Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 186 of 226
Found at i:59223909 original size:23 final size:23
Alignment explanation
Indices: 59223883--59223933 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
59223873 CTAAAGCATA
* *
59223883 AAAAATATAAAT-AATAAATAAAT
1 AAAAATAAAAATAAATAAA-AAAG
59223906 AAAAATAAAAATAAATAAAAAAG
1 AAAAATAAAAATAAATAAAAAAG
59223929 AAAAA
1 AAAAA
59223934 AAAGAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 19 0.76
24 6 0.24
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (23 bp):
AAAAATAAAAATAAATAAAAAAG
Found at i:59223919 original size:27 final size:26
Alignment explanation
Indices: 59223884--59223942 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
59223874 TAAAGCATAA
* * *
59223884 AAAATATAAATAATAAATAAATAAAAAT
1 AAAA-ATAAATAAAAAAGAAA-AAAAAG
59223912 AAAAATAAATAAAAAAGAAAAAAAAG
1 AAAAATAAATAAAAAAGAAAAAAAAG
59223938 AAAAA
1 AAAAA
59223943 GAAAAAGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 10 0.36
27 14 0.50
28 4 0.14
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.15
Consensus pattern (26 bp):
AAAAATAAATAAAAAAGAAAAAAAAG
Found at i:59223926 original size:16 final size:16
Alignment explanation
Indices: 59223885--59223948 Score: 67
Period size: 16 Copynumber: 3.9 Consensus size: 16
59223875 AAAGCATAAA
*
59223885 AAATATAAATAATAAAT
1 AAATAAAAATAA-AAAT
59223902 AAATAAAAATAAAAAT
1 AAATAAAAATAAAAAT
*
59223918 AAATAAAAA-AGAAAAA
1 AAATAAAAATA-AAAAT
* *
59223934 AAAGAAAAAGAAAAA
1 AAATAAAAATAAAAA
59223949 GAATATAATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
15 1 0.02
16 29 0.69
17 12 0.29
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (16 bp):
AAATAAAAATAAAAAT
Found at i:59223935 original size:20 final size:20
Alignment explanation
Indices: 59223880--59223951 Score: 65
Period size: 20 Copynumber: 3.5 Consensus size: 20
59223870 TTCCTAAAGC
* * *
59223880 ATAAAAAATATAAATAATAA
1 ATAAAAAAGAAAAAAAATAA
*
59223900 ATAAATAAA-AATAAAAATAA
1 ATAAA-AAAGAAAAAAAATAA
*
59223920 ATAAAAAAGAAAAAAAAGAA
1 ATAAAAAAGAAAAAAAATAA
*
59223940 AAAGAAAAAGAA
1 ATA-AAAAAGAA
59223952 TATAATTTGG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 3 0.07
20 29 0.67
21 11 0.26
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.14
Consensus pattern (20 bp):
ATAAAAAAGAAAAAAAATAA
Found at i:59224536 original size:28 final size:27
Alignment explanation
Indices: 59224500--59224558 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
59224490 ATTTTAATTA
59224500 TATTAGGA-TAATTAATATTAAGAATAT
1 TATTAGGATTAATTAAT-TTAAGAATAT
* * *
59224527 TATTAAGGATTATTTAATTTTAGAATTT
1 TATT-AGGATTAATTAATTTAAGAATAT
59224555 TATT
1 TATT
59224559 TTATTTATCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.15
28 16 0.59
29 7 0.26
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (27 bp):
TATTAGGATTAATTAATTTAAGAATAT
Found at i:59227860 original size:79 final size:79
Alignment explanation
Indices: 59227759--59227908 Score: 221
Period size: 79 Copynumber: 1.9 Consensus size: 79
59227749 ATTAACAACA
* * * * *
59227759 GAAATCGAATAAATCTTGTTGAACGATAGGAAC-AGAGTCCTGAAACAGAATTGTTGAATTGATT
1 GAAATCGAACAAATCCTGTTGAACGACAGGAACAAGA-TCCTGAAACAGAATTATTCAATTGATT
59227823 TCTGTTTGAAAATAG
65 TCTGTTTGAAAATAG
* *
59227838 GAAATCGAACAAATCCTGTTGAACGACAGGAATAAGATCTTGAAACAGAATTATTCAATTGATTT
1 GAAATCGAACAAATCCTGTTGAACGACAGGAACAAGATCCTGAAACAGAATTATTCAATTGATTT
59227903 CTGTTT
66 CTGTTT
59227909 ACAAACAGAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
79 60 0.95
80 3 0.05
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (79 bp):
GAAATCGAACAAATCCTGTTGAACGACAGGAACAAGATCCTGAAACAGAATTATTCAATTGATTT
CTGTTTGAAAATAG
Found at i:59228488 original size:23 final size:26
Alignment explanation
Indices: 59228442--59228499 Score: 86
Period size: 24 Copynumber: 2.3 Consensus size: 26
59228432 TTGACTAATA
*
59228442 GAGCCAATAACGTCCGTGAATT-AAG
1 GAGCCATTAACGTCCGTGAATTAAAG
59228467 GAGCCATTAACGT-C-TGAATTAAAG
1 GAGCCATTAACGTCCGTGAATTAAAG
59228491 GAGCCATTA
1 GAGCCATTA
59228500 GCCTTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
23 6 0.19
24 13 0.42
25 12 0.39
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.22
Consensus pattern (26 bp):
GAGCCATTAACGTCCGTGAATTAAAG
Found at i:59240866 original size:15 final size:16
Alignment explanation
Indices: 59240846--59240879 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
59240836 TATATGTAAA
59240846 AAAAATTTA-AAATAT
1 AAAAATTTATAAATAT
*
59240861 AAAAATTTATTAATAT
1 AAAAATTTATAAATAT
59240877 AAA
1 AAA
59240880 TTAATATATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAAATTTATAAATAT
Found at i:59241010 original size:20 final size:20
Alignment explanation
Indices: 59240985--59241024 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
59240975 AATATTTTCC
*
59240985 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
59241005 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
59241025 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:59241030 original size:34 final size:34
Alignment explanation
Indices: 59240973--59241038 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 34
59240963 CAAACACCAA
*
59240973 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTAC-GAAAAGT
59241008 AAAACATTTTCCAG-AAATCATTTTACGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACGAAAA
59241039 ACATTTTACT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 5 0.17
34 12 0.40
35 13 0.43
ACGTcount: A:0.47, C:0.14, G:0.08, T:0.32
Consensus pattern (34 bp):
AAAACATTTTCCAGTAAATCATTTTACGAAAAGT
Found at i:59243372 original size:26 final size:26
Alignment explanation
Indices: 59243341--59243397 Score: 87
Period size: 26 Copynumber: 2.2 Consensus size: 26
59243331 CTTTTTGGAG
* **
59243341 AGAACCTGAAGAGTTAGAGTGGAGAA
1 AGAACCCGAAGAGTTAGAACGGAGAA
59243367 AGAACCCGAAGAGTTAGAACGGAGAA
1 AGAACCCGAAGAGTTAGAACGGAGAA
59243393 AGAAC
1 AGAAC
59243398 AAGGATTCGA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.46, C:0.12, G:0.32, T:0.11
Consensus pattern (26 bp):
AGAACCCGAAGAGTTAGAACGGAGAA
Found at i:59248936 original size:25 final size:25
Alignment explanation
Indices: 59248908--59248956 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
59248898 TACAATCTAA
* *
59248908 CTATAGTAGTCTCAGTATATACTAC
1 CTATAGCAGTCTCAGGATATACTAC
*
59248933 CTATAGCAGTGTCAGGATATACTA
1 CTATAGCAGTCTCAGGATATACTA
59248957 TCAAAAATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (25 bp):
CTATAGCAGTCTCAGGATATACTAC
Found at i:59253456 original size:37 final size:37
Alignment explanation
Indices: 59253406--59253480 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
59253396 GACACTCCAA
59253406 ACATTAAAATAAATATATACAATTAAGAAATAAAATT
1 ACATTAAAATAAATATATACAATTAAGAAATAAAATT
59253443 ACATTAAAATAAATATATACAATTAAGAAATAAAATT
1 ACATTAAAATAAATATATACAATTAAGAAATAAAATT
59253480 A
1 A
59253481 AGCAAGCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (37 bp):
ACATTAAAATAAATATATACAATTAAGAAATAAAATT
Found at i:59254320 original size:28 final size:28
Alignment explanation
Indices: 59254274--59254462 Score: 161
Period size: 28 Copynumber: 6.8 Consensus size: 28
59254264 TGTGTTCACT
*
59254274 GTTTTTCAAAAATTT-CAATTTTGCCACA
1 GTTTTTC-AAATTTTACAATTTTGCCACA
*
59254302 GTTTTTTAAATTTTACAATTTTGCCACA
1 GTTTTTCAAATTTTACAATTTTGCCACA
* * * **
59254330 ATTCTTCAGATTTTACAATTTTGCCATT
1 GTTTTTCAAATTTTACAATTTTGCCACA
* * *
59254358 GCTTTTCAAATTTT-CAAATTTTACCACT
1 GTTTTTCAAATTTTAC-AATTTTGCCACA
* *
59254386 G-TTTTGAAATTTTACAGTTTTGCCACA
1 GTTTTTCAAATTTTACAATTTTGCCACA
* * * *
59254413 ATTTTTCAGATTTTACAGTTTTGCTACGA
1 GTTTTTCAAATTTTACAATTTTGCCAC-A
* *
59254442 TTTTTTC-GATTTTACAATTTT
1 GTTTTTCAAATTTTACAATTTT
59254463 CCTCTATTTT
Statistics
Matches: 132, Mismatches: 24, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
27 27 0.20
28 98 0.74
29 7 0.05
ACGTcount: A:0.26, C:0.16, G:0.08, T:0.49
Consensus pattern (28 bp):
GTTTTTCAAATTTTACAATTTTGCCACA
Found at i:59254398 original size:27 final size:28
Alignment explanation
Indices: 59254346--59254398 Score: 72
Period size: 27 Copynumber: 1.9 Consensus size: 28
59254336 CAGATTTTAC
* *
59254346 AATTTTGCCATTGCTTTTCAAATTTTCA
1 AATTTTACCACTGCTTTTCAAATTTTCA
*
59254374 AATTTTACCACTG-TTTTGAAATTTT
1 AATTTTACCACTGCTTTTCAAATTTT
59254399 ACAGTTTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.26, C:0.15, G:0.08, T:0.51
Consensus pattern (28 bp):
AATTTTACCACTGCTTTTCAAATTTTCA
Found at i:59254406 original size:27 final size:27
Alignment explanation
Indices: 59254270--59254482 Score: 139
Period size: 28 Copynumber: 7.7 Consensus size: 27
59254260 GTCGTGTGTT
*
59254270 CACTGTTTTTCAAAAATTT-CAATTTTGC
1 CACTG-TTTTC-AAATTTTACAATTTTGC
* *
59254298 CACAGTTTTTTAAATTTTACAATTTTGC
1 CACTG-TTTTCAAATTTTACAATTTTGC
** *
59254326 CACAATTCTTCAGATTTTACAATTTTGC
1 CACTGTT-TTCAAATTTTACAATTTTGC
* *
59254354 CATTGCTTTTCAAATTTT-CAAATTTTAC
1 CACTG-TTTTCAAATTTTAC-AATTTTGC
* *
59254382 CACTGTTTTGAAATTTTACAGTTTTGC
1 CACTGTTTTCAAATTTTACAATTTTGC
* *
59254409 CACAAT-TTTTCAGATTTTACAGTTTTGC
1 CAC--TGTTTTCAAATTTTACAATTTTGC
* * *
59254437 TACGATTTTTTC-GATTTTACAATTTT-C
1 CAC--TGTTTTCAAATTTTACAATTTTGC
* *
59254464 CTCTATTTTACAAATTTTA
1 CACTGTTTT-CAAATTTTA
59254483 TAGTTTTGAC
Statistics
Matches: 151, Mismatches: 24, Indels: 21
0.77 0.12 0.11
Matches are distributed among these distances:
25 5 0.03
26 1 0.01
27 37 0.25
28 100 0.66
29 8 0.05
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.49
Consensus pattern (27 bp):
CACTGTTTTCAAATTTTACAATTTTGC
Found at i:59254407 original size:83 final size:84
Alignment explanation
Indices: 59254276--59254436 Score: 236
Period size: 83 Copynumber: 1.9 Consensus size: 84
59254266 TGTTCACTGT
* *
59254276 TTTTCAAAAATTTCAATTTTGCCACAGTTTTTTAAATTTTACAATTTTGCCACAATTCTTCAGAT
1 TTTTCAAAAATTTCAATTTTACCACAGTTTTTGAAATTTTACAATTTTGCCACAATTCTTCAGAT
59254341 TTTACAATTTTGCCATTGC
66 TTTACAATTTTGCCATTGC
* * * *
59254360 TTTTC-AAATTTTCAAATTTTACCACTG-TTTTGAAATTTTACAGTTTTGCCACAATTTTTCAGA
1 TTTTCAAAAATTTC-AATTTTACCACAGTTTTTGAAATTTTACAATTTTGCCACAATTCTTCAGA
*
59254423 TTTTACAGTTTTGC
65 TTTTACAATTTTGC
59254437 TACGATTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
83 53 0.77
84 16 0.23
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (84 bp):
TTTTCAAAAATTTCAATTTTACCACAGTTTTTGAAATTTTACAATTTTGCCACAATTCTTCAGAT
TTTACAATTTTGCCATTGC
Found at i:59254419 original size:55 final size:56
Alignment explanation
Indices: 59254289--59254434 Score: 152
Period size: 55 Copynumber: 2.6 Consensus size: 56
59254279 TCAAAAATTT
* * *
59254289 CAATTTTGCCACAGTTTTTTAAATTTTACAATTTTGCCACAATTCTTCAGATTTTA
1 CAATTTTGCCACAGTTTTTCAAATTTTACAATTTTACCACAATTCTTCAAATTTTA
** * ** *
59254345 CAATTTTGCCATTGCTTTTCAAATTTT-CAAATTTTACCACTGTT-TTGAAATTTTA
1 CAATTTTGCCACAGTTTTTCAAATTTTAC-AATTTTACCACAATTCTTCAAATTTTA
* * * *
59254400 CAGTTTTGCCACAATTTTTCAGATTTTACAGTTTT
1 CAATTTTGCCACAGTTTTTCAAATTTTACAATTTT
59254435 GCTACGATTT
Statistics
Matches: 72, Mismatches: 16, Indels: 5
0.77 0.17 0.05
Matches are distributed among these distances:
55 36 0.50
56 36 0.50
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (56 bp):
CAATTTTGCCACAGTTTTTCAAATTTTACAATTTTACCACAATTCTTCAAATTTTA
Found at i:59254454 original size:83 final size:81
Alignment explanation
Indices: 59254276--59254490 Score: 213
Period size: 83 Copynumber: 2.6 Consensus size: 81
59254266 TGTTCACTGT
* * * *
59254276 TTTTCAAAAATTTC-AATTTTGCCACAGTTTTTTAAATTTTACAATTTTGCCACAATTCTTCAGA
1 TTTTC-AAATTTTCAAATTTT-CCACTG-TTTTCAAATTTTACAGTTTTGCCACAATTCTTCAGA
59254340 TTTTACAATTTTGCCATTGC
63 TTTTACAATTTTGCCATT-C
* *
59254360 TTTTCAAATTTTCAAATTTTACCACTGTTTTGAAATTTTACAGTTTTGCCACAATTTTTCAGATT
1 TTTTCAAATTTTCAAATTTT-CCACTGTTTTCAAATTTTACAGTTTTGCCACAATTCTTCAGATT
*
59254425 TTACAGTTTTGCTACGATT-
65 TTACAATTTTGC--C-ATTC
* * * *
59254444 TTTTC-GATTTT-ACAATTTTCCTCTATTTTACAAATTTTATAGTTTTG
1 TTTTCAAATTTTCA-AATTTTCCACTGTTTT-CAAATTTTACAGTTTTG
59254491 ACCTAAGATT
Statistics
Matches: 113, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
82 9 0.08
83 79 0.70
84 21 0.19
85 1 0.01
86 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.50
Consensus pattern (81 bp):
TTTTCAAATTTTCAAATTTTCCACTGTTTTCAAATTTTACAGTTTTGCCACAATTCTTCAGATTT
TACAATTTTGCCATTC
Found at i:59254898 original size:21 final size:21
Alignment explanation
Indices: 59254874--59254939 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
59254864 AGTTTATTTG
*
59254874 CATCGTTTAGTGGTTTATCCA
1 CATCATTTAGTGGTTTATCCA
**
59254895 CATCATTTGAGCAGTTTA-CCTA
1 CATCATTT-AGTGGTTTATCC-A
* *
59254917 CACCATTGAGTGGTTTATCCA
1 CATCATTTAGTGGTTTATCCA
59254938 CA
1 CA
59254940 CCTTATTAGT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.24, C:0.23, G:0.17, T:0.36
Consensus pattern (21 bp):
CATCATTTAGTGGTTTATCCA
Found at i:59254940 original size:21 final size:21
Alignment explanation
Indices: 59254882--59254984 Score: 75
Period size: 21 Copynumber: 4.8 Consensus size: 21
59254872 TGCATCGTTT
*
59254882 AGTGGTTTATCCACATCATTTG
1 AGTGGTTTATCCACACCA-TTG
**
59254904 AGCAGTTTA-CCTACACCATTG
1 AGTGGTTTATCC-ACACCATTG
59254925 AGTGGTTTATCCACACCTTATT-
1 AGTGGTTTATCCACACC--ATTG
* * *
59254947 AGTAGCTTTATCTACACCAATG
1 AGT-GGTTTATCCACACCATTG
* *
59254969 AGAGTTTTATCCACAC
1 AGTGGTTTATCCACAC
59254985 TGTACTAACA
Statistics
Matches: 64, Mismatches: 11, Indels: 13
0.73 0.12 0.15
Matches are distributed among these distances:
21 30 0.47
22 19 0.30
23 15 0.23
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (21 bp):
AGTGGTTTATCCACACCATTG
Found at i:59258971 original size:91 final size:88
Alignment explanation
Indices: 59258815--59259006 Score: 233
Period size: 91 Copynumber: 2.1 Consensus size: 88
59258805 ACTCCTGTTG
* * * * * *
59258815 TTGGATAAACCACCAGTGTTGCAGGTTAATATGCTGGCAGTAGTTGTGAGTACACAATGAGTTTG
1 TTGGATAAACCACAAGTGTTGCAGGTTAATACGCTGCCAGTAGTTATGAATACACAACGAGTTTG
*
59258880 CAGAT-AATAGTTGCTAATATAAGTT
66 CAGATGAA-AGCTGCTAATA-AA-TT
* * *
59258905 TTGGATAAACCACAAGTGCTTGCAGGTTAGTACGCTGCCAGTGGTTATGAATACACAACGATTTT
1 TTGGATAAACCACAAGTG-TTGCAGGTTAATACGCTGCCAGTAGTTATGAATACACAACGAGTTT
*
59258970 GCAGATGAAAGCTGCTAGTAAATT
65 GCAGATGAAAGCTGCTAATAAATT
*
59258994 GTGGATAAACCAC
1 TTGGATAAACCAC
59259007 CAGTATTTGT
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
89 14 0.16
90 19 0.22
91 53 0.60
92 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (88 bp):
TTGGATAAACCACAAGTGTTGCAGGTTAATACGCTGCCAGTAGTTATGAATACACAACGAGTTTG
CAGATGAAAGCTGCTAATAAATT
Found at i:59267130 original size:12 final size:13
Alignment explanation
Indices: 59267106--59267134 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
59267096 GGGTTATAAC
59267106 TATTGCATTTATT
1 TATTGCATTTATT
59267119 TATTGC-TTTATT
1 TATTGCATTTATT
59267131 TATT
1 TATT
59267135 CATGTATGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:59277905 original size:7 final size:7
Alignment explanation
Indices: 59277893--59277922 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
59277883 TTAGTCTTTT
59277893 TTATTTA
1 TTATTTA
59277900 TTATTTA
1 TTATTTA
59277907 TTATTTA
1 TTATTTA
59277914 TTA-TTA
1 TTATTTA
59277920 TTA
1 TTA
59277923 AATTTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (7 bp):
TTATTTA
Found at i:59277910 original size:3 final size:3
Alignment explanation
Indices: 59277897--59277961 Score: 55
Period size: 3 Copynumber: 21.3 Consensus size: 3
59277887 TCTTTTTTAT
* *
59277897 TTA TTA TTTA TTA TTTA TTA TTA TTA -AA TT- TTA TT- TTA TTG TTA
1 TTA TTA -TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
59277941 TTAA GTTA TTA TTA TTA TTA T
1 TT-A -TTA TTA TTA TTA TTA T
59277962 ACATACTCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
2 5 0.10
3 36 0.71
4 8 0.16
5 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:59277910 original size:14 final size:13
Alignment explanation
Indices: 59277893--59277961 Score: 56
Period size: 14 Copynumber: 5.3 Consensus size: 13
59277883 TTAGTCTTTT
59277893 TTATTTATTATTTA
1 TTATTTATTA-TTA
59277907 TTATTTATTATTA
1 TTATTTATTATTA
*
59277920 TTAAATT-TTATT-
1 TT-ATTTATTATTA
*
59277932 TTA-TTGTTATTAA
1 TTATTTATTATT-A
59277945 GTTA-TTATTATTA
1 -TTATTTATTATTA
59277958 TTAT
1 TTAT
59277962 ACATACTCAT
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
10 2 0.04
11 6 0.13
12 5 0.11
13 11 0.23
14 23 0.49
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:59278111 original size:17 final size:17
Alignment explanation
Indices: 59278078--59278123 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
59278068 CATAACTTTT
*
59278078 ATATACATATATATATAC
1 ATATACAT-TTTATATAC
*
59278096 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
59278113 ATATACATTTT
1 ATATACATTTT
59278124 TTATTTCCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:59278294 original size:30 final size:29
Alignment explanation
Indices: 59278260--59278351 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 29
59278250 ATTAATTTCA
*
59278260 ATATATGTAATTATTATTATTTGTTTTTAT
1 ATATATGTAATTATTATTATTT-TTTATAT
* *
59278290 ATATATGTAATTATCT-TT-TTTATAATCTAT
1 ATATATGTAATTAT-TATTATTT-T-TTATAT
*
59278320 ATATATGTAGATAATTATTATTTTTTATAT
1 ATATATGTA-ATTATTATTATTTTTTATAT
59278350 AT
1 AT
59278352 GTACATGTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
29 4 0.08
30 36 0.71
31 8 0.16
32 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (29 bp):
ATATATGTAATTATTATTATTTTTTATAT
Found at i:59283328 original size:11 final size:12
Alignment explanation
Indices: 59283298--59283327 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
59283288 AAAATATAAT
59283298 AAAAAAAGAGCA
1 AAAAAAAGAGCA
59283310 AAAAAAAGAGCA
1 AAAAAAAGAGCA
59283322 AAAAAA
1 AAAAAA
59283328 GGAAAGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAGCA
Found at i:59284708 original size:88 final size:88
Alignment explanation
Indices: 59284556--59285322 Score: 842
Period size: 88 Copynumber: 8.7 Consensus size: 88
59284546 AGAACAGATC
* * * * * *
59284556 ATTGAAGATAGCAGATCTTGTCTTCCTGTAC-CAGTAGCGAAGCAGATCAAAGACACCAGCCTTG
1 ATTGAAGATAGCAGATCTTGCCTTCCTGTACTGA-CAGCGAAGCAGATCGAAGACACTAGTCTTG
* * *
59284620 CCTCCCTAAGTTACAGCGGAGCAG
65 CCTCCCTAGGTTGCAGTGGAGCAG
* * *
59284644 GTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGTAGATCGAAGACACTAGTCTTGC
1 ATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACTAGTCTTGC
*
59284709 CTCCCTAGGTTGCAATGGAGCAG
66 CTCCCTAGGTTGCAGTGGAGCAG
* * *
59284732 ACTGAAGATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGC
1 ATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACTAGTCTTGC
59284797 CTCCCTAGGTTGCAGTGGAGCAG
66 CTCCCTAGGTTGCAGTGGAGCAG
* * * * *
59284820 ACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATC-AAGGGCACCAGCCTTG
1 ATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAA-GACACTAGTCTTG
* * *
59284884 CCTCCCTGGGTTGCAGCGGAGTAG
65 CCTCCCTAGGTTGCAGTGGAGCAG
* * * * * *
59284908 GTTGAAAATAGCAGATCTTGCCTTCCTATATTGACAGCGAAGTAGATCGAAGACACCAGTCTTGC
1 ATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACTAGTCTTGC
*
59284973 CTCCCAAGGTTGCAGTGGAGCAG
66 CTCCCTAGGTTGCAGTGGAGCAG
* * * * *
59284996 ACTGAAGATAGCAGATCTTGCCTTCCTGTACCGGCAGCGAAGCAGATCAAAGACACTAGCCTTGC
1 ATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACTAGTCTTGC
* *
59285061 CTCCCT-GGATTGCGGCGGAGCATG
66 CTCCCTAGG-TTGCAGTGGAGCA-G
* * * * * *
59285085 -TTGAAAATAGTAGATCTTTCCTTCCTGTACTGACAGCGAAGCAGATTGAAGGCACTATTCTTGC
1 ATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACTAGTCTTGC
* * *
59285149 CTCCCTAGGTTGCAGTGCAACAA
66 CTCCCTAGGTTGCAGTGGAGCAG
* * * * * * * * *
59285172 ACTGAAGATAGAAGATCTTGCCTTCCTGTACCGGCAGCGAAGCAGATCGAAAACTCTGGCCTTGT
1 ATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACTAGTCTTGC
* ** * *
59285237 CTCCCTAAGCAGTAGTGGAGTAG
66 CTCCCTAGGTTGCAGTGGAGCAG
* * * * * * *
59285260 GTTGAAAATAGTAGATCTTGCCTTCCTATATTGGCAGTGAAGCAGATCGAAGACA-TCAGTCTT
1 ATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACT-AGTCTT
59285323 ATTGCCTTGA
Statistics
Matches: 567, Mismatches: 104, Indels: 16
0.83 0.15 0.02
Matches are distributed among these distances:
87 5 0.01
88 556 0.98
89 6 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (88 bp):
ATTGAAGATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACTAGTCTTGC
CTCCCTAGGTTGCAGTGGAGCAG
Found at i:59284858 original size:176 final size:176
Alignment explanation
Indices: 59284557--59285322 Score: 953
Period size: 176 Copynumber: 4.4 Consensus size: 176
59284547 GAACAGATCA
* * * * * * *
59284557 TTGAAGATAGCAGATCTTGTCTTCCTGTAC-CAGTAGCGAAGCAGATCAAAGACACCAGCCTTGC
1 TTGAAAATAGTAGATCTTGCCTTCCTGTACTGA-CAGCGAAGCAGATCGAAGACACCAGTCTTGC
* * * ** * *
59284621 CTCCCTAAGTTACAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAG
65 CTCCCTAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAG
* * ** *
59284686 TAGATCGAAGACACTAGTCTTGCCTCCCTAGGTTGCAATGGAGCAGA
130 CAGATCGAAGACACTAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGG
* *
59284733 CTGAAGATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCC
1 TTGAAAATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCC
59284798 TCCCTAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGC
66 TCCCTAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGC
* * * *
59284863 AGATC-AAGGGCACCAGCCTTGCCTCCCTGGGTTGCAGCGGAGTAGG
131 AGATCGAA-GACACTAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGG
* * * *
59284909 TTGAAAATAGCAGATCTTGCCTTCCTATATTGACAGCGAAGTAGATCGAAGACACCAGTCTTGCC
1 TTGAAAATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCC
* *
59284974 TCCCAAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACCGGCAGCGAAGC
66 TCCCTAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGC
* * *
59285039 AGATCAAAGACACTAGCCTTGCCTCCCT-GGATTGCGGCGGAGCATG
131 AGATCGAAGACACTAGCCTTGCCTCCCTAGG-TTGCAGCGGAGCAGG
* * * * *
59285085 TTGAAAATAGTAGATCTTTCCTTCCTGTACTGACAGCGAAGCAGATTGAAGGCACTATTCTTGCC
1 TTGAAAATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCC
* * * * *
59285150 TCCCTAGGTTGCAGTGCAACAAACTGAAGATAGAAGATCTTGCCTTCCTGTACCGGCAGCGAAGC
66 TCCCTAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGC
* * * * * ** * * *
59285215 AGATCGAAAACTCTGGCCTTGTCTCCCTAAGCAGTAGTGGAGTAGG
131 AGATCGAAGACACTAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGG
* * * * *
59285261 TTGAAAATAGTAGATCTTGCCTTCCTATATTGGCAGTGAAGCAGATCGAAGACATCAGTCTT
1 TTGAAAATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTT
59285323 ATTGCCTTGA
Statistics
Matches: 512, Mismatches: 73, Indels: 10
0.86 0.12 0.02
Matches are distributed among these distances:
175 4 0.01
176 504 0.98
177 4 0.01
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (176 bp):
TTGAAAATAGTAGATCTTGCCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCC
TCCCTAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGC
AGATCGAAGACACTAGCCTTGCCTCCCTAGGTTGCAGCGGAGCAGG
Found at i:59285036 original size:264 final size:263
Alignment explanation
Indices: 59284558--59285322 Score: 935
Period size: 264 Copynumber: 2.9 Consensus size: 263
59284548 AACAGATCAT
* * *
59284558 TGAAGATAGCAGATCTTGTCTTCCTGTACC-AGTAGCGAAGCAGATCAAAGACACCAGCCTTGCC
1 TGAAGATAGCAGATCTTGCCTTCCTGTACCGA-CAGCGAAGCAGATC-AAGGCACCAGCCTTGCC
* *
59284622 TCCCTAAGTTACAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGT
64 TCCCTAGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGT
* *
59284687 AGATCGAAGACACTAGTCTTGCCTCCCTAGGTTGCAATGGAGCAGACTGAAGATAGTAGATCTTG
129 AGATCGAAGACACTAGTCTTGCCTCCCAAGGTTGCAGTGGAGCAGACTGAAGATAGTAGATCTTG
* *
59284752 CCTTCCTGTACTGACAGCGAAGCAGATCGAAGACACCAGTCTTGCCTCCCTAGG-TTGCAGTGGA
194 CCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGTCTTGCCTCCCT-GGATTGCAGCGGA
59284816 GCA-GAC
258 GCATG-C
59284822 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCAAGGGCACCAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCAA-GGCACCAGCCTTGCCT
* * * *
59284887 CCCTGGGTTGCAGCGGAGTAGGTTGAAAATAGCAGATCTTGCCTTCCTATATTGACAGCGAAGTA
65 CCCTAGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGTA
* *
59284952 GATCGAAGACACCAGTCTTGCCTCCCAAGGTTGCAGTGGAGCAGACTGAAGATAGCAGATCTTGC
130 GATCGAAGACACTAGTCTTGCCTCCCAAGGTTGCAGTGGAGCAGACTGAAGATAGTAGATCTTGC
* * * * *
59285017 CTTCCTGTACCGGCAGCGAAGCAGATCAAAGACACTAGCCTTGCCTCCCTGGATTGCGGCGGAGC
195 CTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGTCTTGCCTCCCTGGATTGCAGCGGAGC
*
59285082 ATGT
260 ATGC
* * * * * * **
59285086 TGAAAATAGTAGATCTTTCCTTCCTGTACTGACAGCGAAGCAGATTGAAGGCACTATTCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGA-TCAAGGCACCAGCCTTGCCT
* * * *** * * * * *
59285151 CCCTAGGTTGCAGTGCAACAAACTGAAGATAGAAGATCTTGCCTTCCTGTACCGGCAGCGAAGCA
65 CCCTAGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGTA
* * * * * ** * * ** *
59285216 GATCGAAAACTCTGGCCTTGTCTCCCTAA-GCAGTAGTGGAGTAGGTTGAAAATAGTAGATCTTG
130 GATCGAAGACACTAGTCTTGCCTCCC-AAGGTTGCAGTGGAGCAGACTGAAGATAGTAGATCTTG
* * * *
59285280 CCTTCCTATATTGGCAGTGAAGCAGATCGAAGACATCAGTCTT
194 CCTTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGTCTT
59285323 ATTGCCTTGA
Statistics
Matches: 429, Mismatches: 66, Indels: 12
0.85 0.13 0.02
Matches are distributed among these distances:
263 4 0.01
264 418 0.97
265 7 0.02
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (263 bp):
TGAAGATAGCAGATCTTGCCTTCCTGTACCGACAGCGAAGCAGATCAAGGCACCAGCCTTGCCTC
CCTAGGTTGCAGCGGAGCAGGTTGAAAATAGCAGATCTTGCCTTCCTGTACTGACAGCGAAGTAG
ATCGAAGACACTAGTCTTGCCTCCCAAGGTTGCAGTGGAGCAGACTGAAGATAGTAGATCTTGCC
TTCCTGTACTGGCAGCGAAGCAGATCGAAGACACCAGTCTTGCCTCCCTGGATTGCAGCGGAGCA
TGC
Found at i:59285546 original size:117 final size:117
Alignment explanation
Indices: 59285348--59285700 Score: 607
Period size: 117 Copynumber: 3.0 Consensus size: 117
59285338 CAATGAAAAT
*
59285348 GATTGAAGCCACGACGACGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGC
1 GATTGAAGCCACGACGGCGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGC
* *
59285413 GGATTAAAGCTAAGGGCAGTGAATCCTATCTCTTTGGCATTGCAGTGGAGCA
66 GGATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCA
* * *
59285465 GATTGAAGCCACGACGGCGAATCTTATCTTTCTGGAGTTAAGGCTTGGATAAGCTGAAGTGGAGC
1 GATTGAAGCCACGACGGCGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGC
*
59285530 GGATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGTGCA
66 GGATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCA
* * *
59285582 GATTGAAGCCACGATGGCGAATCTTATCTTCCTGGCGTTAAAGTTTGGATTAGCTGAAGTGGAGC
1 GATTGAAGCCACGACGGCGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGC
*
59285647 GGATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTTGCATTGCAGTGGAGCA
66 GGATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCA
59285699 GA
1 GA
59285701 CTGAGTAAGA
Statistics
Matches: 221, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 221 1.00
ACGTcount: A:0.25, C:0.18, G:0.30, T:0.27
Consensus pattern (117 bp):
GATTGAAGCCACGACGGCGAATCTTATCTTCCTGGCGTTAAGGCTTGGATTAGCTGAAGTGGAGC
GGATTAAAGCTGAGGGCAGCGAATCCTATCTCTTTGGCATTGCAGTGGAGCA
Found at i:59285735 original size:44 final size:44
Alignment explanation
Indices: 59285685--59285784 Score: 121
Period size: 44 Copynumber: 2.3 Consensus size: 44
59285675 TCTCTTTTGC
* * *
59285685 ATTGCAGTGGAGCAGACTGAGT-AAGAAAGTCTTATCCCCCTAAA
1 ATTGCAGTGGAGCAGACTGAATGAACAAA-TCATATCCCCCTAAA
* *
59285729 ATTGCAGTGCAGCAGACTGAATGAACAAATCATATCTCCCTAAA
1 ATTGCAGTGGAGCAGACTGAATGAACAAATCATATCCCCCTAAA
* *
59285773 GTTGTAGTGGAG
1 ATTGCAGTGGAG
59285785 TGGATTAGAA
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
44 42 0.89
45 5 0.11
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (44 bp):
ATTGCAGTGGAGCAGACTGAATGAACAAATCATATCCCCCTAAA
Found at i:59286604 original size:3 final size:3
Alignment explanation
Indices: 59286596--59286626 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
59286586 GGTTATTAAG
59286596 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
59286627 ACATACGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:59286756 original size:27 final size:27
Alignment explanation
Indices: 59286726--59286779 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
59286716 ATTATTATTT
*
59286726 TATATGCA-TAAC-TTTTATATACATA
1 TATATACATTAACATTTTATATACATA
*
59286751 TATATACATTTACATTTTATATACATA
1 TATATACATTAACATTTTATATACATA
59286778 TA
1 TA
59286780 CATTTTTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.28
26 3 0.12
27 15 0.60
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.46
Consensus pattern (27 bp):
TATATACATTAACATTTTATATACATA
Found at i:59286773 original size:17 final size:17
Alignment explanation
Indices: 59286742--59286785 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
59286732 CATAACTTTT
*
59286742 ATATACA-TATATATAC
1 ATATACATTTTATATAC
*
59286758 ATTTACATTTTATATAC
1 ATATACATTTTATATAC
59286775 ATATACATTTT
1 ATATACATTTT
59286786 TATTTCCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATACATTTTATATAC
Found at i:59286955 original size:30 final size:29
Alignment explanation
Indices: 59286921--59287012 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 29
59286911 ATTAATTTCA
*
59286921 ATATATGTAATTATTATTATTTGTTTTTAT
1 ATATATGTAATTATTATTATTT-TTTATAT
* *
59286951 ATATATGTAATTATCT-TT-TTTATAATCTAT
1 ATATATGTAATTAT-TATTATTT-T-TTATAT
*
59286981 ATATATGTAGATAATTATTATTTTTTATAT
1 ATATATGTA-ATTATTATTATTTTTTATAT
59287011 AT
1 AT
59287013 GTACATGTAT
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
29 4 0.08
30 36 0.71
31 8 0.16
32 3 0.06
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (29 bp):
ATATATGTAATTATTATTATTTTTTATAT
Found at i:59291244 original size:25 final size:25
Alignment explanation
Indices: 59291215--59291298 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
59291205 CAGATACTCC
*
59291215 ACAGCTCGT-ATGAGCTTATCGATTT
1 ACAGCTCGTGA-GAGCATATCGATTT
*
59291240 ACAGCTCATGAGAGCATATCGATTT
1 ACAGCTCGTGAGAGCATATCGATTT
* * *
59291265 ACAGCTCGAGAGAGCATACCGATTC
1 ACAGCTCGTGAGAGCATATCGATTT
*
59291290 ATAGCTCGT
1 ACAGCTCGT
59291299 ATAAGCATAC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
25 49 0.98
26 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCATATCGATTT
Found at i:59291488 original size:31 final size:30
Alignment explanation
Indices: 59291453--59291513 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
59291443 TATTTAATTG
*
59291453 AGATACATGGAAAT-GATTTTACATGATATAT
1 AGATACAT-GAAATGGATGTTACATG-TATAT
*
59291484 AGATACATGATATGGATGTTACATGTATAT
1 AGATACATGAAATGGATGTTACATGTATAT
59291514 GGAAATTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.36
Consensus pattern (30 bp):
AGATACATGAAATGGATGTTACATGTATAT
Found at i:59296624 original size:18 final size:17
Alignment explanation
Indices: 59296591--59296629 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
59296581 TTTTATAAAT
59296591 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
59296609 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
59296626 TGTG
1 TGTG
59296630 GAAGGAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:59296882 original size:23 final size:23
Alignment explanation
Indices: 59296855--59296968 Score: 138
Period size: 23 Copynumber: 5.0 Consensus size: 23
59296845 AGTGTTATTG
*
59296855 ATCAGTGGTAGCTTCAGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * * *
59296878 TTCAGTGATAGCTACGGCTACCT
1 ATCAGTGGTAGCTTCGGCTACAT
*
59296901 ATCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
59296924 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
59296947 ATCAGTGGTAGTTTCGGCTACA
1 ATCAGTGGTAGCTTCGGCTACA
59296969 AATTAGTGTG
Statistics
Matches: 73, Mismatches: 18, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 73 1.00
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:59296907 original size:46 final size:45
Alignment explanation
Indices: 59296855--59296968 Score: 174
Period size: 46 Copynumber: 2.5 Consensus size: 45
59296845 AGTGTTATTG
59296855 ATCAGTGGTAGCTTCAGCTACATTTCAGTGATAGCTACGGCTACCT
1 ATCAGTGGTAGCTTC-GCTACATTTCAGTGATAGCTACGGCTACCT
* *
59296901 ATCAGTGGTAGCTTCGACTACATTTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCG-CTACATTTCAGTGATAGCTACGGCTACCT
*
59296947 ATCAGTGGTAGTTTCGGCTACA
1 ATCAGTGGTAGCTTC-GCTACA
59296969 AATTAGTGTG
Statistics
Matches: 63, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
45 1 0.02
46 61 0.97
47 1 0.02
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.31
Consensus pattern (45 bp):
ATCAGTGGTAGCTTCGCTACATTTCAGTGATAGCTACGGCTACCT
Found at i:59304609 original size:21 final size:21
Alignment explanation
Indices: 59304566--59304610 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
59304556 TTTAAGTTAC
* *
59304566 GATAATTTCGGCTTGACCCAT
1 GATAATTTCGACTTGACACAT
* *
59304587 GATAATTTCGATTTGACATAT
1 GATAATTTCGACTTGACACAT
59304608 GAT
1 GAT
59304611 TCTTAGTAGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.38
Consensus pattern (21 bp):
GATAATTTCGACTTGACACAT
Found at i:59307343 original size:17 final size:18
Alignment explanation
Indices: 59307309--59307343 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
59307299 GTTTTGAAAT
*
59307309 TGAATAATTATTTGTAAA
1 TGAATAATTATTTCTAAA
59307327 TGAATAA-TATTTCTAAA
1 TGAATAATTATTTCTAAA
59307344 ACGAACGACA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (18 bp):
TGAATAATTATTTCTAAA
Found at i:59322969 original size:6 final size:6
Alignment explanation
Indices: 59322960--59323012 Score: 70
Period size: 6 Copynumber: 8.3 Consensus size: 6
59322950 TCAATTTCAA
*
59322960 TTTCTT TTTCTT TTTCTT TTTCTT TTTCATT TTTCTCT TCTCGTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTC-TT TTTCT-T TTTC-TT TTTCTT
59323011 TT
1 TT
59323013 ACCTCACTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
6 27 0.64
7 14 0.33
8 1 0.02
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.77
Consensus pattern (6 bp):
TTTCTT
Found at i:59322975 original size:18 final size:19
Alignment explanation
Indices: 59322954--59322994 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
59322944 TTTCTTTCAA
59322954 TTTCAATTTCTTTTTC-TT
1 TTTCAATTTCTTTTTCATT
**
59322972 TTTCTTTTTCTTTTTCATT
1 TTTCAATTTCTTTTTCATT
59322991 TTTC
1 TTTC
59322995 TCTTCTCGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTCAATTTCTTTTTCATT
Found at i:59323682 original size:54 final size:54
Alignment explanation
Indices: 59323600--59323709 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
59323590 TCTCATTTTT
59323600 TATTACAAGATGGAGTTGAAATGAAAGAATCAGGATGAAATGATTTGCGTTGGG
1 TATTACAAGATGGAGTTGAAATGAAAGAATCAGGATGAAATGATTTGCGTTGGG
59323654 TATTACAAGATGGAGTTGAAATGAAAGAATCAGGATGAAATGATTTGCGTTGGG
1 TATTACAAGATGGAGTTGAAATGAAAGAATCAGGATGAAATGATTTGCGTTGGG
59323708 TA
1 TA
59323710 AAAGTGGAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.37, C:0.05, G:0.29, T:0.28
Consensus pattern (54 bp):
TATTACAAGATGGAGTTGAAATGAAAGAATCAGGATGAAATGATTTGCGTTGGG
Found at i:59324526 original size:16 final size:17
Alignment explanation
Indices: 59324491--59324537 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
59324481 TATTTTGCAC
*
59324491 ACTTTTTTTATATTCGAA
1 ACTTTTTTT-TACTCGAA
59324509 ACTTTTTTTTACTC-AA
1 ACTTTTTTTTACTCGAA
59324525 ACTTTTTTTTACT
1 ACTTTTTTTTACT
59324538 TCTTTTCAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
16 15 0.54
17 4 0.14
18 9 0.32
ACGTcount: A:0.23, C:0.15, G:0.02, T:0.60
Consensus pattern (17 bp):
ACTTTTTTTTACTCGAA
Found at i:59327896 original size:21 final size:19
Alignment explanation
Indices: 59327861--59327924 Score: 74
Period size: 21 Copynumber: 3.2 Consensus size: 19
59327851 ACCATATTCT
*
59327861 ATTTTTAAAATTTAAAATTA
1 ATTTTTAAAAATT-AAATTA
*
59327881 ATTTTTAGAAAATTAACTTA
1 ATTTTTA-AAAATTAAATTA
59327901 ATTTTTAAAAAAATTAAATTA
1 ATTTTT--AAAAATTAAATTA
59327922 ATT
1 ATT
59327925 AGAAGTATCC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
20 18 0.47
21 19 0.50
22 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
ATTTTTAAAAATTAAATTA
Found at i:59328269 original size:7 final size:7
Alignment explanation
Indices: 59328233--59328284 Score: 54
Period size: 7 Copynumber: 7.6 Consensus size: 7
59328223 ATTATTTCAT
*
59328233 TAAAAAG
1 TAAAAGG
*
59328240 TAAAAGA
1 TAAAAGG
*
59328247 AAAAAGAG
1 TAAAAG-G
59328255 -AAAA-G
1 TAAAAGG
59328260 TAAAAGG
1 TAAAAGG
59328267 TAAAAGG
1 TAAAAGG
59328274 TAAAAGG
1 TAAAAGG
59328281 TAAA
1 TAAA
59328285 TAAAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
5 1 0.03
6 4 0.11
7 33 0.87
ACGTcount: A:0.67, C:0.00, G:0.21, T:0.12
Consensus pattern (7 bp):
TAAAAGG
Found at i:59342572 original size:17 final size:17
Alignment explanation
Indices: 59342550--59342582 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
59342540 CCAAAATCGC
59342550 TATCTGGTCATCTCAAT
1 TATCTGGTCATCTCAAT
59342567 TATCTGGTCATCTCAA
1 TATCTGGTCATCTCAA
59342583 AGGTTGTAGT
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:0.24, C:0.24, G:0.12, T:0.39
Consensus pattern (17 bp):
TATCTGGTCATCTCAAT
Found at i:59345105 original size:20 final size:20
Alignment explanation
Indices: 59345082--59345119 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59345072 ATTTTTTTTT
59345082 ATTTTTTTCA-AATTTTTAGA
1 ATTTTTTT-AGAATTTTTAGA
59345102 ATTTTTTTAGAATTTTTA
1 ATTTTTTTAGAATTTTTA
59345120 AATAATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.29, C:0.03, G:0.05, T:0.63
Consensus pattern (20 bp):
ATTTTTTTAGAATTTTTAGA
Found at i:59345108 original size:11 final size:11
Alignment explanation
Indices: 59345094--59345118 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59345084 TTTTTTCAAA
59345094 TTTTTAGAATT
1 TTTTTAGAATT
59345105 TTTTTAGAATT
1 TTTTTAGAATT
59345116 TTT
1 TTT
59345119 AAATAATTGT
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:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTTAGAATT
Found at i:59348653 original size:20 final size:20
Alignment explanation
Indices: 59348625--59348685 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 20
59348615 AATTGGGAAA
*
59348625 TGGGTTGGGGTAGAAGGGGG
1 TGGGATGGGGTAGAAGGGGG
59348645 TGGGATGGGTTGGGGTAGAAGGGGG
1 TGGGA-----TGGGGTAGAAGGGGG
*
59348670 TGGGATGGGATAGAAG
1 TGGGATGGGGTAGAAG
59348686 TAAAAGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
20 14 0.41
25 20 0.59
ACGTcount: A:0.20, C:0.00, G:0.61, T:0.20
Consensus pattern (20 bp):
TGGGATGGGGTAGAAGGGGG
Found at i:59348656 original size:25 final size:25
Alignment explanation
Indices: 59348624--59348678 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
59348614 AAATTGGGAA
59348624 ATGGGTTGGGGTAGAAGGGGGTGGG
1 ATGGGTTGGGGTAGAAGGGGGTGGG
59348649 ATGGGTTGGGGTAGAAGGGGGTGGG
1 ATGGGTTGGGGTAGAAGGGGGTGGG
59348674 ATGGG
1 ATGGG
59348679 ATAGAAGTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.16, C:0.00, G:0.64, T:0.20
Consensus pattern (25 bp):
ATGGGTTGGGGTAGAAGGGGGTGGG
Found at i:59348742 original size:30 final size:30
Alignment explanation
Indices: 59348684--59348742 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
59348674 ATGGGATAGA
* *
59348684 AGTAAAAGTTTTGAGGGGAAAGTGAGAGGG
1 AGTAAAAGTGTTGAGGGGAAAGTAAGAGGG
59348714 AGTAAAAGTGTT-AGGGGAAAGTAAAGAGG
1 AGTAAAAGTGTTGAGGGGAAAGT-AAGAGG
59348743 TTTGAGAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 10 0.38
30 16 0.62
ACGTcount: A:0.41, C:0.00, G:0.41, T:0.19
Consensus pattern (30 bp):
AGTAAAAGTGTTGAGGGGAAAGTAAGAGGG
Found at i:59354784 original size:44 final size:44
Alignment explanation
Indices: 59354709--59354916 Score: 131
Period size: 44 Copynumber: 4.7 Consensus size: 44
59354699 CCAAGCCTCG
* * * *
59354709 TCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATAGCAGATCTTA
* * * *
59354753 TCTCCCTAAGCAGTAGTGCAGCAGATCGAAGA-CGACAAATCTTA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATAG-CAGATCTTA
* * ** * * *
59354797 TCTTTCC-AAG-A-TAGTAGGAAGCAGATTTAAGCCACCA-AGCCTTG
1 TC-TCCCTAAGCAGTAGT-GG-AGCAGATTGAAGATAGCAGA-TCTTA
* * * *
59354841 TCTCCCTGAA-CAGCAGTGGAGTAGGTTGAAGATAGCAGATCTTG
1 TCTCCCT-AAGCAGTAGTGGAGCAGATTGAAGATAGCAGATCTTA
* *
59354885 TCTCCTTAAGCAGTAGTGGAGCAGATCGAAGA
1 TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGA
59354917 CGACAAATCT
Statistics
Matches: 121, Mismatches: 31, Indels: 24
0.69 0.18 0.14
Matches are distributed among these distances:
42 4 0.03
43 9 0.07
44 96 0.79
45 9 0.07
46 3 0.02
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (44 bp):
TCTCCCTAAGCAGTAGTGGAGCAGATTGAAGATAGCAGATCTTA
Found at i:59354858 original size:132 final size:132
Alignment explanation
Indices: 59354616--59355021 Score: 638
Period size: 132 Copynumber: 3.1 Consensus size: 132
59354606 AAATTACAGG
* * * * * *
59354616 TCTTGTCTCCCTAAGCAGTAGTGGAGAAGATCAAAGACGGCAAATCTTATCTTTCCAAGATAATG
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTA
*
59354681 GGAAGCAGATTTAAGCCACCAAGCCTCGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCA
66 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCA
59354746 GA
131 GA
*
59354748 TCTTATCTCCCTAAGCAGTAGTGCAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTA
*
59354813 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAACAGCAGTGGAGTAGGTTGAAGATAGCA
66 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCA
59354878 GA
131 GA
* *
59354880 TCTTGTCTCCTTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAG--AGTA
1 TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTA
* **
59354943 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCTCTGAGCAGCAACGGAGTAGGTTGAAGATTA-C
66 GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGA-TAGC
*
59355007 AAA
130 AGA
*
59355010 TCCTATCTCCCT
1 TCTTATCTCCCT
59355022 GAAGTTGCAG
Statistics
Matches: 253, Mismatches: 20, Indels: 4
0.91 0.07 0.01
Matches are distributed among these distances:
130 72 0.28
131 2 0.01
132 179 0.71
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (132 bp):
TCTTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACGACAAATCTTATCTTTCCAAGATAGTA
GGAAGCAGATTTAAGCCACCAAGCCTTGTCTCCCTGAGCAGCAGTGGAGTAGGTTGAAGATAGCA
GA
Found at i:59359995 original size:19 final size:18
Alignment explanation
Indices: 59359940--59359992 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
59359930 CCCCTTATTA
*
59359940 AACATAAAAAATAAAATT
1 AACATGAAAAATAAAATT
* *
59359958 AACATTAAAAATGGAAATT
1 AACATGAAAAAT-AAAATT
59359977 AA-AGTGAAAAATAAAA
1 AACA-TGAAAAATAAAA
59359993 ATTTTAAAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.68, C:0.04, G:0.08, T:0.21
Consensus pattern (18 bp):
AACATGAAAAATAAAATT
Found at i:59361940 original size:21 final size:22
Alignment explanation
Indices: 59361889--59361940 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
59361879 ATATTAATAT
*
59361889 TTAA-CATGAAAATAATATAAA
1 TTAAGCATAAAAATAATATAAA
* * *
59361910 TTATGTATAAAAATAATGT-AA
1 TTAAGCATAAAAATAATATAAA
59361931 TTAAGCATAA
1 TTAAGCATAA
59361941 TTTCACATTC
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.33
Consensus pattern (22 bp):
TTAAGCATAAAAATAATATAAA
Found at i:59362463 original size:17 final size:17
Alignment explanation
Indices: 59362426--59362463 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
59362416 CTCTCATATT
* *
59362426 TTTCTTTATTTTTTTTA
1 TTTCTTTACTCTTTTTA
59362443 -TTCTTTACTCTTTTTA
1 TTTCTTTACTCTTTTTA
59362459 TTTCT
1 TTTCT
59362464 CTTTATTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTTTACTCTTTTTA
Found at i:59366485 original size:21 final size:20
Alignment explanation
Indices: 59366453--59366491 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
59366443 TAGATATCAC
59366453 TTATAATCAAAT-AAAAATT
1 TTATAATCAAATCAAAAATT
59366472 TTATATATCAAAATCAAAAA
1 TTATA-ATC-AAATCAAAAA
59366492 AATATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 3 0.18
21 4 0.24
22 5 0.29
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (20 bp):
TTATAATCAAATCAAAAATT
Found at i:59368187 original size:42 final size:42
Alignment explanation
Indices: 59368128--59368228 Score: 168
Period size: 42 Copynumber: 2.4 Consensus size: 42
59368118 TTTGCAGCGT
59368128 TTTAGCGGCGTTTTTTTCTAAGCGCCT-CTAAAGAACATGTTC
1 TTTAGCGGCGTTTTTTTCTAAGCG-CTGCTAAAGAACATGTTC
59368170 TTTAGCGGCGTTTTTTTCTAAGCGCTGCTAAAGAACATGTTC
1 TTTAGCGGCGTTTTTTTCTAAGCGCTGCTAAAGAACATGTTC
* *
59368212 TTTAGCAGCATTTTTTT
1 TTTAGCGGCGTTTTTTT
59368229 TACAAAAATG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
41 2 0.04
42 54 0.96
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTTTCTAAGCGCTGCTAAAGAACATGTTC
Found at i:59368577 original size:21 final size:21
Alignment explanation
Indices: 59368547--59368598 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
59368537 GCTATGCTCT
*
59368547 GCTTCTCTCGCTGCAGCCT-CC
1 GCTTCCCTCGCTGCAG-CTGCC
*
59368568 GCTTCCCTCGCTGCAGCTGCT
1 GCTTCCCTCGCTGCAGCTGCC
59368589 GCTTCCCTCG
1 GCTTCCCTCG
59368599 TTACCGCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 26 0.93
ACGTcount: A:0.04, C:0.46, G:0.21, T:0.29
Consensus pattern (21 bp):
GCTTCCCTCGCTGCAGCTGCC
Found at i:59373746 original size:20 final size:19
Alignment explanation
Indices: 59373709--59373751 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 19
59373699 TTATAGAAAT
*
59373709 AAAATATTTAAATTTTTA-
1 AAAATATATAAATTTTTAC
59373727 AAAATATATATAATTATTTAC
1 AAAATATATA-AATT-TTTAC
59373748 AAAA
1 AAAA
59373752 CGTGTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 4 0.19
20 4 0.19
21 4 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (19 bp):
AAAATATATAAATTTTTAC
Found at i:59373829 original size:61 final size:61
Alignment explanation
Indices: 59373738--59373885 Score: 165
Period size: 61 Copynumber: 2.4 Consensus size: 61
59373728 AAATATATAT
* * * *
59373738 AATTATTTACAAAACGTGTAAAATTGATACTTA-TAAA-TTTTATTAAAAATAAATCTAGAAC
1 AATTATTTACAAAACTTATAAATTTAATAC-TACTAAATTTTTA-TAAAAATAAATCTAGAAC
* * * ** * *
59373799 ACTTTTTTAGAAAACTTATAAATTTAATACTACTAAATTTTTATACTAATAAATTTAGAAT
1 AATTATTTACAAAACTTATAAATTTAATACTACTAAATTTTTATAAAAATAAATCTAGAAC
59373860 AATTATTTACAAAACTTATAAATTTA
1 AATTATTTACAAAACTTATAAATTTA
59373886 GAAAACTTAT
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
60 2 0.03
61 64 0.90
62 5 0.07
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (61 bp):
AATTATTTACAAAACTTATAAATTTAATACTACTAAATTTTTATAAAAATAAATCTAGAAC
Found at i:59373837 original size:15 final size:15
Alignment explanation
Indices: 59373816--59373855 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
59373806 TAGAAAACTT
59373816 ATAAATTTAATACTA
1 ATAAATTTAATACTA
* *
59373831 CTAAATTTTTATACTA
1 ATAAA-TTTAATACTA
59373847 ATAAATTTA
1 ATAAATTTA
59373856 GAATAATTAT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
15 7 0.35
16 13 0.65
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (15 bp):
ATAAATTTAATACTA
Found at i:59373890 original size:17 final size:17
Alignment explanation
Indices: 59373864--59373896 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
59373854 TAGAATAATT
59373864 ATTTACAAAACTTATAA
1 ATTTACAAAACTTATAA
*
59373881 ATTTAGAAAACTTATA
1 ATTTACAAAACTTATA
59373897 TAGAAAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.09, G:0.03, T:0.36
Consensus pattern (17 bp):
ATTTACAAAACTTATAA
Found at i:59374704 original size:2 final size:2
Alignment explanation
Indices: 59374697--59374728 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
59374687 TTTCGTCACT
*
59374697 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59374729 AGAAGGTAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59376229 original size:14 final size:14
Alignment explanation
Indices: 59376210--59376241 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
59376200 TTAATAATAT
59376210 TTTATATGTCTATA
1 TTTATATGTCTATA
59376224 TTTATATGTCTATA
1 TTTATATGTCTATA
59376238 TTTA
1 TTTA
59376242 AATTTTAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.28, C:0.06, G:0.06, T:0.59
Consensus pattern (14 bp):
TTTATATGTCTATA
Found at i:59379449 original size:6 final size:6
Alignment explanation
Indices: 59379438--59379510 Score: 146
Period size: 6 Copynumber: 12.2 Consensus size: 6
59379428 TATAAAAATA
59379438 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
59379486 TTATAT TTATAT TTATAT TTATAT T
1 TTATAT TTATAT TTATAT TTATAT T
59379511 AAATCAATAA
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 67 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTATAT
Found at i:59379967 original size:2 final size:2
Alignment explanation
Indices: 59379960--59379992 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59379950 AAACTGTATT
59379960 TA TA TA 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 TA TA TA T
59379993 TGTTCTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59380168 original size:28 final size:28
Alignment explanation
Indices: 59380129--59380188 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
59380119 ACGAATGAAA
59380129 AAAACAATTAGATAATAAGAAGAAGAAG
1 AAAACAATTAGATAATAAGAAGAAGAAG
59380157 AAAACAATTAGATAATAAGAAGAAGAAG
1 AAAACAATTAGATAATAAGAAGAAGAAG
59380185 AAAA
1 AAAA
59380189 GGGAGGGGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.67, C:0.03, G:0.17, T:0.13
Consensus pattern (28 bp):
AAAACAATTAGATAATAAGAAGAAGAAG
Found at i:59382879 original size:15 final size:16
Alignment explanation
Indices: 59382849--59382880 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
59382839 CAAATAGGTT
59382849 TAGTGCATTATTTTTTA
1 TAGTGCATTA-TTTTTA
59382866 TAGTGCATTATTTTT
1 TAGTGCATTATTTTT
59382881 GAATGAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.22, C:0.06, G:0.12, T:0.59
Consensus pattern (16 bp):
TAGTGCATTATTTTTA
Found at i:59383399 original size:15 final size:15
Alignment explanation
Indices: 59383372--59383400 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59383362 CATATTTAAT
59383372 TACATAATATTTTTC
1 TACATAATATTTTTC
59383387 TACATAATATTTTT
1 TACATAATATTTTT
59383401 GTTTCAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.10, G:0.00, T:0.55
Consensus pattern (15 bp):
TACATAATATTTTTC
Found at i:59389147 original size:12 final size:12
Alignment explanation
Indices: 59389130--59389160 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
59389120 AATTTCAGTC
59389130 TTTAAAGAAAAG
1 TTTAAAGAAAAG
59389142 TTTAAAGAAAAG
1 TTTAAAGAAAAG
59389154 TTTAAAG
1 TTTAAAG
59389161 CTTATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.29
Consensus pattern (12 bp):
TTTAAAGAAAAG
Found at i:59398684 original size:20 final size:21
Alignment explanation
Indices: 59398659--59398706 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
59398649 GTTTCATTCA
*
59398659 AACCCTAGGTT-AAACATGCG
1 AACCCTAGATTCAAACATGCG
*
59398679 AACCCTAGATTCAAATATGCG
1 AACCCTAGATTCAAACATGCG
59398700 AACCCTA
1 AACCCTA
59398707 TATATGTTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.38, C:0.27, G:0.15, T:0.21
Consensus pattern (21 bp):
AACCCTAGATTCAAACATGCG
Found at i:59398754 original size:22 final size:22
Alignment explanation
Indices: 59398729--59398771 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
59398719 GTGAATTCTA
* *
59398729 TATATGTGTTATATGCAAACCC
1 TATATATGATATATGCAAACCC
59398751 TATATATGATATATGCAAACC
1 TATATATGATATATGCAAACC
59398772 ATTGTACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (22 bp):
TATATATGATATATGCAAACCC
Found at i:59399753 original size:13 final size:13
Alignment explanation
Indices: 59399735--59399761 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
59399725 CATATCTTTC
59399735 AATTTAGAAAACT
1 AATTTAGAAAACT
59399748 AATTTAGAAAACT
1 AATTTAGAAAACT
59399761 A
1 A
59399762 TCTTTTGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.07, T:0.30
Consensus pattern (13 bp):
AATTTAGAAAACT
Found at i:59412899 original size:21 final size:21
Alignment explanation
Indices: 59412855--59412899 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
59412845 AAACCTAAGC
**
59412855 TTATTTGACATAATTTTTAAA
1 TTATTTGACATAATCCTTAAA
*
59412876 TTATTTGACATAATCCTTAGA
1 TTATTTGACATAATCCTTAAA
59412897 TTA
1 TTA
59412900 GGCACTCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.49
Consensus pattern (21 bp):
TTATTTGACATAATCCTTAAA
Found at i:59413623 original size:14 final size:14
Alignment explanation
Indices: 59413604--59413636 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
59413594 CATCATTTCG
59413604 TTATTATATTGCTA
1 TTATTATATTGCTA
59413618 TTATTATATTGCTA
1 TTATTATATTGCTA
*
59413632 CTATT
1 TTATT
59413637 TTGTTATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (14 bp):
TTATTATATTGCTA
Found at i:59414623 original size:2 final size:2
Alignment explanation
Indices: 59414618--59414643 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59414608 TATTTTACGA
59414618 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
59414644 TTGCGTTGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59419259 original size:84 final size:86
Alignment explanation
Indices: 59419083--59419261 Score: 249
Period size: 85 Copynumber: 2.1 Consensus size: 86
59419073 TACGTGTAAG
* *
59419083 GTTTTTAGTCTATTTGGGTTGTAATTATATTTTTTTAATCCCAAAATATGCTATTATCATGGGTA
1 GTTTTTAATCTATTT-GGTTGTAATTATATTTTTTTAATCCCAAAATATGCTATTATCAAGGGTA
*
59419148 AGTTTTTAGTTAGGATTATTTTA
65 AG-TTTTAGCTAGGATTATTTTA
* *
59419171 GTTTTTAATCTATTT-GTTGTAGTTATA-TTTTTTAGTCCCATAAA-ATGCTATTATCAAGGGTA
1 GTTTTTAATCTATTTGGTTGTAATTATATTTTTTTAATCCCA-AAATATGCTATTATCAAGGGTA
59419233 CA-TTTTAGCTAGGATTATTTTA
65 -AGTTTTAGCTAGGATTATTTTA
59419255 GTTTTTA
1 GTTTTTA
59419262 GTTGTAATTG
Statistics
Matches: 84, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
84 26 0.31
85 29 0.35
86 15 0.18
88 14 0.17
ACGTcount: A:0.26, C:0.08, G:0.15, T:0.51
Consensus pattern (86 bp):
GTTTTTAATCTATTTGGTTGTAATTATATTTTTTTAATCCCAAAATATGCTATTATCAAGGGTAA
GTTTTAGCTAGGATTATTTTA
Found at i:59419587 original size:28 final size:28
Alignment explanation
Indices: 59419552--59419608 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
59419542 AATTTAAAAG
59419552 TAAAAAGAAATCTAAATAGGTAAATACA
1 TAAAAAGAAATCTAAATAGGTAAATACA
59419580 TAAAAAGAAATCTAAATAGGTAAATACA
1 TAAAAAGAAATCTAAATAGGTAAATACA
59419608 T
1 T
59419609 CTAATTAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.60, C:0.07, G:0.11, T:0.23
Consensus pattern (28 bp):
TAAAAAGAAATCTAAATAGGTAAATACA
Found at i:59419604 original size:14 final size:14
Alignment explanation
Indices: 59419559--59419604 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
59419549 AAGTAAAAAG
59419559 AAATCTAAATAGGT
1 AAATCTAAATAGGT
*
59419573 AAATACATAAA-AAG-
1 AAAT-C-TAAATAGGT
59419587 AAATCTAAATAGGT
1 AAATCTAAATAGGT
59419601 AAAT
1 AAAT
59419605 ACATCTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
12 4 0.15
13 3 0.12
14 12 0.46
15 3 0.12
16 4 0.15
ACGTcount: A:0.59, C:0.07, G:0.11, T:0.24
Consensus pattern (14 bp):
AAATCTAAATAGGT
Found at i:59443069 original size:125 final size:124
Alignment explanation
Indices: 59442840--59443213 Score: 475
Period size: 125 Copynumber: 3.0 Consensus size: 124
59442830 GGTTTTTAGG
* * * *
59442840 TCCTGGAAGAATTAATTTTGAGTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTTTACCAGG
1 TCCTGAAAAAATT-ATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAT-GCTTCTACCAGG
* * * * * *
59442904 ATGTTTTATGAGAATAATTTGTTAAATCGCACCCAT-GTGGACGTGCTTTTGCTACAGTAGA
64 ATGCTTTATGAGAAGAATTTCTAAAATCGCGCCC-TCGTGGACGCGCTTTTGCTACAGTAGA
* *
59442965 TCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAATGCTTCAAGCAGGA
1 TCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAATGCTTCTACCAGGA
* * *
59443030 TGCTATT-TGAGAAGAATTTCTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTTGG
65 TGCT-TTATGAGAAGAATTTCTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGA
* * * *
59443090 TCCTGGAAGAAATAATTTCGAGTTGATGTTTCTGAGCAAATAGTATAAAATTGCTTCTACCAGGA
1 TCCT-GAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAATGCTTCTACCAGGA
* * *
59443155 TACTTTATGAGAAGAATTTCTAAAATCGCGCCCACGTGGATGCGCTTTTGCTACAGTAG
65 TGCTTTATGAGAAGAATTTCTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAG
59443214 CATGTTTGGG
Statistics
Matches: 218, Mismatches: 25, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
124 34 0.16
125 139 0.64
126 45 0.21
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (124 bp):
TCCTGAAAAAATTATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAATGCTTCTACCAGGAT
GCTTTATGAGAAGAATTTCTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTAGA
Found at i:59446470 original size:9 final size:9
Alignment explanation
Indices: 59446452--59446483 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
59446442 TACATAAAAT
59446452 AATA-TCAA
1 AATATTCAA
59446460 AATATTCAA
1 AATATTCAA
59446469 AATATTCAA
1 AATATTCAA
59446478 AATATT
1 AATATT
59446484 TGTACAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (9 bp):
AATATTCAA
Found at i:59446892 original size:18 final size:18
Alignment explanation
Indices: 59446869--59446908 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
59446859 GACTCGGAAA
* *
59446869 AGGATATATATAAGGGTT
1 AGGATACATATAAGGGCT
59446887 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
59446905 AGGA
1 AGGA
59446909 AACGCACCTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.40, C:0.05, G:0.30, T:0.25
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:59447569 original size:7 final size:7
Alignment explanation
Indices: 59447559--59447584 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
59447549 TTATATACAT
59447559 AATACTA
1 AATACTA
59447566 AATACTA
1 AATACTA
59447573 AATACTA
1 AATACTA
59447580 AATAC
1 AATAC
59447585 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:59447791 original size:20 final size:20
Alignment explanation
Indices: 59447754--59447791 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
59447744 TTTATTTTTA
*
59447754 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
59447774 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
59447792 TACCTCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:59448832 original size:11 final size:11
Alignment explanation
Indices: 59448818--59448883 Score: 66
Period size: 11 Copynumber: 5.9 Consensus size: 11
59448808 TTAAATATGG
59448818 ATTTGAGAGAA
1 ATTTGAGAGAA
*
59448829 ATTTG-GAAGGA
1 ATTTGAG-AGAA
59448840 ATTTGAGAGCAA
1 ATTTGAGAG-AA
59448852 A-TTGAGAGCAA
1 ATTTGAGAG-AA
59448863 A-TTGAGAGGAA
1 ATTTGAGA-GAA
59448874 ATTTGAGAGA
1 ATTTGAGAGA
59448884 GGATTAATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
10 1 0.02
11 37 0.77
12 10 0.21
ACGTcount: A:0.42, C:0.03, G:0.30, T:0.24
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:59451378 original size:2 final size:2
Alignment explanation
Indices: 59451371--59451402 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
59451361 TATAGCAGTG
59451371 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59451403 GTCTCTGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59452648 original size:40 final size:40
Alignment explanation
Indices: 59452604--59452696 Score: 125
Period size: 40 Copynumber: 2.3 Consensus size: 40
59452594 GTTTGGATAA
* *
59452604 AAAACGCCGGTAAAAATCGAGCATTAGCGGCGCTTC-AGAG
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGATTCTA-AG
* * *
59452644 AAAACGCAGCTAAAAATTGAGCATTAGCGGCGATTCTAAT
1 AAAACGCCGCTAAAAATCGAGCATTAGCGGCGATTCTAAG
59452684 AAAACGCCGCTAA
1 AAAACGCCGCTAA
59452697 TAATATTAGC
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 45 0.98
41 1 0.02
ACGTcount: A:0.39, C:0.22, G:0.23, T:0.17
Consensus pattern (40 bp):
AAAACGCCGCTAAAAATCGAGCATTAGCGGCGATTCTAAG
Found at i:59453529 original size:21 final size:20
Alignment explanation
Indices: 59453501--59453543 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
59453491 TTATGGTATA
59453501 TTGGGGTTGGTGTTTGAGGT
1 TTGGGGTTGGTGTTTGAGGT
*
59453521 TTGGTGGTTGGTGTTTGTGGT
1 TTGG-GGTTGGTGTTTGAGGT
59453542 TT
1 TT
59453544 ACGGGTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (20 bp):
TTGGGGTTGGTGTTTGAGGT
Found at i:59453550 original size:21 final size:20
Alignment explanation
Indices: 59453504--59453550 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
59453494 TGGTATATTG
*
59453504 GGGTTGGTGTTTGAGGTTTG
1 GGGTTGGTGTTTGAGGTTTC
*
59453524 GTGGTTGGTGTTTGTGGTTTAC
1 G-GGTTGGTGTTTGAGGTTT-C
59453546 GGGTT
1 GGGTT
59453551 TAATGTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
20 1 0.04
21 21 0.91
22 1 0.04
ACGTcount: A:0.04, C:0.02, G:0.47, T:0.47
Consensus pattern (20 bp):
GGGTTGGTGTTTGAGGTTTC
Found at i:59453570 original size:21 final size:22
Alignment explanation
Indices: 59453540--59453587 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
59453530 GGTGTTTGTG
*
59453540 GTTTACGGGTTTAATG-TTTATA
1 GTTTACGGGTTT-ACGATTTATA
59453562 GTTTA-GGGTTTACGATTTATA
1 GTTTACGGGTTTACGATTTATA
59453583 GTTTA
1 GTTTA
59453588 TGATTTAGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 17 0.71
22 5 0.21
ACGTcount: A:0.23, C:0.04, G:0.23, T:0.50
Consensus pattern (22 bp):
GTTTACGGGTTTACGATTTATA
Found at i:59453601 original size:7 final size:7
Alignment explanation
Indices: 59453539--59453621 Score: 51
Period size: 7 Copynumber: 11.9 Consensus size: 7
59453529 TGGTGTTTGT
59453539 GGTTTACG
1 GGTTTA-G
*
59453547 GGTTTAA
1 GGTTTAG
* *
59453554 TGTTTAT
1 GGTTTAG
*
59453561 AGTTTAG
1 GGTTTAG
*
59453568 GGTTTAC
1 GGTTTAG
* *
59453575 GATTTAT
1 GGTTTAG
* *
59453582 AGTTTAT
1 GGTTTAG
*
59453589 GATTTAG
1 GGTTTAG
59453596 GGTTTAG
1 GGTTTAG
59453603 GG-TTAG
1 GGTTTAG
*
59453609 TGTTTAG
1 GGTTTAG
59453616 GGTTTA
1 GGTTTA
59453622 ATTTAAGTTT
Statistics
Matches: 57, Mismatches: 17, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
6 5 0.09
7 46 0.81
8 6 0.11
ACGTcount: A:0.20, C:0.02, G:0.29, T:0.48
Consensus pattern (7 bp):
GGTTTAG
Found at i:59453601 original size:21 final size:21
Alignment explanation
Indices: 59453555--59453601 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
59453545 CGGGTTTAAT
*
59453555 GTTTATAGTTTAGGGTTTACG
1 GTTTATAGTTTAGGATTTACG
* * *
59453576 ATTTATAGTTTATGATTTAGG
1 GTTTATAGTTTAGGATTTACG
59453597 GTTTA
1 GTTTA
59453602 GGGTTAGTGT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.23, C:0.02, G:0.23, T:0.51
Consensus pattern (21 bp):
GTTTATAGTTTAGGATTTACG
Found at i:59454206 original size:147 final size:147
Alignment explanation
Indices: 59453902--59454677 Score: 532
Period size: 147 Copynumber: 5.3 Consensus size: 147
59453892 ATTTTCAAAA
* * * * * * * * *
59453902 TTTCCAAGTTCTTAGTGGCGTTTTATGCAAAAATGCCACAA-AATTGTCCTAATTATCGGGGAAA
1 TTTCCATGTTATTAGTGGCGTTTTATGCCAAAACGCCAGAATATTTG-ACTAATTGT-TGGGAAA
* ** * * * *
59453966 CGACAG-CGTTTC-ACGGTTATTTAGTGGCGCATACGTATAAACGCCACAAA-CGGTTAATTTAA
64 CAAC-GTCGTTTCTACGGTTATTTAGTGGCGCATGTGTATAAACGCCGCAAATGGGTTCATTTAG
* *
59454028 TCCCAT--AAAACGGCGTCGTA
128 T--CATGGAAAACGTCGTCGTT
* * *
59454048 TTACTATGTTCTTAGTGGCGTTTTATGCCAAAACGCCAGAATATTT-ACATAATTGTGTGGGAAA
1 TTTCCATGTTATTAGTGGCGTTTTATGCCAAAACGCCAGAATATTTGAC-TAATTGT-TGGGAAA
* *
59454112 CAACGTCGTTTCTGA-GGTTATTTAGTGGCGCAAGAT-TATAAACGCCGCGAATGGGTTCATTTA
64 CAACGTCGTTTCT-ACGGTTATTTAGTGGCGCATG-TGTATAAACGCCGCAAATGGGTTCATTTA
* *
59454175 GTCAT-GAATACGTCGTCATT
127 GTCATGGAAAACGTCGTCGTT
* * * *
59454195 TTTCCATGTTCTTAGTGGCGTTTTATACCAAAACGCCAGAAT-GTTGTCCTAATTGTTTGGGAAA
1 TTTCCATGTTATTAGTGGCGTTTTATGCCAAAACGCCAGAATATTTG-ACTAATTG-TTGGGAAA
* * * * * * ** * ** *
59454259 CGACTTCGTTTCCATGGTTAATTTAGTGGCACTTACGTGTAAACGCCGCAAA-GTTCTTCGTTTA
64 CAACGTCGTTTCTACGGTT-ATTTAGTGGCGCATGTGTATAAACGCCGCAAATG-GGTTCATTTA
59454323 GTCATGGAAAACGTCGTCGTT
127 GTCATGGAAAACGTCGTCGTT
* * * * * * * * * **
59454344 TTTCCATGTTGTGACTGGCATTTTATGCCTAAGCGCCACAAT-TTTGACTAACTGACTGTTAAA-
1 TTTCCATGTTATTAGTGGCGTTTTATGCCAAAACGCCAGAATATTTGACTAATTG-TTGGGAAAC
** * **
59454407 AGACAG-CGTTTCTACTTTTAGTTT-GTGGCGCTTGTGTATAAACGCCGCAAATGGGTAAATTTA
65 A-AC-GTCGTTTCTACGGTTA-TTTAGTGGCGCATGTGTATAAACGCCGCAAATGGGTTCATTTA
* *
59454470 GTCA-AGAATACGTCGTCGTT
127 GTCATGGAAAACGTCGTCGTT
* * * * * * *
59454490 TTGCTA-GTTAATAGTGGCGTTTTATACCAAAACGCCAGAA-ATTTGTCGTAAGTGTTTGGAAAC
1 TTTCCATGTTATTAGTGGCGTTTTATGCCAAAACGCCAGAATATTTGAC-TAATTGTTGGGAAAC
* * * * * * **
59454553 GACATCGTTTCTAGGGTTATTTAGTGGCGCTTATGTAGAAACGCCGCAAATTTGTT-AGTTTAGT
65 AACGTCGTTTCTACGGTTATTTAGTGGCGCATGTGTATAAACGCCGCAAATGGGTTCA-TTTAGT
*
59454617 CATGGAAAACGTTGTCG-T
129 CATGGAAAACGTCGTCGTT
* *
59454635 TTTCCAATGTTATGAGTGGCGTTTTATGCCAAAACACCAGAAT
1 TTTCC-ATGTTATTAGTGGCGTTTTATGCCAAAACGCCAGAAT
59454678 GAAGACTGTC
Statistics
Matches: 488, Mismatches: 112, Indels: 58
0.74 0.17 0.09
Matches are distributed among these distances:
144 4 0.01
145 89 0.18
146 97 0.20
147 173 0.35
148 75 0.15
149 50 0.10
ACGTcount: A:0.27, C:0.18, G:0.22, T:0.34
Consensus pattern (147 bp):
TTTCCATGTTATTAGTGGCGTTTTATGCCAAAACGCCAGAATATTTGACTAATTGTTGGGAAACA
ACGTCGTTTCTACGGTTATTTAGTGGCGCATGTGTATAAACGCCGCAAATGGGTTCATTTAGTCA
TGGAAAACGTCGTCGTT
Found at i:59454726 original size:292 final size:295
Alignment explanation
Indices: 59454148--59454746 Score: 719
Period size: 292 Copynumber: 2.0 Consensus size: 295
59454138 GGCGCAAGAT
* ** * * **
59454148 TATAAACGCCGCGAATGGGTTCATTTAGTCATGAATACGTCGTCATTTTTCCATGTTCTTAGTGG
1 TATAAACGCCGCAAATGGGTAAATTTAGTCAAGAATACGTCGTCATTTTGCCATGTTAATAGTGG
* * *
59454213 CGTTTTATACCAAAACGCCAGAATGTTGTCCTAATTGTTTGGGAAACGACTTCGTTTCCATGGTT
66 CGTTTTATACCAAAACGCCAGAATGTTGTCCTAAGTGTTTGGGAAACGACATCGTTTCCAGGGTT
*
59454278 AATTTAGTGGCACTTACGTGTAAACGCCGCAAAGTTCTTCGTTTAGTCATGGAAAACGTCGTCGT
131 AATTTAGTGGCACTTACGTGTAAACGCCGCAAAGTTCTTAGTTTAGTCATGGAAAACGTCGTCGT
* * * * *** *
59454343 TTTTCCATGTTGTGACTGGCATTTTATGCCTAAGCGCCACAATTTTGACTAACTGACTGTTAAAA
196 TTTTCCATGTTATGACTGGCATTTTATGCCAAAACACCACAATGAAGACTAACTGACTCTTAAAA
* **
59454408 GACAGCGTTTCTACTTTTAGTTTGTGGCGCTTGTG
261 GACAGCATTTCTACTGATAGTTTGTGGCGCTTGTG
* *
59454443 TATAAACGCCGCAAATGGGTAAATTTAGTCAAGAATACGTCGTCGTTTTGCTA-GTTAATAGTGG
1 TATAAACGCCGCAAATGGGTAAATTTAGTCAAGAATACGTCGTCATTTTGCCATGTTAATAGTGG
* *
59454507 CGTTTTATACCAAAACGCCAGAAAT-TTGTCGTAAGTGTTT-GGAAACGACATCGTTTCTAGGGT
66 CGTTTTATACCAAAACGCCAG-AATGTTGTCCTAAGTGTTTGGGAAACGACATCGTTTCCAGGGT
* * * * *
59454570 T-ATTTAGTGGCGCTTATGTAG-AAACGCCGCAAATTTGTTAGTTTAGTCATGGAAAACGTTGTC
130 TAATTTAGTGGCACTTACGT-GTAAACGCCGCAAAGTTCTTAGTTTAGTCATGGAAAACGTCGTC
* * * **
59454633 G-TTTTCCAATGTTATGAGTGGCGTTTTATGCCAAAACACCAGAATGAAGACTGTCTG-CTTCTT
194 GTTTTTCC-ATGTTATGACTGGCATTTTATGCCAAAACACCACAATGAAGACTAACTGAC-TCTT
* ** * * *
59454696 AAACGACTTCATTTCT-GTGGATATTTTGTGGCGCTTGTT
257 AAAAGACAGCATTTCTACT-GATAGTTTGTGGCGCTTGTG
59454735 TATAAACGCCGC
1 TATAAACGCCGC
59454747 TACCAGTGGG
Statistics
Matches: 257, Mismatches: 42, Indels: 13
0.82 0.13 0.04
Matches are distributed among these distances:
291 8 0.03
292 135 0.53
293 22 0.09
294 43 0.17
295 49 0.19
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (295 bp):
TATAAACGCCGCAAATGGGTAAATTTAGTCAAGAATACGTCGTCATTTTGCCATGTTAATAGTGG
CGTTTTATACCAAAACGCCAGAATGTTGTCCTAAGTGTTTGGGAAACGACATCGTTTCCAGGGTT
AATTTAGTGGCACTTACGTGTAAACGCCGCAAAGTTCTTAGTTTAGTCATGGAAAACGTCGTCGT
TTTTCCATGTTATGACTGGCATTTTATGCCAAAACACCACAATGAAGACTAACTGACTCTTAAAA
GACAGCATTTCTACTGATAGTTTGTGGCGCTTGTG
Found at i:59454966 original size:6 final size:6
Alignment explanation
Indices: 59454955--59454986 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
59454945 ATCTACTGCA
59454955 TCACCG TCACCG TCACCG TCACCG TCACCG TC
1 TCACCG TCACCG TCACCG TCACCG TCACCG TC
59454987 GCTCTTCGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.50, G:0.16, T:0.19
Consensus pattern (6 bp):
TCACCG
Found at i:59455223 original size:14 final size:14
Alignment explanation
Indices: 59455204--59455230 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
59455194 AATATTTCAG
59455204 ATTTTGTTATTCGA
1 ATTTTGTTATTCGA
59455218 ATTTTGTTATTCG
1 ATTTTGTTATTCG
59455231 GGTTTCTGTT
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:0.19, C:0.07, G:0.15, T:0.59
Consensus pattern (14 bp):
ATTTTGTTATTCGA
Found at i:59456381 original size:69 final size:69
Alignment explanation
Indices: 59456308--59456449 Score: 239
Period size: 69 Copynumber: 2.1 Consensus size: 69
59456298 AAATTTTATT
* * *
59456308 AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTTTTTAAATATTAAAACCTATAT
1 AATAATAAATTTTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAAAACCTATAT
59456373 TTTC
66 TTTC
*
59456377 AATAATAAATTTTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAACACCTATAT
1 AATAATAAATTTTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAAAACCTATAT
*
59456442 TTTT
66 TTTC
59456446 AATA
1 AATA
59456450 TATCACCCCA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 68 1.00
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (69 bp):
AATAATAAATTTTATAATTTTAAAAATAATTGAAAATGTTATTTTCTAAAGATTAAAACCTATAT
TTTC
Found at i:59456548 original size:12 final size:12
Alignment explanation
Indices: 59456533--59456610 Score: 56
Period size: 12 Copynumber: 6.4 Consensus size: 12
59456523 ATCATATCAT
59456533 AACTTATATATA
1 AACTTATATATA
*
59456545 AACTTACATAATACA
1 AACTT--AT-ATATA
*
59456560 TAACTTACATA-A
1 -AACTTATATATA
*
59456572 TAAC-T-TACATA
1 -AACTTATATATA
59456583 A-CTTATATATA
1 AACTTATATATA
59456594 AACTTATATATA
1 AACTTATATATA
59456606 AACTT
1 AACTT
59456611 GCATAACTTA
Statistics
Matches: 53, Mismatches: 5, Indels: 16
0.72 0.07 0.22
Matches are distributed among these distances:
9 1 0.02
10 4 0.08
11 8 0.15
12 25 0.47
13 3 0.06
14 3 0.06
15 4 0.08
16 5 0.09
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (12 bp):
AACTTATATATA
Found at i:59456563 original size:28 final size:28
Alignment explanation
Indices: 59456530--59456583 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
59456520 TCAATCATAT
*
59456530 CATAACTTATAT-ATAAACTTACATAATA
1 CATAACTTACATAAT-AACTTACATAATA
59456558 CATAACTTACATAATAACTTACATAA
1 CATAACTTACATAATAACTTACATAA
59456584 CTTATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (28 bp):
CATAACTTACATAATAACTTACATAATA
Found at i:59456570 original size:9 final size:9
Alignment explanation
Indices: 59456545--59456859 Score: 135
Period size: 9 Copynumber: 34.7 Consensus size: 9
59456535 CTTATATATA
59456545 AACTTACAT
1 AACTTACAT
59456554 AA--TACAT
1 AACTTACAT
59456561 AACTTACATAAT
1 AACTTAC---AT
59456573 AACTTACAT
1 AACTTACAT
*
59456582 AACTTATATAT
1 AAC-T-TACAT
*
59456593 AAACTTATATAT
1 -AAC-T-TACAT
*
59456605 AAACTTGCAT
1 -AACTTACAT
59456615 AACTTACAT
1 AACTTACAT
*
59456624 AA-TAACAT
1 AACTTACAT
59456632 AATGACTTACAT
1 -A--ACTTACAT
*
59456644 AA--TATAT
1 AACTTACAT
* *
59456651 AGCCTACAT
1 AACTTACAT
* *
59456660 AAATTGCAT
1 AACTTACAT
*
59456669 AACTCACAT
1 AACTTACAT
*
59456678 AA--TACAC
1 AACTTACAT
*
59456685 GACTTACAT
1 AACTTACAT
*
59456694 AACTTAAAT
1 AACTTACAT
*
59456703 AATTTACAT
1 AACTTACAT
59456712 AA--TACAT
1 AACTTACAT
59456719 AACTTACATT
1 AACTTACA-T
*
59456729 AATATTATACAT
1 -A-ACT-TACAT
59456741 AACTTACAT
1 AACTTACAT
*
59456750 AACATA-ATT
1 AACTTACA-T
59456759 AA-TTA-AT
1 AACTTACAT
*
59456766 -ATTATACAT
1 AACT-TACAT
59456775 AACTTACAT
1 AACTTACAT
59456784 AACTTAC--
1 AACTTACAT
59456791 AACTTACAT
1 AACTTACAT
59456800 AACTTA-ATT
1 AACTTACA-T
* *
59456809 ACATTATACAC
1 A-ACT-TACAT
59456820 AACTTACAT
1 AACTTACAT
*
59456829 AACATACAT
1 AACTTACAT
59456838 AA--TACAT
1 AACTTACAT
59456845 AACTTACAT
1 AACTTACAT
59456854 AACTTA
1 AACTTA
59456860 TATATAAACT
Statistics
Matches: 237, Mismatches: 34, Indels: 70
0.70 0.10 0.21
Matches are distributed among these distances:
6 1 0.00
7 39 0.16
8 12 0.05
9 123 0.52
10 13 0.05
11 12 0.05
12 33 0.14
13 4 0.02
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.34
Consensus pattern (9 bp):
AACTTACAT
Found at i:59456580 original size:21 final size:20
Alignment explanation
Indices: 59456556--59456881 Score: 78
Period size: 16 Copynumber: 17.6 Consensus size: 20
59456546 ACTTACATAA
59456556 TACATAACTTACATAATAACT
1 TACATAACTTACAT-ATAACT
*
59456577 TACATAACTTATATATAAACTT
1 TACATAACTTACATAT-AAC-T
* *
59456599 ATATATAAACTTGC--ATAACT
1 -TACAT-AACTTACATATAACT
* *
59456619 TACATAA-TAACATAATGACT
1 TACATAACTTACAT-ATAACT
* *
59456639 TACATAA--T--ATATAGCC
1 TACATAACTTACATATAACT
* *
59456655 TACATAAATTGC--ATAACT
1 TACATAACTTACATATAACT
* **
59456673 CACATAA--TAC--ACGACT
1 TACATAACTTACATATAACT
*
59456689 TACATAACTTA-A-ATAATT
1 TACATAACTTACATATAACT
59456707 TACATAA--TAC--ATAACT
1 TACATAACTTACATATAACT
* * *
59456723 TACATTAATATTATACATAACT
1 TACA-TAA-CTTACATATAACT
*
59456745 TACATAACATA-AT-TAA-T
1 TACATAACTTACATATAACT
* *
59456762 TA-AT-A-TTATACATAACT
1 TACATAACTTACATATAACT
59456779 TACATAACTTAC----AACT
1 TACATAACTTACATATAACT
*
59456795 TACATAACTTA-AT-TACATT
1 TACATAACTTACATATA-ACT
* *
59456814 ATACACAACTTAC--ATAACA
1 -TACATAACTTACATATAACT
59456833 TACATAA--TAC--ATAACT
1 TACATAACTTACATATAACT
*
59456849 TACATAACTTATATATAAACT
1 TACATAACTTACATAT-AACT
*
59456870 TACATAATTTAC
1 TACATAACTTAC
59456882 TTCATACATA
Statistics
Matches: 227, Mismatches: 39, Indels: 78
0.66 0.11 0.23
Matches are distributed among these distances:
14 2 0.01
15 2 0.01
16 68 0.30
17 13 0.06
18 39 0.17
19 9 0.04
20 36 0.16
21 36 0.16
22 13 0.06
23 4 0.02
24 5 0.02
ACGTcount: A:0.47, C:0.17, G:0.02, T:0.34
Consensus pattern (20 bp):
TACATAACTTACATATAACT
Found at i:59456693 original size:34 final size:34
Alignment explanation
Indices: 59456655--59456751 Score: 86
Period size: 34 Copynumber: 2.7 Consensus size: 34
59456645 ATATATAGCC
** *
59456655 TACATAAATTGCATAACTCACATAATACACGACT
1 TACATAAATTAAATAACTCACATAATACACAACT
* * * *
59456689 TACATAACTTAAATAATTTACATAATACATAACT
1 TACATAAATTAAATAACTCACATAATACACAACT
*
59456723 TACATTAATATTATACATAACTTACATAA
1 TACA-TAA-ATTA-A-ATAACTCACATAA
59456752 CATAATTAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
34 31 0.62
35 3 0.06
36 3 0.06
37 1 0.02
38 12 0.24
ACGTcount: A:0.47, C:0.18, G:0.02, T:0.33
Consensus pattern (34 bp):
TACATAAATTAAATAACTCACATAATACACAACT
Found at i:59456717 original size:25 final size:25
Alignment explanation
Indices: 59456689--59456877 Score: 87
Period size: 25 Copynumber: 7.0 Consensus size: 25
59456679 ATACACGACT
59456689 TACATAACTTAAATAATTTACATAA
1 TACATAACTTAAATAATTTACATAA
*
59456714 TACATAACTTACATTAATATTATACATAA
1 TACATAACTTA-AAT-A-ATT-TACATAA
* * * * *
59456743 CTTACATAACATAATTAATTAATATTA
1 --TACATAACTTAAATAATTTACATAA
* * *
59456770 TACATAACTTACATAACTTACA-ACT
1 TACATAACTTAAATAATTTACATA-A
* *
59456795 TACATAACTTAATTACATTATACACAA
1 TACATAACTTAAATA-ATT-TACATAA
* *
59456822 CTTACATAACATACATAA--TACATAA
1 --TACATAACTTAAATAATTTACATAA
*
59456847 CTTACATAACTTATATATAAACTTACATAA
1 --TACATAACTTA-A-AT-AATTTACATAA
59456877 T
1 T
59456878 TTACTTCATA
Statistics
Matches: 124, Mismatches: 23, Indels: 31
0.70 0.13 0.17
Matches are distributed among these distances:
25 58 0.47
26 4 0.03
27 11 0.09
28 11 0.09
29 20 0.16
30 10 0.08
31 10 0.08
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (25 bp):
TACATAACTTAAATAATTTACATAA
Found at i:59456767 original size:34 final size:36
Alignment explanation
Indices: 59456701--59456786 Score: 131
Period size: 34 Copynumber: 2.4 Consensus size: 36
59456691 CATAACTTAA
*
59456701 ATAATTTACATAATACATAACTTACATTAATATTATAC
1 ATAACTTACAT-A-ACATAACTTACATTAATATTATAC
59456739 ATAACTTACATAACATAA-TTA-ATTAATATTATAC
1 ATAACTTACATAACATAACTTACATTAATATTATAC
59456773 ATAACTTACATAAC
1 ATAACTTACATAAC
59456787 TTACAACTTA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
34 27 0.57
35 3 0.06
36 6 0.13
37 1 0.02
38 10 0.21
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (36 bp):
ATAACTTACATAACATAACTTACATTAATATTATAC
Found at i:59462423 original size:21 final size:21
Alignment explanation
Indices: 59462393--59462443 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
59462383 CTACAACTTA
* *
59462393 AAGCAAAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGAG
* *
59462414 AAGCAGAGGCTGCAGTGAGAG
1 AAGCAGAGGCGGCAGCGAGAG
59462435 AAGCAGAGG
1 AAGCAGAGG
59462444 TTCAAGCTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.35, C:0.16, G:0.45, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGAG
Found at i:59462489 original size:67 final size:67
Alignment explanation
Indices: 59462381--59462509 Score: 186
Period size: 67 Copynumber: 1.9 Consensus size: 67
59462371 GAAGAACTCC
* * **
59462381 AGCTACAACTTAAAGCAAAGGCGGCAGCGAGGGAAGCAGAGGCTGCAGTGAGAGAAGCAGAGGTT
1 AGCTACAACTTAAAGCAAAGGCGACAGCGAGAGAAGCAGAGGCTGCAACGAGAGAAGCAGAGGTT
59462446 CA
66 CA
* * * *
59462448 AGCTACAACTTAAAGCAGATGCGACATCGAGAGAAGCAGAGGCTGCAACGAGGGAAGCAGAG
1 AGCTACAACTTAAAGCAAAGGCGACAGCGAGAGAAGCAGAGGCTGCAACGAGAGAAGCAGAG
59462510 CAGAGCAGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
67 54 1.00
ACGTcount: A:0.37, C:0.19, G:0.34, T:0.10
Consensus pattern (67 bp):
AGCTACAACTTAAAGCAAAGGCGACAGCGAGAGAAGCAGAGGCTGCAACGAGAGAAGCAGAGGTT
CA
Found at i:59462682 original size:26 final size:26
Alignment explanation
Indices: 59462661--59462718 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
59462651 GAATTACATC
*
59462661 TTATTTATTT-ATATTTATATTATATA
1 TTATTCATTTAAT-TTTATATTATATA
59462687 TTATTCATTTAATTTTATATTATATA
1 TTATTCATTTAATTTTATATTATATA
59462713 TTATTC
1 TTATTC
59462719 GGTTAGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 28 0.93
27 2 0.07
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (26 bp):
TTATTCATTTAATTTTATATTATATA
Found at i:59462688 original size:7 final size:7
Alignment explanation
Indices: 59462661--59462716 Score: 50
Period size: 7 Copynumber: 8.6 Consensus size: 7
59462651 GAATTACATC
*
59462661 TTATTTA
1 TTATATA
59462668 TT-TATA
1 TTATATA
59462674 TT-TATA
1 TTATATA
59462680 TTATATA
1 TTATATA
59462687 TTAT-TCA
1 TTATAT-A
59462694 TT-TA-A
1 TTATATA
*
59462699 TTTTATA
1 TTATATA
59462706 TTATATA
1 TTATATA
59462713 TTAT
1 TTAT
59462717 TCGGTTAGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
5 3 0.07
6 15 0.36
7 24 0.57
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (7 bp):
TTATATA
Found at i:59462688 original size:19 final size:20
Alignment explanation
Indices: 59462661--59462714 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 20
59462651 GAATTACATC
*
59462661 TTATTTATT-TATATTT-AT
1 TTATATATTATATATTTAAT
59462679 ATTATATATTAT-TCATTTAAT
1 -TTATATATTATAT-ATTTAAT
59462700 TT-TATATTATATATT
1 TTATATATTATATATT
59462715 ATTCGGTTAG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
19 20 0.67
20 8 0.27
21 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATATATTATATATTTAAT
Found at i:59462886 original size:43 final size:43
Alignment explanation
Indices: 59462825--59463115 Score: 384
Period size: 43 Copynumber: 6.8 Consensus size: 43
59462815 TTATACCAAA
* * *
59462825 CGCCGCTAAAAGTTATGGCCTATAGCGGCGTTTGTGGGAAAAA
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
*
59462868 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAGAAG
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
* * *
59462911 CACCTCTAAAGGTCATGGCCTATAGCGGCATTTGTGGGAAAAG
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
*
59462954 TGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
* *
59462997 CGCCGCTAAAGATCATGGTCTATAGCGGCGTTTGTGGGAAAAG
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
* * * * * * **
59463040 TGTCGCTAAAGATCATAGTCTATAGCGGTGTTTGTGGGAGCAG
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
* ** *
59463083 CGCCGCTAAAGATCATGTTCTATAGCGGTGTTT
1 CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTT
59463116 ATTTCAAAAA
Statistics
Matches: 223, Mismatches: 25, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 223 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (43 bp):
CGCCGCTAAAGGTCATGGCCTATAGCGGCGTTTGTGGGAAAAG
Found at i:59467293 original size:18 final size:19
Alignment explanation
Indices: 59467272--59467328 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 19
59467262 TTAAAAAATA
59467272 TATAAGT-TTTGGAATTTT
1 TATAAGTATTTGGAATTTT
* *
59467290 TATAATTATTTTGAATTTT
1 TATAAGTATTTGGAATTTT
* * * *
59467309 AAAAATTATTTTGAATTTT
1 TATAAGTATTTGGAATTTT
59467328 T
1 T
59467329 TTGTAATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
18 6 0.18
19 27 0.82
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (19 bp):
TATAAGTATTTGGAATTTT
Found at i:59467307 original size:19 final size:19
Alignment explanation
Indices: 59467278--59467328 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
59467268 AATATATAAG
*
59467278 TTTTGGAATTTTTATAATTA
1 TTTT-GAATTTTTAAAATTA
*
59467298 TTTTGAATTTTAAAAATTA
1 TTTTGAATTTTTAAAATTA
59467317 TTTTGAATTTTT
1 TTTTGAATTTTT
59467329 TTGTAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 24 0.86
20 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.61
Consensus pattern (19 bp):
TTTTGAATTTTTAAAATTA
Found at i:59470320 original size:102 final size:102
Alignment explanation
Indices: 59470144--59470475 Score: 465
Period size: 102 Copynumber: 3.3 Consensus size: 102
59470134 TATCGATGAA
* * * *
59470144 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATTGATAAATAATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAATAATGGTCACATGTGTAGTAC
*
59470209 TAAGTGAAGGCTACAATGTGTACCGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* *
59470246 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGGTAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAATAATGGTCACATGTGTAGTAC
*
59470311 TAAGTGAAGGCTACTATGTGTACTGAAAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
* * * * *
59470348 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAA-CTGTAAA-ACTTGATCACGTATGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAATA-ATGGTCACATGTGTAGTA
* * * *
59470411 CTATGTGAAGGCTACTACGTGAACCGTAAAA-C-TTGAT
65 CTAAGTGAAGGCTACTATGTGTACCG-AAAAGCTTTGGT
59470448 CACGTGTGTAGTACTATGTGAAGGCTAC
1 CACGTGTGTAGTACTATGTGAAGGCTAC
59470476 ACTACACCAA
Statistics
Matches: 210, Mismatches: 18, Indels: 6
0.90 0.08 0.03
Matches are distributed among these distances:
100 32 0.15
101 43 0.20
102 135 0.64
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (102 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGGTAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAAGCTTTGGT
Done.