Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 174 of 187
Found at i:52062513 original size:38 final size:38
Alignment explanation
Indices: 52062471--52062550 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
52062461 GTTTCTCAGT
52062471 TTGTGTGGTTTTGTTCAAAGAATTGACAAAAGGGGAGG
1 TTGTGTGGTTTTGTTCAAAGAATTGACAAAAGGGGAGG
52062509 TTGTGTGGTTTTGTTCAAAGAATTGACAAAAGGGGAGG
1 TTGTGTGGTTTTGTTCAAAGAATTGACAAAAGGGGAGG
52062547 TTGT
1 TTGT
52062551 TTAGGCAAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.28, C:0.05, G:0.34, T:0.34
Consensus pattern (38 bp):
TTGTGTGGTTTTGTTCAAAGAATTGACAAAAGGGGAGG
Found at i:52067065 original size:30 final size:30
Alignment explanation
Indices: 52066978--52067128 Score: 151
Period size: 30 Copynumber: 5.1 Consensus size: 30
52066968 CAAAGTATGC
52066978 TAAA-CGATGGTCGAAACCATCCCTTTTCA
1 TAAATCGATGGTCGAAACCATCCCTTTTCA
* * * ** * *
52067007 TTAATCAATGGTTGTCACCGTACCTTTTCA
1 TAAATCGATGGTCGAAACCATCCCTTTTCA
* * * *
52067037 TAAATCAATGGTCAAAATCATCCATTTTCA
1 TAAATCGATGGTCGAAACCATCCCTTTTCA
* * **
52067067 TTAATTGATGGTCGTCACCATCCCTTTTCA
1 TAAATCGATGGTCGAAACCATCCCTTTTCA
*
52067097 TAAACCGATGGTCGAAACCATCCCTTTTCA
1 TAAATCGATGGTCGAAACCATCCCTTTTCA
52067127 TA
1 TA
52067129 TTCAATAGTC
Statistics
Matches: 92, Mismatches: 29, Indels: 1
0.75 0.24 0.01
Matches are distributed among these distances:
29 3 0.03
30 89 0.97
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (30 bp):
TAAATCGATGGTCGAAACCATCCCTTTTCA
Found at i:52067078 original size:60 final size:60
Alignment explanation
Indices: 52066984--52067127 Score: 198
Period size: 60 Copynumber: 2.4 Consensus size: 60
52066974 ATGCTAAACG
* * *
52066984 ATGGTCGAAACCATCCCTTTTCATTAATCAATGGTTGTCACCGTACCTTTTCATAAATCA
1 ATGGTCGAAACCATCCCTTTTCATTAATCAATGGTCGTCACCATACCTTTTCATAAACCA
* * * ** * *
52067044 ATGGTCAAAATCATCCATTTTCATTAATTGATGGTCGTCACCATCCCTTTTCATAAACCG
1 ATGGTCGAAACCATCCCTTTTCATTAATCAATGGTCGTCACCATACCTTTTCATAAACCA
52067104 ATGGTCGAAACCATCCCTTTTCAT
1 ATGGTCGAAACCATCCCTTTTCAT
52067128 ATTCAATAGT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
60 71 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (60 bp):
ATGGTCGAAACCATCCCTTTTCATTAATCAATGGTCGTCACCATACCTTTTCATAAACCA
Found at i:52074004 original size:22 final size:22
Alignment explanation
Indices: 52073978--52074020 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
52073968 TCCTTCTTTT
* *
52073978 TTTGCTGTCTCCTTTTTGTTTC
1 TTTGCTCTCTCCTGTTTGTTTC
*
52074000 TTTGCTCTCTGCTGTTTGTTT
1 TTTGCTCTCTCCTGTTTGTTT
52074021 ATGTGTAGGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.16, T:0.63
Consensus pattern (22 bp):
TTTGCTCTCTCCTGTTTGTTTC
Found at i:52074645 original size:50 final size:50
Alignment explanation
Indices: 52074591--52074746 Score: 133
Period size: 50 Copynumber: 3.1 Consensus size: 50
52074581 TGCATCGCTA
*
52074591 GGGAAGTAACACTCGATGCTGTGTCTTTAGTCTTTTTAACTGCAATGTCG
1 GGGAAGTAACACTCGATGCTGTGGCTTTAGTCTTTTTAACTGCAATGTCG
* * * ** ** * * *
52074641 GGGAAGCAAGA-TACGCCAT-C-GTGGCTTTAATCTGCTCCAGTGC-ATCTCCA
1 GGGAAGTAACACT-CG--ATGCTGTGGCTTTAGTCTTTTTAACTGCAATGT-CG
52074691 GGGAAGTAACACTCG-TCGCTGTGGCTTTAGTCTTTTTAACTGCAATGTCG
1 GGGAAGTAACACTCGAT-GCTGTGGCTTTAGTCTTTTTAACTGCAATGTCG
52074741 GGGAAG
1 GGGAAG
52074747 CAAGATACGC
Statistics
Matches: 76, Mismatches: 21, Indels: 18
0.66 0.18 0.16
Matches are distributed among these distances:
47 1 0.01
49 5 0.07
50 63 0.83
51 5 0.07
52 2 0.03
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (50 bp):
GGGAAGTAACACTCGATGCTGTGGCTTTAGTCTTTTTAACTGCAATGTCG
Found at i:52074671 original size:100 final size:100
Alignment explanation
Indices: 52074526--52075603 Score: 1074
Period size: 100 Copynumber: 10.8 Consensus size: 100
52074516 TTTAATTTGC
** * * * * * * *
52074526 TTAACTGTGATGTTGGGGAAGCAAGATTCGCTGTTGTAGCTTTAATCTGCTCAACTGCATCGCTA
1 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCATCGCCA
* * * *
52074591 GGGAAGTAACACTCGATGCTGT-GTCTTTAGTCTTT
66 GGGAAGTAAGATTCGCTGCTGTAG-CTTTAATCTTT
* * * *
52074626 TTAACTGCAATGTCGGGGAAGCAAGATACGCC-ATCGTGGCTTTAATCTGCTCCAGTGCATCTCC
1 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGAT-GTGGCTTTAATCTGCTCCACTGCATCGCC
* * * *
52074690 AGGGAAGTAACACTCG-TCGCTGTGGCTTTAGTCTTT
65 AGGGAAGTAAGATTCGCT-GCTGTAGCTTTAATCTTT
* * ** * *
52074726 TTAACTGCAATGTCGGGGAAGCAAGATACGCCG-TCGTGGCCATAATCTGCTCGACTGCATTGCC
1 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGAT-GTGGCTTTAATCTGCTCCACTGCATCGCC
* * * * * *
52074790 AAGGAAGTAACACTCGCCGCTGTGGCTTTAGTCTTTT
65 AGGGAAGTAAGATTCGCTGCTGTAGCTTTAATC-TTT
* * * * ** * *
52074827 TTAATTGCAATTTTGGGGAAGCAAGATACGTCG-TCGTGGCTTTAATCTGCTCTACTGTATCGCC
1 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGAT-GTGGCTTTAATCTGCTCCACTGCATCGCC
* * *
52074891 AGGGAAGTAAGATTCGCTGATGTGGTTTTAATCTTT
65 AGGGAAGTAAGATTCGCTGCTGTAGCTTTAATCTTT
* * * *
52074927 TTAACTGCAATGTCAGGAAAGCGAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCACCGCCA
1 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCATCGCCA
* * * * *
52074992 GGGAAGTAGGATTCGCCGCTATGGCTTTAGTCTTT
66 GGGAAGTAAGATTCGCTGCTGTAGCTTTAATCTTT
* * * * * * ** *
52075027 TAAACTGCAATGTC-GAGAAGCAAGATACGCCG-TCGTGGCCTTAATTTGCTCCACTGCGCCACC
1 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGAT-GTGGCTTTAATCTGCTCCACTGCATCGCC
* * * * *
52075090 AGGGAAGT-AGCACTCGCCGCTATGGCTTTAGTCTTT
65 AGGGAAGTAAG-ATTCGCTGCTGTAGCTTTAATCTTT
* * * *
52075126 TTAACAGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCACCGCCT
1 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCATCGCCA
* * *
52075191 GGGGAGTAAGATTCGTTGTTGTAGCTTTAATCTTT
66 GGGAAGTAAGATTCGCTGCTGTAGCTTTAATCTTT
* ** * * * **
52075226 TTAACTGCAATGTCGGGGAAACAAGATTCACCGATGTGGCTTTAATCTATTCCACTACACCACTT
1 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCATCGCCA
* * *
52075291 GGGGAGTAAGATTCGTTGTTGTAGCTTTAATCTTT
66 GGGAAGTAAGATTCGCTGCTGTAGCTTTAATCTTT
* * *
52075326 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCCACTGCATCACCT
1 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCATCGCCA
* * *
52075391 GGGGAGTAAGATTCACTGTTGTAGCTTTAATCTTT
66 GGGAAGTAAGATTCGCTGCTGTAGCTTTAATCTTT
* * * * * * *
52075426 TTAACTGCAATGTCGAGGAAGAAATATTCACCGATGTGGTTTTAATCTGTTCCACTGCATTGCCT
1 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCATCGCCA
* * *
52075491 GGGGAGTAAGATTCGTTGTTGTAGCTTTAATCTTT
66 GGGAAGTAAGATTCGCTGCTGTAGCTTTAATCTTT
** * *
52075526 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTATTCCACTGCATCACCT
1 TTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCATCGCCA
*
52075591 GTGAAGTAAGATT
66 GGGAAGTAAGATT
52075604 TGAAATTCTT
Statistics
Matches: 852, Mismatches: 114, Indels: 24
0.86 0.12 0.02
Matches are distributed among these distances:
98 2 0.00
99 84 0.10
100 677 0.79
101 89 0.10
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.31
Consensus pattern (100 bp):
TTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGCTCCACTGCATCGCCA
GGGAAGTAAGATTCGCTGCTGTAGCTTTAATCTTT
Found at i:52075583 original size:50 final size:50
Alignment explanation
Indices: 52074610--52075584 Score: 434
Period size: 50 Copynumber: 19.5 Consensus size: 50
52074600 CACTCGATGC
* * * * *
52074610 TGTGTCTTTAGTCTTTTTAACTGCAATGTCGGGGAAGCAAGATACGCC-A
1 TGTGGCTTTAATCTTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
** * * * * * * * ** *
52074659 TCGTGGCTTTAATCTGCTCCAGTGC-ATCTCCAGGGAAGTAACACTCGTCGC
1 T-GTGGCTTTAATCTTTTCAACTGCAATGT-CGGGGAAGCAAGATTCACCGA
* * * *
52074710 TGTGGCTTTAGTCTTTTTAACTGCAATGTCGGGGAAGCAAGATACGCCG-
1 TGTGGCTTTAATCTTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
** ** * * * ** * * * * *
52074759 TCGTGGCCATAATCTGCTCGACTGCATTGCCAAGGAAGTAACACTCGCCGC
1 T-GTGGCTTTAATCTTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
* * * * * * **
52074810 TGTGGCTTTAGTCTTTTTTAATTGCAATTTTGGGGAAGCAAGATACGTCG-
1 TGTGGCTTTAATC-TTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
** * * * * * * *
52074860 TCGTGGCTTTAATCTGCTCTACTG-TATCGCCAGGGAAGTAAGATTCGCTGA
1 T-GTGGCTTTAATCTTTTCAACTGCAAT-GTCGGGGAAGCAAGATTCACCGA
* * * * *
52074911 TGTGGTTTTAATCTTTTTAACTGCAATGTCAGGAAAGCGAGATTCACCGA
1 TGTGGCTTTAATCTTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
** * ** * * * * * *
52074961 TGTGGCTTTAATCTGCTCCACTGCACCGCCAGGGAAGTAGGATTCGCCGC
1 TGTGGCTTTAATCTTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
* * * * * *
52075011 TATGGCTTTAGTCTTTTAAACTGCAATGTC-GAGAAGCAAGATACGCCG-
1 TGTGGCTTTAATCTTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
* * * ***** * * * * *
52075059 TCGTGGCCTTAAT-TTGCTCCACTGCGCCACCAGGGAAG-TAGCACTCGCCGC
1 T-GTGGCTTTAATCTT-TTCAACTGCAATGTCGGGGAAGCAAG-ATTCACCGA
* * * *
52075110 TATGGCTTTAGTCTTTTTAACAGCAATGTCGGGGAAGCAAGATTCACCGA
1 TGTGGCTTTAATCTTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
* * ** * * *** *
52075160 TGTGGCTTTAATCTGTTCCACTGCACCGCCTGGGG-AGTAAGATTCGTTGT
1 TGTGGCTTTAATCTTTTCAACTGCAATGTC-GGGGAAGCAAGATTCACCGA
* * *
52075210 TGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAACAAGATTCACCGA
1 TGTGGCTTTAATCTTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
* * * * *** *
52075260 TGTGGCTTTAATCTATTCCACTACACCACT-T-GGGG-AGTAAGATTCGTTGT
1 TGTGGCTTTAATCTTTTCAACTGCA--A-TGTCGGGGAAGCAAGATTCACCGA
* *
52075310 TGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGA
1 TGTGGCTTTAATCTTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
* * ** * * *
52075360 TGTGGCTTTAATCTGTTCCACTGC-ATCACCTGGGG-AGTAAGATTCACTGT
1 TGTGGCTTTAATCTTTTCAACTGCAAT-GTC-GGGGAAGCAAGATTCACCGA
* * * * *
52075410 TGTAGCTTTAATCTTTTTAACTGCAATGTCGAGGAAGAAATATTCACCGA
1 TGTGGCTTTAATCTTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
* * * * * * *** *
52075460 TGTGGTTTTAATCTGTTCCACTGCATTGCCTGGGG-AGTAAGATTCGTTGT
1 TGTGGCTTTAATCTTTTCAACTGCAATGTC-GGGGAAGCAAGATTCACCGA
* *
52075510 TGTAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGA
1 TGTGGCTTTAATCTTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
* *
52075560 TGTGGCTTTAATCTATTCCACTGCA
1 TGTGGCTTTAATCTTTTCAACTGCA
52075585 TCACCTGTGA
Statistics
Matches: 648, Mismatches: 246, Indels: 63
0.68 0.26 0.07
Matches are distributed among these distances:
47 1 0.00
48 5 0.01
49 55 0.08
50 523 0.81
51 61 0.09
52 2 0.00
53 1 0.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (50 bp):
TGTGGCTTTAATCTTTTCAACTGCAATGTCGGGGAAGCAAGATTCACCGA
Found at i:52075748 original size:44 final size:44
Alignment explanation
Indices: 52075626--52075996 Score: 201
Period size: 44 Copynumber: 8.5 Consensus size: 44
52075616 GTCTATGCAC
* * * * * *
52075626 CTGTAATCTCAGGGAGATAAGA--CCT-GATGCTATCTACTCTA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCGA
* * * * * *
52075667 CTGTAATTTCAGAGAGATAAGATCATTTA-TTTTAATCTGCTCGA
1 CTGTAATCTCAGGGAGATAAGATTA-CTAGCTTCAATCTGCTCGA
* * *
52075711 CTGTAATCTCAGGGAAATAGGATTACTGGCTTCAATCTGCTCCG-
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCT-CGA
* * *
52075755 TTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATCTGCTCCA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCGA
* * * ** *
52075799 CTGTAACCTCAGGGAGATAAGATTTGA-AATTCTTCAATCTATTCCA
1 CTGTAATCTCAGGGAGATAAGA-TT-ACTA-GCTTCAATCTGCTCGA
* * * * * * *
52075845 CTGTAATCTCAAGGAGATAAGA--CCT-GATGCTATCTACTCTA
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCGA
* * * * * *
52075886 CTGTAA-CTTCAGAGAGATAAAATCCT-TTA-TTTTAATCTGCTCCA
1 CTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTCAATCTGCTCGA
* * *
52075930 CTGTAATCTCAAGGAGATAGGATTACTAGCTTTAATCTGCTCCG-
1 CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCT-CGA
*
52075974 CTGTAATCTCAGGGATATAAGAT
1 CTGTAATCTCAGGGAGATAAGAT
52075997 CTGAAATTCT
Statistics
Matches: 247, Mismatches: 62, Indels: 39
0.71 0.18 0.11
Matches are distributed among these distances:
40 1 0.00
41 47 0.19
42 1 0.00
43 4 0.02
44 154 0.62
45 7 0.03
46 33 0.13
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (44 bp):
CTGTAATCTCAGGGAGATAAGATTACTAGCTTCAATCTGCTCGA
Found at i:52075955 original size:219 final size:219
Alignment explanation
Indices: 52075597--52075996 Score: 658
Period size: 219 Copynumber: 1.8 Consensus size: 219
52075587 ACCTGTGAAG
** * *
52075597 TAAGATTTGAAATTCTTCGGTCTATGCACCTGTAATCTCAGGGAGATAAGACCTGATGCTATCTA
1 TAAGATTTGAAATTCTTCAATCTATCCACCTGTAATCTCAAGGAGATAAGACCTGATGCTATCTA
* * * *
52075662 CTCTACTGTAATTTCAGAGAGATAAGATCATTTATTTTAATCTGCTCGACTGTAATCTCAGGGAA
66 CTCTACTGTAACTTCAGAGAGATAAAATCATTTATTTTAATCTGCTCCACTGTAATCTCAAGGAA
* *
52075727 ATAGGATTACTGGCTTCAATCTGCTCCGTTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATC
131 ATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATC
52075792 TGCTCCACTGTAACCTCAGGGAGA
196 TGCTCCACTGTAACCTCAGGGAGA
52075816 TAAGATTTGAAATTCTTCAATCTATTCCA-CTGTAATCTCAAGGAGATAAGACCTGATGCTATCT
1 TAAGATTTGAAATTCTTCAATCTA-TCCACCTGTAATCTCAAGGAGATAAGACCTGATGCTATCT
*
52075880 ACTCTACTGTAACTTCAGAGAGATAAAATCCTTTATTTTAATCTGCTCCACTGTAATCTCAAGGA
65 ACTCTACTGTAACTTCAGAGAGATAAAATCATTTATTTTAATCTGCTCCACTGTAATCTCAAGGA
* * *
52075945 GATAGGATTACTAGCTTTAATCTGCTCCGCTGTAATCTCAGGGATATAAGAT
130 AATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT
52075997 CTGAAATTCT
Statistics
Matches: 166, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
219 163 0.98
220 3 0.02
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (219 bp):
TAAGATTTGAAATTCTTCAATCTATCCACCTGTAATCTCAAGGAGATAAGACCTGATGCTATCTA
CTCTACTGTAACTTCAGAGAGATAAAATCATTTATTTTAATCTGCTCCACTGTAATCTCAAGGAA
ATAGGATTACTAGCTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAAGATTTCTAGCTTCAATC
TGCTCCACTGTAACCTCAGGGAGA
Found at i:52077373 original size:13 final size:14
Alignment explanation
Indices: 52077355--52077387 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
52077345 TTAGCCTCTC
52077355 CATTTTAC-TTTTT
1 CATTTTACATTTTT
*
52077368 CATTTTTCATTTTT
1 CATTTTACATTTTT
52077382 CATTTT
1 CATTTT
52077388 TCCATTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (14 bp):
CATTTTACATTTTT
Found at i:52077381 original size:8 final size:7
Alignment explanation
Indices: 52077363--52077396 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
52077353 TCCATTTTAC
52077363 TTTTTCA
1 TTTTTCA
52077370 TTTTTCA
1 TTTTTCA
52077377 TTTTTCA
1 TTTTTCA
52077384 TTTTTCCA
1 TTTTT-CA
52077392 TTTTT
1 TTTTT
52077397 TTGACTAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTTCA
Found at i:52078294 original size:30 final size:31
Alignment explanation
Indices: 52078251--52078309 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
52078241 CTCTTTTCTC
52078251 TTTTTCATATTTTA-TTTTAACTTTGATTGA
1 TTTTTCATATTTTACTTTTAACTTTGATTGA
* * *
52078281 TTTTTCCTTTTTTACTTTTGACTTTGATT
1 TTTTTCATATTTTACTTTTAACTTTGATT
52078310 TTTTTTTTGG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.17, C:0.10, G:0.07, T:0.66
Consensus pattern (31 bp):
TTTTTCATATTTTACTTTTAACTTTGATTGA
Found at i:52086450 original size:8 final size:8
Alignment explanation
Indices: 52086437--52086465 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
52086427 TTTTAAATGA
52086437 TATTTTAT
1 TATTTTAT
52086445 TATTTTAT
1 TATTTTAT
52086453 TATTTTAT
1 TATTTTAT
52086461 TATTT
1 TATTT
52086466 AGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:52089783 original size:28 final size:28
Alignment explanation
Indices: 52089727--52089798 Score: 128
Period size: 28 Copynumber: 2.6 Consensus size: 28
52089717 AAGGCCTTAG
*
52089727 TGTAATATAAATATT-TTTGAAAATAAT
1 TGTAATATAAATATTAATTGAAAATAAT
52089754 TGTAATATAAATATTAATTGAAAATAAT
1 TGTAATATAAATATTAATTGAAAATAAT
52089782 TGTAATATAAATATTAA
1 TGTAATATAAATATTAA
52089799 GTGATTACAG
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
27 15 0.35
28 28 0.65
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (28 bp):
TGTAATATAAATATTAATTGAAAATAAT
Found at i:52090177 original size:6 final size:6
Alignment explanation
Indices: 52090166--52090198 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
52090156 GGATTGTACA
52090166 AAAAAT AAAAAT -AAAAT AAAAAT AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
52090199 CATATATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:52090183 original size:11 final size:12
Alignment explanation
Indices: 52090166--52090198 Score: 59
Period size: 11 Copynumber: 2.8 Consensus size: 12
52090156 GGATTGTACA
52090166 AAAAATAAAAAT
1 AAAAATAAAAAT
52090178 -AAAATAAAAAT
1 AAAAATAAAAAT
52090189 AAAAATAAAA
1 AAAAATAAAA
52090199 CATATATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAAATAAAAAT
Found at i:52090188 original size:17 final size:17
Alignment explanation
Indices: 52090166--52090198 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
52090156 GGATTGTACA
52090166 AAAAATAAAAATAAAAT
1 AAAAATAAAAATAAAAT
52090183 AAAAATAAAAATAAAA
1 AAAAATAAAAATAAAA
52090199 CATATATATT
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAATAAAAATAAAAT
Found at i:52098356 original size:32 final size:32
Alignment explanation
Indices: 52098310--52098511 Score: 125
Period size: 33 Copynumber: 5.6 Consensus size: 32
52098300 TCCTCCAAGG
52098310 GGTTGCTAAGTGCTGATTCCCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCCCGAATCATTGGT
* * *
52098342 GGTTGCTAAATGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATT-C-CCGAATC----AT-TG---GT
*
52098384 GGTTGCTAAGTACTGATTCCTCGAATCATTGGT
1 GGTTGCTAAGTGCTGATTCC-CGAATCATTGGT
* * *
52098417 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGAT-TC-CCGAATC----AT-TG---GT
* *
52098459 GGTTGCTAAGTGATGATTCCCCTAATCATTGGT
1 GGTTGCTAAGTGCTGATT-CCCGAATCATTGGT
52098492 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
52098512 ACCGTATCTT
Statistics
Matches: 131, Mismatches: 17, Indels: 44
0.68 0.09 0.23
Matches are distributed among these distances:
32 19 0.15
33 36 0.27
34 12 0.09
35 1 0.01
36 4 0.03
37 4 0.03
38 4 0.03
39 4 0.03
40 1 0.01
41 11 0.08
42 35 0.27
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (32 bp):
GGTTGCTAAGTGCTGATTCCCGAATCATTGGT
Found at i:52098401 original size:42 final size:41
Alignment explanation
Indices: 52098342--52098554 Score: 181
Period size: 33 Copynumber: 5.5 Consensus size: 41
52098332 AATCATTGGT
*
52098342 GGTTGCTAAATGCTGATTCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTT-AATGTGAAAGG
* * * *
52098384 GGTTGCTAAGTACTGATTCC-TCGAATC---AT-TG---GT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAATGTGAAAGG
*
52098417 GGTTGCTAAGTGCTGATCCCACCGTATCTTAAATGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTT-AATGTGAAAGG
* *
52098459 GGTTGCTAAGTGATGATTCC-CC-TAATC---AT-TG---GT
1 GGTTGCTAAGTGCTGATTCCACCGT-ATCTTAATGTGAAAGG
*
52098492 GGTTGCTAAGTGCTGATTCCACCGTATCTTTGAATGTGAAATG
1 GGTTGCTAAGTGCTGATTCCACCGTATC-TT-AATGTGAAAGG
52098535 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
52098555 CCGAATCACT
Statistics
Matches: 134, Mismatches: 16, Indels: 41
0.70 0.08 0.21
Matches are distributed among these distances:
33 39 0.29
34 10 0.07
35 1 0.01
36 4 0.03
37 4 0.03
38 2 0.01
39 4 0.03
40 3 0.02
41 10 0.07
42 37 0.28
43 20 0.15
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAATGTGAAAGG
Found at i:52098568 original size:76 final size:75
Alignment explanation
Indices: 52098306--52098591 Score: 457
Period size: 75 Copynumber: 3.8 Consensus size: 75
52098296 TGATTCCTCC
*
52098306 AAGGGGTTGCTAAGTGCTGATT-CCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
52098370 TTAAATGTGA
66 TTAAATGTGA
* * *
52098380 AAGGGGTTGCTAAGTACTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
52098445 TTAAATGTGA
66 TTAAATGTGA
* *
52098455 AAGGGGTTGCTAAGTGATGATTCCCCTAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
*
52098520 TTTGAATGTGA
66 -TTAAATGTGA
* * * *
52098531 AATGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTGTTGAATCCACCG
1 AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCG
52098592 ATAACGGGTA
Statistics
Matches: 194, Mismatches: 16, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
74 21 0.11
75 109 0.56
76 64 0.33
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (75 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
TTAAATGTGA
Found at i:52098591 original size:151 final size:149
Alignment explanation
Indices: 52098306--52098579 Score: 458
Period size: 151 Copynumber: 1.8 Consensus size: 149
52098296 TGATTCCTCC
*
52098306 AAGGGGTTGCTAAGTGCTGATTCCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCGTATCT
1 AAGGGGTTGCTAAGTGATGATTCCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCGTATCT
* *
52098371 TAAATGTGAAAGGGGTTGCTAAGTACTGATTCCTCGAATCATTGGTGGTTGCTAAGTGCTGATCC
66 TAAATGTGAAAGGGGTTGCTAAGTACTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATCC
52098436 CACCGTATCTTAAATGTGA
131 CACCGTATCTTAAATGTGA
* *
52098455 AAGGGGTTGCTAAGTGATGATTCCCCTAATCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATC
1 AAGGGGTTGCTAAGTGATGATT-CCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCGTATC
* * *
52098520 TTTGAATGTGAAATGGGTTGCTAAGTGCTGATTCCCCGAATCACTGGTGGTTGCTAAGTG
65 -TTAAATGTGAAAGGGGTTGCTAAGTACTGATTCCCCGAATCACTGGTGGTTGCTAAGTG
52098580 TTGAATCCAC
Statistics
Matches: 115, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
149 21 0.18
150 40 0.35
151 54 0.47
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.32
Consensus pattern (149 bp):
AAGGGGTTGCTAAGTGATGATTCCCGAATCATTGGTGGTTGCTAAATGCTGATTCCACCGTATCT
TAAATGTGAAAGGGGTTGCTAAGTACTGATTCCCCGAATCACTGGTGGTTGCTAAGTGCTGATCC
CACCGTATCTTAAATGTGA
Found at i:52100145 original size:11 final size:11
Alignment explanation
Indices: 52100129--52100153 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
52100119 GTGCTCTTTC
52100129 TTCCTCATTCT
1 TTCCTCATTCT
52100140 TTCCTCATTCT
1 TTCCTCATTCT
52100151 TTC
1 TTC
52100154 TTCTATTCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.36, G:0.00, T:0.56
Consensus pattern (11 bp):
TTCCTCATTCT
Found at i:52105466 original size:29 final size:30
Alignment explanation
Indices: 52105416--52105490 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 30
52105406 TGAAAGTTAT
* * *
52105416 AAAAATTATTAGATTTTAATAAAAAACTATAA
1 AAAAATTA-TAAAATTT-ATAAAAAACTAGAA
* *
52105448 AAATATT-TAAAATTTATAAAAAATTAGAA
1 AAAAATTATAAAATTTATAAAAAACTAGAA
52105477 AAAAATTATAAAAT
1 AAAAATTATAAAAT
52105491 CGTAAAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
29 18 0.50
30 12 0.33
32 6 0.17
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (30 bp):
AAAAATTATAAAATTTATAAAAAACTAGAA
Found at i:52105469 original size:10 final size:10
Alignment explanation
Indices: 52105412--52105559 Score: 60
Period size: 10 Copynumber: 14.9 Consensus size: 10
52105402 TTACTGAAAG
52105412 TTATAAAAA-
1 TTATAAAAAT
* * *
52105421 TTATTAGATT
1 TTATAAAAAT
*
52105431 TTAATAAAAAA
1 TT-ATAAAAAT
*
52105442 CTATAAAAAT
1 TTATAAAAAT
52105452 ATT-T-AAAAT
1 -TTATAAAAAT
*
52105461 TTATAAAAAA
1 TTATAAAAAT
* *
52105471 TTAGAAAAAAA
1 TTA-TAAAAAT
52105482 TTAT-AAAA-
1 TTATAAAAAT
**
52105490 TCGTAAAAAT
1 TTATAAAAAT
*
52105500 ATATAAAAAT
1 TTATAAAAAT
*
52105510 TTAGAAAAAAAT
1 TT--ATAAAAAT
*
52105522 ATATAAAAAT
1 TTATAAAAAT
52105532 TTAT-AAAAT
1 TTATAAAAAT
52105541 TGTA-AGAAAA-
1 T-TATA-AAAAT
52105551 TTATAAAAA
1 TTATAAAAA
52105560 ATGTAAAGAA
Statistics
Matches: 102, Mismatches: 23, Indels: 28
0.67 0.15 0.18
Matches are distributed among these distances:
8 4 0.04
9 32 0.31
10 39 0.38
11 19 0.19
12 8 0.08
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.32
Consensus pattern (10 bp):
TTATAAAAAT
Found at i:52105519 original size:50 final size:49
Alignment explanation
Indices: 52105445--52105577 Score: 130
Period size: 50 Copynumber: 2.7 Consensus size: 49
52105435 TAAAAAACTA
* *
52105445 TAAAAATAT-TTAAAATTTATAAAAAAT-TAGAAAAAAATTATAAAATCG
1 TAAAAATATATAAAAATTTAAAAAAAATATA-AAAAAAATTATAAAATCG
* * *
52105493 TAAAAATATATAAAAATTTAGAAAAAAATATATAAAAATTTATAAAATTG
1 TAAAAATATATAAAAATTTA-AAAAAAATATAAAAAAAATTATAAAATCG
* *
52105543 TAAGAAA-ATTATAAAAAATGT-AAAGAAATATAAAA
1 TAA-AAATA-TAT-AAAAATTTAAAAAAAATATAAAA
52105578 TCCATAAAAA
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
48 9 0.13
49 9 0.13
50 38 0.54
51 8 0.11
52 7 0.10
ACGTcount: A:0.65, C:0.01, G:0.05, T:0.29
Consensus pattern (49 bp):
TAAAAATATATAAAAATTTAAAAAAAATATAAAAAAAATTATAAAATCG
Found at i:52105522 original size:22 final size:22
Alignment explanation
Indices: 52105456--52105539 Score: 88
Period size: 22 Copynumber: 4.0 Consensus size: 22
52105446 AAAAATATTT
* *
52105456 AAAATTTATAAAAAATTAGAAA
1 AAAATATATAAAAATTTAGAAA
* *
52105478 AAAAT-TAT-AAAA--TCG-TA
1 AAAATATATAAAAATTTAGAAA
52105495 AAAATATATAAAAATTTAGAAA
1 AAAATATATAAAAATTTAGAAA
*
52105517 AAAATATATAAAAATTTATAAA
1 AAAATATATAAAAATTTAGAAA
52105539 A
1 A
52105540 TTGTAAGAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
17 6 0.12
18 5 0.10
19 4 0.08
20 4 0.08
21 5 0.10
22 28 0.54
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.29
Consensus pattern (22 bp):
AAAATATATAAAAATTTAGAAA
Found at i:52105571 original size:10 final size:9
Alignment explanation
Indices: 52105434--52105595 Score: 65
Period size: 10 Copynumber: 16.7 Consensus size: 9
52105424 TTAGATTTTA
52105434 ATAAAAAACT
1 ATAAAAAA-T
52105444 ATAAAAATAT
1 ATAAAAA-AT
* **
52105454 TTAAAATTT
1 ATAAAAAAT
52105463 ATAAAAAAT
1 ATAAAAAAT
*
52105472 -TAGAAAAAA
1 ATA-AAAAAT
*
52105481 ATTATAAAAT
1 A-TAAAAAAT
*
52105491 CGTAAAAATAT
1 -ATAAAAA-AT
*
52105502 ATAAAAATTT
1 ATAAAAA-AT
*
52105512 AGAAAAAAAT
1 A-TAAAAAAT
52105522 ATATAAAAAT
1 ATA-AAAAAT
* *
52105532 TTATAAAATT
1 ATA-AAAAAT
*
52105542 GTAAGAAAATT
1 ATAA-AAAA-T
52105553 ATAAAAAAT
1 ATAAAAAAT
*
52105562 GTAAAGAAAT
1 ATAAA-AAAT
***
52105572 ATAAAATCC
1 ATAAAAAAT
52105581 ATAAAAAAT
1 ATAAAAAAT
52105590 ATAAAA
1 ATAAAA
52105596 CTTATCGTTT
Statistics
Matches: 112, Mismatches: 29, Indels: 23
0.68 0.18 0.14
Matches are distributed among these distances:
8 2 0.02
9 32 0.29
10 64 0.57
11 14 0.12
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.28
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:52105835 original size:21 final size:21
Alignment explanation
Indices: 52105791--52105846 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
52105781 TTTTATGATT
* *
52105791 TTTAGAATTTTTA-ATAAATT
1 TTTAAAATTTTTATATAAATA
*
52105811 TTTAAAATTTTTATATTAATA
1 TTTAAAATTTTTATATAAATA
*
52105832 TTTAATATTTTTATA
1 TTTAAAATTTTTATA
52105847 ACTTTTATTG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 12 0.39
21 19 0.61
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTAAAATTTTTATATAAATA
Found at i:52106223 original size:90 final size:89
Alignment explanation
Indices: 52105963--52106244 Score: 320
Period size: 90 Copynumber: 3.1 Consensus size: 89
52105953 TTAACGGTTA
* * * *
52105963 AAGGACCTTTTTGATGCA-TTT-AATAGTTCAAGTATCCAATTAAGTGCAAAAAAAAATTAAAGG
1 AAGGA-CTTTTTGATGCATTTTGAA-AGTTCAAGTACCCAATTGAGTG-AAAAAAAAAGT-AGGG
* *
52106026 GCTTAATTGCTTTTTCTGAAAAGAGTTTG
62 GCTTAATTGCTTTTTTTTAAAA-AGTTTG
* * *
52106055 AAGGACTTTTTGATGCATTTCGAAAGTTCAAGTACCCAATTGAGTGAAAAAAATAAGCAGTGGCT
1 AAGGACTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAA-AAGTAGGGGCT
**
52106120 TAATTGGATTTTTTTAAAAAGTTTG
65 TAATTGCTTTTTTTTAAAAAGTTTG
* * *
52106145 AGGGTCTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGTAAAAAAAA-TAGGGGCTT
1 AAGGACTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGTAGGGGCTT
* *
52106209 AATTGCTTCCTTTTTTTAAATGTTTG
66 AATTGCTT--TTTTTTAAAAAGTTTG
52106235 AA-GACTTTTT
1 AAGGACTTTTT
52106245 ACATCCTTAA
Statistics
Matches: 162, Mismatches: 23, Indels: 13
0.82 0.12 0.07
Matches are distributed among these distances:
88 13 0.08
89 9 0.06
90 70 0.43
91 39 0.24
92 29 0.18
93 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.19, T:0.37
Consensus pattern (89 bp):
AAGGACTTTTTGATGCATTTTGAAAGTTCAAGTACCCAATTGAGTGAAAAAAAAAGTAGGGGCTT
AATTGCTTTTTTTTAAAAAGTTTG
Found at i:52106801 original size:18 final size:18
Alignment explanation
Indices: 52106780--52106823 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
52106770 TTTTTAACTA
52106780 ATAATTATAAATTAAAT-T
1 ATAATTAT-AATTAAATGT
**
52106798 ATAATTATTTTTAAATGT
1 ATAATTATAATTAAATGT
52106816 ATAATTAT
1 ATAATTAT
52106824 CACAACTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 6 0.26
18 17 0.74
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
ATAATTATAATTAAATGT
Found at i:52108041 original size:28 final size:28
Alignment explanation
Indices: 52108008--52108065 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
52107998 GTAATTAAAA
52108008 TCAATCATATAAATGAAGAAAAAAATTG
1 TCAATCATATAAATGAAGAAAAAAATTG
52108036 TCAATCATATAAATGAAGAAAAAAATTG
1 TCAATCATATAAATGAAGAAAAAAATTG
52108064 TC
1 TC
52108066 TTATAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.26
Consensus pattern (28 bp):
TCAATCATATAAATGAAGAAAAAAATTG
Found at i:52108840 original size:40 final size:40
Alignment explanation
Indices: 52108766--52108845 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 40
52108756 TAAACAATTC
* *
52108766 AATAATATAAATAGTACAAAATGTGAAATATATTACTATT
1 AATAATATAAATAGTACAAAATATAAAATATATTACTATT
*
52108806 AATAATATAAATAGTAGATATAA-ATAAAAT-TATTACTATT
1 AATAATATAAATAGTACA-A-AATATAAAATATATTACTATT
52108846 TAGGTTTAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 27 0.77
41 6 0.17
42 2 0.06
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.36
Consensus pattern (40 bp):
AATAATATAAATAGTACAAAATATAAAATATATTACTATT
Found at i:52109005 original size:76 final size:76
Alignment explanation
Indices: 52108904--52109045 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 76
52108894 AAGGGTGAGA
* * *
52108904 AGTAAAAGTTTAAGGGAAAAATAAAAAGTTTTGGGGGTTTTTAGGGGAGTAAAATTTT-AGGAGA
1 AGTAAAAGTTTAAGGGAAAAATAAAAAGTTTTGAGGGTTTTTAAGAGAGTAAAATTTTGAGG-GA
52108968 AAAGCGGAAGAG
65 AAAGCGGAAGAG
** * *
52108980 AGTAAAAGTTTTGGGGGAAATTAAAAAGTTTTGAGGGTTTTTAAGAGAGTAAAATTTTGAGGGAA
1 AGTAAAAGTTTAAGGGAAAAATAAAAAGTTTTGAGGGTTTTTAAGAGAGTAAAATTTTGAGGGAA
52109045 A
66 A
52109046 GGTAATGGAA
Statistics
Matches: 58, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
76 55 0.95
77 3 0.05
ACGTcount: A:0.41, C:0.01, G:0.30, T:0.28
Consensus pattern (76 bp):
AGTAAAAGTTTAAGGGAAAAATAAAAAGTTTTGAGGGTTTTTAAGAGAGTAAAATTTTGAGGGAA
AAGCGGAAGAG
Found at i:52109068 original size:76 final size:78
Alignment explanation
Indices: 52108904--52109078 Score: 195
Period size: 76 Copynumber: 2.3 Consensus size: 78
52108894 AAGGGTGAGA
* * * * * *
52108904 AGTAAAAG-TTT-AAGGGAAAAATAAAAAGTTTTGGGGGTTTTTAGGGGAGTAAAATTTTAGGAG
1 AGTAAAAGTTTTGGAGGGGAAATTAAAAAGTTTTGAGGGTTTTTAAGAGAGTAAAATTTTAGGAG
52108967 AAAAGCGGAAGAG
66 AAAAGCGGAAGAG
52108980 AGTAAAAGTTTT-G-GGGGAAATTAAAAAGTTTTGAGGGTTTTTAAGAGAGTAAAATTTTGAGG-
1 AGTAAAAGTTTTGGAGGGGAAATTAAAAAGTTTTGAGGGTTTTTAAGAGAGTAAAATTTT-AGGA
*
52109042 G-AAAG-GTAATGGAAG
65 GAAAAGCGGAA--G-AG
52109057 AGTAAAA-TTTTGGAGGGGAAAT
1 AGTAAAAGTTTTGGAGGGGAAAT
52109079 ATTAAAAAAA
Statistics
Matches: 85, Mismatches: 7, Indels: 12
0.82 0.07 0.12
Matches are distributed among these distances:
74 3 0.04
75 4 0.05
76 54 0.64
77 16 0.19
78 8 0.09
ACGTcount: A:0.41, C:0.01, G:0.31, T:0.27
Consensus pattern (78 bp):
AGTAAAAGTTTTGGAGGGGAAATTAAAAAGTTTTGAGGGTTTTTAAGAGAGTAAAATTTTAGGAG
AAAAGCGGAAGAG
Found at i:52111655 original size:9 final size:9
Alignment explanation
Indices: 52111641--52111668 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
52111631 CTTTAGTCAA
52111641 CACATTGTC
1 CACATTGTC
52111650 CACATTGTC
1 CACATTGTC
52111659 CACATTGTC
1 CACATTGTC
52111668 C
1 C
52111669 TTAATGTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.36, G:0.11, T:0.32
Consensus pattern (9 bp):
CACATTGTC
Found at i:52119016 original size:48 final size:48
Alignment explanation
Indices: 52118936--52119093 Score: 219
Period size: 48 Copynumber: 3.3 Consensus size: 48
52118926 AGGAAGGATA
* *
52118936 TGAAAAGAGTAAGTTAATATGACTCT-CTATGTGATATATGTTATGTAC
1 TGAAATGAGTAAGTTAATATGACTCTGC-ATGTGATATATGTTATGTAT
* *
52118984 TGAAATGAGTAAGTTAATATGACCCTGCATGTGATATCTGTTATGTAT
1 TGAAATGAGTAAGTTAATATGACTCTGCATGTGATATATGTTATGTAT
* * * *
52119032 TGAAATGAGTAAGTTAAAATAACTTTGTATGTGATATATGTTATGTAT
1 TGAAATGAGTAAGTTAATATGACTCTGCATGTGATATATGTTATGTAT
*
52119080 TGAAATAAGTAAGT
1 TGAAATGAGTAAGT
52119094 GATAACTCCT
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
48 97 0.99
49 1 0.01
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (48 bp):
TGAAATGAGTAAGTTAATATGACTCTGCATGTGATATATGTTATGTAT
Found at i:52152348 original size:38 final size:37
Alignment explanation
Indices: 52152279--52152351 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
52152269 TTTTCATAAT
* *
52152279 TTCACTTTTTCACTTTTAATCACTATTCAATTCAAAA
1 TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
52152316 TTCACTTTTCCA-TTTTCAAGTCAATATTCAATTCAA
1 TTCACTTTTCCACTTTT-AA-TCAATATTCAATTCAA
52152352 TTCCACACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.45
Consensus pattern (37 bp):
TTCACTTTTCCACTTTTAATCAATATTCAATTCAAAA
Found at i:52152382 original size:23 final size:22
Alignment explanation
Indices: 52152339--52152382 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
52152329 TTTCAAGTCA
52152339 ATATTCAATTCAATTCCACACAT
1 ATATTCAATTCAATT-CACACAT
52152362 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
52152383 TTAATCGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.39, C:0.23, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACAT
Found at i:52152507 original size:23 final size:23
Alignment explanation
Indices: 52152481--52152602 Score: 199
Period size: 23 Copynumber: 5.3 Consensus size: 23
52152471 ATAAGTGTCA
52152481 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
52152504 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
52152527 CACTGATATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
52152550 CACTGAAATGTAGCCGAATCTAC
1 CACTGATATGTAGCCGAAGCTAC
52152573 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
52152596 CACTGAT
1 CACTGAT
52152603 CAATAACACT
Statistics
Matches: 89, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 89 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:52160853 original size:15 final size:15
Alignment explanation
Indices: 52160829--52160859 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52160819 TTTATAACAT
*
52160829 GGTATTACCAAATCA
1 GGTATGACCAAATCA
52160844 GGTATGACCAAATCA
1 GGTATGACCAAATCA
52160859 G
1 G
52160860 CTGCAACATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.23
Consensus pattern (15 bp):
GGTATGACCAAATCA
Found at i:52164509 original size:44 final size:44
Alignment explanation
Indices: 52164456--52164545 Score: 180
Period size: 44 Copynumber: 2.0 Consensus size: 44
52164446 AATATGCATT
52164456 AATTGCTTCCTTCTATCGTTAGCTTAGCAAGTAAGAATATTATA
1 AATTGCTTCCTTCTATCGTTAGCTTAGCAAGTAAGAATATTATA
52164500 AATTGCTTCCTTCTATCGTTAGCTTAGCAAGTAAGAATATTATA
1 AATTGCTTCCTTCTATCGTTAGCTTAGCAAGTAAGAATATTATA
52164544 AA
1 AA
52164546 ATGAAAAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (44 bp):
AATTGCTTCCTTCTATCGTTAGCTTAGCAAGTAAGAATATTATA
Found at i:52172799 original size:50 final size:50
Alignment explanation
Indices: 52172722--52172946 Score: 245
Period size: 50 Copynumber: 4.4 Consensus size: 50
52172712 NNNNNNNNNN
** * * *
52172722 GGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCTATGTCCCAGACAT
1 GGTCTTACATGGGACCTCTCATCTCGGTGCCCACGCCATGTCCCAGACAT
* ** *
52172772 GGTCTTGCGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACAT
1 GGTCTTACATGGGACCTCTCATCTCGGTGCCCACGCCATGTCCCAGACAT
*
52172822 GGTCTTACATGGGACCTCTCATCTCGATG-CCAGCGCCATGTCCCAGACAT
1 GGTCTTACATGGGACCTCTCATCTCGGTGCCCA-CGCCATGTCCCAGACAT
* * *
52172872 GGTCTTACATGGGACCTCTCATAATCTCAATGATGCCAATGCCATGTCCCAGACAT
1 GGTCTTACATGGGACCTCTC---ATCTC---GGTGCCCACGCCATGTCCCAGACAT
* *
52172928 GGTCTTAGATGGGATCTCT
1 GGTCTTACATGGGACCTCT
52172947 TTACCCAAAT
Statistics
Matches: 149, Mismatches: 18, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
49 2 0.01
50 103 0.69
53 5 0.03
56 37 0.25
57 2 0.01
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
GGTCTTACATGGGACCTCTCATCTCGGTGCCCACGCCATGTCCCAGACAT
Found at i:52173319 original size:30 final size:29
Alignment explanation
Indices: 52173285--52173354 Score: 72
Period size: 30 Copynumber: 2.4 Consensus size: 29
52173275 CCTTGACTCG
52173285 AACTTTGGAAAAATTACGA-TTTTGCCCCTA
1 AACTTTGGAAAAATTAC-ACTTTTGCCCC-A
* * *
52173315 AACTTTTGCATAATTACACTTTTGCCCCA
1 AACTTTGGAAAAATTACACTTTTGCCCCA
52173344 AAGC-TTGGAAA
1 AA-CTTTGGAAA
52173355 TTAAACTTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
29 8 0.25
30 24 0.75
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (29 bp):
AACTTTGGAAAAATTACACTTTTGCCCCA
Found at i:52177955 original size:2 final size:2
Alignment explanation
Indices: 52177948--52177973 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
52177938 AGAGTGATGT
52177948 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
52177974 GTGGCAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52179432 original size:14 final size:14
Alignment explanation
Indices: 52179412--52179450 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
52179402 TTTAAGGTTA
52179412 ATTTAGGGTTAGAG
1 ATTTAGGGTTAGAG
* *
52179426 GTTTAGGGGTTTGAG
1 ATTTA-GGGTTAGAG
52179441 ATTTAGGGTT
1 ATTTAGGGTT
52179451 TCAACGGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (14 bp):
ATTTAGGGTTAGAG
Found at i:52179451 original size:14 final size:14
Alignment explanation
Indices: 52179385--52179451 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
52179375 TACGGGGTAT
* *
52179385 AGATTTAAGGTTTA
1 AGATTTAGGGTTTG
*
52179399 AGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
52179411 A-ATTTAGGGTTAG
1 AGATTTAGGGTTTG
*
52179424 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
52179439 AGATTTAGGGTTT
1 AGATTTAGGGTTT
52179452 CAACGGTCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
11 7 0.16
12 2 0.05
13 3 0.07
14 20 0.45
15 12 0.27
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:52180767 original size:2 final size:2
Alignment explanation
Indices: 52180762--52180836 Score: 54
Period size: 2 Copynumber: 40.5 Consensus size: 2
52180752 ATATTTTTTG
** **
52180762 AT AT AT AT AT AT GG AT AT AT -T A- AT -T AT AT AT AT AT GG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
**
52180801 AT AT -T A- AT -T AT AT AT AT AT GG AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52180837 GTTATTAATT
Statistics
Matches: 55, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
1 6 0.11
2 49 0.89
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (2 bp):
AT
Found at i:52180791 original size:19 final size:22
Alignment explanation
Indices: 52180762--52180836 Score: 118
Period size: 23 Copynumber: 3.4 Consensus size: 22
52180752 ATATTTTTTG
52180762 ATATATATATATGGATATATTA
1 ATATATATATATGGATATATTA
52180784 ATTATATATATATGGATATATTA
1 A-TATATATATATGGATATATTA
52180807 ATTATATATATATGGATATA-T-
1 A-TATATATATATGGATATATTA
52180828 ATATATATA
1 ATATATATA
52180837 GTTATTAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
20 8 0.15
21 1 0.02
22 2 0.04
23 41 0.79
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (22 bp):
ATATATATATATGGATATATTA
Found at i:52180793 original size:23 final size:23
Alignment explanation
Indices: 52180763--52180827 Score: 130
Period size: 23 Copynumber: 2.8 Consensus size: 23
52180753 TATTTTTTGA
52180763 TATATATATATGGATATATTAAT
1 TATATATATATGGATATATTAAT
52180786 TATATATATATGGATATATTAAT
1 TATATATATATGGATATATTAAT
52180809 TATATATATATGGATATAT
1 TATATATATATGGATATAT
52180828 ATATATATAG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.48
Consensus pattern (23 bp):
TATATATATATGGATATATTAAT
Found at i:52181853 original size:11 final size:11
Alignment explanation
Indices: 52181837--52181863 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
52181827 TTTGTTTAAT
52181837 TTACTTTCATA
1 TTACTTTCATA
52181848 TTACTTTCATA
1 TTACTTTCATA
52181859 TTACT
1 TTACT
52181864 GGTTGAGTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.56
Consensus pattern (11 bp):
TTACTTTCATA
Found at i:52184824 original size:9 final size:9
Alignment explanation
Indices: 52184756--52184858 Score: 60
Period size: 9 Copynumber: 12.0 Consensus size: 9
52184746 ATAATACACA
52184756 ATAACTTAC
1 ATAACTTAC
52184765 --AACTTAC
1 ATAACTTAC
*
52184772 ATAACATAC
1 ATAACTTAC
* *
52184781 AT-ATTTATG
1 ATAACTTA-C
52184790 ATAACTTAC
1 ATAACTTAC
*
52184799 ATAGCTTAC
1 ATAACTTAC
*
52184808 TTAA--TAC
1 ATAACTTAC
*
52184815 ATGACTTAC
1 ATAACTTAC
52184824 ATAACTT--
1 ATAACTTAC
52184831 AT-ACTCGTAC
1 ATAACT--TAC
52184841 ATAACTTAC
1 ATAACTTAC
*
52184850 ATAATTTAC
1 ATAACTTAC
52184859 TTAATACATA
Statistics
Matches: 70, Mismatches: 13, Indels: 22
0.67 0.12 0.21
Matches are distributed among these distances:
6 3 0.04
7 14 0.20
8 4 0.06
9 40 0.57
10 6 0.09
11 3 0.04
ACGTcount: A:0.41, C:0.19, G:0.04, T:0.36
Consensus pattern (9 bp):
ATAACTTAC
Found at i:52197974 original size:22 final size:22
Alignment explanation
Indices: 52197946--52198098 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
52197936 TGTTGATAGT
*
52197946 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
52197968 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
52197990 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
52198012 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
52198034 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
52198056 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
52198078 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
52198099 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:52198289 original size:13 final size:13
Alignment explanation
Indices: 52198273--52198323 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
52198263 TAGCAATAAT
*
52198273 ATTTTAATTGGTA
1 ATTTTAATTGATA
*
52198286 ATTTTATAATT-ATC
1 A-TTT-TAATTGATA
*
52198300 ATTTTAATTTATA
1 ATTTTAATTGATA
52198313 ATTTTAATTGA
1 ATTTTAATTGA
52198324 CAACAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
12 5 0.16
13 16 0.52
14 5 0.16
15 5 0.16
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (13 bp):
ATTTTAATTGATA
Found at i:52199346 original size:4 final size:4
Alignment explanation
Indices: 52199339--52199385 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
52199329 TATATATATA
52199339 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
52199386 ATTGTGTGTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:52201225 original size:23 final size:22
Alignment explanation
Indices: 52201173--52201236 Score: 56
Period size: 23 Copynumber: 2.7 Consensus size: 22
52201163 ATAAATATAT
* *
52201173 AATAAAATTCAAAAAAATATTAT
1 AATAAAATT-AAAAAATTATTAA
* *
52201196 CACAAAATTATAAAAATTATTAA
1 AATAAAATTA-AAAAATTATTAA
52201219 AATAAAATTTAGAAAAAT
1 AATAAAA-TTA-AAAAAT
52201237 ATGGTAAATG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 1 0.03
23 22 0.69
24 9 0.28
ACGTcount: A:0.64, C:0.05, G:0.02, T:0.30
Consensus pattern (22 bp):
AATAAAATTAAAAAATTATTAA
Found at i:52201405 original size:20 final size:21
Alignment explanation
Indices: 52201380--52201424 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
52201370 ATATTTTTAA
*
52201380 AAAAATTGA-TTAAAATTTGT-
1 AAAAATT-ATTTAAAAATTGTG
52201400 AAAAATTATTTAAAAATTGTG
1 AAAAATTATTTAAAAATTGTG
52201421 AAAA
1 AAAA
52201425 CTATAAGAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 17 0.77
21 4 0.18
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.36
Consensus pattern (21 bp):
AAAAATTATTTAAAAATTGTG
Found at i:52202240 original size:3 final size:3
Alignment explanation
Indices: 52202234--52202265 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
52202224 TTTTTTTTCA
52202234 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
52202266 AATTAACATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:52203094 original size:24 final size:24
Alignment explanation
Indices: 52203066--52203119 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
52203056 TCTTTCTAAA
** *
52203066 ATATTTATTATTTATTAGTATAAT
1 ATATTTAGCATTTATTAGCATAAT
52203090 ATATTTAGCATTTATTAGCATAAT
1 ATATTTAGCATTTATTAGCATAAT
*
52203114 TTATTT
1 ATATTT
52203120 GGCCTACGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.06, T:0.56
Consensus pattern (24 bp):
ATATTTAGCATTTATTAGCATAAT
Found at i:52207680 original size:19 final size:19
Alignment explanation
Indices: 52207641--52207694 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 19
52207631 GTTTGTTTGG
*
52207641 AATTTTAGATTTTTA-GAA
1 AATTTTAGAATTTTATGAA
*
52207659 AATTTTAGAATCTTATGAA
1 AATTTTAGAATTTTATGAA
52207678 AATTTTAAGAATTTTAT
1 AATTTT-AGAATTTTAT
52207695 TGGTTTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
18 13 0.42
19 9 0.29
20 9 0.29
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (19 bp):
AATTTTAGAATTTTATGAA
Found at i:52212026 original size:47 final size:47
Alignment explanation
Indices: 52211956--52212068 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
52211946 ATTTTCTTTG
* *
52211956 GCCTTTGTGGCGTATTCTGTATGTTGCGTTTGTGGCATACTCTGTTA
1 GCCTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCATACTCTGATA
* * **
52212003 GCCTTTGTAGCGTATTCTTTATGTTGCCTTTGTGGTGTACTCTGATA
1 GCCTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCATACTCTGATA
* *
52212050 GCTTTTGTGGCGTACTCTG
1 GCCTTTGTGGCGTATTCTG
52212069 ATAACCTTTG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.11, C:0.18, G:0.27, T:0.45
Consensus pattern (47 bp):
GCCTTTGTGGCGTATTCTGTATGTTGCCTTTGTGGCATACTCTGATA
Found at i:52212033 original size:25 final size:23
Alignment explanation
Indices: 52211956--52212036 Score: 67
Period size: 25 Copynumber: 3.4 Consensus size: 23
52211946 ATTTTCTTTG
52211956 GCCTTTGTGGCGTATTCTGTATGTT
1 GCCTTTGT-GCGTATTCT-TATGTT
* * * *
52211981 GCGTTTGTG-GCATAC-TCTGTT
1 GCCTTTGTGCGTATTCTTATGTT
52212002 AGCCTTTGTAGCGTATTCTTTATGTT
1 -GCCTTTGT-GCGTATTC-TTATGTT
52212028 GCCTTTGTG
1 GCCTTTGTG
52212037 GTGTACTCTG
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
21 5 0.12
22 7 0.16
23 5 0.12
24 6 0.14
25 15 0.35
26 5 0.12
ACGTcount: A:0.10, C:0.17, G:0.26, T:0.47
Consensus pattern (23 bp):
GCCTTTGTGCGTATTCTTATGTT
Found at i:52212059 original size:22 final size:22
Alignment explanation
Indices: 52212029--52212085 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
52212019 CTTTATGTTG
* *
52212029 CCTTTGTGGTGTACTCTGATAG
1 CCTTTGTGGCGTACTCTGATAA
*
52212051 CTTTTGTGGCGTACTCTGATAA
1 CCTTTGTGGCGTACTCTGATAA
52212073 CCTTTGTGGCGTA
1 CCTTTGTGGCGTA
52212086 TTTTGTCTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.14, C:0.19, G:0.26, T:0.40
Consensus pattern (22 bp):
CCTTTGTGGCGTACTCTGATAA
Found at i:52214776 original size:16 final size:16
Alignment explanation
Indices: 52214755--52214787 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
52214745 AAAATTTTAG
52214755 TATTGATCCATCTACT
1 TATTGATCCATCTACT
52214771 TATTGATCCATCTACT
1 TATTGATCCATCTACT
52214787 T
1 T
52214788 TGCTAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.24, G:0.06, T:0.45
Consensus pattern (16 bp):
TATTGATCCATCTACT
Found at i:52219249 original size:2 final size:2
Alignment explanation
Indices: 52219244--52219287 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
52219234 AAAAAAGTAC
* * *
52219244 AT AT AT CT AT AT CT AT AG AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52219286 AT
1 AT
52219288 TAAAAACTAC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52239222 original size:22 final size:22
Alignment explanation
Indices: 52239197--52239238 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
52239187 GAAAAATAGA
* *
52239197 TTTTTATTTTAGAGAAAATCTC
1 TTTTTATTTTAAAAAAAATCTC
*
52239219 TTTTTTTTTTAAAAAAAATC
1 TTTTTATTTTAAAAAAAATC
52239239 AAAACTTTTC
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:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTTTATTTTAAAAAAAATCTC
Found at i:52242331 original size:25 final size:25
Alignment explanation
Indices: 52242291--52242340 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
52242281 TTTCTCATCC
*
52242291 CAATTTTACTCAAGTAAAATTTTGA
1 CAATTTTACCCAAGTAAAATTTTGA
*
52242316 CAATTTTACCCTAGTAAAATTTTGA
1 CAATTTTACCCAAGTAAAATTTTGA
52242341 GAAAATTTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (25 bp):
CAATTTTACCCAAGTAAAATTTTGA
Found at i:52263654 original size:73 final size:73
Alignment explanation
Indices: 52263487--52263703 Score: 371
Period size: 73 Copynumber: 3.0 Consensus size: 73
52263477 GAAAATTCAC
*
52263487 AAAAACTTTAACCTCATTCGTCTTGATACGGTGAATATCAATGGCTCAAACACTGAATAGGAATA
1 AAAAACTTTAACCTCATTCGTCTTGATACGGTGAATATCAATGGCTC-AACACTGAATAGGAATG
52263552 ATAATACAG
65 ATAATACAG
*
52263561 AAAAAGTTTAACCTCATTCGTCTTGATACGGTGAATATCAATGGCTCAACACTGAATAGGAATGA
1 AAAAACTTTAACCTCATTCGTCTTGATACGGTGAATATCAATGGCTCAACACTGAATAGGAATGA
52263626 TAATACAG
66 TAATACAG
* * * *
52263634 AAAATCTTTAACCTGATTCGTCTTGATACGGTGAATATCGATGGCTCAACACTCAATAGGAATGA
1 AAAAACTTTAACCTCATTCGTCTTGATACGGTGAATATCAATGGCTCAACACTGAATAGGAATGA
52263699 TAATA
66 TAATA
52263704 GAATAGGGGC
Statistics
Matches: 136, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
73 90 0.66
74 46 0.34
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (73 bp):
AAAAACTTTAACCTCATTCGTCTTGATACGGTGAATATCAATGGCTCAACACTGAATAGGAATGA
TAATACAG
Found at i:52267318 original size:6 final size:6
Alignment explanation
Indices: 52267307--52267344 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
52267297 AATATAATAA
52267307 ATTTTT ATTTTT ATTTTT ATTTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT A-TTTTT ATTTTT ATTTTT A
52267345 AAATACTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
ATTTTT
Found at i:52267330 original size:13 final size:13
Alignment explanation
Indices: 52267307--52267343 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
52267297 AATATAATAA
52267307 ATTTTTA-TTTTT
1 ATTTTTATTTTTT
52267319 ATTTTTATTTTTT
1 ATTTTTATTTTTT
52267332 ATTTTTATTTTT
1 ATTTTTATTTTT
52267344 AAAATACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 7 0.29
13 17 0.71
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (13 bp):
ATTTTTATTTTTT
Found at i:52267332 original size:19 final size:19
Alignment explanation
Indices: 52267308--52267344 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
52267298 ATATAATAAA
52267308 TTTTTATTTTTATTTTTAT
1 TTTTTATTTTTATTTTTAT
52267327 TTTTTATTTTTATTTTTA
1 TTTTTATTTTTATTTTTA
52267345 AAATACTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (19 bp):
TTTTTATTTTTATTTTTAT
Found at i:52267395 original size:20 final size:20
Alignment explanation
Indices: 52267351--52267395 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
52267341 TTTAAAATAC
*
52267351 TTTTAAAATAAATTTTTTTA
1 TTTTAAAATAAATTTTTTAA
52267371 TTTTAAAAT-AATTTTTTAA
1 TTTTAAAATAAATTTTTTAA
52267390 TGTTTA
1 T-TTTA
52267396 TTTTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTTTAAAATAAATTTTTTAA
Found at i:52273901 original size:20 final size:18
Alignment explanation
Indices: 52273851--52273902 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
52273841 CTACAAGATA
52273851 AATATTAAATTAA-ATTT
1 AATATTAAATTAATATTT
52273868 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-A-TTT
52273888 AATATTAAATTAATA
1 AATATTAAATTAATA
52273903 AAATACTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 3 0.10
20 15 0.50
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTAAATTAATATTT
Found at i:52273943 original size:68 final size:72
Alignment explanation
Indices: 52273809--52273943 Score: 206
Period size: 68 Copynumber: 1.9 Consensus size: 72
52273799 TTAAACTTAG
* *
52273809 TCACTTTAATATTAAATTAATATAATATTTATCTACAAGATAAATATTAAATTAAATTTAATATT
1 TCACTTTAATATTAAATTAATAAAATATCTATCTACAAGATAAATATTAAATTAAATTTAATATT
52273874 AAGATAA
66 AAGATAA
* *
52273881 TCACTTTAATATTAAATTAATAAAATA-CTAT-TA-AA-ATAAGTATTAAATTTAATTTAATATT
1 TCACTTTAATATTAAATTAATAAAATATCTATCTACAAGATAAATATTAAATTAAATTTAATATT
52273942 AA
66 AA
52273944 ATCTTTTAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
68 26 0.44
69 2 0.03
70 2 0.03
71 3 0.05
72 26 0.44
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (72 bp):
TCACTTTAATATTAAATTAATAAAATATCTATCTACAAGATAAATATTAAATTAAATTTAATATT
AAGATAA
Found at i:52276529 original size:22 final size:21
Alignment explanation
Indices: 52276503--52276562 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 21
52276493 ATATCCAAAC
52276503 AATAATAACAAAATAGTAGCAA
1 AATAATAA-AAAATAGTAGCAA
* **
52276525 CATAATAGTGAAATAGTAGCAA
1 AATAATA-AAAAATAGTAGCAA
52276547 AATAATTAAAAAATAG
1 AATAA-TAAAAAATAG
52276563 CATTTTTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
22 28 0.93
23 2 0.07
ACGTcount: A:0.60, C:0.07, G:0.12, T:0.22
Consensus pattern (21 bp):
AATAATAAAAAATAGTAGCAA
Found at i:52285462 original size:43 final size:42
Alignment explanation
Indices: 52285395--52285565 Score: 208
Period size: 43 Copynumber: 4.0 Consensus size: 42
52285385 AATAGGATTT
52285395 TCGATATGTG-TTATCGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGAT-TGTGATTA-CGTGTAAGACCACGTCTGGGACGTTGGCA
* * *
52285438 TCGACTTGTGTTTACGTGTAAGACCATGTCTGGGACATTGGCA
1 TCGA-TTGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
52285481 TCGTATT-TGATT-CGTGTAAGACC-CTGTCTGGGACAG-TGGCA
1 TCG-ATTGTGATTACGTGTAAGACCAC-GTCTGGGAC-GTTGGCA
*
52285522 TCGATATGTGATTACATGTAAGACCACGTCTGGGACGTTGGCA
1 TCGAT-TGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
52285565 T
1 T
52285566 TGTACGAGTC
Statistics
Matches: 112, Mismatches: 6, Indels: 20
0.81 0.04 0.14
Matches are distributed among these distances:
40 2 0.02
41 29 0.26
42 10 0.09
43 65 0.58
44 6 0.05
ACGTcount: A:0.22, C:0.19, G:0.29, T:0.31
Consensus pattern (42 bp):
TCGATTGTGATTACGTGTAAGACCACGTCTGGGACGTTGGCA
Found at i:52285553 original size:84 final size:84
Alignment explanation
Indices: 52285408--52285565 Score: 232
Period size: 84 Copynumber: 1.9 Consensus size: 84
52285398 ATATGTGTTA
* * *
52285408 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGTGTAAGACCATGTCTGGGA
1 TCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGA
52285473 CATTGGCATCGTATTTGAT
66 CATTGGCATCGTATTTGAT
52285492 TCGTGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATGTGATTACATGTAAGACCACGTCTG
1 TCGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGATTACATGTAAGACCACGTCTG
*
52285554 GGACGTTGGCAT
63 GGACATTGGCAT
52285566 TGTACGAGTC
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
83 2 0.03
84 64 0.96
85 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (84 bp):
TCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGATTACATGTAAGACCACGTCTGGGA
CATTGGCATCGTATTTGAT
Found at i:52286499 original size:2 final size:2
Alignment explanation
Indices: 52286492--52286518 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
52286482 GCTTATGTGT
52286492 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
52286519 TGATATGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52287790 original size:12 final size:12
Alignment explanation
Indices: 52287773--52287806 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
52287763 CAGCCCGCCC
52287773 ATATTAATTTTT
1 ATATTAATTTTT
*
52287785 ATATTAACTTTT
1 ATATTAATTTTT
52287797 ATA-TAATTTT
1 ATATTAATTTT
52287807 AAAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 6 0.30
12 14 0.70
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:52287831 original size:18 final size:18
Alignment explanation
Indices: 52287808--52287847 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
52287798 TATAATTTTA
*
52287808 AAAAATA-TATAATACATC
1 AAAAATACTA-AAAACATC
52287826 AAAAATACTAAAAACATC
1 AAAAATACTAAAAACATC
52287844 AAAA
1 AAAA
52287848 TAAATATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 18 0.90
19 2 0.10
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAAATACTAAAAACATC
Found at i:52296231 original size:53 final size:53
Alignment explanation
Indices: 52296164--52296270 Score: 187
Period size: 53 Copynumber: 2.0 Consensus size: 53
52296154 TTGTACCATG
** *
52296164 AATTGCTTTGAGTGTGGACTTAACCAATTGAATCAAAATACAGAACTAGAAAA
1 AATTGCTTCAAGTGTGGACTTAACCAATTGAATCAAAACACAGAACTAGAAAA
52296217 AATTGCTTCAAGTGTGGACTTAACCAATTGAATCAAAACACAGAACTAGAAAA
1 AATTGCTTCAAGTGTGGACTTAACCAATTGAATCAAAACACAGAACTAGAAAA
52296270 A
1 A
52296271 GTTTTCTCTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.24
Consensus pattern (53 bp):
AATTGCTTCAAGTGTGGACTTAACCAATTGAATCAAAACACAGAACTAGAAAA
Found at i:52296973 original size:12 final size:12
Alignment explanation
Indices: 52296956--52296980 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
52296946 TGCAAACGGA
52296956 TCATTTCCATTT
1 TCATTTCCATTT
52296968 TCATTTCCATTT
1 TCATTTCCATTT
52296980 T
1 T
52296981 TGAAAACCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:52310101 original size:3 final size:3
Alignment explanation
Indices: 52310093--52310120 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
52310083 TACACTACTT
52310093 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC A
52310121 ACTTATCTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:52312217 original size:5 final size:5
Alignment explanation
Indices: 52312207--52312232 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52312197 TATATATAAA
52312207 TATTT TATTT TATTT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATTT T
52312233 CACAAATCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TATTT
Found at i:52320277 original size:52 final size:51
Alignment explanation
Indices: 52320206--52320414 Score: 293
Period size: 52 Copynumber: 4.1 Consensus size: 51
52320196 ATCAAGTGAC
* *
52320206 AAAGTGATAGGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGT-G
*
52320258 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTG
*
52320304 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTG
**
52320355 AAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 -AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC-AAGTG
52320408 ATAAGTG
1 A-AAGTG
52320415 GCTACACTTA
Statistics
Matches: 141, Mismatches: 8, Indels: 15
0.86 0.05 0.09
Matches are distributed among these distances:
46 44 0.31
52 87 0.62
53 10 0.07
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.27
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTG
Found at i:52320310 original size:46 final size:46
Alignment explanation
Indices: 52320258--52320451 Score: 226
Period size: 46 Copynumber: 4.3 Consensus size: 46
52320248 TGACAAGTGG
*
52320258 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
*
52320304 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
**
52320350 AAGTGAAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
*
52320402 AAAGTG---A-T-A-AG--T-GGCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
52320439 AAAGTGATAAGTG
1 AAAGTGATAAGTG
52320452 GCTACACTTA
Statistics
Matches: 130, Mismatches: 7, Indels: 26
0.80 0.04 0.16
Matches are distributed among these distances:
37 29 0.22
38 1 0.01
40 3 0.02
41 2 0.02
42 1 0.01
43 1 0.01
46 50 0.38
52 43 0.33
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
Found at i:52320361 original size:98 final size:98
Alignment explanation
Indices: 52320192--52320414 Score: 392
Period size: 98 Copynumber: 2.3 Consensus size: 98
52320182 TTTGAGTACT
* *
52320192 TCTGATCAAGTGACAAAGTGATAGGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
* * *
52320257 GAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTGATAGCTTCAGCTACACTTA
52320290 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
*
52320355 AAAAGTGATAAGTGATAGCTTTAGCTACACTTA
66 AAAAGTGATAAGTGATAGCTTCAGCTACACTTA
52320388 TCTGATCAAGAGACAAAGTGATAAGTG
1 TCTGATCAAGAGACAAAGTGATAAGTG
52320415 GCTACACTTA
Statistics
Matches: 119, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 119 1.00
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.27
Consensus pattern (98 bp):
TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTGATAGCTTCAGCTACACTTA
Found at i:52320422 original size:37 final size:37
Alignment explanation
Indices: 52320378--52320486 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
52320368 GATAGCTTTA
52320378 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
52320415 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
52320452 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
52320487 ATCATACGTA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 12 0.17
36 4 0.06
37 53 0.77
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:52338024 original size:16 final size:16
Alignment explanation
Indices: 52338003--52338035 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
52337993 ACATAACAGG
52338003 TTAATATAATATTCTT
1 TTAATATAATATTCTT
52338019 TTAATATAATATTCTT
1 TTAATATAATATTCTT
52338035 T
1 T
52338036 CAAGAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (16 bp):
TTAATATAATATTCTT
Found at i:52338285 original size:33 final size:33
Alignment explanation
Indices: 52338227--52338290 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
52338217 TTTTGTTTGA
** *
52338227 TTAAATCAAGATTAAAAAAGGGGTTAGGGTTAG
1 TTAAATCAAGATTAAAAAAAAGGTTAAGGTTAG
52338260 TTAAATCAAGATTAAAAAAAAGGTTAAGGTT
1 TTAAATCAAGATTAAAAAAAAGGTTAAGGTT
52338291 TTTTGATTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.22, T:0.28
Consensus pattern (33 bp):
TTAAATCAAGATTAAAAAAAAGGTTAAGGTTAG
Found at i:52338350 original size:32 final size:32
Alignment explanation
Indices: 52338238--52338371 Score: 101
Period size: 33 Copynumber: 4.1 Consensus size: 32
52338228 TAAATCAAGA
* **
52338238 TTAAAAAAGGGGTTAGGGTTAGTTAAATCAAGA-
1 TTAAAAAAGGGGTTAAGGTTCTTTAAATC--GAT
** * * *
52338271 TTAAAAAAAAGGTTAAGGTTTTTTGATTCGAGT
1 TTAAAAAAGGGGTTAAGGTTCTTTAAATCGA-T
* * *
52338304 GTACAAAAAAGGGGTTATGGTTTTTTAAAT-GAT
1 -T-TAAAAAAGGGGTTAAGGTTCTTTAAATCGAT
52338337 TTAAAAAAGGGGGTTAAGGTTCTTTAAATCGAT
1 TTAAAAAA-GGGGTTAAGGTTCTTTAAATCGAT
52338370 TT
1 TT
52338372 TGCACTTTCA
Statistics
Matches: 79, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
31 8 0.10
32 19 0.24
33 28 0.35
34 3 0.04
35 21 0.27
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (32 bp):
TTAAAAAAGGGGTTAAGGTTCTTTAAATCGAT
Found at i:52344811 original size:17 final size:18
Alignment explanation
Indices: 52344774--52344812 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
52344764 TCTTCCTGAA
*
52344774 AAAAAAATTATATATGAC
1 AAAAAAATTATAGATGAC
*
52344792 AAAAAAATTA-AGATGGC
1 AAAAAAATTATAGATGAC
52344809 AAAA
1 AAAA
52344813 TGAGAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.64, C:0.05, G:0.10, T:0.21
Consensus pattern (18 bp):
AAAAAAATTATAGATGAC
Found at i:52348332 original size:4 final size:4
Alignment explanation
Indices: 52348316--52348365 Score: 50
Period size: 4 Copynumber: 12.2 Consensus size: 4
52348306 TTCAATCGTC
*
52348316 TCTT T-TT TTTT TCTT TCTT AT-TT TCCTT TCTT TCTT TCTT TCATT TCTT
1 TCTT TCTT TCTT TCTT TCTT -TCTT T-CTT TCTT TCTT TCTT TC-TT TCTT
52348365 T
1 T
52348366 GTTGCTAGAG
Statistics
Matches: 40, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
3 4 0.10
4 28 0.70
5 8 0.20
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:52348345 original size:17 final size:17
Alignment explanation
Indices: 52348325--52348365 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
52348315 CTCTTTTTTT
*
52348325 TTTCTTTCTTAT-TTTCC
1 TTTCTTTCTT-TCTTTCA
52348342 TTTCTTTCTTTCTTTCA
1 TTTCTTTCTTTCTTTCA
52348359 TTTCTTT
1 TTTCTTT
52348366 GTTGCTAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.05
17 21 0.95
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTCTTTCTTTCTTTCA
Found at i:52348353 original size:13 final size:12
Alignment explanation
Indices: 52348316--52348365 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
52348306 TTCAATCGTC
*
52348316 TCTTT-TTTTTT
1 TCTTTCTTTCTT
52348327 TCTTTCTTAT-TT
1 TCTTTCTT-TCTT
52348339 TCCTTTCTTTCTT
1 T-CTTTCTTTCTT
52348352 TCTTTCATTTCTT
1 TCTTTC-TTTCTT
52348365 T
1 T
52348366 GTTGCTAGAG
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.15
12 11 0.32
13 18 0.53
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTTCTTTCTT
Found at i:52364725 original size:19 final size:19
Alignment explanation
Indices: 52364685--52364762 Score: 117
Period size: 19 Copynumber: 4.3 Consensus size: 19
52364675 ACAATAATAA
*
52364685 TTTTTGAAAACACGAAGA-
1 TTTTTGAAAACACGAAAAT
52364703 TTTTTG-AAACACGAAAAT
1 TTTTTGAAAACACGAAAAT
*
52364721 TTTTTGAAAACACGGAAAT
1 TTTTTGAAAACACGAAAAT
52364740 TTTTTGAAAACACG-AAAT
1 TTTTTGAAAACACGAAAAT
52364758 TTTTT
1 TTTTT
52364763 TATTCACGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
17 10 0.18
18 21 0.38
19 25 0.45
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (19 bp):
TTTTTGAAAACACGAAAAT
Found at i:52364763 original size:19 final size:18
Alignment explanation
Indices: 52364685--52364762 Score: 115
Period size: 18 Copynumber: 4.3 Consensus size: 18
52364675 ACAATAATAA
52364685 TTTTTGAAAACACGAAGA-
1 TTTTTGAAAACACGAA-AT
52364703 TTTTTG-AAACACGAAAAT
1 TTTTTGAAAACACG-AAAT
52364721 TTTTTGAAAACACGGAAAT
1 TTTTTGAAAACAC-GAAAT
52364740 TTTTTGAAAACACGAAAT
1 TTTTTGAAAACACGAAAT
52364758 TTTTT
1 TTTTT
52364763 TATTCACGAG
Statistics
Matches: 56, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.14
18 24 0.43
19 23 0.41
20 1 0.02
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.36
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAT
Found at i:52364797 original size:18 final size:18
Alignment explanation
Indices: 52364685--52364796 Score: 92
Period size: 18 Copynumber: 6.3 Consensus size: 18
52364675 ACAATAATAA
52364685 TTTTTGAAAACAC-GAAGA-
1 TTTTTG-AAACACGGAA-AT
*
52364703 TTTTTGAAACACGAAAAT
1 TTTTTGAAACACGGAAAT
52364721 TTTTTGAAAACACGGAAAT
1 TTTTTG-AAACACGGAAAT
52364740 TTTTTGAAAACAC-GAAAT
1 TTTTTG-AAACACGGAAAT
* **
52364758 TTTTTTATTCAC-GAGAA-
1 TTTTTGAAACACGGA-AAT
*
52364775 TTTTTGAAACATGG-AAT
1 TTTTTGAAACACGGAAAT
52364792 TTTTT
1 TTTTT
52364797 TTTTAAGAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
16 2 0.03
17 26 0.33
18 27 0.34
19 24 0.30
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.38
Consensus pattern (18 bp):
TTTTTGAAACACGGAAAT
Found at i:52364894 original size:18 final size:17
Alignment explanation
Indices: 52364853--52364901 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
52364843 TATTATTATT
52364853 ATTTTGAAACACGAGAA
1 ATTTTGAAACACGAGAA
*
52364870 ATTTTGAAGACATGA-AA
1 ATTTTGAA-ACACGAGAA
52364887 ATTTTTGAAACACGA
1 A-TTTTGAAACACGA
52364902 CTTTTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.29
Consensus pattern (17 bp):
ATTTTGAAACACGAGAA
Found at i:52365312 original size:13 final size:14
Alignment explanation
Indices: 52365283--52365317 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
52365273 TACAATATTT
52365283 AAATAAATGGACTA
1 AAATAAATGGACTA
52365297 AAATAAATGGA-TA
1 AAATAAATGGACTA
*
52365310 AAAAAAAT
1 AAATAAAT
52365318 TACCCAAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.66, C:0.03, G:0.11, T:0.20
Consensus pattern (14 bp):
AAATAAATGGACTA
Found at i:52365469 original size:43 final size:42
Alignment explanation
Indices: 52365412--52365494 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 42
52365402 TGCCAGGAAG
* * *
52365412 TGGGCCGAATCTGCTGGCCTGCTGGGCACT-GGTCTGCTGCTAT
1 TGGGCCGAAGCTGCTGGACTGCT--GCACTGGGCCTGCTGCTAT
*
52365455 TGGGCTGAAGCTGCTGGACTGCTGCACTGGGCCTGCTGCT
1 TGGGCCGAAGCTGCTGGACTGCTGCACTGGGCCTGCTGCT
52365495 GGACTGCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 5 0.14
42 10 0.29
43 20 0.57
ACGTcount: A:0.10, C:0.28, G:0.36, T:0.27
Consensus pattern (42 bp):
TGGGCCGAAGCTGCTGGACTGCTGCACTGGGCCTGCTGCTAT
Found at i:52365527 original size:13 final size:13
Alignment explanation
Indices: 52365505--52365558 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
52365495 GGACTGCTTC
*
52365505 TTTCTTCTTCTTT
1 TTTCTGCTTCTTT
52365518 TTTCTGCTTCTTT
1 TTTCTGCTTCTTT
52365531 CTTTCT--TT-TTT
1 -TTTCTGCTTCTTT
52365542 TTCTGCTGCTTCTTT
1 TT-T-CTGCTTCTTT
52365557 TT
1 TT
52365559 CTATTTTGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
10 2 0.06
11 4 0.12
12 4 0.12
13 12 0.35
14 7 0.21
15 5 0.15
ACGTcount: A:0.00, C:0.22, G:0.06, T:0.72
Consensus pattern (13 bp):
TTTCTGCTTCTTT
Found at i:52365528 original size:23 final size:23
Alignment explanation
Indices: 52365498--52365565 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
52365488 TGCTGCTGGA
52365498 CTGCTTCTTTCTTCTTCTTTTTT
1 CTGCTTCTTTCTTCTTCTTTTTT
52365521 CTGCTTCTTTCTTTCTT-TTTTTT
1 CTGCTTCTTTC-TTCTTCTTTTTT
* * *
52365544 CTGCTGC-TTCTTTTTCTATTTT
1 CTGCTTCTTTCTTCTTCTTTTTT
52365566 GGTTTTTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
21 4 0.10
22 8 0.20
23 23 0.57
24 5 0.12
ACGTcount: A:0.01, C:0.24, G:0.06, T:0.69
Consensus pattern (23 bp):
CTGCTTCTTTCTTCTTCTTTTTT
Found at i:52365693 original size:7 final size:7
Alignment explanation
Indices: 52365676--52365750 Score: 64
Period size: 7 Copynumber: 10.3 Consensus size: 7
52365666 TTTAAAAATA
52365676 TTTTTTCC
1 TTTTTT-C
52365684 TTTTTTC
1 TTTTTTC
52365691 -TTTTTC
1 TTTTTTC
52365697 TTTTTTC
1 TTTTTTC
52365704 TTTTCTTC
1 TTTT-TTC
52365712 TCCCTTTTTC
1 T---TTTTTC
*
52365722 -TTCTTC
1 TTTTTTC
52365728 TTTTTTC
1 TTTTTTC
*
52365735 TTTCTTC
1 TTTTTTC
*
52365742 TTTCTTC
1 TTTTTTC
52365749 TT
1 TT
52365751 CTTCGGGCCG
Statistics
Matches: 58, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
6 11 0.19
7 31 0.53
8 10 0.17
10 3 0.05
11 3 0.05
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTTC
Found at i:52365722 original size:31 final size:30
Alignment explanation
Indices: 52365685--52365742 Score: 98
Period size: 31 Copynumber: 1.9 Consensus size: 30
52365675 ATTTTTTCCT
*
52365685 TTTTTCTTTTTCTTTTTTCTTTTCTTCTCCC
1 TTTTTCTTCTTCTTTTTTC-TTTCTTCTCCC
52365716 TTTTTCTTCTTCTTTTTTCTTTCTTCT
1 TTTTTCTTCTTCTTTTTTCTTTCTTCT
52365743 TTCTTCTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 8 0.31
31 18 0.69
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (30 bp):
TTTTTCTTCTTCTTTTTTCTTTCTTCTCCC
Found at i:52365752 original size:13 final size:13
Alignment explanation
Indices: 52365687--52365754 Score: 57
Period size: 13 Copynumber: 5.0 Consensus size: 13
52365677 TTTTTCCTTT
* *
52365687 TTTCTTTTTCTTT
1 TTTCTTCTTCTTC
52365700 TTTCTT-TTCTTC
1 TTTCTTCTTCTTC
*
52365712 TCCCTTTTTCTTCTTC
1 T---TTCTTCTTCTTC
*
52365728 TTTTTTCTTTCTTC
1 TTTCTTC-TTCTTC
52365742 TTTCTTCTTCTTC
1 TTTCTTCTTCTTC
52365755 GGGCCGCACC
Statistics
Matches: 47, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
12 6 0.13
13 18 0.38
14 12 0.26
15 4 0.09
16 7 0.15
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTCTTCTTCTTC
Found at i:52365912 original size:19 final size:17
Alignment explanation
Indices: 52365888--52365926 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
52365878 TTTTCTTGTT
52365888 TTTTGCTGCTGCGTTTTTG
1 TTTTGCTGCT-C-TTTTTG
*
52365907 TTTTGCTTCTCTTTTTG
1 TTTTGCTGCTCTTTTTG
52365924 TTT
1 TTT
52365927 CGATTTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 1 0.05
19 9 0.47
ACGTcount: A:0.00, C:0.15, G:0.18, T:0.67
Consensus pattern (17 bp):
TTTTGCTGCTCTTTTTG
Found at i:52366389 original size:29 final size:30
Alignment explanation
Indices: 52366317--52366456 Score: 153
Period size: 30 Copynumber: 4.7 Consensus size: 30
52366307 GTAATTTCTT
*
52366317 AAAAGTTTAGGGGTTAAAGTG-AAATTTTG
1 AAAAGTTTAGGGGTTAAAATGTAAATTTTG
* *
52366346 AGAAAGTTTAAGGGTTGAAATGT-AATTTTAG
1 A-AAAGTTTAGGGGTTAAAATGTAAATTTT-G
*
52366377 AAAAGTTT-GGGGTTAAAATGTAAATTTTA
1 AAAAGTTTAGGGGTTAAAATGTAAATTTTG
*
52366406 AAAAGGTTT-GGGGTCAAAATGTAAATTTTG
1 AAAA-GTTTAGGGGTTAAAATGTAAATTTTG
* * *
52366436 AAAAATATAGGGGTCAAAATG
1 AAAAGTTTAGGGGTTAAAATG
52366457 CAATTTTTTT
Statistics
Matches: 95, Mismatches: 10, Indels: 11
0.82 0.09 0.09
Matches are distributed among these distances:
29 18 0.19
30 75 0.79
31 2 0.02
ACGTcount: A:0.41, C:0.01, G:0.25, T:0.33
Consensus pattern (30 bp):
AAAAGTTTAGGGGTTAAAATGTAAATTTTG
Found at i:52366439 original size:59 final size:60
Alignment explanation
Indices: 52366317--52366463 Score: 158
Period size: 59 Copynumber: 2.5 Consensus size: 60
52366307 GTAATTTCTT
* * **
52366317 AAAAGTTTAGGGGTTAAAGTGAAATTTTGAGAAAGTTTAAGGGTTGAAATGTAATTTTAG
1 AAAAGTTTAGGGGTTAAAATGAAATTTTGAAAAAGTTTAAGGGTCAAAATGTAATTTTAG
*
52366377 AAAAGTTT-GGGGTTAAAATGTAAATTTT-AAAAAGGTTT-GGGGTCAAAATGTAAATTTT-G
1 AAAAGTTTAGGGGTTAAAATG-AAATTTTGAAAAA-GTTTAAGGGTCAAAATGT-AATTTTAG
* * * *
52366436 AAAAATATAGGGGTCAAAATGCAATTTT
1 AAAAGTTTAGGGGTTAAAATGAAATTTT
52366464 TTTATTTTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 9
0.80 0.10 0.10
Matches are distributed among these distances:
59 38 0.51
60 36 0.49
ACGTcount: A:0.40, C:0.02, G:0.24, T:0.34
Consensus pattern (60 bp):
AAAAGTTTAGGGGTTAAAATGAAATTTTGAAAAAGTTTAAGGGTCAAAATGTAATTTTAG
Found at i:52368556 original size:10 final size:10
Alignment explanation
Indices: 52368502--52368557 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
52368492 AATTTTAACT
52368502 TTTTTTATATA
1 TTTTTTATA-A
* *
52368513 TTTTTAGATTA
1 TTTTT-TATAA
52368524 TTTTTTA-AA
1 TTTTTTATAA
52368533 --TTTTATAA
1 TTTTTTATAA
52368541 TTTTTTATAA
1 TTTTTTATAA
52368551 TTTTTTA
1 TTTTTTA
52368558 AAAATATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
7 5 0.14
8 2 0.05
9 1 0.03
10 16 0.43
11 11 0.30
12 2 0.05
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:52368556 original size:39 final size:39
Alignment explanation
Indices: 52368475--52368579 Score: 114
Period size: 39 Copynumber: 2.8 Consensus size: 39
52368465 AAAATTATTA
*
52368475 TTTTAGAAAATTTTTTAAATTTTAACTTTTTTTATATAT
1 TTTTAGAAAATTTTTTAAATTTTAAATTTTTTTATATAT
**
52368514 TTTTAGATTATTTTTTAAATTTTATAA-TTTTTTATA-ATT
1 TTTTAGAAAATTTTTTAAATTTTA-AATTTTTTTATATA-T
*
52368553 TTTTA-AAAA---TATAAATTTTAAATTTTT
1 TTTTAGAAAATTTTTTAAATTTTAAATTTTT
52368580 GAAAATTATT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
34 2 0.04
35 14 0.25
38 3 0.05
39 37 0.65
40 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.02, T:0.62
Consensus pattern (39 bp):
TTTTAGAAAATTTTTTAAATTTTAAATTTTTTTATATAT
Found at i:52368562 original size:29 final size:29
Alignment explanation
Indices: 52368504--52368559 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 29
52368494 TTTTAACTTT
*
52368504 TTTTATATATTTTTAGATTATTTTTTAAA
1 TTTTATATATTTTTAGATAATTTTTTAAA
*
52368533 TTTTATA-ATTTTT-TATAATTTTTTAAA
1 TTTTATATATTTTTAGATAATTTTTTAAA
52368560 AATATAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 12 0.48
28 6 0.24
29 7 0.28
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (29 bp):
TTTTATATATTTTTAGATAATTTTTTAAA
Found at i:52373537 original size:2 final size:2
Alignment explanation
Indices: 52373532--52373569 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
52373522 TATTCAAATA
* *
52373532 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AC AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52373570 TTGTAAAGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:52384406 original size:3 final size:3
Alignment explanation
Indices: 52384398--52384423 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
52384388 ATCTATCCTT
52384398 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
52384424 TAACTAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:52385976 original size:7 final size:8
Alignment explanation
Indices: 52385936--52386072 Score: 51
Period size: 9 Copynumber: 15.2 Consensus size: 8
52385926 TCATAAAAAT
*
52385936 AATTAAAA
1 AATTATAA
*
52385944 AATCTTTAA
1 AAT-TATAA
*
52385953 AAATATAA
1 AATTATAA
52385961 AA-TATAA
1 AATTATAA
*
52385968 AATTAAAA
1 AATTATAA
*
52385976 ATATTTTAA
1 A-ATTATAA
52385985 AATTAATAAA
1 AATT-AT-AA
52385995 AACTTATAA
1 AA-TTATAA
*
52386004 CAATCATAAA
1 -AATTAT-AA
52386014 AATTAATAAA
1 AATT-AT-AA
52386024 AACTTATAA
1 AA-TTATAA
*
52386033 CAATCATAAAA
1 -AAT--TATAA
*
52386044 AATAATAAA
1 AATTAT-AA
52386053 AACTTATAA
1 AA-TTATAA
52386062 ATATTATAA
1 A-ATTATAA
52386071 AA
1 AA
52386073 AAATCTAATA
Statistics
Matches: 99, Mismatches: 14, Indels: 32
0.68 0.10 0.22
Matches are distributed among these distances:
7 7 0.07
8 19 0.19
9 37 0.37
10 28 0.28
11 8 0.08
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (8 bp):
AATTATAA
Found at i:52386020 original size:29 final size:29
Alignment explanation
Indices: 52385983--52386061 Score: 149
Period size: 29 Copynumber: 2.7 Consensus size: 29
52385973 AAAATATTTT
52385983 AAAATTAATAAAAACTTATAACAATCATA
1 AAAATTAATAAAAACTTATAACAATCATA
52386012 AAAATTAATAAAAACTTATAACAATCATA
1 AAAATTAATAAAAACTTATAACAATCATA
*
52386041 AAAAATAATAAAAACTTATAA
1 AAAATTAATAAAAACTTATAA
52386062 ATATTATAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.27
Consensus pattern (29 bp):
AAAATTAATAAAAACTTATAACAATCATA
Found at i:52386070 original size:19 final size:18
Alignment explanation
Indices: 52385936--52386182 Score: 96
Period size: 19 Copynumber: 13.1 Consensus size: 18
52385926 TCATAAAAAT
*
52385936 AATTA-AAAAATCTTTAAA
1 AATTATAAAAAT-TATAAA
52385954 AA-TAT-AAAA-TAT-AA
1 AATTATAAAAATTATAAA
*
52385968 AATTA-AAAATATT-TTAA
1 AATTATAAAA-ATTATAAA
*
52385985 AATTAATAAAAACTTATAAC
1 AATT-ATAAAAA-TTATAAA
*
52386005 AATCATAAAAATTAATAAA
1 AATTATAAAAATT-ATAAA
* *
52386024 AACTTATAACAATCATAAAA
1 AA-TTATAAAAATTAT-AAA
*
52386044 AATAATAAAAACTTATAAA
1 AATTATAAAAA-TTATAAA
* * *
52386063 TATTATAAAAAAATCTAATA
1 AATTAT-AAAAATTATAA-A
* *
52386083 AATTTTAATAAATTATAAT
1 AATTATAA-AAATTATAAA
** *
52386102 TTTTTTATAAAATTAATGAAA
1 AATTATA-AAAATT-AT-AAA
52386123 ATATT-TAAAATATTATAAA
1 A-ATTATAAAA-ATTATAAA
* * *
52386142 AACGTATACAAATTCTTAAA
1 AA-TTATAAAAATT-ATAAA
*
52386162 AACTTATAAAAATCATAAA
1 AA-TTATAAAAATTATAAA
52386181 AA
1 AA
52386183 AAATATTAAG
Statistics
Matches: 172, Mismatches: 32, Indels: 49
0.68 0.13 0.19
Matches are distributed among these distances:
14 4 0.02
15 7 0.04
16 2 0.01
17 13 0.08
18 7 0.04
19 65 0.38
20 65 0.38
21 7 0.04
22 2 0.01
ACGTcount: A:0.60, C:0.06, G:0.01, T:0.34
Consensus pattern (18 bp):
AATTATAAAAATTATAAA
Found at i:52386070 original size:29 final size:29
Alignment explanation
Indices: 52385983--52386074 Score: 141
Period size: 29 Copynumber: 3.2 Consensus size: 29
52385973 AAAATATTTT
*
52385983 AAAATTAATAAAAACTTATAACAATCATA
1 AAAAATAATAAAAACTTATAACAATCATA
*
52386012 AAAATTAATAAAAACTTATAACAATCATA
1 AAAAATAATAAAAACTTATAACAATCATA
*
52386041 AAAAATAATAAAAACTTATAA-ATATTATA
1 AAAAATAATAAAAACTTATAACA-ATCATA
52386070 AAAAA
1 AAAAA
52386075 ATCTAATAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
28 1 0.02
29 59 0.98
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (29 bp):
AAAAATAATAAAAACTTATAACAATCATA
Found at i:52386075 original size:22 final size:23
Alignment explanation
Indices: 52386044--52386094 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
52386034 AATCATAAAA
* *
52386044 AATAATAAAAACTTATAAATATT
1 AATAAAAAAAACTAATAAATATT
* *
52386067 -ATAAAAAAATCTAATAAATTTT
1 AATAAAAAAAACTAATAAATATT
52386089 AATAAA
1 AATAAA
52386095 TTATAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (23 bp):
AATAAAAAAAACTAATAAATATT
Found at i:52386173 original size:10 final size:9
Alignment explanation
Indices: 52385936--52386182 Score: 96
Period size: 10 Copynumber: 26.2 Consensus size: 9
52385926 TCATAAAAAT
52385936 AATTA-AAA
1 AATTATAAA
*
52385944 AATCTTTAAA
1 AAT-TATAAA
52385954 AA-TAT-AA
1 AATTATAAA
52385961 AA-TAT-AA
1 AATTATAAA
52385968 AATTA-AAA
1 AATTATAAA
*
52385976 ATATT-TTAA
1 A-ATTATAAA
52385985 AATTAATAAA
1 AATT-ATAAA
*
52385995 AACTTATAAC
1 AA-TTATAAA
*
52386005 AATCATAAA
1 AATTATAAA
52386014 AATTAATAAA
1 AATT-ATAAA
*
52386024 AACTTATAAC
1 AA-TTATAAA
*
52386034 AATCATAAAA
1 AATTAT-AAA
*
52386044 AATAATAAA
1 AATTATAAA
52386053 AACTTATAAA
1 AA-TTATAAA
*
52386063 TATTATAAAA
1 AATTAT-AAA
* *
52386073 AAATCTAATA
1 AATTATAA-A
*
52386083 AATTTTAATA
1 AATTATAA-A
*
52386093 AATTATAAT
1 AATTATAAA
** *
52386102 TTTTTTATAA
1 AATTATA-AA
52386112 AATTAATGAAA
1 AATT-AT-AAA
52386123 ATATT-TAAA
1 A-ATTATAAA
52386132 ATATTATAAA
1 A-ATTATAAA
* *
52386142 AACGTATACA
1 AA-TTATAAA
*
52386152 AATTCTTAAA
1 AATT-ATAAA
52386162 AACTTATAAA
1 AA-TTATAAA
*
52386172 AATCATAAA
1 AATTATAAA
52386181 AA
1 AA
52386183 AAATATTAAG
Statistics
Matches: 181, Mismatches: 35, Indels: 45
0.69 0.13 0.17
Matches are distributed among these distances:
7 11 0.06
8 13 0.07
9 51 0.28
10 92 0.51
11 10 0.06
12 4 0.02
ACGTcount: A:0.60, C:0.06, G:0.01, T:0.34
Consensus pattern (9 bp):
AATTATAAA
Found at i:52386771 original size:21 final size:20
Alignment explanation
Indices: 52386737--52386810 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
52386727 ATAGTTCATG
52386737 TTTTTATGATTTTTTAATAA
1 TTTTTATGATTTTTTAATAA
* * *
52386757 TTTTATATCA-TTTTTATTTA
1 TTTT-TATGATTTTTTAATAA
* *
52386777 TTTTTAT-ATTTTTCAATATT
1 TTTTTATGATTTTTTAATA-A
52386797 TTTTTATGATTTTT
1 TTTTTATGATTTTT
52386811 GTAAGTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
18 1 0.02
19 9 0.21
20 23 0.53
21 10 0.23
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (20 bp):
TTTTTATGATTTTTTAATAA
Done.