Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
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: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 100 of 230
Found at i:28454777 original size:83 final size:82
Alignment explanation
Indices: 28454657--28454836 Score: 297
Period size: 83 Copynumber: 2.2 Consensus size: 82
28454647 TTATTAAGTC
* * *
28454657 CGCACACTCAGTGCTATATAATCAACTCGCACACTTAGTGCTACATAATCATACTCGCACACTTA
1 CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
28454722 GTGCTACATAGTCAACT
66 GTGCTACATAGTCAACT
* *
28454739 CGCACACTTAGTGCTACATAGTCAAACTCGCACACTTAGTGCTACATAGTCAAACTCGCACACTT
1 CGCACACTTAGTGCTACATAATC-AACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTT
*
28454804 AGTGCTACATAGTCAATT
65 AGTGCTACATAGTCAACT
28454822 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28454837 GCACAATTTA
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 20 0.22
83 71 0.78
ACGTcount: A:0.31, C:0.29, G:0.14, T:0.27
Consensus pattern (82 bp):
CGCACACTTAGTGCTACATAATCAACTCGCACACTTAGTGCTACATAATCAAACTCGCACACTTA
GTGCTACATAGTCAACT
Found at i:28466969 original size:24 final size:27
Alignment explanation
Indices: 28466917--28466971 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
28466907 TTGTACCGAG
28466917 TTTGTTTGTTCTTGTAAATACTTTATTC
1 TTTGTTTGTTCTTG-AAATACTTTATTC
28466945 TTTG-TTGTTCTTG-AATACTTT-TTC
1 TTTGTTTGTTCTTGAAATACTTTATTC
28466969 TTT
1 TTT
28466972 TCAAGACACT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 6 0.22
25 8 0.30
27 9 0.33
28 4 0.15
ACGTcount: A:0.15, C:0.11, G:0.11, T:0.64
Consensus pattern (27 bp):
TTTGTTTGTTCTTGAAATACTTTATTC
Found at i:28467841 original size:44 final size:43
Alignment explanation
Indices: 28467786--28468460 Score: 281
Period size: 44 Copynumber: 15.6 Consensus size: 43
28467776 CCGATAATCC
* *
28467786 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTTGGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACC-TAGATCT
* * *** *
28467830 TATCTCTCTGAAGATGCAG-AGAGCAGA-TCGCATCTAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTAGATCT
* * * *
28467870 TATCT-TCTTGGAGTTGTAGTGGAGCAGACTAAGTAAGCTAG-TCT
1 TATCTCTC-TGAAGTTGCAGTGGAGCAGATTAA--AACCTAGATCT
* * ** *
28467914 TATC-CTTCTGAAGCTACAGT-GAGGCAGATTGAAGATGGC-AAATCT
1 TATCTC-TCTGAAGTTGCAGTGGA-GCAGATT-AA-A-ACCTAGATCT
* * * *
28467959 TATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCGATA-ATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACC--TAGATCT
* *
28468003 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACC-TAGATCT
* * *** *
28468047 TATCTCTCTGAAGATGCAG-AGAGCAGA-TCGCATCTAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTAGATCT
* * * *
28468087 TATCTC-CTTGGAGTTGCAGTGGAGCAGACTAAGTAAGCAAG-TCT
1 TATCTCTC-TGAAGTTGCAGTGGAGCAGATTAA--AACCTAGATCT
* * *
28468131 TATC-CTCCTGAAGTTGCAAT-GAGGCAGACTGAAGATGA-C-AAATCT
1 TATCTCT-CTGAAGTTGCAGTGGA-GCAGA-TTAA-A--ACCTAGATCT
* * * *
28468176 TATCTCCCTGAGGTTGCAGTGGAGCAGATTAAAGCCGATA-ATCC
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACC--TAGATCT
* * *
28468220 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACC-TAGATCT
* * *** *
28468264 TATCTCTCTGAATTTGCAG-AGAGCAGA-TCGCATCTAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTAGATCT
* * * * *
28468304 TATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTAAACAAG-TCT
1 TATCTCTCTGAAGTTGCAGTGGAGCAGATTAA--AACCTAGATCT
* *** *
28468348 TATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGGAGATGGC-AAATCT
1 TATCTCT-CTGAAGTTGCAGTGGA-GCAGA-T-TA-AAACCTAGATCT
* * *
28468393 TATCTC-CTTAAAGTTGCAGTGGAGCAAATTAAAGCCGATA-ATCT
1 TATCTCTC-TGAAGTTGCAGTGGAGCAGATTAAAACC--TAGATCT
*
28468437 TATCTCCCTGAAGTTGCAGTGGAG
1 TATCTCTCTGAAGTTGCAGTGGAG
28468461 TAGACCCGAG
Statistics
Matches: 477, Mismatches: 101, Indels: 106
0.70 0.15 0.15
Matches are distributed among these distances:
39 3 0.01
40 53 0.11
41 28 0.06
42 18 0.04
43 33 0.07
44 246 0.52
45 84 0.18
46 11 0.02
47 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (43 bp):
TATCTCTCTGAAGTTGCAGTGGAGCAGATTAAAACCTAGATCT
Found at i:28468156 original size:217 final size:217
Alignment explanation
Indices: 28467775--28468460 Score: 1156
Period size: 217 Copynumber: 3.2 Consensus size: 217
28467765 CAGATCGGTG
*
28467775 GCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTTGGATCTTATCTCTCTG
1 GCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTG
* *
28467840 AAGATGCAGAGAGCAGATCGCATCTAGTCTTATCTTCTTGGAGTTGTAGTGGAGCAGACTAAGTA
66 AAGATGCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGGAGTTGCAGTGGAGCAGACTAAGTA
* * * * *
28467905 AGCTAGTCTTATCCTTCTGAAGCTACAGTGAGGCAGATTGAAGATGGCAAATCTTATCTCCCTGA
131 AGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGA
*
28467970 AGTTGTAGTGGAGCAGATTAAA
196 AGTTGCAGTGGAGCAGATTAAA
*
28467992 GCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTAGATCTTATCTCTCTG
1 GCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTG
28468057 AAGATGCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGGAGTTGCAGTGGAGCAGACTAAGTA
66 AAGATGCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGGAGTTGCAGTGGAGCAGACTAAGTA
* *
28468122 AGCAAGTCTTATCCTCCTGAAGTTGCAATGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGA
131 AGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGA
*
28468187 GGTTGCAGTGGAGCAGATTAAA
196 AGTTGCAGTGGAGCAGATTAAA
28468209 GCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTG
1 GCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTG
** * * *
28468274 AATTTGCAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAATGGAGCAGACTAAGTA
66 AAGATGCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGGAGTTGCAGTGGAGCAGACTAAGTA
* * * *
28468339 AACAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGGAGATGGCAAATCTTATCTCCTTAA
131 AGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGA
*
28468404 AGTTGCAGTGGAGCAAATTAAA
196 AGTTGCAGTGGAGCAGATTAAA
*
28468426 GCCGATAATCTTATCTCCCTGAAGTTGCAGTGGAG
1 GCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAG
28468461 TAGACCCGAG
Statistics
Matches: 441, Mismatches: 28, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
217 441 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (217 bp):
GCCGATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGGATCTTATCTCTCTG
AAGATGCAGAGAGCAGATCGCATCTAGTCTTATCTCCTTGGAGTTGCAGTGGAGCAGACTAAGTA
AGCAAGTCTTATCCTCCTGAAGTTGCAGTGAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGA
AGTTGCAGTGGAGCAGATTAAA
Found at i:28470013 original size:17 final size:16
Alignment explanation
Indices: 28470004--28470049 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
28469994 ATATATGTTG
28470004 TTTTTATATACATATT
1 TTTTTATATACATATT
*
28470020 TTTTTATA-A-GTAATT
1 TTTTTATATACAT-ATT
*
28470035 TTTTTATATTCATAT
1 TTTTTATATACATAT
28470050 ATATACACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
14 1 0.04
15 12 0.50
16 10 0.42
17 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.02, T:0.63
Consensus pattern (16 bp):
TTTTTATATACATATT
Found at i:28472910 original size:11 final size:11
Alignment explanation
Indices: 28472883--28472933 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
28472873 TTTATATTTT
28472883 TAAAAAAA-TA
1 TAAAAAAATTA
* *
28472893 TATAAAAATTC
1 TAAAAAAATTA
*
28472904 TAAAAAAATTT
1 TAAAAAAATTA
28472915 TAAAAAAATATA
1 TAAAAAAAT-TA
28472927 TAAAAAA
1 TAAAAAA
28472934 GTTCAAATTT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
10 7 0.21
11 19 0.56
12 8 0.24
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
TAAAAAAATTA
Found at i:28473020 original size:3 final size:3
Alignment explanation
Indices: 28473012--28473049 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
28473002 CTCAAGAATC
28473012 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
28473050 TTGCTTTGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:28477119 original size:40 final size:40
Alignment explanation
Indices: 28477048--28477125 Score: 93
Period size: 40 Copynumber: 1.9 Consensus size: 40
28477038 GATGTCAGGG
* * * *
28477048 GATGTGTCAGCAAAGCGCGGCCACGTCAGCGCGCTTTGAT
1 GATGTGGCAACAAAGCGCGGCCACGACAGCGCGATTTGAT
** *
28477088 GATGTGGCAACAAAGCGCGGCCTTGAGAGCGCGATTTG
1 GATGTGGCAACAAAGCGCGGCCACGACAGCGCGATTTG
28477126 TTGCCACGTC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.22, C:0.24, G:0.35, T:0.19
Consensus pattern (40 bp):
GATGTGGCAACAAAGCGCGGCCACGACAGCGCGATTTGAT
Found at i:28477334 original size:23 final size:23
Alignment explanation
Indices: 28477303--28477358 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
28477293 AAACAAATCC
*
28477303 TCTCTCAAATTTCCTTTC-AATT
1 TCTCTCAAATTTCCTTCCAAATT
28477325 TCCTCTCAAA-TTCCTTCCAAATT
1 T-CTCTCAAATTTCCTTCCAAATT
28477348 TCTCTCAAATT
1 TCTCTCAAATT
28477359 CATATTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 16 0.53
23 14 0.47
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (23 bp):
TCTCTCAAATTTCCTTCCAAATT
Found at i:28477356 original size:11 final size:11
Alignment explanation
Indices: 28477303--28477358 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
28477293 AAACAAATCC
28477303 TCTCTCAAATT
1 TCTCTCAAATT
*
28477314 TCCTTTC-AATT
1 T-CTCTCAAATT
28477325 TCCTCTCAAATT
1 T-CTCTCAAATT
*
28477337 CCT-TCCAAATT
1 TCTCT-CAAATT
28477348 TCTCTCAAATT
1 TCTCTCAAATT
28477359 CATATTTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 1 0.03
11 27 0.73
12 9 0.24
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:28477717 original size:11 final size:12
Alignment explanation
Indices: 28477668--28477719 Score: 67
Period size: 11 Copynumber: 4.6 Consensus size: 12
28477658 AAATCCTCTG
28477668 TCAAATTTCCTC
1 TCAAATTTCCTC
28477680 TC-AATTTCCTC
1 TCAAATTTCCTC
28477691 TC-AATTTCCT-
1 TCAAATTTCCTC
28477701 TCCAAATTT-CTC
1 T-CAAATTTCCTC
28477713 TCAAATT
1 TCAAATT
28477720 CATAGTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
10 1 0.03
11 28 0.76
12 8 0.22
ACGTcount: A:0.25, C:0.31, G:0.00, T:0.44
Consensus pattern (12 bp):
TCAAATTTCCTC
Found at i:28477786 original size:361 final size:363
Alignment explanation
Indices: 28477082--28477808 Score: 1235
Period size: 363 Copynumber: 2.0 Consensus size: 363
28477072 GTCAGCGCGC
*
28477082 TTTGATGATGTGGCAACAAAGCGCGGCCTTGAGAGCGCGATTTGTTGCCACGTCAGCAAAGCAGT
1 TTTGATGACGTGGCAACAAAGCGCGGCCTTGAGAGCGCGATTTGTTGCCACGTCAGCAAAGCAGT
* * * * * *
28477147 CTGACATGGCCGTGATTTGATGATGTGGCGCGTCCTTGGGGACGCGATTTAGACTGCACGTGAAC
66 CTGACATGGCCGCGATTTGATGACGTGGCACATCCCTGGGGACGCGATTTAGACCGCACGTGAAC
*
28477212 AGTGCAACGGTCAAAAATTTGACCATTGCCCCCCCAACGGTAAAAAAAACCCTATAAATACCCCC
131 AGTGCAACGGTCAAAAATTTGACCATTGCCCCCCCAACAGTAAAAAAAACCCTATAAATACCCCC
*
28477277 ACCCCTTTTTTTTCACAAACAAATCCTCTCTCAAATTTCCTTTCAATTTCCTCTCAAATTCCTTC
196 ACCCCTTTTTTTTCACAAACAAATCCTCTCTCAAATTTCCTCTCAATTTCCTCTCAAATTCCTTC
*
28477342 CAAATTTCTCTCAAATTCATATTTAATCTCAATTAGCTCTCAATTTCCTTTTAAATTTCTCTTAA
261 CAAATTTCTCTCAAATTCATAGTTAATCTCAATTAGCTCTCAATTTCCTTTTAAATTTCTCTTAA
**
28477407 ATCCCTATTTTCAAATAATTTTAAAATTTTTTGATTTT
326 ATCCCTATTTTCAAATAATTTTAAAAAATTTTGATTTT
** *
28477445 TTTGATGACGTGGCAACAAAGCGTTGCCTTGAGAGCGCGATTTGTTGCCATGTCAGCAAAGC-GC
1 TTTGATGACGTGGCAACAAAGCGCGGCCTTGAGAGCGCGATTTGTTGCCACGTCAGCAAAGCAG-
* *
28477509 TCTGACGTGGCCGCGATTTGATGACGTGGCACATCCCTGGGGACGCGATTTAGACCGCGCGTGAA
65 TCTGACATGGCCGCGATTTGATGACGTGGCACATCCCTGGGGACGCGATTTAGACCGCACGTGAA
*
28477574 CAGTGCAACGGTCAAAAATTTGACCGTTGCCCCCCCAACAGTAAAAAAAA-CCTATAAATACCCC
130 CAGTGCAACGGTCAAAAATTTGACCATTGCCCCCCCAACAGTAAAAAAAACCCTATAAATACCCC
* *
28477638 CA-CCCTTTTTTTTCACAAACAAATCCTCTGTCAAATTTCCTCTCAATTTCCTCTCAATTTCCTT
195 CACCCCTTTTTTTTCACAAACAAATCCTCTCTCAAATTTCCTCTCAATTTCCTCTCAAATTCCTT
28477702 CCAAATTTCTCTCAAATTCATAGTTAATCTCAATTAGCTCTCAATTTCCTTTTAAATTTCTCTTA
260 CCAAATTTCTCTCAAATTCATAGTTAATCTCAATTAGCTCTCAATTTCCTTTTAAATTTCTCTTA
*
28477767 AATCCCTATTTTTAAATAATTTTAAAAAATTTTGATTTT
325 AATCCCTATTTTCAAATAATTTTAAAAAATTTTGATTTT
28477806 TTT
1 TTT
28477809 AAACCGAAAA
Statistics
Matches: 342, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
361 162 0.47
362 17 0.05
363 163 0.48
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (363 bp):
TTTGATGACGTGGCAACAAAGCGCGGCCTTGAGAGCGCGATTTGTTGCCACGTCAGCAAAGCAGT
CTGACATGGCCGCGATTTGATGACGTGGCACATCCCTGGGGACGCGATTTAGACCGCACGTGAAC
AGTGCAACGGTCAAAAATTTGACCATTGCCCCCCCAACAGTAAAAAAAACCCTATAAATACCCCC
ACCCCTTTTTTTTCACAAACAAATCCTCTCTCAAATTTCCTCTCAATTTCCTCTCAAATTCCTTC
CAAATTTCTCTCAAATTCATAGTTAATCTCAATTAGCTCTCAATTTCCTTTTAAATTTCTCTTAA
ATCCCTATTTTCAAATAATTTTAAAAAATTTTGATTTT
Found at i:28479648 original size:18 final size:18
Alignment explanation
Indices: 28479621--28479658 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
28479611 CAGGTGCGTT
* *
28479621 TCCTAGCCCTTTTATGTA
1 TCCTAACCCTTATATGTA
28479639 TCCTAACCCTTATATGTA
1 TCCTAACCCTTATATGTA
28479657 TC
1 TC
28479659 TTTTTCCCAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.29, G:0.08, T:0.42
Consensus pattern (18 bp):
TCCTAACCCTTATATGTA
Found at i:28480311 original size:22 final size:22
Alignment explanation
Indices: 28480286--28480580 Score: 252
Period size: 22 Copynumber: 12.9 Consensus size: 22
28480276 AAAAAAGGGT
* * *
28480286 AACCTTTACCTTAAAAACCCCA
1 AACCTTAAACTTAAAAACCCTA
* * *
28480308 AACCCTAAACCTAAAAACCATA
1 AACCTTAAACTTAAAAACCCTA
* *
28480330 AGCCCTAAACTTAAAAACCCTA
1 AACCTTAAACTTAAAAACCCTA
* *
28480352 AACCTTAAACATAAAAACCTTA
1 AACCTTAAACTTAAAAACCCTA
* *
28480374 AACCCTAAACTTAAAAACCCCA
1 AACCTTAAACTTAAAAACCCTA
28480396 AACCTTAAACTTAAAAACCTTAAACCCTA
1 AACCTTAAACTT---AA----AAACCCTA
*
28480425 AACCCTAAACTTAAAAACCCTA
1 AACCTTAAACTTAAAAACCCTA
* **
28480447 AACCTTAAACATAAAAACATTA
1 AACCTTAAACTTAAAAACCCTA
* *
28480469 AACCCT-AACTTAAAAACCCCA
1 AACCTTAAACTTAAAAACCCTA
28480490 AACCTTAAACTTAAAAACTTTAAACCCTA
1 AACCTTAAACTT---AA----AAACCCTA
* *
28480519 AACCCTAAACTTAAAAACCCCA
1 AACCTTAAACTTAAAAACCCTA
*
28480541 ACCCTTAAACTTAAAAACCCTA
1 AACCTTAAACTTAAAAACCCTA
*
28480563 ACCCTT-AACTTAAAAACC
1 AACCTTAAACTTAAAAACC
28480581 ACAAAACATA
Statistics
Matches: 222, Mismatches: 36, Indels: 31
0.77 0.12 0.11
Matches are distributed among these distances:
21 28 0.13
22 150 0.68
25 4 0.02
26 4 0.02
29 36 0.16
ACGTcount: A:0.49, C:0.31, G:0.00, T:0.20
Consensus pattern (22 bp):
AACCTTAAACTTAAAAACCCTA
Found at i:28480343 original size:44 final size:44
Alignment explanation
Indices: 28480295--28480665 Score: 318
Period size: 44 Copynumber: 8.0 Consensus size: 44
28480285 TAACCTTTAC
* *
28480295 CTTAAAAACCCCAAACCCTAAACCTAAAAACCATAAGCCCTAAA
1 CTTAAAAACCCCAAACCCTAAACTTAAAAACCATAAACCCTAAA
* * * *
28480339 CTTAAAAACCCTAAACCTTAAACATAAAAACCTTAAACCCTAAA
1 CTTAAAAACCCCAAACCCTAAACTTAAAAACCATAAACCCTAAA
*
28480383 CTTAAAAACCCCAAACCTTAAACTTAAAAACCTTAAACCCTAAACCCTAAA
1 CTTAAAAACCCCAAACCCTAAACTTAAAAACC----A---TAAACCCTAAA
* * *
28480434 CTTAAAAACCCTAAACCTTAAACATAAAAA-CATTAAACCCT-AA
1 CTTAAAAACCCCAAACCCTAAACTTAAAAACCA-TAAACCCTAAA
* *
28480477 CTTAAAAACCCCAAACCTTAAACTTAAAAACTTTAAACCCTAAACCCTAAA
1 CTTAAAAACCCCAAACCCTAAACTT---AA----AAACCATAAACCCTAAA
* *
28480528 CTTAAAAACCCC-AACCCTTAAACTTAAAAACCCT-AACCCTTAA
1 CTTAAAAACCCCAAACCC-TAAACTTAAAAACCATAAACCCTAAA
* *
28480571 CTTAAAAACCACAAAACATAAACCCTAAACCTAAAAACCATAAACCATAAA
1 CTTAAAAACC-C----C--AAACCCTAAACTTAAAAACCATAAACCCTAAA
* ** * *
28480622 CCTAAAAACCTTAAACCCTAAATTTAAAAACCCTAAACCCTAAA
1 CTTAAAAACCCCAAACCCTAAACTTAAAAACCATAAACCCTAAA
28480666 ACCTTAACTT
Statistics
Matches: 274, Mismatches: 27, Indels: 52
0.78 0.08 0.15
Matches are distributed among these distances:
43 43 0.16
44 113 0.41
46 3 0.01
48 3 0.01
50 30 0.11
51 82 0.30
ACGTcount: A:0.51, C:0.30, G:0.00, T:0.19
Consensus pattern (44 bp):
CTTAAAAACCCCAAACCCTAAACTTAAAAACCATAAACCCTAAA
Found at i:28480360 original size:7 final size:7
Alignment explanation
Indices: 28480344--28480456 Score: 61
Period size: 7 Copynumber: 15.6 Consensus size: 7
28480334 CTAAACTTAA
*
28480344 AAACCCT
1 AAACCTT
28480351 AAACCTT
1 AAACCTT
* *
28480358 AAACATAA
1 AAACCT-T
28480366 AAACCTT
1 AAACCTT
*
28480373 AAACCCT
1 AAACCTT
28480380 AAA-CTT
1 AAACCTT
**
28480386 AAAAACCCC
1 --AAACCTT
28480395 AAACCTT
1 AAACCTT
28480402 AAA-CTT
1 AAACCTT
28480408 AAAAACCTT
1 --AAACCTT
*
28480417 AAACCCT
1 AAACCTT
*
28480424 AAACCCT
1 AAACCTT
28480431 AAA-CTT
1 AAACCTT
*
28480437 AAAAACCCT
1 --AAACCTT
28480446 AAACCTT
1 AAACCTT
28480453 AAAC
1 AAAC
28480457 ATAAAAACAT
Statistics
Matches: 81, Mismatches: 15, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
6 7 0.09
7 54 0.67
8 14 0.17
9 6 0.07
ACGTcount: A:0.50, C:0.30, G:0.00, T:0.19
Consensus pattern (7 bp):
AAACCTT
Found at i:28480376 original size:29 final size:29
Alignment explanation
Indices: 28480344--28480476 Score: 90
Period size: 29 Copynumber: 4.3 Consensus size: 29
28480334 CTAAACTTAA
28480344 AAACCCTAAACCTTAAACATAAAAACCTT
1 AAACCCTAAACCTTAAACATAAAAACCTT
* ***
28480373 AAACCCTAAA-CTTAAAAACCCCAAACCTT
1 AAACCCTAAACCTTAAACA-TAAAAACCTT
* * *
28480402 AAA-CTTAAAAACCTTAAACCCTAAACCCTAAACTT
1 AAACCCT--AAACCTTAAA-CATAAA----AACCTT
*
28480437 AAAAACCCTAAACCTTAAACATAAAAACATT
1 --AAACCCTAAACCTTAAACATAAAAACCTT
28480468 AAACCCTAA
1 AAACCCTAA
28480477 CTTAAAAACC
Statistics
Matches: 77, Mismatches: 15, Indels: 24
0.66 0.13 0.21
Matches are distributed among these distances:
28 9 0.12
29 29 0.38
30 3 0.04
31 11 0.14
35 10 0.13
36 10 0.13
37 3 0.04
38 2 0.03
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.20
Consensus pattern (29 bp):
AAACCCTAAACCTTAAACATAAAAACCTT
Found at i:28480377 original size:51 final size:50
Alignment explanation
Indices: 28480322--28480559 Score: 277
Period size: 51 Copynumber: 5.0 Consensus size: 50
28480312 CTAAACCTAA
* *
28480322 AAACCATAAGCCCTAAACTTAAAAACCCTAAACCTTAAACATAAAAACCTT
1 AAACCATAA-CCCTAAACTTAAAAACCCCAAACCTTAAACTTAAAAACCTT
28480373 -----A-AACCCTAAACTTAAAAACCCCAAACCTTAAACTTAAAAACCTT
1 AAACCATAACCCTAAACTTAAAAACCCCAAACCTTAAACTTAAAAACCTT
* * * *
28480417 AAACCCTAAACCCTAAACTTAAAAACCCTAAACCTTAAACATAAAAACATT
1 AAACCAT-AACCCTAAACTTAAAAACCCCAAACCTTAAACTTAAAAACCTT
*
28480468 -----A-AACCCT-AACTTAAAAACCCCAAACCTTAAACTTAAAAACTTT
1 AAACCATAACCCTAAACTTAAAAACCCCAAACCTTAAACTTAAAAACCTT
* *
28480511 AAACCCTAAACCCTAAACTTAAAAACCCCAACCCTTAAACTTAAAAACC
1 AAACCAT-AACCCTAAACTTAAAAACCCCAAACCTTAAACTTAAAAACC
28480560 CTAACCCTTA
Statistics
Matches: 159, Mismatches: 13, Indels: 30
0.79 0.06 0.15
Matches are distributed among these distances:
43 33 0.21
44 45 0.28
45 2 0.01
46 1 0.01
50 6 0.04
51 72 0.45
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.20
Consensus pattern (50 bp):
AAACCATAACCCTAAACTTAAAAACCCCAAACCTTAAACTTAAAAACCTT
Found at i:28480522 original size:29 final size:28
Alignment explanation
Indices: 28480388--28480476 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 28
28480378 CTAAACTTAA
*
28480388 AAACCCCAAACCTTAAACTTAAAAACCTT
1 AAACCCTAAACCTTAAACTTAAAAA-CTT
*
28480417 AAACCCTAAACCCTAAACTT---AA---
1 AAACCCTAAACCTTAAACTTAAAAACTT
*
28480439 AAACCCTAAACCTTAAACATAAAAACATT
1 AAACCCTAAACCTTAAACTTAAAAAC-TT
28480468 AAACCCTAA
1 AAACCCTAA
28480477 CTTAAAAACC
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
22 18 0.37
25 2 0.04
26 2 0.04
29 27 0.55
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (28 bp):
AAACCCTAAACCTTAAACTTAAAAACTT
Found at i:28480524 original size:94 final size:94
Alignment explanation
Indices: 28480322--28480664 Score: 438
Period size: 94 Copynumber: 3.6 Consensus size: 94
28480312 CTAAACCTAA
* *
28480322 AAACCATAAGCCCTAAACTTAAAAACCCTAAACCTTAAACATAAAAACCTTAAACCCTAAACTTA
1 AAACCATAAACCCTAAACTTAAAAACCCTAAACCTTAAACATAAAAACCCTAAACCCT-AACTTA
*
28480387 AAAACCCCAAACCTTAAACTTAAAAACCTT
65 AAAACCCCAAACCTTAAACTTAAAAACTTT
* **
28480417 AAACCCTAAACCCTAAACTTAAAAACCCTAAACCTTAAACATAAAAACATTAAACCCTAACTTAA
1 AAACCATAAACCCTAAACTTAAAAACCCTAAACCTTAAACATAAAAACCCTAAACCCTAACTTAA
28480482 AAACCCCAAACCTTAAACTTAAAAACTTT
66 AAACCCCAAACCTTAAACTTAAAAACTTT
* * * *
28480511 AAACCCTAAACCCTAAACTTAAAAACCCCAACCCTTAAACTTAAAAACCCT-AACCCTTAACTTA
1 AAACCATAAACCCTAAACTTAAAAACCCTAAACCTTAAACATAAAAACCCTAAACCC-TAACTTA
* * * * * **
28480575 AAAACCACAAAACATAAACCCT-AAACCTAA
65 AAAACCCCAAACCTTAAA-CTTAAAAACTTT
* * * * **
28480605 AAACCATAAACCATAAACCTAAAAACCTTAAACCCTAAATTTAAAAACCCTAAACCCTAA
1 AAACCATAAACCCTAAACTTAAAAACCCTAAACCTTAAACATAAAAACCCTAAACCCTAA
28480665 AACCTTAACT
Statistics
Matches: 221, Mismatches: 24, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
93 5 0.02
94 154 0.70
95 62 0.28
ACGTcount: A:0.51, C:0.29, G:0.00, T:0.19
Consensus pattern (94 bp):
AAACCATAAACCCTAAACTTAAAAACCCTAAACCTTAAACATAAAAACCCTAAACCCTAACTTAA
AAACCCCAAACCTTAAACTTAAAAACTTT
Found at i:28480527 original size:29 final size:29
Alignment explanation
Indices: 28480482--28480538 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
28480472 CCTAACTTAA
* * **
28480482 AAACCCCAAACCTTAAACTTAAAAACTTT
1 AAACCCTAAACCCTAAACTTAAAAACCCT
28480511 AAACCCTAAACCCTAAACTTAAAAACCC
1 AAACCCTAAACCCTAAACTTAAAAACCC
28480539 CAACCCTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.49, C:0.32, G:0.00, T:0.19
Consensus pattern (29 bp):
AAACCCTAAACCCTAAACTTAAAAACCCT
Found at i:28480586 original size:29 final size:29
Alignment explanation
Indices: 28480562--28480627 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
28480552 TAAAAACCCT
* *
28480562 AACCCTTAACTTAAAAACCACAAAACATA
1 AACCCTAAACCTAAAAACCACAAAACATA
* *
28480591 AACCCTAAACCTAAAAACCATAAACCATA
1 AACCCTAAACCTAAAAACCACAAAACATA
28480620 AA-CCTAAA
1 AACCCTAAA
28480628 AACCTTAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (29 bp):
AACCCTAAACCTAAAAACCACAAAACATA
Found at i:28480593 original size:43 final size:44
Alignment explanation
Indices: 28480511--28480665 Score: 123
Period size: 43 Copynumber: 3.4 Consensus size: 44
28480501 TAAAAACTTT
* ** *
28480511 AAACCCTAAACCCTAAACTTAAAAACCCCAACCCTTAAACTTAA
1 AAACCCTAAACCCTAAACTTAAAAACCACAAAACATAAACTTAA
*
28480555 AAACCCT-AACCCTTAACTTAAAAACCACAAAACATAAACCCTAAACCTAA
1 AAACCCTAAACCCTAAACTTAAAAACCACAAAACATAAA--CT-----TAA
* * * ** * * *
28480605 AAACCATAAACCATAAACCTAAAAACCTTAAACCCTAAATTTAA
1 AAACCCTAAACCCTAAACTTAAAAACCACAAAACATAAACTTAA
28480649 AAACCCTAAACCCTAAA
1 AAACCCTAAACCCTAAA
28480666 ACCTTAACTT
Statistics
Matches: 87, Mismatches: 16, Indels: 16
0.73 0.13 0.13
Matches are distributed among these distances:
43 26 0.30
44 25 0.29
45 2 0.02
49 1 0.01
50 9 0.10
51 24 0.28
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.17
Consensus pattern (44 bp):
AAACCCTAAACCCTAAACTTAAAAACCACAAAACATAAACTTAA
Found at i:28480614 original size:15 final size:15
Alignment explanation
Indices: 28480590--28480666 Score: 61
Period size: 15 Copynumber: 5.1 Consensus size: 15
28480580 CACAAAACAT
28480590 AAACCCTAAACCTAA
1 AAACCCTAAACCTAA
* *
28480605 AAACCATAAACC-AT
1 AAACCCTAAACCTAA
*
28480619 AAA-CCTAAAAACCT-T
1 AAACCCT--AAACCTAA
**
28480634 AAACCCTAAATTTAA
1 AAACCCTAAACCTAA
28480649 AAACCCTAAACCCTAA
1 AAACCCTAAA-CCTAA
28480665 AA
1 AA
28480667 CCTTAACTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
13 2 0.04
14 8 0.17
15 30 0.62
16 8 0.17
ACGTcount: A:0.55, C:0.29, G:0.00, T:0.17
Consensus pattern (15 bp):
AAACCCTAAACCTAA
Found at i:28480615 original size:22 final size:22
Alignment explanation
Indices: 28480583--28480665 Score: 114
Period size: 22 Copynumber: 3.8 Consensus size: 22
28480573 TAAAAACCAC
28480583 AAAA-CATAAACCCTAAACCTA
1 AAAACCATAAACCCTAAACCTA
*
28480604 AAAACCATAAACCATAAACCTA
1 AAAACCATAAACCCTAAACCTA
* **
28480626 AAAACCTTAAACCCTAAATTTA
1 AAAACCATAAACCCTAAACCTA
*
28480648 AAAACCCTAAACCCTAAA
1 AAAACCATAAACCCTAAA
28480666 ACCTTAACTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
21 4 0.07
22 51 0.93
ACGTcount: A:0.55, C:0.28, G:0.00, T:0.17
Consensus pattern (22 bp):
AAAACCATAAACCCTAAACCTA
Found at i:28480659 original size:29 final size:28
Alignment explanation
Indices: 28480627--28480693 Score: 80
Period size: 30 Copynumber: 2.3 Consensus size: 28
28480617 ATAAACCTAA
28480627 AAACCTTAAACCCTAAATTTAAAAACCCT
1 AAACCTTAAACCCTAAATTT-AAAACCCT
* * *
28480656 AAACCCTAAAACCTTAACTTTAAAACCCT
1 AAA-CCTTAAACCCTAAATTTAAAACCCT
*
28480685 AACCCTTAA
1 AAACCTTAA
28480694 GTTAAATATA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
28 5 0.16
29 13 0.41
30 14 0.44
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.24
Consensus pattern (28 bp):
AAACCTTAAACCCTAAATTTAAAACCCT
Found at i:28480667 original size:15 final size:15
Alignment explanation
Indices: 28480590--28480690 Score: 52
Period size: 15 Copynumber: 6.9 Consensus size: 15
28480580 CACAAAACAT
28480590 AAACCCTAAA-CCTAA
1 AAACCCTAAACCCT-A
* *
28480605 AAACCATAAACCAT-
1 AAACCCTAAACCCTA
* *
28480619 AAA-CCTAAAAACCTT
1 AAACCCT-AAACCCTA
**
28480634 AAACCCTAAA-TTTAA
1 AAACCCTAAACCCT-A
28480649 AAACCCTAAACCCTA
1 AAACCCTAAACCCTA
* **
28480664 AAA-CCTTAACTTTA
1 AAACCCTAAACCCTA
28480678 AAACCCT-AACCCT
1 AAACCCTAAACCCT
28480691 TAAGTTAAAT
Statistics
Matches: 64, Mismatches: 15, Indels: 15
0.68 0.16 0.16
Matches are distributed among these distances:
13 2 0.03
14 24 0.38
15 32 0.50
16 6 0.09
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.20
Consensus pattern (15 bp):
AAACCCTAAACCCTA
Found at i:28496447 original size:39 final size:40
Alignment explanation
Indices: 28496404--28496571 Score: 139
Period size: 40 Copynumber: 4.2 Consensus size: 40
28496394 CTCGTTCAAG
* * * *
28496404 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
28496443 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
28496483 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* ** * *
28496523 GGCCTTCGGGACTTAACCCGGAATTA-ATGACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
28496563 TGCCTTCGG
1 TGCCTTCGG
28496572 ATCTTAGTCC
Statistics
Matches: 110, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
39 26 0.24
40 80 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:28496556 original size:80 final size:80
Alignment explanation
Indices: 28496439--28496624 Score: 220
Period size: 80 Copynumber: 2.3 Consensus size: 80
28496429 AGTAACTCAT
* * *
28496439 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
28496503 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
* **
28496518 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATGACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
28496582 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
28496599 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
28496625 CAGCATTCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
79 11 0.12
80 71 0.76
81 10 0.11
82 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:28496584 original size:40 final size:39
Alignment explanation
Indices: 28496441--28496624 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
28496431 TAACTCATAC
* * *
28496441 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAATACTCGCACA
*
28496481 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAATA-CTCGCACA
*
28496521 AAGGCCTTCGGGACTTAACCCGGAATTAATGACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAAT-ACTCGCACA
** * *
28496561 AATGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGAAT-TAAT-AC-TCGCACA
*
28496602 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28496625 CAGCATTCAA
Statistics
Matches: 124, Mismatches: 13, Indels: 13
0.83 0.09 0.09
Matches are distributed among these distances:
39 9 0.07
40 103 0.83
41 12 0.10
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGAATTAATACTCGCACA
Found at i:28499979 original size:28 final size:30
Alignment explanation
Indices: 28499931--28499994 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 30
28499921 GCAACTATCT
28499931 TTTC-TAT-TTTTTAATAAAAATTAAAT-A
1 TTTCTTATATTTTTAATAAAAATTAAATCA
* *
28499958 TTTCTTATATTTTT-ATTAAAATTTAATCA
1 TTTCTTATATTTTTAATAAAAATTAAATCA
28499987 TTT-TTATA
1 TTTCTTATA
28499995 AAATTTATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
27 4 0.12
28 19 0.59
29 9 0.28
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTCTTATATTTTTAATAAAAATTAAATCA
Found at i:28499991 original size:20 final size:20
Alignment explanation
Indices: 28499966--28500013 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
28499956 TATTTCTTAT
28499966 ATTTTTATTAAAATTTAATC
1 ATTTTTATTAAAATTTAATC
* *
28499986 ATTTTTA-TAAAATTTATTG
1 ATTTTTATTAAAATTTAATC
28500005 ATTTTTATT
1 ATTTTTATT
28500014 TTTTATCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTTTTATTAAAATTTAATC
Found at i:28500939 original size:42 final size:42
Alignment explanation
Indices: 28500880--28500962 Score: 166
Period size: 42 Copynumber: 2.0 Consensus size: 42
28500870 AAAGTCTACC
28500880 ATATTGCATTTATTTCCCAAAAACATCAACAACTAAATCAAA
1 ATATTGCATTTATTTCCCAAAAACATCAACAACTAAATCAAA
28500922 ATATTGCATTTATTTCCCAAAAACATCAACAACTAAATCAA
1 ATATTGCATTTATTTCCCAAAAACATCAACAACTAAATCAA
28500963 CACCTACGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.47, C:0.22, G:0.02, T:0.29
Consensus pattern (42 bp):
ATATTGCATTTATTTCCCAAAAACATCAACAACTAAATCAAA
Found at i:28509499 original size:61 final size:62
Alignment explanation
Indices: 28509321--28509527 Score: 249
Period size: 62 Copynumber: 3.4 Consensus size: 62
28509311 GTATATGTTT
* * * **
28509321 TATACATTTCCAAATTTGATTTGTATATAGATATACATTG-CAGAATTTGAATTGTTTATAAA
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGTCA-AATTTGAATTGTATATGGA
* * * * * *
28509383 TATACATTGCCGAATTTAATTGGTATATGGTTATACATTGTCGAATTTGACTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGTCAAATTTGAATTGTATATGGA
* *
28509445 TATACATTGCCGAA-TTGATTTGTATGTAGATATACATTGTCAAATTTGAGTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGATATACATTGTCAAATTTGAATTGTATATGGA
* *
28509506 TATATATTGTCGAA-TTGATTTG
1 TATACATTGCCGAATTTGATTTG
28509528 AGCATTGGAT
Statistics
Matches: 124, Mismatches: 20, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
61 60 0.48
62 63 0.51
63 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (62 bp):
TATACATTGCCGAATTTGATTTGTATATAGATATACATTGTCAAATTTGAATTGTATATGGA
Found at i:28509515 original size:31 final size:31
Alignment explanation
Indices: 28509333--28509521 Score: 204
Period size: 31 Copynumber: 6.1 Consensus size: 31
28509323 TACATTTCCA
*
28509333 AATTTGATTTGTATATAGATATACATTG-CAG
1 AATTTGAATTGTATATAGATATACATTGTC-G
* * *
28509364 AATTTGAATTGTTTATAAATATACATTGCCG
1 AATTTGAATTGTATATAGATATACATTGTCG
* *
28509395 AATTT-AATTGGTATATGGTTATACATTGTCG
1 AATTTGAATT-GTATATAGATATACATTGTCG
* * *
28509426 AATTTGACTTGTATATGGATATACATTGCCG
1 AATTTGAATTGTATATAGATATACATTGTCG
* * *
28509457 AA-TTGATTTGTATGTAGATATACATTGTCA
1 AATTTGAATTGTATATAGATATACATTGTCG
* * *
28509487 AATTTGAGTTGTATATGGATATATATTGTCG
1 AATTTGAATTGTATATAGATATACATTGTCG
28509518 AATT
1 AATT
28509522 GATTTGAGCA
Statistics
Matches: 133, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
30 29 0.22
31 100 0.75
32 4 0.03
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.43
Consensus pattern (31 bp):
AATTTGAATTGTATATAGATATACATTGTCG
Found at i:28509537 original size:92 final size:93
Alignment explanation
Indices: 28509333--28509521 Score: 229
Period size: 92 Copynumber: 2.0 Consensus size: 93
28509323 TACATTTCCA
* * * * *
28509333 AATTTGATTTGTATATAGATATACATTGCAGAATTTGAATTGTTTATAAATATACATTGCCGAAT
1 AATTTGACTTGCATATGGATATACATTGCAGAATTTGAATTGTATATAAATATACATTGCCAAAT
*
28509398 TTAATTGGTATATGGTTATACATTGTCG
66 TTAATTGGTATATGGATATACATTGTCG
* * * * * *
28509426 AATTTGACTTGTATATGGATATACATTGCCGAA-TTGATTTGTATGTAGATATACATTGTCAAAT
1 AATTTGACTTGCATATGGATATACATTGCAGAATTTGAATTGTATATAAATATACATTGCCAAAT
* *
28509490 TTGAGTT-GTATATGGATATATATTGTCG
66 TT-AATTGGTATATGGATATACATTGTCG
28509518 AATT
1 AATT
28509522 GATTTGAGCA
Statistics
Matches: 83, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
92 50 0.60
93 33 0.40
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.43
Consensus pattern (93 bp):
AATTTGACTTGCATATGGATATACATTGCAGAATTTGAATTGTATATAAATATACATTGCCAAAT
TTAATTGGTATATGGATATACATTGTCG
Found at i:28509693 original size:43 final size:43
Alignment explanation
Indices: 28509645--28509792 Score: 224
Period size: 43 Copynumber: 3.4 Consensus size: 43
28509635 TCTGACGTGT
* *
28509645 GATTTCATGTAAGACCATAGTTGGGCTATTAGCATCGATTTGA
1 GATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
*
28509688 GATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
1 GATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
* * **
28509731 GACTTCATGTAAGACCGTAGCTGGGCTATTGGCATCGATACGA
1 GATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
28509774 GATTTCCATGTAAGACCAT
1 GATTT-CATGTAAGACCAT
28509793 GTCTTGGACA
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
43 82 0.87
44 12 0.13
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (43 bp):
GATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
Found at i:28516056 original size:31 final size:31
Alignment explanation
Indices: 28515862--28516062 Score: 251
Period size: 31 Copynumber: 6.5 Consensus size: 31
28515852 TTATATGTTT
*
28515862 TATACATTGTCGAATTTGATTTGTATATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
28515893 TATACATTGCTGAATTTGAATTGTTTATAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* * *
28515924 TATGCATTGCCGAATTTGATTTGTATATGGT
1 TATACATTGCCGAATTTGATTTGTATATAGA
** *
28515955 TATACATTATCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
** *
28515986 TATACATTTTCGAA-TTGATTTGTATGTAGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
*
28516016 TATACATTGCCGAATTTGATTTGTATATGGA
1 TATACATTGCCGAATTTGATTTGTATATAGA
* *
28516047 TATATATTGCTGAATT
1 TATACATTGCCGAATT
28516063 GCTTTGAGCA
Statistics
Matches: 146, Mismatches: 23, Indels: 2
0.85 0.13 0.01
Matches are distributed among these distances:
30 26 0.18
31 120 0.82
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (31 bp):
TATACATTGCCGAATTTGATTTGTATATAGA
Found at i:28516089 original size:92 final size:92
Alignment explanation
Indices: 28515862--28516050 Score: 245
Period size: 92 Copynumber: 2.0 Consensus size: 92
28515852 TTATATGTTT
* * * * * * * *
28515862 TATACATTGTCGAATTTGATTTGTATATAGATATACA-TTGCTGAATTTGAATTGTTTATAGATA
1 TATACATTATCGAATTTGATTTGCATATGGATAGACATTTTC-GAA-TTGATTTGTATGTAGATA
* *
28515926 TGCATTGCCGAATTTGATTTGTATATGGT
64 TACATTGCCGAATTTGATTTGTATATGGA
* *
28515955 TATACATTATCGAATTTGATTTGTATATGGATATACATTTTCGAATTGATTTGTATGTAGATATA
1 TATACATTATCGAATTTGATTTGCATATGGATAGACATTTTCGAATTGATTTGTATGTAGATATA
28516020 CATTGCCGAATTTGATTTGTATATGGA
66 CATTGCCGAATTTGATTTGTATATGGA
28516047 TATA
1 TATA
28516051 TATTGCTGAA
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
92 46 0.53
93 38 0.44
94 3 0.03
ACGTcount: A:0.30, C:0.07, G:0.17, T:0.45
Consensus pattern (92 bp):
TATACATTATCGAATTTGATTTGCATATGGATAGACATTTTCGAATTGATTTGTATGTAGATATA
CATTGCCGAATTTGATTTGTATATGGA
Found at i:28516250 original size:43 final size:43
Alignment explanation
Indices: 28516186--28516333 Score: 199
Period size: 43 Copynumber: 3.4 Consensus size: 43
28516176 TCTGAGGTGT
* ** *
28516186 GATTTCGTGTAAGACTGTAGCTGGGCTTTTGGCATCGATCTGA
1 GATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGATCTGA
* *
28516229 GATTTTATGTAAGACCATAGCTGGGCTATTGGCATCGATTTGA
1 GATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGATCTGA
* *
28516272 GATTTCGTGTAAGACCATAGTTGGGCTATTGGCATCGATAC-GA
1 GATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGAT-CTGA
28516315 GATTTCCATGTAAGACCAT
1 GATTT-CATGTAAGACCAT
28516334 GTCTGGGACA
Statistics
Matches: 92, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
43 80 0.87
44 12 0.13
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.33
Consensus pattern (43 bp):
GATTTCATGTAAGACCATAGCTGGGCTATTGGCATCGATCTGA
Found at i:28516880 original size:37 final size:37
Alignment explanation
Indices: 28516830--28516904 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
28516820 GAAAGAGTAA
*
28516830 AATTTGCAATAAAACAGTTTTGGACAGAAACATTTGT
1 AATTTGCAATAAAACAGTTTTGGACAGAAACAGTTGT
28516867 AATTTGCAATAAAACAGTTTTGGACAGAAACAGTTGT
1 AATTTGCAATAAAACAGTTTTGGACAGAAACAGTTGT
28516904 A
1 A
28516905 TAACTTTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (37 bp):
AATTTGCAATAAAACAGTTTTGGACAGAAACAGTTGT
Found at i:28525746 original size:31 final size:31
Alignment explanation
Indices: 28525708--28525769 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
28525698 AGGCAAATTA
28525708 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
28525739 CAAGAGTAATTGAATCCTAATAAAACTCTTT
1 CAAGAGTAATTGAATCCTAATAAAACTCTTT
28525770 AAAATTATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (31 bp):
CAAGAGTAATTGAATCCTAATAAAACTCTTT
Found at i:28529195 original size:15 final size:16
Alignment explanation
Indices: 28529175--28529204 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28529165 AAGGTTAAAA
28529175 TCGTC-AAATTTTACC
1 TCGTCAAAATTTTACC
28529190 TCGTCAAAATTTTAC
1 TCGTCAAAATTTTAC
28529205 TAGGGTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (16 bp):
TCGTCAAAATTTTACC
Found at i:28547876 original size:69 final size:70
Alignment explanation
Indices: 28547744--28547876 Score: 214
Period size: 69 Copynumber: 1.9 Consensus size: 70
28547734 TAGTTTATTA
* * * * *
28547744 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCCAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
28547809 CTTAG
66 CTTAG
28547814 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
28547877 GTTATGTACT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
69 35 0.60
70 23 0.40
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:28549317 original size:47 final size:47
Alignment explanation
Indices: 28549263--28549761 Score: 795
Period size: 47 Copynumber: 10.6 Consensus size: 47
28549253 TATTTGAATA
*
28549263 AATGTGAAAGTGTATATATGTGATAAGACCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
28549310 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
28549357 AATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
28549406 AATGTGAAAGTGTATATATATGTGATATGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
28549455 -ATGTG-AAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28549500 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
28549547 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
28549594 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
28549641 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
28549688 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
28549735 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
28549762 TCCCGAAGGG
Statistics
Matches: 427, Mismatches: 21, Indels: 8
0.94 0.05 0.02
Matches are distributed among these distances:
45 33 0.08
46 5 0.01
47 303 0.71
48 5 0.01
49 81 0.19
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:28550749 original size:27 final size:27
Alignment explanation
Indices: 28550719--28550905 Score: 293
Period size: 27 Copynumber: 6.9 Consensus size: 27
28550709 GGTGTTACAT
* *
28550719 GAATTACCCTCACAGGGTAAAATAATC
1 GAATTACCCCCACAGGGTAAAATGATC
28550746 GAATTACCCCCACAGGGTAAAATGATC
1 GAATTACCCCCACAGGGTAAAATGATC
28550773 GAATTACCCCCACAGGGTAAAATGATC
1 GAATTACCCCCACAGGGTAAAATGATC
28550800 GAATTACCCCCACAGGGTAAAATGATC
1 GAATTACCCCCACAGGGTAAAATGATC
28550827 GAATTACCCCCACAGGGTAAAATGATC
1 GAATTACCCCCACAGGGTAAAATGATC
* *
28550854 GAATTACCCCCATAGGGTAAAATGACC
1 GAATTACCCCCACAGGGTAAAATGATC
* * * * *
28550881 AAAATACCTCCATAGTGTAAAATGA
1 GAATTACCCCCACAGGGTAAAATGA
28550906 CTGTTATACC
Statistics
Matches: 152, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 152 1.00
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (27 bp):
GAATTACCCCCACAGGGTAAAATGATC
Found at i:28551312 original size:28 final size:28
Alignment explanation
Indices: 28551271--28551335 Score: 94
Period size: 28 Copynumber: 2.3 Consensus size: 28
28551261 ACTGTACCAA
*
28551271 TACTGTATTAGGCTAGGGACCACATGGT
1 TACTGTATTAGGCTAAGGACCACATGGT
* * *
28551299 TACTGTATTGGGCTAAGGCCCACATTGT
1 TACTGTATTAGGCTAAGGACCACATGGT
28551327 TACTGTATT
1 TACTGTATT
28551336 TCACTAAGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (28 bp):
TACTGTATTAGGCTAAGGACCACATGGT
Found at i:28551342 original size:28 final size:28
Alignment explanation
Indices: 28551290--28551359 Score: 79
Period size: 28 Copynumber: 2.5 Consensus size: 28
28551280 AGGCTAGGGA
* **
28551290 CCACATGGTTACTGTATTGGGCTAAGGC
1 CCACATTGTTACTGTATTGCACTAAGGC
*
28551318 CCACATTGTTACTGTATTTCACTAAGGC
1 CCACATTGTTACTGTATTGCACTAAGGC
* *
28551346 CTACACTG-TACTGT
1 CCACATTGTTACTGT
28551360 TACTGAATAG
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
27 6 0.17
28 30 0.83
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (28 bp):
CCACATTGTTACTGTATTGCACTAAGGC
Found at i:28557253 original size:27 final size:27
Alignment explanation
Indices: 28557223--28557284 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
28557213 AGGGGCATTA
28557223 CGGTCATTTTA-CCTTACAAGGGTATTT
1 CGGTCATTTTATCCTT-CAAGGGTATTT
*
28557250 CGGTCATTTTATCCTTCGAGGGTATTT
1 CGGTCATTTTATCCTTCAAGGGTATTT
*
28557277 CAGTCATT
1 CGGTCATT
28557285 CAACAACCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 28 0.88
28 4 0.12
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (27 bp):
CGGTCATTTTATCCTTCAAGGGTATTT
Found at i:28557813 original size:8 final size:8
Alignment explanation
Indices: 28557771--28557813 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
28557761 GTAGTCATAC
*
28557771 TTTCAGCT
1 TTTCAGCA
*
28557779 TTTCAGCT
1 TTTCAGCA
28557787 TTTCAGCA
1 TTTCAGCA
* *
28557795 TTTCGGGA
1 TTTCAGCA
28557803 TTTCAGCA
1 TTTCAGCA
28557811 TTT
1 TTT
28557814 GCTGATCTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 30 1.00
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.47
Consensus pattern (8 bp):
TTTCAGCA
Found at i:28564361 original size:137 final size:137
Alignment explanation
Indices: 28564115--28564366 Score: 346
Period size: 137 Copynumber: 1.8 Consensus size: 137
28564105 ATGTCATTAG
* * * * *
28564115 GGTTACCATGTTTCGGGTGCTGGTTCTAAATGTCTTACCGATGGCTGAGTTTTGACATTTGTTGC
1 GGTTACAATGTTTCGGGTGCTGGTTCTAAATGTCCTACCGATGGCTAAGGTCTGACATTTGTTGC
28564180 GGATACTCATCAACTTATGTGAGTGGCAACGTGTAGCTACATTCCAACCGCCAGCTTGTGTGAGC
66 GGATACTCATCAACTTATGTGAGTGGCAACGTGTAGCTACATTCCAACCGCCAGCTTGTGTGAGC
28564245 AGACCTA
131 AGACCTA
* **
28564252 GGTTACAATGTTTCGGGTGCTGG-TCTTGAATGTCCTACCGATGGCTAAGGTCTGGTATTTGTTG
1 GGTTACAATGTTTCGGGTGCTGGTTC-TAAATGTCCTACCGATGGCTAAGGTCTGACATTTGTTG
* * * * * *
28564316 TGGATACTCGTCAGCTTGTGTGAAG-GGCATCGTGTAGCTATATTCCAACCG
65 CGGATACTCATCAACTTATGTG-AGTGGCAACGTGTAGCTACATTCCAACCG
28564367 TCACCTTATG
Statistics
Matches: 99, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
136 2 0.02
137 95 0.96
138 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (137 bp):
GGTTACAATGTTTCGGGTGCTGGTTCTAAATGTCCTACCGATGGCTAAGGTCTGACATTTGTTGC
GGATACTCATCAACTTATGTGAGTGGCAACGTGTAGCTACATTCCAACCGCCAGCTTGTGTGAGC
AGACCTA
Found at i:28564421 original size:42 final size:41
Alignment explanation
Indices: 28564327--28564421 Score: 109
Period size: 42 Copynumber: 2.3 Consensus size: 41
28564317 GGATACTCGT
*** * *
28564327 CAGCTTGTGTGAAGGGCATCGTGTAGCTATATTCCAACCGT
1 CAGCTTGTGTGAACAACATCGTGTAGCTACATTCCAACCGC
* * *
28564368 CACCTTATGTGAACAACATTGTGTAGCTTACATTCCAACCGC
1 CAGCTTGTGTGAACAACATCGTGTAGC-TACATTCCAACCGC
28564410 CAGCTTGTGTGA
1 CAGCTTGTGTGA
28564422 GCCACGACTA
Statistics
Matches: 43, Mismatches: 10, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
41 21 0.49
42 22 0.51
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (41 bp):
CAGCTTGTGTGAACAACATCGTGTAGCTACATTCCAACCGC
Found at i:28566633 original size:36 final size:36
Alignment explanation
Indices: 28566527--28566646 Score: 111
Period size: 36 Copynumber: 3.3 Consensus size: 36
28566517 TCTTCGAATG
* *
28566527 CATATATATA-TTATTCAAATACATATGCCAAAAGCA
1 CATATATATACTTA-TCAACTACATATGCCAAATGCA
* * * *
28566563 AATA-ATTATACTTATCAACCACATGTGCCGAATGCA
1 CATATA-TATACTTATCAACTACATATGCCAAATGCA
*
28566599 CATATATATACTTAT-AATTTACATATGCCAAATGCATA
1 CATATATATACTTATCAA-CTACATATGCCAAATGC--A
28566637 CATATATATA
1 CATATATATA
28566647 TCCAACAATT
Statistics
Matches: 67, Mismatches: 11, Indels: 10
0.76 0.12 0.11
Matches are distributed among these distances:
35 3 0.04
36 49 0.73
37 4 0.06
38 11 0.16
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (36 bp):
CATATATATACTTATCAACTACATATGCCAAATGCA
Found at i:28566869 original size:41 final size:41
Alignment explanation
Indices: 28566814--28566935 Score: 190
Period size: 41 Copynumber: 3.0 Consensus size: 41
28566804 TTAATTAAAA
28566814 CAGATTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
* *
28566856 CAGATCACTGGCACTTAGCCTGCTAGGCTTATAGCCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
* * *
28566897 CAGTTCACCGGCACTTAGCCTTCTAGGCTTTAAGCCTGA
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGA
28566936 ATTGATTCAC
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
41 69 0.95
42 4 0.05
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
Found at i:28566964 original size:41 final size:40
Alignment explanation
Indices: 28566816--28566950 Score: 175
Period size: 41 Copynumber: 3.3 Consensus size: 40
28566806 AATTAAAACA
*
28566816 GATTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT
1 GATTCACCGGCACTTAGCCTGCTAGGCTTTAAGCCTGATT
*
28566856 CAGA-TCACTGGCACTTAGCCTGCTAGGC-TTATAGCCTGATT
1 --GATTCACCGGCACTTAGCCTGCTAGGCTTTA-AGCCTGATT
* *
28566897 CAGTTCACCGGCACTTAGCCTTCTAGGCTTTAAGCCTGAATT
1 GA-TTCACCGGCACTTAGCCTGCTAGGCTTTAAGCCTG-ATT
28566939 GATTCACCGGCA
1 GATTCACCGGCA
28566951 ATATACCTAC
Statistics
Matches: 82, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
39 1 0.01
40 2 0.02
41 70 0.85
42 9 0.11
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.28
Consensus pattern (40 bp):
GATTCACCGGCACTTAGCCTGCTAGGCTTTAAGCCTGATT
Found at i:28566974 original size:82 final size:81
Alignment explanation
Indices: 28566818--28566976 Score: 198
Period size: 82 Copynumber: 1.9 Consensus size: 81
28566808 TTAAAACAGA
* * *
28566818 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGATCACTGGCACTTAGCCTGCTAGG
1 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATT-AGATCACCGGCAATTAGCCTACTAGG
*
28566883 CTTATAGCCTGATTCAG
65 CTGATAGCCTGATTCAG
* *
28566900 TTCACCGGCACTTAGCCTTCTAGGCTTTAAGCCTGAATT-GATTCACCGGCAATATA-CCTACTA
1 TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTG-ATTAGA-TCACCGGCAAT-TAGCCTACTA
28566963 GG-TGATGAGCCTGA
63 GGCTGAT-AGCCTGA
28566977 ATACGCAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
81 5 0.07
82 57 0.85
83 5 0.07
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (81 bp):
TTCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTAGATCACCGGCAATTAGCCTACTAGGC
TGATAGCCTGATTCAG
Found at i:28573886 original size:41 final size:41
Alignment explanation
Indices: 28573829--28573974 Score: 208
Period size: 41 Copynumber: 3.6 Consensus size: 41
28573819 TAAAATAGAT
28573829 TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGA
* *
28573870 TCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAGT
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGA
*
28573911 TCACCGGCACTTAGCCTGCTAGGCTTTAAGCCTGAATT--GA
1 TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTG-ATTCAGA
*
28573951 TTCACCGGCAATATA-CCTGCTAGG
1 -TCACCGGCACT-TAGCCTGCTAGG
28573975 TGCTGAGCCT
Statistics
Matches: 96, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
40 1 0.01
41 90 0.94
42 5 0.05
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.27
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGGCTTAAAGCCTGATTCAGA
Found at i:28574355 original size:22 final size:23
Alignment explanation
Indices: 28574307--28574356 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 23
28574297 AAATCTTAAA
* *
28574307 CATATATATACATATACATTTGAC
1 CATATATATAAATATACAATT-AC
*
28574331 CATATATATAAATATATAATT-C
1 CATATATATAAATATACAATTAC
28574353 CATA
1 CATA
28574357 CCTAATTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 5 0.22
24 18 0.78
ACGTcount: A:0.46, C:0.14, G:0.02, T:0.38
Consensus pattern (23 bp):
CATATATATAAATATACAATTAC
Found at i:28586430 original size:25 final size:24
Alignment explanation
Indices: 28586396--28586490 Score: 118
Period size: 25 Copynumber: 3.8 Consensus size: 24
28586386 CAAGCCCATT
*
28586396 TTCACAGCTCGTGTGAGCATTCTAG
1 TTCACAGCTCATGTGAGCATTCT-G
28586421 TTCACAGCTCATGTGAGCATTCTGG
1 TTCACAGCTCATGTGAGCATTCT-G
*
28586446 TTCGCAGCTCATGTGAGCATTCTG
1 TTCACAGCTCATGTGAGCATTCTG
* * *
28586470 ATCCACAGCTCGTGTAAGCAT
1 -TTCACAGCTCATGTGAGCAT
28586491 ACATGTACAT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
24 1 0.02
25 61 0.98
ACGTcount: A:0.21, C:0.25, G:0.23, T:0.31
Consensus pattern (24 bp):
TTCACAGCTCATGTGAGCATTCTG
Found at i:28587155 original size:20 final size:19
Alignment explanation
Indices: 28587132--28587173 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
28587122 TAAAGAAATT
28587132 AAATAC-AATGGAAAGTAATG
1 AAATACAAAT-GAAAGTAA-G
*
28587152 AAATGCAAATGAAAGTAAG
1 AAATACAAATGAAAGTAAG
28587171 AAA
1 AAA
28587174 ATTTGAAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 4 0.20
20 13 0.65
21 3 0.15
ACGTcount: A:0.60, C:0.05, G:0.19, T:0.17
Consensus pattern (19 bp):
AAATACAAATGAAAGTAAG
Found at i:28591423 original size:20 final size:20
Alignment explanation
Indices: 28591392--28591447 Score: 87
Period size: 20 Copynumber: 2.8 Consensus size: 20
28591382 AGACGATGAA
28591392 CCATTCCATTTACTTACTTT
1 CCATTCCATTTACTTACTTT
*
28591412 CTACTT-CATTTACTTACTTT
1 CCA-TTCCATTTACTTACTTT
28591432 CCATTCCATTTACTTA
1 CCATTCCATTTACTTA
28591448 GCATAAGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.21, C:0.29, G:0.00, T:0.50
Consensus pattern (20 bp):
CCATTCCATTTACTTACTTT
Found at i:28601051 original size:10 final size:10
Alignment explanation
Indices: 28601036--28601062 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
28601026 CCGACAATCA
28601036 CAAAATTTTC
1 CAAAATTTTC
28601046 CAAAATTTTC
1 CAAAATTTTC
28601056 CAAAATT
1 CAAAATT
28601063 CCTAGTTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (10 bp):
CAAAATTTTC
Found at i:28614915 original size:10 final size:10
Alignment explanation
Indices: 28614900--28614926 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
28614890 CCGACAATCA
28614900 CAAAATTTTC
1 CAAAATTTTC
28614910 CAAAATTTTC
1 CAAAATTTTC
28614920 CAAAATT
1 CAAAATT
28614927 CCTAGTTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.37
Consensus pattern (10 bp):
CAAAATTTTC
Found at i:28629935 original size:18 final size:18
Alignment explanation
Indices: 28629912--28629948 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
28629902 CTTTTGGTTC
28629912 TTCATGAATGTAAATAGT
1 TTCATGAATGTAAATAGT
28629930 TTCATGAATGTAAATAGT
1 TTCATGAATGTAAATAGT
28629948 T
1 T
28629949 CGAACTCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.16, T:0.41
Consensus pattern (18 bp):
TTCATGAATGTAAATAGT
Found at i:28632197 original size:59 final size:59
Alignment explanation
Indices: 28632088--28632235 Score: 223
Period size: 59 Copynumber: 2.6 Consensus size: 59
28632078 GGTGTAGTGC
28632088 TAATTATGTGGTGTAGTAC--AATAATGCACTTGGACAATATTATTATGTGGTGAACTAT
1 TAATTATGTGGTGTAGTACTAAAT-ATGCACTTGGACAATATTATTATGTGGTGAACTAT
* * * *
28632146 TAATTATGTTGTTTAGTACTAAATATGTACTTGGACAGTATTATTATGTGGTGAACTAT
1 TAATTATGTGGTGTAGTACTAAATATGCACTTGGACAATATTATTATGTGGTGAACTAT
28632205 TAA-T-TGTGGTGTAGTACTAAATATGCACTTG
1 TAATTATGTGGTGTAGTACTAAATATGCACTTG
28632236 AGCAATAATG
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
57 24 0.30
58 18 0.22
59 36 0.44
60 3 0.04
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (59 bp):
TAATTATGTGGTGTAGTACTAAATATGCACTTGGACAATATTATTATGTGGTGAACTAT
Found at i:28632351 original size:3 final size:3
Alignment explanation
Indices: 28632345--28632370 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
28632335 TTTGTTGTTG
28632345 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
28632371 CAATCCTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:28632936 original size:56 final size:56
Alignment explanation
Indices: 28632866--28632979 Score: 165
Period size: 56 Copynumber: 2.0 Consensus size: 56
28632856 CACAAACAAA
* ** *
28632866 CTACAACATTCTTAAAAATGCCTTGCTAATTTCATAACATTAGGAATATAGTTCCG
1 CTACAACATCCTTAAAAATGCCTTGCTAATTTCATAACACCAGGAATATAGTTACG
* * *
28632922 CTACAACATCCTTAAAAATGCTTTGCTAATTTTATAACACCAGGAATCTAGTTACG
1 CTACAACATCCTTAAAAATGCCTTGCTAATTTCATAACACCAGGAATATAGTTACG
28632978 CT
1 CT
28632980 GGCACGACAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 51 1.00
ACGTcount: A:0.35, C:0.21, G:0.11, T:0.33
Consensus pattern (56 bp):
CTACAACATCCTTAAAAATGCCTTGCTAATTTCATAACACCAGGAATATAGTTACG
Found at i:28638073 original size:20 final size:21
Alignment explanation
Indices: 28638045--28638085 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
28638035 CCTGCAGTTC
* *
28638045 AAATTTTCCAACT-TTTTCTT
1 AAATGTTCCAAATGTTTTCTT
28638065 AAATGTTCCAAATGTTTTCTT
1 AAATGTTCCAAATGTTTTCTT
28638086 TTTGGCCCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (21 bp):
AAATGTTCCAAATGTTTTCTT
Found at i:28642897 original size:23 final size:23
Alignment explanation
Indices: 28642871--28642924 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
28642861 ACCTACTTTC
*
28642871 TTACAGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
28642894 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
28642917 TTACAGTA
1 TTACAGTA
28642925 ACATATTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:28648821 original size:6 final size:6
Alignment explanation
Indices: 28648810--28648855 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
28648800 GGTTTTCTCA
* *
28648810 AAATGG AAATGG AAATGG AAATGA AAATGA AAATGAG AAAT-G AAAT
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATG-G AAATGG AAAT
28648856 CTTTTAGAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
5 5 0.14
6 28 0.76
7 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.24, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:28648837 original size:18 final size:19
Alignment explanation
Indices: 28648810--28648854 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
28648800 GGTTTTCTCA
* *
28648810 AAATGGAAATGGAAATG-G
1 AAATGAAAATGAAAATGAG
28648828 AAATGAAAATGAAAATGAG
1 AAATGAAAATGAAAATGAG
28648847 AAATGAAA
1 AAATGAAA
28648855 TCTTTTAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (19 bp):
AAATGAAAATGAAAATGAG
Found at i:28662787 original size:27 final size:27
Alignment explanation
Indices: 28662756--28662890 Score: 189
Period size: 27 Copynumber: 5.0 Consensus size: 27
28662746 CATCGAGCTC
*
28662756 CGAAATACCCGTATAGGGTAAAATGAT
1 CGAAATACCCCTATAGGGTAAAATGAT
* *
28662783 TGAAATACCCCTATAGGGTAAAATGAC
1 CGAAATACCCCTATAGGGTAAAATGAT
* * *
28662810 CAAAATACCCTCTATTGTGTAAAATGAT
1 CGAAATACCC-CTATAGGGTAAAATGAT
*
28662838 CGAAATACCCCCATAGGGTAAAATGAT
1 CGAAATACCCCTATAGGGTAAAATGAT
*
28662865 CGAAATACCCCAATAGGGTAAAATGA
1 CGAAATACCCCTATAGGGTAAAATGA
28662891 CTGTTATACC
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
27 71 0.76
28 23 0.24
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (27 bp):
CGAAATACCCCTATAGGGTAAAATGAT
Found at i:28663314 original size:33 final size:31
Alignment explanation
Indices: 28663277--28663368 Score: 93
Period size: 28 Copynumber: 2.9 Consensus size: 31
28663267 TGTATTATTG
28663277 CACTGTATTGATACTGTAATGGGCTAAGGCCCA
1 CACTGTA-TG-TACTGTAATGGGCTAAGGCCCA
*
28663310 CACTG--T-TACTGTATTGGGCTAAGGCCCA
1 CACTGTATGTACTGTAATGGGCTAAGGCCCA
*
28663338 CACTGTACTGCTACTG-AATAGGGCTCAGGCC
1 CACTGTA-TG-TACTGTAAT-GGGCTAAGGCC
28663369 TAGACTGTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
28 26 0.52
30 1 0.02
31 1 0.02
32 2 0.04
33 20 0.40
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (31 bp):
CACTGTATGTACTGTAATGGGCTAAGGCCCA
Found at i:28663328 original size:28 final size:27
Alignment explanation
Indices: 28663288--28663347 Score: 102
Period size: 28 Copynumber: 2.2 Consensus size: 27
28663278 ACTGTATTGA
28663288 TACTGTAATGGGCTAAGGCCCACACTG
1 TACTGTAATGGGCTAAGGCCCACACTG
*
28663315 TTACTGTATTGGGCTAAGGCCCACACTG
1 -TACTGTAATGGGCTAAGGCCCACACTG
28663343 TACTG
1 TACTG
28663348 CTACTGAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (27 bp):
TACTGTAATGGGCTAAGGCCCACACTG
Found at i:28664969 original size:26 final size:26
Alignment explanation
Indices: 28664940--28664996 Score: 105
Period size: 26 Copynumber: 2.2 Consensus size: 26
28664930 TAATTGTAAG
28664940 CAAAGCAACAGTTTGTCGCGGCATTA
1 CAAAGCAACAGTTTGTCGCGGCATTA
*
28664966 CAAAGCAACAGTTTGTTGCGGCATTA
1 CAAAGCAACAGTTTGTCGCGGCATTA
28664992 CAAAG
1 CAAAG
28664997 AAACGTTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.33, C:0.21, G:0.23, T:0.23
Consensus pattern (26 bp):
CAAAGCAACAGTTTGTCGCGGCATTA
Found at i:28667086 original size:20 final size:23
Alignment explanation
Indices: 28667061--28667101 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
28667051 GTACTCAAGT
28667061 ACATTTT-GTT-GCA-TTTTAGG
1 ACATTTTAGTTAGCAGTTTTAGG
28667081 ACATTTTAGTTAGCAGTTTTA
1 ACATTTTAGTTAGCAGTTTTA
28667102 ATATTGCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 3 0.17
23 5 0.28
ACGTcount: A:0.24, C:0.10, G:0.17, T:0.49
Consensus pattern (23 bp):
ACATTTTAGTTAGCAGTTTTAGG
Found at i:28676740 original size:17 final size:17
Alignment explanation
Indices: 28676718--28676762 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
28676708 GAGTGAGATG
28676718 AAGTGAAAAAGATCA-AA
1 AAGTGAAAAAG-TCACAA
*
28676735 AAGTGACAAAGTCACAA
1 AAGTGAAAAAGTCACAA
28676752 AAGTAGAAAAA
1 AAGT-GAAAAA
28676763 CTCAGTCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 16 0.67
18 5 0.21
ACGTcount: A:0.62, C:0.09, G:0.18, T:0.11
Consensus pattern (17 bp):
AAGTGAAAAAGTCACAA
Found at i:28682764 original size:12 final size:12
Alignment explanation
Indices: 28682746--28682779 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
28682736 TAAGTTTCCA
28682746 AAAATGGAAAT-
1 AAAATGGAAATG
28682757 AGAAATGGAAATG
1 A-AAATGGAAATG
28682770 AAAATGGAAA
1 AAAATGGAAA
28682780 CTTGCAATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 1 0.05
12 19 0.90
13 1 0.05
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:28686057 original size:47 final size:47
Alignment explanation
Indices: 28685884--28686477 Score: 819
Period size: 47 Copynumber: 12.4 Consensus size: 47
28685874 CAGCCAAGAG
* *
28685884 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
28685931 AGTATATGTATATATGTAATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AG----TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
28685982 AGTGTATGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 A--G--TGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
28686033 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
28686080 AGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
*
28686127 AGTGTATGTATATATGTATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTA--TATATGTG-ATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
28686177 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
28686224 AGTGTATATGTGTGACAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * *
28686271 AGTGTATATATGTAATAAGGCCTAATGGCCGATGCGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
28686318 AGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
28686365 AGTGTATATATGTGATAAGGCCCAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * * * * * * * *
28686412 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTAATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* *
28686459 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
28686478 TCCCGAAAGG
Statistics
Matches: 504, Mismatches: 34, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
47 360 0.71
48 6 0.01
49 7 0.01
50 39 0.08
51 91 0.18
53 1 0.00
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
Found at i:28686402 original size:285 final size:288
Alignment explanation
Indices: 28685884--28686418 Score: 860
Period size: 285 Copynumber: 1.9 Consensus size: 288
28685874 CAGCCAAGAG
* *
28685884 AGTGTATATATGTAATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTATATGTATATATGTA
1 AGTGTATATATGTAATAAGGCCTAATAGCCGACGTGATGAATGTGAAAG---ATGTATATATGTA
* *
28685949 ATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTGATAAGGCCTAATGG
63 ACAAGGCCTAATAGCCGATGTGATGAATGTGAAAG-G-ATGTATATATGTAATAAGGCCTAATGG
* * *
28686014 CCGATGTGATGAATGTGAAAGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGA
126 CCGATGCGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGACGCGATGAATGTGA
* *
28686079 AAGTGTATATGTGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATGTATATATGT
191 AAGTGTATATATGTGATAAGGCCCAATAGCCGATGTGATGAATGTGAAAGTGTATGTATATATGT
28686144 ATAAGGCCTAATAGCCGATGTGATGAATGTGAA
256 ATAAGGCCTAATAGCCGATGTGATGAATGTGAA
* * * *
28686177 AGTGTATATGTGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAAAG-TGTATATGTGTGACA
1 AGTGTATATATGTAATAAGGCCTAATAGCCGACGTGATGAATGTGAAAGATGTATATATGTAACA
28686241 AGGCCTAATAGCCGATGTGATGAATGTGAAA-G-TGTATATATGTAATAAGGCCTAATGGCCGAT
66 AGGCCTAATAGCCGATGTGATGAATGTGAAAGGATGTATATATGTAATAAGGCCTAATGGCCGAT
* *
28686304 GCGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGCGATGAATGTGAAAGTG
131 GCGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGACGCGATGAATGTGAAAGTG
*
28686369 TATATATGTGATAAGGCCCAATGGCCGATGTGATGAATGTGAAAGTGTAT
196 TATATATGTGATAAGGCCCAATAGCCGATGTGATGAATGTGAAAGTGTAT
28686419 ATATGTGACA
Statistics
Matches: 226, Mismatches: 16, Indels: 8
0.90 0.06 0.03
Matches are distributed among these distances:
285 137 0.61
287 1 0.00
289 43 0.19
293 45 0.20
ACGTcount: A:0.33, C:0.09, G:0.28, T:0.29
Consensus pattern (288 bp):
AGTGTATATATGTAATAAGGCCTAATAGCCGACGTGATGAATGTGAAAGATGTATATATGTAACA
AGGCCTAATAGCCGATGTGATGAATGTGAAAGGATGTATATATGTAATAAGGCCTAATGGCCGAT
GCGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGACGCGATGAATGTGAAAGTG
TATATATGTGATAAGGCCCAATAGCCGATGTGATGAATGTGAAAGTGTATGTATATATGTATAAG
GCCTAATAGCCGATGTGATGAATGTGAA
Found at i:28686652 original size:37 final size:37
Alignment explanation
Indices: 28686596--28686674 Score: 115
Period size: 37 Copynumber: 2.1 Consensus size: 37
28686586 CCGAGCTCTA
* *
28686596 AAGACCCGATGACTACGTGTGG-GAATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAG-ATTATGTCCGGGT
*
28686633 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
28686670 AAGAC
1 AAGAC
28686675 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
37 37 0.97
38 1 0.03
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:28690126 original size:137 final size:136
Alignment explanation
Indices: 28689876--28690147 Score: 361
Period size: 137 Copynumber: 2.0 Consensus size: 136
28689866 ACTCGAGCCA
*
28689876 TAAATGGGTCTGCTCACACAAGCTGACAGTCGAAATGTAGCTACACGATGCCACTCACACAACTT
1 TAAATGGGTCTACTCACACAAGCTGACAGTCGAAATGTAGCTACACGATGCCACTCACACAACTT
* *
28689941 GAAGAGTATCCACAACAAATGTCAAAACTCAGCCATCGATAGGACATTCAGGACCAGCACCTTGA
66 GAAGAGTATCCACAACAAATGCCAAAACTCAGCCATCGATAGGACATTCAGGACCAGCACCTAGA
28690006 ACATGG
131 ACATGG
* * **
28690012 TAAACTGGGTCTACTCACACAAGCTGACGGTC-AGAATGTAAGCTACGC-ATGCTGCTCACACAA
1 TAAA-TGGGTCTACTCACACAAGCTGACAGTCGA-AATGT-AGCTACACGATGCCACTCACACAA
* * ** ** *
28690075 GTTGACGAGTATCTGCAACAAATGCCTGACCTCAGCCATC-AGTAGGACATTCAGGACCAGCACC
63 CTTGAAGAGTATCCACAACAAATGCCAAAACTCAGCCATCGA-TAGGACATTCAGGACCAGCACC
28690139 TAGAACATG
127 TAGAACATG
28690148 AAAACCCTAA
Statistics
Matches: 118, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
136 6 0.05
137 105 0.89
138 7 0.06
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.19
Consensus pattern (136 bp):
TAAATGGGTCTACTCACACAAGCTGACAGTCGAAATGTAGCTACACGATGCCACTCACACAACTT
GAAGAGTATCCACAACAAATGCCAAAACTCAGCCATCGATAGGACATTCAGGACCAGCACCTAGA
ACATGG
Found at i:28697772 original size:42 final size:42
Alignment explanation
Indices: 28697716--28697812 Score: 167
Period size: 42 Copynumber: 2.3 Consensus size: 42
28697706 CTATATGAAC
28697716 GGCACTAAGTGTGCGAAACTAAAATCACGATGTTGAATAATG
1 GGCACTAAGTGTGCGAAACTAAAATCACGATGTTGAATAATG
* * *
28697758 GGCACTAAGTGTGCGAAATTAAAATGATGATGTTGAATAATG
1 GGCACTAAGTGTGCGAAACTAAAATCACGATGTTGAATAATG
28697800 GGCACTAAGTGTG
1 GGCACTAAGTGTG
28697813 TGATACCAAG
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.36, C:0.11, G:0.27, T:0.26
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACTAAAATCACGATGTTGAATAATG
Found at i:28712228 original size:100 final size:100
Alignment explanation
Indices: 28712055--28712254 Score: 328
Period size: 100 Copynumber: 2.0 Consensus size: 100
28712045 AAAGAAAGTG
* * *
28712055 TGCCTGTATCATATTAAATTATTATACCTCTTAGGATTTTGCCTCAAGAAAGTTACTAAGTCAAT
1 TGCCTATATCATATTAAATTATTATACCTCCTAGGATTTTGCCTCAAGAAAGTTAATAAGTCAAT
*
28712120 TTTAAAGACTTAAACCTTCGTACATGTCTATTTCT
66 TTTAAAGACTTAAACCTTCATACATGTCTATTTCT
* *
28712155 TGCCTATATCATATTAAATTCTTATTCCTCCTAGGATTTTGCCTCAAGAAAGTTAATAAGTCAAT
1 TGCCTATATCATATTAAATTATTATACCTCCTAGGATTTTGCCTCAAGAAAGTTAATAAGTCAAT
**
28712220 TTTAAAGACTTAAACCTTCATGTATGTCTATTTCT
66 TTTAAAGACTTAAACCTTCATACATGTCTATTTCT
28712255 AAAGAAAATG
Statistics
Matches: 92, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 92 1.00
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (100 bp):
TGCCTATATCATATTAAATTATTATACCTCCTAGGATTTTGCCTCAAGAAAGTTAATAAGTCAAT
TTTAAAGACTTAAACCTTCATACATGTCTATTTCT
Found at i:28718862 original size:40 final size:37
Alignment explanation
Indices: 28718805--28719029 Score: 200
Period size: 40 Copynumber: 5.7 Consensus size: 37
28718795 TTGAATGATG
* * *
28718805 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGACTAAGT-CCGAAGGCATTTGTGC-GAGT-ACTA-A
28718845 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGATACTAA
1 TCCGGACTAAG-TCCGAAGGCATTTGTGCGAG-TACTAA
* *
28718884 TTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAAA
1 -TCCGGACTAAGTCCGAAGGCATTTGTGCGAG-TACT-AA
28718924 TCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGACTAAG-TCCGAAGGCATTTGTGCGAG-TACT-AA
** *
28718964 TCCGGGTTAAGTGCCGAAGGCATTTGTGCGAATTACTATA
1 TCCGGACTAAGT-CCGAAGGCATTTGTGCG-AGTACTA-A
* * *
28719004 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGACTAAGT-CCGAAGGCATTTG
28719030 AACGAGGAGC
Statistics
Matches: 161, Mismatches: 15, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
39 36 0.22
40 115 0.71
41 10 0.06
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (37 bp):
TCCGGACTAAGTCCGAAGGCATTTGTGCGAGTACTAA
Found at i:28718937 original size:79 final size:80
Alignment explanation
Indices: 28718805--28719029 Score: 296
Period size: 79 Copynumber: 2.8 Consensus size: 80
28718795 TTGAATGATG
* * * *
28718805 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGACTAAGATCCGAAGGCATT
*
28718869 TGTGCGAGATACTAAT
65 TGTGCGAGATACTAAA
28718885 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
*
28718949 GTGCGAGTTACTAAA
66 GTGCGAGATACTAAA
* * * * *
28718964 TCCGGGTTAAGTGCCGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGACTAAGAT-CCGAAGGCAT
28719027 TTG
64 TTG
28719030 AACGAGGAGC
Statistics
Matches: 130, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
79 65 0.50
80 63 0.48
81 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:28719047 original size:80 final size:79
Alignment explanation
Indices: 28718818--28719062 Score: 216
Period size: 79 Copynumber: 3.1 Consensus size: 79
28718808 GGGCTAAGTC
* * * * **
28718818 CCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTTGTGCGAGAT-AC
1 CCGAAGGCATTTGTGCGAA-TTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAG-TGAC
* *
28718881 TAATTCCGGGCT-AA-G
64 TAAATCC-GGTTAAATG
* ** *
28718896 CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGACTAAGATCCGAAGGCATTTGTGCGAGTTACT
1 -CCGAAGGCATTTGTGCGAATTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTGACT
*
28718961 AAATCCGGGTTAAGTG
65 AAATCC-GGTTAAATG
* *
28718977 CCGAAGGCATTTGTGCGAATTACTATAA-CCGGGCTATG-TCCCGAAGGCATTTGAACGAG-GAG
1 CCGAAGGCATTTGTGCGAATTACTA-AATCCGGACTAAGAT-CCGAAGGCATTTGAACGAGTGA-
* *
28719039 CTATATCCGGTTAAATT
63 CTAAATCCGGTTAAATG
28719056 CCGAAGG
1 CCGAAGG
28719063 TACGTGATTT
Statistics
Matches: 142, Mismatches: 17, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
78 1 0.01
79 73 0.51
80 65 0.46
81 3 0.02
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAATTACTAAATCCGGACTAAGATCCGAAGGCATTTGAACGAGTGACTA
AATCCGGTTAAATG
Found at i:28726842 original size:23 final size:23
Alignment explanation
Indices: 28726816--28726866 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
28726806 TACTACTTTC
* *
28726816 TTACTGTAGTAATTTTCGGGGTA
1 TTACAGTAGTAATTTTCGGGATA
28726839 TTACAGTAGTAATTTTCGGGATA
1 TTACAGTAGTAATTTTCGGGATA
28726862 TTACA
1 TTACA
28726867 TTTCTCTCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.41
Consensus pattern (23 bp):
TTACAGTAGTAATTTTCGGGATA
Found at i:28728478 original size:50 final size:50
Alignment explanation
Indices: 28728351--28728687 Score: 327
Period size: 50 Copynumber: 6.6 Consensus size: 50
28728341 GATAATAACA
* * * ** * * *
28728351 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGAGATGTTTCCTGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * * * **
28728400 TGCCAATGTCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** * **
28728450 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTTATCCCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
28728500 TGCCAACGCCATGTCCCAAACATGGTCTTACATGAGACCTCTCATTTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* *
28728550 TGCGAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
*
28728600 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* *
28728656 TGCCAATGTCATGTCCCAGACATGGTCTTACA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACA
28728688 CTAGCTCACA
Statistics
Matches: 238, Mismatches: 42, Indels: 9
0.82 0.15 0.03
Matches are distributed among these distances:
48 1 0.00
49 35 0.15
50 169 0.71
53 2 0.01
56 31 0.13
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:28729786 original size:25 final size:24
Alignment explanation
Indices: 28729750--28729805 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 24
28729740 TTAAAGCTTC
28729750 ATTT-TCATTTCATTCAATTC-A-CA
1 ATTTCTCATTTCA--CAATTCAATCA
28729773 ATTTCTCATGTTCACAATTCAATCA
1 ATTTCTCAT-TTCACAATTCAATCA
28729798 ATTTCTCA
1 ATTTCTCA
28729806 ATCCAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 10 0.34
24 5 0.17
25 14 0.48
ACGTcount: A:0.30, C:0.23, G:0.02, T:0.45
Consensus pattern (24 bp):
ATTTCTCATTTCACAATTCAATCA
Found at i:28730997 original size:12 final size:12
Alignment explanation
Indices: 28730980--28731023 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
28730970 ATCTTGATGT
28730980 TCTTATATAAGA
1 TCTTATATAAGA
28730992 TCTTATATAAGA
1 TCTTATATAAGA
*
28731004 ----ACATAAGA
1 TCTTATATAAGA
28731012 TCTTATATAAGA
1 TCTTATATAAGA
28731024 AAACTCTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
8 7 0.27
12 19 0.73
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (12 bp):
TCTTATATAAGA
Found at i:28731011 original size:20 final size:20
Alignment explanation
Indices: 28730986--28731024 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
28730976 ATGTTCTTAT
28730986 ATAAGATCTTATATAAGAAC
1 ATAAGATCTTATATAAGAAC
28731006 ATAAGATCTTATATAAGAA
1 ATAAGATCTTATATAAGAA
28731025 AACTCTACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (20 bp):
ATAAGATCTTATATAAGAAC
Found at i:28731089 original size:117 final size:118
Alignment explanation
Indices: 28730877--28731101 Score: 416
Period size: 117 Copynumber: 1.9 Consensus size: 118
28730867 TATTCACTAA
*
28730877 TATATCAAGAACATAAGATCTTATATAAGAAAACTCTACTATAACATTATTTCCTTACTTTTTCA
1 TATATCAAGAACATAAGATCTTATATAAGAAAACTCTACTATAACATTATTTCCTTACATTTTCA
28730942 ATAATATAAAACTTAAAAATATATTGAAATCTTGATGTTCTTATATAAGATCT
66 ATAATATAAAACTTAAAAATATATTGAAATCTTGATGTTCTTATATAAGATCT
28730995 TATAT-AAGAACATAAGATCTTATATAAGAAAACTCTACTATAACATTATTTCCTTACATTTTCA
1 TATATCAAGAACATAAGATCTTATATAAGAAAACTCTACTATAACATTATTTCCTTACATTTTCA
* *
28731059 ATAATATCAAACTTAAAATTATATTGAAATCTTGATGTTCTTA
66 ATAATATAAAACTTAAAAATATATTGAAATCTTGATGTTCTTA
28731102 CCTTGTGCTA
Statistics
Matches: 104, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
117 99 0.95
118 5 0.05
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (118 bp):
TATATCAAGAACATAAGATCTTATATAAGAAAACTCTACTATAACATTATTTCCTTACATTTTCA
ATAATATAAAACTTAAAAATATATTGAAATCTTGATGTTCTTATATAAGATCT
Found at i:28731915 original size:23 final size:23
Alignment explanation
Indices: 28731888--28731937 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
28731878 ACCTACTTTC
*
28731888 TTACTGTAGTAATTTTCGGGGTA
1 TTACTGTAGTAATTTTCGGGATA
28731911 TTACTGTAGTAATTTTCGGGATA
1 TTACTGTAGTAATTTTCGGGATA
28731934 TTAC
1 TTAC
28731938 ACAAACAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.24, C:0.10, G:0.22, T:0.44
Consensus pattern (23 bp):
TTACTGTAGTAATTTTCGGGATA
Found at i:28733115 original size:43 final size:42
Alignment explanation
Indices: 28733052--28733165 Score: 110
Period size: 43 Copynumber: 2.7 Consensus size: 42
28733042 AAGTCGTGCA
* *
28733052 ATGCCATATCCTGGATATGGTCTTACATGTTAACGCATAT-CG
1 ATGCCATATCCTAGACATGGTCTTACATGTTAA-GCATATACG
* * *
28733094 ATGCCACTATCCTAGACATGGTCTTATACG--AATCATATACG
1 ATGCCA-TATCCTAGACATGGTCTTACATGTTAAGCATATACG
* *
28733135 ATGCCAATGTCCCA-ACATGGTCTTACATGTT
1 ATGCC-ATATCCTAGACATGGTCTTACATGTT
28733166 TTCACACTTC
Statistics
Matches: 58, Mismatches: 9, Indels: 10
0.75 0.12 0.13
Matches are distributed among these distances:
40 18 0.31
41 14 0.24
42 7 0.12
43 19 0.33
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (42 bp):
ATGCCATATCCTAGACATGGTCTTACATGTTAAGCATATACG
Found at i:28733215 original size:43 final size:42
Alignment explanation
Indices: 28733092--28733208 Score: 121
Period size: 41 Copynumber: 2.8 Consensus size: 42
28733082 TAACGCATAT
* * * * *
28733092 CGATGCCACTATCCTAGACATGGTCTTATACGAATCATA-TA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGAATCACACTA
* ** *
28733133 CGATGCCAATGTCCCA-ACATGGTCTTACATGTTTTCACACTT
1 CGATGCCAATGTCCCAGACATGGTCTTACACG-AATCACACTA
*
28733175 CGATGTCAATGTCCCAGACATGGTCTTACACGAA
1 CGATGCCAATGTCCCAGACATGGTCTTACACGAA
28733209 ACCACACCTT
Statistics
Matches: 60, Mismatches: 13, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
40 13 0.22
41 17 0.28
42 16 0.27
43 14 0.23
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (42 bp):
CGATGCCAATGTCCCAGACATGGTCTTACACGAATCACACTA
Found at i:28733475 original size:31 final size:31
Alignment explanation
Indices: 28733329--28733463 Score: 182
Period size: 31 Copynumber: 4.4 Consensus size: 31
28733319 ACCCAATGCT
** * *
28733329 CAAATC-AATTCAACAATATATATCCATGTA
1 CAAATCAAATTCGGCAATGTATATCCATATA
* * *
28733359 CGAATCAAATTCGGTAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
28733390 CAAATCAAATTCGGCAATGAATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
*
28733421 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCCATATA
28733452 CAAATCAAATTC
1 CAAATCAAATTC
28733464 AACAATCTAT
Statistics
Matches: 91, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
30 5 0.05
31 86 0.95
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCCATATA
Found at i:28734070 original size:11 final size:10
Alignment explanation
Indices: 28734048--28734077 Score: 51
Period size: 11 Copynumber: 2.9 Consensus size: 10
28734038 CACAAAAACA
28734048 TAAAAATAAT
1 TAAAAATAAT
28734058 TAAAAATAGAT
1 TAAAAATA-AT
28734069 TAAAAATAA
1 TAAAAATAA
28734078 ATTCCAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 9 0.47
11 10 0.53
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (10 bp):
TAAAAATAAT
Found at i:28735930 original size:40 final size:40
Alignment explanation
Indices: 28735808--28736144 Score: 286
Period size: 40 Copynumber: 8.5 Consensus size: 40
28735798 AATTATTGTA
* * * * * *
28735808 TGAATGCACATGCATACCCCTGTTTGTACTTCGGCACCCT
1 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * * * ** *
28735848 TGATTACACATACCTGCCTCGGTTTGCACTTCGGGT---CC
1 TGAATGCACATACGTGCCCCTATTTGTACTTC-GGTACCCC
***
28735886 TGAATGCACATACGCT-CCCCTATTTGTACTTTAATACCCC
1 TGAATGCACATACG-TGCCCCTATTTGTACTTCGGTACCCC
* * *
28735926 TGAATGCACATACGTTCCCCTATTTGTACTTCGATACCCG
1 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* *
28735966 TGAATGCACATACGTGCCCCTGTTTGTACTTTGGTACCCC
1 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* ** * * *
28736006 TGATTGCACATTTGTGCCTCTGTTTGTACTTTGGTACCCC
1 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * * * *
28736046 TGATTACACATTCGTGCCCCTGTTTATACTTCGGTACCCC
1 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
* * * * *
28736086 TGAATGCACATGCATTCCCCTATTTATACTTCGGTACCCT
1 TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
*
28736126 TGAATGCACTTACGTGCCC
1 TGAATGCACATACGTGCCC
28736145 TGTTTATACT
Statistics
Matches: 243, Mismatches: 48, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
37 1 0.00
38 23 0.09
39 2 0.01
40 215 0.88
41 2 0.01
ACGTcount: A:0.19, C:0.31, G:0.17, T:0.34
Consensus pattern (40 bp):
TGAATGCACATACGTGCCCCTATTTGTACTTCGGTACCCC
Found at i:28735992 original size:80 final size:80
Alignment explanation
Indices: 28735884--28736169 Score: 315
Period size: 80 Copynumber: 3.6 Consensus size: 80
28735874 CACTTCGGGT
* * **
28735884 CCTGAATGCACATACGCT-CCCCTATTTGTACTTTAATACCCCTGAATGCACATACGTTCCCCTA
1 CCTGAATGCACATACG-TGCCCCTGTTTATACTTTGGTACCCCTGAATGCACATACGTTCCCCTA
*
28735948 TTTGTACTTCGATACC
65 TTTGTACTTCGGTACC
* * * ** * * *
28735964 CGTGAATGCACATACGTGCCCCTGTTTGTACTTTGGTACCCCTGATTGCACATTTGTGCCTCTGT
1 CCTGAATGCACATACGTGCCCCTGTTTATACTTTGGTACCCCTGAATGCACATACGTTCCCCTAT
*
28736029 TTGTACTTTGGTACC
66 TTGTACTTCGGTACC
* * * * * *
28736044 CCTGATTACACATTCGTGCCCCTGTTTATACTTCGGTACCCCTGAATGCACATGCATTCCCCTAT
1 CCTGAATGCACATACGTGCCCCTGTTTATACTTTGGTACCCCTGAATGCACATACGTTCCCCTAT
*
28736109 TTATACTTCGGTACC
66 TTGTACTTCGGTACC
* * * * *
28736124 CTTGAATGCACTTACGTG-CCCTGTTTATACTCTGGTAACTCTGAAT
1 CCTGAATGCACATACGTGCCCCTGTTTATACTTTGGTACCCCTGAAT
28736170 TATATAATAT
Statistics
Matches: 169, Mismatches: 36, Indels: 3
0.81 0.17 0.01
Matches are distributed among these distances:
79 25 0.15
80 144 0.85
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (80 bp):
CCTGAATGCACATACGTGCCCCTGTTTATACTTTGGTACCCCTGAATGCACATACGTTCCCCTAT
TTGTACTTCGGTACC
Found at i:28736007 original size:20 final size:20
Alignment explanation
Indices: 28735982--28736087 Score: 88
Period size: 20 Copynumber: 5.3 Consensus size: 20
28735972 CACATACGTG
28735982 CCCCTGTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTTGGTA
* * *
28736002 CCCCTGATTGCACATTT-GTG
1 CCCCTGTTTGTAC-TTTGGTA
*
28736022 CCTCTGTTTGTACTTTGGTA
1 CCCCTGTTTGTACTTTGGTA
* ** * * *
28736042 CCCCTGATTACACATTCGTG
1 CCCCTGTTTGTACTTTGGTA
* *
28736062 CCCCTGTTTATACTTCGGTA
1 CCCCTGTTTGTACTTTGGTA
28736082 CCCCTG
1 CCCCTG
28736088 AATGCACATG
Statistics
Matches: 64, Mismatches: 20, Indels: 4
0.73 0.23 0.05
Matches are distributed among these distances:
19 3 0.05
20 58 0.91
21 3 0.05
ACGTcount: A:0.13, C:0.30, G:0.18, T:0.39
Consensus pattern (20 bp):
CCCCTGTTTGTACTTTGGTA
Found at i:28751794 original size:30 final size:30
Alignment explanation
Indices: 28751760--28752016 Score: 164
Period size: 30 Copynumber: 8.6 Consensus size: 30
28751750 AGCATTGGCT
28751760 ATCGAATTATGAAAAGGGATGG-TGACGACC
1 ATCGAATTATGAAAAGGGATGGCT-ACGACC
* * * * *
28751790 ATCGAATTATTAACAGAGATGGCTTC-AGCT
1 ATCGAATTATGAAAAGGGATGGCTACGA-CC
* ** ***
28751820 GTCGAATTATGAAAAGGGATGGCTTTGGTT
1 ATCGAATTATGAAAAGGGATGGCTACGACC
* * * * *
28751850 ATCAAATTATGAAAAGGGACGGCTTCGGCT
1 ATCGAATTATGAAAAGGGATGGCTACGACC
*
28751880 ATCAAATTATGAAAAGGGATGG-TGACGACC
1 ATCGAATTATGAAAAGGGATGGCT-ACGACC
**
28751910 ATC-AACAATGAAAAGGGATGG-TGACGACC
1 ATCGAATTATGAAAAGGGATGGCT-ACGACC
* * *
28751939 ATCGAATTATGAAAAGGGATGGCTTCAACT
1 ATCGAATTATGAAAAGGGATGGCTACGACC
* * * * * * *
28751969 ATCAAAATATGGAAAGGGATAGCTTCGGCT
1 ATCGAATTATGAAAAGGGATGGCTACGACC
* *
28751999 ATTGAAATATGAAAAGGG
1 ATCGAATTATGAAAAGGG
28752017 GTGGTAACAA
Statistics
Matches: 184, Mismatches: 37, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
29 29 0.16
30 153 0.83
31 2 0.01
ACGTcount: A:0.37, C:0.13, G:0.27, T:0.24
Consensus pattern (30 bp):
ATCGAATTATGAAAAGGGATGGCTACGACC
Found at i:28751901 original size:90 final size:90
Alignment explanation
Indices: 28751708--28751901 Score: 210
Period size: 90 Copynumber: 2.2 Consensus size: 90
28751698 TCATTGTCCA
** * *
28751708 ATGAAAAGGTTTGGCTTCAGCTATCAAAATATGGAAAGGGATAGCATTGGCTATCGAATTATGAA
1 ATGAAAAGGGATGGCTTCAGCTATCAAAATATGAAAAGGGATAGCATTGGCTATCAAATTATGAA
* *
28751773 AAGGGATGGTGACGACCATCGAATT
66 AAGGGACGGTGACGACCATCAAATT
* * * * * * * * *
28751798 ATTAACAGAGATGGCTTCAGCTGTCGAATTATGAAAAGGGATGGCTTTGGTTATCAAATTATGAA
1 ATGAAAAGGGATGGCTTCAGCTATCAAAATATGAAAAGGGATAGCATTGGCTATCAAATTATGAA
* * *
28751863 AAGGGACGGCT-TCGGCTATCAAATT
66 AAGGGACGG-TGACGACCATCAAATT
28751888 ATGAAAAGGGATGG
1 ATGAAAAGGGATGG
28751902 TGACGACCAT
Statistics
Matches: 82, Mismatches: 21, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
90 81 0.99
91 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.26
Consensus pattern (90 bp):
ATGAAAAGGGATGGCTTCAGCTATCAAAATATGAAAAGGGATAGCATTGGCTATCAAATTATGAA
AAGGGACGGTGACGACCATCAAATT
Found at i:28751928 original size:29 final size:30
Alignment explanation
Indices: 28751888--28751960 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 30
28751878 CTATCAAATT
28751888 ATGAAAAGGGATGGTGACGACCATC-AACA
1 ATGAAAAGGGATGGTGACGACCATCGAACA
**
28751917 ATGAAAAGGGATGGTGACGACCATCGAATT
1 ATGAAAAGGGATGGTGACGACCATCGAACA
28751947 ATGAAAAGGGATGG
1 ATGAAAAGGGATGG
28751961 CTTCAACTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 25 0.61
30 16 0.39
ACGTcount: A:0.40, C:0.12, G:0.32, T:0.16
Consensus pattern (30 bp):
ATGAAAAGGGATGGTGACGACCATCGAACA
Found at i:28752016 original size:60 final size:60
Alignment explanation
Indices: 28751708--28752016 Score: 252
Period size: 60 Copynumber: 5.2 Consensus size: 60
28751698 TCATTGTCCA
** *
28751708 ATGAAAAGGTTTGGCTTC-AGCTATCAAAATATGGAAAGGGATAGCATT-GGCTATCGAATT
1 ATGAAAAGGGATGGCTTCGA-CTATCAAAATATGAAAAGGGATAGC-TTCGGCTATCGAATT
* * * * * * * * * *
28751768 ATGAAAAGGGATGG-TGACGACCATCGAATTATTAACAGAGATGGCTTCAGCTGTCGAATT
1 ATGAAAAGGGATGGCT-TCGACTATCAAAATATGAAAAGGGATAGCTTCGGCTATCGAATT
* ** * ** *
28751828 ATGAAAAGGGATGGCTTTGGTTATCAAATTATGAAAAGGGACGGCTTCGGCTATCAAATT
1 ATGAAAAGGGATGGCTTCGACTATCAAAATATGAAAAGGGATAGCTTCGGCTATCGAATT
* * * * * * *
28751888 ATGAAAAGGGATGG-TGACGACCATCAACA-ATGAAAAGGGAT-GGTGACGACCATCGAATT
1 ATGAAAAGGGATGGCT-TCGACTATCAAAATATGAAAAGGGATAGCT-TCGGCTATCGAATT
* * * *
28751947 ATGAAAAGGGATGGCTTCAACTATCAAAATATGGAAAGGGATAGCTTCGGCTATTGAAAT
1 ATGAAAAGGGATGGCTTCGACTATCAAAATATGAAAAGGGATAGCTTCGGCTATCGAATT
28752007 ATGAAAAGGG
1 ATGAAAAGGG
28752017 GTGGTAACAA
Statistics
Matches: 190, Mismatches: 50, Indels: 18
0.74 0.19 0.07
Matches are distributed among these distances:
58 2 0.01
59 48 0.25
60 136 0.72
61 4 0.02
ACGTcount: A:0.36, C:0.13, G:0.27, T:0.24
Consensus pattern (60 bp):
ATGAAAAGGGATGGCTTCGACTATCAAAATATGAAAAGGGATAGCTTCGGCTATCGAATT
Found at i:28753938 original size:42 final size:42
Alignment explanation
Indices: 28753806--28753998 Score: 223
Period size: 41 Copynumber: 4.7 Consensus size: 42
28753796 TACCCAGTGT
* * *
28753806 AAACAGGGGCACATATGTGCAATTCAGGGG-AACTAAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTATCTGAAGTAC
* * *
28753847 AAA-ATGGGAACATATGTGCAATTCAGGGGTATC-GAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTATCTGAAGTAC
* * *
28753887 AAATAGGGGCACGTTTGTGCAATTCAGGGGTTTCTGAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTATCTGAAGTAC
* *
28753929 AAACAGGGGCATGTATGTGCAGTTCAGGGGTAT-TGAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTATCTGAAGTAC
* * * *
28753970 AAACACGGGCATGTATGTGGAATTTAGGG
1 AAACAGGGGCACGTATGTGCAATTCAGGG
28753999 AATAATTGAG
Statistics
Matches: 131, Mismatches: 18, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
40 33 0.25
41 63 0.48
42 35 0.27
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.23
Consensus pattern (42 bp):
AAACAGGGGCACGTATGTGCAATTCAGGGGTATCTGAAGTAC
Found at i:28753980 original size:83 final size:81
Alignment explanation
Indices: 28753806--28753998 Score: 224
Period size: 83 Copynumber: 2.4 Consensus size: 81
28753796 TACCCAGTGT
* *
28753806 AAACAGGGGCACATATGTGCAATTCAGGGGAACTAAAGTACAAAATGGGAACATATGTGCAATTC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGAACTAAAGTACAAAAGGGGAACATATGTGCAATTC
28753871 AGGGGTATCGAAGTAC
66 AGGGGTATCGAAGTAC
* * ** * * ** *
28753887 AAATAGGGGCACGTTTGTGCAATTCAGGGGTTTCTGAAGTACAAACAGGGGCATGTATGTGCAGT
1 AAACAGGGGCACGTATGTGCAATTCAGGGG-AACTAAAGTACAAA-AGGGGAACATATGTGCAAT
*
28753952 TCAGGGGTATTGAAGTAC
64 TCAGGGGTATCGAAGTAC
* * * *
28753970 AAACACGGGCATGTATGTGGAATTTAGGG
1 AAACAGGGGCACGTATGTGCAATTCAGGG
28753999 AATAATTGAG
Statistics
Matches: 92, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
81 27 0.29
82 11 0.12
83 54 0.59
ACGTcount: A:0.33, C:0.13, G:0.31, T:0.23
Consensus pattern (81 bp):
AAACAGGGGCACGTATGTGCAATTCAGGGGAACTAAAGTACAAAAGGGGAACATATGTGCAATTC
AGGGGTATCGAAGTAC
Found at i:28755555 original size:107 final size:107
Alignment explanation
Indices: 28755396--28755611 Score: 351
Period size: 107 Copynumber: 2.0 Consensus size: 107
28755386 GGCTCACACT
** *
28755396 ATCCGTCTAAACTGGTTGTTTTTGTATCTCTTAGGGTAGTGGCGTGTATATATATATTTATATAG
1 ATCCGTCTAAACTGGTTGTTTTTGTATCTCTTAAAGTAGTGGCATGTATATATATATTTATATAG
* * * *
28755461 ATGAATTTGTGGTTGAAATTCTTAGGATGTTATGTAATGGTG
66 ATGAATTTGTAGTTGAAATGCTTAGCATGTTATGTAATAGTG
*
28755503 ATCCGTCTAAATTGGTTGTTTTTGTATCTCTTAAAGTAGTGGCATGTATATATATATTTATATAG
1 ATCCGTCTAAACTGGTTGTTTTTGTATCTCTTAAAGTAGTGGCATGTATATATATATTTATATAG
*
28755568 ATGAATTTGTAGTTGAAATGGTTAGCATGTTATGTAATAGTG
66 ATGAATTTGTAGTTGAAATGCTTAGCATGTTATGTAATAGTG
28755610 AT
1 AT
28755612 TTGGATGTTT
Statistics
Matches: 100, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
107 100 1.00
ACGTcount: A:0.27, C:0.07, G:0.22, T:0.44
Consensus pattern (107 bp):
ATCCGTCTAAACTGGTTGTTTTTGTATCTCTTAAAGTAGTGGCATGTATATATATATTTATATAG
ATGAATTTGTAGTTGAAATGCTTAGCATGTTATGTAATAGTG
Found at i:28761721 original size:50 final size:50
Alignment explanation
Indices: 28761618--28761805 Score: 205
Period size: 50 Copynumber: 3.6 Consensus size: 50
28761608 AAAGAGATCT
28761618 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCA---AG---ATGAGAGGTCC
* *
28761674 CATGTAATACCATGTCTGGGACATGGCGTTGGCATCAAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAGATGAGAGGTCC
* * * * * **
28761724 CCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAGATGAGAGGTCC
* * * *
28761774 CATGTAAGACCATATTTTGGATATGGCATTGG
1 CATGTAAGACCATGTCTGGGACATGGCATTGG
28761806 AAGCATAGAA
Statistics
Matches: 115, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
50 78 0.68
53 2 0.02
56 35 0.30
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.26
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCATCAAGATGAGAGGTCC
Found at i:28761800 original size:100 final size:103
Alignment explanation
Indices: 28761620--28761805 Score: 234
Period size: 100 Copynumber: 1.8 Consensus size: 103
28761610 AGAGATCTCA
* ** *
28761620 TGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGGTCCCATGTAATACC
1 TGTAAGACCATGTCTGGGACATGGCATGGGCATC--T-AGATTATGAGAACTCCCATGTAAGACC
* *
28761685 ATGTCTGGGACATGGCGTTGGCATCAAGATGAGAGGTCCCC
63 ATATCTGGGACATGGCATTGGCATCAAGATGAGAGGTCCCC
*
28761726 TGTAAGACCATGTCTGGGACATGGCATGGGCA-C-CGA-TATGAGAACTCCCATGTAAGACCATA
1 TGTAAGACCATGTCTGGGACATGGCATGGGCATCTAGATTATGAGAACTCCCATGTAAGACCATA
* * *
28761788 TTTTGGATATGGCATTGG
66 TCTGGGACATGGCATTGG
28761806 AAGCATAGAA
Statistics
Matches: 70, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
100 36 0.51
101 2 0.03
105 1 0.01
106 31 0.44
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (103 bp):
TGTAAGACCATGTCTGGGACATGGCATGGGCATCTAGATTATGAGAACTCCCATGTAAGACCATA
TCTGGGACATGGCATTGGCATCAAGATGAGAGGTCCCC
Found at i:28761849 original size:49 final size:50
Alignment explanation
Indices: 28761721--28761849 Score: 129
Period size: 50 Copynumber: 2.6 Consensus size: 50
28761711 AGATGAGAGG
* * * * *
28761721 TCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATTTCTAGGACATGGCATGGGAACCGATATGAAAAC
* * * *
28761771 TCCCATGTAAGACCATATT-TTGGATATGGCATTGGAAGC-ATA-GAAAAC
1 TCCCATGTAAGACCAT-TTCTAGGACATGGCATGGGAACCGATATGAAAAC
*
28761819 ATCCCATTTAAGACCATTTCTAGGACATGGC
1 -TCCCATGTAAGACCATTTCTAGGACATGGC
28761850 TTGTAACACC
Statistics
Matches: 65, Mismatches: 11, Indels: 7
0.78 0.13 0.08
Matches are distributed among these distances:
48 7 0.11
49 27 0.42
50 30 0.46
51 1 0.02
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (50 bp):
TCCCATGTAAGACCATTTCTAGGACATGGCATGGGAACCGATATGAAAAC
Found at i:28763757 original size:22 final size:22
Alignment explanation
Indices: 28763729--28763803 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
28763719 TTCCACATCC
28763729 ATCACATTGGCCATTCGGCCTT
1 ATCACATTGGCCATTCGGCCTT
** * * *
28763751 ATCACATATATACACTTTC-ACATT
1 ATCACAT-T-GGC-CATTCGGCCTT
28763775 CATCACATTGGCCATTCGGCCTT
1 -ATCACATTGGCCATTCGGCCTT
28763798 ATCACA
1 ATCACA
28763804 CATACACATG
Statistics
Matches: 38, Mismatches: 10, Indels: 10
0.66 0.17 0.17
Matches are distributed among these distances:
22 17 0.45
23 5 0.13
24 5 0.13
25 11 0.29
ACGTcount: A:0.27, C:0.31, G:0.11, T:0.32
Consensus pattern (22 bp):
ATCACATTGGCCATTCGGCCTT
Found at i:28763764 original size:47 final size:47
Alignment explanation
Indices: 28763701--28764162 Score: 633
Period size: 47 Copynumber: 9.6 Consensus size: 47
28763691 CCCTTCGGGA
* * *
28763701 CTTATCACATTTATACACTTCCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
28763748 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
28763795 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
28763842 CTTATCTCATATATGCA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
* *
28763889 CTTATCACACATACACA-TGTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACT-TTCACATTCATCACATTGGCCATTCGGC
28763936 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
28763985 CTTATCACATATATACACTTTCACATTCATCCATTCATCACATCGGCCATTAGTC
1 CTTATCACATATATACACTTTCACATTCAT-CA--CAT----T-GGCCATTCGGC
* *
28764040 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
28764089 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
28764136 CTTATCACATATATACACTTTCACATT
1 CTTATCACATATATACACTTTCACATT
28764163 TATTCAAATA
Statistics
Matches: 382, Mismatches: 19, Indels: 28
0.89 0.04 0.07
Matches are distributed among these distances:
46 1 0.00
47 269 0.70
48 2 0.01
49 61 0.16
50 4 0.01
54 4 0.01
55 17 0.04
56 2 0.01
57 22 0.06
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:28764026 original size:104 final size:102
Alignment explanation
Indices: 28763908--28764162 Score: 384
Period size: 104 Copynumber: 2.6 Consensus size: 102
28763898 CATACACATG
*
28763908 TTCA-CATTCATCACATTGGCCATTCGGCCTTATCACATATATATACACTTTCACATTCATCACA
1 TTCATCATTCATCACA-TGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
* *
28763972 TTGGCCATTCGGCCTTATCACATATATACACTTTCACA
65 TCGGCCATTAGGCCTTATCACATATATACACTTTCACA
*
28764010 TTCATCCATTCATCACATCGGCCATTAGTCCTTATCACATATATATACACTTTCACATTCATCAC
1 TTCAT-CATTCATCACAT-GGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCAC
28764075 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACA
64 ATCGGCCATTAGGCCTTATCACATATATACACTTTCACA
28764114 TTCATCA--CAT--C--GGCCATTAGGCCTTATCAC--ATATATACACTTTCACATT
1 TTCATCATTCATCACATGGCCATTAGGCCTTATCACATATATATACACTTTCACATT
28764163 TATTCAAATA
Statistics
Matches: 145, Mismatches: 5, Indels: 14
0.88 0.03 0.09
Matches are distributed among these distances:
94 19 0.13
96 18 0.12
99 1 0.01
101 3 0.02
102 4 0.03
103 3 0.02
104 97 0.67
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.34
Consensus pattern (102 bp):
TTCATCATTCATCACATGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACAT
CGGCCATTAGGCCTTATCACATATATACACTTTCACA
Found at i:28767211 original size:40 final size:40
Alignment explanation
Indices: 28767127--28767311 Score: 204
Period size: 40 Copynumber: 4.7 Consensus size: 40
28767117 TTGAATGCTG
* *
28767127 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
28767166 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28767207 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
28767246 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
*
28767285 AACCGGGCTAAGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28767312 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 16
0.82 0.07 0.10
Matches are distributed among these distances:
39 36 0.29
40 77 0.61
41 12 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28767263 original size:79 final size:81
Alignment explanation
Indices: 28767127--28767311 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 81
28767117 TTGAATGCTG
*
28767127 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
28767191 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * * **
28767206 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
28767268 TTTGTGCGAATTACTATA
64 TTTGTGCGAATTACTATA
*
28767286 ACCGGGCTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28767312 AACGAGGAGC
Statistics
Matches: 93, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
78 2 0.02
79 58 0.62
80 33 0.35
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:28767333 original size:79 final size:78
Alignment explanation
Indices: 28767128--28767344 Score: 237
Period size: 79 Copynumber: 2.7 Consensus size: 78
28767118 TGAATGCTGT
* * *
28767128 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACTATATCCGG-TTAAG-TCCGAAGGCATTT
*
28767192 GTGCGAGATACTAATT
63 GTGCGAGATACTAATA
* *
28767208 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCC-GGTTAAGT-CCGAAGGCATTTG
28767272 TGCGA-ATTACT-ATAA
64 TGCGAGA-TACTAAT-A
** *
28767287 CCGGGCTAAGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGA-CTATATCCGGTT-AAGTCCGAAGG
28767345 TACGTGATTT
Statistics
Matches: 118, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
78 4 0.03
79 67 0.57
80 47 0.40
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCCGGTTAAGTCCGAAGGCATTTGTG
CGAGATACTAATA
Found at i:28775036 original size:40 final size:40
Alignment explanation
Indices: 28774952--28775136 Score: 204
Period size: 40 Copynumber: 4.7 Consensus size: 40
28774942 TTGAATGCTG
* *
28774952 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTAAT
*
28774991 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTAAT
* *
28775032 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
*
28775071 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGA-ATTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-TACTAAT
*
28775110 AACCGGGCTAAGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28775137 AACGAGGAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 16
0.82 0.07 0.10
Matches are distributed among these distances:
39 36 0.29
40 77 0.61
41 12 0.10
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTAAT
Found at i:28775088 original size:79 final size:81
Alignment explanation
Indices: 28774952--28775136 Score: 238
Period size: 79 Copynumber: 2.3 Consensus size: 81
28774942 TTGAATGCTG
*
28774952 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
28775016 TGTGCGAGA-TACTA-A
66 TGTGCGA-ATTACTATA
* * * **
28775031 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
28775093 TTTGTGCGAATTACTATA
64 TTTGTGCGAATTACTATA
*
28775111 ACCGGGCTAAGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28775137 AACGAGGAGC
Statistics
Matches: 93, Mismatches: 7, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
78 2 0.02
79 58 0.62
80 33 0.35
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAATTACTATA
Found at i:28775158 original size:79 final size:78
Alignment explanation
Indices: 28774953--28775169 Score: 237
Period size: 79 Copynumber: 2.7 Consensus size: 78
28774943 TGAATGCTGT
* * *
28774953 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTGACTATATCCGG-TTAAG-TCCGAAGGCATTT
*
28775017 GTGCGAGATACTAATT
63 GTGCGAGATACTAATA
* *
28775033 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCC-GGTTAAGT-CCGAAGGCATTTG
28775097 TGCGA-ATTACT-ATAA
64 TGCGAGA-TACTAAT-A
** *
28775112 CCGGGCTAAGTCCCGAAGGCATTTGAACGAG-GAGCTATATCCGGTTAAATTCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGA-CTATATCCGGTT-AAGTCCGAAGG
28775170 TACGTGATTT
Statistics
Matches: 118, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
78 4 0.03
79 67 0.57
80 47 0.40
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (78 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTATATCCGGTTAAGTCCGAAGGCATTTGTG
CGAGATACTAATA
Done.