Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 50 of 131
Found at i:16617321 original size:107 final size:107
Alignment explanation
Indices: 16617131--16617357 Score: 393
Period size: 107 Copynumber: 2.1 Consensus size: 107
16617121 TTTCCTTCAA
* *
16617131 ATAG-TTGCCACAAGGGTTGTTCTTTTGTGTTCTCCACGAAGACATTCCTTTCATCATTTGCCAC
1 ATAGATTGCCACAAGGGTTGTTCTTTTGTGTGCGCCACGAAGACATTCCTTTCATCATTTGCCAC
16617195 AAGGATTTTTCTTTCCTTAGATCGCCACAAGGCTTCCATTTC
66 AAGGATTTTTCTTTCCTTAGATCGCCACAAGGCTTCCATTTC
* * *
16617237 ATAGATTGCCACAAGGGTTGTTCTTTTGTGTGCGCTACGAAGGCATTTCTTTCATCATTTGCCAC
1 ATAGATTGCCACAAGGGTTGTTCTTTTGTGTGCGCCACGAAGACATTCCTTTCATCATTTGCCAC
*
16617302 AAGGATTTTTCTTTCCTTAGATTGCCACAAGGCTTCCATTTC
66 AAGGATTTTTCTTTCCTTAGATCGCCACAAGGCTTCCATTTC
16617344 ATAGATTGCCACAA
1 ATAGATTGCCACAA
16617358 AGGCTTCCAT
Statistics
Matches: 114, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
106 4 0.04
107 110 0.96
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (107 bp):
ATAGATTGCCACAAGGGTTGTTCTTTTGTGTGCGCCACGAAGACATTCCTTTCATCATTTGCCAC
AAGGATTTTTCTTTCCTTAGATCGCCACAAGGCTTCCATTTC
Found at i:16617360 original size:27 final size:27
Alignment explanation
Indices: 16617319--16617398 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
16617309 TTTCTTTCCT
16617319 TAGATTGCCAC-AAGGCTTCCATTTCA
1 TAGATTGCCACAAAGGCTTCCATTTCA
16617345 TAGATTGCCACAAAGGCTTCCATTTCA
1 TAGATTGCCACAAAGGCTTCCATTTCA
* * *
16617372 TGGATTTCCATAAAGGCTTCCACTTTC
1 TAGATTGCCACAAAGGCTTCCA-TTTC
16617399 TTACATGTTC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
26 11 0.22
27 34 0.69
28 4 0.08
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (27 bp):
TAGATTGCCACAAAGGCTTCCATTTCA
Found at i:16619553 original size:31 final size:28
Alignment explanation
Indices: 16619518--16619594 Score: 84
Period size: 28 Copynumber: 2.6 Consensus size: 28
16619508 TCCAGAGATT
*
16619518 GCCACAAAGGCATCCTTTTCATTAAGTACTC
1 GCCACAAAGGCATCCTTTCCA--AAGT-CTC
*
16619549 GCCACAAAGGCTTTCC-TTCCAAAGTCTC
1 GCCACAAAGGC-ATCCTTTCCAAAGTCTC
*
16619577 GCCACAAAAGCATCCTTT
1 GCCACAAAGGCATCCTTT
16619595 AAGAGGTTCA
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
27 3 0.08
28 15 0.38
29 4 0.10
31 15 0.38
32 3 0.08
ACGTcount: A:0.29, C:0.32, G:0.13, T:0.26
Consensus pattern (28 bp):
GCCACAAAGGCATCCTTTCCAAAGTCTC
Found at i:16619661 original size:57 final size:57
Alignment explanation
Indices: 16619589--16619727 Score: 206
Period size: 57 Copynumber: 2.4 Consensus size: 57
16619579 CACAAAAGCA
* * *
16619589 TCCTTTAAGAGGTTCACCACAAAGGCTCACCTTTCTAGAGTTTTGCCGCAAAGGCTG
1 TCCTTTAACAGGTTCACCATAAAGGCTCACCTTTCTAGAGTTTTGCCACAAAGGCTG
* * * *
16619646 TCCTTTAACATGTTCACCATATAGGCTTACCTTTCTAGAGTTTTTCCACAAAGGCTG
1 TCCTTTAACAGGTTCACCATAAAGGCTCACCTTTCTAGAGTTTTGCCACAAAGGCTG
*
16619703 TCCTTTAATAGGTTCACCATAAAGG
1 TCCTTTAACAGGTTCACCATAAAGG
16619728 TTTTTCTTCT
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 72 1.00
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.32
Consensus pattern (57 bp):
TCCTTTAACAGGTTCACCATAAAGGCTCACCTTTCTAGAGTTTTGCCACAAAGGCTG
Found at i:16619701 original size:29 final size:29
Alignment explanation
Indices: 16619604--16619701 Score: 76
Period size: 29 Copynumber: 3.4 Consensus size: 29
16619594 TAAGAGGTTC
*
16619604 ACCACAAAGGCTCACCTTTCTAGAGTTTT
1 ACCACAAAGGCTTACCTTTCTAGAGTTTT
* * * * *
16619633 GCCGCAAAGGCTGT-CCTTT-AACA-TGTTC
1 ACCACAAAGGCT-TACCTTTCTAGAGT-TTT
* *
16619661 ACCATATAGGCTTACCTTTCTAGAGTTTT
1 ACCACAAAGGCTTACCTTTCTAGAGTTTT
*
16619690 TCCACAAAGGCT
1 ACCACAAAGGCT
16619702 GTCCTTTAAT
Statistics
Matches: 48, Mismatches: 16, Indels: 10
0.65 0.22 0.14
Matches are distributed among these distances:
27 2 0.04
28 17 0.35
29 28 0.58
30 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.32
Consensus pattern (29 bp):
ACCACAAAGGCTTACCTTTCTAGAGTTTT
Found at i:16620203 original size:5 final size:5
Alignment explanation
Indices: 16620193--16620222 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
16620183 TGCCATATCA
16620193 AATCT AATCT AATCT AATCT AATCT AATCT
1 AATCT AATCT AATCT AATCT AATCT AATCT
16620223 TTATAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
AATCT
Found at i:16622451 original size:39 final size:39
Alignment explanation
Indices: 16622384--16622535 Score: 157
Period size: 40 Copynumber: 3.8 Consensus size: 39
16622374 TTAGAGTTAT
* * * *
16622384 CGAAGTATAAATAGGGGCAC-TAAAGTGCATTCAATGTAC
1 CGAAGTACAAACAGGGGCACGT-ATGTGCAATCAATGTAC
* **
16622423 CGAAGTATAAACAGGGGCACGTATGTGCAATCAGGGGTAC
1 CGAAGTACAAACAGGGGCACGTATGTGCAATCA-ATGTAC
*
16622463 CGAAGTGCAAACAGGGGCACGTATGTGCAATC-ATGGGTAC
1 CGAAGTACAAACAGGGGCACGTATGTGCAATCAAT--GTAC
*
16622503 C-AAGGTACAAACAGGGGCACGTATGTACAATCA
1 CGAA-GTACAAACAGGGGCACGTATGTGCAATCA
16622536 TACAATAATT
Statistics
Matches: 96, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
39 30 0.31
40 66 0.69
ACGTcount: A:0.35, C:0.18, G:0.28, T:0.18
Consensus pattern (39 bp):
CGAAGTACAAACAGGGGCACGTATGTGCAATCAATGTAC
Found at i:16622459 original size:20 final size:20
Alignment explanation
Indices: 16622434--16622535 Score: 89
Period size: 20 Copynumber: 5.1 Consensus size: 20
16622424 GAAGTATAAA
16622434 CAGGGGCACGTATGTGCAAT
1 CAGGGGCACGTATGTGCAAT
* * *
16622454 CAGGGGTACCG-AAGTGCAAA
1 CAGGGGCA-CGTATGTGCAAT
16622474 CAGGGGCACGTATGTGCAAT
1 CAGGGGCACGTATGTGCAAT
* * ** * * *
16622494 CATGGGTACCAAGGTACAAA
1 CAGGGGCACGTATGTGCAAT
*
16622514 CAGGGGCACGTATGTACAAT
1 CAGGGGCACGTATGTGCAAT
16622534 CA
1 CA
16622536 TACAATAATT
Statistics
Matches: 61, Mismatches: 19, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
19 2 0.03
20 57 0.93
21 2 0.03
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.17
Consensus pattern (20 bp):
CAGGGGCACGTATGTGCAAT
Found at i:16622536 original size:40 final size:40
Alignment explanation
Indices: 16622419--16622536 Score: 184
Period size: 40 Copynumber: 3.0 Consensus size: 40
16622409 TGCATTCAAT
* *
16622419 GTACCGAAGTATAAACAGGGGCACGTATGTGCAATCAGGG
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCAATCATGG
*
16622459 GTACCGAAGTGCAAACAGGGGCACGTATGTGCAATCATGG
1 GTACCGAAGTACAAACAGGGGCACGTATGTGCAATCATGG
*
16622499 GTACC-AAGGTACAAACAGGGGCACGTATGTACAATCAT
1 GTACCGAA-GTACAAACAGGGGCACGTATGTGCAATCAT
16622537 ACAATAATTT
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
39 2 0.03
40 70 0.97
ACGTcount: A:0.33, C:0.19, G:0.30, T:0.18
Consensus pattern (40 bp):
GTACCGAAGTACAAACAGGGGCACGTATGTGCAATCATGG
Found at i:16626729 original size:91 final size:91
Alignment explanation
Indices: 16626574--16626777 Score: 311
Period size: 91 Copynumber: 2.2 Consensus size: 91
16626564 CACAAGCCGT
* *
16626574 CATTTAAAACAAATAAATTTAAGCCTTTCCTTTAGAAATTACTCTATGTTACTATTAGTTTTCTA
1 CATTTAAAATAAATAAATTTAAGCCTTTCCTTTAGAAAATACTCTATGTTACTATTAGTTTTCTA
** *
16626639 TTAAAATATTTTTTATTCTTATTAAA
66 TTAAAATATTTTCCATTCCTATTAAA
* *
16626665 CATTTAAAATGAATAAATTTAAGCCTTTCTTTTAGAAAATACTCTACT-TTACTATTAGTTTTCT
1 CATTTAAAATAAATAAATTTAAGCCTTTCCTTTAGAAAATACTCTA-TGTTACTATTAGTTTTCT
16626729 ATTAAAATATTTTCCATTCCTATTAAA
65 ATTAAAATATTTTCCATTCCTATTAAA
* *
16626756 CATTTAGAATAAATGAATTTAA
1 CATTTAAAATAAATAAATTTAA
16626778 ATTTTAAGCA
Statistics
Matches: 102, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
91 101 0.99
92 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (91 bp):
CATTTAAAATAAATAAATTTAAGCCTTTCCTTTAGAAAATACTCTATGTTACTATTAGTTTTCTA
TTAAAATATTTTCCATTCCTATTAAA
Found at i:16627339 original size:13 final size:15
Alignment explanation
Indices: 16627308--16627339 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
16627298 ATTCATTTAT
16627308 TTTTATATAAAATAA
1 TTTTATATAAAATAA
16627323 TTTTAT-TAAAA-AA
1 TTTTATATAAAATAA
16627336 TTTT
1 TTTT
16627340 GGTGGATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 6 0.35
14 5 0.29
15 6 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTTATATAAAATAA
Found at i:16632473 original size:16 final size:16
Alignment explanation
Indices: 16632452--16632488 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
16632442 ATCCTTAGTT
16632452 GTGGAAAGCTAAGGTA
1 GTGGAAAGCTAAGGTA
*
16632468 GTGGAAAGCTAATGTA
1 GTGGAAAGCTAAGGTA
16632484 GTGGA
1 GTGGA
16632489 GTAGGCAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.35, C:0.05, G:0.38, T:0.22
Consensus pattern (16 bp):
GTGGAAAGCTAAGGTA
Found at i:16635641 original size:19 final size:18
Alignment explanation
Indices: 16635611--16635648 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
16635601 ATTAATTAAT
*
16635611 TTACTATTATTATTTTTA
1 TTACTATTATTATTGTTA
16635629 TTACTATTTATTATTGTTA
1 TTACTA-TTATTATTGTTA
16635648 T
1 T
16635649 CATTATTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.26, C:0.05, G:0.03, T:0.66
Consensus pattern (18 bp):
TTACTATTATTATTGTTA
Found at i:16635655 original size:19 final size:19
Alignment explanation
Indices: 16635613--16635660 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
16635603 TAATTAATTT
* *
16635613 ACTA-TTATTATTTTTATT
1 ACTATTTATTATTGTTATC
16635631 ACTATTTATTATTGTTATC
1 ACTATTTATTATTGTTATC
*
16635650 ATTATTATATT
1 ACTATT-TATT
16635661 CAATTACATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 4 0.16
19 17 0.68
20 4 0.16
ACGTcount: A:0.29, C:0.06, G:0.02, T:0.62
Consensus pattern (19 bp):
ACTATTTATTATTGTTATC
Found at i:16640525 original size:40 final size:40
Alignment explanation
Indices: 16640470--16640551 Score: 164
Period size: 40 Copynumber: 2.0 Consensus size: 40
16640460 TGGAGAAAAA
16640470 GATAGAGCAAATGGAGGCGAAAAAGACGAACTTGAGATTG
1 GATAGAGCAAATGGAGGCGAAAAAGACGAACTTGAGATTG
16640510 GATAGAGCAAATGGAGGCGAAAAAGACGAACTTGAGATTG
1 GATAGAGCAAATGGAGGCGAAAAAGACGAACTTGAGATTG
16640550 GA
1 GA
16640552 CATAGATGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.43, C:0.10, G:0.33, T:0.15
Consensus pattern (40 bp):
GATAGAGCAAATGGAGGCGAAAAAGACGAACTTGAGATTG
Found at i:16641924 original size:13 final size:14
Alignment explanation
Indices: 16641898--16641926 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
16641888 AGCTACCATG
16641898 GAATTGATGCTAGA
1 GAATTGATGCTAGA
16641912 GAATTGA-GCTAGA
1 GAATTGATGCTAGA
16641925 GA
1 GA
16641927 TGGAGGGAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.38, C:0.07, G:0.31, T:0.24
Consensus pattern (14 bp):
GAATTGATGCTAGA
Found at i:16649328 original size:44 final size:43
Alignment explanation
Indices: 16649190--16649555 Score: 225
Period size: 44 Copynumber: 8.5 Consensus size: 43
16649180 CCAATAATCC
* * * * * *
16649190 TATCTCCCTAAAGTTGTAGTGGAGCGGATTAA-AACCTTAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * * *
16649234 TATCTCTCTGAAGTTGCAG-AGAGCAGA-T-CGCATCCAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
*
16649274 TATCTCCCTGAAGATGCAGTGGAGCAGACTAAGTAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAG-AAGCAAGTCT
* * *
16649318 TATC-CTCCTGAAGTTGCAGT-GAGGTAGACTGAAGATGGCAAATCT
1 TATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA-AGCAAGTCT
* ** *
16649363 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTGACAA-TCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGAAG-CAAGTCT
* * * * *
16649407 TATCTCCCTAAAGTTGCAGTGGAGCGGATTAA-AACCTTAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGC-AAG-TCT
* * * * * * *
16649451 TATCTCTCTGAAGTTGCAG-AGAACAGA-T-CGCATCTAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
* *
16649491 TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCGAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGAAGCAAGTCT
16649535 TATC-CTCCTGAAGTTGCAGTG
1 TATCTC-CCTGAAGTTGCAGTG
16649556 AGGCAGATTG
Statistics
Matches: 252, Mismatches: 49, Indels: 42
0.73 0.14 0.12
Matches are distributed among these distances:
40 41 0.16
41 19 0.08
42 9 0.04
43 18 0.07
44 123 0.49
45 39 0.15
46 3 0.01
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (43 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGAAGCAAGTCT
Found at i:16649570 original size:217 final size:216
Alignment explanation
Indices: 16649185--16649607 Score: 711
Period size: 217 Copynumber: 2.0 Consensus size: 216
16649175 GGTGGCCAAT
*
16649185 AATCCTATCTCCCTAAAGTTGTAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTG
* *
16649250 CAGAGAGCAGATCGCATCCAGTCTTATCTCCCTGAAGATGCAGTGGAGCAGACTAAGTAAGCAAG
66 CAGAGAACAGATCGCATCCAGTCTTATCTCCCTGAAGATGCAGTGGAGCAGACTAAATAAGCAAG
* **
16649315 TCTTATCCTCCTGAAGTTGCAGTGAGGTAGACTGAAGATGGCAAATCTTATCTCCCTGAAGTTGC
131 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCT-AAGCAGC
16649380 AGTGGAGCAGATTAAAGCTGAC
195 AGTGGAGCAGATTAAAGCTGAC
16649402 AATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTG
1 AATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTG
* * *
16649467 CAGAGAACAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAATAAGCGAG
66 CAGAGAACAGATCGCATCCAGTCTTATCTCCCTGAAGATGCAGTGGAGCAGACTAAATAAGCAAG
* ** * *
16649532 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGATTGAAGATTTCAGATCTTATCTCCCTAAGCAGTA
131 TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTAAGCAGCA
16649597 GTGGAGCAGAT
196 GTGGAGCAGAT
16649608 CGAAGATGGC
Statistics
Matches: 192, Mismatches: 14, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
216 16 0.08
217 176 0.92
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (216 bp):
AATCCTATCTCCCTAAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTGAAGTTG
CAGAGAACAGATCGCATCCAGTCTTATCTCCCTGAAGATGCAGTGGAGCAGACTAAATAAGCAAG
TCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTAAGCAGCA
GTGGAGCAGATTAAAGCTGAC
Found at i:16651407 original size:43 final size:43
Alignment explanation
Indices: 16651359--16651620 Score: 524
Period size: 43 Copynumber: 6.1 Consensus size: 43
16651349 TTGTCCATTG
16651359 ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
1 ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
16651402 ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
1 ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
16651445 ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
1 ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
16651488 ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
1 ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
16651531 ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
1 ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
16651574 ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
1 ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
16651617 ATTT
1 ATTT
16651621 TGCATGCCAT
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 219 1.00
ACGTcount: A:0.23, C:0.09, G:0.09, T:0.58
Consensus pattern (43 bp):
ATTTAGGTTTATATATTTTTATTATCTTGCCCATTTATTTGAT
Found at i:16651462 original size:21 final size:21
Alignment explanation
Indices: 16651394--16651462 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
16651384 CTTGCCCATT
16651394 TATTTGATATTTAGGTTTATA
1 TATTTGATATTTAGGTTTATA
* *** *
16651415 TATTTTTATTATCTT--GCCCATT
1 TA-TTTGA-TAT-TTAGGTTTATA
16651437 TATTTGATATTTAGGTTTATA
1 TATTTGATATTTAGGTTTATA
16651458 TATTT
1 TATTT
16651463 TTATTATCTT
Statistics
Matches: 33, Mismatches: 10, Indels: 10
0.62 0.19 0.19
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 14 0.42
22 9 0.27
23 3 0.09
24 2 0.06
ACGTcount: A:0.25, C:0.06, G:0.10, T:0.59
Consensus pattern (21 bp):
TATTTGATATTTAGGTTTATA
Found at i:16651991 original size:98 final size:98
Alignment explanation
Indices: 16651822--16652002 Score: 362
Period size: 98 Copynumber: 1.8 Consensus size: 98
16651812 GTATTGGGTT
16651822 AGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAG
1 AGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAG
16651887 TGGATGTTCTTTTAAAGTAAAGGAAATATTCCA
66 TGGATGTTCTTTTAAAGTAAAGGAAATATTCCA
16651920 AGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAG
1 AGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAG
16651985 TGGATGTTCTTTTAAAGT
66 TGGATGTTCTTTTAAAGT
16652003 TTTATTGCAC
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 83 1.00
ACGTcount: A:0.27, C:0.10, G:0.25, T:0.38
Consensus pattern (98 bp):
AGTTTGGGATTTTAGAGGAATCGTGCCCTAACGTATTGGGTGTGATTTCTTAAATCTTGGATAAG
TGGATGTTCTTTTAAAGTAAAGGAAATATTCCA
Found at i:16654368 original size:13 final size:13
Alignment explanation
Indices: 16654350--16654375 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16654340 TGTGATGAAT
16654350 TAATATGGATTTA
1 TAATATGGATTTA
16654363 TAATATGGATTTA
1 TAATATGGATTTA
16654376 GGGCTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (13 bp):
TAATATGGATTTA
Found at i:16655033 original size:21 final size:21
Alignment explanation
Indices: 16655009--16655133 Score: 92
Period size: 21 Copynumber: 6.0 Consensus size: 21
16654999 GTTTGCTTTT
16655009 AGTTTAGCTCTTATGAGCTTC
1 AGTTTAGCTCTTATGAGCTTC
* * * *
16655030 AG-TTAACTCATATGAGTTTT
1 AGTTTAGCTCTTATGAGCTTC
* * * *
16655050 AGTTTAGCCCTTCTGGGTTTC
1 AGTTTAGCTCTTATGAGCTTC
*
16655071 AGTTTAGCTCTTTTGAGCTTC
1 AGTTTAGCTCTTATGAGCTTC
* * *
16655092 AGTTTAAC-CTTTATGGGTTTC
1 AGTTTAGCTC-TTATGAGCTTC
* * *
16655113 CGTTCAGCTCTTATAAGCTTC
1 AGTTTAGCTCTTATGAGCTTC
16655134 CATTTAACCC
Statistics
Matches: 77, Mismatches: 24, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
20 17 0.22
21 59 0.77
22 1 0.01
ACGTcount: A:0.18, C:0.19, G:0.18, T:0.44
Consensus pattern (21 bp):
AGTTTAGCTCTTATGAGCTTC
Found at i:16655053 original size:20 final size:20
Alignment explanation
Indices: 16655005--16655053 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
16654995 CTGTGTTTGC
* *
16655005 TTTTAGTTTAGCTCTTATGAG
1 TTTTAG-TTAACTCATATGAG
* *
16655026 CTTCAGTTAACTCATATGAG
1 TTTTAGTTAACTCATATGAG
16655046 TTTTAGTT
1 TTTTAGTT
16655054 TAGCCCTTCT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.22, C:0.12, G:0.16, T:0.49
Consensus pattern (20 bp):
TTTTAGTTAACTCATATGAG
Found at i:16655175 original size:42 final size:43
Alignment explanation
Indices: 16655050--16655175 Score: 123
Period size: 42 Copynumber: 3.0 Consensus size: 43
16655040 TATGAGTTTT
* ** *
16655050 AGTTTAGCCCTTCTGGG-TTTCAGTTTAGCTCTTTTGAGCTT-C
1 AGTTTAACCCTTAAGGGTTTTC-GTTTAGCTCTTATGAGCTTCC
* * * * *
16655092 AGTTTAACCTTTATGGGTTTCCGTTCAGCTCTTATAAGCTTCC
1 AGTTTAACCCTTAAGGGTTTTCGTTTAGCTCTTATGAGCTTCC
* *
16655135 A-TTTAACCCTTAAGGGTTTTCGTTTAGCACTTATGTGCTTC
1 AGTTTAACCCTTAAGGGTTTTCGTTTAGCTCTTATGAGCTTC
16655176 TGTGCAGCCT
Statistics
Matches: 68, Mismatches: 14, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
42 63 0.93
43 5 0.07
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (43 bp):
AGTTTAACCCTTAAGGGTTTTCGTTTAGCTCTTATGAGCTTCC
Found at i:16665257 original size:21 final size:21
Alignment explanation
Indices: 16665174--16665264 Score: 85
Period size: 21 Copynumber: 4.4 Consensus size: 21
16665164 NNNNNNNNNN
*
16665174 AGTTTAGCTCTTATGAGCTTC
1 AGTTTAACTCTTATGAGCTTC
* *
16665195 AG-TTAACTCATATGAGTTTC
1 AGTTTAACTCTTATGAGCTTC
* ** * *
16665215 AGTTTAACCCTTCGGGGTTTC
1 AGTTTAACTCTTATGAGCTTC
* *
16665236 AGTTTAGCTCTTTTGAGCTTC
1 AGTTTAACTCTTATGAGCTTC
16665257 AGTTTAAC
1 AGTTTAAC
16665265 CTTTATGGGT
Statistics
Matches: 54, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 17 0.31
21 37 0.69
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (21 bp):
AGTTTAACTCTTATGAGCTTC
Found at i:16665261 original size:42 final size:42
Alignment explanation
Indices: 16665192--16665340 Score: 149
Period size: 42 Copynumber: 3.6 Consensus size: 42
16665182 TCTTATGAGC
* * * *
16665192 TTCAG-TTAACTCATATGAGTTTCAGTTTAACCCTTCGGGGT
1 TTCAGTTTAGCTCTTATGAGCTTCAGTTTAACCCTTAGGGGT
* * *
16665233 TTCAGTTTAGCTCTTTTGAGCTTCAGTTTAACCTTTATGGGT
1 TTCAGTTTAGCTCTTATGAGCTTCAGTTTAACCCTTAGGGGT
* * * *
16665275 TTCCGTTCAGCTCTTATAAGCTTCCA-TTTAACCCTTAGGGTT
1 TTCAGTTTAGCTCTTATGAGCTT-CAGTTTAACCCTTAGGGGT
* * *
16665317 TTCGGTTTAGCACTTATGTGCTTC
1 TTCAGTTTAGCTCTTATGAGCTTC
16665341 TGTGCAGCCT
Statistics
Matches: 87, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
41 6 0.07
42 79 0.91
43 2 0.02
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (42 bp):
TTCAGTTTAGCTCTTATGAGCTTCAGTTTAACCCTTAGGGGT
Found at i:16665822 original size:49 final size:50
Alignment explanation
Indices: 16665750--16665848 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 50
16665740 AATGGTTGTG
16665750 TAAACATTAAAATTACATTTTGGCTATGTTTCATATTAA-TTATATATGT
1 TAAACATTAAAATTACATTTTGGCTATGTTTCATATTAACTTATATATGT
16665799 TAAACATTAAAATTACATTTTGGCTATGTTTCATATTAACTTATATATGT
1 TAAACATTAAAATTACATTTTGGCTATGTTTCATATTAACTTATATATGT
16665849 ATGGTTTGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
49 39 0.80
50 10 0.20
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.46
Consensus pattern (50 bp):
TAAACATTAAAATTACATTTTGGCTATGTTTCATATTAACTTATATATGT
Found at i:16670508 original size:6 final size:6
Alignment explanation
Indices: 16670497--16670527 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
16670487 AGATAGAGAA
16670497 TGAGGT TGAGGT TGAGGT TGAGGT TGAGGT T
1 TGAGGT TGAGGT TGAGGT TGAGGT TGAGGT T
16670528 TTCTCCGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.35
Consensus pattern (6 bp):
TGAGGT
Found at i:16675558 original size:47 final size:47
Alignment explanation
Indices: 16675505--16675603 Score: 180
Period size: 47 Copynumber: 2.1 Consensus size: 47
16675495 CCACAAATTA
**
16675505 CTTAGTTTAGAATTTTTCTTTTAAATTTGGCTTAACTTTTCTTTCTT
1 CTTAGTTTAGAATTTTTCTTTTAAATTCAGCTTAACTTTTCTTTCTT
16675552 CTTAGTTTAGAATTTTTCTTTTAAATTCAGCTTAACTTTTCTTTCTT
1 CTTAGTTTAGAATTTTTCTTTTAAATTCAGCTTAACTTTTCTTTCTT
16675599 CTTAG
1 CTTAG
16675604 GTTTTAGGTT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.20, C:0.14, G:0.08, T:0.58
Consensus pattern (47 bp):
CTTAGTTTAGAATTTTTCTTTTAAATTCAGCTTAACTTTTCTTTCTT
Found at i:16686132 original size:16 final size:16
Alignment explanation
Indices: 16686071--16686139 Score: 111
Period size: 16 Copynumber: 4.3 Consensus size: 16
16686061 TTGGTTCGCT
*
16686071 GTAATGGAATAGATGC
1 GTAATGGAATAGAGGC
*
16686087 GTAATGGAATAGAAGC
1 GTAATGGAATAGAGGC
16686103 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
*
16686119 GTAATGGAATAGAGAC
1 GTAATGGAATAGAGGC
16686135 GTAAT
1 GTAAT
16686140 AGGTAATCCT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.41, C:0.06, G:0.32, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:16686184 original size:46 final size:44
Alignment explanation
Indices: 16686119--16686204 Score: 127
Period size: 46 Copynumber: 1.9 Consensus size: 44
16686109 GAATAGAGGC
*
16686119 GTAATGGAATAGAGACGTAATAGGTAATCCTTTTGTTTGGTTCGCT
1 GTAATGGAATAGAGACGTAATA-GT-ATCCTTGTGTTTGGTTCGCT
* *
16686165 GTAATGGAATAGAGGCGTAATAGTATTCTTGTGTTTGGTT
1 GTAATGGAATAGAGACGTAATAGTATCCTTGTGTTTGGTT
16686205 GAATGAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 14 0.38
45 2 0.05
46 21 0.57
ACGTcount: A:0.26, C:0.08, G:0.28, T:0.38
Consensus pattern (44 bp):
GTAATGGAATAGAGACGTAATAGTATCCTTGTGTTTGGTTCGCT
Found at i:16686579 original size:14 final size:15
Alignment explanation
Indices: 16686560--16686592 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
16686550 TTTTATTCTT
*
16686560 AAAATTCAAAAA-TA
1 AAAATTAAAAAACTA
16686574 AAAATTAAAAAACTA
1 AAAATTAAAAAACTA
16686589 AAAA
1 AAAA
16686593 ATTTAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATTAAAAAACTA
Found at i:16687747 original size:58 final size:58
Alignment explanation
Indices: 16687624--16687761 Score: 188
Period size: 59 Copynumber: 2.4 Consensus size: 58
16687614 AAAGTTGCTA
* * *
16687624 TGTTTTGGCACTAAAAGCAACCGCAAGCCACAACTACCAGCATGTCAAGAATTAAATT
1 TGTTTTGGCACTAAAAGAAACCACAAGCCACAACTACCAGAATGTCAAGAATTAAATT
* * *
16687682 TGTTTTGGCACTAAAAGTAAACCACAAGTCACAA-TAACCAGAATGTCAAGGATTGAATT
1 TGTTTTGGCACTAAAAG-AAACCACAAGCCACAACT-ACCAGAATGTCAAGAATTAAATT
*
16687741 TGTTTGGGCACTAAAAGAAAC
1 TGTTTTGGCACTAAAAGAAAC
16687762 AAATGAACAA
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
58 22 0.31
59 49 0.69
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (58 bp):
TGTTTTGGCACTAAAAGAAACCACAAGCCACAACTACCAGAATGTCAAGAATTAAATT
Found at i:16700978 original size:14 final size:14
Alignment explanation
Indices: 16700957--16700989 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16700947 AATAGCATAG
16700957 AAAT-AATATAAAA
1 AAATGAATATAAAA
16700970 AAATGAATATAAAA
1 AAATGAATATAAAA
*
16700984 TAATGA
1 AAATGA
16700990 CATGAAAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (14 bp):
AAATGAATATAAAA
Found at i:16702723 original size:44 final size:44
Alignment explanation
Indices: 16702653--16703161 Score: 314
Period size: 44 Copynumber: 11.7 Consensus size: 44
16702643 ACCTCATTAG
* *
16702653 TCTGCTCCACTGCAACTTCAGAGAGATAGGATTGTCGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTCGGTTTTAA
* ** * *
16702697 TTTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGCCATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGT-CGGT-TTTAA
*
16702742 TCTGC-CTCACTGCAACTTCA-GGAGGATAAGACTTG-C--TTACTTAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGA-TTGTCGGTT--TTAA
* * *
16702786 TCTGCTTCACTGCAACTTCAGGGAGATAAGACTAGATAC-GATTT--
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTG-T-CGGTTTTAA
* * * *
16702830 GCT-CT-CA--GCAACTTCAGAGAGATAAGATCTG-AGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-TGTCGGTTTTAA
*
16702870 TCCT-CTCCACTGCAACTTCAGGGAGATAGGATTGTCGGTTTTAA
1 T-CTGCTCCACTGCAACTTCAGGGAGATAAGATTGTCGGTTTTAA
* ** *
16702914 TCTGCTCCACTGCAACTTTAGGGAGATAAGATT-TGCCATCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGT-CGGT-TTTAA
* *
16702959 TCTGC-CTCACTGCAACTTCA-GGAGGATAAGACTTG-C--TTACTCAG
1 TCTGCTC-CACTGCAACTTCAGGGA-GATAAGA-TTGTCGGTT--TTAA
* * * ***
16703003 TCTGCTCCACTGCAACTTCAGGGAGATAAGA--CT-AGATGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTCGGTTTTAA
* * ** * *
16703044 TATGCT-CTCTGCAACTTCAGAAAGATAAGACTTG-AGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGTCGGTTTTAA
* * * *
16703087 TCCGCTCCACTGTAATTTCAGGGAGATAGGATTGTCGGTTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTCGGTTTTAA
16703131 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
16703162 CTTGCCATCT
Statistics
Matches: 362, Mismatches: 60, Indels: 86
0.71 0.12 0.17
Matches are distributed among these distances:
38 3 0.01
39 1 0.00
40 41 0.11
41 10 0.03
42 6 0.02
43 20 0.06
44 209 0.58
45 64 0.18
46 6 0.02
47 1 0.00
48 1 0.00
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTGTCGGTTTTAA
Found at i:16702971 original size:173 final size:173
Alignment explanation
Indices: 16702664--16702991 Score: 402
Period size: 173 Copynumber: 1.9 Consensus size: 173
16702654 CTGCTCCACT
* * * *
16702664 GCAACTTCAGAGAGATAGGATTGTCGGTTTTAATTTGCTCCACTGCAACTTCAGGGAGATAAGAT
1 GCAACTTCAGAGAGATAAGATTGTAGATTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
* * * *
16702729 TTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAGTCTGCTTC
66 TTGCCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCATACTTAATCTGCCTC
16702794 ACTGCAACTTCAGG-GAGATAAGACTAGATACGATTTGCTCTCA
131 ACTGCAACTTCAGGAG-GATAAGACTAGATACGATTTGCTCTCA
*
16702837 GCAACTTCAGAGAGATAAGATCTG-AGATTTTAATCCT-CTCCACTGCAACTTCAGGGAGATAGG
1 GCAACTTCAGAGAGATAAGAT-TGTAGATTTTAAT-CTGCTCCACTGCAACTTCAGGGAGATAAG
** * * *
16702900 A-TTGTCGGT-TTTAATCTG-CTCCACTGCAACTTTAGG-GAGATAAGATTTGCCAT-CTTCAAT
64 ATTTG-CCATCTTCAATCTGCCT-CACTGCAACTTCAGGAG-GATAAGACTTG-CATACTT-AAT
16702960 CTGCCTCACTGCAACTTCAGGAGGATAAGACT
124 CTGCCTCACTGCAACTTCAGGAGGATAAGACT
16702992 TGCTTACTCA
Statistics
Matches: 133, Mismatches: 14, Indels: 16
0.82 0.09 0.10
Matches are distributed among these distances:
171 3 0.02
172 37 0.28
173 89 0.67
174 4 0.03
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (173 bp):
GCAACTTCAGAGAGATAAGATTGTAGATTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
TTGCCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCATACTTAATCTGCCTC
ACTGCAACTTCAGGAGGATAAGACTAGATACGATTTGCTCTCA
Found at i:16703032 original size:217 final size:217
Alignment explanation
Indices: 16702656--16703180 Score: 899
Period size: 217 Copynumber: 2.4 Consensus size: 217
16702646 TCATTAGTCT
* *
16702656 GCTCCACTGCAACTTCAGAGAGATAGGATTGTCGGTTTTAATTTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGTTTTAATCTGCTCCACTGCAACTTCAGGGA
* *
16702721 GATAAGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTTAG
66 GATAAGATTTGCCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTCAG
* * *
16702786 TCTGCTTCACTGCAACTTCAGGGAGATAAGACTAGATACGATTTGCTCTCAGCAACTTCAGAGAG
131 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATATGCTCTCAGCAACTTCAGAAAG
16702851 ATAAGA-TCTGAGATTTTAATCC
196 ATAAGACT-TGAGATTTTAATCC
* *
16702873 TCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGTTTTAATCTGCTCCACTGCAACTTTAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGTTTTAATCTGCTCCACTGCAACTTCAGGGA
16702938 GATAAGATTTGCCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTCAG
66 GATAAGATTTGCCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTCAG
* *
16703003 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATATGCTCTCTGCAACTTCAGAAAG
131 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATATGCTCTCAGCAACTTCAGAAAG
16703068 ATAAGACTTGAGATTTTAATCC
196 ATAAGACTTGAGATTTTAATCC
* *
16703090 GCTCCACTGTAATTTCAGGGAGATAGGATTGTCGGTTTTAATCTGCTCCACTGCAACTTCAGGGA
1 GCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGTTTTAATCTGCTCCACTGCAACTTCAGGGA
* *
16703155 GATAAGACTTGCCATCTTCGATCTGC
66 GATAAGATTTGCCATCTTCAATCTGC
16703181 TCCGCTGTCG
Statistics
Matches: 290, Mismatches: 17, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
217 289 1.00
218 1 0.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (217 bp):
GCTCCACTGCAACTTCAGGGAGATAGGATTGTCGGTTTTAATCTGCTCCACTGCAACTTCAGGGA
GATAAGATTTGCCATCTTCAATCTGCCTCACTGCAACTTCAGGAGGATAAGACTTGCTTACTCAG
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATACGATATGCTCTCAGCAACTTCAGAAAG
ATAAGACTTGAGATTTTAATCC
Found at i:16704436 original size:15 final size:15
Alignment explanation
Indices: 16704408--16704445 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
16704398 CCTTAGCCTC
16704408 TCCA-TTTTACTTTT
1 TCCATTTTTACTTTT
16704422 T-CATTTTTCACTTTT
1 TCCATTTTT-ACTTTT
16704437 TCCATTTTT
1 TCCATTTTT
16704446 TCATTTCGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 5 0.24
15 7 0.33
16 7 0.33
ACGTcount: A:0.13, C:0.21, G:0.00, T:0.66
Consensus pattern (15 bp):
TCCATTTTTACTTTT
Found at i:16705274 original size:25 final size:25
Alignment explanation
Indices: 16705220--16705276 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
16705210 AAGAAAATCC
* **
16705220 AAAAGAATGAAAGAATAATTACTTG
1 AAAATAATGAAAGAATAATTACTCA
*
16705245 GAAATAATGAAAGAAT-ATTGACTCA
1 AAAATAATGAAAGAATAATT-ACTCA
16705270 AAAATAA
1 AAAATAA
16705277 ATGCCAAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 3 0.12
25 23 0.88
ACGTcount: A:0.58, C:0.05, G:0.14, T:0.23
Consensus pattern (25 bp):
AAAATAATGAAAGAATAATTACTCA
Found at i:16707415 original size:148 final size:148
Alignment explanation
Indices: 16707142--16707442 Score: 467
Period size: 148 Copynumber: 2.0 Consensus size: 148
16707132 ATCTTTTCCG
* * *
16707142 CCTCCATTTGCTCTATCCTTTTCTCCAAGTCCGCATTCTTCCTCTCAAAATCCTGTTTTACCATT
1 CCTCCATTTGCTCTATCCTTTTCTCCAAATCCGCATTCTTCCTCTCAAAATCCTGTCTTACAATT
* *
16707207 TCCAACTCAGAAGGAATGACTCGCAAATGCTCTTCTATTGACTGGCCCTCTTCCTAATTTAACTT
66 TCCAACTCAGAAGGAATGACTCGCAAATGCTCTTCTATTGACTGGCCCTCCTCATAATTTAACTT
*
16707272 AGGTGTATTATCATTTAT
131 AGGTGTATTATCATTAAT
* * *
16707290 CCTCTATTTGCTCTATCCTTTTCTCCAAATCCGCGTTCTTCCTCTCAAAATCTTGTCTTACAATT
1 CCTCCATTTGCTCTATCCTTTTCTCCAAATCCGCATTCTTCCTCTCAAAATCCTGTCTTACAATT
* * * * *
16707355 TCCAATTCCGAAGGGATGACTCGCAAATGCTCTTCTATTGACTGGCCGTCCTCATTATTTAACTT
66 TCCAACTCAGAAGGAATGACTCGCAAATGCTCTTCTATTGACTGGCCCTCCTCATAATTTAACTT
*
16707420 AGGTGTGTTATCATTAAT
131 AGGTGTATTATCATTAAT
16707438 CCTCC
1 CCTCC
16707443 TAGCCCACCA
Statistics
Matches: 137, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
148 137 1.00
ACGTcount: A:0.22, C:0.28, G:0.12, T:0.39
Consensus pattern (148 bp):
CCTCCATTTGCTCTATCCTTTTCTCCAAATCCGCATTCTTCCTCTCAAAATCCTGTCTTACAATT
TCCAACTCAGAAGGAATGACTCGCAAATGCTCTTCTATTGACTGGCCCTCCTCATAATTTAACTT
AGGTGTATTATCATTAAT
Found at i:16714318 original size:27 final size:27
Alignment explanation
Indices: 16714250--16714331 Score: 92
Period size: 27 Copynumber: 3.0 Consensus size: 27
16714240 CAAAGATCAA
* *
16714250 ACACTAGCTCACCAGACCTACTGGCAT
1 ACACTATCTCACCAGACCTGCTGGCAT
* *
16714277 GCACTATCTCACCAGACTTGCTGGCAT
1 ACACTATCTCACCAGACCTGCTGGCAT
* ** *
16714304 ACACTATTTTGCCAGGCCTGCTGGCAT
1 ACACTATCTCACCAGACCTGCTGGCAT
16714331 A
1 A
16714332 TACCATCTTG
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.24
Consensus pattern (27 bp):
ACACTATCTCACCAGACCTGCTGGCAT
Found at i:16714854 original size:20 final size:21
Alignment explanation
Indices: 16714821--16714859 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
16714811 TCCTGGTGTC
*
16714821 GCGACTTTACCAAG-GAATTT
1 GCGACTTCACCAAGTGAATTT
*
16714841 GCGACTTCAGCAAGTGAAT
1 GCGACTTCACCAAGTGAAT
16714860 GTCACGACCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (21 bp):
GCGACTTCACCAAGTGAATTT
Found at i:16715530 original size:18 final size:18
Alignment explanation
Indices: 16715507--16715541 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16715497 GGCCTAGTAC
16715507 CCAAAC-TAAAGCCCAAAA
1 CCAAACTTAAA-CCCAAAA
16715525 CCAAACTTAAACCCAAA
1 CCAAACTTAAACCCAAA
16715542 CCTAACCCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.54, C:0.34, G:0.03, T:0.09
Consensus pattern (18 bp):
CCAAACTTAAACCCAAAA
Found at i:16728126 original size:31 final size:32
Alignment explanation
Indices: 16728085--16728154 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
16728075 AACCATTAAA
* *
16728085 TATTTGTAATTACAT-A-TTAACGCATTTGTAT
1 TATTTTTAATTA-ATGATTTAACACATTTGTAT
*
16728116 TATTTTTAATTAATGATTTTAACACATTTGTGT
1 TATTTTTAATTAATGA-TTTAACACATTTGTAT
16728149 TATTTT
1 TATTTT
16728155 ATTTTAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 2 0.06
31 12 0.36
33 19 0.58
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (32 bp):
TATTTTTAATTAATGATTTAACACATTTGTAT
Found at i:16737249 original size:23 final size:22
Alignment explanation
Indices: 16737168--16737253 Score: 88
Period size: 21 Copynumber: 4.0 Consensus size: 22
16737158 CCTAATCAGT
*
16737168 ATACGACACA-TAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
* *
16737189 A-ACAACACACAAGGTGCCTG-
1 ATACGACACACAAAGTGCCTGA
* *
16737209 ATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTG-A
*
16737232 ATACGACACATAAAGTGCCTGA
1 ATACGACACACAAAGTGCCTGA
16737254 TCGGCAAAAC
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
20 8 0.15
21 26 0.49
22 1 0.02
23 18 0.34
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (22 bp):
ATACGACACACAAAGTGCCTGA
Found at i:16737922 original size:3 final size:3
Alignment explanation
Indices: 16737914--16737949 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
16737904 ACATTAATTT
16737914 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16737950 GAATTTCTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:16738354 original size:20 final size:20
Alignment explanation
Indices: 16738329--16738367 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
16738319 TTATTTAAAA
*
16738329 TATAATAATATAATATATTT
1 TATAATAAAATAATATATTT
16738349 TATAATAAAATAATATATT
1 TATAATAAAATAATATATT
16738368 AATATATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TATAATAAAATAATATATTT
Found at i:16742887 original size:19 final size:22
Alignment explanation
Indices: 16742842--16742887 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 22
16742832 ATTGAAAAAG
16742842 AAAA-AGAGGAAGAAATGATAA
1 AAAAGAGAGGAAGAAATGATAA
*
16742863 AGAAGAGAGGAA-AAAT-A-AA
1 AAAAGAGAGGAAGAAATGATAA
16742882 AAAAGA
1 AAAAGA
16742888 TAAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 7 0.32
20 1 0.05
21 7 0.32
22 7 0.32
ACGTcount: A:0.70, C:0.00, G:0.24, T:0.07
Consensus pattern (22 bp):
AAAAGAGAGGAAGAAATGATAA
Found at i:16743674 original size:36 final size:37
Alignment explanation
Indices: 16743626--16743718 Score: 102
Period size: 36 Copynumber: 2.6 Consensus size: 37
16743616 GGGAAAACTC
* * *
16743626 GATATCTTATTCAGGATCTTGAGATTGAGAAGA-CTA
1 GATATCTCATTCAGGATCTTGAGACTAAGAAGACCTA
*
16743662 GATATCTCATTCAGGAGT-TTGAGACTAAGAATACCTA
1 GATATCTCATTCAGGA-TCTTGAGACTAAGAAGACCTA
* *
16743699 -ATATCTCTTTCAGGAGCTTG
1 GATATCTCATTCAGGATCTTG
16743719 GGAAGATCTA
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
36 44 0.92
37 4 0.08
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.33
Consensus pattern (37 bp):
GATATCTCATTCAGGATCTTGAGACTAAGAAGACCTA
Found at i:16746611 original size:25 final size:25
Alignment explanation
Indices: 16746538--16746611 Score: 64
Period size: 25 Copynumber: 3.0 Consensus size: 25
16746528 GTACATGTAT
16746538 GCTCATACGAGCT--GTAACGGTAA
1 GCTCATACGAGCTGAGTAACGGTAA
* ** * *
16746561 GCTTC-TTCGAGCTGAAAAATGATAA
1 GC-TCATACGAGCTGAGTAACGGTAA
*
16746586 GCTCATGCGAGCTGAGTAACGGTAA
1 GCTCATACGAGCTGAGTAACGGTAA
16746611 G
1 G
16746612 ACCAAACAAG
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
23 9 0.24
24 4 0.11
25 24 0.65
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (25 bp):
GCTCATACGAGCTGAGTAACGGTAA
Found at i:16748889 original size:84 final size:85
Alignment explanation
Indices: 16748790--16748959 Score: 333
Period size: 84 Copynumber: 2.0 Consensus size: 85
16748780 CAAAGGATAT
16748790 ATACTTGTACAAAATTAAAATTTTAAAAAAATTGGTTAATATAAATTAATTCGACATTTAAGCTT
1 ATACTTGTACAAAATTAAAATTTTAAAAAAATTGGTTAATATAAATTAATTCGACATTTAAGCTT
16748855 AAGTAAAA-TCTAAAATCTA
66 AAGTAAAATTCTAAAATCTA
16748874 ATACTTGTACAAAATTAAAATTTTAAAAAAATTGGTTAATATAAATTAATTCGACATTTAAGCTT
1 ATACTTGTACAAAATTAAAATTTTAAAAAAATTGGTTAATATAAATTAATTCGACATTTAAGCTT
16748939 AAGTAAAATTCTAAAATCTA
66 AAGTAAAATTCTAAAATCTA
16748959 A
1 A
16748960 AATAATTTTA
Statistics
Matches: 85, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
84 73 0.86
85 12 0.14
ACGTcount: A:0.49, C:0.08, G:0.07, T:0.36
Consensus pattern (85 bp):
ATACTTGTACAAAATTAAAATTTTAAAAAAATTGGTTAATATAAATTAATTCGACATTTAAGCTT
AAGTAAAATTCTAAAATCTA
Found at i:16748971 original size:18 final size:20
Alignment explanation
Indices: 16748945--16748992 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
16748935 GCTTAAGTAA
*
16748945 AATTCTAAAAT-CT-AAAAT
1 AATTTTAAAATACTAAAAAT
*
16748963 AATTTTAAAATATTAAAAAT
1 AATTTTAAAATACTAAAAAT
16748983 AATTTTAAAA
1 AATTTTAAAA
16748993 ACTTCATAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 10 0.38
19 1 0.04
20 15 0.58
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (20 bp):
AATTTTAAAATACTAAAAAT
Found at i:16749076 original size:27 final size:28
Alignment explanation
Indices: 16749045--16749097 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
16749035 ATAGTATTCA
*
16749045 TTAATTAATAAATTA-TGAAATGTTACT
1 TTAATTAATAAATAACTGAAATGTTACT
* *
16749072 TTAATTTATATATAACTGAAATGTTA
1 TTAATTAATAAATAACTGAAATGTTA
16749098 GAAAATATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 12 0.55
28 10 0.45
ACGTcount: A:0.43, C:0.04, G:0.08, T:0.45
Consensus pattern (28 bp):
TTAATTAATAAATAACTGAAATGTTACT
Found at i:16750252 original size:87 final size:86
Alignment explanation
Indices: 16750098--16750260 Score: 213
Period size: 87 Copynumber: 1.9 Consensus size: 86
16750088 TTAAGTTCAA
* * *
16750098 TGAATTCATCAAGTTCGTCTCAATAGGACCACCCAAATTCTAGAATATGAACTCATAAAGAATAA
1 TGAATTCATCAAGTCCGTCTCAATAAGACCACCAAAATTCTAGAATATGAACTCATAAAGAATAA
*
16750163 GAAATTCAACCTCACATGTTGG
66 G-AAGTCAACCTCACATGTTGG
* * * *
16750185 TGAATTCATCAAGTCCGTCTCAATAATACCACCAAAACTT-TAGGATATGAATTCATTAAGAGA-
1 TGAATTCATCAAGTCCGTCTCAATAAGACCACCAAAA-TTCTAGAATATGAACTCATAAAGA-AT
16750248 AAGAAGTCAACCT
64 AAGAAGTCAACCT
16750261 TATGCATGCA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
86 9 0.14
87 54 0.82
88 3 0.05
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (86 bp):
TGAATTCATCAAGTCCGTCTCAATAAGACCACCAAAATTCTAGAATATGAACTCATAAAGAATAA
GAAGTCAACCTCACATGTTGG
Found at i:16751281 original size:45 final size:45
Alignment explanation
Indices: 16751180--16751284 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 45
16751170 AGTTTTGCAA
* * * *
16751180 ATAAAATCTTCCACTGGGCTGTGGATACAAAGTAAAAATTCATAG
1 ATAAAATCTGCCACTAGGCTGTGGATACAAAGCAAAAATTCACAG
* * * * *
16751225 ATGAAACCTGCCACTAGGTTGTGGGTACACAGC-AAAATATCACAG
1 ATAAAATCTGCCACTAGGCTGTGGATACAAAGCAAAAAT-TCACAG
16751270 ATAAAATCTGCCACT
1 ATAAAATCTGCCACT
16751285 GGGCAATAGA
Statistics
Matches: 48, Mismatches: 11, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
44 5 0.10
45 43 0.90
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (45 bp):
ATAAAATCTGCCACTAGGCTGTGGATACAAAGCAAAAATTCACAG
Found at i:16751417 original size:138 final size:138
Alignment explanation
Indices: 16751234--16751536 Score: 437
Period size: 138 Copynumber: 2.2 Consensus size: 138
16751224 GATGAAACCT
*
16751234 GCCACTAGGTTGTGGGTACACAGCAAAATATCACAGATAAAATCTGCCACTGGGCAATAGATGCA
1 GCCACTAGGTTGTGGGTGCACAGCAAAATATCACAGATAAAATCTGCCACTGGGCAATAGATGCA
* * *
16751299 TAATATATTTGCAGGTAAAAGCTGGCGATGGGTTGTGGATGTAAAACATATTTGCAATTAAAGGA
66 CAACATATTTGCAGGTAAAAGCTGGCGATGGGTTGTAGATGTAAAACATATTTGCAATTAAAGGA
16751364 T-AAACATC
131 TGAAA-ATC
* * * **
16751372 GCCACTAGGCTGTGGGTGCATAGCAAAATATCGCAGATAAAATCTGCCACTGGGCTGTAGATGCA
1 GCCACTAGGTTGTGGGTGCACAGCAAAATATCACAGATAAAATCTGCCACTGGGCAATAGATGCA
* * * * *
16751437 CAACATATTTGCAGGTAAAAGTTGTCGATGGGTTGTAGATGTACAACATATTTGTAGTTAAAGGA
66 CAACATATTTGCAGGTAAAAGCTGGCGATGGGTTGTAGATGTAAAACATATTTGCAATTAAAGGA
*
16751502 TGAAAATT
131 TGAAAATC
* *
16751510 GCCACTGGGTTGTGGGTGCACAACAAA
1 GCCACTAGGTTGTGGGTGCACAGCAAA
16751537 TTTGGAGATA
Statistics
Matches: 145, Mismatches: 19, Indels: 2
0.87 0.11 0.01
Matches are distributed among these distances:
138 142 0.98
139 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.26
Consensus pattern (138 bp):
GCCACTAGGTTGTGGGTGCACAGCAAAATATCACAGATAAAATCTGCCACTGGGCAATAGATGCA
CAACATATTTGCAGGTAAAAGCTGGCGATGGGTTGTAGATGTAAAACATATTTGCAATTAAAGGA
TGAAAATC
Found at i:16752051 original size:28 final size:27
Alignment explanation
Indices: 16752014--16752232 Score: 185
Period size: 28 Copynumber: 7.9 Consensus size: 27
16752004 AAGTAGGGGG
* *
16752014 AAATTGTAAAATCTAAAAAATAAGGGTA
1 AAATTATAAAATCTAAAAAAT-AGGGCA
* *
16752042 AAACTATAAAATCTAGAAAATAGAGGCA
1 AAATTATAAAATCTAAAAAATAG-GGCA
* **
16752070 AAACTGCAAAATCTAAAAAATAGGGCA
1 AAATTATAAAATCTAAAAAATAGGGCA
16752097 AAACTT-TAAAATCTACAAAACATA-GGCA
1 AAA-TTATAAAATCTA-AAAA-ATAGGGCA
* * *
16752125 AAATTGTAAAATCTAGAAAATAGAGGTA
1 AAATTATAAAATCTAAAAAATAG-GGCA
* * *
16752153 AAATTATAAAATTTGAAAAATAAGGGAA
1 AAATTATAAAATCTAAAAAAT-AGGGCA
* *
16752181 AAATTGTAAAATTTAAAAAATGAGGG-A
1 AAATTATAAAATCTAAAAAAT-AGGGCA
*
16752208 AAATTTATAAAATCT-GAAAATAGGG
1 AAA-TTATAAAATCTAAAAAATAGGG
16752233 GACACGACCA
Statistics
Matches: 160, Mismatches: 22, Indels: 20
0.79 0.11 0.10
Matches are distributed among these distances:
26 7 0.04
27 31 0.19
28 117 0.73
29 5 0.03
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.23
Consensus pattern (27 bp):
AAATTATAAAATCTAAAAAATAGGGCA
Found at i:16752107 original size:55 final size:57
Alignment explanation
Indices: 16752014--16752230 Score: 236
Period size: 56 Copynumber: 3.9 Consensus size: 57
16752004 AAGTAGGGGG
16752014 AAATTGTAAAATCTAAAAAATAAGGGTAAAAC-TATAAAATCTAGAAAATAGAGGCA
1 AAATTGTAAAATCTAAAAAATAAGGGTAAAACTTATAAAATCTAGAAAATAGAGGCA
* * * * * *
16752070 AAACTGCAAAATCTAAAAAAT-AGGGCAAAACTT-TAAAATCTACAAAACATAGGCA
1 AAATTGTAAAATCTAAAAAATAAGGGTAAAACTTATAAAATCTAGAAAATAGAGGCA
* * *
16752125 AAATTGTAAAATCTAGAAAAT-AGAGGTAAAA-TTATAAAAT-TTGAAAAATA-AGGGAA
1 AAATTGTAAAATCTAAAAAATAAG-GGTAAAACTTATAAAATCTAG-AAAATAGA-GGCA
* * *
16752181 AAATTGTAAAATTTAAAAAATGAGGG-AAAATTTATAAAATCT-GAAAATAG
1 AAATTGTAAAATCTAAAAAATAAGGGTAAAACTTATAAAATCTAGAAAATAG
16752231 GGGACACGAC
Statistics
Matches: 136, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
55 62 0.46
56 71 0.52
57 3 0.02
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (57 bp):
AAATTGTAAAATCTAAAAAATAAGGGTAAAACTTATAAAATCTAGAAAATAGAGGCA
Found at i:16752111 original size:83 final size:82
Alignment explanation
Indices: 16752014--16752230 Score: 251
Period size: 83 Copynumber: 2.6 Consensus size: 82
16752004 AAGTAGGGGG
* *
16752014 AAATTGTAAAATCTAAAAAATAAGGGTAAAACTATAAAATCTAGAAAATAGAGGCAAAACTGCAA
1 AAATTGTAAAATCTAAAAAAT-AGGG-AAAATTATAAAATCTAGAAAATAGAGGCAAAACTACAA
16752079 AATCTAAAAAAT-AGGGCAA
64 AATCTAAAAAATAAGGG-AA
* * * * * *
16752098 AACTT-TAAAATCTACAAAACATAGGCAAAATTGTAAAATCTAGAAAATAGAGGTAAAATTATAA
1 AAATTGTAAAATCTA-AAAA-ATAGGGAAAATTATAAAATCTAGAAAATAGAGGCAAAACTACAA
* *
16752162 AATTTGAAAAATAAGGGAA
64 AATCTAAAAAATAAGGGAA
*
16752181 AAATTGTAAAATTTAAAAAATGAGGGAAAATTTATAAAATCT-GAAAATAG
1 AAATTGTAAAATCTAAAAAAT-AGGGAAAA-TTATAAAATCTAGAAAATAG
16752231 GGGACACGAC
Statistics
Matches: 113, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
82 2 0.02
83 76 0.67
84 33 0.29
85 2 0.02
ACGTcount: A:0.56, C:0.07, G:0.14, T:0.23
Consensus pattern (82 bp):
AAATTGTAAAATCTAAAAAATAGGGAAAATTATAAAATCTAGAAAATAGAGGCAAAACTACAAAA
TCTAAAAAATAAGGGAA
Found at i:16756744 original size:14 final size:15
Alignment explanation
Indices: 16756727--16756759 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
16756717 ATTTTTAGGG
*
16756727 ACTAT-TTTTTATAA
1 ACTATATTTTTAAAA
16756741 ACTATATTTTTAAAA
1 ACTATATTTTTAAAA
16756756 ACTA
1 ACTA
16756760 ATATCTCAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (15 bp):
ACTATATTTTTAAAA
Found at i:16758117 original size:62 final size:63
Alignment explanation
Indices: 16757993--16758133 Score: 169
Period size: 62 Copynumber: 2.3 Consensus size: 63
16757983 ATTAATTGGA
* * *
16757993 TCCTAAATATAAAAATAAATAAATAAATTTAGCCCTCAATGTTTACAAAATTTTTCATTTTAG
1 TCCTAAATATAAAAATAAATAAATAAATTTAGCCCTCAATATTTACAAAATCTGTCATTTTAG
* * * * *
16758056 TTCTAATTATAAAAA-AAATCAATAATTTTAGCCCTCAATATTTATAAAATCTGTC-TATTTAG
1 TCCTAAATATAAAAATAAATAAATAAATTTAGCCCTCAATATTTACAAAATCTGTCAT-TTTAG
* *
16758118 TCCTAACTCTAAAAAT
1 TCCTAAATATAAAAAT
16758134 TAAAAATTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
61 1 0.02
62 51 0.78
63 13 0.20
ACGTcount: A:0.43, C:0.14, G:0.04, T:0.38
Consensus pattern (63 bp):
TCCTAAATATAAAAATAAATAAATAAATTTAGCCCTCAATATTTACAAAATCTGTCATTTTAG
Found at i:16758146 original size:62 final size:61
Alignment explanation
Indices: 16757993--16758153 Score: 155
Period size: 62 Copynumber: 2.6 Consensus size: 61
16757983 ATTAATTGGA
* * * *
16757993 TCCTAAATATAAAAATAAATAAATAAATTTAGCCCTCAATGTTTACAAAATTTTTCATTTTAG
1 TCCTAAATATAAAAAT-AA-AAATAATTTTAGCCCTCAATATTTACAAAATCTGTCATTTTAG
* * *
16758056 TTCTAATTATAAAAA-AAATCAATAATTTTAGCCCTCAATATTTATAAAATCTGTC-TATTTAG
1 TCCTAAATATAAAAATAAA--AATAATTTTAGCCCTCAATATTTACAAAATCTGTCAT-TTTAG
* * *
16758118 TCCTAACTCTAAAAATTAAAAATTATTTTTAGCCCT
1 TCCTAAATATAAAAA-TAAAAA-TAATTTTAGCCCT
16758154 TTATAACCTA
Statistics
Matches: 81, Mismatches: 11, Indels: 12
0.78 0.11 0.12
Matches are distributed among these distances:
60 1 0.01
61 3 0.04
62 49 0.60
63 25 0.31
64 3 0.04
ACGTcount: A:0.42, C:0.14, G:0.04, T:0.39
Consensus pattern (61 bp):
TCCTAAATATAAAAATAAAAATAATTTTAGCCCTCAATATTTACAAAATCTGTCATTTTAG
Found at i:16760123 original size:345 final size:346
Alignment explanation
Indices: 16759492--16760182 Score: 1366
Period size: 345 Copynumber: 2.0 Consensus size: 346
16759482 CACGGGTAAA
16759492 ATGGCCTCAGTTTAGGGAAAATGTCTTACCAATTTCATTTCCGTAAGACATTTTCCGGAAAATCC
1 ATGGCCTCAGTTTAGGGAAAATGTCTTACCAATTTCATTTCCGTAAGACATTTTCCGGAAAATCC
16759557 CTCCCTCCTTCGGTCCTTCTCCTTCGTCAATCTGTCTTCCCCTCACGAATTTGCAGGATCTAAAA
66 CTCCCTCCTTCGGTCCTTCTCCTTCGTCAATCTGTCTTCCCCTCACGAATTTGCAGGATCTAAAA
16759622 ATCCCAAAGTTGGCCCATTGTCGATATTGTAAGTATCCCTTTCTGTCTTCCCCTTCTGGTAGCTT
131 ATCCCAAAGTTGGCCCATTGTCGATATTGTAAGTATCCCTTTCTGTCTTCCCCTTCTGGTAGCTT
16759687 GCAATTGGGAATTTTTATTGTTCTTTCTGGTATCCCCTTCTGTCTTCCAATATATGTCAACAAAC
196 GCAATTGGGAATTTTTATTGTTCTTTCTGGTATCCCCTTCTGTCTTCCAATATATGTCAACAAAC
16759752 AGCTGCTTGCAATTGGTTGAGACAACTTCAATTCCAGCACCATGGCTTGAACTTCTTCATGTCTC
261 AGCTGCTTGCAATTGGTTGAGACAACTTCAATTCCAGCACCATGGCTTGAACTTCTTCATGTCTC
16759817 GTCAGTTCC-AAATCCCTAAT
326 GTCAGTTCCAAAATCCCTAAT
16759837 ATGGCCTCAGTTTAGGGAAAATGTCTTACCAATTTCATTTCCGTAAGACATTTTCCGGAAAATCC
1 ATGGCCTCAGTTTAGGGAAAATGTCTTACCAATTTCATTTCCGTAAGACATTTTCCGGAAAATCC
*
16759902 CTTCCTCCTTCGGTCCTTCTCCTTCGTCAATCTGTCTTCCCCTCACGAATTTGCAGGATCTAAAA
66 CTCCCTCCTTCGGTCCTTCTCCTTCGTCAATCTGTCTTCCCCTCACGAATTTGCAGGATCTAAAA
16759967 ATCCCAAAGTTGGCCCATTGTCGATATTGTAAGTATCCCTTTCTGTCTTCCCCTTCTGGTAGCTT
131 ATCCCAAAGTTGGCCCATTGTCGATATTGTAAGTATCCCTTTCTGTCTTCCCCTTCTGGTAGCTT
16760032 GCAATTGGGAATTTTTATTGTTCTTTCTGGTATCCCCTTCTGTCTTCCAATATATGTCAACAAAC
196 GCAATTGGGAATTTTTATTGTTCTTTCTGGTATCCCCTTCTGTCTTCCAATATATGTCAACAAAC
16760097 AGCTGCTTGCAATTGGTTGAGACAACTTCAATTCCAGCACCATGGCTTGAACTTCTTCATGTCTC
261 AGCTGCTTGCAATTGGTTGAGACAACTTCAATTCCAGCACCATGGCTTGAACTTCTTCATGTCTC
16760162 GTCAGTTCCAAAATCCCTAAT
326 GTCAGTTCCAAAATCCCTAAT
16760183 GTTAACGCTA
Statistics
Matches: 344, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
345 333 0.97
346 11 0.03
ACGTcount: A:0.22, C:0.27, G:0.15, T:0.35
Consensus pattern (346 bp):
ATGGCCTCAGTTTAGGGAAAATGTCTTACCAATTTCATTTCCGTAAGACATTTTCCGGAAAATCC
CTCCCTCCTTCGGTCCTTCTCCTTCGTCAATCTGTCTTCCCCTCACGAATTTGCAGGATCTAAAA
ATCCCAAAGTTGGCCCATTGTCGATATTGTAAGTATCCCTTTCTGTCTTCCCCTTCTGGTAGCTT
GCAATTGGGAATTTTTATTGTTCTTTCTGGTATCCCCTTCTGTCTTCCAATATATGTCAACAAAC
AGCTGCTTGCAATTGGTTGAGACAACTTCAATTCCAGCACCATGGCTTGAACTTCTTCATGTCTC
GTCAGTTCCAAAATCCCTAAT
Found at i:16762352 original size:32 final size:33
Alignment explanation
Indices: 16762316--16762402 Score: 99
Period size: 33 Copynumber: 2.7 Consensus size: 33
16762306 ACTTTTTCGA
* *
16762316 AAAATATTTT-CAGGAAATC-TGCCAAACAGCAG
1 AAAATATTTTACAGTAAATCAT-CCAAACACCAG
*
16762348 AAAATATTTTACA-TAGATTCATCCAAACACCAG
1 AAAATATTTTACAGTA-AATCATCCAAACACCAG
*
16762381 AAAATATTTTCCAGTAAATCAT
1 AAAATATTTTACAGTAAATCAT
16762403 TTTACAGAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
32 11 0.24
33 32 0.70
34 3 0.07
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.28
Consensus pattern (33 bp):
AAAATATTTTACAGTAAATCATCCAAACACCAG
Found at i:16762418 original size:20 final size:20
Alignment explanation
Indices: 16762393--16762432 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
16762383 AATATTTTCC
*
16762393 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
16762413 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
16762433 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:16766606 original size:10 final size:10
Alignment explanation
Indices: 16766591--16766660 Score: 61
Period size: 10 Copynumber: 6.6 Consensus size: 10
16766581 TAGCATGTTG
16766591 AATTTTAATT
1 AATTTTAATT
*
16766601 AATTTTCATGTT
1 AATTTT-A-ATT
16766613 GAATTTTAATT
1 -AATTTTAATT
16766624 AATTTTATAATT
1 AA-TTT-TAATT
*
16766636 AATTTTGATT
1 AATTTTAATT
*
16766646 AATTTTGATT
1 AATTTTAATT
16766656 -ATTTT
1 AATTTT
16766661 CGATAGATTT
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
9 5 0.10
10 22 0.42
11 9 0.17
12 10 0.19
13 6 0.12
ACGTcount: A:0.33, C:0.01, G:0.06, T:0.60
Consensus pattern (10 bp):
AATTTTAATT
Found at i:16766610 original size:23 final size:23
Alignment explanation
Indices: 16766584--16766651 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
16766574 AAATTATTAG
16766584 CATGTTGAATTTTAATTAATTTT
1 CATGTTGAATTTTAATTAATTTT
16766607 CATGTTGAATTTTAATTAATTTT
1 CATGTTGAATTTTAATTAATTTT
* *
16766630 -ATAATT-AATTTTGATTAATTTT
1 CAT-GTTGAATTTTAATTAATTTT
16766652 GATTATTTTC
Statistics
Matches: 42, Mismatches: 2, Indels: 3
0.89 0.04 0.06
Matches are distributed among these distances:
22 17 0.40
23 25 0.60
ACGTcount: A:0.32, C:0.03, G:0.07, T:0.57
Consensus pattern (23 bp):
CATGTTGAATTTTAATTAATTTT
Found at i:16776904 original size:12 final size:13
Alignment explanation
Indices: 16776887--16776944 Score: 50
Period size: 12 Copynumber: 4.4 Consensus size: 13
16776877 GTCACACGAT
16776887 CGTGT-GTCAGGC
1 CGTGTGGTCAGGC
16776899 CGTGTGGT-AGGC
1 CGTGTGGTCAGGC
*
16776911 CGTGTGAGTCACACGGT
1 CGTGTG-GT--CA-GGC
16776928 CGTGT-GTCAGGC
1 CGTGTGGTCAGGC
16776940 CGTGT
1 CGTGT
16776945 AACTCACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
12 22 0.58
13 6 0.16
15 2 0.05
16 1 0.03
17 7 0.18
ACGTcount: A:0.10, C:0.22, G:0.41, T:0.26
Consensus pattern (13 bp):
CGTGTGGTCAGGC
Found at i:16785529 original size:6 final size:6
Alignment explanation
Indices: 16785518--16785543 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16785508 TTTATTATAT
16785518 TAATTA TAATTA TAATTA TAATTA TA
1 TAATTA TAATTA TAATTA TAATTA TA
16785544 TTAGAAAGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TAATTA
Found at i:16787673 original size:16 final size:17
Alignment explanation
Indices: 16787637--16787673 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
16787627 ATACCACATC
16787637 ACATAAAGTCATCTGAT
1 ACATAAAGTCATCTGAT
*
16787654 ACATAAAGTCGTCT-AT
1 ACATAAAGTCATCTGAT
16787670 ACAT
1 ACAT
16787674 GCCATGTTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.41, C:0.19, G:0.11, T:0.30
Consensus pattern (17 bp):
ACATAAAGTCATCTGAT
Found at i:16789808 original size:40 final size:41
Alignment explanation
Indices: 16789753--16789836 Score: 161
Period size: 40 Copynumber: 2.1 Consensus size: 41
16789743 CAATTTAGAA
16789753 TTTCATAACAATTTGACACTTCTAACATGTA-AACTCAACT
1 TTTCATAACAATTTGACACTTCTAACATGTAGAACTCAACT
16789793 TTTCATAACAATTTGACACTTCTAACATGTAGAACTCAACT
1 TTTCATAACAATTTGACACTTCTAACATGTAGAACTCAACT
16789834 TTT
1 TTT
16789837 GCACTTTTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 31 0.72
41 12 0.28
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (41 bp):
TTTCATAACAATTTGACACTTCTAACATGTAGAACTCAACT
Found at i:16789913 original size:11 final size:12
Alignment explanation
Indices: 16789885--16789918 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
16789875 GCCCAAACGT
16789885 CGAAATTTTTGAA
1 CGAAATTTTT-AA
16789898 CGAAATTTTT-A
1 CGAAATTTTTAA
16789909 CGAAATTTTT
1 CGAAATTTTT
16789919 TCGTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.52
13 10 0.48
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (12 bp):
CGAAATTTTTAA
Found at i:16791546 original size:7 final size:7
Alignment explanation
Indices: 16791534--16791575 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
16791524 TATATTATTA
16791534 CATTTCC
1 CATTTCC
16791541 CATTTCC
1 CATTTCC
*
16791548 C-CTTCC
1 CATTTCC
16791554 CATTTCC
1 CATTTCC
*
16791561 CGTTTCC
1 CATTTCC
*
16791568 CCTTTCC
1 CATTTCC
16791575 C
1 C
16791576 CGTGCATCTG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 5 0.17
7 25 0.83
ACGTcount: A:0.07, C:0.50, G:0.02, T:0.40
Consensus pattern (7 bp):
CATTTCC
Found at i:16791555 original size:13 final size:13
Alignment explanation
Indices: 16791537--16791576 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
16791527 ATTATTACAT
16791537 TTCCCATTTCCCC
1 TTCCCATTTCCCC
*
16791550 TTCCCATTTCCCGT
1 TTCCCATTTCCC-C
*
16791564 TTCCCCTTTCCCC
1 TTCCCATTTCCCC
16791577 GTGCATCTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.05, C:0.53, G:0.03, T:0.40
Consensus pattern (13 bp):
TTCCCATTTCCCC
Found at i:16791559 original size:20 final size:20
Alignment explanation
Indices: 16791534--16791571 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
16791524 TATATTATTA
16791534 CATTTCCCATTTCCCCTTCC
1 CATTTCCCATTTCCCCTTCC
*
16791554 CATTTCCCGTTTCCCCTT
1 CATTTCCCATTTCCCCTT
16791572 TCCCCGTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.08, C:0.47, G:0.03, T:0.42
Consensus pattern (20 bp):
CATTTCCCATTTCCCCTTCC
Found at i:16793851 original size:22 final size:23
Alignment explanation
Indices: 16793808--16793876 Score: 77
Period size: 22 Copynumber: 2.9 Consensus size: 23
16793798 ATATACAAAA
16793808 AAAAATATAATTTGATAAAATTTTAAT
1 AAAAATATAATTT--T--AATTTTAAT
* *
16793835 AACAAT-TAGTTTTAATTTTAAT
1 AAAAATATAATTTTAATTTTAAT
16793857 AAAAATATAATTTTAATTTT
1 AAAAATATAATTTTAATTTT
16793877 TAAAAAACGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
22 14 0.38
23 12 0.32
24 1 0.03
26 5 0.14
27 5 0.14
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (23 bp):
AAAAATATAATTTTAATTTTAAT
Found at i:16795548 original size:3 final size:3
Alignment explanation
Indices: 16795540--16795569 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
16795530 ATAGGATTTC
16795540 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
16795570 CCTATACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:16796375 original size:29 final size:28
Alignment explanation
Indices: 16796331--16796400 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
16796321 AAATAAAAAA
*
16796331 TTACCAAAATGT-TATAACTTTTTTTTAT
1 TTACCAAAATATATATAA-TTTTTTTTAT
16796359 TTACCAAAATATATATAATTTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTTAT
16796387 TTACCAAAATATAT
1 TTACCAAAATATAT
16796401 CAAAAACAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
28 35 0.88
29 5 0.12
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.50
Consensus pattern (28 bp):
TTACCAAAATATATATAATTTTTTTTAT
Found at i:16796421 original size:16 final size:17
Alignment explanation
Indices: 16796402--16796439 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
16796392 AAAATATATC
16796402 AAAAACAAAAAACA-AA
1 AAAAACAAAAAACAGAA
* *
16796418 AAAAATAAAAAATAGAA
1 AAAAACAAAAAACAGAA
16796435 AAAAA
1 AAAAA
16796440 AAACTGAACT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.87, C:0.05, G:0.03, T:0.05
Consensus pattern (17 bp):
AAAAACAAAAAACAGAA
Found at i:16796529 original size:27 final size:27
Alignment explanation
Indices: 16796468--16796529 Score: 88
Period size: 27 Copynumber: 2.3 Consensus size: 27
16796458 AACTCCCTGG
16796468 GTGGAGGGAAGCAGGTTGGCGGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
****
16796495 AACAAGGGAAGCAGGTTGGCGGCACCA
1 GTGGAGGGAAGCAGGTTGGCGGCACCA
16796522 GTGGAGGG
1 GTGGAGGG
16796530 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.26, C:0.18, G:0.47, T:0.10
Consensus pattern (27 bp):
GTGGAGGGAAGCAGGTTGGCGGCACCA
Found at i:16797506 original size:19 final size:18
Alignment explanation
Indices: 16797466--16797516 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
16797456 AAAATATATA
**
16797466 TAATATTTTGGTATTTTT
1 TAATATTTTATTATTTTT
16797484 TAATATTTTATTATTTTT
1 TAATATTTTATTATTTTT
*
16797502 GTAATGTTTTATTAT
1 -TAATATTTTATTAT
16797517 GGGTTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TAATATTTTATTATTTTT
Found at i:16797541 original size:13 final size:13
Alignment explanation
Indices: 16797523--16797548 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
16797513 TTATGGGTTT
16797523 TATAAAAAAATAA
1 TATAAAAAAATAA
16797536 TATAAAAAAATAA
1 TATAAAAAAATAA
16797549 AAAAATTACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
TATAAAAAAATAA
Found at i:16799597 original size:25 final size:25
Alignment explanation
Indices: 16799563--16799614 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
16799553 CCCAGCCAGA
16799563 TCCGAAACAATCTGGATTTGTCGGT
1 TCCGAAACAATCTGGATTTGTCGGT
16799588 TCCGAAACAATCTGGATTTGTCGGT
1 TCCGAAACAATCTGGATTTGTCGGT
16799613 TC
1 TC
16799615 AGATAGCTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (25 bp):
TCCGAAACAATCTGGATTTGTCGGT
Found at i:16800149 original size:10 final size:10
Alignment explanation
Indices: 16800134--16800237 Score: 55
Period size: 10 Copynumber: 9.1 Consensus size: 10
16800124 TCCAAACGCC
16800134 TTCTTTTTCT
1 TTCTTTTTCT
16800144 TTCTTTCCTCCTCT
1 TTCTTT--T--TCT
*
16800158 TTCCTTTTCT
1 TTCTTTTTCT
16800168 TTCCTTCTTTTCT
1 TT-C-T-TTTTCT
16800181 TTCTTTCCTCTCAT
1 TTCTTT--T-TC-T
* *
16800195 TTCCTTTTCC
1 TTCTTTTTCT
16800205 TTCTTTTTCT
1 TTCTTTTTCT
16800215 TTCTTCCTTTCT
1 TTCTT--TTTCT
*
16800227 TTCTTCTTCT
1 TTCTTTTTCT
16800237 T
1 T
16800238 CCCCTCTCCT
Statistics
Matches: 74, Mismatches: 7, Indels: 26
0.69 0.07 0.24
Matches are distributed among these distances:
10 31 0.42
11 4 0.05
12 15 0.20
13 10 0.14
14 14 0.19
ACGTcount: A:0.01, C:0.32, G:0.00, T:0.67
Consensus pattern (10 bp):
TTCTTTTTCT
Found at i:16800183 original size:37 final size:37
Alignment explanation
Indices: 16800132--16800219 Score: 121
Period size: 37 Copynumber: 2.4 Consensus size: 37
16800122 ATTCCAAACG
*
16800132 CCTTCTTTTTCTTTCTTTCCTCCTC-TTTCCTTTTCTTT
1 CCTTC-TTTTCTTTCTTTCCT-CTCATTTCCTTTTCCTT
16800170 CCTTCTTTTCTTTCTTTCCTCTCATTTCCTTTTCCTT
1 CCTTCTTTTCTTTCTTTCCTCTCATTTCCTTTTCCTT
16800207 -C-T-TTTTCTTTCTT
1 CCTTCTTTTCTTTCTT
16800220 CCTTTCTTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
34 11 0.23
35 1 0.02
36 4 0.08
37 27 0.56
38 5 0.10
ACGTcount: A:0.01, C:0.33, G:0.00, T:0.66
Consensus pattern (37 bp):
CCTTCTTTTCTTTCTTTCCTCTCATTTCCTTTTCCTT
Found at i:16800466 original size:24 final size:24
Alignment explanation
Indices: 16800415--16800472 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
16800405 TTTTTAATAT
*
16800415 ATTTTGGTAAATAAAAATATATAT
1 ATTTTGGTAAATAAAAATATATAA
16800439 ATTTTGGTAAA-AAAAAGT-TATAAA
1 ATTTTGGTAAATAAAAA-TATAT-AA
*
16800463 ATTTTAGTAA
1 ATTTTGGTAA
16800473 TTTTTTATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 8 0.27
24 22 0.73
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (24 bp):
ATTTTGGTAAATAAAAATATATAA
Found at i:16802805 original size:3 final size:3
Alignment explanation
Indices: 16802790--16802828 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
16802780 TATTTATTGA
*
16802790 TAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
16802829 ATACGCCTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:16803127 original size:16 final size:16
Alignment explanation
Indices: 16803106--16803138 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
16803096 CATTTTCTAA
*
16803106 TTCATATGCATTTTTT
1 TTCATATACATTTTTT
16803122 TTCATATACATTTTTT
1 TTCATATACATTTTTT
16803138 T
1 T
16803139 AGAAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.21, C:0.12, G:0.03, T:0.64
Consensus pattern (16 bp):
TTCATATACATTTTTT
Found at i:16809824 original size:33 final size:33
Alignment explanation
Indices: 16809787--16809853 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
16809777 GATGGAAATG
*
16809787 TACTGTGTATTTGTTTAAACTATGCATAAGTGC
1 TACTGTGTATTTGTTTAAACTAAGCATAAGTGC
*
16809820 TACTGTGTATTTGTTTAAACTAAGCATGAGTGC
1 TACTGTGTATTTGTTTAAACTAAGCATAAGTGC
16809853 T
1 T
16809854 GCTTTCATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (33 bp):
TACTGTGTATTTGTTTAAACTAAGCATAAGTGC
Found at i:16820189 original size:16 final size:17
Alignment explanation
Indices: 16820159--16820192 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
16820149 GACCCGATCC
16820159 TTTTTAGATTCGAATTT
1 TTTTTAGATTCGAATTT
*
16820176 TTTTTAGCTT-GAATTT
1 TTTTTAGATTCGAATTT
16820192 T
1 T
16820193 CTCGGATTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.21, C:0.06, G:0.12, T:0.62
Consensus pattern (17 bp):
TTTTTAGATTCGAATTT
Found at i:16821918 original size:23 final size:23
Alignment explanation
Indices: 16821892--16821940 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
16821882 CTTTGGTGCG
16821892 ATTTGT-TCTGGCAATTCGATGCA
1 ATTTGTAT-TGGCAATTCGATGCA
* *
16821915 ATTTGTATTGGCACTTCGGTGCA
1 ATTTGTATTGGCAATTCGATGCA
16821938 ATT
1 ATT
16821941 ACCTTTGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.41
Consensus pattern (23 bp):
ATTTGTATTGGCAATTCGATGCA
Found at i:16823522 original size:7 final size:7
Alignment explanation
Indices: 16823510--16823534 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
16823500 ATACGGTAAT
16823510 ATATTAA
1 ATATTAA
16823517 ATATTAA
1 ATATTAA
16823524 ATATTAA
1 ATATTAA
16823531 ATAT
1 ATAT
16823535 ATTTTTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
ATATTAA
Found at i:16823976 original size:19 final size:19
Alignment explanation
Indices: 16823952--16824044 Score: 150
Period size: 19 Copynumber: 4.8 Consensus size: 19
16823942 AATTTTTGAG
16823952 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
16823971 GATATGCAATCCTAGATAT
1 GATATGCAATCTTAGATAT
16823990 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
**
16824009 GATATATAATCTTTAGATAT
1 GATATGCAATC-TTAGATAT
16824029 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
16824045 ATATATGATT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 50 0.75
20 17 0.25
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:16824656 original size:25 final size:25
Alignment explanation
Indices: 16824605--16824656 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
16824595 AATTTTGTTA
**
16824605 ATGTAATTATTATTATTATTTTCAT
1 ATGTAATTATTATTATTATTAGCAT
16824630 ATGTAATTATTATTATT-TTAGCTAT
1 ATGTAATTATTATTATTATTAGC-AT
16824655 AT
1 AT
16824657 ATATATNNNN
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.58
Consensus pattern (25 bp):
ATGTAATTATTATTATTATTAGCAT
Found at i:16825704 original size:98 final size:98
Alignment explanation
Indices: 16825584--16826464 Score: 1699
Period size: 98 Copynumber: 9.0 Consensus size: 98
16825574 TTAAAAATAA
* * * * * *
16825584 TAAAGGAAATATTCCGAATTTGGGATTTTAAAGGAATTGTGCCCTAACGTATTGGGTGTGATTTC
1 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
16825649 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
16825682 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
1 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
16825747 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
16825780 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
1 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
16825845 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
16825878 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
1 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
16825943 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
16825976 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
1 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
16826041 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
16826074 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
1 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
16826139 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
16826172 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
1 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
16826237 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
16826270 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
1 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
16826335 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
16826368 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
1 TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
*
16826433 TTAAATCTTGGATAAGTGGATGTTCTTCTAAA
66 TTAAATCTTGGATAAGTGGATGTTCTTTTAAA
16826465 ATTTTATTGT
Statistics
Matches: 776, Mismatches: 7, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 776 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (98 bp):
TAAAGGAAATACTCCGAGTTTGGGATTCTAGAGGAATCGTGCCCTAACGTATTGAGTGTGATTTC
TTAAATCTTGGATAAGTGGATGTTCTTTTAAAG
Found at i:16828006 original size:96 final size:97
Alignment explanation
Indices: 16827901--16828099 Score: 382
Period size: 96 Copynumber: 2.1 Consensus size: 97
16827891 TCATTCATAT
16827901 TTATTTAATTTAAGTTTAGTTTTATAGAAATATGTCTACAGTTTTCTCAAGGTCACCCACATTTT
1 TTATTTAATTTAAGTTTAGTTTTATAGAAATATGTCTACAGTTTTCTCAAGGTCACCCACATTTT
16827966 TTTTATTTTTAAAAATAAAA-TATTTTATTTA
66 TTTTATTTTTAAAAATAAAATTATTTTATTTA
16827997 TTATTTAATTTAAGTTTAGTTTTATAGAAATATGTCTACAGTTTTCTCAAGGTCACCCACATTTT
1 TTATTTAATTTAAGTTTAGTTTTATAGAAATATGTCTACAGTTTTCTCAAGGTCACCCACATTTT
16828062 TTTTATTTTTAAAAATAAAATTATTTTATTTA
66 TTTTATTTTTAAAAATAAAATTATTTTATTTA
*
16828094 ATATTT
1 TTATTT
16828100 TAAACGTAAA
Statistics
Matches: 101, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
96 85 0.84
97 16 0.16
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (97 bp):
TTATTTAATTTAAGTTTAGTTTTATAGAAATATGTCTACAGTTTTCTCAAGGTCACCCACATTTT
TTTTATTTTTAAAAATAAAATTATTTTATTTA
Found at i:16835913 original size:96 final size:97
Alignment explanation
Indices: 16835749--16835945 Score: 387
Period size: 96 Copynumber: 2.0 Consensus size: 97
16835739 CTTGAACACG
16835749 TTTACAAATAATATCATGAAGAATAAACTAACAAACAATAAATAAACATACATATTATCTTTTAG
1 TTTACAAATAATATCATGAAGAATAAACTAACAAACAATAAATAAACATACATATTATCTTTTAG
16835814 ATATAAAATAATTAAATATAAATATCAA-AGT
66 ATATAAAATAATTAAATATAAATATCAATAGT
16835845 TTTACAAATAATATCATGAAGAATAAACTAACAAACAATAAATAAACATACATATTATCTTTTAG
1 TTTACAAATAATATCATGAAGAATAAACTAACAAACAATAAATAAACATACATATTATCTTTTAG
16835910 ATATAAAATAATTAAATATAAATATCAATAGT
66 ATATAAAATAATTAAATATAAATATCAATAGT
16835942 TTTA
1 TTTA
16835946 ATATAAATAG
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
96 93 0.93
97 7 0.07
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.32
Consensus pattern (97 bp):
TTTACAAATAATATCATGAAGAATAAACTAACAAACAATAAATAAACATACATATTATCTTTTAG
ATATAAAATAATTAAATATAAATATCAATAGT
Found at i:16856133 original size:19 final size:19
Alignment explanation
Indices: 16856106--16856142 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16856096 GCAATTACGA
*
16856106 AAATTAAAAATTATATATT
1 AAATCAAAAATTATATATT
*
16856125 AAATCAAAATTTATATAT
1 AAATCAAAAATTATATAT
16856143 AATTTTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATCAAAAATTATATATT
Found at i:16857939 original size:20 final size:20
Alignment explanation
Indices: 16857903--16857940 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
16857893 AAGAAGCAAC
*
16857903 ACAGAAACATCAACAAAAAG
1 ACAGAAACATAAACAAAAAG
16857923 ACAGAAACA-AAAGCAAAA
1 ACAGAAACATAAA-CAAAA
16857941 CATAGCAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.12
20 14 0.88
ACGTcount: A:0.68, C:0.18, G:0.11, T:0.03
Consensus pattern (20 bp):
ACAGAAACATAAACAAAAAG
Found at i:16859242 original size:43 final size:43
Alignment explanation
Indices: 16859180--16859384 Score: 216
Period size: 43 Copynumber: 4.8 Consensus size: 43
16859170 CGTCGCTAAC
16859180 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGACA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGACA
* * *
16859223 TTTAGTGGCGCTTTCCCCACAAACGCCGCTAAAGACCAC-ATA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGACA
* * *
16859265 TTTTAGCGGCGCTTTTCCCACAAACGTCGCTAAATACCAAGATC-
1 -TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGA-CA
* ** * * * *
16859309 TTTAGCGGTGCTTTTATCACAAACGCCGATATAGACCATGACC
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGACA
* * ** *
16859352 TTTAGCGGTGCTTCTAGCAAAAACGCCGCTAAA
1 TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAA
16859385 AAACATAAAC
Statistics
Matches: 136, Mismatches: 22, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
42 3 0.02
43 132 0.97
44 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCACGACA
Found at i:16859398 original size:43 final size:43
Alignment explanation
Indices: 16859308--16859398 Score: 101
Period size: 43 Copynumber: 2.1 Consensus size: 43
16859298 ATACCAAGAT
* * * * * * * *
16859308 CTTTAGCGGTGCTTTTATCACAAACGCCGATATAGACCATGAC
1 CTTTAGCGGTGCTTCTAGCAAAAACGCCGATAAAAAACATAAA
*
16859351 CTTTAGCGGTGCTTCTAGCAAAAACGCCGCTAAAAAACATAAA
1 CTTTAGCGGTGCTTCTAGCAAAAACGCCGATAAAAAACATAAA
16859394 CTTTA
1 CTTTA
16859399 AAAAAAATTA
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
43 39 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.26
Consensus pattern (43 bp):
CTTTAGCGGTGCTTCTAGCAAAAACGCCGATAAAAAACATAAA
Found at i:16861407 original size:15 final size:15
Alignment explanation
Indices: 16861383--16861419 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
16861373 AACACTCACA
*
16861383 AAAATTCCAAGAATG
1 AAAATCCCAAGAATG
16861398 AAAATCCCAAGAATG
1 AAAATCCCAAGAATG
16861413 AAAATCC
1 AAAATCC
16861420 AAGTTCATGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.54, C:0.19, G:0.11, T:0.16
Consensus pattern (15 bp):
AAAATCCCAAGAATG
Found at i:16861686 original size:22 final size:22
Alignment explanation
Indices: 16861645--16861686 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
16861635 TGTAAAAATG
** *
16861645 AAATTGAAATTTATTCAAAACA
1 AAATTGAAATAAATTAAAAACA
16861667 AAATTGAAATAAATTAAAAA
1 AAATTGAAATAAATTAAAAA
16861687 GGAAGAGTGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.05, T:0.29
Consensus pattern (22 bp):
AAATTGAAATAAATTAAAAACA
Found at i:16861989 original size:41 final size:41
Alignment explanation
Indices: 16861932--16862086 Score: 195
Period size: 41 Copynumber: 3.8 Consensus size: 41
16861922 TTTTATTATT
* *
16861932 ATTAGCGGCGCTTTTCAAAAAACACCGCTAAAGGCCCGAAC
1 ATTAGCGGCGCTTTTCAAAAAACGCCGCTAAAGGCCCGAGC
* *
16861973 ATTAGCGGCGCTTTTCAAAAAACGCCGCTAAAGTCCTGAGC
1 ATTAGCGGCGCTTTTCAAAAAACGCCGCTAAAGGCCCGAGC
* * *
16862014 ATTAGCGGCGCTTCTT-TAAAAACGCCGCCAAAGGCCCGAGT
1 ATTAGCGGCGCTT-TTCAAAAAACGCCGCTAAAGGCCCGAGC
* ** *
16862055 ATTGGCGGCGCTTTTTTAAAAATGCCGCTAAA
1 ATTAGCGGCGCTTTTCAAAAAACGCCGCTAAA
16862087 AAAAGCGCCG
Statistics
Matches: 100, Mismatches: 12, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
40 2 0.02
41 96 0.96
42 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.22
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTCAAAAAACGCCGCTAAAGGCCCGAGC
Found at i:16862119 original size:56 final size:55
Alignment explanation
Indices: 16862031--16862142 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 55
16862021 GCGCTTCTTT
* * * * *
16862031 AAAAACGCCGCCAAAGGCCCGAGTATTGGCGGCGCTTTTTTAAAAATGCCGCTAA
1 AAAAACGCCGCCAAAGGCCCGAGCATTAGCGGCGATTTTTCAAAAACGCCGCTAA
*
16862086 AAAAAGCGCCGCTAAAGGCCCGAGCATTAGCGGCGATTTTTCAAAAACGCCGCTAA
1 AAAAA-CGCCGCCAAAGGCCCGAGCATTAGCGGCGATTTTTCAAAAACGCCGCTAA
16862142 A
1 A
16862143 TGCCCCCCAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
55 5 0.10
56 45 0.90
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (55 bp):
AAAAACGCCGCCAAAGGCCCGAGCATTAGCGGCGATTTTTCAAAAACGCCGCTAA
Found at i:16862255 original size:39 final size:39
Alignment explanation
Indices: 16862202--16862317 Score: 144
Period size: 40 Copynumber: 2.9 Consensus size: 39
16862192 CCGCTTTTTG
* *
16862202 AAAAA-CGCCGCTAATACTTATTTTTAGTGGCATTTTCC
1 AAAAAGCGCCGCTAATGCTTATTTTTAGTGGCGTTTTCC
* ** *
16862240 AAAAAGCGCCGCTAATGCTAGACCTTTAGTGGCGTTTTTC
1 AAAAAGCGCCGCTAATGCT-TATTTTTAGTGGCGTTTTCC
*
16862280 AAAAAGCACCGCTAATGCTTGATTTTTAGTGGCGTTTT
1 AAAAAGCGCCGCTAATGCTT-ATTTTTAGTGGCGTTTT
16862318 TTGTCCAAAC
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
38 5 0.08
39 12 0.18
40 48 0.74
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (39 bp):
AAAAAGCGCCGCTAATGCTTATTTTTAGTGGCGTTTTCC
Found at i:16867145 original size:47 final size:47
Alignment explanation
Indices: 16867080--16867319 Score: 312
Period size: 47 Copynumber: 5.1 Consensus size: 47
16867070 TTGTTGAATA
*
16867080 ATTT-ATTTATTTATTTTACACTATATAATAATTGAATAATTTGTTT
1 ATTTAATTTATTTATTTTACACTATATAATAATTGAATAATTTATTT
*
16867126 ATTTAATTTATTTACTTTACACTATA-AATAATTGAAATAATTTATTT
1 ATTTAATTTATTTATTTTACACTATATAATAATTG-AATAATTTATTT
***
16867173 ATTTAAGACATTTATTTTACAC--TATAATAATTGAATAATTTATTT
1 ATTTAATTTATTTATTTTACACTATATAATAATTGAATAATTTATTT
*
16867218 ATTTAATTTATTTACTTTAACACTATATAATAACTT-AATAATTTATTT
1 ATTTAATTTATTTA-TTTTACACTATATAATAA-TTGAATAATTTATTT
*** *
16867266 ATTTAAAACATTTATTTTACACTATATAATAATT-AAAAATTTTATTT
1 ATTTAATTTATTTATTTTACACTATATAATAATTGAATAA-TTTATTT
16867313 ATTTAAT
1 ATTTAAT
16867320 AATTGGATAA
Statistics
Matches: 170, Mismatches: 16, Indels: 15
0.85 0.08 0.07
Matches are distributed among these distances:
45 25 0.15
46 33 0.19
47 79 0.46
48 31 0.18
49 2 0.01
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (47 bp):
ATTTAATTTATTTATTTTACACTATATAATAATTGAATAATTTATTT
Found at i:16867226 original size:13 final size:14
Alignment explanation
Indices: 16867208--16867237 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
16867198 AATAATTGAA
16867208 TAATTTATTTA-TT
1 TAATTTATTTACTT
16867221 TAATTTATTTACTT
1 TAATTTATTTACTT
16867235 TAA
1 TAA
16867238 CACTATATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (14 bp):
TAATTTATTTACTT
Found at i:16867234 original size:92 final size:94
Alignment explanation
Indices: 16867088--16867319 Score: 357
Period size: 93 Copynumber: 2.5 Consensus size: 94
16867078 TAATTTATTT
*
16867088 ATTTATTTTACACTATATAATAATTGAATAATTTGTTTATTTAATTTATTTACTTT-ACACTATA
1 ATTTATTTTACAC-ATATAATAATTGAATAATTTATTTATTTAATTTATTTACTTTAACACTATA
*
16867152 -AATAA-TTGAAATAATTTATTTATTTAAGAC
65 TAATAACTT--AATAATTTATTTATTTAAAAC
16867182 ATTTATTTTACAC-TATAATAATTGAATAATTTATTTATTTAATTTATTTACTTTAACACTATAT
1 ATTTATTTTACACATATAATAATTGAATAATTTATTTATTTAATTTATTTACTTTAACACTATAT
16867246 AATAACTTAATAATTTATTTATTTAAAAC
66 AATAACTTAATAATTTATTTATTTAAAAC
*
16867275 ATTTATTTTACACTATATAATAATT-AAAAATTTTATTTATTTAAT
1 ATTTATTTTACAC-ATATAATAATTGAATAA-TTTATTTATTTAAT
16867320 AATTGGATAA
Statistics
Matches: 129, Mismatches: 3, Indels: 11
0.90 0.02 0.08
Matches are distributed among these distances:
92 40 0.31
93 41 0.32
94 22 0.17
95 26 0.20
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (94 bp):
ATTTATTTTACACATATAATAATTGAATAATTTATTTATTTAATTTATTTACTTTAACACTATAT
AATAACTTAATAATTTATTTATTTAAAAC
Found at i:16870506 original size:55 final size:55
Alignment explanation
Indices: 16870420--16870584 Score: 206
Period size: 56 Copynumber: 3.0 Consensus size: 55
16870410 ACTTCACTTG
* * **
16870420 ACCCAAAATTTTTTT-TAAAATTCTAGCACAAGGGTGTTAACCATCAGTGTCCCAGC
1 ACCC-AAATTTTTTTCTCAAA-TCTAGTACAAGGGTGTCGACCATCAGTGTCCCAGC
* *
16870476 ACCCAAATTTTTTTCTCAAATCTAGTACAAGGGTGTCGACCATCAGTGTGCTAGC
1 ACCCAAATTTTTTTCTCAAATCTAGTACAAGGGTGTCGACCATCAGTGTCCCAGC
* * * *
16870531 ACCCAATTTTTTTTTCTCGAATCTAGTACAAGGATGTCGACCATCAATGTCCCA
1 ACCCAA-ATTTTTTTCTCAAATCTAGTACAAGGGTGTCGACCATCAGTGTCCCA
16870585 ACAATTAGAA
Statistics
Matches: 95, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
55 46 0.48
56 49 0.52
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (55 bp):
ACCCAAATTTTTTTCTCAAATCTAGTACAAGGGTGTCGACCATCAGTGTCCCAGC
Found at i:16875034 original size:7 final size:8
Alignment explanation
Indices: 16875005--16875037 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
16874995 TGAAATTCTT
16875005 TTTAAAAA
1 TTTAAAAA
16875013 TTTAAAAA
1 TTTAAAAA
16875021 TTCTAAAAA
1 TT-TAAAAA
16875030 -TTAAAAA
1 TTTAAAAA
16875037 T
1 T
16875038 AGATAAAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
7 6 0.26
8 11 0.48
9 6 0.26
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (8 bp):
TTTAAAAA
Found at i:16886640 original size:27 final size:27
Alignment explanation
Indices: 16886602--16886673 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 27
16886592 TGCAGGGGTG
* *
16886602 TGGTAGGCGGCACTAGTGGCCCTTATC
1 TGGTAGGCGGCACTAGTGACCCCTATC
* *
16886629 TGGTAGGCGGCACTGGTGACCCCTATT
1 TGGTAGGCGGCACTAGTGACCCCTATC
* *
16886656 TGATAGGCGGCACCAGTG
1 TGGTAGGCGGCACTAGTG
16886674 TATTAAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.24
Consensus pattern (27 bp):
TGGTAGGCGGCACTAGTGACCCCTATC
Found at i:16886822 original size:5 final size:6
Alignment explanation
Indices: 16886805--16886830 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16886795 AAAGAAAATG
16886805 TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TA
16886831 AAGAGAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:16887035 original size:94 final size:94
Alignment explanation
Indices: 16886928--16887139 Score: 424
Period size: 94 Copynumber: 2.3 Consensus size: 94
16886918 TTTTGTTTAT
16886928 TGATTTGTTAGGTTATGAATGTTATGTTAAAGTTTTAAAGTTTTTTTGTTAGTAAGTTTTGTGTT
1 TGATTTGTTAGGTTATGAATGTTATGTTAAAGTTTTAAAGTTTTTTTGTTAGTAAGTTTTGTGTT
16886993 TAGGTTAATTATTTGTTTAGGGTTTATTG
66 TAGGTTAATTATTTGTTTAGGGTTTATTG
16887022 TGATTTGTTAGGTTATGAATGTTATGTTAAAGTTTTAAAGTTTTTTTGTTAGTAAGTTTTGTGTT
1 TGATTTGTTAGGTTATGAATGTTATGTTAAAGTTTTAAAGTTTTTTTGTTAGTAAGTTTTGTGTT
16887087 TAGGTTAATTATTTGTTTAGGGTTTATTG
66 TAGGTTAATTATTTGTTTAGGGTTTATTG
16887116 TGATTTGTTAGGTTATGAATGTTA
1 TGATTTGTTAGGTTATGAATGTTA
16887140 CGTTTTAATA
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 118 1.00
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.55
Consensus pattern (94 bp):
TGATTTGTTAGGTTATGAATGTTATGTTAAAGTTTTAAAGTTTTTTTGTTAGTAAGTTTTGTGTT
TAGGTTAATTATTTGTTTAGGGTTTATTG
Found at i:16890937 original size:27 final size:26
Alignment explanation
Indices: 16890905--16890984 Score: 64
Period size: 27 Copynumber: 3.2 Consensus size: 26
16890895 TATCTAATTT
16890905 ATATTACAAATTTTGTTCATCATTTTA
1 ATATTACAAA-TTTGTTCATCATTTTA
* *
16890932 ATATTA-TAA--TG-T-ATCTAATTT-
1 ATATTACAAATTTGTTCATC-ATTTTA
*
16890953 ATATTGCAAAGTTTGTTCATCATTTTA
1 ATATTACAAA-TTTGTTCATCATTTTA
16890980 ATATT
1 ATATT
16890985 GTAATGTATT
Statistics
Matches: 40, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
21 8 0.20
22 7 0.17
23 2 0.05
25 2 0.05
26 7 0.17
27 14 0.35
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (26 bp):
ATATTACAAATTTGTTCATCATTTTA
Found at i:16891020 original size:48 final size:48
Alignment explanation
Indices: 16890706--16891020 Score: 463
Period size: 48 Copynumber: 6.6 Consensus size: 48
16890696 GCTAAGGTAC
*
16890706 CTAATTTATATTACAAAGTTTGTT-ATTCATTTTAATGTTGTAATGCAT
1 CTAATTTATATTACAAAGTTTGTTCA-TCATTTTAATGTTGTAATGTAT
* * *
16890754 CTAATTTATATTACAAAGTTTGTTCCTCGTTTTAATGTTGTAATATAT
1 CTAATTTATATTACAAAGTTTGTTCATCATTTTAATGTTGTAATGTAT
*
16890802 CTAATTTATATTACAAAGTTTGTTTC-TCGTTTTAATGTTGTAATGTAT
1 CTAATTTATATTACAAAGTTTG-TTCATCATTTTAATGTTGTAATGTAT
* * *
16890850 CTAATTTATATTACAAAGTTTGTTCCTCGTTTTAATGCTGTAATGTAT
1 CTAATTTATATTACAAAGTTTGTTCATCATTTTAATGTTGTAATGTAT
* * *
16890898 CTAATTTATATTACAAATTTTGTTCATCATTTTAATATTATAATGTAT
1 CTAATTTATATTACAAAGTTTGTTCATCATTTTAATGTTGTAATGTAT
* *
16890946 CTAATTTATATTGCAAAGTTTGTTCATCATTTTAATATTGTAATGTAT
1 CTAATTTATATTACAAAGTTTGTTCATCATTTTAATGTTGTAATGTAT
* *
16890994 TTAATTTATATTACAAAGTTTATTCAT
1 CTAATTTATATTACAAAGTTTGTTCAT
16891021 ATTACAGAGT
Statistics
Matches: 246, Mismatches: 18, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
47 3 0.01
48 240 0.98
49 3 0.01
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50
Consensus pattern (48 bp):
CTAATTTATATTACAAAGTTTGTTCATCATTTTAATGTTGTAATGTAT
Found at i:16891382 original size:31 final size:32
Alignment explanation
Indices: 16891322--16891384 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
16891312 TGAACTTGAG
*
16891322 CCGGGAGGAGTGGAGTACTACGGTGGATACGAT
1 CCGGGAGGAG-GGAGTACTACGGTAGATACGAT
* *
16891355 CCGGGAGGA-GGAGTATTGCGGTAGATACGA
1 CCGGGAGGAGGGAGTACTACGGTAGATACGA
16891385 GCAAAGAGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 18 0.67
33 9 0.33
ACGTcount: A:0.25, C:0.14, G:0.43, T:0.17
Consensus pattern (32 bp):
CCGGGAGGAGGGAGTACTACGGTAGATACGAT
Found at i:16892248 original size:14 final size:14
Alignment explanation
Indices: 16892229--16892255 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
16892219 AAAATTACAT
16892229 GTTAGAATAGTATC
1 GTTAGAATAGTATC
16892243 GTTAGAATAGTAT
1 GTTAGAATAGTAT
16892256 TATTAGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (14 bp):
GTTAGAATAGTATC
Found at i:16892261 original size:14 final size:14
Alignment explanation
Indices: 16892230--16892263 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
16892220 AAATTACATG
*
16892230 TTAGAATAGTATCG
1 TTAGAATAGTATCA
*
16892244 TTAGAATAGTATTA
1 TTAGAATAGTATCA
16892258 TTAGAA
1 TTAGAA
16892264 AAAAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.18, T:0.38
Consensus pattern (14 bp):
TTAGAATAGTATCA
Done.