611 AATGTTGTAT
*
38605621 AATTTCAATATCTCTTTAAC
1 AATTTTAATAT-T-TTTAAC
38605641 AATTTTAAAATATTTTTAAC
1 AATTTT--AATATTTTTAAC
38605661 AATATTTAAT-TTTTT-AC
1 AAT-TTTAATATTTTTAAC
*
38605678 AATTTTTAAATATTTTTTTAC
1 AA-TTTT-AATA-TTTTTAAC
*
38605699 GATTATTAATATTTTTAAC
1 AATT-TTAATATTTTTAAC
38605718 AATTTT
1 AATTTT
38605724 TTGGTCTGGT
Statistics
Matches: 70, Mismatches: 4, Indels: 20
0.74 0.04 0.21
Matches are distributed among these distances:
17 7 0.10
18 11 0.16
19 13 0.19
20 25 0.36
21 9 0.13
22 5 0.07
ACGTcount: A:0.37, C:0.08, G:0.01, T:0.54
Consensus pattern (18 bp):
AATTTTAATATTTTTAAC
Found at i:38605674 original size:17 final size:17
Alignment explanation
Indices: 38605652--38605686 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38605642 ATTTTAAAAT
38605652 ATTTTTAACAATATTTA
1 ATTTTTAACAATATTTA
* *
38605669 ATTTTTTACAATTTTTA
1 ATTTTTAACAATATTTA
38605686 A
1 A
38605687 ATATTTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTTTTAACAATATTTA
Found at i:38605695 original size:38 final size:39
Alignment explanation
Indices: 38605635--38605724 Score: 114
Period size: 38 Copynumber: 2.3 Consensus size: 39
38605625 TCAATATCTC
*
38605635 TTTAACAATTTTAAAATATTTTTAACAA-TATTTAAT-TT
1 TTTAACAATTTTTAAATATTTTTAACAATTA-TTAATATT
* *
38605673 TTT-ACAATTTTTAAATATTTTTTTACGATTATTAATATT
1 TTTAACAATTTTTAAATA-TTTTTAACAATTATTAATATT
38605712 TTTAACAATTTTT
1 TTTAACAATTTTT
38605725 TGGTCTGGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
37 13 0.29
38 16 0.36
39 7 0.16
40 9 0.20
ACGTcount: A:0.37, C:0.06, G:0.01, T:0.57
Consensus pattern (39 bp):
TTTAACAATTTTTAAATATTTTTAACAATTATTAATATT
Found at i:38613035 original size:48 final size:48
Alignment explanation
Indices: 38612966--38613196 Score: 240
Period size: 48 Copynumber: 4.9 Consensus size: 48
38612956 TAGGCTTATG
38612966 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
*
38613014 TGTGATCCCATGTAAGACCATGTCTGGGACATAGCATTGGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
* * * * * *
38613062 TTTGATACCATGTAATACCATATCTGGGATATGGCATTAGCATCGATA
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
*** * * * *
38613110 TGTGAAATCATGTAAGACCATAG-CTAGG-C-T---ATCGGCTTCGATC
1 TGTGATCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGATA
* * * * *
38613153 TGTAATCCCATGTAAGACCATATTTGGGATATGGCACTGGCATC
1 TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC
38613197 TTATTATGTG
Statistics
Matches: 146, Mismatches: 30, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
43 29 0.20
45 1 0.01
46 1 0.01
48 115 0.79
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (48 bp):
TGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATA
Found at i:38620831 original size:26 final size:26
Alignment explanation
Indices: 38620786--38620860 Score: 87
Period size: 26 Copynumber: 2.9 Consensus size: 26
38620776 CATATTTTCT
* *
38620786 CAAAATTTTACTAGGGGTAAAATCGC
1 CAAAATTTTACTAGAGGTAAAATCAC
* * *
38620812 CAAAATTTTATTAGATGTAAAATCAT
1 CAAAATTTTACTAGAGGTAAAATCAC
* *
38620838 CAAAATTTTACTGGGGGTAAAAT
1 CAAAATTTTACTAGAGGTAAAAT
38620861 AGGGATAAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (26 bp):
CAAAATTTTACTAGAGGTAAAATCAC
Found at i:38627657 original size:58 final size:57
Alignment explanation
Indices: 38627511--38627657 Score: 147
Period size: 57 Copynumber: 2.6 Consensus size: 57
38627501 GTATAACAAG
*
38627511 ATTACCAGTCCAGGCTAAATCCTTTATATAACGTATGCTCAGAGGAGCTCGATTAGA
1 ATTACCAGTCCAGGCTAAATCCTTTATATAACGTATGCTCAGAGGAGATCGATTAGA
* * * * ** * *
38627568 ATTACCAGTCCAGGC-AAAACCCTAATCATAACGTATGTTC-GA-GAGATATTATATCGGT
1 ATTACCAGTCCAGGCTAAATCCTTTAT-ATAACGTATGCTCAGAGGAGAT-CGAT-T-AGA
*
38627626 ATTACCTGTCCAGGCTAAATCCTTTATATAAC
1 ATTACCAGTCCAGGCTAAATCCTTTATATAAC
38627658 AAAGTCATTA
Statistics
Matches: 72, Mismatches: 13, Indels: 9
0.77 0.14 0.10
Matches are distributed among these distances:
55 4 0.06
56 12 0.17
57 28 0.39
58 20 0.28
59 8 0.11
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (57 bp):
ATTACCAGTCCAGGCTAAATCCTTTATATAACGTATGCTCAGAGGAGATCGATTAGA
Found at i:38628228 original size:20 final size:20
Alignment explanation
Indices: 38628199--38628244 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
38628189 AGCACATGTA
* *
38628199 TTCATAAAATTTCAAAATTT
1 TTCATTAAATTTCAAAACTT
* *
38628219 TTCATTAAATTTTACAACTT
1 TTCATTAAATTTCAAAACTT
38628239 TTCATT
1 TTCATT
38628245 TTAGTCCCTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (20 bp):
TTCATTAAATTTCAAAACTT
Found at i:38630332 original size:27 final size:27
Alignment explanation
Indices: 38630120--38630401 Score: 205
Period size: 27 Copynumber: 10.4 Consensus size: 27
38630110 ATTACCAAAG
* * * *
38630120 TACCCCCGATTTACAGAATTA-TCGTTC
1 TACCCTCGATTTATAGAATTACT-ATTT
* *
38630147 TACCCTTGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACTATTT
38630174 TACCCTCGATTTATAGAATTATCT-TTT
1 TACCCTCGATTTATAGAATTA-CTATTT
* * ***
38630201 TACCCTCGATTTACAAAATTACTAAAA
1 TACCCTCGATTTATAGAATTACTATTT
* * * ***
38630228 TACCC-CTGGTTTGTAAAATTACTAAAA
1 TACCCTC-GATTTATAGAATTACTATTT
* * ***
38630255 TACCCTCGACTTGTA-AAAATTACCAAAG
1 TACCCTCGA-TT-TATAGAATTACTATTT
*
38630283 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTATTT
*
38630310 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACTATTT
* *
38630337 TACCCTCGATTTACAGAATTATTATTT
1 TACCCTCGATTTATAGAATTACTATTT
* * * *
38630364 TACCC-CTAATTTACAAAATTACCATTT
1 TACCCTC-GATTTATAGAATTACTATTT
38630391 TACCCTCGATT
1 TACCCTCGATT
38630402 GTGAAATTAC
Statistics
Matches: 211, Mismatches: 34, Indels: 20
0.80 0.13 0.08
Matches are distributed among these distances:
26 6 0.03
27 179 0.85
28 25 0.12
29 1 0.00
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACTATTT
Found at i:38630395 original size:136 final size:134
Alignment explanation
Indices: 38630147--38630411 Score: 343
Period size: 136 Copynumber: 2.0 Consensus size: 134
38630137 ATTATCGTTC
*
38630147 TACCCTTGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTATCTTTTTACCCTCGATT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTATCTTTTTACCCTCGATT
** ** *
38630212 TACAAAATTACTAAAATACCCCTGGTTTGTAAAATTACTAAAATACCCTCGACTTGTAAAAATTA
66 TACAAAATTACTAAAATACCCCTAATTTACAAAATTACCAAAATACCCTCGA-TTGT-AAAATTA
38630277 CCAAAG
129 CCAAAG
**
38630283 TACCCTCGATTTATAGAATTACTGTTTTACCCTCGATTTATAGAATTA-CTGTTTTACCCTCGAT
1 TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTATCT-TTTTACCCTCGAT
* * *** *** *
38630347 TTACAGAATTATTATTTTACCCCTAATTTACAAAATTACCATTTTACCCTCGATTGTGAAATTAC
65 TTACAAAATTACTAAAATACCCCTAATTTACAAAATTACCAAAATACCCTCGATTGTAAAATTAC
38630412 TGAAATACCC
Statistics
Matches: 111, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
134 7 0.06
135 6 0.05
136 98 0.88
ACGTcount: A:0.32, C:0.21, G:0.08, T:0.38
Consensus pattern (134 bp):
TACCCTCGATTTATAGAATTACCATTTTACCCTCGATTTATAGAATTATCTTTTTACCCTCGATT
TACAAAATTACTAAAATACCCCTAATTTACAAAATTACCAAAATACCCTCGATTGTAAAATTACC
AAAG
Found at i:38630473 original size:54 final size:52
Alignment explanation
Indices: 38630392--38630529 Score: 120
Period size: 54 Copynumber: 2.6 Consensus size: 52
38630382 TTACCATTTT
* * **
38630392 ACCCTCGA-TTGTGAAATTACTGAAATACCC-GTATAGGGTAGAATTACCAAAAC
1 ACCCTCAATTTGTAAAATTACCAAAATACCCGGT-TAGGG-A-AATTACCAAAAC
* * * * *
38630445 ACCC-CTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAAT
1 ACCCTC-AATTTGTAAAATTACCAAAATACC-C-GGTTAGGGAAATTACCAAAAC
38630499 ACCCTCAATTTGTAAAATTACCAAAATACCC
1 ACCCTCAATTTGTAAAATTACCAAAATACCC
38630530 CTGATTTACA
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
52 1 0.01
53 5 0.07
54 55 0.80
55 3 0.04
56 3 0.04
57 2 0.03
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.27
Consensus pattern (52 bp):
ACCCTCAATTTGTAAAATTACCAAAATACCCGGTTAGGGAAATTACCAAAAC
Found at i:38630536 original size:27 final size:27
Alignment explanation
Indices: 38630433--38630583 Score: 135
Period size: 27 Copynumber: 5.6 Consensus size: 27
38630423 TATAGGGTAG
*
38630433 AATTACCAAAACACCCCT-AGTTTGTAA
1 AATTACCAAAATACCCCTGA-TTTGTAA
* * *
38630460 AATTACCAAAATACCACTGGTTTGTGA
1 AATTACCAAAATACCCCTGATTTGTAA
* *
38630487 AATTACCGAAATA-CCCTCAATTTGTAA
1 AATTACCAAAATACCCCT-GATTTGTAA
**
38630514 AATTACCAAAATACCCCTGATTTACAA
1 AATTACCAAAATACCCCTGATTTGTAA
* * * * *
38630541 AATTACAAAAAAAACCTTGATTTGTAG
1 AATTACCAAAATACCCCTGATTTGTAA
* *
38630568 ATTTACCAAAACACCC
1 AATTACCAAAATACCC
38630584 TTGTAGGATG
Statistics
Matches: 97, Mismatches: 24, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
26 3 0.03
27 90 0.93
28 4 0.04
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (27 bp):
AATTACCAAAATACCCCTGATTTGTAA
Found at i:38630543 original size:81 final size:79
Alignment explanation
Indices: 38630364--38630551 Score: 191
Period size: 81 Copynumber: 2.3 Consensus size: 79
38630354 ATTATTATTT
*** *
38630364 TACCCCTAATTTACAAAATTACCATTTTACCCTCGATTGTGAAATTACTGAAATACCCGTATAGG
1 TACCCCT-ATTTACAAAATTACCAAAATACCCTCGATTGTGAAATTACCGAAATACCCGTATAGG
*
38630429 GTAGAATTACCAAAA
65 GTAAAATTACCAAAA
* ** * *
38630444 CACCCCTAGTTTGTAAAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATACCC-TCA-A
1 TACCCCTA-TTTACAAAATTACCAAAATACC-CTCGATTGTGAAATTACCGAAATACCCGT-ATA
**
38630507 TTTGTAAAATTACCAAAA
63 -GGGTAAAATTACCAAAA
*
38630525 TACCCCTGATTTACAAAATTACAAAAA
1 TACCCCT-ATTTACAAAATTACCAAAA
38630552 AAACCTTGAT
Statistics
Matches: 87, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
79 1 0.01
80 25 0.29
81 60 0.69
82 1 0.01
ACGTcount: A:0.40, C:0.22, G:0.10, T:0.29
Consensus pattern (79 bp):
TACCCCTATTTACAAAATTACCAAAATACCCTCGATTGTGAAATTACCGAAATACCCGTATAGGG
TAAAATTACCAAAA
Found at i:38631330 original size:25 final size:25
Alignment explanation
Indices: 38631302--38631361 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
38631292 CCTTATAGTA
*
38631302 TGAAAATGATTGTTTTGCCCCTAGG
1 TGAAAATGACTGTTTTGCCCCTAGG
38631327 TGAAAATGACTGTTTTGCCCCTAGG
1 TGAAAATGACTGTTTTGCCCCTAGG
*
38631352 TAAAAATGAC
1 TGAAAATGAC
38631362 CATTATACCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.32
Consensus pattern (25 bp):
TGAAAATGACTGTTTTGCCCCTAGG
Found at i:38631372 original size:25 final size:25
Alignment explanation
Indices: 38631319--38631376 Score: 71
Period size: 25 Copynumber: 2.3 Consensus size: 25
38631309 GATTGTTTTG
* ** * *
38631319 CCCCTAGGTGAAAATGACTGTTTTG
1 CCCCTAGGTAAAAATGACCATTATA
38631344 CCCCTAGGTAAAAATGACCATTATA
1 CCCCTAGGTAAAAATGACCATTATA
38631369 CCCCTAGG
1 CCCCTAGG
38631377 GTTTAATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (25 bp):
CCCCTAGGTAAAAATGACCATTATA
Found at i:38631455 original size:20 final size:20
Alignment explanation
Indices: 38631432--38631498 Score: 125
Period size: 20 Copynumber: 3.4 Consensus size: 20
38631422 TATGATAAGT
*
38631432 ACATGATATGTATAAAATGC
1 ACATGATATGTATGAAATGC
38631452 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
38631472 ACATGATATGTATGAAATGC
1 ACATGATATGTATGAAATGC
38631492 ACATGAT
1 ACATGAT
38631499 GTATTCATAA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (20 bp):
ACATGATATGTATGAAATGC
Found at i:38631577 original size:26 final size:26
Alignment explanation
Indices: 38631548--38631683 Score: 174
Period size: 26 Copynumber: 5.3 Consensus size: 26
38631538 GAGGAAGTGC
38631548 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
38631574 AAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGCTTATGCCCCAGTTTATTG
*
38631600 AAAAGGGCGTATGCCCCAGTTTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
**
38631625 AGAAAGGGCTT-TGCCCCAGTTTACCG
1 A-AAAGGGCTTATGCCCCAGTTTATTG
38631651 AAAAGGGCTT-TGCCCCAG-TTATT-
1 AAAAGGGCTTATGCCCCAGTTTATTG
38631674 AAAAGAGGCT
1 AAAAG-GGCT
38631684 AGGCCTCCAG
Statistics
Matches: 97, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
23 5 0.05
24 7 0.07
25 30 0.31
26 55 0.57
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (26 bp):
AAAAGGGCTTATGCCCCAGTTTATTG
Found at i:38631631 original size:52 final size:50
Alignment explanation
Indices: 38631548--38631683 Score: 197
Period size: 52 Copynumber: 2.7 Consensus size: 50
38631538 GAGGAAGTGC
38631548 AAAAGGGCTTATGCCCCAGTTTATT-GAAAAGGGCTTATGCCCCAGTTTACCG
1 AAAAGGGC-TATGCCCCAGTTTATTAG-AAAGGGCTT-TGCCCCAGTTTACCG
38631600 AAAAGGGCGTATGCCCCAGTTTATTAGAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGC-TATGCCCCAGTTTATTAGAAAGGGCTTTGCCCCAGTTTACCG
*
38631651 AAAAGGGCTTTGCCCCAG-TTATTA-AAAGAGGCT
1 AAAAGGGCTATGCCCCAGTTTATTAGAAAG-GGCT
38631684 AGGCCTCCAG
Statistics
Matches: 80, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
48 4 0.05
49 10 0.12
50 9 0.11
51 23 0.29
52 33 0.41
53 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (50 bp):
AAAAGGGCTATGCCCCAGTTTATTAGAAAGGGCTTTGCCCCAGTTTACCG
Found at i:38631875 original size:42 final size:42
Alignment explanation
Indices: 38631816--38631907 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
38631806 TAGTCTCCCC
* * ** *
38631816 AAATGGGCTTGCATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTACATACATCCATTGACATTACATATGATATTG
* *
38631858 AAATGGGCTTACATACATCCCTTGACATTACATGTGATATTG
1 AAATGGGCTTACATACATCCATTGACATTACATATGATATTG
38631900 AAATGGGC
1 AAATGGGC
38631908 CTATGGGCCA
Statistics
Matches: 43, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTACATACATCCATTGACATTACATATGATATTG
Found at i:38631970 original size:31 final size:31
Alignment explanation
Indices: 38631931--38632069 Score: 171
Period size: 31 Copynumber: 4.6 Consensus size: 31
38631921 CGTTTACAGT
38631931 AAAA-GCTTCGGCCCAGTGAAATGATTTATA
1 AAAAGGCTTCGGCCCAGTGAAATGATTTATA
* *
38631961 AAAAGGCTTCGGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGAAATGATTTATA
* *
38631992 AAAAGGCTTCGGCCCAGTGATATGATTTATG
1 AAAAGGCTTCGGCCCAGTGAAATGATTTATA
* *
38632023 AAAACGCTTCGGCCCAGT-AACTG--TTA-A
1 AAAAGGCTTCGGCCCAGTGAAATGATTTATA
38632050 ACGAAAGGCTTCGGCCCAGT
1 A--AAAGGCTTCGGCCCAGT
38632070 ATATGTCAAG
Statistics
Matches: 99, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
27 1 0.01
28 3 0.03
29 16 0.16
30 7 0.07
31 72 0.73
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (31 bp):
AAAAGGCTTCGGCCCAGTGAAATGATTTATA
Found at i:38633625 original size:39 final size:39
Alignment explanation
Indices: 38633571--38633645 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
38633561 TTATTAGCCA
38633571 AATAGCTAAGAACATAAGGTAGCAAGATAAAAATTTACG
1 AATAGCTAAGAACATAAGGTAGCAAGATAAAAATTTACG
38633610 AATAGCTAAGAACATAAGGTAGCAAGATAAAAATTT
1 AATAGCTAAGAACATAAGGTAGCAAGATAAAAATTT
38633646 TACCATGTCG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.21
Consensus pattern (39 bp):
AATAGCTAAGAACATAAGGTAGCAAGATAAAAATTTACG
Found at i:38634057 original size:29 final size:29
Alignment explanation
Indices: 38634022--38634095 Score: 105
Period size: 29 Copynumber: 2.6 Consensus size: 29
38634012 GTTGTGAGAT
*
38634022 TGGCACTAAGTGTGCGAGCTTGAAA-TGCA
1 TGGCACTAAGTGTGCGAG-TTGAAAGTACA
* *
38634051 TGGCACTAAGTGTGCAAGTTTAAAGTACA
1 TGGCACTAAGTGTGCGAGTTGAAAGTACA
38634080 TGGCACTAAGTGTGCG
1 TGGCACTAAGTGTGCG
38634096 TGGTTGATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 5 0.12
29 35 0.88
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGAGTTGAAAGTACA
Found at i:38644093 original size:40 final size:40
Alignment explanation
Indices: 38644033--38644169 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 40
38644023 TCGAGAATAT
* *
38644033 AAAGTGGATAGGATTCGTTCCTGATTCACTATAATACCTC
1 AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAACTC
* ** * *
38644073 AAAGTGGATAGGATTTGTTCCTAATTCACTATGGTAATTT
1 AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAACTC
* * ** *
38644113 AAAGTGAATAGGATTTATTCCTGATTCACTATGGTAACTT
1 AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAACTC
* *
38644153 AAGGCGGATAGGATTTG
1 AAAGTGGATAGGATTTG
38644170 ACCTGAAAAG
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (40 bp):
AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAACTC
Found at i:38644224 original size:78 final size:78
Alignment explanation
Indices: 38644134--38644363 Score: 388
Period size: 78 Copynumber: 2.9 Consensus size: 78
38644124 GATTTATTCC
38644134 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACA
1 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACA
*
38644199 ATTACATGATATA
66 GTTACATGATATA
* *
38644212 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATCCTAATCCGCTACA
1 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACA
38644277 GTTACATGATATA
66 GTTACATGATATA
* * * *
38644290 TGATTCATTATGGTAACCTAAGGTGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCACTACA
1 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACA
*
38644355 GTTATATGA
66 GTTACATGA
38644364 GATGTGACTC
Statistics
Matches: 142, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 142 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (78 bp):
TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCGCTACA
GTTACATGATATA
Found at i:38649768 original size:40 final size:40
Alignment explanation
Indices: 38649708--38649844 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 40
38649698 TCGAGAATAT
* *
38649708 AAAGTGGATAGGATTCGTTCCTGATTCACTATAATACCTC
1 AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAACTC
* ** * *
38649748 AAAGTGGATAGGATTTGTTCCTAATTCACTATGGTAATTT
1 AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAACTC
* * ** *
38649788 AAAGTGAATAGGATTTATTCCTGATTCACTATGGTAACTT
1 AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAACTC
* *
38649828 AAGGCGGATAGGATTTG
1 AAAGTGGATAGGATTTG
38649845 ACCTGAAAAG
Statistics
Matches: 82, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (40 bp):
AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAACTC
Found at i:38649899 original size:78 final size:78
Alignment explanation
Indices: 38649809--38650044 Score: 364
Period size: 78 Copynumber: 2.9 Consensus size: 78
38649799 GATTTATTCC
*
38649809 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATCTTGATTCGCTACA
1 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATCTTGATTCACTACA
38649874 GTTACATGATATA
66 GTTACATGATATA
38649887 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATCTAAATCCTGATTC
1 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATC----T--TGATTC
38649952 ACTACAGTTACATGATATA
60 ACTACAGTTACATGATATA
* * * * *
38649971 TGATTCATTATGGTAACCTAAGGTGGATAGGATTTGACCAGAAAAGGTAATCCTGATTCACTACA
1 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATCTTGATTCACTACA
38650036 GTTACATGA
66 GTTACATGA
38650045 GATGTGACTC
Statistics
Matches: 146, Mismatches: 6, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
78 73 0.50
82 1 0.01
84 72 0.49
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (78 bp):
TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAAGGTAATCTTGATTCACTACA
GTTACATGATATA
Found at i:38651432 original size:22 final size:22
Alignment explanation
Indices: 38651407--38651451 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
38651397 TGTTTGACAC
38651407 ATCAAAATTTAAAAATAACATA
1 ATCAAAATTTAAAAATAACATA
38651429 ATCAAAATTTAAAAATAACATA
1 ATCAAAATTTAAAAATAACATA
38651451 A
1 A
38651452 CTTAATGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.27
Consensus pattern (22 bp):
ATCAAAATTTAAAAATAACATA
Found at i:38653371 original size:18 final size:18
Alignment explanation
Indices: 38653350--38653408 Score: 66
Period size: 18 Copynumber: 3.3 Consensus size: 18
38653340 TTTATACAAA
* *
38653350 TAATTCAGTTTATTCGGT
1 TAATTCGGTTAATTCGGT
* *
38653368 TAATTTGGGTAATTCGAG-
1 TAATTCGGTTAATTCG-GT
38653386 TAATTCGGTTAATTCGGT
1 TAATTCGGTTAATTCGGT
38653404 TAATT
1 TAATT
38653409 TTATACTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 1 0.03
18 31 0.94
19 1 0.03
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.46
Consensus pattern (18 bp):
TAATTCGGTTAATTCGGT
Found at i:38653380 original size:9 final size:9
Alignment explanation
Indices: 38653361--38653408 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
38653351 AATTCAGTTT
*
38653361 ATTCGGTTA
1 ATTCGGGTA
*
38653370 ATTTGGGTA
1 ATTCGGGTA
*
38653379 ATTCGAGTA
1 ATTCGGGTA
*
38653388 ATTCGGTTA
1 ATTCGGGTA
*
38653397 ATTCGGTTA
1 ATTCGGGTA
38653406 ATT
1 ATT
38653409 TTATACTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 33 1.00
ACGTcount: A:0.25, C:0.08, G:0.23, T:0.44
Consensus pattern (9 bp):
ATTCGGGTA
Found at i:38658845 original size:23 final size:24
Alignment explanation
Indices: 38658805--38658854 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
38658795 GAAGATTTTT
38658805 AATCTTAGTAAATTTGATTCTGTA
1 AATCTTAGTAAATTTGATTCTGTA
* *
38658829 AATCTTA-TAGATTTGATTTTGTA
1 AATCTTAGTAAATTTGATTCTGTA
38658852 AAT
1 AAT
38658855 TGCTTTTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (24 bp):
AATCTTAGTAAATTTGATTCTGTA
Found at i:38659460 original size:88 final size:88
Alignment explanation
Indices: 38659345--38659506 Score: 229
Period size: 88 Copynumber: 1.8 Consensus size: 88
38659335 TTGTGATACT
* *
38659345 TGAACTATCAATTTATGTAGTATTTGGT-ACTTGTACCTTCATAAAATATTCAATGTGGTA-TCT
1 TGAACTATCAATTTATGTAGTATTTGGTAAATT-TACCTTCATAAAATATCCAATGTGGTACT-T
38659408 ATACTTTGAAATTTCCAGTGGTACA
64 ATACTTTGAAATTTCCAGTGGTACA
* * ** *
38659433 TGAACTATCAATTTGTGTATTATTTGGTAAATTTATTTTCATAAAATGTCCAATGTGGTACTTAT
1 TGAACTATCAATTTATGTAGTATTTGGTAAATTTACCTTCATAAAATATCCAATGTGGTACTTAT
38659498 ACTTTGAAA
66 ACTTTGAAA
38659507 GTATTTAATG
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
88 61 0.94
89 4 0.06
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (88 bp):
TGAACTATCAATTTATGTAGTATTTGGTAAATTTACCTTCATAAAATATCCAATGTGGTACTTAT
ACTTTGAAATTTCCAGTGGTACA
Found at i:38660071 original size:29 final size:31
Alignment explanation
Indices: 38660037--38660104 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
38660027 TTGATAGTTC
38660037 AAGTACCAC-ATTGAACA-TTT-TCAAAGTAT
1 AAGTACCACAATTG-ACATTTTATCAAAGTAT
* *
38660066 AAGTACAACAATTGACATTTTATGAAAGTAT
1 AAGTACCACAATTGACATTTTATCAAAGTAT
*
38660097 ATGTACCA
1 AAGTACCA
38660105 AATAATGCAC
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 11 0.34
30 7 0.22
31 14 0.44
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.31
Consensus pattern (31 bp):
AAGTACCACAATTGACATTTTATCAAAGTAT
Found at i:38663550 original size:39 final size:39
Alignment explanation
Indices: 38663492--38663677 Score: 309
Period size: 39 Copynumber: 4.8 Consensus size: 39
38663482 GGCTTATGCT
38663492 CTAAACGGAAGCCCGAAGGCTAACTGAAGCACACAAGTG
1 CTAAACGGAAGCCCGAAGGCTAACTGAAGCACACAAGTG
* *
38663531 CTAAATGGAAGCCCAAAGGCTAACTGAAGCACACAAGTG
1 CTAAACGGAAGCCCGAAGGCTAACTGAAGCACACAAGTG
* * *
38663570 CCAAACGGAAGCCCGAAGGCTAACTGAAGTACATAAGTG
1 CTAAACGGAAGCCCGAAGGCTAACTGAAGCACACAAGTG
*
38663609 CTAAATGGAAGCCCGAAGGCTAACTGAAGCACACAAGTG
1 CTAAACGGAAGCCCGAAGGCTAACTGAAGCACACAAGTG
*
38663648 CTAAACGGAAGCCCGAAGGCTAACGGAAGC
1 CTAAACGGAAGCCCGAAGGCTAACTGAAGC
38663678 CCGAAGGCTA
Statistics
Matches: 134, Mismatches: 13, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 134 1.00
ACGTcount: A:0.39, C:0.24, G:0.26, T:0.11
Consensus pattern (39 bp):
CTAAACGGAAGCCCGAAGGCTAACTGAAGCACACAAGTG
Found at i:38665881 original size:28 final size:28
Alignment explanation
Indices: 38665832--38665888 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
38665822 ATTAAAGTGA
*
38665832 TTATCTTAATATTAATTTAATTTAATAT
1 TTATCTTAATATTAATTAAATTTAATAT
*
38665860 TTATCTT-GTATTAGATTAAATTTAATAT
1 TTATCTTAATATTA-ATTAAATTTAATAT
38665888 T
1 T
38665889 AAAGTGATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 5 0.19
28 21 0.81
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (28 bp):
TTATCTTAATATTAATTAAATTTAATAT
Found at i:38668629 original size:16 final size:16
Alignment explanation
Indices: 38668608--38668639 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38668598 TCCATGACAA
38668608 GTGATATATGTAATAT
1 GTGATATATGTAATAT
*
38668624 GTGATATATGTTATAT
1 GTGATATATGTAATAT
38668640 AAATTCTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (16 bp):
GTGATATATGTAATAT
Found at i:38668932 original size:44 final size:44
Alignment explanation
Indices: 38668875--38668961 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
38668865 GGCATCTGAG
*
38668875 CTTGTTGAGTTGGTCCGAGTTCATTATGGATGCGAGCATCCAAA
1 CTTGTTGAATTGGTCCGAGTTCATTATGGATGCGAGCATCCAAA
*
38668919 CTTGTTGAATTGGTCTGAGTTCATTATGGATGCGAGCATCCAA
1 CTTGTTGAATTGGTCCGAGTTCATTATGGATGCGAGCATCCAA
38668962 TGGTCTTGTG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.33
Consensus pattern (44 bp):
CTTGTTGAATTGGTCCGAGTTCATTATGGATGCGAGCATCCAAA
Found at i:38672643 original size:8 final size:8
Alignment explanation
Indices: 38672630--38672654 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
38672620 GATTGCTAAC
38672630 GTTTATTG
1 GTTTATTG
38672638 GTTTATTG
1 GTTTATTG
38672646 GTTTATTG
1 GTTTATTG
38672654 G
1 G
38672655 GGATAGCCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.28, T:0.60
Consensus pattern (8 bp):
GTTTATTG
Found at i:38674101 original size:86 final size:86
Alignment explanation
Indices: 38673952--38674119 Score: 275
Period size: 86 Copynumber: 2.0 Consensus size: 86
38673942 CGAAATAAAA
* *
38673952 ACATAGTAACACAAAGAAAAGGGAGAGATTATCAATTCTTTTTTACTTTCTCTTCCCTGTTAAAA
1 ACATAGTAACACAAAGAAAAGGGAGAGACTATCAATTCTTTTTTACTTTCTCTTCCCTATTAAAA
*
38674017 CATGTTATCCATATGAATCCT
66 CATGTTATCCAAATGAATCCT
*
38674038 ACATAGTAACACAAAG-AAAGGGAGAGACTATTAATTCTTTTTTTACTTTCTCTTCCCTATTAAA
1 ACATAGTAACACAAAGAAAAGGGAGAGACTATCAATTC-TTTTTTACTTTCTCTTCCCTATTAAA
*
38674102 ACGTGTTATCCAAATGAA
65 ACATGTTATCCAAATGAA
38674120 CCATTCTCTT
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
85 19 0.25
86 57 0.75
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.35
Consensus pattern (86 bp):
ACATAGTAACACAAAGAAAAGGGAGAGACTATCAATTCTTTTTTACTTTCTCTTCCCTATTAAAA
CATGTTATCCAAATGAATCCT
Found at i:38676019 original size:11 final size:11
Alignment explanation
Indices: 38676003--38676027 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38675993 ATATCTAGAA
38676003 TTCTCTTCATT
1 TTCTCTTCATT
38676014 TTCTCTTCATT
1 TTCTCTTCATT
38676025 TTC
1 TTC
38676028 ATCAGCTGAA
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:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (11 bp):
TTCTCTTCATT
Found at i:38679236 original size:24 final size:24
Alignment explanation
Indices: 38679188--38679249 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 24
38679178 TTTACTATTT
* *
38679188 TTAATATAAAATATTTATTTTTATA
1 TTAATA-AAAATATTTAATTATATA
38679213 -TAATAAAAATATATTAATTATATA
1 TTAATAAAAATAT-TTAATTATATA
38679237 TTAAATAAAAATA
1 TT-AATAAAAATA
38679250 AAATTTGACT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 7 0.22
24 14 0.44
25 1 0.03
26 10 0.31
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTAATAAAAATATTTAATTATATA
Found at i:38679834 original size:26 final size:28
Alignment explanation
Indices: 38679795--38679847 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
38679785 TTAATATAAC
*
38679795 TTTTAGTCTCACTTTGATATTTATATTT
1 TTTTAGTCTCACTTTGATATTAATATTT
*
38679823 TTTTA-TCT-ACTTTGATCTTAATATT
1 TTTTAGTCTCACTTTGATATTAATATT
38679848 GGTAATTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 15 0.65
27 3 0.13
28 5 0.22
ACGTcount: A:0.23, C:0.11, G:0.06, T:0.60
Consensus pattern (28 bp):
TTTTAGTCTCACTTTGATATTAATATTT
Found at i:38686917 original size:12 final size:12
Alignment explanation
Indices: 38686900--38686935 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
38686890 GGACTAAAAC
38686900 ACCAAAGTTAGG
1 ACCAAAGTTAGG
**
38686912 ACCAAAGTTAAC
1 ACCAAAGTTAGG
38686924 ACCAAAGTTAGG
1 ACCAAAGTTAGG
38686936 TCGTGTTATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (12 bp):
ACCAAAGTTAGG
Found at i:38689603 original size:1 final size:1
Alignment explanation
Indices: 38689597--38689627 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
38689587 GACTGAAGCG
*
38689597 AAAAAAAAAAAAAAAAAAGAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
38689628 CAGATTAGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:38693950 original size:2 final size:2
Alignment explanation
Indices: 38693945--38693970 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38693935 TTTGTTTAAA
38693945 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
38693971 TTCACAACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38695648 original size:7 final size:7
Alignment explanation
Indices: 38695624--38695663 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
38695614 CCTCCCCTTT
38695624 GCTATTG
1 GCTATTG
*
38695631 GC-CTTG
1 GCTATTG
*
38695637 GCTATGG
1 GCTATTG
38695644 GCTATTG
1 GCTATTG
38695651 GCTATTG
1 GCTATTG
38695658 GCTATT
1 GCTATT
38695664 CTCTACCCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.12, C:0.17, G:0.30, T:0.40
Consensus pattern (7 bp):
GCTATTG
Found at i:38700365 original size:48 final size:48
Alignment explanation
Indices: 38700313--38700495 Score: 303
Period size: 48 Copynumber: 3.8 Consensus size: 48
38700303 TATTAGGGTT
* *
38700313 ATATGTGATCCCATATAAGACCGTGTCTGGGACATGGCATTGACATCG
1 ATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCG
*
38700361 ATATGTTATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCG
1 ATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCG
*
38700409 ATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCG
1 ATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCG
** *
38700457 ATATGTGATTTCGTGTAAGACCATGTCTGGGACATGGCA
1 ATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCA
38700496 CCGATATGAG
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 127 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (48 bp):
ATATGTGATCCCATGTAAGACCATGTCTGGGACATGGCATTGACATCG
Found at i:38700513 original size:42 final size:44
Alignment explanation
Indices: 38700374--38700522 Score: 133
Period size: 48 Copynumber: 3.2 Consensus size: 44
38700364 TGTTATCCCA
* * *
38700374 TGTAAGACCATGTCTGGGACATGGCATTGACATCGATATGTGATC-CCA
1 TGTAAGACCATGTCTGGGACATGGCA--G-CA-CGATATGAGA-CATCG
* **
38700422 TGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTGATTTCG
1 TGTAAGACCATGTCTGGGACATGGCA---GCA-CGATATGAGACATCG
38700470 TGTAAGACCATGTCTGGGACATGGCA-C-CGATATGAGACATCG
1 TGTAAGACCATGTCTGGGACATGGCAGCACGATATGAGACATCG
*
38700512 TGTAATACCAT
1 TGTAAGACCAT
38700523 AGCTGGGCTA
Statistics
Matches: 91, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
42 22 0.24
44 1 0.01
48 66 0.73
49 2 0.02
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACATGGCAGCACGATATGAGACATCG
Found at i:38702252 original size:16 final size:14
Alignment explanation
Indices: 38702214--38702245 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
38702204 ATATGTAAAA
*
38702214 GAAAATATATGCAT
1 GAAAATATATACAT
38702228 GAAAATATATACAT
1 GAAAATATATACAT
38702242 GAAA
1 GAAA
38702246 TATTATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.25
Consensus pattern (14 bp):
GAAAATATATACAT
Found at i:38702857 original size:3 final size:3
Alignment explanation
Indices: 38702788--38702838 Score: 93
Period size: 3 Copynumber: 16.7 Consensus size: 3
38702778 GAGTATATAC
38702788 TAA TAA GTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38702834 TAA TA
1 TAA TA
38702839 GAGATGGCAA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 44 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:38702869 original size:15 final size:15
Alignment explanation
Indices: 38702847--38702880 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
38702837 TAGAGATGGC
*
38702847 AATA-AATAATAGTA
1 AATATAATAATAGAA
38702861 AATATAATAATAGAA
1 AATATAATAATAGAA
38702876 AATAT
1 AATAT
38702881 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 4 0.22
15 14 0.78
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (15 bp):
AATATAATAATAGAA
Found at i:38703520 original size:12 final size:12
Alignment explanation
Indices: 38703480--38703521 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
38703470 AAGGTAAAAC
38703480 TTTTATATTTTT
1 TTTTATATTTTT
*
38703492 TTTTGT-TTTTT
1 TTTTATATTTTT
*
38703503 TATTTATATTTCT
1 T-TTTATATTTTT
38703516 TTTTAT
1 TTTTAT
38703522 CTATGTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 6 0.24
12 14 0.56
13 5 0.20
ACGTcount: A:0.14, C:0.02, G:0.02, T:0.81
Consensus pattern (12 bp):
TTTTATATTTTT
Found at i:38710811 original size:2 final size:2
Alignment explanation
Indices: 38710804--38710839 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
38710794 TGTTAAAAAG
38710804 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
38710840 CCATCCTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38715508 original size:3 final size:3
Alignment explanation
Indices: 38715500--38715533 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
38715490 TGCATAAGGG
38715500 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
38715534 TCTTTTTGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (3 bp):
CAT
Found at i:38723493 original size:44 final size:47
Alignment explanation
Indices: 38723343--38723652 Score: 174
Period size: 47 Copynumber: 6.6 Consensus size: 47
38723333 TTGCCGCTGC
* * * *
38723343 CATGTCCCAGACATGGTCTTACGCTGGCTATC-TCCATCGAGGCCGATG
1 CATGTCCCAGACAT-GTCTTACACTAGCTAACAT-CATTGAGGCCGATG
* ** * * ** * *
38723391 CCATGTCTCAGACATGGTCTTACACTAGCTCTCGTGTATACATGCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCTAACAT-CATTGAGGCCGATG
38723441 CATGTCCCAGACATGTCTTACACTAGCATGAA-A-C-TT-A-GCCGATG
1 CATGTCCCAGACATGTCTTACACTAGC-T-AACATCATTGAGGCCGATG
* * **
38723485 CATGTCCCAGACACGTCTTACACTGGCTAACATCATTGAGGCTAATG
1 CATGTCCCAGACATGTCTTACACTAGCTAACATCATTGAGGCCGATG
* *
38723532 CATGTCCCAGACATGTCTTACACTGGC--AC-TCACCTCT-ACGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTAACATCA--T-TGAGGCCGATG
** ** * * * *
38723578 CCATGTCCCAGATGTGGTCTTACACGGGCTATCATGA-TGCGGCTGATG
1 -CATGTCCCAGACAT-GTCTTACACTAGCTAACATCATTGAGGCCGATG
* *
38723626 CATGTACCAGACACGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
38723653 CCCCGTCTCA
Statistics
Matches: 205, Mismatches: 39, Indels: 37
0.73 0.14 0.13
Matches are distributed among these distances:
42 2 0.01
43 2 0.01
44 35 0.17
45 5 0.02
46 20 0.10
47 55 0.27
48 31 0.15
49 42 0.20
50 11 0.05
51 2 0.01
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (47 bp):
CATGTCCCAGACATGTCTTACACTAGCTAACATCATTGAGGCCGATG
Found at i:38723644 original size:94 final size:91
Alignment explanation
Indices: 38723384--38723652 Score: 274
Period size: 94 Copynumber: 2.9 Consensus size: 91
38723374 CTCCATCGAG
* * * * * *
38723384 GCCGATGCCATGTCTCAGACATGGTCTTACACTAGCTCTCGTGTATACATGCTGATGCATGTCCC
1 GCCGATGCCATGTCCCAGA-ATGGTCTTACACTGGCTATCATG-ATGC-GGCTGATGCATGTCCC
38723449 AGACATGTCTTACACTAGCATGAAACTTA
63 AGACATGTCTTACACTAGCATGAAACTTA
* * * * *
38723478 GCCGATG-CATGTCCCAGACA-CGTCTTACACTGGCTAACATCATTGAGGCTAATGCATGTCCCA
1 GCCGATGCCATGTCCCAGA-ATGGTCTTACACTGGCTATCATGA-TGCGGCTGATGCATGTCCCA
* * *
38723541 GACATGTCTTACACTGGCACT-CACCTCTA
64 GACATGTCTTACACTAGCA-TGAAACT-TA
* * *
38723570 CGCCGATGCCATGTCCCAGATGTGGTCTTACACGGGCTATCATGATGCGGCTGATGCATGTACCA
1 -GCCGATGCCATGTCCCAGA-ATGGTCTTACACTGGCTATCATGATGCGGCTGATGCATGTCCCA
*
38723635 GACACGTCTTACACTAGC
64 GACATGTCTTACACTAGC
38723653 CCCCGTCTCA
Statistics
Matches: 144, Mismatches: 25, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
91 37 0.26
92 19 0.13
93 19 0.13
94 51 0.35
95 18 0.12
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (91 bp):
GCCGATGCCATGTCCCAGAATGGTCTTACACTGGCTATCATGATGCGGCTGATGCATGTCCCAGA
CATGTCTTACACTAGCATGAAACTTA
Found at i:38729210 original size:16 final size:16
Alignment explanation
Indices: 38729189--38729232 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
38729179 GTTCTATTTC
38729189 ATTTATTATACTTAAT
1 ATTTATTATACTTAAT
* *
38729205 ATTTATT-TATCATATT
1 ATTTATTATA-CTTAAT
38729221 ATTTATTATACT
1 ATTTATTATACT
38729233 ACATATACTT
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (16 bp):
ATTTATTATACTTAAT
Found at i:38730675 original size:24 final size:24
Alignment explanation
Indices: 38730639--38730767 Score: 215
Period size: 24 Copynumber: 5.4 Consensus size: 24
38730629 CTGGAGGCCT
*
38730639 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
38730664 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
38730688 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
38730711 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
38730735 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
38730759 AGCCCTTTT
1 AGCCCTTTT
38730768 TCACTTCCTC
Statistics
Matches: 101, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
23 23 0.23
24 74 0.73
25 4 0.04
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:38730715 original size:47 final size:48
Alignment explanation
Indices: 38730639--38730767 Score: 215
Period size: 47 Copynumber: 2.7 Consensus size: 48
38730629 CTGGAGGCCT
*
38730639 AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATA
1 AGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
*
38730688 AGCCC-TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
*
38730735 AGCCCTTTTGATAACTGGGGCATAAGCCCTTTT
1 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
38730768 TCACTTCCTC
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
47 45 0.59
48 27 0.36
49 4 0.05
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (48 bp):
AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
Found at i:38730841 original size:20 final size:20
Alignment explanation
Indices: 38730816--38730862 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
38730806 TTATGATTAC
38730816 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
38730836 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
38730856 ACCATGT
1 ATCATGT
38730863 TTATCAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.11, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:38730931 original size:25 final size:25
Alignment explanation
Indices: 38730899--38730946 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
38730889 ATACATAAAC
* * *
38730899 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
38730924 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
38730947 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:38738712 original size:24 final size:24
Alignment explanation
Indices: 38738676--38738827 Score: 254
Period size: 24 Copynumber: 6.4 Consensus size: 24
38738666 CTGGAGGCCT
*
38738676 AGCCTCTTTTAATAACTGGGGCAAA
1 AGCC-CTTTTAATAACTGGGGCATA
38738701 AGCCCTTTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
38738725 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
38738748 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
*
38738772 AGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
38738796 AGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATA
38738819 AGCCCTTTT
1 AGCCCTTTT
38738828 TCACTTCCTC
Statistics
Matches: 122, Mismatches: 3, Indels: 5
0.94 0.02 0.04
Matches are distributed among these distances:
23 45 0.37
24 73 0.60
25 4 0.03
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
AGCCCTTTTAATAACTGGGGCATA
Found at i:38738762 original size:71 final size:71
Alignment explanation
Indices: 38738676--38738827 Score: 268
Period size: 71 Copynumber: 2.1 Consensus size: 71
38738666 CTGGAGGCCT
38738676 AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTG
1 AGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTG
38738741 GGGCATA
65 GGGCATA
* * *
38738748 AGCCCTTTTGATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTAATAACTGG
1 AGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGG
38738813 GGCATA
66 GGCATA
38738819 AGCCCTTTT
1 AGCCCTTTT
38738828 TCACTTCCTC
Statistics
Matches: 77, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
71 73 0.95
72 4 0.05
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (71 bp):
AGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTAATAACTGG
GGCATA
Found at i:38738827 original size:47 final size:48
Alignment explanation
Indices: 38738676--38738827 Score: 254
Period size: 47 Copynumber: 3.2 Consensus size: 48
38738666 CTGGAGGCCT
*
38738676 AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTAATAACTGGGGCATA
1 AGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
*
38738725 AGCCC-TTTAATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
*
38738772 AGCCCTTTTGATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATA
1 AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
38738819 AGCCCTTTT
1 AGCCCTTTT
38738828 TCACTTCCTC
Statistics
Matches: 98, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
47 71 0.72
48 23 0.23
49 4 0.04
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.29
Consensus pattern (48 bp):
AGCCCTTTTAATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATA
Found at i:38738901 original size:20 final size:20
Alignment explanation
Indices: 38738876--38738942 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
38738866 TTATGATTAC
38738876 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
38738896 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
38738916 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
38738936 ACCATGT
1 ATCATGT
38738943 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:38738907 original size:11 final size:11
Alignment explanation
Indices: 38738876--38738931 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
38738866 TTATGATTAC
38738876 ATCATGTGCAT
1 ATCATGTGCAT
*
38738887 ATCA--TACAT
1 ATCATGTGCAT
38738896 ATCATGTGCAT
1 ATCATGTGCAT
*
38738907 ATCA--TACAT
1 ATCATGTGCAT
*
38738916 GTCATGTGCAT
1 ATCATGTGCAT
38738927 ATCAT
1 ATCAT
38738932 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:38739011 original size:25 final size:25
Alignment explanation
Indices: 38738979--38739026 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
38738969 ATACATAAAC
* * *
38738979 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
38739004 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
38739027 CATGTTATAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:38743648 original size:40 final size:40
Alignment explanation
Indices: 38743592--38743754 Score: 290
Period size: 40 Copynumber: 4.1 Consensus size: 40
38743582 AATTGTGCTA
*
38743592 GTTATTATAACTGGGTTAAGTCCCGAAGGCATTCGTGCGG
1 GTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGG
38743632 GTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGG
1 GTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGG
*
38743672 GTTATTATAACCGGGTTAAGTCCCGAAGGCATTTGTGCGG
1 GTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGG
* *
38743712 GTTATTATAACCGGGTTAAGTCTCGAAGGCATTCGTGCTG
1 GTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGG
38743752 GTT
1 GTT
38743755 GTTACATCCG
Statistics
Matches: 118, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 118 1.00
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (40 bp):
GTTATTATAACCGGGTTAAGTCCCGAAGGCATTCGTGCGG
Found at i:38752888 original size:19 final size:20
Alignment explanation
Indices: 38752851--38752888 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38752841 CTTCATTTTT
*
38752851 CTCCCCTCTCTCTCTCCCTC
1 CTCCCCTCTCTCTCACCCTC
38752871 CTCCCCTCT-TCTCACCCT
1 CTCCCCTCTCTCTCACCCT
38752889 TGCACACCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.03, C:0.63, G:0.00, T:0.34
Consensus pattern (20 bp):
CTCCCCTCTCTCTCACCCTC
Found at i:38762540 original size:68 final size:64
Alignment explanation
Indices: 38762417--38762675 Score: 202
Period size: 68 Copynumber: 3.9 Consensus size: 64
38762407 TGGATGATAC
** * * *
38762417 AGATAGTATGTAGCTAGGTCACATGTATGATGCTGA-GTGCACATCATGTGTACAAGAGAGCTAC
1 AGATA-TATGTAGCTAGGTCACATGGGTGATACT-ATGTGTACACCATGTGTACAAGAGAGCTAC
38762481 AAG
64 --G
* *
38762484 ACATTATGATGTAGCTAGGTCGCATGGGTGATACTATGTGTACACCATGTAG-ACAAGAGAGCTA
1 AGA-TAT-ATGTAGCTAGGTCACATGGGTGATACTATGTGTACACCATGT-GTACAAGAGAGCTA
38762548 CG
63 CG
* ** * * * * * *
38762550 GGATATATGTAGCTAGGTTGCATGCGTGGTTCCAGGTGAAGGACACCATGTAG-ACAAGAGAGCT
1 AGATATATGTAGCTAGGTCACATGGGTGATACTA--TG-TGTACACCATGT-GTACAAGAGAGCT
38762614 ACG
62 ACG
* * * * *
38762617 AGATAAAT-TGGCTAGGTCACATGGGTGGTACTAAGTGTTCACCATGTGTACAAGAGAGC
1 AGATATATGTAGCTAGGTCACATGGGTGATACTATGTGTACACCATGTGTACAAGAGAGC
38762676 CGAACTATAT
Statistics
Matches: 156, Mismatches: 28, Indels: 20
0.76 0.14 0.10
Matches are distributed among these distances:
62 1 0.01
63 19 0.12
64 24 0.15
65 3 0.02
66 23 0.15
67 36 0.23
68 49 0.31
69 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.25
Consensus pattern (64 bp):
AGATATATGTAGCTAGGTCACATGGGTGATACTATGTGTACACCATGTGTACAAGAGAGCTACG
Found at i:38766637 original size:49 final size:49
Alignment explanation
Indices: 38766537--38766661 Score: 164
Period size: 49 Copynumber: 2.5 Consensus size: 49
38766527 GATGCCGACT
*
38766537 CCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGTGAGGCCGATG
1 CCATGTCCCAGACA-GGTCTTACACTGGCTTTCATATAGTGAGGCCAATG
* * * *
38766587 CCATGTCCTAGACAGGTCTTACACTGG-TTCTCATCTA-TCGATGTCAATG
1 CCATGTCCCAGACAGGTCTTACACTGGCTT-TCATATAGT-GAGGCCAATG
38766636 CCATGTCCCAGACAGGTCTTACACTG
1 CCATGTCCCAGACAGGTCTTACACTG
38766662 ACACCCCACA
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
48 3 0.04
49 51 0.76
50 13 0.19
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.29
Consensus pattern (49 bp):
CCATGTCCCAGACAGGTCTTACACTGGCTTTCATATAGTGAGGCCAATG
Found at i:38766789 original size:46 final size:48
Alignment explanation
Indices: 38766676--38766895 Score: 200
Period size: 46 Copynumber: 4.6 Consensus size: 48
38766666 CCCACAAGCT
* * * *
38766676 GATGCCATGTCCCAGATAGGTCTTACACTAGCTTGT-ATATCGCGAGGCC
1 GATG-CATGTCCCAGACATGTCTTACACTAGC-TGTAATATCTCAAGGCC
* * *
38766725 GATGCATGTCCCAAACATGTCTTACACTAGCTGT-A-GTCTCAATGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTGTAATATCTCAAGGCC
* * *
38766771 GATGTATGTCCCAGACATGTCTTACACTGGCT-TAAATATCTTAAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTGT-AATATCTCAAGGCC
* * * * * * * * *
38766819 GTTGCATGTCCCATACATGTTTTACACTGGCTCTCAT-GCT-ATGGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCTGTAATATCTCAAGGCC
38766865 GATGCATGTCCCAGACATGTCTTACACTAGC
1 GATGCATGTCCCAGACATGTCTTACACTAGC
38766896 ACACATATCA
Statistics
Matches: 142, Mismatches: 25, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
45 1 0.01
46 67 0.47
47 7 0.05
48 62 0.44
49 5 0.04
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (48 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTGTAATATCTCAAGGCC
Found at i:38766904 original size:94 final size:93
Alignment explanation
Indices: 38766673--38766895 Score: 252
Period size: 94 Copynumber: 2.4 Consensus size: 93
38766663 CACCCCACAA
* * ** *
38766673 GCTGATGCCATGTCCCAGATAGGTCTTACACTAGCTTGTATATCGCGAGGCCGATGCATGTCCCA
1 GCTGATG-CATGTCCCAGACATGTCTTACACTAGCTTAAATATCGCAAGGCCGATGCATGTCCCA
*
38766738 AACATGTCTTACACTAGCTGTAGTCTCAAT
65 AACATGTCTTACACTAGCTCTAGTCT-AAT
* * * ** * *
38766768 GCCGATGTATGTCCCAGACATGTCTTACACTGGCTTAAATATCTTAAGGCCGTTGCATGTCCCAT
1 GCTGATGCATGTCCCAGACATGTCTTACACTAGCTTAAATATCGCAAGGCCGATGCATGTCCCAA
* *
38766833 ACATGTTTTACACTGGCTCTCA-TGCT-AT
66 ACATGTCTTACACTAGCTCT-AGT-CTAAT
38766861 GGCTGATGCATGTCCCAGACATGTCTTACACTAGC
1 -GCTGATGCATGTCCCAGACATGTCTTACACTAGC
38766896 ACACATATCA
Statistics
Matches: 107, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
93 2 0.02
94 96 0.90
95 9 0.08
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.30
Consensus pattern (93 bp):
GCTGATGCATGTCCCAGACATGTCTTACACTAGCTTAAATATCGCAAGGCCGATGCATGTCCCAA
ACATGTCTTACACTAGCTCTAGTCTAAT
Found at i:38767388 original size:19 final size:18
Alignment explanation
Indices: 38767358--38767399 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
38767348 AAAAGCAGCC
38767358 CACAATTTTCAT-TATTT
1 CACAATTTTCATCTATTT
38767375 CACACATTTATCATCTATTT
1 CACA-ATTT-TCATCTATTT
*
38767395 TACAA
1 CACAA
38767400 CTTATGCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 4 0.19
18 4 0.19
19 5 0.24
20 8 0.38
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.45
Consensus pattern (18 bp):
CACAATTTTCATCTATTT
Found at i:38771803 original size:53 final size:54
Alignment explanation
Indices: 38771735--38772050 Score: 352
Period size: 53 Copynumber: 5.9 Consensus size: 54
38771725 TTTCCTTTTT
* * * *
38771735 GAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * * *
38771788 GAACTCACCAATGCCATGCCTTGGCATGATCTTACATGGGA-CCTTTACCTTATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATA
* ** *
38771842 GTAATTCATTAATGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-
1 G-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * *
38771896 GAATTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTATA
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCCTTATA
* * * * *
38771950 GTAACTCATCAATGTCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATA
1 G-AACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
* * * *
38772005 GAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
38772051 ATCTTACCAA
Statistics
Matches: 221, Mismatches: 34, Indels: 15
0.82 0.13 0.06
Matches are distributed among these distances:
52 4 0.02
53 86 0.39
54 43 0.19
55 84 0.38
56 4 0.02
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (54 bp):
GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATA
Found at i:38771876 original size:55 final size:53
Alignment explanation
Indices: 38771746--38772042 Score: 330
Period size: 55 Copynumber: 5.5 Consensus size: 53
38771736 AACTTACCAT
* * * *
38771746 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAATTCATCAA
* * * * *
38771799 TGCCATGCCTTGGCATGATCTTACATGGGACCTTTACCTTATAGTAATTCATTAA
1 TGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AATTCATCAA
* *
38771854 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAATTCACCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAATTCATCAA
* * *
38771907 TGCCATGCCTTGGCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
1 TGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTTATAG-AATTCATCAA
* * * *
38771962 TGTCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTT-ATCAA
1 TGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAA-TTCATCAA
*
38772016 TGCCATGCCTTGGCATGGTCTTACATG
1 TGCCATGCCTTGACATGGTCTTACATG
38772043 ATATCCTTAT
Statistics
Matches: 204, Mismatches: 31, Indels: 17
0.81 0.12 0.07
Matches are distributed among these distances:
52 4 0.02
53 77 0.38
54 34 0.17
55 85 0.42
56 4 0.02
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (53 bp):
TGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAATTCATCAA
Found at i:38771935 original size:108 final size:108
Alignment explanation
Indices: 38771746--38772042 Score: 479
Period size: 108 Copynumber: 2.7 Consensus size: 108
38771736 AACTTACCAT
* *
38771746 TGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTATGAACTCACCAATGCCATGCCTTG
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAATTCACCAATGCCATGCCTTG
* * *
38771811 GCATGATCTTACATGGGACCTTTACCTTATAGTAATTCATTAA
66 GCATGGTCTTACATGGGACCTTTACCTTATAGTAACTCATCAA
38771854 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAATTCACCAATGCCATGCCTTG
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAATTCACCAATGCCATGCCTTG
*
38771919 GCATGGTCTTACATGGGACCTTTGCCTTATAGTAACTCATCAA
66 GCATGGTCTTACATGGGACCTTTACCTTATAGTAACTCATCAA
* * * *
38771962 TGTCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAACTT-ATCAATGCCATGCCT
1 TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTAT-GAA-TTCACCAATGCCATGCCT
38772026 TGGCATGGTCTTACATG
64 TGGCATGGTCTTACATG
38772043 ATATCCTTAT
Statistics
Matches: 177, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
108 141 0.80
109 34 0.19
110 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (108 bp):
TGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCCTTATGAATTCACCAATGCCATGCCTTG
GCATGGTCTTACATGGGACCTTTACCTTATAGTAACTCATCAA
Found at i:38772082 original size:47 final size:47
Alignment explanation
Indices: 38772029--38772150 Score: 192
Period size: 47 Copynumber: 2.6 Consensus size: 47
38772019 CATGCCTTGG
*
38772029 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCA-AGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCACA-TTCCAAA
* *
38772076 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCACATTTCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCACATTCCAAA
*
38772123 CATGGTCTTACATGGTATCCTTCTCTTA
1 CATGGTCTTACATGGTATCCTTATCTTA
38772151 GTGCCAATGC
Statistics
Matches: 70, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
47 69 0.99
48 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.12, T:0.35
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCACATTCCAAA
Found at i:38772338 original size:44 final size:44
Alignment explanation
Indices: 38772288--38772373 Score: 111
Period size: 44 Copynumber: 2.0 Consensus size: 44
38772278 TATCCTTAAT
* *
38772288 CGTCAATTCCTCATTAAATGCCATGTTATGAA-CATGGACTTTTC
1 CGTCAATTCCTCATTAAATGCCATGGTA-CAACCATGGACTTTTC
* * *
38772332 CGTCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 CGTCAATTCCTCATTAAATGCCATGGTACAACCATGGACTTT
38772374 GAGATATCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
43 2 0.06
44 34 0.94
ACGTcount: A:0.26, C:0.24, G:0.14, T:0.36
Consensus pattern (44 bp):
CGTCAATTCCTCATTAAATGCCATGGTACAACCATGGACTTTTC
Found at i:38776722 original size:20 final size:21
Alignment explanation
Indices: 38776667--38776722 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
38776657 AAAATAGGGC
*
38776667 ACATGCCAGTGTGGAAGGGTA
1 ACATGCCAGTGTGGTAGGGTA
*
38776688 ACACGCCCA-TGTGGTAGGGTA
1 ACATG-CCAGTGTGGTAGGGTA
*
38776709 A-ATGCCTGTGTGGT
1 ACATGCCAGTGTGGT
38776723 CTTTATGACA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
19 2 0.07
20 8 0.28
21 16 0.55
22 3 0.10
ACGTcount: A:0.23, C:0.18, G:0.36, T:0.23
Consensus pattern (21 bp):
ACATGCCAGTGTGGTAGGGTA
Found at i:38780371 original size:40 final size:40
Alignment explanation
Indices: 38780316--38780539 Score: 279
Period size: 40 Copynumber: 5.5 Consensus size: 40
38780306 TATTCGGATG
*
38780316 ATATCCGGGCTAAGTCCTGAAGGCATTTGTGCAAGTTACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
*
38780356 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGC-A--AGTTACT
* * *
38780399 ATACCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
** * *
38780439 ATATCCGGGCTAAGTCCCGAAGGCATTCATGCTAGTGACT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* * * *
38780479 ATATCTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGCT
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
* *
38780519 ATATCC-TGCTAAATCCCGAAG
1 ATATCCGGGCTAAGTCCCGAAG
38780540 ATACTTGGGT
Statistics
Matches: 161, Mismatches: 20, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
39 12 0.07
40 111 0.69
41 1 0.01
43 37 0.23
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACT
Found at i:38780459 original size:83 final size:80
Alignment explanation
Indices: 38780320--38780539 Score: 275
Period size: 83 Copynumber: 2.7 Consensus size: 80
38780310 CGGATGATAT
* * **
38780320 CCGGGCTAAGTCCTGAAGGCATTTGTGCAAGTTACTATATCCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
38780385 TGCGAGTAGTTG-CTATAC
66 TGC---TAG-TGACTATAC
*
38780403 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
*
38780468 TGCTAGTGACTATAT
66 TGCTAGTGACTATAC
* * * * *
38780483 CTGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTATATCC-TGCTAAATCCCGAAG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAG-TGACTATATCCGGGCTAAGTCCCGAAG
38780540 ATACTTGGGT
Statistics
Matches: 124, Mismatches: 11, Indels: 8
0.87 0.08 0.06
Matches are distributed among these distances:
79 15 0.12
80 44 0.35
81 2 0.02
83 63 0.51
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTGACTATATCCGGGCTAAGTCCCGAAGGCATTCA
TGCTAGTGACTATAC
Found at i:38784800 original size:31 final size:31
Alignment explanation
Indices: 38784765--38784838 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
38784755 TGTTAGATTG
38784765 TGTGGCCTACACAGCCAAACAAACCAAACCA
1 TGTGGCCTACACAGCCAAACAAACCAAACCA
* * * * *
38784796 TGTGGCCTACACGGCCCAACAGACCAGACCG
1 TGTGGCCTACACAGCCAAACAAACCAAACCA
*
38784827 TGTGGCCCACAC
1 TGTGGCCTACAC
38784839 TGCCTAATTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.31, C:0.38, G:0.20, T:0.11
Consensus pattern (31 bp):
TGTGGCCTACACAGCCAAACAAACCAAACCA
Found at i:38785141 original size:140 final size:141
Alignment explanation
Indices: 38784888--38785169 Score: 523
Period size: 140 Copynumber: 2.0 Consensus size: 141
38784878 TGCTCCATAA
38784888 GGCTTAACACACAGCCGTGTGACATAAACTGCAATTTGAAAACAACTTGTTTTATTTTCAAAATT
1 GGCTTAACACACAGCCGTGTGACATAAACTGCAATTTGAAAACAACTTGTTTTATTTTCAAAATT
38784953 TCCAAGTTCTATTTAATGATTTCAGGTTAGAATCACACATCTGATGCTATTAGAATATTTACACT
66 TCCAAGTTCTATTTAATGATTTCAGGTTAGAATCACACATCTGATGCTATTAGAATATTTACACT
38785018 AATGCAGCAAT
131 AATGCAGCAAT
*
38785029 GGCTTAACACACGGCCGTGTGACATAAACTGCAATTCT-AAAACAACTTGTTTT-TTTTCAAAAT
1 GGCTTAACACACAGCCGTGTGACATAAACTGCAATT-TGAAAACAACTTGTTTTATTTTCAAAAT
*
38785092 TTCCAAGTTCTATTTGATGATTTCAGGTTAGAATCACACATCTGATGCTATTAGAATATTTACAC
65 TTCCAAGTTCTATTTAATGATTTCAGGTTAGAATCACACATCTGATGCTATTAGAATATTTACAC
38785157 TAATGCAGCAAT
130 TAATGCAGCAAT
38785169 G
1 G
38785170 AGACCTTAAA
Statistics
Matches: 138, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
140 87 0.63
141 50 0.36
142 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (141 bp):
GGCTTAACACACAGCCGTGTGACATAAACTGCAATTTGAAAACAACTTGTTTTATTTTCAAAATT
TCCAAGTTCTATTTAATGATTTCAGGTTAGAATCACACATCTGATGCTATTAGAATATTTACACT
AATGCAGCAAT
Found at i:38790251 original size:46 final size:46
Alignment explanation
Indices: 38790198--38790346 Score: 133
Period size: 46 Copynumber: 3.2 Consensus size: 46
38790188 CCCAAATATG
38790198 GTCTTACACT-GACAATCATCTCGTA-GCCGATGCAAGTCCTAGACAT
1 GTCTTACACTAGACAA-CATCTCG-AGGCCGATGCAAGTCCTAGACAT
* * * * *
38790244 GTCTTACACTAGCCTACGTCTCGAGGCCGATGCATGTCCTGGACAT
1 GTCTTACACTAGACAACATCTCGAGGCCGATGCAAGTCCTAGACAT
* ** * * *
38790290 GTCTTACACTAG-CATTCGCCTCGATGCCGATGCCATGTCCCAGACAT
1 GTCTTACACTAGACA-ACATCTCGAGGCCGATG-CAAGTCCTAGACAT
38790337 GGTCTTACAC
1 -GTCTTACAC
38790347 AGGCTCTCAT
Statistics
Matches: 87, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
45 2 0.02
46 61 0.70
47 15 0.17
48 9 0.10
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (46 bp):
GTCTTACACTAGACAACATCTCGAGGCCGATGCAAGTCCTAGACAT
Found at i:38792411 original size:41 final size:41
Alignment explanation
Indices: 38792354--38792497 Score: 170
Period size: 40 Copynumber: 3.6 Consensus size: 41
38792344 CGAGCTTGGG
38792354 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
* *
38792395 TTCGAAGGGCTTTTGAGCCAGTG-TCATAACCGGACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
* * * * *
38792435 TCCGAAGGGCCTTCGAGCCAGTGGCCTAAT--CCGAGCTTGGT
1 TTCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGT
*
38792476 CTCGAAGGGC-TTTGAGCCAGTG
1 TTCGAAGGGCTTTTGAGCCAGTG
38792498 TTAAGAATCG
Statistics
Matches: 88, Mismatches: 12, Indels: 8
0.81 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 44 0.50
41 40 0.45
43 3 0.03
ACGTcount: A:0.22, C:0.23, G:0.29, T:0.26
Consensus pattern (41 bp):
TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
Found at i:38800838 original size:41 final size:41
Alignment explanation
Indices: 38800777--38800920 Score: 152
Period size: 40 Copynumber: 3.6 Consensus size: 41
38800767 CGAGCTTGGG
38800777 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
* * * *
38800818 TTCAAAGGGCTTTTGAGCCAGTG-TCATAACTGGACTTAGT
1 TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
* * * * *
38800858 TCCGAAGGGCCTTCGAGCCAGTGGCCTAAT--CCGAGCTTGGT
1 TTCGAAGGGCTTTTGAGCCAGT-G-CTAATAACCGAACTTAGT
*
38800899 CTCGAAGGGC-TTTGAGCCAGTG
1 TTCGAAGGGCTTTTGAGCCAGTG
38800921 TTAAGAATCG
Statistics
Matches: 84, Mismatches: 16, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
39 1 0.01
40 42 0.50
41 38 0.45
43 3 0.04
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.27
Consensus pattern (41 bp):
TTCGAAGGGCTTTTGAGCCAGTGCTAATAACCGAACTTAGT
Found at i:38800916 original size:40 final size:40
Alignment explanation
Indices: 38800763--38800920 Score: 137
Period size: 41 Copynumber: 3.9 Consensus size: 40
38800753 TCGGGGTGTA
*
38800763 AATCCGAGCTTGGGTTCGAAGGGCTTTTGAGCCAGT-G-CT
1 AATCCGAGCTT-AGTTCGAAGGGCTTTTGAGCCAGTGGCCT
* * * *
38800802 AATAACCGAACTTAGTTTCAAAGGGCTTTTGAGCCAGTGTCAT
1 AAT--CCGAGCTTAG-TTCGAAGGGCTTTTGAGCCAGTGGCCT
* * *
38800845 AA-CTG-GACTTAGTTCCGAAGGGCCTTCGAGCCAGTGGCCT
1 AATCCGAG-CTTAGTT-CGAAGGGCTTTTGAGCCAGTGGCCT
*
38800885 AATCCGAGCTTGGTCTCGAAGGGC-TTTGAGCCAGTG
1 AATCCGAGCTTAGT-TCGAAGGGCTTTTGAGCCAGTG
38800921 TTAAGAATCG
Statistics
Matches: 94, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
39 5 0.05
40 41 0.44
41 43 0.46
42 2 0.02
43 3 0.03
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.27
Consensus pattern (40 bp):
AATCCGAGCTTAGTTCGAAGGGCTTTTGAGCCAGTGGCCT
Found at i:38810428 original size:25 final size:26
Alignment explanation
Indices: 38810380--38810428 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
38810370 CTTTTCTTTT
* *
38810380 CTTTTCATTTTTAGATTAGGTTTTCC
1 CTTTTCATTTTTAGACTAGATTTTCC
38810406 CTTTTC-TTTTTAGACTAGATTTT
1 CTTTTCATTTTTAGACTAGATTTT
38810429 ATTTTTGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.16, C:0.14, G:0.10, T:0.59
Consensus pattern (26 bp):
CTTTTCATTTTTAGACTAGATTTTCC
Found at i:38815307 original size:19 final size:19
Alignment explanation
Indices: 38815285--38815332 Score: 96
Period size: 19 Copynumber: 2.5 Consensus size: 19
38815275 TCCAAGTTGG
38815285 TAAAATTGAGATCAAGAGA
1 TAAAATTGAGATCAAGAGA
38815304 TAAAATTGAGATCAAGAGA
1 TAAAATTGAGATCAAGAGA
38815323 TAAAATTGAG
1 TAAAATTGAG
38815333 TCACTTAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.52, C:0.04, G:0.21, T:0.23
Consensus pattern (19 bp):
TAAAATTGAGATCAAGAGA
Found at i:38821083 original size:5 final size:5
Alignment explanation
Indices: 38821073--38821098 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
38821063 TTGTGTGTTC
38821073 TTTAT TTTAT TTTAT TTTAT TTTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T
38821099 ACAATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTAT
Found at i:38824335 original size:58 final size:58
Alignment explanation
Indices: 38824264--38824387 Score: 230
Period size: 58 Copynumber: 2.1 Consensus size: 58
38824254 GACTTTGATT
*
38824264 AGGCTTTGTGCCTAGCAGGCTTAGTGCCGGTGAATAAATATCAGACCTTGGGTCTAGC
1 AGGCTTTGCGCCTAGCAGGCTTAGTGCCGGTGAATAAATATCAGACCTTGGGTCTAGC
*
38824322 AGGCTTTGCGCCTAGCAGGCTTAGTGCCGGTGAATAAATATCAGACCTTGGGTCTAGT
1 AGGCTTTGCGCCTAGCAGGCTTAGTGCCGGTGAATAAATATCAGACCTTGGGTCTAGC
38824380 AGGCTTTG
1 AGGCTTTG
38824388 TGCCAGTGTG
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
58 64 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.28
Consensus pattern (58 bp):
AGGCTTTGCGCCTAGCAGGCTTAGTGCCGGTGAATAAATATCAGACCTTGGGTCTAGC
Found at i:38824615 original size:35 final size:35
Alignment explanation
Indices: 38824576--38824663 Score: 83
Period size: 35 Copynumber: 2.5 Consensus size: 35
38824566 ATTTAATTAC
* ** *
38824576 ATGTGAGTTTATATTGAATTTGTGTATT-TGGTCAT
1 ATGTGAGTTTATATTGAATGTGCATATTCT-GCCAT
*
38824611 ATGTGAAG-TTATTTTGAATGTGCATATTCTGCCAT
1 ATGTG-AGTTTATATTGAATGTGCATATTCTGCCAT
38824646 ATGTGA-TGTTATATTGAA
1 ATGTGAGT-TTATATTGAA
38824664 ATTGAACTAT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
34 1 0.02
35 39 0.91
36 3 0.07
ACGTcount: A:0.26, C:0.06, G:0.22, T:0.47
Consensus pattern (35 bp):
ATGTGAGTTTATATTGAATGTGCATATTCTGCCAT
Found at i:38833731 original size:35 final size:35
Alignment explanation
Indices: 38833692--38833779 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 35
38833682 ATTTGATTAC
* ** *
38833692 ATGTGAGTTTATATTGAATTTGTGTATTTGGTCAT
1 ATGTGAGTTTATATTGAATGTGCATATTTGGCCAT
*
38833727 ATGTGCAG-TTATTTTGAATGTGCATATTTGGCCAT
1 ATGTG-AGTTTATATTGAATGTGCATATTTGGCCAT
38833762 ATGTGA-TGTTATATTGAA
1 ATGTGAGT-TTATATTGAA
38833780 ACTGAACTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
34 1 0.02
35 41 0.93
36 2 0.05
ACGTcount: A:0.25, C:0.06, G:0.23, T:0.47
Consensus pattern (35 bp):
ATGTGAGTTTATATTGAATGTGCATATTTGGCCAT
Found at i:38838775 original size:27 final size:27
Alignment explanation
Indices: 38838744--38838797 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
38838734 TGTCATGTGA
*
38838744 AATTGAATGGCAAATTATTATCACATG
1 AATTGAATGGCAAATTACTATCACATG
** *
38838771 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATCACATG
38838798 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATCACATG
Found at i:38839122 original size:49 final size:49
Alignment explanation
Indices: 38839045--38839274 Score: 244
Period size: 49 Copynumber: 4.6 Consensus size: 49
38839035 TATTGTGAGG
* * *
38839045 TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCGGATAATTGG
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGA
* * * * *
38839094 TCGCATGTGTAGTACTAAGTGCAAGCTACTATGCGTACCCGATAACTTTGA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAA--TTGA
* * * * * **
38839145 TCACGTGTGTAGTACTAAGTGTAGGCTACTACATGTATCAGATGGTTAGA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATT-GA
* * * *
38839195 TCACATGTTTAGTACTAAGTGCAGGCTACTACGTGTAACGAATAATTGG
1 TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGA
* *
38839244 TCGCATGTGTAGTACTAAGTGTAGGCTACTA
1 TCACATGTGTAGTACTAAGTGCAGGCTACTA
38839275 TGCGTACCAG
Statistics
Matches: 148, Mismatches: 30, Indels: 6
0.80 0.16 0.03
Matches are distributed among these distances:
49 71 0.48
50 40 0.27
51 37 0.25
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.30
Consensus pattern (49 bp):
TCACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGA
Found at i:38839286 original size:99 final size:99
Alignment explanation
Indices: 38839045--38839287 Score: 265
Period size: 100 Copynumber: 2.4 Consensus size: 99
38839035 TATTGTGAGG
* * * * * *
38839045 TCACGTGTGTAGTACTAAGTGCAAGCTACTACGTGTACCGGATAATTGGTCGCATGTGTAGTACT
1 TCACATGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAATTGATCACATGTGTAGTACT
* *
38839110 AAGTGCAAGCTACTATGCGTACCCGATAACTTTGA
66 AAGTGCAAGCTACTACGCGTACACGATAAC-TTGA
* * * ** *
38839145 TCACGTGTGTAGTACTAAGTGTAGGCTACTACATGTATCAGATGGTTAGATCACATGTTTAGTAC
1 TCACATGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAATT-GATCACATGTGTAGTAC
* * *
38839210 TAAGTGCAGGCTACTACGTGTA-ACGAATAA-TTGG
65 TAAGTGCAAGCTACTACGCGTACACG-ATAACTTGA
* * *
38839244 TCGCATGTGTAGTACTAAGTGTAGGCTACTATGCGTACCAGATA
1 TCACATGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATA
38839288 GCCTTGTCTA
Statistics
Matches: 119, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
99 40 0.34
100 42 0.35
101 37 0.31
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (99 bp):
TCACATGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATAATTGATCACATGTGTAGTACT
AAGTGCAAGCTACTACGCGTACACGATAACTTGA
Found at i:38840427 original size:78 final size:79
Alignment explanation
Indices: 38840277--38840438 Score: 281
Period size: 78 Copynumber: 2.0 Consensus size: 79
38840267 TTAATTCAAA
38840277 TATTAGAAATATCAAGTGAATGGCATGTATAGGAAGAAGTTGGTTTGTGATATGTATTATTATTA
1 TATTAGAAATATCAAGTGAATGGCATGTAT--GAAGAAGTTGGTTTGTGATATGTATTATTATTA
38840342 TGACTTTGACCATACG
64 TGACTTTGACCATACG
* *
38840358 TATTAGAAATATCAAGTGAGTGGCATGTAT-AAGAATTTGGTTTGTGATATGTATTATTATTATG
1 TATTAGAAATATCAAGTGAATGGCATGTATGAAGAAGTTGGTTTGTGATATGTATTATTATTATG
38840422 ACTTTGACCATACG
66 ACTTTGACCATACG
38840436 TAT
1 TAT
38840439 CAGTTTGCAA
Statistics
Matches: 79, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
78 50 0.63
81 29 0.37
ACGTcount: A:0.33, C:0.07, G:0.21, T:0.39
Consensus pattern (79 bp):
TATTAGAAATATCAAGTGAATGGCATGTATGAAGAAGTTGGTTTGTGATATGTATTATTATTATG
ACTTTGACCATACG
Found at i:38844794 original size:25 final size:27
Alignment explanation
Indices: 38844764--38844815 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
38844754 TGTCATGTGA
38844764 AATTGAATGGCAAATTA-T-TTACATG
1 AATTGAATGGCAAATTACTATTACATG
**
38844789 AATTGAATGTTAAATTACTATTACATG
1 AATTGAATGGCAAATTACTATTACATG
38844816 GGTTGTATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 15 0.65
26 1 0.04
27 7 0.30
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.38
Consensus pattern (27 bp):
AATTGAATGGCAAATTACTATTACATG
Found at i:38845138 original size:48 final size:50
Alignment explanation
Indices: 38845062--38845182 Score: 174
Period size: 48 Copynumber: 2.5 Consensus size: 50
38845052 TCTATTGTGA
* *
38845062 GGTCACATGTGTAGTACTAAGTGCAGCTACTACGTGTACCGGATAA-TT-
1 GGTCACATGTGTAGTACTAAGTGCAGCTACTACGCGTACCCGATAACTTC
* *
38845110 GGTCGCATGTGTAGTACTAAGTGCAGCTACTATGCGTACCCGATAACTTC
1 GGTCACATGTGTAGTACTAAGTGCAGCTACTACGCGTACCCGATAACTTC
* *
38845160 GATCACGTGTGTAGTACTAAGTG
1 GGTCACATGTGTAGTACTAAGTG
38845183 TTGGCTACTA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
48 42 0.66
49 2 0.03
50 20 0.31
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (50 bp):
GGTCACATGTGTAGTACTAAGTGCAGCTACTACGCGTACCCGATAACTTC
Found at i:38845233 original size:31 final size:32
Alignment explanation
Indices: 38845195--38845258 Score: 121
Period size: 31 Copynumber: 2.0 Consensus size: 32
38845185 GGCTACTACA
38845195 TGTATCAGATGGTTAGG-TACATGTGTAGTAC
1 TGTATCAGATGGTTAGGTTACATGTGTAGTAC
38845226 TGTATCAGATGGTTAGGTTACATGTGTAGTAC
1 TGTATCAGATGGTTAGGTTACATGTGTAGTAC
38845258 T
1 T
38845259 AAGTGCGGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 17 0.53
32 15 0.47
ACGTcount: A:0.25, C:0.09, G:0.28, T:0.38
Consensus pattern (32 bp):
TGTATCAGATGGTTAGGTTACATGTGTAGTAC
Found at i:38851259 original size:26 final size:26
Alignment explanation
Indices: 38851223--38851276 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
38851213 AGGAAAGAAA
*
38851223 GAAAGAATATTGGAATTTGTTTGTAT
1 GAAAGAATATTGGAATTTGTTGGTAT
38851249 GAAAGAATATTGGAATTTGTTGGTAT
1 GAAAGAATATTGGAATTTGTTGGTAT
38851275 GA
1 GA
38851277 TTTCCAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (26 bp):
GAAAGAATATTGGAATTTGTTGGTAT
Found at i:38858259 original size:17 final size:18
Alignment explanation
Indices: 38858237--38858270 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
38858227 GAAAATTCAA
38858237 TATATATATATA-TATTG
1 TATATATATATACTATTG
*
38858254 TATATATTTATACTATT
1 TATATATATATACTATT
38858271 TATTAAGCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TATATATATATACTATTG
Found at i:38861125 original size:27 final size:27
Alignment explanation
Indices: 38861087--38861139 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
38861077 GGTAGGGGTC
38861087 AGTCTCTTCCTATAATGGAAATTGAAT
1 AGTCTCTTCCTATAATGGAAATTGAAT
38861114 AGTCTCTTCCTATAATGGAAATTGAA
1 AGTCTCTTCCTATAATGGAAATTGAA
38861140 CCTTTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (27 bp):
AGTCTCTTCCTATAATGGAAATTGAAT
Found at i:38861520 original size:17 final size:17
Alignment explanation
Indices: 38861498--38861546 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
38861488 TTATAATATC
38861498 ATTAATTACTTTAAATA
1 ATTAATTACTTTAAATA
**
38861515 ATTAA-TACTATTATCTA
1 ATTAATTACT-TTAAATA
*
38861532 ATTAGTTACTTTAAA
1 ATTAATTACTTTAAA
38861547 ATCATATTTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
16 4 0.16
17 17 0.68
18 4 0.16
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (17 bp):
ATTAATTACTTTAAATA
Found at i:38863986 original size:22 final size:22
Alignment explanation
Indices: 38863961--38864014 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
38863951 AATTAATAAA
38863961 AATATTAAATATATTT-TAAATT
1 AATATTAAATATATTTAT-AATT
*
38863983 AATATTATATATATTTATAATT
1 AATATTAAATATATTTATAATT
38864005 AA-ATTTAAAT
1 AATA-TTAAAT
38864015 TAAAAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 1 0.04
22 26 0.93
23 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
AATATTAAATATATTTATAATT
Found at i:38868593 original size:20 final size:20
Alignment explanation
Indices: 38868568--38868631 Score: 83
Period size: 20 Copynumber: 3.1 Consensus size: 20
38868558 CTTGTACAGG
*
38868568 TTTGCACTTTGGTGCCTCTA
1 TTTGCACTTCGGTGCCTCTA
*
38868588 TTTGCACTTCGATGCCTCTGTA
1 TTTGCACTTCGGTGCCTC--TA
*
38868610 TTTGCACTACGGTGCCTCTA
1 TTTGCACTTCGGTGCCTCTA
38868630 TT
1 TT
38868632 AGCATTTCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
20 20 0.53
22 18 0.47
ACGTcount: A:0.12, C:0.27, G:0.19, T:0.42
Consensus pattern (20 bp):
TTTGCACTTCGGTGCCTCTA
Found at i:38868614 original size:22 final size:21
Alignment explanation
Indices: 38868568--38868628 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 21
38868558 CTTGTACAGG
*
38868568 TTTGCACTTTGGTGCCTC-TA
1 TTTGCACTTCGGTGCCTCTTA
*
38868588 TTTGCACTTCGATGCCTCTGTA
1 TTTGCACTTCGGTGCCTCT-TA
*
38868610 TTTGCACTACGGTGCCTCT
1 TTTGCACTTCGGTGCCTCT
38868629 ATTAGCATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 16 0.46
22 19 0.54
ACGTcount: A:0.11, C:0.28, G:0.20, T:0.41
Consensus pattern (21 bp):
TTTGCACTTCGGTGCCTCTTA
Found at i:38870975 original size:30 final size:30
Alignment explanation
Indices: 38870940--38870996 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
38870930 AGGCACTTCT
38870940 ACACGGGT-GATCCACACGT-CCGTGTGTGAC
1 ACACGGGTAGA-CCACAC-TCCCGTGTGTGAC
38870970 ACACGGGTAGACCACACTCCCGTGTGT
1 ACACGGGTAGACCACACTCCCGTGTGT
38870997 CACGCCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
29 1 0.04
30 22 0.88
31 2 0.08
ACGTcount: A:0.21, C:0.32, G:0.28, T:0.19
Consensus pattern (30 bp):
ACACGGGTAGACCACACTCCCGTGTGTGAC
Found at i:38874443 original size:47 final size:47
Alignment explanation
Indices: 38874389--38874766 Score: 535
Period size: 47 Copynumber: 8.1 Consensus size: 47
38874379 TTAGGATTTT
** * * * *
38874389 ATGTGATGAATGTGAATGTGTATATATGAGATAAGGTCGAATGGCAA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
38874436 ATGTGATGAATGTGAACATGCATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
38874483 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
38874530 ATGTGATGAATGTGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * *
38874577 ATGTGATGAATATGAACATGCGTATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
*
38874624 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAGTGG-CA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* *
38874670 ATGTGATGAATGTGAACATGCATATATGTGACAAGGCAGAATGGCCA
1 ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
* * * * * * *
38874717 ATGTGATGAACGTGGAA-GTGTATAAATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGT-GAACATGCATATATGTGATAAGGCCGAATGGCCA
38874764 ATG
1 ATG
38874767 CGAAATGTGT
Statistics
Matches: 304, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
46 43 0.14
47 258 0.85
48 3 0.01
ACGTcount: A:0.34, C:0.11, G:0.30, T:0.26
Consensus pattern (47 bp):
ATGTGATGAATGTGAACATGCATATATGTGATAAGGCCGAATGGCCA
Found at i:38874536 original size:22 final size:22
Alignment explanation
Indices: 38874465--38874536 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 22
38874455 GCATATATGA
38874465 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
* * *
38874487 GATGAATG-TGAACAT-GCATATATGT
1 GAT-AAGGCCG-A-ATGGC-CA-ATGT
38874512 GATAAGGCCGAATGGCCAATGT
1 GATAAGGCCGAATGGCCAATGT
38874534 GAT
1 GAT
38874537 GAATGTGAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 14
0.65 0.11 0.25
Matches are distributed among these distances:
22 11 0.30
23 9 0.24
24 9 0.24
25 8 0.22
ACGTcount: A:0.33, C:0.14, G:0.29, T:0.24
Consensus pattern (22 bp):
GATAAGGCCGAATGGCCAATGT
Found at i:38876236 original size:29 final size:29
Alignment explanation
Indices: 38876202--38876362 Score: 81
Period size: 29 Copynumber: 5.6 Consensus size: 29
38876192 TACTCGATTT
*
38876202 CGCACACTTAGTGCCATGCGATTTAG-GCC
1 CGCACACTTAGTGCCATGC-ACTTAGAGCC
** * * *
38876231 CGCACACACAGTGCCATGCCCTTCGAGCT
1 CGCACACTTAGTGCCATGCACTTAGAGCC
** * ** *
38876260 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATGCACTTAGAGCC
* ** * ** *
38876289 TGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATGCACTTAGAGCC
** * ** *
38876318 CGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATGCACTTAGAGCC
38876347 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
38876363 ATCTCGTCAC
Statistics
Matches: 115, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
28 3 0.03
29 112 0.97
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.25
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTAGAGCC
Found at i:38876294 original size:58 final size:58
Alignment explanation
Indices: 38876231--38876362 Score: 183
Period size: 58 Copynumber: 2.3 Consensus size: 58
38876221 GATTTAGGCC
** * * * *
38876231 CGCACACACAGTGCCATGCCCTTCGAGCTCGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
* * *
38876289 TGCACACTTAGTGCCATATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCATACACTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
38876347 CGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
38876363 ATCTCGTCAC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
58 64 1.00
ACGTcount: A:0.26, C:0.33, G:0.16, T:0.25
Consensus pattern (58 bp):
CGCACACTTAGTGCCATACACTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
Found at i:38877629 original size:1 final size:1
Alignment explanation
Indices: 38877623--38877655 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
38877613 CATGAGACCA
38877623 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
38877656 GTTCCCTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:38878112 original size:46 final size:46
Alignment explanation
Indices: 38878045--38878146 Score: 132
Period size: 46 Copynumber: 2.2 Consensus size: 46
38878035 GGCTGTCACA
* * * *
38878045 GTATGAGATGGATATGAGGTAAAGCCGAATGGCTAATGCGAAACGT
1 GTATGAGATGGACATGAGGTAAAGCCAAATGGATAATGCGAAACAT
* * * *
38878091 GTATGAGATGGACATGCGGTAAAGCCAAATGGATAATGTGAGATAT
1 GTATGAGATGGACATGAGGTAAAGCCAAATGGATAATGCGAAACAT
38878137 GTATGAGATG
1 GTATGAGATG
38878147 TGTATATATA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 48 1.00
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.24
Consensus pattern (46 bp):
GTATGAGATGGACATGAGGTAAAGCCAAATGGATAATGCGAAACAT
Found at i:38879689 original size:40 final size:40
Alignment explanation
Indices: 38879637--38879952 Score: 533
Period size: 40 Copynumber: 7.9 Consensus size: 40
38879627 GTTATATATG
*
38879637 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGAGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
38879677 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
* *
38879717 ATCCGGGCTAAGTCCTGAAGAGCATACGTACTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
* *
38879757 ATCTGGGCTAAGTCCCGAAAAGCATACGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
*
38879797 ATCCGGGCTAAGTCCCGAAGAGCATACATGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
*
38879837 ATCTGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
* *
38879877 ATCCGGGCTAAGTCCCGAAGCGCATACGTACTGGTGTTAT
1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
* *
38879917 ATCCGGGCTAAGTCCCGAAGAGCATTCATGCTGGTG
1 ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTG
38879953 ATGTGTATTC
Statistics
Matches: 257, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 257 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGAGCATACGTGCTGGTGTTAT
Found at i:38880166 original size:25 final size:25
Alignment explanation
Indices: 38880116--38880168 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
38880106 TGTGTAACAA
* *
38880116 CAAATGAATAGGGGCACTATGTGTG
1 CAAATGAATAGAGGCACTATGAGTG
*
38880141 CAAATGATTAGAGGCACTGA-GAGTG
1 CAAATGAATAGAGGCACT-ATGAGTG
38880166 CAA
1 CAA
38880169 GTTCTTCAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 23 0.96
26 1 0.04
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (25 bp):
CAAATGAATAGAGGCACTATGAGTG
Found at i:38891756 original size:11 final size:11
Alignment explanation
Indices: 38891740--38891764 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
38891730 TTTCAACACT
38891740 TCAAATTTACA
1 TCAAATTTACA
38891751 TCAAATTTACA
1 TCAAATTTACA
38891762 TCA
1 TCA
38891765 TTCAATCTCA
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:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (11 bp):
TCAAATTTACA
Found at i:38892515 original size:43 final size:43
Alignment explanation
Indices: 38892449--38892605 Score: 167
Period size: 43 Copynumber: 3.7 Consensus size: 43
38892439 AACTCGTACA
*
38892449 ATGCCAATGTCCTAGAC-GTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACATGTAATCAAATATCG
* * *
38892492 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAATA-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGTAATCAAATATCG
* * * *
38892534 ATGCTAATGTCCCAGACATGGTCTTACGTGTAAATCATAA-GTCG
1 ATGCCAATGTCCCAGACAGGGTCTTACATGT-AATCA-AATATCG
* * *
38892578 ATGCCAACGTCCCATACATGGTCTTACA
1 ATGCCAATGTCCCAGACAGGGTCTTACA
38892606 CGAAAAAACA
Statistics
Matches: 95, Mismatches: 15, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
42 27 0.28
43 39 0.41
44 29 0.31
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
ATGCCAATGTCCCAGACAGGGTCTTACATGTAATCAAATATCG
Done.