Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 188 of 427
Found at i:51889307 original size:27 final size:26
Alignment explanation
Indices: 51889277--51889422 Score: 166
Period size: 27 Copynumber: 5.4 Consensus size: 26
51889267 ATTACCAAAG
* *
51889277 TACCCTTGATTTACAAATTTACCGTTT
1 TACCCTCGATTTATAAA-TTACCGTTT
51889304 TACCCTCGATTTATAAAATTACCGTTT
1 TACCCTCGATTTAT-AAATTACCGTTT
51889331 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTATA-AATTACCGTTT
* ** *
51889358 TACCTTTAATTTATAGAATTACCATTT
1 TACCCTCGATTTATA-AATTACCGTTT
* **
51889385 TACCCTCGATTTACAAAATTATTGTTT
1 TACCCTCGATTTA-TAAATTACCGTTT
51889412 TACCCTCGATT
1 TACCCTCGATT
51889423 GTGAAATTAC
Statistics
Matches: 103, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.01
27 98 0.95
28 4 0.04
ACGTcount: A:0.28, C:0.21, G:0.08, T:0.43
Consensus pattern (26 bp):
TACCCTCGATTTATAAATTACCGTTT
Found at i:51889321 original size:54 final size:53
Alignment explanation
Indices: 51889252--51889422 Score: 189
Period size: 54 Copynumber: 3.2 Consensus size: 53
51889242 CATTGAAATG
* * *** *
51889252 CCCTCGACTTGTAAAATTACCAAAGTACCCTTGATTTACAAATTTACCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAAA-TTACCGTTTTA
* *
51889306 CCCTCGATTTATAAAATTACCGTTTTACCCTCGATTTATAGAATTACCGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACA-AATTACCGTTTTA
* ** * **
51889360 CCTTTAATTTATAGAATTACCATTTTACCCTCGATTTACAAAATTATTGTTTTA
1 CCCTCGATTTATAAAATTACCATTTTACCCTCGATTTAC-AAATTACCGTTTTA
51889414 CCCTCGATT
1 CCCTCGATT
51889423 GTGAAATTAC
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
54 93 0.97
55 3 0.03
ACGTcount: A:0.29, C:0.22, G:0.08, T:0.40
Consensus pattern (53 bp):
CCCTCGATTTATAAAATTACCATTTTACCCTCGATTTACAAATTACCGTTTTA
Found at i:51889441 original size:26 final size:26
Alignment explanation
Indices: 51889412--51889548 Score: 100
Period size: 26 Copynumber: 5.2 Consensus size: 26
51889402 ATTATTGTTT
**
51889412 TACCCTCGATTGTGAAATTACTGAAA
1 TACCCTCGATTGTGAAATTACCAAAA
* * *
51889438 TACCC-CTATAG-GATAGAATTTCCAAAA
1 TACCCTCGATTGTG--A-AATTACCAAAA
* * *
51889465 TACCCTAGTTTGTAAAATTACCAAAA
1 TACCCTCGATTGTGAAATTACCAAAA
* *
51889491 TACCACT-GTTTGTGAAATTACCGAAA
1 TACC-CTCGATTGTGAAATTACCAAAA
* *
51889517 TACCCTCAATTTGTAAAATTACCAAAA
1 TACCCTCGA-TTGTGAAATTACCAAAA
51889544 TACCC
1 TACCC
51889549 CTAATTTACA
Statistics
Matches: 86, Mismatches: 17, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
24 1 0.01
25 6 0.07
26 41 0.48
27 36 0.42
28 2 0.02
ACGTcount: A:0.39, C:0.22, G:0.10, T:0.29
Consensus pattern (26 bp):
TACCCTCGATTGTGAAATTACCAAAA
Found at i:51889537 original size:27 final size:26
Alignment explanation
Indices: 51889454--51889564 Score: 125
Period size: 26 Copynumber: 4.2 Consensus size: 26
51889444 TATAGGATAG
* *
51889454 AATTTCCAAAATACCCTAGTTTGTAA
1 AATTACCAAAATACCCTAATTTGTAA
* *
51889480 AATTACCAAAATACCACT-GTTTGTGA
1 AATTACCAAAATACC-CTAATTTGTAA
*
51889506 AATTACCGAAATACCCTCAATTTGTAA
1 AATTACCAAAATACCCT-AATTTGTAA
**
51889533 AATTACCAAAATACCCCTAATTTACAA
1 AATTACCAAAATA-CCCTAATTTGTAA
51889560 AATTA
1 AATTA
51889565 TAGAAATACC
Statistics
Matches: 73, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
25 2 0.03
26 35 0.48
27 32 0.44
28 4 0.05
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.31
Consensus pattern (26 bp):
AATTACCAAAATACCCTAATTTGTAA
Found at i:51889571 original size:27 final size:27
Alignment explanation
Indices: 51889513--51889633 Score: 86
Period size: 27 Copynumber: 4.4 Consensus size: 27
51889503 TGAAATTACC
* ** *
51889513 GAAATACCCTCAATTTGTAAAATTACCA
1 GAAATACCCTTAATTTACAAAATTA-TA
*
51889541 -AAATACCCCTAATTTACAAAATTATA
1 GAAATACCCTTAATTTACAAAATTATA
* *
51889567 GAAATACCATTGACTTT-CTAAAAATTATA
1 GAAATACCCTT-AATTTAC--AAAATTATA
* **
51889596 GAAATACCTTTGGTTTACAAAATTAGT-
1 GAAATACCCTTAATTTACAAAATTA-TA
51889623 GAAATACCCTT
1 GAAATACCCTT
51889634 GGTTTGTAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
26 1 0.01
27 46 0.61
28 8 0.11
29 20 0.27
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.32
Consensus pattern (27 bp):
GAAATACCCTTAATTTACAAAATTATA
Found at i:51889635 original size:27 final size:27
Alignment explanation
Indices: 51889553--51889638 Score: 95
Period size: 27 Copynumber: 3.1 Consensus size: 27
51889543 ATACCCCTAA
*
51889553 TTTACAAAATTATAGAAATACCATTGAC
1 TTTACAAAATTATAGAAATACCATTG-G
*
51889581 TTT-CTAAAAATTATAGAAATACCTTTGG
1 TTTAC--AAAATTATAGAAATACCATTGG
*
51889609 TTTACAAAATTAGT-GAAATACCCTTGG
1 TTTACAAAATTA-TAGAAATACCATTGG
51889636 TTT
1 TTT
51889639 GTAGATTTAC
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
27 23 0.45
28 7 0.14
29 21 0.41
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.37
Consensus pattern (27 bp):
TTTACAAAATTATAGAAATACCATTGG
Found at i:51889734 original size:27 final size:27
Alignment explanation
Indices: 51889679--51889756 Score: 70
Period size: 27 Copynumber: 2.9 Consensus size: 27
51889669 AAATGACTAA
* * *
51889679 AATACCCCTAATA-GGTAAAAAGACTGT
1 AATACCCCT-GTAGGGTAAAATGACCGT
*
51889706 AA-AGCCCCTGTAGGGTAAAGTGACCGT
1 AATA-CCCCTGTAGGGTAAAATGACCGT
* *
51889733 AATACCCTTGTATGGTAAAATGAC
1 AATACCCCTGTAGGGTAAAATGAC
51889757 GAATATGCCC
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
26 3 0.07
27 37 0.90
28 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (27 bp):
AATACCCCTGTAGGGTAAAATGACCGT
Found at i:51890601 original size:25 final size:24
Alignment explanation
Indices: 51890562--51890628 Score: 91
Period size: 25 Copynumber: 2.7 Consensus size: 24
51890552 AGGAAGTGCT
51890562 AAAAGGGC-TCTGCCCCAGTTTATC
1 AAAAGGGCTTC-GCCCCAGTTTATC
51890586 GAAAAGGGCTTCGCCCCAGTTTATC
1 -AAAAGGGCTTCGCCCCAGTTTATC
*
51890611 AGAAAGGGCTTTGCCCCA
1 A-AAAGGGCTTCGCCCCA
51890629 ATTATTAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
24 1 0.03
25 36 0.92
26 2 0.05
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.22
Consensus pattern (24 bp):
AAAAGGGCTTCGCCCCAGTTTATC
Found at i:51890899 original size:31 final size:31
Alignment explanation
Indices: 51890850--51890932 Score: 134
Period size: 31 Copynumber: 2.7 Consensus size: 31
51890840 CGCTTACAGT
*
51890850 AAAGGCTTCGG-CCAGTGATATTATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
*
51890880 AAGGGCTTCGGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGATATGATTTATGA
51890911 AAAGGCTTCGGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
51890933 TCGAGACTGA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 15 0.31
31 34 0.69
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGATTTATGA
Found at i:51893169 original size:18 final size:19
Alignment explanation
Indices: 51893146--51893181 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
51893136 CCCATTTGGG
51893146 CCGAGAAT-GGCTTTAGGA
1 CCGAGAATGGGCTTTAGGA
51893164 CCGAGAATGGGCTTTAGG
1 CCGAGAATGGGCTTTAGG
51893182 CCATTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.25, C:0.17, G:0.36, T:0.22
Consensus pattern (19 bp):
CCGAGAATGGGCTTTAGGA
Found at i:51893290 original size:27 final size:27
Alignment explanation
Indices: 51893260--51893405 Score: 238
Period size: 27 Copynumber: 5.4 Consensus size: 27
51893250 ATTACCAAAG
51893260 TACCCTCGATTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
**
51893287 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTATAGAATTACCATTT
* *
51893314 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTATAGAATTACCATTT
*
51893341 TACCCTCGACTTATAGAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
*
51893368 TACCCTCGATTTATAAAATTACCATTT
1 TACCCTCGATTTATAGAATTACCATTT
51893395 TACCCTCGATT
1 TACCCTCGATT
51893406 GTGAAATTAA
Statistics
Matches: 110, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 110 1.00
ACGTcount: A:0.28, C:0.24, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTATAGAATTACCATTT
Found at i:51893466 original size:26 final size:27
Alignment explanation
Indices: 51893437--51893531 Score: 115
Period size: 26 Copynumber: 3.6 Consensus size: 27
51893427 TGTAGGATAG
*
51893437 AATTAGCAAAATACCCTTAGTTTGT-A
1 AATTACCAAAATACCCTTAGTTTGTGA
*
51893463 AATTACCAAAATACCAC-TGGTTTGTGA
1 AATTACCAAAATACC-CTTAGTTTGTGA
* * *
51893490 AATTACCGAAATA-CCTCAATTTGTGA
1 AATTACCAAAATACCCTTAGTTTGTGA
51893516 AATTACCAAAATACCC
1 AATTACCAAAATACCC
51893532 CTGATTTACA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
25 1 0.02
26 41 0.71
27 16 0.28
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (27 bp):
AATTACCAAAATACCCTTAGTTTGTGA
Found at i:51893475 original size:53 final size:52
Alignment explanation
Indices: 51893404--51893534 Score: 122
Period size: 53 Copynumber: 2.5 Consensus size: 52
51893394 TTACCCTCGA
*** * * *
51893404 TTGTGAAATTAATGAAATACCCCTGTAGGAT-AGAATTAGCAAAATACCCTTAGT
1 TTGTGAAATTACCAAAATACCCCTGTAGG-TGA-AATTACCAAAATA-CCTCAAT
* ** *
51893458 TTGT-AAATTACCAAAATACCACTGGTTTGTGAAATTACCGAAATACCTCAAT
1 TTGTGAAATTACCAAAATACCCCT-GTAGGTGAAATTACCAAAATACCTCAAT
51893510 TTGTGAAATTACCAAAATACCCCTG
1 TTGTGAAATTACCAAAATACCCCTG
51893535 ATTTACAAAA
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
52 10 0.16
53 45 0.71
54 8 0.13
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (52 bp):
TTGTGAAATTACCAAAATACCCCTGTAGGTGAAATTACCAAAATACCTCAAT
Found at i:51893546 original size:27 final size:27
Alignment explanation
Indices: 51893462--51893613 Score: 87
Period size: 27 Copynumber: 5.6 Consensus size: 27
51893452 CTTAGTTTGT
* * ***
51893462 AAATTACCAAAATACCACTGGTTTGTG
1 AAATTACCAAAATACCCCTGATTTACA
* * * ***
51893489 AAATTACCGAAATACCTC-AATTTGTG
1 AAATTACCAAAATACCCCTGATTTACA
51893515 AAATTACCAAAATACCCCTGATTTACA
1 AAATTACCAAAATACCCCTGATTTACA
*
51893542 AAATTA-CAAAATACCCTTGACTTT-CTAA
1 AAATTACCAAAATACCCCTGA-TTTAC--A
* ** *
51893570 AAATTA-TAGAAATACCATTGGTTTACA
1 AAATTACCA-AAATACCCCTGATTTACA
*
51893597 AAATTACTAAAATACCC
1 AAATTACCAAAATACCC
51893614 TTGGTTTGTA
Statistics
Matches: 103, Mismatches: 15, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
26 36 0.35
27 43 0.42
28 13 0.13
29 11 0.11
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.30
Consensus pattern (27 bp):
AAATTACCAAAATACCCCTGATTTACA
Found at i:51893546 original size:53 final size:51
Alignment explanation
Indices: 51893437--51893556 Score: 132
Period size: 53 Copynumber: 2.3 Consensus size: 51
51893427 TGTAGGATAG
* * * ***
51893437 AATTAGCAAAATACCCTTAGTTTGTAAATTACCAAAATACCACTGGTTTGTGA
1 AATTA-CAAAATA-CCTCAATTTGTAAATTACCAAAATACCACTGATTTACAA
* *
51893490 AATTACCGAAATACCTCAATTTGTGAAATTACCAAAATACCCCTGATTTACAA
1 AATTA-CAAAATACCTCAATTTGT-AAATTACCAAAATACCACTGATTTACAA
51893543 AATTACAAAATACC
1 AATTACAAAATACC
51893557 CTTGACTTTC
Statistics
Matches: 56, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
52 17 0.30
53 39 0.70
ACGTcount: A:0.42, C:0.20, G:0.09, T:0.29
Consensus pattern (51 bp):
AATTACAAAATACCTCAATTTGTAAATTACCAAAATACCACTGATTTACAA
Found at i:51893617 original size:27 final size:27
Alignment explanation
Indices: 51893515--51893620 Score: 110
Period size: 27 Copynumber: 3.9 Consensus size: 27
51893505 TCAATTTGTG
* * *
51893515 AAATTACCAAAATACCCCTGATTTACA
1 AAATTACTAAAATACCCTTGGTTTACA
*
51893542 AAATTAC-AAAATACCCTTGACTTT-CTAA
1 AAATTACTAAAATACCCTTG-GTTTAC--A
*
51893570 AAATTA-TAGAAATACCATTGGTTTACA
1 AAATTACTA-AAATACCCTTGGTTTACA
51893597 AAATTACTAAAATACCCTTGGTTT
1 AAATTACTAAAATACCCTTGGTTT
51893621 GTAGATTTAC
Statistics
Matches: 67, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
26 12 0.18
27 31 0.46
28 13 0.19
29 11 0.16
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (27 bp):
AAATTACTAAAATACCCTTGGTTTACA
Found at i:51893737 original size:27 final size:26
Alignment explanation
Indices: 51893674--51893737 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
51893664 ACCCCTAATA
*
51893674 GGTAAAAAGACCGTAAAGCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCTGTAG
* *
51893700 GGTAAAGTGACCGTAATA-CCCTTGTAT
1 GGTAAAATGACCGTAA-AGCCC-TGTAG
51893727 GGTAAAATGAC
1 GGTAAAATGAC
51893738 GAATATGCCC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 17 0.53
27 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.22
Consensus pattern (26 bp):
GGTAAAATGACCGTAAAGCCCTGTAG
Found at i:51894578 original size:25 final size:24
Alignment explanation
Indices: 51894540--51894606 Score: 107
Period size: 25 Copynumber: 2.7 Consensus size: 24
51894530 AGGAAGTGCT
*
51894540 AAAAGGGCTCTGCCCCAGTTTATC
1 AAAAGGGCTTTGCCCCAGTTTATC
51894564 GAAAAGGGCTTTGCCCCAGTTTATC
1 -AAAAGGGCTTTGCCCCAGTTTATC
51894589 AGAAAGGGCTTTGCCCCA
1 A-AAAGGGCTTTGCCCCA
51894607 ATTATTAAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
24 1 0.03
25 39 0.98
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (24 bp):
AAAAGGGCTTTGCCCCAGTTTATC
Found at i:51894622 original size:24 final size:24
Alignment explanation
Indices: 51894539--51894622 Score: 89
Period size: 25 Copynumber: 3.4 Consensus size: 24
51894529 GAGGAAGTGC
* *
51894539 TAAAAGGGCTCTGCCCCAGTTTAT
1 TAAAAGGGCTTTGCCCCAGATTAT
* *
51894563 CGAAAAGGGCTTTGCCCCAGTTTAT
1 -TAAAAGGGCTTTGCCCCAGATTAT
*
51894588 CAGAAAGGGCTTTGCCCCA-ATTAT
1 TA-AAAGGGCTTTGCCCCAGATTAT
51894612 TAAAAGAGGCT
1 TAAAAG-GGCT
51894623 AGGCCTCCAA
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.08
24 10 0.19
25 38 0.73
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (24 bp):
TAAAAGGGCTTTGCCCCAGATTAT
Found at i:51896413 original size:28 final size:28
Alignment explanation
Indices: 51896364--51896475 Score: 100
Period size: 28 Copynumber: 4.0 Consensus size: 28
51896354 ACATACCTGT
*** * *
51896364 ATATGGCCCACTAGGTATAATCTCTTTC
1 ATATGGCCCACTAGGCCCAATCACATTC
* *
51896392 ATATGGCCCATTAGGCCCAATCACATTA
1 ATATGGCCCACTAGGCCCAATCACATTC
* * * *
51896420 ATGTGGCCTATTAGGCTCAAATCACATTC
1 ATATGGCCCACTAGGC-CCAATCACATTC
51896449 ATATGG-CCACTAGGCCCAAATCACATT
1 ATATGGCCCACTAGGCCC-AATCACATT
51896476 TACAGTCATG
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
27 1 0.01
28 51 0.76
29 15 0.22
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (28 bp):
ATATGGCCCACTAGGCCCAATCACATTC
Found at i:51903701 original size:21 final size:21
Alignment explanation
Indices: 51903635--51903702 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
51903625 CACATAGCCT
*
51903635 TGTGACTGAGGCACACGCCCG
1 TGTGACTAAGGCACACGCCCG
* ** * *
51903656 TGTAAAGAGAGGCACACGGCTG
1 TGTGACTA-AGGCACACGCCCG
*
51903678 TGTGACTAAGGCACACGTCCG
1 TGTGACTAAGGCACACGCCCG
51903699 TGTG
1 TGTG
51903703 GACCAGGGAC
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.24, C:0.25, G:0.34, T:0.18
Consensus pattern (21 bp):
TGTGACTAAGGCACACGCCCG
Found at i:51904416 original size:17 final size:17
Alignment explanation
Indices: 51904380--51904417 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
51904370 CACTATTTTC
*
51904380 AAAGAGACAAGAAACAA
1 AAAGAGACAAGAAAAAA
51904397 AAAGA-ACAAGAAAAAGA
1 AAAGAGACAAGAAAAA-A
51904414 AAAG
1 AAAG
51904418 CTAAGAGCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.74, C:0.08, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAGAGACAAGAAAAAA
Found at i:51910946 original size:24 final size:24
Alignment explanation
Indices: 51910730--51910946 Score: 319
Period size: 24 Copynumber: 9.0 Consensus size: 24
51910720 GCTTTATCAT
* *
51910730 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
* * *
51910755 ATAACTGGGGCAAAAGCCCGTTTA
1 ATAACTGGGGCATAAGCCCTTTTG
*
51910779 ATAACTGAGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
51910803 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTG
51910827 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
51910851 ATAATTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
51910875 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTG
51910899 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
51910923 ATAACTGGGGCATAAACCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
51910947 CACTTCCTCC
Statistics
Matches: 176, Mismatches: 15, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
24 164 0.93
25 12 0.07
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:51911023 original size:20 final size:20
Alignment explanation
Indices: 51910995--51911061 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
51910985 TTATGAATAC
*
51910995 ATCACGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
51911015 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
51911035 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
51911055 ACCATGT
1 ATCATGT
51911062 TTATCAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.33, C:0.22, G:0.12, T:0.33
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:51911126 original size:25 final size:25
Alignment explanation
Indices: 51911098--51911145 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
51911088 ACATATAAAC
* *
51911098 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAATGGTCATTTTTA
51911123 CCTAGGGGCAAAATGGTCATTTT
1 CCTAGGGGCAAAATGGTCATTTT
51911146 CATATTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAATGGTCATTTTTA
Found at i:51926484 original size:40 final size:40
Alignment explanation
Indices: 51926429--51926676 Score: 347
Period size: 40 Copynumber: 6.2 Consensus size: 40
51926419 TGAATGATAC
*
51926429 CCGGGCTAAGCCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
51926469 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
*
51926509 CCGAGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
*
51926549 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
* * * * *
51926589 CCGGGCCAAGACCCGAAGGCATTTGTGCGAGTTG-CTATAC
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTATAT
* * * * * *
51926629 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTGTAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
51926669 CC-GGCTAA
1 CCGGGCTAA
51926677 ATTCTGAAGA
Statistics
Matches: 188, Mismatches: 18, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
39 7 0.04
40 179 0.95
41 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
Found at i:51930823 original size:40 final size:40
Alignment explanation
Indices: 51930657--51930841 Score: 164
Period size: 40 Copynumber: 4.6 Consensus size: 40
51930647 TTCGAATGAT
* * *
51930657 ATCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTAA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAA
** *
51930697 ATCCGGAATAAGAT-CCGATA-GCATACGTGCGAGTTACTAA
1 ATCCGGGCTAAG-TCCCGA-AGGCATTCGTGCGAGTTACTAA
* * * *
51930737 ATCCGGACTAAGAT-CCGAAGGCTTTCGAGCGAGCTACTAA
1 ATCCGGGCTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAA
* *
51930777 ATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTGTA
1 ATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACT-AA
* *
51930818 A-CCGGGCCATGTCCCGAAGGCATT
1 ATCCGGGCTAAGTCCCGAAGGCATT
51930842 TGAATGTGTA
Statistics
Matches: 119, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
39 2 0.02
40 108 0.91
41 9 0.08
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGTCCCGAAGGCATTCGTGCGAGTTACTAA
Found at i:51932286 original size:28 final size:28
Alignment explanation
Indices: 51932246--51932305 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
51932236 ACCTTTAGGT
* *
51932246 CCAATCTCGTTCACATGGCCCATCAGGC
1 CCAATCACATTCACATGGCCCATCAGGC
*
51932274 CCAATCACATTCATATGGCCCATCAGGC
1 CCAATCACATTCACATGGCCCATCAGGC
51932302 CCAA
1 CCAA
51932306 CTACTTCCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.27, C:0.38, G:0.15, T:0.20
Consensus pattern (28 bp):
CCAATCACATTCACATGGCCCATCAGGC
Found at i:51935242 original size:28 final size:28
Alignment explanation
Indices: 51935198--51935311 Score: 165
Period size: 28 Copynumber: 4.0 Consensus size: 28
51935188 TGGCCCCTTT
* * *
51935198 AGGCCCAATCTCGTTCACATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
*
51935226 AGACCCAATCACATTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
*
51935254 AGGCCCAATCACCTTCATATGGCCCATC
1 AGGCCCAATCACATTCATATGGCCCATC
*
51935282 AGGCCCCATCACATTCATATGGCCCCATC
1 AGGCCCAATCACATTCATATGG-CCCATC
51935311 A
1 A
51935312 CATTCATATG
Statistics
Matches: 77, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
28 70 0.91
29 7 0.09
ACGTcount: A:0.26, C:0.39, G:0.14, T:0.21
Consensus pattern (28 bp):
AGGCCCAATCACATTCATATGGCCCATC
Found at i:51935276 original size:56 final size:57
Alignment explanation
Indices: 51935181--51935311 Score: 183
Period size: 56 Copynumber: 2.3 Consensus size: 57
51935171 ATCCACACTT
* * * * *
51935181 ATTCATTTGGCCCCTTTAGGCCCAATCTCGTTCACATGGCCCATCAGACCCAATCAC
1 ATTCATATGGCCCCATCAGGCCCAATCACCTTCACATGGCCCATCAGACCCAATCAC
* * *
51935238 ATTCATATGG-CCCATCAGGCCCAATCACCTTCATATGGCCCATCAGGCCCCATCAC
1 ATTCATATGGCCCCATCAGGCCCAATCACCTTCACATGGCCCATCAGACCCAATCAC
51935294 ATTCATATGGCCCCATCA
1 ATTCATATGGCCCCATCA
51935312 CATTCATATG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
56 49 0.75
57 16 0.25
ACGTcount: A:0.24, C:0.37, G:0.14, T:0.24
Consensus pattern (57 bp):
ATTCATATGGCCCCATCAGGCCCAATCACCTTCACATGGCCCATCAGACCCAATCAC
Found at i:51935328 original size:18 final size:19
Alignment explanation
Indices: 51935283--51935329 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
51935273 TGGCCCATCA
51935283 GGCCCCATCACATTCATAT
1 GGCCCCATCACATTCATAT
51935302 GGCCCCATCACATTCATAT
1 GGCCCCATCACATTCATAT
51935321 GG-CCCATCA
1 GGCCCCATCA
51935330 GGCCCAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 7 0.25
19 21 0.75
ACGTcount: A:0.26, C:0.38, G:0.13, T:0.23
Consensus pattern (19 bp):
GGCCCCATCACATTCATAT
Found at i:51943321 original size:23 final size:23
Alignment explanation
Indices: 51943294--51943350 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
51943284 AATGATAAAT
51943294 CAAGCAATTAACATATATAAACA
1 CAAGCAATTAACATATATAAACA
51943317 CAAGCAATTAACATATATAAACA
1 CAAGCAATTAACATATATAAACA
51943340 CAAGCAATTAA
1 CAAGCAATTAA
51943351 ATCTATCCCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.56, C:0.18, G:0.05, T:0.21
Consensus pattern (23 bp):
CAAGCAATTAACATATATAAACA
Found at i:51943544 original size:9 final size:9
Alignment explanation
Indices: 51943530--51943554 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
51943520 ACACATTTTA
51943530 CAATTTATT
1 CAATTTATT
51943539 CAATTTATT
1 CAATTTATT
51943548 CAATTTA
1 CAATTTA
51943555 GTCCCTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (9 bp):
CAATTTATT
Found at i:51944616 original size:17 final size:18
Alignment explanation
Indices: 51944596--51944630 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
51944586 TTATTTTTTG
*
51944596 TAATTGTTTTCA-AAAAA
1 TAATTATTTTCATAAAAA
51944613 TAATTATTTTCATAAAAA
1 TAATTATTTTCATAAAAA
51944631 GTATTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (18 bp):
TAATTATTTTCATAAAAA
Found at i:51947054 original size:30 final size:29
Alignment explanation
Indices: 51947019--51947092 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
51947009 CTTCGAGCTC
* *
51947019 GCACACCCAGTGCCGTATTTTTTCCAGCAT
1 GCACACCCAGTGCCATA-TATTTCCAGCAT
**
51947049 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
51947078 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
51947093 ATCTCGTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 26 0.65
30 14 0.35
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.28
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:51954955 original size:30 final size:29
Alignment explanation
Indices: 51954920--51954993 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
51954910 CTTCGAGCTC
* *
51954920 GCACACCCAGTGCCGTATTTTTTCCAGCAT
1 GCACACCCAGTGCCATA-TATTTCCAGCAT
**
51954950 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACCCAGTGCCATATATTTCCAGCAT
**
51954979 GCACACTTAGTGCCA
1 GCACACCCAGTGCCA
51954994 ATCTCGTCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
29 26 0.65
30 14 0.35
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.28
Consensus pattern (29 bp):
GCACACCCAGTGCCATATATTTCCAGCAT
Found at i:51956211 original size:15 final size:15
Alignment explanation
Indices: 51956158--51956213 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
51956148 AATGAACACT
51956158 TTTTTTTTC-TTTTC
1 TTTTTTTTCTTTTTC
51956172 TTTGTTTTTCTTCATATTC
1 TTT-TTTTTCTT--T-TTC
*
51956191 TCTTTTTTCTTTTTC
1 TTTTTTTTCTTTTTC
51956206 TTTTTTTT
1 TTTTTTTT
51956214 TTCATTTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 3 0.09
15 16 0.46
16 2 0.06
18 9 0.26
19 5 0.14
ACGTcount: A:0.04, C:0.14, G:0.02, T:0.80
Consensus pattern (15 bp):
TTTTTTTTCTTTTTC
Found at i:51960736 original size:49 final size:48
Alignment explanation
Indices: 51960613--51960757 Score: 182
Period size: 49 Copynumber: 2.9 Consensus size: 48
51960603 TCTATTGTGA
* * *
51960613 GGTCGCATGTGTAGTACTAAGTACAGGCTACTATGCGTACCCGAAAACTGT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTA-CC--AGATTGT
* * * * *
51960664 GATCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTG-T
51960713 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAT
1 GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGAT
51960758 AGCTTCGGCT
Statistics
Matches: 80, Mismatches: 13, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
48 4 0.05
49 41 0.51
50 2 0.03
51 33 0.41
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.28
Consensus pattern (48 bp):
GGTCGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGATTGT
Found at i:51963780 original size:15 final size:15
Alignment explanation
Indices: 51963760--51963824 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
51963750 GTATCTTGGG
51963760 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
51963775 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
51963790 TTT-TTCTA-TCTTGGA
1 TTTCTT-TATTC-TGGA
*
51963805 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
51963819 TTTCTT
1 TTTCTT
51963825 GTTATCTTTA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 12 0.28
15 27 0.63
16 4 0.09
ACGTcount: A:0.09, C:0.14, G:0.14, T:0.63
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:51963790 original size:30 final size:31
Alignment explanation
Indices: 51963756--51963824 Score: 92
Period size: 30 Copynumber: 2.3 Consensus size: 31
51963746 TATCGTATCT
51963756 TGGGTTTCTT-TAT-TCTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCT-TGGATTTCTTTATTC
51963786 TGGGTTT-TTCTATCTTGGATTTCTTTATTC
1 TGGGTTTCTTCTATCTTGGATTTCTTTATTC
*
51963816 -GGTTTTCTT
1 TGGGTTTCTT
51963825 GTTATCTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
29 7 0.20
30 27 0.77
31 1 0.03
ACGTcount: A:0.09, C:0.13, G:0.17, T:0.61
Consensus pattern (31 bp):
TGGGTTTCTTCTATCTTGGATTTCTTTATTC
Found at i:51967324 original size:26 final size:23
Alignment explanation
Indices: 51967267--51967314 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
51967257 CTACCATTTA
51967267 TCCTTATTAAAATGAGTGAACCT
1 TCCTTATTAAAATGAGTGAACCT
*
51967290 TCCTCATTAAAATGAGTGAACCT
1 TCCTTATTAAAATGAGTGAACCT
51967313 TC
1 TC
51967315 TTCTTTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.33
Consensus pattern (23 bp):
TCCTTATTAAAATGAGTGAACCT
Found at i:51971365 original size:40 final size:39
Alignment explanation
Indices: 51971291--51971598 Score: 375
Period size: 40 Copynumber: 7.6 Consensus size: 39
51971281 AACCCAAGTA
* * * *
51971291 CCTTCAGGATTTAG-CCGGATATAGCAATTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGC-ACTAGCACAAATG
* *
51971330 CCTTCAGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CACTAGCACAAATG
*
51971370 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTGACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGC-ACTA--G-CACAAATG
* *
51971413 CCTTTGGGACTTCGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CACTAGCACAAATG
*
51971453 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGC-ACTA---GCACAAATG
*
51971496 CCTTCGGGACTTCGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CACTAGCACAAATG
* *
51971536 CCTTCGGGACTTAGCCCGGATATAGGAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATA-GCACTAGCACAAATG
51971576 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
51971599 CATCCGAATA
Statistics
Matches: 238, Mismatches: 18, Indels: 25
0.85 0.06 0.09
Matches are distributed among these distances:
39 14 0.06
40 148 0.62
41 3 0.01
42 1 0.00
43 70 0.29
44 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAGCACTAGCACAAATG
Found at i:51971411 original size:83 final size:82
Alignment explanation
Indices: 51971291--51971598 Score: 464
Period size: 83 Copynumber: 3.8 Consensus size: 82
51971281 AACCCAAGTA
* * * * * *
51971291 CCTTCAGGATTTAG-CCGGATATAGCAA-TTC-GCACAAATGCCTTCAGGTCTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
51971353 AGTCACTAGCACAAATG
66 AGTCACTAGCACAAATG
* *
51971370 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTGACACAAATGCCTTTGGGACTTCGCCCGGATA
1 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTG-CACAAATGCCTTCGGGACTTAGCCCGGATA
51971435 TAGTCACTAGCACAAATG
65 TAGTCACTAGCACAAATG
*
51971453 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTCGCACAAATGCCTTCGGGACTTCGCCCGGATA
1 CCTTCGGGACTTAGCCCGGGTATAGCAACTACT-GCACAAATGCCTTCGGGACTTAGCCCGGATA
51971518 TAGTCACTAGCACAAATG
65 TAGTCACTAGCACAAATG
* *
51971536 CCTTCGGGACTTAGCCCGGATATAGGAACT-C-GCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGGTATAGCAACTACTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
51971599 CATCCGAATA
Statistics
Matches: 212, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
79 12 0.06
80 43 0.20
81 2 0.01
82 2 0.01
83 152 0.72
84 1 0.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (82 bp):
CCTTCGGGACTTAGCCCGGGTATAGCAACTACTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
AGTCACTAGCACAAATG
Found at i:51971532 original size:123 final size:122
Alignment explanation
Indices: 51971291--51971598 Score: 392
Period size: 123 Copynumber: 2.5 Consensus size: 122
51971281 AACCCAAGTA
* * * * * * *
51971291 CCTTCAGGATTTAG-CCGGATATAGCAATTCGCACAAATGCCTTCAGGTCTTAGCCCGGATATAG
1 CCTTCGGGACTTAGCCCGGATATAGGAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
51971355 TCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAGCAACTACTGACACAAATG
66 TCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGCAACTAC-GACACAAATG
* * ** *
51971413 CCTTTGGGACTTCGCCCGGATATAGTCACTAGCACAAATGCCTTCGGGACTTAGCCCGGGTATAG
1 CCTTCGGGACTTAGCCCGGATATAGGAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
*
51971478 -CAACTACTCGCACAAATGCCTTCGGGACTTCGCCCGGATATAGTC-ACTA-G-CACAAATG
66 TC-ACTA---GCACAAATGCCTTCGGGACTTAGCCCGGATATAG-CAACTACGACACAAATG
*
51971536 CCTTCGGGACTTAGCCCGGATATAGGAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATATAGGAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
51971599 CATCCGAATA
Statistics
Matches: 161, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
122 11 0.07
123 112 0.70
124 1 0.01
126 36 0.22
127 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (122 bp):
CCTTCGGGACTTAGCCCGGATATAGGAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAG
TCACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGCAACTACGACACAAATG
Found at i:51972843 original size:19 final size:19
Alignment explanation
Indices: 51972807--51972845 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
51972797 TTTTCATCAT
* *
51972807 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
51972826 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
51972845 A
1 A
51972846 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:51973357 original size:28 final size:28
Alignment explanation
Indices: 51973309--51973399 Score: 139
Period size: 28 Copynumber: 3.2 Consensus size: 28
51973299 GTGACAGAGT
*
51973309 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGTGC
*
51973338 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGTGC
51973366 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGATAATTTGTGGCAGT-GC
51973394 CACCAG
1 CACCAG
51973400 GACGCTTCCT
Statistics
Matches: 58, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
28 51 0.88
29 7 0.12
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.21
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGTGC
Found at i:51973551 original size:28 final size:28
Alignment explanation
Indices: 51973504--51973568 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
51973494 AAATTAACCC
*
51973504 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
51973532 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
51973560 TAGGGGTAT
1 TAGGGGTAT
51973569 TAGCACATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:51980698 original size:19 final size:19
Alignment explanation
Indices: 51980662--51980700 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
51980652 TTTTCATCAT
* *
51980662 AGTAAAATAAAATAATAAA
1 AGTAAAACAAAACAATAAA
*
51980681 AGTAAAACAAAACCATAAA
1 AGTAAAACAAAACAATAAA
51980700 A
1 A
51980701 ATAATTAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.72, C:0.08, G:0.05, T:0.15
Consensus pattern (19 bp):
AGTAAAACAAAACAATAAA
Found at i:51980793 original size:19 final size:19
Alignment explanation
Indices: 51980771--51980809 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 19
51980761 CCAGTTCACC
51980771 AGAAAGAAACCAGGTTCGT
1 AGAAAGAAACCAGGTTCGT
51980790 ----AGAAACCAGGTTCGT
1 AGAAAGAAACCAGGTTCGT
51980805 AGAAA
1 AGAAA
51980810 CATGTGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 8
0.67 0.00 0.33
Matches are distributed among these distances:
15 15 0.94
19 1 0.06
ACGTcount: A:0.44, C:0.15, G:0.26, T:0.15
Consensus pattern (19 bp):
AGAAAGAAACCAGGTTCGT
Found at i:51980795 original size:15 final size:15
Alignment explanation
Indices: 51980775--51980810 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
51980765 TTCACCAGAA
51980775 AGAAACCAGGTTCGT
1 AGAAACCAGGTTCGT
51980790 AGAAACCAGGTTCGT
1 AGAAACCAGGTTCGT
51980805 AGAAAC
1 AGAAAC
51980811 ATGTGGCCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (15 bp):
AGAAACCAGGTTCGT
Found at i:51981219 original size:55 final size:56
Alignment explanation
Indices: 51981154--51981268 Score: 146
Period size: 55 Copynumber: 2.1 Consensus size: 56
51981144 AGCATGGCTG
* *
51981154 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGCAGT-GCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCA-TAGCCA
* * *
51981210 CCAGA-ACAGATAATTGTGGCAGGGCCACCAGAACAGATAATTTGTGGCATAGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
51981265 CCAG
1 CCAG
51981269 GACGCTTCCT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
54 1 0.02
55 29 0.56
56 22 0.42
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.19
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCATAGCCA
Found at i:51981264 original size:28 final size:27
Alignment explanation
Indices: 51981179--51981268 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
51981169 GTGACAGAGT
*
51981179 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATAATTTGTGGCA-TGC
*
51981208 CACCAGAACAGATAA-TTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCA-TGC
51981235 CACCAGAACAGATAATTTGTGGCATAGC
1 CACCAGAACAGATAATTTGTGGCAT-GC
51981263 CACCAG
1 CACCAG
51981269 GACGCTTCCT
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
27 26 0.46
28 23 0.41
29 7 0.12
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATAATTTGTGGCATGC
Found at i:51981421 original size:28 final size:28
Alignment explanation
Indices: 51981374--51981438 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
51981364 AAATTAACCC
*
51981374 TAGGGGTATAAAGGTCATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
*
51981402 TAGGGGTATAATGGTAATTTTGCATACA
1 TAGGGGTATAAAGGTAATTTTGCATACA
51981430 TAGGGGTAT
1 TAGGGGTAT
51981439 TAAATCTAAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.31, C:0.08, G:0.28, T:0.34
Consensus pattern (28 bp):
TAGGGGTATAAAGGTAATTTTGCATACA
Found at i:51990361 original size:40 final size:39
Alignment explanation
Indices: 51990287--51990509 Score: 290
Period size: 40 Copynumber: 5.6 Consensus size: 39
51990277 AACCCAAGTA
* *
51990287 CCTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGC-ACTAGCACAAATG
*
51990326 CCTTCGGGTCTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CACTAGCACAAATG
*
51990366 CCTTCGGGACTTAG-CCGG-TATAGCAACTACTCGTACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGC-ACTA---GCACAAATG
*
51990407 CCTTCGGGACTTCGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-CACTAGCACAAATG
* *
51990447 CCTTCGGGACTTAGCCCGGATATAGGAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATA-GCACTAGCACAAATG
51990487 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
51990510 CATCCGAATA
Statistics
Matches: 164, Mismatches: 10, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
37 1 0.01
38 9 0.05
39 16 0.10
40 101 0.62
41 23 0.14
42 4 0.02
43 9 0.05
44 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGATATAGCACTAGCACAAATG
Found at i:51990411 original size:81 final size:79
Alignment explanation
Indices: 51990287--51990509 Score: 358
Period size: 81 Copynumber: 2.8 Consensus size: 79
51990277 AACCCAAGTA
* *
51990287 CCTTCGGGATTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CCTTCGGGACTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
51990352 CACTAGCACAAATG
66 CACTAGCACAAATG
* *
51990366 CCTTCGGGACTTAGCCGG-TATAGCAACTACTCGTACAAATGCCTTCGGGACTTCGCCCGGATAT
1 CCTTCGGGACTTAGCCGGATATAGC-A--ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
51990430 AGTCACTAGCACAAATG
63 AGTCACTAGCACAAATG
*
51990447 CCTTCGGGACTTAGCCCGGATATAGGAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
51990510 CATCCGAATA
Statistics
Matches: 132, Mismatches: 7, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
78 6 0.05
79 18 0.14
80 34 0.26
81 64 0.48
82 5 0.04
83 5 0.04
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (79 bp):
CCTTCGGGACTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATG
Found at i:51996256 original size:22 final size:19
Alignment explanation
Indices: 51996231--51996278 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 19
51996221 TACCGTTTTG
51996231 ATTAAATTCTTGTCAAAAAATA
1 ATTAAATT-TT-T-AAAAAATA
*
51996253 ATT-AATTTTTATAAAATA
1 ATTAAATTTTTAAAAAATA
51996271 ATTAAATT
1 ATTAAATT
51996279 ATACTTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.42
19 5 0.21
20 2 0.08
21 4 0.17
22 3 0.12
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTAAATTTTTAAAAAATA
Found at i:52002319 original size:39 final size:39
Alignment explanation
Indices: 52002201--52002383 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
52002191 TCGTTCAAAC
* * ** * **
52002201 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
52002241 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
*
52002281 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
52002320 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
52002359 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
52002384 CTCGAACATT
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:52009754 original size:39 final size:39
Alignment explanation
Indices: 52009636--52009818 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
52009626 TCGTTCAAAC
* * ** * **
52009636 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
52009676 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
*
52009716 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
52009755 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
52009794 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
52009819 CTCGAACATT
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:52015816 original size:9 final size:9
Alignment explanation
Indices: 52015780--52016054 Score: 77
Period size: 9 Copynumber: 29.8 Consensus size: 9
52015770 TTAAAATGTT
52015780 TAAAAAATCA
1 TAAAAAAT-A
*
52015790 TAATAAATTA
1 TAA-AAAATA
*
52015800 TCAAAAAT-
1 TAAAAAATA
52015808 TAGAAAAATA
1 TA-AAAAATA
52015818 TAAAAAATA
1 TAAAAAATA
*
52015827 T--TAAATA
1 TAAAAAATA
*
52015834 TGAGAAAATA
1 T-AAAAAATA
*
52015844 TAAAAATTGA
1 TAAAAAAT-A
* *
52015854 TATAAACT-
1 TAAAAAATA
**
52015862 TAAAATTTA
1 TAAAAAATA
52015871 -AAAAAAT-
1 TAAAAAATA
52015878 TAAAAAAT-
1 TAAAAAATA
52015886 TAAAAAAATA
1 T-AAAAAATA
* * *
52015896 TTAAAATTC
1 TAAAAAATA
*
52015905 TAATAAAT-
1 TAAAAAATA
*
52015913 TATAAAATA
1 TAAAAAATA
*
52015922 TATAAAAT-
1 TAAAAAATA
52015930 TAAAAAACATA
1 T-AAAAA-ATA
* *
52015941 TTTAAAATATT
1 --TAAAAAATA
***
52015952 TAAATTTTTA
1 TAAA-AAATA
52015962 TAAAAACATA
1 TAAAAA-ATA
**
52015972 TTAAAATTCTA
1 -TAAAA-AATA
52015983 TAAAAAATCA
1 TAAAAAAT-A
*
52015993 -AAAAATTA
1 TAAAAAATA
52016001 TAAAAAATA
1 TAAAAAATA
52016010 TATAAAAATA
1 TA-AAAAATA
* *
52016020 TTAAAATTGA
1 TAAAAAAT-A
*
52016030 TATAAAAT-
1 TAAAAAATA
52016038 TATAAAAATA
1 TA-AAAAATA
52016048 TAAAAAA
1 TAAAAAA
52016055 ATCATAAAAT
Statistics
Matches: 194, Mismatches: 44, Indels: 55
0.66 0.15 0.19
Matches are distributed among these distances:
7 6 0.03
8 29 0.15
9 87 0.45
10 54 0.28
11 13 0.07
12 4 0.02
13 1 0.01
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (9 bp):
TAAAAAATA
Found at i:52015883 original size:17 final size:16
Alignment explanation
Indices: 52015863--52015935 Score: 56
Period size: 17 Copynumber: 4.2 Consensus size: 16
52015853 ATATAAACTT
52015863 AAAATTTAAAAAAATTAA
1 AAAATTT-AAAAAATT-A
* *
52015881 AAAATTAAAAAAATATT
1 AAAATTTAAAAAAT-TA
*
52015898 AAAATTCTAATAAATTA
1 AAAATT-TAAAAAATTA
* *
52015915 TAAAATATATAAAATTA
1 -AAAATTTAAAAAATTA
52015932 AAAA
1 AAAA
52015936 ACATATTTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
16 4 0.09
17 22 0.50
18 18 0.41
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.30
Consensus pattern (16 bp):
AAAATTTAAAAAATTA
Found at i:52015911 original size:52 final size:52
Alignment explanation
Indices: 52015812--52015936 Score: 121
Period size: 52 Copynumber: 2.4 Consensus size: 52
52015802 AAAAATTAGA
** * *
52015812 AAAATATAAAAAA-TATTAAATATGAGAAAATATAAAAATTGATATAAACT-T
1 AAAATATAAAAAATTAAAAAAT-TAAAAAAATATAAAAATTGATATAAACTAT
* * * *
52015863 AAAATTTAAAAAAATTAAAAAATTAAAAAAATATTAAAATT-CTAATAAATTAT
1 AAAATAT-AAAAAATTAAAAAATTAAAAAAATATAAAAATTGAT-ATAAACTAT
*
52015916 AAAATATATAAAATTAAAAAA
1 AAAATATAAAAAATTAAAAAA
52015937 CATATTTAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
51 7 0.12
52 40 0.67
53 13 0.22
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (52 bp):
AAAATATAAAAAATTAAAAAATTAAAAAAATATAAAAATTGATATAAACTAT
Found at i:52015936 original size:17 final size:17
Alignment explanation
Indices: 52015803--52015941 Score: 52
Period size: 17 Copynumber: 8.0 Consensus size: 17
52015793 TAAATTATCA
52015803 AAAATTAGAAAAATATA-
1 AAAATTA-AAAAATATAT
* ** *
52015820 AAAAATATTAAATATGAG
1 AAAATTAAAAAATAT-AT
*
52015838 AAAATATAAAAATTGATAT
1 AAAAT-TAAAAAAT-ATAT
* ** *
52015857 AAACTTAAAATTTA-AA
1 AAAATTAAAAAATATAT
*
52015873 AAAATTAAAAAAT-TAA
1 AAAATTAAAAAATATAT
* * *
52015889 AAAAATATTAAAAT-TCT
1 AAAATTA-AAAAATATAT
*
52015906 AATAAATTATAAAATATAT
1 -A-AAATTAAAAAATATAT
*
52015925 AAAATTAAAAAACATAT
1 AAAATTAAAAAATATAT
52015942 TTAAAATATT
Statistics
Matches: 91, Mismatches: 22, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
16 25 0.27
17 28 0.31
18 19 0.21
19 17 0.19
20 2 0.02
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.29
Consensus pattern (17 bp):
AAAATTAAAAAATATAT
Found at i:52016047 original size:28 final size:28
Alignment explanation
Indices: 52015993--52016053 Score: 88
Period size: 28 Copynumber: 2.2 Consensus size: 28
52015983 TAAAAAATCA
52015993 AAAAATTATAAAAAATATATAAAAATAT
1 AAAAATTATAAAAAATATATAAAAATAT
* *
52016021 TAAAATTGATATAAAAT-TATAAAAATAT
1 AAAAATT-ATAAAAAATATATAAAAATAT
52016049 AAAAA
1 AAAAA
52016054 AATCATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 21 0.72
29 8 0.28
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (28 bp):
AAAAATTATAAAAAATATATAAAAATAT
Found at i:52016205 original size:16 final size:16
Alignment explanation
Indices: 52016180--52016219 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
52016170 GAATCAAATT
*
52016180 TTTTTA-TTTTTAATA
1 TTTTTATTTTTTAAAA
52016195 TTTTTATTTTTTAAAA
1 TTTTTATTTTTTAAAA
*
52016211 GTTTTATTT
1 TTTTTATTT
52016220 AATTGAACTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.27
16 16 0.73
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (16 bp):
TTTTTATTTTTTAAAA
Found at i:52016531 original size:28 final size:29
Alignment explanation
Indices: 52016476--52016534 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 29
52016466 TAAATATATT
* *
52016476 TTTTTATTTTTAATCATATTTACATTTTA
1 TTTTTAATTTTAATCATAATTACATTTTA
* *
52016505 TTTTTAATTTTAGT-ATAATTACTTTTTA
1 TTTTTAATTTTAATCATAATTACATTTTA
52016533 TT
1 TT
52016535 ATATTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 14 0.54
29 12 0.46
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.66
Consensus pattern (29 bp):
TTTTTAATTTTAATCATAATTACATTTTA
Found at i:52017043 original size:9 final size:9
Alignment explanation
Indices: 52017031--52017252 Score: 53
Period size: 9 Copynumber: 23.3 Consensus size: 9
52017021 TTTAATTATT
52017031 TTTTTATAA
1 TTTTTATAA
52017040 TTTTTA-AA
1 TTTTTATAA
52017048 TTTTATATGAA
1 TTTT-TAT-AA
* *
52017059 TTTTAATAT
1 TTTTTATAA
52017068 TTTTTAT-A
1 TTTTTATAA
*
52017076 TTTTTTTGCAA
1 TTTTTAT--AA
**
52017087 TTTTTATTC
1 TTTTTATAA
*
52017096 TTTTTAAGAA
1 TTTTT-ATAA
* *
52017106 TTCTAATAAAA
1 TT-T-TTATAA
52017117 TTTTT-TAA
1 TTTTTATAA
52017125 -TTTTA-AA
1 TTTTTATAA
52017132 TATTTTAAATAA
1 T-TTTT--ATAA
*
52017144 GTTTTACTAA
1 TTTTTA-TAA
* *
52017154 TTTAATAAAA
1 TTT-TTATAA
52017164 TTTTTAATAA
1 TTTTT-ATAA
* *
52017174 ATTTAATAA
1 TTTTTATAA
*
52017183 TTTATTGT-A
1 TTT-TTATAA
52017192 TTTTTATAA
1 TTTTTATAA
* *
52017201 -TATTATAG
1 TTTTTATAA
* *
52017209 GTTTTATTACTT
1 TTTTTA-TA--A
52017221 TTTTTATAA
1 TTTTTATAA
*
52017230 TTTTAATAA
1 TTTTTATAA
52017239 TTTTGTATCAA
1 TTTT-TAT-AA
52017250 TTT
1 TTT
52017253 CAATATTTTT
Statistics
Matches: 152, Mismatches: 35, Indels: 50
0.64 0.15 0.21
Matches are distributed among these distances:
7 6 0.04
8 23 0.15
9 54 0.36
10 28 0.18
11 33 0.22
12 8 0.05
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:52017062 original size:28 final size:28
Alignment explanation
Indices: 52017031--52017102 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
52017021 TTTAATTATT
52017031 TTTTTATAATTTTTAAATTTTATATG-AA
1 TTTTTATAATTTTTAAATTTT-TATGCAA
* * * *
52017059 TTTTAATATTTTTTATATTTTTTTGCAA
1 TTTTTATAATTTTTAAATTTTTATGCAA
**
52017087 TTTTTATTCTTTTTAA
1 TTTTTATAATTTTTAA
52017103 GAATTCTAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
27 3 0.09
28 32 0.91
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (28 bp):
TTTTTATAATTTTTAAATTTTTATGCAA
Found at i:52017081 original size:19 final size:18
Alignment explanation
Indices: 52017020--52017080 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
52017010 TCCTATTCAG
52017020 TTTTAATTATTTTTTTATAAT
1 TTTTAA-TA-TTTTTTAT-AT
* *
52017041 TTTTAA-ATTTTATATGAA
1 TTTTAATATTTTTTAT-AT
52017059 TTTTAATATTTTTTATAT
1 TTTTAATATTTTTTATAT
52017077 TTTT
1 TTTT
52017081 TTGCAATTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 19 0.56
19 9 0.26
21 6 0.18
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (18 bp):
TTTTAATATTTTTTATAT
Found at i:52017173 original size:30 final size:30
Alignment explanation
Indices: 52017128--52017186 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
52017118 TTTTTAATTT
* *
52017128 TAAATATTTTAAATAAGTTTTACTAATTTAA
1 TAAATATTTTAAATAA-ATTTAATAATTTAA
*
52017159 TAAA-ATTTTTAATAAATTTAATAATTTA
1 TAAATATTTTAAATAAATTTAATAATTTA
52017187 TTGTATTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 11 0.44
30 10 0.40
31 4 0.16
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (30 bp):
TAAATATTTTAAATAAATTTAATAATTTAA
Found at i:52017242 original size:29 final size:28
Alignment explanation
Indices: 52017164--52017242 Score: 72
Period size: 29 Copynumber: 2.8 Consensus size: 28
52017154 TTTAATAAAA
* * *
52017164 TTTTTAATAAATTTAATAA-TTTATTGT
1 TTTTTTATAATTTTAATAATTTTATTCT
* * *
52017191 ATTTTTATAATATT-ATAGGTTTTATTACT
1 TTTTTTATAATTTTAATA-ATTTTATT-CT
52017220 TTTTTTATAATTTTAATAATTTT
1 TTTTTTATAATTTTAATAATTTT
52017243 GTATCAATTT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
26 3 0.08
27 10 0.26
28 6 0.15
29 17 0.44
30 3 0.08
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (28 bp):
TTTTTTATAATTTTAATAATTTTATTCT
Found at i:52017262 original size:20 final size:19
Alignment explanation
Indices: 52017219--52017262 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
52017209 GTTTTATTAC
* *
52017219 TTTTTTTATAATTTTAATA
1 TTTTTGTATAATTTCAATA
*
52017238 ATTTTGTATCAATTTCAATA
1 TTTTTGTAT-AATTTCAATA
52017258 TTTTT
1 TTTTT
52017263 AATTTTTTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTTGTATAATTTCAATA
Found at i:52017959 original size:3 final size:3
Alignment explanation
Indices: 52017951--52017995 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
52017941 TTTCGGTGAT
52017951 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
52017996 GTAGACCTAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:52018851 original size:21 final size:20
Alignment explanation
Indices: 52018813--52018852 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
52018803 CTAAAAATTA
*
52018813 TAAAAATTCAAAAAAAAACT
1 TAAAAAATCAAAAAAAAACT
52018833 TAAAAAATCATAAATAAAAA
1 TAAAAAATCA-AAA-AAAAA
52018853 ACCATAATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 3 0.18
22 5 0.29
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (20 bp):
TAAAAAATCAAAAAAAAACT
Found at i:52018851 original size:22 final size:22
Alignment explanation
Indices: 52018804--52018852 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
52018794 ACAATAAATC
52018804 TAAAAATTATAAAAATTCAAAA
1 TAAAAATTATAAAAATTCAAAA
52018826 -AAAAACTTA-AAAAA-TCATAAA
1 TAAAAA-TTATAAAAATTCA-AAA
52018847 TAAAAA
1 TAAAAA
52018853 ACCATAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.12
21 13 0.54
22 8 0.33
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.22
Consensus pattern (22 bp):
TAAAAATTATAAAAATTCAAAA
Found at i:52028428 original size:28 final size:28
Alignment explanation
Indices: 52028356--52028457 Score: 116
Period size: 27 Copynumber: 3.6 Consensus size: 28
52028346 ATCATGAGAA
* * * *
52028356 TAGCACTAAGTGTGCGGGTTTAAAACTTG
1 TAGCACTAAGTGTGCGAGTTT-GATCATG
52028385 TACAGCACTAAGTGTGCGAGTTTGATCATG
1 T--AGCACTAAGTGTGCGAGTTTGATCATG
* *
52028415 TAGCACTAAGTGTGCGAG-TTGATTATA
1 TAGCACTAAGTGTGCGAGTTTGATCATG
52028442 TAGCACTAAGTGTGCG
1 TAGCACTAAGTGTGCG
52028458 GACACACTAT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
27 23 0.35
28 17 0.26
29 1 0.02
30 5 0.08
31 19 0.29
ACGTcount: A:0.27, C:0.15, G:0.27, T:0.30
Consensus pattern (28 bp):
TAGCACTAAGTGTGCGAGTTTGATCATG
Found at i:52037823 original size:49 final size:49
Alignment explanation
Indices: 52037687--52037993 Score: 505
Period size: 49 Copynumber: 6.3 Consensus size: 49
52037677 CCCTTCGGAA
* * *
52037687 CTTATCACAT-T-TATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * *
52037734 CCTATCAC--ATATATACACTTTCACATTCATCACGTTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
52037781 CTTATCACATATATATGCACTTTCACATTCTTCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52037830 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52037879 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52037928 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52037977 CTTATCACATATATATA
1 CTTATCACATATATATA
52037994 TATCTCATAC
Statistics
Matches: 245, Mismatches: 11, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
46 1 0.00
47 48 0.20
49 196 0.80
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.34
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52041329 original size:40 final size:40
Alignment explanation
Indices: 52041285--52041475 Score: 278
Period size: 40 Copynumber: 4.7 Consensus size: 40
52041275 CCAGCATGAT
* * *
52041285 TGCTCTTCGGGACCTAGCCCGGATATAACACTAGCACGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
* *
52041325 TGCTCTTCGGAACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
52041365 TGCTCTT-GGGACTTAGCCCGGATACATCACTAGCATGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCA--C--GAA
*
52041408 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCATGAA
1 TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
52041448 TGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TGCTCTTCGGGACTTAGCCCGGATACATC
52041476 GTCGAGACCT
Statistics
Matches: 138, Mismatches: 8, Indels: 11
0.88 0.05 0.07
Matches are distributed among these distances:
39 31 0.22
40 69 0.50
43 10 0.07
44 28 0.20
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.25
Consensus pattern (40 bp):
TGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAA
Found at i:52041429 original size:83 final size:80
Alignment explanation
Indices: 52041272--52041475 Score: 304
Period size: 83 Copynumber: 2.5 Consensus size: 80
52041262 CGAATACACG
* * * * *
52041272 TCACCAGCATGATTGCTCTTCGGGACCTAGCCCGGATATAACACTAGCACGAATGCTCTTCGGAA
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAA
52041337 CTTAGCCCGGATACA
66 CTTAGCCCGGATACA
52041352 TCACTAGCATGAATGCTCTT-GGGACTTAGCCCGGATACATCACTAGCATGCATGAATGCTCTTC
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCA--C--GAATGCTCTTC
*
52041416 GGGACTTAGCCCGGATACA
62 GGAACTTAGCCCGGATACA
52041435 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGAT-CATC
1 TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATC
52041476 GTCGAGACCT
Statistics
Matches: 113, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
79 25 0.22
80 18 0.16
81 1 0.01
83 53 0.47
84 16 0.14
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.25
Consensus pattern (80 bp):
TCACTAGCATGAATGCTCTTCGGGACTTAGCCCGGATACATCACTAGCACGAATGCTCTTCGGAA
CTTAGCCCGGATACA
Found at i:52043908 original size:25 final size:24
Alignment explanation
Indices: 52043833--52043909 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 24
52043823 TTCGGAACTT
52043833 ATCACATTTATACACATTCACATTC
1 ATCACA-TTATACACATTCACATTC
** * **
52043858 ATCACATT-GGC-CATTCGGCCCT-
1 ATCACATTATACACATTC-ACATTC
52043880 ATCACATATATACACATTCACATTC
1 ATCACAT-TATACACATTCACATTC
52043905 ATCAC
1 ATCAC
52043910 GTTGGCCATT
Statistics
Matches: 37, Mismatches: 10, Indels: 10
0.65 0.18 0.18
Matches are distributed among these distances:
22 12 0.32
23 4 0.11
24 5 0.14
25 16 0.43
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.31
Consensus pattern (24 bp):
ATCACATTATACACATTCACATTC
Found at i:52043966 original size:49 final size:49
Alignment explanation
Indices: 52043830--52044233 Score: 647
Period size: 49 Copynumber: 8.3 Consensus size: 49
52043820 CCCTTCGGAA
* * *
52043830 CTTATCACAT-T-TATACACATTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * * * *
52043877 CCTATCAC--ATATATACACATTCACATTCATCACGTTGGCCATTCGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
52043924 CTTATCACATATATATGCACTTTCACATTCTTCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52043973 CTTATCACATATATATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52044022 CTTATCACATATATACACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52044071 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTTGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52044120 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATT-GGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
52044168 CTTATCACATATATATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
52044217 CTTATCACATATATATA
1 CTTATCACATATATATA
52044234 TATCTCATAC
Statistics
Matches: 335, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
46 1 0.00
47 49 0.15
48 47 0.14
49 238 0.71
ACGTcount: A:0.29, C:0.28, G:0.08, T:0.34
Consensus pattern (49 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:52049387 original size:26 final size:26
Alignment explanation
Indices: 52049351--52049415 Score: 130
Period size: 26 Copynumber: 2.5 Consensus size: 26
52049341 TTATATCATT
52049351 ACTCACACGAGCTGTGAAATAGTCTA
1 ACTCACACGAGCTGTGAAATAGTCTA
52049377 ACTCACACGAGCTGTGAAATAGTCTA
1 ACTCACACGAGCTGTGAAATAGTCTA
52049403 ACTCACACGAGCT
1 ACTCACACGAGCT
52049416 ATAGGTCAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (26 bp):
ACTCACACGAGCTGTGAAATAGTCTA
Found at i:52050905 original size:68 final size:68
Alignment explanation
Indices: 52050781--52050915 Score: 159
Period size: 68 Copynumber: 2.0 Consensus size: 68
52050771 AAGCCTATGG
* ** **
52050781 GTAAACATGACACCTTATTACGTAAGACCATAGCTGGGCTATAGCAACATCTGAAGTCCGCCAGG
1 GTAAACATGACACCATATTACGTAAGACCATAAATGGGCTATAGCAACATAAGAAGTCCGCCAGG
52050846 ATA
66 ATA
* *
52050849 GTAAACATGACACCATATTGA-GTAAGACCATAAATGGGCTA-AGGCAATGA-AAGAAGTCTGCC
1 GTAAACATGACACCATATT-ACGTAAGACCATAAATGGGCTATA-GCAA-CATAAGAAGTCCGCC
52050911 AGGAT
63 AGGAT
52050916 GGTGAACCAA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
67 1 0.02
68 54 0.95
69 2 0.04
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (68 bp):
GTAAACATGACACCATATTACGTAAGACCATAAATGGGCTATAGCAACATAAGAAGTCCGCCAGG
ATA
Found at i:52051384 original size:14 final size:14
Alignment explanation
Indices: 52051365--52051395 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
52051355 GCTTTCTGTT
52051365 ATGGGATAATCCAC
1 ATGGGATAATCCAC
52051379 ATGGGATAATCCAC
1 ATGGGATAATCCAC
52051393 ATG
1 ATG
52051396 AGGCTAACTG
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:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (14 bp):
ATGGGATAATCCAC
Found at i:52051878 original size:18 final size:18
Alignment explanation
Indices: 52051851--52051886 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
52051841 AGGGAAAGTA
*
52051851 TGGAAGTCTGAGATAGAG
1 TGGAAATCTGAGATAGAG
52051869 TGGAAATCTGAGATAGAG
1 TGGAAATCTGAGATAGAG
52051887 CCTGATGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.36, T:0.22
Consensus pattern (18 bp):
TGGAAATCTGAGATAGAG
Found at i:52055304 original size:18 final size:18
Alignment explanation
Indices: 52055283--52055317 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52055273 CATAAATCAC
* *
52055283 ATAAACTTGATAAATAAG
1 ATAAACATGAAAAATAAG
52055301 ATAAACATGAAAAATAA
1 ATAAACATGAAAAATAA
52055318 ATCAAGACTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.23
Consensus pattern (18 bp):
ATAAACATGAAAAATAAG
Found at i:52056385 original size:104 final size:104
Alignment explanation
Indices: 52056200--52056387 Score: 286
Period size: 104 Copynumber: 1.8 Consensus size: 104
52056190 GCCTATTACA
* * * * * *
52056200 GAATGTATGTGCAAGTTGTCATTGCATTGAATGCATGAATTGTTTTGTGTTGGAATGTATATGTG
1 GAATGTATATGCAAGTTGCCATTGCATCGAATGCATGAATTATTTTGTGATGGAATATATATGTG
* ** *
52056265 AGTTTCCATTGGATCGAATGCATGAACTGGTTTGTGATG
66 AGCTGACATTGCATCGAATGCATGAACTGGTTTGTGATG
52056304 GAATGTATATGCAAGTTGCCATTGCATCGAATGCATGAATTATTTTGTGATGGAATATATATGTG
1 GAATGTATATGCAAGTTGCCATTGCATCGAATGCATGAATTATTTTGTGATGGAATATATATGTG
52056369 AGCTGACATTGCATCGAAT
66 AGCTGACATTGCATCGAAT
52056388 ATATGAAATG
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
104 74 1.00
ACGTcount: A:0.27, C:0.10, G:0.26, T:0.37
Consensus pattern (104 bp):
GAATGTATATGCAAGTTGCCATTGCATCGAATGCATGAATTATTTTGTGATGGAATATATATGTG
AGCTGACATTGCATCGAATGCATGAACTGGTTTGTGATG
Found at i:52056394 original size:52 final size:52
Alignment explanation
Indices: 52056213--52056387 Score: 233
Period size: 52 Copynumber: 3.4 Consensus size: 52
52056203 TGTATGTGCA
* * *
52056213 AGTTGTCATTGCATTGAATGCATGAATTGTTTTGTGTTGGAATGTATATGTG
1 AGTTGCCATTGCATCGAATGCATGAATTGTTTTGTGATGGAATGTATATGTG
* * * * **
52056265 AGTTTCCATTGGATCGAATGCATGAACTGGTTTGTGATGGAATGTATATGCA
1 AGTTGCCATTGCATCGAATGCATGAATTGTTTTGTGATGGAATGTATATGTG
* *
52056317 AGTTGCCATTGCATCGAATGCATGAATTATTTTGTGATGGAATATATATGTG
1 AGTTGCCATTGCATCGAATGCATGAATTGTTTTGTGATGGAATGTATATGTG
* *
52056369 AGCTGACATTGCATCGAAT
1 AGTTGCCATTGCATCGAAT
52056388 ATATGAAATG
Statistics
Matches: 104, Mismatches: 19, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
52 104 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (52 bp):
AGTTGCCATTGCATCGAATGCATGAATTGTTTTGTGATGGAATGTATATGTG
Found at i:52056628 original size:27 final size:25
Alignment explanation
Indices: 52056597--52056649 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 25
52056587 GGATTTTGTA
*
52056597 AAGTATTCATGTGTGTGCTAACTCTAT
1 AAGTATTCATGTGCGTGCT--CTCTAT
52056624 AAGTATTCATGTGCGTGCTCTCTAT
1 AAGTATTCATGTGCGTGCTCTCTAT
52056649 A
1 A
52056650 GAAAGTAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 7 0.28
27 18 0.72
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.40
Consensus pattern (25 bp):
AAGTATTCATGTGCGTGCTCTCTAT
Found at i:52056865 original size:17 final size:17
Alignment explanation
Indices: 52056829--52056867 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
52056819 TCCGTGCCAA
*
52056829 ATGTGCGAGTTGTGCCC
1 ATGTGCGAGTTGTGACC
*
52056846 ATGTGCGAGTTGTGATC
1 ATGTGCGAGTTGTGACC
52056863 ATGTG
1 ATGTG
52056868 TGAACTGTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.36, T:0.33
Consensus pattern (17 bp):
ATGTGCGAGTTGTGACC
Found at i:52060012 original size:31 final size:31
Alignment explanation
Indices: 52059976--52060038 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
52059966 GACATGTCAC
* *
52059976 TAGGAACTATGTGGATATCAGCTTATGAATA
1 TAGGAACTATGTGGATATCAACTCATGAATA
52060007 TAGGAACTATGTGGATATCAACTCATGAATA
1 TAGGAACTATGTGGATATCAACTCATGAATA
52060038 T
1 T
52060039 GTGTGTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (31 bp):
TAGGAACTATGTGGATATCAACTCATGAATA
Found at i:52062682 original size:30 final size:30
Alignment explanation
Indices: 52062646--52062705 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
52062636 AAATGAGACA
52062646 AGGGATTATAATGTAATGAACTTATCTATG
1 AGGGATTATAATGTAATGAACTTATCTATG
52062676 AGGGATTATAATGTAATGAACTTATCTATG
1 AGGGATTATAATGTAATGAACTTATCTATG
52062706 TTAAATTGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.37, C:0.07, G:0.20, T:0.37
Consensus pattern (30 bp):
AGGGATTATAATGTAATGAACTTATCTATG
Found at i:52063791 original size:15 final size:15
Alignment explanation
Indices: 52063771--52063838 Score: 82
Period size: 15 Copynumber: 4.5 Consensus size: 15
52063761 ATTATGATAT
52063771 TGTATCTTGGATTTC
1 TGTATCTTGGATTTC
*
52063786 TGTATCTTGAATTTC
1 TGTATCTTGGATTTC
* *
52063801 TTTATCTAGGATTTC
1 TGTATCTTGGATTTC
* * *
52063816 TTTGTCTTGGACTTC
1 TGTATCTTGGATTTC
52063831 TGTATCTT
1 TGTATCTT
52063839 AGTTTTTATG
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.15, C:0.15, G:0.16, T:0.54
Consensus pattern (15 bp):
TGTATCTTGGATTTC
Found at i:52071290 original size:20 final size:20
Alignment explanation
Indices: 52071265--52071330 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
52071255 CATACATAAT
52071265 ATGCCACAAAGGCTAGA-AGA
1 ATGCCACAAAGGCTA-ACAGA
* *
52071285 ATGCCATAAAGGCTAACAAA
1 ATGCCACAAAGGCTAACAGA
52071305 ATGTGCCACAAAGGCTAACAGA
1 A--TGCCACAAAGGCTAACAGA
52071327 ATGC
1 ATGC
52071331 ATTACAAATG
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.03
20 20 0.51
22 18 0.46
ACGTcount: A:0.44, C:0.21, G:0.21, T:0.14
Consensus pattern (20 bp):
ATGCCACAAAGGCTAACAGA
Found at i:52071317 original size:22 final size:22
Alignment explanation
Indices: 52071266--52071329 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
52071256 ATACATAATA
52071266 TGCCACAAAGGCTAGA-AGAA--
1 TGCCACAAAGGCTA-ACAGAATG
* *
52071286 TGCCATAAAGGCTAACAAAATG
1 TGCCACAAAGGCTAACAGAATG
52071308 TGCCACAAAGGCTAACAGAATG
1 TGCCACAAAGGCTAACAGAATG
52071330 CATTACAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 16 0.43
22 20 0.54
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (22 bp):
TGCCACAAAGGCTAACAGAATG
Found at i:52079886 original size:29 final size:29
Alignment explanation
Indices: 52079825--52079923 Score: 168
Period size: 28 Copynumber: 3.5 Consensus size: 29
52079815 ACAGTAAGTC
52079825 CGCACACTTAGTGCT-TA-ATATTCAAACT
1 CGCACACTTAGTGCTATACA-ATTCAAACT
52079853 CGCACACTTAGTGCTATACAATTCAAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
52079882 CGCACACTTAGTGCTATACAATT-AAACT
1 CGCACACTTAGTGCTATACAATTCAAACT
52079910 CGCACACTTAGTGC
1 CGCACACTTAGTGC
52079924 CAATCTCATT
Statistics
Matches: 69, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
28 34 0.49
29 34 0.49
30 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCTATACAATTCAAACT
Found at i:52082237 original size:26 final size:27
Alignment explanation
Indices: 52082184--52082239 Score: 71
Period size: 25 Copynumber: 2.1 Consensus size: 27
52082174 TTTTAAATAC
52082184 TTTAATATAATTTAATATAAAATTTTA
1 TTTAATATAATTTAATATAAAATTTTA
* *
52082211 TTTAA-AT-ATTTGATATTAAATTATTA
1 TTTAATATAATTTAATATAAAATT-TTA
52082237 TTT
1 TTT
52082240 TATAGAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 13 0.50
26 8 0.31
27 5 0.19
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
TTTAATATAATTTAATATAAAATTTTA
Found at i:52090913 original size:15 final size:15
Alignment explanation
Indices: 52090893--52090933 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
52090883 TATTTTGAAA
52090893 AATATATAAAAATAC
1 AATATATAAAAATAC
*
52090908 AATATAT-AATATAC
1 AATATATAAAAATAC
*
52090922 AA-ATAAAAAAAT
1 AATATATAAAAAT
52090934 TAAGATTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
13 3 0.14
14 12 0.55
15 7 0.32
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (15 bp):
AATATATAAAAATAC
Found at i:52105144 original size:47 final size:46
Alignment explanation
Indices: 52105025--52105198 Score: 196
Period size: 46 Copynumber: 3.8 Consensus size: 46
52105015 GGGATATTTG
*
52105025 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGA
* * *
52105072 -GCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA-GATGTAACTA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATG---CGA
*
52105118 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGA-GGATGCGA
* * *
52105165 -AC-GCCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
52105199 TATGGGCGGG
Statistics
Matches: 109, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
43 4 0.04
45 32 0.29
46 34 0.31
47 33 0.30
48 2 0.02
50 4 0.04
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTGAGGATGCGA
Found at i:52105192 original size:45 final size:46
Alignment explanation
Indices: 52105029--52105203 Score: 225
Period size: 45 Copynumber: 3.8 Consensus size: 46
52105019 TATTTGGGCA
*
52105029 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
52105075 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC---G
52105120 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
*
52105168 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
52105204 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 8, Indels: 19
0.81 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
45 38 0.34
46 29 0.26
47 29 0.26
48 3 0.03
50 4 0.04
51 3 0.03
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:52108448 original size:42 final size:42
Alignment explanation
Indices: 52108389--52108483 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
52108379 GCTGTGTAAG
* *
52108389 ACGCCCGTGTCCCAGGCCGTGTCAACCACACAGCTGAGACAC
1 ACGCCCGTGTCCCAGGCCATGTCAACCACACAGCTAAGACAC
* *
52108431 ACGCCCATGTCCCAGGCCATGTCAACCACACGGCTAAGACAC
1 ACGCCCGTGTCCCAGGCCATGTCAACCACACAGCTAAGACAC
52108473 ACGCCCGTGTC
1 ACGCCCGTGTC
52108484 TCTGCCTGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.24, C:0.41, G:0.22, T:0.13
Consensus pattern (42 bp):
ACGCCCGTGTCCCAGGCCATGTCAACCACACAGCTAAGACAC
Found at i:52109436 original size:15 final size:15
Alignment explanation
Indices: 52109416--52109446 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
52109406 TTGGGCACTC
52109416 AATTTAGTCAAAAGG
1 AATTTAGTCAAAAGG
52109431 AATTTAGTCAAAAGG
1 AATTTAGTCAAAAGG
52109446 A
1 A
52109447 CTAAATTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.19, T:0.26
Consensus pattern (15 bp):
AATTTAGTCAAAAGG
Found at i:52111425 original size:34 final size:34
Alignment explanation
Indices: 52111381--52111453 Score: 137
Period size: 34 Copynumber: 2.1 Consensus size: 34
52111371 TTCGAATTCT
*
52111381 TGTTAGACAGAGTCAGAATGAGTTCGAAATCCCC
1 TGTTCGACAGAGTCAGAATGAGTTCGAAATCCCC
52111415 TGTTCGACAGAGTCAGAATGAGTTCGAAATCCCC
1 TGTTCGACAGAGTCAGAATGAGTTCGAAATCCCC
52111449 TGTTC
1 TGTTC
52111454 TAACTTGGGA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.26
Consensus pattern (34 bp):
TGTTCGACAGAGTCAGAATGAGTTCGAAATCCCC
Found at i:52113889 original size:20 final size:19
Alignment explanation
Indices: 52113838--52113891 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
52113828 AATTAGATAA
52113838 TTATTATTTATTTAATATT
1 TTATTATTTATTTAATATT
* ** *
52113857 TTAATAAGATATTTATTATT
1 TT-ATTATTTATTTAATATT
52113877 TTATTATTTTATTTA
1 TTATTA-TTTATTTA
52113892 GTATATATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 3
0.72 0.19 0.08
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (19 bp):
TTATTATTTATTTAATATT
Found at i:52131561 original size:41 final size:41
Alignment explanation
Indices: 52131516--52131633 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
52131506 TGAAAGATAA
52131516 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
52131557 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
52131587 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
52131628 ATGTAG
1 ATGTAG
52131634 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:52131572 original size:71 final size:71
Alignment explanation
Indices: 52131484--52131647 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
52131474 GAGATGTATC
52131484 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
52131549 AGGACA
66 AGGACA
52131555 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
52131620 AGGACA
66 AGGACA
52131626 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
52131648 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:52138950 original size:41 final size:41
Alignment explanation
Indices: 52138905--52139022 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
52138895 TGAAAGATAA
52138905 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
52138946 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
52138976 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
52139017 ATGTAG
1 ATGTAG
52139023 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:52138961 original size:71 final size:71
Alignment explanation
Indices: 52138873--52139036 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
52138863 GAGATGTATC
52138873 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
52138938 AGGACA
66 AGGACA
52138944 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
52139009 AGGACA
66 AGGACA
52139015 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
52139037 AGACAAATCG
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:52141522 original size:30 final size:30
Alignment explanation
Indices: 52141482--52141547 Score: 105
Period size: 30 Copynumber: 2.2 Consensus size: 30
52141472 TGTCTCAACT
*
52141482 GTGTGAGTCATACGGCCTGGCCCCACGACC
1 GTGTGAGTCATACGGCCTGGCCACACGACC
* *
52141512 GTGTGTGTCATATGGCCTGGCCACACGACC
1 GTGTGAGTCATACGGCCTGGCCACACGACC
52141542 GTGTGA
1 GTGTGA
52141548 CCCTTGCAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.17, C:0.30, G:0.32, T:0.21
Consensus pattern (30 bp):
GTGTGAGTCATACGGCCTGGCCACACGACC
Found at i:52144059 original size:28 final size:29
Alignment explanation
Indices: 52144005--52144066 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 29
52143995 GAAAACGTGT
*
52144005 ATATGAATGTGATTTGGGCATAATGGGCC
1 ATATGAATGAGATTTGGGCATAATGGGCC
* *
52144034 ATATGAATGAGA-TTGGGCCTAGTGGGCC
1 ATATGAATGAGATTTGGGCATAATGGGCC
52144062 ATATG
1 ATATG
52144067 CATGTATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 19 0.63
29 11 0.37
ACGTcount: A:0.27, C:0.11, G:0.32, T:0.29
Consensus pattern (29 bp):
ATATGAATGAGATTTGGGCATAATGGGCC
Found at i:52146079 original size:46 final size:46
Alignment explanation
Indices: 52145984--52146152 Score: 159
Period size: 46 Copynumber: 3.6 Consensus size: 46
52145974 AAATCGATGC
* * * *
52145984 CATGTCCCAGACATGGTCTTACACTGAC-TATCATCTCGTAGCCGATG
1 CATGTCCCAGACATGGTCTTACACTGGCTTA-CGTCTC-AAGCCGTTG
52146031 CATGTCCCAGACAT-GTCTTACACTGGCTTACGTCTCAAGGCCGTTG
1 CATGTCCCAGACATGGTCTTACACTGGCTTACGTCTCAA-GCCGTTG
* * * *
52146077 CATGTCCCAGACAT-GTCTTACACTAGCCCTT--GTCTCAATCCCAATTC
1 CATGTCCCAGACATGGTCTTACACT-G-GCTTACGTCTCAA-GCC-GTTG
*
52146124 CATGTCCCAGACATGGTCTTACATTGGCT
1 CATGTCCCAGACATGGTCTTACACTGGCT
52146153 CTCATAATGT
Statistics
Matches: 105, Mismatches: 11, Indels: 13
0.81 0.09 0.10
Matches are distributed among these distances:
45 1 0.01
46 58 0.55
47 34 0.32
48 12 0.11
ACGTcount: A:0.22, C:0.31, G:0.18, T:0.29
Consensus pattern (46 bp):
CATGTCCCAGACATGGTCTTACACTGGCTTACGTCTCAAGCCGTTG
Found at i:52152351 original size:21 final size:22
Alignment explanation
Indices: 52152311--52152351 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
52152301 CACTTGACAT
*
52152311 AGGGGCAACATGCCCATGTGAA
1 AGGGGCAACACGCCCATGTGAA
*
52152333 AGGGGC-ACACGCCCGTGTG
1 AGGGGCAACACGCCCATGTG
52152352 GCCAATTCCG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.24, C:0.27, G:0.37, T:0.12
Consensus pattern (22 bp):
AGGGGCAACACGCCCATGTGAA
Found at i:52153596 original size:46 final size:46
Alignment explanation
Indices: 52153523--52153644 Score: 149
Period size: 46 Copynumber: 2.6 Consensus size: 46
52153513 ATCTCAAATT
* *
52153523 GATGCCATGTCCCAAACATTGTCTTACACTGAC-TATCATCTTGTA-GCC
1 GATG-CATGTCCCAGACA-TGTCTTACACTGACTTA-CATCTCG-AGGCC
* *
52153571 GATGCATGTCCCAGACATGTCTTACACTGGCTTACTTCTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGACTTACATCTCGAGGCC
*
52153617 GTTGCATGTCCCAGACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
52153645 AGCCCTCGTC
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
45 1 0.01
46 48 0.72
47 14 0.21
48 4 0.06
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTGACTTACATCTCGAGGCC
Found at i:52156988 original size:26 final size:26
Alignment explanation
Indices: 52156952--52157018 Score: 107
Period size: 26 Copynumber: 2.6 Consensus size: 26
52156942 CATTCTGACC
*
52156952 CACAGCTCGTGTGAGCAGGCCCATTT
1 CACAGCTCGTGTGAGCAGACCCATTT
*
52156978 CACAGCTCGTGTGAGCAGATCCATTT
1 CACAGCTCGTGTGAGCAGACCCATTT
*
52157004 CATAGCTCGTGTGAG
1 CACAGCTCGTGTGAG
52157019 TAATGATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.21, C:0.27, G:0.27, T:0.25
Consensus pattern (26 bp):
CACAGCTCGTGTGAGCAGACCCATTT
Found at i:52157302 original size:17 final size:17
Alignment explanation
Indices: 52157280--52157312 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
52157270 TAAATTCATA
52157280 TGAGTTATGGTTAAATC
1 TGAGTTATGGTTAAATC
52157297 TGAGTTATGGTTAAAT
1 TGAGTTATGGTTAAAT
52157313 GAGCTAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.24, T:0.42
Consensus pattern (17 bp):
TGAGTTATGGTTAAATC
Found at i:52160482 original size:25 final size:24
Alignment explanation
Indices: 52160454--52160526 Score: 83
Period size: 25 Copynumber: 3.0 Consensus size: 24
52160444 TAGTTTACCG
*
52160454 AAAAGGGGTTTTGCCCCAGTTTATT
1 AAAAGGGGCTTTGCCCCAG-TTATT
*
52160479 AAAAAGGGCTTTGCCCCAGTTATT
1 AAAAGGGGCTTTGCCCCAGTTATT
* **
52160503 AAAAGAGGCTAGGCCTCCAGTTAT
1 AAAAGGGGCTTTGCC-CCAGTTAT
52160527 ATGTTAAAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
24 16 0.39
25 25 0.61
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (24 bp):
AAAAGGGGCTTTGCCCCAGTTATT
Found at i:52160757 original size:31 final size:31
Alignment explanation
Indices: 52160719--52160833 Score: 178
Period size: 31 Copynumber: 3.7 Consensus size: 31
52160709 TTGTTACAGT
*
52160719 AAAGGCTTCGACCCAGTGATATGAATAATGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
52160750 AAAGGCTTCGGCCCAGTGATATGAATAACGA
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
*
52160781 AAAGGCTTCGGCCCAGTGATATGAATAATGT
1 AAAGGCTTCGGCCCAGTGATATGAATAATGA
* *
52160812 AAAGGCTTCAGCCCCGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
52160834 CTGAGCTTGA
Statistics
Matches: 78, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
30 5 0.06
31 73 0.94
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATGA
Found at i:52163096 original size:43 final size:41
Alignment explanation
Indices: 52162952--52163095 Score: 171
Period size: 43 Copynumber: 3.4 Consensus size: 41
52162942 CCATATATGA
* * *
52162952 TCTTACATGTCATCATATATCGATGCCACTGTCCTAGACAGTG
1 TCTTACATGTAATCATATA-CGATGCCAATGTCCCAGACA-TG
* *
52162995 TCTTACACGAAATCATATAACGATGCCAATGTCCCAGACATGG
1 TCTTACATGTAATCATAT-ACGATGCCAATGTCCCAGACAT-G
* *
52163038 TCTTACATGTAATCACAATACAATGCCAATGTCCCAGACATAG
1 TCTTACATGTAATCA-TATACGATGCCAATGTCCCAGACAT-G
52163081 TCTTACATGTAATCA
1 TCTTACATGTAATCA
52163096 CCTCTCGGTA
Statistics
Matches: 88, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
42 1 0.01
43 84 0.95
44 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (41 bp):
TCTTACATGTAATCATATACGATGCCAATGTCCCAGACATG
Found at i:52164582 original size:27 final size:27
Alignment explanation
Indices: 52164547--52164602 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
52164537 AAATTAAAAC
*
52164547 AAAATAAAAATAAAAGT-AATGTTCTAA
1 AAAATAAAAATAAAA-TCAATGTCCTAA
52164574 AAAATAAAAATAAAATCAATGTCCTAA
1 AAAATAAAAATAAAATCAATGTCCTAA
52164601 AA
1 AA
52164603 TAAAGAAAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.23
Consensus pattern (27 bp):
AAAATAAAAATAAAATCAATGTCCTAA
Found at i:52165350 original size:6 final size:6
Alignment explanation
Indices: 52165296--52165389 Score: 59
Period size: 6 Copynumber: 15.3 Consensus size: 6
52165286 AAGAAACATT
* * * * *
52165296 ATCAGA A-CTAGA ATCAAA ATGAGA ATTAGA ATCAAA ATCAG- GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
* *
52165345 ATCAGA ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
52165390 GTGAATGCAA
Statistics
Matches: 67, Mismatches: 13, Indels: 16
0.70 0.14 0.17
Matches are distributed among these distances:
5 4 0.06
6 54 0.81
7 7 0.10
8 2 0.03
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:52165351 original size:25 final size:25
Alignment explanation
Indices: 52165317--52165386 Score: 74
Period size: 25 Copynumber: 2.8 Consensus size: 25
52165307 AATCAAAATG
*
52165317 AGAATTAGAATCAAAATCAGGTGA-C
1 AGAATCAGAATCAAAATCAGGT-ATC
*
52165342 AGAATCAGAATCAGAATCA-GTATC
1 AGAATCAGAATCAAAATCAGGTATC
52165366 AGGTAA-CAGAATCAAAATCAG
1 A-G-AATCAGAATCAAAATCAG
52165387 AATGTGAATG
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 1 0.03
24 4 0.11
25 31 0.82
26 2 0.05
ACGTcount: A:0.49, C:0.14, G:0.19, T:0.19
Consensus pattern (25 bp):
AGAATCAGAATCAAAATCAGGTATC
Done.