Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007709.1 Hibiscus syriacus cultivar Beakdansim tig00109924_pilon, whole genome shotgun sequence
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: 657132
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 3
Found at i:322787 original size:2 final size:2
Alignment explanation
Indices: 322743--322772 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
322733 TCGTATCTAG
322743 AT AT 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 AT AT
322773 TATGGTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:326475 original size:2 final size:2
Alignment explanation
Indices: 326468--326502 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
326458 AATATGAATG
326468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
326503 CGTACGTATG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:336924 original size:23 final size:23
Alignment explanation
Indices: 336898--336945 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
336888 ATAAAGTACA
* *
336898 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
**
336921 ATAATGTAATAGATAGCGCTTAT
1 ATAACATAATAGATAGCGCTTAT
336944 AT
1 AT
336946 TTACCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGATAGCGCTTAT
Found at i:337331 original size:21 final size:22
Alignment explanation
Indices: 337306--337358 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
337296 GATAGACACT
337306 TTACA-ATAT-AACCACTACCTA
1 TTACATATATAAACCA-TACCTA
*
337327 TTACATTATATAAACGATACCTA
1 TTACA-TATATAAACCATACCTA
*
337350 TTACTTATA
1 TTACATATA
337359 AGGGCTACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 5 0.19
22 4 0.15
23 14 0.52
24 4 0.15
ACGTcount: A:0.42, C:0.21, G:0.02, T:0.36
Consensus pattern (22 bp):
TTACATATATAAACCATACCTA
Found at i:337756 original size:39 final size:39
Alignment explanation
Indices: 337702--337788 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
337692 TCAAGTTGTA
*
337702 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
337741 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
337780 GATTTTGAT
1 GATTTTGAT
337789 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:338658 original size:21 final size:22
Alignment explanation
Indices: 338633--338684 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
338623 ACACTTTACA
*
338633 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
338656 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
338679 ATATAA
1 ATATAA
338685 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:338669 original size:23 final size:23
Alignment explanation
Indices: 338643--338705 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
338633 ATATAACCAC
338643 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
338666 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
338689 TACCTATTACATCATAT
1 TACCTATTACATTATAT
338706 GTTTACTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:339080 original size:39 final size:39
Alignment explanation
Indices: 339026--339112 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
339016 TCAAGTTGTA
*
339026 GATTTTGATTTCCTTTTGCTTGGCATCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
*
339065 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
339104 GATTTTGAT
1 GATTTTGAT
339113 GAGCATCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.17, C:0.14, G:0.21, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:339392 original size:18 final size:18
Alignment explanation
Indices: 339369--339405 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
339359 CGAAATATAT
339369 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
339387 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
339405 A
1 A
339406 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:339681 original size:25 final size:25
Alignment explanation
Indices: 339653--339703 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
339643 TTAATCCAAA
*
339653 TAATGTACCCATAACAATGTTCAAT
1 TAATGTACCCACAACAATGTTCAAT
*
339678 TAATGTACCCACAACAATGTTTAAT
1 TAATGTACCCACAACAATGTTCAAT
339703 T
1 T
339704 GATTTGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (25 bp):
TAATGTACCCACAACAATGTTCAAT
Found at i:339963 original size:18 final size:19
Alignment explanation
Indices: 339926--339962 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
339916 TCCACAGTGA
* *
339926 AAAAAGTATGGACACTTTT
1 AAAAAGGATAGACACTTTT
339945 AAAAAGGATAGACACTTT
1 AAAAAGGATAGACACTTT
339963 ACAATATAAC
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:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (19 bp):
AAAAAGGATAGACACTTTT
Found at i:339991 original size:21 final size:22
Alignment explanation
Indices: 339966--340017 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
339956 ACACTTTACA
*
339966 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
339989 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
340012 ATATAA
1 ATATAA
340018 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:340002 original size:23 final size:23
Alignment explanation
Indices: 339976--340038 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
339966 ATATAACCAC
339976 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
339999 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
340022 TACCTATTACATCATAT
1 TACCTATTACATTATAT
340039 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:340455 original size:23 final size:22
Alignment explanation
Indices: 340393--340464 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 22
340383 ACACTTTACA
*
340393 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
* *
340416 ATATAACGATACCTATTTCATT
1 ATATAACGCTACCTATTACATT
* *
340438 ATATAAGGGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
340461 ATAT
1 ATAT
340465 GTTTACCTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
22 19 0.46
23 22 0.54
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:340842 original size:21 final size:22
Alignment explanation
Indices: 340817--340868 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
340807 AAACTTTACA
*
340817 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
340840 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
340863 ATATAA
1 ATATAA
340869 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:340853 original size:23 final size:23
Alignment explanation
Indices: 340827--340889 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
340817 ATATAACCAC
340827 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
340850 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
340873 TACCTATTACATCATAT
1 TACCTATTACATTATAT
340890 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:341269 original size:21 final size:22
Alignment explanation
Indices: 341244--341295 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 22
341234 AAACTTTACA
*
341244 ATATAACCACTACCTATTACATT
1 ATATAAACA-TACCTATTACATT
341267 ATATAAACGATACCTATTACATT
1 ATATAAAC-ATACCTATTACATT
341290 ATATAA
1 ATATAA
341296 GGGCTACCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 26 0.96
24 1 0.04
ACGTcount: A:0.44, C:0.19, G:0.02, T:0.35
Consensus pattern (22 bp):
ATATAAACATACCTATTACATT
Found at i:341280 original size:23 final size:23
Alignment explanation
Indices: 341254--341316 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
341244 ATATAACCAC
341254 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
341277 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
341300 TACCTATTACATCATAT
1 TACCTATTACATTATAT
341317 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:341311 original size:427 final size:429
Alignment explanation
Indices: 339738--341414 Score: 3007
Period size: 425 Copynumber: 3.9 Consensus size: 429
339728 GAATTATTTA
* *
339738 ATTTAATAATTTCATTTGCACAAAAAATTATTTGA-TGTTTTGATATTTTATAAAATAATATTTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
* *
339802 GAATTTTAA-TTAATAATAATATATATCGCAACGT-AAAAATAAATCATTAGACGCCTATAATTA
66 GAATTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTA
*
339865 CTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAA
131 CTAAATTAATATCTTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAA
*
339930 AGTATGGACAC-TTT-TAAAAAGGATAGACACTTTACAATATAACCACTACCTATTACATTATAT
196 AGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATAT
339993 AAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAA
261 AAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAA
340058 AGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAA
326 AGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAA
*
340123 TTTTTTTAACATTGTTTCATGTTTTCCA-CTACA-ATTG
391 TTTTTTTAACAGTGTTTCATGTTTTCCACCTACATATTG
340160 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
340225 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAAT-AATCATTAGACGCCTATAATT
66 GAA-TTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
* *
340289 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACATTGAAAA
130 ACTAAATTAATATCTTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAA
* *
340354 AAGTATGGACACTTTTATAAAAAGGATATACACTTTACAATATAACCACTACCTATTACATTATA
195 AAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
*
340419 T-AACGATACCTATTTCATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATA-TGA
260 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
340482 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAA-TTATGTTTCA
325 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
340546 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACATATTG
390 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTACATATTG
*
340586 ATTTAATAATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTA-TTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
*
340650 GAATTTTAATTTAATAATAATATATACCATAACGTAAAAAATAAATCATTAGACGCCTATAATTA
66 GAATTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTA
*
340715 CTAAATTAATATCTTAAAACTCACTCAAAA-ATTAATATTAAATTAATG-TTTCCACAGTGAAAA
131 CTAAATTAATATCTTAAAACTCACTCAAAAGA-TAACATTAAATTAATGTTTTCCACAGTGAAAA
*
340778 AAGTATAGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
195 AAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATA
340843 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
260 TAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGA
340908 AAGTGTCCATAC-TTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
325 AAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCA
340972 A-TTTTTTAACAGTGTTTCATGTTTTCCACCTACAATATTG
390 ATTTTTTTAACAGTGTTTCATGTTTTCCACCTAC-ATATTG
*
341012 ATTTAATAATTTCATTTGCAGAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
1 ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
341077 GAATTTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
66 GAA-TTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATT
*
341142 ACTAAATTAATATCTTAAAACTCACTCAAAA-ATTAATATT-AATTAATGTTTTCCACAGTG-AA
130 ACTAAATTAATATCTTAAAACTCACTCAAAAGA-TAACATTAAATTAATGTTTTCCACAGTGAAA
341204 AAAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTAT
194 AAAGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTAT
341269 ATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTG
259 ATAAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTG
341334 AAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTC
324 AAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTC
341399 AA-TTTTTTAACAGTGT
389 AATTTTTTTAACAGTGT
341415 ACTGCGAATT
Statistics
Matches: 1218, Mismatches: 19, Indels: 30
0.96 0.01 0.02
Matches are distributed among these distances:
422 35 0.03
423 30 0.02
424 160 0.13
425 385 0.32
426 224 0.18
427 206 0.17
428 178 0.15
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.40
Consensus pattern (429 bp):
ATTTAATAATTTCATTTGCACAAAAAATTATTTGATTGTTTTTATATTTTATAAAATATTATTTA
GAATTTTAATTTAATAATAATATATACCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTA
CTAAATTAATATCTTAAAACTCACTCAAAAGATAACATTAAATTAATGTTTTCCACAGTGAAAAA
AGTATGGACACTTTTATAAAAAGGATAGAAACTTTACAATATAACCACTACCTATTACATTATAT
AAACGATACCTATTACATTATATAAGGGCTACCTATTACATCATATGTTTACCTATTATATTGAA
AGTGTCCATACTTTTTATAAAAAGGATCGATACTTTTTTTAAAACTTATGTAATTTATGTTTCAA
TTTTTTTAACAGTGTTTCATGTTTTCCACCTACATATTG
Found at i:343412 original size:197 final size:198
Alignment explanation
Indices: 342935--343720 Score: 1405
Period size: 196 Copynumber: 4.0 Consensus size: 198
342925 AGAAGACATA
342935 TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC
1 TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC
343000 CTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTT
66 CTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTT
*
343065 AGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACATT
131 AGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACA-ATTACATT
343130 ATAC
195 ATAC
343134 -TTTGGGTTCGATGATTTTGGGATCGACAC--TTT-TATATGGATCGACACTTTATGGGTGCACC
1 TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC
343195 CTGTTTTCCATTCATTCTGGAAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATT
66 CTGTTTTCCATTCATTCTGG-AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATT
343260 TAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTAC-ATTACATT
130 TAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAATTACATT
343324 ATAC
195 ATAC
343328 TTTTGGGTTCGATGA-TTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC
1 TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC
*
343392 TTGTTTTCCATTCATTCTGGAAAAAAAAATATCGACACAAACTATA-TAGTGTCGACACATTATT
66 CTGTTTTCCATTCATTCTGG-AAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATT
*
343456 TAGACATATTCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACAT
130 TAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACA-ATTACAT
343521 TATAC
194 TATAC
343526 TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTTATGGGTGCAC
1 TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACAC-TTTATGGGTGCAC
*
343591 CCTGTTTTCCATTAATTCTGG-AAAAAAATATCGACACAAACTATATTAGTGTCG--ACATTATT
65 CCTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATT
343653 TAGACATATCCTCTCATAAAA-CGGTATAATTGTACCGGTTAGATTGAAAAATTACATATTACAT
130 TAGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACA-ATTACAT
343717 TATA
194 TATA
343721 TGGATCGACA
Statistics
Matches: 571, Mismatches: 6, Indels: 23
0.95 0.01 0.04
Matches are distributed among these distances:
194 26 0.05
195 63 0.11
196 225 0.39
197 102 0.18
198 80 0.14
199 43 0.08
200 32 0.06
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (198 bp):
TTTTGGGTTCGATGATTTTGGGATCGACACTTTTTATATATGGATCGACACTTTATGGGTGCACC
CTGTTTTCCATTCATTCTGGAAAAAAAATATCGACACAAACTATATTAGTGTCGACACATTATTT
AGACATATCCTCTCATAAAACCGGTATAATTGTACCGGTTAGATTGAAAAATTACAATTACATTA
TAC
Found at i:343915 original size:19 final size:19
Alignment explanation
Indices: 343869--343917 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
343859 TTATATTCAC
*
343869 ATACAAAAATATAAATCGT
1 ATACAAAATTATAAATCGT
*
343888 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
343907 ATACAAAATTA
1 ATACAAAATTA
343918 ACTCGACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:345736 original size:33 final size:33
Alignment explanation
Indices: 345699--345761 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
345689 CATCTTAATA
*
345699 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
345732 TCACCCCTCAACACCTCTACTTCTTTCACC
1 TCACCCCTCAACACCGAAACTTCTTTCACC
345762 CTCCATCTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.24, C:0.46, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:348125 original size:19 final size:19
Alignment explanation
Indices: 348070--348116 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 19
348060 ATCCGGTATC
348070 ATTTTACCGGTTTTATCAT
1 ATTTTACCGGTTTTATCAT
348089 -TTTGATACCGGTTTTATCAT
1 ATTT--TACCGGTTTTATCAT
348109 ATTTTACC
1 ATTTTACC
348117 TGTTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
18 3 0.12
19 4 0.16
20 15 0.60
21 3 0.12
ACGTcount: A:0.21, C:0.17, G:0.11, T:0.51
Consensus pattern (19 bp):
ATTTTACCGGTTTTATCAT
Found at i:348263 original size:20 final size:20
Alignment explanation
Indices: 348237--348282 Score: 76
Period size: 20 Copynumber: 2.3 Consensus size: 20
348227 CACTTTTAAA
348237 TTTACCGGTTTTATCAT-TT
1 TTTACCGGTTTTATCATATT
348256 TGTTACCGGTTTTATCATATT
1 T-TTACCGGTTTTATCATATT
348277 TTTACC
1 TTTACC
348283 TGGTATATCG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.54
Consensus pattern (20 bp):
TTTACCGGTTTTATCATATT
Found at i:348748 original size:229 final size:228
Alignment explanation
Indices: 348347--348795 Score: 808
Period size: 229 Copynumber: 2.0 Consensus size: 228
348337 TTAAAACTGC
348347 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
**
348412 TTAATTTAATAATTTAATTTACACAAAATTTTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
348477 TTAGAATTTAAATTTAACAATATTAACCAAATATAATAATAAATATGTTTTCAACAGTGAAATAA
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTC-ACAGTGAAATAA
*
348542 GTATGGACACTTTTATAAAAATGATATATACTTT
195 GTATGGACACTTTTATAAAAAGGATATATACTTT
*
348576 TTTGAAAGTTATGTAATTTATGTTTCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATA
1 TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
*
348641 TTAATTTAATAATTTCATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
66 TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
* *
348706 TTAGATTTTAAATTTAACAATATTAACTAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
131 TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
348771 TATGGACACTTTTATAAAAAGGATA
196 TATGGACACTTTTATAAAAAGGATA
348796 GATAATTTAC
Statistics
Matches: 211, Mismatches: 9, Indels: 1
0.95 0.04 0.00
Matches are distributed among these distances:
228 37 0.18
229 174 0.82
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.45
Consensus pattern (228 bp):
TTTGAAAGTTATGTAATTTATGTTTCAATTTATTTAATAGTGTTTCATGTTTTCCACCTACAATA
TTAATTTAATAATTTAATTTACACAAAAAATTATTTGATTGTTTTGATATTTTATAAAATATTAT
TTAGAATTTAAATTTAACAATATTAACCAAAGATAATAATAAATATATTTTCACAGTGAAATAAG
TATGGACACTTTTATAAAAAGGATATATACTTT
Found at i:362940 original size:2 final size:2
Alignment explanation
Indices: 362930--362959 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
362920 TTTTTTCTAA
*
362930 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
362960 TATTAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:362982 original size:15 final size:16
Alignment explanation
Indices: 362935--362992 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
362925 TCTAAATATT
*
362935 TATATATA-TATATATA
1 TATATATATTAT-TAAA
362951 TATATATATTATTAAA
1 TATATATATTATTAAA
362967 TAT-TATATT-TTAAA
1 TATATATATTATTAAA
*
362981 -ATATAGATTATT
1 TATATATATTATT
362993 TTTTAATCCC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
13 2 0.05
14 10 0.27
15 8 0.22
16 14 0.38
17 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
TATATATATTATTAAA
Found at i:362985 original size:12 final size:14
Alignment explanation
Indices: 362936--362992 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
362926 CTAAATATTT
*
362936 ATATATATATATATAT
1 ATATATAT-TAT-TAA
362952 ATATATATTATTAA
1 ATATATATTATTAA
362966 ATATTATATT-TTAAA
1 ATA-TATATTATT-AA
*
362981 ATATAGATTATT
1 ATATATATTATT
362993 TTTTAATCCC
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
14 12 0.33
15 16 0.44
16 8 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
ATATATATTATTAA
Found at i:364694 original size:17 final size:17
Alignment explanation
Indices: 364672--364705 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
364662 GTCAACGGTA
364672 AACGGTCGGGTCGGGTC
1 AACGGTCGGGTCGGGTC
364689 AACGGTCGGGTCGGGTC
1 AACGGTCGGGTCGGGTC
364706 GGGTCAGACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.24, G:0.47, T:0.18
Consensus pattern (17 bp):
AACGGTCGGGTCGGGTC
Found at i:364744 original size:10 final size:10
Alignment explanation
Indices: 364713--364767 Score: 53
Period size: 9 Copynumber: 5.6 Consensus size: 10
364703 GTCGGGTCAG
364713 ACCGGTCAAA
1 ACCGGTCAAA
*
364723 A-CGGTTC-GA
1 ACCGG-TCAAA
364732 ACCGGTCAAA
1 ACCGGTCAAA
*
364742 ACCGGTTGAAA
1 ACCGG-TCAAA
364753 ACCGGTC-AA
1 ACCGGTCAAA
364762 ACCGGT
1 ACCGGT
364768 TTCCAACAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
9 15 0.41
10 13 0.35
11 9 0.24
ACGTcount: A:0.33, C:0.27, G:0.25, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:364763 original size:20 final size:19
Alignment explanation
Indices: 364713--364768 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 19
364703 GTCGGGTCAG
*
364713 ACCGGTCAAAACGGTTCGA
1 ACCGGTCAAACCGGTTCGA
364732 ACCGGTCAAAACCGGTT-GAAA
1 ACCGGTC-AAACCGGTTCG--A
364753 ACCGGTCAAACCGGTT
1 ACCGGTCAAACCGGTT
364769 TCCAACAGCG
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 8 0.24
20 17 0.52
21 8 0.24
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Found at i:365536 original size:11 final size:11
Alignment explanation
Indices: 365504--365537 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
365494 TCAGTGTATG
*
365504 TACCTAACAAG
1 TACCTAACAAA
365515 TACCTAACAAA
1 TACCTAACAAA
*
365526 TATCTAACAAA
1 TACCTAACAAA
365537 T
1 T
365538 GGCAGATGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.50, C:0.24, G:0.03, T:0.24
Consensus pattern (11 bp):
TACCTAACAAA
Found at i:367276 original size:22 final size:24
Alignment explanation
Indices: 367250--367293 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
367240 TTTAAAAAGT
367250 AAAT-AATTA-ATAAAAATATATA
1 AAATAAATTATATAAAAATATATA
*
367272 AAATAAATTATATTAAAATATA
1 AAATAAATTATATAAAAATATA
367294 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 5 0.26
24 10 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
AAATAAATTATATAAAAATATATA
Found at i:368183 original size:4 final size:4
Alignment explanation
Indices: 368161--368200 Score: 53
Period size: 4 Copynumber: 9.5 Consensus size: 4
368151 TATCAATAAA
*
368161 TATT TAATT TGATT GATT TATT TATT TATT TATT TATT TA
1 TATT T-ATT T-ATT TATT TATT TATT TATT TATT TATT TA
368201 ATTCAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
4 25 0.78
5 7 0.22
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (4 bp):
TATT
Found at i:371050 original size:59 final size:58
Alignment explanation
Indices: 370940--371101 Score: 157
Period size: 59 Copynumber: 2.7 Consensus size: 58
370930 AATATGACCT
* * *
370940 TCATTTTAAATTAATCCTTAAATTTTTAAATATTTCAATTT-TTCCTTAAACTATCACTA
1 TCATTTTAAATTAATCCTCAAACTTTTAAA-ATTTCAATTTCATCC-TAAACTATCACTA
** *
370999 TCATTTTAAATTAATCCTCAAACTTTTAAACATTTCAATTTCATCAC-AAACTATGTCTT
1 TCATTTTAAATTAATCCTCAAACTTTTAAA-ATTTCAATTTCATC-CTAAACTATCACTA
* ** * *
371058 TCATTCTAAATTGGTCCCCAAACTTTTTGAAAATTCCAATTTCA
1 TCATTTTAAATTAATCCTCAAAC-TTTT-AAAATTTCAATTTCA
371102 AGTATATGTA
Statistics
Matches: 87, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
59 66 0.76
60 17 0.20
61 4 0.05
ACGTcount: A:0.35, C:0.19, G:0.02, T:0.44
Consensus pattern (58 bp):
TCATTTTAAATTAATCCTCAAACTTTTAAAATTTCAATTTCATCCTAAACTATCACTA
Found at i:371262 original size:61 final size:59
Alignment explanation
Indices: 371185--371352 Score: 183
Period size: 60 Copynumber: 2.8 Consensus size: 59
371175 TATTTGGATG
* * * *
371185 AATTTGGGGATAAAATTAAAATATTCAAAAGGTTGGGGAACCAATTTAGAAAGAGGGTCAT
1 AATTT-GGGATGAAATTAAAATATTCAAAAGTTTGAGG-ACCAATTTAGAAAGAGAGTCAT
* * * * * *
371246 AATTTAGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAGTTTAGAATGAGAGTCAT
1 AATTT-GGGATGAAATTAAAATATTCAAAAGTTTGAGGACCAATTTAGAAAGAGAGTCAT
* * *
371306 AGTTTGGAGATGAAATTGAAATATGCAAAAGTTTGAGGACCAATTTA
1 AATTTGG-GATGAAATTAAAATATTCAAAAGTTTGAGGACCAATTTA
371353 AAATAAATGT
Statistics
Matches: 87, Mismatches: 19, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
59 2 0.02
60 54 0.62
61 31 0.36
ACGTcount: A:0.41, C:0.06, G:0.24, T:0.29
Consensus pattern (59 bp):
AATTTGGGATGAAATTAAAATATTCAAAAGTTTGAGGACCAATTTAGAAAGAGAGTCAT
Found at i:371840 original size:24 final size:27
Alignment explanation
Indices: 371812--371862 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
371802 ACGGTCAACT
371812 ATGTATT-TA-TTTA-TTTATTTATAC
1 ATGTATTATATTTTATTTTATTTATAC
371836 ATGTATTATATTTTATTTTTATTTATA
1 ATGTATTATATTTTA-TTTTATTTATA
371863 ATTTTTATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.30
25 2 0.09
26 4 0.17
28 10 0.43
ACGTcount: A:0.29, C:0.02, G:0.04, T:0.65
Consensus pattern (27 bp):
ATGTATTATATTTTATTTTATTTATAC
Found at i:377717 original size:22 final size:23
Alignment explanation
Indices: 377689--377738 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
377679 AAAAATGTCA
377689 AAAGACAG-AAGAAACATATCAT
1 AAAGACAGAAAGAAACATATCAT
* *
377711 AAAGACAGAAATAAATATATCAT
1 AAAGACAGAAAGAAACATATCAT
377734 AAAGA
1 AAAGA
377739 TAAAAAATGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.62, C:0.10, G:0.12, T:0.16
Consensus pattern (23 bp):
AAAGACAGAAAGAAACATATCAT
Found at i:382006 original size:18 final size:19
Alignment explanation
Indices: 381983--382019 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
381973 TTAATTGAAA
*
381983 AACCGATAAA-CCGAACCG
1 AACCGAAAAACCCGAACCG
382001 AACCGAAAAACCCGAACCG
1 AACCGAAAAACCCGAACCG
382020 TTAAAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.46, C:0.35, G:0.16, T:0.03
Consensus pattern (19 bp):
AACCGAAAAACCCGAACCG
Found at i:391959 original size:21 final size:21
Alignment explanation
Indices: 391933--392018 Score: 104
Period size: 21 Copynumber: 4.1 Consensus size: 21
391923 CCAGTCGTTG
391933 CGAATTTGGAATAAATCGCAA
1 CGAATTTGGAATAAATCGCAA
*
391954 CGAATTTGTAATAAATCGCAA
1 CGAATTTGGAATAAATCGCAA
* *
391975 CGTGAACTTGGACT--ATCGCAA
1 C--GAATTTGGAATAAATCGCAA
*
391996 CAAATTTGGAATAAATCGCAA
1 CGAATTTGGAATAAATCGCAA
392017 CG
1 CG
392019 CGAACTTGGA
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
19 8 0.15
21 37 0.70
23 8 0.15
ACGTcount: A:0.40, C:0.17, G:0.19, T:0.24
Consensus pattern (21 bp):
CGAATTTGGAATAAATCGCAA
Found at i:392002 original size:42 final size:41
Alignment explanation
Indices: 391945--392036 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 41
391935 AATTTGGAAT
* * *
391945 AAATCGCAACGAATTTGTAATAAATCGCAACGTGAACTTGG
1 AAATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGG
*
391986 ACTATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGG
1 A-AATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGG
392028 AAATCGCAA
1 AAATCGCAA
392037 TGCGAATATG
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
41 8 0.18
42 37 0.82
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (41 bp):
AAATCGCAACAAATTTGGAATAAATCGCAACGCGAACTTGG
Found at i:392033 original size:20 final size:20
Alignment explanation
Indices: 392008--392061 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
391998 AATTTGGAAT
*
392008 AAATCGCAACGCGAACT-TGG
1 AAATCGCAATGCGAA-TATGG
*
392028 AAATCGCAATGCGAATATGT
1 AAATCGCAATGCGAATATGG
392048 AAATCGCAATGCGA
1 AAATCGCAATGCGA
392062 TAGTCGAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 30 0.97
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.19
Consensus pattern (20 bp):
AAATCGCAATGCGAATATGG
Found at i:392118 original size:40 final size:40
Alignment explanation
Indices: 392072--392164 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
392062 TAGTCGAAGT
*
392072 TCGCGTTGTGAATCTGGAAACTGATTTGCGATACCGGAGA
1 TCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGA
* * *
392112 TCGCGTTGCGAATCTGGAAACTGATTTTCGATATCGTAGA
1 TCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGA
392152 TCGCGTTGCGAAT
1 TCGCGTTGCGAAT
392165 TATCGATCGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (40 bp):
TCGCGTTGCGAATCTGGAAACTGATTTGCGATACCGGAGA
Found at i:393880 original size:14 final size:14
Alignment explanation
Indices: 393861--393904 Score: 52
Period size: 14 Copynumber: 2.9 Consensus size: 14
393851 AATTTTGTTA
393861 AATTATTATAAAAT
1 AATTATTATAAAAT
*
393875 AATTATTATAATATT
1 AATTATTATAA-AAT
393890 ATATTAATTATAAAA
1 A-ATT-ATTATAAAA
393905 ATCCGATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 11 0.44
15 3 0.12
16 4 0.16
17 7 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
AATTATTATAAAAT
Found at i:405321 original size:2 final size:2
Alignment explanation
Indices: 405314--405346 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
405304 AAGAATTAAA
405314 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
405347 ATTCTATAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:407158 original size:24 final size:24
Alignment explanation
Indices: 407130--407207 Score: 65
Period size: 24 Copynumber: 3.2 Consensus size: 24
407120 ATTTTAATTA
407130 AATTATTTAATATATGATAATTTT
1 AATTATTTAATATATGATAATTTT
**
407154 AATTA--T-ATATGATGCAATGAA-TCA
1 AATTATTTAATAT-ATG--AT-AATTTT
*
407178 AATCATTTAATATATGATAATTTT
1 AATTATTTAATATATGATAATTTT
407202 AATTAT
1 AATTAT
407208 AAACATATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 16
0.65 0.10 0.26
Matches are distributed among these distances:
21 4 0.10
22 4 0.10
23 2 0.05
24 20 0.50
25 2 0.05
26 4 0.10
27 4 0.10
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (24 bp):
AATTATTTAATATATGATAATTTT
Found at i:426323 original size:2 final size:2
Alignment explanation
Indices: 426316--426341 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
426306 CTTAAAACTT
426316 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
426342 TATATATCTT
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:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:427375 original size:19 final size:19
Alignment explanation
Indices: 427339--427383 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
427329 ATTTAAAGCC
427339 AAAAGAA-CAAAAGGAAAA
1 AAAAGAACCAAAAGGAAAA
* *
427357 AAAAGAACCCAAAGTAAAA
1 AAAAGAACCAAAAGGAAAA
*
427376 GAAAGAAC
1 AAAAGAAC
427384 GGGAAATTTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.71, C:0.11, G:0.16, T:0.02
Consensus pattern (19 bp):
AAAAGAACCAAAAGGAAAA
Found at i:427795 original size:3 final size:3
Alignment explanation
Indices: 427787--427818 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
427777 AATTGATATC
*
427787 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
427819 TCTTTACATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:429051 original size:85 final size:86
Alignment explanation
Indices: 428911--429096 Score: 320
Period size: 85 Copynumber: 2.2 Consensus size: 86
428901 GAAGCCAATA
* *
428911 AAAAGATCATGCCAGTTGCTGCTTGTGGTAATAAAAAATTGTATGAATTGCAGGGG-GAAACAAC
1 AAAAGATCATGTCAGTTGCTGCTTGTGGTAATAAAAAATTGTATGAATTGCAGGGGAAAAACAAC
*
428975 TTCAATGTTGCTTGTGGTAAT
66 TTCAATGCTGCTTGTGGTAAT
*
428996 AAAAGATCATGTCAGTTGCTGCTTGTGGTAATAAAAAATTGTTTGAATTGCAGGGGAAAAACAAC
1 AAAAGATCATGTCAGTTGCTGCTTGTGGTAATAAAAAATTGTATGAATTGCAGGGGAAAAACAAC
*
429061 TTCGATGCTGCTTGTGGTAAT
66 TTCAATGCTGCTTGTGGTAAT
429082 AAAAGATCATGTCAG
1 AAAAGATCATGTCAG
429097 ATTTAATTTA
Statistics
Matches: 95, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
85 54 0.57
86 41 0.43
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (86 bp):
AAAAGATCATGTCAGTTGCTGCTTGTGGTAATAAAAAATTGTATGAATTGCAGGGGAAAAACAAC
TTCAATGCTGCTTGTGGTAAT
Found at i:429671 original size:2 final size:2
Alignment explanation
Indices: 429664--429697 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
429654 TTCAGAATTA
429664 AT AT AT AT 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 AT AT AT AT
429698 TGTCTAGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:430223 original size:3 final size:3
Alignment explanation
Indices: 430215--430258 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
430205 AATTAGTTTC
430215 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
430259 CATCATCATC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:435100 original size:21 final size:20
Alignment explanation
Indices: 435014--435171 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
435004 AAATGACCAA
**
435014 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
435033 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
435053 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
435073 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
435094 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
435115 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
435135 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
435156 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
435172 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:435200 original size:20 final size:20
Alignment explanation
Indices: 435139--435347 Score: 199
Period size: 20 Copynumber: 10.4 Consensus size: 20
435129 GATTTTCCAG
* ** *
435139 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
435159 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
435179 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
435199 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
435219 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
435239 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
435259 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
435279 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
435299 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
435319 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
435339 AATCACAAC
1 AATCGCAAC
435348 ACTGAAATTT
Statistics
Matches: 157, Mismatches: 26, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 153 0.97
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:436078 original size:24 final size:24
Alignment explanation
Indices: 436039--436085 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
436029 AAATTTGGTC
436039 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
436063 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
436086 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:438618 original size:33 final size:33
Alignment explanation
Indices: 438581--438709 Score: 118
Period size: 34 Copynumber: 3.7 Consensus size: 33
438571 GCAACGAGAG
*
438581 ATCGCAATGCGAAATGAAAATCCCAACATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACATGAAA
438614 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGC-GAAATGAAAATCGCAA--C---ATGAAA
* * * *
438653 ATCGCAACGAGAGAATCG-CAATGCGGAA-ATGAAA
1 ATCGCAATGCGA-AAT-GAAAAT-CGCAACATGAAA
438687 ATCGCAATGCGAAATGAAAATCG
1 ATCGCAATGCGAAATGAAAATCG
438710 TATTGCGATT
Statistics
Matches: 78, Mismatches: 8, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
32 3 0.04
33 16 0.21
34 31 0.40
36 1 0.01
38 2 0.03
39 20 0.26
40 5 0.06
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACATGAAA
Found at i:438709 original size:53 final size:53
Alignment explanation
Indices: 438581--438709 Score: 224
Period size: 53 Copynumber: 2.4 Consensus size: 53
438571 GCAACGAGAG
*
438581 ATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATGAAA
*
438634 ATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAAC-ATGAAAATCGCAATGCGGAAATGAAA
438687 ATCGCAATGCGAAATGAAAATCG
1 ATCGCAATGCGAAATGAAAATCG
438710 TATTGCGATT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
53 72 0.99
54 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAACATGAAAATCGCAATGCGGAAATGAAA
Found at i:438717 original size:19 final size:19
Alignment explanation
Indices: 438581--438709 Score: 152
Period size: 19 Copynumber: 7.2 Consensus size: 19
438571 GCAACGAGAG
438581 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
438600 ATCCCAA--C---ATGAAA
1 ATCGCAATGCGAAATGAAA
438614 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
438634 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
438653 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
438667 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
438687 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
438706 ATCG
1 ATCG
438710 TATTGCGATT
Statistics
Matches: 94, Mismatches: 4, Indels: 24
0.77 0.03 0.20
Matches are distributed among these distances:
14 22 0.23
15 1 0.01
16 2 0.02
17 4 0.04
19 36 0.38
20 29 0.31
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:438751 original size:53 final size:52
Alignment explanation
Indices: 438688--438803 Score: 151
Period size: 53 Copynumber: 2.2 Consensus size: 52
438678 GAAATGAAAA
* *
438688 TCGCAATGCGAAATGAAAATCGTATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
** ** **
438740 TCCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 T-CGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
438793 TCGCATTGCGA
1 TCGCATTGCGA
438804 TTTTCATTTC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
52 11 0.20
53 44 0.80
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.40
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:438766 original size:19 final size:19
Alignment explanation
Indices: 438726--438824 Score: 127
Period size: 19 Copynumber: 5.4 Consensus size: 19
438716 GATTCTCTCG
438726 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
438746 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
438765 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
438779 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
438798 TTGCGATTTTCATTTCCACA
1 TTGCGATTTTCATTT-CGCA
438818 TTGCGAT
1 TTGCGAT
438825 AGTCATTTTT
Statistics
Matches: 70, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.10
17 7 0.10
19 25 0.36
20 25 0.36
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:438820 original size:53 final size:53
Alignment explanation
Indices: 438711--438824 Score: 203
Period size: 53 Copynumber: 2.2 Consensus size: 53
438701 TGAAAATCGT
*
438711 ATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGC
1 ATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCAC
438764 ATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCAC
1 ATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTT-CAC
438817 ATTGCGAT
1 ATTGCGAT
438825 AGTCATTTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
52 19 0.32
53 40 0.68
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.45
Consensus pattern (53 bp):
ATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCAC
Found at i:438950 original size:14 final size:14
Alignment explanation
Indices: 438931--438967 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
438921 CATCAATTAC
438931 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
438945 ACAAATCATCTTTT
1 ACAAATCAACTTTT
438959 ACAAATCAA
1 ACAAATCAA
438968 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:440928 original size:19 final size:19
Alignment explanation
Indices: 440886--441058 Score: 152
Period size: 19 Copynumber: 9.6 Consensus size: 19
440876 TAGTTTACTT
* *
440886 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
440906 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
440925 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
440944 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
440963 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
440982 TCGCAACGACG----G--AA
1 TCGCAACG-CGAAATGAAAA
*
440996 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
441015 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
441029 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
441048 TCGCAATGCGA
1 TCGCAACGCGA
441059 TTTTGGTTTC
Statistics
Matches: 127, Mismatches: 14, Indels: 25
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.02
14 19 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 1 0.01
19 84 0.66
20 14 0.11
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.10
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:441007 original size:33 final size:33
Alignment explanation
Indices: 440961--441053 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
440951 GCGAAACCAA
440961 AATCGCAACGCGAAATGAAAATCGCAACGACG-G
1 AATCGCAACGCGAAATGAAAATCGCAACGA-GAG
*
440994 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
441027 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
441054 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 1 0.02
33 56 0.98
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:441089 original size:14 final size:14
Alignment explanation
Indices: 441070--441128 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
441060 TTTGGTTTCG
441070 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
441084 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
*
441101 CGCGTTGCGATTCTGT
1 --CGTTGCGATTTTGT
441117 CGTTGCGATTTT
1 CGTTGCGATTTT
441129 CATTTCGCGT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 23 0.61
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
19 11 0.29
ACGTcount: A:0.07, C:0.17, G:0.29, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:441096 original size:33 final size:33
Alignment explanation
Indices: 441054--441161 Score: 180
Period size: 33 Copynumber: 3.3 Consensus size: 33
441044 AAAATCGCAA
*
441054 TGCGATTTTGGTTTCGCGTTGCGATTTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
441087 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
** *
441120 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
441153 TGCGATTTT
1 TGCGATTTT
441162 AAGTTTCGTG
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 71 1.00
ACGTcount: A:0.07, C:0.19, G:0.27, T:0.47
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:441108 original size:19 final size:18
Alignment explanation
Indices: 441054--441145 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 18
441044 AAAATCGCAA
441054 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
441073 TGCGATTTTG--T--CGT
1 TGCGATTTTGTTTCGCGT
441087 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-GTTTCGCGT
*
441106 TGCGATTCTG--T--CGT
1 TGCGATTTTGTTTCGCGT
*
441120 TGCGATTTTCATTTCGCGT
1 TGCGATTTT-GTTTCGCGT
441139 TGCGATT
1 TGCGATT
441146 CTCTCGTTGC
Statistics
Matches: 60, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
14 23 0.38
15 1 0.02
16 2 0.03
17 2 0.03
18 2 0.03
19 30 0.50
ACGTcount: A:0.08, C:0.17, G:0.28, T:0.47
Consensus pattern (18 bp):
TGCGATTTTGTTTCGCGT
Found at i:441155 original size:14 final size:14
Alignment explanation
Indices: 441103--441159 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
441093 TTTGGTTTCG
*
441103 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
441117 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
441136 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
441150 CGTTGCGATT
1 CGTTGCGATT
441160 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:443118 original size:20 final size:20
Alignment explanation
Indices: 443087--443183 Score: 100
Period size: 20 Copynumber: 5.2 Consensus size: 20
443077 TTTTGGTTGA
443087 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
***
443107 AATGACTGTCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
443127 AAATGAAAATCGCAAC--GAG
1 -AATGAAAATCGCAACGAGAG
*
443146 -A-G--AATCGCAACGCGA-
1 AATGAAAATCGCAACGAGAG
443161 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
443181 AAT
1 AAT
443184 CGCAACGCGA
Statistics
Matches: 62, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
14 9 0.15
16 4 0.06
17 2 0.03
19 15 0.24
20 20 0.32
21 12 0.19
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:443139 original size:21 final size:21
Alignment explanation
Indices: 443085--443149 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
443075 TCTTTTGGTT
443085 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
***
443106 G-AATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
443126 GAAATGAAAATCGCAACGAGA
1 GAAATGAAAATCGCAACGAGA
443147 GAA
1 GAA
443150 TCGCAACGCG
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.48, C:0.15, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAATGAAAATCGCAACGAGA
Found at i:443153 original size:14 final size:14
Alignment explanation
Indices: 443134--443190 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
443124 GAGAAATGAA
443134 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
443148 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
443167 AATCGCAACGAGAG
1 AATCGCAACGAGAG
443181 AATCGCAACG
1 AATCGCAACG
443191 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:443166 original size:33 final size:33
Alignment explanation
Indices: 443085--443207 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
443075 TCTTTTGGTT
*
443085 GAAATGAAAATCGCAACGAGAGAATGACTGTCGCAACGAGA
1 GAAATGAAAATCGCAACGAGAG-A--A---TCGCAAC--GC
443126 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
443159 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
443192 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
443208 TGCGATTTTG
Statistics
Matches: 81, Mismatches: 1, Indels: 8
0.90 0.01 0.09
Matches are distributed among these distances:
33 50 0.62
35 7 0.09
38 1 0.01
40 1 0.01
41 22 0.27
ACGTcount: A:0.46, C:0.19, G:0.24, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:443243 original size:14 final size:14
Alignment explanation
Indices: 443224--443313 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
443214 TTTGGTTTCG
443224 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
443238 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
443257 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
443271 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
443290 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
443304 CGTTGCGATT
1 CGTTGCGATT
443314 TTCATTTTTC
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
16 6 0.10
17 6 0.10
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:443256 original size:33 final size:33
Alignment explanation
Indices: 443208--443320 Score: 208
Period size: 33 Copynumber: 3.4 Consensus size: 33
443198 AAAATCGCAA
**
443208 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
443241 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
443274 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
443307 TGCGATTTTCATTT
1 TGCGATTTTCATTT
443321 TTCTCGTTGC
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:443262 original size:19 final size:19
Alignment explanation
Indices: 443235--443365 Score: 111
Period size: 19 Copynumber: 7.2 Consensus size: 19
443225 GTTGCGATTC
443235 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTTTCATT
*
443254 TCGCGTTGCGA--TTC---
1 TCTCGTTGCGATTTTCATT
443268 TCTCGTTGCGATTTTCATT
1 TCTCGTTGCGATTTTCATT
*
443287 TCGCGTTGCGA--TTC---
1 TCTCGTTGCGATTTTCATT
443301 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCA--TT
**
443322 TCTCGTTGCAGATAGTCATTT
1 TCTCGTTGC-GATTTTCA-TT
*
443343 TCACGTTGCGATTTTCATT
1 TCTCGTTGCGATTTTCATT
443362 TCTC
1 TCTC
443366 TCGTTGCGAC
Statistics
Matches: 89, Mismatches: 10, Indels: 26
0.71 0.08 0.21
Matches are distributed among these distances:
14 20 0.22
16 6 0.07
17 6 0.07
19 25 0.28
20 6 0.07
21 20 0.22
22 6 0.07
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.47
Consensus pattern (19 bp):
TCTCGTTGCGATTTTCATT
Found at i:443326 original size:21 final size:21
Alignment explanation
Indices: 443301--443374 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
443291 GTTGCGATTC
443301 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
443322 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
443343 TCACGTTGCGATTTTCATTTC
1 TCTCGTTGCGATTTTCATTTT
443364 TCTCGTTGCGA
1 TCTCGTTGCGA
443375 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:443496 original size:32 final size:32
Alignment explanation
Indices: 443457--443525 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
443447 ACTAACTTGA
443457 AAATCGCAACGAGAGAATAGCAACGCGAAATG
1 AAATCGCAACGAGAGAATAGCAACGCGAAATG
* *
443489 AAATCGCAACGAGAGAATCGTAACGCGAAATG
1 AAATCGCAACGAGAGAATAGCAACGCGAAATG
443521 AAATC
1 AAATC
443526 TAAGTGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (32 bp):
AAATCGCAACGAGAGAATAGCAACGCGAAATG
Found at i:443499 original size:18 final size:18
Alignment explanation
Indices: 443476--443525 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
443466 CGAGAGAATA
443476 GCAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
*
443494 GCAA--CGAGA-G-AATC
1 GCAACGCGAAATGAAATC
*
443508 GTAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
443526 TAAGTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 1 0.04
16 8 0.32
17 1 0.04
18 8 0.32
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.12
Consensus pattern (18 bp):
GCAACGCGAAATGAAATC
Found at i:443939 original size:20 final size:20
Alignment explanation
Indices: 443926--444075 Score: 194
Period size: 20 Copynumber: 7.5 Consensus size: 20
443916 TACGTATTGT
443926 CGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
443946 CGTTGCGATATACGGATACG
1 CGTTGCGATTTACGGATACG
*
443966 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACG
*
443986 CGTTGCGATTTACGGATACA
1 CGTTGCGATTTACGGATACG
*
444006 CGTTGCGGTTTACGGATACG
1 CGTTGCGATTTACGGATACG
* *
444026 CGTTGCGATTTATGTG-TTCG
1 CGTTGCGATTTACG-GATACG
* ** *
444046 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTACGGATACG
444066 CGTTGCGATT
1 CGTTGCGATT
444076 CTGGAAAATC
Statistics
Matches: 114, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
20 113 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.28, T:0.34
Consensus pattern (20 bp):
CGTTGCGATTTACGGATACG
Found at i:444128 original size:21 final size:21
Alignment explanation
Indices: 444104--444161 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
444094 AATTTGTACT
*
444104 ATCGCATTGCGATTTTCAAGA
1 ATCGCGTTGCGATTTTCAAGA
444125 ATCGCGTTGCGATTTTCAAGA
1 ATCGCGTTGCGATTTTCAAGA
444146 ATCGCGTTGCGATTTT
1 ATCGCGTTGCGATTTT
444162 GGAAACTGAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.36
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTCAAGA
Found at i:451893 original size:22 final size:22
Alignment explanation
Indices: 451876--451942 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
451866 CTCGTATAAA
451876 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
451898 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
451920 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
451942 T
1 T
451943 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:452976 original size:18 final size:18
Alignment explanation
Indices: 452955--452989 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
452945 TCCCCTCTAG
452955 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
452973 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
452990 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:453617 original size:22 final size:21
Alignment explanation
Indices: 453571--453613 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
453561 TTCATATTCG
* *
453571 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
453592 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
453613 C
1 C
453614 CTTGCCCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:456766 original size:22 final size:22
Alignment explanation
Indices: 456749--456815 Score: 134
Period size: 22 Copynumber: 3.0 Consensus size: 22
456739 CTCGTATAAA
456749 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
456771 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
456793 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
456815 T
1 T
456816 ATGTCCATAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:457849 original size:18 final size:18
Alignment explanation
Indices: 457828--457862 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
457818 TCCCCTCTAG
457828 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
457846 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
457863 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:458490 original size:22 final size:21
Alignment explanation
Indices: 458444--458486 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
458434 TTCATATTCG
* *
458444 CTTGAAGGGGTATCGGTTCCC
1 CTTGAAGGGGTACCGATTCCC
*
458465 CTTGAATGGGTACCGATTCCC
1 CTTGAAGGGGTACCGATTCCC
458486 C
1 C
458487 CTTGCCCAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.28, G:0.28, T:0.28
Consensus pattern (21 bp):
CTTGAAGGGGTACCGATTCCC
Found at i:484941 original size:5 final size:5
Alignment explanation
Indices: 484908--484959 Score: 50
Period size: 5 Copynumber: 10.4 Consensus size: 5
484898 AACTGGGTAA
* * * * * *
484908 TCTTT TATTT TCCTT TCCTT TCCTC TCTTT TCTTT TCTTT TATTT TCTTT
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT
484958 TC
1 TC
484960 CTTCAAGAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 39 1.00
ACGTcount: A:0.04, C:0.25, G:0.00, T:0.71
Consensus pattern (5 bp):
TCTTT
Found at i:493158 original size:29 final size:30
Alignment explanation
Indices: 493095--493163 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
493085 AAAAACTTGG
* *
493095 ATTTTGAAATAAGAAAATAGAGGGACTATA
1 ATTTTGAAATAAGAAAATAGAGAGACTAAA
* *
493125 TTTTTGGAAAT-A-AAAATAGATAGACTAAA
1 ATTTT-GAAATAAGAAAATAGAGAGACTAAA
*
493154 ATTTTAAAAT
1 ATTTTGAAAT
493164 CTATAGAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
28 4 0.12
29 18 0.56
30 5 0.16
31 5 0.16
ACGTcount: A:0.51, C:0.03, G:0.14, T:0.32
Consensus pattern (30 bp):
ATTTTGAAATAAGAAAATAGAGAGACTAAA
Found at i:493341 original size:31 final size:31
Alignment explanation
Indices: 493306--493364 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
493296 TGTTGTCTCC
* * *
493306 GTTTTTATTTAATTAAGATTTTGTCACTTTA
1 GTTTTAATTTAATTAAGATGTAGTCACTTTA
*
493337 GTTTTAATTTAGTTAAGATGTAGTCACT
1 GTTTTAATTTAATTAAGATGTAGTCACT
493365 AAAGATTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.27, C:0.07, G:0.14, T:0.53
Consensus pattern (31 bp):
GTTTTAATTTAATTAAGATGTAGTCACTTTA
Found at i:493639 original size:2 final size:2
Alignment explanation
Indices: 493632--493660 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
493622 ATTTAAAAAG
493632 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 T
493661 TGAAAAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:501953 original size:39 final size:39
Alignment explanation
Indices: 501880--501955 Score: 109
Period size: 39 Copynumber: 1.9 Consensus size: 39
501870 GCGTTTATTT
* * *
501880 ATTAAATGAACGAACATGAACAAGATTTTTGTTCGTTTA
1 ATTAAATGAACAAACATGAACAAGAGTTTCGTTCGTTTA
501919 ATTAAATGAACAAACATGAACATAG-GTTTCGTTCGTT
1 ATTAAATGAACAAACATGAACA-AGAGTTTCGTTCGTT
501956 CATTTAGGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 31 0.94
40 2 0.06
ACGTcount: A:0.38, C:0.12, G:0.16, T:0.34
Consensus pattern (39 bp):
ATTAAATGAACAAACATGAACAAGAGTTTCGTTCGTTTA
Found at i:501994 original size:14 final size:14
Alignment explanation
Indices: 501972--502028 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 14
501962 GGTTCGTGAA
*
501972 CGTTCGGTTATGTT
1 CGTTTGGTTATGTT
501986 CGTTTGGTTATGTT
1 CGTTTGGTTATGTT
502000 CG--T--TTATGTT
1 CGTTTGGTTATGTT
* *
502010 CGTTCGATTATGTT
1 CGTTTGGTTATGTT
502024 CGTTT
1 CGTTT
502029 ATGTTCATTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.25
12 1 0.03
14 26 0.72
ACGTcount: A:0.09, C:0.12, G:0.25, T:0.54
Consensus pattern (14 bp):
CGTTTGGTTATGTT
Found at i:502000 original size:24 final size:24
Alignment explanation
Indices: 501973--502047 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
501963 GTTCGTGAAC
* * *
501973 GTTCGGTTATGTTCGTTTGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
501997 GTTCGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
502021 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
502045 GTT
1 GTT
502048 TAACCCAATC
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
23 1 0.02
24 45 0.98
ACGTcount: A:0.12, C:0.11, G:0.21, T:0.56
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:502781 original size:10 final size:10
Alignment explanation
Indices: 502766--502839 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
502756 GGGTCTCCAA
502766 CGTTTATGTT
1 CGTTTATGTT
502776 CGTTTATGTT
1 CGTTTATGTT
502786 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
502797 ATGTTCGTGTT
1 -CGTTTATGTT
502808 CGTTTATGTT
1 CGTTTATGTT
502818 CG----TGTT
1 CGTTTATGTT
502824 C-TTTATGTT
1 CGTTTATGTT
502833 CGTTTAT
1 CGTTTAT
502840 TTATTAAATG
Statistics
Matches: 49, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
6 5 0.10
9 5 0.10
10 28 0.57
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.20, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:502797 original size:16 final size:16
Alignment explanation
Indices: 502772--502843 Score: 105
Period size: 16 Copynumber: 4.7 Consensus size: 16
502762 CCAACGTTTA
*
502772 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
502788 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
502804 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
502820 TGTTC-TTTATGTTCG
1 TGTTCATTTATGTTCG
502835 T-TT-ATTTAT
1 TGTTCATTTAT
502844 TAAATGAACG
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
14 7 0.13
15 11 0.21
16 35 0.66
ACGTcount: A:0.10, C:0.11, G:0.19, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:502813 original size:32 final size:31
Alignment explanation
Indices: 502772--502835 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 31
502762 CCAACGTTTA
502772 TGTTCGTTTATGTTCGTGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCGTGTTC-TTTATGTTCG
502804 TGTTCGTTTATGTTCGTGTTCTTTATGTTCG
1 TGTTCGTTTATGTTCGTGTTCTTTATGTTCG
502835 T
1 T
502836 TTATTTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 11 0.34
32 21 0.66
ACGTcount: A:0.08, C:0.12, G:0.22, T:0.58
Consensus pattern (31 bp):
TGTTCGTTTATGTTCGTGTTCTTTATGTTCG
Found at i:502926 original size:16 final size:16
Alignment explanation
Indices: 502905--502937 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
502895 AAAAAAATTT
502905 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
502921 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
502937 T
1 T
502938 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:506757 original size:20 final size:20
Alignment explanation
Indices: 506732--506769 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
506722 TTTGGTTCAC
506732 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
506752 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
506770 GAAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:507206 original size:506 final size:504
Alignment explanation
Indices: 506245--507206 Score: 1608
Period size: 506 Copynumber: 1.9 Consensus size: 504
506235 TTTGGTTCAC
* * * *
506245 GGAATGTAAGATTACCAGTGGGAATACAAGATTACTGGGAATGTTGTATTTTGTGTTTGGTTGGT
1 GGAATGTAAGATTACCA--GGGAATACAAGATTACAGGGAATATTATATTTTGTGTTTGGTTGGC
506310 TTAGCAGGAATGTAAGATTACCGTATTTGGTTAAAGGAATAAAAGATTATTGAAATGTATATTTG
64 TTAGCAGGAATGTAAGATTACCGTATTTGGTTAAAGGAATAAAAGATTATTGAAATGTATATTTG
*
506375 ACCAAATTGTCATTATATATTTGTATAATATTACAAATTGTAAAATATTTATATATTTTCTTTAA
129 ACCAAATTGTCATTATATATTTGTATAATATTACAAATTGGAAAATATTTATATATTTTCTTTAA
*
506440 AAAATTAAATTCATAATATTTATATAATTTTTTTACAAAATTAAAAATATAAAAAAGGTTGAATG
194 AAAATTAAATTCATAATATTTATATAATTTTTTTACAAAATTAAAAATATAAAAAAGATTGAATG
*
506505 AAAGGGTAAAATTTTTTTAACCCCTAAACTTCATATAAAATTTTAATTATAGATTTTTTTTTGTA
259 AAAGGGTAAAATTTTTTTAACCCCTAAACTTCATATAAAATTTTAATTATAGACTTTTTTTTGTA
*
506570 AATCTAAAATAATTTAAGGATAAATTTGTAATTTAACCTTCGTAGAATTTTTATTATTCAATGAT
324 AATCTAAAATAATTTAAGGATAAATTTGTAATTTAACCTTCGTAGAATTTTTATTATTCAATGAC
* * *
506635 AGAAGAATAATATTTTTGAAAAAAAAATAAAAATTTAAGGGCATTTTAGTTCAAAACGCCGGTAA
389 AGAAGAATAATATTTTTG-AAAAAAAATAAAAATTTAAGGACATTTTAGTCCAAAACACCGGTAA
506700 TGTTACAATACCTAAGGGTGCGTTTGGTTCACGGAATGTAAGATTACCAGTG
453 TGTTACAATACCTAAGGGTGCGTTTGGTTCACGGAATGTAAGATTACCAGTG
* *
506752 GGAATGTAAGATTACCA-GGAA-ATAGGATTACAGGGAATATTATATTTTGTGTTTGGTTGGCTT
1 GGAATGTAAGATTACCAGGGAATACAAGATTACAGGGAATATTATATTTTGTGTTTGGTTGGCTT
*
506815 AGCAGGAATGTAAGATTACCGTGTTTGGTTAAAGGAATAAAAGATTATTGAAATGTATATTTGAC
66 AGCAGGAATGTAAGATTACCGTATTTGGTTAAAGGAATAAAAGATTATTGAAATGTATATTTGAC
*
506880 CAAATTGTCCTTATTATATATTTGTATAATATTACAAGTTGGAAAATATTTATATATTTTCTTTA
131 CAAATTGT-C--ATTATATATTTGTATAATATTACAAATTGGAAAATATTTATATATTTTCTTTA
* *
506945 AAAATTTAAATTCATAATATTTATATATATTTTTTTACAAAATTAAAAATAT-AAAAAGATTTAA
193 AAAAATTAAATTCATAATATTTATATA-ATTTTTTTACAAAATTAAAAATATAAAAAAGATTGAA
* *
507009 TGAAAGGGTAAAATTTTATTTTAACCCCTGAACTTCATATAAAATTTTAATTATATACTTTTTTT
257 TGAAAGGGTAAAA-TTT-TTTTAACCCCTAAACTTCATATAAAATTTTAATTATAGACTTTTTTT
* *
507074 TGTAAATCTATAATAATTTAAGGATAAATTTGTAATTTAACCTTTGTAGAATTTTTATTATTCAA
320 TGTAAATCTAAAATAATTTAAGGATAAATTTGTAATTTAACCTTCGTAGAATTTTTATTATTCAA
* *
507139 TGACAGAAGAATGATGTTTTTG-AAAAAAATAAAAATTTAAGGACATTTTAGTCCAAAACACCGG
385 TGACAGAAGAATAATATTTTTGAAAAAAAATAAAAATTTAAGGACATTTTAGTCCAAAACACCGG
507203 TAAT
450 TAAT
507207 CCAATAATAC
Statistics
Matches: 426, Mismatches: 23, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
503 108 0.25
504 5 0.01
506 143 0.34
507 44 0.10
508 126 0.30
ACGTcount: A:0.39, C:0.07, G:0.14, T:0.39
Consensus pattern (504 bp):
GGAATGTAAGATTACCAGGGAATACAAGATTACAGGGAATATTATATTTTGTGTTTGGTTGGCTT
AGCAGGAATGTAAGATTACCGTATTTGGTTAAAGGAATAAAAGATTATTGAAATGTATATTTGAC
CAAATTGTCATTATATATTTGTATAATATTACAAATTGGAAAATATTTATATATTTTCTTTAAAA
AATTAAATTCATAATATTTATATAATTTTTTTACAAAATTAAAAATATAAAAAAGATTGAATGAA
AGGGTAAAATTTTTTTAACCCCTAAACTTCATATAAAATTTTAATTATAGACTTTTTTTTGTAAA
TCTAAAATAATTTAAGGATAAATTTGTAATTTAACCTTCGTAGAATTTTTATTATTCAATGACAG
AAGAATAATATTTTTGAAAAAAAATAAAAATTTAAGGACATTTTAGTCCAAAACACCGGTAATGT
TACAATACCTAAGGGTGCGTTTGGTTCACGGAATGTAAGATTACCAGTG
Found at i:507479 original size:157 final size:158
Alignment explanation
Indices: 507216--507499 Score: 405
Period size: 157 Copynumber: 1.8 Consensus size: 158
507206 TCCAATAATA
* ***
507216 CCTAAGGAAAGGGAGGTAATGACATTCCCGGTAATATACCCAAAAAATTCACTATTGGTAATCTT
1 CCTAAGGAAAGGGAGGTAATGACATTCCCGGCAATATACCCAAAAAATTCACTATTGGTAATAAA
* * * *
507281 ACATTACCGGTAATGGGATTCCCGGGCTAACCAAACGTGGGAATGT-GGATT-CCATTCCCATGG
66 ACATTACCGGGAATGAGATTCCCGGGCCAACCAAACATGGGAATGTGGGATTCCCA-TCCCATGG
507344 GAATCCAACATTCCCCCATCCAAACACCC
130 GAATCCAACATTCCCCCATCCAAACACCC
*
507373 CCTAAGGGAAGGGAGGTAATGACATTCCCGGCAATATACCCCAAAAAA-TCTACTATTGGTAATA
1 CCTAAGGAAAGGGAGGTAATGACATTCCCGGCAATATA-CCCAAAAAATTC-ACTATTGGTAATA
* * *
507437 AAATATTACTGGGAATGAGATTCTC-GGCCAACCAAACATGGGAATGTGGGATTCCCATCCCAT
64 AAACATTACCGGGAATGAGATTCCCGGGCCAACCAAACATGGGAATGTGGGATTCCCATCCCAT
507500 TGGTAATAAA
Statistics
Matches: 111, Mismatches: 12, Indels: 7
0.85 0.09 0.05
Matches are distributed among these distances:
157 58 0.52
158 50 0.45
159 3 0.03
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.23
Consensus pattern (158 bp):
CCTAAGGAAAGGGAGGTAATGACATTCCCGGCAATATACCCAAAAAATTCACTATTGGTAATAAA
ACATTACCGGGAATGAGATTCCCGGGCCAACCAAACATGGGAATGTGGGATTCCCATCCCATGGG
AATCCAACATTCCCCCATCCAAACACCC
Found at i:517984 original size:13 final size:13
Alignment explanation
Indices: 517966--517991 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
517956 AAGGGAGATG
517966 AACTTATAAAATT
1 AACTTATAAAATT
517979 AACTTATAAAATT
1 AACTTATAAAATT
517992 TTAGAGGGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (13 bp):
AACTTATAAAATT
Found at i:519017 original size:2 final size:2
Alignment explanation
Indices: 519010--519051 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
519000 ACATTCTATC
519010 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
519052 TAGGTAGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:526841 original size:2 final size:2
Alignment explanation
Indices: 526834--526875 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
526824 ACCGTAAACA
526834 AT AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT AT
526876 GAAAAAATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:532034 original size:24 final size:24
Alignment explanation
Indices: 531999--532052 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
531989 AAATAAACGC
* *
531999 ATTTTAAGA-TTTTAAAGAATCAAA
1 ATTTTAACATTTTTAAAAAAT-AAA
*
532023 ATTTTAACATTTTTAAAAAATAAT
1 ATTTTAACATTTTTAAAAAATAAA
532047 ATTTTA
1 ATTTTA
532053 TATGATTGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (24 bp):
ATTTTAACATTTTTAAAAAATAAA
Found at i:535554 original size:29 final size:29
Alignment explanation
Indices: 535511--535571 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
535501 TTTGGATGAA
*
535511 TTTGTGGATGAAATTGGAA-GATTCAAAAG
1 TTTGGGGATGAAATTGGAATG-TTCAAAAG
* *
535540 TTTGGGGATGCAATTGGAATGTTTAAAAG
1 TTTGGGGATGAAATTGGAATGTTCAAAAG
535569 TTT
1 TTT
535572 AAGGATCAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (29 bp):
TTTGGGGATGAAATTGGAATGTTCAAAAG
Found at i:535577 original size:29 final size:29
Alignment explanation
Indices: 535516--535582 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
535506 ATGAATTTGT
* **
535516 GGATGAAATTGGAAGATTCAAAAGTTTGG
1 GGATGCAATTGGAAGATTCAAAAGTTTAA
*
535545 GGATGCAATTGGAATG-TTTAAAAGTTTAA
1 GGATGCAATTGGAA-GATTCAAAAGTTTAA
535574 GGAT-CAATT
1 GGATGCAATT
535583 TAGAATGAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 5 0.15
29 27 0.82
30 1 0.03
ACGTcount: A:0.37, C:0.04, G:0.27, T:0.31
Consensus pattern (29 bp):
GGATGCAATTGGAAGATTCAAAAGTTTAA
Found at i:536254 original size:2 final size:2
Alignment explanation
Indices: 536247--536281 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
536237 CATAAAGGCA
536247 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
536282 GTACAAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:549280 original size:32 final size:32
Alignment explanation
Indices: 549239--549318 Score: 142
Period size: 32 Copynumber: 2.5 Consensus size: 32
549229 CATAGGTATA
549239 CTGTCCATATGTCCCGAAAGACACAGGTAATT
1 CTGTCCATATGTCCCGAAAGACACAGGTAATT
*
549271 CTGTCCATATGTCCCGAAAGACATAGGTAATT
1 CTGTCCATATGTCCCGAAAGACACAGGTAATT
*
549303 ATGTCCATATGTCCCG
1 CTGTCCATATGTCCCG
549319 TAGAATATAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.29, C:0.25, G:0.19, T:0.28
Consensus pattern (32 bp):
CTGTCCATATGTCCCGAAAGACACAGGTAATT
Found at i:549332 original size:32 final size:32
Alignment explanation
Indices: 549228--549318 Score: 141
Period size: 32 Copynumber: 2.9 Consensus size: 32
549218 GTTCCTTATA
549228 ACATAGGT-A-TACTGTCCATATGTCCCGAAAG
1 ACATAGGTAATTA-TGTCCATATGTCCCGAAAG
* *
549259 ACACAGGTAATTCTGTCCATATGTCCCGAAAG
1 ACATAGGTAATTATGTCCATATGTCCCGAAAG
549291 ACATAGGTAATTATGTCCATATGTCCCG
1 ACATAGGTAATTATGTCCATATGTCCCG
549319 TAGAATATAG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
31 7 0.13
32 46 0.85
33 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (32 bp):
ACATAGGTAATTATGTCCATATGTCCCGAAAG
Found at i:550483 original size:19 final size:20
Alignment explanation
Indices: 550451--550488 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
550441 TTCTCTCATC
550451 TCTTCTTCCTTCTT-TCTTA
1 TCTTCTTCCTTCTTCTCTTA
550470 TCTTCTTCAC-TCTTCTCTT
1 TCTTCTTC-CTTCTTCTCTT
550489 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCCTTCTTCTCTTA
Found at i:550991 original size:21 final size:21
Alignment explanation
Indices: 550949--550991 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
550939 TTTCTGGGCT
* *
550949 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
550970 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
550991 A
1 A
550992 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:557280 original size:19 final size:20
Alignment explanation
Indices: 557248--557285 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
557238 TTCTCTCATC
557248 TCTTCTTCCTTCTT-TCTTA
1 TCTTCTTCCTTCTTCTCTTA
557267 TCTTCTTCAC-TCTTCTCTT
1 TCTTCTTC-CTTCTTCTCTT
557286 CTTCCAAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.05, C:0.34, G:0.00, T:0.61
Consensus pattern (20 bp):
TCTTCTTCCTTCTTCTCTTA
Found at i:557786 original size:21 final size:21
Alignment explanation
Indices: 557744--557786 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
557734 TTTCTGGGCT
* *
557744 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
557765 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
557786 A
1 A
557787 CGAATATGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:567395 original size:10 final size:10
Alignment explanation
Indices: 567380--567465 Score: 51
Period size: 10 Copynumber: 9.0 Consensus size: 10
567370 GGTAAAAATT
567380 ATAATAAAAA
1 ATAATAAAAA
*
567390 ATAATAAAAG
1 ATAATAAAAA
567400 ATAA-AATAAA
1 ATAATAA-AAA
*
567410 AT-A-AAATA
1 ATAATAAAAA
567418 AT-ATAATAAA
1 ATAATAA-AAA
*
567428 A-GA-AAAAA
1 ATAATAAAAA
*
567436 ATAACAAAAA
1 ATAATAAAAA
567446 A-AAGTAAAAA
1 ATAA-TAAAAA
*
567456 ATAACAAAAA
1 ATAATAAAAA
567466 CCAAAATCAT
Statistics
Matches: 61, Mismatches: 7, Indels: 16
0.73 0.08 0.19
Matches are distributed among these distances:
8 9 0.15
9 12 0.20
10 38 0.62
11 2 0.03
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.16
Consensus pattern (10 bp):
ATAATAAAAA
Found at i:567427 original size:18 final size:18
Alignment explanation
Indices: 567404--567438 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
567394 TAAAAGATAA
* *
567404 AATAAAATAAAATAATAT
1 AATAAAAGAAAAAAATAT
567422 AATAAAAGAAAAAAATA
1 AATAAAAGAAAAAAATA
567439 ACAAAAAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (18 bp):
AATAAAAGAAAAAAATAT
Found at i:567435 original size:20 final size:20
Alignment explanation
Indices: 567425--567465 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
567415 ATAATATAAT
567425 AAAAGAAAAAAATAACAAAA
1 AAAAGAAAAAAATAACAAAA
*
567445 AAAAGTAAAAAATAACAAAA
1 AAAAGAAAAAAATAACAAAA
567465 A
1 A
567466 CCAAAATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.83, C:0.05, G:0.05, T:0.07
Consensus pattern (20 bp):
AAAAGAAAAAAATAACAAAA
Found at i:568159 original size:16 final size:16
Alignment explanation
Indices: 568138--568172 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
568128 TTAGTATTTT
568138 TTTAATTATTTTATTA
1 TTTAATTATTTTATTA
*
568154 TTTAATTTTTTTATTA
1 TTTAATTATTTTATTA
568170 TTT
1 TTT
568173 TATTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTAATTATTTTATTA
Found at i:568175 original size:21 final size:21
Alignment explanation
Indices: 568133--568194 Score: 70
Period size: 21 Copynumber: 2.8 Consensus size: 21
568123 TTTTGTTAGT
568133 ATTTTTTTAATTATTTTATTATTTA
1 ATTTTTTT-ATTA--TT-TTATTTA
568158 ATTTTTTTATTATTTTATTTA
1 ATTTTTTTATTATTTTATTTA
* *
568179 ATTATTTTATTTTTTT
1 ATTTTTTTATTATTTT
568195 GTAGTTATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 21 0.60
22 2 0.06
24 4 0.11
25 8 0.23
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (21 bp):
ATTTTTTTATTATTTTATTTA
Found at i:568177 original size:16 final size:16
Alignment explanation
Indices: 568132--568194 Score: 60
Period size: 16 Copynumber: 4.1 Consensus size: 16
568122 ATTTTGTTAG
* *
568132 TATTTTTTTAATTATTT
1 TATTATTTT-ATTTTTT
*
568149 TATTATTTAATTTTTT
1 TATTATTTTATTTTTT
568165 TATTATTTTA---TTT
1 TATTATTTTATTTTTT
*
568178 AATTATTTTATTTTTT
1 TATTATTTTATTTTTT
568194 T
1 T
568195 GTAGTTATAA
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
13 12 0.32
16 18 0.49
17 7 0.19
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TATTATTTTATTTTTT
Found at i:568182 original size:13 final size:13
Alignment explanation
Indices: 568132--568190 Score: 72
Period size: 13 Copynumber: 4.8 Consensus size: 13
568122 ATTTTGTTAG
568132 TATTTT-TTTAAT
1 TATTTTATTTAAT
*
568144 TATTTTA-TTATT
1 TATTTTATTTAAT
568156 TAATTTT-TTT-AT
1 T-ATTTTATTTAAT
568168 TATTTTATTTAAT
1 TATTTTATTTAAT
568181 TATTTTATTT
1 TATTTTATTT
568191 TTTTGTAGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
11 5 0.12
12 16 0.40
13 19 0.47
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TATTTTATTTAAT
Done.