Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr8
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: 78745976
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 2640508 characters in sequence are not A, C, G, or T
File 97 of 235
Found at i:33496441 original size:17 final size:16
Alignment explanation
Indices: 33496409--33496450 Score: 66
Period size: 17 Copynumber: 2.6 Consensus size: 16
33496399 TAAAAACAGT
*
33496409 TTAAAATATAAATTTA
1 TTAATATATAAATTTA
33496425 TTAATATATATAATTTA
1 TTAATATATA-AATTTA
33496442 TTAATATAT
1 TTAATATAT
33496451 GTAAAAACAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.38
17 15 0.62
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TTAATATATAAATTTA
Found at i:33497162 original size:49 final size:49
Alignment explanation
Indices: 33497107--33497240 Score: 142
Period size: 49 Copynumber: 2.7 Consensus size: 49
33497097 AGTACATTAA
* * * *
33497107 AGTCGATGCCGTTTCCTAAACAAGTTTTACACTGACTTTCATATATCAG
1 AGTCGATGCCATATCCTAAACAAGTCTTACACTGACTCTCATATATCAG
* * * * *
33497156 AGTCGATGCCATATCCTAGACAGGTCTTACACTGGCTCTCATCTATCGG
1 AGTCGATGCCATATCCTAAACAAGTCTTACACTGACTCTCATATATCAG
* * * * *
33497205 TGTCGATGCCATGTCCCAGACAGGTCTTACACTGAC
1 AGTCGATGCCATATCCTAAACAAGTCTTACACTGAC
33497241 ACACAACAAG
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 72 1.00
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.30
Consensus pattern (49 bp):
AGTCGATGCCATATCCTAAACAAGTCTTACACTGACTCTCATATATCAG
Found at i:33497395 original size:45 final size:42
Alignment explanation
Indices: 33497301--33497429 Score: 132
Period size: 46 Copynumber: 2.9 Consensus size: 42
33497291 TCCCAAGGCT
* *
33497301 GATGCATGTCCGAGACATGTCTTACCCTAGCTCTCGTCTCAAAATC
1 GATGCATGTCC-AGACATGTCTTACACTAGCTCTC--AT-AAAATC
*
33497347 GATGCATGTCCAGACATGTCTTACACTAGCTCTCATAATATGGAC
1 GATGCATGTCCAGACATGTCTTACACTAGCTCTCATAAAAT---C
* * *
33497392 GATGCATGTCTCAGATATGTCTTACACTGGCTCACATA
1 GATGCATGTC-CAGACATGTCTTACACTAGCTCTCATA
33497430 CCACCCAATG
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
42 4 0.05
43 1 0.01
45 33 0.45
46 35 0.48
ACGTcount: A:0.26, C:0.26, G:0.18, T:0.29
Consensus pattern (42 bp):
GATGCATGTCCAGACATGTCTTACACTAGCTCTCATAAAATC
Found at i:33503850 original size:22 final size:20
Alignment explanation
Indices: 33503802--33503851 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 20
33503792 CTTAAATTTT
33503802 AAAATTTTAAAAATAAAAAA
1 AAAATTTTAAAAATAAAAAA
*
33503822 ACTAAATTTTTAAAATAAAATATA
1 A--AAATTTTAAAAATAAAA-A-A
33503846 AAAATT
1 AAAATT
33503852 AAATTTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 1 0.04
22 21 0.84
23 1 0.04
24 2 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAATTTTAAAAATAAAAAA
Found at i:33504470 original size:24 final size:23
Alignment explanation
Indices: 33504431--33504485 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
33504421 TCTTTTAACT
* *
33504431 TTCT-TTCTTCTTCTTTTTTTTA
1 TTCTCTTCTTCTCCTTTGTTTTA
*
33504453 TTCTCTTCTTCTCCCTTTGTTTTC
1 TTCTCTTCTTCT-CCTTTGTTTTA
*
33504477 CTCTCTTCT
1 TTCTCTTCT
33504486 CAATTTCTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.02, C:0.29, G:0.02, T:0.67
Consensus pattern (23 bp):
TTCTCTTCTTCTCCTTTGTTTTA
Found at i:33505982 original size:21 final size:19
Alignment explanation
Indices: 33505943--33505991 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 19
33505933 ATTCATAAAG
33505943 TTTAATTTAATTGTATTTTA
1 TTTAATTTAATT-TATTTTA
33505963 TTTAACTTTAATTTATTTTTA
1 TTTAA-TTTAATTTA-TTTTA
*
33505984 ATTAATTT
1 TTTAATTT
33505992 TTATTTTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTAATTTAATTTATTTTA
Found at i:33505997 original size:21 final size:21
Alignment explanation
Indices: 33505944--33505997 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
33505934 TTCATAAAGT
*
33505944 TTAA-TTTAATTGTA-TTTTAT
1 TTAACTTTAATT-TATTTTTAA
33505964 TTAACTTTAATTTATTTTTAA
1 TTAACTTTAATTTATTTTTAA
* *
33505985 TTAATTTTTATTT
1 TTAACTTTAATTT
33505998 TGAGTTATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.21
21 23 0.79
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTAACTTTAATTTATTTTTAA
Found at i:33506672 original size:15 final size:14
Alignment explanation
Indices: 33506642--33506679 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
33506632 AGTTACTTTC
33506642 TATTA-TTTTATTT
1 TATTATTTTTATTT
33506655 TATTATTTTTATTTT
1 TATTATTTTTA-TTT
33506670 TATTATTTTT
1 TATTATTTTT
33506680 GTCTTCTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.22
14 5 0.22
15 13 0.57
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TATTATTTTTATTT
Found at i:33507447 original size:22 final size:22
Alignment explanation
Indices: 33507421--33507462 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
33507411 TATGCCTTAG
*
33507421 TCATA-TGGCTGTGTGCCTCTCT
1 TCATACTGGC-GTGTACCTCTCT
33507443 TCATACTGGCGTGTACCTCT
1 TCATACTGGCGTGTACCTCT
33507463 GCCACACGGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.12, C:0.29, G:0.21, T:0.38
Consensus pattern (22 bp):
TCATACTGGCGTGTACCTCTCT
Found at i:33508726 original size:310 final size:310
Alignment explanation
Indices: 33508164--33509738 Score: 2540
Period size: 310 Copynumber: 5.0 Consensus size: 310
33508154 GGGTTTCATT
* *
33508164 GTTTGACTGCTTTTCATACGTATCTTTTTGAGCATTCTAGATGCTAGACCGTTTGACTGTTCTTT
1 GTTTGACTGCTTTTCATACGTATCTTTTTGAGCATTCTGGATGCTAGACCGTCTGACTGTTCTTT
33508229 GTCTAACTGTAAATATATATATGACTGAGTGTTTGTGTTTGAGATGTTACGTTCCATTAGGATGT
66 GTCTAACTGTAAATATATATATGACTGAGTGTTTGTGTTTGAGATGTTACGTTCCATTAGGATGT
33508294 TGATTTCGGTATTACCTCTGTAGTTGTTCGATATTGAATTGTGTACTATATTTCTGTTTTCATCT
131 TGATTTCGGTATTACCTCTGTAGTTGTTCGATATTGAATTGTGTACTATATTTCTGTTTTCATCT
33508359 TGATTCGAACTCACACTGAGCTCATATGGCTCACCCCCTCTTAGTGTTTCCTTTTTAGGTACACT
196 TGATTCGAACTCACACTGAGCTCATATGGCTCACCCCCTCTTAGTGTTTCCTTTTTAGGTACACT
33508424 TTTCTTTTCTGCAACTAGACTCCACAAGTCAGAGGTCTCAAAATCGTCGC
261 TTTCTTTTCTGCAACTAGACTCCACAAGTCAGAGGTCTCAAAATCGTCGC
33508474 GTTTGACTGCTTTTCATACGTATCTTTTTGAGCATTCTGGATGCTAGACCGTCTGACTGTTCTTT
1 GTTTGACTGCTTTTCATACGTATCTTTTTGAGCATTCTGGATGCTAGACCGTCTGACTGTTCTTT
33508539 GTCTAACTGTAAATATATATATGACTGAGTGTTTGTGTTTGAGATGTTACGTTCCATTAGGATGT
66 GTCTAACTGTAAATATATATATGACTGAGTGTTTGTGTTTGAGATGTTACGTTCCATTAGGATGT
33508604 TGATTTCGGTATTACCTCTGTAGTTGTTCGATATTGAATTGTGTACTATATTTCTGTTTTCATCT
131 TGATTTCGGTATTACCTCTGTAGTTGTTCGATATTGAATTGTGTACTATATTTCTGTTTTCATCT
33508669 TGATTCGAACTCACACTGAGCTCATATGGCTCACCCCCTCTTAGTGTTTCCTTTTTAGGTACACT
196 TGATTCGAACTCACACTGAGCTCATATGGCTCACCCCCTCTTAGTGTTTCCTTTTTAGGTACACT
33508734 TTTCTTTTCTGCAACTAGACTCCACAAGTCAGAGGTCTCAAAATCGTCGC
261 TTTCTTTTCTGCAACTAGACTCCACAAGTCAGAGGTCTCAAAATCGTCGC
33508784 GTTTGACTGCTTTTCATACGTATCTTTTTGAGCATTCTGGATGCTAGACCGTCTGACTGTTCTTT
1 GTTTGACTGCTTTTCATACGTATCTTTTTGAGCATTCTGGATGCTAGACCGTCTGACTGTTCTTT
33508849 GTCTAACTGTAAATATATATATGACTGAGTGTTTGTGTTTGAGATGTTACGTTCCATTAGGATGT
66 GTCTAACTGTAAATATATATATGACTGAGTGTTTGTGTTTGAGATGTTACGTTCCATTAGGATGT
33508914 TGATTTCGGTATTACCTCTGTAGTTGTTCGATATTGAATTGTGTACTATATTTCTGTTTTCATCT
131 TGATTTCGGTATTACCTCTGTAGTTGTTCGATATTGAATTGTGTACTATATTTCTGTTTTCATCT
33508979 TGATTCGAACTCACACTGAGCTCATATGGCTCACCCCCTCTTAGTGTTTCCTTTTTAGGTACACT
196 TGATTCGAACTCACACTGAGCTCATATGGCTCACCCCCTCTTAGTGTTTCCTTTTTAGGTACACT
33509044 TTTCTTTTCTGCAACTAGACTCCACAAGTCAGAGGTCTCAAAATCGTCGC
261 TTTCTTTTCTGCAACTAGACTCCACAAGTCAGAGGTCTCAAAATCGTCGC
33509094 GTTTGACTGCTTTTCATACGTATCTTTTTGAGCATTCTGGATGCTAGACCGTCTGACTGTTCTTT
1 GTTTGACTGCTTTTCATACGTATCTTTTTGAGCATTCTGGATGCTAGACCGTCTGACTGTTCTTT
* *
33509159 GTCTAACTGTAAATATATATATGACTGAGTGTTTGTGTTTGAGATGTTACGTTCCGTTGGGATGT
66 GTCTAACTGTAAATATATATATGACTGAGTGTTTGTGTTTGAGATGTTACGTTCCATTAGGATGT
*
33509224 TGATTCCGGTATTACCTTTTGCTTCTGAATATATATCTGTAGTTGTTCGATATTGAATTGTGTAC
131 TGATTTCGGTATTA-------C--C----------TCTGTAGTTGTTCGATATTGAATTGTGTAC
* **
33509289 TGTATTTCTGTTTTCATCTTGATTCGAACTCACACTGAGCTTGTATGGCTCA-CCCCTCTTAGTG
177 TATATTTCTGTTTTCATCTTGATTCGAACTCACACTGAGCTCATATGGCTCACCCCCTCTTAGTG
* * * * *
33509353 TTTCTTTTTTAGGTACACTTTTCTTTTCTGCAACTAGACTCGACAAGTCGGAGGTCTAAAAATCA
242 TTTCCTTTTTAGGTACACTTTTCTTTTCTGCAACTAGACTCCACAAGTCAGAGGTCTCAAAATCG
33509418 TCGC
307 TCGC
* * * *
33509422 GTTTGACTACTATTCATACGTATCTTTTTGAGCATTCTGGATGCTAGATCGTCTAACTGTTCTTT
1 GTTTGACTGCTTTTCATACGTATCTTTTTGAGCATTCTGGATGCTAGACCGTCTGACTGTTCTTT
*
33509487 GTCTAACTGTAAATATATATATGACTGAGTGTTTGTGTTTGAGATGTTACGTTCCATTGGGATGT
66 GTCTAACTGTAAATATATATATGACTGAGTGTTTGTGTTTGAGATGTTACGTTCCATTAGGATGT
*
33509552 TGATTCCGGTATTACCTTTTGCTTCTGAATATGTATCTGTAGTTGTTCGATATTGAATTGTGTAC
131 TGATTTCGGTATTA-------C--C----------TCTGTAGTTGTTCGATATTGAATTGTGTAC
* * * * *
33509617 TGTATTTCTGTTTTCATCTTGATTTGGACTCACACTGAGCTCGTATGGCTCACCCCATCTTAGTG
177 TATATTTCTGTTTTCATCTTGATTCGAACTCACACTGAGCTCATATGGCTCACCCCCTCTTAGTG
* * * **
33509682 TTTCCTTTTTAGGTACACTTTTCTTTTTTGCAACTGGATTCGGCAAGTCAGAGGTCT
242 TTTCCTTTTTAGGTACACTTTTCTTTTCTGCAACTAGACTCCACAAGTCAGAGGTCT
33509739 TAGAATCATC
Statistics
Matches: 1216, Mismatches: 29, Indels: 21
0.96 0.02 0.02
Matches are distributed among these distances:
310 759 0.62
317 1 0.00
319 1 0.00
328 314 0.26
329 141 0.12
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (310 bp):
GTTTGACTGCTTTTCATACGTATCTTTTTGAGCATTCTGGATGCTAGACCGTCTGACTGTTCTTT
GTCTAACTGTAAATATATATATGACTGAGTGTTTGTGTTTGAGATGTTACGTTCCATTAGGATGT
TGATTTCGGTATTACCTCTGTAGTTGTTCGATATTGAATTGTGTACTATATTTCTGTTTTCATCT
TGATTCGAACTCACACTGAGCTCATATGGCTCACCCCCTCTTAGTGTTTCCTTTTTAGGTACACT
TTTCTTTTCTGCAACTAGACTCCACAAGTCAGAGGTCTCAAAATCGTCGC
Found at i:33509528 original size:328 final size:328
Alignment explanation
Indices: 33508930--33509754 Score: 1425
Period size: 328 Copynumber: 2.5 Consensus size: 328
33508920 CGGTATTACC
*
33508930 TCTGTAGTTGTTCGATATTGAATTGTGTACTATATTTCTGTTTTCATCTTGATTCGAACTCACAC
1 TCTGTAGTTGTTCGATATTGAATTGTGTACTGTATTTCTGTTTTCATCTTGATTCGAACTCACAC
*
33508995 TGAGCTCATATGGCTCACCCCCTCTTAGTGTTTCCTTTTTAGGTACACTTTTCTTTTCTGCAACT
66 TGAGCTCGTATGGCTCA-CCCCTCTTAGTGTTTCCTTTTTAGGTACACTTTTCTTTTCTGCAACT
* * * * *
33509060 AGACTCCACAAGTCAGAGGTCTCAAAATCGTCGCGTTTGACTGCTTTTCATACGTATCTTTTTGA
130 AGACTCGACAAGTCAGAGGTCTAAAAATCATCGCGTTTGACTACTATTCATACGTATCTTTTTGA
*
33509125 GCATTCTGGATGCTAGACCGTCTGACTGTTCTTTGTCTAACTGTAAATATATATATGACTGAGTG
195 GCATTCTGGATGCTAGACCGTCTAACTGTTCTTTGTCTAACTGTAAATATATATATGACTGAGTG
*
33509190 TTTGTGTTTGAGATGTTACGTTCCGTTGGGATGTTGATTCCGGTATTACCTTTTGCTTCTGAATA
260 TTTGTGTTTGAGATGTTACGTTCCATTGGGATGTTGATTCCGGTATTACCTTTTGCTTCTGAATA
33509255 TATA
325 TATA
33509259 TCTGTAGTTGTTCGATATTGAATTGTGTACTGTATTTCTGTTTTCATCTTGATTCGAACTCACAC
1 TCTGTAGTTGTTCGATATTGAATTGTGTACTGTATTTCTGTTTTCATCTTGATTCGAACTCACAC
* *
33509324 TGAGCTTGTATGGCTCACCCCTCTTAGTGTTTCTTTTTTAGGTACACTTTTCTTTTCTGCAACTA
66 TGAGCTCGTATGGCTCACCCCTCTTAGTGTTTCCTTTTTAGGTACACTTTTCTTTTCTGCAACTA
*
33509389 GACTCGACAAGTCGGAGGTCTAAAAATCATCGCGTTTGACTACTATTCATACGTATCTTTTTGAG
131 GACTCGACAAGTCAGAGGTCTAAAAATCATCGCGTTTGACTACTATTCATACGTATCTTTTTGAG
*
33509454 CATTCTGGATGCTAGATCGTCTAACTGTTCTTTGTCTAACTGTAAATATATATATGACTGAGTGT
196 CATTCTGGATGCTAGACCGTCTAACTGTTCTTTGTCTAACTGTAAATATATATATGACTGAGTGT
33509519 TTGTGTTTGAGATGTTACGTTCCATTGGGATGTTGATTCCGGTATTACCTTTTGCTTCTGAATAT
261 TTGTGTTTGAGATGTTACGTTCCATTGGGATGTTGATTCCGGTATTACCTTTTGCTTCTGAATAT
*
33509584 GTA
326 ATA
* *
33509587 TCTGTAGTTGTTCGATATTGAATTGTGTACTGTATTTCTGTTTTCATCTTGATTTGGACTCACAC
1 TCTGTAGTTGTTCGATATTGAATTGTGTACTGTATTTCTGTTTTCATCTTGATTCGAACTCACAC
*
33509652 TGAGCTCGTATGGCTCACCCCATCTTAGTGTTTCCTTTTTAGGTACACTTTTCTTTTTTGCAACT
66 TGAGCTCGTATGGCTCACCCC-TCTTAGTGTTTCCTTTTTAGGTACACTTTTCTTTTCTGCAACT
* * * * * *
33509717 GGATTCGGCAAGTCAGAGGTCTTAGAATCATCACGTTT
130 AGACTCGACAAGTCAGAGGTCTAAAAATCATCGCGTTT
33509755 TTTTGTAACT
Statistics
Matches: 469, Mismatches: 26, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
328 318 0.68
329 151 0.32
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.42
Consensus pattern (328 bp):
TCTGTAGTTGTTCGATATTGAATTGTGTACTGTATTTCTGTTTTCATCTTGATTCGAACTCACAC
TGAGCTCGTATGGCTCACCCCTCTTAGTGTTTCCTTTTTAGGTACACTTTTCTTTTCTGCAACTA
GACTCGACAAGTCAGAGGTCTAAAAATCATCGCGTTTGACTACTATTCATACGTATCTTTTTGAG
CATTCTGGATGCTAGACCGTCTAACTGTTCTTTGTCTAACTGTAAATATATATATGACTGAGTGT
TTGTGTTTGAGATGTTACGTTCCATTGGGATGTTGATTCCGGTATTACCTTTTGCTTCTGAATAT
ATA
Found at i:33509965 original size:31 final size:31
Alignment explanation
Indices: 33509927--33509985 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
33509917 TTTATGTAAC
33509927 TTAAATAAACTAGGTGTTTTCTAATTGGAAT
1 TTAAATAAACTAGGTGTTTTCTAATTGGAAT
*
33509958 TTAAATAAACTAGGTGTTTTTTAATTGG
1 TTAAATAAACTAGGTGTTTTCTAATTGG
33509986 TTAACTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (31 bp):
TTAAATAAACTAGGTGTTTTCTAATTGGAAT
Found at i:33510892 original size:18 final size:18
Alignment explanation
Indices: 33510869--33510920 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
33510859 GTGATTTTAA
33510869 TGAGATTACTTATTCATT
1 TGAGATTACTTATTCATT
33510887 TGAGATT--TTA---A--
1 TGAGATTACTTATTCATT
33510898 TGAGATTACTTATTCATT
1 TGAGATTACTTATTCATT
33510916 TGAGA
1 TGAGA
33510921 AACAAAGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 14
0.66 0.00 0.34
Matches are distributed among these distances:
11 7 0.26
13 4 0.15
16 4 0.15
18 12 0.44
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (18 bp):
TGAGATTACTTATTCATT
Found at i:33510903 original size:29 final size:29
Alignment explanation
Indices: 33510861--33510920 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
33510851 TGTTGTGGGT
33510861 GATTTTAATGAGATTACTTATTCATTTGA
1 GATTTTAATGAGATTACTTATTCATTTGA
33510890 GATTTTAATGAGATTACTTATTCATTTGA
1 GATTTTAATGAGATTACTTATTCATTTGA
33510919 GA
1 GA
33510921 AACAAAGTGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.47
Consensus pattern (29 bp):
GATTTTAATGAGATTACTTATTCATTTGA
Found at i:33512285 original size:29 final size:29
Alignment explanation
Indices: 33512241--33512299 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
33512231 GGTAGGTGAG
* *
33512241 CCAGTGTAAGATATGTCTGGGACATGCAT
1 CCAGTGTAAGACATGTCTAGGACATGCAT
33512270 CCAGTGTAAGACATGTCTAGGACATGCAT
1 CCAGTGTAAGACATGTCTAGGACATGCAT
33512299 C
1 C
33512300 AGCATTGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (29 bp):
CCAGTGTAAGACATGTCTAGGACATGCAT
Found at i:33512482 original size:49 final size:49
Alignment explanation
Indices: 33512329--33512581 Score: 202
Period size: 49 Copynumber: 5.3 Consensus size: 49
33512319 GTGTAGGATA
* ** * *
33512329 TGTCTGGGACAT-GCATTGACCTCGGGATAT-ACAAGCTAGTGTAAGACC
1 TGTCTGGGACATGGCATCGACCTCGATAGATGA-AAGCCAGTGTAAGACC
* * * * *
33512377 TGTCTGGGACATGGCATC-AGCTTG-T-TATG--TGTCAGTGTAAGACC
1 TGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCCAGTGTAAGACC
* * *
33512421 TATATGGGACATGGCATCGACAC-CGATAGATGAGAGCCAGTGTAAGACC
1 TGTCTGGGACATGGCATCGAC-CTCGATAGATGAAAGCCAGTGTAAGACC
* * * * *
33512470 TGTCTGGAACATGGCATCGGCCTCGATATATGAAAGTCAGTGTAAGACA
1 TGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCCAGTGTAAGACC
* ** **
33512519 TGTCTGGGACATGGCATCGACTTTAAT-G-TGCTAGCCAGTGTAAGACC
1 TGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCCAGTGTAAGACC
33512566 ATGTCTGGGACATGGC
1 -TGTCTGGGACATGGC
33512582 GTCGGCATTT
Statistics
Matches: 163, Mismatches: 32, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
44 28 0.17
45 2 0.01
46 5 0.03
47 18 0.11
48 32 0.20
49 78 0.48
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.25
Consensus pattern (49 bp):
TGTCTGGGACATGGCATCGACCTCGATAGATGAAAGCCAGTGTAAGACC
Found at i:33512537 original size:98 final size:92
Alignment explanation
Indices: 33512366--33512587 Score: 248
Period size: 98 Copynumber: 2.3 Consensus size: 92
33512356 TATACAAGCT
* * * *
33512366 AGTGTAAGACCTGTCTGGGACATGGCATCAG-CTTGTTATGTGTCAGTGTAAGACCTATATGGGA
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGTTATGAGTCAGTGTAAGACATATATGGGA
*
33512430 CATGGCATCGACACCGATAGATGAGAGCC
66 CATGGCATCGACACCAAT-G-TGAGAGCC
* * *
33512459 AGTGTAAGACCTGTCTGGAACATGGCATCGGCCTCGATATATGAAAGTCAGTGTAAGACATGTCT
1 AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCG-T-TATG--AGTCAGTGTAAGACATATAT
*** **
33512524 GGGACATGGCATCGACTTTAATGTGCTAGCC
62 GGGACATGGCATCGACACCAATGTGAGAGCC
*
33512555 AGTGTAAGACCATGTCTGGGACATGGCGTCGGC
1 AGTGTAAGACC-TGTCTGGGACATGGCATCGGC
33512588 ATTTTATCCC
Statistics
Matches: 108, Mismatches: 15, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
93 29 0.27
94 3 0.03
95 1 0.01
96 21 0.19
97 20 0.19
98 34 0.31
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (92 bp):
AGTGTAAGACCTGTCTGGGACATGGCATCGGCCTCGTTATGAGTCAGTGTAAGACATATATGGGA
CATGGCATCGACACCAATGTGAGAGCC
Found at i:33516047 original size:14 final size:15
Alignment explanation
Indices: 33516028--33516057 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
33516018 ATTTTTATGC
33516028 TTATAA-GATTTTTA
1 TTATAAGGATTTTTA
33516042 TTATAAGGATTTTTA
1 TTATAAGGATTTTTA
33516057 T
1 T
33516058 ACTAATTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (15 bp):
TTATAAGGATTTTTA
Found at i:33516075 original size:31 final size:32
Alignment explanation
Indices: 33516018--33516078 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
33516008 AAAAATTTAA
* *
33516018 ATTTTTATGCTTATAAGATTTTTATTATAAGG
1 ATTTTTATACTAATAAGATTTTTATTATAAGG
*
33516050 ATTTTTATACTAATTAGA-TTTTATTATAA
1 ATTTTTATACTAATAAGATTTTTATTATAA
33516079 TTACTATATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.54
Consensus pattern (32 bp):
ATTTTTATACTAATAAGATTTTTATTATAAGG
Found at i:33517025 original size:54 final size:54
Alignment explanation
Indices: 33516931--33517033 Score: 122
Period size: 54 Copynumber: 1.9 Consensus size: 54
33516921 AATTTTTTTT
*
33516931 AAATTCTAAAAATTATTAAAATGAATAAACATTATAAAATT-TCAAATATGTAAC
1 AAATTATAAAAATTATTAAAATGAATAAACATTATAAAATTAT-AAATATGTAAC
* * *
33516985 AAATTATAAAATTTATTAAAATTTACTATAA-ATTAT-AAATTATAAATAT
1 AAATTATAAAAATTATTAAAA-TGAATA-AACATTATAAAATTATAAATAT
33517034 TTTACTTATA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
54 30 0.71
55 10 0.24
56 2 0.05
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (54 bp):
AAATTATAAAAATTATTAAAATGAATAAACATTATAAAATTATAAATATGTAAC
Found at i:33517307 original size:28 final size:26
Alignment explanation
Indices: 33517251--33517319 Score: 72
Period size: 28 Copynumber: 2.7 Consensus size: 26
33517241 TTTTTTTTGT
*
33517251 TTTTA-TATATTTAAAATTTATAAAT
1 TTTTATTATATTTAAAATTTATAAAA
33517276 TTTTATTATATTTACTAAATTT-TAATAA
1 TTTTATTATATTTA--AAATTTATAA-AA
*
33517304 TTTTA-TATTTTTAAAA
1 TTTTATTATATTTAAAA
33517320 AATTAAAGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
25 8 0.21
26 8 0.21
27 10 0.26
28 12 0.32
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (26 bp):
TTTTATTATATTTAAAATTTATAAAA
Found at i:33517308 original size:19 final size:19
Alignment explanation
Indices: 33517266--33517310 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
33517256 TATATTTAAA
* *
33517266 ATTTATAAATTTTTATTAT
1 ATTTATAAATTTTAATAAT
33517285 ATTTACTAAATTTTAATAAT
1 ATTTA-TAAATTTTAATAAT
33517305 -TTTATA
1 ATTTATA
33517311 TTTTTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 2 0.09
19 9 0.39
20 12 0.52
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTATAAATTTTAATAAT
Found at i:33520541 original size:27 final size:27
Alignment explanation
Indices: 33520478--33520570 Score: 98
Period size: 27 Copynumber: 3.4 Consensus size: 27
33520468 TATTCCCGAT
* * *
33520478 GAACTCTCAAGAGATAGTATGTGTGGC
1 GAACTCTGAAGGGATAGTATGTATGGC
33520505 GAACAT-TGAAGGGATAGTATGTATGGC
1 GAAC-TCTGAAGGGATAGTATGTATGGC
* * * **
33520532 GAACTCTGAAGGAATGGTAGGTATAAC
1 GAACTCTGAAGGGATAGTATGTATGGC
33520559 GAACTCTGAAGG
1 GAACTCTGAAGG
33520571 AAAATCCCTT
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.02
27 54 0.96
28 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (27 bp):
GAACTCTGAAGGGATAGTATGTATGGC
Found at i:33522672 original size:33 final size:33
Alignment explanation
Indices: 33522635--33522702 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
33522625 ATTTCATTTT
*
33522635 TTCCTTTCAATTTTGCATTAACATTCTATAGCA
1 TTCCTTTCAATTTGGCATTAACATTCTATAGCA
33522668 TTCCTTTCAATTTGGCATTAACATTCTATAGCA
1 TTCCTTTCAATTTGGCATTAACATTCTATAGCA
33522701 TT
1 TT
33522703 GTGTCCAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.46
Consensus pattern (33 bp):
TTCCTTTCAATTTGGCATTAACATTCTATAGCA
Found at i:33534063 original size:46 final size:46
Alignment explanation
Indices: 33533975--33534194 Score: 166
Period size: 46 Copynumber: 4.7 Consensus size: 46
33533965 GGTAAGGTTT
33533975 CGATGCCATGTCCCAGACATGGTCTTACACTGACTATCATCTCG-TAGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGACTATCATCTCGAT-GC
* * *
33534023 CGATGCATGTCCCAAACATGTCTTACATTGGCT-TACATCTCGATGC
1 CGATGCATGTCCCAGACATGTCTTACACTGACTAT-CATCTCGATGC
* *
33534069 CGCTGCATGTCGCAGACATGTCTTACACTAGCACT-TGC--CTCGATGC
1 CGATGCATGTCCCAGACATGTCTTACACT-G-ACTAT-CATCTCGATGC
* * * * * *
33534115 CAATGCCATGTCCCAGACACAGTCTTACACTGGCTCTCATAAT-G-TGGT
1 CGATG-CATGTCCCAGACA-TGTCTTACACTGACTATCAT-CTCGAT-GC
** *
33534163 TAATGCATGTCCTAGACATGTCTTACACTGAC
1 CGATGCATGTCCCAGACATGTCTTACACTGAC
33534195 CCACAATAAC
Statistics
Matches: 141, Mismatches: 20, Indels: 24
0.76 0.11 0.13
Matches are distributed among these distances:
45 1 0.01
46 72 0.51
47 42 0.30
48 25 0.18
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.28
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTGACTATCATCTCGATGC
Found at i:33537312 original size:68 final size:69
Alignment explanation
Indices: 33537232--33537395 Score: 215
Period size: 69 Copynumber: 2.4 Consensus size: 69
33537222 TGAGTGCACA
* **
33537232 TCATGT-GTACAAGAGAGCTACGAGATACTATGTA-GTAGCTAGGTCGCATGTGTGATACGGGAT
1 TCATGTAG-ACAAGAGAGCTACGAGATACGATAAATGTAGCTAGGTCGCATGTGTGATACGGGAT
33537295 GTATC
65 GTATC
* * *
33537300 TCATGTAGACAAGAGAGCTACGGGAGAGGATAAATGTAGCTAGGTCGCATGTGTGATACGGGATG
1 TCATGTAGACAAGAGAGCTACGAGATACGATAAATGTAGCTAGGTCGCATGTGTGATACGGGATG
33537365 TATC
66 TATC
* * * *
33537369 CCACGTAGACAAGAGAGGTATGAGATA
1 TCATGTAGACAAGAGAGCTACGAGATA
33537396 AATTGGCTAG
Statistics
Matches: 82, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
68 26 0.32
69 56 0.68
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (69 bp):
TCATGTAGACAAGAGAGCTACGAGATACGATAAATGTAGCTAGGTCGCATGTGTGATACGGGATG
TATC
Found at i:33545051 original size:49 final size:49
Alignment explanation
Indices: 33544982--33545079 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
33544972 ATGAAATATG
33544982 ATGGTGGGGCTGTGTGCTGAAACCATCAAGTATCGAGGATTGATCCGAA
1 ATGGTGGGGCTGTGTGCTGAAACCATCAAGTATCGAGGATTGATCCGAA
33545031 ATGGTGGGGCTGTGTGCTGAAACCATCAAGTATCGAGGATTGATCCGAA
1 ATGGTGGGGCTGTGTGCTGAAACCATCAAGTATCGAGGATTGATCCGAA
33545080 TTGTTCAACG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (49 bp):
ATGGTGGGGCTGTGTGCTGAAACCATCAAGTATCGAGGATTGATCCGAA
Found at i:33547471 original size:19 final size:19
Alignment explanation
Indices: 33547447--33547484 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
33547437 TGAAAAAATG
*
33547447 TTTGCTTGTATATAAATAA
1 TTTGCTTGTACATAAATAA
33547466 TTTGCTTGTACATAAATAA
1 TTTGCTTGTACATAAATAA
33547485 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTGCTTGTACATAAATAA
Found at i:33548267 original size:16 final size:16
Alignment explanation
Indices: 33548246--33548281 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
33548236 AAAAAAAATC
*
33548246 TTATTTTATTTTTATT
1 TTATTTTATTTTGATT
*
33548262 TTATTTTCTTTTGATT
1 TTATTTTATTTTGATT
33548278 TTAT
1 TTAT
33548282 ATTAAATTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.78
Consensus pattern (16 bp):
TTATTTTATTTTGATT
Found at i:33559316 original size:27 final size:27
Alignment explanation
Indices: 33559279--33559581 Score: 294
Period size: 27 Copynumber: 11.3 Consensus size: 27
33559269 TTAGTTTACC
* * *
33559279 AAATTATCAAAATACCCTCGATTAGCA
1 AAATTACCAAAATACCCTCGATTTGTA
* ***
33559306 AAATTACCAAAATACCCTTGATTAACA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
33559333 AAATTACCAAAATACCCTCGATTAGCA
1 AAATTACCAAAATACCCTCGATTTGTA
*
33559360 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
*
33559387 AAATTACCAAATTACCC-CTGATTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
*
33559414 AAATTACCAAATTACCC-CTGATTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
*
33559441 AAATTACCGAAATA-CCTCCGATTTGTA
1 AAATTACCAAAATACCCT-CGATTTGTA
* *
33559468 AAATTACCGAAATA-CATCTGATTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
**
33559495 AAATTACTGAAATACCC-CGATTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* ** *
33559521 AAATTACTAAAATACTTTCGACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* * **
33559548 AAATTACCAAAGTACCCCCGATTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
33559575 AAATTAC
1 AAATTAC
33559582 AGTTTTACCC
Statistics
Matches: 243, Mismatches: 27, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
26 26 0.11
27 215 0.88
28 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.29
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:33559633 original size:27 final size:27
Alignment explanation
Indices: 33559603--33559852 Score: 322
Period size: 27 Copynumber: 9.3 Consensus size: 27
33559593 CGATTTACAA
* *
33559603 AATTACCGAAACACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
33559630 AATTACTGAAATATCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
33559657 AATTACCGAAATACCCCTATAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
*
33559684 AATTACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
** *
33559711 AATTATTGAAATACCCCTATAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
33559738 AATTACCGAAATACCCCTGTAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
33559765 AATTACTGAAATACCCTTGTAGGGTAGG
1 AATTACCGAAATACCCCTGTAGGGTA-G
*
33559793 AA-TACCAAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * *
33559819 AATTACCGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
33559846 AATTACC
1 AATTACC
33559853 ATTTTTCCCC
Statistics
Matches: 191, Mismatches: 30, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
26 3 0.02
27 185 0.97
28 3 0.02
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:33565610 original size:27 final size:27
Alignment explanation
Indices: 33565575--33565887 Score: 260
Period size: 27 Copynumber: 11.6 Consensus size: 27
33565565 TTAGTTTACC
* *
33565575 AAATTACCAAAATACCCTCGATTAGCA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
33565602 AAATTACCAAAATACCCTCGATTAGCA
1 AAATTACCAAAATACCCTCGATTTGTA
* *
33565629 AAATTACCAAAATACCCTTGGTTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
*
33565656 AAATTACCAAAATACCC-CTGGTTTGTA
1 AAATTACCAAAATACCCTC-GATTTGTA
* *
33565683 AAATTACCAAATTACCCCCGATTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
*
33565710 AAATTACCGAAATA-CCTCCGATTTG-A
1 AAATTACCAAAATACCCT-CGATTTGTA
**
33565736 AAATTTACTGAAATACCC-CGATTTGTA
1 AAA-TTACCAAAATACCCTCGATTTGTA
* * * *
33565763 AAATTACTAAAATACCTTCAACTTGTA
1 AAATTACCAAAATACCCTCGATTTGTA
* **
33565790 AAATTACCAAAGTA-CCTCCGATTTACA
1 AAATTACCAAAATACCCT-CGATTTGTA
**** **
33565817 AAATTACCGTTTTACCCTCGATTTACA
1 AAATTACCAAAATACCCTCGATTTGTA
* * * **
33565844 AAATTACCGAAACACCC-CTATAGGGTA
1 AAATTACCAAAATACCCTCGAT-TTGTA
*
33565871 AAATTACCGAAATACCC
1 AAATTACCAAAATACCC
33565888 CTGTAGGGTA
Statistics
Matches: 240, Mismatches: 36, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
26 30 0.12
27 204 0.85
28 6 0.03
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.28
Consensus pattern (27 bp):
AAATTACCAAAATACCCTCGATTTGTA
Found at i:33565883 original size:134 final size:133
Alignment explanation
Indices: 33565601--33565888 Score: 303
Period size: 134 Copynumber: 2.1 Consensus size: 133
33565591 CTCGATTAGC
* ***
33565601 AAAATTACCAAAATACCCTCGATTAGCAAAATTACCAAAATACCCTTGGTTTGTAAAATTACCAA
1 AAAATTACCGAAATACCC-CGATTAGCAAAATTACCAAAATACCCTTAACTTGTAAAATTACCAA
* ** ** *
33565666 AATACCCCTGGTTTGTAAAATTACCAAATTACCCCCGATTTGTAAAATTACCGAAATACCTCCGA
65 AATACCCCTGATTTACAAAATTACCAAATTACCCCCGATTTACAAAATTACCGAAACACCTCCGA
**
33565731 TTTG
130 TGGG
* * * *
33565735 AAAATTTACTGAAATACCCCGATTTGTAAAATTACTAAAATA-CCTTCAACTTGTAAAATTACCA
1 AAAA-TTACCGAAATACCCCGATTAGCAAAATTACCAAAATACCCTT-AACTTGTAAAATTACCA
* *** *
33565799 AAGTACCTCC-GATTTACAAAATTACCGTTTTACCCTCGATTTACAAAATTACCGAAACACC-CC
64 AAATACC-CCTGATTTACAAAATTACCAAATTACCCCCGATTTACAAAATTACCGAAACACCTCC
*
33565862 TATAGGG
128 GAT-GGG
33565869 TAAAATTACCGAAATACCCC
1 -AAAATTACCGAAATACCCC
33565889 TGTAGGGTAG
Statistics
Matches: 126, Mismatches: 23, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
133 8 0.06
134 100 0.79
135 18 0.14
ACGTcount: A:0.39, C:0.24, G:0.09, T:0.28
Consensus pattern (133 bp):
AAAATTACCGAAATACCCCGATTAGCAAAATTACCAAAATACCCTTAACTTGTAAAATTACCAAA
ATACCCCTGATTTACAAAATTACCAAATTACCCCCGATTTACAAAATTACCGAAACACCTCCGAT
GGG
Found at i:33565888 original size:27 final size:27
Alignment explanation
Indices: 33565845--33566094 Score: 360
Period size: 27 Copynumber: 9.3 Consensus size: 27
33565835 CGATTTACAA
* * *
33565845 AATTACCGAAACACCCCTATAGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
33565872 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
33565899 AATTACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
33565926 AATTACCGAAATACCCCTGTTGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
*
33565953 AATTACTGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* *
33565980 AATTACCGAAATACCCCTATAGGATAG
1 AATTACCGAAATACCCCTGTAGGGTAG
33566007 AATTACCGAAAT-CCCCTTGTAGGGTAGG
1 AATTACCGAAATACCCC-TGTAGGGTA-G
33566035 AA-TACCGAAATACCCCTGTAGGGTAG
1 AATTACCGAAATACCCCTGTAGGGTAG
* * * * *
33566061 AATTACTGAGATACCCTTGTGGGGTAA
1 AATTACCGAAATACCCCTGTAGGGTAG
33566088 AATTACC
1 AATTACC
33566095 ATTTTGCCCC
Statistics
Matches: 202, Mismatches: 17, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.03
27 188 0.93
28 7 0.03
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.24
Consensus pattern (27 bp):
AATTACCGAAATACCCCTGTAGGGTAG
Found at i:33566786 original size:27 final size:26
Alignment explanation
Indices: 33566746--33566797 Score: 77
Period size: 27 Copynumber: 2.0 Consensus size: 26
33566736 CTCGCTGCAA
*
33566746 TCTGGTGGCCTCGTCACATATATCTGT
1 TCTGGTGACCTCGTCACA-ATATCTGT
*
33566773 TCTGGTGACTTCGTCACAATATCTG
1 TCTGGTGACCTCGTCACAATATCTG
33566798 GCAGCCTCGC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (26 bp):
TCTGGTGACCTCGTCACAATATCTGT
Found at i:33569918 original size:18 final size:18
Alignment explanation
Indices: 33569895--33569947 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 18
33569885 AGAGATATGT
33569895 ATAAAAGAAAATTTTAAA
1 ATAAAAGAAAATTTTAAA
*
33569913 AT-AAA-AAAATTTT-AT
1 ATAAAAGAAAATTTTAAA
*
33569928 ATAATAGAACAA-TTTAAA
1 ATAAAAGAA-AATTTTAAA
33569946 AT
1 AT
33569948 TTTATACAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
15 3 0.11
16 10 0.36
17 8 0.29
18 7 0.25
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (18 bp):
ATAAAAGAAAATTTTAAA
Found at i:33571368 original size:14 final size:15
Alignment explanation
Indices: 33571349--33571378 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
33571339 TTTTAATTAA
33571349 TTTGGTTTTA-TTTT
1 TTTGGTTTTAGTTTT
33571363 TTTGGTTTTAGTTTT
1 TTTGGTTTTAGTTTT
33571378 T
1 T
33571379 GTATGGGCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.07, C:0.00, G:0.17, T:0.77
Consensus pattern (15 bp):
TTTGGTTTTAGTTTT
Found at i:33575602 original size:22 final size:22
Alignment explanation
Indices: 33575561--33575603 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
33575551 TATTAAAATA
**
33575561 ATAAAATTTTAATTTTTTAATG
1 ATAAAATTTTAATTAATTAATG
*
33575583 ATAAATTTTTAATTAATTAAT
1 ATAAAATTTTAATTAATTAAT
33575604 TTAATAAAAT
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:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATAAAATTTTAATTAATTAATG
Found at i:33579154 original size:19 final size:15
Alignment explanation
Indices: 33579108--33579145 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
33579098 TGATGAAATT
33579108 ATTGAATTTATATTG
1 ATTGAATTTATATTG
33579123 ATTGAATTTATATTG
1 ATTGAATTTATATTG
33579138 ATTGAATT
1 ATTGAATT
33579146 GGCGTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (15 bp):
ATTGAATTTATATTG
Found at i:33579186 original size:18 final size:19
Alignment explanation
Indices: 33579163--33579201 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
33579153 ATATATAGAT
33579163 ATATATATTGAATA-TTGA
1 ATATATATTGAATATTTGA
*
33579181 ATATATATTGATTATTTGA
1 ATATATATTGAATATTTGA
33579200 AT
1 AT
33579202 TGAATTGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.49
Consensus pattern (19 bp):
ATATATATTGAATATTTGA
Found at i:33579551 original size:39 final size:39
Alignment explanation
Indices: 33579441--33579575 Score: 112
Period size: 39 Copynumber: 3.4 Consensus size: 39
33579431 GACCTCGAGT
* * * *
33579441 CGATGAGACACTGGGTGTCACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA-AATATTCCTTCGGCTAG-TC
** ** * *
33579482 CGATGAGGTACTGGGTACCAACT-TTCCTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAAATATTCCTTCGGCTAGTC
* *
33579520 CGATGAGACACTGGGTGTCAAATATTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAAATATTCCTTCG-GCTAGTC
*
33579559 CGATGAGGCACTGGGTG
1 CGATGAGACACTGGGTG
33579576 CCATATTGGT
Statistics
Matches: 73, Mismatches: 19, Indels: 6
0.74 0.19 0.06
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATATTCCTTCGGCTAGTC
Found at i:33579719 original size:18 final size:19
Alignment explanation
Indices: 33579698--33579738 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
33579688 AATGAAATGA
33579698 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
33579716 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
33579735 GAAA
1 GAAA
33579739 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:33584724 original size:19 final size:19
Alignment explanation
Indices: 33584700--33584736 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33584690 ATTTATGTTT
*
33584700 TAGATACAGGACCTTTTAA
1 TAGATACAGCACCTTTTAA
*
33584719 TAGATATAGCACCTTTTA
1 TAGATACAGCACCTTTTA
33584737 TATTAATAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (19 bp):
TAGATACAGCACCTTTTAA
Found at i:33585893 original size:18 final size:18
Alignment explanation
Indices: 33585870--33585917 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
33585860 AAAATGTGAG
*
33585870 AAATGATGTTCACATTTT
1 AAATGATGTTCACATTTC
33585888 AAATGATGTTCACATTTC
1 AAATGATGTTCACATTTC
33585906 AAATGATGTTCA
1 AAATGATGTTCA
33585918 AATTGATGGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (18 bp):
AAATGATGTTCACATTTC
Found at i:33586468 original size:72 final size:72
Alignment explanation
Indices: 33586346--33586651 Score: 454
Period size: 72 Copynumber: 4.2 Consensus size: 72
33586336 AAATGCTAAA
* * * *
33586346 CTAGTTTTATCAATAGTTATTTATGTTTGGTTTTTGGATATTGAACTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTAGTTTTTGAATATTGAATTTATGTTCTACTTATTTAT
33586411 GTGTAAT
66 GTGTAAT
*
33586418 CTAGTTTTATCAATGGTTGTTTATGTTTAGTTTTTGAATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTAGTTTTTGAATATTGAATTTATGTTCTACTTATTTAT
33586483 GTGTAAT
66 GTGTAAT
*
33586490 CTAGTTTTATCAATGGTTGTTTATGTTTAGTTTTTGAATATTGAATTTATGTTCTACTTATTTAT
1 CTAGTTTTATCAATAGTTGTTTATGTTTAGTTTTTGAATATTGAATTTATGTTCTACTTATTTAT
33586555 GTGTAAT
66 GTGTAAT
* * * * * *
33586562 CTACTTTTATTAATAGTTGTTTATGTTTGGTCTTTGGGATATTGAATTTATGCTCTACTTATTTA
1 CTAGTTTTATCAATAGTTGTTTATGTTTAGT-TTTTGAATATTGAATTTATGTTCTACTTATTTA
* *
33586627 TACT-AAAT
65 T-GTGTAAT
33586635 -TAGTTTTATCAATAGTT
1 CTAGTTTTATCAATAGTT
33586652 ATTAATATAT
Statistics
Matches: 216, Mismatches: 16, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
72 181 0.84
73 34 0.16
74 1 0.00
ACGTcount: A:0.24, C:0.07, G:0.15, T:0.54
Consensus pattern (72 bp):
CTAGTTTTATCAATAGTTGTTTATGTTTAGTTTTTGAATATTGAATTTATGTTCTACTTATTTAT
GTGTAAT
Found at i:33588463 original size:13 final size:13
Alignment explanation
Indices: 33588442--33588505 Score: 83
Period size: 13 Copynumber: 4.9 Consensus size: 13
33588432 ACACCTAAAA
33588442 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
*
33588455 TTCTCAAAAGCAC
1 TTTTCAAAAGCAC
* **
33588468 TTTTCCACCGCAC
1 TTTTCAAAAGCAC
*
33588481 TTTTTAAAAGCAC
1 TTTTCAAAAGCAC
33588494 TTTTCAAAAGCA
1 TTTTCAAAAGCA
33588506 TTGCCAAACA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.34, C:0.27, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:33588913 original size:13 final size:13
Alignment explanation
Indices: 33588895--33588924 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
33588885 ACTCAATATC
*
33588895 ATGCGAGCTCGAT
1 ATGCGAGCTCAAT
33588908 ATGCGAGCTCAAT
1 ATGCGAGCTCAAT
33588921 ATGC
1 ATGC
33588925 AAACCACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (13 bp):
ATGCGAGCTCAAT
Found at i:33590324 original size:6 final size:6
Alignment explanation
Indices: 33590313--33590340 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
33590303 TAGAACCTTA
33590313 AACCAT AACCAT AACCAT AACCAT AACC
1 AACCAT AACCAT AACCAT AACCAT AACC
33590341 CCAAACTCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.50, C:0.36, G:0.00, T:0.14
Consensus pattern (6 bp):
AACCAT
Found at i:33590361 original size:14 final size:13
Alignment explanation
Indices: 33590315--33590360 Score: 51
Period size: 12 Copynumber: 3.5 Consensus size: 13
33590305 GAACCTTAAA
33590315 CCATAACCATAA-
1 CCATAACCATAAC
33590327 CCATAACCATAACC
1 CCATAACCATAA-C
33590341 CCA-AACTCATAAC
1 CCATAAC-CATAAC
*
33590354 CCGTAAC
1 CCATAAC
33590361 TTTGAACCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 12 0.41
13 6 0.21
14 11 0.38
ACGTcount: A:0.43, C:0.39, G:0.02, T:0.15
Consensus pattern (13 bp):
CCATAACCATAAC
Found at i:33590936 original size:22 final size:22
Alignment explanation
Indices: 33590867--33590937 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
33590857 TTTACTAACA
33590867 TAACAATTTTATAATATAAATT
1 TAACAATTTTATAATATAAATT
* * *
33590889 TAAC-ATTTATTTAGTTCTAACA--
1 TAACAATTT-TATA-ATATAA-ATT
33590911 TAACAATTTTATAATATAAATT
1 TAACAATTTTATAATATAAATT
33590933 TAACA
1 TAACA
33590938 CTTATTTAGT
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
20 1 0.03
21 8 0.22
22 19 0.51
23 8 0.22
24 1 0.03
ACGTcount: A:0.46, C:0.08, G:0.01, T:0.44
Consensus pattern (22 bp):
TAACAATTTTATAATATAAATT
Found at i:33590946 original size:44 final size:44
Alignment explanation
Indices: 33590861--33590952 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
33590851 TTAAATTTTA
*
33590861 CTAACATAACAATTTTATAATATAAATTTAACATTTATTTAGTT
1 CTAACATAACAATTTTATAATATAAATTTAACACTTATTTAGTT
33590905 CTAACATAACAATTTTATAATATAAATTTAACACTTATTTAGTT
1 CTAACATAACAATTTTATAATATAAATTTAACACTTATTTAGTT
33590949 CTAA
1 CTAA
33590953 AAATTATGTC
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (44 bp):
CTAACATAACAATTTTATAATATAAATTTAACACTTATTTAGTT
Found at i:33591419 original size:7 final size:8
Alignment explanation
Indices: 33591407--33591444 Score: 60
Period size: 8 Copynumber: 4.9 Consensus size: 8
33591397 ATTCTTCACT
*
33591407 CTTTTTTT
1 CTTTTTTC
33591415 CTTTTTT-
1 CTTTTTTC
33591422 CTTTTTTC
1 CTTTTTTC
33591430 CTTTTTTC
1 CTTTTTTC
33591438 CTTTTTT
1 CTTTTTT
33591445 TCCACCCAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (8 bp):
CTTTTTTC
Found at i:33591424 original size:15 final size:15
Alignment explanation
Indices: 33591406--33591446 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
33591396 CATTCTTCAC
33591406 TCTTTTTTTCTTTTT
1 TCTTTTTTTCTTTTT
*
33591421 TCTTTTTTCCTTTTT
1 TCTTTTTTTCTTTTT
33591436 TCCTTTTTTTC
1 T-CTTTTTTTC
33591447 CACCCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TCTTTTTTTCTTTTT
Found at i:33592890 original size:9 final size:9
Alignment explanation
Indices: 33592876--33592908 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
33592866 TGTTTGTGTC
33592876 TTTAAAAAT
1 TTTAAAAAT
33592885 TTTAAAAAT
1 TTTAAAAAT
33592894 TTTAAAAAT
1 TTTAAAAAT
33592903 TTTAAA
1 TTTAAA
33592909 TTAATATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTTAAAAAT
Found at i:33603541 original size:24 final size:24
Alignment explanation
Indices: 33603509--33603557 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
33603499 TTGGTCAGGC
33603509 TATGAATTCCACTACTATGAATGA
1 TATGAATTCCACTACTATGAATGA
* *
33603533 TATGAATTCCACTATTGTGAATGA
1 TATGAATTCCACTACTATGAATGA
33603557 T
1 T
33603558 GCTACATACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (24 bp):
TATGAATTCCACTACTATGAATGA
Found at i:33605854 original size:13 final size:14
Alignment explanation
Indices: 33605821--33605854 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
33605811 TTAGTGTTTA
33605821 AGGG-TTTAAAGCT
1 AGGGTTTTAAAGCT
33605834 AGGGTTTTAAAG-T
1 AGGGTTTTAAAGCT
33605847 AGGGTTTT
1 AGGGTTTT
33605855 GGATTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.26, C:0.03, G:0.32, T:0.38
Consensus pattern (14 bp):
AGGGTTTTAAAGCT
Found at i:33619636 original size:16 final size:16
Alignment explanation
Indices: 33619611--33619642 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
33619601 ACTATGACAT
*
33619611 TAAGGTAAAAATAGAA
1 TAAGGCAAAAATAGAA
33619627 TAAGGCAAAAATAGAA
1 TAAGGCAAAAATAGAA
33619643 ACTAACTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.19, T:0.16
Consensus pattern (16 bp):
TAAGGCAAAAATAGAA
Found at i:33619725 original size:19 final size:19
Alignment explanation
Indices: 33619681--33619717 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33619671 TAAAAGTTTT
* *
33619681 AAATTATTTAAAATCTATA
1 AAATTATTAAAAATATATA
33619700 AAATTATTAAAAATATAT
1 AAATTATTAAAAATATAT
33619718 CCAATTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATTATTAAAAATATATA
Found at i:33628637 original size:23 final size:25
Alignment explanation
Indices: 33628590--33628639 Score: 77
Period size: 25 Copynumber: 2.1 Consensus size: 25
33628580 ATGCAATACT
33628590 ATAAATATAAAAAATTAGAACAAAA
1 ATAAATATAAAAAATTAGAACAAAA
*
33628615 ATAAATATAAAATATTA-AA-AAAA
1 ATAAATATAAAAAATTAGAACAAAA
33628638 AT
1 AT
33628640 TTCTCCCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 6 0.25
24 2 0.08
25 16 0.67
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (25 bp):
ATAAATATAAAAAATTAGAACAAAA
Found at i:33629158 original size:21 final size:19
Alignment explanation
Indices: 33629133--33629174 Score: 57
Period size: 21 Copynumber: 2.1 Consensus size: 19
33629123 AAAATTAAAA
33629133 TTTTAAAATTCTTTATATATT
1 TTTTAAAATT-TTTATA-ATT
*
33629154 TTTTAGAATTTTTATAATT
1 TTTTAAAATTTTTATAATT
33629173 TT
1 TT
33629175 AAAAAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 5 0.25
20 6 0.30
21 9 0.45
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTTAAAATTTTTATAATT
Found at i:33629205 original size:18 final size:18
Alignment explanation
Indices: 33629130--33629206 Score: 68
Period size: 17 Copynumber: 4.2 Consensus size: 18
33629120 AAAAAAATTA
33629130 AAATTTTAAAATTCTTTAT
1 AAATTTTAAAATT-TTTAT
* *
33629149 ATATTTTTTAGAATTTTTAT
1 A-A-ATTTTAAAATTTTTAT
***
33629169 -AATTTTAAAA-AAATAT
1 AAATTTTAAAATTTTTAT
33629185 AAATTTTAAAATTTTTAT
1 AAATTTTAAAATTTTTAT
33629203 AAAT
1 AAAT
33629207 ATTATGAATT
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
16 3 0.07
17 17 0.39
18 8 0.18
19 1 0.02
20 6 0.14
21 9 0.20
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (18 bp):
AAATTTTAAAATTTTTAT
Found at i:33629225 original size:19 final size:22
Alignment explanation
Indices: 33629194--33629241 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 22
33629184 TAAATTTTAA
33629194 AATTTTT-ATAAA-TATTATG-
1 AATTTTTGATAAATTATTATGT
*
33629213 AATTTTTGA-AAATTATTTTGT
1 AATTTTTGATAAATTATTATGT
33629234 AATTTTTG
1 AATTTTTG
33629242 TTGAAAAAGA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 10 0.40
20 7 0.28
21 8 0.32
ACGTcount: A:0.35, C:0.00, G:0.08, T:0.56
Consensus pattern (22 bp):
AATTTTTGATAAATTATTATGT
Found at i:33631999 original size:17 final size:18
Alignment explanation
Indices: 33631979--33632018 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
33631969 AAAATAATAT
33631979 TATTTTAA-TAAATTTAA
1 TATTTTAATTAAATTTAA
*
33631996 TA-TTTAATTTAATTTAA
1 TATTTTAATTAAATTTAA
33632013 T-TTTTA
1 TATTTTA
33632019 TCTTGTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
16 5 0.25
17 15 0.75
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATTTTAATTAAATTTAA
Found at i:33632070 original size:12 final size:12
Alignment explanation
Indices: 33632053--33632116 Score: 55
Period size: 12 Copynumber: 5.2 Consensus size: 12
33632043 AATTTAATAG
33632053 ATTTAATATTAA
1 ATTTAATATTAA
33632065 ATTTAAT-TTAA
1 ATTTAATATTAA
33632076 TATTTACAT-TGATAA
1 -ATTTA-ATAT--TAA
33632091 ATATT-ATATT-A
1 AT-TTAATATTAA
33632102 ATTTAATATTAA
1 ATTTAATATTAA
33632114 ATT
1 ATT
33632117 AATTAAGTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
10 2 0.05
11 12 0.27
12 17 0.39
13 5 0.11
14 3 0.07
15 5 0.11
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:33632108 original size:63 final size:64
Alignment explanation
Indices: 33631973--33632113 Score: 173
Period size: 63 Copynumber: 2.2 Consensus size: 64
33631963 ATTTCAAAAA
* * * *
33631973 TAATATTATTTTAATAAATTTAATATTTAATTTAATTTAATTTTTATCTTGTAGATAATTATAT
1 TAATATTAATTTAATAAATTTAATATTAAATTTAATTTAATATTTATCTTGTAAATAATTATAT
* *
33632037 T-CTATTAATTTAATAGATTTAATATTAAATTTAATTTAATATTTA-CATTGATAAAT-ATTATA
1 TAATATTAATTTAATAAATTTAATATTAAATTTAATTTAATATTTATC-TTG-TAAATAATTATA
33632099 T
64 T
33632100 TAAT-TTAATATTAA
1 TAATATTAAT-TTAA
33632114 ATTAATTAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
62 1 0.02
63 55 0.83
64 10 0.15
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (64 bp):
TAATATTAATTTAATAAATTTAATATTAAATTTAATTTAATATTTATCTTGTAAATAATTATAT
Found at i:33632122 original size:58 final size:61
Alignment explanation
Indices: 33631975--33632129 Score: 158
Period size: 63 Copynumber: 2.5 Consensus size: 61
33631965 TTCAAAAATA
* * * * *
33631975 ATATTATTTTAATAAATTTAATATTTAATTTAATTTAATTTTTATCTTGTAGATAATTATATT
1 ATATTAATTTAAT-AATTAAATATTAAATTTAATTTAATATTTATCATGTAGATAA-TATATT
* *
33632038 CTATTAATTTAATAGATTTAATATTAAATTTAATTTAATATTTA-CAT-T-GATAA-ATATT
1 ATATTAATTTAATA-ATTAAATATTAAATTTAATTTAATATTTATCATGTAGATAATATATT
*
33632096 ATATTAATTTAAT-ATTAAATTAATTAAGTTTAAT
1 ATATTAATTTAATAATTAAA-T-ATTAAATTTAAT
33632130 CAAAGTTTAA
Statistics
Matches: 81, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
56 5 0.06
57 1 0.01
58 28 0.35
60 5 0.06
61 1 0.01
62 3 0.04
63 38 0.47
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (61 bp):
ATATTAATTTAATAATTAAATATTAAATTTAATTTAATATTTATCATGTAGATAATATATT
Found at i:33634956 original size:52 final size:52
Alignment explanation
Indices: 33634899--33635002 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
33634889 GAGAAGTTAT
*
33634899 TTTACATTTTGATAATTTTAGAAAGATTGTTTTAAAGGATGTCTTTTATGTA
1 TTTACATTTTGATAATTTTAGAAAGATTGTTTTAAAGGACGTCTTTTATGTA
* * *
33634951 TTTACATTTTGATAATTTTAGGAAGATTGTTTTAAAGGGCGTGTTTTATGTA
1 TTTACATTTTGATAATTTTAGAAAGATTGTTTTAAAGGACGTCTTTTATGTA
33635003 CCTTATTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.29, C:0.04, G:0.18, T:0.49
Consensus pattern (52 bp):
TTTACATTTTGATAATTTTAGAAAGATTGTTTTAAAGGACGTCTTTTATGTA
Found at i:33638798 original size:49 final size:50
Alignment explanation
Indices: 33638707--33638879 Score: 170
Period size: 49 Copynumber: 3.5 Consensus size: 50
33638697 AAAGGATTTC
* * ** * *
33638707 CAAATAACTTTGCCACTAAGGCTACCCAAATAATATGTCACATAGGCCTTT
1 CAAATAAC-TCGCCACAAAGGCTTTCCAAACAATATGCCACATAGGCCTTT
* * * *
33638758 CAAATAACTCGCCAC-AATGCTTTCTAGACAATATGCCACATAGGTCTTT
1 CAAATAACTCGCCACAAAGGCTTTCCAAACAATATGCCACATAGGCCTTT
* * * *
33638807 TAGATAACTTGCCACAAAGGCTTTCCAAACAATATGCTACA-AGGCCTTT
1 CAAATAACTCGCCACAAAGGCTTTCCAAACAATATGCCACATAGGCCTTT
* * *
33638856 GAAATAACTCGCCAAAAAAGCTTT
1 CAAATAACTCGCCACAAAGGCTTT
33638880 GTTTGGTTTG
Statistics
Matches: 99, Mismatches: 22, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
49 64 0.65
50 27 0.27
51 8 0.08
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.27
Consensus pattern (50 bp):
CAAATAACTCGCCACAAAGGCTTTCCAAACAATATGCCACATAGGCCTTT
Found at i:33641435 original size:17 final size:18
Alignment explanation
Indices: 33641415--33641453 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
33641405 AAAATAATAT
33641415 TATTTTAA-TAAATTTAA
1 TATTTTAATTAAATTTAA
*
33641432 TA-TTTAATTTAATTTAA
1 TATTTTAATTAAATTTAA
33641449 TATTT
1 TATTT
33641454 ATTTTGATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 5 0.26
17 12 0.63
18 2 0.11
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATTTTAATTAAATTTAA
Found at i:33641478 original size:31 final size:32
Alignment explanation
Indices: 33641429--33641489 Score: 106
Period size: 31 Copynumber: 1.9 Consensus size: 32
33641419 TTAATAAATT
33641429 TAATATTTAATTTAATTTAATATTTATTTTGA
1 TAATATTTAATTTAATTTAATATTTATTTTGA
*
33641461 TAATATTTTA-TTAATTTAATATTTATTTT
1 TAATATTTAATTTAATTTAATATTTATTTT
33641490 AATCTAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
31 19 0.68
32 9 0.32
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (32 bp):
TAATATTTAATTTAATTTAATATTTATTTTGA
Found at i:33641498 original size:48 final size:49
Alignment explanation
Indices: 33641415--33641531 Score: 166
Period size: 48 Copynumber: 2.4 Consensus size: 49
33641405 AAAATAATAT
* * *
33641415 TATTTTAATAAATTTAATATTTAATTTAATTTAATATTTATTTTGATAA-
1 TATTTT-ATTAATTTAATATTTAATTTAATCTAATATTTATCTTGATAAG
*
33641464 TATTTTATTAATTTAATATTTATTTTAATCTAATATTTATCTTGATAAG
1 TATTTTATTAATTTAATATTTAATTTAATCTAATATTTATCTTGATAAG
*
33641513 T-TTATATTAATTTAATATT
1 TATTTTATTAATTTAATATT
33641532 AAAGTGATCA
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
48 55 0.89
49 7 0.11
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.58
Consensus pattern (49 bp):
TATTTTATTAATTTAATATTTAATTTAATCTAATATTTATCTTGATAAG
Found at i:33641503 original size:17 final size:17
Alignment explanation
Indices: 33641425--33641503 Score: 101
Period size: 17 Copynumber: 4.8 Consensus size: 17
33641415 TATTTTAATA
*
33641425 AATTTAATATTTAATTT
1 AATTTAATATTTATTTT
33641442 AATTTAATATTTATTTT
1 AATTTAATATTTATTTT
* *
33641459 GA--TAATATTT-TATT
1 AATTTAATATTTATTTT
33641473 AATTTAATATTTATTTT
1 AATTTAATATTTATTTT
*
33641490 AATCTAATATTTAT
1 AATTTAATATTTAT
33641504 CTTGATAAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.08
15 8 0.15
16 8 0.15
17 33 0.62
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (17 bp):
AATTTAATATTTATTTT
Found at i:33642853 original size:103 final size:101
Alignment explanation
Indices: 33642731--33642921 Score: 310
Period size: 103 Copynumber: 1.9 Consensus size: 101
33642721 TTTTTTTTAC
* *
33642731 TATTTTGATATATTGTCAGTGTTTTACAACATAAAAAGGTGACTTAACATTATTGAATACCTACT
1 TATTTTGATATATTATCAGTGTTTTACAACATAAAAAGGTGACTTAACATTACTGAATACCTACT
*
33642796 GAATAAATGTTGCAACAATAAAAAAAATAAAAAAATAT
66 GAATAAATGTTACAA-AA-AAAAAAAATAAAAAAATAT
* * *
33642834 TATTTTGGTATATTATCAGTGTTTTACAACATAAAAAGGTGACTTAACATTACTGAATGCCTATT
1 TATTTTGATATATTATCAGTGTTTTACAACATAAAAAGGTGACTTAACATTACTGAATACCTACT
33642899 GAATAAATGTTACAAAAAAAAAA
66 GAATAAATGTTACAAAAAAAAAA
33642922 CTATTTTGAT
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
101 6 0.07
102 2 0.02
103 74 0.90
ACGTcount: A:0.45, C:0.10, G:0.12, T:0.34
Consensus pattern (101 bp):
TATTTTGATATATTATCAGTGTTTTACAACATAAAAAGGTGACTTAACATTACTGAATACCTACT
GAATAAATGTTACAAAAAAAAAAAATAAAAAAATAT
Found at i:33645959 original size:5 final size:5
Alignment explanation
Indices: 33645949--33645978 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
33645939 ATATCTTATA
*
33645949 TGATT TGATT TGATT TGATT TGGTT TGATT
1 TGATT TGATT TGATT TGATT TGATT TGATT
33645979 ATGTAATCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.23, T:0.60
Consensus pattern (5 bp):
TGATT
Found at i:33651935 original size:20 final size:19
Alignment explanation
Indices: 33651912--33651955 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
33651902 ATTACATATT
33651912 GGTGCCCTGTTATGCACTTC
1 GGTGCCCTGTT-TGCACTTC
*
33651932 GGTGCCTTGTTTGCACTTC
1 GGTGCCCTGTTTGCACTTC
33651951 GGTGC
1 GGTGC
33651956 TCTTGTGTGC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.07, C:0.27, G:0.30, T:0.36
Consensus pattern (19 bp):
GGTGCCCTGTTTGCACTTC
Found at i:33651960 original size:20 final size:19
Alignment explanation
Indices: 33651912--33651967 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
33651902 ATTACATATT
*
33651912 GGTGCCCTGTTATGCACTTC
1 GGTGCCTTGTT-TGCACTTC
33651932 GGTGCCTTGTTTGCACTTC
1 GGTGCCTTGTTTGCACTTC
*
33651951 GGTGCTCTTGTGTGCAC
1 GGTGC-CTTGTTTGCAC
33651968 ATTTGTGCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.39
20 20 0.61
ACGTcount: A:0.07, C:0.27, G:0.29, T:0.38
Consensus pattern (19 bp):
GGTGCCTTGTTTGCACTTC
Found at i:33652896 original size:64 final size:64
Alignment explanation
Indices: 33652825--33652955 Score: 244
Period size: 64 Copynumber: 2.0 Consensus size: 64
33652815 GTTAGAGTGA
33652825 GAATTTGATGTTGCCATAGAAGGGAAAAATGATAAGCATGTCATAAAACATAAGAAAATAGGCT
1 GAATTTGATGTTGCCATAGAAGGGAAAAATGATAAGCATGTCATAAAACATAAGAAAATAGGCT
* *
33652889 GAATTTGATGTTGCCATAGAAGGGAAAAATGATCAGCATGTCATAAAATATAAGAAAATAGGCT
1 GAATTTGATGTTGCCATAGAAGGGAAAAATGATAAGCATGTCATAAAACATAAGAAAATAGGCT
33652953 GAA
1 GAA
33652956 GTTTAATTTA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.45, C:0.09, G:0.22, T:0.24
Consensus pattern (64 bp):
GAATTTGATGTTGCCATAGAAGGGAAAAATGATAAGCATGTCATAAAACATAAGAAAATAGGCT
Found at i:33653486 original size:46 final size:46
Alignment explanation
Indices: 33653433--33653522 Score: 162
Period size: 46 Copynumber: 2.0 Consensus size: 46
33653423 TACAAGTGAC
* *
33653433 ATGTCACTAGGATGTTTGGGCATCCGAACTCGTTGAGTTGAGTCTG
1 ATGTCACTAGGATGGTTGAGCATCCGAACTCGTTGAGTTGAGTCTG
33653479 ATGTCACTAGGATGGTTGAGCATCCGAACTCGTTGAGTTGAGTC
1 ATGTCACTAGGATGGTTGAGCATCCGAACTCGTTGAGTTGAGTC
33653523 CGAGTTCAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 42 1.00
ACGTcount: A:0.21, C:0.18, G:0.30, T:0.31
Consensus pattern (46 bp):
ATGTCACTAGGATGGTTGAGCATCCGAACTCGTTGAGTTGAGTCTG
Found at i:33653614 original size:92 final size:93
Alignment explanation
Indices: 33653498--33653667 Score: 279
Period size: 92 Copynumber: 1.8 Consensus size: 93
33653488 GGATGGTTGA
* *
33653498 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATGCGAATG-TCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATGCGAACGCCCGAACTCGTTGAGT
33653562 TGAGTCCAAGTTCGATAGATGTAATTAG
66 TGAGTCCAAGTTCGATAGATGTAATTAG
* * *
33653590 GCATCCGAGCTCTTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATGCGAACGCCCGAACTCGTTGAGT
*
33653655 TGAGTCCGAGTTC
66 TGAGTCCAAGTTC
33653668 ACTTGTGGGC
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
92 45 0.63
93 26 0.37
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCAAGTTCGATAGATGTAATTAG
Found at i:33653662 original size:46 final size:46
Alignment explanation
Indices: 33653502--33653671 Score: 179
Period size: 46 Copynumber: 3.7 Consensus size: 46
33653492 GGTTGAGCAT
* *
33653502 CCGAACTCGTTGAGTTGAGTCCGAGTTCAATTATGGATGCGAATG-
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* * ** *
33653547 TCGAACTCGTTGAGTTGAGTCCAAGTTCGA--TA--GATGTAATTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGA--ACGC
* *
33653592 ATCCGAGCTCTTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
33653640 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTT
33653672 GTGGGCGGGT
Statistics
Matches: 101, Mismatches: 14, Indels: 19
0.75 0.10 0.14
Matches are distributed among these distances:
42 5 0.05
44 4 0.04
45 26 0.26
46 32 0.32
47 24 0.24
48 5 0.05
50 5 0.05
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (46 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:33656608 original size:15 final size:15
Alignment explanation
Indices: 33656588--33656641 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
33656578 GTATCTTGGG
33656588 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* * *
33656603 TCTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
33656618 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
33656633 TTTCTTTAT
1 TTTCTTTAT
33656642 TCGGTTTTCT
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.11, C:0.19, G:0.13, T:0.57
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:33656618 original size:30 final size:30
Alignment explanation
Indices: 33656584--33656652 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
33656574 TATCGTATCT
33656584 TGGGTTTCTTTATCCTGGATCTCTTTATTC
1 TGGGTTTCTTTATCCTGGATCTCTTTATTC
* * *
33656614 TGGGTTTCTCTATCTTGGATTTCTTTATTC
1 TGGGTTTCTTTATCCTGGATCTCTTTATTC
*
33656644 -GGTTTTCTT
1 TGGGTTTCTT
33656653 GTTATCTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 7 0.21
30 27 0.79
ACGTcount: A:0.09, C:0.17, G:0.17, T:0.57
Consensus pattern (30 bp):
TGGGTTTCTTTATCCTGGATCTCTTTATTC
Found at i:33666228 original size:18 final size:19
Alignment explanation
Indices: 33666199--33666235 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
33666189 TTCGTCATTT
33666199 CATATCCCATTTCCCATCC
1 CATATCCCATTTCCCATCC
*
33666218 CATAT-CCATTTCTCATCC
1 CATATCCCATTTCCCATCC
33666236 TTGTCATCCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.22, C:0.43, G:0.00, T:0.35
Consensus pattern (19 bp):
CATATCCCATTTCCCATCC
Found at i:33667617 original size:32 final size:32
Alignment explanation
Indices: 33667580--33667648 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
33667570 TCTATAATTC
33667580 AACTTTTAGCCCTTTCATGATTTTGTCCATAT
1 AACTTTTAGCCCTTTCATGATTTTGTCCATAT
33667612 AACTTTTAGCCCTTTCATGATTTTGTCCATAT
1 AACTTTTAGCCCTTTCATGATTTTGTCCATAT
33667644 -ACTTT
1 AACTTT
33667649 AATAGCTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 5 0.14
32 32 0.86
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.48
Consensus pattern (32 bp):
AACTTTTAGCCCTTTCATGATTTTGTCCATAT
Found at i:33678996 original size:40 final size:39
Alignment explanation
Indices: 33678929--33679055 Score: 134
Period size: 37 Copynumber: 3.2 Consensus size: 39
33678919 ACCAGTTTGG
*
33678929 CACCCAGTGCCTCATCAGATAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCA-ATAAATCGAAGTAATAAATTGA
* * *
33678969 CACCCAGTGTCTCATTAACTAAATCGAAG---TAAATTGG
1 CACCCAGTGCCTCATCAA-TAAATCGAAGTAATAAATTGA
* * *
33679006 CACCTAGTGCCTCATCGAATTAATCCGAAGTAATAGATTGA
1 CACCCAGTGCCTCATC-AATAAAT-CGAAGTAATAAATTGA
33679047 CACCCAGTG
1 CACCCAGTG
33679056 TCTTATCGAC
Statistics
Matches: 70, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
37 24 0.34
38 7 0.10
39 1 0.01
40 24 0.34
41 14 0.20
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.25
Consensus pattern (39 bp):
CACCCAGTGCCTCATCAATAAATCGAAGTAATAAATTGA
Found at i:33679020 original size:37 final size:38
Alignment explanation
Indices: 33678925--33679021 Score: 108
Period size: 40 Copynumber: 2.5 Consensus size: 38
33678915 ACACACCAGT
*
33678925 TTGGCACCCAGTGCCTCATCAGATAATTCGAAGTAATAAA
1 TTGGCACCCAGTGCCTCATCAGATAAATCGAAG--ATAAA
* * *
33678965 TTGACACCCAGTGTCTCATTA-ACTAAATCGAAG-TAAA
1 TTGGCACCCAGTGCCTCATCAGA-TAAATCGAAGATAAA
*
33679002 TTGGCACCTAGTGCCTCATC
1 TTGGCACCCAGTGCCTCATC
33679022 GAATTAATCC
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
37 20 0.42
39 1 0.02
40 27 0.56
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.27
Consensus pattern (38 bp):
TTGGCACCCAGTGCCTCATCAGATAAATCGAAGATAAA
Found at i:33679430 original size:13 final size:13
Alignment explanation
Indices: 33679408--33679440 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
33679398 AAGGGTTTGT
33679408 TTAT-TAAACTAA
1 TTATCTAAACTAA
33679420 TTATCTAAACTAA
1 TTATCTAAACTAA
*
33679433 TTAACTAA
1 TTATCTAA
33679441 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:33680676 original size:15 final size:15
Alignment explanation
Indices: 33680658--33680689 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
33680648 ATATGTATAT
*
33680658 ATATCAATTCAATAA
1 ATATAAATTCAATAA
33680673 ATATAAATTCAATAA
1 ATATAAATTCAATAA
33680688 AT
1 AT
33680690 TCATCACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.34
Consensus pattern (15 bp):
ATATAAATTCAATAA
Found at i:33686753 original size:23 final size:24
Alignment explanation
Indices: 33686723--33686903 Score: 135
Period size: 23 Copynumber: 7.9 Consensus size: 24
33686713 AGACTCACCA
* *
33686723 CAGCTCGTAT-GAGTTTACCGATT
1 CAGCTCGTATAGAGCTTACTGATT
*
33686746 CAGCTCGTAT-GAGCTTACTGTTT
1 CAGCTCGTATAGAGCTTACTGATT
* *
33686769 CAGCTCAT-TGGAGCTTACTGATT
1 CAGCTCGTATAGAGCTTACTGATT
* ** *
33686792 CAGCTCG-ATAGAGTTTTTTGTTT
1 CAGCTCGTATAGAGCTTACTGATT
* **
33686815 CAGCTCAT-TAGAGCTTACCAATT
1 CAGCTCGTATAGAGCTTACTGATT
* *
33686838 CAGCTCG-ATAGAGCTTATTGTTT
1 CAGCTCGTATAGAGCTTACTGATT
* * * *
33686861 TAGCTCAT-TGGAGCTTACCGATT
1 CAGCTCGTATAGAGCTTACTGATT
*
33686884 CAGCTC-AATAGAGCTTACTG
1 CAGCTCGTATAGAGCTTACTG
33686904 TCCATCAGCT
Statistics
Matches: 119, Mismatches: 33, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
22 1 0.01
23 118 0.99
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.36
Consensus pattern (24 bp):
CAGCTCGTATAGAGCTTACTGATT
Found at i:33686794 original size:46 final size:46
Alignment explanation
Indices: 33686737--33686904 Score: 239
Period size: 46 Copynumber: 3.7 Consensus size: 46
33686727 TCGTATGAGT
33686737 TTACCGATTCAGCTCG-TATGAGCTTACTGTTTCAGCTCATTGGAGC
1 TTACCGATTCAGCTCGATA-GAGCTTACTGTTTCAGCTCATTGGAGC
* * ** *
33686783 TTACTGATTCAGCTCGATAGAGTTTTTTGTTTCAGCTCATTAGAGC
1 TTACCGATTCAGCTCGATAGAGCTTACTGTTTCAGCTCATTGGAGC
* * *
33686829 TTACCAATTCAGCTCGATAGAGCTTATTGTTTTAGCTCATTGGAGC
1 TTACCGATTCAGCTCGATAGAGCTTACTGTTTCAGCTCATTGGAGC
*
33686875 TTACCGATTCAGCTCAATAGAGCTTACTGT
1 TTACCGATTCAGCTCGATAGAGCTTACTGT
33686905 CCATCAGCTC
Statistics
Matches: 107, Mismatches: 14, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 105 0.98
47 2 0.02
ACGTcount: A:0.23, C:0.21, G:0.20, T:0.37
Consensus pattern (46 bp):
TTACCGATTCAGCTCGATAGAGCTTACTGTTTCAGCTCATTGGAGC
Found at i:33690926 original size:45 final size:45
Alignment explanation
Indices: 33690875--33690965 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 45
33690865 AATTAAATTA
** *
33690875 ACCATTATTAACATTTTTAGTTTCATTTAAGTC-ATGCATATATAT
1 ACCATTATTAACAGGTTTAGCTTCATTTAAGTCAAT-CATATATAT
*
33690920 ACCATTATTAGCAGGTTTAGCTTCATTTAAGTCAATCATATATAT
1 ACCATTATTAACAGGTTTAGCTTCATTTAAGTCAATCATATATAT
33690965 A
1 A
33690966 TTAATGCATA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
45 39 0.95
46 2 0.05
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (45 bp):
ACCATTATTAACAGGTTTAGCTTCATTTAAGTCAATCATATATAT
Found at i:33691003 original size:36 final size:36
Alignment explanation
Indices: 33690963--33691035 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 36
33690953 AATCATATAT
* * *
33690963 ATATTAATGCATATGTATACTGTTTAGCTTCATTTA
1 ATATTAATGCATATATATAATGTTTACCTTCATTTA
*
33690999 ATATTAATGCATATATATAATGTTTTCCTTCATTTA
1 ATATTAATGCATATATATAATGTTTACCTTCATTTA
33691035 A
1 A
33691036 GTCATGCGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.48
Consensus pattern (36 bp):
ATATTAATGCATATATATAATGTTTACCTTCATTTA
Found at i:33691059 original size:56 final size:57
Alignment explanation
Indices: 33690999--33691115 Score: 155
Period size: 56 Copynumber: 2.1 Consensus size: 57
33690989 GCTTCATTTA
** * *
33690999 ATATTAATGCATATATATAATGTTTTCCTTCATTTAAGTCATGCGCATA-TATATAT
1 ATATTAATGCATATATATAACATTTACCTTCATTTAAGTCATGCACATATTATATAT
** * *
33691055 ATATTAATGCATATATATTCCATTTAGCTTCATTTAAGTCATGCATATATTATATAT
1 ATATTAATGCATATATATAACATTTACCTTCATTTAAGTCATGCACATATTATATAT
33691112 ATAT
1 ATAT
33691116 ATTACAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
56 41 0.79
57 11 0.21
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (57 bp):
ATATTAATGCATATATATAACATTTACCTTCATTTAAGTCATGCACATATTATATAT
Found at i:33693456 original size:20 final size:21
Alignment explanation
Indices: 33693431--33693470 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
33693421 AGCTCCAAGT
33693431 TCAAGTGAAAA-TGAA-ATAGA
1 TCAAGT-AAAACTGAAGATAGA
33693451 TCAAGTAAAACTGAAGATAG
1 TCAAGTAAAACTGAAGATAG
33693471 GCTTAGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 10 0.56
21 4 0.22
ACGTcount: A:0.53, C:0.07, G:0.20, T:0.20
Consensus pattern (21 bp):
TCAAGTAAAACTGAAGATAGA
Found at i:33704742 original size:42 final size:43
Alignment explanation
Indices: 33704639--33704780 Score: 155
Period size: 42 Copynumber: 3.3 Consensus size: 43
33704629 ATCTGAGATA
** * *
33704639 TCGTGTAAGACTGTGTCTGGGACACAGGCCTCGAT-TTTAGATT
1 TCGTGTAAGACCATGTCTGGGACACAGGCATCGATATCT-GATT
*
33704682 TACGTGTAAGACCATGTCTGGGACATAGGCATC-ATATCTGATT
1 T-CGTGTAAGACCATGTCTGGGACACAGGCATCGATATCTGATT
* *
33704725 TCGTGTAAGACCCTGTCTGGGACAGAGGCATCGATA-CTGAATT
1 TCGTGTAAGACCATGTCTGGGACACAGGCATCGATATCTG-ATT
* *
33704768 ACATGTAAGACCA
1 TCGTGTAAGACCA
33704781 CGTCCAGGAT
Statistics
Matches: 85, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
42 32 0.38
43 24 0.28
44 29 0.34
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (43 bp):
TCGTGTAAGACCATGTCTGGGACACAGGCATCGATATCTGATT
Found at i:33708093 original size:23 final size:23
Alignment explanation
Indices: 33708043--33708162 Score: 98
Period size: 23 Copynumber: 5.2 Consensus size: 23
33708033 GGACTCACCA
* * * *
33708043 TAGCTTGTATGAGCTTACCGATT
1 TAGCTCGTAAGAGCTTACTGTTT
*
33708066 CAGCTCGTAAGAGCTTACTGTTT
1 TAGCTCGTAAGAGCTTACTGTTT
* ** *
33708089 TAGCTCATTGGTGCTTACTGTTT
1 TAGCTCGTAAGAGCTTACTGTTT
* * ** *
33708112 CAGCTCATTGGAGCTTACTGATT
1 TAGCTCGTAAGAGCTTACTGTTT
33708135 TAGCTCG-ATAGAGCTTACTGTTT
1 TAGCTCGTA-AGAGCTTACTGTTT
33708158 TAGCT
1 TAGCT
33708163 AATTAGAGCT
Statistics
Matches: 78, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
23 78 1.00
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (23 bp):
TAGCTCGTAAGAGCTTACTGTTT
Found at i:33708114 original size:46 final size:46
Alignment explanation
Indices: 33708053--33708201 Score: 147
Period size: 46 Copynumber: 3.2 Consensus size: 46
33708043 TAGCTTGTAT
* * * * *
33708053 GAGCTTACCGATTCAGCTCGTAAGAGCTTACTGTTTTAGCTC-ATTG
1 GAGCTTACTGTTTCAGCTCATAAGAGCTTACTGATTTAGCTCGA-TA
* **
33708099 GTGCTTACTGTTTCAGCTCATTGGAGCTTACTGATTTAGCTCGATA
1 GAGCTTACTGTTTCAGCTCATAAGAGCTTACTGATTTAGCTCGATA
* * * * * **
33708145 GAGCTTACTGTTTTAGCTAATTAGAGCTTACCGATTCAGCTTAATA
1 GAGCTTACTGTTTCAGCTCATAAGAGCTTACTGATTTAGCTCGATA
33708191 GAGCTTACTGT
1 GAGCTTACTGT
33708202 CCATCAGCTC
Statistics
Matches: 86, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
46 85 0.99
47 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (46 bp):
GAGCTTACTGTTTCAGCTCATAAGAGCTTACTGATTTAGCTCGATA
Found at i:33708169 original size:23 final size:23
Alignment explanation
Indices: 33708075--33708201 Score: 123
Period size: 23 Copynumber: 5.5 Consensus size: 23
33708065 TCAGCTCGTA
*
33708075 AGAGCTTACTGTTTTAGCTCATT
1 AGAGCTTACTGTTTTAGCTAATT
* * * *
33708098 GGTGCTTACTGTTTCAGCTCATT
1 AGAGCTTACTGTTTTAGCTAATT
* * *
33708121 GGAGCTTACTGATTTAGCTCGA-T
1 AGAGCTTACTGTTTTAGCT-AATT
33708144 AGAGCTTACTGTTTTAGCTAATT
1 AGAGCTTACTGTTTTAGCTAATT
* * *
33708167 AGAGCTTACCGATTCAGCTTAA-T
1 AGAGCTTACTGTTTTAGC-TAATT
33708190 AGAGCTTACTGT
1 AGAGCTTACTGT
33708202 CCATCAGCTC
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
22 1 0.01
23 81 0.94
24 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (23 bp):
AGAGCTTACTGTTTTAGCTAATT
Found at i:33708174 original size:69 final size:69
Alignment explanation
Indices: 33708053--33708200 Score: 190
Period size: 69 Copynumber: 2.1 Consensus size: 69
33708043 TAGCTTGTAT
* * * * * *
33708053 GAGCTTACCGATTCAGCTCGTAAGAGCTTACTGTTTTAGCTCATTGGTGCTTACTGTTTCAGCTC
1 GAGCTTACTGATTCAGCTCGTAAGAGCTTACTGTTTTAGCTAATTAGAGCTTACCGATTCAGCTC
* *
33708118 ATTG
66 AATA
*
33708122 GAGCTTACTGATTTAGCTCG-ATAGAGCTTACTGTTTTAGCTAATTAGAGCTTACCGATTCAGCT
1 GAGCTTACTGATTCAGCTCGTA-AGAGCTTACTGTTTTAGCTAATTAGAGCTTACCGATTCAGCT
*
33708186 TAATA
65 CAATA
33708191 GAGCTTACTG
1 GAGCTTACTG
33708201 TCCATCAGCT
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
68 1 0.01
69 67 0.99
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (69 bp):
GAGCTTACTGATTCAGCTCGTAAGAGCTTACTGTTTTAGCTAATTAGAGCTTACCGATTCAGCTC
AATA
Found at i:33711395 original size:51 final size:51
Alignment explanation
Indices: 33711319--33711423 Score: 201
Period size: 51 Copynumber: 2.1 Consensus size: 51
33711309 GGGATTTTTG
33711319 TCCCCGAAAATCTTACCAGTGAATAGGTTTGAATATTGTTTTCTCATAGAA
1 TCCCCGAAAATCTTACCAGTGAATAGGTTTGAATATTGTTTTCTCATAGAA
*
33711370 TCCCCGAAAATCTTACCAGTGAATAGGTTTGAATATTGTTTTCTCATAGCA
1 TCCCCGAAAATCTTACCAGTGAATAGGTTTGAATATTGTTTTCTCATAGAA
33711421 TCC
1 TCC
33711424 TCGAGTTCCC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (51 bp):
TCCCCGAAAATCTTACCAGTGAATAGGTTTGAATATTGTTTTCTCATAGAA
Found at i:33713992 original size:17 final size:17
Alignment explanation
Indices: 33713970--33714002 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
33713960 TTTTCAGACC
33713970 TTTCAAACTTTACATCT
1 TTTCAAACTTTACATCT
33713987 TTTCAAACTTTACATC
1 TTTCAAACTTTACATC
33714003 AAAACCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTCAAACTTTACATCT
Found at i:33718062 original size:40 final size:41
Alignment explanation
Indices: 33717997--33718092 Score: 101
Period size: 40 Copynumber: 2.4 Consensus size: 41
33717987 TATCTCGGTA
33717997 TCGCACACTTAGTGCCTCATATAGCCGAAA-CTA-TTCCAAC
1 TCGCACACTTAGTGCCTCATATAGCC-AAAGCTATTTCCAAC
* * * *
33718037 TCGCACACTTAGTGCCAT-TTGTAGCCAAAGTTATTTCTAAC
1 TCGCACACTTAGTGCC-TCATATAGCCAAAGCTATTTCCAAC
*
33718078 T-GCATACTTAGTGCC
1 TCGCACACTTAGTGCC
33718093 GAACATAGTC
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
39 3 0.06
40 37 0.77
41 8 0.17
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (41 bp):
TCGCACACTTAGTGCCTCATATAGCCAAAGCTATTTCCAAC
Found at i:33724781 original size:20 final size:21
Alignment explanation
Indices: 33724756--33724795 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
33724746 CTCTTGGAAC
33724756 AGGGC-ACACGCCCGTGTGGA
1 AGGGCAACACGCCCGTGTGGA
33724776 AGGGCAACACGCCCGTGTGG
1 AGGGCAACACGCCCGTGTGG
33724796 TCATTATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.20, C:0.30, G:0.40, T:0.10
Consensus pattern (21 bp):
AGGGCAACACGCCCGTGTGGA
Found at i:33726086 original size:47 final size:46
Alignment explanation
Indices: 33726029--33726144 Score: 139
Period size: 47 Copynumber: 2.5 Consensus size: 46
33726019 TGAGGCTGAC
33726029 GCCATGTCCCAGACATGTCTTACACTAGCTCTCGTCACAA-T-GCCGAT
1 GCCATGTCCCAGACATGTCTTACACTAGCTC-C--CACAAGTGGCCGAT
* *
33726076 GCCATGTCCCAGACATGGTCTTACACTGGCTCCCATAATGTGGCCGAT
1 GCCATGTCCCAGACAT-GTCTTACACTAGCTCCCACAA-GTGGCCGAT
*
33726124 G-CATGTCCCAAACATGTCTTA
1 GCCATGTCCCAGACATGTCTTA
33726145 TATTAGCACA
Statistics
Matches: 62, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
45 4 0.06
46 6 0.10
47 31 0.50
48 21 0.34
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (46 bp):
GCCATGTCCCAGACATGTCTTACACTAGCTCCCACAAGTGGCCGAT
Found at i:33727865 original size:46 final size:46
Alignment explanation
Indices: 33727808--33727931 Score: 160
Period size: 46 Copynumber: 2.7 Consensus size: 46
33727798 CAGCTCGTAT
* *
33727808 GAGCTTACCGATTCAGCTCG-TAAGAGTTTACTATTTCAGCTCAATG
1 GAGCTTACCGATTCAGCTCGAT-AGAGCTTACTATTTCAACTCAATG
* * * *
33727854 GAGCTTACCGATTCAACTCGATAGAGCTTGCTGTTTCAACTCATTG
1 GAGCTTACCGATTCAGCTCGATAGAGCTTACTATTTCAACTCAATG
**
33727900 GAGCTTACCGATTCAGCTTAATAGAGCTTACT
1 GAGCTTACCGATTCAGCTCGATAGAGCTTACT
33727932 GTCCATCAGC
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
46 66 0.99
47 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (46 bp):
GAGCTTACCGATTCAGCTCGATAGAGCTTACTATTTCAACTCAATG
Found at i:33727926 original size:23 final size:23
Alignment explanation
Indices: 33727808--33727930 Score: 97
Period size: 23 Copynumber: 5.3 Consensus size: 23
33727798 CAGCTCGTAT
*
33727808 GAGCTTACCGATTCAGCTC-GTAA
1 GAGCTTACCGATTCAGCTCAAT-A
* * *
33727831 GAGTTTA-CTATTTCAGCTCAATG
1 GAGCTTACCGA-TTCAGCTCAATA
* *
33727854 GAGCTTACCGATTCAACTCGATA
1 GAGCTTACCGATTCAGCTCAATA
* * * * * *
33727877 GAGCTTGCTGTTTCAACTCATTG
1 GAGCTTACCGATTCAGCTCAATA
*
33727900 GAGCTTACCGATTCAGCTTAATA
1 GAGCTTACCGATTCAGCTCAATA
33727923 GAGCTTAC
1 GAGCTTAC
33727931 TGTCCATCAG
Statistics
Matches: 75, Mismatches: 22, Indels: 6
0.73 0.21 0.06
Matches are distributed among these distances:
22 2 0.03
23 70 0.93
24 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.32
Consensus pattern (23 bp):
GAGCTTACCGATTCAGCTCAATA
Found at i:33731924 original size:13 final size:14
Alignment explanation
Indices: 33731891--33731929 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
33731881 TTCAAATTAG
33731891 TTAAAAACCAATTC
1 TTAAAAACCAATTC
33731905 TTAAAAACCAAGTT-
1 TTAAAAACCAA-TTC
*
33731919 TTAAAACCCAA
1 TTAAAAACCAA
33731930 ATCCACAGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 21 0.91
15 2 0.09
ACGTcount: A:0.51, C:0.21, G:0.03, T:0.26
Consensus pattern (14 bp):
TTAAAAACCAATTC
Found at i:33734647 original size:13 final size:14
Alignment explanation
Indices: 33734631--33734671 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
33734621 CTTTTTCTCC
33734631 TTTTTCTTTC--TT
1 TTTTTCTTTCATTT
* *
33734643 TTTTTCCTTCTTTT
1 TTTTTCTTTCATTT
33734657 TTTTTCTTTCATTT
1 TTTTTCTTTCATTT
33734671 T
1 T
33734672 ACTTATTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
12 9 0.38
14 15 0.62
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTCTTTCATTT
Found at i:33734655 original size:22 final size:21
Alignment explanation
Indices: 33734622--33734665 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
33734612 AAACCCTAGC
33734622 TTTTTCTCCTTTTTCTTTCTT
1 TTTTTCTCCTTTTTCTTTCTT
* *
33734643 TTTTTCCTTCTTTTTTTTTCTT
1 TTTTT-CTCCTTTTTCTTTCTT
33734665 T
1 T
33734666 CATTTTACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (21 bp):
TTTTTCTCCTTTTTCTTTCTT
Found at i:33734811 original size:20 final size:19
Alignment explanation
Indices: 33734786--33734833 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
33734776 AAGTATTACA
*
33734786 TATATTATTATATACATATG
1 TATATTATT-TATACACATG
*
33734806 TATATTATTTTTACACATG
1 TATATTATTTATACACATG
33734825 TA-ATTATTT
1 TATATTATTT
33734834 TTACCATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 7 0.27
19 10 0.38
20 9 0.35
ACGTcount: A:0.35, C:0.06, G:0.04, T:0.54
Consensus pattern (19 bp):
TATATTATTTATACACATG
Found at i:33734832 original size:18 final size:19
Alignment explanation
Indices: 33734786--33734837 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
33734776 AAGTATTACA
* *
33734786 TATATTATTATATACATATG
1 TATATTATT-TTTACACATG
33734806 TATATTATTTTTACACATG
1 TATATTATTTTTACACATG
33734825 TA-ATTATTTTTAC
1 TATATTATTTTTAC
33734838 CATACACTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 11 0.37
19 10 0.33
20 9 0.30
ACGTcount: A:0.35, C:0.08, G:0.04, T:0.54
Consensus pattern (19 bp):
TATATTATTTTTACACATG
Found at i:33738914 original size:15 final size:15
Alignment explanation
Indices: 33738894--33738930 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
33738884 GACAATTGTA
33738894 GTGGGAATCATTTCC
1 GTGGGAATCATTTCC
33738909 GTGGGAATCATTTCC
1 GTGGGAATCATTTCC
*
33738924 GTAGGAA
1 GTGGGAA
33738931 CTCACTAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (15 bp):
GTGGGAATCATTTCC
Found at i:33743769 original size:30 final size:30
Alignment explanation
Indices: 33743721--33743779 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
33743711 TTTATGAGCC
* * *
33743721 TAGGGGCCAAAGTGCAAATATGTGAAAGTT
1 TAGGGGCCAAAATACAAATATGTAAAAGTT
* *
33743751 TAGGGGTCAAAATACAAATTTGTAAAAGT
1 TAGGGGCCAAAATACAAATATGTAAAAGT
33743780 ATGATTTTTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.25, T:0.25
Consensus pattern (30 bp):
TAGGGGCCAAAATACAAATATGTAAAAGTT
Found at i:33744539 original size:50 final size:50
Alignment explanation
Indices: 33744421--33744865 Score: 410
Period size: 50 Copynumber: 8.8 Consensus size: 50
33744411 GTTGTGAGAA
* * * ** *
33744421 CACATGTGTAATACTATGTGCAGGCTACTATGTGTTTAAGACGGTT-TTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTG--TACCA-GATTGTTAGGT
* * *
33744473 TACGTGTGTAGCACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
** * * * * *
33744523 TGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTC-GATAGTTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-CAGATTG-TTAGGT
* *
33744574 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * * * * * * *
33744624 TACGTATGTAGTAATAAGTGTAGGCTACTACGTATACCAAATTGATAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * * * * * *
33744674 CGCATGTATAGTACTAAGTGCAGGCTACTATGTGTACCCG-TTAACTTCGAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATT--GTTAGGT
* * * * *
33744725 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGATAAGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* **
33744775 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTCATAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
* * *
33744825 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACCAGA
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGA
33744866 GAGCTTCGGT
Statistics
Matches: 316, Mismatches: 70, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
49 5 0.02
50 204 0.65
51 78 0.25
52 29 0.09
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.31
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
Found at i:33744606 original size:101 final size:99
Alignment explanation
Indices: 33744421--33744860 Score: 393
Period size: 101 Copynumber: 4.4 Consensus size: 99
33744411 GTTGTGAGAA
* * * * * ** * * *
33744421 CACATGTGTAATACTATGTGCAGGCTACTATGTGTTTAAGACGGTTTTAGGTTACGTGTGTAGCA
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTAT-CGATAG-TTTA-GTCACATGTGTAGTA
*
33744486 CTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGT
63 CTAAGTGCAGGCTACTACGTGTACCAGATTCTTAGGT
** *
33744523 TGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCGATAGTTTCGATCACATGTGTAGTAC
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTA-TCGATAGTTTAG-TCACATGTGTAGTAC
* **
33744588 TAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGT
64 TAAGTGCAGGCTACTACGTGTACCAGATTCTTAGGT
* * * * * * * * *
33744624 TACGTATGTAGTAATAAGTGTAGGCTACTA--CGTATACCA-AATTGATAGGTCGCATGTATAGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTAT-CGATAGTT--TA-GTCACATGTGTAGT
* * * *
33744686 ACTAAGTGCAGGCTACTATGTGTACCCG-TTAACTTCGAT
62 ACTAAGTGCAGGCTACTACGTGTACCAGATT--CTTAGGT
* * * * * * *
33744725 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGATAAGTCACGTGTGTAGTACT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTATC-GATAGTTTAGTCACATGTGTAGTACT
*
33744790 AAGTGCAGGCTACTACGTGTACCAGATTCATAGGT
65 AAGTGCAGGCTACTACGTGTACCAGATTCTTAGGT
*
33744825 CGCATGTGTAGTACTAAGTGCAGGCTACTATGCGTA
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTA
33744861 CCAGAGAGCT
Statistics
Matches: 271, Mismatches: 54, Indels: 28
0.77 0.15 0.08
Matches are distributed among these distances:
98 4 0.01
99 7 0.03
100 74 0.27
101 142 0.52
102 37 0.14
103 6 0.02
104 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (99 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGCGTATCGATAGTTTAGTCACATGTGTAGTACTA
AGTGCAGGCTACTACGTGTACCAGATTCTTAGGT
Found at i:33744697 original size:151 final size:151
Alignment explanation
Indices: 33744421--33744862 Score: 641
Period size: 151 Copynumber: 2.9 Consensus size: 151
33744411 GTTGTGAGAA
* * * * * * *
33744421 CACATGTGTAATACTATGTGCAGGCTACTATGTGTTTAAGACGGTTTTAGGTTACGTGTGTAGCA
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGG--TTAGGTTACGTGTGTAGTA
* *
33744486 CTAAGTGCAGGCTACTACGTGTACCAGATTGTTAGGTTGCATGTGTAGTACTAAGTGCAGGCTAC
64 CTAAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGTACTAAGTGCAGGCTAC
* **
33744551 TATGCGTACTCGATAGTTTCGAT
129 TATGCGTACCCGATAACTTCGAT
* *
33744574 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTTACGTATGTAGTAAT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTTACGTGTGTAGTACT
* * * *
33744639 AAGTGTAGGCTACTACGTATACCAAATTGATAGGTCGCATGTATAGTACTAAGTGCAGGCTACTA
66 AAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
* *
33744704 TGTGTACCCGTTAACTTCGAT
131 TGCGTACCCGATAACTTCGAT
* * * *
33744725 CACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGATAAGTCACGTGTGTAGTACT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTTACGTGTGTAGTACT
*
33744790 AAGTGCAGGCTACTACGTGTACCAGATTCATAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
66 AAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
33744855 TGCGTACC
131 TGCGTACC
33744863 AGAGAGCTTC
Statistics
Matches: 257, Mismatches: 32, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
151 219 0.85
153 38 0.15
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (151 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTTAGGTTACGTGTGTAGTACT
AAGTGCAGGCTACTACGTGTACCAGATTGATAGGTCGCATGTGTAGTACTAAGTGCAGGCTACTA
TGCGTACCCGATAACTTCGAT
Found at i:33745744 original size:180 final size:180
Alignment explanation
Indices: 33745421--33745747 Score: 478
Period size: 180 Copynumber: 1.8 Consensus size: 180
33745411 TCCGAGAGCT
* ** *
33745421 GTACCATGAAATAAATAATTATTAGTGAAGAGAGGTCAGAACTGTCGGACAGTGAAACAGGGGTA
1 GTACCATGAAATAAATAATTATTAGTGAAGAGAGCTCAGAACTGTCGGACAGCAAAACAGAGGTA
* * * * *
33745486 TCTTTAATGAATAAACTGTACTAATTAGCTAAACTAAAAATTCTAAAAATTTTATGATAATAATA
66 TATTTAATGAATAAACTATACTAATTAGCTAAACGAAAAATTCTAAAAATTTTATGATAAGAAGA
*
33745551 TATGTGAGTCTAGTTTCTGGTAAAATTAGTTGTTCTCAATTTGGAGTCTC
131 TATATGAGTCTAGTTTCTGGTAAAATTAGTTGTTCTCAATTTGGAGTCTC
*
33745601 GTACCATGAAATAAATAATTTTTAGTGAAGAGAGCTC-GAAACTGTCGGACAGCAAAACAGAGGT
1 GTACCATGAAATAAATAATTATTAGTGAAGAGAGCTCAG-AACTGTCGGACAGCAAAACAGAGGT
* * * * *
33745665 ATATTTAATGAATAAACTATACTTATTGGCTAGACGAAAAATTCTGAAAATTTTATGGTAAGAAG
65 ATATTTAATGAATAAACTATACTAATTAGCTAAACGAAAAATTCTAAAAATTTTATGATAAGAAG
33745730 ATATAT-ACGTCTAGTTTC
130 ATATATGA-GTCTAGTTTC
33745748 ATAGAAAATT
Statistics
Matches: 129, Mismatches: 16, Indels: 4
0.87 0.11 0.03
Matches are distributed among these distances:
179 2 0.02
180 127 0.98
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (180 bp):
GTACCATGAAATAAATAATTATTAGTGAAGAGAGCTCAGAACTGTCGGACAGCAAAACAGAGGTA
TATTTAATGAATAAACTATACTAATTAGCTAAACGAAAAATTCTAAAAATTTTATGATAAGAAGA
TATATGAGTCTAGTTTCTGGTAAAATTAGTTGTTCTCAATTTGGAGTCTC
Found at i:33753361 original size:43 final size:42
Alignment explanation
Indices: 33753307--33753401 Score: 111
Period size: 43 Copynumber: 2.2 Consensus size: 42
33753297 CTGGGACATC
* *
33753307 GGCATTGTATTTGATTTCGTGTAAAACC-CTGTCTAGGACAAT
1 GGCATTGTATTTGATTACATGTAAAACCAC-GTCTAGGACAAT
* * **
33753349 GGCATTGATATTTGGTTACATGTAAGACCACGTCTAGGACGTT
1 GGCATTG-TATTTGATTACATGTAAAACCACGTCTAGGACAAT
33753392 GGCATTGTAT
1 GGCATTGTAT
33753402 GAGCTTTCCG
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
42 10 0.22
43 34 0.76
44 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (42 bp):
GGCATTGTATTTGATTACATGTAAAACCACGTCTAGGACAAT
Found at i:33754162 original size:22 final size:24
Alignment explanation
Indices: 33754137--33754181 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
33754127 GTTTTTGGCT
33754137 TATGAAATG-ACATGA-ATTGGTA
1 TATGAAATGAACATGAGATTGGTA
**
33754159 TATGTTATGAACATGAGATTGGT
1 TATGAAATGAACATGAGATTGGT
33754182 TGATAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 6 0.32
24 6 0.32
ACGTcount: A:0.36, C:0.04, G:0.24, T:0.36
Consensus pattern (24 bp):
TATGAAATGAACATGAGATTGGTA
Found at i:33758803 original size:6 final size:6
Alignment explanation
Indices: 33758784--33758826 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
33758774 GAAGCAGTGG
* * *
33758784 AGAAAA AGAGAA AGAAAA AGGAAA AGAAAA ATAAAA TAGAAAA
1 AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA AGAAAA -AGAAAA
33758827 CTAAGGATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
6 25 0.83
7 5 0.17
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (6 bp):
AGAAAA
Done.